Set up deploy/stage branch for ubuntu 22.04 upgrade #680
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The UserAccountTable on the StudySite detail page was showing inactive users. Hide the users in the queryset and add a test for this case.
…dy-site-table Hide inactive users in study site table
This way we can reference it using an environment variable when deploying.
Bumps [types-requests](https://github.com/python/typeshed) from 2.32.0.20240622 to 2.32.0.20240712. - [Commits](https://github.com/python/typeshed/commits) --- updated-dependencies: - dependency-name: types-requests dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]>
test_dbgap_project_id_does_not_match was failing only in mysql likely because in mysql tests, the pk field does not reset to 1 for each test. A (new) previous test likely created a dbGaP application, so when this test had the project_id hard-coded, it failed. Now, set the dbGaP application project_id using the application that the test created in the setup method.
Fix failing test for mysql
Bumps [github/combine-prs](https://github.com/github/combine-prs) from 5.0.0 to 5.1.0. - [Release notes](https://github.com/github/combine-prs/releases) - [Commits](github/combine-prs@v5.0.0...v5.1.0) --- updated-dependencies: - dependency-name: github/combine-prs dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]>
Bumps [pytest](https://github.com/pytest-dev/pytest) from 8.2.2 to 8.3.1. - [Release notes](https://github.com/pytest-dev/pytest/releases) - [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst) - [Commits](pytest-dev/pytest@8.2.2...8.3.1) --- updated-dependencies: - dependency-name: pytest dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]>
Bumps [django-debug-toolbar](https://github.com/jazzband/django-debug-toolbar) from 4.4.5 to 4.4.6. - [Release notes](https://github.com/jazzband/django-debug-toolbar/releases) - [Changelog](https://github.com/jazzband/django-debug-toolbar/blob/main/docs/changes.rst) - [Commits](django-commons/django-debug-toolbar@4.4.5...4.4.6) --- updated-dependencies: - dependency-name: django-debug-toolbar dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]>
Bumps [mypy](https://github.com/python/mypy) from 1.10.1 to 1.11.0. - [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md) - [Commits](python/mypy@v1.10.1...v1.11) --- updated-dependencies: - dependency-name: mypy dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]>
Bumps [ruff](https://github.com/astral-sh/ruff) from 0.5.1 to 0.5.4. - [Release notes](https://github.com/astral-sh/ruff/releases) - [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md) - [Commits](astral-sh/ruff@0.5.1...0.5.4) --- updated-dependencies: - dependency-name: ruff dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]>
Bumps [jsonschema](https://github.com/python-jsonschema/jsonschema) from 4.22.0 to 4.23.0. - [Release notes](https://github.com/python-jsonschema/jsonschema/releases) - [Changelog](https://github.com/python-jsonschema/jsonschema/blob/main/CHANGELOG.rst) - [Commits](python-jsonschema/jsonschema@v4.22.0...v4.23.0) --- updated-dependencies: - dependency-name: jsonschema dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]>
Bumps [django-crispy-forms](https://github.com/django-crispy-forms/django-crispy-forms) from 2.2 to 2.3. - [Release notes](https://github.com/django-crispy-forms/django-crispy-forms/releases) - [Changelog](https://github.com/django-crispy-forms/django-crispy-forms/blob/main/CHANGELOG.md) - [Commits](django-crispy-forms/django-crispy-forms@2.2...2.3) --- updated-dependencies: - dependency-name: django-crispy-forms dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]>
Bumps [sqlparse](https://github.com/andialbrecht/sqlparse) from 0.5.0 to 0.5.1. - [Changelog](https://github.com/andialbrecht/sqlparse/blob/master/CHANGELOG) - [Commits](andialbrecht/sqlparse@0.5.0...0.5.1) --- updated-dependencies: - dependency-name: sqlparse dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]>
Combined PRs
These were previously used to update packages for security requirements but are no longer necessary, because we can just update the requirements.txt file.
For some reason, the github action to open a pull request is returning a 403 error.
This is not needed in UW-GAC/gregor-django so something else must be going on.
Security updates
…e-scripts Add the crontab file to the activate script
Change python version to 3.10 and mariadb version to 10.6.
Otherwise, the python version is interested as 3.1 - not what we want.
…es/669 Update requirements file for maint/ubuntu-22.04
The badge next to the consortium members with data access is using the wrong table; use the correct table to calculate the count to show in the badge.
…h-access-badge Fix badge for consortium members with data access
They stand out a little more this way.
It will come back on the next page you load but that's ok.
…ive-users Better behavior for inactive users
We've found a bug associated with the inventory inputs view/helper. From inspecting prod data, it seems to occur when there are multiple workspaces associated with more than 1 study. I added a test that might fix this, but it isn't failing in sqlite. I'm not sure if this is an issue with the test or if it will only fail for mysql, so I'm commiting and pushing to check against CI. However I can't get it to fail on mysql
The last test didn't fail; still trying to figure out exactly what condition triggers it.
Test is still not failing
This time, I checked the object creation on the staging server and it does show the bug. This *should* fail in CI, finally (hopefully).
This isn't really testing the bug, per se, but it might catch the bug. We also want to make sure the querysets are ordered, since we need to rely on the ordering when using itertools.groupby.
The get_workspace_for_phenotype_inventory helper function had a bug when workspaces were not properly sorted before calling itertools.groupby. This was only apparent on the stage/prod servers, and not in mariadb. I couldn't reproduce the bug in CI (possibly because the charset was different between prod and stage?), and I'm not entirely sure why. However, this fix to the code makes an interactive check in stage work correctly.
Since we now have a genotype inventory, it better fits the use case.
…ple-studies Fix bug where only a single study is shown for a workspace linked to multiple studies
Ubuntu 22.04 upgrade
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