Deploy to prod #635
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Deploy to prod #635
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Add a mixin that checks if the user has Staff View permission or is the PI of the application in question. Update the context and template to show links based on permission level.
As part of this update, rework the new view mixin to require views to implement a "get_dbgap_application" method. This method already existed for dbaPDataAccessSnapshotDetail; I had to add it for the dbGaPApplicationDetail view. Note that database queries are not optimized here, so many of the views are making multiple queries for the same object.
Since the viewmixin sets self.dbgap_application, we can use that attribute in the view without having to make additional database queries.
Rework the url and view such that both the dbgap_application and the DAR id are required. This should be unnecessary (e.g., a DAR id is only associated with a single dbGaP application at dbGaP), but it's a little safer and it's easier to check if the user has permission to see the page.
This field allows the CC to set the collaborators for a dbGaP Application, even if the users have not linked their AnVIL accounts.
This is in preparation for adding a table of collaborators.
This table will be used on the dbGaP application page to show the list of collaborators, their AnVIL accounts, and whether or not the user is a member of the access group.
This table shows the list of named collaborators, their AnVIL account (if linked), and whether the account is a member of the access group.
Bumps [responses](https://github.com/getsentry/responses) from 0.25.0 to 0.25.2. - [Release notes](https://github.com/getsentry/responses/releases) - [Changelog](https://github.com/getsentry/responses/blob/master/CHANGES) - [Commits](getsentry/responses@0.25.0...0.25.2) --- updated-dependencies: - dependency-name: responses dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]>
Bumps [pytest](https://github.com/pytest-dev/pytest) from 8.2.1 to 8.2.2. - [Release notes](https://github.com/pytest-dev/pytest/releases) - [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst) - [Commits](pytest-dev/pytest@8.2.1...8.2.2) --- updated-dependencies: - dependency-name: pytest dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]>
Bumps [ruff](https://github.com/astral-sh/ruff) from 0.4.7 to 0.4.8. - [Release notes](https://github.com/astral-sh/ruff/releases) - [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md) - [Commits](astral-sh/ruff@v0.4.7...v0.4.8) --- updated-dependencies: - dependency-name: ruff dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]>
Combined PRs
Bumps [tornado](https://github.com/tornadoweb/tornado) from 6.4 to 6.4.1. - [Changelog](https://github.com/tornadoweb/tornado/blob/master/docs/releases.rst) - [Commits](tornadoweb/tornado@v6.4.0...v6.4.1) --- updated-dependencies: - dependency-name: tornado dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]>
Dependabot security updates appear to run from the directory in which the requirements files are stored, not the root directory of the repository (like regular dependabot updates). See issue: dependabot/dependabot-core#9490
See previous commit for info.
…do-6.4.1 Bump tornado from 6.4 to 6.4.1 in /requirements
We're going to add an audit for dbGaP application collaborators, so rework the current audits to include "access" in the namespace and urls.
Also rename some of the audit classes and views to include "Access" in the name. This will help when we add a collaborator audit, and matches how the audit is done for CDSAs.
Add skeleton classes for the collaborator audits, mostly copy-pasted from the access audits. Add views that currently do nothing, some urls for those views, and test classes with one failing test. These will be fleshed out in future commits.
Write the class definitions for dbGaPCollaboratorAudit and related classes (audit results, tables). Also add some tests; other tests can be added once the views are closer to working.
…es/622 Update requirements file for maint/security-updates
Security updates
Deploy to stage
Add a button on the dbGaPApplicationDetail view to update the collaborators for that application.
Instead of just creating a Study or StudySite, first check if it exists and get the object if it does. This means that the dbgap example script can be run, and then the CDSA example script can be run afterward, or vice versa.
Add StudyListFilter to StudyList view Add filter form to study_list template Add tests for StudyList view
Show CDSAs where the user is the representative on the user detail page. Previously it was just showing accessors and uploaders.
Change the spacing in the details box such that the definition list has a better appearance. Add alert boxes to the accessors, uploaders, and collaborators tables indicating that the a can contact the CDSA if changes need to be made.
It failed with what looks like some sort of server error somewhere.
Harmonize dbgap and cdsa updates
Bumps [ruff](https://github.com/astral-sh/ruff) from 0.4.10 to 0.5.0. - [Release notes](https://github.com/astral-sh/ruff/releases) - [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md) - [Commits](astral-sh/ruff@v0.4.10...0.5.0) --- updated-dependencies: - dependency-name: ruff dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]>
Bumps [mypy](https://github.com/python/mypy) from 1.10.0 to 1.10.1. - [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md) - [Commits](python/mypy@v1.10.0...v1.10.1) --- updated-dependencies: - dependency-name: mypy dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]>
the 3.10 was converted to 3.1 without them.
Update CI to run ubuntu 22.04 defaults
Combined PRs
Add search to Study List
Deploy to stage
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