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26080 Commits
Author SHA1 Message Date
Dannon 06b306b044 Merge pull request #11596 from mvdbeek/runtime_data_column_fix 
[21.01] Fix workflow runs with data_column runtime parameter changes
 2021-03-15 10:14:46 -04:00
Dannon 602e3e8328 Merge pull request #11602 from mvdbeek/fix_on_copy_bugs 
[21.01] Various fixes for copying workflow nodes
 2021-03-15 09:39:01 -04:00
Marius van den Beek f1a98b9846 Merge pull request #11621 from jmchilton/collection_mapping_issue 
[21.01] Fix collection mapping over filtered output problem.
 2021-03-15 13:21:08 +01:00
Marius van den Beek 7242774fda Merge pull request #11595 from mvdbeek/tighten_phylip_datatype 
[21.01] Avoid false positives in Phylip sniffer
 2021-03-15 13:04:02 +01:00
John Chilton 25a930a948 Fix failing test. 2021-03-14 21:40:13 -04:00
John Chilton 8f9bdd6eb5 Failing test case for output problem. 2021-03-14 19:58:31 -04:00
mvdbeek 991b86ce8a Add selenium test for editing and copying workflow nodes 2021-03-13 19:49:01 +01:00
Nicola Soranzo 283ec1772f Merge branch 'release_20.09' into release_21.01 2021-03-12 17:12:04 +00:00
Nicola Soranzo 0573e95128 Add server name, PID and thread name to each handler log message 
Also:
- Add server name to each uWSGI log message.
- Add the server name to each uWSGI log message (and moved thread name in
  the same "section" of the message).
- Update the process name to the configured server name.

Follow-up on https://github.com/galaxyproject/galaxy/pull/11598#issuecomment-796961045
 2021-03-12 11:55:09 +00:00
Nicola Soranzo 3506abcc80 Fix `metadata_bcf` framework test 
Somewhere between file/libmagic 5.36 and 5.39, the output of `file` on a
`.csi` file changed, breaking the ``metadata_bcf`` framework test with
the following error:

```
        if found_exceptions:
>           raise JobOutputsError(found_exceptions, job_stdio)
E           galaxy.tool_util.verify.interactor.JobOutputsError: Output output_of_input_metadata:  different than expected, difference (using contains):
E           ( /tmp/tmpu1a3dgjcbcf_index_metadata_test.txt v. /tmp/tmpkt78tzggbcf_index_metadata_test.txt )
E           Failed to find 'gzip compressed data, extra field' in history data. (lines_diff=0):

lib/galaxy/tool_util/verify/interactor.py:1222: JobOutputsError
```

So add a requirement for the latest `file` version and update the test
accordingly.
 2021-03-11 20:21:00 +00:00
Nicola Soranzo d2afd63146 Sniff relaxed and strict interleaved PHYLIP files 2021-03-11 17:40:08 +00:00
mvdbeek 5e4e04d8b3 Add workflow that tests runtime data column parameters 
This test only needs the previous 2 commits to pass.
 2021-03-11 16:57:31 +01:00
mvdbeek 8146fcb50d Only strip c from column definition if it precedes integers 2021-03-11 16:57:31 +01:00
mvdbeek ca0af28d52 Fix workflow runs with data_column runtime parameter changes 
The issue is that the fallback when no data is available uses the
default tool state but ignores values that are set at runtime.

Fixes https://github.com/galaxyproject/galaxy/issues/11593
 2021-03-11 16:56:13 +01:00
Marius van den Beek de7b74bd0b Name variable 2021-03-11 16:18:05 +01:00
Dannon Baker 68fa01e300 Add handler name and pid to item grab logging 2021-03-11 10:14:48 -05:00
Marius van den Beek f8e6755aa9 Verify exactly two integers in phylip header 2021-03-11 15:45:01 +01:00
Marius van den BeekandNicola Soranzo 11777d0e7e Use encode 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2021-03-11 14:25:26 +01:00
Nicola Soranzo 23ce02fc27 Replace assert 
Asserts can be ignored when running Python in optimized mode
 2021-03-11 12:52:00 +00:00
mvdbeek 10c99cc146 Work around str.isasci not available on python 3.6 2021-03-11 13:46:36 +01:00
mvdbeek 6252c11532 Avoid false positives in Phylip sniffer 
Following the definition at
http://scikit-bio.org/docs/0.2.3/generated/skbio.io.phylip.html.

Previously this would have been sniffed as Phylip:
```
1	2
1	2
```
Also had to update our test file since it is not valid Phylip (the
identifier is more than 10 characters, which is out of spec).
 2021-03-11 13:24:37 +01:00
John Chilton 482417460b Merge pull request #11532 from mvdbeek/add_step_label_when_extracting_workflows 
[21.01] Add input step data label when extracting workflow
 2021-03-10 12:12:00 -05:00
John Chilton 275acb4af1 Merge pull request #11589 from mvdbeek/backport_anvilfs_conditional_dependency 
[21.01] Backport anvilfs conditional dependency
 2021-03-10 11:36:50 -05:00
John Chilton 9be9dc797d Lint fix. 2021-03-10 17:20:35 +01:00
almahmoud 97d5d1578c Luke's AnVILFS conditional dependency 2021-03-10 17:20:35 +01:00
John Chilton b28b784406 Merge pull request #11585 from mvdbeek/backport_empty_column_fix 
[21.01] Backport Handle the case where column list is a comma-separated string
 2021-03-10 09:38:48 -05:00
Kaivan Kamali d423b29336 Added another test for when columns are a comma separated string 2021-03-10 10:26:41 +01:00
Marius van den Beek 61b7cdd504 Add regression test for allowing data column selection on empty files 
A test for https://github.com/galaxyproject/galaxy/pull/10981.
 2021-03-10 10:26:41 +01:00
Kaivan Kamali 6e74674775 Removed whitespace 2021-03-10 10:26:41 +01:00
Kaivan Kamali 3e6aee1b4e Using utility function per code review feedback. 2021-03-10 10:26:41 +01:00
Kaivan Kamali 42a103291e Handle the case where column list is a comma-separated string 2021-03-10 10:26:41 +01:00
Juleen Graham 347388326e Implement logout without extra api call 
utilise localStorage
 2021-03-10 10:23:18 +01:00
Juleen Graham 30eacaa8a4 log out of oidc on galaxy logout 2021-03-10 10:23:18 +01:00
John Chilton 6a8725a641 Bug fix - poor feedback for remote file listing exceptions. 2021-03-09 11:21:03 -05:00
mvdbeek 45460cfac8 Merge branch 'release_20.09' into release_21.01 2021-03-09 15:27:49 +01:00
Dannon 81ddf7e1b5 Merge pull request #11574 from mvdbeek/anndata_select2_fix 
[20.09] Don't display obs_names in select list
 2021-03-09 07:38:13 -05:00
mvdbeek 358a1e52a6 Don't display obs_names in select list 
This would result in thousands of select items, which breaks Select2
atm. Fixes https://github.com/galaxyproject/galaxy/issues/11406 while we
replace select2 hopefully soon.
 2021-03-09 11:37:46 +01:00
Marius van den Beek 54830aa1f7 Merge pull request #11540 from dannon/remote_user_logout 
[21.01] Remote user logout redirect fix
 2021-03-09 10:13:53 +01:00
Alexander OSTROVSKY 58e183ae15 add compressed paf datatype 2021-03-08 13:59:19 -08:00
Dave Bouvier 3c2f919ff0 Add display_in_upload for protobuf datatypes. 
These datatypes are used as an input for a tool, UShER, which is
currently being wrapped.
 2021-03-05 13:10:41 -05:00
Björn Grüning 56af70cdc1 Merge pull request #11543 from jmchilton/dbkey_tests 
[21.01] Bug fix - cannot set dbkeys in workflow tests.
 2021-03-05 09:31:28 +01:00
John Chilton d128734d65 Bug fix - cannot set dbkeys in workflow tests. 2021-03-04 21:07:25 -05:00
Nicola Soranzo 454e755f06 Check for "format" attribute only once in output linter 
Also "ext" attribute takes precedence over "format".
 2021-03-04 20:40:59 +00:00
Matthias Bernt 6d229fcd6f Extend xsd doc for format attribute 2021-03-04 18:37:17 +01:00
Matthias Bernt 566f216945 allow format attribute in output collections 
this works already but xsd does not allow for it
and the linter complains
 2021-03-04 18:37:17 +01:00
Dannon Baker f46d965c01 This logout response is intended to be json 2021-03-04 10:52:49 -05:00
Dannon Baker ef4df2fe9d Correctly include redirect_uri in logout request 2021-03-04 10:52:49 -05:00
Björn Grüning 87978aad43 Merge pull request #11218 from guerler/add_ffindex_datatype 
[21.01] Add ffindex and ffdata database file types
 2021-03-04 10:03:14 +01:00
Dannon e5e4f727c8 Merge pull request #11535 from davelopez/fix_#11451 
[21.01] Fix unhandled error when creating tags with multiple dots
 2021-03-03 20:39:47 -05:00
Dannon Baker 77f1c8c906 Merge remote-tracking branch 'upstream/release_20.09' into release_21.01 2021-03-03 18:21:43 -05:00