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
mvdbeek
73aeb4c363
Minor fix, don't need to manage handler assignment methods like this
2021-04-14 17:58:45 +02:00
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
John Chilton
094bc49e38
Drop legacy metadata handling special case from pulsar.py that is no longer supported.
2021-04-09 16:24:32 -04:00
John Chilton
cb2ddef8d4
Improved assertion error messages.
2021-04-09 16:24:32 -04:00
John Chilton
c502649104
Get extended metadata working with Pulsar.
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Work started in https://github.com/galaxyproject/pulsar/pull/192 .
2021-04-09 16:24:22 -04:00
Dannon
16ad3aba1e
Merge pull request #11808 from natefoo/no-overwrite-memory-var
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Don't overwrite $GALAXY_MEMORY_MB if it's already set
2021-04-09 09:07:23 -04:00
Dannon
4b26e8528a
Merge pull request #11812 from annefou/jp2-newtype
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add new datatype JPEG 2000 in Galaxy
2021-04-09 09:06:33 -04:00
Anne Fouilloux
7d5a54ada4
add JPEG2000 test file for testing new datatype
2021-04-09 09:19:36 +00:00
Nicola Soranzo
04787115ed
Merge pull request #11575 from bernt-matthias/topic/slurm-noedit-errorfile
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SLURM: stop editing job stderr file
2021-04-09 02:23:42 +01:00
Anne Fouilloux
f733a30ad1
add JP2 in sniff_order<1 section
2021-04-08 21:11:47 +00:00
Anne Fouilloux
69b5b16dfe
fix linting issues
2021-04-08 21:07:52 +00:00
Anne Fouilloux
0860549e08
add JP2 in datatypes_conf.xml.sample
2021-04-08 20:48:14 +00:00
Nate Coraor
f31d4bcc0d
Lint fixes
2021-04-08 16:42:58 -04:00
Anne Fouilloux
c1c20db884
add new datatype JPEG 2000 in Galaxy:
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JPEG 2000 is an image compression standard and coding system. It is widely used for storing satellite imagery; for instance from EU Copernicus Sentinel
2021-04-08 20:34:42 +00:00
Nate Coraor
7a0f14de20
Fix import of galaxy.jobs-level name in
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galaxy.jobs.runners.util.cli.job.lsf when this module is loaded e.g. in
Pulsar where galaxy.jobs is not present.
xref: galaxyproject/pulsar#177
2021-04-08 15:32:51 -04:00
Nate Coraor
1003d572e3
Merge changes to galaxy.jobs.runners.util.condor that were applied
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directly to the Pulsar copy in pulsar.managers.util.
xref: galaxyproject/pulsar#213 galaxyproject/pulsar#229
2021-04-08 14:33:37 -04:00
Helena
e5000e24c8
Merge pull request #11351 from selten/analytics
2021-04-08 16:45:34 +00:00
Nate Coraor
90217822bd
Don't overwrite $GALAXY_MEMORY_MB if it's already set.
2021-04-08 10:29:59 -04:00
Marius van den Beek
c87a0dd9a7
Merge pull request #11801 from qiagu/ometiff2
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Make Avivator GEDA and sniffer for ome.tiff datatype
2021-04-08 15:47:58 +02:00
mvdbeek
dec78b7204
Merge branch 'release_21.01' into dev
2021-04-08 15:44:44 +02:00
Marius van den Beek
c767adbed1
Merge pull request #11654 from brinkmanlab/revert_11448
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Refactor default mounting of $tmp_directory in containers
2021-04-08 15:43:39 +02:00
Nicola Soranzo
135b13548b
Merge pull request #11798 from nsoranzo/fix_profile_docs
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Fix tool profile details in schema docs
2021-04-08 03:07:40 +01:00
Nicola Soranzo
7d32450ba8
Merge pull request #11727 from bernt-matthias/topic/lint-checkboxes
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lint for checkboxes select
2021-04-07 23:19:18 +01:00
qiagu
56f715c59d
Merge branch 'dev' into ometiff2_new
2021-04-07 10:45:40 -07:00
M Bernt and Nicola Soranzo
cb3d03df0c
Apply suggestions from code review
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Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2021-04-07 19:39:31 +02:00
qiagu
3278d01dcb
Lower down tifffile version to fit python 3.6
2021-04-07 10:37:05 -07:00
Nicola Soranzo
0e43c82a49
Fix tool profile details in schema docs
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Per the GitHub Flavored Markdown Spec: "Block-level elements cannot be
inserted in a table.", see
https://github.github.com/gfm/#tables-extension-
2021-04-07 17:34:47 +01:00
Marius van den Beek
ba88c91d24
Merge pull request #10496 from almahmoud/patch-8
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Handle unschedulable jobs in k8s runner
2021-04-07 17:29:54 +02:00
John Chilton
0553f8d58b
Merge pull request #11425 from pcm32/feature/binary_checking_fcs
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Check for binary files at the middle of the file instead of at the beginning
2021-04-07 10:25:48 -04:00
Nicola Soranzo