Unable to update HTAPP Biospecimen manifests

[clarisse-lau]

Describe the bug I'm attempting to update 3 HTAPP biospecimen manifests through staging. All three pass validation, but the app disconnects after ~10sec at the submission step.

To Reproduce Steps to reproduce the behavior: Upload HTAPP biospecimen_neuroblastoma, biospecimen_lung, biospecimen_breast manifests

htapp_bios_neuroblastoma.csv htapp_bios_lung.csv htapp_bios_breast.csv

Expected behavior Manifest is submitted to Synapse

Priority (select one)

• [ ] Minor ⬇️
• [x] Major 📢
• [ ] Critical 🆘

Screenshots If applicable, add screenshots to help explain your problem.

Desktop (if applicable, please complete the following information):

• OS: [MacOS]
• Browser [chrome]
• Version [Version 103.0.5060.114 (Official Build) (x86_64)]

Additional context

[adamjtaylor]

Thanks for reporting @clarisse-lau Weirdly this looks like it was a synapse authentication error.

2022-11-21T23:32:38.602511+00:00 shinyapps[5750996]: INFO: [2022-11-21 23:32:38] synapseclient_default - Welcome, clarisselau!
2022-11-21T23:33:15.660080+00:00 shinyapps[5750996]: Warning: Setting row names on a tibble is deprecated.
2022-11-21T23:33:28.198723+00:00 shinyapps[5750996]: Warning: Setting row names on a tibble is deprecated.
2022-11-21T23:33:46.707217+00:00 shinyapps[5750996]: [WARNING] /srv/connect/apps/HTAN-data-curator-staging/.venv/lib/python3.8/site-packages/synapseclient/table.py:2063: FutureWarning: the 'line_terminator'' keyword is deprecated, use 'lineterminator' instead.
2022-11-21T23:33:46.707259+00:00 shinyapps[5750996]:   df.to_csv(f,
2022-11-21T23:33:46.707270+00:00 shinyapps[5750996]: WARNING: [2022-11-21 23:33:46] py.warnings - /srv/connect/apps/HTAN-data-curator-staging/.venv/lib/python3.8/site-packages/synapseclient/table.py:2063: FutureWarning: the 'line_terminator'' keyword is deprecated, use 'lineterminator' instead.
2022-11-21T23:33:46.707275+00:00 shinyapps[5750996]:   df.to_csv(f,
2022-11-21T23:33:57.964839+00:00 shinyapps[5750996]: Warning: Error in py_call_impl: SynapseAuthenticationError: You are not logged in and do not have access to a requested resource.
2022-11-21T23:33:57.964885+00:00 shinyapps[5750996]: Detailed traceback:
2022-11-21T23:33:57.964889+00:00 shinyapps[5750996]:   File "/srv/connect/apps/HTAN-data-curator-staging/.venv/lib/python3.8/site-packages/schematic/store/synapse.py", line 1108, in associateMetadataWithFiles
2022-11-21T23:33:57.964893+00:00 shinyapps[5750996]:     annos = self.format_row_annotations(se, schemaGenerator, row, entityId, useSchemaLabel, hideBlanks)
2022-11-21T23:33:57.964897+00:00 shinyapps[5750996]:   File "/srv/connect/apps/HTAN-data-curator-staging/.venv/lib/python3.8/site-packages/schematic/store/synapse.py", line 146, in wrapper
2022-11-21T23:33:57.964911+00:00 shinyapps[5750996]:     return method(*args, **kwargs)
2022-11-21T23:33:57.964914+00:00 shinyapps[5750996]:   File "/srv/connect/apps/HTAN-data-curator-staging/.venv/lib/python3.8/site-packages/schematic/store/synapse.py", line 858, in format_row_annotations
2022-11-21T23:33:57.964917+00:00 shinyapps[5750996]:     annos = self.syn.get_annotations(entityId)
2022-11-21T23:33:57.964924+00:00 shinyapps[5750996]:   File "/srv/connect/apps/HTAN-data-curator-staging/.venv/lib/python3.8/site-packages/synapseclient/client.py", line 1525, in get_annotations
2022-11-21T23:33:57.964927+00:00 shinyapps[5750996]:     return from_synapse_annotations(self._getRawAnnotations(entity, version))
2022-11-21T23:33:57.964930+00:00 shinyapps[5750996]:   File "/ [... truncated]
2022-11-21T23:33:57.971099+00:00 shinyapps[5750996]:   15: <Anonymous>
2022-11-21T23:33:57.971118+00:00 shinyapps[5750996]:   13: fn
2022-11-21T23:33:57.971122+00:00 shinyapps[5750996]:    8: retry
2022-11-21T23:33:57.971125+00:00 shinyapps[5750996]:    7: connect$retryingStartServer
2022-11-21T23:33:57.971129+00:00 shinyapps[5750996]:    6: eval
2022-11-21T23:33:57.971139+00:00 shinyapps[5750996]:    5: eval
2022-11-21T23:33:57.971144+00:00 shinyapps[5750996]:    4: eval
2022-11-21T23:33:57.971157+00:00 shinyapps[5750996]:    3: eval
2022-11-21T23:33:57.971161+00:00 shinyapps[5750996]:    2: eval.parent
2022-11-21T23:33:57.971165+00:00 shinyapps[5750996]:    1: local

[adamjtaylor]

I was able to successfully submit the neuroblastoma table provided above in staging. @clarisse-lau - Can you try logging in and out of synapse before accessing DCA and see if you can resubmit the others successfully

[clarisse-lau]

Thanks Adam! I just tried logging in and out, but am still getting disconnected after a while at submission (for both breast and lung manifests)... any other tips?

[clarisse-lau]

Just tried the following with schematic CLI

schematic model --config config.yml submit --manifest_path htapp_bios_lung.csv --dataset_id syn25585684

and got the following: error: 'syn25585684' is not in the asset view (or file view for Synapse user)

[adamjtaylor]

Interesting. Let's check on the fileview scope here

[clarisse-lau]

Ah sorry- I had the wrong fileview specified in config! I'm now able to submit the lung and breast manifests.

Still having trouble with the app, but will close for now. Thanks @adamjtaylor

[adamjtaylor]

Great!