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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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Data Dashboard causes disconnect for HTAN HTAPP #55

Open adamjtaylor opened 1 year ago

adamjtaylor commented 1 year ago 
2022-11-29T10:31:52.216506+00:00 shinyapps[5806160]: ERROR: [2022-11-29 10:31:52] root - For the attribute 'PhysicalSizeZUnit', on row 5613, '' is not one of ['mm', 'Å', 'cm', 'µm', 'nm'].
2022-11-29T10:31:52.216552+00:00 shinyapps[5806160]: ERROR: [2022-11-29 10:31:52] root - For the attribute 'PhysicalSizeZ', on row 5613, '' is too short.
2022-11-29T10:31:52.217052+00:00 shinyapps[5806160]: ERROR: [2022-11-29 10:31:52] root - For the attribute 'PhysicalSizeZUnit', on row 5614, '' is not one of ['mm', 'Å', 'cm', 'µm', 'nm'].
2022-11-29T10:31:52.217110+00:00 shinyapps[5806160]: ERROR: [2022-11-29 10:31:52] root - For the attribute 'PhysicalSizeZ', on row 5614, '' is too short.
2022-11-29T10:31:52.217628+00:00 shinyapps[5806160]: ERROR: [2022-11-29 10:31:52] root - For the attribute 'PhysicalSizeZUnit', on row 5615, '' is not one of ['mm', 'Å', 'cm', 'µm', 'nm'].
2022-11-29T10:31:52.217679+00:00 shinyapps[5806160]: ERROR: [2022-11-29 10:31:52] root - For the attribute 'PhysicalSizeZ', on row 5615, '' is too short.
2022-11-29T10:31:52.218189+00:00 shinyapps[5806160]: ERROR: [2022-11-29 10:31:52] root - For the attribute 'PhysicalSizeZUnit', on row 5616, '' is not one of ['mm', 'Å', 'cm', 'µm', 'nm'].
2022-11-29T10:31:52.218251+00:00 shinyapps[5806160]: ERROR: [2022-11-29 10:31:52] root - For the attribute 'PhysicalSizeZ', on row 5616, '' is too short.
2022-11-29T10:31:52.218785+00:00 shinyapps[5806160]: ERROR: [2022-11-29 10:31:52] root - For the attribute 'PhysicalSizeZUnit', on row 5617, '' is not one of ['mm', 'Å', 'cm', 'µm', 'nm'].
2022-11-29T10:31:52.218834+00:00 shinyapps[5806160]: ERROR: [2022-11-29 10:31:52] root - For the attribute 'PhysicalSizeZ', on row 5617, '' is too short.
2022-11-29T10:32:31.537092+00:00 shinyapps[5806160]: ERROR: [2022-11-29 10:32:31] root - On row 2 the attribute Start Days from Index does not contain the proper value type int.
2022-11-29T10:32:31.537127+00:00 shinyapps[5806160]: ERROR: [2022-11-29 10:32:31] root - On row 3 the attribute Start Days from Index does not contain the proper value type int.
2022-11-29T10:33:40.774818+00:00 shinyapps[5806160]: WARNING: [2022-11-29 10:33:40] root - On row 12 the attribute Days to Progression does not contain the proper value type int.
2022-11-29T10:33:40.790546+00:00 shinyapps[5806160]: ERROR: [2022-11-29 10:33:40] root - On row 4 the attribute Days to Recurrence does not contain the proper value type int.
2022-11-29T10:33:40.790587+00:00 shinyapps[5806160]: ERROR: [2022-11-29 10:33:40] root - On row 12 the attribute Days to Recurrence does not contain the proper value type int.
2022-11-29T10:33:40.827939+00:00 shinyapps[5806160]: WARNING: [2022-11-29 10:33:40] root - For the attribute 'Prior Malignancy', on row 12, 'unknown' is not one of ['No', 'Not Allowed To Collect', 'Unknown', 'Not Reported', 'Yes', ''].
2022-11-29T10:33:40.827966+00:00 shinyapps[5806160]: WARNING: [2022-11-29 10:33:40] root - For the attribute 'Prior Treatment', on row 12, 'unknown' is not one of ['No', 'Not Allowed To Collect', 'Unknown', 'Not Reported', 'Yes', ''].
2022-11-29T10:34:10.180714+00:00 shinyapps[5806160]: Warning in parallel::mclapply(1:nrow(metadata), function(i) { :
2022-11-29T10:34:10.180751+00:00 shinyapps[5806160]:   scheduled cores 11, 10, 14, 8, 6, 12, 13, 3 encountered errors in user code, all values of the jobs will be affected
2022-11-29T10:34:10.273787+00:00 shinyapps[5806160]: Warning: Error in bind_rows: Argument 3 must have names.
2022-11-29T10:34:10.286598+00:00 shinyapps[5806160]:   15: <Anonymous>
2022-11-29T10:34:10.286624+00:00 shinyapps[5806160]:   13: fn
2022-11-29T10:34:10.286628+00:00 shinyapps[5806160]:    8: retry
2022-11-29T10:34:10.286632+00:00 shinyapps[5806160]:    7: connect$retryingStartServer
2022-11-29T10:34:10.286635+00:00 shinyapps[5806160]:    6: eval
2022-11-29T10:34:10.286638+00:00 shinyapps[5806160]:    5: eval
2022-11-29T10:34:10.286650+00:00 shinyapps[5806160]:    4: eval
2022-11-29T10:34:10.286654+00:00 shinyapps[5806160]:    3: eval
2022-11-29T10:34:10.286657+00:00 shinyapps[5806160]:    2: eval.parent
2022-11-29T10:34:10.286662+00:00 shinyapps[5806160]:    1: local
aclayton555 commented 1 year ago

Included in escalation to FAIR in this issue: https://sagebionetworks.jira.com/servicedesk/customer/portal/5/IBCSPRT-115