search

ncihtan / HTAN-data-curator

HTAN Data Ingest Shiny App
https://sagebio.shinyapps.io/HTAN-data-curator/
Apache License 2.0
1 stars 0 forks source link

Data Dashboard causes disconnect for HTAN Duke project #48

Open adamjtaylor opened 1 year ago

adamjtaylor commented 1 year ago

Reproduce in v22.11.1 production DCA. Select HTAN Duke project. Open data dashboard Loading, please wait.... shows for a few minutes before Disconnected from server error shows Screenshot 2022-11-29 at 09 37 27

2022-11-29T09:34:26.326368+00:00 shinyapps[5806160]: ERROR: [2022-11-29 09:34:26] root - For the attribute 'Tumor Tissue Type', on row 1032, 'primary' is not one of ['Metastatic', 'Recurrent', 'Premalignant', 'Primary', 'Normal distant', 'Normal adjacent', 'Premalignant - in situ', 'Atypia - hyperplasia', 'Not Otherwise Specified', 'Local recurrence', 'Normal', 'Post therapy adjuvant', 'Post therapy', 'Additional Primary', 'Post therapy neoadjuvant', 'Not analyzed', ''].
2022-11-29T09:34:26.326465+00:00 shinyapps[5806160]: ERROR: [2022-11-29 09:34:26] root - For the attribute 'Tumor Tissue Type', on row 1032, 'primary' is not one of ['Metastatic', 'Recurrent', 'Premalignant', 'Primary', 'Normal distant', 'Normal adjacent', 'Premalignant - in situ', 'Atypia - hyperplasia', 'Not Otherwise Specified', 'Local recurrence', 'Normal', 'Post therapy adjuvant', 'Post therapy', 'Additional Primary', 'Post therapy neoadjuvant', 'Not analyzed'].
2022-11-29T09:34:26.328456+00:00 shinyapps[5806160]: ERROR: [2022-11-29 09:34:26] root - For the attribute 'Tumor Tissue Type', on row 1034, 'primary' is not one of ['Metastatic', 'Recurrent', 'Premalignant', 'Primary', 'Normal distant', 'Normal adjacent', 'Premalignant - in situ', 'Atypia - hyperplasia', 'Not Otherwise Specified', 'Local recurrence', 'Normal', 'Post therapy adjuvant', 'Post therapy', 'Additional Primary', 'Post therapy neoadjuvant', 'Not analyzed', ''].
2022-11-29T09:34:26.328521+00:00 shinyapps[5806160]: ERROR: [2022-11-29 09:34:26] root - For the attribute 'Tumor Tissue Type', on row 1034, 'primary' is not one of ['Metastatic', 'Recurrent', 'Premalignant', 'Primary', 'Normal distant', 'Normal adjacent', 'Premalignant - in situ', 'Atypia - hyperplasia', 'Not Otherwise Specified', 'Local recurrence', 'Normal', 'Post therapy adjuvant', 'Post therapy', 'Additional Primary', 'Post therapy neoadjuvant', 'Not analyzed'].
2022-11-29T09:34:26.330600+00:00 shinyapps[5806160]: ERROR: [2022-11-29 09:34:26] root - For the attribute 'Tumor Tissue Type', on row 1036, 'primary' is not one of ['Metastatic', 'Recurrent', 'Premalignant', 'Primary', 'Normal distant', 'Normal adjacent', 'Premalignant - in situ', 'Atypia - hyperplasia', 'Not Otherwise Specified', 'Local recurrence', 'Normal', 'Post therapy adjuvant', 'Post therapy', 'Additional Primary', 'Post therapy neoadjuvant', 'Not analyzed', ''].
2022-11-29T09:34:26.394459+00:00 shinyapps[5806160]: ERROR: [2022-11-29 09:34:26] root - For the attribute 'Tumor Tissue Type', on row 1036, 'primary' is not one of ['Metastatic', 'Recurrent', 'Premalignant', 'Primary', 'Normal distant', 'Normal adjacent', 'Premalignant - in situ', 'Atypia - hyperplasia', 'Not Otherwise Specified', 'Local recurrence', 'Normal', 'Post therapy adjuvant', 'Post therapy', 'Additional Primary', 'Post therapy neoadjuvant', 'Not analyzed'].
2022-11-29T09:34:26.394496+00:00 shinyapps[5806160]: ERROR: [2022-11-29 09:34:26] root - For the attribute 'Tumor Tissue Type', on row 1037, 'primary' is not one of ['Metastatic', 'Recurrent', 'Premalignant', 'Primary', 'Normal distant', 'Normal adjacent', 'Premalignant - in situ', 'Atypia - hyperplasia', 'Not Otherwise Specified', 'Local recurrence', 'Normal', 'Post therapy adjuvant', 'Post therapy', 'Additional Primary', 'Post therapy neoadjuvant', 'Not analyzed', ''].
2022-11-29T09:34:26.394502+00:00 shinyapps[5806160]: ERROR: [2022-11-29 09:34:26] root - For the attribute 'Tumor Tissue Type', on row 1037, 'primary' is not one of ['Metastatic', 'Recurrent', 'Premalignant', 'Primary', 'Normal distant', 'Normal adjacent', 'Premalignant - in situ', 'Atypia - hyperplasia', 'Not Otherwise Specified', 'Local recurrence', 'Normal', 'Post therapy adjuvant', 'Post therapy', 'Additional Primary', 'Post therapy neoadjuvant', 'Not analyzed'].
2022-11-29T09:34:26.394521+00:00 shinyapps[5806160]: ERROR: [2022-11-29 09:34:26] root - For the attribute 'Tumor Tissue Type', on row 1039, 'primary' is not one of ['Metastatic', 'Recurrent', 'Premalignant', 'Primary', 'Normal distant', 'Normal adjacent', 'Premalignant - in situ', 'Atypia - hyperplasia', 'Not Otherwise Specified', 'Local recurrence', 'Normal', 'Post therapy adjuvant', 'Post therapy', 'Additional Primary', 'Post therapy neoadjuvant', 'Not analyzed', ''].
2022-11-29T09:34:26.394524+00:00 shinyapps[5806160]: ERROR: [2022-11-29 09:34:26] root - For the attribute 'Tumor Tissue Type', on row 1039, 'primary' is not one of ['Metastatic', 'Recurrent', 'Premalignant', 'Primary', 'Normal distant', 'Normal adjacent', 'Premalignant - in situ', 'Atypia - hyperplasia', 'Not Otherwise Specified', 'Local recurrence', 'Normal', 'Post therapy adjuvant', 'Post therapy', 'Additional Primary', 'Post therapy neoadjuvant', 'Not analyzed'].
2022-11-29T09:35:14.547842+00:00 shinyapps[5806160]: Warning in parallel::mclapply(1:nrow(metadata), function(i) { :
2022-11-29T09:35:14.547875+00:00 shinyapps[5806160]:   scheduled core 1 encountered error in user code, all values of the job will be affected
2022-11-29T09:35:14.644244+00:00 shinyapps[5806160]: Warning: Error in bind_rows: Argument 1 must have names.
2022-11-29T09:35:14.674802+00:00 shinyapps[5806160]:   15: <Anonymous>
2022-11-29T09:35:14.674831+00:00 shinyapps[5806160]:   13: fn
2022-11-29T09:35:14.674835+00:00 shinyapps[5806160]:    8: retry
2022-11-29T09:35:14.674839+00:00 shinyapps[5806160]:    7: connect$retryingStartServer
2022-11-29T09:35:14.674842+00:00 shinyapps[5806160]:    6: eval
2022-11-29T09:35:14.674846+00:00 shinyapps[5806160]:    5: eval
2022-11-29T09:35:14.674849+00:00 shinyapps[5806160]:    4: eval
2022-11-29T09:35:14.674863+00:00 shinyapps[5806160]:    3: eval
2022-11-29T09:35:14.674866+00:00 shinyapps[5806160]:    2: eval.parent
2022-11-29T09:35:14.674869+00:00 shinyapps[5806160]:    1: local
adamjtaylor commented 1 year ago

In the full logs there are hundreds of errors being generated all of the same form. I wonder if this is timing out?

aclayton555 commented 1 year ago

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