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Author SHA1 Message Date
Sergey YakubovandJohn Davis d930fc638d update comment about file check for cloud object store 
Co-authored-by: John Davis <jdavcs@gmail.com>
 2023-11-16 10:25:49 -05:00
Yakubov, Sergey 9858c5971b irods - download file even if already in cache 2023-11-16 10:11:50 -05:00
Yakubov, Sergey f9182d9bd3 fix xml parsing for irods 2023-11-14 13:48:45 -05:00
Yakubov, Sergey 898c5c942d optimize object store pull 
added sync_cache parameter to the get_filename function that allows
skip pulling to cache when not needed
 2023-11-14 11:57:40 -05:00
mvdbeek c85298b48e Merge branch 'release_23.1' into dev 2023-11-13 15:07:27 +01:00
mvdbeek d0c583ec0e Merge branch 'release_23.0' into release_23.1 2023-11-13 15:06:55 +01:00
Marius van den Beek 1b0c0bb353 Merge pull request #17013 from bernt-matthias/bump/conda 
[23.0] Upgrade minimum conda to be compatible with latest conda-build
 2023-11-13 15:04:29 +01:00
Matthias Bernt 0aafa22154 bump required conda version 
potential solution for the build prblems in https://github.com/galaxyproject/planemo/pull/1388
 2023-11-13 13:19:10 +01:00
mvdbeek 8468162302 Merge branch 'release_23.1' into dev 2023-11-13 11:37:20 +01:00
Martin Cech 2319bc31af Merge pull request #16991 from dannon/tool_panels-doc 
Update API tool_panels route conditions
 2023-11-11 17:49:55 +01:00
Nicola Soranzo 0cb54186b9 Merge pull request #17011 from galaxybot/dev_auto_update_dependencies 
Update Python dependencies
 2023-11-11 15:33:27 +00:00
galaxybot 8f67b00750 Update Python dependencies 2023-11-11 03:16:14 +00:00
Martin Cech 70d41851f4 Merge pull request #17009 from mvdbeek/update_tar_to_directory_dependency 
[23.1] Update tar_to_directory dependency
 2023-11-11 00:53:23 +01:00
Björn Grüning 643b0d4147 Merge pull request #17007 from mvdbeek/fix_copied_outputs_metadata 
[23.1] Fix copying metadata to copied job outputs
 2023-11-10 20:56:26 +01:00
mvdbeek 93d11dc04a Update tar_to_directory dependency 
Should fix:
```
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/usr/local/lib/python3.7/site-packages/galaxy/util/compression_utils.py", line 114, in extract
    common_prefix_dir = self.common_prefix_dir
  File "/usr/local/lib/python3.7/site-packages/galaxy/util/compression_utils.py", line 103, in common_prefix_dir
    if len(common_prefix) >= 1 and not common_prefix.endswith(os.sep) and self.isdir(self.getmember(common_prefix)) \
  File "/usr/local/lib/python3.7/site-packages/galaxy/util/compression_utils.py", line 186, in isdir
    return getattr(self, 'isdir_%s' % self.type)(member)
  File "/usr/local/lib/python3.7/site-packages/galaxy/util/compression_utils.py", line 189, in isdir_tar
    return member.isdir()
AttributeError: 'NoneType' object has no attribute 'isdir'

```

seen on usegalaxy.eu with https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE176031&format=file
 2023-11-10 18:37:34 +01:00
mvdbeek 2fc1b64742 Fix copying metadata to copied job outputs 
Fixes https://github.com/galaxyproject/galaxy/issues/17003
 2023-11-10 18:03:45 +01:00
Marius van den Beek 1956639a8e Merge pull request #16852 from jdavcs/dev_sa20_fix20 
SQLAlchemy 2.0 upgrades (part 4)
 2023-11-10 11:35:30 +01:00
John Davis 2fa96dfb11 Fix SA2.0 usage in managers.history_contents 2023-11-09 15:33:46 -05:00
John Davis c6622de620 Fix SA2.0 usage in managers.sharable (2) 2023-11-09 15:33:46 -05:00
John Davis 5731bf5739 Fix SA2.0 usage in managers.sharable 2023-11-09 15:33:46 -05:00
John Davis ffd226687b Fix SA2.0 usage in webapps.base.controller (3) 
Reuse slug_exists function
 2023-11-09 15:33:46 -05:00
John Davis 67e4c3fe9f Fix SA2.0 usage in webapps.base.controller (2) 
Add forms manager module for FormDefinition/FormDefintionCurrent data access functions.
 2023-11-09 15:33:46 -05:00
John Davis c5df598af0 Fix SA2.0 usage in webapps.base.controller (1), simplify exists 2023-11-09 15:33:46 -05:00
John Davis 5f319d6b49 Drop unused method 2023-11-09 15:33:46 -05:00
John Davis 0352ed8e55 Fix SA2.0 usage in managers.ratable 2023-11-09 15:33:46 -05:00
John Davis c419e42197 Fix SA2.0 usage in managers.hdas; simplify exists query 
We don't need eagerloads(False): it's an `exists` statement; there
were no joins in the first place.
 2023-11-09 15:33:46 -05:00
John Davis 93d4f6b30d Fix SA2.0 usage in managers.notification 2023-11-09 15:33:46 -05:00
John Davis 54b87a4852 Fix SA2.0 usage in managers.context 2023-11-09 15:33:46 -05:00
John Davis f47586ab5a Fix SA2.0 in managers.session 2023-11-09 15:33:46 -05:00
John Davis dc32fee36c Fix SA2.0 usage in managers.tags 2023-11-09 15:33:46 -05:00
John Davis 20d2d4a51d Fix SA2.0 usage in managers.history 2023-11-09 15:33:46 -05:00
John Davis 884e1ed38a Fix SA2.0 usage in managers.tools; refactor 
Refactor: use native SA one_or_none method instead of calling
self._one_or_none >> self._one_with_recast_errors.
Reason: old code duplicated SA's error catching logic while not
providing a useful error message. Using SA's native method achieves the
same result with a more useful error message and without adding custom code.
The _one_or_none method is dropped as it is not used anywhere else.
 2023-11-09 15:33:46 -05:00
John Davis 792ac5015a Fix union operation (see note) 
Can't call union() more than once because on second call we have a
CompoundSelect. Reversing stmt with all-stmts will result in improper
nesting. Proposed fix solves this: we collect Select statements into a
list, then union the first item with the rest. The list is guaranteed to
have at least one item.
 2023-11-09 15:33:46 -05:00
John Davis fbcabb2aff Fix SA2.0 usage in managers.users 2023-11-09 15:33:46 -05:00
John Davis 7c5f60095d Fix SA2.0 usage in managers.library_datasets 2023-11-09 15:33:46 -05:00
John Davis c4ecdf57cf Fix SA2.0 usage in managers.datasets 2023-11-09 15:33:46 -05:00
John Davis b1ee6b98d1 Fix SA2.0 in managers.workflows (5) 2023-11-09 15:33:46 -05:00
John Davis 9ce277919d Fix SA2.0 usage in managers.workflows (4) 2023-11-09 15:33:46 -05:00
John Davis c907cfca72 Fix SA2.0 usage in managers.workflows (3) 2023-11-09 15:33:46 -05:00
John Davis b799811b3a Fix SA2.0 usage in managers.workflows, refactor (2) 2023-11-09 15:33:46 -05:00
John Davis b94cbff4a0 Fix SA2.0 usage in managers.workflows, refactor (1) 2023-11-09 15:33:46 -05:00
John Davis ec36ea7e57 Fix SA2.0 usage in managers.interactivetool, refactor 2023-11-09 15:33:46 -05:00
John Davis fc69968a9d Fix SA2.0 usage in managers.pages (2) 2023-11-09 15:33:46 -05:00
John Davis 564eab73e9 Fix SA2.0 usage in managers.pages (1) 2023-11-09 15:33:46 -05:00
John Davis cc56de6442 Fix SA2.0 usage in managers.jobs (1) 2023-11-09 15:33:46 -05:00
John Davis eadc457949 Fix SA2.0 usage in managers.collections 2023-11-09 15:33:46 -05:00
John Davis fa46d0ab90 Fix SA2.0 usage in managers.libraries (2); refactor 
Factor out SA statement building logic into 2 separate helpers (I think
the filtering criteria for admin and nonadmin users is sufficiently
different, so 2 methods make for cleaner code here).
 2023-11-09 15:33:46 -05:00
John Davis 5b906eedec Fix SA2.0 usage in managers.libraries (1) 2023-11-09 15:33:46 -05:00
John Davis 311fe028da Fix SA2.0 usage in managers.folders 2023-11-09 15:33:46 -05:00
Dannon a1b548556d Merge pull request #17000 from mvdbeek/dev 
Merge 23.1 into dev
 2023-11-09 11:04:11 -05:00