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ncihtan / HTAN-data-curator

HTAN Data Ingest Shiny App
https://sagebio.shinyapps.io/HTAN-data-curator/
Apache License 2.0
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Update to DCA v22.11.3 #63

Closed rrchai closed 1 year ago

rrchai commented 1 year ago

I will look into where the issues come from.

DO NOT MERGE

rrchai commented 1 year ago

By testing this branch, the dashboard can be successfully launched locally using the latest release of schematic.

Screen Shot 2022-12-08 at 2 30 21 AM

But it failed to load using the latest develop branch of schematic.

rrchai commented 1 year ago

✅ Just tested with the latest release of schematic in shinyapps.io - the dashboard can be rendered.

I think it might be a bug from the backend. Here is what might cause the error.

The dashboard is expecting "errors" and "warnings" two outputs from the validation results, where "warnings" should return the cross-manifest check results with certain format. However, using the latest develop of schematic, one(s) of manifests have invalid errors from "warnings" output, which makes the app crashed. For example:

synapse get syn24994554  
schematic model -c schematic_config.yml validate -mp synapse_storage_manifest.csv -dt Diagnosis -rr

warning: For the attribute 'AJCC Clinical T', on row 4, 1670472942462 is not one of ['T2a1', 'T3b', 'T1b1', 'T2a2', 'T1', 'T2b', 'T2', 'Ta', "Tis (Paget's)", 'Tis', 'T2a', 'TX', 'T1a1', 'T2c', 'T4a', 'T1a2', 'T2d', 'T4e', 'Tis (LCIS)', 'T0', 'T1c', 'T3', 'T3d', 'T4b', 'T4', 'Tis (DCIS)', 'unknown', 'T1mi', 'Not Reported', 'T3c', 'T3a', 'T1a', 'T4d', 'T4c', 'T1b', 'T1b2', ''].
warning: For the attribute 'AJCC Pathologic T', on row 4, 1670472942789 is not one of ['T2a1', 'T3b', 'T1b1', 'T2a2', 'T1', 'T2b', 'T2', 'Ta', "Tis (Paget's)", 'Tis', 'T2a', 'TX', 'T1a1', 'T2c', 'T4a', 'T1a2', 'T2d', 'T4e', 'Tis (LCIS)', 'T0', 'T1c', 'T3', 'T3d', 'T4b', 'T4', 'Tis (DCIS)', 'unknown', 'T1mi', 'Not Reported', 'T3c', 'T3a', 'T1a', 'T4d', 'T4c', 'T1b', 'T1b2', ''].
warning: For the attribute 'AJCC Clinical T', on row 6, 1667884542480 is not one of ['T2a1', 'T3b', 'T1b1', 'T2a2', 'T1', 'T2b', 'T2', 'Ta', "Tis (Paget's)", 'Tis', 'T2a', 'TX', 'T1a1', 'T2c', 'T4a', 'T1a2', 'T2d', 'T4e', 'Tis (LCIS)', 'T0', 'T1c', 'T3', 'T3d', 'T4b', 'T4', 'Tis (DCIS)', 'unknown', 'T1mi', 'Not Reported', 'T3c', 'T3a', 'T1a', 'T4d', 'T4c', 'T1b', 'T1b2', ''].
warning: For the attribute 'AJCC Pathologic T', on row 6, 1667884542807 is not one of ['T2a1', 'T3b', 'T1b1', 'T2a2', 'T1', 'T2b', 'T2', 'Ta', "Tis (Paget's)", 'Tis', 'T2a', 'TX', 'T1a1', 'T2c', 'T4a', 'T1a2', 'T2d', 'T4e', 'Tis (LCIS)', 'T0', 'T1c', 'T3', 'T3d', 'T4b', 'T4', 'Tis (DCIS)', 'unknown', 'T1mi', 'Not Reported', 'T3c', 'T3a', 'T1a', 'T4d', 'T4c', 'T1b', 'T1b2', ''].
adamjtaylor commented 1 year ago

@rrchai is it OK for this PR to be closed?

rrchai commented 1 year ago

@adamjtaylor Thanks for reminding! Close as it's out of date.