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knowledgesystems / pipelines-scrum

Repository for tracking uncategorizable issues related to backend pipelines work
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PDX Pipeline Followup #935

Closed averyniceday closed 2 years ago

averyniceday commented 2 years ago

Done Condition (What do we need? Why do we need it? Keep this is small as possible!)

Confirm PDX pipeline is working and importing main subsets (e.g. mixed_pdx_msk)

Technical Description (How are we going to achieve the above)

Potential Issues

Dependencies

Technical Requirements

Outside People/Teams

Changes

sheridancbio commented 2 years ago

A few studies were successfully updated over night last night: mixed_pdx_ntrk mixed_pdx_janjigian mixed_aac

Remaining problems captured on Aug 30:

Most failures seem to be related to missing "case_lists" subdirectories in the study directories. These studies failed to import because of that: mixed_pdx_rudin mcc_pdx mixed_pdx_kung mixed_pdx_chiosis mixed_pdx_scaltriti mixed_gyn_pdx mixed_pdx_singer mixed_pdx_head_and_neck mixed_gyn_pdx_rosen mixed_pdx_lowe prostate_pdx_scher breast_pdx_chandarlapaty mixed_pdx_cheung mixed_pdx_somwar mixed_pdx_abou_alfa And there were these other causes for failures: melanoma_pdx_rw (Caused by: java.lang.IllegalArgumentException: melanoma is not a supported cancer type.) mixed_pdx_msk (Caused by: java.lang.NullPointerException: Sample is not found in database (is it missing from clinical data file?): P-0012443-T01-IM5) colorectal_pdx_larson (Caused by: java.lang.IllegalArgumentException: colorectal is not a supported cancer type.)

sheridancbio commented 2 years ago

Problems related to imports reported to pdx team ... ball is in their court to do data corrections.