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Author SHA1 Message Date
mvdbeek bf31260192 Call tool_script.sh with shell 2019-06-01 13:24:51 +02:00
Aysam Guerler a763c89180 Merge pull request #8035 from martenson/changesets-search-index 
enhance TS repo search capabilities
 2019-05-30 23:25:14 -04:00
Nate Coraor 51b39b82e6 Merge remote-tracking branch 'upstream/release_19.05' into dev 2019-05-30 15:03:50 -04:00
Nate Coraor bff203f48c Merge remote-tracking branch 'upstream/release_19.01' into release_19.05 2019-05-30 15:03:00 -04:00
Martin Cech 91041c2ba4 minor refactoring 2019-05-30 14:27:59 -04:00
John Chilton bef00770ba Merge pull request #8036 from WilliamHolden/update_layout_folder_es6 
Prefer const and let over var in layout folder
 2019-05-30 14:16:21 -04:00
John Chilton 9c960c2db8 Merge pull request #8056 from mvdbeek/possibly_fix_amqp_issue_on_mules 
[19.05] Release ampq connection after initial connect
 2019-05-30 14:15:21 -04:00
Martin Cech 7addeb952f the alphabet 2019-05-30 13:51:25 -04:00
Nicola Soranzo c7decb1d3c Merge pull request #8061 from natefoo/max-grab-typo 
Fix typo grap -> grab
 2019-05-30 16:43:39 +01:00
Martin Cech 2eb02c613c refactor filtering method and add doctest 2019-05-30 11:24:26 -04:00
Björn Grüning da0f5f290c [19.01] Document the handler max_grab config param (#8060) 
[19.01] Document the handler max_grab config param
 2019-05-30 17:16:06 +02:00
mvdbeek 514154e36b Release ampq connection after initial connect 
We need to call `connection.connect()` to avoid
`'kombu.transport.sqlalchemy.Message' is not mapped`` errrors.
This is fine for for sqlalchemy transports, but the connection
is still open if we don't release the connection.

This is a problem when acquiring the connection with rabbitmq
transports. So instead we release the connection and acquire
a blocking connection from the connection pool. This sets up
the mapping and avoids `'kombu.transport.sqlalchemy.Message' is not
mapped`.
Not sure if this will fix @natefoo's issue as I haven't exactly
been able to reproduce the same error, but acquiring a blocking
connection failed outright without releasing the connection, so this is
probably a step in the right direction.
 2019-05-30 15:54:56 +02:00
Nate Coraor 466366c242 Fix typo grap -> grab 2019-05-30 09:28:46 -04:00
Nate Coraor dfb591caf6 Document the handler max_grab config param 2019-05-30 09:18:42 -04:00
Nicola Soranzo e7b411dbca Merge branch 'release_19.05' into dev 2019-05-30 10:43:27 +01:00
Nicola Soranzo e0a5e39435 Merge branch 'release_19.01' into release_19.05 2019-05-30 10:33:51 +01:00
Björn Grüning d25dcc4fe4 [19.01] Fixes for job handler and worklflow scheduler self-assignment grab limits (#8059) 
[19.01] Fixes for job handler and worklflow scheduler self-assignment grab limits
 2019-05-30 09:30:40 +02:00
Martin Cech 676d913c05 add option to specify category boost for searching repos 2019-05-29 16:20:33 -04:00
Martin Cech d6a26e1ba5 enhance repository search API capabilities 
* include categories as keywords for repository index
* allow filtering on category/owner using github-like wildards "category:name"
* only log metadtaa like matched terms, do not return in http response
* refactoring
 2019-05-29 16:17:09 -04:00
Nate Coraor c0c39d5969 Default the maximum grab limit for handler database preassignment 
methods to unlimited as intended. Document the config param.
 2019-05-29 15:25:55 -04:00
John Chilton 62d5e8b68c Merge pull request #8050 from mvdbeek/fix_stream_to_open_named_file_for_text_files_with_funky_encoding 
Fix stream_to_open_named_file for non-utf8 text
 2019-05-29 00:11:31 -04:00
Martin Cech fd82ec013b repo search - prefix hash with changeset number, stringify as list 2019-05-28 11:38:16 -04:00
mvdbeek 5bcfa3c5b7 Fix stream_to_open_named_file for non-utf8 text 
We only recode the file if a target encoding is given,
and make the assumption that the file is not binary
or compressed if a target encoding is set.

This is required to upload the imzml test data by url
in https://github.com/galaxyproject/galaxy/issues/7412#issuecomment-469379295
 2019-05-28 16:42:23 +02:00
John Chilton 530077a1be Merge pull request #8040 from mvdbeek/bwlang_editor_fixes 
[19.05] Update node.post_job_actions when changing post job actions
 2019-05-28 09:37:13 -04:00
Marius van den Beek 40196a5950 Merge pull request #8045 from jmchilton/job_parameters 
Fixes for JobParameters Vue components.
 2019-05-28 14:58:23 +02:00
John Chilton 73832b7b69 Merge pull request #8038 from mvdbeek/database_operation_tool_improvements 
Database operation tool improvements
 2019-05-28 08:50:49 -04:00
Marius van den Beek c654406725 Merge pull request #8046 from jmchilton/selenium_workflow_data 
Fix Selenium DatasetPopulator for more interesting uploads.
 2019-05-28 14:42:47 +02:00
Marius van den Beek ea107d79d8 Merge pull request #8048 from nsoranzo/release_19.05_update_conda 
[19.05] Update Conda for new installs to v4.6.14
 2019-05-28 13:28:12 +02:00
mvdbeek b1ea3d2da6 Don't add new outputView because it resets mapOver 
This means we don't see the forced datataype on the node itself, but we
maintain the noodle type, and the connection hints are correct.
 2019-05-28 12:33:41 +02:00
mvdbeek c70310946d Update node.post_job_actions when changing post job actions 
I broke persisting pot job actions in
https://github.com/galaxyproject/galaxy/pull/7989.
The onchange function prevented updating the post job action.
 2019-05-28 10:14:20 +02:00
Nicola Soranzo 25ea088647 Update Conda for new installs to v4.6.14 
and conda-build to v3.17.8 .
 2019-05-28 00:36:22 +01:00
John Chilton 79ce86bce5 Fix Selenium DatasetPopulator for more interesting uploads. 
This is a bug, that interface consumes files and so should this method.
 2019-05-27 17:56:55 -04:00
Nicola Soranzo 0e14a47e6c Merge branch 'release_19.05' into dev 2019-05-27 22:50:04 +01:00
John Chilton 9a63c4e2f5 Fixes for JobParameters Vue components. 
Based on comments from @inkuzmin use scoped styling and fix notes conditional logic.
 2019-05-27 17:47:01 -04:00
John Chilton 0e33056989 Merge pull request #8039 from mvdbeek/non_legacy_object_store_fix 
[19.05] Backport 7939: Fix non-eager object store with nested object stores
 2019-05-27 12:09:34 -04:00
mvdbeek dd91b14b6d Add testcase for new tag from file behavior 2019-05-27 14:58:16 +02:00
mvdbeek 5b05866545 Explicitly create extra_files_path when discovering outputs with extra files 2019-05-27 14:37:53 +02:00
mvdbeek 563ae4d7d3 Raise ObjectNotFound if file does not exist in object store 
And return an empty string if a path does not exist when calling
`get_filename` or` get_extra_files_path` on a Dataset.
 2019-05-27 14:37:53 +02:00
John Chilton 419bae1f09 Don't calculate real path in tool action code if unused. 2019-05-27 14:37:53 +02:00
John Chilton 7ea502be77 Run API tests with a nested object store. 2019-05-27 14:37:53 +02:00
Nicola Soranzo 5c2da643c6 [19.05] Use byte comparison for contains and files_re_match (#8010) 
[19.05] Use byte comparison for contains and files_re_match
 2019-05-27 12:27:17 +01:00
mvdbeek b3d7989a85 Convert tags starting with # to name: tags 
I think we want name tags to be `name:` tags in the backend,
this keeps processing more uniform.
 2019-05-27 12:44:18 +02:00
Steffen Neumann f7fd73249b Update help text for Relabel List Identifiers 
This addresses https://github.com/galaxyproject/galaxy/issues/6156#issuecomment-494290527.
The rest of #6156 might require python-hacking. Yours, Steffen
 2019-05-27 11:52:19 +02:00
mvdbeek 62f5572a43 Add carriage return unit test 2019-05-27 11:35:20 +02:00
Nicola Soranzo c78416a9fc Merge branch 'release_19.05' into dev 2019-05-26 15:57:10 +01:00
Nicola Soranzo 1eea5def3f Merge branch 'release_19.01' into release_19.05 2019-05-26 15:55:20 +01:00
Nicola Soranzo d9b0f54906 Try to verify tool test output first as Unicode 2019-05-26 15:07:36 +01:00
Martin Cech 55c0861a13 Merge pull request #8034 from WilliamHolden/update_entry_folder_es6 
es6 upgrades in entry folder
 2019-05-24 16:16:19 -04:00
Martin Cech a8d1a4f965 Merge pull request #8023 from mvdbeek/fix_column_assign_bug 
Fix column assign bug
 2019-05-24 16:14:27 -04:00
Martin Cech 73ac1114a4 Merge pull request #8028 from WilliamHolden/update_to_let_and_const_vue_components 
switch var to let and const for vue components
 2019-05-24 16:12:44 -04:00