guerler
b29cd4e824
Remove unused import
2021-04-19 13:52:56 -04:00
guerler
2208de874a
Parse history name to page client, post import request to histories api
2021-04-19 13:46:45 -04:00
guerler
54a927af7c
Add new element to pages, allow history import
2021-04-19 12:51:52 -04:00
Ruben Vorderman
4361e1001d
Also check for boolean True, not just string 'True' when evaluating conditional dependencies.
...
When people know how actual yaml works they might have
galaxy:
watch_tools: true
as their config. Which signifies an actual Boolean value. This should be considered by the script as well.
2021-04-19 14:12:02 +02:00
Marius van den Beek
7cf7e1b737
Merge pull request #11844 from simonbray/wf-check-tools
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Do not invoke workflow if not all tools are available
2021-04-19 09:34:05 +02:00
Marius van den Beek
87a71e061f
Merge pull request #11856 from davelopez/unify_security_decode_id_exceptions
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Unify security decode id exceptions
2021-04-19 09:15:37 +02:00
davelopez
37f32c444d
Remove helper _decode_id in resource_parser
2021-04-17 21:23:48 +02:00
David López and Nicola Soranzo
1c41c8d8af
Apply suggestions from code review
...
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2021-04-17 20:49:16 +02:00
davelopez
cc4847e4fd
Replace helpers with direct call as suggested by code review
2021-04-17 20:08:21 +02:00
Simon Bray
51ee555b40
do not invoke workflow if not all tools are available
2021-04-17 15:41:50 +02:00
David López and Nicola Soranzo
1a456b1624
Update lib/galaxy/managers/folders.py
...
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2021-04-17 14:56:58 +02:00
Marius van den Beek
c8f881f0ba
Merge pull request #11852 from jmchilton/less_transfer
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Test a better Pulsar configuration for extended metadata.
2021-04-17 09:24:40 +02:00
John Chilton
7c77975b58
Merge pull request #11831 from gregvonkuster/relion_star
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Add support for the Relion STAR data format
2021-04-16 11:46:47 -04:00
davelopez
2158498371
Add specific exception
2021-04-16 15:57:29 +02:00
davelopez
ebe6e30d1a
Check for bootstrap admin user (master API key) specifically
2021-04-16 15:57:29 +02:00
davelopez
cb3bd5047f
Check session when creating history using the API.
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This will return a BadRequest instead of a InternalServerError when trying to create a history with the master API key.
2021-04-16 15:57:29 +02:00
davelopez
92092ce975
Add API test to create history without session
2021-04-16 15:57:29 +02:00
davelopez
3eb10b69f5
Remove unused __decode_id function
2021-04-16 14:03:16 +02:00
davelopez
ebb68213cb
Slightly enhance decode_id error message
2021-04-16 13:59:35 +02:00
davelopez
4c9ffef89c
Remove redundant decode_id exception checks
2021-04-16 13:57:56 +02:00
Marius van den Beek
5b0fe015ff
Merge pull request #11843 from nsoranzo/restore_triggers
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Restore triggers dropped in #10821
2021-04-16 13:44:20 +02:00
davelopez
639fe87b92
Raise MalformedId exception when IdEncodingHelper.decode_id() fails
2021-04-16 13:08:54 +02:00
John Chilton
cc41f30af6
Better extended metadata configuration for Pulsar (don't copy outputs)
2021-04-15 15:01:28 -04:00
John Chilton
289862d384
Merge pull request #11716 from OlegZharkov/library-collections-test
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[Selenium] Library collections export
2021-04-15 10:31:16 -04:00
Nicola Soranzo
ef03871a74
Add migration to re-add the triggers
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Make sure that any BEFORE/AFTER trigger is removed.
2021-04-15 12:09:21 +01:00
Nicola Soranzo
a414444a59
Restore triggers dropped in #10821
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Partially revert commit 33883fe5eb
2021-04-15 12:09:21 +01:00
greg
767b90c757
Improve approach to sniffing STAR data
2021-04-14 18:22:17 -04:00
John Chilton
d9ca2ed983
Transfer fewer files when using extended + remote metadata.
2021-04-14 13:21:15 -04:00
mvdbeek
73aeb4c363
Minor fix, don't need to manage handler assignment methods like this
2021-04-14 17:58:45 +02:00
greg
f20d8b7f3c
Add support for the Relion STAR data format
2021-04-13 13:58:33 -04:00
Marius van den Beek
b7078f51fa
Merge pull request #11788 from jmchilton/pulsar_extended_metadata
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Fixes for extended metadata working with Pulsar.
2021-04-13 18:39:45 +02:00
mvdbeek
de8ef76092
Make sure web handlers don't become job handlers if handlers section exists
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And add a default pool, so that exisiting job setups that don't specify
a pool (for instance those that previously used db-preassign) will just
continue working.
2021-04-13 10:13:42 +02:00
mvdbeek
fddaaec2ae
Restore stack pool default setup
2021-04-13 10:13:42 +02:00
mvdbeek
bb83f97af5
Move get_preferred_handler_assignment_method into ApplicationStack
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and simplify _set_default_job_handler_assignment_methods
2021-04-13 10:13:42 +02:00
mvdbeek
e52c33033b
Remove db-self, db-preassign fallback options
2021-04-13 10:13:42 +02:00
mvdbeek
c0f2c751d1
Workaround missing RETURNING for transaction isolation
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In that case there just won't be any logs about which jobs were grabbed,
but that's probably justified by being able to drop db-self and
db-preassgin which would have no real reason to remain options.
2021-04-13 10:13:42 +02:00
mvdbeek
a5f0b88c12
Shut down pulsar app on Galaxy shutdown if embedded
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Fixes occasional error in pulsar embedded integration tests,
which is a neverending stream of:
```
2021-04-12T08:09:18.5912970Z FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmpk0dfc3gg/tmp539e3wrp/tmp3zkj6xnj/database/pulsar_persisted_data/_default_-active-jobs'
2021-04-12T08:09:18.5916534Z pulsar.managers.stateful ERROR 2021-04-12 08:09:18,347 [pN:main,p:3088,tN:[manager=_default_]-[action=monitor]] Failure in stateful manager monitor step.
2021-04-12T08:09:18.5917629Z Traceback (most recent call last):
2021-04-12T08:09:18.5919687Z File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/pulsar/managers/stateful.py", line 361, in _run
2021-04-12T08:09:18.5920924Z self._monitor_active_jobs()
2021-04-12T08:09:18.5924333Z File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/pulsar/managers/stateful.py", line 366, in _monitor_active_jobs
2021-04-12T08:09:18.5925618Z active_job_ids = self.stateful_manager.active_jobs.active_job_ids()
2021-04-12T08:09:18.5927558Z File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/pulsar/managers/stateful.py", line 307, in active_job_ids
2021-04-12T08:09:18.5929117Z job_ids = os.listdir(target_directory)
```
2021-04-13 10:13:42 +02:00
mvdbeek
f0463477b9
Setup grabber query after fork
2021-04-13 10:13:42 +02:00
mvdbeek
9ce1eb85be
Fix log statement
2021-04-13 10:13:42 +02:00
mvdbeek
333ebb75d9
Fix workflow_handler_configuration tests
2021-04-13 10:13:42 +02:00
mvdbeek
6a106e4938
Fix handlers pools, job handler capacilities
2021-04-13 10:13:42 +02:00
mvdbeek
1507cc80f4
Add generic GALAXY_WEB_PORT variable to infrastructure_url parsing
2021-04-13 10:13:42 +02:00
mvdbeek
546935a5fb
Add log statements when determining best handler assignment method
2021-04-13 10:13:42 +02:00
mvdbeek
1bf92038fa
Figure out which assignment method is best given the deployed database
2021-04-13 10:13:42 +02:00
mvdbeek
cdbfd8720f
Change default handler assignment to db-skip-locked
2021-04-13 10:13:42 +02:00
John Chilton
c313635676
Merge pull request #11772 from mvdbeek/run_sh_gunicorn
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Add circus + gunicorn option when using run.sh
2021-04-12 10:31:30 -04:00
Björn Grüning
240829a472
Merge pull request #11815 from mvdbeek/performance_fix_setup_external_metadata
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[21.01] Don't write job and job-related attributes when creating export model
2021-04-12 00:40:09 +02:00
mvdbeek
897590b2f3
Add separate option for including jobs to model store
2021-04-11 20:33:57 +02:00
mvdbeek
0a4aa468bf
Don't write job and job-related attributes when creating export model
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These aren't used in regular jobs (should only be needed for history
export currently).
2021-04-11 10:56:39 +02:00
John Chilton
5f62b6e485
Merge pull request #11810 from natefoo/merge-pulsar-managers-util
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Incorporate changes from Pulsar's copy of galaxy.jobs.runners.util
2021-04-09 16:30:51 -04:00
guerler