From 864a52b6f3295c0fcf7b8dbe6dff78156e9f5488 Mon Sep 17 00:00:00 2001 From: Mitchell Shiell <59712867+MitchellShiell@users.noreply.github.com> Date: Sun, 12 Nov 2023 14:07:37 -0500 Subject: [PATCH 1/8] initial commit, file and folder setup --- .../arranger-metadata/aggs-state.json | 236 +++++++ .../arranger-metadata/columns-state.json | 530 ++++++++++++++ .../arranger-metadata/extended.json | 646 ++++++++++++++++++ .../arranger-metadata/matchbox-state.json | 42 ++ playground-data/song-schemas/VariantCall.json | 81 +++ 5 files changed, 1535 insertions(+) create mode 100644 playground-data/arranger-metadata/aggs-state.json create mode 100644 playground-data/arranger-metadata/columns-state.json create mode 100644 playground-data/arranger-metadata/extended.json create mode 100644 playground-data/arranger-metadata/matchbox-state.json create mode 100644 playground-data/song-schemas/VariantCall.json diff --git a/playground-data/arranger-metadata/aggs-state.json 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"dmsdefault::file::extended::donors.specimens.samples.sample_id", + "field": "donors.specimens.samples.sample_id", + "type": "keyword", + "displayName": "SampleId", + "active": true, + "isArray": false, + "primaryKey": true, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::donors.specimens.samples.sample_type", + "field": "donors.specimens.samples.sample_type", + "type": "keyword", + "displayName": "Sample Type", + "active": true, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::donors.specimens.samples.submitter_sample_id", + "field": "donors.specimens.samples.submitter_sample_id", + "type": "keyword", + "displayName": "Submitter Sample Id", + "active": true, + "isArray": false, + 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"donors.specimens.specimen_type", + "type": "keyword", + "displayName": "Specimen Type", + "active": true, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::donors.specimens.submitter_specimen_id", + "field": "donors.specimens.submitter_specimen_id", + "type": "keyword", + "displayName": "Submitter Specimen Id", + "active": true, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::donors.specimens.tumour_normal_designation", + "field": "donors.specimens.tumour_normal_designation", + "type": "keyword", + "displayName": "Tumour Normal Designation", + "active": true, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::donors.submitter_donor_id", + "field": "donors.submitter_donor_id", + "type": "keyword", + "displayName": "Submitter Donor Id", + "active": true, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::file", + "field": "file", + "type": "object", + "displayName": "File", + "active": false, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::file.index_file", + "field": "file.index_file", + "type": "object", + "displayName": "File Index File", + "active": false, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::file.index_file.file_type", + "field": "file.index_file.file_type", + "type": "keyword", + "displayName": "Index File Type", + "active": true, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::file.index_file.md5sum", + "field": "file.index_file.md5sum", + "type": "keyword", + "displayName": "Index File Md5sum", + "active": true, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::file.index_file.name", + "field": "file.index_file.name", + "type": "keyword", + "displayName": "Index File Name", + "active": true, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::file.index_file.object_id", + "field": "file.index_file.object_id", + "type": "keyword", + "displayName": "Index File Object Id", + "active": true, + "isArray": false, + "primaryKey": true, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::file.index_file.size", + "field": "file.index_file.size", + "type": "long", + "displayName": "Index File Size", + "active": true, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::file.md5sum", + "field": "file.md5sum", + "type": "keyword", + "displayName": "File Md5sum", + "active": true, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::file.name", + "field": "file.name", + "type": "keyword", + "displayName": "File Name", + "active": true, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::file.size", + "field": "file.size", + "type": "long", + "displayName": "File Size", + "active": true, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::file_access", + "field": "file_access", + "type": "keyword", + "displayName": "File Access", + "active": true, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::file_autocomplete", + "field": "file_autocomplete", + "type": "keyword", + "displayName": "File Autocomplete", + "active": false, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::file_type", + "field": "file_type", + "type": "keyword", + "displayName": "File Type", + "active": true, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::object_id", + "field": "object_id", + "type": "keyword", + "displayName": "Object Id", + "active": true, + "isArray": false, + "primaryKey": true, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::repositories", + "field": "repositories", + "type": "nested", + "displayName": "Repositories", + "active": false, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::repositories.code", + "field": "repositories.code", + "type": "keyword", + "displayName": "Repositories Code", + "active": true, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::repositories.country", + "field": "repositories.country", + "type": "keyword", + "displayName": "Repositories Country", + "active": true, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::repositories.name", + "field": "repositories.name", + "type": "keyword", + "displayName": "Repositories Name", + "active": true, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::repositories.organization", + "field": "repositories.organization", + "type": "keyword", + "displayName": "Repositories Organization", + "active": true, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::repositories.url", + "field": "repositories.url", + "type": "keyword", + "displayName": "Repositories Url", + "active": true, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::study_id", + "field": "study_id", + "type": "keyword", + "displayName": "Study Id", + "active": true, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::analysis.first_published_at", + "field": "analysis.first_published_at", + "type": "date", + "displayName": "Analysis First Published At", + "active": false, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::analysis.published_at", + "field": "analysis.published_at", + "type": "date", + "displayName": "Analysis Published At", + "active": false, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + }, + { + "gqlId": "dmsdefault::file::extended::analysis.updated_at", + "field": "analysis.updated_at", + "type": "date", + "displayName": "Analysis Updated At", + "active": false, + "isArray": false, + "primaryKey": false, + "quickSearchEnabled": false, + "unit": null, + "displayValues": {}, + "rangeStep": 1, + "__typename": "ExtendedFieldMapping" + } +] \ No newline at end of file diff --git a/playground-data/arranger-metadata/matchbox-state.json b/playground-data/arranger-metadata/matchbox-state.json new file mode 100644 index 00000000..1929bf43 --- /dev/null +++ b/playground-data/arranger-metadata/matchbox-state.json @@ -0,0 +1,42 @@ +[ + { + "displayName": "some_alias", + "field": "", + "isActive": false, + "keyField": null, + "searchFields": [], + "__typename": "MatchBoxField" + }, + { + "displayName": "Donors", + "field": "donors", + "isActive": true, + "keyField": null, + "searchFields": [], + "__typename": "MatchBoxField" + }, + { + "displayName": "Donors Specimens", + "field": "donors.specimens", + "isActive": true, + "keyField": null, + "searchFields": [], + "__typename": "MatchBoxField" + }, + { + "displayName": "Donors Specimens Samples", + "field": "donors.specimens.samples", + "isActive": true, + "keyField": null, + "searchFields": [], + "__typename": "MatchBoxField" + }, + { + "displayName": "Repositories", + "field": "repositories", + "isActive": true, + "keyField": null, + "searchFields": [], + "__typename": "MatchBoxField" + } +] \ No newline at end of file diff --git a/playground-data/song-schemas/VariantCall.json b/playground-data/song-schemas/VariantCall.json new file mode 100644 index 00000000..c658fd64 --- /dev/null +++ b/playground-data/song-schemas/VariantCall.json @@ -0,0 +1,81 @@ +{ + "studyId" : "ABC123", + "analysisType" : { + "name" : "variantCall" + }, + "experiment": { + "variantCallingTool": "silver bullet", + "matchedNormalSampleSubmitterId": "sample-x24-11a", + "randomField14" : "we can define any EXPERIMENT field. For example, randomField14", + "randomField15" : "as a second example, we can define another random EXPERIMENT field called randomField15", + "info" : { + "randomField16" : "alternatively, put some extra EXPERIMENT fields here" + } + }, + "samples": [ + { + "submitterSampleId": "internal_sample_1", + "sampleType": "Total RNA", + "matchedNormalSubmitterSampleId": "sample-x24-11a", + "specimen": { + "submitterSpecimenId": "internal_specimen_1", + "specimenType": "Primary tumour", + "specimenTissueSource": "Solid tissue", + "tumourNormalDesignation": "Tumour", + "randomField1" : "we can define any SPECIMEN field. For example, randomField1", + "randomField2" : "as a second example, we can define another random SPECIMEN field called randomField2", + "info" : { + "randomField3" : "alternatively, put some extra SPECIMEN fields here" + } + }, + "donor": { + "submitterDonorId": "internal_donor_123456789-00", + "gender": "Female", + "age": 30, + "randomField4" : "we can define any DONOR field. For example, randomField4", + "randomField5" : "as a second example, we can define another random DONOR field called randomField5", + "info" : { + "randomField6" : "alternatively, put some extra DONOR fields here" + } + }, + "randomField7" : "we can define any SAMPLE field. For example, randomField7", + "randomField8" : "as a second example, we can define another random SAMPLE field called randomField8", + "info" : { + "randomField9" : "alternatively, put some extra SAMPLE fields here" + } + } + ], + "files": [ + { + "dataType": "Variant Calling Data", + "fileName": "example.vcf.gz", + "fileSize": 52, + "fileMd5sum": "9a793e90d0d1e11301ea8da996446e59", + "fileAccess" : "open", + "fileType": "VCF", + "randomField10" : "we can define any FILE field. For example, randomField10", + "randomField11" : "as a second example, we can define another random FILE field called randomField11", + "info" : { + "randomField12" : "alternatively, put some extra FILE fields here" + } + }, + { + "dataType": "Variant Calling Index", + "fileName": "example.vcf.gz.idx", + "fileSize": 24, + "fileMd5sum": "c03274816eb4907a92b8e5632cd6eb81", + "fileAccess" : "open", + "fileType": "IDX", + "randomField10" : "we can define any FILE field. For example, randomField10", + "randomField13" : "as a second example, we can define another random FILE field called randomField13", + "info" : { + "randomField12" : "alternatively, put some extra FILE fields here" + } + } + ], + "randomField17" : "we can define any ANALYSIS field. For example, randomField17", + "randomField18" : "as a second example, we can define another random ANALYSIS field called randomField18", + "info" : { + "randomField19" : "alternatively, put some extra ANALYSIS fields here" + } +} From cf71f9952342bebbcfd74e4d1fa43f1c0ed2b72f Mon Sep 17 00:00:00 2001 From: edsu7 <22638361+edsu7@users.noreply.github.com> Date: Fri, 15 Dec 2023 16:37:59 -0500 Subject: [PATCH 2/8] adding data and payloads --- .DS_Store | Bin 0 -> 6148 bytes playground-data/.DS_Store | Bin 0 -> 8196 bytes ...wgs.20200513.sanger-wgs.somatic.snv.vcf.gz | Bin 0 -> 23947 bytes ...20200513.sanger-wgs.somatic.snv.vcf.gz.tbi | Bin 0 -> 185 bytes ...s.20200922.gatk-mutect2.somatic.snv.vcf.gz | Bin 0 -> 23947 bytes ...200922.gatk-mutect2.somatic.snv.vcf.gz.tbi | Bin 0 -> 185 bytes ...s.20200911.sanger-wxs.somatic.indel.vcf.gz | Bin 0 -> 23947 bytes ...200911.sanger-wxs.somatic.indel.vcf.gz.tbi | Bin 0 -> 185 bytes ...QA.DO263273.SA624744.wgs.20230728.aln.cram | Bin 0 -> 19423 bytes ...263273.SA624744.wgs.20230728.aln.cram.crai | Bin 0 -> 79 bytes ...CIMEN_hjdxmpeccamrjzybhqrl_N1.indel.vcf.gz | Bin 0 -> 17414 bytes ...N_hjdxmpeccamrjzybhqrl_N1.indel.vcf.gz.tbi | Bin 0 -> 405 bytes ...CIMEN_hjdxmpeccamrjzybhqrl_N2.indel.vcf.gz | Bin 0 -> 17325 bytes ...N_hjdxmpeccamrjzybhqrl_N2.indel.vcf.gz.tbi | Bin 0 -> 409 bytes ...CIMEN_hjdxmpeccamrjzybhqrl_T1.indel.vcf.gz | Bin 0 -> 17339 bytes ...N_hjdxmpeccamrjzybhqrl_T1.indel.vcf.gz.tbi | Bin 0 -> 400 bytes ...CIMEN_hjdxmpeccamrjzybhqrl_T2.indel.vcf.gz | Bin 0 -> 17334 bytes ...N_hjdxmpeccamrjzybhqrl_T2.indel.vcf.gz.tbi | Bin 0 -> 423 bytes ...PECIMEN_hlmegwbcehzqgmuaopom_N1.snv.vcf.gz | Bin 0 -> 17259 bytes ...MEN_hlmegwbcehzqgmuaopom_N1.snv.vcf.gz.tbi | Bin 0 -> 377 bytes ...CIMEN_hlmegwbcehzqgmuaopom_N2.indel.vcf.gz | Bin 0 -> 17334 bytes ...N_hlmegwbcehzqgmuaopom_N2.indel.vcf.gz.tbi | Bin 0 -> 411 bytes ...PECIMEN_hlmegwbcehzqgmuaopom_T1.snv.vcf.gz | Bin 0 -> 17255 bytes ...MEN_hlmegwbcehzqgmuaopom_T1.snv.vcf.gz.tbi | Bin 0 -> 413 bytes ...CIMEN_hlmegwbcehzqgmuaopom_T2.indel.vcf.gz | Bin 0 -> 17345 bytes ...N_hlmegwbcehzqgmuaopom_T2.indel.vcf.gz.tbi | Bin 0 -> 256 bytes ...CIMEN_hsreltpusctapirhgwpr_N1.indel.vcf.gz | Bin 0 -> 17347 bytes ...N_hsreltpusctapirhgwpr_N1.indel.vcf.gz.tbi | Bin 0 -> 370 bytes ...CIMEN_hsreltpusctapirhgwpr_N2.indel.vcf.gz | Bin 0 -> 17328 bytes ...N_hsreltpusctapirhgwpr_N2.indel.vcf.gz.tbi | Bin 0 -> 374 bytes ...PECIMEN_hsreltpusctapirhgwpr_T1.snv.vcf.gz | Bin 0 -> 17257 bytes ...MEN_hsreltpusctapirhgwpr_T1.snv.vcf.gz.tbi | Bin 0 -> 382 bytes ...CIMEN_hsreltpusctapirhgwpr_T2.indel.vcf.gz | Bin 0 -> 17336 bytes ...N_hsreltpusctapirhgwpr_T2.indel.vcf.gz.tbi | Bin 0 -> 404 bytes ...PECIMEN_kemubcrdlsbqgbcnnchc_N1.snv.vcf.gz | Bin 0 -> 17253 bytes ...MEN_kemubcrdlsbqgbcnnchc_N1.snv.vcf.gz.tbi | Bin 0 -> 371 bytes ...PECIMEN_kemubcrdlsbqgbcnnchc_N2.snv.vcf.gz | Bin 0 -> 17257 bytes ...MEN_kemubcrdlsbqgbcnnchc_N2.snv.vcf.gz.tbi | Bin 0 -> 396 bytes ...PECIMEN_kemubcrdlsbqgbcnnchc_T1.snv.vcf.gz | Bin 0 -> 17259 bytes ...MEN_kemubcrdlsbqgbcnnchc_T1.snv.vcf.gz.tbi | Bin 0 -> 398 bytes ...CIMEN_kemubcrdlsbqgbcnnchc_T2.indel.vcf.gz | Bin 0 -> 17302 bytes ...N_kemubcrdlsbqgbcnnchc_T2.indel.vcf.gz.tbi | Bin 0 -> 368 bytes ...PECIMEN_mynbiqpmzjplsgqejeyd_N1.snv.vcf.gz | Bin 0 -> 17256 bytes ...MEN_mynbiqpmzjplsgqejeyd_N1.snv.vcf.gz.tbi | Bin 0 -> 369 bytes ...CIMEN_mynbiqpmzjplsgqejeyd_N2.indel.vcf.gz | Bin 0 -> 17346 bytes ...N_mynbiqpmzjplsgqejeyd_N2.indel.vcf.gz.tbi | Bin 0 -> 389 bytes ...PECIMEN_mynbiqpmzjplsgqejeyd_T1.snv.vcf.gz | Bin 0 -> 17257 bytes ...MEN_mynbiqpmzjplsgqejeyd_T1.snv.vcf.gz.tbi | Bin 0 -> 414 bytes ...PECIMEN_mynbiqpmzjplsgqejeyd_T2.snv.vcf.gz | Bin 0 -> 17260 bytes ...MEN_mynbiqpmzjplsgqejeyd_T2.snv.vcf.gz.tbi | Bin 0 -> 415 bytes ...PECIMEN_otliefvakqotckrtwbxm_N1.snv.vcf.gz | Bin 0 -> 17258 bytes ...MEN_otliefvakqotckrtwbxm_N1.snv.vcf.gz.tbi | Bin 0 -> 375 bytes ...CIMEN_otliefvakqotckrtwbxm_N2.indel.vcf.gz | Bin 0 -> 17330 bytes ...N_otliefvakqotckrtwbxm_N2.indel.vcf.gz.tbi | Bin 0 -> 412 bytes ...PECIMEN_otliefvakqotckrtwbxm_T1.snv.vcf.gz | Bin 0 -> 17261 bytes ...MEN_otliefvakqotckrtwbxm_T1.snv.vcf.gz.tbi | Bin 0 -> 404 bytes ...CIMEN_otliefvakqotckrtwbxm_T2.indel.vcf.gz | Bin 0 -> 17339 bytes ...N_otliefvakqotckrtwbxm_T2.indel.vcf.gz.tbi | Bin 0 -> 393 bytes ...PECIMEN_tixlzwxuqaoyhubfdlph_N1.snv.vcf.gz | Bin 0 -> 17252 bytes ...MEN_tixlzwxuqaoyhubfdlph_N1.snv.vcf.gz.tbi | Bin 0 -> 259 bytes ...CIMEN_tixlzwxuqaoyhubfdlph_T1.indel.vcf.gz | Bin 0 -> 17354 bytes ...N_tixlzwxuqaoyhubfdlph_T1.indel.vcf.gz.tbi | Bin 0 -> 393 bytes .../data_files/anon_chr1_complete.bam | Bin 0 -> 258104 bytes .../data_files/anon_chr1_complete.bam.bai | Bin 0 -> 1232 bytes .../alignment_bam-checkpoint.json | 174 ++ .../alignment_cram-checkpoint.json | 174 ++ .../wgbs_coverage_bigwig-checkpoint.json | 150 ++ ...TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N1.json | 1 + ...TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N2.json | 1 + ...TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_T1.json | 1 + ...TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_T2.json | 1 + ...TEST_SPECIMEN_hlmegwbcehzqgmuaopom_N1.json | 1 + ...TEST_SPECIMEN_hlmegwbcehzqgmuaopom_N2.json | 1 + ...TEST_SPECIMEN_hlmegwbcehzqgmuaopom_T1.json | 1 + ...TEST_SPECIMEN_hlmegwbcehzqgmuaopom_T2.json | 1 + ...TEST_SPECIMEN_hsreltpusctapirhgwpr_N1.json | 1 + ...TEST_SPECIMEN_hsreltpusctapirhgwpr_N2.json | 1 + ...TEST_SPECIMEN_hsreltpusctapirhgwpr_T1.json | 1 + ...TEST_SPECIMEN_hsreltpusctapirhgwpr_T2.json | 1 + ...TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_N1.json | 1 + ...TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_N2.json | 1 + ...TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_T1.json | 1 + ...TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_T2.json | 1 + ...TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_N1.json | 1 + ...TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_N2.json | 1 + ...TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_T1.json | 1 + ...TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_T2.json | 1 + ...TEST_SPECIMEN_otliefvakqotckrtwbxm_N1.json | 1 + ...TEST_SPECIMEN_otliefvakqotckrtwbxm_N2.json | 1 + ...TEST_SPECIMEN_otliefvakqotckrtwbxm_T1.json | 1 + ...TEST_SPECIMEN_otliefvakqotckrtwbxm_T2.json | 1 + ...TEST_SPECIMEN_tixlzwxuqaoyhubfdlph_N1.json | 1 + ...TEST_SPECIMEN_tixlzwxuqaoyhubfdlph_T1.json | 1 + .../example-payloads/alignment_bam.json | 1 + .../example-payloads/alignment_cram.json | 1 + .../chipseq_foldchange_bigwig.json | 1 + .../example-payloads/chipseq_idr_bigbed.json | 1 + .../example-payloads/chipseq_pval_bigwig.json | 1 + playground-data/example-payloads/hic_hic.json | 1 + .../hic_insulation_bigwig.json | 1 + .../example-payloads/hic_pc1_bigwig.json | 1 + .../example-payloads/hichipseq_bedpe.json | 1 + .../wgbs_coverage_bigwig.json | 1 + .../wgbs_methylation_bigbed.json | 1 + .../example-payloads/wgs_indel_vcf.json | 1 + .../example-payloads/wgs_mutect_snv_vcf.json | 1 + .../example-payloads/wgs_sanger_snv_vcf.json | 1 + .../alignment_bam_hg38-checkpoint.json | 64 + .../alignment_cram.hg38-checkpoint.json | 62 + .../chipseq_IDR_bigBed-checkpoint.json | 25 + .../chipseq_bedpe-checkpoint.json | 29 + .../chipseq_foldchange_bigwig-checkpoint.json | 21 + .../chipseq_pval_bigwig-checkpoint.json | 21 + .../hic_hic-checkpoint.json | 21 + .../hic_insulation_bigwig-checkpoint.json | 21 + .../hic_pc1_bigwig-checkpoint.json | 21 + .../wgbs_cpg_coverage_bigWig-checkpoint.json | 21 + ...gbs_cpg_methylation_bigBed-checkpoint.json | 25 + .../jbrowse-config/alignment_bam_hg38.json | 64 + .../jbrowse-config/alignment_cram.hg38.json | 62 + .../jbrowse-config/chipseq_IDR_bigBed.json | 25 + .../jbrowse-config/chipseq_bedpe.json | 29 + .../chipseq_foldchange_bigwig.json | 21 + .../jbrowse-config/chipseq_pval_bigwig.json | 21 + playground-data/jbrowse-config/hic_hic.json | 21 + .../jbrowse-config/hic_insulation_bigwig.json | 21 + .../jbrowse-config/hic_pc1_bigwig.json | 21 + .../wgbs_cpg_coverage_bigWig.json | 21 + .../wgbs_cpg_methylation_bigBed.json | 25 + .../general-checkpoint.json | 1452 +++++++++++++++++ playground-data/song-schemas/general.json | 1452 +++++++++++++++++ 131 files changed, 4104 insertions(+) create mode 100644 .DS_Store create mode 100644 playground-data/.DS_Store create mode 100644 playground-data/data_files/TEST-PR.DO250183.SA610229.wgs.20200513.sanger-wgs.somatic.snv.vcf.gz create mode 100644 playground-data/data_files/TEST-PR.DO250183.SA610229.wgs.20200513.sanger-wgs.somatic.snv.vcf.gz.tbi create mode 100644 playground-data/data_files/TEST-PR.DO250183.SA610229.wgs.20200922.gatk-mutect2.somatic.snv.vcf.gz create mode 100644 playground-data/data_files/TEST-PR.DO250183.SA610229.wgs.20200922.gatk-mutect2.somatic.snv.vcf.gz.tbi create mode 100644 playground-data/data_files/TEST-PR.DO250183.SA610229.wxs.20200911.sanger-wxs.somatic.indel.vcf.gz create mode 100644 playground-data/data_files/TEST-PR.DO250183.SA610229.wxs.20200911.sanger-wxs.somatic.indel.vcf.gz.tbi create mode 100644 playground-data/data_files/TEST-QA.DO263273.SA624744.wgs.20230728.aln.cram create mode 100644 playground-data/data_files/TEST-QA.DO263273.SA624744.wgs.20230728.aln.cram.crai create mode 100644 playground-data/data_files/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N1.indel.vcf.gz create mode 100644 playground-data/data_files/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N1.indel.vcf.gz.tbi create mode 100644 playground-data/data_files/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N2.indel.vcf.gz create mode 100644 playground-data/data_files/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N2.indel.vcf.gz.tbi create mode 100644 playground-data/data_files/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_T1.indel.vcf.gz create mode 100644 playground-data/data_files/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_T1.indel.vcf.gz.tbi create mode 100644 playground-data/data_files/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_T2.indel.vcf.gz create mode 100644 playground-data/data_files/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_T2.indel.vcf.gz.tbi create mode 100644 playground-data/data_files/TEST_SPECIMEN_hlmegwbcehzqgmuaopom_N1.snv.vcf.gz create mode 100644 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playground-data/data_files/TEST_SPECIMEN_tixlzwxuqaoyhubfdlph_N1.snv.vcf.gz.tbi create mode 100644 playground-data/data_files/TEST_SPECIMEN_tixlzwxuqaoyhubfdlph_T1.indel.vcf.gz create mode 100644 playground-data/data_files/TEST_SPECIMEN_tixlzwxuqaoyhubfdlph_T1.indel.vcf.gz.tbi create mode 100644 playground-data/data_files/anon_chr1_complete.bam create mode 100644 playground-data/data_files/anon_chr1_complete.bam.bai create mode 100644 playground-data/example-payloads/.ipynb_checkpoints/alignment_bam-checkpoint.json create mode 100644 playground-data/example-payloads/.ipynb_checkpoints/alignment_cram-checkpoint.json create mode 100644 playground-data/example-payloads/.ipynb_checkpoints/wgbs_coverage_bigwig-checkpoint.json create mode 100644 playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N1.json create mode 100644 playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N2.json create mode 100644 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a/playground-data/example-payloads/.ipynb_checkpoints/alignment_bam-checkpoint.json b/playground-data/example-payloads/.ipynb_checkpoints/alignment_bam-checkpoint.json new file mode 100644 index 00000000..7be8365d --- /dev/null +++ b/playground-data/example-payloads/.ipynb_checkpoints/alignment_bam-checkpoint.json @@ -0,0 +1,174 @@ +{ + "samples": [ + { + "submitterSampleId": "TEST_SPECIMEN_bcclfxzvjitgtbsvfnum_N1", + "sampleType": "Total DNA", + "matchedNormalSubmitterSampleId": null, + "specimen": { + "submitterSpecimenId": "TEST_SPECIMEN_bcclfxzvjitgtbsvfnum_N1", + "specimenType": "Normal - tissue adjacent to primary tumour", + "specimenTissueSource": "Urine", + "tumourNormalDesignation": "Normal" + }, + "donor": { + "submitterDonorId": "TEST_DONOR_bcclfxzvjitgtbsvfnum", + "gender": "Female" + } + } + ], + "donor": { + "submitter_donor_id": "TEST_DONOR_bcclfxzvjitgtbsvfnum", + "primary_site": "Testis", + "vital_status": "Deceased", + "survival_time": 1550, + "cause_of_death": 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"surgery_location": "Metastatic", + "residual_tumour_classification": "R1" + } + ] + } + ], + "follow_up": [ + { + "submitter_follow_up_id": "TEST_FOLLOW_UP_bcclfxzvjitgtbsvfnum_0", + "interval_of_followup": 77, + "disease_status_at_followup": "Complete remission" + } + ] + }, + { + "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_bcclfxzvjitgtbsvfnum_1", + "age_at_diagnosis": 57, + "cancer_type_code": "D43.2", + "laterality": "Left", + "clinical_tumour_staging_system": "AJCC 7th edition", + "clinical_stage_group": "Stage IV", + "lymph_nodes_examined_status": "No lymph nodes found in resected specimen", + "performance_status": "Unknown", + "treatment": [ + { + "submitter_treatment_id": "TEST_TREATMENT_bcclfxzvjitgtbsvfnum_1", + "treatment_type": [ + "Chemotherapy" + ], + "treatment_intent": "Unknown", + "treatment_start_interval": 24, + "treatment_duration": 32, + "response_to_treatment": "Stable disease", + "chemotherapy": [ + { + "drug_name": "leucovorin", + 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"test-qa.do263273.sa624744.wgs.20230728.aln.cram-1702318770555-sessionTrack-LinearSNPCoverageDisplay" + }, + { + "type": "LinearReadArcsDisplay", + "displayId": "test-qa.do263273.sa624744.wgs.20230728.aln.cram-1702318770555-sessionTrack-LinearReadArcsDisplay" + }, + { + "type": "LinearReadCloudDisplay", + "displayId": "test-qa.do263273.sa624744.wgs.20230728.aln.cram-1702318770555-sessionTrack-LinearReadCloudDisplay" + } + ] +} \ No newline at end of file diff --git a/playground-data/jbrowse-config/.ipynb_checkpoints/chipseq_IDR_bigBed-checkpoint.json b/playground-data/jbrowse-config/.ipynb_checkpoints/chipseq_IDR_bigBed-checkpoint.json new file mode 100644 index 00000000..cde5021c --- /dev/null +++ b/playground-data/jbrowse-config/.ipynb_checkpoints/chipseq_IDR_bigBed-checkpoint.json @@ -0,0 +1,25 @@ +{ + "type": "FeatureTrack", + "trackId": "encff772oad.bigbed-1702320934124-sessionTrack", + "name": "ENCFF772OAD.bigBed", + "assemblyNames": [ + "hg38" + ], + "adapter": { + "type": "BigBedAdapter", + "bigBedLocation": { + "locationType": "UriLocation", + "uri": "https://www.encodeproject.org/files/ENCFF772OAD/@@download/ENCFF772OAD.bigBed" + } + }, + "displays": [ + { + "type": "LinearBasicDisplay", + "displayId": "encff772oad.bigbed-1702320934124-sessionTrack-LinearBasicDisplay" + }, + { + "type": "LinearArcDisplay", + "displayId": "encff772oad.bigbed-1702320934124-sessionTrack-LinearArcDisplay" + } + ] +} \ No newline at end of file diff --git a/playground-data/jbrowse-config/.ipynb_checkpoints/chipseq_bedpe-checkpoint.json b/playground-data/jbrowse-config/.ipynb_checkpoints/chipseq_bedpe-checkpoint.json new file mode 100644 index 00000000..fdb3cdf8 --- /dev/null +++ b/playground-data/jbrowse-config/.ipynb_checkpoints/chipseq_bedpe-checkpoint.json @@ -0,0 +1,29 @@ +{ + "type": "VariantTrack", + "trackId": "encff327gbz.bedpe.gz-1702322266543-sessionTrack", + "name": "ENCFF327GBZ.bedpe.gz", + "assemblyNames": [ + "hg38" + ], + "adapter": { + "type": "BedpeAdapter", + "bedpeLocation": { + "locationType": "UriLocation", + "uri": "https://www.encodeproject.org/files/ENCFF327GBZ/@@download/ENCFF327GBZ.bedpe.gz" + } + }, + "displays": [ + { + "type": "LinearVariantDisplay", + "displayId": "encff327gbz.bedpe.gz-1702322266543-sessionTrack-LinearVariantDisplay" + }, + { + "type": "ChordVariantDisplay", + "displayId": "encff327gbz.bedpe.gz-1702322266543-sessionTrack-ChordVariantDisplay" + }, + { + "type": "LinearPairedArcDisplay", + "displayId": "encff327gbz.bedpe.gz-1702322266543-sessionTrack-LinearPairedArcDisplay" + } + ] +} \ No newline at end of file diff --git a/playground-data/jbrowse-config/.ipynb_checkpoints/chipseq_foldchange_bigwig-checkpoint.json b/playground-data/jbrowse-config/.ipynb_checkpoints/chipseq_foldchange_bigwig-checkpoint.json new file mode 100644 index 00000000..ba247071 --- /dev/null +++ b/playground-data/jbrowse-config/.ipynb_checkpoints/chipseq_foldchange_bigwig-checkpoint.json @@ -0,0 +1,21 @@ +{ + "type": "QuantitativeTrack", + "trackId": "encff140qly.bigwig-1702320857138-sessionTrack", + "name": "ENCFF140QLY.bigWig", + "assemblyNames": [ + "hg38" + ], + "adapter": { + "type": "BigWigAdapter", + "bigWigLocation": { + "locationType": "UriLocation", + "uri": "https://www.encodeproject.org/files/ENCFF140QLY/@@download/ENCFF140QLY.bigWig" + } + }, + "displays": [ + { + "type": "LinearWiggleDisplay", + "displayId": "encff140qly.bigwig-1702320857138-sessionTrack-LinearWiggleDisplay" + } + ] +} \ No newline at end of file diff --git a/playground-data/jbrowse-config/.ipynb_checkpoints/chipseq_pval_bigwig-checkpoint.json b/playground-data/jbrowse-config/.ipynb_checkpoints/chipseq_pval_bigwig-checkpoint.json new file mode 100644 index 00000000..44db553b --- /dev/null +++ b/playground-data/jbrowse-config/.ipynb_checkpoints/chipseq_pval_bigwig-checkpoint.json @@ -0,0 +1,21 @@ +{ + "type": "QuantitativeTrack", + "trackId": "encff561sgx.bigwig-1702321270752-sessionTrack", + "name": "ENCFF561SGX.bigWig", + "assemblyNames": [ + "hg38" + ], + "adapter": { + "type": "BigWigAdapter", + "bigWigLocation": { + "locationType": "UriLocation", + "uri": "https://www.encodeproject.org/files/ENCFF561SGX/@@download/ENCFF561SGX.bigWig" + } + }, + "displays": [ + { + "type": "LinearWiggleDisplay", + "displayId": "encff561sgx.bigwig-1702321270752-sessionTrack-LinearWiggleDisplay" + } + ] +} \ No newline at end of file diff --git a/playground-data/jbrowse-config/.ipynb_checkpoints/hic_hic-checkpoint.json b/playground-data/jbrowse-config/.ipynb_checkpoints/hic_hic-checkpoint.json new file mode 100644 index 00000000..1ef9fdc6 --- /dev/null +++ b/playground-data/jbrowse-config/.ipynb_checkpoints/hic_hic-checkpoint.json @@ -0,0 +1,21 @@ +{ + "type": "HicTrack", + "trackId": "gse174533%5f1%2dc11%2dcb1.2%2dc11%2dcb2.merge.hic-1702319986845-sessionTrack", + "name": "GSE174533%5F1%2DC11%2DCB1.2%2DC11%2DCB2.merge.hic", + "assemblyNames": [ + "hg38" + ], + "adapter": { + "type": "HicAdapter", + "hicLocation": { + "locationType": "UriLocation", + "uri": "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE174nnn/GSE174533/suppl/GSE174533%5F1%2DC11%2DCB1.2%2DC11%2DCB2.merge.hic" + } + }, + "displays": [ + { + "type": "LinearHicDisplay", + "displayId": "gse174533%5f1%2dc11%2dcb1.2%2dc11%2dcb2.merge.hic-1702319986845-sessionTrack-LinearHicDisplay" + } + ] +} \ No newline at end of file diff --git a/playground-data/jbrowse-config/.ipynb_checkpoints/hic_insulation_bigwig-checkpoint.json b/playground-data/jbrowse-config/.ipynb_checkpoints/hic_insulation_bigwig-checkpoint.json new file mode 100644 index 00000000..38c3c1f4 --- /dev/null +++ b/playground-data/jbrowse-config/.ipynb_checkpoints/hic_insulation_bigwig-checkpoint.json @@ -0,0 +1,21 @@ +{ + "type": "QuantitativeTrack", + "trackId": "gse174533%5f1%2dc11%2dcb1.2%2dc11%2dcb2.insulationscore.bw-1702320154801-sessionTrack", + "name": "GSE174533%5F1%2DC11%2DCB1.2%2DC11%2DCB2.insulationScore.bw", + "assemblyNames": [ + "hg38" + ], + "adapter": { + "type": "BigWigAdapter", + "bigWigLocation": { + "locationType": "UriLocation", + "uri": "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE174nnn/GSE174533/suppl/GSE174533%5F1%2DC11%2DCB1.2%2DC11%2DCB2.insulationScore.bw" + } + }, + "displays": [ + { + "type": "LinearWiggleDisplay", + "displayId": "gse174533%5f1%2dc11%2dcb1.2%2dc11%2dcb2.insulationscore.bw-1702320154801-sessionTrack-LinearWiggleDisplay" + } + ] +} \ No newline at end of file diff --git a/playground-data/jbrowse-config/.ipynb_checkpoints/hic_pc1_bigwig-checkpoint.json b/playground-data/jbrowse-config/.ipynb_checkpoints/hic_pc1_bigwig-checkpoint.json new file mode 100644 index 00000000..e87b2f71 --- /dev/null +++ b/playground-data/jbrowse-config/.ipynb_checkpoints/hic_pc1_bigwig-checkpoint.json @@ -0,0 +1,21 @@ +{ + "type": "QuantitativeTrack", + "trackId": "gse174533%5f11%2dp53%2d15%2dd23.pc1.bw-1702320228955-sessionTrack", + "name": "GSE174533%5F11%2DP53%2D15%2Dd23.PC1.bw", + "assemblyNames": [ + "hg38" + ], + "adapter": { + "type": "BigWigAdapter", + "bigWigLocation": { + "locationType": "UriLocation", + "uri": "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE174nnn/GSE174533/suppl/GSE174533%5F11%2DP53%2D15%2Dd23.PC1.bw" + } + }, + "displays": [ + { + "type": "LinearWiggleDisplay", + "displayId": "gse174533%5f11%2dp53%2d15%2dd23.pc1.bw-1702320228955-sessionTrack-LinearWiggleDisplay" + } + ] +} \ No newline at end of file diff --git a/playground-data/jbrowse-config/.ipynb_checkpoints/wgbs_cpg_coverage_bigWig-checkpoint.json b/playground-data/jbrowse-config/.ipynb_checkpoints/wgbs_cpg_coverage_bigWig-checkpoint.json new file mode 100644 index 00000000..347361ac --- /dev/null +++ b/playground-data/jbrowse-config/.ipynb_checkpoints/wgbs_cpg_coverage_bigWig-checkpoint.json @@ -0,0 +1,21 @@ +{ + "type": "QuantitativeTrack", + "trackId": "encff750ori.bigwig-1702321769798-sessionTrack", + "name": "ENCFF750ORI.bigWig", + "assemblyNames": [ + "hg38" + ], + "adapter": { + "type": "BigWigAdapter", + "bigWigLocation": { + "locationType": "UriLocation", + "uri": "https://www.encodeproject.org/files/ENCFF750ORI/@@download/ENCFF750ORI.bigWig" + } + }, + "displays": [ + { + "type": "LinearWiggleDisplay", + "displayId": "encff750ori.bigwig-1702321769798-sessionTrack-LinearWiggleDisplay" + } + ] +} \ No newline at end of file diff --git a/playground-data/jbrowse-config/.ipynb_checkpoints/wgbs_cpg_methylation_bigBed-checkpoint.json b/playground-data/jbrowse-config/.ipynb_checkpoints/wgbs_cpg_methylation_bigBed-checkpoint.json new file mode 100644 index 00000000..5df18341 --- /dev/null +++ b/playground-data/jbrowse-config/.ipynb_checkpoints/wgbs_cpg_methylation_bigBed-checkpoint.json @@ -0,0 +1,25 @@ +{ + "type": "FeatureTrack", + "trackId": "encff256off.bigbed-1702321430813-sessionTrack", + "name": "ENCFF256OFF.bigBed", + "assemblyNames": [ + "hg38" + ], + "adapter": { + "type": "BigBedAdapter", + "bigBedLocation": { + "locationType": "UriLocation", + "uri": "https://www.encodeproject.org/files/ENCFF256OFF/@@download/ENCFF256OFF.bigBed" + } + }, + "displays": [ + { + "type": "LinearBasicDisplay", + "displayId": "encff256off.bigbed-1702321430813-sessionTrack-LinearBasicDisplay" + }, + { + "type": "LinearArcDisplay", + "displayId": "encff256off.bigbed-1702321430813-sessionTrack-LinearArcDisplay" + } + ] +} \ No newline at end of file diff --git a/playground-data/jbrowse-config/alignment_bam_hg38.json b/playground-data/jbrowse-config/alignment_bam_hg38.json new file mode 100644 index 00000000..cc2240c5 --- /dev/null +++ b/playground-data/jbrowse-config/alignment_bam_hg38.json @@ -0,0 +1,64 @@ +{ + "type": "AlignmentsTrack", + "trackId": "anon_chr1_complete.bam-1702318669309-sessionTrack", + "name": "anon_chr1_complete.bam", + "assemblyNames": [ + "hg38" + ], + "adapter": { + "type": "BamAdapter", + "bamLocation": { + "locationType": "BlobLocation", + "name": "anon_chr1_complete.bam", + "blobId": "b1702318658137-0" + }, + "index": { + "location": { + "locationType": "BlobLocation", + "name": "anon_chr1_complete.bam.bai", + "blobId": "b1702318664524-1" + } + }, + "sequenceAdapter": { + "type": "BgzipFastaAdapter", + "fastaLocation": { + "locationType": "UriLocation", + "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz" + }, + "faiLocation": { + "locationType": "UriLocation", + "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.fai" + }, + "metadataLocation": { + "locationType": "UriLocation", + "uri": "/path/to/fa.metadata.yaml" + }, + "gziLocation": { + "locationType": "UriLocation", + "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.gzi" + } + } + }, + "displays": [ + { + "type": "LinearAlignmentsDisplay", + "displayId": "anon_chr1_complete.bam-1702318669309-sessionTrack-LinearAlignmentsDisplay" + }, + { + "type": "LinearPileupDisplay", + "displayId": "anon_chr1_complete.bam-1702318669309-sessionTrack-LinearPileupDisplay" + }, + { + "type": "LinearSNPCoverageDisplay", + "displayId": "anon_chr1_complete.bam-1702318669309-sessionTrack-LinearSNPCoverageDisplay" + }, + { + "type": "LinearReadArcsDisplay", + "displayId": "anon_chr1_complete.bam-1702318669309-sessionTrack-LinearReadArcsDisplay" + }, + { + "type": "LinearReadCloudDisplay", + "displayId": "anon_chr1_complete.bam-1702318669309-sessionTrack-LinearReadCloudDisplay" + } + ] +} \ No newline at end of file diff --git a/playground-data/jbrowse-config/alignment_cram.hg38.json b/playground-data/jbrowse-config/alignment_cram.hg38.json new file mode 100644 index 00000000..67329452 --- /dev/null +++ b/playground-data/jbrowse-config/alignment_cram.hg38.json @@ -0,0 +1,62 @@ +{ + "type": "AlignmentsTrack", + "trackId": "test-qa.do263273.sa624744.wgs.20230728.aln.cram-1702318770555-sessionTrack", + "name": "TEST-QA.DO263273.SA624744.wgs.20230728.aln.cram", + "assemblyNames": [ + "hg38" + ], + "adapter": { + "type": "CramAdapter", + "cramLocation": { + "locationType": "BlobLocation", + "name": "TEST-QA.DO263273.SA624744.wgs.20230728.aln.cram", + "blobId": "b1702318762933-2" + }, + "craiLocation": { + "locationType": "BlobLocation", + "name": "TEST-QA.DO263273.SA624744.wgs.20230728.aln.cram.crai", + "blobId": "b1702318767264-3" + }, + "sequenceAdapter": { + "type": "BgzipFastaAdapter", + "fastaLocation": { + "locationType": "UriLocation", + "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz" + }, + "faiLocation": { + "locationType": "UriLocation", + "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.fai" + }, + "metadataLocation": { + "locationType": "UriLocation", + "uri": "/path/to/fa.metadata.yaml" + }, + "gziLocation": { + "locationType": "UriLocation", + "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.gzi" + } + } + }, + "displays": [ + { + "type": "LinearAlignmentsDisplay", + "displayId": "test-qa.do263273.sa624744.wgs.20230728.aln.cram-1702318770555-sessionTrack-LinearAlignmentsDisplay" + }, + { + "type": "LinearPileupDisplay", + "displayId": "test-qa.do263273.sa624744.wgs.20230728.aln.cram-1702318770555-sessionTrack-LinearPileupDisplay" + }, + { + "type": "LinearSNPCoverageDisplay", + "displayId": "test-qa.do263273.sa624744.wgs.20230728.aln.cram-1702318770555-sessionTrack-LinearSNPCoverageDisplay" + }, + { + "type": "LinearReadArcsDisplay", + "displayId": "test-qa.do263273.sa624744.wgs.20230728.aln.cram-1702318770555-sessionTrack-LinearReadArcsDisplay" + }, + { + "type": "LinearReadCloudDisplay", + "displayId": "test-qa.do263273.sa624744.wgs.20230728.aln.cram-1702318770555-sessionTrack-LinearReadCloudDisplay" + } + ] +} \ No newline at end of file diff --git a/playground-data/jbrowse-config/chipseq_IDR_bigBed.json b/playground-data/jbrowse-config/chipseq_IDR_bigBed.json new file mode 100644 index 00000000..cde5021c --- /dev/null +++ b/playground-data/jbrowse-config/chipseq_IDR_bigBed.json @@ -0,0 +1,25 @@ +{ + "type": "FeatureTrack", + "trackId": "encff772oad.bigbed-1702320934124-sessionTrack", + "name": "ENCFF772OAD.bigBed", + "assemblyNames": [ + "hg38" + ], + "adapter": { + "type": "BigBedAdapter", + "bigBedLocation": { + "locationType": "UriLocation", + "uri": "https://www.encodeproject.org/files/ENCFF772OAD/@@download/ENCFF772OAD.bigBed" + } + }, + "displays": [ + { + "type": "LinearBasicDisplay", + "displayId": "encff772oad.bigbed-1702320934124-sessionTrack-LinearBasicDisplay" + }, + { + "type": "LinearArcDisplay", + "displayId": "encff772oad.bigbed-1702320934124-sessionTrack-LinearArcDisplay" + } + ] +} \ No newline at end of file diff --git a/playground-data/jbrowse-config/chipseq_bedpe.json b/playground-data/jbrowse-config/chipseq_bedpe.json new file mode 100644 index 00000000..fdb3cdf8 --- /dev/null +++ b/playground-data/jbrowse-config/chipseq_bedpe.json @@ -0,0 +1,29 @@ +{ + "type": "VariantTrack", + "trackId": "encff327gbz.bedpe.gz-1702322266543-sessionTrack", + "name": "ENCFF327GBZ.bedpe.gz", + "assemblyNames": [ + "hg38" + ], + "adapter": { + "type": "BedpeAdapter", + "bedpeLocation": { + "locationType": "UriLocation", + "uri": "https://www.encodeproject.org/files/ENCFF327GBZ/@@download/ENCFF327GBZ.bedpe.gz" + } + }, + "displays": [ + { + "type": "LinearVariantDisplay", + "displayId": "encff327gbz.bedpe.gz-1702322266543-sessionTrack-LinearVariantDisplay" + }, + { + "type": "ChordVariantDisplay", + "displayId": "encff327gbz.bedpe.gz-1702322266543-sessionTrack-ChordVariantDisplay" + }, + { + "type": "LinearPairedArcDisplay", + "displayId": "encff327gbz.bedpe.gz-1702322266543-sessionTrack-LinearPairedArcDisplay" + } + ] +} \ No newline at end of file diff --git a/playground-data/jbrowse-config/chipseq_foldchange_bigwig.json b/playground-data/jbrowse-config/chipseq_foldchange_bigwig.json new file mode 100644 index 00000000..ba247071 --- /dev/null +++ b/playground-data/jbrowse-config/chipseq_foldchange_bigwig.json @@ -0,0 +1,21 @@ +{ + "type": "QuantitativeTrack", + "trackId": "encff140qly.bigwig-1702320857138-sessionTrack", + "name": "ENCFF140QLY.bigWig", + "assemblyNames": [ + "hg38" + ], + "adapter": { + "type": "BigWigAdapter", + "bigWigLocation": { + "locationType": "UriLocation", + "uri": "https://www.encodeproject.org/files/ENCFF140QLY/@@download/ENCFF140QLY.bigWig" + } + }, + "displays": [ + { + "type": "LinearWiggleDisplay", + "displayId": "encff140qly.bigwig-1702320857138-sessionTrack-LinearWiggleDisplay" + } + ] +} \ No newline at end of file diff --git a/playground-data/jbrowse-config/chipseq_pval_bigwig.json b/playground-data/jbrowse-config/chipseq_pval_bigwig.json new file mode 100644 index 00000000..44db553b --- /dev/null +++ b/playground-data/jbrowse-config/chipseq_pval_bigwig.json @@ -0,0 +1,21 @@ +{ + "type": "QuantitativeTrack", + "trackId": "encff561sgx.bigwig-1702321270752-sessionTrack", + "name": "ENCFF561SGX.bigWig", + "assemblyNames": [ + "hg38" + ], + "adapter": { + "type": "BigWigAdapter", + "bigWigLocation": { + "locationType": 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"Surgery" + ] + } + }, + "treatment_intent": { + "type": "string", + "enum": [ + "Curative", + "Palliative", + "Unknown" + ] + }, + "treatment_start_interval": { + "type": "integer", + "minimum": 0 + }, + "treatment_duration": { + "type": "integer", + "minimum": 0 + }, + "response_to_treatment": { + "type": "string", + "enum": [ + "Complete response", + "Disease progression", + "NED", + "Partial response", + "Stable disease" + ] + }, + "chemotherapy": { + "type": "array", + "items": { + "type": "object", + "propertyNames": { + "enum": [ + "drug_name", + "drug_rxnormcui", + "cumulative_drug_dosage", + "chemotherapy_dosage_units" + ] + }, + "required": [ + "drug_name", + "drug_rxnormcui", + "cumulative_drug_dosage", + "chemotherapy_dosage_units" + ], + "properties": { + "drug_name": { + "type": "string" + }, + "drug_rxnormcui": { + "type": "string" + }, + "cumulative_drug_dosage": { + "type": "integer", + "minimum": 0 + }, + "chemotherapy_dosage_units": { + "type": "string", + "enum": [ + "mg/m2", + "IU/m2", + "ug/m2", + "g/m2", + "mg/kg" + ] + } + } + } + }, + "hormone_therapy": { + "type": "array", + "items": { + "type": "object", + "propertyNames": { + "enum": [ + "drug_name", + "drug_rxnormcui", + "cumulative_drug_dosage", + "hormone_drug_dosage_units" + ] + }, + "required": [ + "drug_rxnormcui", + "drug_name", + "cumulative_drug_dosage", + "hormone_drug_dosage_units" + ], + "properties": { + "drug_name": { + "type": "string" + }, + "drug_rxnormcui": { + "type": "string" + }, + "cumulative_drug_dosage": { + "type": "integer", + "minimum": 0 + }, + "hormone_drug_dosage_units": { + "type": "string", + "enum": [ + "mg/m2", + "IU/m2", + "ug/m2", + "g/m2", + "mg/kg" + ] + } + } + } + }, + "radiation": { + "type": "array", + "items": { + "type": "object", + "propertyNames": { + "enum": [ + "radiation_therapy_modality", + "radiation_therapy_type", + "anatomical_site_irradiated", + "radiation_therapy_dosage", + "radiation_therapy_fractions" + ] + }, + "required": [ + "radiation_therapy_modality", + "radiation_therapy_type", + "anatomical_site_irradiated", + "radiation_therapy_dosage", + "radiation_therapy_fractions" + ], + "properties": { + "radiation_therapy_modality": { + "type": "string", + "enum": [ + "Electron", + "Heavy Ions", + "Photon", + "Proton" + ] + }, + "radiation_therapy_type": { + "type": "string", + "enum": [ + "External", + "Internal" + ] + }, + "anatomical_site_irradiated": { + "type": "string", + "enum": [ + "Abdomen", + "Body", + "Brain", + "Chest", + "Head", + "Liver", + "Lower Limb", + "Lung", + "Neck", + "Pelvis", + "Skin", + "Spine", + "Thorax", + "Upper Limb" + ] + }, + "radiation_therapy_dosage": { + "type": "number" + }, + "radiation_therapy_fractions": { + "type": "integer" + } + } + } + }, + "immunotherapy": { + "type": "array", + "items": { + "type": "object", + "propertyNames": { + "enum": [ + "drug_name", + "drug_rxnormcui", + "immunotherapy_type" + ] + }, + "required": [ + "drug_name", + "drug_rxnormcui", + "immunotherapy_type" + ], + "properties": { + "immunotherapy_type": { + "type": "string", + "enum": [ + "Cell-based", + "Immune checkpoint inhibitors", + "Monoclonal antibodies other than immune checkpoint inhibitors", + "Other immunomodulatory substances" + ] + }, + "drug_name": { + "type": "string" + }, + "drug_rxnormcui": { + "type": "string" + } + } + } + }, + "surgery": { + "type": "array", + "items": { + "type": "object", + "propertyNames": { + "enum": [ + "surgery_type", + "surgery_site", + "surgery_location", + "residual_tumour_classification" + ] + }, + "required": [ + "surgery_type" + ], + "properties": { + "surgery_type": { + "type": "string" + }, + "surgery_site": { + "type": "string" + }, + "surgery_location": { + "type": "string", + "enum": [ + "Local recurrence", + "Metastatic", + "Primary" + ] + }, + "residual_tumour_classification": { + "type": "string", + "enum": [ + "RX", + "R0", + "R1", + "R2", + "Not applicable", + "Unknown" + ] + } + } + } + } + }, + "allOf": [ + { + "if": { + "properties": { + "treatment_type": { + "contains": { + "const": "Chemotherapy" + } + } + } + }, + "then": { + "required": [ + "chemotherapy" + ] + } + }, + { + "if": { + "properties": { + "treatment_type": { + "contains": { + "const": "Radiation therapy" + } + } + } + }, + "then": { + "required": [ + "radiation" + ] + } + }, + { + "if": { + "properties": { + "treatment_type": { + "contains": { + "const": "Hormonal therapy" + } + } + } + }, + "then": { + "required": [ + "hormone_therapy" + ] + } + }, + { + "if": { + "properties": { + "treatment_type": { + "contains": { + "const": "Immunotherapy" + } + } + } + }, + "then": { + "required": [ + "immunotherapy" + ] + } + }, + { + "if": { + "properties": { + "treatment_type": { + "contains": { + "const": "Surgery" + } + } + } + }, + "then": { + "required": [ + "surgery" + ] + } + } + ] + } + } + } + } + }, + "comorbidity": { + "type": "array", + "items": { + "type": "object", + "propertyNames": { + "enum": [ + "age_at_comorbidity_diagnosis", + "comorbidity_type_code" + ] + }, + "required": [ + "comorbidity_type_code" + ], + "properties": { + "age_at_comorbidity_diagnosis": { + "type": "integer", + "minimum": 0 + }, + "comorbidity_type_code": { + "type": "string", + "pattern": "^[A-Z][0-9]{2}(.[0-9]{1,3}[A-Z]{0,1})?$" + } + } + } + } + }, + "if": { + "properties": { + "vital_status": { + "const": "Deceased" + } + } + }, + "then": { + "required": [ + "cause_of_death", + "survival_time" + ] + } + }, + "specimen": { + "type": "object", + "propertyNames": { + "enum": [ + "submitter_specimen_id", + "submitter_primary_diagnosis_id", + "specimen_acquisition_interval", + "specimen_anatomic_location", + "specimen_laterality", + "tumour_histological_type", + "pathological_tumour_staging_system", + "pathological_stage_group", + "tumour_grading_system", + "tumour_grade", + "percent_tumour_cells", + "reference_pathology_confirmed", + "cell_line" + ] + }, + "required": [ + "submitter_specimen_id", + "submitter_primary_diagnosis_id", + "specimen_acquisition_interval", + "specimen_anatomic_location", + "pathological_tumour_staging_system", + "pathological_stage_group", + "tumour_histological_type", + "reference_pathology_confirmed", + "tumour_grading_system", + "tumour_grade", + "percent_tumour_cells" + ], + "properties": { + "submitter_specimen_id": { + "type": "string" + }, + "submitter_primary_diagnosis_id": { + "type": "string" + }, + "specimen_acquisition_interval": { + "type": "integer", + "minimum": 0 + }, + "specimen_anatomic_location": { + "type": "string", + "pattern": "^[C][0-9]{2}(.[0-9]{1})?$" + }, + "specimen_laterality": { + "type": "string", + "enum": [ + "Left", + "Right", + "Not applicable", + "Unknown" + ] + }, + "tumour_histological_type": { + "type": "string", + "pattern": "^[8,9]{1}[0-9]{3}/[0,1,2,3,6,9]{1}[1-9]{0,1}$" + }, + "pathological_tumour_staging_system": { + "type": "string", + "enum": [ + "AJCC 8th edition", + "AJCC 7th edition", + "AJCC 6th edition", + "Ann Arbor staging system", + "Binet staging system", + "Durie-Salmon staging system", + "FIGO staging system", + "Lugano staging system", + "Rai staging system", + "Revised International staging system (RISS)", + "St Jude staging system" + ] + }, + "pathological_stage_group": { + "type": "string", + "enum": [ + "Occult Carcinoma", + "Stage 0", + "Stage 0a", + "Stage 0is", + "Stage 1", + "Stage 1A", + "Stage 1B", + "Stage A", + "Stage B", + "Stage C", + "Stage I", + "Stage IA", + "Stage IA1", + "Stage IA2", + "Stage IA3", + "Stage IAB", + "Stage IAE", + "Stage IAES", + "Stage IAS", + "Stage IB", + "Stage IB1", + "Stage IB2", + "Stage IBE", + "Stage IBES", + "Stage IBS", + "Stage IC", + "Stage IE", + "Stage IEA", + "Stage IEB", + "Stage IES", + "Stage II", + "Stage II bulky", + "Stage IIA", + "Stage IIA1", + "Stage IIA2", + "Stage IIAE", + "Stage IIAES", + "Stage IIAS", + "Stage IIB", + "Stage IIBE", + "Stage IIBES", + "Stage IIBS", + "Stage IIC", + "Stage IIE", + "Stage IIEA", + "Stage IIEB", + "Stage IIES", + "Stage III", + "Stage IIIA", + "Stage IIIA1", + "Stage IIIA2", + "Stage IIIAE", + "Stage IIIAES", + "Stage IIIAS", + "Stage IIIB", + "Stage IIIBE", + "Stage IIIBES", + "Stage IIIBS", + "Stage IIIC", + "Stage IIIC1", + "Stage IIIC2", + "Stage IIID", + "Stage IIIE", + "Stage IIIES", + "Stage IIIS", + "Stage IIS", + "Stage IS", + "Stage IV", + "Stage IVA", + "Stage IVA1", + "Stage IVA2", + "Stage IVAE", + "Stage IVAES", + "Stage IVAS", + "Stage IVB", + "Stage IVBE", + "Stage IVBES", + "Stage IVBS", + "Stage IVC", + "Stage IVE", + "Stage IVES", + "Stage IVS", + "Cannot be assessed" + ] + }, + "tumour_grading_system": { + "type": "string", + "enum": [ + "FNCLCC grading system", + "Four-tier grading system", + "Gleason grade group system", + "Grading system for GISTs", + "Grading system for GNETs", + "ISUP grading system", + "Nuclear grading system for DCIS", + "Scarff-Bloom-Richardson grading system", + "Three-tier grading system", + "Two-tier grading system", + "WHO grading system for CNS tumours" + ] + }, + "tumour_grade": { + "type": "string", + "enum": [ + "Low grade", + "High grade", + "GX", + "G1", + "G2", + "G3", + "G4", + "Low", + "High", + "Grade I", + "Grade II", + "Grade III", + "Grade IV", + "Grade Group 1", + "Grade Group 2", + "Grade Group 3", + "Grade Group 4", + "Grade Group 5" + ] + }, + "percent_tumour_cells": { + "type": "integer", + "minimum": 0 + }, + "reference_pathology_confirmed": { + "type": "string", + "enum": [ + "Yes", + "No", + "Unknown" + ] + }, + "cell_line": { + "type": "array", + "items": { + "type": "object", + "propertyNames": { + "enum": [ + "cell_line_name", + "cellosaurus_id", + "treatment" + ] + }, + "required": [ + "cell_line_name" + ], + "properties": { + "cell_line_name": { + "type": "string" + }, + "cellosaurus_id": { + "type": ["string","null"] + }, + "treatment": { + "type": "array", + "items": { + "type": "object", + "propertyNames": { + "enum":[ + "treatment_type", + "compound_name", + "duration", + "time_point", + "dosage", + "dosage_units" + ] + }, + "properties":{ + "treatment_typed": { + "type": ["string","null"] + }, + "compound_name": { + "type": ["string","null"] + }, + "duration": { + "type": ["string","null"] + }, + "time_point": { + "type": ["integer","null"] + }, + "dosage": { + "type": ["integer","null"] + }, + "dosage_units": { + "type": ["string"] + } + } + } + } + } + } + } + } + }, + "qualityControl" : { + "type":"array", + "items": { + "type": "object", + "propertyNames": { + "enum": [ + "test_name", + "test_value", + "expected_value", + "test_measurement_method", + "test_pass" + ] + }, + "properties": { + "test_name": { + "type": "string" + }, + "test_value": { + "type": "string" + }, + "expected_value": { + "type": "string" + }, + "test_measurement_method": { + "type": "string" + }, + "test_pass": { + "type": "string", + "enum":[ + "PASS", + "FAIL", + "WARN" + ] + } + } + } + }, + "publication" : { + "type":"object", + "propertyNames": { + "enum": [ + "title", + "doi" + ] + }, + "properties": { + "title": { + "type": ["string","null"] + }, + "doi": { + "type": ["string","null"] + } + } + }, + "archive" : { + "type":"object", + "propertyNames": { + "enum": [ + "ega", + "sra", + "icgc_argo" + ] + }, + "properties":{ + "EGA": { + "type": "array", + "items": { + "type": "object", + "properties": { + "EGAF": { + "type": "string" + } + } + } + }, + "SRA": { + "type": "array", + "items": { + "type": "object", + "properties": { + "GSE": { + "type": "string" + } + } + } + }, + "icgc_argo": { + "type": "array", + "items": { + "type": "object", + "properties": { + "fileID": { + "type": "string" + } + } + } + } + } + }, + "collaborator" : { + "type":"array", + "items": { + "type": "object", + "propertyNames": { + "enum": [ + "name", + "contact_email", + "affiliation" + ] + }, + "properties": { + "name": { + "type": "string" + }, + "contact_email": { + "type": ["string","null"], + "pattern": "^\\S+@\\S+\\.\\S+$" + }, + "affiliation": { + "type": ["string","null"] + } + } + } + } + } + } + } \ No newline at end of file From 38359bf9937009b700e6f542b09bac0f786cbc9f Mon Sep 17 00:00:00 2001 From: edsu7 <22638361+edsu7@users.noreply.github.com> Date: Thu, 18 Jan 2024 16:56:26 -0500 Subject: [PATCH 3/8] update to address dms/173 --- ...TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N1.json | 171 ++++++++++++++- ...TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N2.json | 171 ++++++++++++++- ...TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_T1.json | 178 +++++++++++++++- ...TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_T2.json | 178 +++++++++++++++- ...TEST_SPECIMEN_hlmegwbcehzqgmuaopom_N1.json | 130 +++++++++++- ...TEST_SPECIMEN_hlmegwbcehzqgmuaopom_N2.json | 130 +++++++++++- ...TEST_SPECIMEN_hlmegwbcehzqgmuaopom_T1.json | 137 +++++++++++- ...TEST_SPECIMEN_hlmegwbcehzqgmuaopom_T2.json | 137 +++++++++++- ...TEST_SPECIMEN_hsreltpusctapirhgwpr_N1.json | 174 +++++++++++++++- ...TEST_SPECIMEN_hsreltpusctapirhgwpr_N2.json | 174 +++++++++++++++- ...TEST_SPECIMEN_hsreltpusctapirhgwpr_T1.json | 181 +++++++++++++++- ...TEST_SPECIMEN_hsreltpusctapirhgwpr_T2.json | 181 +++++++++++++++- ...TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_N1.json | 161 +++++++++++++- ...TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_N2.json | 161 +++++++++++++- ...TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_T1.json | 168 ++++++++++++++- ...TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_T2.json | 168 ++++++++++++++- ...TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_N1.json | 180 +++++++++++++++- ...TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_N2.json | 180 +++++++++++++++- ...TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_T1.json | 187 ++++++++++++++++- ...TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_T2.json | 187 ++++++++++++++++- ...TEST_SPECIMEN_otliefvakqotckrtwbxm_N1.json | 169 ++++++++++++++- ...TEST_SPECIMEN_otliefvakqotckrtwbxm_N2.json | 169 ++++++++++++++- ...TEST_SPECIMEN_otliefvakqotckrtwbxm_T1.json | 176 +++++++++++++++- ...TEST_SPECIMEN_otliefvakqotckrtwbxm_T2.json | 176 +++++++++++++++- ...TEST_SPECIMEN_tixlzwxuqaoyhubfdlph_N1.json | 170 ++++++++++++++- ...TEST_SPECIMEN_tixlzwxuqaoyhubfdlph_T1.json | 177 +++++++++++++++- .../example-payloads/alignment_bam.json | 1 - .../alignment_bam_bcclfxzvjitgtbsvfnum.json | 182 ++++++++++++++++ .../example-payloads/alignment_cram.json | 1 - .../alignment_cram_bcclfxzvjitgtbsvfnum.json | 182 ++++++++++++++++ .../chipseq_foldchange_bigwig.json | 1 - ...oldchange_bigwig_zscpyibaevspyxlkyaip.json | 196 ++++++++++++++++++ .../example-payloads/chipseq_idr_bigbed.json | 1 - ...ipseq_idr_bigbed_zscpyibaevspyxlkyaip.json | 196 ++++++++++++++++++ .../example-payloads/chipseq_pval_bigwig.json | 1 - ...pseq_pval_bigwig_zscpyibaevspyxlkyaip.json | 196 ++++++++++++++++++ playground-data/example-payloads/hic_hic.json | 1 - .../hic_hic_eszycidpyopumzgdpamn.json | 156 ++++++++++++++ .../hic_insulation_bigwig.json | 1 - ...nsulation_bigwig_eszycidpyopumzgdpamn.json | 153 ++++++++++++++ .../example-payloads/hic_pc1_bigwig.json | 1 - .../hic_pc1_bigwig_eszycidpyopumzgdpamn.json | 153 ++++++++++++++ .../example-payloads/hichipseq_bedpe.json | 1 - .../hichipseq_bedpe_zscpyibaevspyxlkyaip.json | 193 +++++++++++++++++ .../wgbs_coverage_bigwig.json | 1 - ..._coverage_bigwig_eszycidpyopumzgdpamn.json | 155 ++++++++++++++ .../wgbs_methylation_bigbed.json | 1 - ...thylation_bigbed_eszycidpyopumzgdpamn.json | 156 ++++++++++++++ .../example-payloads/wgs_indel_vcf.json | 1 - .../wgs_indel_vcf_zscpyibaevspyxlkyaip.json | 190 +++++++++++++++++ .../example-payloads/wgs_mutect_snv_vcf.json | 1 - ...s_mutect_snv_vcf_zscpyibaevspyxlkyaip.json | 190 +++++++++++++++++ .../example-payloads/wgs_sanger_snv_vcf.json | 1 - ...s_sanger_snv_vcf_zscpyibaevspyxlkyaip.json | 190 +++++++++++++++++ 54 files changed, 6833 insertions(+), 40 deletions(-) delete mode 100644 playground-data/example-payloads/alignment_bam.json create mode 100644 playground-data/example-payloads/alignment_bam_bcclfxzvjitgtbsvfnum.json delete mode 100644 playground-data/example-payloads/alignment_cram.json create mode 100644 playground-data/example-payloads/alignment_cram_bcclfxzvjitgtbsvfnum.json delete mode 100644 playground-data/example-payloads/chipseq_foldchange_bigwig.json create mode 100644 playground-data/example-payloads/chipseq_foldchange_bigwig_zscpyibaevspyxlkyaip.json delete mode 100644 playground-data/example-payloads/chipseq_idr_bigbed.json create mode 100644 playground-data/example-payloads/chipseq_idr_bigbed_zscpyibaevspyxlkyaip.json delete mode 100644 playground-data/example-payloads/chipseq_pval_bigwig.json create mode 100644 playground-data/example-payloads/chipseq_pval_bigwig_zscpyibaevspyxlkyaip.json delete mode 100644 playground-data/example-payloads/hic_hic.json create mode 100644 playground-data/example-payloads/hic_hic_eszycidpyopumzgdpamn.json delete mode 100644 playground-data/example-payloads/hic_insulation_bigwig.json create mode 100644 playground-data/example-payloads/hic_insulation_bigwig_eszycidpyopumzgdpamn.json delete mode 100644 playground-data/example-payloads/hic_pc1_bigwig.json create mode 100644 playground-data/example-payloads/hic_pc1_bigwig_eszycidpyopumzgdpamn.json delete mode 100644 playground-data/example-payloads/hichipseq_bedpe.json create mode 100644 playground-data/example-payloads/hichipseq_bedpe_zscpyibaevspyxlkyaip.json delete mode 100644 playground-data/example-payloads/wgbs_coverage_bigwig.json create mode 100644 playground-data/example-payloads/wgbs_coverage_bigwig_eszycidpyopumzgdpamn.json delete mode 100644 playground-data/example-payloads/wgbs_methylation_bigbed.json create mode 100644 playground-data/example-payloads/wgbs_methylation_bigbed_eszycidpyopumzgdpamn.json delete mode 100644 playground-data/example-payloads/wgs_indel_vcf.json create mode 100644 playground-data/example-payloads/wgs_indel_vcf_zscpyibaevspyxlkyaip.json delete mode 100644 playground-data/example-payloads/wgs_mutect_snv_vcf.json create mode 100644 playground-data/example-payloads/wgs_mutect_snv_vcf_zscpyibaevspyxlkyaip.json delete mode 100644 playground-data/example-payloads/wgs_sanger_snv_vcf.json create mode 100644 playground-data/example-payloads/wgs_sanger_snv_vcf_zscpyibaevspyxlkyaip.json diff --git a/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N1.json b/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N1.json index 6f954d87..d78ea087 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N1.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N1.json @@ -1 +1,170 @@ -{"path": "/Users/esu/Desktop/GitHub/dms/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N1.json", "json": {"samples": [{"submitterSampleId": "TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N1", "sampleType": "Total DNA", "matchedNormalSubmitterSampleId": null, "specimen": 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"surgery_site": "C46.7", "surgery_location": "Metastatic", "residual_tumour_classification": "R2"}], "chemotherapy": [{"drug_name": "leucovorin", "drug_rxnormcui": "6313", "cumulative_drug_dosage": 29, "chemotherapy_dosage_units": "IU/m2"}]}], "follow_up": [{"submitter_follow_up_id": "TEST_FOLLOW_UP_zscpyibaevspyxlkyaip_1", "interval_of_followup": 59, "disease_status_at_followup": "Complete remission"}]}], "comorbidity": [{"age_at_comorbidity_diagnosis": 42, "comorbidity_type_code": "B07.48"}, {"age_at_comorbidity_diagnosis": 83, "comorbidity_type_code": "A66.7"}, {"age_at_comorbidity_diagnosis": 70, "comorbidity_type_code": "E15.40"}]}, "specimen": {"submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_zscpyibaevspyxlkyaip_0", "submitter_specimen_id": "TEST_SPECIMEN_zscpyibaevspyxlkyaip_N1", "specimen_acquisition_interval": 19, "specimen_anatomic_location": "C05", "specimen_laterality": "Right", "tumour_histological_type": "9672/68", "pathological_tumour_staging_system": "Rai staging system", "pathological_stage_group": "Stage IV", "tumour_grading_system": "FNCLCC grading system", "tumour_grade": "G2", "percent_tumour_cells": 47, "reference_pathology_confirmed": "Unknown"}, "files": [{"dataType": "SNV Variant Calls", "fileName": "EST-PR.DO250183.SA610229.wgs.20200513.sanger-wgs.somatic.snv.vcf.gz", "fileSize": 52, "fileMd5sum": "9a793e90d0d1e11301ea8da996446e59", "fileAccess": "controlled", "fileType": "VCF", "info": {"notes_for_mitchell": "hg38:21:29896103-36188915", "dataCategory": "Simple Nucelotide Variation"}}], "collaborator": [{"contact_email": "batman@batman_inc.org", "name": "batman", "affiliation": "batman inc"}], "experiment": {"platform": "ILLUMINA", "experimental_strategy": "WGS", "submitter_sequencing_experiment_id": "EXPERIMENT"}, "workflow": {"workflow_name": "sanger", "genome_build": "GRCh38_hla_decoy_ebv", "inputs": [{"analysis_type": "sequencing_alignment", "tumour_analysis_id": "00000000-0000-0000-0000-000000000000", "normal_analysis_id": "00000000-0000-0000-0000-000000000000"}]}}} \ No newline at end of file diff --git a/playground-data/example-payloads/wgs_sanger_snv_vcf_zscpyibaevspyxlkyaip.json b/playground-data/example-payloads/wgs_sanger_snv_vcf_zscpyibaevspyxlkyaip.json new file mode 100644 index 00000000..9c73a8a2 --- /dev/null +++ b/playground-data/example-payloads/wgs_sanger_snv_vcf_zscpyibaevspyxlkyaip.json @@ -0,0 +1,190 @@ +{ + "samples": [ + { + "submitterSampleId": "TEST_SPECIMEN_zscpyibaevspyxlkyaip_T1", + "sampleType": "Total DNA", + "matchedNormalSubmitterSampleId": "TEST_SPECIMEN_zscpyibaevspyxlkyaip_N1", + "specimen": { + "submitterSpecimenId": "TEST_SPECIMEN_zscpyibaevspyxlkyaip_N1", + "specimenType": "Tumour - unknown if derived from primary or metastatic", + "specimenTissueSource": "Blood derived - peripheral blood", + "tumourNormalDesignation": "Tumour" + }, + "donor": { + "submitterDonorId": "TEST_DONOR_zscpyibaevspyxlkyaip", + "gender": "Male" + } + } + ], + "donor": { + "submitter_donor_id": "TEST_DONOR_zscpyibaevspyxlkyaip", + "primary_site": "Hematopoietic and reticuloendothelial systems", + "vital_status": "Deceased", + "survival_time": 1520, + "cause_of_death": "Died of cancer", + "primary_diagnosis": [ + { + "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_zscpyibaevspyxlkyaip_0", + "age_at_diagnosis": 9, + "cancer_type_code": "D72.3", + "laterality": "Midline", + "clinical_tumour_staging_system": "FIGO staging system", + "clinical_stage_group": "Stage IVB", + "lymph_nodes_examined_status": "Not applicable", + "performance_status": "Unknown", + "treatment": [ + { + "submitter_treatment_id": "TEST_TREATMENT_zscpyibaevspyxlkyaip_0", + "treatment_type": [ + "Surgery" + ], + "treatment_intent": "Curative", + "treatment_start_interval": 26, + "treatment_duration": 36, + "response_to_treatment": "Complete response", + "surgery": [ + { + "surgery_type": "Bypass Gastrojejunostomy", + "surgery_site": "C27.8", + "surgery_location": "Metastatic", + "residual_tumour_classification": "R0" + } + ] + } + ], + "follow_up": [ + { + "submitter_follow_up_id": "TEST_FOLLOW_UP_zscpyibaevspyxlkyaip_0", + "interval_of_followup": 82, + "disease_status_at_followup": "Partial remission" + } + ] + }, + { + "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_zscpyibaevspyxlkyaip_1", + "age_at_diagnosis": 10, + "cancer_type_code": "D30.8", + "laterality": "Unilateral, side not specified", + "clinical_tumour_staging_system": "Revised International staging system (RISS)", + "clinical_stage_group": "Stage III", + "lymph_nodes_examined_status": "Not applicable", + "performance_status": "Grade 4", + "treatment": [ + { + "submitter_treatment_id": "TEST_TREATMENT_zscpyibaevspyxlkyaip_1", + "treatment_type": [ + "Hormonal therapy", + "Surgery", + "Chemotherapy" + ], + "treatment_intent": "Palliative", + "treatment_start_interval": 7, + "treatment_duration": 16, + "response_to_treatment": "Stable disease", + "hormone_therapy": [ + { + "drug_name": "leucovorin", + "drug_rxnormcui": "6313", + "cumulative_drug_dosage": 98, + "hormone_drug_dosage_units": "mg/kg" + } + ], + "surgery": [ + { + "surgery_type": "Cholecystectomy", + "surgery_site": "C46.7", + "surgery_location": "Metastatic", + "residual_tumour_classification": "R2" + } + ], + "chemotherapy": [ + { + "drug_name": "leucovorin", + "drug_rxnormcui": "6313", + "cumulative_drug_dosage": 29, + "chemotherapy_dosage_units": "IU/m2" + } + ] + } + ], + "follow_up": [ + { + "submitter_follow_up_id": "TEST_FOLLOW_UP_zscpyibaevspyxlkyaip_1", + "interval_of_followup": 59, + "disease_status_at_followup": "Loco-regional progression" + } + ] + } + ], + "comorbidity": [ + { + "age_at_comorbidity_diagnosis": 42, + "comorbidity_type_code": "B07.48" + }, + { + "age_at_comorbidity_diagnosis": 83, + "comorbidity_type_code": "A66.7" + }, + { + "age_at_comorbidity_diagnosis": 70, + "comorbidity_type_code": "E15.40" + } + ] + }, + "specimen": { + "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_zscpyibaevspyxlkyaip_0", + "submitter_specimen_id": "TEST_SPECIMEN_zscpyibaevspyxlkyaip_N1", + "specimen_acquisition_interval": 19, + "specimen_anatomic_location": "C42", + "specimen_laterality": "Right" + }, + "files": [ + { + "dataType": "SNV Variant Calls", + "fileName": "TEST-PR.DO250183.SA610229.wgs.20200513.sanger-wgs.somatic.snv.vcf.gz", + "fileSize": 23947, + "fileMd5sum": "1ebce71c8231aeb7ac6c06c92adfd5db", + "fileAccess": "controlled", + "fileType": "VCF", + "info": { + "notes_for_mitchell": "hg38:21:29896103-36188915", + "dataCategory": "Simple Nucelotide Variation" + } + }, + { + "dataType": "VCF Index", + "fileName": "TEST-PR.DO250183.SA610229.wgs.20200513.sanger-wgs.somatic.snv.vcf.gz.tbi", + "fileSize": 185, + "fileMd5sum": "7a8482dc43849a4ee8bdd4c9c77fae0c", + "fileAccess": "controlled", + "fileType": "TBI", + "info": { + "notes_for_mitchell": "hg38:21:29896103-36188915", + "dataCategory": "Simple Nucelotide Variation" + } + } + ], + "collaborator": [ + { + "contact_email": "batman@batman_inc.org", + "name": "batman", + "affiliation": "batman inc" + } + ], + "experiment": { + "platform": "ILLUMINA", + "experimental_strategy": "WGS", + "submitter_sequencing_experiment_id": "EXPERIMENT" + }, + "workflow": { + "workflow_name": "sanger", + "genome_build": "GRCh38_hla_decoy_ebv", + "inputs": [ + { + "analysis_type": "sequencing_alignment", + "tumour_analysis_id": "00000000-0000-0000-0000-000000000000", + "normal_analysis_id": "00000000-0000-0000-0000-000000000000" + } + ] + } +} From 54c696fd918acfd41d03b2cfbca57f7cd0fa384f Mon Sep 17 00:00:00 2001 From: edsu7 <22638361+edsu7@users.noreply.github.com> Date: Thu, 18 Jan 2024 17:34:38 -0500 Subject: [PATCH 4/8] update payloads and general.json general.json - add support for multiple primary_sites - capitalize external repos payloads - adjust to array to suit primary_sitee --- ...TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N1.json | 2 +- ...TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N2.json | 2 +- ...TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_T1.json | 2 +- ...TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_T2.json | 4 +- ...TEST_SPECIMEN_hlmegwbcehzqgmuaopom_N1.json | 2 +- ...TEST_SPECIMEN_hlmegwbcehzqgmuaopom_N2.json | 2 +- ...TEST_SPECIMEN_hlmegwbcehzqgmuaopom_T1.json | 2 +- ...TEST_SPECIMEN_hlmegwbcehzqgmuaopom_T2.json | 2 +- ...TEST_SPECIMEN_hsreltpusctapirhgwpr_N1.json | 2 +- ...TEST_SPECIMEN_hsreltpusctapirhgwpr_N2.json | 2 +- ...TEST_SPECIMEN_hsreltpusctapirhgwpr_T1.json | 2 +- ...TEST_SPECIMEN_hsreltpusctapirhgwpr_T2.json | 2 +- ...TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_N1.json | 2 +- ...TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_N2.json | 2 +- ...TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_T1.json | 2 +- ...TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_T2.json | 2 +- ...TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_N1.json | 4 +- ...TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_N2.json | 4 +- ...TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_T1.json | 4 +- ...TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_T2.json | 4 +- ...TEST_SPECIMEN_otliefvakqotckrtwbxm_N1.json | 2 +- ...TEST_SPECIMEN_otliefvakqotckrtwbxm_N2.json | 2 +- ...TEST_SPECIMEN_otliefvakqotckrtwbxm_T1.json | 2 +- ...TEST_SPECIMEN_otliefvakqotckrtwbxm_T2.json | 2 +- ...TEST_SPECIMEN_tixlzwxuqaoyhubfdlph_N1.json | 2 +- ...TEST_SPECIMEN_tixlzwxuqaoyhubfdlph_T1.json | 2 +- .../alignment_bam_bcclfxzvjitgtbsvfnum.json | 4 +- .../alignment_cram_bcclfxzvjitgtbsvfnum.json | 4 +- ...oldchange_bigwig_zscpyibaevspyxlkyaip.json | 2 +- ...ipseq_idr_bigbed_zscpyibaevspyxlkyaip.json | 2 +- ...pseq_pval_bigwig_zscpyibaevspyxlkyaip.json | 2 +- .../hic_hic_eszycidpyopumzgdpamn.json | 2 +- ...nsulation_bigwig_eszycidpyopumzgdpamn.json | 2 +- .../hic_pc1_bigwig_eszycidpyopumzgdpamn.json | 2 +- .../hichipseq_bedpe_zscpyibaevspyxlkyaip.json | 2 +- ..._coverage_bigwig_eszycidpyopumzgdpamn.json | 2 +- ...thylation_bigbed_eszycidpyopumzgdpamn.json | 2 +- .../wgs_indel_vcf_zscpyibaevspyxlkyaip.json | 2 +- ...s_mutect_snv_vcf_zscpyibaevspyxlkyaip.json | 2 +- ...s_sanger_snv_vcf_zscpyibaevspyxlkyaip.json | 2 +- playground-data/song-schemas/general.json | 180 +++++++++--------- 41 files changed, 142 insertions(+), 132 deletions(-) diff --git a/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N1.json b/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N1.json index d78ea087..e7e150bf 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N1.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N1.json @@ -18,7 +18,7 @@ ], "donor": { "submitter_donor_id": "TEST_DONOR_hjdxmpeccamrjzybhqrl", - "primary_site": "Anus and anal canal", + "primary_site": ["Anus and anal canal"], "vital_status": "Alive", "survival_time": null, "cause_of_death": null, diff --git a/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N2.json b/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N2.json index 39ee4b55..dbe12301 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N2.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N2.json @@ -18,7 +18,7 @@ ], "donor": { "submitter_donor_id": "TEST_DONOR_hjdxmpeccamrjzybhqrl", - "primary_site": "Anus and anal canal", + "primary_site": ["Anus and anal canal"], "vital_status": "Alive", "survival_time": null, "cause_of_death": null, diff --git a/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_T1.json b/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_T1.json index 6b496c0a..3e5206cf 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_T1.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_T1.json @@ -18,7 +18,7 @@ ], "donor": { "submitter_donor_id": "TEST_DONOR_hjdxmpeccamrjzybhqrl", - "primary_site": "Anus and anal canal", + "primary_site": ["Anus and anal canal"], "vital_status": "Alive", "survival_time": null, "cause_of_death": null, diff --git a/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_T2.json b/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_T2.json index 6c83c349..9842711b 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_T2.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_T2.json @@ -18,7 +18,7 @@ ], "donor": { "submitter_donor_id": "TEST_DONOR_hjdxmpeccamrjzybhqrl", - "primary_site": "Anus and anal canal", + "primary_site": ["Anus and anal canal"], "vital_status": "Alive", "survival_time": null, "cause_of_death": null, @@ -117,7 +117,7 @@ "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_hjdxmpeccamrjzybhqrl_0", "submitter_specimen_id": "TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N2", "specimen_acquisition_interval": 72, - "specimen_anatomic_location": "C1u", + "specimen_anatomic_location": "C18", "specimen_laterality": "Unknown", "tumour_histological_type": "8643/34", "pathological_tumour_staging_system": "Durie-Salmon staging system", diff --git a/playground-data/example-payloads/TEST_SPECIMEN_hlmegwbcehzqgmuaopom_N1.json b/playground-data/example-payloads/TEST_SPECIMEN_hlmegwbcehzqgmuaopom_N1.json index a388d9c7..87d77505 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_hlmegwbcehzqgmuaopom_N1.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_hlmegwbcehzqgmuaopom_N1.json @@ -18,7 +18,7 @@ ], "donor": { "submitter_donor_id": "TEST_DONOR_hlmegwbcehzqgmuaopom", - "primary_site": "Esophagus", + "primary_site": ["Esophagus"], "vital_status": "Deceased", "survival_time": 373, "cause_of_death": "Died of other reasons", diff --git a/playground-data/example-payloads/TEST_SPECIMEN_hlmegwbcehzqgmuaopom_N2.json b/playground-data/example-payloads/TEST_SPECIMEN_hlmegwbcehzqgmuaopom_N2.json index 5f8c95d2..1bc562db 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_hlmegwbcehzqgmuaopom_N2.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_hlmegwbcehzqgmuaopom_N2.json @@ -18,7 +18,7 @@ ], "donor": { "submitter_donor_id": "TEST_DONOR_hlmegwbcehzqgmuaopom", - "primary_site": "Esophagus", + "primary_site": ["Esophagus"], "vital_status": "Deceased", "survival_time": 373, "cause_of_death": "Died of other reasons", diff --git a/playground-data/example-payloads/TEST_SPECIMEN_hlmegwbcehzqgmuaopom_T1.json b/playground-data/example-payloads/TEST_SPECIMEN_hlmegwbcehzqgmuaopom_T1.json index 8614a562..1d03d85b 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_hlmegwbcehzqgmuaopom_T1.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_hlmegwbcehzqgmuaopom_T1.json @@ -18,7 +18,7 @@ ], "donor": { "submitter_donor_id": "TEST_DONOR_hlmegwbcehzqgmuaopom", - "primary_site": "Esophagus", + "primary_site": ["Esophagus"], "vital_status": "Deceased", "survival_time": 373, "cause_of_death": "Died of other reasons", diff --git a/playground-data/example-payloads/TEST_SPECIMEN_hlmegwbcehzqgmuaopom_T2.json b/playground-data/example-payloads/TEST_SPECIMEN_hlmegwbcehzqgmuaopom_T2.json index 340abfd1..2ba035cf 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_hlmegwbcehzqgmuaopom_T2.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_hlmegwbcehzqgmuaopom_T2.json @@ -18,7 +18,7 @@ ], "donor": { "submitter_donor_id": "TEST_DONOR_hlmegwbcehzqgmuaopom", - "primary_site": "Esophagus", + "primary_site": ["Esophagus"], "vital_status": "Deceased", "survival_time": 373, "cause_of_death": "Died of other reasons", diff --git a/playground-data/example-payloads/TEST_SPECIMEN_hsreltpusctapirhgwpr_N1.json b/playground-data/example-payloads/TEST_SPECIMEN_hsreltpusctapirhgwpr_N1.json index e1b8b0d9..2a8d43c7 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_hsreltpusctapirhgwpr_N1.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_hsreltpusctapirhgwpr_N1.json @@ -18,7 +18,7 @@ ], "donor": { "submitter_donor_id": "TEST_DONOR_hsreltpusctapirhgwpr", - "primary_site": "Brain", + "primary_site": ["Brain"], "vital_status": "Deceased", "survival_time": 884, "cause_of_death": "Died of cancer", diff --git a/playground-data/example-payloads/TEST_SPECIMEN_hsreltpusctapirhgwpr_N2.json b/playground-data/example-payloads/TEST_SPECIMEN_hsreltpusctapirhgwpr_N2.json index a7e563b5..9301cc26 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_hsreltpusctapirhgwpr_N2.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_hsreltpusctapirhgwpr_N2.json @@ -18,7 +18,7 @@ ], "donor": { "submitter_donor_id": "TEST_DONOR_hsreltpusctapirhgwpr", - "primary_site": "Brain", + "primary_site": ["Brain"], "vital_status": "Deceased", "survival_time": 884, "cause_of_death": "Died of cancer", diff --git a/playground-data/example-payloads/TEST_SPECIMEN_hsreltpusctapirhgwpr_T1.json b/playground-data/example-payloads/TEST_SPECIMEN_hsreltpusctapirhgwpr_T1.json index 5101b31b..6f9fa27e 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_hsreltpusctapirhgwpr_T1.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_hsreltpusctapirhgwpr_T1.json @@ -18,7 +18,7 @@ ], "donor": { "submitter_donor_id": "TEST_DONOR_hsreltpusctapirhgwpr", - "primary_site": "Brain", + "primary_site": ["Brain"], "vital_status": "Deceased", "survival_time": 884, "cause_of_death": "Died of cancer", diff --git a/playground-data/example-payloads/TEST_SPECIMEN_hsreltpusctapirhgwpr_T2.json b/playground-data/example-payloads/TEST_SPECIMEN_hsreltpusctapirhgwpr_T2.json index 93183628..31ffe521 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_hsreltpusctapirhgwpr_T2.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_hsreltpusctapirhgwpr_T2.json @@ -18,7 +18,7 @@ ], "donor": { "submitter_donor_id": "TEST_DONOR_hsreltpusctapirhgwpr", - "primary_site": "Brain", + "primary_site": ["Brain"], "vital_status": "Deceased", "survival_time": 884, "cause_of_death": "Died of cancer", diff --git a/playground-data/example-payloads/TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_N1.json b/playground-data/example-payloads/TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_N1.json index 6abef62e..15dec6fe 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_N1.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_N1.json @@ -18,7 +18,7 @@ ], "donor": { "submitter_donor_id": "TEST_DONOR_kemubcrdlsbqgbcnnchc", - "primary_site": "Bladder", + "primary_site": ["Bladder"], "vital_status": "Alive", "survival_time": null, "cause_of_death": null, diff --git a/playground-data/example-payloads/TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_N2.json b/playground-data/example-payloads/TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_N2.json index 100cc9e8..4b89128a 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_N2.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_N2.json @@ -18,7 +18,7 @@ ], "donor": { "submitter_donor_id": "TEST_DONOR_kemubcrdlsbqgbcnnchc", - "primary_site": "Bladder", + "primary_site": ["Bladder"], "vital_status": "Alive", "survival_time": null, "cause_of_death": null, diff --git a/playground-data/example-payloads/TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_T1.json b/playground-data/example-payloads/TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_T1.json index 815d1184..e61919c0 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_T1.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_T1.json @@ -18,7 +18,7 @@ ], "donor": { "submitter_donor_id": "TEST_DONOR_kemubcrdlsbqgbcnnchc", - "primary_site": "Bladder", + "primary_site": ["Bladder"], "vital_status": "Alive", "survival_time": null, "cause_of_death": null, diff --git a/playground-data/example-payloads/TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_T2.json b/playground-data/example-payloads/TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_T2.json index 2fcbaf22..59dea9c9 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_T2.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_T2.json @@ -18,7 +18,7 @@ ], "donor": { "submitter_donor_id": "TEST_DONOR_kemubcrdlsbqgbcnnchc", - "primary_site": "Bladder", + "primary_site": ["Bladder"], "vital_status": "Alive", "survival_time": null, "cause_of_death": null, diff --git a/playground-data/example-payloads/TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_N1.json b/playground-data/example-payloads/TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_N1.json index 7755a002..d277274f 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_N1.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_N1.json @@ -18,7 +18,7 @@ ], "donor": { "submitter_donor_id": "TEST_DONOR_mynbiqpmzjplsgqejeyd", - "primary_site": "Pyriform sinus", + "primary_site": ["Pyriform sinus"], "vital_status": "Deceased", "survival_time": 180, "cause_of_death": "Unknown", @@ -63,7 +63,7 @@ { "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_mynbiqpmzjplsgqejeyd_1", "age_at_diagnosis": 51, - "cancer_type_code": "C79.89s", + "cancer_type_code": "C79.89", "laterality": "Unilateral, side not specified", "clinical_tumour_staging_system": "FIGO staging system", "clinical_stage_group": "Stage IVA", diff --git a/playground-data/example-payloads/TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_N2.json b/playground-data/example-payloads/TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_N2.json index f9d66e78..cea4e6c5 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_N2.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_N2.json @@ -18,7 +18,7 @@ ], "donor": { "submitter_donor_id": "TEST_DONOR_mynbiqpmzjplsgqejeyd", - "primary_site": "Pyriform sinus", + "primary_site": ["Pyriform sinus"], "vital_status": "Deceased", "survival_time": 180, "cause_of_death": "Unknown", @@ -63,7 +63,7 @@ { "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_mynbiqpmzjplsgqejeyd_1", "age_at_diagnosis": 51, - "cancer_type_code": "C79.89s", + "cancer_type_code": "C79.89", "laterality": "Unilateral, side not specified", "clinical_tumour_staging_system": "FIGO staging system", "clinical_stage_group": "Stage IVA", diff --git a/playground-data/example-payloads/TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_T1.json b/playground-data/example-payloads/TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_T1.json index 6368e681..32608483 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_T1.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_T1.json @@ -18,7 +18,7 @@ ], "donor": { "submitter_donor_id": "TEST_DONOR_mynbiqpmzjplsgqejeyd", - "primary_site": "Pyriform sinus", + "primary_site": ["Pyriform sinus"], "vital_status": "Deceased", "survival_time": 180, "cause_of_death": "Unknown", @@ -63,7 +63,7 @@ { "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_mynbiqpmzjplsgqejeyd_1", "age_at_diagnosis": 51, - "cancer_type_code": "C79.89s", + "cancer_type_code": "C79.89", "laterality": "Unilateral, side not specified", "clinical_tumour_staging_system": "FIGO staging system", "clinical_stage_group": "Stage IVA", diff --git a/playground-data/example-payloads/TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_T2.json b/playground-data/example-payloads/TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_T2.json index 53736833..8cbeb88c 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_T2.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_T2.json @@ -18,7 +18,7 @@ ], "donor": { "submitter_donor_id": "TEST_DONOR_mynbiqpmzjplsgqejeyd", - "primary_site": "Pyriform sinus", + "primary_site": ["Pyriform sinus"], "vital_status": "Deceased", "survival_time": 180, "cause_of_death": "Unknown", @@ -63,7 +63,7 @@ { "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_mynbiqpmzjplsgqejeyd_1", "age_at_diagnosis": 51, - "cancer_type_code": "C79.89s", + "cancer_type_code": "C79.89", "laterality": "Unilateral, side not specified", "clinical_tumour_staging_system": "FIGO staging system", "clinical_stage_group": "Stage IVA", diff --git a/playground-data/example-payloads/TEST_SPECIMEN_otliefvakqotckrtwbxm_N1.json b/playground-data/example-payloads/TEST_SPECIMEN_otliefvakqotckrtwbxm_N1.json index a25e577f..b866c192 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_otliefvakqotckrtwbxm_N1.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_otliefvakqotckrtwbxm_N1.json @@ -18,7 +18,7 @@ ], "donor": { "submitter_donor_id": "TEST_DONOR_otliefvakqotckrtwbxm", - "primary_site": "Trachea|Colon", + "primary_site": ["Trachea","Colon"], "vital_status": "Alive", "survival_time": null, "cause_of_death": null, diff --git a/playground-data/example-payloads/TEST_SPECIMEN_otliefvakqotckrtwbxm_N2.json b/playground-data/example-payloads/TEST_SPECIMEN_otliefvakqotckrtwbxm_N2.json index 92132117..1b75e384 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_otliefvakqotckrtwbxm_N2.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_otliefvakqotckrtwbxm_N2.json @@ -18,7 +18,7 @@ ], "donor": { "submitter_donor_id": "TEST_DONOR_otliefvakqotckrtwbxm", - "primary_site": "Trachea|Colon", + "primary_site": ["Trachea","Colon"], "vital_status": "Alive", "survival_time": null, "cause_of_death": null, diff --git a/playground-data/example-payloads/TEST_SPECIMEN_otliefvakqotckrtwbxm_T1.json b/playground-data/example-payloads/TEST_SPECIMEN_otliefvakqotckrtwbxm_T1.json index 48df5ff2..c2164983 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_otliefvakqotckrtwbxm_T1.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_otliefvakqotckrtwbxm_T1.json @@ -18,7 +18,7 @@ ], "donor": { "submitter_donor_id": "TEST_DONOR_otliefvakqotckrtwbxm", - "primary_site": "Trachea|Colon", + "primary_site": ["Trachea","Colon"], "vital_status": "Alive", "survival_time": null, "cause_of_death": null, diff --git a/playground-data/example-payloads/TEST_SPECIMEN_otliefvakqotckrtwbxm_T2.json b/playground-data/example-payloads/TEST_SPECIMEN_otliefvakqotckrtwbxm_T2.json index 79b3db66..640b5804 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_otliefvakqotckrtwbxm_T2.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_otliefvakqotckrtwbxm_T2.json @@ -18,7 +18,7 @@ ], "donor": { "submitter_donor_id": "TEST_DONOR_otliefvakqotckrtwbxm", - "primary_site": "Trachea|Colon", + "primary_site": ["Trachea","Colon"], "vital_status": "Alive", "survival_time": null, "cause_of_death": null, diff --git a/playground-data/example-payloads/TEST_SPECIMEN_tixlzwxuqaoyhubfdlph_N1.json b/playground-data/example-payloads/TEST_SPECIMEN_tixlzwxuqaoyhubfdlph_N1.json index d2ca0fd2..192c4a29 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_tixlzwxuqaoyhubfdlph_N1.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_tixlzwxuqaoyhubfdlph_N1.json @@ -18,7 +18,7 @@ ], "donor": { "submitter_donor_id": "TEST_DONOR_tixlzwxuqaoyhubfdlph", - "primary_site": "Bones, joints and articular cartilage of other and unspecified", + "primary_site": ["Bones, joints and articular cartilage of other and unspecified sites"], "vital_status": "Deceased", "survival_time": 1711, "cause_of_death": "Unknown", diff --git a/playground-data/example-payloads/TEST_SPECIMEN_tixlzwxuqaoyhubfdlph_T1.json b/playground-data/example-payloads/TEST_SPECIMEN_tixlzwxuqaoyhubfdlph_T1.json index f5bb6aa9..0232044d 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_tixlzwxuqaoyhubfdlph_T1.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_tixlzwxuqaoyhubfdlph_T1.json @@ -18,7 +18,7 @@ ], "donor": { "submitter_donor_id": "TEST_DONOR_tixlzwxuqaoyhubfdlph", - "primary_site": "Bones, joints and articular cartilage of other and unspecified", + "primary_site": ["Bones, joints and articular cartilage of other and unspecified sites"], "vital_status": "Deceased", "survival_time": 1711, "cause_of_death": "Unknown", diff --git a/playground-data/example-payloads/alignment_bam_bcclfxzvjitgtbsvfnum.json b/playground-data/example-payloads/alignment_bam_bcclfxzvjitgtbsvfnum.json index adc19a7b..35405400 100644 --- a/playground-data/example-payloads/alignment_bam_bcclfxzvjitgtbsvfnum.json +++ b/playground-data/example-payloads/alignment_bam_bcclfxzvjitgtbsvfnum.json @@ -18,7 +18,7 @@ ], "donor": { "submitter_donor_id": "TEST_DONOR_bcclfxzvjitgtbsvfnum", - "primary_site": "Brain", + "primary_site": ["Brain"], "vital_status": "Deceased", "survival_time": 1550, "cause_of_death": "Unknown", @@ -173,7 +173,7 @@ "genome_build": "GRCh38_hla_decoy_ebv", "inputs": [ { - "analysis_type": "Sequence Experiment", + "analysis_type": "sequencing_alignment", "tumour_analysis_id": "00000000-0000-0000-0000-000000000000", "normal_analysis_id": "00000000-0000-0000-0000-000000000000" } diff --git a/playground-data/example-payloads/alignment_cram_bcclfxzvjitgtbsvfnum.json b/playground-data/example-payloads/alignment_cram_bcclfxzvjitgtbsvfnum.json index 81ccec6e..96d28545 100644 --- a/playground-data/example-payloads/alignment_cram_bcclfxzvjitgtbsvfnum.json +++ b/playground-data/example-payloads/alignment_cram_bcclfxzvjitgtbsvfnum.json @@ -18,7 +18,7 @@ ], "donor": { "submitter_donor_id": "TEST_DONOR_bcclfxzvjitgtbsvfnum", - "primary_site": "Bones, joints and articular cartilage of limbs", + "primary_site": ["Bones, joints and articular cartilage of limbs"], "vital_status": "Deceased", "survival_time": 1550, "cause_of_death": "Unknown", @@ -173,7 +173,7 @@ "genome_build": "GRCh38_hla_decoy_ebv", "inputs": [ { - "analysis_type": "Sequence Experiment", + "analysis_type": "sequencing_alignment", "tumour_analysis_id": "00000000-0000-0000-0000-000000000000", "normal_analysis_id": "00000000-0000-0000-0000-000000000000" } diff --git a/playground-data/example-payloads/chipseq_foldchange_bigwig_zscpyibaevspyxlkyaip.json b/playground-data/example-payloads/chipseq_foldchange_bigwig_zscpyibaevspyxlkyaip.json index b0cee6cf..4b2e371a 100644 --- a/playground-data/example-payloads/chipseq_foldchange_bigwig_zscpyibaevspyxlkyaip.json +++ b/playground-data/example-payloads/chipseq_foldchange_bigwig_zscpyibaevspyxlkyaip.json @@ -18,7 +18,7 @@ ], "donor": { "submitter_donor_id": "TEST_DONOR_zscpyibaevspyxlkyaip", - "primary_site": "Hematopoietic and reticuloendothelial systems", + "primary_site": ["Hematopoietic and reticuloendothelial systems"], "vital_status": "Deceased", "survival_time": 1520, "cause_of_death": "Died of cancer", diff --git a/playground-data/example-payloads/chipseq_idr_bigbed_zscpyibaevspyxlkyaip.json b/playground-data/example-payloads/chipseq_idr_bigbed_zscpyibaevspyxlkyaip.json index 0b9f5ca4..c9ad6f7a 100644 --- a/playground-data/example-payloads/chipseq_idr_bigbed_zscpyibaevspyxlkyaip.json +++ b/playground-data/example-payloads/chipseq_idr_bigbed_zscpyibaevspyxlkyaip.json @@ -18,7 +18,7 @@ ], "donor": { "submitter_donor_id": "TEST_DONOR_zscpyibaevspyxlkyaip", - "primary_site": "Hematopoietic and reticuloendothelial systems", + "primary_site": ["Hematopoietic and reticuloendothelial systems"], "vital_status": "Deceased", "survival_time": 1520, "cause_of_death": "Died of cancer", diff --git a/playground-data/example-payloads/chipseq_pval_bigwig_zscpyibaevspyxlkyaip.json b/playground-data/example-payloads/chipseq_pval_bigwig_zscpyibaevspyxlkyaip.json index 0caebbe1..7083d8a4 100644 --- a/playground-data/example-payloads/chipseq_pval_bigwig_zscpyibaevspyxlkyaip.json +++ b/playground-data/example-payloads/chipseq_pval_bigwig_zscpyibaevspyxlkyaip.json @@ -18,7 +18,7 @@ ], "donor": { "submitter_donor_id": "TEST_DONOR_zscpyibaevspyxlkyaip", - "primary_site": "Hematopoietic and reticuloendothelial systems", + "primary_site": ["Hematopoietic and reticuloendothelial systems"], "vital_status": "Deceased", "survival_time": 1520, "cause_of_death": "Died of cancer", diff --git a/playground-data/example-payloads/hic_hic_eszycidpyopumzgdpamn.json b/playground-data/example-payloads/hic_hic_eszycidpyopumzgdpamn.json index dfbd2711..938e3f29 100644 --- a/playground-data/example-payloads/hic_hic_eszycidpyopumzgdpamn.json +++ b/playground-data/example-payloads/hic_hic_eszycidpyopumzgdpamn.json @@ -18,7 +18,7 @@ ], "donor": { "submitter_donor_id": "TEST_DONOR_eszycidpyopumzgdpamn", - "primary_site": "Nasal cavity and middle ear", + "primary_site": ["Nasal cavity and middle ear"], "vital_status": "Alive", "survival_time": null, "cause_of_death": null, diff --git a/playground-data/example-payloads/hic_insulation_bigwig_eszycidpyopumzgdpamn.json b/playground-data/example-payloads/hic_insulation_bigwig_eszycidpyopumzgdpamn.json index 3fe0f7f7..6eae33c8 100644 --- a/playground-data/example-payloads/hic_insulation_bigwig_eszycidpyopumzgdpamn.json +++ b/playground-data/example-payloads/hic_insulation_bigwig_eszycidpyopumzgdpamn.json @@ -18,7 +18,7 @@ ], "donor": { "submitter_donor_id": "TEST_DONOR_eszycidpyopumzgdpamn", - "primary_site": "Hematopoietic and reticuloendothelial systems", + "primary_site": ["Hematopoietic and reticuloendothelial systems"], "vital_status": "Alive", "survival_time": null, "cause_of_death": null, diff --git a/playground-data/example-payloads/hic_pc1_bigwig_eszycidpyopumzgdpamn.json b/playground-data/example-payloads/hic_pc1_bigwig_eszycidpyopumzgdpamn.json index f5bd968c..06b3f0ba 100644 --- a/playground-data/example-payloads/hic_pc1_bigwig_eszycidpyopumzgdpamn.json +++ b/playground-data/example-payloads/hic_pc1_bigwig_eszycidpyopumzgdpamn.json @@ -18,7 +18,7 @@ ], "donor": { "submitter_donor_id": "TEST_DONOR_eszycidpyopumzgdpamn", - "primary_site": "Hematopoietic and reticuloendothelial systems", + "primary_site": ["Hematopoietic and reticuloendothelial systems"], "vital_status": "Alive", "survival_time": null, "cause_of_death": null, diff --git a/playground-data/example-payloads/hichipseq_bedpe_zscpyibaevspyxlkyaip.json b/playground-data/example-payloads/hichipseq_bedpe_zscpyibaevspyxlkyaip.json index 9cfd18f3..c1cbad20 100644 --- a/playground-data/example-payloads/hichipseq_bedpe_zscpyibaevspyxlkyaip.json +++ b/playground-data/example-payloads/hichipseq_bedpe_zscpyibaevspyxlkyaip.json @@ -18,7 +18,7 @@ ], "donor": { "submitter_donor_id": "TEST_DONOR_zscpyibaevspyxlkyaip", - "primary_site": "Hematopoietic and reticuloendothelial systems", + "primary_site": ["Hematopoietic and reticuloendothelial systems"], "vital_status": "Deceased", "survival_time": 1520, "cause_of_death": "Died of cancer", diff --git a/playground-data/example-payloads/wgbs_coverage_bigwig_eszycidpyopumzgdpamn.json b/playground-data/example-payloads/wgbs_coverage_bigwig_eszycidpyopumzgdpamn.json index 48f11903..850427d0 100644 --- a/playground-data/example-payloads/wgbs_coverage_bigwig_eszycidpyopumzgdpamn.json +++ b/playground-data/example-payloads/wgbs_coverage_bigwig_eszycidpyopumzgdpamn.json @@ -18,7 +18,7 @@ ], "donor": { "submitter_donor_id": "TEST_DONOR_eszycidpyopumzgdpamn", - "primary_site": "Hematopoietic and reticuloendothelial systems", + "primary_site": ["Hematopoietic and reticuloendothelial systems"], "vital_status": "Alive", "survival_time": null, "cause_of_death": null, diff --git a/playground-data/example-payloads/wgbs_methylation_bigbed_eszycidpyopumzgdpamn.json b/playground-data/example-payloads/wgbs_methylation_bigbed_eszycidpyopumzgdpamn.json index 3450415c..8aca680a 100644 --- a/playground-data/example-payloads/wgbs_methylation_bigbed_eszycidpyopumzgdpamn.json +++ b/playground-data/example-payloads/wgbs_methylation_bigbed_eszycidpyopumzgdpamn.json @@ -18,7 +18,7 @@ ], "donor": { "submitter_donor_id": "TEST_DONOR_eszycidpyopumzgdpamn", - "primary_site": "Hematopoietic and reticuloendothelial systems", + "primary_site": ["Hematopoietic and reticuloendothelial systems"], "vital_status": "Alive", "survival_time": null, "cause_of_death": null, diff --git a/playground-data/example-payloads/wgs_indel_vcf_zscpyibaevspyxlkyaip.json b/playground-data/example-payloads/wgs_indel_vcf_zscpyibaevspyxlkyaip.json index 09145ce7..c35832c5 100644 --- a/playground-data/example-payloads/wgs_indel_vcf_zscpyibaevspyxlkyaip.json +++ b/playground-data/example-payloads/wgs_indel_vcf_zscpyibaevspyxlkyaip.json @@ -18,7 +18,7 @@ ], "donor": { "submitter_donor_id": "TEST_DONOR_zscpyibaevspyxlkyaip", - "primary_site": "Hematopoietic and reticuloendothelial systems", + "primary_site": ["Hematopoietic and reticuloendothelial systems"], "vital_status": "Deceased", "survival_time": 1520, "cause_of_death": "Died of cancer", diff --git a/playground-data/example-payloads/wgs_mutect_snv_vcf_zscpyibaevspyxlkyaip.json b/playground-data/example-payloads/wgs_mutect_snv_vcf_zscpyibaevspyxlkyaip.json index a81bce02..9f969eaf 100644 --- a/playground-data/example-payloads/wgs_mutect_snv_vcf_zscpyibaevspyxlkyaip.json +++ b/playground-data/example-payloads/wgs_mutect_snv_vcf_zscpyibaevspyxlkyaip.json @@ -18,7 +18,7 @@ ], "donor": { "submitter_donor_id": "TEST_DONOR_zscpyibaevspyxlkyaip", - "primary_site": "Hematopoietic and reticuloendothelial systems", + "primary_site": ["Hematopoietic and reticuloendothelial systems"], "vital_status": "Deceased", "survival_time": 1520, "cause_of_death": "Died of cancer", diff --git a/playground-data/example-payloads/wgs_sanger_snv_vcf_zscpyibaevspyxlkyaip.json b/playground-data/example-payloads/wgs_sanger_snv_vcf_zscpyibaevspyxlkyaip.json index 9c73a8a2..4c7e747a 100644 --- a/playground-data/example-payloads/wgs_sanger_snv_vcf_zscpyibaevspyxlkyaip.json +++ b/playground-data/example-payloads/wgs_sanger_snv_vcf_zscpyibaevspyxlkyaip.json @@ -18,7 +18,7 @@ ], "donor": { "submitter_donor_id": "TEST_DONOR_zscpyibaevspyxlkyaip", - "primary_site": "Hematopoietic and reticuloendothelial systems", + "primary_site": ["Hematopoietic and reticuloendothelial systems"], "vital_status": "Deceased", "survival_time": 1520, "cause_of_death": "Died of cancer", diff --git a/playground-data/song-schemas/general.json b/playground-data/song-schemas/general.json index 89341df3..854613d8 100644 --- a/playground-data/song-schemas/general.json +++ b/playground-data/song-schemas/general.json @@ -296,79 +296,84 @@ "type": "string" }, "primary_site": { - "type": "string", - "enum": [ - "Accessory sinuses", - "Adrenal gland", - "Anus and anal canal", - "Base of tongue", - "Bladder", - "Bones, joints and articular cartilage of limbs", - "Bones, joints and articular cartilage of other and unspecified sites", - "Brain", - "Breast", - "Bronchus and lung", - "Cervix uteri", - "Colon", - "Connective, subcutaneous and other soft tissues", - "Corpus uteri", - "Esophagus", - "Eye and adnexa", - "Floor of mouth", - "Gallbladder", - "Gum", - "Heart, mediastinum, and pleura", - "Hematopoietic and reticuloendothelial systems", - "Hypopharynx", - "Kidney", - "Larynx", - "Lip", - "Liver and intrahepatic bile ducts", - "Lymph nodes", - "Meninges", - "Nasal cavity and middle ear", - "Nasopharynx", - "Oropharynx", - "Other and ill-defined digestive organs", - "Other and ill-defined sites", - "Other and ill-defined sites in lip, oral cavity and pharynx", - "Other and ill-defined sites within respiratory system and intrathoracic organs", - "Other and unspecified female genital organs", - "Other and unspecified major salivary glands", - "Other and unspecified male genital organs", - "Other and unspecified parts of biliary tract", - "Other and unspecified parts of mouth", - "Other and unspecified parts of tongue", - "Other and unspecified urinary organs", - "Other endocrine glands and related structures", - "Ovary", - "Palate", - "Pancreas", - "Parotid gland", - "Penis", - "Peripheral nerves and autonomic nervous system", - "Placenta", - "Prostate gland", - "Pyriform sinus", - "Rectosigmoid junction", - "Rectum", - "Renal pelvis", - "Retroperitoneum and peritoneum", - "Skin", - "Small intestine", - "Spinal cord, cranial nerves, and other parts of central nervous system", - "Stomach", - "Testis", - "Thymus", - "Thyroid gland", - "Tonsil", - "Trachea", - "Ureter", - "Uterus, NOS", - "Vagina", - "Vulva" - ] - }, + "type": "array", + "minItems": 1, + "items": { + "type": "string", + "enum": [ + "Accessory sinuses", + "Adrenal gland", + "Anus and anal canal", + "Base of tongue", + "Bladder", + "Bones, joints and articular cartilage of limbs", + "Bones, joints and articular cartilage of other and unspecified sites", + "Brain", + "Breast", + "Bronchus and lung", + "Cervix uteri", + "Colon", + "Connective, subcutaneous and other soft tissues", + "Corpus uteri", + "Esophagus", + "Eye and adnexa", + "Floor of mouth", + "Gallbladder", + "Gum", + "Heart, mediastinum, and pleura", + "Hematopoietic and reticuloendothelial systems", + "Hypopharynx", + "Kidney", + "Larynx", + "Lip", + "Liver and intrahepatic bile ducts", + "Lymph nodes", + "Meninges", + "Nasal cavity and middle ear", + "Nasopharynx", + "Oropharynx", + "Other and ill-defined digestive organs", + "Other and ill-defined sites", + "Other and ill-defined sites in lip, oral cavity and pharynx", + "Other and ill-defined sites within respiratory system and intrathoracic organs", + "Other and unspecified female genital organs", + "Other and unspecified major salivary glands", + "Other and unspecified male genital organs", + "Other and unspecified parts of biliary tract", + "Other and unspecified parts of mouth", + "Other and unspecified parts of tongue", + "Other and unspecified urinary organs", + "Other endocrine glands and related structures", + "Ovary", + "Palate", + "Pancreas", + "Parotid gland", + "Penis", + "Peripheral nerves and autonomic nervous system", + "Placenta", + "Prostate gland", + "Pyriform sinus", + "Rectosigmoid junction", + "Rectum", + "Renal pelvis", + "Retroperitoneum and peritoneum", + "Skin", + "Small intestine", + "Spinal cord, cranial nerves, and other parts of central nervous system", + "Stomach", + "Testis", + "Thymus", + "Thyroid gland", + "Tonsil", + "Trachea", + "Ureter", + "Uterus, NOS", + "Vagina", + "Vulva" + ] + } + } + , "vital_status": { "type": "string", "enum": [ @@ -1069,14 +1074,7 @@ "submitter_specimen_id", "submitter_primary_diagnosis_id", "specimen_acquisition_interval", - "specimen_anatomic_location", - "pathological_tumour_staging_system", - "pathological_stage_group", - "tumour_histological_type", - "reference_pathology_confirmed", - "tumour_grading_system", - "tumour_grade", - "percent_tumour_cells" + "specimen_anatomic_location" ], "properties": { "submitter_specimen_id": { @@ -1381,9 +1379,10 @@ "type":"object", "propertyNames": { "enum": [ - "ega", - "sra", - "icgc_argo" + "EGA", + "SRA", + "ICGC_ARGO", + "ENCODE" ] }, "properties":{ @@ -1409,7 +1408,18 @@ } } }, - "icgc_argo": { + "ICGC_ARGO": { + "type": "array", + "items": { + "type": "object", + "properties": { + "fileID": { + "type": "string" + } + } + } + }, + "ENCODE": { "type": "array", "items": { "type": "object", From 4d963a18519ef2d285ebece317df2b0be95ba947 Mon Sep 17 00:00:00 2001 From: edsu7 <22638361+edsu7@users.noreply.github.com> Date: Thu, 18 Jan 2024 17:36:18 -0500 Subject: [PATCH 5/8] add files to gitignorre --- .gitignore | 4 +++- .gitignore.swp | Bin 0 -> 12288 bytes 2 files changed, 3 insertions(+), 1 deletion(-) create mode 100644 .gitignore.swp diff --git a/.gitignore b/.gitignore index 0abed450..13414f8b 100644 --- a/.gitignore +++ b/.gitignore @@ -35,4 +35,6 @@ build/ ## others -run.sh \ No newline at end of file +run.sh +.ipynb_checkpoints/data_generate-checkpoint.ipynb +data_generate.ipynb diff --git a/.gitignore.swp b/.gitignore.swp new file mode 100644 index 0000000000000000000000000000000000000000..b517bfb130353fd09027bb3e70e438f2a04f07fc GIT binary patch literal 12288 zcmeI1F^dyH6vro5X>oU=SlR3uun1%(YCuz}IlPF9lJh`Cj@jLDGr8T_b!L(%h;~}| z0kjfpd%?mlV0YMA3sx3(TKZ428zha*6(_ub-_E?rn>Q~%NU6{86X2>fDDiUGC&5%02v?yWPl8if&b8ej2U~s%GkX% zG>`xPtM~uk>x}&b``{yZ2i}0!;1zfZ9)TF#2e&~NTm%=u1~>&yf^~2d909*@&o}TD zd;y=qC-4Eh1uwx1Fa{Y&!5)xc+T&e7gA9-XGC&5%02v?yWPl8i0Wv@a4wC^pGTaSV zy&mL#psYi0eC(n;Rsx&#V5c8kK@eb#*TqIdI2#GCoEKP!Bb~-#v7Je6{@N}-72Jf) z#L75DNnyfR<1iEDWWp-VgoVwAD)OSRdMtg}z)j^ZD{0)kg9g`yWq4-k^f_^i>sZNI zt3BgYn(Avoue*6^p3a?j?PesSfnwaDu1RLa5Gd~v;e2^3;}2!zbNi%_e!zH?O6TTF zS@_*V8D-H^JiDpC-JjPVPCWOI{lY*c#!H(he9KB$WoEI@v#}8qD~m!|k;$<#%`)Oc PX<3!GwR!y(&tmomXp*;r literal 0 HcmV?d00001 From af390deadda150393b182592090fc4475e488f21 Mon Sep 17 00:00:00 2001 From: Mitchell Shiell <59712867+MitchellShiell@users.noreply.github.com> Date: Fri, 19 Jan 2024 11:54:30 -0500 Subject: [PATCH 6/8] gtg --- example-data/sequencing_alignment_sample_schema.json | 2 +- example-data/sequencing_experiment_sample_schema.json | 2 +- example-data/variant_calling_sample_schema.json | 2 +- .../TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N1.json | 4 ++-- .../TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N2.json | 4 ++-- .../TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_T1.json | 4 ++-- .../TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_T2.json | 4 ++-- ...pyxlkyaip.json => wxs_indel_vcf_zscpyibaevspyxlkyaip.json} | 0 .../song-schemas/.ipynb_checkpoints/general-checkpoint.json | 2 +- playground-data/song-schemas/general.json | 2 +- 10 files changed, 13 insertions(+), 13 deletions(-) rename playground-data/example-payloads/{wgs_indel_vcf_zscpyibaevspyxlkyaip.json => wxs_indel_vcf_zscpyibaevspyxlkyaip.json} (100%) diff --git a/example-data/sequencing_alignment_sample_schema.json b/example-data/sequencing_alignment_sample_schema.json index 19833a50..05e43fd4 100644 --- a/example-data/sequencing_alignment_sample_schema.json +++ b/example-data/sequencing_alignment_sample_schema.json @@ -347,7 +347,7 @@ "enum":[ "Accessory sinuses", "Adrenal gland", - "Anus and anal canal", + "Pancreas", "Base of tongue", "Bladder", "Bones, joints and articular cartilage of limbs", diff --git a/example-data/sequencing_experiment_sample_schema.json b/example-data/sequencing_experiment_sample_schema.json index ee28a7cb..6524dc0b 100644 --- a/example-data/sequencing_experiment_sample_schema.json +++ b/example-data/sequencing_experiment_sample_schema.json @@ -274,7 +274,7 @@ "enum":[ "Accessory sinuses", "Adrenal gland", - "Anus and anal canal", + "Pancreas", "Base of tongue", "Bladder", "Bones, joints and articular cartilage of limbs", diff --git a/example-data/variant_calling_sample_schema.json b/example-data/variant_calling_sample_schema.json index 72a3fbe7..8911b745 100644 --- a/example-data/variant_calling_sample_schema.json +++ b/example-data/variant_calling_sample_schema.json @@ -158,7 +158,7 @@ "enum":[ "Accessory sinuses", "Adrenal gland", - "Anus and anal canal", + "Pancreas", "Base of tongue", "Bladder", "Bones, joints and articular cartilage of limbs", diff --git a/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N1.json b/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N1.json index e7e150bf..e600d4b7 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N1.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N1.json @@ -6,7 +6,7 @@ "matchedNormalSubmitterSampleId": null, "specimen": { "submitterSpecimenId": "TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N1", - "specimenType": "Anus and anal canal", + "specimenType": "Pancreas", "specimenTissueSource": "Sputum", "tumourNormalDesignation": "Normal" }, @@ -18,7 +18,7 @@ ], "donor": { "submitter_donor_id": "TEST_DONOR_hjdxmpeccamrjzybhqrl", - "primary_site": ["Anus and anal canal"], + "primary_site": ["Pancreas"], "vital_status": "Alive", "survival_time": null, "cause_of_death": null, diff --git a/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N2.json b/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N2.json index dbe12301..2d1ddddb 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N2.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N2.json @@ -7,7 +7,7 @@ "specimen": { "submitterSpecimenId": "TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N2", "specimenType": "Normal", - "specimenTissueSource": "Anus and anal canal", + "specimenTissueSource": "Pancreas", "tumourNormalDesignation": "Normal" }, "donor": { @@ -18,7 +18,7 @@ ], "donor": { "submitter_donor_id": "TEST_DONOR_hjdxmpeccamrjzybhqrl", - "primary_site": ["Anus and anal canal"], + "primary_site": ["Pancreas"], "vital_status": "Alive", "survival_time": null, "cause_of_death": null, diff --git a/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_T1.json b/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_T1.json index 3e5206cf..326daf9c 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_T1.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_T1.json @@ -7,7 +7,7 @@ "specimen": { "submitterSpecimenId": "TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N1", "specimenType": "Cell line - derived from normal", - "specimenTissueSource": "Anus and anal canal", + "specimenTissueSource": "Pancreas", "tumourNormalDesignation": "Tumour" }, "donor": { @@ -18,7 +18,7 @@ ], "donor": { "submitter_donor_id": "TEST_DONOR_hjdxmpeccamrjzybhqrl", - "primary_site": ["Anus and anal canal"], + "primary_site": ["Pancreas"], "vital_status": "Alive", "survival_time": null, "cause_of_death": null, diff --git a/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_T2.json b/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_T2.json index 9842711b..7a039af2 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_T2.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_T2.json @@ -7,7 +7,7 @@ "specimen": { "submitterSpecimenId": "TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N2", "specimenType": "Primary Tumour", - "specimenTissueSource": "Anus and anal canal", + "specimenTissueSource": "Pancreas", "tumourNormalDesignation": "Tumour" }, "donor": { @@ -18,7 +18,7 @@ ], "donor": { "submitter_donor_id": "TEST_DONOR_hjdxmpeccamrjzybhqrl", - "primary_site": ["Anus and anal canal"], + "primary_site": ["Pancreas"], "vital_status": "Alive", "survival_time": null, "cause_of_death": null, diff --git a/playground-data/example-payloads/wgs_indel_vcf_zscpyibaevspyxlkyaip.json b/playground-data/example-payloads/wxs_indel_vcf_zscpyibaevspyxlkyaip.json similarity index 100% rename from playground-data/example-payloads/wgs_indel_vcf_zscpyibaevspyxlkyaip.json rename to playground-data/example-payloads/wxs_indel_vcf_zscpyibaevspyxlkyaip.json diff --git a/playground-data/song-schemas/.ipynb_checkpoints/general-checkpoint.json b/playground-data/song-schemas/.ipynb_checkpoints/general-checkpoint.json index 89341df3..d674e1d8 100644 --- a/playground-data/song-schemas/.ipynb_checkpoints/general-checkpoint.json +++ b/playground-data/song-schemas/.ipynb_checkpoints/general-checkpoint.json @@ -300,7 +300,7 @@ "enum": [ "Accessory sinuses", "Adrenal gland", - "Anus and anal canal", + "Pancreas", "Base of tongue", "Bladder", "Bones, joints and articular cartilage of limbs", diff --git a/playground-data/song-schemas/general.json b/playground-data/song-schemas/general.json index 854613d8..ea5dde61 100644 --- a/playground-data/song-schemas/general.json +++ b/playground-data/song-schemas/general.json @@ -303,7 +303,7 @@ "enum": [ "Accessory sinuses", "Adrenal gland", - "Anus and anal canal", + "Pancreas", "Base of tongue", "Bladder", "Bones, joints and articular cartilage of limbs", From 4beb1afdc84d5ffc69387178cc1a1ad82070a2f0 Mon Sep 17 00:00:00 2001 From: Mitchell Shiell <59712867+MitchellShiell@users.noreply.github.com> Date: Fri, 19 Jan 2024 11:57:12 -0500 Subject: [PATCH 7/8] removed double entry of pancreas --- playground-data/song-schemas/general.json | 1 - 1 file changed, 1 deletion(-) diff --git a/playground-data/song-schemas/general.json b/playground-data/song-schemas/general.json index ea5dde61..7390e20a 100644 --- a/playground-data/song-schemas/general.json +++ b/playground-data/song-schemas/general.json @@ -303,7 +303,6 @@ "enum": [ "Accessory sinuses", "Adrenal gland", - "Pancreas", "Base of tongue", "Bladder", "Bones, joints and articular cartilage of limbs", From ce2a1010845be7133966f580ef236a321edb24ea Mon Sep 17 00:00:00 2001 From: Mitchell Shiell <59712867+MitchellShiell@users.noreply.github.com> Date: Mon, 4 Mar 2024 17:18:59 -0500 Subject: [PATCH 8/8] camilization + various minor updates --- .../wgbs_coverage_bigwig-checkpoint.json | 10 +- ...TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N1.json | 136 +- ...TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N2.json | 138 +- ...TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_T1.json | 154 +- ...TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_T2.json | 156 +- ...TEST_SPECIMEN_hlmegwbcehzqgmuaopom_N1.json | 96 +- ...TEST_SPECIMEN_hlmegwbcehzqgmuaopom_N2.json | 96 +- ...TEST_SPECIMEN_hlmegwbcehzqgmuaopom_T1.json | 112 +- ...TEST_SPECIMEN_hlmegwbcehzqgmuaopom_T2.json | 112 +- ...TEST_SPECIMEN_hsreltpusctapirhgwpr_N1.json | 140 +- ...TEST_SPECIMEN_hsreltpusctapirhgwpr_N2.json | 140 +- ...TEST_SPECIMEN_hsreltpusctapirhgwpr_T1.json | 156 +- ...TEST_SPECIMEN_hsreltpusctapirhgwpr_T2.json | 156 +- ...TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_N1.json | 126 +- ...TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_N2.json | 126 +- ...TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_T1.json | 144 +- ...TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_T2.json | 144 +- ...TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_N1.json | 154 +- ...TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_N2.json | 154 +- ...TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_T1.json | 170 +- ...TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_T2.json | 170 +- ...TEST_SPECIMEN_otliefvakqotckrtwbxm_N1.json | 137 +- ...TEST_SPECIMEN_otliefvakqotckrtwbxm_N2.json | 137 +- ...TEST_SPECIMEN_otliefvakqotckrtwbxm_T1.json | 153 +- ...TEST_SPECIMEN_otliefvakqotckrtwbxm_T2.json | 157 +- ...TEST_SPECIMEN_tixlzwxuqaoyhubfdlph_N1.json | 136 +- ...TEST_SPECIMEN_tixlzwxuqaoyhubfdlph_T1.json | 152 +- .../alignment_bam_bcclfxzvjitgtbsvfnum.json | 156 +- .../alignment_cram_bcclfxzvjitgtbsvfnum.json | 162 +- ...oldchange_bigwig_zscpyibaevspyxlkyaip.json | 176 +- ...ipseq_idr_bigbed_zscpyibaevspyxlkyaip.json | 176 +- ...pseq_pval_bigwig_zscpyibaevspyxlkyaip.json | 176 +- .../hic_hic_eszycidpyopumzgdpamn.json | 134 +- ...nsulation_bigwig_eszycidpyopumzgdpamn.json | 138 +- .../hic_pc1_bigwig_eszycidpyopumzgdpamn.json | 138 +- .../hichipseq_bedpe_zscpyibaevspyxlkyaip.json | 170 +- ..._coverage_bigwig_eszycidpyopumzgdpamn.json | 138 +- ...thylation_bigbed_eszycidpyopumzgdpamn.json | 142 +- ...s_mutect_snv_vcf_zscpyibaevspyxlkyaip.json | 168 +- ...s_sanger_snv_vcf_zscpyibaevspyxlkyaip.json | 166 +- .../wxs_indel_vcf_zscpyibaevspyxlkyaip.json | 168 +- .../song-schemas/playgroundSchema.json | 1498 +++++++++++++++++ 42 files changed, 4555 insertions(+), 2813 deletions(-) create mode 100644 playground-data/song-schemas/playgroundSchema.json diff --git a/playground-data/example-payloads/.ipynb_checkpoints/wgbs_coverage_bigwig-checkpoint.json b/playground-data/example-payloads/.ipynb_checkpoints/wgbs_coverage_bigwig-checkpoint.json index 1a2df069..eefed508 100644 --- a/playground-data/example-payloads/.ipynb_checkpoints/wgbs_coverage_bigwig-checkpoint.json +++ b/playground-data/example-payloads/.ipynb_checkpoints/wgbs_coverage_bigwig-checkpoint.json @@ -99,7 +99,7 @@ "files": [ { "dataType": "coverageCpgSites", - "fileName": "ENCFF750ORI.bigWig", + "fileName": "encfF750ORI.bigWig", "fileSize": 52, "fileMd5sum": "9a793e90d0d1e11301ea8da996446e59", "fileAccess": "controlled", @@ -136,11 +136,11 @@ ] }, "archive":{ - "SRA": [ - {"GSE":"GSE215679"} + "sra": [ + {"gse":"gse215679"} ], - "ENCODE": [ - {"ENCF":"ENCFF750ORI"} + "encode": [ + {"encf":"encfF750ORI"} ] }, "publication":{ diff --git a/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N1.json b/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N1.json index e600d4b7..5e381b1f 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N1.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N1.json @@ -1,4 +1,8 @@ { + "analysisType": { + "name": "playgroundSchema" + }, + "studyId": "OVPLG-01", "samples": [ { "submitterSampleId": "TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N1", @@ -17,108 +21,110 @@ } ], "donor": { - "submitter_donor_id": "TEST_DONOR_hjdxmpeccamrjzybhqrl", - "primary_site": ["Pancreas"], - "vital_status": "Alive", - "survival_time": null, - "cause_of_death": null, - "primary_diagnosis": [ + "submitterDonorId": "TEST_DONOR_hjdxmpeccamrjzybhqrl", + "primarySite": [ + "Pancreas" + ], + "vitalStatus": "Alive", + "survivalTime": null, + "causeOfDeath": null, + "primaryDiagnosis": [ { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_hjdxmpeccamrjzybhqrl_0", - "age_at_diagnosis": 27, - "cancer_type_code": "C21.2", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_hjdxmpeccamrjzybhqrl_0", + "ageAtDiagnosis": 27, + "cancerTypeCode": "C21.2", "laterality": "Bilateral", - "clinical_tumour_staging_system": "Durie-Salmon staging system", - "clinical_stage_group": "Stage II", - "lymph_nodes_examined_status": "Yes", - "performance_status": "Grade 4", + "clinicalTumourStagingSystem": "Durie-Salmon staging system", + "clinicalStageGroup": "Stage II", + "lymphNodesExaminedStatus": "Yes", + "performanceStatus": "Grade 4", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_hjdxmpeccamrjzybhqrl_0", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_hjdxmpeccamrjzybhqrl_0", + "treatmentType": [ "Hormonal therapy", "Radiation therapy", "Immunotherapy", "Surgery", "Chemotherapy" ], - "treatment_intent": "Curative", - "treatment_start_interval": 15, - "treatment_duration": 91, - "response_to_treatment": "NED", - "hormone_therapy": [ + "treatmentIntent": "Curative", + "treatmentStartInterval": 15, + "treatmentDuration": 91, + "responseToTreatment": "NED", + "hormoneTherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 76, - "hormone_drug_dosage_units": "IU/m2" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 76, + "hormoneDrugDosageUnits": "IU/m2" } ], "radiation": [ { - "radiation_therapy_modality": "Heavy Ions", - "radiation_therapy_type": "Internal", - "anatomical_site_irradiated": "Head", - "radiation_therapy_dosage": 24, - "radiation_therapy_fractions": 97 + "radiationTherapyModality": "Heavy Ions", + "radiationTherapyType": "Internal", + "anatomicalSiteIrradiated": "Head", + "radiationTherapyDosage": 24, + "radiationTherapyFractions": 97 } ], "immunotherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "immunotherapy_type": "Monoclonal antibodies other than immune checkpoint inhibitors" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "immunotherapyType": "Monoclonal antibodies other than immune checkpoint inhibitors" } ], "surgery": [ { - "surgery_type": "Biopsy", - "surgery_site": "C83.5", - "surgery_location": "Metastatic", - "residual_tumour_classification": "RX" + "surgeryType": "Biopsy", + "surgerySite": "C83.5", + "surgeryLocation": "Metastatic", + "residualTumourClassification": "RX" } ], "chemotherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 41, - "chemotherapy_dosage_units": "g/m2" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 41, + "chemotherapyDosageUnits": "g/m2" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_hjdxmpeccamrjzybhqrl_0", - "interval_of_followup": 54, - "disease_status_at_followup": "Progression NOS", - "relapse_type": "Local recurrence" + "submitterFollowUpId": "TEST_FOLLOW_UP_hjdxmpeccamrjzybhqrl_0", + "intervalOfFollowup": 54, + "diseaseStatusAtFollowup": "Progression NOS", + "relapseType": "Local recurrence" } ] } ], "comorbidity": [ { - "age_at_comorbidity_diagnosis": 60, - "comorbidity_type_code": "E12.51" + "ageAtComorbidityDiagnosis": 60, + "comorbidityTypeCode": "E12.51" }, { - "age_at_comorbidity_diagnosis": 54, - "comorbidity_type_code": "B40.46" + "ageAtComorbidityDiagnosis": 54, + "comorbidityTypeCode": "B40.46" }, { - "age_at_comorbidity_diagnosis": 63, - "comorbidity_type_code": "A72.22" + "ageAtComorbidityDiagnosis": 63, + "comorbidityTypeCode": "A72.22" } ] }, "specimen": { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_hjdxmpeccamrjzybhqrl_0", - "submitter_specimen_id": "TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N1", - "specimen_acquisition_interval": 53, - "specimen_anatomic_location": "C18", - "specimen_laterality": "Unknown" + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_hjdxmpeccamrjzybhqrl_0", + "submitterSpecimenId": "TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N1", + "specimenAcquisitionInterval": 53, + "specimenAnatomicLocation": "C18", + "specimenLaterality": "Unknown" }, "files": [ { @@ -146,25 +152,25 @@ ], "collaborator": [ { - "contact_email": "batman@batman_inc.org", + "contactEmail": "batman@batman_inc.org", "name": "batman", "affiliation": "batman inc" } ], "experiment": { "platform": "ILLUMINA", - "experimental_strategy": "WGS", - "submitter_sequencing_experiment_id": "EXPERIMENT" + "experimentalStrategy": "WGS", + "submitterSequencingExperimentId": "EXPERIMENT" }, "workflow": { - "workflow_name": "batman_stuff", - "genome_build": "GRCh38_hla_decoy_ebv", + "workflowName": "batman_stuff", + "genomeBuild": "GRCh38_hla_decoy_ebv", "inputs": [ { - "analysis_type": "sequencing_alignment", - "tumour_analysis_id": "00000000-0000-0000-0000-000000000000", - "normal_analysis_id": "00000000-0000-0000-0000-000000000000" + "analysisType": "sequencing_alignment", + "tumourAnalysisId": "00000000-0000-0000-0000-000000000000", + "normalAnalysisId": "00000000-0000-0000-0000-000000000000" } ] } -} +} \ No newline at end of file diff --git a/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N2.json b/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N2.json index 2d1ddddb..4ca2e4eb 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N2.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N2.json @@ -1,4 +1,8 @@ { + "analysisType": { + "name": "playgroundSchema" + }, + "studyId": "OVPLG-01", "samples": [ { "submitterSampleId": "TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N2", @@ -7,7 +11,7 @@ "specimen": { "submitterSpecimenId": "TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N2", "specimenType": "Normal", - "specimenTissueSource": "Pancreas", + "specimenTissueSource": "Plasma", "tumourNormalDesignation": "Normal" }, "donor": { @@ -17,108 +21,110 @@ } ], "donor": { - "submitter_donor_id": "TEST_DONOR_hjdxmpeccamrjzybhqrl", - "primary_site": ["Pancreas"], - "vital_status": "Alive", - "survival_time": null, - "cause_of_death": null, - "primary_diagnosis": [ + "submitterDonorId": "TEST_DONOR_hjdxmpeccamrjzybhqrl", + "primarySite": [ + "Pancreas" + ], + "vitalStatus": "Alive", + "survivalTime": null, + "causeOfDeath": null, + "primaryDiagnosis": [ { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_hjdxmpeccamrjzybhqrl_0", - "age_at_diagnosis": 27, - "cancer_type_code": "C21.2", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_hjdxmpeccamrjzybhqrl_0", + "ageAtDiagnosis": 27, + "cancerTypeCode": "C21.2", "laterality": "Bilateral", - "clinical_tumour_staging_system": "Durie-Salmon staging system", - "clinical_stage_group": "Stage II", - "lymph_nodes_examined_status": "Yes", - "performance_status": "Grade 4", + "clinicalTumourStagingSystem": "Durie-Salmon staging system", + "clinicalStageGroup": "Stage II", + "lymphNodesExaminedStatus": "Yes", + "performanceStatus": "Grade 4", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_hjdxmpeccamrjzybhqrl_0", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_hjdxmpeccamrjzybhqrl_0", + "treatmentType": [ "Hormonal therapy", "Radiation therapy", "Immunotherapy", "Surgery", "Chemotherapy" ], - "treatment_intent": "Curative", - "treatment_start_interval": 15, - "treatment_duration": 91, - "response_to_treatment": "NED", - "hormone_therapy": [ + "treatmentIntent": "Curative", + "treatmentStartInterval": 15, + "treatmentDuration": 91, + "responseToTreatment": "NED", + "hormoneTherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 76, - "hormone_drug_dosage_units": "IU/m2" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 76, + "hormoneDrugDosageUnits": "IU/m2" } ], "radiation": [ { - "radiation_therapy_modality": "Heavy Ions", - "radiation_therapy_type": "Internal", - "anatomical_site_irradiated": "Head", - "radiation_therapy_dosage": 24, - "radiation_therapy_fractions": 97 + "radiationTherapyModality": "Heavy Ions", + "radiationTherapyType": "Internal", + "anatomicalSiteIrradiated": "Head", + "radiationTherapyDosage": 24, + "radiationTherapyFractions": 97 } ], "immunotherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "immunotherapy_type": "Monoclonal antibodies other than immune checkpoint inhibitors" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "immunotherapyType": "Monoclonal antibodies other than immune checkpoint inhibitors" } ], "surgery": [ { - "surgery_type": "Biopsy", - "surgery_site": "C83.5", - "surgery_location": "Metastatic", - "residual_tumour_classification": "RX" + "surgeryType": "Biopsy", + "surgerySite": "C83.5", + "surgeryLocation": "Metastatic", + "residualTumourClassification": "RX" } ], "chemotherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 41, - "chemotherapy_dosage_units": "g/m2" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 41, + "chemotherapyDosageUnits": "g/m2" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_hjdxmpeccamrjzybhqrl_0", - "interval_of_followup": 54, - "disease_status_at_followup": "Progression NOS", - "relapse_type": "Local recurrence" + "submitterFollowUpId": "TEST_FOLLOW_UP_hjdxmpeccamrjzybhqrl_0", + "intervalOfFollowup": 54, + "diseaseStatusAtFollowup": "Progression NOS", + "relapseType": "Local recurrence" } ] } ], "comorbidity": [ { - "age_at_comorbidity_diagnosis": 60, - "comorbidity_type_code": "E12.51" + "ageAtComorbidityDiagnosis": 60, + "comorbidityTypeCode": "E12.51" }, { - "age_at_comorbidity_diagnosis": 54, - "comorbidity_type_code": "B40.46" + "ageAtComorbidityDiagnosis": 54, + "comorbidityTypeCode": "B40.46" }, { - "age_at_comorbidity_diagnosis": 63, - "comorbidity_type_code": "A72.22" + "ageAtComorbidityDiagnosis": 63, + "comorbidityTypeCode": "A72.22" } ] }, "specimen": { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_hjdxmpeccamrjzybhqrl_0", - "submitter_specimen_id": "TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N2", - "specimen_acquisition_interval": 38, - "specimen_anatomic_location": "C18", - "specimen_laterality": "Unknown" + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_hjdxmpeccamrjzybhqrl_0", + "submitterSpecimenId": "TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N2", + "specimenAcquisitionInterval": 38, + "specimenAnatomicLocation": "C18", + "specimenLaterality": "Unknown" }, "files": [ { @@ -146,25 +152,25 @@ ], "collaborator": [ { - "contact_email": "batman@batman_inc.org", + "contactEmail": "batman@batman_inc.org", "name": "batman", "affiliation": "batman inc" } ], "experiment": { "platform": "ILLUMINA", - "experimental_strategy": "WGS", - "submitter_sequencing_experiment_id": "EXPERIMENT" + "experimentalStrategy": "WGS", + "submitterSequencingExperimentId": "EXPERIMENT" }, "workflow": { - "workflow_name": "batman_stuff", - "genome_build": "GRCh38_hla_decoy_ebv", + "workflowName": "batman_stuff", + "genomeBuild": "GRCh38_hla_decoy_ebv", "inputs": [ { - "analysis_type": "sequencing_alignment", - "tumour_analysis_id": "00000000-0000-0000-0000-000000000000", - "normal_analysis_id": "00000000-0000-0000-0000-000000000000" + "analysisType": "sequencing_alignment", + "tumourAnalysisId": "00000000-0000-0000-0000-000000000000", + "normalAnalysisId": "00000000-0000-0000-0000-000000000000" } ] } -} +} \ No newline at end of file diff --git a/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_T1.json b/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_T1.json index 326daf9c..81c53c3c 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_T1.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_T1.json @@ -1,13 +1,17 @@ { + "analysisType": { + "name": "playgroundSchema" + }, + "studyId": "OVPLG-01", "samples": [ { "submitterSampleId": "TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_T1", "sampleType": "Total DNA", "matchedNormalSubmitterSampleId": "TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N1", "specimen": { - "submitterSpecimenId": "TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N1", + "submitterSpecimenId": "TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_T1", "specimenType": "Cell line - derived from normal", - "specimenTissueSource": "Pancreas", + "specimenTissueSource": "Solid tissue", "tumourNormalDesignation": "Tumour" }, "donor": { @@ -17,115 +21,117 @@ } ], "donor": { - "submitter_donor_id": "TEST_DONOR_hjdxmpeccamrjzybhqrl", - "primary_site": ["Pancreas"], - "vital_status": "Alive", - "survival_time": null, - "cause_of_death": null, - "primary_diagnosis": [ + "submitterDonorId": "TEST_DONOR_hjdxmpeccamrjzybhqrl", + "primarySite": [ + "Pancreas" + ], + "vitalStatus": "Alive", + "survivalTime": null, + "causeOfDeath": null, + "primaryDiagnosis": [ { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_hjdxmpeccamrjzybhqrl_0", - "age_at_diagnosis": 27, - "cancer_type_code": "C21.2", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_hjdxmpeccamrjzybhqrl_0", + "ageAtDiagnosis": 27, + "cancerTypeCode": "C21.2", "laterality": "Bilateral", - "clinical_tumour_staging_system": "Durie-Salmon staging system", - "clinical_stage_group": "Stage II", - "lymph_nodes_examined_status": "Yes", - "performance_status": "Grade 4", + "clinicalTumourStagingSystem": "Durie-Salmon staging system", + "clinicalStageGroup": "Stage II", + "lymphNodesExaminedStatus": "Yes", + "performanceStatus": "Grade 4", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_hjdxmpeccamrjzybhqrl_0", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_hjdxmpeccamrjzybhqrl_0", + "treatmentType": [ "Hormonal therapy", "Radiation therapy", "Immunotherapy", "Surgery", "Chemotherapy" ], - "treatment_intent": "Curative", - "treatment_start_interval": 15, - "treatment_duration": 91, - "response_to_treatment": "NED", - "hormone_therapy": [ + "treatmentIntent": "Curative", + "treatmentStartInterval": 15, + "treatmentDuration": 91, + "responseToTreatment": "NED", + "hormoneTherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 76, - "hormone_drug_dosage_units": "IU/m2" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 76, + "hormoneDrugDosageUnits": "IU/m2" } ], "radiation": [ { - "radiation_therapy_modality": "Heavy Ions", - "radiation_therapy_type": "Internal", - "anatomical_site_irradiated": "Head", - "radiation_therapy_dosage": 24, - "radiation_therapy_fractions": 97 + "radiationTherapyModality": "Heavy Ions", + "radiationTherapyType": "Internal", + "anatomicalSiteIrradiated": "Head", + "radiationTherapyDosage": 24, + "radiationTherapyFractions": 97 } ], "immunotherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "immunotherapy_type": "Monoclonal antibodies other than immune checkpoint inhibitors" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "immunotherapyType": "Monoclonal antibodies other than immune checkpoint inhibitors" } ], "surgery": [ { - "surgery_type": "Biopsy", - "surgery_site": "C83.5", - "surgery_location": "Metastatic", - "residual_tumour_classification": "RX" + "surgeryType": "Biopsy", + "surgerySite": "C83.5", + "surgeryLocation": "Metastatic", + "residualTumourClassification": "RX" } ], "chemotherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 41, - "chemotherapy_dosage_units": "g/m2" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 41, + "chemotherapyDosageUnits": "g/m2" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_hjdxmpeccamrjzybhqrl_0", - "interval_of_followup": 54, - "disease_status_at_followup": "Progression NOS", - "relapse_type": "Local recurrence" + "submitterFollowUpId": "TEST_FOLLOW_UP_hjdxmpeccamrjzybhqrl_0", + "intervalOfFollowup": 54, + "diseaseStatusAtFollowup": "Progression NOS", + "relapseType": "Local recurrence" } ] } ], "comorbidity": [ { - "age_at_comorbidity_diagnosis": 60, - "comorbidity_type_code": "E12.51" + "ageAtComorbidityDiagnosis": 60, + "comorbidityTypeCode": "E12.51" }, { - "age_at_comorbidity_diagnosis": 54, - "comorbidity_type_code": "B40.46" + "ageAtComorbidityDiagnosis": 54, + "comorbidityTypeCode": "B40.46" }, { - "age_at_comorbidity_diagnosis": 63, - "comorbidity_type_code": "A72.22" + "ageAtComorbidityDiagnosis": 63, + "comorbidityTypeCode": "A72.22" } ] }, "specimen": { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_hjdxmpeccamrjzybhqrl_0", - "submitter_specimen_id": "TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N1", - "specimen_acquisition_interval": 39, - "specimen_anatomic_location": "C18", - "specimen_laterality": "Unknown", - "tumour_histological_type": "8126/11", - "pathological_tumour_staging_system": "Revised International staging system (RISS)", - "pathological_stage_group": "Stage III", - "tumour_grading_system": "Two-tier grading system", - "tumour_grade": "High grade", - "percent_tumour_cells": 2, - "reference_pathology_confirmed": "Yes" + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_hjdxmpeccamrjzybhqrl_0", + "submitterSpecimenId": "TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N1", + "specimenAcquisitionInterval": 39, + "specimenAnatomicLocation": "C18", + "specimenLaterality": "Unknown", + "tumourHistologicalType": "8126/11", + "pathologicalTumourStagingSystem": "Revised International staging system (RISS)", + "pathologicalStageGroup": "Stage III", + "tumourGradingSystem": "Two-tier grading system", + "tumourGrade": "High grade", + "percentTumourCells": 2, + "referencePathologyConfirmed": "Yes" }, "files": [ { @@ -153,25 +159,25 @@ ], "collaborator": [ { - "contact_email": "batman@batman_inc.org", + "contactEmail": "batman@batman_inc.org", "name": "batman", "affiliation": "batman inc" } ], "experiment": { "platform": "ILLUMINA", - "experimental_strategy": "WGS", - "submitter_sequencing_experiment_id": "EXPERIMENT" + "experimentalStrategy": "WGS", + "submitterSequencingExperimentId": "EXPERIMENT" }, "workflow": { - "workflow_name": "batman_stuff", - "genome_build": "GRCh38_hla_decoy_ebv", + "workflowName": "batman_stuff", + "genomeBuild": "GRCh38_hla_decoy_ebv", "inputs": [ { - "analysis_type": "sequencing_alignment", - "tumour_analysis_id": "00000000-0000-0000-0000-000000000000", - "normal_analysis_id": "00000000-0000-0000-0000-000000000000" + "analysisType": "sequencing_alignment", + "tumourAnalysisId": "00000000-0000-0000-0000-000000000000", + "normalAnalysisId": "00000000-0000-0000-0000-000000000000" } ] } -} +} \ No newline at end of file diff --git a/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_T2.json b/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_T2.json index 7a039af2..80732bb3 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_T2.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_T2.json @@ -1,13 +1,17 @@ { + "analysisType": { + "name": "playgroundSchema" + }, + "studyId": "OVPLG-01", "samples": [ { "submitterSampleId": "TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_T2", "sampleType": "Total DNA", "matchedNormalSubmitterSampleId": "TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N2", "specimen": { - "submitterSpecimenId": "TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N2", - "specimenType": "Primary Tumour", - "specimenTissueSource": "Pancreas", + "submitterSpecimenId": "TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_T2", + "specimenType": "Primary tumour", + "specimenTissueSource": "Solid tissue", "tumourNormalDesignation": "Tumour" }, "donor": { @@ -17,115 +21,117 @@ } ], "donor": { - "submitter_donor_id": "TEST_DONOR_hjdxmpeccamrjzybhqrl", - "primary_site": ["Pancreas"], - "vital_status": "Alive", - "survival_time": null, - "cause_of_death": null, - "primary_diagnosis": [ + "submitterDonorId": "TEST_DONOR_hjdxmpeccamrjzybhqrl", + "primarySite": [ + "Pancreas" + ], + "vitalStatus": "Alive", + "survivalTime": null, + "causeOfDeath": null, + "primaryDiagnosis": [ { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_hjdxmpeccamrjzybhqrl_0", - "age_at_diagnosis": 27, - "cancer_type_code": "C21.2", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_hjdxmpeccamrjzybhqrl_0", + "ageAtDiagnosis": 27, + "cancerTypeCode": "C21.2", "laterality": "Bilateral", - "clinical_tumour_staging_system": "Durie-Salmon staging system", - "clinical_stage_group": "Stage II", - "lymph_nodes_examined_status": "Yes", - "performance_status": "Grade 4", + "clinicalTumourStagingSystem": "Durie-Salmon staging system", + "clinicalStageGroup": "Stage II", + "lymphNodesExaminedStatus": "Yes", + "performanceStatus": "Grade 4", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_hjdxmpeccamrjzybhqrl_0", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_hjdxmpeccamrjzybhqrl_0", + "treatmentType": [ "Hormonal therapy", "Radiation therapy", "Immunotherapy", "Surgery", "Chemotherapy" ], - "treatment_intent": "Curative", - "treatment_start_interval": 15, - "treatment_duration": 91, - "response_to_treatment": "NED", - "hormone_therapy": [ + "treatmentIntent": "Curative", + "treatmentStartInterval": 15, + "treatmentDuration": 91, + "responseToTreatment": "NED", + "hormoneTherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 76, - "hormone_drug_dosage_units": "IU/m2" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 76, + "hormoneDrugDosageUnits": "IU/m2" } ], "radiation": [ { - "radiation_therapy_modality": "Heavy Ions", - "radiation_therapy_type": "Internal", - "anatomical_site_irradiated": "Head", - "radiation_therapy_dosage": 24, - "radiation_therapy_fractions": 97 + "radiationTherapyModality": "Heavy Ions", + "radiationTherapyType": "Internal", + "anatomicalSiteIrradiated": "Head", + "radiationTherapyDosage": 24, + "radiationTherapyFractions": 97 } ], "immunotherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "immunotherapy_type": "Monoclonal antibodies other than immune checkpoint inhibitors" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "immunotherapyType": "Monoclonal antibodies other than immune checkpoint inhibitors" } ], "surgery": [ { - "surgery_type": "Biopsy", - "surgery_site": "C83.5", - "surgery_location": "Metastatic", - "residual_tumour_classification": "RX" + "surgeryType": "Biopsy", + "surgerySite": "C83.5", + "surgeryLocation": "Metastatic", + "residualTumourClassification": "RX" } ], "chemotherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 41, - "chemotherapy_dosage_units": "g/m2" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 41, + "chemotherapyDosageUnits": "g/m2" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_hjdxmpeccamrjzybhqrl_0", - "interval_of_followup": 54, - "disease_status_at_followup": "Progression NOS", - "relapse_type": "Local recurrence" + "submitterFollowUpId": "TEST_FOLLOW_UP_hjdxmpeccamrjzybhqrl_0", + "intervalOfFollowup": 54, + "diseaseStatusAtFollowup": "Progression NOS", + "relapseType": "Local recurrence" } ] } ], "comorbidity": [ { - "age_at_comorbidity_diagnosis": 60, - "comorbidity_type_code": "E12.51" + "ageAtComorbidityDiagnosis": 60, + "comorbidityTypeCode": "E12.51" }, { - "age_at_comorbidity_diagnosis": 54, - "comorbidity_type_code": "B40.46" + "ageAtComorbidityDiagnosis": 54, + "comorbidityTypeCode": "B40.46" }, { - "age_at_comorbidity_diagnosis": 63, - "comorbidity_type_code": "A72.22" + "ageAtComorbidityDiagnosis": 63, + "comorbidityTypeCode": "A72.22" } ] }, "specimen": { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_hjdxmpeccamrjzybhqrl_0", - "submitter_specimen_id": "TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N2", - "specimen_acquisition_interval": 72, - "specimen_anatomic_location": "C18", - "specimen_laterality": "Unknown", - "tumour_histological_type": "8643/34", - "pathological_tumour_staging_system": "Durie-Salmon staging system", - "pathological_stage_group": "Stage II", - "tumour_grading_system": "Gleason grade group system", - "tumour_grade": "Grade Group 1", - "percent_tumour_cells": 73, - "reference_pathology_confirmed": "Yes" + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_hjdxmpeccamrjzybhqrl_0", + "submitterSpecimenId": "TEST_SPECIMEN_hjdxmpeccamrjzybhqrl_N2", + "specimenAcquisitionInterval": 72, + "specimenAnatomicLocation": "C18", + "specimenLaterality": "Unknown", + "tumourHistologicalType": "8643/34", + "pathologicalTumourStagingSystem": "Durie-Salmon staging system", + "pathologicalStageGroup": "Stage II", + "tumourGradingSystem": "Gleason grade group system", + "tumourGrade": "Grade Group 1", + "percentTumourCells": 73, + "referencePathologyConfirmed": "Yes" }, "files": [ { @@ -153,25 +159,25 @@ ], "collaborator": [ { - "contact_email": "batman@batman_inc.org", + "contactEmail": "batman@batman_inc.org", "name": "batman", "affiliation": "batman inc" } ], "experiment": { "platform": "ILLUMINA", - "experimental_strategy": "WGS", - "submitter_sequencing_experiment_id": "EXPERIMENT" + "experimentalStrategy": "WGS", + "submitterSequencingExperimentId": "EXPERIMENT" }, "workflow": { - "workflow_name": "batman_stuff", - "genome_build": "GRCh38_hla_decoy_ebv", + "workflowName": "batman_stuff", + "genomeBuild": "GRCh38_hla_decoy_ebv", "inputs": [ { - "analysis_type": "sequencing_alignment", - "tumour_analysis_id": "00000000-0000-0000-0000-000000000000", - "normal_analysis_id": "00000000-0000-0000-0000-000000000000" + "analysisType": "sequencing_alignment", + "tumourAnalysisId": "00000000-0000-0000-0000-000000000000", + "normalAnalysisId": "00000000-0000-0000-0000-000000000000" } ] } -} +} \ No newline at end of file diff --git a/playground-data/example-payloads/TEST_SPECIMEN_hlmegwbcehzqgmuaopom_N1.json b/playground-data/example-payloads/TEST_SPECIMEN_hlmegwbcehzqgmuaopom_N1.json index 87d77505..7fa1c2ef 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_hlmegwbcehzqgmuaopom_N1.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_hlmegwbcehzqgmuaopom_N1.json @@ -1,4 +1,8 @@ { + "analysisType": { + "name": "playgroundSchema" + }, + "studyId": "OVPLG-01", "samples": [ { "submitterSampleId": "TEST_SPECIMEN_hlmegwbcehzqgmuaopom_N1", @@ -17,55 +21,57 @@ } ], "donor": { - "submitter_donor_id": "TEST_DONOR_hlmegwbcehzqgmuaopom", - "primary_site": ["Esophagus"], - "vital_status": "Deceased", - "survival_time": 373, - "cause_of_death": "Died of other reasons", - "primary_diagnosis": [ + "submitterDonorId": "TEST_DONOR_hlmegwbcehzqgmuaopom", + "primarySite": [ + "Esophagus" + ], + "vitalStatus": "Deceased", + "survivalTime": 373, + "causeOfDeath": "Died of other reasons", + "primaryDiagnosis": [ { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_hlmegwbcehzqgmuaopom_0", - "age_at_diagnosis": 85, - "cancer_type_code": "C26", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_hlmegwbcehzqgmuaopom_0", + "ageAtDiagnosis": 85, + "cancerTypeCode": "C26", "laterality": "Right", - "clinical_tumour_staging_system": "FIGO staging system", - "clinical_stage_group": "Stage IVB", - "lymph_nodes_examined_status": "Cannot be determined", - "performance_status": "Grade 0", + "clinicalTumourStagingSystem": "FIGO staging system", + "clinicalStageGroup": "Stage IVB", + "lymphNodesExaminedStatus": "Cannot be determined", + "performanceStatus": "Grade 0", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_hlmegwbcehzqgmuaopom_0", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_hlmegwbcehzqgmuaopom_0", + "treatmentType": [ "Radiation therapy", "Immunotherapy" ], - "treatment_intent": "Curative", - "treatment_start_interval": 81, - "treatment_duration": 46, - "response_to_treatment": "Complete response", + "treatmentIntent": "Curative", + "treatmentStartInterval": 81, + "treatmentDuration": 46, + "responseToTreatment": "Complete response", "radiation": [ { - "radiation_therapy_modality": "Heavy Ions", - "radiation_therapy_type": "Internal", - "anatomical_site_irradiated": "Abdomen", - "radiation_therapy_dosage": 82, - "radiation_therapy_fractions": 89 + "radiationTherapyModality": "Heavy Ions", + "radiationTherapyType": "Internal", + "anatomicalSiteIrradiated": "Abdomen", + "radiationTherapyDosage": 82, + "radiationTherapyFractions": 89 } ], "immunotherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "immunotherapy_type": "Monoclonal antibodies other than immune checkpoint inhibitors" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "immunotherapyType": "Monoclonal antibodies other than immune checkpoint inhibitors" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_hlmegwbcehzqgmuaopom_0", - "interval_of_followup": 59, - "disease_status_at_followup": "No evidence of disease" + "submitterFollowUpId": "TEST_FOLLOW_UP_hlmegwbcehzqgmuaopom_0", + "intervalOfFollowup": 59, + "diseaseStatusAtFollowup": "No evidence of disease" } ] } @@ -73,11 +79,11 @@ "comorbidity": [] }, "specimen": { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_hlmegwbcehzqgmuaopom_0", - "submitter_specimen_id": "TEST_SPECIMEN_hlmegwbcehzqgmuaopom_N1", - "specimen_acquisition_interval": 26, - "specimen_anatomic_location": "C76", - "specimen_laterality": "Left" + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_hlmegwbcehzqgmuaopom_0", + "submitterSpecimenId": "TEST_SPECIMEN_hlmegwbcehzqgmuaopom_N1", + "specimenAcquisitionInterval": 26, + "specimenAnatomicLocation": "C76", + "specimenLaterality": "Left" }, "files": [ { @@ -105,25 +111,25 @@ ], "collaborator": [ { - "contact_email": "batman@batman_inc.org", + "contactEmail": "batman@batman_inc.org", "name": "batman", "affiliation": "batman inc" } ], "experiment": { "platform": "ILLUMINA", - "experimental_strategy": "WGS", - "submitter_sequencing_experiment_id": "EXPERIMENT" + "experimentalStrategy": "WGS", + "submitterSequencingExperimentId": "EXPERIMENT" }, "workflow": { - "workflow_name": "batman_stuff", - "genome_build": "GRCh38_hla_decoy_ebv", + "workflowName": "batman_stuff", + "genomeBuild": "GRCh38_hla_decoy_ebv", "inputs": [ { - "analysis_type": "sequencing_alignment", - "tumour_analysis_id": "00000000-0000-0000-0000-000000000000", - "normal_analysis_id": "00000000-0000-0000-0000-000000000000" + "analysisType": "sequencing_alignment", + "tumourAnalysisId": "00000000-0000-0000-0000-000000000000", + "normalAnalysisId": "00000000-0000-0000-0000-000000000000" } ] } -} +} \ No newline at end of file diff --git a/playground-data/example-payloads/TEST_SPECIMEN_hlmegwbcehzqgmuaopom_N2.json b/playground-data/example-payloads/TEST_SPECIMEN_hlmegwbcehzqgmuaopom_N2.json index 1bc562db..26e47eca 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_hlmegwbcehzqgmuaopom_N2.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_hlmegwbcehzqgmuaopom_N2.json @@ -1,4 +1,8 @@ { + "analysisType": { + "name": "playgroundSchema" + }, + "studyId": "OVPLG-01", "samples": [ { "submitterSampleId": "TEST_SPECIMEN_hlmegwbcehzqgmuaopom_N2", @@ -17,55 +21,57 @@ } ], "donor": { - "submitter_donor_id": "TEST_DONOR_hlmegwbcehzqgmuaopom", - "primary_site": ["Esophagus"], - "vital_status": "Deceased", - "survival_time": 373, - "cause_of_death": "Died of other reasons", - "primary_diagnosis": [ + "submitterDonorId": "TEST_DONOR_hlmegwbcehzqgmuaopom", + "primarySite": [ + "Esophagus" + ], + "vitalStatus": "Deceased", + "survivalTime": 373, + "causeOfDeath": "Died of other reasons", + "primaryDiagnosis": [ { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_hlmegwbcehzqgmuaopom_0", - "age_at_diagnosis": 85, - "cancer_type_code": "D74.7", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_hlmegwbcehzqgmuaopom_0", + "ageAtDiagnosis": 85, + "cancerTypeCode": "D74.7", "laterality": "Right", - "clinical_tumour_staging_system": "FIGO staging system", - "clinical_stage_group": "Stage IVB", - "lymph_nodes_examined_status": "Cannot be determined", - "performance_status": "Grade 0", + "clinicalTumourStagingSystem": "FIGO staging system", + "clinicalStageGroup": "Stage IVB", + "lymphNodesExaminedStatus": "Cannot be determined", + "performanceStatus": "Grade 0", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_hlmegwbcehzqgmuaopom_0", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_hlmegwbcehzqgmuaopom_0", + "treatmentType": [ "Radiation therapy", "Immunotherapy" ], - "treatment_intent": "Curative", - "treatment_start_interval": 81, - "treatment_duration": 46, - "response_to_treatment": "Complete response", + "treatmentIntent": "Curative", + "treatmentStartInterval": 81, + "treatmentDuration": 46, + "responseToTreatment": "Complete response", "radiation": [ { - "radiation_therapy_modality": "Heavy Ions", - "radiation_therapy_type": "Internal", - "anatomical_site_irradiated": "Abdomen", - "radiation_therapy_dosage": 82, - "radiation_therapy_fractions": 89 + "radiationTherapyModality": "Heavy Ions", + "radiationTherapyType": "Internal", + "anatomicalSiteIrradiated": "Abdomen", + "radiationTherapyDosage": 82, + "radiationTherapyFractions": 89 } ], "immunotherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "immunotherapy_type": "Monoclonal antibodies other than immune checkpoint inhibitors" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "immunotherapyType": "Monoclonal antibodies other than immune checkpoint inhibitors" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_hlmegwbcehzqgmuaopom_0", - "interval_of_followup": 59, - "disease_status_at_followup": "No evidence of disease" + "submitterFollowUpId": "TEST_FOLLOW_UP_hlmegwbcehzqgmuaopom_0", + "intervalOfFollowup": 59, + "diseaseStatusAtFollowup": "No evidence of disease" } ] } @@ -73,11 +79,11 @@ "comorbidity": [] }, "specimen": { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_hlmegwbcehzqgmuaopom_0", - "submitter_specimen_id": "TEST_SPECIMEN_hlmegwbcehzqgmuaopom_N2", - "specimen_acquisition_interval": 35, - "specimen_anatomic_location": "C76", - "specimen_laterality": "Left" + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_hlmegwbcehzqgmuaopom_0", + "submitterSpecimenId": "TEST_SPECIMEN_hlmegwbcehzqgmuaopom_N2", + "specimenAcquisitionInterval": 35, + "specimenAnatomicLocation": "C76", + "specimenLaterality": "Left" }, "files": [ { @@ -105,25 +111,25 @@ ], "collaborator": [ { - "contact_email": "batman@batman_inc.org", + "contactEmail": "batman@batman_inc.org", "name": "batman", "affiliation": "batman inc" } ], "experiment": { "platform": "ILLUMINA", - "experimental_strategy": "WGS", - "submitter_sequencing_experiment_id": "EXPERIMENT" + "experimentalStrategy": "WGS", + "submitterSequencingExperimentId": "EXPERIMENT" }, "workflow": { - "workflow_name": "batman_stuff", - "genome_build": "GRCh38_hla_decoy_ebv", + "workflowName": "batman_stuff", + "genomeBuild": "GRCh38_hla_decoy_ebv", "inputs": [ { - "analysis_type": "sequencing_alignment", - "tumour_analysis_id": "00000000-0000-0000-0000-000000000000", - "normal_analysis_id": "00000000-0000-0000-0000-000000000000" + "analysisType": "sequencing_alignment", + "tumourAnalysisId": "00000000-0000-0000-0000-000000000000", + "normalAnalysisId": "00000000-0000-0000-0000-000000000000" } ] } -} +} \ No newline at end of file diff --git a/playground-data/example-payloads/TEST_SPECIMEN_hlmegwbcehzqgmuaopom_T1.json b/playground-data/example-payloads/TEST_SPECIMEN_hlmegwbcehzqgmuaopom_T1.json index 1d03d85b..111d1c15 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_hlmegwbcehzqgmuaopom_T1.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_hlmegwbcehzqgmuaopom_T1.json @@ -1,11 +1,15 @@ { + "analysisType": { + "name": "playgroundSchema" + }, + "studyId": "OVPLG-01", "samples": [ { "submitterSampleId": "TEST_SPECIMEN_hlmegwbcehzqgmuaopom_T1", "sampleType": "Total DNA", "matchedNormalSubmitterSampleId": "TEST_SPECIMEN_hlmegwbcehzqgmuaopom_N1", "specimen": { - "submitterSpecimenId": "TEST_SPECIMEN_hlmegwbcehzqgmuaopom_N1", + "submitterSpecimenId": "TEST_SPECIMEN_hlmegwbcehzqgmuaopom_T1", "specimenType": "Primary tumour - additional new primary", "specimenTissueSource": "Intestine", "tumourNormalDesignation": "Tumour" @@ -17,55 +21,57 @@ } ], "donor": { - "submitter_donor_id": "TEST_DONOR_hlmegwbcehzqgmuaopom", - "primary_site": ["Esophagus"], - "vital_status": "Deceased", - "survival_time": 373, - "cause_of_death": "Died of other reasons", - "primary_diagnosis": [ + "submitterDonorId": "TEST_DONOR_hlmegwbcehzqgmuaopom", + "primarySite": [ + "Esophagus" + ], + "vitalStatus": "Deceased", + "survivalTime": 373, + "causeOfDeath": "Died of other reasons", + "primaryDiagnosis": [ { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_hlmegwbcehzqgmuaopom_0", - "age_at_diagnosis": 85, - "cancer_type_code": "D74.7", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_hlmegwbcehzqgmuaopom_0", + "ageAtDiagnosis": 85, + "cancerTypeCode": "D74.7", "laterality": "Right", - "clinical_tumour_staging_system": "FIGO staging system", - "clinical_stage_group": "Stage IVB", - "lymph_nodes_examined_status": "Cannot be determined", - "performance_status": "Grade 0", + "clinicalTumourStagingSystem": "FIGO staging system", + "clinicalStageGroup": "Stage IVB", + "lymphNodesExaminedStatus": "Cannot be determined", + "performanceStatus": "Grade 0", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_hlmegwbcehzqgmuaopom_0", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_hlmegwbcehzqgmuaopom_0", + "treatmentType": [ "Radiation therapy", "Immunotherapy" ], - "treatment_intent": "Curative", - "treatment_start_interval": 81, - "treatment_duration": 46, - "response_to_treatment": "Complete response", + "treatmentIntent": "Curative", + "treatmentStartInterval": 81, + "treatmentDuration": 46, + "responseToTreatment": "Complete response", "radiation": [ { - "radiation_therapy_modality": "Heavy Ions", - "radiation_therapy_type": "Internal", - "anatomical_site_irradiated": "Abdomen", - "radiation_therapy_dosage": 82, - "radiation_therapy_fractions": 89 + "radiationTherapyModality": "Heavy Ions", + "radiationTherapyType": "Internal", + "anatomicalSiteIrradiated": "Abdomen", + "radiationTherapyDosage": 82, + "radiationTherapyFractions": 89 } ], "immunotherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "immunotherapy_type": "Monoclonal antibodies other than immune checkpoint inhibitors" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "immunotherapyType": "Monoclonal antibodies other than immune checkpoint inhibitors" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_hlmegwbcehzqgmuaopom_0", - "interval_of_followup": 59, - "disease_status_at_followup": "No evidence of disease" + "submitterFollowUpId": "TEST_FOLLOW_UP_hlmegwbcehzqgmuaopom_0", + "intervalOfFollowup": 59, + "diseaseStatusAtFollowup": "No evidence of disease" } ] } @@ -73,18 +79,18 @@ "comorbidity": [] }, "specimen": { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_hlmegwbcehzqgmuaopom_0", - "submitter_specimen_id": "TEST_SPECIMEN_hlmegwbcehzqgmuaopom_N1", - "specimen_acquisition_interval": 95, - "specimen_anatomic_location": "C76", - "specimen_laterality": "Left", - "tumour_histological_type": "9627/03", - "pathological_tumour_staging_system": "Binet staging system", - "pathological_stage_group": "Stage C", - "tumour_grading_system": "Scarff-Bloom-Richardson grading system", - "tumour_grade": "GX", - "percent_tumour_cells": 39, - "reference_pathology_confirmed": "Yes" + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_hlmegwbcehzqgmuaopom_0", + "submitterSpecimenId": "TEST_SPECIMEN_hlmegwbcehzqgmuaopom_N1", + "specimenAcquisitionInterval": 95, + "specimenAnatomicLocation": "C76", + "specimenLaterality": "Left", + "tumourHistologicalType": "9627/03", + "pathologicalTumourStagingSystem": "Binet staging system", + "pathologicalStageGroup": "Stage C", + "tumourGradingSystem": "Scarff-Bloom-Richardson grading system", + "tumourGrade": "GX", + "percentTumourCells": 39, + "referencePathologyConfirmed": "Yes" }, "files": [ { @@ -112,25 +118,25 @@ ], "collaborator": [ { - "contact_email": "batman@batman_inc.org", + "contactEmail": "batman@batman_inc.org", "name": "batman", "affiliation": "batman inc" } ], "experiment": { "platform": "ILLUMINA", - "experimental_strategy": "WGS", - "submitter_sequencing_experiment_id": "EXPERIMENT" + "experimentalStrategy": "WGS", + "submitterSequencingExperimentId": "EXPERIMENT" }, "workflow": { - "workflow_name": "batman_stuff", - "genome_build": "GRCh38_hla_decoy_ebv", + "workflowName": "batman_stuff", + "genomeBuild": "GRCh38_hla_decoy_ebv", "inputs": [ { - "analysis_type": "sequencing_alignment", - "tumour_analysis_id": "00000000-0000-0000-0000-000000000000", - "normal_analysis_id": "00000000-0000-0000-0000-000000000000" + "analysisType": "sequencing_alignment", + "tumourAnalysisId": "00000000-0000-0000-0000-000000000000", + "normalAnalysisId": "00000000-0000-0000-0000-000000000000" } ] } -} +} \ No newline at end of file diff --git a/playground-data/example-payloads/TEST_SPECIMEN_hlmegwbcehzqgmuaopom_T2.json b/playground-data/example-payloads/TEST_SPECIMEN_hlmegwbcehzqgmuaopom_T2.json index 2ba035cf..cd38a3bc 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_hlmegwbcehzqgmuaopom_T2.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_hlmegwbcehzqgmuaopom_T2.json @@ -1,11 +1,15 @@ { + "analysisType": { + "name": "playgroundSchema" + }, + "studyId": "OVPLG-01", "samples": [ { "submitterSampleId": "TEST_SPECIMEN_hlmegwbcehzqgmuaopom_T2", "sampleType": "Total DNA", "matchedNormalSubmitterSampleId": "TEST_SPECIMEN_hlmegwbcehzqgmuaopom_N2", "specimen": { - "submitterSpecimenId": "TEST_SPECIMEN_hlmegwbcehzqgmuaopom_N2", + "submitterSpecimenId": "TEST_SPECIMEN_hlmegwbcehzqgmuaopom_T2", "specimenType": "Primary tumour", "specimenTissueSource": "Intestine", "tumourNormalDesignation": "Tumour" @@ -17,55 +21,57 @@ } ], "donor": { - "submitter_donor_id": "TEST_DONOR_hlmegwbcehzqgmuaopom", - "primary_site": ["Esophagus"], - "vital_status": "Deceased", - "survival_time": 373, - "cause_of_death": "Died of other reasons", - "primary_diagnosis": [ + "submitterDonorId": "TEST_DONOR_hlmegwbcehzqgmuaopom", + "primarySite": [ + "Esophagus" + ], + "vitalStatus": "Deceased", + "survivalTime": 373, + "causeOfDeath": "Died of other reasons", + "primaryDiagnosis": [ { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_hlmegwbcehzqgmuaopom_0", - "age_at_diagnosis": 85, - "cancer_type_code": "C76", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_hlmegwbcehzqgmuaopom_0", + "ageAtDiagnosis": 85, + "cancerTypeCode": "C76", "laterality": "Right", - "clinical_tumour_staging_system": "FIGO staging system", - "clinical_stage_group": "Stage IVB", - "lymph_nodes_examined_status": "Cannot be determined", - "performance_status": "Grade 0", + "clinicalTumourStagingSystem": "FIGO staging system", + "clinicalStageGroup": "Stage IVB", + "lymphNodesExaminedStatus": "Cannot be determined", + "performanceStatus": "Grade 0", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_hlmegwbcehzqgmuaopom_0", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_hlmegwbcehzqgmuaopom_0", + "treatmentType": [ "Radiation therapy", "Immunotherapy" ], - "treatment_intent": "Curative", - "treatment_start_interval": 81, - "treatment_duration": 46, - "response_to_treatment": "Complete response", + "treatmentIntent": "Curative", + "treatmentStartInterval": 81, + "treatmentDuration": 46, + "responseToTreatment": "Complete response", "radiation": [ { - "radiation_therapy_modality": "Heavy Ions", - "radiation_therapy_type": "Internal", - "anatomical_site_irradiated": "Abdomen", - "radiation_therapy_dosage": 82, - "radiation_therapy_fractions": 89 + "radiationTherapyModality": "Heavy Ions", + "radiationTherapyType": "Internal", + "anatomicalSiteIrradiated": "Abdomen", + "radiationTherapyDosage": 82, + "radiationTherapyFractions": 89 } ], "immunotherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "immunotherapy_type": "Monoclonal antibodies other than immune checkpoint inhibitors" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "immunotherapyType": "Monoclonal antibodies other than immune checkpoint inhibitors" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_hlmegwbcehzqgmuaopom_0", - "interval_of_followup": 59, - "disease_status_at_followup": "No evidence of disease" + "submitterFollowUpId": "TEST_FOLLOW_UP_hlmegwbcehzqgmuaopom_0", + "intervalOfFollowup": 59, + "diseaseStatusAtFollowup": "No evidence of disease" } ] } @@ -73,18 +79,18 @@ "comorbidity": [] }, "specimen": { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_hlmegwbcehzqgmuaopom_0", - "submitter_specimen_id": "TEST_SPECIMEN_hlmegwbcehzqgmuaopom_N2", - "specimen_acquisition_interval": 81, - "specimen_anatomic_location": "C54", - "specimen_laterality": "Left", - "tumour_histological_type": "8575/02", - "pathological_tumour_staging_system": "AJCC 8th edition", - "pathological_stage_group": "Stage IA2", - "tumour_grading_system": "Scarff-Bloom-Richardson grading system", - "tumour_grade": "G2", - "percent_tumour_cells": 43, - "reference_pathology_confirmed": "No" + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_hlmegwbcehzqgmuaopom_0", + "submitterSpecimenId": "TEST_SPECIMEN_hlmegwbcehzqgmuaopom_N2", + "specimenAcquisitionInterval": 81, + "specimenAnatomicLocation": "C54", + "specimenLaterality": "Left", + "tumourHistologicalType": "8575/02", + "pathologicalTumourStagingSystem": "AJCC 8th edition", + "pathologicalStageGroup": "Stage IA2", + "tumourGradingSystem": "Scarff-Bloom-Richardson grading system", + "tumourGrade": "G2", + "percentTumourCells": 43, + "referencePathologyConfirmed": "No" }, "files": [ { @@ -112,25 +118,25 @@ ], "collaborator": [ { - "contact_email": "batman@batman_inc.org", + "contactEmail": "batman@batman_inc.org", "name": "batman", "affiliation": "batman inc" } ], "experiment": { "platform": "ILLUMINA", - "experimental_strategy": "WGS", - "submitter_sequencing_experiment_id": "EXPERIMENT" + "experimentalStrategy": "WGS", + "submitterSequencingExperimentId": "EXPERIMENT" }, "workflow": { - "workflow_name": "batman_stuff", - "genome_build": "GRCh38_hla_decoy_ebv", + "workflowName": "batman_stuff", + "genomeBuild": "GRCh38_hla_decoy_ebv", "inputs": [ { - "analysis_type": "sequencing_alignment", - "tumour_analysis_id": "00000000-0000-0000-0000-000000000000", - "normal_analysis_id": "00000000-0000-0000-0000-000000000000" + "analysisType": "sequencing_alignment", + "tumourAnalysisId": "00000000-0000-0000-0000-000000000000", + "normalAnalysisId": "00000000-0000-0000-0000-000000000000" } ] } -} +} \ No newline at end of file diff --git a/playground-data/example-payloads/TEST_SPECIMEN_hsreltpusctapirhgwpr_N1.json b/playground-data/example-payloads/TEST_SPECIMEN_hsreltpusctapirhgwpr_N1.json index 2a8d43c7..c9748db4 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_hsreltpusctapirhgwpr_N1.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_hsreltpusctapirhgwpr_N1.json @@ -1,4 +1,8 @@ { + "analysisType": { + "name": "playgroundSchema" + }, + "studyId": "OVPLG-01", "samples": [ { "submitterSampleId": "TEST_SPECIMEN_hsreltpusctapirhgwpr_N1", @@ -17,111 +21,113 @@ } ], "donor": { - "submitter_donor_id": "TEST_DONOR_hsreltpusctapirhgwpr", - "primary_site": ["Brain"], - "vital_status": "Deceased", - "survival_time": 884, - "cause_of_death": "Died of cancer", - "primary_diagnosis": [ + "submitterDonorId": "TEST_DONOR_hsreltpusctapirhgwpr", + "primarySite": [ + "Brain" + ], + "vitalStatus": "Deceased", + "survivalTime": 884, + "causeOfDeath": "Died of cancer", + "primaryDiagnosis": [ { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_hsreltpusctapirhgwpr_0", - "age_at_diagnosis": 70, - "cancer_type_code": "C71.9", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_hsreltpusctapirhgwpr_0", + "ageAtDiagnosis": 70, + "cancerTypeCode": "C71.9", "laterality": "Unilateral, side not specified", - "clinical_tumour_staging_system": "FIGO staging system", - "clinical_stage_group": "Stage IB", - "lymph_nodes_examined_status": "No lymph nodes found in resected specimen", - "performance_status": "Grade 1", + "clinicalTumourStagingSystem": "FIGO staging system", + "clinicalStageGroup": "Stage IB", + "lymphNodesExaminedStatus": "No lymph nodes found in resected specimen", + "performanceStatus": "Grade 1", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_hsreltpusctapirhgwpr_0", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_hsreltpusctapirhgwpr_0", + "treatmentType": [ "No treatment" ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_hsreltpusctapirhgwpr_0", - "interval_of_followup": 95, - "disease_status_at_followup": "Loco-regional progression" + "submitterFollowUpId": "TEST_FOLLOW_UP_hsreltpusctapirhgwpr_0", + "intervalOfFollowup": 95, + "diseaseStatusAtFollowup": "Loco-regional progression" } ] }, { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_hsreltpusctapirhgwpr_1", - "age_at_diagnosis": 49, - "cancer_type_code": "D76.5", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_hsreltpusctapirhgwpr_1", + "ageAtDiagnosis": 49, + "cancerTypeCode": "D76.5", "laterality": "Right", - "clinical_tumour_staging_system": "AJCC 7th edition", - "clinical_stage_group": "Stage IVA2", - "lymph_nodes_examined_status": "No", - "performance_status": "Grade 3", + "clinicalTumourStagingSystem": "AJCC 7th edition", + "clinicalStageGroup": "Stage IVA2", + "lymphNodesExaminedStatus": "No", + "performanceStatus": "Grade 3", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_hsreltpusctapirhgwpr_1", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_hsreltpusctapirhgwpr_1", + "treatmentType": [ "Radiation therapy", "Surgery", "Chemotherapy" ], - "treatment_intent": "Unknown", - "treatment_start_interval": 51, - "treatment_duration": 32, - "response_to_treatment": "NED", + "treatmentIntent": "Unknown", + "treatmentStartInterval": 51, + "treatmentDuration": 32, + "responseToTreatment": "NED", "radiation": [ { - "radiation_therapy_modality": "Heavy Ions", - "radiation_therapy_type": "Internal", - "anatomical_site_irradiated": "Body", - "radiation_therapy_dosage": 48, - "radiation_therapy_fractions": 45 + "radiationTherapyModality": "Heavy Ions", + "radiationTherapyType": "Internal", + "anatomicalSiteIrradiated": "Body", + "radiationTherapyDosage": 48, + "radiationTherapyFractions": 45 } ], "surgery": [ { - "surgery_type": "Cholecystectomy", - "surgery_site": "C42.6", - "surgery_location": "Local recurrence", - "residual_tumour_classification": "R1" + "surgeryType": "Cholecystectomy", + "surgerySite": "C42.6", + "surgeryLocation": "Local recurrence", + "residualTumourClassification": "R1" } ], "chemotherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 54, - "chemotherapy_dosage_units": "ug/m2" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 54, + "chemotherapyDosageUnits": "ug/m2" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_hsreltpusctapirhgwpr_1", - "interval_of_followup": 56, - "disease_status_at_followup": "No evidence of disease" + "submitterFollowUpId": "TEST_FOLLOW_UP_hsreltpusctapirhgwpr_1", + "intervalOfFollowup": 56, + "diseaseStatusAtFollowup": "No evidence of disease" } ] } ], "comorbidity": [ { - "age_at_comorbidity_diagnosis": 70, - "comorbidity_type_code": "B78.90" + "ageAtComorbidityDiagnosis": 70, + "comorbidityTypeCode": "B78.90" }, { - "age_at_comorbidity_diagnosis": 29, - "comorbidity_type_code": "E45.94" + "ageAtComorbidityDiagnosis": 29, + "comorbidityTypeCode": "E45.94" } ] }, "specimen": { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_hsreltpusctapirhgwpr_0", - "submitter_specimen_id": "TEST_SPECIMEN_hsreltpusctapirhgwpr_N1", - "specimen_acquisition_interval": 56, - "specimen_anatomic_location": "C71.0", - "specimen_laterality": "Unknown" + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_hsreltpusctapirhgwpr_0", + "submitterSpecimenId": "TEST_SPECIMEN_hsreltpusctapirhgwpr_N1", + "specimenAcquisitionInterval": 56, + "specimenAnatomicLocation": "C71.0", + "specimenLaterality": "Unknown" }, "files": [ { @@ -149,25 +155,25 @@ ], "collaborator": [ { - "contact_email": "batman@batman_inc.org", + "contactEmail": "batman@batman_inc.org", "name": "batman", "affiliation": "batman inc" } ], "experiment": { "platform": "ILLUMINA", - "experimental_strategy": "WGS", - "submitter_sequencing_experiment_id": "EXPERIMENT" + "experimentalStrategy": "WGS", + "submitterSequencingExperimentId": "EXPERIMENT" }, "workflow": { - "workflow_name": "batman_stuff", - "genome_build": "GRCh38_hla_decoy_ebv", + "workflowName": "batman_stuff", + "genomeBuild": "GRCh38_hla_decoy_ebv", "inputs": [ { - "analysis_type": "sequencing_alignment", - "tumour_analysis_id": "00000000-0000-0000-0000-000000000000", - "normal_analysis_id": "00000000-0000-0000-0000-000000000000" + "analysisType": "sequencing_alignment", + "tumourAnalysisId": "00000000-0000-0000-0000-000000000000", + "normalAnalysisId": "00000000-0000-0000-0000-000000000000" } ] } -} +} \ No newline at end of file diff --git a/playground-data/example-payloads/TEST_SPECIMEN_hsreltpusctapirhgwpr_N2.json b/playground-data/example-payloads/TEST_SPECIMEN_hsreltpusctapirhgwpr_N2.json index 9301cc26..03f52277 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_hsreltpusctapirhgwpr_N2.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_hsreltpusctapirhgwpr_N2.json @@ -1,4 +1,8 @@ { + "analysisType": { + "name": "playgroundSchema" + }, + "studyId": "OVPLG-01", "samples": [ { "submitterSampleId": "TEST_SPECIMEN_hsreltpusctapirhgwpr_N2", @@ -17,111 +21,113 @@ } ], "donor": { - "submitter_donor_id": "TEST_DONOR_hsreltpusctapirhgwpr", - "primary_site": ["Brain"], - "vital_status": "Deceased", - "survival_time": 884, - "cause_of_death": "Died of cancer", - "primary_diagnosis": [ + "submitterDonorId": "TEST_DONOR_hsreltpusctapirhgwpr", + "primarySite": [ + "Brain" + ], + "vitalStatus": "Deceased", + "survivalTime": 884, + "causeOfDeath": "Died of cancer", + "primaryDiagnosis": [ { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_hsreltpusctapirhgwpr_0", - "age_at_diagnosis": 70, - "cancer_type_code": "C71.9", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_hsreltpusctapirhgwpr_0", + "ageAtDiagnosis": 70, + "cancerTypeCode": "C71.9", "laterality": "Unilateral, side not specified", - "clinical_tumour_staging_system": "FIGO staging system", - "clinical_stage_group": "Stage IB", - "lymph_nodes_examined_status": "No lymph nodes found in resected specimen", - "performance_status": "Grade 1", + "clinicalTumourStagingSystem": "FIGO staging system", + "clinicalStageGroup": "Stage IB", + "lymphNodesExaminedStatus": "No lymph nodes found in resected specimen", + "performanceStatus": "Grade 1", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_hsreltpusctapirhgwpr_0", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_hsreltpusctapirhgwpr_0", + "treatmentType": [ "No treatment" ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_hsreltpusctapirhgwpr_0", - "interval_of_followup": 95, - "disease_status_at_followup": "Loco-regional progression" + "submitterFollowUpId": "TEST_FOLLOW_UP_hsreltpusctapirhgwpr_0", + "intervalOfFollowup": 95, + "diseaseStatusAtFollowup": "Loco-regional progression" } ] }, { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_hsreltpusctapirhgwpr_1", - "age_at_diagnosis": 49, - "cancer_type_code": "D76.5", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_hsreltpusctapirhgwpr_1", + "ageAtDiagnosis": 49, + "cancerTypeCode": "D76.5", "laterality": "Right", - "clinical_tumour_staging_system": "AJCC 7th edition", - "clinical_stage_group": "Stage IVA2", - "lymph_nodes_examined_status": "No", - "performance_status": "Grade 3", + "clinicalTumourStagingSystem": "AJCC 7th edition", + "clinicalStageGroup": "Stage IVA2", + "lymphNodesExaminedStatus": "No", + "performanceStatus": "Grade 3", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_hsreltpusctapirhgwpr_1", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_hsreltpusctapirhgwpr_1", + "treatmentType": [ "Radiation therapy", "Surgery", "Chemotherapy" ], - "treatment_intent": "Unknown", - "treatment_start_interval": 51, - "treatment_duration": 32, - "response_to_treatment": "NED", + "treatmentIntent": "Unknown", + "treatmentStartInterval": 51, + "treatmentDuration": 32, + "responseToTreatment": "NED", "radiation": [ { - "radiation_therapy_modality": "Heavy Ions", - "radiation_therapy_type": "Internal", - "anatomical_site_irradiated": "Body", - "radiation_therapy_dosage": 48, - "radiation_therapy_fractions": 45 + "radiationTherapyModality": "Heavy Ions", + "radiationTherapyType": "Internal", + "anatomicalSiteIrradiated": "Body", + "radiationTherapyDosage": 48, + "radiationTherapyFractions": 45 } ], "surgery": [ { - "surgery_type": "Cholecystectomy", - "surgery_site": "C42.6", - "surgery_location": "Local recurrence", - "residual_tumour_classification": "R1" + "surgeryType": "Cholecystectomy", + "surgerySite": "C42.6", + "surgeryLocation": "Local recurrence", + "residualTumourClassification": "R1" } ], "chemotherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 54, - "chemotherapy_dosage_units": "ug/m2" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 54, + "chemotherapyDosageUnits": "ug/m2" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_hsreltpusctapirhgwpr_1", - "interval_of_followup": 56, - "disease_status_at_followup": "No evidence of disease" + "submitterFollowUpId": "TEST_FOLLOW_UP_hsreltpusctapirhgwpr_1", + "intervalOfFollowup": 56, + "diseaseStatusAtFollowup": "No evidence of disease" } ] } ], "comorbidity": [ { - "age_at_comorbidity_diagnosis": 70, - "comorbidity_type_code": "B78.90" + "ageAtComorbidityDiagnosis": 70, + "comorbidityTypeCode": "B78.90" }, { - "age_at_comorbidity_diagnosis": 29, - "comorbidity_type_code": "E45.94" + "ageAtComorbidityDiagnosis": 29, + "comorbidityTypeCode": "E45.94" } ] }, "specimen": { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_hsreltpusctapirhgwpr_1", - "submitter_specimen_id": "TEST_SPECIMEN_hsreltpusctapirhgwpr_N2", - "specimen_acquisition_interval": 31, - "specimen_anatomic_location": "C71.0", - "specimen_laterality": "Unknown" + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_hsreltpusctapirhgwpr_1", + "submitterSpecimenId": "TEST_SPECIMEN_hsreltpusctapirhgwpr_N2", + "specimenAcquisitionInterval": 31, + "specimenAnatomicLocation": "C71.0", + "specimenLaterality": "Unknown" }, "files": [ { @@ -149,25 +155,25 @@ ], "collaborator": [ { - "contact_email": "batman@batman_inc.org", + "contactEmail": "batman@batman_inc.org", "name": "batman", "affiliation": "batman inc" } ], "experiment": { "platform": "ILLUMINA", - "experimental_strategy": "WGS", - "submitter_sequencing_experiment_id": "EXPERIMENT" + "experimentalStrategy": "WGS", + "submitterSequencingExperimentId": "EXPERIMENT" }, "workflow": { - "workflow_name": "batman_stuff", - "genome_build": "GRCh38_hla_decoy_ebv", + "workflowName": "batman_stuff", + "genomeBuild": "GRCh38_hla_decoy_ebv", "inputs": [ { - "analysis_type": "sequencing_alignment", - "tumour_analysis_id": "00000000-0000-0000-0000-000000000000", - "normal_analysis_id": "00000000-0000-0000-0000-000000000000" + "analysisType": "sequencing_alignment", + "tumourAnalysisId": "00000000-0000-0000-0000-000000000000", + "normalAnalysisId": "00000000-0000-0000-0000-000000000000" } ] } -} +} \ No newline at end of file diff --git a/playground-data/example-payloads/TEST_SPECIMEN_hsreltpusctapirhgwpr_T1.json b/playground-data/example-payloads/TEST_SPECIMEN_hsreltpusctapirhgwpr_T1.json index 6f9fa27e..1b99a65b 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_hsreltpusctapirhgwpr_T1.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_hsreltpusctapirhgwpr_T1.json @@ -1,11 +1,15 @@ { + "analysisType": { + "name": "playgroundSchema" + }, + "studyId": "OVPLG-01", "samples": [ { "submitterSampleId": "TEST_SPECIMEN_hsreltpusctapirhgwpr_T1", "sampleType": "Total DNA", "matchedNormalSubmitterSampleId": "TEST_SPECIMEN_hsreltpusctapirhgwpr_N1", "specimen": { - "submitterSpecimenId": "TEST_SPECIMEN_hsreltpusctapirhgwpr_N1", + "submitterSpecimenId": "TEST_SPECIMEN_hsreltpusctapirhgwpr_T1", "specimenType": "Xenograft - derived from tumour cell line", "specimenTissueSource": "Cerebellum", "tumourNormalDesignation": "Tumour" @@ -17,118 +21,120 @@ } ], "donor": { - "submitter_donor_id": "TEST_DONOR_hsreltpusctapirhgwpr", - "primary_site": ["Brain"], - "vital_status": "Deceased", - "survival_time": 884, - "cause_of_death": "Died of cancer", - "primary_diagnosis": [ + "submitterDonorId": "TEST_DONOR_hsreltpusctapirhgwpr", + "primarySite": [ + "Brain" + ], + "vitalStatus": "Deceased", + "survivalTime": 884, + "causeOfDeath": "Died of cancer", + "primaryDiagnosis": [ { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_hsreltpusctapirhgwpr_0", - "age_at_diagnosis": 70, - "cancer_type_code": "C71.9", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_hsreltpusctapirhgwpr_0", + "ageAtDiagnosis": 70, + "cancerTypeCode": "C71.9", "laterality": "Unilateral, side not specified", - "clinical_tumour_staging_system": "FIGO staging system", - "clinical_stage_group": "Stage IB", - "lymph_nodes_examined_status": "No lymph nodes found in resected specimen", - "performance_status": "Grade 1", + "clinicalTumourStagingSystem": "FIGO staging system", + "clinicalStageGroup": "Stage IB", + "lymphNodesExaminedStatus": "No lymph nodes found in resected specimen", + "performanceStatus": "Grade 1", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_hsreltpusctapirhgwpr_0", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_hsreltpusctapirhgwpr_0", + "treatmentType": [ "No treatment" ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_hsreltpusctapirhgwpr_0", - "interval_of_followup": 95, - "disease_status_at_followup": "Loco-regional progression" + "submitterFollowUpId": "TEST_FOLLOW_UP_hsreltpusctapirhgwpr_0", + "intervalOfFollowup": 95, + "diseaseStatusAtFollowup": "Loco-regional progression" } ] }, { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_hsreltpusctapirhgwpr_1", - "age_at_diagnosis": 49, - "cancer_type_code": "D76.5", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_hsreltpusctapirhgwpr_1", + "ageAtDiagnosis": 49, + "cancerTypeCode": "D76.5", "laterality": "Right", - "clinical_tumour_staging_system": "AJCC 7th edition", - "clinical_stage_group": "Stage IVA2", - "lymph_nodes_examined_status": "No", - "performance_status": "Grade 3", + "clinicalTumourStagingSystem": "AJCC 7th edition", + "clinicalStageGroup": "Stage IVA2", + "lymphNodesExaminedStatus": "No", + "performanceStatus": "Grade 3", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_hsreltpusctapirhgwpr_1", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_hsreltpusctapirhgwpr_1", + "treatmentType": [ "Radiation therapy", "Surgery", "Chemotherapy" ], - "treatment_intent": "Unknown", - "treatment_start_interval": 51, - "treatment_duration": 32, - "response_to_treatment": "NED", + "treatmentIntent": "Unknown", + "treatmentStartInterval": 51, + "treatmentDuration": 32, + "responseToTreatment": "NED", "radiation": [ { - "radiation_therapy_modality": "Heavy Ions", - "radiation_therapy_type": "Internal", - "anatomical_site_irradiated": "Body", - "radiation_therapy_dosage": 48, - "radiation_therapy_fractions": 45 + "radiationTherapyModality": "Heavy Ions", + "radiationTherapyType": "Internal", + "anatomicalSiteIrradiated": "Body", + "radiationTherapyDosage": 48, + "radiationTherapyFractions": 45 } ], "surgery": [ { - "surgery_type": "Cholecystectomy", - "surgery_site": "C42.6", - "surgery_location": "Local recurrence", - "residual_tumour_classification": "R1" + "surgeryType": "Cholecystectomy", + "surgerySite": "C42.6", + "surgeryLocation": "Local recurrence", + "residualTumourClassification": "R1" } ], "chemotherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 54, - "chemotherapy_dosage_units": "ug/m2" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 54, + "chemotherapyDosageUnits": "ug/m2" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_hsreltpusctapirhgwpr_1", - "interval_of_followup": 56, - "disease_status_at_followup": "No evidence of disease" + "submitterFollowUpId": "TEST_FOLLOW_UP_hsreltpusctapirhgwpr_1", + "intervalOfFollowup": 56, + "diseaseStatusAtFollowup": "No evidence of disease" } ] } ], "comorbidity": [ { - "age_at_comorbidity_diagnosis": 70, - "comorbidity_type_code": "B78.90" + "ageAtComorbidityDiagnosis": 70, + "comorbidityTypeCode": "B78.90" }, { - "age_at_comorbidity_diagnosis": 29, - "comorbidity_type_code": "E45.94" + "ageAtComorbidityDiagnosis": 29, + "comorbidityTypeCode": "E45.94" } ] }, "specimen": { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_hsreltpusctapirhgwpr_0", - "submitter_specimen_id": "TEST_SPECIMEN_hsreltpusctapirhgwpr_N1", - "specimen_acquisition_interval": 72, - "specimen_anatomic_location": "C71.0", - "specimen_laterality": "Right", - "tumour_histological_type": "8151/63", - "pathological_tumour_staging_system": "AJCC 7th edition", - "pathological_stage_group": "Stage IVA", - "tumour_grading_system": "ISUP grading system", - "tumour_grade": "G1", - "percent_tumour_cells": 16, - "reference_pathology_confirmed": "Unknown" + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_hsreltpusctapirhgwpr_0", + "submitterSpecimenId": "TEST_SPECIMEN_hsreltpusctapirhgwpr_N1", + "specimenAcquisitionInterval": 72, + "specimenAnatomicLocation": "C71.0", + "specimenLaterality": "Right", + "tumourHistologicalType": "8151/63", + "pathologicalTumourStagingSystem": "AJCC 7th edition", + "pathologicalStageGroup": "Stage IVA", + "tumourGradingSystem": "ISUP grading system", + "tumourGrade": "G1", + "percentTumourCells": 16, + "referencePathologyConfirmed": "Unknown" }, "files": [ { @@ -156,25 +162,25 @@ ], "collaborator": [ { - "contact_email": "batman@batman_inc.org", + "contactEmail": "batman@batman_inc.org", "name": "batman", "affiliation": "batman inc" } ], "experiment": { "platform": "ILLUMINA", - "experimental_strategy": "WGS", - "submitter_sequencing_experiment_id": "EXPERIMENT" + "experimentalStrategy": "WGS", + "submitterSequencingExperimentId": "EXPERIMENT" }, "workflow": { - "workflow_name": "batman_stuff", - "genome_build": "GRCh38_hla_decoy_ebv", + "workflowName": "batman_stuff", + "genomeBuild": "GRCh38_hla_decoy_ebv", "inputs": [ { - "analysis_type": "sequencing_alignment", - "tumour_analysis_id": "00000000-0000-0000-0000-000000000000", - "normal_analysis_id": "00000000-0000-0000-0000-000000000000" + "analysisType": "sequencing_alignment", + "tumourAnalysisId": "00000000-0000-0000-0000-000000000000", + "normalAnalysisId": "00000000-0000-0000-0000-000000000000" } ] } -} +} \ No newline at end of file diff --git a/playground-data/example-payloads/TEST_SPECIMEN_hsreltpusctapirhgwpr_T2.json b/playground-data/example-payloads/TEST_SPECIMEN_hsreltpusctapirhgwpr_T2.json index 31ffe521..8ae3b709 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_hsreltpusctapirhgwpr_T2.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_hsreltpusctapirhgwpr_T2.json @@ -1,11 +1,15 @@ { + "analysisType": { + "name": "playgroundSchema" + }, + "studyId": "OVPLG-01", "samples": [ { "submitterSampleId": "TEST_SPECIMEN_hsreltpusctapirhgwpr_T2", "sampleType": "Total DNA", "matchedNormalSubmitterSampleId": "TEST_SPECIMEN_hsreltpusctapirhgwpr_N2", "specimen": { - "submitterSpecimenId": "TEST_SPECIMEN_hsreltpusctapirhgwpr_N2", + "submitterSpecimenId": "TEST_SPECIMEN_hsreltpusctapirhgwpr_T2", "specimenType": "Cell line - derived from xenograft tumour", "specimenTissueSource": "Cerebellum", "tumourNormalDesignation": "Tumour" @@ -17,118 +21,120 @@ } ], "donor": { - "submitter_donor_id": "TEST_DONOR_hsreltpusctapirhgwpr", - "primary_site": ["Brain"], - "vital_status": "Deceased", - "survival_time": 884, - "cause_of_death": "Died of cancer", - "primary_diagnosis": [ + "submitterDonorId": "TEST_DONOR_hsreltpusctapirhgwpr", + "primarySite": [ + "Brain" + ], + "vitalStatus": "Deceased", + "survivalTime": 884, + "causeOfDeath": "Died of cancer", + "primaryDiagnosis": [ { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_hsreltpusctapirhgwpr_0", - "age_at_diagnosis": 70, - "cancer_type_code": "C71.9", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_hsreltpusctapirhgwpr_0", + "ageAtDiagnosis": 70, + "cancerTypeCode": "C71.9", "laterality": "Unilateral, side not specified", - "clinical_tumour_staging_system": "FIGO staging system", - "clinical_stage_group": "Stage IB", - "lymph_nodes_examined_status": "No lymph nodes found in resected specimen", - "performance_status": "Grade 1", + "clinicalTumourStagingSystem": "FIGO staging system", + "clinicalStageGroup": "Stage IB", + "lymphNodesExaminedStatus": "No lymph nodes found in resected specimen", + "performanceStatus": "Grade 1", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_hsreltpusctapirhgwpr_0", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_hsreltpusctapirhgwpr_0", + "treatmentType": [ "No treatment" ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_hsreltpusctapirhgwpr_0", - "interval_of_followup": 95, - "disease_status_at_followup": "Loco-regional progression" + "submitterFollowUpId": "TEST_FOLLOW_UP_hsreltpusctapirhgwpr_0", + "intervalOfFollowup": 95, + "diseaseStatusAtFollowup": "Loco-regional progression" } ] }, { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_hsreltpusctapirhgwpr_1", - "age_at_diagnosis": 49, - "cancer_type_code": "D76.5", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_hsreltpusctapirhgwpr_1", + "ageAtDiagnosis": 49, + "cancerTypeCode": "D76.5", "laterality": "Right", - "clinical_tumour_staging_system": "AJCC 7th edition", - "clinical_stage_group": "Stage IVA2", - "lymph_nodes_examined_status": "No", - "performance_status": "Grade 3", + "clinicalTumourStagingSystem": "AJCC 7th edition", + "clinicalStageGroup": "Stage IVA2", + "lymphNodesExaminedStatus": "No", + "performanceStatus": "Grade 3", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_hsreltpusctapirhgwpr_1", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_hsreltpusctapirhgwpr_1", + "treatmentType": [ "Radiation therapy", "Surgery", "Chemotherapy" ], - "treatment_intent": "Unknown", - "treatment_start_interval": 51, - "treatment_duration": 32, - "response_to_treatment": "NED", + "treatmentIntent": "Unknown", + "treatmentStartInterval": 51, + "treatmentDuration": 32, + "responseToTreatment": "NED", "radiation": [ { - "radiation_therapy_modality": "Heavy Ions", - "radiation_therapy_type": "Internal", - "anatomical_site_irradiated": "Body", - "radiation_therapy_dosage": 48, - "radiation_therapy_fractions": 45 + "radiationTherapyModality": "Heavy Ions", + "radiationTherapyType": "Internal", + "anatomicalSiteIrradiated": "Body", + "radiationTherapyDosage": 48, + "radiationTherapyFractions": 45 } ], "surgery": [ { - "surgery_type": "Cholecystectomy", - "surgery_site": "C42.6", - "surgery_location": "Local recurrence", - "residual_tumour_classification": "R1" + "surgeryType": "Cholecystectomy", + "surgerySite": "C42.6", + "surgeryLocation": "Local recurrence", + "residualTumourClassification": "R1" } ], "chemotherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 54, - "chemotherapy_dosage_units": "ug/m2" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 54, + "chemotherapyDosageUnits": "ug/m2" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_hsreltpusctapirhgwpr_1", - "interval_of_followup": 56, - "disease_status_at_followup": "No evidence of disease" + "submitterFollowUpId": "TEST_FOLLOW_UP_hsreltpusctapirhgwpr_1", + "intervalOfFollowup": 56, + "diseaseStatusAtFollowup": "No evidence of disease" } ] } ], "comorbidity": [ { - "age_at_comorbidity_diagnosis": 70, - "comorbidity_type_code": "B78.90" + "ageAtComorbidityDiagnosis": 70, + "comorbidityTypeCode": "B78.90" }, { - "age_at_comorbidity_diagnosis": 29, - "comorbidity_type_code": "E45.94" + "ageAtComorbidityDiagnosis": 29, + "comorbidityTypeCode": "E45.94" } ] }, "specimen": { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_hsreltpusctapirhgwpr_1", - "submitter_specimen_id": "TEST_SPECIMEN_hsreltpusctapirhgwpr_N2", - "specimen_acquisition_interval": 71, - "specimen_anatomic_location": "C71.0", - "specimen_laterality": "Not applicable", - "tumour_histological_type": "8156/96", - "pathological_tumour_staging_system": "Durie-Salmon staging system", - "pathological_stage_group": "Stage 1A", - "tumour_grading_system": "FNCLCC grading system", - "tumour_grade": "G2", - "percent_tumour_cells": 16, - "reference_pathology_confirmed": "Yes" + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_hsreltpusctapirhgwpr_1", + "submitterSpecimenId": "TEST_SPECIMEN_hsreltpusctapirhgwpr_N2", + "specimenAcquisitionInterval": 71, + "specimenAnatomicLocation": "C71.0", + "specimenLaterality": "Not applicable", + "tumourHistologicalType": "8156/96", + "pathologicalTumourStagingSystem": "Durie-Salmon staging system", + "pathologicalStageGroup": "Stage 1A", + "tumourGradingSystem": "FNCLCC grading system", + "tumourGrade": "G2", + "percentTumourCells": 16, + "referencePathologyConfirmed": "Yes" }, "files": [ { @@ -156,25 +162,25 @@ ], "collaborator": [ { - "contact_email": "batman@batman_inc.org", + "contactEmail": "batman@batman_inc.org", "name": "batman", "affiliation": "batman inc" } ], "experiment": { "platform": "ILLUMINA", - "experimental_strategy": "WGS", - "submitter_sequencing_experiment_id": "EXPERIMENT" + "experimentalStrategy": "WGS", + "submitterSequencingExperimentId": "EXPERIMENT" }, "workflow": { - "workflow_name": "batman_stuff", - "genome_build": "GRCh38_hla_decoy_ebv", + "workflowName": "batman_stuff", + "genomeBuild": "GRCh38_hla_decoy_ebv", "inputs": [ { - "analysis_type": "sequencing_alignment", - "tumour_analysis_id": "00000000-0000-0000-0000-000000000000", - "normal_analysis_id": "00000000-0000-0000-0000-000000000000" + "analysisType": "sequencing_alignment", + "tumourAnalysisId": "00000000-0000-0000-0000-000000000000", + "normalAnalysisId": "00000000-0000-0000-0000-000000000000" } ] } -} +} \ No newline at end of file diff --git a/playground-data/example-payloads/TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_N1.json b/playground-data/example-payloads/TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_N1.json index 15dec6fe..78b00549 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_N1.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_N1.json @@ -1,4 +1,8 @@ { + "analysisType": { + "name": "playgroundSchema" + }, + "studyId": "OVPLG-01", "samples": [ { "submitterSampleId": "TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_N1", @@ -17,98 +21,100 @@ } ], "donor": { - "submitter_donor_id": "TEST_DONOR_kemubcrdlsbqgbcnnchc", - "primary_site": ["Bladder"], - "vital_status": "Alive", - "survival_time": null, - "cause_of_death": null, - "primary_diagnosis": [ + "submitterDonorId": "TEST_DONOR_kemubcrdlsbqgbcnnchc", + "primarySite": [ + "Bladder" + ], + "vitalStatus": "Alive", + "survivalTime": null, + "causeOfDeath": null, + "primaryDiagnosis": [ { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_kemubcrdlsbqgbcnnchc_0", - "age_at_diagnosis": 25, - "cancer_type_code": "C67.2", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_kemubcrdlsbqgbcnnchc_0", + "ageAtDiagnosis": 25, + "cancerTypeCode": "C67.2", "laterality": "Midline", - "clinical_tumour_staging_system": "Ann Arbor staging system", - "clinical_stage_group": "Stage IIA", - "lymph_nodes_examined_status": "Not applicable", - "performance_status": "Grade 0", + "clinicalTumourStagingSystem": "Ann Arbor staging system", + "clinicalStageGroup": "Stage IIA", + "lymphNodesExaminedStatus": "Not applicable", + "performanceStatus": "Grade 0", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_kemubcrdlsbqgbcnnchc_0", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_kemubcrdlsbqgbcnnchc_0", + "treatmentType": [ "Radiation therapy", "Immunotherapy", "Chemotherapy", "Hormonal therapy" ], - "treatment_intent": "Curative", - "treatment_start_interval": 5, - "treatment_duration": 8, - "response_to_treatment": "NED", + "treatmentIntent": "Curative", + "treatmentStartInterval": 5, + "treatmentDuration": 8, + "responseToTreatment": "NED", "radiation": [ { - "radiation_therapy_modality": "Electron", - "radiation_therapy_type": "Internal", - "anatomical_site_irradiated": "Head", - "radiation_therapy_dosage": 67, - "radiation_therapy_fractions": 53 + "radiationTherapyModality": "Electron", + "radiationTherapyType": "Internal", + "anatomicalSiteIrradiated": "Head", + "radiationTherapyDosage": 67, + "radiationTherapyFractions": 53 } ], "immunotherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "immunotherapy_type": "Monoclonal antibodies other than immune checkpoint inhibitors" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "immunotherapyType": "Monoclonal antibodies other than immune checkpoint inhibitors" } ], "chemotherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 29, - "chemotherapy_dosage_units": "mg/kg" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 29, + "chemotherapyDosageUnits": "mg/kg" } ], - "hormone_therapy": [ + "hormoneTherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 83, - "hormone_drug_dosage_units": "IU/m2" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 83, + "hormoneDrugDosageUnits": "IU/m2" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_kemubcrdlsbqgbcnnchc_0", - "interval_of_followup": 35, - "disease_status_at_followup": "No evidence of disease" + "submitterFollowUpId": "TEST_FOLLOW_UP_kemubcrdlsbqgbcnnchc_0", + "intervalOfFollowup": 35, + "diseaseStatusAtFollowup": "No evidence of disease" } ] } ], "comorbidity": [ { - "age_at_comorbidity_diagnosis": 15, - "comorbidity_type_code": "A28.15" + "ageAtComorbidityDiagnosis": 15, + "comorbidityTypeCode": "A28.15" }, { - "age_at_comorbidity_diagnosis": 48, - "comorbidity_type_code": "F03.21" + "ageAtComorbidityDiagnosis": 48, + "comorbidityTypeCode": "F03.21" }, { - "age_at_comorbidity_diagnosis": 26, - "comorbidity_type_code": "F31.70" + "ageAtComorbidityDiagnosis": 26, + "comorbidityTypeCode": "F31.70" } ] }, "specimen": { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_kemubcrdlsbqgbcnnchc_0", - "submitter_specimen_id": "TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_N1", - "specimen_acquisition_interval": 3, - "specimen_anatomic_location": "C67.3", - "specimen_laterality": "Left" + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_kemubcrdlsbqgbcnnchc_0", + "submitterSpecimenId": "TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_N1", + "specimenAcquisitionInterval": 3, + "specimenAnatomicLocation": "C67.3", + "specimenLaterality": "Left" }, "files": [ { @@ -136,25 +142,25 @@ ], "collaborator": [ { - "contact_email": "batman@batman_inc.org", + "contactEmail": "batman@batman_inc.org", "name": "batman", "affiliation": "batman inc" } ], "experiment": { "platform": "ILLUMINA", - "experimental_strategy": "WGS", - "submitter_sequencing_experiment_id": "EXPERIMENT" + "experimentalStrategy": "WGS", + "submitterSequencingExperimentId": "EXPERIMENT" }, "workflow": { - "workflow_name": "batman_stuff", - "genome_build": "GRCh38_hla_decoy_ebv", + "workflowName": "batman_stuff", + "genomeBuild": "GRCh38_hla_decoy_ebv", "inputs": [ { - "analysis_type": "sequencing_alignment", - "tumour_analysis_id": "00000000-0000-0000-0000-000000000000", - "normal_analysis_id": "00000000-0000-0000-0000-000000000000" + "analysisType": "sequencing_alignment", + "tumourAnalysisId": "00000000-0000-0000-0000-000000000000", + "normalAnalysisId": "00000000-0000-0000-0000-000000000000" } ] } -} +} \ No newline at end of file diff --git a/playground-data/example-payloads/TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_N2.json b/playground-data/example-payloads/TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_N2.json index 4b89128a..b44a45a8 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_N2.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_N2.json @@ -1,4 +1,8 @@ { + "analysisType": { + "name": "playgroundSchema" + }, + "studyId": "OVPLG-01", "samples": [ { "submitterSampleId": "TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_N2", @@ -17,98 +21,100 @@ } ], "donor": { - "submitter_donor_id": "TEST_DONOR_kemubcrdlsbqgbcnnchc", - "primary_site": ["Bladder"], - "vital_status": "Alive", - "survival_time": null, - "cause_of_death": null, - "primary_diagnosis": [ + "submitterDonorId": "TEST_DONOR_kemubcrdlsbqgbcnnchc", + "primarySite": [ + "Bladder" + ], + "vitalStatus": "Alive", + "survivalTime": null, + "causeOfDeath": null, + "primaryDiagnosis": [ { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_kemubcrdlsbqgbcnnchc_0", - "age_at_diagnosis": 25, - "cancer_type_code": "C67.2", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_kemubcrdlsbqgbcnnchc_0", + "ageAtDiagnosis": 25, + "cancerTypeCode": "C67.2", "laterality": "Midline", - "clinical_tumour_staging_system": "Ann Arbor staging system", - "clinical_stage_group": "Stage IIA", - "lymph_nodes_examined_status": "Not applicable", - "performance_status": "Grade 0", + "clinicalTumourStagingSystem": "Ann Arbor staging system", + "clinicalStageGroup": "Stage IIA", + "lymphNodesExaminedStatus": "Not applicable", + "performanceStatus": "Grade 0", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_kemubcrdlsbqgbcnnchc_0", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_kemubcrdlsbqgbcnnchc_0", + "treatmentType": [ "Radiation therapy", "Immunotherapy", "Chemotherapy", "Hormonal therapy" ], - "treatment_intent": "Curative", - "treatment_start_interval": 5, - "treatment_duration": 8, - "response_to_treatment": "NED", + "treatmentIntent": "Curative", + "treatmentStartInterval": 5, + "treatmentDuration": 8, + "responseToTreatment": "NED", "radiation": [ { - "radiation_therapy_modality": "Electron", - "radiation_therapy_type": "Internal", - "anatomical_site_irradiated": "Head", - "radiation_therapy_dosage": 67, - "radiation_therapy_fractions": 53 + "radiationTherapyModality": "Electron", + "radiationTherapyType": "Internal", + "anatomicalSiteIrradiated": "Head", + "radiationTherapyDosage": 67, + "radiationTherapyFractions": 53 } ], "immunotherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "immunotherapy_type": "Monoclonal antibodies other than immune checkpoint inhibitors" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "immunotherapyType": "Monoclonal antibodies other than immune checkpoint inhibitors" } ], "chemotherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 29, - "chemotherapy_dosage_units": "mg/kg" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 29, + "chemotherapyDosageUnits": "mg/kg" } ], - "hormone_therapy": [ + "hormoneTherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 83, - "hormone_drug_dosage_units": "IU/m2" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 83, + "hormoneDrugDosageUnits": "IU/m2" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_kemubcrdlsbqgbcnnchc_0", - "interval_of_followup": 35, - "disease_status_at_followup": "No evidence of disease" + "submitterFollowUpId": "TEST_FOLLOW_UP_kemubcrdlsbqgbcnnchc_0", + "intervalOfFollowup": 35, + "diseaseStatusAtFollowup": "No evidence of disease" } ] } ], "comorbidity": [ { - "age_at_comorbidity_diagnosis": 15, - "comorbidity_type_code": "A28.15" + "ageAtComorbidityDiagnosis": 15, + "comorbidityTypeCode": "A28.15" }, { - "age_at_comorbidity_diagnosis": 48, - "comorbidity_type_code": "F03.21" + "ageAtComorbidityDiagnosis": 48, + "comorbidityTypeCode": "F03.21" }, { - "age_at_comorbidity_diagnosis": 26, - "comorbidity_type_code": "F31.70" + "ageAtComorbidityDiagnosis": 26, + "comorbidityTypeCode": "F31.70" } ] }, "specimen": { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_kemubcrdlsbqgbcnnchc_0", - "submitter_specimen_id": "TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_N2", - "specimen_acquisition_interval": 31, - "specimen_anatomic_location": "C67.3", - "specimen_laterality": "Unknown" + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_kemubcrdlsbqgbcnnchc_0", + "submitterSpecimenId": "TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_N2", + "specimenAcquisitionInterval": 31, + "specimenAnatomicLocation": "C67.3", + "specimenLaterality": "Unknown" }, "files": [ { @@ -136,25 +142,25 @@ ], "collaborator": [ { - "contact_email": "batman@batman_inc.org", + "contactEmail": "batman@batman_inc.org", "name": "batman", "affiliation": "batman inc" } ], "experiment": { "platform": "ILLUMINA", - "experimental_strategy": "WGS", - "submitter_sequencing_experiment_id": "EXPERIMENT" + "experimentalStrategy": "WGS", + "submitterSequencingExperimentId": "EXPERIMENT" }, "workflow": { - "workflow_name": "batman_stuff", - "genome_build": "GRCh38_hla_decoy_ebv", + "workflowName": "batman_stuff", + "genomeBuild": "GRCh38_hla_decoy_ebv", "inputs": [ { - "analysis_type": "sequencing_alignment", - "tumour_analysis_id": "00000000-0000-0000-0000-000000000000", - "normal_analysis_id": "00000000-0000-0000-0000-000000000000" + "analysisType": "sequencing_alignment", + "tumourAnalysisId": "00000000-0000-0000-0000-000000000000", + "normalAnalysisId": "00000000-0000-0000-0000-000000000000" } ] } -} +} \ No newline at end of file diff --git a/playground-data/example-payloads/TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_T1.json b/playground-data/example-payloads/TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_T1.json index e61919c0..054e6d46 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_T1.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_T1.json @@ -1,12 +1,16 @@ { + "analysisType": { + "name": "playgroundSchema" + }, + "studyId": "OVPLG-01", "samples": [ { "submitterSampleId": "TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_T1", "sampleType": "Total DNA", "matchedNormalSubmitterSampleId": "TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_N1", "specimen": { - "submitterSpecimenId": "TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_N1", - "specimenType": "Primary Tumour", + "submitterSpecimenId": "TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_T1", + "specimenType": "Primary tumour", "specimenTissueSource": "Solid tissue", "tumourNormalDesignation": "Tumour" }, @@ -17,105 +21,107 @@ } ], "donor": { - "submitter_donor_id": "TEST_DONOR_kemubcrdlsbqgbcnnchc", - "primary_site": ["Bladder"], - "vital_status": "Alive", - "survival_time": null, - "cause_of_death": null, - "primary_diagnosis": [ + "submitterDonorId": "TEST_DONOR_kemubcrdlsbqgbcnnchc", + "primarySite": [ + "Bladder" + ], + "vitalStatus": "Alive", + "survivalTime": null, + "causeOfDeath": null, + "primaryDiagnosis": [ { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_kemubcrdlsbqgbcnnchc_0", - "age_at_diagnosis": 25, - "cancer_type_code": "C67.2", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_kemubcrdlsbqgbcnnchc_0", + "ageAtDiagnosis": 25, + "cancerTypeCode": "C67.2", "laterality": "Midline", - "clinical_tumour_staging_system": "Ann Arbor staging system", - "clinical_stage_group": "Stage IIA", - "lymph_nodes_examined_status": "Not applicable", - "performance_status": "Grade 0", + "clinicalTumourStagingSystem": "Ann Arbor staging system", + "clinicalStageGroup": "Stage IIA", + "lymphNodesExaminedStatus": "Not applicable", + "performanceStatus": "Grade 0", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_kemubcrdlsbqgbcnnchc_0", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_kemubcrdlsbqgbcnnchc_0", + "treatmentType": [ "Radiation therapy", "Immunotherapy", "Chemotherapy", "Hormonal therapy" ], - "treatment_intent": "Curative", - "treatment_start_interval": 5, - "treatment_duration": 8, - "response_to_treatment": "NED", + "treatmentIntent": "Curative", + "treatmentStartInterval": 5, + "treatmentDuration": 8, + "responseToTreatment": "NED", "radiation": [ { - "radiation_therapy_modality": "Electron", - "radiation_therapy_type": "Internal", - "anatomical_site_irradiated": "Head", - "radiation_therapy_dosage": 67, - "radiation_therapy_fractions": 53 + "radiationTherapyModality": "Electron", + "radiationTherapyType": "Internal", + "anatomicalSiteIrradiated": "Head", + "radiationTherapyDosage": 67, + "radiationTherapyFractions": 53 } ], "immunotherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "immunotherapy_type": "Monoclonal antibodies other than immune checkpoint inhibitors" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "immunotherapyType": "Monoclonal antibodies other than immune checkpoint inhibitors" } ], "chemotherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 29, - "chemotherapy_dosage_units": "mg/kg" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 29, + "chemotherapyDosageUnits": "mg/kg" } ], - "hormone_therapy": [ + "hormoneTherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 83, - "hormone_drug_dosage_units": "IU/m2" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 83, + "hormoneDrugDosageUnits": "IU/m2" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_kemubcrdlsbqgbcnnchc_0", - "interval_of_followup": 35, - "disease_status_at_followup": "No evidence of disease" + "submitterFollowUpId": "TEST_FOLLOW_UP_kemubcrdlsbqgbcnnchc_0", + "intervalOfFollowup": 35, + "diseaseStatusAtFollowup": "No evidence of disease" } ] } ], "comorbidity": [ { - "age_at_comorbidity_diagnosis": 15, - "comorbidity_type_code": "A28.15" + "ageAtComorbidityDiagnosis": 15, + "comorbidityTypeCode": "A28.15" }, { - "age_at_comorbidity_diagnosis": 48, - "comorbidity_type_code": "F03.21" + "ageAtComorbidityDiagnosis": 48, + "comorbidityTypeCode": "F03.21" }, { - "age_at_comorbidity_diagnosis": 26, - "comorbidity_type_code": "F31.70" + "ageAtComorbidityDiagnosis": 26, + "comorbidityTypeCode": "F31.70" } ] }, "specimen": { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_kemubcrdlsbqgbcnnchc_0", - "submitter_specimen_id": "TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_N1", - "specimen_acquisition_interval": 26, - "specimen_anatomic_location": "C67.3", - "specimen_laterality": "Not applicable", - "tumour_histological_type": "8276/08", - "pathological_tumour_staging_system": "Binet staging system", - "pathological_stage_group": "Stage C", - "tumour_grading_system": "Grading system for GNETs", - "tumour_grade": "G2", - "percent_tumour_cells": 71, - "reference_pathology_confirmed": "No" + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_kemubcrdlsbqgbcnnchc_0", + "submitterSpecimenId": "TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_N1", + "specimenAcquisitionInterval": 26, + "specimenAnatomicLocation": "C67.3", + "specimenLaterality": "Not applicable", + "tumourHistologicalType": "8276/08", + "pathologicalTumourStagingSystem": "Binet staging system", + "pathologicalStageGroup": "Stage C", + "tumourGradingSystem": "Grading system for GNETs", + "tumourGrade": "G2", + "percentTumourCells": 71, + "referencePathologyConfirmed": "No" }, "files": [ { @@ -143,25 +149,25 @@ ], "collaborator": [ { - "contact_email": "batman@batman_inc.org", + "contactEmail": "batman@batman_inc.org", "name": "batman", "affiliation": "batman inc" } ], "experiment": { "platform": "ILLUMINA", - "experimental_strategy": "WGS", - "submitter_sequencing_experiment_id": "EXPERIMENT" + "experimentalStrategy": "WGS", + "submitterSequencingExperimentId": "EXPERIMENT" }, "workflow": { - "workflow_name": "batman_stuff", - "genome_build": "GRCh38_hla_decoy_ebv", + "workflowName": "batman_stuff", + "genomeBuild": "GRCh38_hla_decoy_ebv", "inputs": [ { - "analysis_type": "sequencing_alignment", - "tumour_analysis_id": "00000000-0000-0000-0000-000000000000", - "normal_analysis_id": "00000000-0000-0000-0000-000000000000" + "analysisType": "sequencing_alignment", + "tumourAnalysisId": "00000000-0000-0000-0000-000000000000", + "normalAnalysisId": "00000000-0000-0000-0000-000000000000" } ] } -} +} \ No newline at end of file diff --git a/playground-data/example-payloads/TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_T2.json b/playground-data/example-payloads/TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_T2.json index 59dea9c9..301ddd5f 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_T2.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_T2.json @@ -1,12 +1,16 @@ { + "analysisType": { + "name": "playgroundSchema" + }, + "studyId": "OVPLG-01", "samples": [ { "submitterSampleId": "TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_T2", "sampleType": "Total DNA", "matchedNormalSubmitterSampleId": "TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_N2", "specimen": { - "submitterSpecimenId": "TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_N2", - "specimenType": "Primary Tumour", + "submitterSpecimenId": "TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_T2", + "specimenType": "Primary tumour", "specimenTissueSource": "Solid tissue", "tumourNormalDesignation": "Tumour" }, @@ -17,105 +21,107 @@ } ], "donor": { - "submitter_donor_id": "TEST_DONOR_kemubcrdlsbqgbcnnchc", - "primary_site": ["Bladder"], - "vital_status": "Alive", - "survival_time": null, - "cause_of_death": null, - "primary_diagnosis": [ + "submitterDonorId": "TEST_DONOR_kemubcrdlsbqgbcnnchc", + "primarySite": [ + "Bladder" + ], + "vitalStatus": "Alive", + "survivalTime": null, + "causeOfDeath": null, + "primaryDiagnosis": [ { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_kemubcrdlsbqgbcnnchc_0", - "age_at_diagnosis": 25, - "cancer_type_code": "C67.2", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_kemubcrdlsbqgbcnnchc_0", + "ageAtDiagnosis": 25, + "cancerTypeCode": "C67.2", "laterality": "Midline", - "clinical_tumour_staging_system": "Ann Arbor staging system", - "clinical_stage_group": "Stage IIA", - "lymph_nodes_examined_status": "Not applicable", - "performance_status": "Grade 0", + "clinicalTumourStagingSystem": "Ann Arbor staging system", + "clinicalStageGroup": "Stage IIA", + "lymphNodesExaminedStatus": "Not applicable", + "performanceStatus": "Grade 0", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_kemubcrdlsbqgbcnnchc_0", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_kemubcrdlsbqgbcnnchc_0", + "treatmentType": [ "Radiation therapy", "Immunotherapy", "Chemotherapy", "Hormonal therapy" ], - "treatment_intent": "Curative", - "treatment_start_interval": 5, - "treatment_duration": 8, - "response_to_treatment": "NED", + "treatmentIntent": "Curative", + "treatmentStartInterval": 5, + "treatmentDuration": 8, + "responseToTreatment": "NED", "radiation": [ { - "radiation_therapy_modality": "Electron", - "radiation_therapy_type": "Internal", - "anatomical_site_irradiated": "Head", - "radiation_therapy_dosage": 67, - "radiation_therapy_fractions": 53 + "radiationTherapyModality": "Electron", + "radiationTherapyType": "Internal", + "anatomicalSiteIrradiated": "Head", + "radiationTherapyDosage": 67, + "radiationTherapyFractions": 53 } ], "immunotherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "immunotherapy_type": "Monoclonal antibodies other than immune checkpoint inhibitors" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "immunotherapyType": "Monoclonal antibodies other than immune checkpoint inhibitors" } ], "chemotherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 29, - "chemotherapy_dosage_units": "mg/kg" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 29, + "chemotherapyDosageUnits": "mg/kg" } ], - "hormone_therapy": [ + "hormoneTherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 83, - "hormone_drug_dosage_units": "IU/m2" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 83, + "hormoneDrugDosageUnits": "IU/m2" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_kemubcrdlsbqgbcnnchc_0", - "interval_of_followup": 35, - "disease_status_at_followup": "No evidence of disease" + "submitterFollowUpId": "TEST_FOLLOW_UP_kemubcrdlsbqgbcnnchc_0", + "intervalOfFollowup": 35, + "diseaseStatusAtFollowup": "No evidence of disease" } ] } ], "comorbidity": [ { - "age_at_comorbidity_diagnosis": 15, - "comorbidity_type_code": "A28.15" + "ageAtComorbidityDiagnosis": 15, + "comorbidityTypeCode": "A28.15" }, { - "age_at_comorbidity_diagnosis": 48, - "comorbidity_type_code": "F03.21" + "ageAtComorbidityDiagnosis": 48, + "comorbidityTypeCode": "F03.21" }, { - "age_at_comorbidity_diagnosis": 26, - "comorbidity_type_code": "F31.70" + "ageAtComorbidityDiagnosis": 26, + "comorbidityTypeCode": "F31.70" } ] }, "specimen": { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_kemubcrdlsbqgbcnnchc_0", - "submitter_specimen_id": "TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_N2", - "specimen_acquisition_interval": 59, - "specimen_anatomic_location": "C67.3", - "specimen_laterality": "Not applicable", - "tumour_histological_type": "9466/08", - "pathological_tumour_staging_system": "St Jude staging system", - "pathological_stage_group": "Stage III", - "tumour_grading_system": "Three-tier grading system", - "tumour_grade": "G2", - "percent_tumour_cells": 61, - "reference_pathology_confirmed": "Unknown" + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_kemubcrdlsbqgbcnnchc_0", + "submitterSpecimenId": "TEST_SPECIMEN_kemubcrdlsbqgbcnnchc_N2", + "specimenAcquisitionInterval": 59, + "specimenAnatomicLocation": "C67.3", + "specimenLaterality": "Not applicable", + "tumourHistologicalType": "9466/08", + "pathologicalTumourStagingSystem": "St Jude staging system", + "pathologicalStageGroup": "Stage III", + "tumourGradingSystem": "Three-tier grading system", + "tumourGrade": "G2", + "percentTumourCells": 61, + "referencePathologyConfirmed": "Unknown" }, "files": [ { @@ -143,25 +149,25 @@ ], "collaborator": [ { - "contact_email": "batman@batman_inc.org", + "contactEmail": "batman@batman_inc.org", "name": "batman", "affiliation": "batman inc" } ], "experiment": { "platform": "ILLUMINA", - "experimental_strategy": "WGS", - "submitter_sequencing_experiment_id": "EXPERIMENT" + "experimentalStrategy": "WGS", + "submitterSequencingExperimentId": "EXPERIMENT" }, "workflow": { - "workflow_name": "batman_stuff", - "genome_build": "GRCh38_hla_decoy_ebv", + "workflowName": "batman_stuff", + "genomeBuild": "GRCh38_hla_decoy_ebv", "inputs": [ { - "analysis_type": "sequencing_alignment", - "tumour_analysis_id": "00000000-0000-0000-0000-000000000000", - "normal_analysis_id": "00000000-0000-0000-0000-000000000000" + "analysisType": "sequencing_alignment", + "tumourAnalysisId": "00000000-0000-0000-0000-000000000000", + "normalAnalysisId": "00000000-0000-0000-0000-000000000000" } ] } -} +} \ No newline at end of file diff --git a/playground-data/example-payloads/TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_N1.json b/playground-data/example-payloads/TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_N1.json index d277274f..11a004a5 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_N1.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_N1.json @@ -1,4 +1,8 @@ { + "analysisType": { + "name": "playgroundSchema" + }, + "studyId": "OVPLG-01", "samples": [ { "submitterSampleId": "TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_N1", @@ -17,117 +21,119 @@ } ], "donor": { - "submitter_donor_id": "TEST_DONOR_mynbiqpmzjplsgqejeyd", - "primary_site": ["Pyriform sinus"], - "vital_status": "Deceased", - "survival_time": 180, - "cause_of_death": "Unknown", - "primary_diagnosis": [ + "submitterDonorId": "TEST_DONOR_mynbiqpmzjplsgqejeyd", + "primarySite": [ + "Pyriform sinus" + ], + "vitalStatus": "Deceased", + "survivalTime": 180, + "causeOfDeath": "Unknown", + "primaryDiagnosis": [ { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_mynbiqpmzjplsgqejeyd_0", - "age_at_diagnosis": 16, - "cancer_type_code": "C50.11", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_mynbiqpmzjplsgqejeyd_0", + "ageAtDiagnosis": 16, + "cancerTypeCode": "C50.11", "laterality": "Unknown", - "clinical_tumour_staging_system": "AJCC 6th edition", - "clinical_stage_group": "Stage IVB", - "lymph_nodes_examined_status": "Cannot be determined", - "performance_status": "Unknown", + "clinicalTumourStagingSystem": "AJCC 6th edition", + "clinicalStageGroup": "Stage IVB", + "lymphNodesExaminedStatus": "Cannot be determined", + "performanceStatus": "Unknown", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_mynbiqpmzjplsgqejeyd_0", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_mynbiqpmzjplsgqejeyd_0", + "treatmentType": [ "Hormonal therapy" ], - "treatment_intent": "Curative", - "treatment_start_interval": 95, - "treatment_duration": 2, - "response_to_treatment": "Stable disease", - "hormone_therapy": [ + "treatmentIntent": "Curative", + "treatmentStartInterval": 95, + "treatmentDuration": 2, + "responseToTreatment": "Stable disease", + "hormoneTherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 35, - "hormone_drug_dosage_units": "ug/m2" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 35, + "hormoneDrugDosageUnits": "ug/m2" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_mynbiqpmzjplsgqejeyd_0", - "interval_of_followup": 53, - "disease_status_at_followup": "Stable" + "submitterFollowUpId": "TEST_FOLLOW_UP_mynbiqpmzjplsgqejeyd_0", + "intervalOfFollowup": 53, + "diseaseStatusAtFollowup": "Stable" } ] }, { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_mynbiqpmzjplsgqejeyd_1", - "age_at_diagnosis": 51, - "cancer_type_code": "C79.89", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_mynbiqpmzjplsgqejeyd_1", + "ageAtDiagnosis": 51, + "cancerTypeCode": "C79.89", "laterality": "Unilateral, side not specified", - "clinical_tumour_staging_system": "FIGO staging system", - "clinical_stage_group": "Stage IVA", - "lymph_nodes_examined_status": "Not applicable", - "performance_status": "Grade 1", + "clinicalTumourStagingSystem": "FIGO staging system", + "clinicalStageGroup": "Stage IVA", + "lymphNodesExaminedStatus": "Not applicable", + "performanceStatus": "Grade 1", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_mynbiqpmzjplsgqejeyd_1", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_mynbiqpmzjplsgqejeyd_1", + "treatmentType": [ "Hormonal therapy", "Chemotherapy" ], - "treatment_intent": "Palliative", - "treatment_start_interval": 65, - "treatment_duration": 27, - "response_to_treatment": "Disease progression", - "hormone_therapy": [ + "treatmentIntent": "Palliative", + "treatmentStartInterval": 65, + "treatmentDuration": 27, + "responseToTreatment": "Disease progression", + "hormoneTherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 84, - "hormone_drug_dosage_units": "mg/kg" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 84, + "hormoneDrugDosageUnits": "mg/kg" } ], "chemotherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 45, - "chemotherapy_dosage_units": "mg/kg" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 45, + "chemotherapyDosageUnits": "mg/kg" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_mynbiqpmzjplsgqejeyd_1", - "interval_of_followup": 90, - "disease_status_at_followup": "Relapse or recurrence" + "submitterFollowUpId": "TEST_FOLLOW_UP_mynbiqpmzjplsgqejeyd_1", + "intervalOfFollowup": 90, + "diseaseStatusAtFollowup": "Relapse or recurrence" } ] } ], "comorbidity": [ { - "age_at_comorbidity_diagnosis": 5, - "comorbidity_type_code": "B02.68" + "ageAtComorbidityDiagnosis": 5, + "comorbidityTypeCode": "B02.68" }, { - "age_at_comorbidity_diagnosis": 91, - "comorbidity_type_code": "B88.93" + "ageAtComorbidityDiagnosis": 91, + "comorbidityTypeCode": "B88.93" }, { - "age_at_comorbidity_diagnosis": 61, - "comorbidity_type_code": "E17.42" + "ageAtComorbidityDiagnosis": 61, + "comorbidityTypeCode": "E17.42" } ] }, "specimen": { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_mynbiqpmzjplsgqejeyd_0", - "submitter_specimen_id": "TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_N1", - "specimen_acquisition_interval": 27, - "specimen_anatomic_location": "C50", - "specimen_laterality": "Left" + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_mynbiqpmzjplsgqejeyd_0", + "submitterSpecimenId": "TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_N1", + "specimenAcquisitionInterval": 27, + "specimenAnatomicLocation": "C50", + "specimenLaterality": "Left" }, "files": [ { @@ -155,25 +161,25 @@ ], "collaborator": [ { - "contact_email": "batman@batman_inc.org", + "contactEmail": "batman@batman_inc.org", "name": "batman", "affiliation": "batman inc" } ], "experiment": { "platform": "ILLUMINA", - "experimental_strategy": "WGS", - "submitter_sequencing_experiment_id": "EXPERIMENT" + "experimentalStrategy": "WGS", + "submitterSequencingExperimentId": "EXPERIMENT" }, "workflow": { - "workflow_name": "batman_stuff", - "genome_build": "GRCh38_hla_decoy_ebv", + "workflowName": "batman_stuff", + "genomeBuild": "GRCh38_hla_decoy_ebv", "inputs": [ { - "analysis_type": "sequencing_alignment", - "tumour_analysis_id": "00000000-0000-0000-0000-000000000000", - "normal_analysis_id": "00000000-0000-0000-0000-000000000000" + "analysisType": "sequencing_alignment", + "tumourAnalysisId": "00000000-0000-0000-0000-000000000000", + "normalAnalysisId": "00000000-0000-0000-0000-000000000000" } ] } -} +} \ No newline at end of file diff --git a/playground-data/example-payloads/TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_N2.json b/playground-data/example-payloads/TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_N2.json index cea4e6c5..942a5d77 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_N2.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_N2.json @@ -1,4 +1,8 @@ { + "analysisType": { + "name": "playgroundSchema" + }, + "studyId": "OVPLG-01", "samples": [ { "submitterSampleId": "TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_N2", @@ -17,117 +21,119 @@ } ], "donor": { - "submitter_donor_id": "TEST_DONOR_mynbiqpmzjplsgqejeyd", - "primary_site": ["Pyriform sinus"], - "vital_status": "Deceased", - "survival_time": 180, - "cause_of_death": "Unknown", - "primary_diagnosis": [ + "submitterDonorId": "TEST_DONOR_mynbiqpmzjplsgqejeyd", + "primarySite": [ + "Pyriform sinus" + ], + "vitalStatus": "Deceased", + "survivalTime": 180, + "causeOfDeath": "Unknown", + "primaryDiagnosis": [ { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_mynbiqpmzjplsgqejeyd_0", - "age_at_diagnosis": 16, - "cancer_type_code": "C50.11", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_mynbiqpmzjplsgqejeyd_0", + "ageAtDiagnosis": 16, + "cancerTypeCode": "C50.11", "laterality": "Unknown", - "clinical_tumour_staging_system": "AJCC 6th edition", - "clinical_stage_group": "Stage IVB", - "lymph_nodes_examined_status": "Cannot be determined", - "performance_status": "Unknown", + "clinicalTumourStagingSystem": "AJCC 6th edition", + "clinicalStageGroup": "Stage IVB", + "lymphNodesExaminedStatus": "Cannot be determined", + "performanceStatus": "Unknown", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_mynbiqpmzjplsgqejeyd_0", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_mynbiqpmzjplsgqejeyd_0", + "treatmentType": [ "Hormonal therapy" ], - "treatment_intent": "Curative", - "treatment_start_interval": 95, - "treatment_duration": 2, - "response_to_treatment": "Stable disease", - "hormone_therapy": [ + "treatmentIntent": "Curative", + "treatmentStartInterval": 95, + "treatmentDuration": 2, + "responseToTreatment": "Stable disease", + "hormoneTherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 35, - "hormone_drug_dosage_units": "ug/m2" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 35, + "hormoneDrugDosageUnits": "ug/m2" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_mynbiqpmzjplsgqejeyd_0", - "interval_of_followup": 53, - "disease_status_at_followup": "Stable" + "submitterFollowUpId": "TEST_FOLLOW_UP_mynbiqpmzjplsgqejeyd_0", + "intervalOfFollowup": 53, + "diseaseStatusAtFollowup": "Stable" } ] }, { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_mynbiqpmzjplsgqejeyd_1", - "age_at_diagnosis": 51, - "cancer_type_code": "C79.89", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_mynbiqpmzjplsgqejeyd_1", + "ageAtDiagnosis": 51, + "cancerTypeCode": "C79.89", "laterality": "Unilateral, side not specified", - "clinical_tumour_staging_system": "FIGO staging system", - "clinical_stage_group": "Stage IVA", - "lymph_nodes_examined_status": "Not applicable", - "performance_status": "Grade 1", + "clinicalTumourStagingSystem": "FIGO staging system", + "clinicalStageGroup": "Stage IVA", + "lymphNodesExaminedStatus": "Not applicable", + "performanceStatus": "Grade 1", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_mynbiqpmzjplsgqejeyd_1", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_mynbiqpmzjplsgqejeyd_1", + "treatmentType": [ "Hormonal therapy", "Chemotherapy" ], - "treatment_intent": "Palliative", - "treatment_start_interval": 65, - "treatment_duration": 27, - "response_to_treatment": "Disease progression", - "hormone_therapy": [ + "treatmentIntent": "Palliative", + "treatmentStartInterval": 65, + "treatmentDuration": 27, + "responseToTreatment": "Disease progression", + "hormoneTherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 84, - "hormone_drug_dosage_units": "mg/kg" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 84, + "hormoneDrugDosageUnits": "mg/kg" } ], "chemotherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 45, - "chemotherapy_dosage_units": "mg/kg" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 45, + "chemotherapyDosageUnits": "mg/kg" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_mynbiqpmzjplsgqejeyd_1", - "interval_of_followup": 90, - "disease_status_at_followup": "Relapse or recurrence" + "submitterFollowUpId": "TEST_FOLLOW_UP_mynbiqpmzjplsgqejeyd_1", + "intervalOfFollowup": 90, + "diseaseStatusAtFollowup": "Relapse or recurrence" } ] } ], "comorbidity": [ { - "age_at_comorbidity_diagnosis": 5, - "comorbidity_type_code": "B02.68" + "ageAtComorbidityDiagnosis": 5, + "comorbidityTypeCode": "B02.68" }, { - "age_at_comorbidity_diagnosis": 91, - "comorbidity_type_code": "B88.93" + "ageAtComorbidityDiagnosis": 91, + "comorbidityTypeCode": "B88.93" }, { - "age_at_comorbidity_diagnosis": 61, - "comorbidity_type_code": "E17.42" + "ageAtComorbidityDiagnosis": 61, + "comorbidityTypeCode": "E17.42" } ] }, "specimen": { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_mynbiqpmzjplsgqejeyd_0", - "submitter_specimen_id": "TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_N2", - "specimen_acquisition_interval": 55, - "specimen_anatomic_location": "C50", - "specimen_laterality": "Not applicable" + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_mynbiqpmzjplsgqejeyd_0", + "submitterSpecimenId": "TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_N2", + "specimenAcquisitionInterval": 55, + "specimenAnatomicLocation": "C50", + "specimenLaterality": "Not applicable" }, "files": [ { @@ -155,25 +161,25 @@ ], "collaborator": [ { - "contact_email": "batman@batman_inc.org", + "contactEmail": "batman@batman_inc.org", "name": "batman", "affiliation": "batman inc" } ], "experiment": { "platform": "ILLUMINA", - "experimental_strategy": "WGS", - "submitter_sequencing_experiment_id": "EXPERIMENT" + "experimentalStrategy": "WGS", + "submitterSequencingExperimentId": "EXPERIMENT" }, "workflow": { - "workflow_name": "batman_stuff", - "genome_build": "GRCh38_hla_decoy_ebv", + "workflowName": "batman_stuff", + "genomeBuild": "GRCh38_hla_decoy_ebv", "inputs": [ { - "analysis_type": "sequencing_alignment", - "tumour_analysis_id": "00000000-0000-0000-0000-000000000000", - "normal_analysis_id": "00000000-0000-0000-0000-000000000000" + "analysisType": "sequencing_alignment", + "tumourAnalysisId": "00000000-0000-0000-0000-000000000000", + "normalAnalysisId": "00000000-0000-0000-0000-000000000000" } ] } -} +} \ No newline at end of file diff --git a/playground-data/example-payloads/TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_T1.json b/playground-data/example-payloads/TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_T1.json index 32608483..9ea25f17 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_T1.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_T1.json @@ -1,11 +1,15 @@ { + "analysisType": { + "name": "playgroundSchema" + }, + "studyId": "OVPLG-01", "samples": [ { "submitterSampleId": "TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_T1", "sampleType": "Total DNA", "matchedNormalSubmitterSampleId": "TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_N1", "specimen": { - "submitterSpecimenId": "TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_N1", + "submitterSpecimenId": "TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_T1", "specimenType": "Metastatic tumour - additional metastatic", "specimenTissueSource": "Cerebrospinal fluid", "tumourNormalDesignation": "Tumour" @@ -17,124 +21,126 @@ } ], "donor": { - "submitter_donor_id": "TEST_DONOR_mynbiqpmzjplsgqejeyd", - "primary_site": ["Pyriform sinus"], - "vital_status": "Deceased", - "survival_time": 180, - "cause_of_death": "Unknown", - "primary_diagnosis": [ + "submitterDonorId": "TEST_DONOR_mynbiqpmzjplsgqejeyd", + "primarySite": [ + "Pyriform sinus" + ], + "vitalStatus": "Deceased", + "survivalTime": 180, + "causeOfDeath": "Unknown", + "primaryDiagnosis": [ { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_mynbiqpmzjplsgqejeyd_0", - "age_at_diagnosis": 16, - "cancer_type_code": "C50.11", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_mynbiqpmzjplsgqejeyd_0", + "ageAtDiagnosis": 16, + "cancerTypeCode": "C50.11", "laterality": "Unknown", - "clinical_tumour_staging_system": "AJCC 6th edition", - "clinical_stage_group": "Stage IVB", - "lymph_nodes_examined_status": "Cannot be determined", - "performance_status": "Unknown", + "clinicalTumourStagingSystem": "AJCC 6th edition", + "clinicalStageGroup": "Stage IVB", + "lymphNodesExaminedStatus": "Cannot be determined", + "performanceStatus": "Unknown", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_mynbiqpmzjplsgqejeyd_0", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_mynbiqpmzjplsgqejeyd_0", + "treatmentType": [ "Hormonal therapy" ], - "treatment_intent": "Curative", - "treatment_start_interval": 95, - "treatment_duration": 2, - "response_to_treatment": "Stable disease", - "hormone_therapy": [ + "treatmentIntent": "Curative", + "treatmentStartInterval": 95, + "treatmentDuration": 2, + "responseToTreatment": "Stable disease", + "hormoneTherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 35, - "hormone_drug_dosage_units": "ug/m2" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 35, + "hormoneDrugDosageUnits": "ug/m2" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_mynbiqpmzjplsgqejeyd_0", - "interval_of_followup": 53, - "disease_status_at_followup": "Stable" + "submitterFollowUpId": "TEST_FOLLOW_UP_mynbiqpmzjplsgqejeyd_0", + "intervalOfFollowup": 53, + "diseaseStatusAtFollowup": "Stable" } ] }, { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_mynbiqpmzjplsgqejeyd_1", - "age_at_diagnosis": 51, - "cancer_type_code": "C79.89", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_mynbiqpmzjplsgqejeyd_1", + "ageAtDiagnosis": 51, + "cancerTypeCode": "C79.89", "laterality": "Unilateral, side not specified", - "clinical_tumour_staging_system": "FIGO staging system", - "clinical_stage_group": "Stage IVA", - "lymph_nodes_examined_status": "Not applicable", - "performance_status": "Grade 1", + "clinicalTumourStagingSystem": "FIGO staging system", + "clinicalStageGroup": "Stage IVA", + "lymphNodesExaminedStatus": "Not applicable", + "performanceStatus": "Grade 1", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_mynbiqpmzjplsgqejeyd_1", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_mynbiqpmzjplsgqejeyd_1", + "treatmentType": [ "Hormonal therapy", "Chemotherapy" ], - "treatment_intent": "Palliative", - "treatment_start_interval": 65, - "treatment_duration": 27, - "response_to_treatment": "Disease progression", - "hormone_therapy": [ + "treatmentIntent": "Palliative", + "treatmentStartInterval": 65, + "treatmentDuration": 27, + "responseToTreatment": "Disease progression", + "hormoneTherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 84, - "hormone_drug_dosage_units": "mg/kg" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 84, + "hormoneDrugDosageUnits": "mg/kg" } ], "chemotherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 45, - "chemotherapy_dosage_units": "mg/kg" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 45, + "chemotherapyDosageUnits": "mg/kg" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_mynbiqpmzjplsgqejeyd_1", - "interval_of_followup": 90, - "disease_status_at_followup": "Relapse or recurrence" + "submitterFollowUpId": "TEST_FOLLOW_UP_mynbiqpmzjplsgqejeyd_1", + "intervalOfFollowup": 90, + "diseaseStatusAtFollowup": "Relapse or recurrence" } ] } ], "comorbidity": [ { - "age_at_comorbidity_diagnosis": 5, - "comorbidity_type_code": "B02.68" + "ageAtComorbidityDiagnosis": 5, + "comorbidityTypeCode": "B02.68" }, { - "age_at_comorbidity_diagnosis": 91, - "comorbidity_type_code": "B88.93" + "ageAtComorbidityDiagnosis": 91, + "comorbidityTypeCode": "B88.93" }, { - "age_at_comorbidity_diagnosis": 61, - "comorbidity_type_code": "E17.42" + "ageAtComorbidityDiagnosis": 61, + "comorbidityTypeCode": "E17.42" } ] }, "specimen": { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_mynbiqpmzjplsgqejeyd_1", - "submitter_specimen_id": "TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_N1", - "specimen_acquisition_interval": 54, - "specimen_anatomic_location": "C50", - "specimen_laterality": "Right", - "tumour_histological_type": "9697/68", - "pathological_tumour_staging_system": "Binet staging system", - "pathological_stage_group": "Stage B", - "tumour_grading_system": "Three-tier grading system", - "tumour_grade": "G3", - "percent_tumour_cells": 55, - "reference_pathology_confirmed": "Yes" + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_mynbiqpmzjplsgqejeyd_1", + "submitterSpecimenId": "TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_N1", + "specimenAcquisitionInterval": 54, + "specimenAnatomicLocation": "C50", + "specimenLaterality": "Right", + "tumourHistologicalType": "9697/68", + "pathologicalTumourStagingSystem": "Binet staging system", + "pathologicalStageGroup": "Stage B", + "tumourGradingSystem": "Three-tier grading system", + "tumourGrade": "G3", + "percentTumourCells": 55, + "referencePathologyConfirmed": "Yes" }, "files": [ { @@ -162,25 +168,25 @@ ], "collaborator": [ { - "contact_email": "batman@batman_inc.org", + "contactEmail": "batman@batman_inc.org", "name": "batman", "affiliation": "batman inc" } ], "experiment": { "platform": "ILLUMINA", - "experimental_strategy": "WGS", - "submitter_sequencing_experiment_id": "EXPERIMENT" + "experimentalStrategy": "WGS", + "submitterSequencingExperimentId": "EXPERIMENT" }, "workflow": { - "workflow_name": "batman_stuff", - "genome_build": "GRCh38_hla_decoy_ebv", + "workflowName": "batman_stuff", + "genomeBuild": "GRCh38_hla_decoy_ebv", "inputs": [ { - "analysis_type": "sequencing_alignment", - "tumour_analysis_id": "00000000-0000-0000-0000-000000000000", - "normal_analysis_id": "00000000-0000-0000-0000-000000000000" + "analysisType": "sequencing_alignment", + "tumourAnalysisId": "00000000-0000-0000-0000-000000000000", + "normalAnalysisId": "00000000-0000-0000-0000-000000000000" } ] } -} +} \ No newline at end of file diff --git a/playground-data/example-payloads/TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_T2.json b/playground-data/example-payloads/TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_T2.json index 8cbeb88c..abc36c80 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_T2.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_T2.json @@ -1,11 +1,15 @@ { + "analysisType": { + "name": "playgroundSchema" + }, + "studyId": "OVPLG-01", "samples": [ { "submitterSampleId": "TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_T2", "sampleType": "Total DNA", "matchedNormalSubmitterSampleId": "TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_N2", "specimen": { - "submitterSpecimenId": "TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_N2", + "submitterSpecimenId": "TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_T2", "specimenType": "Cell line - derived from tumour", "specimenTissueSource": "Lymph node", "tumourNormalDesignation": "Tumour" @@ -17,124 +21,126 @@ } ], "donor": { - "submitter_donor_id": "TEST_DONOR_mynbiqpmzjplsgqejeyd", - "primary_site": ["Pyriform sinus"], - "vital_status": "Deceased", - "survival_time": 180, - "cause_of_death": "Unknown", - "primary_diagnosis": [ + "submitterDonorId": "TEST_DONOR_mynbiqpmzjplsgqejeyd", + "primarySite": [ + "Pyriform sinus" + ], + "vitalStatus": "Deceased", + "survivalTime": 180, + "causeOfDeath": "Unknown", + "primaryDiagnosis": [ { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_mynbiqpmzjplsgqejeyd_0", - "age_at_diagnosis": 16, - "cancer_type_code": "C50.11", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_mynbiqpmzjplsgqejeyd_0", + "ageAtDiagnosis": 16, + "cancerTypeCode": "C50.11", "laterality": "Unknown", - "clinical_tumour_staging_system": "AJCC 6th edition", - "clinical_stage_group": "Stage IVB", - "lymph_nodes_examined_status": "Cannot be determined", - "performance_status": "Unknown", + "clinicalTumourStagingSystem": "AJCC 6th edition", + "clinicalStageGroup": "Stage IVB", + "lymphNodesExaminedStatus": "Cannot be determined", + "performanceStatus": "Unknown", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_mynbiqpmzjplsgqejeyd_0", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_mynbiqpmzjplsgqejeyd_0", + "treatmentType": [ "Hormonal therapy" ], - "treatment_intent": "Curative", - "treatment_start_interval": 95, - "treatment_duration": 2, - "response_to_treatment": "Stable disease", - "hormone_therapy": [ + "treatmentIntent": "Curative", + "treatmentStartInterval": 95, + "treatmentDuration": 2, + "responseToTreatment": "Stable disease", + "hormoneTherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 35, - "hormone_drug_dosage_units": "ug/m2" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 35, + "hormoneDrugDosageUnits": "ug/m2" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_mynbiqpmzjplsgqejeyd_0", - "interval_of_followup": 53, - "disease_status_at_followup": "Stable" + "submitterFollowUpId": "TEST_FOLLOW_UP_mynbiqpmzjplsgqejeyd_0", + "intervalOfFollowup": 53, + "diseaseStatusAtFollowup": "Stable" } ] }, { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_mynbiqpmzjplsgqejeyd_1", - "age_at_diagnosis": 51, - "cancer_type_code": "C79.89", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_mynbiqpmzjplsgqejeyd_1", + "ageAtDiagnosis": 51, + "cancerTypeCode": "C79.89", "laterality": "Unilateral, side not specified", - "clinical_tumour_staging_system": "FIGO staging system", - "clinical_stage_group": "Stage IVA", - "lymph_nodes_examined_status": "Not applicable", - "performance_status": "Grade 1", + "clinicalTumourStagingSystem": "FIGO staging system", + "clinicalStageGroup": "Stage IVA", + "lymphNodesExaminedStatus": "Not applicable", + "performanceStatus": "Grade 1", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_mynbiqpmzjplsgqejeyd_1", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_mynbiqpmzjplsgqejeyd_1", + "treatmentType": [ "Hormonal therapy", "Chemotherapy" ], - "treatment_intent": "Palliative", - "treatment_start_interval": 65, - "treatment_duration": 27, - "response_to_treatment": "Disease progression", - "hormone_therapy": [ + "treatmentIntent": "Palliative", + "treatmentStartInterval": 65, + "treatmentDuration": 27, + "responseToTreatment": "Disease progression", + "hormoneTherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 84, - "hormone_drug_dosage_units": "mg/kg" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 84, + "hormoneDrugDosageUnits": "mg/kg" } ], "chemotherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 45, - "chemotherapy_dosage_units": "mg/kg" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 45, + "chemotherapyDosageUnits": "mg/kg" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_mynbiqpmzjplsgqejeyd_1", - "interval_of_followup": 90, - "disease_status_at_followup": "Relapse or recurrence" + "submitterFollowUpId": "TEST_FOLLOW_UP_mynbiqpmzjplsgqejeyd_1", + "intervalOfFollowup": 90, + "diseaseStatusAtFollowup": "Relapse or recurrence" } ] } ], "comorbidity": [ { - "age_at_comorbidity_diagnosis": 5, - "comorbidity_type_code": "B02.68" + "ageAtComorbidityDiagnosis": 5, + "comorbidityTypeCode": "B02.68" }, { - "age_at_comorbidity_diagnosis": 91, - "comorbidity_type_code": "B88.93" + "ageAtComorbidityDiagnosis": 91, + "comorbidityTypeCode": "B88.93" }, { - "age_at_comorbidity_diagnosis": 61, - "comorbidity_type_code": "E17.42" + "ageAtComorbidityDiagnosis": 61, + "comorbidityTypeCode": "E17.42" } ] }, "specimen": { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_mynbiqpmzjplsgqejeyd_0", - "submitter_specimen_id": "TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_N2", - "specimen_acquisition_interval": 26, - "specimen_anatomic_location": "C50", - "specimen_laterality": "Right", - "tumour_histological_type": "9521/25", - "pathological_tumour_staging_system": "Lugano staging system", - "pathological_stage_group": "Stage IB", - "tumour_grading_system": "Two-tier grading system", - "tumour_grade": "Low grade", - "percent_tumour_cells": 40, - "reference_pathology_confirmed": "Unknown" + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_mynbiqpmzjplsgqejeyd_0", + "submitterSpecimenId": "TEST_SPECIMEN_mynbiqpmzjplsgqejeyd_N2", + "specimenAcquisitionInterval": 26, + "specimenAnatomicLocation": "C50", + "specimenLaterality": "Right", + "tumourHistologicalType": "9521/25", + "pathologicalTumourStagingSystem": "Lugano staging system", + "pathologicalStageGroup": "Stage IB", + "tumourGradingSystem": "Two-tier grading system", + "tumourGrade": "Low grade", + "percentTumourCells": 40, + "referencePathologyConfirmed": "Unknown" }, "files": [ { @@ -162,25 +168,25 @@ ], "collaborator": [ { - "contact_email": "batman@batman_inc.org", + "contactEmail": "batman@batman_inc.org", "name": "batman", "affiliation": "batman inc" } ], "experiment": { "platform": "ILLUMINA", - "experimental_strategy": "WGS", - "submitter_sequencing_experiment_id": "EXPERIMENT" + "experimentalStrategy": "WGS", + "submitterSequencingExperimentId": "EXPERIMENT" }, "workflow": { - "workflow_name": "batman_stuff", - "genome_build": "GRCh38_hla_decoy_ebv", + "workflowName": "batman_stuff", + "genomeBuild": "GRCh38_hla_decoy_ebv", "inputs": [ { - "analysis_type": "sequencing_alignment", - "tumour_analysis_id": "00000000-0000-0000-0000-000000000000", - "normal_analysis_id": "00000000-0000-0000-0000-000000000000" + "analysisType": "sequencing_alignment", + "tumourAnalysisId": "00000000-0000-0000-0000-000000000000", + "normalAnalysisId": "00000000-0000-0000-0000-000000000000" } ] } -} +} \ No newline at end of file diff --git a/playground-data/example-payloads/TEST_SPECIMEN_otliefvakqotckrtwbxm_N1.json b/playground-data/example-payloads/TEST_SPECIMEN_otliefvakqotckrtwbxm_N1.json index b866c192..6abbfd80 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_otliefvakqotckrtwbxm_N1.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_otliefvakqotckrtwbxm_N1.json @@ -1,4 +1,8 @@ { + "analysisType": { + "name": "playgroundSchema" + }, + "studyId": "OVPLG-01", "samples": [ { "submitterSampleId": "TEST_SPECIMEN_otliefvakqotckrtwbxm_N1", @@ -17,106 +21,109 @@ } ], "donor": { - "submitter_donor_id": "TEST_DONOR_otliefvakqotckrtwbxm", - "primary_site": ["Trachea","Colon"], - "vital_status": "Alive", - "survival_time": null, - "cause_of_death": null, - "primary_diagnosis": [ + "submitterDonorId": "TEST_DONOR_otliefvakqotckrtwbxm", + "primarySite": [ + "Trachea", + "Colon" + ], + "vitalStatus": "Alive", + "survivalTime": null, + "causeOfDeath": null, + "primaryDiagnosis": [ { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_otliefvakqotckrtwbxm_0", - "age_at_diagnosis": 20, - "cancer_type_code": "C13.6", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_otliefvakqotckrtwbxm_0", + "ageAtDiagnosis": 20, + "cancerTypeCode": "C13.6", "laterality": "Unilateral, side not specified", - "clinical_tumour_staging_system": "AJCC 7th edition", - "clinical_stage_group": "Stage IIIB", - "lymph_nodes_examined_status": "Not applicable", - "performance_status": "Grade 1", + "clinicalTumourStagingSystem": "AJCC 7th edition", + "clinicalStageGroup": "Stage IIIB", + "lymphNodesExaminedStatus": "Not applicable", + "performanceStatus": "Grade 1", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_otliefvakqotckrtwbxm_0", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_otliefvakqotckrtwbxm_0", + "treatmentType": [ "Radiation therapy", "Chemotherapy" ], - "treatment_intent": "Curative", - "treatment_start_interval": 67, - "treatment_duration": 85, - "response_to_treatment": "Disease progression", + "treatmentIntent": "Curative", + "treatmentStartInterval": 67, + "treatmentDuration": 85, + "responseToTreatment": "Disease progression", "radiation": [ { - "radiation_therapy_modality": "Photon", - "radiation_therapy_type": "External", - "anatomical_site_irradiated": "Head", - "radiation_therapy_dosage": 71, - "radiation_therapy_fractions": 69 + "radiationTherapyModality": "Photon", + "radiationTherapyType": "External", + "anatomicalSiteIrradiated": "Head", + "radiationTherapyDosage": 71, + "radiationTherapyFractions": 69 } ], "chemotherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 79, - "chemotherapy_dosage_units": "mg/m2" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 79, + "chemotherapyDosageUnits": "mg/m2" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_otliefvakqotckrtwbxm_0", - "interval_of_followup": 65, - "disease_status_at_followup": "Complete remission" + "submitterFollowUpId": "TEST_FOLLOW_UP_otliefvakqotckrtwbxm_0", + "intervalOfFollowup": 65, + "diseaseStatusAtFollowup": "Complete remission" } ] }, { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_otliefvakqotckrtwbxm_1", - "age_at_diagnosis": 25, - "cancer_type_code": "D01.0", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_otliefvakqotckrtwbxm_1", + "ageAtDiagnosis": 25, + "cancerTypeCode": "D01.0", "laterality": "Not a paired site", - "clinical_tumour_staging_system": "Ann Arbor staging system", - "clinical_stage_group": "Stage IIIBE", - "lymph_nodes_examined_status": "Yes", - "performance_status": "Grade 1", + "clinicalTumourStagingSystem": "Ann Arbor staging system", + "clinicalStageGroup": "Stage IIIBE", + "lymphNodesExaminedStatus": "Yes", + "performanceStatus": "Grade 1", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_otliefvakqotckrtwbxm_1", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_otliefvakqotckrtwbxm_1", + "treatmentType": [ "No treatment" ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_otliefvakqotckrtwbxm_1", - "interval_of_followup": 69, - "disease_status_at_followup": "Stable" + "submitterFollowUpId": "TEST_FOLLOW_UP_otliefvakqotckrtwbxm_1", + "intervalOfFollowup": 69, + "diseaseStatusAtFollowup": "Stable" } ] } ], "comorbidity": [ { - "age_at_comorbidity_diagnosis": 18, - "comorbidity_type_code": "E13.87" + "ageAtComorbidityDiagnosis": 18, + "comorbidityTypeCode": "E13.87" }, { - "age_at_comorbidity_diagnosis": 19, - "comorbidity_type_code": "A22.74" + "ageAtComorbidityDiagnosis": 19, + "comorbidityTypeCode": "A22.74" }, { - "age_at_comorbidity_diagnosis": 20, - "comorbidity_type_code": "E67.38" + "ageAtComorbidityDiagnosis": 20, + "comorbidityTypeCode": "E67.38" } ] }, "specimen": { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_otliefvakqotckrtwbxm_0", - "submitter_specimen_id": "TEST_SPECIMEN_otliefvakqotckrtwbxm_N1", - "specimen_acquisition_interval": 42, - "specimen_anatomic_location": "C09.1", - "specimen_laterality": "Right" + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_otliefvakqotckrtwbxm_0", + "submitterSpecimenId": "TEST_SPECIMEN_otliefvakqotckrtwbxm_N1", + "specimenAcquisitionInterval": 42, + "specimenAnatomicLocation": "C09.1", + "specimenLaterality": "Right" }, "files": [ { @@ -144,25 +151,25 @@ ], "collaborator": [ { - "contact_email": "batman@batman_inc.org", + "contactEmail": "batman@batman_inc.org", "name": "batman", "affiliation": "batman inc" } ], "experiment": { "platform": "ILLUMINA", - "experimental_strategy": "WGS", - "submitter_sequencing_experiment_id": "EXPERIMENT" + "experimentalStrategy": "WGS", + "submitterSequencingExperimentId": "EXPERIMENT" }, "workflow": { - "workflow_name": "batman_stuff", - "genome_build": "GRCh38_hla_decoy_ebv", + "workflowName": "batman_stuff", + "genomeBuild": "GRCh38_hla_decoy_ebv", "inputs": [ { - "analysis_type": "sequencing_alignment", - "tumour_analysis_id": "00000000-0000-0000-0000-000000000000", - "normal_analysis_id": "00000000-0000-0000-0000-000000000000" + "analysisType": "sequencing_alignment", + "tumourAnalysisId": "00000000-0000-0000-0000-000000000000", + "normalAnalysisId": "00000000-0000-0000-0000-000000000000" } ] } -} +} \ No newline at end of file diff --git a/playground-data/example-payloads/TEST_SPECIMEN_otliefvakqotckrtwbxm_N2.json b/playground-data/example-payloads/TEST_SPECIMEN_otliefvakqotckrtwbxm_N2.json index 1b75e384..2934c908 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_otliefvakqotckrtwbxm_N2.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_otliefvakqotckrtwbxm_N2.json @@ -1,4 +1,8 @@ { + "analysisType": { + "name": "playgroundSchema" + }, + "studyId": "OVPLG-01", "samples": [ { "submitterSampleId": "TEST_SPECIMEN_otliefvakqotckrtwbxm_N2", @@ -17,106 +21,109 @@ } ], "donor": { - "submitter_donor_id": "TEST_DONOR_otliefvakqotckrtwbxm", - "primary_site": ["Trachea","Colon"], - "vital_status": "Alive", - "survival_time": null, - "cause_of_death": null, - "primary_diagnosis": [ + "submitterDonorId": "TEST_DONOR_otliefvakqotckrtwbxm", + "primarySite": [ + "Trachea", + "Colon" + ], + "vitalStatus": "Alive", + "survivalTime": null, + "causeOfDeath": null, + "primaryDiagnosis": [ { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_otliefvakqotckrtwbxm_0", - "age_at_diagnosis": 20, - "cancer_type_code": "C13.6", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_otliefvakqotckrtwbxm_0", + "ageAtDiagnosis": 20, + "cancerTypeCode": "C13.6", "laterality": "Unilateral, side not specified", - "clinical_tumour_staging_system": "AJCC 7th edition", - "clinical_stage_group": "Stage IIIB", - "lymph_nodes_examined_status": "Not applicable", - "performance_status": "Grade 1", + "clinicalTumourStagingSystem": "AJCC 7th edition", + "clinicalStageGroup": "Stage IIIB", + "lymphNodesExaminedStatus": "Not applicable", + "performanceStatus": "Grade 1", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_otliefvakqotckrtwbxm_0", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_otliefvakqotckrtwbxm_0", + "treatmentType": [ "Radiation therapy", "Chemotherapy" ], - "treatment_intent": "Curative", - "treatment_start_interval": 67, - "treatment_duration": 85, - "response_to_treatment": "Disease progression", + "treatmentIntent": "Curative", + "treatmentStartInterval": 67, + "treatmentDuration": 85, + "responseToTreatment": "Disease progression", "radiation": [ { - "radiation_therapy_modality": "Photon", - "radiation_therapy_type": "External", - "anatomical_site_irradiated": "Head", - "radiation_therapy_dosage": 71, - "radiation_therapy_fractions": 69 + "radiationTherapyModality": "Photon", + "radiationTherapyType": "External", + "anatomicalSiteIrradiated": "Head", + "radiationTherapyDosage": 71, + "radiationTherapyFractions": 69 } ], "chemotherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 79, - "chemotherapy_dosage_units": "mg/m2" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 79, + "chemotherapyDosageUnits": "mg/m2" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_otliefvakqotckrtwbxm_0", - "interval_of_followup": 65, - "disease_status_at_followup": "Complete remission" + "submitterFollowUpId": "TEST_FOLLOW_UP_otliefvakqotckrtwbxm_0", + "intervalOfFollowup": 65, + "diseaseStatusAtFollowup": "Complete remission" } ] }, { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_otliefvakqotckrtwbxm_1", - "age_at_diagnosis": 25, - "cancer_type_code": "D01.0", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_otliefvakqotckrtwbxm_1", + "ageAtDiagnosis": 25, + "cancerTypeCode": "D01.0", "laterality": "Not a paired site", - "clinical_tumour_staging_system": "Ann Arbor staging system", - "clinical_stage_group": "Stage IIIBE", - "lymph_nodes_examined_status": "Yes", - "performance_status": "Grade 1", + "clinicalTumourStagingSystem": "Ann Arbor staging system", + "clinicalStageGroup": "Stage IIIBE", + "lymphNodesExaminedStatus": "Yes", + "performanceStatus": "Grade 1", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_otliefvakqotckrtwbxm_1", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_otliefvakqotckrtwbxm_1", + "treatmentType": [ "No treatment" ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_otliefvakqotckrtwbxm_1", - "interval_of_followup": 69, - "disease_status_at_followup": "Stable" + "submitterFollowUpId": "TEST_FOLLOW_UP_otliefvakqotckrtwbxm_1", + "intervalOfFollowup": 69, + "diseaseStatusAtFollowup": "Stable" } ] } ], "comorbidity": [ { - "age_at_comorbidity_diagnosis": 18, - "comorbidity_type_code": "E13.87" + "ageAtComorbidityDiagnosis": 18, + "comorbidityTypeCode": "E13.87" }, { - "age_at_comorbidity_diagnosis": 19, - "comorbidity_type_code": "A22.74" + "ageAtComorbidityDiagnosis": 19, + "comorbidityTypeCode": "A22.74" }, { - "age_at_comorbidity_diagnosis": 20, - "comorbidity_type_code": "E67.38" + "ageAtComorbidityDiagnosis": 20, + "comorbidityTypeCode": "E67.38" } ] }, "specimen": { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_otliefvakqotckrtwbxm_0", - "submitter_specimen_id": "TEST_SPECIMEN_otliefvakqotckrtwbxm_N2", - "specimen_acquisition_interval": 33, - "specimen_anatomic_location": "C13", - "specimen_laterality": "Right" + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_otliefvakqotckrtwbxm_0", + "submitterSpecimenId": "TEST_SPECIMEN_otliefvakqotckrtwbxm_N2", + "specimenAcquisitionInterval": 33, + "specimenAnatomicLocation": "C13", + "specimenLaterality": "Right" }, "files": [ { @@ -144,25 +151,25 @@ ], "collaborator": [ { - "contact_email": "batman@batman_inc.org", + "contactEmail": "batman@batman_inc.org", "name": "batman", "affiliation": "batman inc" } ], "experiment": { "platform": "ILLUMINA", - "experimental_strategy": "WGS", - "submitter_sequencing_experiment_id": "EXPERIMENT" + "experimentalStrategy": "WGS", + "submitterSequencingExperimentId": "EXPERIMENT" }, "workflow": { - "workflow_name": "batman_stuff", - "genome_build": "GRCh38_hla_decoy_ebv", + "workflowName": "batman_stuff", + "genomeBuild": "GRCh38_hla_decoy_ebv", "inputs": [ { - "analysis_type": "sequencing_alignment", - "tumour_analysis_id": "00000000-0000-0000-0000-000000000000", - "normal_analysis_id": "00000000-0000-0000-0000-000000000000" + "analysisType": "sequencing_alignment", + "tumourAnalysisId": "00000000-0000-0000-0000-000000000000", + "normalAnalysisId": "00000000-0000-0000-0000-000000000000" } ] } -} +} \ No newline at end of file diff --git a/playground-data/example-payloads/TEST_SPECIMEN_otliefvakqotckrtwbxm_T1.json b/playground-data/example-payloads/TEST_SPECIMEN_otliefvakqotckrtwbxm_T1.json index c2164983..28f61095 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_otliefvakqotckrtwbxm_T1.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_otliefvakqotckrtwbxm_T1.json @@ -1,11 +1,15 @@ { + "analysisType": { + "name": "playgroundSchema" + }, + "studyId": "OVPLG-01", "samples": [ { "submitterSampleId": "TEST_SPECIMEN_otliefvakqotckrtwbxm_T1", "sampleType": "Total DNA", "matchedNormalSubmitterSampleId": "TEST_SPECIMEN_otliefvakqotckrtwbxm_N1", "specimen": { - "submitterSpecimenId": "TEST_SPECIMEN_otliefvakqotckrtwbxm_N1", + "submitterSpecimenId": "TEST_SPECIMEN_otliefvakqotckrtwbxm_T1", "specimenType": "Tumour - unknown if derived from primary or metastatic", "specimenTissueSource": "Solid tissue", "tumourNormalDesignation": "Tumour" @@ -17,113 +21,116 @@ } ], "donor": { - "submitter_donor_id": "TEST_DONOR_otliefvakqotckrtwbxm", - "primary_site": ["Trachea","Colon"], - "vital_status": "Alive", - "survival_time": null, - "cause_of_death": null, - "primary_diagnosis": [ + "submitterDonorId": "TEST_DONOR_otliefvakqotckrtwbxm", + "primarySite": [ + "Trachea", + "Colon" + ], + "vitalStatus": "Alive", + "survivalTime": null, + "causeOfDeath": null, + "primaryDiagnosis": [ { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_otliefvakqotckrtwbxm_0", - "age_at_diagnosis": 20, - "cancer_type_code": "C13.6", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_otliefvakqotckrtwbxm_0", + "ageAtDiagnosis": 20, + "cancerTypeCode": "C13.6", "laterality": "Unilateral, side not specified", - "clinical_tumour_staging_system": "AJCC 7th edition", - "clinical_stage_group": "Stage IIIB", - "lymph_nodes_examined_status": "Not applicable", - "performance_status": "Grade 1", + "clinicalTumourStagingSystem": "AJCC 7th edition", + "clinicalStageGroup": "Stage IIIB", + "lymphNodesExaminedStatus": "Not applicable", + "performanceStatus": "Grade 1", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_otliefvakqotckrtwbxm_0", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_otliefvakqotckrtwbxm_0", + "treatmentType": [ "Radiation therapy", "Chemotherapy" ], - "treatment_intent": "Curative", - "treatment_start_interval": 67, - "treatment_duration": 85, - "response_to_treatment": "Disease progression", + "treatmentIntent": "Curative", + "treatmentStartInterval": 67, + "treatmentDuration": 85, + "responseToTreatment": "Disease progression", "radiation": [ { - "radiation_therapy_modality": "Photon", - "radiation_therapy_type": "External", - "anatomical_site_irradiated": "Head", - "radiation_therapy_dosage": 71, - "radiation_therapy_fractions": 69 + "radiationTherapyModality": "Photon", + "radiationTherapyType": "External", + "anatomicalSiteIrradiated": "Head", + "radiationTherapyDosage": 71, + "radiationTherapyFractions": 69 } ], "chemotherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 79, - "chemotherapy_dosage_units": "mg/m2" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 79, + "chemotherapyDosageUnits": "mg/m2" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_otliefvakqotckrtwbxm_0", - "interval_of_followup": 65, - "disease_status_at_followup": "Complete remission" + "submitterFollowUpId": "TEST_FOLLOW_UP_otliefvakqotckrtwbxm_0", + "intervalOfFollowup": 65, + "diseaseStatusAtFollowup": "Complete remission" } ] }, { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_otliefvakqotckrtwbxm_1", - "age_at_diagnosis": 25, - "cancer_type_code": "D01.0", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_otliefvakqotckrtwbxm_1", + "ageAtDiagnosis": 25, + "cancerTypeCode": "D01.0", "laterality": "Not a paired site", - "clinical_tumour_staging_system": "Ann Arbor staging system", - "clinical_stage_group": "Stage IIIBE", - "lymph_nodes_examined_status": "Yes", - "performance_status": "Grade 1", + "clinicalTumourStagingSystem": "Ann Arbor staging system", + "clinicalStageGroup": "Stage IIIBE", + "lymphNodesExaminedStatus": "Yes", + "performanceStatus": "Grade 1", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_otliefvakqotckrtwbxm_1", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_otliefvakqotckrtwbxm_1", + "treatmentType": [ "No treatment" ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_otliefvakqotckrtwbxm_1", - "interval_of_followup": 69, - "disease_status_at_followup": "Stable" + "submitterFollowUpId": "TEST_FOLLOW_UP_otliefvakqotckrtwbxm_1", + "intervalOfFollowup": 69, + "diseaseStatusAtFollowup": "Stable" } ] } ], "comorbidity": [ { - "age_at_comorbidity_diagnosis": 18, - "comorbidity_type_code": "E13.87" + "ageAtComorbidityDiagnosis": 18, + "comorbidityTypeCode": "E13.87" }, { - "age_at_comorbidity_diagnosis": 19, - "comorbidity_type_code": "A22.74" + "ageAtComorbidityDiagnosis": 19, + "comorbidityTypeCode": "A22.74" }, { - "age_at_comorbidity_diagnosis": 20, - "comorbidity_type_code": "E67.38" + "ageAtComorbidityDiagnosis": 20, + "comorbidityTypeCode": "E67.38" } ] }, "specimen": { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_otliefvakqotckrtwbxm_0", - "submitter_specimen_id": "TEST_SPECIMEN_otliefvakqotckrtwbxm_N1", - "specimen_acquisition_interval": 84, - "specimen_anatomic_location": "C14.0", - "specimen_laterality": "Left", - "tumour_histological_type": "8878/13", - "pathological_tumour_staging_system": "Binet staging system", - "pathological_stage_group": "Stage A", - "tumour_grading_system": "Grading system for GISTs", - "tumour_grade": "Low", - "percent_tumour_cells": 46, - "reference_pathology_confirmed": "No" + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_otliefvakqotckrtwbxm_0", + "submitterSpecimenId": "TEST_SPECIMEN_otliefvakqotckrtwbxm_N1", + "specimenAcquisitionInterval": 84, + "specimenAnatomicLocation": "C14.0", + "specimenLaterality": "Left", + "tumourHistologicalType": "8878/13", + "pathologicalTumourStagingSystem": "Binet staging system", + "pathologicalStageGroup": "Stage A", + "tumourGradingSystem": "Grading system for GISTs", + "tumourGrade": "Low", + "percentTumourCells": 46, + "referencePathologyConfirmed": "No" }, "files": [ { @@ -151,25 +158,25 @@ ], "collaborator": [ { - "contact_email": "batman@batman_inc.org", + "contactEmail": "batman@batman_inc.org", "name": "batman", "affiliation": "batman inc" } ], "experiment": { "platform": "ILLUMINA", - "experimental_strategy": "WGS", - "submitter_sequencing_experiment_id": "EXPERIMENT" + "experimentalStrategy": "WGS", + "submitterSequencingExperimentId": "EXPERIMENT" }, "workflow": { - "workflow_name": "batman_stuff", - "genome_build": "GRCh38_hla_decoy_ebv", + "workflowName": "batman_stuff", + "genomeBuild": "GRCh38_hla_decoy_ebv", "inputs": [ { - "analysis_type": "sequencing_alignment", - "tumour_analysis_id": "00000000-0000-0000-0000-000000000000", - "normal_analysis_id": "00000000-0000-0000-0000-000000000000" + "analysisType": "sequencing_alignment", + "tumourAnalysisId": "00000000-0000-0000-0000-000000000000", + "normalAnalysisId": "00000000-0000-0000-0000-000000000000" } ] } -} +} \ No newline at end of file diff --git a/playground-data/example-payloads/TEST_SPECIMEN_otliefvakqotckrtwbxm_T2.json b/playground-data/example-payloads/TEST_SPECIMEN_otliefvakqotckrtwbxm_T2.json index 640b5804..577cf11a 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_otliefvakqotckrtwbxm_T2.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_otliefvakqotckrtwbxm_T2.json @@ -1,13 +1,17 @@ { + "analysisType": { + "name": "playgroundSchema" + }, + "studyId": "OVPLG-01", "samples": [ { "submitterSampleId": "TEST_SPECIMEN_otliefvakqotckrtwbxm_T2", "sampleType": "Total DNA", "matchedNormalSubmitterSampleId": "TEST_SPECIMEN_otliefvakqotckrtwbxm_N2", "specimen": { - "submitterSpecimenId": "TEST_SPECIMEN_otliefvakqotckrtwbxm_N2", - "specimenType": "Xenograft - derived from metastatic tumour", - "specimenTissueSource": "Blood derived - bone marrow", + "submitterSpecimenId": "TEST_SPECIMEN_otliefvakqotckrtwbxm_T2", + "specimenType": "Metastatic tumour", + "specimenTissueSource": "Buccal cell", "tumourNormalDesignation": "Tumour" }, "donor": { @@ -17,113 +21,116 @@ } ], "donor": { - "submitter_donor_id": "TEST_DONOR_otliefvakqotckrtwbxm", - "primary_site": ["Trachea","Colon"], - "vital_status": "Alive", - "survival_time": null, - "cause_of_death": null, - "primary_diagnosis": [ + "submitterDonorId": "TEST_DONOR_otliefvakqotckrtwbxm", + "primarySite": [ + "Trachea", + "Colon" + ], + "vitalStatus": "Alive", + "survivalTime": null, + "causeOfDeath": null, + "primaryDiagnosis": [ { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_otliefvakqotckrtwbxm_0", - "age_at_diagnosis": 20, - "cancer_type_code": "C13.6", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_otliefvakqotckrtwbxm_0", + "ageAtDiagnosis": 20, + "cancerTypeCode": "C13.6", "laterality": "Unilateral, side not specified", - "clinical_tumour_staging_system": "AJCC 7th edition", - "clinical_stage_group": "Stage IIIB", - "lymph_nodes_examined_status": "Not applicable", - "performance_status": "Grade 1", + "clinicalTumourStagingSystem": "AJCC 7th edition", + "clinicalStageGroup": "Stage IIIB", + "lymphNodesExaminedStatus": "Not applicable", + "performanceStatus": "Grade 1", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_otliefvakqotckrtwbxm_0", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_otliefvakqotckrtwbxm_0", + "treatmentType": [ "Radiation therapy", "Chemotherapy" ], - "treatment_intent": "Curative", - "treatment_start_interval": 67, - "treatment_duration": 85, - "response_to_treatment": "Disease progression", + "treatmentIntent": "Curative", + "treatmentStartInterval": 67, + "treatmentDuration": 85, + "responseToTreatment": "Disease progression", "radiation": [ { - "radiation_therapy_modality": "Photon", - "radiation_therapy_type": "External", - "anatomical_site_irradiated": "Head", - "radiation_therapy_dosage": 71, - "radiation_therapy_fractions": 69 + "radiationTherapyModality": "Photon", + "radiationTherapyType": "External", + "anatomicalSiteIrradiated": "Head", + "radiationTherapyDosage": 71, + "radiationTherapyFractions": 69 } ], "chemotherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 79, - "chemotherapy_dosage_units": "mg/m2" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 79, + "chemotherapyDosageUnits": "mg/m2" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_otliefvakqotckrtwbxm_0", - "interval_of_followup": 65, - "disease_status_at_followup": "Complete remission" + "submitterFollowUpId": "TEST_FOLLOW_UP_otliefvakqotckrtwbxm_0", + "intervalOfFollowup": 65, + "diseaseStatusAtFollowup": "Complete remission" } ] }, { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_otliefvakqotckrtwbxm_1", - "age_at_diagnosis": 25, - "cancer_type_code": "D01.0", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_otliefvakqotckrtwbxm_1", + "ageAtDiagnosis": 25, + "cancerTypeCode": "D01.0", "laterality": "Not a paired site", - "clinical_tumour_staging_system": "Ann Arbor staging system", - "clinical_stage_group": "Stage IIIBE", - "lymph_nodes_examined_status": "Yes", - "performance_status": "Grade 1", + "clinicalTumourStagingSystem": "Ann Arbor staging system", + "clinicalStageGroup": "Stage IIIBE", + "lymphNodesExaminedStatus": "Yes", + "performanceStatus": "Grade 1", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_otliefvakqotckrtwbxm_1", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_otliefvakqotckrtwbxm_1", + "treatmentType": [ "No treatment" ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_otliefvakqotckrtwbxm_1", - "interval_of_followup": 69, - "disease_status_at_followup": "Stable" + "submitterFollowUpId": "TEST_FOLLOW_UP_otliefvakqotckrtwbxm_1", + "intervalOfFollowup": 69, + "diseaseStatusAtFollowup": "Stable" } ] } ], "comorbidity": [ { - "age_at_comorbidity_diagnosis": 18, - "comorbidity_type_code": "E13.87" + "ageAtComorbidityDiagnosis": 18, + "comorbidityTypeCode": "E13.87" }, { - "age_at_comorbidity_diagnosis": 19, - "comorbidity_type_code": "A22.74" + "ageAtComorbidityDiagnosis": 19, + "comorbidityTypeCode": "A22.74" }, { - "age_at_comorbidity_diagnosis": 20, - "comorbidity_type_code": "E67.38" + "ageAtComorbidityDiagnosis": 20, + "comorbidityTypeCode": "E67.38" } ] }, "specimen": { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_otliefvakqotckrtwbxm_0", - "submitter_specimen_id": "TEST_SPECIMEN_otliefvakqotckrtwbxm_N2", - "specimen_acquisition_interval": 22, - "specimen_anatomic_location": "C13.9", - "specimen_laterality": "Unknown", - "tumour_histological_type": "9681/98", - "pathological_tumour_staging_system": "AJCC 8th edition", - "pathological_stage_group": "Stage IVA2", - "tumour_grading_system": "Grading system for GISTs", - "tumour_grade": "Low", - "percent_tumour_cells": 45, - "reference_pathology_confirmed": "No" + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_otliefvakqotckrtwbxm_0", + "submitterSpecimenId": "TEST_SPECIMEN_otliefvakqotckrtwbxm_N2", + "specimenAcquisitionInterval": 22, + "specimenAnatomicLocation": "C13.9", + "specimenLaterality": "Unknown", + "tumourHistologicalType": "9681/98", + "pathologicalTumourStagingSystem": "AJCC 8th edition", + "pathologicalStageGroup": "Stage IVA2", + "tumourGradingSystem": "Grading system for GISTs", + "tumourGrade": "Low", + "percentTumourCells": 45, + "referencePathologyConfirmed": "No" }, "files": [ { @@ -151,25 +158,25 @@ ], "collaborator": [ { - "contact_email": "batman@batman_inc.org", + "contactEmail": "batman@batman_inc.org", "name": "batman", "affiliation": "batman inc" } ], "experiment": { "platform": "ILLUMINA", - "experimental_strategy": "WGS", - "submitter_sequencing_experiment_id": "EXPERIMENT" + "experimentalStrategy": "WGS", + "submitterSequencingExperimentId": "EXPERIMENT" }, "workflow": { - "workflow_name": "batman_stuff", - "genome_build": "GRCh38_hla_decoy_ebv", + "workflowName": "batman_stuff", + "genomeBuild": "GRCh38_hla_decoy_ebv", "inputs": [ { - "analysis_type": "sequencing_alignment", - "tumour_analysis_id": "00000000-0000-0000-0000-000000000000", - "normal_analysis_id": "00000000-0000-0000-0000-000000000000" + "analysisType": "sequencing_alignment", + "tumourAnalysisId": "00000000-0000-0000-0000-000000000000", + "normalAnalysisId": "00000000-0000-0000-0000-000000000000" } ] } -} +} \ No newline at end of file diff --git a/playground-data/example-payloads/TEST_SPECIMEN_tixlzwxuqaoyhubfdlph_N1.json b/playground-data/example-payloads/TEST_SPECIMEN_tixlzwxuqaoyhubfdlph_N1.json index 192c4a29..f73e37a5 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_tixlzwxuqaoyhubfdlph_N1.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_tixlzwxuqaoyhubfdlph_N1.json @@ -1,4 +1,8 @@ { + "analysisType": { + "name": "playgroundSchema" + }, + "studyId": "OVPLG-01", "samples": [ { "submitterSampleId": "TEST_SPECIMEN_tixlzwxuqaoyhubfdlph_N1", @@ -6,7 +10,7 @@ "matchedNormalSubmitterSampleId": null, "specimen": { "submitterSpecimenId": "TEST_SPECIMEN_tixlzwxuqaoyhubfdlph_N1", - "specimenType": "Cell line - derived from normal", + "specimenType": "Primary tumour", "specimenTissueSource": "Bone", "tumourNormalDesignation": "Normal" }, @@ -17,107 +21,109 @@ } ], "donor": { - "submitter_donor_id": "TEST_DONOR_tixlzwxuqaoyhubfdlph", - "primary_site": ["Bones, joints and articular cartilage of other and unspecified sites"], - "vital_status": "Deceased", - "survival_time": 1711, - "cause_of_death": "Unknown", - "primary_diagnosis": [ + "submitterDonorId": "TEST_DONOR_tixlzwxuqaoyhubfdlph", + "primarySite": [ + "Bones, joints and articular cartilage of other and unspecified sites" + ], + "vitalStatus": "Deceased", + "survivalTime": 1711, + "causeOfDeath": "Unknown", + "primaryDiagnosis": [ { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_tixlzwxuqaoyhubfdlph_0", - "age_at_diagnosis": 72, - "cancer_type_code": "C79.51", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_tixlzwxuqaoyhubfdlph_0", + "ageAtDiagnosis": 72, + "cancerTypeCode": "C79.51", "laterality": "Not a paired site", - "clinical_tumour_staging_system": "St Jude staging system", - "clinical_stage_group": "Stage III", - "lymph_nodes_examined_status": "Not applicable", - "performance_status": "Grade 4", + "clinicalTumourStagingSystem": "St Jude staging system", + "clinicalStageGroup": "Stage III", + "lymphNodesExaminedStatus": "Not applicable", + "performanceStatus": "Grade 4", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_tixlzwxuqaoyhubfdlph_0", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_tixlzwxuqaoyhubfdlph_0", + "treatmentType": [ "Hormonal therapy", "Radiation therapy", "Immunotherapy", "Surgery", "Chemotherapy" ], - "treatment_intent": "Curative", - "treatment_start_interval": 39, - "treatment_duration": 44, - "response_to_treatment": "Complete response", - "hormone_therapy": [ + "treatmentIntent": "Curative", + "treatmentStartInterval": 39, + "treatmentDuration": 44, + "responseToTreatment": "Complete response", + "hormoneTherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 16, - "hormone_drug_dosage_units": "mg/m2" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 16, + "hormoneDrugDosageUnits": "mg/m2" } ], "radiation": [ { - "radiation_therapy_modality": "Heavy Ions", - "radiation_therapy_type": "Internal", - "anatomical_site_irradiated": "Lung", - "radiation_therapy_dosage": 86, - "radiation_therapy_fractions": 67 + "radiationTherapyModality": "Heavy Ions", + "radiationTherapyType": "Internal", + "anatomicalSiteIrradiated": "Lung", + "radiationTherapyDosage": 86, + "radiationTherapyFractions": 67 } ], "immunotherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "immunotherapy_type": "Other immunomodulatory substances" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "immunotherapyType": "Other immunomodulatory substances" } ], "surgery": [ { - "surgery_type": "Axillary Clearance", - "surgery_site": "C27.7", - "surgery_location": "Local recurrence", - "residual_tumour_classification": "R1" + "surgeryType": "Axillary Clearance", + "surgerySite": "C27.7", + "surgeryLocation": "Local recurrence", + "residualTumourClassification": "R1" } ], "chemotherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 53, - "chemotherapy_dosage_units": "IU/m2" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 53, + "chemotherapyDosageUnits": "IU/m2" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_tixlzwxuqaoyhubfdlph_0", - "interval_of_followup": 65, - "disease_status_at_followup": "No evidence of disease" + "submitterFollowUpId": "TEST_FOLLOW_UP_tixlzwxuqaoyhubfdlph_0", + "intervalOfFollowup": 65, + "diseaseStatusAtFollowup": "No evidence of disease" } ] } ], "comorbidity": [ { - "age_at_comorbidity_diagnosis": 48, - "comorbidity_type_code": "A23.79" + "ageAtComorbidityDiagnosis": 48, + "comorbidityTypeCode": "A23.79" }, { - "age_at_comorbidity_diagnosis": 66, - "comorbidity_type_code": "A01.8" + "ageAtComorbidityDiagnosis": 66, + "comorbidityTypeCode": "A01.8" }, { - "age_at_comorbidity_diagnosis": 58, - "comorbidity_type_code": "A25.43" + "ageAtComorbidityDiagnosis": 58, + "comorbidityTypeCode": "A25.43" } ] }, "specimen": { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_tixlzwxuqaoyhubfdlph_0", - "submitter_specimen_id": "TEST_SPECIMEN_tixlzwxuqaoyhubfdlph_N1", - "specimen_acquisition_interval": 94, - "specimen_anatomic_location": "C41.4", - "specimen_laterality": "Not applicable" + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_tixlzwxuqaoyhubfdlph_0", + "submitterSpecimenId": "TEST_SPECIMEN_tixlzwxuqaoyhubfdlph_N1", + "specimenAcquisitionInterval": 94, + "specimenAnatomicLocation": "C41.4", + "specimenLaterality": "Not applicable" }, "files": [ { @@ -145,25 +151,25 @@ ], "collaborator": [ { - "contact_email": "batman@batman_inc.org", + "contactEmail": "batman@batman_inc.org", "name": "batman", "affiliation": "batman inc" } ], "experiment": { "platform": "ILLUMINA", - "experimental_strategy": "WGS", - "submitter_sequencing_experiment_id": "EXPERIMENT" + "experimentalStrategy": "WGS", + "submitterSequencingExperimentId": "EXPERIMENT" }, "workflow": { - "workflow_name": "batman_stuff", - "genome_build": "GRCh38_hla_decoy_ebv", + "workflowName": "batman_stuff", + "genomeBuild": "GRCh38_hla_decoy_ebv", "inputs": [ { - "analysis_type": "sequencing_alignment", - "tumour_analysis_id": "00000000-0000-0000-0000-000000000000", - "normal_analysis_id": "00000000-0000-0000-0000-000000000000" + "analysisType": "sequencing_alignment", + "tumourAnalysisId": "00000000-0000-0000-0000-000000000000", + "normalAnalysisId": "00000000-0000-0000-0000-000000000000" } ] } -} +} \ No newline at end of file diff --git a/playground-data/example-payloads/TEST_SPECIMEN_tixlzwxuqaoyhubfdlph_T1.json b/playground-data/example-payloads/TEST_SPECIMEN_tixlzwxuqaoyhubfdlph_T1.json index 0232044d..0a900d68 100644 --- a/playground-data/example-payloads/TEST_SPECIMEN_tixlzwxuqaoyhubfdlph_T1.json +++ b/playground-data/example-payloads/TEST_SPECIMEN_tixlzwxuqaoyhubfdlph_T1.json @@ -1,12 +1,16 @@ { + "analysisType": { + "name": "playgroundSchema" + }, + "studyId": "OVPLG-01", "samples": [ { "submitterSampleId": "TEST_SPECIMEN_tixlzwxuqaoyhubfdlph_T1", "sampleType": "Total DNA", "matchedNormalSubmitterSampleId": "TEST_SPECIMEN_tixlzwxuqaoyhubfdlph_N1", "specimen": { - "submitterSpecimenId": "TEST_SPECIMEN_tixlzwxuqaoyhubfdlph_N1", - "specimenType": "Cell line - derived from tumour", + "submitterSpecimenId": "TEST_SPECIMEN_tixlzwxuqaoyhubfdlph_T1", + "specimenType": "Primary tumour", "specimenTissueSource": "Bone", "tumourNormalDesignation": "Tumour" }, @@ -17,114 +21,116 @@ } ], "donor": { - "submitter_donor_id": "TEST_DONOR_tixlzwxuqaoyhubfdlph", - "primary_site": ["Bones, joints and articular cartilage of other and unspecified sites"], - "vital_status": "Deceased", - "survival_time": 1711, - "cause_of_death": "Unknown", - "primary_diagnosis": [ + "submitterDonorId": "TEST_DONOR_tixlzwxuqaoyhubfdlph", + "primarySite": [ + "Bones, joints and articular cartilage of other and unspecified sites" + ], + "vitalStatus": "Deceased", + "survivalTime": 1711, + "causeOfDeath": "Unknown", + "primaryDiagnosis": [ { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_tixlzwxuqaoyhubfdlph_0", - "age_at_diagnosis": 72, - "cancer_type_code": "C79.51", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_tixlzwxuqaoyhubfdlph_0", + "ageAtDiagnosis": 72, + "cancerTypeCode": "C79.51", "laterality": "Not a paired site", - "clinical_tumour_staging_system": "St Jude staging system", - "clinical_stage_group": "Stage III", - "lymph_nodes_examined_status": "Not applicable", - "performance_status": "Grade 4", + "clinicalTumourStagingSystem": "St Jude staging system", + "clinicalStageGroup": "Stage III", + "lymphNodesExaminedStatus": "Not applicable", + "performanceStatus": "Grade 4", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_tixlzwxuqaoyhubfdlph_0", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_tixlzwxuqaoyhubfdlph_0", + "treatmentType": [ "Hormonal therapy", "Radiation therapy", "Immunotherapy", "Surgery", "Chemotherapy" ], - "treatment_intent": "Curative", - "treatment_start_interval": 39, - "treatment_duration": 44, - "response_to_treatment": "Complete response", - "hormone_therapy": [ + "treatmentIntent": "Curative", + "treatmentStartInterval": 39, + "treatmentDuration": 44, + "responseToTreatment": "Complete response", + "hormoneTherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 16, - "hormone_drug_dosage_units": "mg/m2" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 16, + "hormoneDrugDosageUnits": "mg/m2" } ], "radiation": [ { - "radiation_therapy_modality": "Heavy Ions", - "radiation_therapy_type": "Internal", - "anatomical_site_irradiated": "Lung", - "radiation_therapy_dosage": 86, - "radiation_therapy_fractions": 67 + "radiationTherapyModality": "Heavy Ions", + "radiationTherapyType": "Internal", + "anatomicalSiteIrradiated": "Lung", + "radiationTherapyDosage": 86, + "radiationTherapyFractions": 67 } ], "immunotherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "immunotherapy_type": "Other immunomodulatory substances" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "immunotherapyType": "Other immunomodulatory substances" } ], "surgery": [ { - "surgery_type": "Axillary Clearance", - "surgery_site": "C27.7", - "surgery_location": "Local recurrence", - "residual_tumour_classification": "R1" + "surgeryType": "Axillary Clearance", + "surgerySite": "C27.7", + "surgeryLocation": "Local recurrence", + "residualTumourClassification": "R1" } ], "chemotherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 53, - "chemotherapy_dosage_units": "IU/m2" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 53, + "chemotherapyDosageUnits": "IU/m2" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_tixlzwxuqaoyhubfdlph_0", - "interval_of_followup": 65, - "disease_status_at_followup": "No evidence of disease" + "submitterFollowUpId": "TEST_FOLLOW_UP_tixlzwxuqaoyhubfdlph_0", + "intervalOfFollowup": 65, + "diseaseStatusAtFollowup": "No evidence of disease" } ] } ], "comorbidity": [ { - "age_at_comorbidity_diagnosis": 48, - "comorbidity_type_code": "A23.79" + "ageAtComorbidityDiagnosis": 48, + "comorbidityTypeCode": "A23.79" }, { - "age_at_comorbidity_diagnosis": 66, - "comorbidity_type_code": "A01.8" + "ageAtComorbidityDiagnosis": 66, + "comorbidityTypeCode": "A01.8" }, { - "age_at_comorbidity_diagnosis": 58, - "comorbidity_type_code": "A25.43" + "ageAtComorbidityDiagnosis": 58, + "comorbidityTypeCode": "A25.43" } ] }, "specimen": { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_tixlzwxuqaoyhubfdlph_0", - "submitter_specimen_id": "TEST_SPECIMEN_tixlzwxuqaoyhubfdlph_N1", - "specimen_acquisition_interval": 92, - "specimen_anatomic_location": "C41.4", - "specimen_laterality": "Left", - "tumour_histological_type": "8137/14", - "pathological_tumour_staging_system": "AJCC 8th edition", - "pathological_stage_group": "Stage IA2", - "tumour_grading_system": "Nuclear grading system for DCIS", - "tumour_grade": "G1", - "percent_tumour_cells": 95, - "reference_pathology_confirmed": "No" + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_tixlzwxuqaoyhubfdlph_0", + "submitterSpecimenId": "TEST_SPECIMEN_tixlzwxuqaoyhubfdlph_N1", + "specimenAcquisitionInterval": 92, + "specimenAnatomicLocation": "C41.4", + "specimenLaterality": "Left", + "tumourHistologicalType": "8137/14", + "pathologicalTumourStagingSystem": "AJCC 8th edition", + "pathologicalStageGroup": "Stage IA2", + "tumourGradingSystem": "Nuclear grading system for DCIS", + "tumourGrade": "G1", + "percentTumourCells": 95, + "referencePathologyConfirmed": "No" }, "files": [ { @@ -152,25 +158,25 @@ ], "collaborator": [ { - "contact_email": "batman@batman_inc.org", + "contactEmail": "batman@batman_inc.org", "name": "batman", "affiliation": "batman inc" } ], "experiment": { "platform": "ILLUMINA", - "experimental_strategy": "WGS", - "submitter_sequencing_experiment_id": "EXPERIMENT" + "experimentalStrategy": "WGS", + "submitterSequencingExperimentId": "EXPERIMENT" }, "workflow": { - "workflow_name": "batman_stuff", - "genome_build": "GRCh38_hla_decoy_ebv", + "workflowName": "batman_stuff", + "genomeBuild": "GRCh38_hla_decoy_ebv", "inputs": [ { - "analysis_type": "sequencing_alignment", - "tumour_analysis_id": "00000000-0000-0000-0000-000000000000", - "normal_analysis_id": "00000000-0000-0000-0000-000000000000" + "analysisType": "sequencing_alignment", + "tumourAnalysisId": "00000000-0000-0000-0000-000000000000", + "normalAnalysisId": "00000000-0000-0000-0000-000000000000" } ] } -} +} \ No newline at end of file diff --git a/playground-data/example-payloads/alignment_bam_bcclfxzvjitgtbsvfnum.json b/playground-data/example-payloads/alignment_bam_bcclfxzvjitgtbsvfnum.json index 35405400..677b4e25 100644 --- a/playground-data/example-payloads/alignment_bam_bcclfxzvjitgtbsvfnum.json +++ b/playground-data/example-payloads/alignment_bam_bcclfxzvjitgtbsvfnum.json @@ -1,4 +1,8 @@ { + "analysisType": { + "name": "playgroundSchema" + }, + "studyId": "OVPLG-01", "samples": [ { "submitterSampleId": "TEST_SPECIMEN_bcclfxzvjitgtbsvfnum_N1", @@ -17,118 +21,120 @@ } ], "donor": { - "submitter_donor_id": "TEST_DONOR_bcclfxzvjitgtbsvfnum", - "primary_site": ["Brain"], - "vital_status": "Deceased", - "survival_time": 1550, - "cause_of_death": "Unknown", - "primary_diagnosis": [ + "submitterDonorId": "TEST_DONOR_bcclfxzvjitgtbsvfnum", + "primarySite": [ + "Brain" + ], + "vitalStatus": "Deceased", + "survivalTime": 1550, + "causeOfDeath": "Unknown", + "primaryDiagnosis": [ { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_bcclfxzvjitgtbsvfnum_0", - "age_at_diagnosis": 59, - "cancer_type_code": "D72.5", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_bcclfxzvjitgtbsvfnum_0", + "ageAtDiagnosis": 59, + "cancerTypeCode": "D72.5", "laterality": "Unknown", - "clinical_tumour_staging_system": "AJCC 8th edition", - "clinical_stage_group": "Stage IIE", - "lymph_nodes_examined_status": "No", - "performance_status": "Unknown", + "clinicalTumourStagingSystem": "AJCC 8th edition", + "clinicalStageGroup": "Stage IIE", + "lymphNodesExaminedStatus": "No", + "performanceStatus": "Unknown", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_bcclfxzvjitgtbsvfnum_0", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_bcclfxzvjitgtbsvfnum_0", + "treatmentType": [ "Radiation therapy", "Surgery" ], - "treatment_intent": "Curative", - "treatment_start_interval": 65, - "treatment_duration": 48, - "response_to_treatment": "NED", + "treatmentIntent": "Curative", + "treatmentStartInterval": 65, + "treatmentDuration": 48, + "responseToTreatment": "NED", "radiation": [ { - "radiation_therapy_modality": "Electron", - "radiation_therapy_type": "Internal", - "anatomical_site_irradiated": "Upper Limb", - "radiation_therapy_dosage": 24, - "radiation_therapy_fractions": 60 + "radiationTherapyModality": "Electron", + "radiationTherapyType": "Internal", + "anatomicalSiteIrradiated": "Upper Limb", + "radiationTherapyDosage": 24, + "radiationTherapyFractions": 60 } ], "surgery": [ { - "surgery_type": "Axillary lymph nodes sampling", - "surgery_site": "C80.3", - "surgery_location": "Metastatic", - "residual_tumour_classification": "R1" + "surgeryType": "Axillary lymph nodes sampling", + "surgerySite": "C80.3", + "surgeryLocation": "Metastatic", + "residualTumourClassification": "R1" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_bcclfxzvjitgtbsvfnum_0", - "interval_of_followup": 77, - "disease_status_at_followup": "Complete remission" + "submitterFollowUpId": "TEST_FOLLOW_UP_bcclfxzvjitgtbsvfnum_0", + "intervalOfFollowup": 77, + "diseaseStatusAtFollowup": "Complete remission" } ] }, { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_bcclfxzvjitgtbsvfnum_1", - "age_at_diagnosis": 57, - "cancer_type_code": "D43.2", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_bcclfxzvjitgtbsvfnum_1", + "ageAtDiagnosis": 57, + "cancerTypeCode": "D43.2", "laterality": "Left", - "clinical_tumour_staging_system": "AJCC 7th edition", - "clinical_stage_group": "Stage IV", - "lymph_nodes_examined_status": "No lymph nodes found in resected specimen", - "performance_status": "Unknown", + "clinicalTumourStagingSystem": "AJCC 7th edition", + "clinicalStageGroup": "Stage IV", + "lymphNodesExaminedStatus": "No lymph nodes found in resected specimen", + "performanceStatus": "Unknown", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_bcclfxzvjitgtbsvfnum_1", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_bcclfxzvjitgtbsvfnum_1", + "treatmentType": [ "Chemotherapy" ], - "treatment_intent": "Unknown", - "treatment_start_interval": 24, - "treatment_duration": 32, - "response_to_treatment": "Stable disease", + "treatmentIntent": "Unknown", + "treatmentStartInterval": 24, + "treatmentDuration": 32, + "responseToTreatment": "Stable disease", "chemotherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 24, - "chemotherapy_dosage_units": "mg/m2" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 24, + "chemotherapyDosageUnits": "mg/m2" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_bcclfxzvjitgtbsvfnum_1", - "interval_of_followup": 95, - "disease_status_at_followup": "Complete remission" + "submitterFollowUpId": "TEST_FOLLOW_UP_bcclfxzvjitgtbsvfnum_1", + "intervalOfFollowup": 95, + "diseaseStatusAtFollowup": "Complete remission" } ] } ], "comorbidity": [ { - "age_at_comorbidity_diagnosis": 35, - "comorbidity_type_code": "E34.13" + "ageAtComorbidityDiagnosis": 35, + "comorbidityTypeCode": "E34.13" }, { - "age_at_comorbidity_diagnosis": 30, - "comorbidity_type_code": "B75.65" + "ageAtComorbidityDiagnosis": 30, + "comorbidityTypeCode": "B75.65" }, { - "age_at_comorbidity_diagnosis": 99, - "comorbidity_type_code": "A03.43" + "ageAtComorbidityDiagnosis": 99, + "comorbidityTypeCode": "A03.43" } ] }, "specimen": { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_bcclfxzvjitgtbsvfnum_0", - "submitter_specimen_id": "TEST_SPECIMEN_bcclfxzvjitgtbsvfnum_N1", - "specimen_acquisition_interval": 35, - "specimen_anatomic_location": "C71.6", - "specimen_laterality": "Right" + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_bcclfxzvjitgtbsvfnum_0", + "submitterSpecimenId": "TEST_SPECIMEN_bcclfxzvjitgtbsvfnum_N1", + "specimenAcquisitionInterval": 35, + "specimenAnatomicLocation": "C71.6", + "specimenLaterality": "Right" }, "files": [ { @@ -139,7 +145,7 @@ "fileAccess": "controlled", "fileType": "BAM", "info": { - "notes_for_mitchell": "hg19:1:14418-18000", + "notesForMitchell": "hg19:1:14418-18000", "dataCategory": "Sequencing Reads" } }, @@ -151,32 +157,32 @@ "fileAccess": "controlled", "fileType": "BAI", "info": { - "notes_for_mitchell": "hg19:1:14418-18000", + "notesForMitchell": "hg19:1:14418-18000", "dataCategory": "Sequencing Reads" } } ], "collaborator": [ { - "contact_email": "batman@batman_inc.org", + "contactEmail": "batman@batman_inc.org", "name": "batman", "affiliation": "batman inc" } ], "experiment": { "platform": "ILLUMINA", - "experimental_strategy": "WGS", - "submitter_sequencing_experiment_id": "EXPERIMENT" + "experimentalStrategy": "WGS", + "submitterSequencingExperimentId": "EXPERIMENT" }, "workflow": { - "workflow_name": "batman_stuff", - "genome_build": "GRCh38_hla_decoy_ebv", + "workflowName": "batman_stuff", + "genomeBuild": "GRCh38_hla_decoy_ebv", "inputs": [ { - "analysis_type": "sequencing_alignment", - "tumour_analysis_id": "00000000-0000-0000-0000-000000000000", - "normal_analysis_id": "00000000-0000-0000-0000-000000000000" + "analysisType": "sequencing_alignment", + "tumourAnalysisId": "00000000-0000-0000-0000-000000000000", + "normalAnalysisId": "00000000-0000-0000-0000-000000000000" } ] } -} +} \ No newline at end of file diff --git a/playground-data/example-payloads/alignment_cram_bcclfxzvjitgtbsvfnum.json b/playground-data/example-payloads/alignment_cram_bcclfxzvjitgtbsvfnum.json index 96d28545..aa4af7fd 100644 --- a/playground-data/example-payloads/alignment_cram_bcclfxzvjitgtbsvfnum.json +++ b/playground-data/example-payloads/alignment_cram_bcclfxzvjitgtbsvfnum.json @@ -1,11 +1,15 @@ { + "analysisType": { + "name": "playgroundSchema" + }, + "studyId": "OVPLG-01", "samples": [ { "submitterSampleId": "TEST_SPECIMEN_bcclfxzvjitgtbsvfnum_T1", "sampleType": "Total DNA", "matchedNormalSubmitterSampleId": "TEST_SPECIMEN_bcclfxzvjitgtbsvfnum_N1", "specimen": { - "submitterSpecimenId": "TEST_SPECIMEN_bcclfxzvjitgtbsvfnum_N1", + "submitterSpecimenId": "TEST_SPECIMEN_bcclfxzvjitgtbsvfnum_T1", "specimenType": "Metastatic tumour - metastasis to distant location", "specimenTissueSource": "Bone", "tumourNormalDesignation": "Tumour" @@ -17,166 +21,168 @@ } ], "donor": { - "submitter_donor_id": "TEST_DONOR_bcclfxzvjitgtbsvfnum", - "primary_site": ["Bones, joints and articular cartilage of limbs"], - "vital_status": "Deceased", - "survival_time": 1550, - "cause_of_death": "Unknown", - "primary_diagnosis": [ + "submitterDonorId": "TEST_DONOR_bcclfxzvjitgtbsvfnum", + "primarySite": [ + "Bones, joints and articular cartilage of limbs" + ], + "vitalStatus": "Deceased", + "survivalTime": 1550, + "causeOfDeath": "Unknown", + "primaryDiagnosis": [ { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_bcclfxzvjitgtbsvfnum_0", - "age_at_diagnosis": 59, - "cancer_type_code": "D72.5", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_bcclfxzvjitgtbsvfnum_0", + "ageAtDiagnosis": 59, + "cancerTypeCode": "D72.5", "laterality": "Unknown", - "clinical_tumour_staging_system": "AJCC 8th edition", - "clinical_stage_group": "Stage IIE", - "lymph_nodes_examined_status": "No", - "performance_status": "Unknown", + "clinicalTumourStagingSystem": "AJCC 8th edition", + "clinicalStageGroup": "Stage IIE", + "lymphNodesExaminedStatus": "No", + "performanceStatus": "Unknown", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_bcclfxzvjitgtbsvfnum_0", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_bcclfxzvjitgtbsvfnum_0", + "treatmentType": [ "Radiation therapy", "Surgery" ], - "treatment_intent": "Curative", - "treatment_start_interval": 65, - "treatment_duration": 48, - "response_to_treatment": "NED", + "treatmentIntent": "Curative", + "treatmentStartInterval": 65, + "treatmentDuration": 48, + "responseToTreatment": "NED", "radiation": [ { - "radiation_therapy_modality": "Electron", - "radiation_therapy_type": "Internal", - "anatomical_site_irradiated": "Upper Limb", - "radiation_therapy_dosage": 24, - "radiation_therapy_fractions": 60 + "radiationTherapyModality": "Electron", + "radiationTherapyType": "Internal", + "anatomicalSiteIrradiated": "Upper Limb", + "radiationTherapyDosage": 24, + "radiationTherapyFractions": 60 } ], "surgery": [ { - "surgery_type": "Axillary lymph nodes sampling", - "surgery_site": "C80.3", - "surgery_location": "Metastatic", - "residual_tumour_classification": "R1" + "surgeryType": "Axillary lymph nodes sampling", + "surgerySite": "C80.3", + "surgeryLocation": "Metastatic", + "residualTumourClassification": "R1" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_bcclfxzvjitgtbsvfnum_0", - "interval_of_followup": 77, - "disease_status_at_followup": "Complete remission" + "submitterFollowUpId": "TEST_FOLLOW_UP_bcclfxzvjitgtbsvfnum_0", + "intervalOfFollowup": 77, + "diseaseStatusAtFollowup": "Complete remission" } ] }, { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_bcclfxzvjitgtbsvfnum_1", - "age_at_diagnosis": 57, - "cancer_type_code": "D43.2", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_bcclfxzvjitgtbsvfnum_1", + "ageAtDiagnosis": 57, + "cancerTypeCode": "D43.2", "laterality": "Left", - "clinical_tumour_staging_system": "AJCC 7th edition", - "clinical_stage_group": "Stage IV", - "lymph_nodes_examined_status": "No lymph nodes found in resected specimen", - "performance_status": "Unknown", + "clinicalTumourStagingSystem": "AJCC 7th edition", + "clinicalStageGroup": "Stage IV", + "lymphNodesExaminedStatus": "No lymph nodes found in resected specimen", + "performanceStatus": "Unknown", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_bcclfxzvjitgtbsvfnum_1", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_bcclfxzvjitgtbsvfnum_1", + "treatmentType": [ "Chemotherapy" ], - "treatment_intent": "Unknown", - "treatment_start_interval": 24, - "treatment_duration": 32, - "response_to_treatment": "Stable disease", + "treatmentIntent": "Unknown", + "treatmentStartInterval": 24, + "treatmentDuration": 32, + "responseToTreatment": "Stable disease", "chemotherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 24, - "chemotherapy_dosage_units": "mg/m2" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 24, + "chemotherapyDosageUnits": "mg/m2" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_bcclfxzvjitgtbsvfnum_1", - "interval_of_followup": 95, - "disease_status_at_followup": "Complete remission" + "submitterFollowUpId": "TEST_FOLLOW_UP_bcclfxzvjitgtbsvfnum_1", + "intervalOfFollowup": 95, + "diseaseStatusAtFollowup": "Complete remission" } ] } ], "comorbidity": [ { - "age_at_comorbidity_diagnosis": 35, - "comorbidity_type_code": "E34.13" + "ageAtComorbidityDiagnosis": 35, + "comorbidityTypeCode": "E34.13" }, { - "age_at_comorbidity_diagnosis": 30, - "comorbidity_type_code": "B75.65" + "ageAtComorbidityDiagnosis": 30, + "comorbidityTypeCode": "B75.65" }, { - "age_at_comorbidity_diagnosis": 99, - "comorbidity_type_code": "A03.43" + "ageAtComorbidityDiagnosis": 99, + "comorbidityTypeCode": "A03.43" } ] }, "specimen": { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_bcclfxzvjitgtbsvfnum_0", - "submitter_specimen_id": "TEST_SPECIMEN_bcclfxzvjitgtbsvfnum_N1", - "specimen_acquisition_interval": 21, - "specimen_anatomic_location": "C87", - "specimen_laterality": "Unknown" + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_bcclfxzvjitgtbsvfnum_0", + "submitterSpecimenId": "TEST_SPECIMEN_bcclfxzvjitgtbsvfnum_N1", + "specimenAcquisitionInterval": 21, + "specimenAnatomicLocation": "C87", + "specimenLaterality": "Unknown" }, "files": [ { - "DataType": "Sequence Alignment", + "dataType": "Sequence Alignment", "fileName": "TEST-QA.DO263273.SA624744.wgs.20230728.aln.cram", "fileSize": 19423, "fileMd5sum": "03dba6ebed01c26401b190e6d591aafc", "fileAccess": "controlled", "fileType": "CRAM", "info": { - "notes_for_mitchell": "hg19:20:61512874-61513499", + "notesForMitchell": "hg19:20:61512874-61513499", "dataCategory": "Simple Nucelotide Variation" } }, { - "DataType": "Sequence Alignment", + "dataType": "Sequence Alignment", "fileName": "TEST-QA.DO263273.SA624744.wgs.20230728.aln.cram.crai", "fileSize": 79, "fileMd5sum": "d9070baed15f3331adda5528a8a9cda1", "fileAccess": "controlled", "fileType": "CRAI", "info": { - "notes_for_mitchell": "hg19:20:61512874-61513499", + "notesForMitchell": "hg19:20:61512874-61513499", "dataCategory": "Simple Nucelotide Variation" } } ], "collaborator": [ { - "contact_email": "batman@batman_inc.org", + "contactEmail": "batman@batman_inc.org", "name": "batman", "affiliation": "batman inc" } ], "experiment": { "platform": "ILLUMINA", - "experimental_strategy": "WGS", - "submitter_sequencing_experiment_id": "EXPERIMENT" + "experimentalStrategy": "WGS", + "submitterSequencingExperimentId": "EXPERIMENT" }, "workflow": { - "workflow_name": "batman_stuff", - "genome_build": "GRCh38_hla_decoy_ebv", + "workflowName": "batman_stuff", + "genomeBuild": "GRCh38_hla_decoy_ebv", "inputs": [ { - "analysis_type": "sequencing_alignment", - "tumour_analysis_id": "00000000-0000-0000-0000-000000000000", - "normal_analysis_id": "00000000-0000-0000-0000-000000000000" + "analysisType": "sequencing_alignment", + "tumourAnalysisId": "00000000-0000-0000-0000-000000000000", + "normalAnalysisId": "00000000-0000-0000-0000-000000000000" } ] } -} +} \ No newline at end of file diff --git a/playground-data/example-payloads/chipseq_foldchange_bigwig_zscpyibaevspyxlkyaip.json b/playground-data/example-payloads/chipseq_foldchange_bigwig_zscpyibaevspyxlkyaip.json index 4b2e371a..71b2464f 100644 --- a/playground-data/example-payloads/chipseq_foldchange_bigwig_zscpyibaevspyxlkyaip.json +++ b/playground-data/example-payloads/chipseq_foldchange_bigwig_zscpyibaevspyxlkyaip.json @@ -1,4 +1,8 @@ { + "analysisType": { + "name": "playgroundSchema" + }, + "studyId": "OVPLG-01", "samples": [ { "submitterSampleId": "TEST_SPECIMEN_zscpyibaevspyxlkyaip_N1", @@ -17,175 +21,177 @@ } ], "donor": { - "submitter_donor_id": "TEST_DONOR_zscpyibaevspyxlkyaip", - "primary_site": ["Hematopoietic and reticuloendothelial systems"], - "vital_status": "Deceased", - "survival_time": 1520, - "cause_of_death": "Died of cancer", - "primary_diagnosis": [ + "submitterDonorId": "TEST_DONOR_zscpyibaevspyxlkyaip", + "primarySite": [ + "Hematopoietic and reticuloendothelial systems" + ], + "vitalStatus": "Deceased", + "survivalTime": 1520, + "causeOfDeath": "Died of cancer", + "primaryDiagnosis": [ { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_zscpyibaevspyxlkyaip_0", - "age_at_diagnosis": 9, - "cancer_type_code": "D72.3", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_zscpyibaevspyxlkyaip_0", + "ageAtDiagnosis": 9, + "cancerTypeCode": "D72.3", "laterality": "Midline", - "clinical_tumour_staging_system": "FIGO staging system", - "clinical_stage_group": "Stage IVB", - "lymph_nodes_examined_status": "Not applicable", - "performance_status": "Unknown", + "clinicalTumourStagingSystem": "FIGO staging system", + "clinicalStageGroup": "Stage IVB", + "lymphNodesExaminedStatus": "Not applicable", + "performanceStatus": "Unknown", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_zscpyibaevspyxlkyaip_0", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_zscpyibaevspyxlkyaip_0", + "treatmentType": [ "Surgery" ], - "treatment_intent": "Curative", - "treatment_start_interval": 26, - "treatment_duration": 36, - "response_to_treatment": "Complete response", + "treatmentIntent": "Curative", + "treatmentStartInterval": 26, + "treatmentDuration": 36, + "responseToTreatment": "Complete response", "surgery": [ { - "surgery_type": "Bypass Gastrojejunostomy", - "surgery_site": "C27.8", - "surgery_location": "Metastatic", - "residual_tumour_classification": "R0" + "surgeryType": "Bypass Gastrojejunostomy", + "surgerySite": "C27.8", + "surgeryLocation": "Metastatic", + "residualTumourClassification": "R0" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_zscpyibaevspyxlkyaip_0", - "interval_of_followup": 82, - "disease_status_at_followup": "Partial remission" + "submitterFollowUpId": "TEST_FOLLOW_UP_zscpyibaevspyxlkyaip_0", + "intervalOfFollowup": 82, + "diseaseStatusAtFollowup": "Partial remission" } ] }, { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_zscpyibaevspyxlkyaip_1", - "age_at_diagnosis": 10, - "cancer_type_code": "D30.8", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_zscpyibaevspyxlkyaip_1", + "ageAtDiagnosis": 10, + "cancerTypeCode": "D30.8", "laterality": "Unilateral, side not specified", - "clinical_tumour_staging_system": "Revised International staging system (RISS)", - "clinical_stage_group": "Stage III", - "lymph_nodes_examined_status": "Not applicable", - "performance_status": "Grade 4", + "clinicalTumourStagingSystem": "Revised International staging system (RISS)", + "clinicalStageGroup": "Stage III", + "lymphNodesExaminedStatus": "Not applicable", + "performanceStatus": "Grade 4", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_zscpyibaevspyxlkyaip_1", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_zscpyibaevspyxlkyaip_1", + "treatmentType": [ "Hormonal therapy", "Surgery", "Chemotherapy" ], - "treatment_intent": "Palliative", - "treatment_start_interval": 7, - "treatment_duration": 16, - "response_to_treatment": "Stable disease", - "hormone_therapy": [ + "treatmentIntent": "Palliative", + "treatmentStartInterval": 7, + "treatmentDuration": 16, + "responseToTreatment": "Stable disease", + "hormoneTherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 98, - "hormone_drug_dosage_units": "mg/kg" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 98, + "hormoneDrugDosageUnits": "mg/kg" } ], "surgery": [ { - "surgery_type": "Cholecystectomy", - "surgery_site": "C46.7", - "surgery_location": "Metastatic", - "residual_tumour_classification": "R2" + "surgeryType": "Cholecystectomy", + "surgerySite": "C46.7", + "surgeryLocation": "Metastatic", + "residualTumourClassification": "R2" } ], "chemotherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 29, - "chemotherapy_dosage_units": "IU/m2" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 29, + "chemotherapyDosageUnits": "IU/m2" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_zscpyibaevspyxlkyaip_1", - "interval_of_followup": 59, - "disease_status_at_followup": "Loco-regional progression" + "submitterFollowUpId": "TEST_FOLLOW_UP_zscpyibaevspyxlkyaip_1", + "intervalOfFollowup": 59, + "diseaseStatusAtFollowup": "Loco-regional progression" } ] } ], "comorbidity": [ { - "age_at_comorbidity_diagnosis": 42, - "comorbidity_type_code": "B07.48" + "ageAtComorbidityDiagnosis": 42, + "comorbidityTypeCode": "B07.48" }, { - "age_at_comorbidity_diagnosis": 83, - "comorbidity_type_code": "A66.7" + "ageAtComorbidityDiagnosis": 83, + "comorbidityTypeCode": "A66.7" }, { - "age_at_comorbidity_diagnosis": 70, - "comorbidity_type_code": "E15.40" + "ageAtComorbidityDiagnosis": 70, + "comorbidityTypeCode": "E15.40" } ] }, "specimen": { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_zscpyibaevspyxlkyaip_0", - "submitter_specimen_id": "TEST_SPECIMEN_zscpyibaevspyxlkyaip_N1", - "specimen_acquisition_interval": 88, - "specimen_anatomic_location": "C42.1", - "specimen_laterality": "Right" + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_zscpyibaevspyxlkyaip_0", + "submitterSpecimenId": "TEST_SPECIMEN_zscpyibaevspyxlkyaip_N1", + "specimenAcquisitionInterval": 88, + "specimenAnatomicLocation": "C42.1", + "specimenLaterality": "Right" }, "files": [ { "dataType": "peakCalling", - "fileName": "ENCFF140QLY.bigWig", + "fileName": "encfF140QLY.bigWig", "fileSize": 580725880, "fileMd5sum": "143909a2e46921589058701a1b46e341", "fileAccess": "controlled", "fileType": "BIGWIG", "info": { - "bigwig_measurement": "FoldChange", - "notes_for_mitchell": "hg38:1:42432049-45561097", + "bigwigMeasurement": "FoldChange", + "notesForMitchell": "hg38:1:42432049-45561097", "dataCategory": "ChIP-Seq Peak Calling" } } ], "collaborator": [ { - "contact_email": "batman@batman_inc.org", + "contactEmail": "batman@batman_inc.org", "name": "Richard Myers", "affiliation": "HudsonAlpha Institute for Biotechnology" } ], "experiment": { "platform": "ILLUMINA", - "experimental_strategy": "ChIP-Seq", - "chip_target": "ATF3", - "submitter_sequencing_experiment_id": "EXPERIMENT" + "experimentalStrategy": "ChIP-Seq", + "chipTarget": "ATF3", + "submitterSequencingExperimentId": "EXPERIMENT" }, "workflow": { - "workflow_name": "batman_stuff", - "genome_build": "GRCh38_hla_decoy_ebv", + "workflowName": "batman_stuff", + "genomeBuild": "GRCh38_hla_decoy_ebv", "inputs": [ { - "analysis_type": "sequencing_alignment", - "tumour_analysis_id": "00000000-0000-0000-0000-000000000000", - "normal_analysis_id": "00000000-0000-0000-0000-000000000000" + "analysisType": "sequencing_alignment", + "tumourAnalysisId": "00000000-0000-0000-0000-000000000000", + "normalAnalysisId": "00000000-0000-0000-0000-000000000000" } ] }, "archive": { - "SRA": [ + "sra": [ { - "GSE": "GSE230918" + "gse": "gse230918" } ], - "ENCODE": [ + "encode": [ { - "ENCF": "ENCFF140QLY" + "encf": "encfF140QLY" } ] }, @@ -193,4 +199,4 @@ "title": "An integrated encyclopedia of DNA elements in the human genome", "doi": "10.1038/nature11247" } -} +} \ No newline at end of file diff --git a/playground-data/example-payloads/chipseq_idr_bigbed_zscpyibaevspyxlkyaip.json b/playground-data/example-payloads/chipseq_idr_bigbed_zscpyibaevspyxlkyaip.json index c9ad6f7a..96660dc2 100644 --- a/playground-data/example-payloads/chipseq_idr_bigbed_zscpyibaevspyxlkyaip.json +++ b/playground-data/example-payloads/chipseq_idr_bigbed_zscpyibaevspyxlkyaip.json @@ -1,4 +1,8 @@ { + "analysisType": { + "name": "playgroundSchema" + }, + "studyId": "OVPLG-01", "samples": [ { "submitterSampleId": "TEST_SPECIMEN_zscpyibaevspyxlkyaip_N1", @@ -17,175 +21,177 @@ } ], "donor": { - "submitter_donor_id": "TEST_DONOR_zscpyibaevspyxlkyaip", - "primary_site": ["Hematopoietic and reticuloendothelial systems"], - "vital_status": "Deceased", - "survival_time": 1520, - "cause_of_death": "Died of cancer", - "primary_diagnosis": [ + "submitterDonorId": "TEST_DONOR_zscpyibaevspyxlkyaip", + "primarySite": [ + "Hematopoietic and reticuloendothelial systems" + ], + "vitalStatus": "Deceased", + "survivalTime": 1520, + "causeOfDeath": "Died of cancer", + "primaryDiagnosis": [ { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_zscpyibaevspyxlkyaip_0", - "age_at_diagnosis": 9, - "cancer_type_code": "D72.3", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_zscpyibaevspyxlkyaip_0", + "ageAtDiagnosis": 9, + "cancerTypeCode": "D72.3", "laterality": "Midline", - "clinical_tumour_staging_system": "FIGO staging system", - "clinical_stage_group": "Stage IVB", - "lymph_nodes_examined_status": "Not applicable", - "performance_status": "Unknown", + "clinicalTumourStagingSystem": "FIGO staging system", + "clinicalStageGroup": "Stage IVB", + "lymphNodesExaminedStatus": "Not applicable", + "performanceStatus": "Unknown", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_zscpyibaevspyxlkyaip_0", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_zscpyibaevspyxlkyaip_0", + "treatmentType": [ "Surgery" ], - "treatment_intent": "Curative", - "treatment_start_interval": 26, - "treatment_duration": 36, - "response_to_treatment": "Complete response", + "treatmentIntent": "Curative", + "treatmentStartInterval": 26, + "treatmentDuration": 36, + "responseToTreatment": "Complete response", "surgery": [ { - "surgery_type": "Bypass Gastrojejunostomy", - "surgery_site": "C27.8", - "surgery_location": "Metastatic", - "residual_tumour_classification": "R0" + "surgeryType": "Bypass Gastrojejunostomy", + "surgerySite": "C27.8", + "surgeryLocation": "Metastatic", + "residualTumourClassification": "R0" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_zscpyibaevspyxlkyaip_0", - "interval_of_followup": 82, - "disease_status_at_followup": "Partial remission" + "submitterFollowUpId": "TEST_FOLLOW_UP_zscpyibaevspyxlkyaip_0", + "intervalOfFollowup": 82, + "diseaseStatusAtFollowup": "Partial remission" } ] }, { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_zscpyibaevspyxlkyaip_1", - "age_at_diagnosis": 10, - "cancer_type_code": "D30.8", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_zscpyibaevspyxlkyaip_1", + "ageAtDiagnosis": 10, + "cancerTypeCode": "D30.8", "laterality": "Unilateral, side not specified", - "clinical_tumour_staging_system": "Revised International staging system (RISS)", - "clinical_stage_group": "Stage III", - "lymph_nodes_examined_status": "Not applicable", - "performance_status": "Grade 4", + "clinicalTumourStagingSystem": "Revised International staging system (RISS)", + "clinicalStageGroup": "Stage III", + "lymphNodesExaminedStatus": "Not applicable", + "performanceStatus": "Grade 4", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_zscpyibaevspyxlkyaip_1", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_zscpyibaevspyxlkyaip_1", + "treatmentType": [ "Hormonal therapy", "Surgery", "Chemotherapy" ], - "treatment_intent": "Palliative", - "treatment_start_interval": 7, - "treatment_duration": 16, - "response_to_treatment": "Stable disease", - "hormone_therapy": [ + "treatmentIntent": "Palliative", + "treatmentStartInterval": 7, + "treatmentDuration": 16, + "responseToTreatment": "Stable disease", + "hormoneTherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 98, - "hormone_drug_dosage_units": "mg/kg" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 98, + "hormoneDrugDosageUnits": "mg/kg" } ], "surgery": [ { - "surgery_type": "Cholecystectomy", - "surgery_site": "C46.7", - "surgery_location": "Metastatic", - "residual_tumour_classification": "R2" + "surgeryType": "Cholecystectomy", + "surgerySite": "C46.7", + "surgeryLocation": "Metastatic", + "residualTumourClassification": "R2" } ], "chemotherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 29, - "chemotherapy_dosage_units": "IU/m2" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 29, + "chemotherapyDosageUnits": "IU/m2" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_zscpyibaevspyxlkyaip_1", - "interval_of_followup": 59, - "disease_status_at_followup": "Loco-regional progression" + "submitterFollowUpId": "TEST_FOLLOW_UP_zscpyibaevspyxlkyaip_1", + "intervalOfFollowup": 59, + "diseaseStatusAtFollowup": "Loco-regional progression" } ] } ], "comorbidity": [ { - "age_at_comorbidity_diagnosis": 42, - "comorbidity_type_code": "B07.48" + "ageAtComorbidityDiagnosis": 42, + "comorbidityTypeCode": "B07.48" }, { - "age_at_comorbidity_diagnosis": 83, - "comorbidity_type_code": "A66.7" + "ageAtComorbidityDiagnosis": 83, + "comorbidityTypeCode": "A66.7" }, { - "age_at_comorbidity_diagnosis": 70, - "comorbidity_type_code": "E15.40" + "ageAtComorbidityDiagnosis": 70, + "comorbidityTypeCode": "E15.40" } ] }, "specimen": { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_zscpyibaevspyxlkyaip_0", - "submitter_specimen_id": "TEST_SPECIMEN_zscpyibaevspyxlkyaip_N1", - "specimen_acquisition_interval": 88, - "specimen_anatomic_location": "C42.1", - "specimen_laterality": "Right" + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_zscpyibaevspyxlkyaip_0", + "submitterSpecimenId": "TEST_SPECIMEN_zscpyibaevspyxlkyaip_N1", + "specimenAcquisitionInterval": 88, + "specimenAnatomicLocation": "C42.1", + "specimenLaterality": "Right" }, "files": [ { "dataType": "peakCalling", - "fileName": "ENCFF772OAD.bigBed", + "fileName": "encfF772OAD.bigBed", "fileSize": 163717, "fileMd5sum": "05b60bdb392ba3ef0bdbfcfa5a0c4435", "fileAccess": "controlled", "fileType": "BIGBED", "info": { - "bigbed_feature_highlight": "IDR enriched regions", - "notes_for_mitchell": "hg38:1:42432049-45561097", + "bigbedFeatureHighlight": "IDR enriched regions", + "notesForMitchell": "hg38:1:42432049-45561097", "dataCategory": "ChIP-Seq Peak Calling" } } ], "collaborator": [ { - "contact_email": "batman@batman_inc.org", + "contactEmail": "batman@batman_inc.org", "name": "Richard Myers", "affiliation": "HudsonAlpha Institute for Biotechnology" } ], "experiment": { "platform": "ILLUMINA", - "experimental_strategy": "ChIP-Seq", - "chip_target": "ATF3", - "submitter_sequencing_experiment_id": "EXPERIMENT" + "experimentalStrategy": "ChIP-Seq", + "chipTarget": "ATF3", + "submitterSequencingExperimentId": "EXPERIMENT" }, "workflow": { - "workflow_name": "batman_stuff", - "genome_build": "GRCh38_hla_decoy_ebv", + "workflowName": "batman_stuff", + "genomeBuild": "GRCh38_hla_decoy_ebv", "inputs": [ { - "analysis_type": "sequencing_alignment", - "tumour_analysis_id": "00000000-0000-0000-0000-000000000000", - "normal_analysis_id": "00000000-0000-0000-0000-000000000000" + "analysisType": "sequencing_alignment", + "tumourAnalysisId": "00000000-0000-0000-0000-000000000000", + "normalAnalysisId": "00000000-0000-0000-0000-000000000000" } ] }, "archive": { - "SRA": [ + "sra": [ { - "GSE": "GSE230918" + "gse": "gse230918" } ], - "ENCODE": [ + "encode": [ { - "ENCF": "ENCFF140QLY" + "encf": "encfF140QLY" } ] }, @@ -193,4 +199,4 @@ "title": "An integrated encyclopedia of DNA elements in the human genome", "doi": "10.1038/nature11247" } -} +} \ No newline at end of file diff --git a/playground-data/example-payloads/chipseq_pval_bigwig_zscpyibaevspyxlkyaip.json b/playground-data/example-payloads/chipseq_pval_bigwig_zscpyibaevspyxlkyaip.json index 7083d8a4..e2135b42 100644 --- a/playground-data/example-payloads/chipseq_pval_bigwig_zscpyibaevspyxlkyaip.json +++ b/playground-data/example-payloads/chipseq_pval_bigwig_zscpyibaevspyxlkyaip.json @@ -1,4 +1,8 @@ { + "analysisType": { + "name": "playgroundSchema" + }, + "studyId": "OVPLG-01", "samples": [ { "submitterSampleId": "TEST_SPECIMEN_zscpyibaevspyxlkyaip_N1", @@ -17,175 +21,177 @@ } ], "donor": { - "submitter_donor_id": "TEST_DONOR_zscpyibaevspyxlkyaip", - "primary_site": ["Hematopoietic and reticuloendothelial systems"], - "vital_status": "Deceased", - "survival_time": 1520, - "cause_of_death": "Died of cancer", - "primary_diagnosis": [ + "submitterDonorId": "TEST_DONOR_zscpyibaevspyxlkyaip", + "primarySite": [ + "Hematopoietic and reticuloendothelial systems" + ], + "vitalStatus": "Deceased", + "survivalTime": 1520, + "causeOfDeath": "Died of cancer", + "primaryDiagnosis": [ { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_zscpyibaevspyxlkyaip_0", - "age_at_diagnosis": 9, - "cancer_type_code": "D72.3", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_zscpyibaevspyxlkyaip_0", + "ageAtDiagnosis": 9, + "cancerTypeCode": "D72.3", "laterality": "Midline", - "clinical_tumour_staging_system": "FIGO staging system", - "clinical_stage_group": "Stage IVB", - "lymph_nodes_examined_status": "Not applicable", - "performance_status": "Unknown", + "clinicalTumourStagingSystem": "FIGO staging system", + "clinicalStageGroup": "Stage IVB", + "lymphNodesExaminedStatus": "Not applicable", + "performanceStatus": "Unknown", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_zscpyibaevspyxlkyaip_0", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_zscpyibaevspyxlkyaip_0", + "treatmentType": [ "Surgery" ], - "treatment_intent": "Curative", - "treatment_start_interval": 26, - "treatment_duration": 36, - "response_to_treatment": "Complete response", + "treatmentIntent": "Curative", + "treatmentStartInterval": 26, + "treatmentDuration": 36, + "responseToTreatment": "Complete response", "surgery": [ { - "surgery_type": "Bypass Gastrojejunostomy", - "surgery_site": "C27.8", - "surgery_location": "Metastatic", - "residual_tumour_classification": "R0" + "surgeryType": "Bypass Gastrojejunostomy", + "surgerySite": "C27.8", + "surgeryLocation": "Metastatic", + "residualTumourClassification": "R0" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_zscpyibaevspyxlkyaip_0", - "interval_of_followup": 82, - "disease_status_at_followup": "Partial remission" + "submitterFollowUpId": "TEST_FOLLOW_UP_zscpyibaevspyxlkyaip_0", + "intervalOfFollowup": 82, + "diseaseStatusAtFollowup": "Partial remission" } ] }, { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_zscpyibaevspyxlkyaip_1", - "age_at_diagnosis": 10, - "cancer_type_code": "D30.8", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_zscpyibaevspyxlkyaip_1", + "ageAtDiagnosis": 10, + "cancerTypeCode": "D30.8", "laterality": "Unilateral, side not specified", - "clinical_tumour_staging_system": "Revised International staging system (RISS)", - "clinical_stage_group": "Stage III", - "lymph_nodes_examined_status": "Not applicable", - "performance_status": "Grade 4", + "clinicalTumourStagingSystem": "Revised International staging system (RISS)", + "clinicalStageGroup": "Stage III", + "lymphNodesExaminedStatus": "Not applicable", + "performanceStatus": "Grade 4", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_zscpyibaevspyxlkyaip_1", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_zscpyibaevspyxlkyaip_1", + "treatmentType": [ "Hormonal therapy", "Surgery", "Chemotherapy" ], - "treatment_intent": "Palliative", - "treatment_start_interval": 7, - "treatment_duration": 16, - "response_to_treatment": "Stable disease", - "hormone_therapy": [ + "treatmentIntent": "Palliative", + "treatmentStartInterval": 7, + "treatmentDuration": 16, + "responseToTreatment": "Stable disease", + "hormoneTherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 98, - "hormone_drug_dosage_units": "mg/kg" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 98, + "hormoneDrugDosageUnits": "mg/kg" } ], "surgery": [ { - "surgery_type": "Cholecystectomy", - "surgery_site": "C46.7", - "surgery_location": "Metastatic", - "residual_tumour_classification": "R2" + "surgeryType": "Cholecystectomy", + "surgerySite": "C46.7", + "surgeryLocation": "Metastatic", + "residualTumourClassification": "R2" } ], "chemotherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 29, - "chemotherapy_dosage_units": "IU/m2" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 29, + "chemotherapyDosageUnits": "IU/m2" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_zscpyibaevspyxlkyaip_1", - "interval_of_followup": 59, - "disease_status_at_followup": "Loco-regional progression" + "submitterFollowUpId": "TEST_FOLLOW_UP_zscpyibaevspyxlkyaip_1", + "intervalOfFollowup": 59, + "diseaseStatusAtFollowup": "Loco-regional progression" } ] } ], "comorbidity": [ { - "age_at_comorbidity_diagnosis": 42, - "comorbidity_type_code": "B07.48" + "ageAtComorbidityDiagnosis": 42, + "comorbidityTypeCode": "B07.48" }, { - "age_at_comorbidity_diagnosis": 83, - "comorbidity_type_code": "A66.7" + "ageAtComorbidityDiagnosis": 83, + "comorbidityTypeCode": "A66.7" }, { - "age_at_comorbidity_diagnosis": 70, - "comorbidity_type_code": "E15.40" + "ageAtComorbidityDiagnosis": 70, + "comorbidityTypeCode": "E15.40" } ] }, "specimen": { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_zscpyibaevspyxlkyaip_0", - "submitter_specimen_id": "TEST_SPECIMEN_zscpyibaevspyxlkyaip_N1", - "specimen_acquisition_interval": 88, - "specimen_anatomic_location": "C42.1", - "specimen_laterality": "Right" + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_zscpyibaevspyxlkyaip_0", + "submitterSpecimenId": "TEST_SPECIMEN_zscpyibaevspyxlkyaip_N1", + "specimenAcquisitionInterval": 88, + "specimenAnatomicLocation": "C42.1", + "specimenLaterality": "Right" }, "files": [ { "dataType": "peakCalling", - "fileName": "ENCFF561SGX.bigWig", + "fileName": "encfF561SGX.bigWig", "fileSize": 1188429149, "fileMd5sum": "cce20c1b3232cba83560b9c2e4d504f8", "fileAccess": "controlled", "fileType": "BIGWIG", "info": { - "bigwig_measurement": "P-value", - "notes_for_mitchell": "hg38:1:25623191-58795484", + "bigwigMeasurement": "P-value", + "notesForMitchell": "hg38:1:25623191-58795484", "dataCategory": "ChIP-Seq Peak Calling" } } ], "collaborator": [ { - "contact_email": "batman@batman_inc.org", + "contactEmail": "batman@batman_inc.org", "name": "Richard Myers", "affiliation": "HudsonAlpha Institute for Biotechnology" } ], "experiment": { "platform": "ILLUMINA", - "experimental_strategy": "ChIP-Seq", - "chip_target": "ATF3", - "submitter_sequencing_experiment_id": "EXPERIMENT" + "experimentalStrategy": "ChIP-Seq", + "chipTarget": "ATF3", + "submitterSequencingExperimentId": "EXPERIMENT" }, "workflow": { - "workflow_name": "batman_stuff", - "genome_build": "GRCh38_hla_decoy_ebv", + "workflowName": "batman_stuff", + "genomeBuild": "GRCh38_hla_decoy_ebv", "inputs": [ { - "analysis_type": "sequencing_alignment", - "tumour_analysis_id": "00000000-0000-0000-0000-000000000000", - "normal_analysis_id": "00000000-0000-0000-0000-000000000000" + "analysisType": "sequencing_alignment", + "tumourAnalysisId": "00000000-0000-0000-0000-000000000000", + "normalAnalysisId": "00000000-0000-0000-0000-000000000000" } ] }, "archive": { - "SRA": [ + "sra": [ { - "GSE": "GSE230918" + "gse": "gse230918" } ], - "ENCODE": [ + "encode": [ { - "ENCF": "ENCFF140QLY" + "encf": "encfF140QLY" } ] }, @@ -193,4 +199,4 @@ "title": "An integrated encyclopedia of DNA elements in the human genome", "doi": "10.1038/nature11247" } -} +} \ No newline at end of file diff --git a/playground-data/example-payloads/hic_hic_eszycidpyopumzgdpamn.json b/playground-data/example-payloads/hic_hic_eszycidpyopumzgdpamn.json index 938e3f29..ff1ae047 100644 --- a/playground-data/example-payloads/hic_hic_eszycidpyopumzgdpamn.json +++ b/playground-data/example-payloads/hic_hic_eszycidpyopumzgdpamn.json @@ -1,4 +1,8 @@ { + "analysisType": { + "name": "playgroundSchema" + }, + "studyId": "OVPLG-01", "samples": [ { "submitterSampleId": "TEST_SPECIMEN_eszycidpyopumzgdpamn_N1", @@ -17,95 +21,97 @@ } ], "donor": { - "submitter_donor_id": "TEST_DONOR_eszycidpyopumzgdpamn", - "primary_site": ["Nasal cavity and middle ear"], - "vital_status": "Alive", - "survival_time": null, - "cause_of_death": null, - "primary_diagnosis": [ + "submitterDonorId": "TEST_DONOR_eszycidpyopumzgdpamn", + "primarySite": [ + "Nasal cavity and middle ear" + ], + "vitalStatus": "Alive", + "survivalTime": null, + "causeOfDeath": null, + "primaryDiagnosis": [ { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_eszycidpyopumzgdpamn_0", - "age_at_diagnosis": 75, - "cancer_type_code": "D35.1", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_eszycidpyopumzgdpamn_0", + "ageAtDiagnosis": 75, + "cancerTypeCode": "D35.1", "laterality": "Right", - "clinical_tumour_staging_system": "FIGO staging system", - "clinical_stage_group": "Stage IA2", - "lymph_nodes_examined_status": "Cannot be determined", - "performance_status": "Grade 2", + "clinicalTumourStagingSystem": "FIGO staging system", + "clinicalStageGroup": "Stage IA2", + "lymphNodesExaminedStatus": "Cannot be determined", + "performanceStatus": "Grade 2", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_eszycidpyopumzgdpamn_0", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_eszycidpyopumzgdpamn_0", + "treatmentType": [ "Radiation therapy", "Hormonal therapy" ], - "treatment_intent": "Curative", - "treatment_start_interval": 37, - "treatment_duration": 3, - "response_to_treatment": "NED", + "treatmentIntent": "Curative", + "treatmentStartInterval": 37, + "treatmentDuration": 3, + "responseToTreatment": "NED", "radiation": [ { - "radiation_therapy_modality": "Electron", - "radiation_therapy_type": "External", - "anatomical_site_irradiated": "Pelvis", - "radiation_therapy_dosage": 40, - "radiation_therapy_fractions": 24 + "radiationTherapyModality": "Electron", + "radiationTherapyType": "External", + "anatomicalSiteIrradiated": "Pelvis", + "radiationTherapyDosage": 40, + "radiationTherapyFractions": 24 } ], - "hormone_therapy": [ + "hormoneTherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 44, - "hormone_drug_dosage_units": "mg/m2" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 44, + "hormoneDrugDosageUnits": "mg/m2" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_eszycidpyopumzgdpamn_0", - "interval_of_followup": 84, - "disease_status_at_followup": "Complete remission" + "submitterFollowUpId": "TEST_FOLLOW_UP_eszycidpyopumzgdpamn_0", + "intervalOfFollowup": 84, + "diseaseStatusAtFollowup": "Complete remission" } ] } ], "comorbidity": [ { - "age_at_comorbidity_diagnosis": 97, - "comorbidity_type_code": "E02.58" + "ageAtComorbidityDiagnosis": 97, + "comorbidityTypeCode": "E02.58" }, { - "age_at_comorbidity_diagnosis": 26, - "comorbidity_type_code": "B07.38" + "ageAtComorbidityDiagnosis": 26, + "comorbidityTypeCode": "B07.38" } ] }, "specimen": { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_eszycidpyopumzgdpamn_0", - "submitter_specimen_id": "TEST_SPECIMEN_eszycidpyopumzgdpamn_N1", - "specimen_acquisition_interval": 0, - "specimen_anatomic_location": "C42", - "specimen_laterality": "Unknown", - "tumour_histological_type": "8578/23", - "pathological_tumour_staging_system": "Binet staging system", - "pathological_stage_group": "Stage C", - "tumour_grading_system": "Scarff-Bloom-Richardson grading system", - "tumour_grade": "G3", - "percent_tumour_cells": 40, - "reference_pathology_confirmed": "Yes" + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_eszycidpyopumzgdpamn_0", + "submitterSpecimenId": "TEST_SPECIMEN_eszycidpyopumzgdpamn_N1", + "specimenAcquisitionInterval": 0, + "specimenAnatomicLocation": "C42", + "specimenLaterality": "Unknown", + "tumourHistologicalType": "8578/23", + "pathologicalTumourStagingSystem": "Binet staging system", + "pathologicalStageGroup": "Stage C", + "tumourGradingSystem": "Scarff-Bloom-Richardson grading system", + "tumourGrade": "G3", + "percentTumourCells": 40, + "referencePathologyConfirmed": "Yes" }, "files": [ { "dataType": "HicAnalysisPostAlignment", - "fileName": "GSE174533_1-C11-CB1.2-C11-CB2.merge.hic", + "fileName": "gse174533_1-C11-CB1.2-C11-CB2.merge.hic", "fileSize": 1251245702, "fileMd5sum": "933faf4efa8f0c267e2187fa2205c4dc", "fileAccess": "controlled", "fileType": "HIC", "info": { - "hic_resolution": [ + "hicResolution": [ "5kb", "10kb", "25kb", @@ -113,39 +119,39 @@ "100kb", "250kb" ], - "hic_normalization_method": "KR", - "notes_for_mitchell": "hg38:20:22840771-31212931", + "hicNormalizationMethod": "KR", + "notesForMitchell": "hg38:20:22840771-31212931", "dataCategory": "Hi-C profiling" } } ], "collaborator": [ { - "contact_email": "batman@batman_inc.org", + "contactEmail": "batman@batman_inc.org", "name": "Sergei Doulatov", "affiliation": "Washington University" } ], "experiment": { "platform": "ILLUMINA", - "experimental_strategy": "Hi-C", - "submitter_sequencing_experiment_id": "EXPERIMENT" + "experimentalStrategy": "Hi-C", + "submitterSequencingExperimentId": "EXPERIMENT" }, "workflow": { - "workflow_name": "batman_stuff", - "genome_build": "GRCh38_hla_decoy_ebv", + "workflowName": "batman_stuff", + "genomeBuild": "GRCh38_hla_decoy_ebv", "inputs": [ { - "analysis_type": "sequencing_alignment", - "tumour_analysis_id": "00000000-0000-0000-0000-000000000000", - "normal_analysis_id": "00000000-0000-0000-0000-000000000000" + "analysisType": "sequencing_alignment", + "tumourAnalysisId": "00000000-0000-0000-0000-000000000000", + "normalAnalysisId": "00000000-0000-0000-0000-000000000000" } ] }, "archive": { - "SRA": [ + "sra": [ { - "GSE": "GSE174533" + "gse": "gse174533" } ] }, @@ -153,4 +159,4 @@ "title": "Lamin B1 deletion in myeloid neoplasms causes nuclear anomaly and altered hematopoietic stem cell function", "doi": "10.1016/j.stem.2022.02.010" } -} +} \ No newline at end of file diff --git a/playground-data/example-payloads/hic_insulation_bigwig_eszycidpyopumzgdpamn.json b/playground-data/example-payloads/hic_insulation_bigwig_eszycidpyopumzgdpamn.json index 6eae33c8..4bad7c09 100644 --- a/playground-data/example-payloads/hic_insulation_bigwig_eszycidpyopumzgdpamn.json +++ b/playground-data/example-payloads/hic_insulation_bigwig_eszycidpyopumzgdpamn.json @@ -1,4 +1,8 @@ { + "analysisType": { + "name": "playgroundSchema" + }, + "studyId": "OVPLG-01", "samples": [ { "submitterSampleId": "TEST_SPECIMEN_eszycidpyopumzgdpamn_N1", @@ -17,132 +21,134 @@ } ], "donor": { - "submitter_donor_id": "TEST_DONOR_eszycidpyopumzgdpamn", - "primary_site": ["Hematopoietic and reticuloendothelial systems"], - "vital_status": "Alive", - "survival_time": null, - "cause_of_death": null, - "primary_diagnosis": [ + "submitterDonorId": "TEST_DONOR_eszycidpyopumzgdpamn", + "primarySite": [ + "Hematopoietic and reticuloendothelial systems" + ], + "vitalStatus": "Alive", + "survivalTime": null, + "causeOfDeath": null, + "primaryDiagnosis": [ { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_eszycidpyopumzgdpamn_0", - "age_at_diagnosis": 75, - "cancer_type_code": "D35.1", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_eszycidpyopumzgdpamn_0", + "ageAtDiagnosis": 75, + "cancerTypeCode": "D35.1", "laterality": "Right", - "clinical_tumour_staging_system": "FIGO staging system", - "clinical_stage_group": "Stage IA2", - "lymph_nodes_examined_status": "Cannot be determined", - "performance_status": "Grade 2", + "clinicalTumourStagingSystem": "FIGO staging system", + "clinicalStageGroup": "Stage IA2", + "lymphNodesExaminedStatus": "Cannot be determined", + "performanceStatus": "Grade 2", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_eszycidpyopumzgdpamn_0", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_eszycidpyopumzgdpamn_0", + "treatmentType": [ "Radiation therapy", "Hormonal therapy" ], - "treatment_intent": "Curative", - "treatment_start_interval": 37, - "treatment_duration": 3, - "response_to_treatment": "NED", + "treatmentIntent": "Curative", + "treatmentStartInterval": 37, + "treatmentDuration": 3, + "responseToTreatment": "NED", "radiation": [ { - "radiation_therapy_modality": "Electron", - "radiation_therapy_type": "External", - "anatomical_site_irradiated": "Pelvis", - "radiation_therapy_dosage": 40, - "radiation_therapy_fractions": 24 + "radiationTherapyModality": "Electron", + "radiationTherapyType": "External", + "anatomicalSiteIrradiated": "Pelvis", + "radiationTherapyDosage": 40, + "radiationTherapyFractions": 24 } ], - "hormone_therapy": [ + "hormoneTherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 44, - "hormone_drug_dosage_units": "mg/m2" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 44, + "hormoneDrugDosageUnits": "mg/m2" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_eszycidpyopumzgdpamn_0", - "interval_of_followup": 84, - "disease_status_at_followup": "Complete remission" + "submitterFollowUpId": "TEST_FOLLOW_UP_eszycidpyopumzgdpamn_0", + "intervalOfFollowup": 84, + "diseaseStatusAtFollowup": "Complete remission" } ] } ], "comorbidity": [ { - "age_at_comorbidity_diagnosis": 97, - "comorbidity_type_code": "E02.58" + "ageAtComorbidityDiagnosis": 97, + "comorbidityTypeCode": "E02.58" }, { - "age_at_comorbidity_diagnosis": 26, - "comorbidity_type_code": "B07.38" + "ageAtComorbidityDiagnosis": 26, + "comorbidityTypeCode": "B07.38" } ] }, "specimen": { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_eszycidpyopumzgdpamn_0", - "submitter_specimen_id": "TEST_SPECIMEN_eszycidpyopumzgdpamn_N1", - "specimen_acquisition_interval": 0, - "specimen_anatomic_location": "C42.1", - "specimen_laterality": "Unknown", - "tumour_histological_type": "8578/23", - "pathological_tumour_staging_system": "Binet staging system", - "pathological_stage_group": "Stage C", - "tumour_grading_system": "Scarff-Bloom-Richardson grading system", - "tumour_grade": "G3", - "percent_tumour_cells": 40, - "reference_pathology_confirmed": "Yes" + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_eszycidpyopumzgdpamn_0", + "submitterSpecimenId": "TEST_SPECIMEN_eszycidpyopumzgdpamn_N1", + "specimenAcquisitionInterval": 0, + "specimenAnatomicLocation": "C42.1", + "specimenLaterality": "Unknown", + "tumourHistologicalType": "8578/23", + "pathologicalTumourStagingSystem": "Binet staging system", + "pathologicalStageGroup": "Stage C", + "tumourGradingSystem": "Scarff-Bloom-Richardson grading system", + "tumourGrade": "G3", + "percentTumourCells": 40, + "referencePathologyConfirmed": "Yes" }, "files": [ { "dataType": "HicAnalysisPostAlignment", - "fileName": "GSE174533_1-C11-CB1.2-C11-CB2.insulationScore.bw", + "fileName": "gse174533_1-C11-CB1.2-C11-CB2.insulationScore.bw", "fileSize": 2950606, "fileMd5sum": "b6b462a91f6765b8149fbada91d82fe6", "fileAccess": "controlled", "fileType": "BIGWIG", "info": { - "hic_resolution": [ + "hicResolution": [ "10kb" ], - "hic_normalization_method": "KR", - "correct_for_multiple_testing": "FDR", - "bigwig_measurement": "insulation_score", - "notes_for_mitchell": "hg38:1:144128680-178932610", + "hicNormalizationMethod": "KR", + "correctForMultipleTesting": "FDR", + "bigwigMeasurement": "insulation_score", + "notesForMitchell": "hg38:1:144128680-178932610", "dataCategory": "Hi-C profiling" } } ], "collaborator": [ { - "contact_email": "batman@batman_inc.org", + "contactEmail": "batman@batman_inc.org", "name": "Sergei Doulatov", "affiliation": "Washington University" } ], "experiment": { "platform": "ILLUMINA", - "experimental_strategy": "Hi-C", - "submitter_sequencing_experiment_id": "EXPERIMENT" + "experimentalStrategy": "Hi-C", + "submitterSequencingExperimentId": "EXPERIMENT" }, "workflow": { - "workflow_name": "batman_stuff", - "genome_build": "GRCh38_hla_decoy_ebv", + "workflowName": "batman_stuff", + "genomeBuild": "GRCh38_hla_decoy_ebv", "inputs": [ { - "analysis_type": "sequencing_alignment", - "tumour_analysis_id": "00000000-0000-0000-0000-000000000000", - "normal_analysis_id": "00000000-0000-0000-0000-000000000000" + "analysisType": "sequencing_alignment", + "tumourAnalysisId": "00000000-0000-0000-0000-000000000000", + "normalAnalysisId": "00000000-0000-0000-0000-000000000000" } ] }, "archive": { - "SRA": [ + "sra": [ { - "GSE": "GSE174533" + "gse": "gse174533" } ] }, @@ -150,4 +156,4 @@ "title": "Lamin B1 deletion in myeloid neoplasms causes nuclear anomaly and altered hematopoietic stem cell function", "doi": "10.1016/j.stem.2022.02.010" } -} +} \ No newline at end of file diff --git a/playground-data/example-payloads/hic_pc1_bigwig_eszycidpyopumzgdpamn.json b/playground-data/example-payloads/hic_pc1_bigwig_eszycidpyopumzgdpamn.json index 06b3f0ba..a614f3f7 100644 --- a/playground-data/example-payloads/hic_pc1_bigwig_eszycidpyopumzgdpamn.json +++ b/playground-data/example-payloads/hic_pc1_bigwig_eszycidpyopumzgdpamn.json @@ -1,4 +1,8 @@ { + "analysisType": { + "name": "playgroundSchema" + }, + "studyId": "OVPLG-01", "samples": [ { "submitterSampleId": "TEST_SPECIMEN_eszycidpyopumzgdpamn_N1", @@ -17,132 +21,134 @@ } ], "donor": { - "submitter_donor_id": "TEST_DONOR_eszycidpyopumzgdpamn", - "primary_site": ["Hematopoietic and reticuloendothelial systems"], - "vital_status": "Alive", - "survival_time": null, - "cause_of_death": null, - "primary_diagnosis": [ + "submitterDonorId": "TEST_DONOR_eszycidpyopumzgdpamn", + "primarySite": [ + "Hematopoietic and reticuloendothelial systems" + ], + "vitalStatus": "Alive", + "survivalTime": null, + "causeOfDeath": null, + "primaryDiagnosis": [ { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_eszycidpyopumzgdpamn_0", - "age_at_diagnosis": 75, - "cancer_type_code": "D35.1", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_eszycidpyopumzgdpamn_0", + "ageAtDiagnosis": 75, + "cancerTypeCode": "D35.1", "laterality": "Right", - "clinical_tumour_staging_system": "FIGO staging system", - "clinical_stage_group": "Stage IA2", - "lymph_nodes_examined_status": "Cannot be determined", - "performance_status": "Grade 2", + "clinicalTumourStagingSystem": "FIGO staging system", + "clinicalStageGroup": "Stage IA2", + "lymphNodesExaminedStatus": "Cannot be determined", + "performanceStatus": "Grade 2", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_eszycidpyopumzgdpamn_0", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_eszycidpyopumzgdpamn_0", + "treatmentType": [ "Radiation therapy", "Hormonal therapy" ], - "treatment_intent": "Curative", - "treatment_start_interval": 37, - "treatment_duration": 3, - "response_to_treatment": "NED", + "treatmentIntent": "Curative", + "treatmentStartInterval": 37, + "treatmentDuration": 3, + "responseToTreatment": "NED", "radiation": [ { - "radiation_therapy_modality": "Electron", - "radiation_therapy_type": "External", - "anatomical_site_irradiated": "Pelvis", - "radiation_therapy_dosage": 40, - "radiation_therapy_fractions": 24 + "radiationTherapyModality": "Electron", + "radiationTherapyType": "External", + "anatomicalSiteIrradiated": "Pelvis", + "radiationTherapyDosage": 40, + "radiationTherapyFractions": 24 } ], - "hormone_therapy": [ + "hormoneTherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 44, - "hormone_drug_dosage_units": "mg/m2" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 44, + "hormoneDrugDosageUnits": "mg/m2" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_eszycidpyopumzgdpamn_0", - "interval_of_followup": 84, - "disease_status_at_followup": "Complete remission" + "submitterFollowUpId": "TEST_FOLLOW_UP_eszycidpyopumzgdpamn_0", + "intervalOfFollowup": 84, + "diseaseStatusAtFollowup": "Complete remission" } ] } ], "comorbidity": [ { - "age_at_comorbidity_diagnosis": 97, - "comorbidity_type_code": "E02.58" + "ageAtComorbidityDiagnosis": 97, + "comorbidityTypeCode": "E02.58" }, { - "age_at_comorbidity_diagnosis": 26, - "comorbidity_type_code": "B07.38" + "ageAtComorbidityDiagnosis": 26, + "comorbidityTypeCode": "B07.38" } ] }, "specimen": { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_eszycidpyopumzgdpamn_0", - "submitter_specimen_id": "TEST_SPECIMEN_eszycidpyopumzgdpamn_N1", - "specimen_acquisition_interval": 0, - "specimen_anatomic_location": "C42.1", - "specimen_laterality": "Unknown", - "tumour_histological_type": "8578/23", - "pathological_tumour_staging_system": "Binet staging system", - "pathological_stage_group": "Stage C", - "tumour_grading_system": "Scarff-Bloom-Richardson grading system", - "tumour_grade": "G3", - "percent_tumour_cells": 40, - "reference_pathology_confirmed": "Yes" + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_eszycidpyopumzgdpamn_0", + "submitterSpecimenId": "TEST_SPECIMEN_eszycidpyopumzgdpamn_N1", + "specimenAcquisitionInterval": 0, + "specimenAnatomicLocation": "C42.1", + "specimenLaterality": "Unknown", + "tumourHistologicalType": "8578/23", + "pathologicalTumourStagingSystem": "Binet staging system", + "pathologicalStageGroup": "Stage C", + "tumourGradingSystem": "Scarff-Bloom-Richardson grading system", + "tumourGrade": "G3", + "percentTumourCells": 40, + "referencePathologyConfirmed": "Yes" }, "files": [ { "dataType": "HicAnalysisPostAlignment", - "fileName": "GSE174533_11-P53-15-d23.PC1.bw", + "fileName": "gse174533_11-P53-15-d23.PC1.bw", "fileSize": 1877046, "fileMd5sum": "42c639c3472d1573c25a674da2ff9c61", "fileAccess": "controlled", "fileType": "BIGWIG", "info": { - "hic_resolution": [ + "hicResolution": [ "10kb" ], - "hic_normalization_method": "KR", - "correct_for_multiple_testing": "FDR", - "bigwig_measurement": "Principle Component 1", - "notes_for_mitchell": "hg38:1:144128680-178932610", + "hicNormalizationMethod": "KR", + "correctForMultipleTesting": "FDR", + "bigwigMeasurement": "Principle Component 1", + "notesForMitchell": "hg38:1:144128680-178932610", "dataCategory": "Hi-C profiling" } } ], "collaborator": [ { - "contact_email": "batman@batman_inc.org", + "contactEmail": "batman@batman_inc.org", "name": "Sergei Doulatov", "affiliation": "Washington University" } ], "experiment": { "platform": "ILLUMINA", - "experimental_strategy": "Hi-C", - "submitter_sequencing_experiment_id": "EXPERIMENT" + "experimentalStrategy": "Hi-C", + "submitterSequencingExperimentId": "EXPERIMENT" }, "workflow": { - "workflow_name": "batman_stuff", - "genome_build": "GRCh38_hla_decoy_ebv", + "workflowName": "batman_stuff", + "genomeBuild": "GRCh38_hla_decoy_ebv", "inputs": [ { - "analysis_type": "sequencing_alignment", - "tumour_analysis_id": "00000000-0000-0000-0000-000000000000", - "normal_analysis_id": "00000000-0000-0000-0000-000000000000" + "analysisType": "sequencing_alignment", + "tumourAnalysisId": "00000000-0000-0000-0000-000000000000", + "normalAnalysisId": "00000000-0000-0000-0000-000000000000" } ] }, "archive": { - "SRA": [ + "sra": [ { - "GSE": "GSE174533" + "gse": "gse174533" } ] }, @@ -150,4 +156,4 @@ "title": "Lamin B1 deletion in myeloid neoplasms causes nuclear anomaly and altered hematopoietic stem cell function", "doi": "10.1016/j.stem.2022.02.010" } -} +} \ No newline at end of file diff --git a/playground-data/example-payloads/hichipseq_bedpe_zscpyibaevspyxlkyaip.json b/playground-data/example-payloads/hichipseq_bedpe_zscpyibaevspyxlkyaip.json index c1cbad20..f8683710 100644 --- a/playground-data/example-payloads/hichipseq_bedpe_zscpyibaevspyxlkyaip.json +++ b/playground-data/example-payloads/hichipseq_bedpe_zscpyibaevspyxlkyaip.json @@ -1,4 +1,8 @@ { + "analysisType": { + "name": "playgroundSchema" + }, + "studyId": "OVPLG-01", "samples": [ { "submitterSampleId": "TEST_SPECIMEN_zscpyibaevspyxlkyaip_N1", @@ -17,137 +21,139 @@ } ], "donor": { - "submitter_donor_id": "TEST_DONOR_zscpyibaevspyxlkyaip", - "primary_site": ["Hematopoietic and reticuloendothelial systems"], - "vital_status": "Deceased", - "survival_time": 1520, - "cause_of_death": "Died of cancer", - "primary_diagnosis": [ + "submitterDonorId": "TEST_DONOR_zscpyibaevspyxlkyaip", + "primarySite": [ + "Hematopoietic and reticuloendothelial systems" + ], + "vitalStatus": "Deceased", + "survivalTime": 1520, + "causeOfDeath": "Died of cancer", + "primaryDiagnosis": [ { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_zscpyibaevspyxlkyaip_0", - "age_at_diagnosis": 9, - "cancer_type_code": "D72.3", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_zscpyibaevspyxlkyaip_0", + "ageAtDiagnosis": 9, + "cancerTypeCode": "D72.3", "laterality": "Midline", - "clinical_tumour_staging_system": "FIGO staging system", - "clinical_stage_group": "Stage IVB", - "lymph_nodes_examined_status": "Not applicable", - "performance_status": "Unknown", + "clinicalTumourStagingSystem": "FIGO staging system", + "clinicalStageGroup": "Stage IVB", + "lymphNodesExaminedStatus": "Not applicable", + "performanceStatus": "Unknown", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_zscpyibaevspyxlkyaip_0", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_zscpyibaevspyxlkyaip_0", + "treatmentType": [ "Surgery" ], - "treatment_intent": "Curative", - "treatment_start_interval": 26, - "treatment_duration": 36, - "response_to_treatment": "Complete response", + "treatmentIntent": "Curative", + "treatmentStartInterval": 26, + "treatmentDuration": 36, + "responseToTreatment": "Complete response", "surgery": [ { - "surgery_type": "Bypass Gastrojejunostomy", - "surgery_site": "C27.8", - "surgery_location": "Metastatic", - "residual_tumour_classification": "R0" + "surgeryType": "Bypass Gastrojejunostomy", + "surgerySite": "C27.8", + "surgeryLocation": "Metastatic", + "residualTumourClassification": "R0" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_zscpyibaevspyxlkyaip_0", - "interval_of_followup": 82, - "disease_status_at_followup": "Partial remission" + "submitterFollowUpId": "TEST_FOLLOW_UP_zscpyibaevspyxlkyaip_0", + "intervalOfFollowup": 82, + "diseaseStatusAtFollowup": "Partial remission" } ] }, { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_zscpyibaevspyxlkyaip_1", - "age_at_diagnosis": 10, - "cancer_type_code": "D30.8", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_zscpyibaevspyxlkyaip_1", + "ageAtDiagnosis": 10, + "cancerTypeCode": "D30.8", "laterality": "Unilateral, side not specified", - "clinical_tumour_staging_system": "Revised International staging system (RISS)", - "clinical_stage_group": "Stage III", - "lymph_nodes_examined_status": "Not applicable", - "performance_status": "Grade 4", + "clinicalTumourStagingSystem": "Revised International staging system (RISS)", + "clinicalStageGroup": "Stage III", + "lymphNodesExaminedStatus": "Not applicable", + "performanceStatus": "Grade 4", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_zscpyibaevspyxlkyaip_1", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_zscpyibaevspyxlkyaip_1", + "treatmentType": [ "Hormonal therapy", "Surgery", "Chemotherapy" ], - "treatment_intent": "Palliative", - "treatment_start_interval": 7, - "treatment_duration": 16, - "response_to_treatment": "Stable disease", - "hormone_therapy": [ + "treatmentIntent": "Palliative", + "treatmentStartInterval": 7, + "treatmentDuration": 16, + "responseToTreatment": "Stable disease", + "hormoneTherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 98, - "hormone_drug_dosage_units": "mg/kg" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 98, + "hormoneDrugDosageUnits": "mg/kg" } ], "surgery": [ { - "surgery_type": "Cholecystectomy", - "surgery_site": "C46.7", - "surgery_location": "Metastatic", - "residual_tumour_classification": "R2" + "surgeryType": "Cholecystectomy", + "surgerySite": "C46.7", + "surgeryLocation": "Metastatic", + "residualTumourClassification": "R2" } ], "chemotherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 29, - "chemotherapy_dosage_units": "IU/m2" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 29, + "chemotherapyDosageUnits": "IU/m2" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_zscpyibaevspyxlkyaip_1", - "interval_of_followup": 59, - "disease_status_at_followup": "Loco-regional progression" + "submitterFollowUpId": "TEST_FOLLOW_UP_zscpyibaevspyxlkyaip_1", + "intervalOfFollowup": 59, + "diseaseStatusAtFollowup": "Loco-regional progression" } ] } ], "comorbidity": [ { - "age_at_comorbidity_diagnosis": 42, - "comorbidity_type_code": "B07.48" + "ageAtComorbidityDiagnosis": 42, + "comorbidityTypeCode": "B07.48" }, { - "age_at_comorbidity_diagnosis": 83, - "comorbidity_type_code": "A66.7" + "ageAtComorbidityDiagnosis": 83, + "comorbidityTypeCode": "A66.7" }, { - "age_at_comorbidity_diagnosis": 70, - "comorbidity_type_code": "E15.40" + "ageAtComorbidityDiagnosis": 70, + "comorbidityTypeCode": "E15.40" } ] }, "specimen": { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_zscpyibaevspyxlkyaip_0", - "submitter_specimen_id": "TEST_SPECIMEN_zscpyibaevspyxlkyaip_N1", - "specimen_acquisition_interval": 88, - "specimen_anatomic_location": "C42.1", - "specimen_laterality": "Right" + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_zscpyibaevspyxlkyaip_0", + "submitterSpecimenId": "TEST_SPECIMEN_zscpyibaevspyxlkyaip_N1", + "specimenAcquisitionInterval": 88, + "specimenAnatomicLocation": "C42.1", + "specimenLaterality": "Right" }, "files": [ { "dataType": "Thresholded links", - "fileName": "ENCFF327GBZ.bedpe.gz", + "fileName": "encfF327GBZ.bedpe.gz", "fileSize": 1877046, "fileMd5sum": "42c639c3472d1573c25a674da2ff9c61", "fileAccess": "controlled", "fileType": "BEDPE", "info": { - "bigwig_measurement": [ + "bigwigMeasurement": [ "hg38:1:160986116-162349231", "Run with arc mode on" ], @@ -157,32 +163,32 @@ ], "collaborator": [ { - "contact_email": "batman@batman_inc.org", + "contactEmail": "batman@batman_inc.org", "name": "Jesse Engreitz", "affiliation": "Stanford" } ], "experiment": { "platform": "ILLUMINA", - "experimental_strategy": "HiChIP-Seq", - "chip_target": "DNase-seq", - "submitter_sequencing_experiment_id": "EXPERIMENT" + "experimentalStrategy": "HiChIP-Seq", + "chipTarget": "DNase-seq", + "submitterSequencingExperimentId": "EXPERIMENT" }, "workflow": { - "workflow_name": "batman_stuff", - "genome_build": "GRCh38_hla_decoy_ebv", + "workflowName": "batman_stuff", + "genomeBuild": "GRCh38_hla_decoy_ebv", "inputs": [ { - "analysis_type": "sequencing_alignment", - "tumour_analysis_id": "00000000-0000-0000-0000-000000000000", - "normal_analysis_id": "00000000-0000-0000-0000-000000000000" + "analysisType": "sequencing_alignment", + "tumourAnalysisId": "00000000-0000-0000-0000-000000000000", + "normalAnalysisId": "00000000-0000-0000-0000-000000000000" } ] }, "archive": { - "ENCODE": [ + "encode": [ { - "ENCF": "ENCFF327GBZ" + "encf": "encfF327GBZ" } ] }, @@ -190,4 +196,4 @@ "title": "An integrated encyclopedia of DNA elements in the human genome", "doi": "10.1038/nature11247" } -} +} \ No newline at end of file diff --git a/playground-data/example-payloads/wgbs_coverage_bigwig_eszycidpyopumzgdpamn.json b/playground-data/example-payloads/wgbs_coverage_bigwig_eszycidpyopumzgdpamn.json index 850427d0..b95ff294 100644 --- a/playground-data/example-payloads/wgbs_coverage_bigwig_eszycidpyopumzgdpamn.json +++ b/playground-data/example-payloads/wgbs_coverage_bigwig_eszycidpyopumzgdpamn.json @@ -1,11 +1,15 @@ { + "analysisType": { + "name": "playgroundSchema" + }, + "studyId": "OVPLG-01", "samples": [ { "submitterSampleId": "TEST_SPECIMEN_eszycidpyopumzgdpamn_T1", "sampleType": "Total DNA", "matchedNormalSubmitterSampleId": "TEST_SPECIMEN_eszycidpyopumzgdpamn_N1", "specimen": { - "submitterSpecimenId": "TEST_SPECIMEN_eszycidpyopumzgdpamn_N1", + "submitterSpecimenId": "TEST_SPECIMEN_eszycidpyopumzgdpamn_T1", "specimenType": "Primary Tumour", "specimenTissueSource": "Mononuclear cells from bone marrow", "tumourNormalDesignation": "Tumour" @@ -17,134 +21,136 @@ } ], "donor": { - "submitter_donor_id": "TEST_DONOR_eszycidpyopumzgdpamn", - "primary_site": ["Hematopoietic and reticuloendothelial systems"], - "vital_status": "Alive", - "survival_time": null, - "cause_of_death": null, - "primary_diagnosis": [ + "submitterDonorId": "TEST_DONOR_eszycidpyopumzgdpamn", + "primarySite": [ + "Hematopoietic and reticuloendothelial systems" + ], + "vitalStatus": "Alive", + "survivalTime": null, + "causeOfDeath": null, + "primaryDiagnosis": [ { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_eszycidpyopumzgdpamn_0", - "age_at_diagnosis": 75, - "cancer_type_code": "D35.1", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_eszycidpyopumzgdpamn_0", + "ageAtDiagnosis": 75, + "cancerTypeCode": "D35.1", "laterality": "Right", - "clinical_tumour_staging_system": "FIGO staging system", - "clinical_stage_group": "Stage IA2", - "lymph_nodes_examined_status": "Cannot be determined", - "performance_status": "Grade 2", + "clinicalTumourStagingSystem": "FIGO staging system", + "clinicalStageGroup": "Stage IA2", + "lymphNodesExaminedStatus": "Cannot be determined", + "performanceStatus": "Grade 2", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_eszycidpyopumzgdpamn_0", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_eszycidpyopumzgdpamn_0", + "treatmentType": [ "Radiation therapy", "Hormonal therapy" ], - "treatment_intent": "Curative", - "treatment_start_interval": 37, - "treatment_duration": 3, - "response_to_treatment": "NED", + "treatmentIntent": "Curative", + "treatmentStartInterval": 37, + "treatmentDuration": 3, + "responseToTreatment": "NED", "radiation": [ { - "radiation_therapy_modality": "Electron", - "radiation_therapy_type": "External", - "anatomical_site_irradiated": "Pelvis", - "radiation_therapy_dosage": 40, - "radiation_therapy_fractions": 24 + "radiationTherapyModality": "Electron", + "radiationTherapyType": "External", + "anatomicalSiteIrradiated": "Pelvis", + "radiationTherapyDosage": 40, + "radiationTherapyFractions": 24 } ], - "hormone_therapy": [ + "hormoneTherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 44, - "hormone_drug_dosage_units": "mg/m2" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 44, + "hormoneDrugDosageUnits": "mg/m2" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_eszycidpyopumzgdpamn_0", - "interval_of_followup": 84, - "disease_status_at_followup": "Complete remission" + "submitterFollowUpId": "TEST_FOLLOW_UP_eszycidpyopumzgdpamn_0", + "intervalOfFollowup": 84, + "diseaseStatusAtFollowup": "Complete remission" } ] } ], "comorbidity": [ { - "age_at_comorbidity_diagnosis": 97, - "comorbidity_type_code": "E02.58" + "ageAtComorbidityDiagnosis": 97, + "comorbidityTypeCode": "E02.58" }, { - "age_at_comorbidity_diagnosis": 26, - "comorbidity_type_code": "B07.38" + "ageAtComorbidityDiagnosis": 26, + "comorbidityTypeCode": "B07.38" } ] }, "specimen": { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_eszycidpyopumzgdpamn_0", - "submitter_specimen_id": "TEST_SPECIMEN_eszycidpyopumzgdpamn_N1", - "specimen_acquisition_interval": 48, - "specimen_anatomic_location": "C42.1", - "specimen_laterality": "Unknown", - "tumour_histological_type": "9556/31", - "pathological_tumour_staging_system": "Binet staging system", - "pathological_stage_group": "Stage C", - "tumour_grading_system": "ISUP grading system", - "tumour_grade": "G4", - "percent_tumour_cells": 25, - "reference_pathology_confirmed": "No" + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_eszycidpyopumzgdpamn_0", + "submitterSpecimenId": "TEST_SPECIMEN_eszycidpyopumzgdpamn_N1", + "specimenAcquisitionInterval": 48, + "specimenAnatomicLocation": "C42.1", + "specimenLaterality": "Unknown", + "tumourHistologicalType": "9556/31", + "pathologicalTumourStagingSystem": "Binet staging system", + "pathologicalStageGroup": "Stage C", + "tumourGradingSystem": "ISUP grading system", + "tumourGrade": "G4", + "percentTumourCells": 25, + "referencePathologyConfirmed": "No" }, "files": [ { "dataType": "coverageCpgSites", - "fileName": "ENCFF750ORI.bigWig", + "fileName": "encfF750ORI.bigWig", "fileSize": 295418867, "fileMd5sum": "63b0da7d7b95475a7df47cd5e1da4a4e", "fileAccess": "controlled", "fileType": "BIGWIG", "info": { - "bigwig_measurement": "Coverage at CpG", + "bigwigMeasurement": "Coverage at CpG", "minimumMappingQ": 30, "deduplicated": true, - "notes_for_mitchell": "hg38:1:43940960-43947020", + "notesForMitchell": "hg38:1:43940960-43947020", "dataCategory": "WGBS profiling" } } ], "collaborator": [ { - "contact_email": "batman@batman_inc.org", + "contactEmail": "batman@batman_inc.org", "name": "Michael Snyder", "affiliation": "Stanford" } ], "experiment": { "platform": "ILLUMINA", - "experimental_strategy": "WGBS", - "submitter_sequencing_experiment_id": "EXPERIMENT" + "experimentalStrategy": "WGBS", + "submitterSequencingExperimentId": "EXPERIMENT" }, "workflow": { - "workflow_name": "gemBS", - "genome_build": "GRCh38_hla_decoy_ebv", + "workflowName": "gemBS", + "genomeBuild": "GRCh38_hla_decoy_ebv", "inputs": [ { - "analysis_type": "sequencing_alignment", - "tumour_analysis_id": "00000000-0000-0000-0000-000000000000", - "normal_analysis_id": "00000000-0000-0000-0000-000000000000" + "analysisType": "sequencing_alignment", + "tumourAnalysisId": "00000000-0000-0000-0000-000000000000", + "normalAnalysisId": "00000000-0000-0000-0000-000000000000" } ] }, "archive": { - "SRA": [ + "sra": [ { - "GSE": "GSE215679" + "gse": "gse215679" } ], - "ENCODE": [ + "encode": [ { - "ENCF": "ENCFF750ORI" + "encf": "encfF750ORI" } ] }, @@ -152,4 +158,4 @@ "title": "An integrated encyclopedia of DNA elements in the human genome", "doi": "10.1038/nature11247" } -} +} \ No newline at end of file diff --git a/playground-data/example-payloads/wgbs_methylation_bigbed_eszycidpyopumzgdpamn.json b/playground-data/example-payloads/wgbs_methylation_bigbed_eszycidpyopumzgdpamn.json index 8aca680a..96370bcf 100644 --- a/playground-data/example-payloads/wgbs_methylation_bigbed_eszycidpyopumzgdpamn.json +++ b/playground-data/example-payloads/wgbs_methylation_bigbed_eszycidpyopumzgdpamn.json @@ -1,12 +1,16 @@ { + "analysisType": { + "name": "playgroundSchema" + }, + "studyId": "OVPLG-01", "samples": [ { "submitterSampleId": "TEST_SPECIMEN_eszycidpyopumzgdpamn_T1", "sampleType": "Total DNA", "matchedNormalSubmitterSampleId": "TEST_SPECIMEN_eszycidpyopumzgdpamn_N1", "specimen": { - "submitterSpecimenId": "TEST_SPECIMEN_eszycidpyopumzgdpamn_N1", - "specimenType": "Primary Tumour", + "submitterSpecimenId": "TEST_SPECIMEN_eszycidpyopumzgdpamn_T1", + "specimenType": "Primary tumour", "specimenTissueSource": "Mononuclear cells from bone marrow", "tumourNormalDesignation": "Tumour" }, @@ -17,135 +21,137 @@ } ], "donor": { - "submitter_donor_id": "TEST_DONOR_eszycidpyopumzgdpamn", - "primary_site": ["Hematopoietic and reticuloendothelial systems"], - "vital_status": "Alive", - "survival_time": null, - "cause_of_death": null, - "primary_diagnosis": [ + "submitterDonorId": "TEST_DONOR_eszycidpyopumzgdpamn", + "primarySite": [ + "Hematopoietic and reticuloendothelial systems" + ], + "vitalStatus": "Alive", + "survivalTime": null, + "causeOfDeath": null, + "primaryDiagnosis": [ { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_eszycidpyopumzgdpamn_0", - "age_at_diagnosis": 75, - "cancer_type_code": "D35.1", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_eszycidpyopumzgdpamn_0", + "ageAtDiagnosis": 75, + "cancerTypeCode": "D35.1", "laterality": "Right", - "clinical_tumour_staging_system": "FIGO staging system", - "clinical_stage_group": "Stage IA2", - "lymph_nodes_examined_status": "Cannot be determined", - "performance_status": "Grade 2", + "clinicalTumourStagingSystem": "FIGO staging system", + "clinicalStageGroup": "Stage IA2", + "lymphNodesExaminedStatus": "Cannot be determined", + "performanceStatus": "Grade 2", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_eszycidpyopumzgdpamn_0", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_eszycidpyopumzgdpamn_0", + "treatmentType": [ "Radiation therapy", "Hormonal therapy" ], - "treatment_intent": "Curative", - "treatment_start_interval": 37, - "treatment_duration": 3, - "response_to_treatment": "NED", + "treatmentIntent": "Curative", + "treatmentStartInterval": 37, + "treatmentDuration": 3, + "responseToTreatment": "NED", "radiation": [ { - "radiation_therapy_modality": "Electron", - "radiation_therapy_type": "External", - "anatomical_site_irradiated": "Pelvis", - "radiation_therapy_dosage": 40, - "radiation_therapy_fractions": 24 + "radiationTherapyModality": "Electron", + "radiationTherapyType": "External", + "anatomicalSiteIrradiated": "Pelvis", + "radiationTherapyDosage": 40, + "radiationTherapyFractions": 24 } ], - "hormone_therapy": [ + "hormoneTherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 44, - "hormone_drug_dosage_units": "mg/m2" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 44, + "hormoneDrugDosageUnits": "mg/m2" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_eszycidpyopumzgdpamn_0", - "interval_of_followup": 84, - "disease_status_at_followup": "Complete remission" + "submitterFollowUpId": "TEST_FOLLOW_UP_eszycidpyopumzgdpamn_0", + "intervalOfFollowup": 84, + "diseaseStatusAtFollowup": "Complete remission" } ] } ], "comorbidity": [ { - "age_at_comorbidity_diagnosis": 97, - "comorbidity_type_code": "E02.58" + "ageAtComorbidityDiagnosis": 97, + "comorbidityTypeCode": "E02.58" }, { - "age_at_comorbidity_diagnosis": 26, - "comorbidity_type_code": "B07.38" + "ageAtComorbidityDiagnosis": 26, + "comorbidityTypeCode": "B07.38" } ] }, "specimen": { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_eszycidpyopumzgdpamn_0", - "submitter_specimen_id": "TEST_SPECIMEN_eszycidpyopumzgdpamn_N1", - "specimen_acquisition_interval": 48, - "specimen_anatomic_location": "C42.1", - "specimen_laterality": "Unknown", - "tumour_histological_type": "9556/31", - "pathological_tumour_staging_system": "Binet staging system", - "pathological_stage_group": "Stage C", - "tumour_grading_system": "ISUP grading system", - "tumour_grade": "G4", - "percent_tumour_cells": 25, - "reference_pathology_confirmed": "No" + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_eszycidpyopumzgdpamn_0", + "submitterSpecimenId": "TEST_SPECIMEN_eszycidpyopumzgdpamn_N1", + "specimenAcquisitionInterval": 48, + "specimenAnatomicLocation": "C42.1", + "specimenLaterality": "Unknown", + "tumourHistologicalType": "9556/31", + "pathologicalTumourStagingSystem": "Binet staging system", + "pathologicalStageGroup": "Stage C", + "tumourGradingSystem": "ISUP grading system", + "tumourGrade": "G4", + "percentTumourCells": 25, + "referencePathologyConfirmed": "No" }, "files": [ { "dataType": "cpgMethylation", - "fileName": "ENCFF256OFF.bigBed", + "fileName": "encfF256OFF.bigBed", "fileSize": 1032910837, "fileMd5sum": "12340e1995c429170f09e13c9c7a7f70", "fileAccess": "controlled", "fileType": "BIGBED", "info": { - "bigbed_measurement": "methylation", - "bigbed_feature_highlight": "CpG", + "bigbedMeasurement": "methylation", + "bigbedFeatureHighlight": "CpG", "minimumMappingQ": 30, "deduplicated": true, - "notes_for_mitchell": "hg38:1:43940960-43947081", + "notesForMitchell": "hg38:1:43940960-43947081", "dataCategory": "WGBS profiling" } } ], "collaborator": [ { - "contact_email": "batman@batman_inc.org", + "contactEmail": "batman@batman_inc.org", "name": "Michael Snyder", "affiliation": "Stanford" } ], "experiment": { "platform": "ILLUMINA", - "experimental_strategy": "WGBS", - "submitter_sequencing_experiment_id": "EXPERIMENT" + "experimentalStrategy": "WGBS", + "submitterSequencingExperimentId": "EXPERIMENT" }, "workflow": { - "workflow_name": "gemBS", - "genome_build": "GRCh38_hla_decoy_ebv", + "workflowName": "gemBS", + "genomeBuild": "GRCh38_hla_decoy_ebv", "inputs": [ { - "analysis_type": "sequencing_alignment", - "tumour_analysis_id": "00000000-0000-0000-0000-000000000000", - "normal_analysis_id": "00000000-0000-0000-0000-000000000000" + "analysisType": "sequencing_alignment", + "tumourAnalysisId": "00000000-0000-0000-0000-000000000000", + "normalAnalysisId": "00000000-0000-0000-0000-000000000000" } ] }, "archive": { - "SRA": [ + "sra": [ { - "GSE": "GSE215679" + "gse": "gse215679" } ], - "ENCODE": [ + "encode": [ { - "ENCF": "ENCFF256OFF" + "encf": "encfF256OFF" } ] }, @@ -153,4 +159,4 @@ "title": "An integrated encyclopedia of DNA elements in the human genome", "doi": "10.1038/nature11247" } -} +} \ No newline at end of file diff --git a/playground-data/example-payloads/wgs_mutect_snv_vcf_zscpyibaevspyxlkyaip.json b/playground-data/example-payloads/wgs_mutect_snv_vcf_zscpyibaevspyxlkyaip.json index 9f969eaf..26d79a5e 100644 --- a/playground-data/example-payloads/wgs_mutect_snv_vcf_zscpyibaevspyxlkyaip.json +++ b/playground-data/example-payloads/wgs_mutect_snv_vcf_zscpyibaevspyxlkyaip.json @@ -1,12 +1,16 @@ { + "analysisType": { + "name": "playgroundSchema" + }, + "studyId": "OVPLG-01", "samples": [ { "submitterSampleId": "TEST_SPECIMEN_zscpyibaevspyxlkyaip_T1", "sampleType": "Total DNA", "matchedNormalSubmitterSampleId": "TEST_SPECIMEN_zscpyibaevspyxlkyaip_N1", "specimen": { - "submitterSpecimenId": "TEST_SPECIMEN_zscpyibaevspyxlkyaip_N1", - "specimenType": "Tumour - unknown if derived from primary or metastatic", + "submitterSpecimenId": "TEST_SPECIMEN_zscpyibaevspyxlkyaip_T1", + "specimenType": "Primary tumour", "specimenTissueSource": "Blood derived - peripheral blood", "tumourNormalDesignation": "Tumour" }, @@ -17,126 +21,128 @@ } ], "donor": { - "submitter_donor_id": "TEST_DONOR_zscpyibaevspyxlkyaip", - "primary_site": ["Hematopoietic and reticuloendothelial systems"], - "vital_status": "Deceased", - "survival_time": 1520, - "cause_of_death": "Died of cancer", - "primary_diagnosis": [ + "submitterDonorId": "TEST_DONOR_zscpyibaevspyxlkyaip", + "primarySite": [ + "Hematopoietic and reticuloendothelial systems" + ], + "vitalStatus": "Deceased", + "survivalTime": 1520, + "causeOfDeath": "Died of cancer", + "primaryDiagnosis": [ { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_zscpyibaevspyxlkyaip_0", - "age_at_diagnosis": 9, - "cancer_type_code": "D72.3", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_zscpyibaevspyxlkyaip_0", + "ageAtDiagnosis": 9, + "cancerTypeCode": "D72.3", "laterality": "Midline", - "clinical_tumour_staging_system": "FIGO staging system", - "clinical_stage_group": "Stage IVB", - "lymph_nodes_examined_status": "Not applicable", - "performance_status": "Unknown", + "clinicalTumourStagingSystem": "FIGO staging system", + "clinicalStageGroup": "Stage IVB", + "lymphNodesExaminedStatus": "Not applicable", + "performanceStatus": "Unknown", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_zscpyibaevspyxlkyaip_0", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_zscpyibaevspyxlkyaip_0", + "treatmentType": [ "Surgery" ], - "treatment_intent": "Curative", - "treatment_start_interval": 26, - "treatment_duration": 36, - "response_to_treatment": "Complete response", + "treatmentIntent": "Curative", + "treatmentStartInterval": 26, + "treatmentDuration": 36, + "responseToTreatment": "Complete response", "surgery": [ { - "surgery_type": "Bypass Gastrojejunostomy", - "surgery_site": "C27.8", - "surgery_location": "Metastatic", - "residual_tumour_classification": "R0" + "surgeryType": "Bypass Gastrojejunostomy", + "surgerySite": "C27.8", + "surgeryLocation": "Metastatic", + "residualTumourClassification": "R0" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_zscpyibaevspyxlkyaip_0", - "interval_of_followup": 82, - "disease_status_at_followup": "Partial remission" + "submitterFollowUpId": "TEST_FOLLOW_UP_zscpyibaevspyxlkyaip_0", + "intervalOfFollowup": 82, + "diseaseStatusAtFollowup": "Partial remission" } ] }, { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_zscpyibaevspyxlkyaip_1", - "age_at_diagnosis": 10, - "cancer_type_code": "D30.8", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_zscpyibaevspyxlkyaip_1", + "ageAtDiagnosis": 10, + "cancerTypeCode": "D30.8", "laterality": "Unilateral, side not specified", - "clinical_tumour_staging_system": "Revised International staging system (RISS)", - "clinical_stage_group": "Stage III", - "lymph_nodes_examined_status": "Not applicable", - "performance_status": "Grade 4", + "clinicalTumourStagingSystem": "Revised International staging system (RISS)", + "clinicalStageGroup": "Stage III", + "lymphNodesExaminedStatus": "Not applicable", + "performanceStatus": "Grade 4", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_zscpyibaevspyxlkyaip_1", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_zscpyibaevspyxlkyaip_1", + "treatmentType": [ "Hormonal therapy", "Surgery", "Chemotherapy" ], - "treatment_intent": "Palliative", - "treatment_start_interval": 7, - "treatment_duration": 16, - "response_to_treatment": "Stable disease", - "hormone_therapy": [ + "treatmentIntent": "Palliative", + "treatmentStartInterval": 7, + "treatmentDuration": 16, + "responseToTreatment": "Stable disease", + "hormoneTherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 98, - "hormone_drug_dosage_units": "mg/kg" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 98, + "hormoneDrugDosageUnits": "mg/kg" } ], "surgery": [ { - "surgery_type": "Cholecystectomy", - "surgery_site": "C46.7", - "surgery_location": "Metastatic", - "residual_tumour_classification": "R2" + "surgeryType": "Cholecystectomy", + "surgerySite": "C46.7", + "surgeryLocation": "Metastatic", + "residualTumourClassification": "R2" } ], "chemotherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 29, - "chemotherapy_dosage_units": "IU/m2" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 29, + "chemotherapyDosageUnits": "IU/m2" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_zscpyibaevspyxlkyaip_1", - "interval_of_followup": 59, - "disease_status_at_followup": "Loco-regional progression" + "submitterFollowUpId": "TEST_FOLLOW_UP_zscpyibaevspyxlkyaip_1", + "intervalOfFollowup": 59, + "diseaseStatusAtFollowup": "Loco-regional progression" } ] } ], "comorbidity": [ { - "age_at_comorbidity_diagnosis": 42, - "comorbidity_type_code": "B07.48" + "ageAtComorbidityDiagnosis": 42, + "comorbidityTypeCode": "B07.48" }, { - "age_at_comorbidity_diagnosis": 83, - "comorbidity_type_code": "A66.7" + "ageAtComorbidityDiagnosis": 83, + "comorbidityTypeCode": "A66.7" }, { - "age_at_comorbidity_diagnosis": 70, - "comorbidity_type_code": "E15.40" + "ageAtComorbidityDiagnosis": 70, + "comorbidityTypeCode": "E15.40" } ] }, "specimen": { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_zscpyibaevspyxlkyaip_0", - "submitter_specimen_id": "TEST_SPECIMEN_zscpyibaevspyxlkyaip_N1", - "specimen_acquisition_interval": 19, - "specimen_anatomic_location": "C42", - "specimen_laterality": "Right" + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_zscpyibaevspyxlkyaip_0", + "submitterSpecimenId": "TEST_SPECIMEN_zscpyibaevspyxlkyaip_N1", + "specimenAcquisitionInterval": 19, + "specimenAnatomicLocation": "C42", + "specimenLaterality": "Right" }, "files": [ { @@ -147,7 +153,7 @@ "fileAccess": "controlled", "fileType": "VCF", "info": { - "notes_for_mitchell": "hg38:21:29896103-36188915", + "notesForMitchell": "hg38:21:29896103-36188915", "dataCategory": "Simple Nucelotide Variation" } }, @@ -159,32 +165,32 @@ "fileAccess": "controlled", "fileType": "TBI", "info": { - "notes_for_mitchell": "hg38:21:29896103-36188915", + "notesForMitchell": "hg38:21:29896103-36188915", "dataCategory": "Simple Nucelotide Variation" } } ], "collaborator": [ { - "contact_email": "batman@batman_inc.org", + "contactEmail": "batman@batman_inc.org", "name": "batman", "affiliation": "batman inc" } ], "experiment": { "platform": "ILLUMINA", - "experimental_strategy": "WGS", - "submitter_sequencing_experiment_id": "EXPERIMENT" + "experimentalStrategy": "WGS", + "submitterSequencingExperimentId": "EXPERIMENT" }, "workflow": { - "workflow_name": "mutect2", - "genome_build": "GRCh38_hla_decoy_ebv", + "workflowName": "mutect2", + "genomeBuild": "GRCh38_hla_decoy_ebv", "inputs": [ { - "analysis_type": "sequencing_alignment", - "tumour_analysis_id": "00000000-0000-0000-0000-000000000000", - "normal_analysis_id": "00000000-0000-0000-0000-000000000000" + "analysisType": "sequencing_alignment", + "tumourAnalysisId": "00000000-0000-0000-0000-000000000000", + "normalAnalysisId": "00000000-0000-0000-0000-000000000000" } ] } -} +} \ No newline at end of file diff --git a/playground-data/example-payloads/wgs_sanger_snv_vcf_zscpyibaevspyxlkyaip.json b/playground-data/example-payloads/wgs_sanger_snv_vcf_zscpyibaevspyxlkyaip.json index 4c7e747a..464a76e9 100644 --- a/playground-data/example-payloads/wgs_sanger_snv_vcf_zscpyibaevspyxlkyaip.json +++ b/playground-data/example-payloads/wgs_sanger_snv_vcf_zscpyibaevspyxlkyaip.json @@ -1,11 +1,15 @@ { + "analysisType": { + "name": "playgroundSchema" + }, + "studyId": "OVPLG-01", "samples": [ { "submitterSampleId": "TEST_SPECIMEN_zscpyibaevspyxlkyaip_T1", "sampleType": "Total DNA", "matchedNormalSubmitterSampleId": "TEST_SPECIMEN_zscpyibaevspyxlkyaip_N1", "specimen": { - "submitterSpecimenId": "TEST_SPECIMEN_zscpyibaevspyxlkyaip_N1", + "submitterSpecimenId": "TEST_SPECIMEN_zscpyibaevspyxlkyaip_T1", "specimenType": "Tumour - unknown if derived from primary or metastatic", "specimenTissueSource": "Blood derived - peripheral blood", "tumourNormalDesignation": "Tumour" @@ -17,126 +21,128 @@ } ], "donor": { - "submitter_donor_id": "TEST_DONOR_zscpyibaevspyxlkyaip", - "primary_site": ["Hematopoietic and reticuloendothelial systems"], - "vital_status": "Deceased", - "survival_time": 1520, - "cause_of_death": "Died of cancer", - "primary_diagnosis": [ + "submitterDonorId": "TEST_DONOR_zscpyibaevspyxlkyaip", + "primarySite": [ + "Hematopoietic and reticuloendothelial systems" + ], + "vitalStatus": "Deceased", + "survivalTime": 1520, + "causeOfDeath": "Died of cancer", + "primaryDiagnosis": [ { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_zscpyibaevspyxlkyaip_0", - "age_at_diagnosis": 9, - "cancer_type_code": "D72.3", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_zscpyibaevspyxlkyaip_0", + "ageAtDiagnosis": 9, + "cancerTypeCode": "D72.3", "laterality": "Midline", - "clinical_tumour_staging_system": "FIGO staging system", - "clinical_stage_group": "Stage IVB", - "lymph_nodes_examined_status": "Not applicable", - "performance_status": "Unknown", + "clinicalTumourStagingSystem": "FIGO staging system", + "clinicalStageGroup": "Stage IVB", + "lymphNodesExaminedStatus": "Not applicable", + "performanceStatus": "Unknown", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_zscpyibaevspyxlkyaip_0", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_zscpyibaevspyxlkyaip_0", + "treatmentType": [ "Surgery" ], - "treatment_intent": "Curative", - "treatment_start_interval": 26, - "treatment_duration": 36, - "response_to_treatment": "Complete response", + "treatmentIntent": "Curative", + "treatmentStartInterval": 26, + "treatmentDuration": 36, + "responseToTreatment": "Complete response", "surgery": [ { - "surgery_type": "Bypass Gastrojejunostomy", - "surgery_site": "C27.8", - "surgery_location": "Metastatic", - "residual_tumour_classification": "R0" + "surgeryType": "Bypass Gastrojejunostomy", + "surgerySite": "C27.8", + "surgeryLocation": "Metastatic", + "residualTumourClassification": "R0" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_zscpyibaevspyxlkyaip_0", - "interval_of_followup": 82, - "disease_status_at_followup": "Partial remission" + "submitterFollowUpId": "TEST_FOLLOW_UP_zscpyibaevspyxlkyaip_0", + "intervalOfFollowup": 82, + "diseaseStatusAtFollowup": "Partial remission" } ] }, { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_zscpyibaevspyxlkyaip_1", - "age_at_diagnosis": 10, - "cancer_type_code": "D30.8", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_zscpyibaevspyxlkyaip_1", + "ageAtDiagnosis": 10, + "cancerTypeCode": "D30.8", "laterality": "Unilateral, side not specified", - "clinical_tumour_staging_system": "Revised International staging system (RISS)", - "clinical_stage_group": "Stage III", - "lymph_nodes_examined_status": "Not applicable", - "performance_status": "Grade 4", + "clinicalTumourStagingSystem": "Revised International staging system (RISS)", + "clinicalStageGroup": "Stage III", + "lymphNodesExaminedStatus": "Not applicable", + "performanceStatus": "Grade 4", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_zscpyibaevspyxlkyaip_1", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_zscpyibaevspyxlkyaip_1", + "treatmentType": [ "Hormonal therapy", "Surgery", "Chemotherapy" ], - "treatment_intent": "Palliative", - "treatment_start_interval": 7, - "treatment_duration": 16, - "response_to_treatment": "Stable disease", - "hormone_therapy": [ + "treatmentIntent": "Palliative", + "treatmentStartInterval": 7, + "treatmentDuration": 16, + "responseToTreatment": "Stable disease", + "hormoneTherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 98, - "hormone_drug_dosage_units": "mg/kg" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 98, + "hormoneDrugDosageUnits": "mg/kg" } ], "surgery": [ { - "surgery_type": "Cholecystectomy", - "surgery_site": "C46.7", - "surgery_location": "Metastatic", - "residual_tumour_classification": "R2" + "surgeryType": "Cholecystectomy", + "surgerySite": "C46.7", + "surgeryLocation": "Metastatic", + "residualTumourClassification": "R2" } ], "chemotherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 29, - "chemotherapy_dosage_units": "IU/m2" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 29, + "chemotherapyDosageUnits": "IU/m2" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_zscpyibaevspyxlkyaip_1", - "interval_of_followup": 59, - "disease_status_at_followup": "Loco-regional progression" + "submitterFollowUpId": "TEST_FOLLOW_UP_zscpyibaevspyxlkyaip_1", + "intervalOfFollowup": 59, + "diseaseStatusAtFollowup": "Loco-regional progression" } ] } ], "comorbidity": [ { - "age_at_comorbidity_diagnosis": 42, - "comorbidity_type_code": "B07.48" + "ageAtComorbidityDiagnosis": 42, + "comorbidityTypeCode": "B07.48" }, { - "age_at_comorbidity_diagnosis": 83, - "comorbidity_type_code": "A66.7" + "ageAtComorbidityDiagnosis": 83, + "comorbidityTypeCode": "A66.7" }, { - "age_at_comorbidity_diagnosis": 70, - "comorbidity_type_code": "E15.40" + "ageAtComorbidityDiagnosis": 70, + "comorbidityTypeCode": "E15.40" } ] }, "specimen": { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_zscpyibaevspyxlkyaip_0", - "submitter_specimen_id": "TEST_SPECIMEN_zscpyibaevspyxlkyaip_N1", - "specimen_acquisition_interval": 19, - "specimen_anatomic_location": "C42", - "specimen_laterality": "Right" + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_zscpyibaevspyxlkyaip_0", + "submitterSpecimenId": "TEST_SPECIMEN_zscpyibaevspyxlkyaip_N1", + "specimenAcquisitionInterval": 19, + "specimenAnatomicLocation": "C42", + "specimenLaterality": "Right" }, "files": [ { @@ -147,7 +153,7 @@ "fileAccess": "controlled", "fileType": "VCF", "info": { - "notes_for_mitchell": "hg38:21:29896103-36188915", + "notesForMitchell": "hg38:21:29896103-36188915", "dataCategory": "Simple Nucelotide Variation" } }, @@ -159,32 +165,32 @@ "fileAccess": "controlled", "fileType": "TBI", "info": { - "notes_for_mitchell": "hg38:21:29896103-36188915", + "notesForMitchell": "hg38:21:29896103-36188915", "dataCategory": "Simple Nucelotide Variation" } } ], "collaborator": [ { - "contact_email": "batman@batman_inc.org", + "contactEmail": "batman@batman_inc.org", "name": "batman", "affiliation": "batman inc" } ], "experiment": { "platform": "ILLUMINA", - "experimental_strategy": "WGS", - "submitter_sequencing_experiment_id": "EXPERIMENT" + "experimentalStrategy": "WGS", + "submitterSequencingExperimentId": "EXPERIMENT" }, "workflow": { - "workflow_name": "sanger", - "genome_build": "GRCh38_hla_decoy_ebv", + "workflowName": "sanger", + "genomeBuild": "GRCh38_hla_decoy_ebv", "inputs": [ { - "analysis_type": "sequencing_alignment", - "tumour_analysis_id": "00000000-0000-0000-0000-000000000000", - "normal_analysis_id": "00000000-0000-0000-0000-000000000000" + "analysisType": "sequencing_alignment", + "tumourAnalysisId": "00000000-0000-0000-0000-000000000000", + "normalAnalysisId": "00000000-0000-0000-0000-000000000000" } ] } -} +} \ No newline at end of file diff --git a/playground-data/example-payloads/wxs_indel_vcf_zscpyibaevspyxlkyaip.json b/playground-data/example-payloads/wxs_indel_vcf_zscpyibaevspyxlkyaip.json index c35832c5..ae407ca4 100644 --- a/playground-data/example-payloads/wxs_indel_vcf_zscpyibaevspyxlkyaip.json +++ b/playground-data/example-payloads/wxs_indel_vcf_zscpyibaevspyxlkyaip.json @@ -1,12 +1,16 @@ { + "analysisType": { + "name": "playgroundSchema" + }, + "studyId": "OVPLG-01", "samples": [ { "submitterSampleId": "TEST_SPECIMEN_zscpyibaevspyxlkyaip_T1", "sampleType": "Total DNA", "matchedNormalSubmitterSampleId": "TEST_SPECIMEN_zscpyibaevspyxlkyaip_N1", "specimen": { - "submitterSpecimenId": "TEST_SPECIMEN_zscpyibaevspyxlkyaip_N1", - "specimenType": "Tumour - unknown if derived from primary or metastatic", + "submitterSpecimenId": "TEST_SPECIMEN_zscpyibaevspyxlkyaip_T1", + "specimenType": "Primary tumour", "specimenTissueSource": "Solid tissue", "tumourNormalDesignation": "Tumour" }, @@ -17,126 +21,128 @@ } ], "donor": { - "submitter_donor_id": "TEST_DONOR_zscpyibaevspyxlkyaip", - "primary_site": ["Hematopoietic and reticuloendothelial systems"], - "vital_status": "Deceased", - "survival_time": 1520, - "cause_of_death": "Died of cancer", - "primary_diagnosis": [ + "submitterDonorId": "TEST_DONOR_zscpyibaevspyxlkyaip", + "primarySite": [ + "Hematopoietic and reticuloendothelial systems" + ], + "vitalStatus": "Deceased", + "survivalTime": 1520, + "causeOfDeath": "Died of cancer", + "primaryDiagnosis": [ { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_zscpyibaevspyxlkyaip_0", - "age_at_diagnosis": 9, - "cancer_type_code": "D72.3", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_zscpyibaevspyxlkyaip_0", + "ageAtDiagnosis": 9, + "cancerTypeCode": "D72.3", "laterality": "Midline", - "clinical_tumour_staging_system": "FIGO staging system", - "clinical_stage_group": "Stage IVB", - "lymph_nodes_examined_status": "Not applicable", - "performance_status": "Unknown", + "clinicalTumourStagingSystem": "FIGO staging system", + "clinicalStageGroup": "Stage IVB", + "lymphNodesExaminedStatus": "Not applicable", + "performanceStatus": "Unknown", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_zscpyibaevspyxlkyaip_0", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_zscpyibaevspyxlkyaip_0", + "treatmentType": [ "Surgery" ], - "treatment_intent": "Curative", - "treatment_start_interval": 26, - "treatment_duration": 36, - "response_to_treatment": "Complete response", + "treatmentIntent": "Curative", + "treatmentStartInterval": 26, + "treatmentDuration": 36, + "responseToTreatment": "Complete response", "surgery": [ { - "surgery_type": "Bypass Gastrojejunostomy", - "surgery_site": "C27.8", - "surgery_location": "Metastatic", - "residual_tumour_classification": "R0" + "surgeryType": "Bypass Gastrojejunostomy", + "surgerySite": "C27.8", + "surgeryLocation": "Metastatic", + "residualTumourClassification": "R0" } ] } ], - "follow_up": [ + "followUp": [ { - "submitter_follow_up_id": "TEST_FOLLOW_UP_zscpyibaevspyxlkyaip_0", - "interval_of_followup": 82, - "disease_status_at_followup": "Partial remission" + "submitterFollowUpId": "TEST_FOLLOW_UP_zscpyibaevspyxlkyaip_0", + "intervalOfFollowup": 82, + "diseaseStatusAtFollowup": "Partial remission" } ] }, { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_zscpyibaevspyxlkyaip_1", - "age_at_diagnosis": 10, - "cancer_type_code": "D30.8", + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_zscpyibaevspyxlkyaip_1", + "ageAtDiagnosis": 10, + "cancerTypeCode": "D30.8", "laterality": "Unilateral, side not specified", - "clinical_tumour_staging_system": "Revised International staging system (RISS)", - "clinical_stage_group": "Stage III", - "lymph_nodes_examined_status": "Not applicable", - "performance_status": "Grade 4", + "clinicalTumourStagingSystem": "Revised International staging system (RISS)", + "clinicalStageGroup": "Stage III", + "lymphNodesExaminedStatus": "Not applicable", + "performanceStatus": "Grade 4", "treatment": [ { - "submitter_treatment_id": "TEST_TREATMENT_zscpyibaevspyxlkyaip_1", - "treatment_type": [ + "submitterTreatmentId": "TEST_TREATMENT_zscpyibaevspyxlkyaip_1", + "treatmentType": [ "Hormonal therapy", "Surgery", "Chemotherapy" ], - "treatment_intent": "Palliative", - "treatment_start_interval": 7, - "treatment_duration": 16, - "response_to_treatment": "Stable disease", - "hormone_therapy": [ + "treatmentIntent": "Palliative", + "treatmentStartInterval": 7, + "treatmentDuration": 16, + "responseToTreatment": "Stable disease", + "hormoneTherapy": [ { - "drug_name": "leucovorin", - "drug_rxnormcui": "6313", - "cumulative_drug_dosage": 98, - "hormone_drug_dosage_units": "mg/kg" + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 98, + "hormoneDrugDosageUnits": "mg/kg" } ], "surgery": [ { - 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"B07.48" + "ageAtComorbidityDiagnosis": 42, + "comorbidityTypeCode": "B07.48" }, { - "age_at_comorbidity_diagnosis": 83, - "comorbidity_type_code": "A66.7" + "ageAtComorbidityDiagnosis": 83, + "comorbidityTypeCode": "A66.7" }, { - "age_at_comorbidity_diagnosis": 70, - "comorbidity_type_code": "E15.40" + "ageAtComorbidityDiagnosis": 70, + "comorbidityTypeCode": "E15.40" } ] }, "specimen": { - "submitter_primary_diagnosis_id": "TEST_PRIMARY_DIAGNOSIS_zscpyibaevspyxlkyaip_0", - "submitter_specimen_id": "TEST_SPECIMEN_zscpyibaevspyxlkyaip_N1", - "specimen_acquisition_interval": 19, - "specimen_anatomic_location": "C42", - "specimen_laterality": "Right" + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_zscpyibaevspyxlkyaip_0", + "submitterSpecimenId": "TEST_SPECIMEN_zscpyibaevspyxlkyaip_N1", + "specimenAcquisitionInterval": 19, + "specimenAnatomicLocation": "C42", + "specimenLaterality": "Right" }, "files": [ { @@ -147,7 +153,7 @@ "fileAccess": "controlled", "fileType": "VCF", "info": { - "notes_for_mitchell": "hg38:21:29896103-36188915", + "notesForMitchell": "hg38:21:29896103-36188915", "dataCategory": "Simple Nucelotide Variation" } }, @@ -159,32 +165,32 @@ "fileAccess": "controlled", "fileType": "TBI", "info": { - "notes_for_mitchell": "hg38:21:29896103-36188915", + "notesForMitchell": "hg38:21:29896103-36188915", "dataCategory": "Simple Nucelotide Variation" } } ], "collaborator": [ { - "contact_email": "batman@batman_inc.org", + "contactEmail": "batman@batman_inc.org", "name": "batman", "affiliation": "batman inc" } ], "experiment": { "platform": "ILLUMINA", - "experimental_strategy": "WGS", - "submitter_sequencing_experiment_id": "EXPERIMENT" + "experimentalStrategy": "WGS", + "submitterSequencingExperimentId": "EXPERIMENT" }, "workflow": { - "workflow_name": "sanger", - "genome_build": "GRCh38_hla_decoy_ebv", + "workflowName": "sanger", + "genomeBuild": "GRCh38_hla_decoy_ebv", "inputs": [ { - "analysis_type": "sequencing_alignment", - 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{ + "if": { + "properties": { + "treatmentType": { + "contains": { + "const": "Hormonal therapy" + } + } + } + }, + "then": { + "required": [ + "hormoneTherapy" + ] + } + }, + { + "if": { + "properties": { + "treatmentType": { + "contains": { + "const": "Immunotherapy" + } + } + } + }, + "then": { + "required": [ + "immunotherapy" + ] + } + }, + { + "if": { + "properties": { + "treatmentType": { + "contains": { + "const": "Surgery" + } + } + } + }, + "then": { + "required": [ + "surgery" + ] + } + } + ] + } + } + } + } + }, + "comorbidity": { + "type": "array", + "items": { + "type": "object", + "propertyNames": { + "enum": [ + "ageAtComorbidityDiagnosis", + "comorbidityTypeCode" + ] + }, + "required": [ + "comorbidityTypeCode" + ], + "properties": { + "ageAtComorbidityDiagnosis": { + "type": "integer", + "minimum": 0 + }, + "comorbidityTypeCode": { + "type": "string", + "pattern": "^[A-Z][0-9]{2}(.[0-9]{1,3}[A-Z]{0,1})?$" + } + } + } + } + }, + "if": { + "properties": { + "vitalStatus": { + "const": "Deceased" + } + } + }, + "then": { + "required": [ + "causeOfDeath", + "survivalTime" + ] + } + }, + "specimen": { + "type": "object", + "propertyNames": { + "enum": [ + "submitterSpecimenId", + "submitterPrimaryDiagnosisId", + "specimenAcquisitionInterval", + "specimenAnatomicLocation", + "specimenLaterality", + "tumourHistologicalType", + "pathologicalTumourStagingSystem", + "pathologicalStageGroup", + "tumourGradingSystem", + "tumourGrade", + "percentTumourCells", + "referencePathologyConfirmed", + "cellLine" + ] + }, + "required": [ + "submitterSpecimenId", + "submitterPrimaryDiagnosisId", + "specimenAcquisitionInterval", + "specimenAnatomicLocation" + ], + "properties": { + "submitterSpecimenId": { + "type": "string" + }, + "submitterPrimaryDiagnosisId": { + "type": "string" + }, + "specimenAcquisitionInterval": { + "type": "integer", + "minimum": 0 + }, + "specimenAnatomicLocation": { + "type": "string", + "pattern": "^[C][0-9]{2}(.[0-9]{1})?$" + }, + "specimenLaterality": { + "type": "string", + "enum": [ + "Left", + "Right", + "Not applicable", + "Unknown" + ] + }, + "tumourHistologicalType": { + "type": "string", + "pattern": "^[8,9]{1}[0-9]{3}/[0,1,2,3,6,9]{1}[1-9]{0,1}$" + }, + "pathologicalTumourStagingSystem": { + "type": "string", + "enum": [ + "AJCC 8th edition", + "AJCC 7th edition", + "AJCC 6th edition", + "Ann Arbor staging system", + "Binet staging system", + "Durie-Salmon staging system", + "FIGO staging system", + "Lugano staging system", + "Rai staging system", + "Revised International staging system (RISS)", + "St Jude staging system" + ] + }, + "pathologicalStageGroup": { + "type": "string", + "enum": [ + "Occult Carcinoma", + "Stage 0", + "Stage 0a", + "Stage 0is", + "Stage 1", + "Stage 1A", + "Stage 1B", + "Stage A", + "Stage B", + "Stage C", + "Stage I", + "Stage IA", + "Stage IA1", + "Stage IA2", + "Stage IA3", + "Stage IAB", + "Stage IAE", + "Stage IAES", + "Stage IAS", + "Stage IB", + "Stage IB1", + "Stage IB2", + "Stage IBE", + "Stage IBES", + "Stage IBS", + "Stage IC", + "Stage IE", + "Stage IEA", + "Stage IEB", + "Stage IES", + "Stage II", + "Stage II bulky", + "Stage IIA", + "Stage IIA1", + "Stage IIA2", + "Stage IIAE", + "Stage IIAES", + "Stage IIAS", + "Stage IIB", + "Stage IIBE", + "Stage IIBES", + "Stage IIBS", + "Stage IIC", + "Stage IIE", + "Stage IIEA", + "Stage IIEB", + "Stage IIES", + "Stage III", + "Stage IIIA", + "Stage IIIA1", + "Stage IIIA2", + "Stage IIIAE", + "Stage IIIAES", + "Stage IIIAS", + "Stage IIIB", + "Stage IIIBE", + "Stage IIIBES", + "Stage IIIBS", + "Stage IIIC", + "Stage IIIC1", + "Stage IIIC2", + "Stage IIID", + "Stage IIIE", + "Stage IIIES", + "Stage IIIS", + "Stage IIS", + "Stage IS", + "Stage IV", + "Stage IVA", + "Stage IVA1", + "Stage IVA2", + "Stage IVAE", + "Stage IVAES", + "Stage IVAS", + "Stage IVB", + "Stage IVBE", + "Stage IVBES", + "Stage IVBS", + "Stage IVC", + "Stage IVE", + "Stage IVES", + "Stage IVS", + "Cannot be assessed" + ] + }, + "tumourGradingSystem": { + "type": "string", + "enum": [ + "FNCLCC grading system", + "Four-tier grading system", + "Gleason grade group system", + "Grading system for GISTs", + "Grading system for GNETs", + "ISUP grading system", + "Nuclear grading system for DCIS", + "Scarff-Bloom-Richardson grading system", + "Three-tier grading system", + "Two-tier grading system", + "WHO grading system for CNS tumours" + ] + }, + "tumourGrade": { + "type": "string", + "enum": [ + "Low grade", + "High grade", + "GX", + "G1", + "G2", + "G3", + "G4", + "Low", + "High", + "Grade I", + "Grade II", + "Grade III", + "Grade IV", + "Grade Group 1", + "Grade Group 2", + "Grade Group 3", + "Grade Group 4", + "Grade Group 5" + ] + }, + "percentTumourCells": { + "type": "integer", + "minimum": 0 + }, + "referencePathologyConfirmed": { + "type": "string", + "enum": [ + "Yes", + "No", + "Unknown" + ] + }, + "cellLine": { + "type": "array", + "items": { + "type": "object", + "propertyNames": { + "enum": [ + "cellLineName", + "cellosaurusId", + "treatment" + ] + }, + "required": [ + "cellLineName" + ], + "properties": { + "cellLineName": { + "type": "string" + }, + "cellosaurusId": { + "type": [ + "string", + "null" + ] + }, + "treatment": { + "type": "array", + "items": { + "type": "object", + "propertyNames": { + "enum": [ + "treatmentType", + "compoundName", + "duration", + "timePoint", + "dosage", + "dosageUnits" + ] + }, + "properties": { + "treatmentType": { + "type": [ + "string", + "null" + ] + }, + "compoundName": { + "type": [ + "string", + "null" + ] + }, + "duration": { + "type": [ + "string", + "null" + ] + }, + "timePoint": { + "type": [ + "integer", + "null" + ] + }, + "dosage": { + "type": [ + "integer", + "null" + ] + }, + "dosageUnits": { + "type": [ + "string" + ] + } + } + } + } + } + } + } + } + }, + "qualityControl": { + "type": "array", + "items": { + "type": "object", + "propertyNames": { + "enum": [ + "testName", + "testValue", + "expectedValue", + "testMeasurementMethod", + "testPass" + ] + }, + "properties": { + "testName": { + "type": "string" + }, + "testValue": { + "type": "string" + }, + "expectedValue": { + "type": "string" + }, + "testMeasurementMethod": { + "type": "string" + }, + "testPass": { + "type": "string", + "enum": [ + "PASS", + "FAIL", + "WARN" + ] + } + } + } + }, + "publication": { + "type": "object", + "propertyNames": { + "enum": [ + "title", + "doi" + ] + }, + "properties": { + "title": { + "type": [ + "string", + "null" + ] + }, + "doi": { + "type": [ + "string", + "null" + ] + } + } + }, + "archive": { + "type": "object", + "propertyNames": { + "enum": [ + "ega", + "sra", + "icgcargo", + "encode" + ] + }, + "properties": { + "ega": { + "type": "array", + "items": { + "type": "object", + "properties": { + "egaf": { + "type": "string" + } + } + } + }, + "sra": { + "type": "array", + "items": { + "type": "object", + "properties": { + "gse": { + "type": "string" + } + } + } + }, + "icgcargo": { + "type": "array", + "items": { + "type": "object", + "properties": { + "fileId": { + "type": "string" + } + } + } + }, + "encode": { + "type": "array", + "items": { + "type": "object", + "properties": { + "fileId": { + "type": "string" + } + } + } + } + } + }, + "collaborators": { + "type": "array", + "items": { + "type": "object", + "propertyNames": { + "enum": [ + "name", + "contactEmail", + "affiliation" + ] + }, + "properties": { + "name": { + "type": "string" + }, + "contactEmail": { + "type": [ + "string", + "null" + ], + "pattern": "^\\S+@\\S+\\.\\S+$" + }, + "affiliation": { + "type": [ + "string", + "null" + ] + } + } + } + } + } + } +} \ No newline at end of file