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29906 Commits
Author SHA1 Message Date
Cristóbal GallardoandMarius van den Beek 60db87fa51 Update lib/galaxy/datatypes/converters/uncompressed_to_gz.xml 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2022-01-25 12:09:31 +01:00
Cristóbal Gallardo adc9723c2d Add tabix dependency 2022-01-24 14:42:25 +01:00
Cristóbal Gallardo feb42f086f Add converter to format 2022-01-24 14:38:58 +01:00
Cristóbal Gallardo 6431d16407 Modify datatypes_conf.xml file 2022-01-21 20:33:25 +01:00
Cristóbal Gallardo 72cd90374b Modify XML file 2022-01-21 19:26:13 +01:00
Cristóbal Gallardo 1bd4f2cac8 Include compressor 2022-01-21 19:22:19 +01:00
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 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
mvdbeek 15d4d2952d Fix ToolApp 2022-01-20 08:39:20 +01:00
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 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
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
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 6c354e2203 Merge pull request #13182 from kxk302/release_21.09 
[21.09] Backport of iRODS Object Store path name fix in #13080
 2022-01-18 18:57:46 +01:00
John Chilton d3b272fd10 Merge pull request #13170 from mvdbeek/max_discovered_files 
Limit maximum number of discovered files per job
 2022-01-18 12:45:01 -05:00
Kaivan Kamali 2b70e34a61 Revised code based on code review 2022-01-18 10:14:35 -05:00
David López 8f72ec5efb Merge pull request #12099 from knutwa-ext/iml_dataset_branch 
Add datatype iml_dataset subclassing html
 2022-01-18 16:08:35 +01:00
mvdbeek faddbeeca9 Use job.get_user_email systematically 2022-01-18 14:21:09 +01:00
Ruben Vorderman 9e546f7d97 Catch exceptions when job.user is None 
prevents the following error:

galaxy.web.framework.decorators ERROR 2022-01-17 14:52:09,619 [p:18,w:1,m:0] [uWSGIWorker1Core1] Uncaught exception in exposed API method:
Traceback (most recent call last):
  File "lib/galaxy/web/framework/decorators.py", line 282, in decorator
    rval = func(self, trans, *args, **kwargs)
  File "lib/galaxy/webapps/galaxy/api/jobs.py", line 113, in index
    j['user_email'] = job.user.email
AttributeError: 'NoneType' object has no attribute 'email'
 2022-01-18 14:21:08 +01:00
mvdbeek 26a98ae8f4 Implement max_discovered_files 2022-01-18 11:49:00 +01:00
David López 2817fdb5b3 Simplify html extension check 
Simplified the check a bit here since `endswith` will cover the previous check and also I've removed the preceding `.` to make sure the old check is still covered.
 2022-01-18 11:39:34 +01:00
mvdbeek 9dcea35ae5 Show yaml files in preview 
The `application/yaml` mediatype might be the logical mediatype for yaml
(there's no standard yet), but we want to see a textual preview (in the
absence of a viewer).
Fixes https://github.com/galaxyproject/galaxy/issues/13168
 2022-01-17 19:10:49 +01:00
mvdbeek 7c4568fe90 Set collection update_time when replacing failed elements 
That allows the new history to update the collection.
 2022-01-17 18:59:40 +01:00
mvdbeek 8a16c56cac Fix re-run with rerun_remap_job_id hiding collection 
Fixes https://github.com/galaxyproject/galaxy/issues/13052
 2022-01-17 18:59:39 +01:00
Matthias BerntandMarius van den Beek 304e1cdc38 catch exceptions in build_sniff_from_prefix 
if sniff_prefix raises ant exception the sniffer
should return False

Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2022-01-17 14:24:02 +01:00
Björn Grüning 48e725717a Merge pull request #13176 from mvdbeek/fix_yaml_downloaded_in_preview 
[21.09] Show yaml files in preview
 2022-01-17 12:27:08 +01:00
Matthias Bernt c37dcd1e98 add TODO for later 2022-01-17 11:07:48 +01:00
Matthias Bernt 16070ccbb5 full test coverage for tests linter 2022-01-17 11:07:48 +01:00
Matthias Bernt 706048c62f full test coverage for outputs linter 
- fix warning for invalid cheetah placeholder
 2022-01-17 11:07:48 +01:00