Submit-cgap

Latest version: v4.1.2

Safety actively analyzes 627119 Python packages for vulnerabilities to keep your Python projects secure.

Scan your dependencies

Page 1 of 6

4.1.2

=====

* Fix ``pip install`` command in installation docs

4.1.1

=====

* Various documentation changes, mostly ported back from the ``submitr`` fork:
* Change Submit-CGAP throughout to SubmitCGAP for internal branding consistency.
* Small wording changes for clarity, especially in Overview.
* Fix some ``.rtf`` syntax errors (especially uses of single-backquote where double-backquote required).
* Clearer section names.
* "Installing Prerequisites" (instead of "Basic Setup") for clarity about what content to expect.
* "Using SubmitCGAP" (instead of "Getting Started") again for clarity.
* "Implementation of submit_cgap package" instead of "submit_cgap package" so that the user is less likely
to feel they need to understand this section to use the tool.
* Put information about ``rclone`` at the end, and make it clear that it's an alternative to using this tool
rather than the main documentation of how to use this tool.
* Put subpackage information at the end of package list, not at the beginning.
* Don't show package content ``submit_cgap.tests`` or ``submit_cgap.scripts`` (which would show info from
``__init__.py``, which we don't do). This avoids some useless/confusing section headings.

* Add some additional ``Makefile`` recipes, most importantly ``make preview-locally`` to preview what Sphinx
will do on ReadTheDocs.

* Backport some improvements to GithubActions (GA) workflows that were debugged for ``submitr``.
* Use ``make build`` rather than explicit ``poetry`` initialization (to avoid extra dependency on version).
* Use ``ref=`` instead of ``branches=`` when submitting a doc build job.
* Trigger auto-build of doc on any non-beta checkin.
(For betas, use the new ``make preview-locally`` since
the recipe for building will just build from master and
doesn't parameterize the branch.)

4.1.0

=====

* Support for a check-submission command.
* Very basic support for SMaHT.
* Commands can now take ``--app smaht`` (which will use ``~/.smaht-keys.json``)
* submit-ontology takes ``--consortium`` and ``submission_center`` arguments.
* Some other functionality may still be missing. Send email if you're missing something you need.

4.0.0

=====

* Add command submit-ontology with new SubmissionProtocol.S3 support that allows upload first via S3
when initiating a connection. This is not an incompatible change, but it is a very major feature addition,
so I'm going to bump the major version.

* In ``base.py``:

* New class ``GenericKeyManager`` to manage possibility of either Fourfront or CGAP keys files
(``~/.fourfront-keys.json`` vs ``~/.cgap-keys.json``)

* Appropriate unit test coverage.

* Use poetry 1.3.2 for building. Update other dependencies.

* -------

* Verify ontology file first before processing in submit-ontology.

* Added --verbose and --debug options to submit-xyz and show-upload-info.

* Fixed show-upload-info to work with new --app option etc.

* Updated show-upload-info to show more info on the given ingestion uuid.

3.1.0

=====

`PR 34: Increase submission timeout <https://github.com/dbmi-bgm/SubmitCGAP/pull/34>`_

* Increase submission timeout from 2 to 10 minutes

3.0.0

=====

* Updates to use creds_utils (C4-779):

* Removed ``auth.py``, and in ``base.py`` removes:

* class ``KeyManager`` class

* decorator``UsingCGAPKeysFile``

* Changed other existing functionality to use new ``dcicutils.creds_utils`` in place of
removed functionality. (See
`SubmitCGAP PR 24 <https://github.com/dbmi-bgm/SubmitCGAP/pull/24>`_
for additional detail.)

* Added a ``make`` target named ``clear-poetry-cache``
to help with certain ``poetry`` solver problems that result from improper caching.

* Upgrades to dcicutils 6.0 (C4-896):

* Avoid use of ``full_cgap_env_name``. Just don't adjust the name.

* Avoid use of ``get_real_env_url`` by changing ``submission.resolve_server``
to not use heuristics based on it.

**NOTE:** These changes are slightly incompatible, but not materially so.
There aren't programmatic dependencies on this library, unless maybe scripts.
It will be necessary after this change to use environment names and hostnames
that are properly declard in ``~/.cgap-keys.json``.

Page 1 of 6

© 2024 Safety CLI Cybersecurity Inc. All Rights Reserved.