mvdbeek
d2597738cb
Make to_cwl compatible with pulsar
2025-05-12 10:54:56 +02:00
mvdbeek
e6b0783194
Enable (Javascript) requirements on frontend/backend
2025-05-12 10:54:42 +02:00
mvdbeek
152bc2ffa5
Add runtime model to API
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Like job_internal but replaces dataset and dataset collection with file
and array / object of files.
2025-05-12 10:54:30 +02:00
mvdbeek
90b21f7212
YamlToolSource parser fixes
2025-05-12 10:54:24 +02:00
mvdbeek
a6d6477122
Bypass global toolbox for unprivileged tools
2025-05-12 10:54:23 +02:00
mvdbeek
eb38fd8ec9
Merge branch 'release_24.2' into dev
2025-05-12 09:05:28 +02:00
John Chilton
219796f049
Implement paired_or_unpaired collections, list wizards.
2025-05-09 17:39:38 -04:00
John Chilton
9c7770d3aa
More dataset collection unit testing...
2025-05-09 16:38:20 -04:00
John Chilton
0b3b408b50
Migrate doctests to unit tests.
2025-05-09 16:38:19 -04:00
John Chilton
518fa136d9
[WIP] Implement records - heterogenous dataset collections.
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Existing dataset colleciton types are meant to be homogenous - all datasets of the same time. This introduces CWL-style record dataset collections.
2025-05-09 16:38:19 -04:00
John Chilton
8e3e86a706
Option for add_column_regex to be unmatched, improved testing.
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Can easily be combined concatenate and such to get conditionals on rewriting values. Used for new tests in new collection types branch that mirror I think useful, real-world examples. Also extends the test framework a bit to allow testing errors during evaluation and not just errors that can be caught statically by inspecting the rule itself.
2025-05-09 16:38:18 -04:00
Marius van den Beek
9fb00287e4
Merge pull request #20054 from davelopez/explore_rocrate_import
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Add ZIP explorer to import individual files from local or remote ZIP archives
2025-05-09 12:07:14 +02:00
Marius van den Beek
de1e356e35
Merge pull request #18628 from rhpvorderman/singularity_settings
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Isolate singularity containers more thoroughly for better reproducibility.
2025-05-09 11:39:50 +02:00
Ruben Vorderman
9eb9274cb5
fix tests for singularity
2025-05-09 09:27:53 +02:00
davelopez
e73723b3e2
Add test to ensure local file access is restricted
2025-05-08 23:57:55 +02:00
davelopez
f080d5d73e
Add basic test for remote zip extractor file source
2025-05-08 23:51:48 +02:00
pauldg
d1ac29c049
a basic template and an ssl template
2025-05-08 23:40:03 +02:00
pauldg
2b5d35ffc5
added unit test
2025-05-08 23:40:01 +02:00
John Davis
421d43eabb
Merge pull request #16696 from natefoo/clean-working
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Run the tool working dir backup/restore on Pulsar
2025-05-08 16:38:19 -04:00
Marius van den Beek
0ac67b5247
Merge pull request #19720 from SergeyYakubov/rucio-templates
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Rucio templates
2025-05-08 17:38:53 +02:00
davelopez
e699452006
Add missing download scheme configuration to Rucio object store template for tests
2025-05-08 12:49:01 +02:00
Yakubov, Sergey
5282940a32
fix liniting
2025-05-07 16:10:47 +02:00
Yakubov, Sergey
50a1d5b6a2
add examples, refactor templates
2025-05-07 16:10:47 +02:00
Eli Chadwick
70cd4511b0
avoid caching in python 3.9
2025-05-07 10:45:12 +01:00
Eli Chadwick
f9688c43a7
isort
2025-05-07 10:45:11 +01:00
Eli Chadwick
09458577b2
linting
2025-05-07 10:45:10 +01:00
Eli Chadwick
007541d1e3
add version check to xfail
2025-05-07 10:45:10 +01:00
Eli Chadwick
a4fbf706b4
fix version check
2025-05-07 10:45:09 +01:00
Eli Chadwick
bd4da7a339
fix problem with non-existent files failing validation
2025-05-07 10:45:08 +01:00
Eli Chadwick
d1906cbf54
work around dependency issues
2025-05-07 10:45:08 +01:00
Eli Chadwick
419930627b
work around dependency issues
2025-05-07 10:45:08 +01:00
Eli Chadwick
5cf1dde60c
checked tests
2025-05-07 10:45:07 +01:00
Eli Chadwick
ed36c907b7
add tests using roc_validator
2025-05-07 10:45:06 +01:00
Ahmed Hamid Awan
d7fa1d19ce
Merge pull request #19054 from jmchilton/tool_markdown
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Implement tool markdown reports.
2025-05-06 20:49:30 +05:00
Marius van den Beek
79638b883a
Merge pull request #19753 from bernt-matthias/env-fix-24.1
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Fix setting env and tags on resubmission
2025-05-06 17:23:45 +02:00
mvdbeek
b99112c337
Fix DataCollectionParameterModel factory
2025-05-06 14:23:23 +02:00
Marius van den Beek
6d99fb3706
Merge pull request #20109 from nsoranzo/dont_prune_docker
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Remove only the Docker images specific for the test
2025-05-06 09:34:11 +02:00
Marius van den Beek
2266a09e68
Merge pull request #20158 from mvdbeek/yaml_parser_fixes
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Yaml parser fixes and improvements (part 1)
2025-05-06 09:25:58 +02:00
Marius van den Beek
507719beb5
Merge pull request #20162 from mvdbeek/yaml_parser_fixes_part2
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Yaml parser fixes part2
2025-05-06 09:13:11 +02:00
John Chilton
4e4017c1be
Merge pull request #20152 from jmchilton/collection_cleanup_2
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Fix certain cases of collection parameter handling during workflow execution.
2025-05-05 15:45:36 -04:00
mvdbeek
7ed247059a
Fix conditional parsing
2025-05-05 20:37:17 +02:00
Marius van den Beek
48423962ca
Merge pull request #20004 from mvdbeek/dataset_collection_support_in_landing_request
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Implement dataset collection support in workflow landing requests
2025-05-05 19:24:53 +02:00
mvdbeek
bd05b3d0e1
Settle on type instead of reftyp inside xref
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We could also make it an alias, but it seems muich simpler to not refer
to the same attribute with different names. So far this has used
internally only.
2025-05-05 19:07:27 +02:00
Marius van den Beek
37a26a6926
Merge pull request #20150 from mvdbeek/add_workflow_dict_run_typing
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Additional type hints for ``toolbox.get_tool`` / ``toolbox.has_tool``
2025-05-05 16:58:02 +02:00
mvdbeek
fa3c19c2a4
Merge branch 'release_24.2' into dev
2025-05-05 16:52:31 +02:00
Dannon
e7d8e66b48
Merge pull request #20134 from mvdbeek/fix_edam_selenium_test
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[24.2] Fix edam selenium test
2025-05-05 10:41:51 -04:00
mvdbeek
073acf5801
Add typing around get_tool / has_tool
2025-05-05 15:16:31 +02:00
Marius van den Beek
18c68b067f
Merge pull request #20144 from mvdbeek/fix_param_value_restriction
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[24.2] Skip ``param_value`` filter if ref value is runtime value
2025-05-05 13:42:20 +02:00
mvdbeek
a53b4125aa
Skip `param_value` filter if ref value is runtime value
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Fixes https://github.com/galaxyproject/galaxy/issues/20136
2025-05-04 16:48:33 +02:00
John Chilton
9b0fb38a76
More workflow mapping test cases.
2025-05-03 10:21:17 -04:00
mvdbeek