New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Add `poetry run` for fence-create with backwards compatibility #2708

Open

nss10 wants to merge 2 commits into master from chore/fence_create_add_poetry_run

+156 −62

Contributor

nss10 commented Jan 24, 2025

New Features

Increase support to amazon linux fence image with adding poetry run fence-create


          Add poetry run for fence-create with backwards compatibility

dab257a

nss10 commented

View reviewed changes

kube/services/jobs/client-modify-job.yaml Show resolved Hide resolved

github-actions bot commented Jan 24, 2025

filepath	$$\textcolor{#f14c4c}{\tt{error}}$$	$$\textcolor{#ffa500}{\tt{skipped}}$$	SUBTOTAL
$$\textcolor{#f14c4c}{\tt{tests/test\_centralized\_auth.py}}$$	$$\textcolor{#f14c4c}{\tt{16}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#f14c4c}{\tt{16}}$$
$$\textcolor{#f14c4c}{\tt{tests/test\_oauth2.py}}$$	$$\textcolor{#f14c4c}{\tt{15}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#f14c4c}{\tt{15}}$$
$$\textcolor{#f14c4c}{\tt{tests/test\_graph\_submit\_and\_query.py}}$$	$$\textcolor{#f14c4c}{\tt{14}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#f14c4c}{\tt{14}}$$
$$\textcolor{#f14c4c}{\tt{tests/test\_data\_upload.py}}$$	$$\textcolor{#f14c4c}{\tt{9}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#f14c4c}{\tt{9}}$$
$$\textcolor{#f14c4c}{\tt{tests/test\_guppy\_service.py}}$$	$$\textcolor{#f14c4c}{\tt{8}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#f14c4c}{\tt{8}}$$
$$\textcolor{#f14c4c}{\tt{tests/test\_presigned\_url.py}}$$	$$\textcolor{#f14c4c}{\tt{7}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#f14c4c}{\tt{7}}$$
$$\textcolor{#f14c4c}{\tt{tests/test\_audit\_service.py}}$$	$$\textcolor{#f14c4c}{\tt{5}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#f14c4c}{\tt{5}}$$
$$\textcolor{#f14c4c}{\tt{tests/test\_dbgap.py}}$$	$$\textcolor{#f14c4c}{\tt{4}}$$	$$\textcolor{#ffa500}{\tt{1}}$$	$$\textcolor{#f14c4c}{\tt{5}}$$
$$\textcolor{#f14c4c}{\tt{tests/test\_requestor.py}}$$	$$\textcolor{#f14c4c}{\tt{5}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#f14c4c}{\tt{5}}$$
$$\textcolor{#f14c4c}{\tt{tests/test\_user\_token.py}}$$	$$\textcolor{#f14c4c}{\tt{5}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#f14c4c}{\tt{5}}$$
$$\textcolor{#f14c4c}{\tt{tests/test\_drs\_endpoint.py}}$$	$$\textcolor{#f14c4c}{\tt{4}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#f14c4c}{\tt{4}}$$
$$\textcolor{#f14c4c}{\tt{tests/test\_ras\_authn.py}}$$	$$\textcolor{#f14c4c}{\tt{3}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#f14c4c}{\tt{3}}$$
$$\textcolor{#f14c4c}{\tt{tests/test\_study\_viewer.py}}$$	$$\textcolor{#f14c4c}{\tt{3}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#f14c4c}{\tt{3}}$$
$$\textcolor{#f14c4c}{\tt{tests/test\_discoverypage.py}}$$	$$\textcolor{#f14c4c}{\tt{1}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#f14c4c}{\tt{1}}$$
$$\textcolor{#f14c4c}{\tt{tests/test\_workspace.py}}$$	$$\textcolor{#f14c4c}{\tt{1}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#f14c4c}{\tt{1}}$$
$$\textcolor{#f14c4c}{\tt{tests/test\_login\_page.py}}$$	$$\textcolor{#f14c4c}{\tt{2}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#f14c4c}{\tt{2}}$$
$$\textcolor{#f14c4c}{\tt{tests/test\_indexing\_page.py}}$$	$$\textcolor{#f14c4c}{\tt{2}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#f14c4c}{\tt{2}}$$
$$\textcolor{#f14c4c}{\tt{tests/test\_oidc\_client.py}}$$	$$\textcolor{#f14c4c}{\tt{2}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#f14c4c}{\tt{2}}$$
$$\textcolor{#f14c4c}{\tt{tests/test\_aggregate\_mds.py}}$$	$$\textcolor{#f14c4c}{\tt{1}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#f14c4c}{\tt{1}}$$
$$\textcolor{#f14c4c}{\tt{tests/test\_homepage.py}}$$	$$\textcolor{#f14c4c}{\tt{1}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#f14c4c}{\tt{1}}$$
$$\textcolor{#f14c4c}{\tt{tests/test\_google\_data\_access.py}}$$	$$\textcolor{#f14c4c}{\tt{1}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#f14c4c}{\tt{1}}$$
$$\textcolor{#f14c4c}{\tt{tests/test\_pfb\_export.py}}$$	$$\textcolor{#f14c4c}{\tt{1}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#f14c4c}{\tt{1}}$$
$$\textcolor{#f14c4c}{\tt{tests/test\_client\_credentials.py}}$$	$$\textcolor{#f14c4c}{\tt{1}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#f14c4c}{\tt{1}}$$
$$\textcolor{#f14c4c}{\tt{tests/test\_etl.py}}$$	$$\textcolor{#f14c4c}{\tt{1}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#f14c4c}{\tt{1}}$$
$$\textcolor{#f14c4c}{\tt{tests/test\_gen3client.py}}$$	$$\textcolor{#f14c4c}{\tt{1}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#f14c4c}{\tt{1}}$$
$$\textcolor{#f14c4c}{\tt{tests/test\_manifest\_service.py}}$$	$$\textcolor{#f14c4c}{\tt{1}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#f14c4c}{\tt{1}}$$
$$\textcolor{#f14c4c}{\tt{tests/test\_metadata\_ingestion.py}}$$	$$\textcolor{#f14c4c}{\tt{1}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#f14c4c}{\tt{1}}$$
$$\textcolor{#ffa500}{\tt{tests/test\_gen3ff\_landing\_page.py}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#ffa500}{\tt{2}}$$	$$\textcolor{#ffa500}{\tt{2}}$$
$$\textcolor{#ffa500}{\tt{tests/test\_register\_user.py}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#ffa500}{\tt{2}}$$	$$\textcolor{#ffa500}{\tt{2}}$$
$$\textcolor{#f14c4c}{\tt{TOTAL}}$$	$$\textcolor{#f14c4c}{\tt{115}}$$	$$\textcolor{#ffa500}{\tt{5}}$$	$$\textcolor{#f14c4c}{\tt{120}}$$

Please find the detailed integration test report here

Please find the ci env pod logs here

github-actions bot commented Jan 24, 2025

filepath	$$\textcolor{#23d18b}{\tt{passed}}$$	$$\textcolor{#f14c4c}{\tt{failed}}$$	$$\textcolor{#ffa500}{\tt{skipped}}$$	SUBTOTAL
$$\textcolor{#23d18b}{\tt{tests/test\_oauth2.py}}$$	$$\textcolor{#23d18b}{\tt{15}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#23d18b}{\tt{15}}$$
$$\textcolor{#23d18b}{\tt{tests/test\_centralized\_auth.py}}$$	$$\textcolor{#23d18b}{\tt{16}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#23d18b}{\tt{16}}$$
$$\textcolor{#ffa500}{\tt{tests/test\_graph\_submit\_and\_query.py}}$$	$$\textcolor{#23d18b}{\tt{13}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#ffa500}{\tt{1}}$$	$$\textcolor{#ffa500}{\tt{14}}$$
$$\textcolor{#ffa500}{\tt{tests/test\_data\_upload.py}}$$	$$\textcolor{#23d18b}{\tt{8}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#ffa500}{\tt{1}}$$	$$\textcolor{#ffa500}{\tt{9}}$$
$$\textcolor{#23d18b}{\tt{tests/test\_guppy\_service.py}}$$	$$\textcolor{#23d18b}{\tt{8}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#23d18b}{\tt{8}}$$
$$\textcolor{#23d18b}{\tt{tests/test\_presigned\_url.py}}$$	$$\textcolor{#23d18b}{\tt{7}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#23d18b}{\tt{7}}$$
$$\textcolor{#ffa500}{\tt{tests/test\_dbgap.py}}$$	$$\textcolor{#23d18b}{\tt{4}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#ffa500}{\tt{1}}$$	$$\textcolor{#ffa500}{\tt{5}}$$
$$\textcolor{#f14c4c}{\tt{tests/test\_audit\_service.py}}$$	$$\textcolor{#23d18b}{\tt{4}}$$	$$\textcolor{#f14c4c}{\tt{1}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#f14c4c}{\tt{5}}$$
$$\textcolor{#23d18b}{\tt{tests/test\_requestor.py}}$$	$$\textcolor{#23d18b}{\tt{5}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#23d18b}{\tt{5}}$$
$$\textcolor{#23d18b}{\tt{tests/test\_user\_token.py}}$$	$$\textcolor{#23d18b}{\tt{5}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#23d18b}{\tt{5}}$$
$$\textcolor{#23d18b}{\tt{tests/test\_ras\_authn.py}}$$	$$\textcolor{#23d18b}{\tt{3}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#23d18b}{\tt{3}}$$
$$\textcolor{#23d18b}{\tt{tests/test\_study\_viewer.py}}$$	$$\textcolor{#23d18b}{\tt{3}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#23d18b}{\tt{3}}$$
$$\textcolor{#23d18b}{\tt{tests/test\_discoverypage.py}}$$	$$\textcolor{#23d18b}{\tt{1}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#23d18b}{\tt{1}}$$
$$\textcolor{#23d18b}{\tt{tests/test\_drs\_endpoint.py}}$$	$$\textcolor{#23d18b}{\tt{4}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#23d18b}{\tt{4}}$$
$$\textcolor{#23d18b}{\tt{tests/test\_workspace.py}}$$	$$\textcolor{#23d18b}{\tt{1}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#23d18b}{\tt{1}}$$
$$\textcolor{#23d18b}{\tt{tests/test\_oidc\_client.py}}$$	$$\textcolor{#23d18b}{\tt{2}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#23d18b}{\tt{2}}$$
$$\textcolor{#23d18b}{\tt{tests/test\_indexing\_page.py}}$$	$$\textcolor{#23d18b}{\tt{2}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#23d18b}{\tt{2}}$$
$$\textcolor{#23d18b}{\tt{tests/test\_login\_page.py}}$$	$$\textcolor{#23d18b}{\tt{2}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#23d18b}{\tt{2}}$$
$$\textcolor{#23d18b}{\tt{tests/test\_pfb\_export.py}}$$	$$\textcolor{#23d18b}{\tt{1}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#23d18b}{\tt{1}}$$
$$\textcolor{#23d18b}{\tt{tests/test\_client\_credentials.py}}$$	$$\textcolor{#23d18b}{\tt{1}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#23d18b}{\tt{1}}$$
$$\textcolor{#23d18b}{\tt{tests/test\_aggregate\_mds.py}}$$	$$\textcolor{#23d18b}{\tt{1}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#23d18b}{\tt{1}}$$
$$\textcolor{#23d18b}{\tt{tests/test\_google\_data\_access.py}}$$	$$\textcolor{#23d18b}{\tt{1}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#23d18b}{\tt{1}}$$
$$\textcolor{#23d18b}{\tt{tests/test\_homepage.py}}$$	$$\textcolor{#23d18b}{\tt{1}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#23d18b}{\tt{1}}$$
$$\textcolor{#23d18b}{\tt{tests/test\_metadata\_ingestion.py}}$$	$$\textcolor{#23d18b}{\tt{1}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#23d18b}{\tt{1}}$$
$$\textcolor{#23d18b}{\tt{tests/test\_etl.py}}$$	$$\textcolor{#23d18b}{\tt{1}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#23d18b}{\tt{1}}$$
$$\textcolor{#23d18b}{\tt{tests/test\_gen3client.py}}$$	$$\textcolor{#23d18b}{\tt{1}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#23d18b}{\tt{1}}$$
$$\textcolor{#23d18b}{\tt{tests/test\_manifest\_service.py}}$$	$$\textcolor{#23d18b}{\tt{1}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#23d18b}{\tt{1}}$$
$$\textcolor{#ffa500}{\tt{tests/test\_gen3ff\_landing\_page.py}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#ffa500}{\tt{2}}$$	$$\textcolor{#ffa500}{\tt{2}}$$
$$\textcolor{#ffa500}{\tt{tests/test\_register\_user.py}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#666666}{\tt{0}}$$	$$\textcolor{#ffa500}{\tt{2}}$$	$$\textcolor{#ffa500}{\tt{2}}$$
$$\textcolor{#f14c4c}{\tt{TOTAL}}$$	$$\textcolor{#23d18b}{\tt{112}}$$	$$\textcolor{#f14c4c}{\tt{1}}$$	$$\textcolor{#ffa500}{\tt{7}}$$	$$\textcolor{#f14c4c}{\tt{120}}$$

Please find the detailed integration test report here

Please find the ci env pod logs here

nss10 added the TestAuditService label

github-actions bot commented Jan 24, 2025

filepath	$$\textcolor{#23d18b}{\tt{passed}}$$	SUBTOTAL
$$\textcolor{#23d18b}{\tt{tests/test\_audit\_service.py}}$$	$$\textcolor{#23d18b}{\tt{5}}$$	$$\textcolor{#23d18b}{\tt{5}}$$
$$\textcolor{#23d18b}{\tt{TOTAL}}$$	$$\textcolor{#23d18b}{\tt{5}}$$	$$\textcolor{#23d18b}{\tt{5}}$$

Please find the detailed integration test report here

Please find the ci env pod logs here

AlbertSnows reviewed

View reviewed changes

gen3/bin/kube-setup-ohdsi.sh Show resolved Hide resolved

AlbertSnows commented Jan 24, 2025

Github is recommending changing line 129 of the Dockerfile to something like this:
CMD ["/bin/bash"]

AlbertSnows approved these changes

View reviewed changes

AlbertSnows left a comment

looks like most of the changes are adding poetry run which should be fine, but I would suggest getting another review before merging.


          Merge branch 'master' into chore/fence_create_add_poetry_run

063528d

github-actions bot commented Jan 24, 2025

filepath	$$\textcolor{#23d18b}{\tt{passed}}$$	SUBTOTAL
$$\textcolor{#23d18b}{\tt{tests/test\_audit\_service.py}}$$	$$\textcolor{#23d18b}{\tt{5}}$$	$$\textcolor{#23d18b}{\tt{5}}$$
$$\textcolor{#23d18b}{\tt{TOTAL}}$$	$$\textcolor{#23d18b}{\tt{5}}$$	$$\textcolor{#23d18b}{\tt{5}}$$

Please find the detailed integration test report here

Please find the ci env pod logs here

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

TestAuditService