[QA-1585] Noticed errors in cos_container logs pertaining to nbconvert incompatibility issue

[xuscrbw]

Was troubleshooting QA-1585. The issue seems to be tied to kernel flakiness.

We noticed a few Asyncio errors, which let us to this known issue. jupyter/notebook#6164

We are updating the jupyter config to use AsyncMappingKernelManager to hopefully resolve this issue

While trying to merge the PR, noticed that we had an error related to cwltool:

ERROR: Cannot install cwltool because these package versions have conflicting dependencies.

The conflict is caused by:
schema-salad 4.5.20191229160203 depends on rdflib-jsonld<0.5.0 and >=0.3.0
schema-salad 4.5.20191204060541 depends on rdflib-jsonld<0.5.0 and >=0.3.0
schema-salad 4.5.20191203162929 depends on rdflib-jsonld<0.5.0 and >=0.3.0
schema-salad 4.5.20191023134839 depends on rdflib-jsonld<0.5.0 and >=0.3.0
schema-salad 4.5.20191017101802 ...

Have tried to fix this by unpinning the cwltool version in terra-jupyter-r

[Qi77Qi]

hi @ravi9, we're trying to fix an issue where the jupyter kernel fails to start up properly sometimes. The only thing changed in this PR is this, but for some reason, the gatk-ovtf image fails to build. Let us know if you have any insights. Since the latest ovtf image is currently broken as I understand it (gpu is broken), we might release the fix for all other images first, and will table the fix for ovtf for now.

[ravi9]

Hi @Qi77Qi , I will build it locally with this commit and debug the issue.

[ravi9]

Hi @Qi77Qi, looking at the error: /bin/bash: pytest: command not found , Is it something related to the test framework setup ?