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Author SHA1 Message Date
Marius van den Beek c767adbed1 Merge pull request #11654 from brinkmanlab/revert_11448 
Refactor default mounting of $tmp_directory in containers
 2021-04-08 15:43:39 +02:00
mvdbeek e22f218bcf Merge branch 'release_20.09' into release_21.01 2021-04-07 14:31:58 +02:00
mvdbeek 84e1d54140 Merge branch 'release_20.05' into release_20.09 2021-04-07 14:30:48 +02:00
mvdbeek b71a4c5bd9 Merge branch 'release_20.01' into release_20.05 2021-04-07 14:30:03 +02:00
Dannon 7f519b4c8e Merge pull request #11794 from nsoranzo/release_21.01_fix_upstream_mod_zip_docs 
[21.01] Fix typo in `upstream_mod_zip` admin docs
 2021-04-06 22:12:45 -04:00
Nicola Soranzo 13d91da1f4 Fix typo in upstream_mod_zip admin docs 2021-04-06 20:04:19 +01:00
Estelle Ancelet d5cb3c3e2f Lower tool id case while populating resource params 2021-04-06 18:08:22 +02:00
John Chilton 5a2985db39 Merge pull request #11776 from dannon/scroll-library-list 
[21.01] Fix library scrolling
 2021-04-03 13:39:43 -04:00
Björn Grüning 635c6f805a Merge pull request #11758 from bgruening/meryldb_new 
[21.0] add new datatype class for meryldb
 2021-04-02 22:43:09 +02:00
Dannon Baker 19acbd5b34 Fix library scrolling 
For good this time, I hope.  As implemented, we always want that
container to take 100% height, handle its own padding,  and scroll
internal contents.
 2021-04-02 11:01:48 -04:00
Björn Grüning 2ae087b88c fix spelling in test 2021-04-01 21:02:51 +02:00
John Chilton 950856002f Merge pull request #11762 from mvdbeek/assorted_tool_shed_fixes 
[21.01] Assorted tool shed fixes
 2021-04-01 10:46:38 -04:00
John Chilton a6f3b255cb Merge pull request #11764 from mvdbeek/fix_format_input_implicit_conversion 
[21.01] Fix format="input" with implicit conversions
 2021-04-01 10:45:55 -04:00
Marius van den Beek b6c24cfce0 Merge pull request #11765 from almahmoud/webapp 
[21.01] galaxy.webapps.tool_shed to webapp.tool_shed
 2021-04-01 16:32:53 +02:00
Marius van den Beek 9711b31eba Merge pull request #11763 from abretaud/pulsar_flood 
[21.01] Pulsar: mark cancelled jobs as finished
 2021-04-01 15:30:45 +02:00
almahmoud 619f1e7a11 galaxy.webapps.tool_shed to webapp.tool_shed 2021-03-31 17:37:36 -04:00
mvdbeek 7eb853d703 Fix format="input" with implicit conversions 
where the implicit converter uses galaxy.json.

Add test, fix fix
 2021-03-31 22:06:39 +02:00
Anthony Bretaudeau 8d7736d0a5 catch cancelled state for pulsar jobs 2021-03-31 17:23:59 +02:00
Marius van den Beek 69d6e78a3d Merge pull request #11599 from abretaud/pulsar_tool_dir 
[21.01] Fix bug with Pulsar and $__tool_directory__
 2021-03-31 15:37:23 +02:00
mvdbeek f0e299cb9b Fix tool shed search returning matched terms as bytestrings 2021-03-31 14:02:41 +02:00
mvdbeek ea747f1983 Don't serialize ratings, reviews and reviewers 
These would need need custom to_dict functions, else they fail with
```
TypeError: Object of type RepositoryRatingAssociation is not JSON serializable
  File "galaxy/web/framework/decorators.py", line 171, in decorator
    rval = format_return_as_json(rval, jsonp_callback, pretty=trans.debug)
  File "galaxy/web/framework/decorators.py", line 329, in format_return_as_json
    json = safe_dumps(rval, **dumps_kwargs)
  File "galaxy/util/json.py", line 67, in safe_dumps
    dumped = json.dumps(*args, allow_nan=False, **kwargs)
  File "json/__init__.py", line 234, in dumps
    return cls(
  File "json/encoder.py", line 199, in encode
    chunks = self.iterencode(o, _one_shot=True)
  File "json/encoder.py", line 257, in iterencode
    return _iterencode(o, 0)
  File "json/encoder.py", line 179, in default
    raise TypeError(f'Object of type {o.__class__.__name__} '
```
I think this has never worked since its addition in
https://github.com/galaxyproject/galaxy/pull/8661.
 2021-03-31 14:02:39 +02:00
mvdbeek 1a12c3df9e Revert "Fix usage of email_alerts column" 
This reverts commit c9dc398bf0.

The default argument has no effect in our custom JSONType
implementation. This only worked with the sqlalchemy-mutable,
which we've removed again in the meantime.
 2021-03-31 14:02:37 +02:00
Anthony Bretaudeau b5e2ea9877 try something else 2021-03-31 13:42:17 +02:00
Anthony Bretaudeau b9c6fc6b23 debug unending ci 2021-03-31 12:09:15 +02:00
Bjoern Gruening 2828c7140b add example meryldb 2021-03-30 23:51:31 +02:00
Bjoern Gruening 6e5d6c09e1 add meryldb 2021-03-30 23:47:27 +02:00
Bjoern Gruening 1518abd615 add merydb datatype class 2021-03-30 23:43:33 +02:00
Dannon 56db84fa4c Merge pull request #11753 from mvdbeek/create_ts_database_if_no_install_database 
[21.01] Create install database with create_db.sh
 2021-03-30 09:41:30 -04:00
mvdbeek ca6f2fa68e Create install database with create_db.sh 2021-03-30 13:44:36 +02:00
John Chilton 1f8aac784a Merge pull request #11741 from jmchilton/fix_mo_tools 
[21.01] Fix a bug when unzipping collections with nametags.
 2021-03-27 16:41:18 -04:00
John Chilton f360f6498f Fix copy tags bug - broken in #10761 I think. 2021-03-26 16:48:15 -04:00
John Chilton d983fc72e8 Exhibit bug when unzipping collections with nametags. 2021-03-26 15:43:12 -04:00
Anthony Bretaudeau 4adeca0e86 Merge remote-tracking branch 'upstream/release_21.01' into pulsar_tool_dir 2021-03-25 16:53:34 +01:00
Marius van den Beek 91aeaa3f8a Merge pull request #11728 from abretaud/refgenie_table_del 
[21.01] Refgenie table del
 2021-03-25 16:36:47 +01:00
Anthony Bretaudeau b5ad804b64 lint 2021-03-25 14:08:14 +01:00
Anthony Bretaudeau 340caa1174 add more tests 2021-03-25 14:01:17 +01:00
Anthony Bretaudeau 7e136c83b3 fix 2021-03-25 14:01:12 +01:00
Marius van den Beek c4ca1a612a Merge pull request #11724 from assuntad23/hotfix/remove-extensions-console-error 
[21.01] Removedreference to remove-extensions
 2021-03-24 20:34:44 +01:00
Björn Grüning b0b3d4bf0a Merge pull request #11718 from mvdbeek/library_elements 
[21.01] Fix importing collections to new history and import correct elements
 2021-03-24 18:30:25 +01:00
Assunta DeSanto 1f7170ff66 removed reference to remove-extensions 2021-03-24 12:21:25 -04:00
Marius van den BeekandOleg Zharkov 5292bedabd Switch to newly created history 
Co-authored-by: Oleg Zharkov <jos.to.new@gmail.com>
 2021-03-24 14:54:24 +01:00
mvdbeek ba6dbe9513 Fix importing collection from library into new history 2021-03-24 11:51:45 +01:00
mvdbeek cf647412fb Make sure elements are ldda when importing from library 2021-03-24 11:51:45 +01:00
Anthony Bretaudeau cbf3a62ef8 Don't block data table deletion when using refgenie 2021-03-24 11:42:35 +01:00
Anthony Bretaudeau 703406efe6 empty lines 2021-03-24 10:52:43 +01:00
Anthony Bretaudeau ffcbb4ee98 simpler solution 2021-03-24 10:51:15 +01:00
mvdbeek 1ffd226625 Merge branch 'release_20.09' into release_21.01 2021-03-23 17:24:10 +01:00
Anthony Bretaudeau 73208d1fb8 possible fix for failing test 2021-03-23 17:05:23 +01:00
John Chilton 4bc8b9a868 Merge pull request #11708 from mvdbeek/make_all_extra_user_preferences_behave_like_defaultdict 
[20.09] Make extra user preferences behave like defaultdict
 2021-03-23 09:05:05 -04:00
mvdbeek 27b7d57080 Make extra user preferences behave like defaultdict 
This was the intention in
https://github.com/galaxyproject/galaxy/pull/10747 and is an alternative
to https://github.com/galaxyproject/galaxy/pull/11707

To test this, enable the file sources, and make sure you add a plugin
you haven't configured in your user preferences.
 2021-03-23 12:04:49 +01:00