Nicola Soranzo
13d0f92fc0
Merge pull request #13071 from mvdbeek/drop_wsgi_mode
2022-03-18 13:41:33 +00:00
John Chilton
4dae7c6f21
Disable implicit re-imports across the projects.
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Exclude galaxy.util for now, but the exclusion is tracked in setup.cfg. Elimiantes a bunch of flake exception markers.
2022-03-15 19:58:42 -04:00
mvdbeek
9277af6657
Raise exception when waiting for entry point
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There's a retry loop, I suppose it was meant to be used that way.
2022-03-15 21:32:00 +01:00
mvdbeek
fd51314a88
Drop more uWSGI legacy things
2022-03-15 21:32:00 +01:00
mvdbeek
b39e8ad9a2
First pass in dropping uwsgi specific things
2022-03-15 21:31:59 +01:00
Sergey Golitsynskiy
3c992a608f
Add create/migrate scripts for Alembic dbs (squashed)
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Also add exec permissions to create/migrate python scripts.
(not sure this is required, adding for consistency with previous
version)
+ A few fixes for TS scripts, tests
Squashed:
- pick b62443245e Add create/migrate scripts for Alembic dbs
- squash 06f0a923ca Fix integration test (test only relevant for TS)
2022-03-09 18:41:02 -05:00
Marius van den Beek
f3d85eb28b
Merge pull request #13335 from simonbray/wf-exec-tool-versions
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Block workflow invocation if wrong tool versions installed
2022-02-11 15:14:16 +01:00
mvdbeek
2aca80d070
Can't change API endpoint parameter, is already used
2022-02-10 18:13:34 +01:00
mvdbeek
fc493c9280
Add test for storing metadata file in object store
2022-02-10 15:58:16 +01:00
Simon Bray
865a3b915e
add integration test for invoking workflows with nonexistent tool_ids or tool_versions
2022-02-10 11:30:36 +01:00
Dannon Baker
623a5e165a
Apply black formatting.
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Apply isort.
2022-02-03 07:42:20 -05:00
mvdbeek
d0fb11c015
Drop OpenID post authentication protocols
2022-02-01 11:04:48 +01:00
mvdbeek
597ee75396
Merge branch 'release_21.09' into dev
2022-01-31 08:57:46 +01:00
Nicola Soranzo and Marius van den Beek
4b46c898a7
Add comment
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Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com >
2022-01-29 13:00:33 +00:00
mvdbeek
be43f1d1a7
Use updated test images for CLI runner
2022-01-28 19:55:45 +01:00
Simon Bray
381d218180
ensure tool_id/content_id is updated when refactoring workflows
2022-01-24 13:39:27 +01:00
mvdbeek
f0baddd905
Merge branch 'release_21.09' into dev
2022-01-21 16:38:36 +01:00
mvdbeek
d5b31ee55a
Fix tool id not getting updated on tool update
2022-01-19 14:46:31 +01:00
John Chilton
d3b272fd10
Merge pull request #13170 from mvdbeek/max_discovered_files
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Limit maximum number of discovered files per job
2022-01-18 12:45:01 -05:00
Kaivan Kamali
28423d27ef
Clear the cache before fetching a file from irods object store, to verify file is fetched from the object store, not from the cache
2022-01-18 09:51:56 -05:00
mvdbeek
26a98ae8f4
Implement max_discovered_files
2022-01-18 11:49:00 +01:00
Kaivan Kamali
85ade3df4f
Clear the cache before fetching a file from irods object store, to verify file is fetched from the object store, not from the cache
2022-01-13 15:19:10 -05:00
mvdbeek
43f9dbe760
Fix test_workflow_scheduling_options
2022-01-05 13:31:58 +01:00
mvdbeek
9a1b0753c5
Fix install_repo_request/delete_repo_request url
2022-01-05 13:31:55 +01:00
Nuwan Goonasekera
01ca66fa98
Merge branch 'dev' into vault_impl
2021-12-22 23:55:37 +05:30
Nuwan Goonasekera
be9f210901
Change vault api test case to integration test case and add missing conditional requirements
2021-12-20 18:23:00 +05:30
Nuwan Goonasekera and Marius van den Beek
592603eb41
Add file upload test to vault
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Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com >
2021-12-20 18:00:53 +05:30
Nicola Soranzo
eea0c8b673
Update pulsar-galaxy-lib to 0.14.13 and enable assert for EmbeddedPulsarDefaultJobEnvironmentIntegrationTestCase
2021-12-06 17:45:58 +00:00
Nicola Soranzo
db566d4627
Check that jobs don't inherit env variables from Galaxy
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in integration tests.
Also:
- Merge `RunsEnvironmentJobs` class into
`BaseJobEnvironmentIntegrationTestCase`
- Remove redundant checks in `DefaultJobEnvironmentIntegrationTestCase`
2021-12-06 17:43:22 +00:00
Nuwan Goonasekera
7f663fad6e
Add new secret type to user preferences that is not sent to client
2021-12-01 10:48:36 +05:30
John Chilton
4ce8c35023
Merge pull request #12459 from mvdbeek/wip_remote_command_line
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Remote / Late evaluation of tools
2021-11-30 15:22:31 -05:00
mvdbeek
1a08eb57b3
Make tool_evaluation_strategy configurable on app and destination level
2021-11-30 12:27:14 +01:00
mvdbeek
2384875073
Disable remote evaluation for JEHA history export jobs
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We'd have the add `JobExportHistoryArchive` to the supported job outputs
in the model export store or move the `JobExportHistoryArchive` creation
from `execute()` ToolAction to the handler and skip creating
`JobExportHistoryArchive` altogether, but we want to perform the
job export in the Celery workers anyway, so I think it's not worth the
effort.
Note that exporting to file sources doesn't use
`JobExportHistoryArchive`, so for those we can still create the command
line remotely (and e.g materialize deferred datasets in a history).
2021-11-30 10:58:40 +01:00
Nicola Soranzo
7b67cea7d0
Remove unnecessary list creations
2021-11-29 16:33:05 +00:00
mvdbeek
1bac1157ba
Construct ToolEvaluator only when needed
2021-11-29 11:22:44 +01:00
mvdbeek
be52b2e0f8
Test implicit conversion
2021-11-29 11:22:44 +01:00
mvdbeek
511383f1fc
Restore ConfiguredFileSources on ToolApp object
2021-11-29 11:22:44 +01:00
mvdbeek
f1ea0f0db4
Run data manager tests with metadata_strategy: extended
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Which currently also means we run with remote_command_line: True.
2021-11-29 11:22:43 +01:00
Nuwan Goonasekera
76951a4bda
Make sure filesources can access user level and app level vaults
2021-11-28 06:56:35 +05:30
Nicola Soranzo
6a6abf37ef
Split run_tool_raw() out of BaseDatasetPopulator.run_tool()
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so that the former always returns a `Response` object while the latter
returns the response content.
Also:
- In `CwlPopulator.run_cwl_job()` wait for the run only if `assert_ok`
is True; if the `wait()` call fails, summarize history also for
workflow runs.
2021-11-27 03:14:52 +00:00
Nuwan Goonasekera
e1535db412
Add vault conditional dependencies
2021-11-18 01:12:23 +05:30
Nicola Soranzo
8199dbd5d9
Merge branch 'release_21.09' into dev
2021-11-16 01:36:35 +00:00
mvdbeek
0941c2d85d
Fix installation of tools with biotools id
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Fixes https://github.com/galaxyproject/galaxy/issues/12918 :
```
galaxy.tool_shed.tools.tool_validator ERROR 2021-11-15 15:55:52,992 [pN:main.web.1,p:5536,w:1,m:0,tN:uWSGIWorker1Core3] Caught exception loading tool from /Users/cat/dev/galaxy/database/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastqc/3d0c7bdf12f5/fastqc/rgFastQC.xml:
Traceback (most recent call last):
File "lib/galaxy/tool_shed/tools/tool_validator.py", line 80, in load_tool_from_config
tool = create_tool_from_source(config_file=full_path, app=self.app, tool_source=tool_source, repository_id=repository_id, allow_code_files=False)
File "lib/galaxy/tools/__init__.py", line 266, in create_tool_from_source
tool = ToolClass(config_file, tool_source, app, **kwds)
File "lib/galaxy/tools/__init__.py", line 585, in __init__
raise e
File "lib/galaxy/tools/__init__.py", line 582, in __init__
self.parse(tool_source, guid=guid, dynamic=dynamic)
File "lib/galaxy/tools/__init__.py", line 1025, in parse
biotools_entry = self.app.biotools_metadata_source.get_biotools_metadata(biotools_reference)
AttributeError: 'ValidationContext' object has no attribute 'biotools_metadata_source'
```
2021-11-15 10:14:56 +01:00
Michael R. Crusoe
36c2e33ed9
improve type hints for test/integration/test_upload_configuration_options.py.
2021-11-12 19:00:33 +01:00
Nicola Soranzo
d10b97ac78
Merge pull request #12897 from mvdbeek/fix_history_new_state
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Consider a history not new once there are any items in it
2021-11-12 15:32:22 +01:00
mvdbeek
c063939484
Consider a history not new once there are any items in it
2021-11-12 08:27:39 +01:00
Nicola Soranzo
f355da5865
Move ssh_util from galaxy_test.base to galaxy.security
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so it can be used by both unit tests of the `galaxy-app` package and by integration tests
2021-11-09 14:37:48 +01:00
mvdbeek
8b7614ccd9
Fix mypy tests that broke while merging forward
2021-11-01 18:46:05 +01:00
mvdbeek
58b2837c7c
Merge branch 'release_21.09' into dev
2021-11-01 18:17:54 +01:00
Marius van den Beek
48996b1aaa
Merge pull request #12816 from mvdbeek/fix_from_work_dir_glob_with_extended_metadata
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[21.09] Fix ``from_work_dir`` glob with extended metadata and pulsar
2021-11-01 18:14:10 +01:00
Nicola Soranzo