Removed deprecated synth datasets and scripts used to create. - #34
Merged
Conversation
There was a problem hiding this comment.
Pull request overview
This PR removes the deprecated synthetic oncology protocol dataset for NCT01797120 (CSV “test_data”) and the local scripts that generated it, aligning with the stated intent to maintain those artifacts in a separate repository. It also includes a formatting-only change to an SDTM Dataset-JSON file (ta.json) under the LZZT source data.
Changes:
- Deleted
data/protocol/NCT01797120/test_data/*synthetic CSVs and accompanying markdown docs. - Deleted deprecated generation scripts under
data/protocol/NCT01797120/scripts/. - Reformatted
data/source/LZZT/sdtm/ta.jsonfrom minified JSON to pretty-printed JSON.
Reviewed changes
Copilot reviewed 13 out of 15 changed files in this pull request and generated 3 comments.
Show a summary per file
| File | Description |
|---|---|
| data/source/LZZT/sdtm/ta.json | Reformats SDTM TA Dataset-JSON (content-preserving formatting change). |
| data/protocol/NCT01797120/test_data/TV.csv | Removes synthetic TV domain CSV. |
| data/protocol/NCT01797120/test_data/TA.csv | Removes synthetic TA domain CSV. |
| data/protocol/NCT01797120/test_data/RS.csv | Removes synthetic RS domain CSV. |
| data/protocol/NCT01797120/test_data/README.md | Removes synthetic dataset README. |
| data/protocol/NCT01797120/test_data/FEEDBACK.md | Removes feedback notes for the synthetic dataset generation. |
| data/protocol/NCT01797120/test_data/DM.csv | Removes synthetic DM domain CSV. |
| data/protocol/NCT01797120/test_data/ADTTE.csv | Removes synthetic ADTTE analysis CSV. |
| data/protocol/NCT01797120/test_data/ADSL.csv | Removes synthetic ADSL analysis CSV. |
| data/protocol/NCT01797120/scripts/generate_subject_data_NCT01797120-deprecated.py | Removes deprecated subject-level synthetic data generator script. |
| data/protocol/NCT01797120/scripts/cdisc_generation_functions.py | Removes deprecated CDISC generation helper functions. |
💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.
Comment on lines
+1
to
+3
| { | ||
| "datasetJSONCreationDateTime": "2024-12-18T15:34:16", | ||
| "datasetJSONVersion": "1.1.0", |
| @@ -1 +1,190 @@ | |||
| {"datasetJSONCreationDateTime":"2024-12-18T15:34:16","datasetJSONVersion":"1.1.0","fileOID":"CDISCPILOT01.ta","dbLastModifiedDateTime":"2012-04-04T22:16:22","originator":"CDISC Data Exchange Standards Team","sourceSystem":{"name":"SAS on X64_10PRO","version":"9.0401M7"},"studyOID":"CDISCPILOT01","metaDataVersionOID":"CDISC.SDTMIG.3.1.2","metaDataRef":"define.xml","itemGroupOID":"TA","records":8,"name":"TA","label":"Trial Arms","columns":[{"itemOID":"TA.STUDYID","name":"STUDYID","label":"Study Identifier","dataType":"string","length":12,"keySequence":1},{"itemOID":"TA.DOMAIN","name":"DOMAIN","label":"Domain Abbreviation","dataType":"string","length":2},{"itemOID":"TA.ARMCD","name":"ARMCD","label":"Planned Arm Code","dataType":"string","length":8,"keySequence":2},{"itemOID":"TA.ARM","name":"ARM","label":"Description of Planned Arm","dataType":"string","length":20},{"itemOID":"TA.TAETORD","name":"TAETORD","label":"Order of Element within Arm","dataType":"integer","keySequence":3},{"itemOID":"TA.ETCD","name":"ETCD","label":"Element Code","dataType":"string","length":200},{"itemOID":"TA.ELEMENT","name":"ELEMENT","label":"Description of Element","dataType":"string","length":200},{"itemOID":"TA.TABRANCH","name":"TABRANCH","label":"Branch","dataType":"string","length":200},{"itemOID":"TA.TATRANS","name":"TATRANS","label":"Transition Rule","dataType":"string","length":200},{"itemOID":"TA.EPOCH","name":"EPOCH","label":"Epoch","dataType":"string","length":200}],"rows":[["CDISCPILOT01","TA","Pbo","Placebo",1,"SCRN","Screen","Randomized to Placebo","","Screening"],["CDISCPILOT01","TA","Pbo","Placebo",2,"PBO","Placebo","","","Treatment"],["CDISCPILOT01","TA","Xan_Hi","Xanomeline High Dose",1,"SCRN","Screen","Randomized to High Dose","","Screening"],["CDISCPILOT01","TA","Xan_Hi","Xanomeline High Dose",2,"HIS","High_Start","","","Treatment"],["CDISCPILOT01","TA","Xan_Hi","Xanomeline High Dose",3,"HIM","High_Middle","","","Treatment"],["CDISCPILOT01","TA","Xan_Hi","Xanomeline High Dose",4,"HIE","High_End","","","Treatment"],["CDISCPILOT01","TA","Xan_Lo","Xanomeline Low Dose",1,"SCRN","Screen","Randomized to Low Dose","","Screening"],["CDISCPILOT01","TA","Xan_Lo","Xanomeline Low Dose",2,"LO","Low","","","Treatment"]]} No newline at end of file | |||
| { | |||
Comment on lines
+1
to
+2
| { | ||
| "datasetJSONCreationDateTime": "2024-12-18T15:34:16", |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Removed protocol synth datasets and scripts for creating these datasets.
These files are maintained in their own project repository: bc-supporting-synthetic-data.