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Author SHA1 Message Date
Martin Cech b0dc3feded Merge branch 'release_19.01' into release_19.05 2019-06-05 15:06:43 -04:00
Martin Cech cb53c7390e Merge pull request #8085 from dannon/fix-multipanel-history-search 
[19.01] Fix multipanel history search.
 2019-06-05 15:04:58 -04:00
Nicola Soranzo 7aa5d562e1 Merge branch 'release_19.01' into release_19.05 2019-06-05 15:16:13 +01:00
Marius van den Beek 2a19b2151f Merge pull request #8097 from bgruening/fix_macro_backport_19.01 
[19.01] Fix nested macro/token expansion
 2019-06-05 15:48:00 +02:00
Nicola Soranzo fc2bff63b3 Remove recursion from `expand_nested_tokens()` 
Also add test for recursive nested token.
 2019-06-05 13:54:18 +02:00
mvdbeek 574d9ad1f5 Fix nested macro/token expansion on python 3 
I noticed that in multiqc @ESCAPE_IDENTIFIER@ wasn't being replaced.
It's surprising that this didn't cause any issues on python 2,
but might have to do with the iteration order changes.
 2019-06-05 13:44:46 +02:00
Dannon Baker 8edffb118a const, formatting 2019-06-04 11:47:21 -04:00
Dannon Baker b732950c70 Actually search in onfirstsearch of history search in multipanel 2019-06-04 11:46:24 -04:00
Dannon Baker edcce00aab Fix multipanel history search. 2019-06-04 11:46:24 -04:00
Nicola Soranzo 4a87bb42e6 Merge branch 'release_19.01' into release_19.05 2019-06-03 18:13:05 +01:00
Nicola Soranzo fd02b745c3 Merge branch 'release_18.09' into release_19.01 2019-06-03 18:06:45 +01:00
John Chilton 115157cdf9 Merge pull request #8071 from dannon/axios-sec-upgrade 
[19.05] Upgrade axios to handle CVE-2019-10742
 2019-06-03 10:00:38 -04:00
Björn Grüning 2f21e73ff4 [18.09] Backport 8023: Fix ColumnSetAction post job action (#8069) 
[18.09] Backport 8023: Fix ColumnSetAction post job action
 2019-06-01 10:50:02 +02:00
Dannon Baker b346565402 Upgrade axios to handle https://snyk.io/vuln/SNYK-JS-AXIOS-174505 2019-05-31 07:55:21 -04:00
mvdbeek 44256971eb Fix ColumnSetAction post job action 
If columns are specified as integers this would fail currently.
Reported by Peter Briggs on the [mailing list](https://lists.galaxyproject.org/archives/list/galaxy-dev@lists.galaxyproject.org/thread/PXLCVKIZ5LW3MLI6333PFMANYGOCDLD2/)
 2019-05-31 10:44:45 +02:00
Nate Coraor bff203f48c Merge remote-tracking branch 'upstream/release_19.01' into release_19.05 2019-05-30 15:03:00 -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
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 dfb591caf6 Document the handler max_grab config param 2019-05-30 09:18:42 -04:00
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
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 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 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 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 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 62f5572a43 Add carriage return unit test 2019-05-27 11:35:20 +02:00
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
John Chilton 374526357f Merge pull request #8032 from mvdbeek/backport_param_as_output_fix 
[19.01] Backport #7799 Skip recording workflow outputs for input parameters
 2019-05-24 09:29:41 -04:00
Dannon 877b115aad Merge pull request #8029 from guerler/disable_register_button 
[19.05] Disable create user button while request is being processed
 2019-05-24 09:15:57 -04:00
mvdbeek e988fdee87 Skip recording workflow outputs for input parameters 
These can come in as a literal parameter value, or as a dictionary like
{'id': 'encoded_id', 'src': 'hda'}, none of which is quite right.
 2019-05-24 10:45:18 +02:00
guerler 0949c3896e Disable create user button while request is being processed 2019-05-23 19:27:54 -04:00
Nate Coraor 12f394c1be Merge pull request #8021 from mvdbeek/fix_databaseless_tools 
[19.05] Fix repo cache when no install database is present
 2019-05-23 10:34:12 -04:00
mvdbeek 6ea862ff79 Use sqlalchemy.inspect to find detached repositories 
Thanks for the suggestion Nicola!
 2019-05-23 14:05:30 +02:00
mvdbeek a398127ede Work with bytestrings in files_contains, files_re_match_* 
But read utf-8 unicode in `lines_diff`. This will replace non-utf8
characters and seems like a reasonable tradeoff for text files
mixed with byte contents, like pdfs.
 2019-05-23 13:43:59 +02:00
mvdbeek f204b33bf3 Fix repo cache when no install database is present 
Fixes https://github.com/galaxyproject/galaxy/issues/8015
 2019-05-23 11:55:19 +02:00
mvdbeek 2d71b0bdfe Use io.open with errors="repalce" instead of comparing byte strings 2019-05-23 11:07:06 +02:00
mvdbeek 9f6bc89d69 Do non-shallow file comparison 2019-05-22 17:59:49 +02:00
mvdbeek 30bec0028d Use bytestring comparisons in verify module 2019-05-22 17:45:00 +02:00
mvdbeek ab7a38631e Unit test verify module 2019-05-22 17:45:00 +02:00
mvdbeek 8fea7e9048 Use byte comparison for contains 
I don't think there's any drawback open this
in byte mode.

Fixes https://github.com/galaxyproject/galaxy/issues/7957#issuecomment-493954901
 2019-05-21 11:09:13 +02:00