diff --git a/.gitignore b/.gitignore index 510ed8c8..c3026287 100644 --- a/.gitignore +++ b/.gitignore @@ -36,3 +36,14 @@ build/ ## others run.sh .DS_Store +.ipynb_checkpoints/data_generate_v2-checkpoint.ipynb +.ipynb_checkpoints/data_generate-checkpoint.ipynb +data_generate.ipynb +data_generate_v2.ipynb +playground-data/header +.demoData/schemas/.prettierrc +data_generate_v3.ipynb +.ipynb_checkpoints/data_generate_v3-checkpoint.ipynb +fixdata.ipynb +demoData/schemas/demoDataSchemaV3.json +.ipynb_checkpoints/fixdata-checkpoint.ipynb diff --git a/demoData/arrangerConfigs/base.json b/demoData/arrangerConfigs/base.json new file mode 100644 index 00000000..2daec630 --- /dev/null +++ b/demoData/arrangerConfigs/base.json @@ -0,0 +1,6 @@ +{ + "baseConfigs": { + "documentType": "analysis", + "index": "analysis_centric_1.0" + } +} diff --git a/demoData/arrangerConfigs/extended.json b/demoData/arrangerConfigs/extended.json new file mode 100644 index 00000000..7998c784 --- /dev/null +++ b/demoData/arrangerConfigs/extended.json @@ -0,0 +1,318 @@ +{ + "extendedConfigs": { + "extended": [ + { + "fieldName": "samples.subitterSampleId", + "displayName": "Submitter Sample ID" + }, + { + "fieldName": "samples.sampleType", + "displayName": "Sample Type" + }, + { + "fieldName": "samples.matchedNormalSubmitterSampleId", + "displayName": "Matched Normal Sample ID" + }, + { + "fieldName": "samples.specimen.submitterSpecimenId", + "displayName": "Submitter Specimen ID" + }, + { + "fieldName": "samples.specimen.specimenType", + "displayName": "Specimen Type" + }, + { + "fieldName": "samples.specimen.tumourNormalDesignation", + "displayName": "Tumour Normal Designation" + }, + { + "fieldName": "samples.specimen.specimenTissueSource", + "displayName": "Tissue Source" + }, + { + "fieldName": "samples.donor.submitterDonorId", + "displayName": "Submitter Donor ID" + }, + { + "fieldName": "samples.donor.gender", + "displayName": "Gender" + }, + { + "fieldName": "samples.donor.submitterDonorId", + "displayName": "Sample Submitter Donor ID" + }, + { + "fieldName": "donor.submitterDonorId", + "displayName": "Donor ID" + }, + { + "fieldName": "donor.primarySite", + "displayName": "Primary Site" + }, + { + "fieldName": "donor.vitalStatus", + "displayName": "Vital Status" + }, + { + "fieldName": "donor.survivalTime", + "displayName": "Survival Time" + }, + { + "fieldName": "donor.primaryDiagnosis.ageAtDiagnosis", + "displayName": "Age At Diagnosis" + }, + { + "fieldName": "donor.primaryDiagnosis.cancerTypeCode", + "displayName": "Cancer Type Code" + }, + { + "fieldName": "donor.primaryDiagnosis.laterality", + "displayName": "Laterality" + }, + { + "fieldName": "donor.primaryDiagnosis.clinicalTumourStagingSystem", + "displayName": "Tumour Staging System" + }, + { + "fieldName": "donor.primaryDiagnosis.clinicalStageGroup", + "displayName": "Staging Group" + }, + { + "fieldName": "donor.primaryDiagnosis.lymphNodesExaminedStatus", + "displayName": "Examination Status" + }, + { + "fieldName": "donor.primaryDiagnosis.performanceStatus", + "displayName": "Performance Status" + }, + { + "fieldName": "donor.primaryDiagnosis.treatment.treatmentType", + "displayName": "Treatment" + }, + { + "fieldName": "donor.primaryDiagnosis.treatment.treatmentIntent", + "displayName": "Treatment Intent" + }, + { + "fieldName": "donor.primaryDiagnosis.treatment.treatmentStartInterval", + "displayName": "Treatment Start Interval" + }, + { + "fieldName": "donor.primaryDiagnosis.treatment.treatmentDuration", + "displayName": "Treatment Duration" + }, + { + "fieldName": "donor.primaryDiagnosis.treatment.responseToTreatment", + "displayName": "Response To Treatment" + }, + { + "fieldName": "donor.primaryDiagnosis.treatment.surgery.surgeryType", + "displayName": "Surgery Type" + }, + { + "fieldName": "donor.primaryDiagnosis.treatment.surgery.surgerySite", + "displayName": "Surgery Site" + }, + { + "fieldName": "donor.primaryDiagnosis.treatment.surgery.surgeryLocation", + "displayName": "Surgery Location" + }, + { + "fieldName": "donor.primaryDiagnosis.treatment.surgery.residualTumourClassification", + "displayName": "Residual Tumour Classification" + }, + { + "fieldName": "donor.primaryDiagnosis.treatment.hormoneTherapy.drugName", + "displayName": "Hormone Therapy" + }, + { + "fieldName": "donor.primaryDiagnosis.treatment.hormoneTherapy.drugRxnormcui", + "displayName": "RxNorm" + }, + { + "fieldName": "donor.primaryDiagnosis.treatment.hormoneTherapy.cumulativeDrugDosage", + "displayName": "Hormone Dosage" + }, + { + "fieldName": "donor.primaryDiagnosis.treatment.hormoneTherapy.hormoneDrugDosageUnits", + "displayName": "Dosage Units" + }, + { + "fieldName": "donor.primaryDiagnosis.treatment.chemotherapy.drugName", + "displayName": "Chemotherapy" + }, + { + "fieldName": "donor.primaryDiagnosis.treatment.chemotherapy.drugRxnormcui", + "displayName": "RxNorm" + }, + { + "fieldName": "donor.primaryDiagnosis.treatment.chemotherapy.cumulativeDrugDosage", + "displayName": "Chemotherapy Dosage" + }, + { + "fieldName": "donor.primaryDiagnosis.treatment.chemotherapy.chemotherapyDosageUnits", + "displayName": "Chemotherapy Dosage Units" + }, + { + "fieldName": "donor.primaryDiagnosis.treatment.immunotherapy.drugName", + "displayName": "Immunotherapy" + }, + { + "fieldName": "donor.primaryDiagnosis.treatment.immunotherapy.drugRxnormcui", + "displayName": "Immunotherapy RxNorm" + }, + { + "fieldName": "donor.primaryDiagnosis.treatment.immunotherapy.immunotherapyType", + "displayName": "Immunotherapy Type" + }, + { + "fieldName": "donor.primaryDiagnosis.treatment.radiation.radiationTherapyModality", + "displayName": "Radiation Modality" + }, + { + "fieldName": "donor.primaryDiagnosis.treatment.radiation.radiationTherapyType", + "displayName": "Radiation Therapy Type" + }, + { + "fieldName": "donor.primaryDiagnosis.treatment.radiation.anatomicalSiteIrradiated", + "displayName": "Radiation Site" + }, + { + "fieldName": "donor.primaryDiagnosis.treatment.radiation.radiationTherapyDosage", + "displayName": "Radiation Dosage" + }, + { + "fieldName": "donor.primaryDiagnosis.treatment.radiation.radiationTherapyFractions", + "displayName": "Radiation Therapy Fractions" + }, + { + "fieldName": "donor.primaryDiagnosis.followUp.intervalOfFollowup", + "displayName": "Follow Up Interval (Days)" + }, + { + "fieldName": "donor.primaryDiagnosis.followUp.diseaseStatusAtFollowup", + "displayName": "Status At Followup" + }, + { + "fieldName": "donor.primaryDiagnosis.ageAtDiagnosis", + "displayName": "Age At Diagnosis" + }, + { + "fieldName": "donor.primaryDiagnosis.cancerTypeCode", + "displayName": "Cancer Type Code" + }, + { + "fieldName": "donor.primaryDiagnosis.comorbidity.ageAtComorbidityDiagnosis", + "displayName": "Age at Comorbidity Diagnosis" + }, + { + "fieldName": "donor.primaryDiagnosis.comorbidity.comorbidityTypeCode", + "displayName": "Comorbidity Type Code" + }, + { + "fieldName": "specimen.specimenAcquisitionInterval", + "displayName": "Specimen Acquisition Interval" + }, + { + "fieldName": "specimen.specimenAnatomicLocation", + "displayName": "Specimen Anatomic Location" + }, + { + "fieldName": "specimen.specimenLaterality", + "displayName": "Specimen Laterality" + }, + { + "fieldName": "specimen.tumourHistologicalType", + "displayName": "Tumour Histological Type" + }, + { + "fieldName": "specimen.pathologicalTumourStagingSystem", + "displayName": "Pathological Tumour Staging System" + }, + { + "fieldName": "specimen.pathologicalStageGroup", + "displayName": "Pathological Stage Group" + }, + { + "fieldName": "specimen.tumourGradingSystem", + "displayName": "Tumour Grading System" + }, + { + "fieldName": "specimen.tumourGrade", + "displayName": "Tumour Grade" + }, + { + "fieldName": "specimen.percentTumourCells", + "displayName": "Percent Tumour Cells" + }, + { + "fieldName": "specimen.referencePathologyConfirmed", + "displayName": "Refernce Pathology Confirmed" + }, + { + "fieldName": "files.dataType", + "displayName": "Data Type" + }, + { + "fieldName": "files.fileName", + "displayName": "File Name" + }, + { + "fieldName": "files.fileSize", + "displayName": "File Size" + }, + { + "fieldName": "files.fileMd5sum", + "displayName": "File Md5sum" + }, + { + "fieldName": "files.fileAccess", + "displayName": "File Access" + }, + { + "fieldName": "files.fileType", + "displayName": "File Type" + }, + { + "fieldName": "files.info.dataCategory", + "displayName": "Data Category" + }, + { + "fieldName": "files.info.jbrowseCoordinates", + "displayName": "jbrowse Coordinate" + }, + { + "fieldName": "collaborator.contactEmail", + "displayName": "Contact Email" + }, + { + "fieldName": "collaborator.name", + "displayName": "Collaborator" + }, + { + "fieldName": "collaborator.affiliation", + "displayName": "Affiliation" + }, + { + "fieldName": "experiment.platform", + "displayName": "Sequencing Platform" + }, + { + "fieldName": "experiment.experimentalStrategy", + "displayName": "Experimental Strategy" + }, + { + "fieldName": "experiment.submitterSequencingExperimentId", + "displayName": "Experiment Id" + }, + { + "fieldName": "workflow.workflowName", + "displayName": "Workflow" + }, + { + "fieldName": "workflow.genomeBuild", + "displayName": "Genome Build" + } + ] + } +} \ No newline at end of file diff --git a/demoData/arrangerConfigs/facets.json b/demoData/arrangerConfigs/facets.json new file mode 100644 index 00000000..bd0db9e1 --- /dev/null +++ b/demoData/arrangerConfigs/facets.json @@ -0,0 +1,78 @@ +{ + "facetsConfigs": { + "facets": { + "aggregations": [ + { + "active": true, + "fieldName": "sample.sampleType", + "show": true + }, + { + "active": true, + "fieldName": "sample.specimen.tumourNormalDesignation", + "show": true + }, + { + "active": true, + "fieldName": "donor.primarySite", + "show": true + }, + { + "active": true, + "fieldName": "donor.clinicalTumourStagingSystem", + "show": true + }, + { + "active": true, + "fieldName": "sample.specimen.specimenTissueSource", + "show": true + }, + { + "active": true, + "fieldName": "sample.specimen.specimenType", + "show": true + }, + { + "active": true, + "fieldName": "sample.donor.gender", + "show": true + }, + { + "active": true, + "fieldName": "files.info.dataCategory", + "show": true + }, + { + "active": true, + "fieldName": "files.fileSize", + "show": true + }, + { + "active": true, + "fieldName": "files.fileType", + "show": true + }, + { + "active": true, + "fieldName": "files.fileAccess", + "show": true + }, + { + "active": true, + "fieldName": "files.dataType", + "show": true + }, + { + "active": true, + "fieldName": "experiment.experimentalStrategy", + "show": true + }, + { + "active": true, + "fieldName": "experiment.platform", + "show": true + } + ] + } + } +} diff --git a/demoData/arrangerConfigs/matchbox.json b/demoData/arrangerConfigs/matchbox.json new file mode 100644 index 00000000..fa0202da --- /dev/null +++ b/demoData/arrangerConfigs/matchbox.json @@ -0,0 +1,41 @@ +{ + "matchboxConfigs": { + "matchbox": [ + { + "displayName": "file", + "fieldName": "", + "isActive": false, + "keyFieldName": null, + "searchFields": [] + }, + { + "displayName": "Donors", + "fieldName": "donors", + "isActive": false, + "keyFieldName": null, + "searchFields": [] + }, + { + "displayName": "Donors Specimens", + "fieldName": "donors.specimens", + "isActive": false, + "keyFieldName": null, + "searchFields": [] + }, + { + "displayName": "Donors Specimens Samples", + "fieldName": "donors.specimens.samples", + "isActive": false, + "keyFieldName": null, + "searchFields": [] + }, + { + "displayName": "Repositories", + "fieldName": "repositories", + "isActive": false, + "keyFieldName": null, + "searchFields": [] + } + ] + } +} diff --git a/demoData/arrangerConfigs/table.json b/demoData/arrangerConfigs/table.json new file mode 100644 index 00000000..f670744e --- /dev/null +++ b/demoData/arrangerConfigs/table.json @@ -0,0 +1,111 @@ +{ + "tableConfigs": { + "table": { + "columns": [ + { + "canChangeShow": true, + "displayType": "string", + "fieldName": "donor.submitterDonorId", + "jsonPath": "$.donor.submitterDonorId", + "query": "donor.submitterDonorId", + "show": true + }, + { + "canChangeShow": true, + "displayType": "list", + "fieldName": "sample.sampleType", + "jsonPath": "$.sample.sampleType", + "query": "sample.sampleType", + "show": true + }, + { + "canChangeShow": true, + "displayType": "list", + "fieldName": "sample.specimen.tumourNormalDesignation", + "jsonPath": "$.sample.specimen.tumourNormalDesignation", + "query": "sample.specimen.tumourNormalDesignation", + "show": true + }, + { + "canChangeShow": true, + "displayType": "list", + "fieldName": "donor.primaryDiagnosis.clinicalStageGroup", + "jsonPath": "$.donor.primaryDiagnosis.clinicalStageGroup", + "query": "donor.primaryDiagnosis.clinicalStageGroup", + "show": true + }, + { + "canChangeShow": true, + "displayType": "list", + "fieldName": "sample.specimen.specimenTissueSource", + "jsonPath": "$.sample.specimen.specimenTissueSource", + "query": "sample.specimen.specimenTissueSource", + "show": true + }, + { + "canChangeShow": true, + "displayType": "list", + "fieldName": "sample.specimen.specimenType", + "jsonPath": "$.sample.specimen.specimenType", + "query": "sample.specimen.specimenType", + "show": true + }, + { + "canChangeShow": true, + "displayType": "list", + "fieldName": "donor.gender", + "jsonPath": "$.donor.gender", + "query": "donor.gender", + "show": true + }, + { + "canChangeShow": true, + "displayType": "list", + "fieldName": "files.fileType", + "jsonPath": "$.files.fileType", + "query": "files.fileType", + "show": true + }, + { + "canChangeShow": true, + "displayType": "list", + "fieldName": "files.fileAccess", + "jsonPath": "$.files.fileAccess", + "query": "files.fileAccess", + "show": true + }, + { + "canChangeShow": true, + "displayType": "list", + "fieldName": "files.dataType", + "jsonPath": "$.files.dataType", + "query": "files.dataType", + "show": true + }, + { + "canChangeShow": true, + "displayType": "list", + "fieldName": "donor.primarySite", + "jsonPath": "$.donor.primarySite", + "query": "donor.primarySite", + "show": true + }, + { + "canChangeShow": true, + "displayType": "list", + "fieldName": "donor.vitalStatus", + "jsonPath": "$.donor.vitalStatus", + "query": "donor.vitalStatus", + "show": true + } + ], + "defaultSorting": [ + { + "fieldName": "donor.submitterDonorId" + } + ], + "maxResultsWindow": 10000, + "rowIdFieldName": "id" + } + } +} diff --git a/demoData/data/README.md b/demoData/data/README.md new file mode 100644 index 00000000..a2b682f9 --- /dev/null +++ b/demoData/data/README.md @@ -0,0 +1 @@ +python submit_payloads.py -t 338a94cd-NNNN-NNNN-NNNN-f3d2519d119c -d /Users/esu/Desktop/GitHub/dms/playground-data -j TEST_SPECIMEN_rfdijnavpljntiranaxn_T2_copy.json -s demoData diff --git a/demoData/data/TEST_SPECIMEN_apdymevbedrhwyeexbvb_N1.json b/demoData/data/TEST_SPECIMEN_apdymevbedrhwyeexbvb_N1.json new file mode 100644 index 00000000..d37cc5eb --- /dev/null +++ b/demoData/data/TEST_SPECIMEN_apdymevbedrhwyeexbvb_N1.json @@ -0,0 +1,183 @@ +{ + "samples": [ + { + "submitterSampleId": "TEST_SPECIMEN_apdymevbedrhwyeexbvb_N1", + "sampleType": "Total DNA", + "matchedNormalSubmitterSampleId": null, + "specimen": { + "submitterSpecimenId": "TEST_SPECIMEN_apdymevbedrhwyeexbvb_N1", + "specimenType": "Normal", + "tumourNormalDesignation": "Normal", + "specimenTissueSource": "Lymph node" + }, + "donor": { + "submitterDonorId": "TEST_DONOR_apdymevbedrhwyeexbvb", + "gender": "Other" + } + } + ], + "donor": { + "submitterDonorId": "TEST_DONOR_apdymevbedrhwyeexbvb", + "primarySite": [ + "Hematopoietic and reticuloendothelial systems" + ], + "vitalStatus": "Deceased", + "survivalTime": 126, + "causeOfDeath": "Died of cancer", + "primaryDiagnosis": [ + { + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_apdymevbedrhwyeexbvb_0", + "ageAtDiagnosis": 56, + "cancerTypeCode": "C88.2", + "laterality": "Unilateral, side not specified", + "clinicalTumourStagingSystem": "St Jude staging system", + "clinicalStageGroup": "Stage II", + "lymphNodesExaminedStatus": "No lymph nodes found in resected specimen", + "performanceStatus": "Grade 0", + "treatment": [ + { + "submitterTreatmentId": "TEST_TREATMENT_apdymevbedrhwyeexbvb_0", + "treatmentType": [ + "No treatment" + ] + } + ], + "followUp": [ + { + "submitterFollowUpId": "TEST_FOLLOW_UP_apdymevbedrhwyeexbvb_0", + "intervalOfFollowup": 93, + "diseaseStatusAtFollowup": "No evidence of disease" + } + ] + }, + { + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_apdymevbedrhwyeexbvb_1", + "ageAtDiagnosis": 4, + "cancerTypeCode": "C88.2", + "laterality": "Unknown", + "clinicalTumourStagingSystem": "Durie-Salmon staging system", + "clinicalStageGroup": "Stage III", + "lymphNodesExaminedStatus": "No lymph nodes found in resected specimen", + "performanceStatus": "Grade 1", + "treatment": [ + { + "submitterTreatmentId": "TEST_TREATMENT_apdymevbedrhwyeexbvb_1", + "treatmentType": [ + "Surgery", + "Hormonal therapy", + "Chemotherapy" + ], + "treatmentIntent": "Unknown", + "treatmentStartInterval": 70, + "treatmentDuration": 56, + "responseToTreatment": "Partial response", + "surgery": [ + { + "surgeryType": "Cholecystectomy", + "surgerySite": "C78.4", + "surgeryLocation": "Metastatic", + "residualTumourClassification": "R2" + } + ], + "hormoneTherapy": [ + { + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 98, + "hormoneDrugDosageUnits": "ug/m2" + } + ], + "chemotherapy": [ + { + "drugName": "leucovorin", + "drugRxnormcui": "6313", + "cumulativeDrugDosage": 88, + "chemotherapyDosageUnits": "g/m2" + } + ] + } + ], + "followUp": [ + { + "submitterFollowUpId": "TEST_FOLLOW_UP_apdymevbedrhwyeexbvb_1", + "intervalOfFollowup": 3, + "diseaseStatusAtFollowup": "Relapse or recurrence" + } + ] + } + ], + "comorbidity": [ + { + "ageAtComorbidityDiagnosis": 59, + "comorbidityTypeCode": "A76.39" + } + ] + }, + "specimen": { + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_apdymevbedrhwyeexbvb_0", + "submitterSpecimenId": "TEST_SPECIMEN_apdymevbedrhwyeexbvb_N1", + "specimenAcquisitionInterval": 48, + "specimenAnatomicLocation": "C75", + "specimenLaterality": "Right", + "tumourHistologicalType": "9556/03", + "pathologicalTumourStagingSystem": "AJCC 7th edition", + "pathologicalStageGroup": "Stage I", + "tumourGradingSystem": "Four-tier grading system", + "tumourGrade": "G1", + "percentTumourCells": 63, + "referencePathologyConfirmed": "Yes" + }, + "files": [ + { + "dataType": "VCF Index", + "fileName": "TEST_SPECIMEN_apdymevbedrhwyeexbvb_N1.snv.vcf.gz.tbi", + "fileSize": 143, + "fileMd5sum": "86f616bd1e1fb5933aa615618fd2faba", + "fileAccess": "controlled", + "fileType": "TBI", + "info": { + "dataCategory": "Simple Nucelotide Variation", + "jbrowseCoordinates": "hg38:chr1:103573-197390" + } + }, + { + "dataType": "Raw SV Calls", + "fileName": "TEST_SPECIMEN_apdymevbedrhwyeexbvb_N1.snv.vcf.gz", + "fileSize": 17246, + "fileMd5sum": "a9f4ad275d7df9941a62406a7cc6fa85", + "fileAccess": "controlled", + "fileType": "VCF", + "info": { + "dataCategory": "Simple Nucelotide Variation", + "jbrowseCoordinates": "hg38:chr1:103573-197390" + } + } + ], + "collaborator": [ + { + "contactEmail": "sturedman@sturedman_inc.org", + "name": "sturedman", + "affiliation": "sturedman inc" + } + ], + "experiment": { + "platform": "ILLUMINA", + "experimentalStrategy": "WGS", + "submitterSequencingExperimentId": "EXPERIMENT" + }, + "workflow": { + "workflowName": "informatics_workflow", + "genomeBuild": "GRCh38_hla_decoy_ebv", + "inputs": [ + { + "analysisType": "sequencing_alignment", + "tumourAnalysisId": "00000000-0000-0000-0000-000000000000", + "normalAnalysisId": "00000000-0000-0000-0000-000000000000" + } + ] + }, + "analysisType": { + "name": "demoDataSchema" + }, + "studyId": "demoData" +} diff --git a/demoData/data/TEST_SPECIMEN_apdymevbedrhwyeexbvb_N1.snv.vcf.gz b/demoData/data/TEST_SPECIMEN_apdymevbedrhwyeexbvb_N1.snv.vcf.gz new file mode 100644 index 00000000..022c2b8f Binary files /dev/null and b/demoData/data/TEST_SPECIMEN_apdymevbedrhwyeexbvb_N1.snv.vcf.gz differ diff --git a/demoData/data/TEST_SPECIMEN_apdymevbedrhwyeexbvb_N1.snv.vcf.gz.tbi b/demoData/data/TEST_SPECIMEN_apdymevbedrhwyeexbvb_N1.snv.vcf.gz.tbi new file mode 100644 index 00000000..7fe72d7e Binary files /dev/null and b/demoData/data/TEST_SPECIMEN_apdymevbedrhwyeexbvb_N1.snv.vcf.gz.tbi differ diff --git a/demoData/data/TEST_SPECIMEN_apdymevbedrhwyeexbvb_N2.indel.vcf.gz b/demoData/data/TEST_SPECIMEN_apdymevbedrhwyeexbvb_N2.indel.vcf.gz new file mode 100644 index 00000000..113ef939 Binary files /dev/null and b/demoData/data/TEST_SPECIMEN_apdymevbedrhwyeexbvb_N2.indel.vcf.gz differ diff --git a/demoData/data/TEST_SPECIMEN_apdymevbedrhwyeexbvb_N2.indel.vcf.gz.tbi b/demoData/data/TEST_SPECIMEN_apdymevbedrhwyeexbvb_N2.indel.vcf.gz.tbi new file mode 100644 index 00000000..0cc1cf6d Binary files /dev/null and b/demoData/data/TEST_SPECIMEN_apdymevbedrhwyeexbvb_N2.indel.vcf.gz.tbi differ diff --git a/demoData/data/TEST_SPECIMEN_apdymevbedrhwyeexbvb_N2.json b/demoData/data/TEST_SPECIMEN_apdymevbedrhwyeexbvb_N2.json new file mode 100644 index 00000000..d54434a1 --- /dev/null +++ b/demoData/data/TEST_SPECIMEN_apdymevbedrhwyeexbvb_N2.json @@ -0,0 +1,171 @@ +{ + "samples": [ + { + "submitterSampleId": "TEST_SPECIMEN_apdymevbedrhwyeexbvb_N2", + "sampleType": "Total DNA", + "matchedNormalSubmitterSampleId": null, + "specimen": { + "submitterSpecimenId": "TEST_SPECIMEN_apdymevbedrhwyeexbvb_N2", + "specimenType": "Cell line - derived from normal", + "tumourNormalDesignation": "Normal", + "specimenTissueSource": "Blood derived - peripheral blood" + }, + "donor": { + "submitterDonorId": "TEST_DONOR_apdymevbedrhwyeexbvb", + "gender": "Other" + } + } + ], + "donor": { + "submitterDonorId": "TEST_DONOR_apdymevbedrhwyeexbvb", + "primarySite": [ + "Hematopoietic and reticuloendothelial systems" + ], + "vitalStatus": "Deceased", + "survivalTime": 126, + "causeOfDeath": "Died of cancer", + "primaryDiagnosis": [ + { + "submitterPrimaryDiagnosisId": "TEST_PRIMARY_DIAGNOSIS_apdymevbedrhwyeexbvb_0", + "ageAtDiagnosis": 56, + "cancerTypeCode": "C88.2", + "laterality": "Unilateral, side not specified", + "clinicalTumourStagingSystem": "St Jude staging system", + "clinicalStageGroup": "Stage II", + "lymphNodesExaminedStatus": "No lymph nodes found in resected specimen", + "performanceStatus": "Grade 0", + "treatment": [ + { + "submitterTreatmentId": "TEST_TREATMENT_apdymevbedrhwyeexbvb_0", + "treatmentType": [ + "No treatment" + ] + } + ], + "followUp": [ + { + "submitterFollowUpId": "TEST_FOLLOW_UP_apdymevbedrhwyeexbvb_0", + "intervalOfFollowup": 93, + "diseaseStatusAtFollowup": "No evidence of disease" + } + ] + }, + { + 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"submitterSequencingExperimentId": "EXPERIMENT" + }, + "workflow": { + "workflowName": "informatics_workflow", + "genomeBuild": "GRCh38_hla_decoy_ebv", + "inputs": [ + { + "analysisType": "sequencing_alignment", + "tumourAnalysisId": "00000000-0000-0000-0000-000000000000", + "normalAnalysisId": "00000000-0000-0000-0000-000000000000" + } + ] + }, + "analysisType": { + "name": "demoDataSchema" + }, + "studyId": "demoData" +} diff --git a/demoData/data/manifest.txt b/demoData/data/manifest.txt new file mode 100644 index 00000000..93c20767 --- /dev/null +++ b/demoData/data/manifest.txt @@ -0,0 +1,2 @@ +b9ba9f9c-2831-48ef-ba9f-9c2831a8effd +c7795bf4-28c1-5122-81b2-3b8609d4a42c /output/TEST_SPECIMEN_eoltfhhxwpeclagdxpwj_T1.snv.vcf.gz.tbi 4a6e898d26dd9663eed1c95264bd4505 diff --git a/demoData/data/package-lock.json b/demoData/data/package-lock.json new file mode 100644 index 00000000..c0a8fc7b --- /dev/null +++ b/demoData/data/package-lock.json @@ -0,0 +1,27 @@ +{ + "name": "playground-data", + "lockfileVersion": 2, + "requires": true, + "packages": { + "": { + "dependencies": { + "python": "^0.0.4" + } + }, + "node_modules/python": { + "version": "0.0.4", + "resolved": "https://registry.npmjs.org/python/-/python-0.0.4.tgz", + "integrity": "sha512-7avKA/6XxrwcGSDes8xGn7FHAUdAUQXKHtpjDulyv5/nm7TcPblmPRvXjjwx5knWHqeRiipqH/TZR2HhmJ4CGQ==", + "engines": { + "node": ">= 0.4.1" + } + } + }, + "dependencies": { + "python": { + "version": "0.0.4", + "resolved": "https://registry.npmjs.org/python/-/python-0.0.4.tgz", + "integrity": "sha512-7avKA/6XxrwcGSDes8xGn7FHAUdAUQXKHtpjDulyv5/nm7TcPblmPRvXjjwx5knWHqeRiipqH/TZR2HhmJ4CGQ==" + } + } +} diff --git a/demoData/data/package.json b/demoData/data/package.json new file mode 100644 index 00000000..d126a004 --- /dev/null +++ b/demoData/data/package.json @@ -0,0 +1,5 @@ +{ + "dependencies": { + "python": "^0.0.4" + } +} diff --git a/demoData/data/submit_payloads.py b/demoData/data/submit_payloads.py new file mode 100644 index 00000000..d7471477 --- /dev/null +++ b/demoData/data/submit_payloads.py @@ -0,0 +1,153 @@ +#!/usr/bin/env python3 +# -*- coding: utf-8 -*- + + +import subprocess +import re +from argparse import ArgumentParser + + +parser = ArgumentParser(description='Tool: Quick song score submit files') +parser.add_argument("-t", "--token", dest="token", required=True, + help="API token", type=str, default ="88fe6ab2-8a5a-4ece-8f32-48a3e4db41fd") +parser.add_argument("-a", "--song", dest="song_url", + help="SONG URL", type=str, default ="https://song.demo.overture.bio") +parser.add_argument("-b", "--score", dest="score_url", + help="SCORE URL", type=str, default ="https://score.demo.overture.bio") +parser.add_argument("-s", "--study", dest="studyId", + help="studyId", type=str, default ="demoData") +parser.add_argument("-j", "--json", dest="json", + help="JSON file", type=str) +parser.add_argument("-d", "--directory", dest="directory", + help="JSON and data directory", type=str) + +args = parser.parse_args() + + +token=args.token +song_url=args.song_url +studyId=args.studyId +score_url=args.score_url +json_directory=args.directory +json_file=args.json + +submit_cmd=\ +""" +docker run \ +-e CLIENT_ACCESS_TOKEN=%s \ +-e CLIENT_STUDY_ID=%s \ +-e CLIENT_SERVER_URL=%s \ +--network="host" \ +--mount type=bind,source=%s,target=/output \ +ghcr.io/overture-stack/song-client \ +sing submit -f /output/%s +""" % (token,studyId,song_url,json_directory,json_file) + +print("Running %s :" % submit_cmd) +proc = subprocess.Popen( + submit_cmd, + shell=True, + stdin=subprocess.PIPE, + stdout=subprocess.PIPE, + stderr=subprocess.PIPE + ) + +stdout, stderr = proc.communicate() + +if proc.returncode!=0: + print("ERRORCODE : %s " % (str(proc.returncode))) + print("STDOUT : %s " % (stdout.decode("utf-8").strip())) + print("STDERR : %s " % (stderr.decode("utf-8").strip())) +else: + print("SUCCESS") + analysisId=re.findall('[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}',stdout.decode("utf-8").strip())[0] + print("analysisId generated : %s" % (analysisId)) + + +manifest_cmd=\ +""" +docker run \ +-e CLIENT_ACCESS_TOKEN=%s \ +-e CLIENT_STUDY_ID=%s \ +-e CLIENT_SERVER_URL=%s \ +--network="host" \ +--mount type=bind,source=%s,target=/output \ +ghcr.io/overture-stack/song-client \ +sing manifest -a %s -f /output/manifest.txt -d /output/ +""" % (token,studyId,song_url,json_directory,analysisId) + +print("Running : %s " % manifest_cmd) +proc = subprocess.Popen( + manifest_cmd, + shell=True, + stdin=subprocess.PIPE, + stdout=subprocess.PIPE, + stderr=subprocess.PIPE + ) + +stdout, stderr = proc.communicate() + +if proc.returncode!=0: + print("ERRORCODE : %s " % (str(proc.returncode))) + print("STDOUT : %s " % (stdout.decode("utf-8").strip())) + print("STDERR : %s " % (stderr.decode("utf-8").strip())) +else: + print("SUCCESS") + +upload_cmd=\ +""" +docker run \ +-e ACCESSTOKEN=%s \ +-e STORAGE_URL=%s \ +-e METADATA_URL=%s \ +--network="host" \ +--mount type=bind,source="%s",target=/output \ +ghcr.io/overture-stack/score \ +score-client upload --manifest /output/manifest.txt +""" % (token,score_url,song_url,json_directory) +print("Running : %s" % upload_cmd) +proc = subprocess.Popen( + upload_cmd, + shell=True, + stdin=subprocess.PIPE, + stdout=subprocess.PIPE, + stderr=subprocess.PIPE + ) + +stdout, stderr = proc.communicate() + +if proc.returncode!=0: + print("ERRORCODE : %s " % (str(proc.returncode))) + print("STDOUT : %s " % (stdout.decode("utf-8").strip())) + print("STDERR : %s " % (stderr.decode("utf-8").strip())) +else: + print("SUCCESS") + +publish_cmd=\ +""" +docker run \ +-e CLIENT_ACCESS_TOKEN=%s \ +-e CLIENT_STUDY_ID=%s \ +-e CLIENT_SERVER_URL=%s \ +--network="host" \ +--mount type=bind,source=%s,target=/output \ +ghcr.io/overture-stack/song-client \ +sing publish -a %s +""" % (token,studyId,song_url,json_directory,analysisId) +print("Running : %s" % publish_cmd) +proc = subprocess.Popen( + publish_cmd, + shell=True, + stdin=subprocess.PIPE, + stdout=subprocess.PIPE, + stderr=subprocess.PIPE + ) + +stdout, stderr = proc.communicate() + +if proc.returncode!=0: + print("ERRORCODE : %s " % (str(proc.returncode))) + print("STDOUT : %s " % (stdout.decode("utf-8").strip())) + print("STDERR : %s " % (stderr.decode("utf-8").strip())) +else: + print("SUCCESS") diff --git a/demoData/schemas/.prettierrc b/demoData/schemas/.prettierrc new file mode 100644 index 00000000..7bfe8b71 --- /dev/null +++ b/demoData/schemas/.prettierrc @@ -0,0 +1,13 @@ +{ + "printWidth": 100, + "tabWidth": 2, + "useTabs": false, + "semi": true, + "singleQuote": false, + "quoteProps": "as-needed", + "trailingComma": "all", + "bracketSpacing": true, + "jsxBracketSameLine": false, + "arrowParens": "always", + "endOfLine": "auto" +} diff --git a/demoData/schemas/baseSchema.json b/demoData/schemas/baseSchema.json new file mode 100644 index 00000000..f373984c --- /dev/null +++ b/demoData/schemas/baseSchema.json @@ -0,0 +1,263 @@ +{ + "$schema": "http://json-schema.org/draft-07/schema#", + "id": "analysisPayload", + "type": "object", + "definitions": { + "common": { + "md5": { + "type": "string", + "pattern": "^[a-fA-F0-9]{32}$" + }, + "submitterId": { + "type": "string", + "pattern": "^[A-Za-z0-9\\-\\._]{1,64}$" + }, + "info": { + "type": "object" + } + }, + "file": { + "fileType": { + "type": "string", + "enum": [ + "FASTA", + "FAI", + "FASTQ", + "BAM", + "BAI", + "VCF", + "TBI", + "IDX", + "XML", + "TGZ", + "CRAM", + "CRAI", + "TXT" + ] + }, + "fileData": { + "type": "object", + "required": ["dataType", "fileName", "fileSize", "fileType", "fileAccess", "fileMd5sum"], + "properties": { + "dataType": { + "type": "string" + }, + "fileName": { + "type": "string", + "pattern": "^[A-Za-z0-9_\\.\\-\\[\\]\\(\\)]+$" + }, + "fileSize": { + "type": "integer", + "min": 0 + }, + "fileAccess": { + "type": "string", + "enum": ["open", "controlled"] + }, + "fileType": { "$ref": "#/definitions/file/fileType" }, + "fileMd5sum": { "$ref": "#/definitions/common/md5" }, + "info": { "$ref": "#/definitions/common/info" } + } + } + }, + "donor": { + "gender": { + "type": "string", + "enum": ["Male", "Female", "Other"] + }, + "donorData": { + "type": "object", + "required": ["submitterDonorId", "gender"], + "properties": { + "submitterDonorId": { "$ref": "#/definitions/common/submitterId" }, + "gender": { "$ref": "#/definitions/donor/gender" }, + "info": { "$ref": "#/definitions/common/info" } + } + } + }, + "specimen": { + "specimenTissueSource": { + "type": "string", + "enum": [ + "Blood derived", + "Blood derived - bone marrow", + "Blood derived - peripheral blood", + "Bone marrow", + "Buccal cell", + "Lymph node", + "Solid tissue", + "Plasma", + "Serum", + "Urine", + "Cerebrospinal fluid", + "Sputum", + "Other", + "Pleural effusion", + "Mononuclear cells from bone marrow", + "Saliva", + "Skin", + "Intestine", + "Buffy coat", + "Stomach", + "Esophagus", + "Tonsil", + "Spleen", + "Bone", + "Cerebellum", + "Endometrium" + ] + }, + "specimenType": { + "type": "string", + "enum": [ + "Normal", + "Normal - tissue adjacent to primary tumour", + "Primary tumour", + "Primary tumour - adjacent to normal", + "Primary tumour - additional new primary", + "Recurrent tumour", + "Metastatic tumour", + "Metastatic tumour - metastasis local to lymph node", + "Metastatic tumour - metastasis to distant location", + "Metastatic tumour - additional metastatic", + "Xenograft - derived from primary tumour", + "Xenograft - derived from tumour cell line", + "Cell line - derived from xenograft tumour", + "Cell line - derived from tumour", + "Cell line - derived from normal", + "Tumour - unknown if derived from primary or metastatic", + "Cell line – derived from metastatic tumour", + "Xenograft – derived from metastatic tumour" + ] + }, + "tumourNormalDesignation": { + "type": "string", + "enum": ["Normal", "Tumour"] + }, + "specimenData": { + "type": "object", + "required": [ + "submitterSpecimenId", + "specimenTissueSource", + "tumourNormalDesignation", + "specimenType" + ], + "properties": { + "submitterSpecimenId": { "$ref": "#/definitions/common/submitterId" }, + "specimenTissueSource": { + "$ref": "#/definitions/specimen/specimenTissueSource" + }, + "tumourNormalDesignation": { + "$ref": "#/definitions/specimen/tumourNormalDesignation" + }, + "specimenType": { "$ref": "#/definitions/specimen/specimenType" }, + "specimenClass": { + "not": {} + }, + "info": { "$ref": "#/definitions/common/info" } + } + } + }, + "analysisType": { + "type": "object", + "required": ["name"], + "properties": { + "name": { + "type": "string" + }, + "version": { + "type": ["integer", "null"] + } + } + }, + "sample": { + "sampleTypes": { + "type": "string", + "enum": [ + "Total DNA", + "Amplified DNA", + "ctDNA", + "Other DNA enrichments", + "Total RNA", + "Ribo-Zero RNA", + "polyA+ RNA", + "Other RNA fractions" + ] + }, + "sampleData": { + "type": "object", + "required": ["submitterSampleId", "sampleType"], + "properties": { + "submitterSampleId": { "$ref": "#/definitions/common/submitterId" }, + "sampleType": { "$ref": "#/definitions/sample/sampleTypes" }, + "info": { "$ref": "#/definitions/common/info" } + } + } + } + }, + "required": ["studyId", "analysisType", "samples", "files"], + "properties": { + "analysisId": { + "not": {} + }, + "studyId": { + "type": "string", + "minLength": 1 + }, + "analysisType": { + "allOf": [{ "$ref": "#/definitions/analysisType" }] + }, + "samples": { + "type": "array", + "minItems": 1, + "items": { + "type": "object", + "allOf": [{ "$ref": "#/definitions/sample/sampleData" }], + "required": ["specimen", "donor"], + "properties": { + "specimen": { "$ref": "#/definitions/specimen/specimenData" }, + "donor": { "$ref": "#/definitions/donor/donorData" } + }, + "if": { + "properties": { + "specimen": { + "properties": { + "tumourNormalDesignation": { + "const": "Tumour" + } + } + } + } + }, + "then": { + "properties": { + "matchedNormalSubmitterSampleId": { + "oneOf": [ + { + "const": null + }, + { + "$ref": "#/definitions/common/submitterId" + } + ] + } + }, + "required": ["matchedNormalSubmitterSampleId"] + }, + "else": { + "properties": { + "matchedNormalSubmitterSampleId": { + "const": null + } + }, + "required": ["matchedNormalSubmitterSampleId"] + } + } + }, + "files": { + "type": "array", + "minItems": 1, + "items": { "$ref": "#/definitions/file/fileData" } + } + } +} diff --git a/demoData/schemas/demoDataSchema.json b/demoData/schemas/demoDataSchema.json new file mode 100644 index 00000000..7fad76a9 --- /dev/null +++ b/demoData/schemas/demoDataSchema.json @@ -0,0 +1,1498 @@ +{ + "name": "demoDataSchema", + "schema": { + "type": "object", + "required": [ + "workflow", + "experiment", + "donor", + "specimen" + ], + "properties": { + "workflow": { + "propertyNames": { + "enum": [ + "workflowName", + "workflowShortName", + "workflowVersion", + "genomeBuild", + "inputs", + "workflowTools" + ] + }, + "required": [ + "workflowName", + "genomeBuild", + "inputs" + ], + "type": "object", + "properties": { + "workflowName": { + "type": "string", + "pattern": "^[a-zA-Z][a-zA-Z0-9 _\\-]+[a-zA-Z0-9]+$" + }, + "workflowShortName": { + "type": "string", + "pattern": "^[a-zA-Z][a-zA-Z0-9_\\-]+[a-zA-Z0-9]+$" + }, + "workflowVersion": { + "type": "string" + }, + "genomeBuild": { + "type": "string", + "enum": [ + "GRCh37", + "GRCh38_hla_decoy_ebv", + "GRCh38_Verily_v1" + ] + }, + "inputs": { + "type": "array", + "items": { + "type": "object", + "properties": { + "tumourAnalysisId": { + "type": "string", + "pattern": "^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$" + }, + "normalAnalysisId": { + "type": "string", + "pattern": "^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$" + }, + "analysisType": { + "type": "string", + "const": "sequencing_alignment" + } + } + }, + "minItems": 1, + "maxItems": 2 + }, + "runId": { + "type": "string" + }, + "sessionId": { + "type": "string", + "pattern": "^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$" + } + } + }, + "experiment": { + "propertyNames": { + "enum": [ + "platform", + "experimentalStrategy", + "platformModel", + "sequencingCentre", + "experimentalProtocol", + "libraryIsolationProtocol", + "submitterSequencingExperimentId", + "libraryStrandedness", + "chipTarget", + "targetCaptureKit", + "primaryTargetRegions", + "captureTargetRegions" + ] + }, + "required": [ + "platform", + "experimentalStrategy", + "submitterSequencingExperimentId" + ], + "type": "object", + "properties": { + "platform": { + "type": [ + "string", + "null" + ] + }, + "experimentalStrategy": { + "type": [ + "string", + "null" + ] + }, + "experimentalProtocol": { + "type": [ + "string", + "null" + ] + }, + "libraryIsolationProtocol": { + "enum": [ + "TRIzol Reagent (Thermo Fisher)", + "RNeasy kits (QIAGEN)", + "RNase free DNase I (Thermo Fisher)", + "Pico Pure RNA isolation kit (Thermo Fisher)", + "mirVANA microRNA isolation kit (Thermo Fisher)", + "Absolutely Total RNA, miRNA & mRNA Purification Kits (Stratagene, Agilent technologies)", + "SV total RNA isolation kit (Promega)", + "RNAqueous Kit (Thermo Fisher)", + "AllPrep DNA/RNA Micro Kit (QIAGEN)", + "GenElute Mammalian Total RNA Miniprep kit (MilliporeSigma)", + "Spectrum Plant Total RNA kit (MilliporeSigma)", + "peqGOLD Total RNA kits (PeqLab Biotechnologie)", + "RNAlater (Thermo Fisher)", + null + ] + }, + "submitterSequencingExperimentId": { + "type": [ + "string", + "null" + ] + }, + "libraryStrandedness": { + "enum": [ + "UNSTRANDED", + "FIRST_READ_SENSE_STRAND", + "FIRST_READ_ANTISENSE_STRAND", + null + ] + }, + "chipTarget": { + "type": [ + "string", + "null" + ] + }, + "platformModel": { + "type": [ + "string", + "null" + ] + }, + "sequencingCentre": { + "type": [ + "string", + "null" + ] + }, + "targetCaptureKit": { + "enum": [ + "xGen Exome Research Panel V1 (IDT)", + "SeqCap EZ MedExome (Roche)", + "SureSelect Human All Exon V6 (Agilent)", + "Human Core Exome Kit + RefSeq V1 (Twist)", + null + ] + }, + "primaryTargetRegions": { + "type": [ + "string", + "null" + ] + }, + "captureTargetRegions": { + "type": [ + "string", + "null" + ] + } + }, + "allOf": [ + { + "if": { + "properties": { + "experimentalStrategy": { + "const": "RNA-Seq" + } + } + }, + "then": { + "properties": { + "libraryStrandedness": { + "enum": [ + "UNSTRANDED", + "FIRST_READ_SENSE_STRAND", + "FIRST_READ_ANTISENSE_STRAND" + ] + } + }, + "required": [ + "libraryStrandedness" + ] + } + }, + { + "if": { + "properties": { + "experimentalStrategy": { + "enum": [ + "WXS", + "Targeted-Seq" + ] + } + } + }, + "then": { + "properties": { + "targetCaptureKit": { + "type": "string", + "pattern": "^[a-zA-Z0-9]{1}[a-zA-Z0-9\\-_\\.:']{0,98}[a-zA-Z0-9]{1}$" + }, + "primaryTargetRegions": { + "type": "string", + "pattern": "^[a-zA-Z0-9]{1}[a-zA-Z0-9\\-_\\.:']{0,98}[a-zA-Z0-9]{1}$" + }, + "captureTargetRegions": { + "type": "string", + "pattern": "^[a-zA-Z0-9]{1}[a-zA-Z0-9\\-_\\.:']{0,98}[a-zA-Z0-9]{1}$" + } + }, + "required": [ + "targetCaptureKit", + "primaryTargetRegions", + "captureTargetRegions" + ] + } + }, + { + "if": { + "properties": { + "experimentalStrategy": { + "const": "ChIP-Seq" + } + } + }, + "then": { + "properties": { + "chipTarget": { + "type": [ + "string", + "null" + ] + } + }, + "required": [ + "chipTarget" + ] + } + } + ] + }, + "donor": { + "type": "object", + "propertyNames": { + "enum": [ + "submitterDonorId", + "primarySite", + "vitalStatus", + "survivalTime", + "causeOfDeath", + "primaryDiagnosis", + "comorbidity" + ] + }, + "required": [ + "submitterDonorId", + "primarySite", + "vitalStatus", + "primaryDiagnosis" + ], + "properties": { + "submitterDonorId": { + "type": "string" + }, + "primarySite": { + "type": "array", + "minItems": 1, + "items": { + "type": "string", + "enum": [ + "Accessory sinuses", + "Adrenal gland", + "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" + ] + } + }, + "vitalStatus": { + "type": "string", + "enum": [ + "Alive", + "Deceased" + ] + }, + "survivalTime": { + "type": [ + "null", + "integer" + ], + "minimum": 0 + }, + "causeOfDeath": { + "type": [ + "null", + "string" + ], + "enum": [ + "Died of 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}, + "donor": { + "type": "object", + "propertyNames": { + "enum": [ + "submitterDonorId", + "primarySite", + "vitalStatus", + "survivalTime", + "causeOfDeath", + "primaryDiagnosis" + ] + }, + "required": ["submitterDonorId", "primarySite", "vitalStatus", "primaryDiagnosis"], + "properties": { + "submitterDonorId": { + "type": "string" + }, + "primarySite": { + "type": "array", + "minItems": 1, + "items": { + "type": "string", + "enum": [ + "Accessory sinuses", + "Adrenal gland", + "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", + 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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" + ] + } + }, + "vitalStatus": { + "type": "string", + "enum": ["Alive", "Deceased"] + }, + "survivalTime": { + "type": ["null", "integer"], + "minimum": 0 + }, + "causeOfDeath": { + "type": ["null", "string"], + "enum": ["Died of cancer", "Died of other reasons", "Unknown", null] + }, + "primaryDiagnosis": { + "type": "array", + "minItems": 1, + "items": { + "type": "object", + "propertyNames": { + "enum": [ + "submitterPrimaryDiagnosisId", + "ageAtDiagnosis", + "cancerTypeCode", + "clinicalTumourStagingSystem", + "clinicalStageGroup", + "treatment", + "followUp" + ] + }, + "required": ["submitterPrimaryDiagnosisId", "ageAtDiagnosis", "cancerTypeCode"], + "properties": { + "submitterPrimaryDiagnosisId": { + "type": "string" + }, + "ageAtDiagnosis": { + "type": "integer", + "minimum": 0 + }, + "cancerTypeCode": { + "type": "string", + "pattern": "^[C|D][0-9]{2}(.[0-9]{1,3}[A-Z]{0,1})?$" + }, + "clinicalTumourStagingSystem": { + "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" + ] + }, + "clinicalStageGroup": { + "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" + ] + }, + "followUp": { + "type": "array", + "items": { + "type": "object", + "propertyNames": { + "enum": [ + "submitterFollowUpId", + "intervalOfFollowUp", + "diseaseStatusAtFollowUp", + "relapseType", + "submitterTreatmentId" + ] + }, + "required": [ + "submitterFollowUpId", + "intervalOfFollowUp", + "diseaseStatusAtFollowUp" + ], + "properties": { + "submitterFollowUpId": { + "type": "string" + }, + "submitterTreatmentId": { + "type": "string" + }, + "intervalOfFollowUp": { + "type": "integer", + "minimum": 0 + }, + "diseaseStatusAtFollowUp": { + "type": "string", + "enum": [ + "Complete remission", + "Distant progression", + "Loco-regional progression", + "No evidence of disease", + "Partial remission", + "Progression NOS", + "Relapse or recurrence", + "Stable" + ] + }, + "relapseType": { + "type": ["string", "null"], + "enum": [ + "Distant recurrence/metastasis", + "Local recurrence", + "Local recurrence and distant metastasis", + "Progression (liquid tumours)", + null + ] + } + } + } + }, + "treatment": { + "type": "array", + "items": { + "type": "object", + "propertyNames": { + "enum": [ + "submitterTreatmentId", + "treatmentType", + "treatmentStartInterval", + "treatmentDuration", + "responseToTreatment", + "chemotherapy", + "hormoneTherapy", + "radiation" + ] + }, + "required": ["submitterTreatmentId", "treatmentType"], + "properties": { + "submitterTreatmentId": { + "type": "string" + }, + "treatmentType": { + "type": "array", + "items": { + "type": "string", + "enum": [ + "Ablation", + "Bone marrow transplant", + "Chemotherapy", + "Endoscopic therapy", + "Hormonal therapy", + "No treatment", + "Other targeting molecular therapy", + "Photodynamic therapy", + "Radiation therapy", + "Stem cell transplant", + "Surgery" + ] + } + }, + "treatmentStartInterval": { + "type": "integer", + "minimum": 0 + }, + "treatmentDuration": { + "type": "integer", + "minimum": 0 + }, + "responseToTreatment": { + "type": "string", + "enum": [ + "Complete response", + "Disease progression", + "NED", + "Minor response", + "Partial response", + "Stable disease" + ] + }, + "chemotherapy": { + "type": "array", + "items": { + "type": "object", + "propertyNames": { + "enum": ["drugName"] + }, + "required": ["drugName"], + "properties": { + "drugName": { + "type": "array" + } + } + } + }, + "hormoneTherapy": { + "type": "array", + "items": { + "type": "object", + "propertyNames": { + "enum": ["drugName"] + }, + "required": ["drugName"], + "properties": { + "drugName": { + "type": "array" + } + } + } + }, + "radiation": { + "type": "array", + "items": { + "type": "object", + "propertyNames": { + "enum": ["radiationTherapyModality", "anatomicalSiteIrradiated"] + }, + "required": ["radiationTherapyModality", "anatomicalSiteIrradiated"], + "properties": { + "radiationTherapyModality": { + "type": "string", + "enum": ["Electron", "Heavy Ions", "Photon", "Proton"] + }, + "anatomicalSiteIrradiated": { + "type": "string", + "enum": [ + "Abdomen", + "Body", + "Brain", + "Chest", + "Head", + "Liver", + "Lower Limb", + "Lung", + "Neck", + "Pelvis", + "Skin", + "Spine", + "Thorax", + "Upper Limb" + ] + } + } + } + } + }, + "allOf": [ + { + "if": { + "properties": { + "treatmentType": { + "contains": { + "const": "Chemotherapy" + } + } + } + }, + "then": { + "required": ["chemotherapy"] + } + }, + { + "if": { + "properties": { + "treatmentType": { + "contains": { + "const": "Radiation therapy" + } + } + } + }, + "then": { + "required": ["radiation"] + } + }, + { + "if": { + "properties": { + "treatmentType": { + "contains": { + "const": "Hormonal therapy" + } + } + } + }, + "then": { + "required": ["hormoneTherapy"] + } + } + ] + } + } + } + } + } + }, + "if": { + "properties": { + "vitalStatus": { + "const": "Deceased" + } + } + }, + "then": { + "required": ["causeOfDeath", "survivalTime"] + } + }, + "specimen": { + "type": "object", + "propertyNames": { + "enum": [ + "submitterSpecimenId", + "submitterPrimaryDiagnosisId", + "specimenAnatomicLocation", + "tumourGradingSystem", + "tumourGrade" + ] + }, + "required": [ + "submitterSpecimenId", + "submitterPrimaryDiagnosisId", + "specimenAnatomicLocation" + ], + "properties": { + "submitterSpecimenId": { + "type": "string" + }, + "submitterPrimaryDiagnosisId": { + "type": "string" + }, + "specimenAnatomicLocation": { + "type": "string", + "pattern": "^[C][0-9]{2}(.[0-9]{1})?$" + }, + "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" + ] + } + } + }, + "publication": { + "type": "object", + "propertyNames": { + "enum": ["publication", "doi"] + }, + "properties": { + "publication": { + "type": ["string", "null"] + }, + "doi": { + "type": ["string", "null"] + } + } + } + } + } +} diff --git a/example-data/COLO-829-BL_ex.bam b/example-data/COLO-829-BL_ex.bam deleted file mode 100644 index efcd9170..00000000 Binary files a/example-data/COLO-829-BL_ex.bam and /dev/null differ diff --git a/example-data/COLO-829_ex.bam b/example-data/COLO-829_ex.bam deleted file mode 100644 index 3b8b2130..00000000 Binary files a/example-data/COLO-829_ex.bam and /dev/null differ diff --git a/example-data/EXAMPLE-FR/example_donor1_normal.json b/example-data/EXAMPLE-FR/example_donor1_normal.json deleted file mode 100755 index 8b0cd802..00000000 --- a/example-data/EXAMPLE-FR/example_donor1_normal.json +++ /dev/null @@ -1,859 +0,0 @@ -{ - "studyId": "EXAMPLE-FR", - "analysisType": { - "name": "sequencing_experiment" - }, - "samples": [ - { - "submitterSampleId": "sample-6", - "matchedNormalSubmitterSampleId": null, - "sampleType": "Total DNA", - "specimen": { - "submitterSpecimenId": "specimen-6", - "tumourNormalDesignation": "Normal", - "specimenTissueSource": "Blood derived", - "specimenType": "Normal" - }, - "donor": { - "gender": "Male", - "submitterDonorId": "example-donor-1" - } - } - ], - "files": [ - { - "info": { - "data_category": "Sequencing Reads" - }, - "fileName": "COLO-829-BL_ex.bam", - "fileSize": 2951856, - "fileType": "BAM", - "fileMd5sum": "69426aaad85e2aed435d3271af6bf828", - "fileAccess": "controlled", - "dataType": "Submitted Reads" - } - ], - "experiment": { - "platform": "ILLUMINA", - "platform_model": "HiSeq 2000", - "sequencing_date": "2014-12-12", - "sequencing_center": "EXT", - "experimental_strategy": "WXS", - "submitter_sequencing_experiment_id": "TEST_EXP" - }, - "read_groups": [ - { - "file_r1": "COLO-829-BL_ex.bam", - "file_r2": 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a/example-data/STUDY1-CA/study1_donor1_normal.json +++ /dev/null @@ -1,864 +0,0 @@ -{ - "studyId": "TESTSTUDY-CA", - "analysisType": { - "name": "sequencing_experiment" - }, - "samples": [ - { - "submitterSampleId": "sample1-1", - "matchedNormalSubmitterSampleId": null, - "sampleType": "Total DNA", - "specimen": { - "submitterSpecimenId": "specimen1-1", - "tumourNormalDesignation": "Normal", - "specimenTissueSource": "Blood derived", - "specimenType": "Normal" - }, - "donor": { - "gender": "Male", - "submitterDonorId": "donor-id-1" - } - } - ], - "files": [ - { - "info": { - "data_category": "Sequencing Reads" - }, - "fileName": "COLO-829-BL_ex.bam", - "fileSize": 2951856, - "fileType": "BAM", - "fileMd5sum": "69426aaad85e2aed435d3271af6bf828", - "fileAccess": "controlled", - "dataType": "Submitted Reads" - } - ], - "experiment": { - "platform": "ILLUMINA", - "platform_model": "HiSeq 2000", - "sequencing_date": "2014-12-12", - "sequencing_center": "EXT", - "experimental_strategy": 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"file_r1": "COLO-829-BL_ex.bam", - "file_r2": "COLO-829-BL_ex.bam", - "insert_size": 298, - "library_name": "531", - "is_paired_end": true, - "platform_unit": "0_2790", - "read_length_r1": 75, - "read_length_r2": 75, - "sample_barcode": null, - "submitter_read_group_id": "2790" - }, - { - "file_r1": "COLO-829-BL_ex.bam", - "file_r2": "COLO-829-BL_ex.bam", - "insert_size": 298, - "library_name": "531", - "is_paired_end": true, - "platform_unit": "0_2792", - "read_length_r1": 75, - "read_length_r2": 75, - "sample_barcode": null, - "submitter_read_group_id": "2792" - } - ], - "read_group_count": 67, - "donor_clinical_data":[{ - "submitter_donor_id":"donor-id-1", - "primary_site":"Brain", - "cancer_code_type":"C71", - "age_at_diagnosis":55, - "basis_of_diagnosis":"Histology of a primary tumour", - "vital_status":"Deceased", - "cause_of_death":"Died of cancer", - "survival_time":371, - "height":183, - "weight":68, - "bmi":20 - }] -} diff --git a/example-data/STUDY1-CA/study1_donor1_tumour.json b/example-data/STUDY1-CA/study1_donor1_tumour.json deleted file mode 100755 index 77753af5..00000000 --- a/example-data/STUDY1-CA/study1_donor1_tumour.json +++ /dev/null @@ -1,1298 +0,0 @@ -{ - "studyId": "TESTSTUDY-CA", - "analysisType": { - "name": "sequencing_experiment" - }, - "samples": [ - { - "submitterSampleId": "sample1-2", - "matchedNormalSubmitterSampleId": "sample1-1", - "sampleType": "Total DNA", - "specimen": { - "submitterSpecimenId": "specimen1-2", - "tumourNormalDesignation": "Tumour", - "specimenTissueSource": "Cerebellum", - "specimenType": "Primary tumour" - }, - "donor": { - "gender": "Male", - "submitterDonorId": "donor-id-1" - } - } - ], - "files": [ - { - "info": { - "data_category": "Sequencing Reads" - }, - "fileName": "COLO-829_ex.bam", - "fileSize": 4071038, - "fileType": "BAM", - "fileMd5sum": "cd0afbe6cb02bd5b0da0b76b50d5b3b7", - "fileAccess": "controlled", - "dataType": "Submitted Reads" - } - ], - 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"cause_of_death": "Died of cancer", - "survival_time": 371, - "height": 183, - "weight": 68, - "bmi": 20 - } - ] -} diff --git a/example-data/STUDY1-CA/study1_donor2_normal.json b/example-data/STUDY1-CA/study1_donor2_normal.json deleted file mode 100755 index f79493f5..00000000 --- a/example-data/STUDY1-CA/study1_donor2_normal.json +++ /dev/null @@ -1,865 +0,0 @@ -{ - "studyId": "TESTSTUDY-CA", - "analysisType": { - "name": "sequencing_experiment" - }, - "samples": [ - { - "submitterSampleId": "sample1-4", - "matchedNormalSubmitterSampleId": null, - "sampleType": "Total DNA", - "specimen": { - "submitterSpecimenId": "specimen1-4", - "tumourNormalDesignation": "Normal", - "specimenTissueSource": "Blood derived", - "specimenType": "Normal" - }, - "donor": { - "gender": "Female", - "submitterDonorId": "donor-id-2" - } - } - ], - "files": [ - { - "info": { - "data_category": "Sequencing Reads" - }, - "fileName": "COLO-829-BL_ex.bam", - "fileSize": 2951856, - "fileType": "BAM", - 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"2792" - } - ], - "read_group_count": 67, - "donor_clinical_data":[{ - "submitter_donor_id":"donor-id-3", - "primary_site":"Brain", - "cancer_code_type":"C70", - "age_at_diagnosis":14, - "basis_of_diagnosis":"Histology of a primary tumour", - "vital_status":"Deceased", - "cause_of_death":"Died of cancer", - "survival_time":125, - "height":150, - "weight":43, - "bmi":19 - }] -} diff --git a/example-data/arranger_metadata/aggs-state.json b/example-data/arranger_metadata/aggs-state.json deleted file mode 100644 index 5e3d9aff..00000000 --- a/example-data/arranger_metadata/aggs-state.json +++ /dev/null @@ -1,236 +0,0 @@ -[ - { - "field": "analysis__first_published_at", - "active": true, - "show": false, - "__typename": "AggState" - }, - { - "field": "analysis__published_at", - "active": true, - "show": false, - "__typename": "AggState" - }, - { - "field": "analysis__updated_at", - "active": true, - "show": false, - "__typename": "AggState" - }, - { - "field": "study_id", - "active": true, 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a/example-data/arranger_metadata/columns-state.json b/example-data/arranger_metadata/columns-state.json deleted file mode 100644 index f1b7debc..00000000 --- a/example-data/arranger_metadata/columns-state.json +++ /dev/null @@ -1,530 +0,0 @@ -{ - "type": "file", - "keyField": "id", - "defaultSorted": [ - { - "id": "analysis.analysis_id", - "desc": false, - "__typename": "ColumnSort" - } - ], - "columns": [ - { - "show": true, - "type": "string", - "sortable": true, - "canChangeShow": true, - "query": null, - "jsonPath": null, - "id": null, - "field": "object_id", - "accessor": "object_id", - "__typename": "Column" - }, - { - "show": true, - "type": "list", - "sortable": false, - "canChangeShow": true, - "query": "donors {\n hits {\n edges {\n node {\n donor_id\n }\n }\n }\n }", - "jsonPath": "$.donors.hits.edges[*].node.donor_id", - "id": null, - "field": "donors.donor_id", - "accessor": null, - "__typename": "Column" - }, - { - "show": true, - "type": "list", - "sortable": false, - 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"query": "donors {\n hits {\n edges {\n node {\n specimens {\n hits {\n edges {\n node {\n samples {\n hits {\n edges {\n node {\n submitter_sample_id\n }\n }\n }\n }\n }\n }\n }\n }\n }\n }\n }\n }", - "jsonPath": "$.donors.hits.edges[*].node.specimens.hits.edges[*].node.samples.hits.edges[*].node.submitter_sample_id", - "id": null, - "field": "donors.specimens.samples.submitter_sample_id", - "accessor": null, - "__typename": "Column" - }, - { - "show": false, - "type": "number", - "sortable": false, - "canChangeShow": false, - "query": null, - "jsonPath": null, - "id": null, - "field": "donors.specimens.samples.hits.total", - "accessor": "donors.hits.edges[0].node.specimens.hits.edges[0].node.samples.hits.total", - "__typename": "Column" - }, - { - "show": false, - "type": "number", - "sortable": false, - "canChangeShow": false, - "query": null, - "jsonPath": null, - "id": null, - "field": "donors.specimens.hits.total", - "accessor": "donors.hits.edges[0].node.specimens.hits.total", 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"accessor": null, - "__typename": "Column" - }, - { - "show": false, - "type": "list", - "sortable": false, - "canChangeShow": true, - "query": "repositories {\n hits {\n edges {\n node {\n country\n }\n }\n }\n }", - "jsonPath": "$.repositories.hits.edges[*].node.country", - "id": null, - "field": "repositories.country", - "accessor": null, - "__typename": "Column" - }, - { - "show": false, - "type": "list", - "sortable": false, - "canChangeShow": true, - "query": "repositories {\n hits {\n edges {\n node {\n name\n }\n }\n }\n }", - "jsonPath": "$.repositories.hits.edges[*].node.name", - "id": null, - "field": "repositories.name", - "accessor": null, - "__typename": "Column" - }, - { - "show": false, - "type": "list", - "sortable": false, - "canChangeShow": true, - "query": "repositories {\n hits {\n edges {\n node {\n organization\n }\n }\n }\n }", - "jsonPath": "$.repositories.hits.edges[*].node.organization", - "id": null, - "field": "repositories.organization", - "accessor": 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"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/example-data/arranger_metadata/matchbox-state.json b/example-data/arranger_metadata/matchbox-state.json deleted file mode 100644 index 1929bf43..00000000 --- a/example-data/arranger_metadata/matchbox-state.json +++ /dev/null @@ -1,42 +0,0 @@ -[ - { - "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/example-data/example.vcf.gz b/example-data/example.vcf.gz deleted file mode 100644 index 89e752a6..00000000 Binary files a/example-data/example.vcf.gz and /dev/null differ diff --git a/example-data/example.vcf.gz.idx b/example-data/example.vcf.gz.idx deleted file mode 100644 index b1c922c9..00000000 --- a/example-data/example.vcf.gz.idx +++ /dev/null @@ -1 +0,0 @@ -this is the first index diff --git a/example-data/exampleVariantCall.json b/example-data/exampleVariantCall.json deleted file mode 100644 index c658fd64..00000000 --- a/example-data/exampleVariantCall.json +++ /dev/null @@ -1,81 +0,0 @@ -{ - "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" - } -} diff --git a/example-data/sequencing_alignment_sample_schema.json b/example-data/sequencing_alignment_sample_schema.json deleted file mode 100644 index 19833a50..00000000 --- a/example-data/sequencing_alignment_sample_schema.json +++ /dev/null @@ -1,496 +0,0 @@ -{ - "name": "sequencing_alignment", - "schema": { - "type": "object", - "required": [ - "workflow", - "experiment", - "read_group_count", - "read_groups", - "donor_clinical_data" - ], - "properties": { - "workflow": { - "propertyNames": { - "enum": [ - "workflow_name", - "workflow_version", - "genome_build", - "run_id", - "inputs" - ] - }, - "required": [ - "workflow_name", - "workflow_version", - "genome_build", - "inputs" - ], - "allOf": [ - { - "type": "object", - "properties": { - "workflow_name": { - "type": "string", - "pattern": "^[a-zA-Z][a-zA-Z0-9 _\\-]+[a-zA-Z0-9]+$" - }, - "genome_build": { - "type": "string", - "enum": ["GRCh38_hla_decoy_ebv"] - }, - "inputs": { - "type": "array", - "items": { - "type": "object", - "properties": { - "input_analysis_id": { - "type": "string", - "pattern": "^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$" - }, - "analysis_type": { - "type": "string", - "pattern": "^[a-zA-Z][a-zA-Z0-9_]+$" - } - } - }, - "minItems": 1 - }, - "run_id": { - "type": "string" - }, - "workflow_version": { - "type": "string" - } - } - }, - { - "properties": { - "inputs": { - "type": "array", - "items": { - "type": "object", - "properties": { - "analysis_type": { - "enum": [ - "sequencing_experiment", - "read_group_ubam" - ] - } - } - } - } - } - } - ] - }, - "experiment": { - "propertyNames": { - "enum": [ - "platform", - "platform_model", - "sequencing_date", - "experimental_strategy", - "sequencing_center", - "submitter_sequencing_experiment_id" - ] - }, - "required": [ - "platform", - "experimental_strategy" - ], - "type": "object", - "properties": { - "submitter_sequencing_experiment_id": { - "type": ["string", "null"], - "pattern": "^[a-zA-Z0-9]{1}[a-zA-Z0-9\\-_\\.:']{0,98}[a-zA-Z0-9]{1}$" - }, - "platform": { - "enum": [ - "CAPILLARY", - "LS454", - "ILLUMINA", - "SOLID", - "HELICOS", - "IONTORRENT", - "ONT", - "PACBIO", - "Nanopore", - "BGI" - ] - }, - "platform_model": { - "type": [ - "string", - "null" - ] - }, - "sequencing_date": { - "oneOf": [ - { - "type": "string", - "oneOf": [ - { - "format": "date" - }, - { - "format": "date-time" - } - ], - "example": [ - "2019-06-16", - "2019-06-16T20:20:39+00:00" - ] - }, - { - "type": "null" - } - ] - }, - "experimental_strategy": { - "enum": [ - "WGS", - "WXS", - "RNA-Seq", - "Bisulfite-Seq", - "ChIP-Seq", - "Targeted-Seq" - ] - }, - "sequencing_center": { - "type": [ - "string", - "null" - ] - } - } - }, - "read_group_count": { - "type": "integer", - "minimum": 1 - }, - "read_groups": { - "type": "array", - "items": { - "type": "object", - "minItems": 1, - "propertyNames": { - "enum": [ - "library_name", - "platform_unit", - "is_paired_end", - "read_length_r1", - "file_r1", - "insert_size", - "read_length_r2", - "file_r2", - "sample_barcode", - "read_group_id_in_bam", - "submitter_read_group_id" - ] - }, - "required": [ - "library_name", - "platform_unit", - "is_paired_end", - "read_length_r1", - "file_r1", - "insert_size", - "read_length_r2", - "file_r2", - "sample_barcode", - "submitter_read_group_id" - ], - "allOf": [ - { - "properties": { - "submitter_read_group_id": { - "type": "string", - "pattern": "^[a-zA-Z0-9\\-_:\\.]+$" - }, - "read_group_id_in_bam": { - "type": [ - "string", - "null" - ], - "pattern": "^[a-zA-Z0-9\\-_:\\.']+$" - }, - "library_name": { - "type": "string" - }, - "platform_unit": { - "type": "string" - }, - "is_paired_end": { - "type": "boolean" - }, - "file_r1": { - "type": "string" - }, - "file_r2": { - "type": [ - "string", - "null" - ] - }, - "read_length_r1": { - "type": [ - "integer", - "null" - ], - "minimum": 20 - }, - "read_length_r2": { - "type": [ - "integer", - "null" - ], - "minimum": 20 - }, - "insert_size": { - "type": [ - "integer", - "null" - ], - "minimum": 0 - }, - "sample_barcode": { - "type": [ - "string", - "null" - ] - } - } - }, - { - "if": { - "properties": { - "is_paired_end": { - "const": true - } - } - }, - "then": { - "properties": { - "file_r2": { - "type": "string" - }, - "read_length_r2": { - "type": [ - "integer", - "null" - ], - "minimum": 20 - }, - "insert_size": { - "type": [ - "integer", - "null" - ], - "minimum": 0 - } - } - }, - "else": { - "properties": { - "file_r2": { - "const": null - }, - "read_length_r2": { - "const": null - }, - "insert_size": { - "const": null - } - } - } - } - ] - } - }, - "donor_clinical_data": { - "type": "array", - "items": { - "type": "object", - "minItems": 1, - "propertyNames": { - "enum": [ - "submitter_donor_id", - "primary_site", - "cancer_code_type", - "age_at_diagnosis", - "basis_of_diagnosis", - "vital_status", - "cause_of_death", - "survival_time", - "height", - "weight", - "bmi" - ] - }, - "required": [ - "submitter_donor_id", - "primary_site", - "cancer_code_type", - "age_at_diagnosis", - "basis_of_diagnosis", - "vital_status" - ], - "allOf":[ - { - "properties": { - "submitter_donor_id": { - "type": "string", - "pattern": "^[A-Za-z0-9\\-\\._]{1,64}" - }, - "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", - "Not Reported", - "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", - "Unknown" - ] - }, - "cancer_code_type": { - "type": "string", - "pattern": "^[C|D][0-9]{2}(.[0-9]{1,3}[A-Z]{0,1})?$" - }, - "age_at_diagnosis": { - "type": "integer", - "minimum": 0 - }, - "basis_of_diagnosis": { - "type": "string", - "enum":[ - "Clinical investigation", - "Clinical", - "Cytology", - "Death certificate only", - "Histology of a metastasis", - "Histology of a primary tumour", - "Specific tumour markers", - "Unknown" - ] - }, - "vital_status": { - "type": "string", - "enum":[ - "Alive", - "Deceased", - "Unknown" - ] - }, - "cause_of_death": { - "type": "string", - "enum":[ - "Died of cancer", - "Died of other reasons", - "Unknown" - ] - }, - "survival_time": { - "type": "integer", - "minimum": 0 - }, - "height": { - "type": "integer", - "minimum": 1 - }, - "weight": { - "type": "integer", - "minimum": 1 - }, - "bmi": { - "type": "integer", - "minimum": 1 - } - } - }, - { - "if": { - "properties": { - "vital_status": { - "const": "Deceased" - } - } - }, - "then": { - "required": [ - "cause_of_death", - "survival_time" - ] - } - } - ] - } - } - } - } -} \ No newline at end of file diff --git a/example-data/sequencing_experiment_sample_schema.json b/example-data/sequencing_experiment_sample_schema.json deleted file mode 100644 index ee28a7cb..00000000 --- a/example-data/sequencing_experiment_sample_schema.json +++ /dev/null @@ -1,423 +0,0 @@ -{ - "name": "sequencing_experiment", - "schema": { - "type": "object", - "required": [ - "experiment", - "read_group_count", - "read_groups", - "donor_clinical_data" - ], - "properties": { - "experiment": { - "propertyNames": { - "enum": [ - "submitter_sequencing_experiment_id", - "platform", - "platform_model", - "sequencing_date", - "experimental_strategy", - "sequencing_center" - ] - }, - "required": [ - "submitter_sequencing_experiment_id", - "platform", - "experimental_strategy" - ], - "type": "object", - "properties": { - "submitter_sequencing_experiment_id": { - "type": ["string", "null"], - "pattern": "^[a-zA-Z0-9]{1}[a-zA-Z0-9\\-_\\.:']{0,98}[a-zA-Z0-9]{1}$" - }, - "platform": { - "enum": [ - "CAPILLARY", - "LS454", - "ILLUMINA", - "SOLID", - "HELICOS", - "IONTORRENT", - "ONT", - "PACBIO", - "Nanopore", - "BGI" - ] - }, - "platform_model": { - "type": [ - "string", - "null" - ] - }, - "sequencing_date": { - "oneOf": [ - { - "type": "string", - "oneOf": [ - { - "format": "date" - }, - { - "format": "date-time" - } - ], - "example": [ - "2019-06-16", - "2019-06-16T20:20:39+00:00" - ] - }, - { - "type": "null" - } - ] - }, - "experimental_strategy": { - "enum": [ - "WGS", - "WXS", - "RNA-Seq", - "Bisulfite-Seq", - "ChIP-Seq", - "Targeted-Seq" - ] - }, - "sequencing_center": { - "type": [ - "string", - "null" - ] - } - } - }, - "read_group_count": { - "type": "integer", - "minimum": 1 - }, - "read_groups": { - "type": "array", - "items": { - "type": "object", - "minItems": 1, - "propertyNames": { - "enum": [ - "library_name", - "platform_unit", - "is_paired_end", - "read_length_r1", - "file_r1", - "insert_size", - "read_length_r2", - "file_r2", - "sample_barcode", - "read_group_id_in_bam", - "submitter_read_group_id" - ] - }, - "required": [ - "library_name", - "platform_unit", - "is_paired_end", - "read_length_r1", - "file_r1", - "insert_size", - "read_length_r2", - "file_r2", - "sample_barcode", - "submitter_read_group_id" - ], - "allOf": [ - { - "properties": { - "submitter_read_group_id": { - "type": "string", - "pattern": "^[a-zA-Z0-9\\-_:\\.]+$" - }, - "read_group_id_in_bam": { - "type": [ - "string", - "null" - ], - "pattern": "^[a-zA-Z0-9\\-_:\\.']+$" - }, - "library_name": { - "type": "string" - }, - "platform_unit": { - "type": "string" - }, - "is_paired_end": { - "type": "boolean" - }, - "file_r1": { - "type": "string" - }, - "file_r2": { - "type": [ - "string", - "null" - ] - }, - "read_length_r1": { - "type": [ - "integer", - "null" - ], - "minimum": 20 - }, - "read_length_r2": { - "type": [ - "integer", - "null" - ], - "minimum": 20 - }, - "insert_size": { - "type": [ - "integer", - "null" - ], - "minimum": 0 - }, - "sample_barcode": { - "type": [ - "string", - "null" - ] - } - } - }, - { - "if": { - "properties": { - "is_paired_end": { - "const": true - } - } - }, - "then": { - "properties": { - "file_r2": { - "type": "string" - }, - "read_length_r2": { - "type": [ - "integer", - "null" - ], - "minimum": 20 - }, - "insert_size": { - "type": [ - "integer", - "null" - ], - "minimum": 0 - } - } - }, - "else": { - "properties": { - "file_r2": { - "const": null - }, - "read_length_r2": { - "const": null - }, - "insert_size": { - "const": null - } - } - } - } - ] - } - }, - "donor_clinical_data": { - "type": "array", - "items": { - "type": "object", - "minItems": 1, - "propertyNames": { - "enum": [ - "submitter_donor_id", - "primary_site", - "cancer_code_type", - "age_at_diagnosis", - "basis_of_diagnosis", - "vital_status", - "cause_of_death", - "survival_time", - "height", - "weight", - "bmi" - ] - }, - "required": [ - "submitter_donor_id", - "primary_site", - "cancer_code_type", - "age_at_diagnosis", - "basis_of_diagnosis", - "vital_status" - ], - "allOf":[ - { - "properties": { - "submitter_donor_id": { - "type": "string", - "pattern": "^[A-Za-z0-9\\-\\._]{1,64}" - }, - "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", - "Not Reported", - "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", - "Unknown" - ] - }, - "cancer_code_type": { - "type": "string", - "pattern": "^[C|D][0-9]{2}(.[0-9]{1,3}[A-Z]{0,1})?$" - }, - "age_at_diagnosis": { - "type": "integer", - "minimum": 0 - }, - "basis_of_diagnosis": { - "type": "string", - "enum":[ - "Clinical investigation", - "Clinical", - "Cytology", - "Death certificate only", - "Histology of a metastasis", - "Histology of a primary tumour", - "Specific tumour markers", - "Unknown" - ] - }, - "vital_status": { - "type": "string", - "enum":[ - "Alive", - "Deceased", - "Unknown" - ] - }, - "cause_of_death": { - "type": "string", - "enum":[ - "Died of cancer", - "Died of other reasons", - "Unknown" - ] - }, - "survival_time": { - "type": "integer", - "minimum": 0 - }, - "height": { - "type": "integer", - "minimum": 1 - }, - "weight": { - "type": "integer", - "minimum": 1 - }, - "bmi": { - "type": "integer", - "minimum": 1 - } - } - }, - { - "if": { - "properties": { - "vital_status": { - "const": "Deceased" - } - } - }, - "then": { - "required": [ - "cause_of_death", - "survival_time" - ] - } - } - ] - } - } - } - } -} \ No newline at end of file diff --git a/example-data/variant_calling_sample_schema.json b/example-data/variant_calling_sample_schema.json deleted file mode 100644 index 72a3fbe7..00000000 --- a/example-data/variant_calling_sample_schema.json +++ /dev/null @@ -1,307 +0,0 @@ -{ - "name": "variant_calling", - "schema": { - "type": "object", - "required": [ - "workflow", - "experiment", - "variant_class", - "donor_clinical_data" - ], - "properties": { - "workflow": { - "propertyNames": { - "enum": [ - "workflow_name", - "workflow_short_name", - "workflow_version", - "genome_build", - "run_id", - "inputs" - ] - }, - "required": [ - "workflow_name", - "workflow_short_name", - "workflow_version", - "genome_build", - "inputs" - ], - "type": "object", - "properties": { - "workflow_name": { - "type": "string", - "pattern": "^[a-zA-Z][a-zA-Z0-9 _\\-]+[a-zA-Z0-9]+$" - }, - "workflow_short_name": { - "type": "string", - "pattern": "^[a-zA-Z][a-zA-Z0-9_\\-]+[a-zA-Z0-9]+$" - }, - "genome_build": { - "type": "string", - "enum": ["GRCh38_hla_decoy_ebv"] - }, - "inputs": { - "type": "array", - "items": { - "type": "object", - "properties": { - "tumour_analysis_id": { - "type": "string", - "pattern": "^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$" - }, - "normal_analysis_id": { - "type": "string", - "pattern": "^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$" - }, - "analysis_type": { - "type": "string", - "const": "sequencing_alignment" - } - } - }, - "minItems": 2, - "maxItems": 2 - }, - "run_id": { - "type": "string" - }, - "workflow_version": { - "type": "string" - } - } - }, - "experiment": { - "type": "object", - "propertyNames": { - "enum": [ - "platform", - "experimental_strategy" - ] - }, - "required": [ - "platform", - "experimental_strategy" - ], - "properties": { - "platform": { - "enum": [ - "CAPILLARY", - "LS454", - "ILLUMINA", - "SOLID", - "HELICOS", - "IONTORRENT", - "ONT", - "PACBIO", - "Nanopore", - "BGI" - ] - }, - "experimental_strategy": { - "type": "string", - "enum": [ - "WGS", - "WXS", - "RNA-Seq", - "Bisulfite-Seq", - "ChIP-Seq", - "Targeted-Seq" - ] - } - } - }, - "variant_class": { - "type": "string", - "enum": [ - "Germline", - "Somatic" - ] - }, - "donor_clinical_data": { - "type": "array", - "items": { - "type": "object", - "minItems": 1, - "propertyNames": { - "enum": [ - "submitter_donor_id", - "primary_site", - "cancer_code_type", - "age_at_diagnosis", - "basis_of_diagnosis", - "vital_status", - "cause_of_death", - "survival_time", - "height", - "weight", - "bmi" - ] - }, - "required": [ - "submitter_donor_id", - "primary_site", - "cancer_code_type", - "age_at_diagnosis", - "basis_of_diagnosis", - "vital_status" - ], - "allOf":[ - { - "properties": { - "submitter_donor_id": { - "type": "string", - "pattern": "^[A-Za-z0-9\\-\\._]{1,64}" - }, - "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", - "Not Reported", - "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", - "Unknown" - ] - }, - "cancer_code_type": { - "type": "string", - "pattern": "^[C|D][0-9]{2}(.[0-9]{1,3}[A-Z]{0,1})?$" - }, - "age_at_diagnosis": { - "type": "integer", - "minimum": 0 - }, - "basis_of_diagnosis": { - "type": "string", - "enum":[ - "Clinical investigation", - "Clinical", - "Cytology", - "Death certificate only", - "Histology of a metastasis", - "Histology of a primary tumour", - "Specific tumour markers", - "Unknown" - ] - }, - "vital_status": { - "type": "string", - "enum":[ - "Alive", - "Deceased", - "Unknown" - ] - }, - "cause_of_death": { - "type": "string", - "enum":[ - "Died of cancer", - "Died of other reasons", - "Unknown" - ] - }, - "survival_time": { - "type": "integer", - "minimum": 0 - }, - "height": { - "type": "integer", - "minimum": 1 - }, - "weight": { - "type": "integer", - "minimum": 1 - }, - "bmi": { - "type": "integer", - "minimum": 1 - } - } - }, - { - "if": { - "properties": { - "vital_status": { - "const": "Deceased" - } - } - }, - "then": { - "required": [ - "cause_of_death", - "survival_time" - ] - } - } - ] - } - } - } - } -} diff --git a/playground-data/README.md b/playground-data/README.md new file mode 100644 index 00000000..a2b682f9 --- /dev/null +++ b/playground-data/README.md @@ -0,0 +1 @@ +python submit_payloads.py -t 338a94cd-NNNN-NNNN-NNNN-f3d2519d119c -d /Users/esu/Desktop/GitHub/dms/playground-data -j TEST_SPECIMEN_rfdijnavpljntiranaxn_T2_copy.json -s demoData diff --git a/playground-data/SP011501.indel.vcf.gz b/playground-data/SP011501.indel.vcf.gz new file mode 100644 index 00000000..b9c6228b Binary files /dev/null and b/playground-data/SP011501.indel.vcf.gz differ diff --git a/playground-data/SP011501.indel.vcf.gz.tbi b/playground-data/SP011501.indel.vcf.gz.tbi new file mode 100644 index 00000000..75dae1ec Binary files /dev/null and b/playground-data/SP011501.indel.vcf.gz.tbi differ diff --git a/playground-data/SP011501.vcf.json b/playground-data/SP011501.vcf.json new file mode 100644 index 00000000..1b4a4d78 --- /dev/null +++ b/playground-data/SP011501.vcf.json @@ -0,0 +1,168 @@ +{ + "studyId": "SECA-CA", + "analysisType": { + "name": "demoDataSchemaV5" + }, + "samples": [ + { + "submitterSampleId": "SP011501", + "sampleType": "Total DNA", + "matchedNormalSubmitterSampleId": null, + "specimen": { + "submitterSpecimenId": "SP011501", + "specimenType": "Normal - tissue adjacent to primary tumour", + "tumourNormalDesignation": "Normal", + "specimenTissueSource": "Solid tissue" + }, + "donor": { + "submitterDonorId": "DO0115", + "gender": "Female" + } + } + ], + "files": [ + { + "dataType": "Raw InDel Calls", + "fileName": "SP011501.indel.vcf.gz", + "fileSize": 17346, + "fileMd5sum": "a5e32b78bd52dc2cfe1cffcdaadcb335", + "fileAccess": "open", + "fileType": "VCF", + "info": { + "dataCategory": "Simple Nucelotide Variation", + "jbrowseCoordinates": "hg38:chr1:100000-200000" + } + }, + { + "dataType": "Raw InDel Calls", + "fileName": "SP011501.indel.vcf.gz.tbi", + "fileSize": 144, + "fileMd5sum": "e4d3b0751f2824bac22f42147dd41fd8", + "fileAccess": "open", + "fileType": "TBI", + "info": { + "dataCategory": "Simple Nucelotide Variation", + "jbrowseCoordinates": "hg38:chr1:100000-200000" + } + } + ], + "specimen": { + "submitterPrimaryDiagnosisId": "PD011501", + "submitterSpecimenId": "SP011501", + "specimenAnatomicLocation": "C01", + "tumourGradingSystem": "Grading system for GNETs", + "tumourGrade": "G2" + }, + "donor": { + "submitterDonorId": "DO0115", + "primarySite": [ + "Bronchus and lung" + ], + "vitalStatus": "Deceased", + "survivalTime": 439, + "causeOfDeath": "Died of other reasons", + "primaryDiagnosis": [ + { + "submitterPrimaryDiagnosisId": "PD011501", + "ageAtDiagnosis": 36, + "cancerTypeCode": "C34.3", + "clinicalTumourStagingSystem": "AJCC 6th edition", + "clinicalStageGroup": "Stage III", + "treatment": [ + { + "submitterTreatmentId": "TR011501", + "treatmentType": [ + "Chemotherapy" + ], + "treatmentStartInterval": 79, + "treatmentDuration": 34, + "responseToTreatment": "Minor response", + "chemotherapy": [ + { + "drugName": [ + "Azacitidine" + ] + } + ] + } + ], + "followUp": [ + { + "submitterFollowUpId": "FO011501", + "submitterTreatmentId": "TR011501", + "intervalOfFollowUp": 50, + "diseaseStatusAtFollowUp": "Partial remission", + "relapseType": null + } + ] + }, + { + "submitterPrimaryDiagnosisId": "PD011502", + "ageAtDiagnosis": 1, + "cancerTypeCode": "C34.2", + "clinicalTumourStagingSystem": "FIGO staging system", + "clinicalStageGroup": "Stage IB", + "treatment": [ + { + "submitterTreatmentId": "TR011502", + "treatmentType": [ + "Chemotherapy", + "Radiation therapy" + ], + "treatmentStartInterval": 70, + "treatmentDuration": 56, + "responseToTreatment": "Complete response", + "chemotherapy": [ + { + "drugName": [ + "Paclitaxel" + ] + } + ], + "radiation": [ + { + "radiationTherapyModality": "Photon", + "anatomicalSiteIrradiated": "Body" + } + ] + } + ], + "followUp": [ + { + "submitterFollowUpId": "FO011502", + "submitterTreatmentId": "TR011502", + "intervalOfFollowUp": 33, + "diseaseStatusAtFollowUp": "Relapse or recurrence", + "relapseType": null + } + ] + } + ] + }, + "experiment": { + "platform": "PacBio", + "experimentalStrategy": "WXS", + "model": "SEQUEL IIe", + "sequencingCenter": "CGTA", + "sequencingDate": "2021-03-08T19:00:00.000Z" + }, + "workflow": { + "workflowName": "Sanger Variant Calling", + "workflowShortName": "SangerVariant", + "workflowVersion": "0.9.8", + "genomeBuild": "GRCh38_hla_decoy_ebv", + "inputs": [ + { + "analysisType": "sequencing_alignment", + "tumourAnalysisId": "00000000-0000-0000-0000-0000000000115", + "normalAnalysisId": "00000000-0000-0000-0000-0000000000115" + } + ], + "runId": "RI0115", + "sessionId": "SI0115" + }, + "publication": { + "publication": "NAR", + "doi": "10.1093/nar/gkae188" + } +} diff --git a/playground-data/SP011511.indel.vcf.gz b/playground-data/SP011511.indel.vcf.gz new file mode 100644 index 00000000..426ed8b0 Binary files /dev/null and b/playground-data/SP011511.indel.vcf.gz differ diff --git a/playground-data/SP011511.indel.vcf.gz.tbi b/playground-data/SP011511.indel.vcf.gz.tbi new file mode 100644 index 00000000..57b43738 Binary files /dev/null and b/playground-data/SP011511.indel.vcf.gz.tbi differ diff --git a/playground-data/SP011511.vcf.json b/playground-data/SP011511.vcf.json new file mode 100644 index 00000000..8c8db855 --- /dev/null +++ b/playground-data/SP011511.vcf.json @@ -0,0 +1,168 @@ +{ + "studyId": "SECA-CA", + "analysisType": { + "name": "demoDataSchemaV5" + }, + "samples": [ + { + "submitterSampleId": "SP011511", + "sampleType": "Total DNA", + "matchedNormalSubmitterSampleId": "SP011501", + "specimen": { + "submitterSpecimenId": "SP011511", + "specimenType": "Primary tumour - adjacent to normal", + "tumourNormalDesignation": "Tumour", + "specimenTissueSource": "Blood derived - bone marrow" + }, + "donor": { + "submitterDonorId": "DO0115", + "gender": "Female" + } + } + ], + "files": [ + { + "dataType": "Raw InDel Calls", + "fileName": "SP011511.indel.vcf.gz", + "fileSize": 17328, + "fileMd5sum": "c445d6cd5e1aa1d7dec13096feae788c", + "fileAccess": "open", + "fileType": "VCF", + "info": { + "dataCategory": "Simple Nucelotide Variation", + "jbrowseCoordinates": "hg38:chr1:100000-200000" + } + }, + { + "dataType": "Raw InDel Calls", + "fileName": "SP011511.indel.vcf.gz.tbi", + "fileSize": 148, + "fileMd5sum": "ae025b596b2fb562d33073338eb23a7d", + "fileAccess": "open", + "fileType": "TBI", + "info": { + "dataCategory": "Simple Nucelotide Variation", + "jbrowseCoordinates": "hg38:chr1:100000-200000" + } + } + ], + "specimen": { + "submitterPrimaryDiagnosisId": "PD011501", + "submitterSpecimenId": "SP011501", + "specimenAnatomicLocation": "C14", + "tumourGradingSystem": "Three-tier grading system", + "tumourGrade": "G3" + }, + "donor": { + "submitterDonorId": "DO0115", + "primarySite": [ + "Bronchus and lung" + ], + "vitalStatus": "Deceased", + "survivalTime": 439, + "causeOfDeath": "Died of other reasons", + "primaryDiagnosis": [ + { + "submitterPrimaryDiagnosisId": "PD011501", + "ageAtDiagnosis": 36, + "cancerTypeCode": "C34.3", + "clinicalTumourStagingSystem": "AJCC 6th edition", + "clinicalStageGroup": "Stage III", + "treatment": [ + { + "submitterTreatmentId": "TR011501", + "treatmentType": [ + "Chemotherapy" + ], + "treatmentStartInterval": 79, + "treatmentDuration": 34, + "responseToTreatment": "Minor response", + "chemotherapy": [ + { + "drugName": [ + "Azacitidine" + ] + } + ] + } + ], + "followUp": [ + { + "submitterFollowUpId": "FO011501", + "submitterTreatmentId": "TR011501", + "intervalOfFollowUp": 50, + "diseaseStatusAtFollowUp": "Partial remission", + "relapseType": null + } + ] + }, + { + "submitterPrimaryDiagnosisId": "PD011502", + "ageAtDiagnosis": 1, + "cancerTypeCode": "C34.2", + "clinicalTumourStagingSystem": "FIGO staging system", + "clinicalStageGroup": "Stage IB", + "treatment": [ + { + "submitterTreatmentId": "TR011502", + "treatmentType": [ + "Chemotherapy", + "Radiation therapy" + ], + "treatmentStartInterval": 70, + "treatmentDuration": 56, + "responseToTreatment": "Complete response", + "chemotherapy": [ + { + "drugName": [ + "Paclitaxel" + ] + } + ], + "radiation": [ + { + "radiationTherapyModality": "Photon", + "anatomicalSiteIrradiated": "Body" + } + ] + } + ], + "followUp": [ + { + "submitterFollowUpId": "FO011502", + "submitterTreatmentId": "TR011502", + "intervalOfFollowUp": 33, + "diseaseStatusAtFollowUp": "Relapse or recurrence", + "relapseType": null + } + ] + } + ] + }, + "experiment": { + "platform": "PacBio", + "experimentalStrategy": "WXS", + "model": "SEQUEL IIe", + "sequencingCenter": "CGTA", + "sequencingDate": "2021-03-08T19:00:00.000Z" + }, + "workflow": { + "workflowName": "Sanger Variant Calling", + "workflowShortName": "SangerVariant", + "workflowVersion": "0.9.8", + "genomeBuild": "GRCh38_hla_decoy_ebv", + "inputs": [ + { + "analysisType": "sequencing_alignment", + "tumourAnalysisId": "00000000-0000-0000-0000-0000000000115", + "normalAnalysisId": "00000000-0000-0000-0000-0000000000115" + } + ], + "runId": "RI0115", + "sessionId": "SI0115" + }, + "publication": { + "publication": "NAR", + "doi": "10.1093/nar/gkae188" + } +} diff --git a/playground-data/SP042701.cram b/playground-data/SP042701.cram new file mode 100644 index 00000000..7bef84bb Binary files /dev/null and b/playground-data/SP042701.cram differ diff --git a/playground-data/SP042701.cram.crai b/playground-data/SP042701.cram.crai new file mode 100644 index 00000000..6b7da94c Binary files /dev/null and b/playground-data/SP042701.cram.crai differ diff --git a/playground-data/SP042701.cram.json b/playground-data/SP042701.cram.json new file mode 100644 index 00000000..9d50f99b --- /dev/null +++ b/playground-data/SP042701.cram.json @@ -0,0 +1,157 @@ +{ + "studyId": "BRCA-MX", + "analysisType": { + "name": "demoDataSchemaV5" + }, + "samples": [ + { + "submitterSampleId": "SP042701", + "sampleType": "ctDNA", + "matchedNormalSubmitterSampleId": null, + "specimen": { + "submitterSpecimenId": "SP042701", + "specimenType": "Normal - tissue adjacent to primary tumour", + "tumourNormalDesignation": "Normal", + "specimenTissueSource": "Blood derived - peripheral blood" + }, + "donor": { + "submitterDonorId": "DO0427", + "gender": "Male" + } + } + ], + "files": [ + { + "dataType": "Aligned Reads", + "fileName": "SP042701.cram", + "fileSize": 116014, + "fileMd5sum": "2870377f867846dbb575b264f3d5fe21", + "fileAccess": "open", + "fileType": "CRAM", + "info": { + "dataCategory": "Sequencing Reads", + "jbrowseCoordinates": "hg38:chr1:100000-200000" + } + }, + { + "dataType": "Aligned Reads", + "fileName": "SP042701.cram.crai", + "fileSize": 53, + "fileMd5sum": "7e40df3cfcad31297106ac8760d979c8", + "fileAccess": "open", + "fileType": "CRAI", + "info": { + "dataCategory": "Sequencing Reads", + "jbrowseCoordinates": "hg38:chr1:100000-200000" + } + } + ], + "specimen": { + "submitterPrimaryDiagnosisId": "PD042701", + "submitterSpecimenId": "SP042701", + "specimenAnatomicLocation": "C06", + "tumourGradingSystem": "Two-tier grading system", + "tumourGrade": "High grade" + }, + "donor": { + "submitterDonorId": "DO0427", + "primarySite": [ + "Bronchus and lung" + ], + "vitalStatus": "Deceased", + "survivalTime": 1945, + "causeOfDeath": "Died of cancer", + "primaryDiagnosis": [ + { + "submitterPrimaryDiagnosisId": "PD042701", + "ageAtDiagnosis": 64, + "cancerTypeCode": "C34.8", + "clinicalTumourStagingSystem": "Revised International staging system (RISS)", + "clinicalStageGroup": "Stage I", + "treatment": [ + { + "submitterTreatmentId": "TR042701", + "treatmentType": [ + "No treatment" + ] + } + ], + "followUp": [ + { + "submitterFollowUpId": "FO042701", + "submitterTreatmentId": "TR042701", + "intervalOfFollowUp": 65, + "diseaseStatusAtFollowUp": "Distant progression", + "relapseType": null + } + ] + }, + { + "submitterPrimaryDiagnosisId": "PD042702", + "ageAtDiagnosis": 52, + "cancerTypeCode": "C34.0", + "clinicalTumourStagingSystem": "AJCC 8th edition", + "clinicalStageGroup": "Stage IIIC1", + "treatment": [ + { + "submitterTreatmentId": "TR042702", + "treatmentType": [ + "Chemotherapy", + "Radiation therapy" + ], + "treatmentStartInterval": 9, + "treatmentDuration": 43, + "responseToTreatment": "Partial response", + "chemotherapy": [ + { + "drugName": [ + "Azacitidine" + ] + } + ], + "radiation": [ + { + "radiationTherapyModality": "Photon", + "anatomicalSiteIrradiated": "Spine" + } + ] + } + ], + "followUp": [ + { + "submitterFollowUpId": "FO042702", + "submitterTreatmentId": "TR042702", + "intervalOfFollowUp": 72, + "diseaseStatusAtFollowUp": "Distant progression", + "relapseType": null + } + ] + } + ] + }, + "experiment": { + "platform": "ILLUMINA", + "experimentalStrategy": "WGS", + "model": "NovaSeq X", + "sequencingCenter": "ACGT", + "sequencingDate": "2020-08-09T19:00:00.000Z" + }, + "workflow": { + "workflowName": "BWA mem2 Alignment", + "workflowShortName": "BWAmem2Aln", + "workflowVersion": "0.8", + "genomeBuild": "GRCh38_hla_decoy_ebv", + "inputs": [ + { + "analysisType": "sequencing_experiment", + "analysisId": "00000000-0000-0000-0000-0000000000427" + } + ], + "runId": "RI0427", + "sessionId": "SI0427" + }, + "publication": { + "publication": "Cell Genomics", + "doi": "10.1016/j.xgen.2024.100537" + } +} diff --git a/playground-data/SP042711.cram b/playground-data/SP042711.cram new file mode 100644 index 00000000..2b3fc124 Binary files /dev/null and b/playground-data/SP042711.cram differ diff --git a/playground-data/SP042711.cram.crai b/playground-data/SP042711.cram.crai new file mode 100644 index 00000000..092bbc72 Binary files /dev/null and b/playground-data/SP042711.cram.crai differ diff --git a/playground-data/SP042711.cram.json b/playground-data/SP042711.cram.json new file mode 100644 index 00000000..786e8c1e --- /dev/null +++ b/playground-data/SP042711.cram.json @@ -0,0 +1,157 @@ +{ + "studyId": "BRCA-MX", + "analysisType": { + "name": "demoDataSchemaV5" + }, + "samples": [ + { + "submitterSampleId": "SP042711", + "sampleType": "ctDNA", + "matchedNormalSubmitterSampleId": "SP042701", + "specimen": { + "submitterSpecimenId": "SP042711", + "specimenType": "Metastatic tumour", + "tumourNormalDesignation": "Tumour", + "specimenTissueSource": "Solid tissue" + }, + "donor": { + "submitterDonorId": "DO0427", + "gender": "Male" + } + } + ], + "files": [ + { + "dataType": "Aligned Reads", + "fileName": "SP042711.cram", + "fileSize": 116051, + "fileMd5sum": "7551669b421718f5e9d8b32349c899b4", + "fileAccess": "open", + "fileType": "CRAM", + "info": { + "dataCategory": "Sequencing Reads", + "jbrowseCoordinates": "hg38:chr1:100000-200000" + } + }, + { + "dataType": "Aligned Reads", + "fileName": "SP042711.cram.crai", + "fileSize": 52, + "fileMd5sum": "068971084f3f865fa5fdb91636f312f0", + "fileAccess": "open", + "fileType": "CRAI", + "info": { + "dataCategory": "Sequencing Reads", + "jbrowseCoordinates": "hg38:chr1:100000-200000" + } + } + ], + "specimen": { + "submitterPrimaryDiagnosisId": "PD042701", + "submitterSpecimenId": "SP042701", + "specimenAnatomicLocation": "C66", + "tumourGradingSystem": "Three-tier grading system", + "tumourGrade": "G2" + }, + "donor": { + "submitterDonorId": "DO0427", + "primarySite": [ + "Bronchus and lung" + ], + "vitalStatus": "Deceased", + "survivalTime": 1945, + "causeOfDeath": "Died of cancer", + "primaryDiagnosis": [ + { + "submitterPrimaryDiagnosisId": "PD042701", + "ageAtDiagnosis": 64, + "cancerTypeCode": "C34.8", + "clinicalTumourStagingSystem": "Revised International staging system (RISS)", + "clinicalStageGroup": "Stage I", + "treatment": [ + { + "submitterTreatmentId": "TR042701", + "treatmentType": [ + "No treatment" + ] + } + ], + "followUp": [ + { + "submitterFollowUpId": "FO042701", + "submitterTreatmentId": "TR042701", + "intervalOfFollowUp": 65, + "diseaseStatusAtFollowUp": "Distant progression", + "relapseType": null + } + ] + }, + { + "submitterPrimaryDiagnosisId": "PD042702", + "ageAtDiagnosis": 52, + "cancerTypeCode": "C34.0", + "clinicalTumourStagingSystem": "AJCC 8th edition", + "clinicalStageGroup": "Stage IIIC1", + "treatment": [ + { + "submitterTreatmentId": "TR042702", + "treatmentType": [ + "Chemotherapy", + "Radiation therapy" + ], + "treatmentStartInterval": 9, + "treatmentDuration": 43, + "responseToTreatment": "Partial response", + "chemotherapy": [ + { + "drugName": [ + "Azacitidine" + ] + } + ], + "radiation": [ + { + "radiationTherapyModality": "Photon", + "anatomicalSiteIrradiated": "Spine" + } + ] + } + ], + "followUp": [ + { + "submitterFollowUpId": "FO042702", + "submitterTreatmentId": "TR042702", + "intervalOfFollowUp": 72, + "diseaseStatusAtFollowUp": "Distant progression", + "relapseType": null + } + ] + } + ] + }, + "experiment": { + "platform": "ILLUMINA", + "experimentalStrategy": "WGS", + "model": "NovaSeq X", + "sequencingCenter": "ACGT", + "sequencingDate": "2020-08-09T19:00:00.000Z" + }, + "workflow": { + "workflowName": "BWA mem2 Alignment", + "workflowShortName": "BWAmem2Aln", + "workflowVersion": "0.8", + "genomeBuild": "GRCh38_hla_decoy_ebv", + "inputs": [ + { + "analysisType": "sequencing_experiment", + "analysisId": "00000000-0000-0000-0000-0000000000427" + } + ], + "runId": "RI0427", + "sessionId": "SI0427" + }, + "publication": { + "publication": "Cell Genomics", + "doi": "10.1016/j.xgen.2024.100537" + } +} diff --git a/playground-data/SP042711.cram.log b/playground-data/SP042711.cram.log new file mode 100644 index 00000000..3ac0f91a --- /dev/null +++ b/playground-data/SP042711.cram.log @@ -0,0 +1,17 @@ +Running +docker run -e CLIENT_ACCESS_TOKEN=995d255f-5482-4201-aa31-b8d69420b591 -e CLIENT_STUDY_ID=BRCA-MX -e CLIENT_SERVER_URL=https://song.demo.overture.bio --network="host" --mount type=bind,source=/Users/esu/Desktop/GitHub/dms/playground-data,target=/output ghcr.io/overture-stack/song-client sing submit -f /output/SP042711.cram.json + : +SUCCESS +analysisId generated : b245ae48-8da8-4561-85ae-488da8156124 +Running : +docker run -e CLIENT_ACCESS_TOKEN=995d255f-5482-4201-aa31-b8d69420b591 -e CLIENT_STUDY_ID=BRCA-MX -e CLIENT_SERVER_URL=https://song.demo.overture.bio --network="host" --mount type=bind,source=/Users/esu/Desktop/GitHub/dms/playground-data,target=/output ghcr.io/overture-stack/song-client sing manifest -a b245ae48-8da8-4561-85ae-488da8156124 -f /output/manifest.txt -d /output/ + +SUCCESS +Running : +docker run -e ACCESSTOKEN=995d255f-5482-4201-aa31-b8d69420b591 -e STORAGE_URL=https://score.demo.overture.bio -e METADATA_URL=https://song.demo.overture.bio --network="host" --mount type=bind,source="/Users/esu/Desktop/GitHub/dms/playground-data",target=/output ghcr.io/overture-stack/score score-client upload --manifest /output/manifest.txt + +SUCCESS +Running : +docker run -e CLIENT_ACCESS_TOKEN=995d255f-5482-4201-aa31-b8d69420b591 -e CLIENT_STUDY_ID=BRCA-MX -e CLIENT_SERVER_URL=https://song.demo.overture.bio --network="host" --mount type=bind,source=/Users/esu/Desktop/GitHub/dms/playground-data,target=/output ghcr.io/overture-stack/song-client sing publish -a b245ae48-8da8-4561-85ae-488da8156124 + +SUCCESS diff --git a/playground-data/SP059901.snv.vcf.gz b/playground-data/SP059901.snv.vcf.gz new file mode 100644 index 00000000..48e493cf Binary files /dev/null and b/playground-data/SP059901.snv.vcf.gz differ diff --git a/playground-data/SP059901.snv.vcf.gz.tbi b/playground-data/SP059901.snv.vcf.gz.tbi new file mode 100644 index 00000000..e52fd645 Binary files /dev/null and b/playground-data/SP059901.snv.vcf.gz.tbi differ diff --git a/playground-data/SP059901.vcf.json b/playground-data/SP059901.vcf.json new file mode 100644 index 00000000..c39fc17d --- /dev/null +++ b/playground-data/SP059901.vcf.json @@ -0,0 +1,127 @@ +{ + "studyId": "SECA-CA", + "analysisType": { + "name": "demoDataSchemaV5" + }, + "samples": [ + { + "submitterSampleId": "SP059901", + "sampleType": "ctDNA", + "matchedNormalSubmitterSampleId": null, + "specimen": { + "submitterSpecimenId": "SP059901", + "specimenType": "Normal", + "tumourNormalDesignation": "Normal", + "specimenTissueSource": "Solid tissue" + }, + "donor": { + "submitterDonorId": "DO0599", + "gender": "Female" + } + } + ], + "files": [ + { + "dataType": "Raw SV Calls", + "fileName": "SP059901.snv.vcf.gz", + "fileSize": 17249, + "fileMd5sum": "e1bd8b61ec914637d7541455012f20ca", + "fileAccess": "open", + "fileType": "VCF", + "info": { + "dataCategory": "Simple Nucelotide Variation", + "jbrowseCoordinates": "hg38:chr1:100000-200000" + } + }, + { + "dataType": "Raw SV Calls", + "fileName": "SP059901.snv.vcf.gz.tbi", + "fileSize": 147, + "fileMd5sum": "fc7d16793329206461cc789ae978ad5d", + "fileAccess": "open", + "fileType": "TBI", + "info": { + "dataCategory": "Simple Nucelotide Variation", + "jbrowseCoordinates": "hg38:chr1:100000-200000" + } + } + ], + "specimen": { + "submitterPrimaryDiagnosisId": "PD059901", + "submitterSpecimenId": "SP059901", + "specimenAnatomicLocation": "C14", + "tumourGradingSystem": "Two-tier grading system", + "tumourGrade": "Low grade" + }, + "donor": { + "submitterDonorId": "DO0599", + "primarySite": [ + "Bronchus and lung" + ], + "vitalStatus": "Alive", + "survivalTime": null, + "causeOfDeath": null, + "primaryDiagnosis": [ + { + "submitterPrimaryDiagnosisId": "PD059901", + "ageAtDiagnosis": 50, + "cancerTypeCode": "C34.2", + "clinicalTumourStagingSystem": "Binet staging system", + "clinicalStageGroup": "Stage A", + "treatment": [ + { + "submitterTreatmentId": "TR059901", + "treatmentType": [ + "Chemotherapy" + ], + "treatmentStartInterval": 58, + "treatmentDuration": 52, + "responseToTreatment": "Complete response", + "chemotherapy": [ + { + "drugName": [ + "Tamoxifen" + ] + } + ] + } + ], + "followUp": [ + { + "submitterFollowUpId": "FO059901", + "submitterTreatmentId": "TR059901", + "intervalOfFollowUp": 45, + "diseaseStatusAtFollowUp": "Stable", + "relapseType": null + } + ] + } + ] + }, + "experiment": { + "platform": "PacBio", + "experimentalStrategy": "WGS", + "model": "SEQUEL IIe", + "sequencingCenter": "CGTA", + "sequencingDate": "2021-03-08T19:00:00.000Z" + }, + "workflow": { + "workflowName": "Sanger Variant Calling", + "workflowShortName": "SangerVariant", + "workflowVersion": "0.9.8", + "genomeBuild": "GRCh38_hla_decoy_ebv", + "inputs": [ + { + "analysisType": "sequencing_alignment", + "tumourAnalysisId": "00000000-0000-0000-0000-0000000000599", + "normalAnalysisId": "00000000-0000-0000-0000-0000000000599" + } + ], + "runId": "RI0599", + "sessionId": "SI0599" + }, + "publication": { + "publication": "NAR", + "doi": "10.1093/nar/gkae188" + } +} diff --git a/playground-data/SP059902.snv.vcf.gz b/playground-data/SP059902.snv.vcf.gz new file mode 100644 index 00000000..731ae2b4 Binary files /dev/null and b/playground-data/SP059902.snv.vcf.gz differ diff --git a/playground-data/SP059902.snv.vcf.gz.tbi b/playground-data/SP059902.snv.vcf.gz.tbi new file mode 100644 index 00000000..28eb7822 Binary files /dev/null and b/playground-data/SP059902.snv.vcf.gz.tbi differ diff --git a/playground-data/SP059902.vcf.json b/playground-data/SP059902.vcf.json new file mode 100644 index 00000000..426cea92 --- /dev/null +++ b/playground-data/SP059902.vcf.json @@ -0,0 +1,127 @@ +{ + "studyId": "CESC-US", + "analysisType": { + "name": "demoDataSchemaV5" + }, + "samples": [ + { + "submitterSampleId": "SP059902", + "sampleType": "Total DNA", + "matchedNormalSubmitterSampleId": null, + "specimen": { + "submitterSpecimenId": "SP059902", + "specimenType": "Normal - tissue adjacent to primary tumour", + "tumourNormalDesignation": "Normal", + "specimenTissueSource": "Blood derived - bone marrow" + }, + "donor": { + "submitterDonorId": "DO0599", + "gender": "Female" + } + } + ], + "files": [ + { + "dataType": "Raw SV Calls", + "fileName": "SP059902.snv.vcf.gz", + "fileSize": 17246, + "fileMd5sum": "94b790078d8e98ad08ffc42389e2fa68", + "fileAccess": "open", + "fileType": "VCF", + "info": { + "dataCategory": "Simple Nucelotide Variation", + "jbrowseCoordinates": "hg38:chr1:100000-200000" + } + }, + { + "dataType": "Raw SV Calls", + "fileName": "SP059902.snv.vcf.gz.tbi", + "fileSize": 141, + "fileMd5sum": "f5cca6ace25d076d1f76cebf4ce3defd", + "fileAccess": "open", + "fileType": "TBI", + "info": { + "dataCategory": "Simple Nucelotide Variation", + "jbrowseCoordinates": "hg38:chr1:100000-200000" + } + } + ], + "specimen": { + "submitterPrimaryDiagnosisId": "PD059901", + "submitterSpecimenId": "SP059902", + "specimenAnatomicLocation": "C31", + "tumourGradingSystem": "Nuclear grading system for DCIS", + "tumourGrade": "G1" + }, + "donor": { + "submitterDonorId": "DO0599", + "primarySite": [ + "Bronchus and lung" + ], + "vitalStatus": "Alive", + "survivalTime": null, + "causeOfDeath": null, + "primaryDiagnosis": [ + { + "submitterPrimaryDiagnosisId": "PD059901", + "ageAtDiagnosis": 50, + "cancerTypeCode": "C34.2", + "clinicalTumourStagingSystem": "Binet staging system", + "clinicalStageGroup": "Stage A", + "treatment": [ + { + "submitterTreatmentId": "TR059901", + "treatmentType": [ + "Chemotherapy" + ], + "treatmentStartInterval": 58, + "treatmentDuration": 52, + "responseToTreatment": "Complete response", + "chemotherapy": [ + { + "drugName": [ + "Tamoxifen" + ] + } + ] + } + ], + "followUp": [ + { + "submitterFollowUpId": "FO059901", + "submitterTreatmentId": "TR059901", + "intervalOfFollowUp": 45, + "diseaseStatusAtFollowUp": "Stable", + "relapseType": null + } + ] + } + ] + }, + "experiment": { + "platform": "PacBio", + "experimentalStrategy": "WXS", + 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"specimen": { + "submitterPrimaryDiagnosisId": "PD945801", + "submitterSpecimenId": "SP945802", + "specimenAnatomicLocation": "C30", + "tumourGradingSystem": "ISUP grading system", + "tumourGrade": "G2" + }, + "donor": { + "submitterDonorId": "DO9458", + "primarySite": [ + "Bronchus and lung" + ], + "vitalStatus": "Deceased", + "survivalTime": 1108, + "causeOfDeath": "Died of other reasons", + "primaryDiagnosis": [ + { + "submitterPrimaryDiagnosisId": "PD945801", + "ageAtDiagnosis": 44, + "cancerTypeCode": "C34.3", + "clinicalTumourStagingSystem": "FIGO staging system", + "clinicalStageGroup": "Stage IA2", + "treatment": [ + { + "submitterTreatmentId": "TR945801", + "treatmentType": [ + "No treatment" + ] + } + ], + "followUp": [ + { + "submitterFollowUpId": "FO945801", + "submitterTreatmentId": "TR945801", + "intervalOfFollowUp": 92, + "diseaseStatusAtFollowUp": "Relapse or recurrence", + "relapseType": null + } + ] + }, + { + "submitterPrimaryDiagnosisId": "PD945802", + "ageAtDiagnosis": 3, + "cancerTypeCode": "C34.3", + "clinicalTumourStagingSystem": "AJCC 7th edition", + "clinicalStageGroup": "Stage IIIC", + "treatment": [ + { + "submitterTreatmentId": "TR945802", + "treatmentType": [ + "Hormonal therapy" + ], + "treatmentStartInterval": 11, + "treatmentDuration": 61, + "responseToTreatment": "Complete response", + "hormoneTherapy": [ + { + "drugName": [ + "Exemestane" + ] + } + ] + } + ], + "followUp": [ + { + "submitterFollowUpId": "FO945802", + "submitterTreatmentId": "TR945802", + "intervalOfFollowUp": 33, + "diseaseStatusAtFollowUp": "Relapse or recurrence", + "relapseType": null + } + ] + } + ] + }, + "experiment": { + "platform": "PacBio", + "experimentalStrategy": "WGS", + "model": "SEQUEL IIe", + "sequencingCenter": "CGTA", + "sequencingDate": "2021-03-08T19:00:00.000Z" + }, + "workflow": { + "workflowName": "Mutect2 Variant Calling", + "workflowShortName": "Mutect2Variant", + "workflowVersion": "0.1.1.1", + "genomeBuild": "GRCh38_hla_decoy_ebv", + "inputs": [ + { + "analysisType": "sequencing_alignment", + "tumourAnalysisId": "00000000-0000-0000-0000-0000000009458", + "normalAnalysisId": "00000000-0000-0000-0000-0000000009458" + } + ], + "runId": "RI9458", + "sessionId": "SI9458" + }, + "publication": { + "publication": "NAR", + "doi": "10.1093/nar/gkae188" + } +} diff --git a/playground-data/manifest.txt b/playground-data/manifest.txt new file mode 100644 index 00000000..1751485c --- /dev/null +++ b/playground-data/manifest.txt @@ -0,0 +1,3 @@ +b245ae48-8da8-4561-85ae-488da8156124 +791977ba-2f45-5b32-8414-aad392f8e760 /output/SP042711.cram 7551669b421718f5e9d8b32349c899b4 +4ce6be5f-d7a8-53ed-9f06-db4a84121996 /output/SP042711.cram.crai 068971084f3f865fa5fdb91636f312f0 diff --git a/playground-data/submit_payload.py b/playground-data/submit_payload.py new file mode 100644 index 00000000..ded66c08 --- /dev/null +++ b/playground-data/submit_payload.py @@ -0,0 +1,158 @@ +#!/usr/bin/env python3 +# -*- coding: utf-8 -*- + + +import subprocess +import re +import sys +from argparse import ArgumentParser + + +parser = ArgumentParser(description='Tool: Quick song score submit files') +parser.add_argument("-t", "--token", dest="token", required=True, + help="API token", type=str, default ="88fe6ab2-8a5a-4ece-8f32-48a3e4db41fd") +parser.add_argument("-a", "--song", dest="song_url", + help="SONG URL", type=str, default ="https://song.demo.overture.bio") +parser.add_argument("-b", "--score", dest="score_url", + help="SCORE URL", type=str, default ="https://score.demo.overture.bio") +parser.add_argument("-s", "--study", dest="studyId", + help="studyId", type=str, default ="demoData") +parser.add_argument("-j", "--json", dest="json", + help="JSON file", type=str) +parser.add_argument("-d", "--directory", dest="directory", + help="JSON and data directory", type=str) + +args = parser.parse_args() + + +token=args.token +song_url=args.song_url +studyId=args.studyId +score_url=args.score_url +json_directory=args.directory +json_file=args.json + +submit_cmd=\ +""" +docker run \ +-e CLIENT_ACCESS_TOKEN=%s \ +-e CLIENT_STUDY_ID=%s \ +-e CLIENT_SERVER_URL=%s \ +--network="host" \ +--mount type=bind,source=%s,target=/output \ +ghcr.io/overture-stack/song-client \ +sing submit -f /output/%s +""" % (token,studyId,song_url,json_directory,json_file) + +print("Running %s :" % submit_cmd) +proc = subprocess.Popen( + submit_cmd, + shell=True, + stdin=subprocess.PIPE, + stdout=subprocess.PIPE, + stderr=subprocess.PIPE + ) + +stdout, stderr = proc.communicate() + +if proc.returncode!=0: + print("ERRORCODE : %s " % (str(proc.returncode))) + print("STDOUT : %s " % (stdout.decode("utf-8").strip())) + print("STDERR : %s " % (stderr.decode("utf-8").strip())) + sys.exit(1) +else: + print("SUCCESS") + analysisId=re.findall('[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}',stdout.decode("utf-8").strip())[0] + print("analysisId generated : %s" % (analysisId)) + + +manifest_cmd=\ +""" +docker run \ +-e CLIENT_ACCESS_TOKEN=%s \ +-e CLIENT_STUDY_ID=%s \ +-e CLIENT_SERVER_URL=%s \ +--network="host" \ +--mount type=bind,source=%s,target=/output \ +ghcr.io/overture-stack/song-client \ +sing manifest -a %s -f /output/manifest.txt -d /output/ +""" % (token,studyId,song_url,json_directory,analysisId) + +print("Running : %s " % manifest_cmd) +proc = subprocess.Popen( + manifest_cmd, + shell=True, + stdin=subprocess.PIPE, + stdout=subprocess.PIPE, + stderr=subprocess.PIPE + ) + +stdout, stderr = proc.communicate() + +if proc.returncode!=0: + print("ERRORCODE : %s " % (str(proc.returncode))) + print("STDOUT : %s " % (stdout.decode("utf-8").strip())) + print("STDERR : %s " % (stderr.decode("utf-8").strip())) + sys.exit(1) +else: + print("SUCCESS") + +upload_cmd=\ +""" +docker run \ +-e ACCESSTOKEN=%s \ +-e STORAGE_URL=%s \ +-e METADATA_URL=%s \ +--network="host" \ +--mount type=bind,source="%s",target=/output \ +ghcr.io/overture-stack/score \ +score-client upload --manifest /output/manifest.txt +""" % (token,score_url,song_url,json_directory) +print("Running : %s" % upload_cmd) +proc = subprocess.Popen( + upload_cmd, + shell=True, + stdin=subprocess.PIPE, + stdout=subprocess.PIPE, + stderr=subprocess.PIPE + ) + +stdout, stderr = proc.communicate() + +if proc.returncode!=0: + print("ERRORCODE : %s " % (str(proc.returncode))) + print("STDOUT : %s " % (stdout.decode("utf-8").strip())) + print("STDERR : %s " % (stderr.decode("utf-8").strip())) + sys.exit(1) +else: + print("SUCCESS") + +publish_cmd=\ +""" +docker run \ +-e CLIENT_ACCESS_TOKEN=%s \ +-e CLIENT_STUDY_ID=%s \ +-e CLIENT_SERVER_URL=%s \ +--network="host" \ +--mount type=bind,source=%s,target=/output \ +ghcr.io/overture-stack/song-client \ +sing publish -a %s +""" % (token,studyId,song_url,json_directory,analysisId) +print("Running : %s" % publish_cmd) +proc = subprocess.Popen( + publish_cmd, + shell=True, + stdin=subprocess.PIPE, + stdout=subprocess.PIPE, + stderr=subprocess.PIPE + ) + +stdout, stderr = proc.communicate() + +if proc.returncode!=0: + print("ERRORCODE : %s " % (str(proc.returncode))) + print("STDOUT : %s " % (stdout.decode("utf-8").strip())) + print("STDERR : %s " % (stderr.decode("utf-8").strip())) + sys.exit(1) +else: + print("SUCCESS")