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31787 Commits
Author SHA1 Message Date
davelopez 2688e1818a Ignore mypy error 
Mypy cannot easily infer the proper type from partial without additional plugins
 2022-08-15 13:27:38 +02:00
Marius van den Beek d64adb4c72 Merge pull request #14439 from qiagu/param_filter 
Improve dynamic option filter efficiency
 2022-08-15 12:49:20 +02:00
galaxybot a549bf1318 Update Python dependencies 2022-08-13 03:37:53 +00:00
Nicola Soranzo 575a1d8358 Merge pull request #14430 from bernt-matthias/unlink-job-template 
Deprecate `cluster_files_directory` and store DRMAA job template and PBS shell, error and out files in job working directory
 2022-08-13 01:00:10 +01:00
Dannon Baker 3112181f3e Merge remote-tracking branch 'upstream/release_22.05' into dev 2022-08-12 13:18:53 -04:00
qiagu 878b2d86f8 Improve efficiency of unique options filter 2022-08-12 09:50:04 -07:00
Marius van den Beek df3d5a1992 Merge pull request #14429 from mvdbeek/singularity_no_host_env_vars 
[22.05] Pass ``--cleanenv`` by default to singularity command
 2022-08-12 15:58:05 +02:00
Dannon 9c0fcad2cb Merge pull request #14417 from mvdbeek/crc32_for_specific_file_sizes 
[22.05] Calculate CRC32 for files in size between 1444 and 1459 bytes
 2022-08-12 09:52:34 -04:00
Marius van den Beek a9027459c3 Merge pull request #14426 from davelopez/22.05_make_contains_filter_case_insensitive 
[22.05] Make history contents filter with `contains` case insensitive
 2022-08-12 13:42:13 +02:00
M BerntandNicola Soranzo f8383c036b Update lib/galaxy/jobs/runners/drmaa.py 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-08-12 11:58:06 +02:00
Marius van den Beek bb19e41ebc Merge pull request #14277 from astrovsky01/agp_sniff 
[22.05] Make Agp set_meta more lenient
 2022-08-12 11:31:14 +02:00
Marius van den Beek 9dd74fc953 Merge pull request #14431 from mvdbeek/cached_image_path_identifier_fix 
[22.05] Fix cache image singularity resolver if path contains uppercase chars
 2022-08-12 11:21:49 +02:00
mvdbeek 034ea59200 Use func.lower and autoescape for contains filters 2022-08-11 19:38:27 +02:00
Nicola Soranzo 9874507e20 Merge branch 'release_22.05' into dev 2022-08-11 16:52:52 +01:00
Marius van den BeekandNicola Soranzo b4a8c061c2 Use os.sep.join 
Much nicer!

Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-08-11 17:21:34 +02:00
Marius van den Beek 403dcdd7ea Merge pull request #13453 from bernt-matthias/topic/slurm-self-cancel 
[22.05] SLURM: check first if stopped for cancelled jobs
 2022-08-11 16:55:26 +02:00
Marius van den Beek f53edd1f18 Merge pull request #14314 from bernt-matthias/topic/cond_out_action_bool 
Extend docs and tests for conditional output actions
 2022-08-11 16:53:41 +02:00
mvdbeek 0560e43a48 Fix cache image singularity resolver if path contains uppercase chars 
Fixes https://github.com/galaxyproject/galaxy/issues/14425
 2022-08-11 13:32:21 +02:00
mvdbeek 27efc1d572 Change test file to test relaxed valid_lines function 2022-08-11 12:22:46 +02:00
Alexander OSTROVSKY d0c1751f00 Log warning if agp file has `na` linkage evidence 
Salsa2 and YAHS may produce such files.
 2022-08-11 12:09:43 +02:00
Marius van den Beek f06f0ade38 Merge pull request #14392 from davelopez/refactor_history_contents_id_decoding 
Refactor history contents API ID encoding
 2022-08-11 11:59:39 +02:00
Matthias Bernt e225244818 deprecate cluster_files_directory config option 2022-08-10 20:21:01 +02:00
Matthias Bernt e29579bf9d pbs runner: use job working dir 
instead of cluster_files_directory for error, out, and sh
 2022-08-10 20:20:05 +02:00
Dannon Baker 58d43a0070 Merge remote-tracking branch 'upstream/release_22.05' into dev 2022-08-10 13:17:40 -04:00
David López a37658a348 Merge pull request #14419 from ElectronicBlueberry/logged-out-users 
Present unavailable options to logged-out users
 2022-08-10 17:54:39 +02:00
Matthias Bernt 9e6f9c8820 store drmaa job template files in job working dir 2022-08-10 17:43:55 +02:00
mvdbeek 728ceebc8a Fix nested archive unzipping on windows 
We need the directory markers in order for the default windows zip
utility to be able to extract the archives. Also requires
https://github.com/evanmiller/mod_zip/commit/51cf45d3e9f51e02224af017b235d1d30fbf28fb
or newer on the mod_zip side.
 2022-08-10 17:33:29 +02:00
mvdbeek f83aefd82a Calculate CRC32 for files in size between 1444 and 1459 bytes 2022-08-10 17:33:25 +02:00
Matthias Bernt 0a9c75658b open job template file in mode w 
w+ seems not necessary
 2022-08-10 17:20:53 +02:00
Matthias Bernt d163bdef0d unlink drmaa job template files 
for successful jobs
 2022-08-10 17:20:09 +02:00
Marius van den BeekandNicola Soranzo b3c8e38f8b Fix typo in sample variable 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-08-10 17:09:25 +02:00
mvdbeek 0eff482466 Pass --cleanenv by default to singularity command 2022-08-10 16:52:59 +02:00
mvdbeek fc86a42880 Update pylibmagic and gravity 2022-08-10 16:12:17 +02:00
davelopez a22d62ea38 Ignore case when filtering using contains 
The `contains` function is case sensitive so we must apply first `func.lower` to the column and the value. I tried this first but it doesn't work... so replacing contains with `ilike` made the trick, but I don't like it at all...
 2022-08-10 15:26:37 +02:00
davelopez cf32b547d1 Add API test for history contents filtering 
Filtering history contents by name should be case insensitive
 2022-08-10 15:14:53 +02:00
Laila Los 37a8de7f33 update selenium test_anon_history 
add assert_disabled to SmartComponent
 2022-08-10 10:56:32 +02:00
Nicola Soranzo 08a7a11dd5 Merge branch 'release_22.05' into dev 2022-08-10 08:55:08 +01:00
Marius van den Beek 6090fb1fcd Merge pull request #14406 from davelopez/support_quoted_strings_in_bool_expression 
[22.05] Support quoted strings in bool expressions
 2022-08-09 18:42:30 +02:00
mvdbeek c4d5ac1afb Merge branch 'release_22.05' into dev 2022-08-09 16:44:16 +02:00
mvdbeek a351bd1ce9 Merge branch 'release_22.05' into dev 2022-08-09 15:12:15 +02:00
davelopez 48ea02faa3 Rename EncodedEntityIdField to EntityIdField 2022-08-09 12:22:34 +02:00
davelopez 7fa9fc7f81 Encode IDs automatically when serializing models 2022-08-09 12:22:34 +02:00
davelopez 08bbe241e6 Refactor history contents API ID encoding 
Replace `EncodedDatabaseIdField` with `DecodedDatabaseIdField` to remove manual ID decodings from the service layer.
 2022-08-09 12:22:34 +02:00
davelopez ef9da3426c Handle history index params validation properly 
Instead of trying to raise an error for each possible case, just wrap the ValidationError with our custom exceptions.

This will finally return a 400 instead of 500 error code when any query parameter is invalid.
 2022-08-09 12:01:48 +02:00
davelopez b46b1ae282 Add more API tests for errors in dataset details 2022-08-09 11:58:14 +02:00
galaxybot d0a596185d Update Python dependencies 2022-08-06 03:34:48 +00:00
davelopez bcff4a1995 Update integration test 
Test boolean expression with group names containing spaces and surrounded by single quotes
 2022-08-05 15:56:21 +02:00
davelopez aff0c5da9b Add quoted string support to boolean expressions 2022-08-05 15:53:16 +02:00
davelopez 083978d042 Raise exception when details contains empty IDs 
Otherwise the pydantic validation will raise an unhandled exception with a rather cryptic error message
 2022-08-04 13:59:52 +02:00
davelopez e2cec35654 Add API test for history content details 
With empty ids it should return a 400 Bad Request a not just a 500 error
 2022-08-04 13:58:11 +02:00