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20667 Commits
Author SHA1 Message Date
John Chilton 8564eabb43 Merge branch 'release_19.05' into dev 2019-06-10 15:01:42 -04:00
John Chilton e00e41557a Merge pull request #8118 from jmchilton/dependency_resolver_config 
Allow declaring depedency resolvers right in Galaxy config, serialization.
 2019-06-10 14:53:25 -04:00
John Chilton 696f9f9f00 Merge pull request #8103 from nuwang/fix_k8s_runasuser 
[19.05] Fix k8s runasuser
 2019-06-10 10:02:56 -04:00
John Chilton f821d3f834 Merge pull request #8092 from nuwang/fix_k8s_namespace_19_05 
[19.05] Filter all pykube queries by namespace
 2019-06-10 10:01:30 -04:00
John ChiltonandMarius van den Beek 5651edcf24 Update lib/galaxy/webapps/galaxy/config_schema.yml 
Co-Authored-By: Marius van den Beek <m.vandenbeek@gmail.com>
 2019-06-10 09:19:40 -04:00
John ChiltonandMarius van den Beek d787a2827a Update lib/galaxy/util/plugin_config.py 
Co-Authored-By: Marius van den Beek <m.vandenbeek@gmail.com>
 2019-06-10 09:19:20 -04:00
Nicola Soranzo dafe9dd30b Merge branch 'release_19.05' into dev 2019-06-10 14:15:02 +01:00
Nicola Soranzo 6b899ce732 Merge branch 'release_19.01' into release_19.05 2019-06-10 14:09:26 +01:00
Dannon 0bbcb4fe40 Merge pull request #8047 from jmchilton/pages_api_and_component 
Toward a more modern frontend and backend for Pages.
 2019-06-10 09:08:48 -04:00
Nicola Soranzo fed80f19f6 Pin SQLAlchemy and update social_auth_core pin 
- SQLAlchemy 1.3 introduced changes that break some queries.

- Commit 5723e15cce did not update the pin
  on `social_auth_core` in the Pipfile.

- Remove spurious `; python_version == '2.7'` produced by pipenv for
  `paste`.

- Run `make update-dependencies`.
 2019-06-09 19:06:53 +01:00
vahid 35629c33db Revert social-auth-core version change. 2019-06-09 09:46:10 -07:00
vahid 96e15d25c5 Result of running make update-dependencies. 2019-06-08 13:57:46 -07:00
vahid b5b1d82c99 Change cloudauthz version to 0.3.0. 2019-06-08 11:37:31 -07:00
John Chilton 70730f673d Allow declaring depedency resolvers right in Galaxy config, serialization. 2019-06-07 15:17:21 -04:00
Nicola Soranzo 68ba4e4f32 Merge branch 'release_19.05' into dev 2019-06-07 16:01:46 +01:00
Martin Cech 23a6b925b9 Merge pull request #8112 from nsoranzo/release_19.05_galaxy-lib_sync 
[19.05] Report a lint error if a citation is empty
 2019-06-07 10:55:24 -04:00
John Chilton 2dad5011e1 Merge pull request #8116 from nuwang/fix_default_container_image 
[19.05] Fix error in recognizing destination default container image
 2019-06-07 08:30:06 -04:00
Nuwan Goonasekera 39d265b907 Fix error in recognizing destination default container image 2019-06-07 07:19:25 +05:30
Nicola Soranzo a69e03c9c7 Add missing files from galaxy-lib 2019-06-07 01:31:56 +01:00
Nicola Soranzo aa25ff5355 Report a lint error if a citation is empty 
xref. https://github.com/galaxyproject/planemo/issues/929
Sync with https://github.com/galaxyproject/galaxy-lib/pull/151
 2019-06-07 00:04:55 +01:00
Nate Coraor f1775a3582 Merge remote-tracking branch 'upstream/release_19.05' into dev 2019-06-06 16:24:26 -04:00
Nate Coraor 3837440aac Merge pull request #8065 from jmchilton/metadata_output_pulsar 
[19.05] Fix metadata output collection on Pulsar with new metadata strategy.
 2019-06-06 16:21:36 -04:00
John Chilton dc4785a59b Fixes(?) to galaxy.metadata. 2019-06-06 11:05:28 -04:00
Nicola Soranzo 9ec952c0a7 Do not use dict iter methods for Python3 compatibility 2019-06-06 15:58:15 +01:00
Nuwan Goonasekera aa463ce070 Default to none if run_as_user or group are not specified 2019-06-06 17:11:04 +05:30
Nuwan Goonasekera 91b6774f18 Added support for runAsUser and runAsGroup to k8srunner 2019-06-05 23:38:09 +05:30
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
Nuwan Goonasekera f577541357 Filter all pykube queries by namespace 2019-06-04 22:30:10 +05:30
Aysam Guerler 3de955731d Merge pull request #7825 from martenson/tool-install-interface 
Beta tool install interface improvements
 2019-06-04 07:53:17 -04:00
John Chilton 5a8514701c Fix job metrics collection from them returning into metadata/ 
Ideally all job metrics should be placed here to mimic Pulsar but this is a bug fix to an almost stable branch.
 2019-06-03 13:36:11 -04:00
John Chilton cbb578e6fa Spelling fix. 2019-06-03 13:36:11 -04:00
John Chilton c6e5a86e80 Fix finding datatype's registry for metadata collection on Pulsar. 2019-06-03 13:35:59 -04:00
John Chilton 5f4bebd2ce Fix portable remote metadata output files... 
... three features not working together super well.
 2019-06-03 13:35:58 -04:00
John Chilton a80a49b491 Fix metadata output collection on Pulsar. 2019-06-03 13:35:58 -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 2a0f04e82e Merge pull request #8076 from martenson/allow-quoted-query 
allow for filter values in repository search to be quoted
 2019-06-03 10:05:48 -04:00
John Chilton f4ea424015 Merge pull request #8077 from mvdbeek/include_shell_for_tool_script_sh 
Call tool_script.sh with shell
 2019-06-03 09:59:40 -04:00
Nuwan Goonasekera 4a7708b7e0 Fix wording for pod retries while maintaining backward compatibility 2019-06-03 14:36:44 +05:30
mvdbeek bf31260192 Call tool_script.sh with shell 2019-06-01 13:24:51 +02:00
Martin Cech 2dc6998eaa allow for filter values in repository search to be quoted 
i.e. they can contain space(s)
 2019-05-31 15:58:25 -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
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
Martin Cech 91041c2ba4 minor refactoring 2019-05-30 14:27:59 -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
Martin Cech 2eb02c613c refactor filtering method and add doctest 2019-05-30 11:24:26 -04:00
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