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Author SHA1 Message Date
Marius van den Beek 06d879ee1f Merge pull request #13218 from ic4f/dev_safeguard_vault 
Prevent a future regression
 2022-01-21 13:09:42 +01:00
Marius van den Beek 233237b1ad Merge pull request #13215 from dannon/admin-jobs-all-running 
Support "show all running" in admin job interface
 2022-01-21 13:08:19 +01:00
Sergey Golitsynskiy 262c30a4d5 Wrap drop_table in db revision 180 in try/except 2022-01-20 23:11:17 -05:00
Dannon Baker 953ca8cdf1 Fix a bug with info box appearing unnecessarily 2022-01-20 14:45:06 -05:00
Dannon Baker 47a755f525 Trigger update when toggling switch 2022-01-20 13:55:37 -05:00
Dannon Baker bd40980c3b Add a showAllRunning option for the admin jobs view 2022-01-20 13:49:00 -05:00
John Chilton 9f8223d845 Merge pull request #10304 from bernt-matthias/topic/test-sort-order-multiple 
Reimplement collection order test, add wrong order, add `expect_test_failure` attribute
 2022-01-20 12:31:01 -05:00
Dannon d34e43d3ce Merge pull request #12571 from natefoo/fix-nested-object-store-example 
Update and correct sample object store config file
 2022-01-20 09:31:15 -05:00
Dannon 410b4e125f Merge pull request #13206 from galaxyproject/dependabot/npm_and_yarn/client/engine.io-4.1.2 
Bump engine.io from 4.1.1 to 4.1.2 in /client
 2022-01-20 09:24:14 -05:00
Dannon 529ca10e09 Merge pull request #13209 from cat-bro/admin-user-list-sort-by-last-login_rebased 
make admin user list sortable by last login
 2022-01-20 09:23:15 -05:00
cat-bro 7bfeddf57d sort admin user list by last login 2022-01-20 21:21:16 +11:00
Nicola Soranzo 7c34b058d8 Merge pull request #13208 from nsoranzo/fix_test_tool_deserialization 2022-01-20 09:42:05 +00:00
Marius van den Beek 594a999652 Merge pull request #13189 from guerler/parameter_collection 
Allow mapping of collection outputs to parameter inputs
 2022-01-20 09:56:10 +01:00
mvdbeek 15d4d2952d Fix ToolApp 2022-01-20 08:39:20 +01:00
guerler 1725ad9c27 Separate qunit test cases for data and parameter input terminals 2022-01-19 22:16:04 -05:00
Dannon 87b743eb76 Merge pull request #13207 from galaxyproject/dependabot/npm_and_yarn/client/follow-redirects-1.14.7 
Bump follow-redirects from 1.14.4 to 1.14.7 in /client
 2022-01-19 19:43:55 -05:00
Nicola Soranzo 53f14908ef Fix test_deserialize_* unit tests 
Fix:

```
    def test_deserialize_xml_tool(tool_app):

>       tool = _deserialize(tool_app, tool_source_class='XmlToolSource', raw_tool_source=XML_TOOL)

test/unit/app/tools/test_tool_deserialization.py:59:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
test/unit/app/tools/test_tool_deserialization.py:54: in _deserialize
    return create_tool_from_source(app, tool_source=tool_source)
lib/galaxy/tools/__init__.py:278: in create_tool_from_source
    tool = ToolClass(config_file, tool_source, app, **kwds)
lib/galaxy/tools/__init__.py:606: in __init__
    raise e
lib/galaxy/tools/__init__.py:603: in __init__
    self.parse(tool_source, guid=guid, dynamic=dynamic)

        if has_missing_data:
            biotools_reference = self.biotools_reference
>           metadata_source = self.app.biotools_metadata_source
E           AttributeError: 'ToolApp' object has no attribute 'biotools_metadata_source'

lib/galaxy/tools/__init__.py:1032: AttributeError
```

introduced merging forward https://github.com/galaxyproject/galaxy/pull/13202 .
 2022-01-19 23:37:27 +00:00
dependabot[bot] 128dd4af0f Bump follow-redirects from 1.14.4 to 1.14.7 in /client 
Bumps [follow-redirects](https://github.com/follow-redirects/follow-redirects) from 1.14.4 to 1.14.7.
- [Release notes](https://github.com/follow-redirects/follow-redirects/releases)
- [Commits](https://github.com/follow-redirects/follow-redirects/compare/v1.14.4...v1.14.7)

---
updated-dependencies:
- dependency-name: follow-redirects
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
 2022-01-19 23:01:06 +00:00
dependabot[bot] 7a4d6f0ad4 Bump engine.io from 4.1.1 to 4.1.2 in /client 
Bumps [engine.io](https://github.com/socketio/engine.io) from 4.1.1 to 4.1.2.
- [Release notes](https://github.com/socketio/engine.io/releases)
- [Changelog](https://github.com/socketio/engine.io/blob/4.1.2/CHANGELOG.md)
- [Commits](https://github.com/socketio/engine.io/compare/4.1.1...4.1.2)

---
updated-dependencies:
- dependency-name: engine.io
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
 2022-01-19 23:01:04 +00:00
Nicola Soranzo a8f1a900a1 Merge pull request #13147 from mvdbeek/mako_fix 2022-01-19 23:00:15 +00:00
Nicola Soranzo c6058f126b Merge branch 'release_21.09' into dev 2022-01-19 19:22:05 +00:00
Nicola Soranzo 25ba40ee9c Merge pull request #13203 from simonbray/patch-2 2022-01-19 19:20:53 +00:00
Nicola Soranzo 5390a07224 Merge branch 'release_21.09' into dev 2022-01-19 19:05:56 +00:00
Nicola Soranzo 178d97222d Merge pull request #13202 from mvdbeek/fix_metadata_source_access 2022-01-19 18:40:47 +00:00
Nicola Soranzo da47f8e844 Simplify PACKAGE_DATA 2022-01-19 18:35:06 +00:00
Nicola Soranzo 60976ec69b Use importlib.resources.files() for ToolShed config_schema.yml 2022-01-19 18:20:21 +00:00
Nicola Soranzo bcc505cbbd Drop remaining uses of template_path config 2022-01-19 18:20:20 +00:00
Nicola Soranzo 6bb9d87d7e Use super() 2022-01-19 18:20:20 +00:00
mvdbeek 4484f0d2f3 Adjust release-diff.py 
For the 22.01 release I will just create symlinks to the old locations.
 2022-01-19 18:20:19 +00:00
Marius van den BeekandNicola Soranzo f6915cf9cf Replace only use of app_template_path 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-01-19 18:20:19 +00:00
Marius van den BeekandNicola Soranzo 6fb840f361 Update manifest for new schema location 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-01-19 18:20:18 +00:00
mvdbeek 817272085e Move uwsgi_schema.yml as well 2022-01-19 18:20:18 +00:00
mvdbeek f1e62b1e0d Fix template resolition for tool shed 2022-01-19 18:20:17 +00:00
mvdbeek 03e218df68 Fix config schema packaging 2022-01-19 18:20:16 +00:00
mvdbeek d3cfb72266 Use importlib_resources 2022-01-19 18:20:16 +00:00
mvdbeek 19e9e55ca3 Fix uvloop message 2022-01-19 18:20:15 +00:00
mvdbeek 01a5cbba37 Fix resolving mako paths for installed Galaxy 2022-01-19 18:20:15 +00:00
mvdbeek f403fd8fcd Fix resolving path to config_schema.yml for installed Galaxy 2022-01-19 18:20:14 +00:00
Simon Bray ee62798b0c fix error getting toolshed repo metadata when no repo found 2022-01-19 17:54:31 +01:00
Nicola Soranzo 7226e2b7bd Merge pull request #12685 from bernt-matthias/topic/illumina-sniffer 2022-01-19 16:42:38 +00:00
mvdbeek 98b7b120b5 Fix metadata source access in tool shed 
Fixes:
```
Unexpected HTTP status code: 500: {"err_msg": "Metadata may have been defined for some items in revision '8f1b150a2487'.  Correct the following problems if necessary and reset metadata.<br/><b>abyss-pe.xml<\/b> - 'NoneType' object has no attribute 'get_biotools_metadata'<br/>"}
```
in https://github.com/galaxyproject/tools-iuc/runs/4792653893?check_suite_focus=true
 2022-01-19 17:32:47 +01:00
Marius van den Beek 68e509912f Merge pull request #13152 from bernt-matthias/topic/xml-replace-fix-test 
XML macros: add named yields, tokenized macros, tokens for attributes, and fix replacement of toplevel yield
 2022-01-19 15:32:22 +01:00
Matthias Bernt a216858e27 fix deprecation warning 
if macros copy is actually an `Element` then this gives a deprecation
warning:

xml_macros.py:41: FutureWarning: The behavior of this method will change in future versions. Use specific 'len(elem)' or 'elem is not None' test instead.
  if macros_copy:
 2022-01-19 15:08:25 +01:00
Matthias BerntNicola SoranzoMarius van den Beek
 		37a2edf00a catch sniffing exceptions in handle uploads 
Co-authored-by: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2022-01-19 14:14:54 +01:00
Matthias Bernt 8594b13036 Revert "catch exceptions in build_sniff_from_prefix" 
This reverts commit 304e1cdc38.
 2022-01-19 14:12:29 +01:00
Marius van den Beek 63ef9d524e Merge pull request #13185 from guerler/fix_tool_version 
Sync tool identifier string with tool version in workflow editor
 2022-01-19 12:33:29 +01:00
guerler 1764f134ed Remove currently unused options from qunit terminal creation helpers 2022-01-19 00:59:31 -05:00
guerler b6890ec09c Add test to validate correct mapping of parameter input terminals 2022-01-19 00:32:06 -05:00
guerler 98a7f820ee Call setMapOver routine in input parameter terminals to detect mapped collections 2022-01-19 00:08:45 -05:00
guerler 7a9513c8e4 Fix order of test assertions, remove unused properties 2022-01-18 19:28:30 -05:00