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Add CCDH Pilot examples#22

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gaurav merged 54 commits intomaincancerDHC/example-data:mainfrom add-pilot-examplescancerDHC/example-data:add-pilot-examplesCopy head branch name to clipboardJan 5, 2022

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Commits on Nov 18, 2021

• Added demonstrator files from data-model-harmonization.

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• First stab at trying to read d1 data as Python Data Classes.

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• Commented out parts of d1 examples so that they pass testing.

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• Commented out non-functional pieces of ccdh-pilot.

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• Commented out non-functional code.

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• Cleaned up test_all.py.

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• Added JSON Schema validation for specimens, commented out some lines.

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• Passed all JSON Schema validation.

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• Added test_import.py to transform some GDC data.

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• Added GDC-to-CRDC-H transformed data.

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• Added age_at_diagnosis.

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• Renamed test_all to test_validate_all; removed days as text.

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• Added condition.

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• Added primary_site.

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• Added ICD-10 codes.

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• Added code for constructing CancerStageObservations.

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• Added AJCC cancer staging, but commented it out.

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• Added diagnosis_date.

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• Added basic related specimen.

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• Added related specimen IDs.

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• Apparently we can get identifiers working if we add a system?!

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• Added a Diagnosis.subject (from GDC:Diagnosis.submitter_id)

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• Added some additional specimen fields.

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• Added creation times.

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• Added additional Specimen.creation_activity fields.

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• Added time-between-excision-and-freezing.

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• Added processing activity.

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• Added sample_submitter_id.

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• Added submitter IDs.

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• Added a link as per Python style requirements.

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• Renamed test_input to clearly indicate that it is the GDC import only.

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• Renamed test_import_gdc.py to reflect that it's a transform.

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• Deleted redundant test_build.py test.

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• Optimized imports.

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• Added and disambiguated submitter IDs and case IDs.

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• Added case and submitter identifiers for diagnoses.

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• Updated some comments.

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• Added diagnosis date from year of diagnosis.

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• Added issue for approx date bug.

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• First stab at transforming PDC.

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• Tweaked outputs.

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• Updated PDC to pass testing.

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• Centralized some shared code.

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• Added a note about why we are truncating value_decimal.

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• Deliberately created a validation error for demo.

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• Reverting to truncating integers.

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• Added morphology.

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• Added morphology to PDC head and mouth example.

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Commits on Jan 5, 2022

• Updated crdch-model to 1.2.

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• Updated expected JSONLD/TTL files.

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• Merge branch 'main' into add-pilot-examples

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• Reformatted source files with black.

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• Renamed GitHub workflow pytest.yaml to be accurate.

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• Added some README files to document content in these folders.

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