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Author SHA1 Message Date
davelopezandNicola Soranzo 5dc7dae7c1 Use pydantic[email] instead of email-validator 
Co-authored-by: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
 2022-10-14 12:20:24 +02:00
davelopez 8aebe9079e Fix some BCO fields 
- Pass the workflow url for the execution_domain instead of a fixed galaxy url
- Fix step annotations in PipelineStep description
- Use API url for downloading collections in InputSubdomainItem
 2022-10-14 12:20:24 +02:00
davelopez 0950722c7c Exclude null values when serializing BCO 
+ fix typo
 2022-10-14 12:20:24 +02:00
davelopez 70e7600968 Fix some pydantic validation issues 2022-10-14 12:20:24 +02:00
davelopez 2140df7eed Add basic BCO export integration tests 2022-10-14 12:20:24 +02:00
John Chilton 61b9e57c7f Implement Workflow Invocation -> BCO export. 2022-10-14 12:20:24 +02:00
John Davis 1b9e465195 Merge pull request #14788 from jdavcs/dev_set_from_env_and_prefix 
Add a utility function that returns first available value for prefix+key set in the environment; fix bug
 2022-10-13 17:27:30 -04:00
John Davis 66ceff374a Ignore type error in test: wrong value is intentional 2022-10-13 13:42:00 -04:00
John Davis c8a1581e06 Assign values from env using new utility function 
Also, fix error: don't break out early as both values should be
assigned.
 2022-10-13 13:17:33 -04:00
John Davis 4818c8dadf Add get_from_env utility + tests 2022-10-13 13:17:15 -04:00
Nicola Soranzo 6069023d86 Merge pull request #14740 from bernt-matthias/topic/doc-security-datatables 
Extend security docs
 2022-10-13 14:29:52 +01:00
Dannon Baker d157331ffd Merge remote-tracking branch 'upstream/release_22.05' into dev 2022-10-13 07:56:53 -04:00
M BerntandMarius van den Beek ffc26d5ddd Update doc/source/admin/security.md 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2022-10-13 13:53:06 +02:00
Dannon 64b75762f1 Merge pull request #14786 from davelopez/22.05_fix_deleted_library_buttons 
[22.05] Fix deleted library buttons visibility
 2022-10-13 07:39:19 -04:00
davelopez 35c9dc434b Fix deleted library buttons visibility 
Also:
- Unify Undelete button size
- Fix aria-label warning
 2022-10-13 11:44:51 +02:00
Marius van den Beek 5f30153180 Merge pull request #14784 from jmchilton/sync_job_script 
Synchronize job script module with Pulsar fixes.
 2022-10-13 10:19:32 +02:00
Marius van den Beek 08b6c67737 Merge pull request #14782 from nsoranzo/skip_tests_if_bio.tools_down 
Skip 2 unit tests if bio.tools is down
 2022-10-13 10:17:45 +02:00
Dannon 7aec7175d3 Merge pull request #14725 from guerler/fix_rerun_reload 
Allow to force push client routes
 2022-10-12 21:11:46 -04:00
Dannon b1fcc1c267 Merge pull request #14775 from itisAliRH/workflow-import-composition 
Migrate `workflow import` to composition API
 2022-10-12 20:07:24 -04:00
John Chilton 5dde30a9db Synchronize job script module with Pulsar fixes. 
- Allows memory_statement.log to be written to a better location than the working directory.
- Allow Pulsar to handle home directory outside the command_factory abstraction.
 2022-10-12 14:36:57 -04:00
Nicola Soranzo a5ff54489c Set default verbosity of pytest to 1 
This is equivalent to the `-v` option, which e.g. shows each test inside a
file as a separate line in the output, showing the reason why a test was
skipped.

xref. https://docs.pytest.org/en/7.1.x/how-to/output.html#verbosity
 2022-10-12 18:13:47 +01:00
Nicola Soranzo c9e5a89c15 Skip unit tests requiring bio.tools if it's down 2022-10-12 18:13:47 +01:00
Nicola Soranzo 847946a887 Move `skip_if_site_down` test decorator to be reusable in unit tests 
Also:
- Add type annotations
 2022-10-12 18:13:46 +01:00
Nicola Soranzo d266eb7f80 Add missing package requirements 
Packages that are imported directly in galaxy-tool-util that were already
required through the galaxy-util dependency.
 2022-10-12 18:13:46 +01:00
Nicola Soranzo c810ebf9e1 Make 2 test decorators usable on both functions and methods 2022-10-12 18:13:45 +01:00
David López f733734299 Merge pull request #14736 from jmchilton/ts_service_models_2 
Migrate index and show tool shed repositories endpoints to Pydantic and FastAPI
 2022-10-12 18:25:14 +02:00
Alireza Heidari 674f4d7378 fix integration_selenium tests 2022-10-12 14:39:01 +02:00
Marius van den Beek 258479a824 Merge pull request #14778 from dannon/fix-history-disappearing-anchor 
[22.05] Fix disappearing right anchor
 2022-10-12 08:38:46 +02:00
Dannon Baker 21b4ed92e8 Fix disappearing right anchor 2022-10-11 17:27:18 -04:00
Nicola Soranzo a81d680cca Merge branch 'release_22.05' into dev 2022-10-11 21:34:31 +01:00
Dannon bbac935f50 Merge pull request #14769 from martenson/admin-jobs-page 
improve UX of admin job page
 2022-10-11 14:17:11 -04:00
Dannon a6acbffee1 Merge pull request #14549 from ElectronicBlueberry/tool-form-improvements 
Tool form improvements
 2022-10-11 11:54:32 -04:00
Alireza Heidari 35e720b5cf Update WorkflowList.vue 2022-10-11 16:04:37 +02:00
Alireza Heidari fe3d02fe22 Delete rxjsAxios.js 
`rxjs` completely deleted from `workflow` components
 2022-10-11 15:34:44 +02:00
Dannon 1221904383 Merge pull request #14703 from itisAliRH/store-multi-view-selected-list 
Storing selected histories in multiple view into local storage
 2022-10-11 09:30:22 -04:00
Alireza Heidari 672564bf90 remove not used services from Workflow/services and replace getAppRoot with safePath 
and update components uses this services files
 2022-10-11 15:28:47 +02:00
Dannon 15364b72c7 Merge pull request #14752 from guerler/safe_path_upgrade 
Align url handling for more consistency
 2022-10-11 09:15:25 -04:00
Dannon 3574b08d5b Merge pull request #14766 from xtrojak/visualisation_visjs_transition_system 
[Visualization] visjs-based transition system visualization
 2022-10-11 09:06:59 -04:00
Nicola Soranzo b31e2f02f2 Merge branch 'release_22.01' into release_22.05 2022-10-11 13:28:32 +01:00
Dannon 577a7d198a Merge pull request #14773 from nsoranzo/release_22.01_fix_provenance_follow 
[22.01] Fix dataset provenance API when ``follow=False``
 2022-10-11 08:01:10 -04:00
Dannon Baker d0bebf23ba Minor stop job message tweak 2022-10-11 07:53:31 -04:00
Alireza Heidari b3d646bfe1 update TrsImport and TrsSearch routes 2022-10-11 12:26:02 +02:00
Alireza Heidari e0100476b4 update WorkflowImport ui 2022-10-11 12:25:45 +02:00
Alireza Heidari 29a808fc74 Delete trsMixin.js 2022-10-11 12:25:18 +02:00
Alireza Heidari daa3f4d0d0 migrate TrsTool to vue composition api 2022-10-11 12:25:07 +02:00
Alireza Heidari f5244bcba3 migrate TrsServerSelection to vue composition api 2022-10-11 12:24:21 +02:00
Alireza Heidari 662e60bc5b migrate TrsSearch to vue composition api 2022-10-11 11:34:59 +02:00
Alireza Heidari d4d7e1e982 migrate TrsImport to vue composition api 2022-10-11 11:33:14 +02:00
Alireza Heidari 08af75743d Create FromFileOrUrl.vue 2022-10-11 11:01:37 +02:00
Nicola Soranzo bb3006df87 Fix dataset provenance API when `follow=False` 2022-10-11 00:45:37 +01:00