Comments (2)
This collection has clinical data spread across different sheets in the Excel file corresponding to different types of attributes (demographics, patient response, weight etc). This was not recorded correctly in the clinical_notes.json file. The code was trying to create the same table hnscc_3dct_rt_clinical, for each of these sheets, creating a race condition. The sheet with the weight information 'won'. The column_metadata table recorded the columns for all of the different versions of hnscc_3dct_rt_clinical being created.
Updating the clinical_notes.json file data should fix this problem. As noted in #35, new regression testing will hopefully pick these errors in the future.
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Visual inspection of the tables confirms consistency between hnscc-3dct_rt table column names and metadata in column_metadata
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Related Issues (20)
- [clinical] Add PatientID to the per-collection tables (whenever it is not already available) HOT 7
- Map the patient identifier column in the clinical collections to the DICOM patientID HOT 2
- [clinical] Support NLST clinical data HOT 9
- Clinical data per-table metadata tracking HOT 3
- Define BQ layout of clinical data tables HOT 1
- [clinical] collection_id should not be an array HOT 3
- variable_label should not be blank HOT 3
- Consider renaming "variable" to "column" in "column_metadata" HOT 2
- Add regression testing to confirm consistency of clinical table schemas with column_metadata HOT 2
- Integrate 'Legacy' Clinical data into new clinical dataset.
- Inconsistencies identified for the ISPY1 clinical table HOT 4
- dicom_patient_id appears to be missing in several clinical tables HOT 2
- Use fully resolved versioned table names in all places HOT 1
- table_metadata should indicate whether table dictionary was parsed from sources or derived HOT 2
- acrin_6698 sbrgrade NAs are replaced with nulls HOT 2
- Values for `dicom_patient_id` are invalid for the `acrin_6698` collection HOT 2
- Duke-Breast-Cancer-MRI clinical data is missing HOT 1
- Investigate ingestion of HTAN related data HOT 2
- Ingest RMS clinical data HOT 18
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