opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-10-25 18:31:53 +08:00
Code Issues Packages Projects Releases Wiki Activity
52,397 Commits 62 Branches 243 Tags
e06bb0dfaecd7da5edc467c193853e40dd5eedbe
Commit Graph
26604 Commits
Author SHA1 Message Date
Nicola Soranzo ccde3bc237 Merge pull request #11655 from rupertnash/cwltool-relax 
update to cope with impending changes to cwltool internals
 2021-03-18 14:27:19 +00:00
Rupert Nash 20e7018b90 update to cope with impending changes to cwltool internals 2021-03-17 19:57:32 +00:00
John Chilton 067d0b2592 Merge pull request #11650 from davelopez/library_folder_contents_api_tests 
Library folder_contents API tests + small fixes
 2021-03-17 13:36:40 -04:00
davelopez 1e253d22e6 Fix limit and offset pagination options in folder_contents API 
When using `limit` or `offset` options independently of one another, the pagination was returning all elements instead of applying the corresponding option.
 2021-03-17 15:04:45 +01:00
davelopez e36052d790 Add subfolders to folder_contents API test 2021-03-17 15:04:45 +01:00
davelopez 7ed6f37a91 Fix library folder datasets search_text condition 
If the search_text was matching the name of the dataset but the dataset had no description it was not included in the results.
 2021-03-17 15:04:45 +01:00
davelopez aa708b9f41 Add tests for folder_contents search 2021-03-17 15:04:45 +01:00
davelopez 26695e4e77 Add basic tests for folder_contents API 2021-03-17 15:04:45 +01:00
Nicola Soranzo ca3492b26c Update all Python dependencies 
using `make update-dependencies` .
 2021-03-17 12:42:01 +00:00
Marius van den Beek ff18e80022 Merge pull request #11560 from rikeshi/api_jobs_filtering 
Add more filtering options to api/jobs endpoint
 2021-03-17 11:14:19 +01:00
Sergey GolitsynskiyandNicola Soranzo 1791bc7693 Update lib/galaxy/dependencies/update.sh 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2021-03-16 22:26:38 -04:00
Sergey GolitsynskiyandNicola Soranzo e507a1f6c7 Update lib/galaxy/dependencies/update.sh 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2021-03-16 22:26:38 -04:00
Sergey GolitsynskiyandNicola Soranzo bab73a6cfd Update lib/galaxy/dependencies/update.sh 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2021-03-16 22:26:38 -04:00
Sergey GolitsynskiyandNicola Soranzo 6580a82a25 Update lib/galaxy/dependencies/update.sh 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2021-03-16 22:26:38 -04:00
Sergey Golitsynskiy b7ec222897 Install poetry into tmp venv; allow arg for update 2021-03-16 22:26:38 -04:00
mvdbeek 4e58fcfbde Merge branch 'release_21.01' into dev 2021-03-16 19:13:50 +01:00
John Chilton 0ac567d6f6 Merge pull request #11626 from mvdbeek/fix_optional_input_set_outputs 
[21.01] Fix optional workflow parameter inputs not recovered when setting step outputs
 2021-03-16 14:09:13 -04:00
mvdbeek 2d43996ef9 Remove pointless exception 2021-03-16 18:35:22 +01:00
mvdbeek e2a30a0408 Restructure invocation query to include implicit collection jobs 2021-03-16 17:59:07 +01:00
mvdbeek 8892802400 Use OR instead of union_all 2021-03-16 17:32:44 +01:00
Dannon Baker 3ae00d18e6 Merge remote-tracking branch 'upstream/release_21.01' into dev 2021-03-16 11:25:32 -04:00
mvdbeek f842787e29 Add workflow test for rescheduled steps referencing optional parameters 2021-03-16 16:21:34 +01:00
mvdbeek 1f2188e0fb Fix optional inputs not recevered when setting step outputs 
Not exactly certain about this fix, need to write some tests here.
 2021-03-16 13:28:37 +01:00
Dannon 695e723aa2 Merge pull request #11614 from OlegZharkov/lib-route-refactor 
Front-end Library Routing refactor
 2021-03-15 21:29:44 -04:00
Oleg Zharkov 20d0701015 go back to history code, 
apply wildcard in buildapp.py
 2021-03-15 22:23:46 +02:00
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
mvdbeek d03c7af02a Merge branch 'release_21.01' into dev 2021-03-15 14:53:07 +01:00
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
Oleg Zharkov ed98995b8e python linting 2021-03-15 14:46:06 +02:00
Oleg Zharkov 38bdf7e56b refactor libraries routes 2021-03-15 14:26:12 +02:00
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
John Chilton b13eaed493 Merge pull request #11485 from OlegZharkov/libraries-rewrite 
Libraries rewrite
 2021-03-13 08:02:00 -05:00
Nicola Soranzo 700f91ad07 Remove unused `TraceLogger` class 
It has been unused since it was introduced in 2012.
 2021-03-13 01:03:13 +00:00
Aysam Guerler 743fd76e91 Merge pull request #11600 from davelopez/pages_api_allow_extra_fields 
Allow any extra field in Pages API
 2021-03-12 17:49:11 -05:00
Nicola Soranzo 6c540932c7 Merge branch 'release_21.01' into dev 2021-03-12 19:01:35 +00:00
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
rikeshi cb97603dc4 apply query fix suggested by simonbray 2021-03-12 11:47:08 +01:00
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
John Chilton 9755358808 Merge pull request #11568 from davelopez/fastapi_metrics_api 
Migrate metrics API to FastAPI
 2021-03-11 12:27:38 -05:00
davelopez 9661fd48ef Allow any extra field in CreatePagePayload and PageDetails 2021-03-11 17:36:56 +01:00
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