opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-11-02 19:52:14 +08:00
Code Issues Packages Projects Releases Wiki Activity
36,721 Commits 64 Branches 246 Tags
v18.09
Commit Graph
36721 Commits
This Branch
This Branch
All Branches
Author SHA1 Message Date
Nicola Soranzo d0a93ff628 Merge pull request #6934 from dannon/doc_update 
[18.09] Additional 18.09 doc update for toolshed bugfix.
v18.09 		2018-10-29 14:11:44 +00:00
Dannon Baker 1fd1848a81 Additional 18.09 bugfix 2018-10-29 09:49:02 -04:00
John Chilton e89f746a07 Merge pull request #6932 from mvdbeek/fix_toolshed_bugs 
[18.09] Fix toolshed error in display_tool if tool is invalid
 2018-10-29 09:26:30 -04:00
mvdbeek cf2645f9a6 Fix toolshed error in display_tool if tool is invalid 
Fixes the following exception:

```
AttributeError: 'NoneType' object has no attribute 'id'
  File "galaxy/web/framework/middleware/sentry.py", line 43, in __call__
    iterable = self.application(environ, start_response)
  File "/srv/toolshed/main/venv/local/lib/python2.7/site-packages/paste/translogger.py", line 69, in __call__
    return self.application(environ, replacement_start_response)
  File "/srv/toolshed/main/venv/local/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__
    return self.application(environ, start_response)
  File "routes/middleware.py", line 141, in __call__
    response = self.app(environ, start_response)
  File "/srv/toolshed/main/venv/local/lib/python2.7/site-packages/paste/httpexceptions.py", line 640, in __call__
    return self.application(environ, start_response)
  File "galaxy/web/framework/base.py", line 143, in __call__
    return self.handle_request(environ, start_response)
  File "galaxy/web/framework/base.py", line 222, in handle_request
    body = method(trans, **kwargs)
  File "galaxy/webapps/tool_shed/controllers/repository.py", line 888, in display_tool
    tool_state = tool_util.new_state(trans, tool, invalid=False)
  File "tool_shed/util/tool_util.py", line 211, in new_state
    log.debug('Failed to build tool state for tool "%s" using standard method, will try to fall back on custom method: %s', tool.id, e)
```

(from https://sentry.galaxyproject.org/sentry/toolshed/issues/279820/).

Might also fix some other issues when redering workflow svg for
workflows with invalid tools.
 2018-10-29 10:34:37 +01:00
Nicola Soranzo 1651238639 Merge pull request #6930 from dannon/index-update 
[18.09] Add 18.09_announce to releases index.
 2018-10-26 19:28:29 +01:00
Dannon Baker 79cff3ea6b Add 18.09_announce to releases index. 2018-10-26 14:23:08 -04:00
Dannon Baker 9b24afc592 Update version to 18.09 show 2018-10-25 14:57:25 -04:00
Martin Cech 43d9787295 Merge pull request #6923 from dannon/18.09_final_notes 
[18.09] Final release notes updates
 2018-10-25 12:36:12 -04:00
Nate Coraor 3263aba44a Add a warning to the 18.09 release notes informing admins that job 
handling will block until old `new` state jobs have been migrated to a
terminal state.
 2018-10-25 12:08:37 -04:00
Dannon Baker 17f4f7955f s/sources/artifacts 2018-10-25 11:58:53 -04:00
Dannon Baker b6e716b289 Correct javascript caps 2018-10-25 10:37:45 -04:00
Dannon Baker 5a71a744ed Add client artifact note 2018-10-25 10:36:38 -04:00
Dannon Baker 6a072ab29d Four more RN PRs. 2018-10-25 10:14:44 -04:00
Nicola Soranzo 843474e5e3 Merge pull request #6915 from mvdbeek/6904_followup 
[18.09] Small followup to #6904
 2018-10-24 10:37:37 +01:00
mvdbeek 91a9dbaf5c Revert unncessary double logging of exception 2018-10-24 09:50:56 +02:00
mvdbeek c862d55ec8 Use with statement when handling NamedTemporaryFile 2018-10-24 09:50:33 +02:00
John Chilton 328c410fdc Merge pull request #6904 from mvdbeek/fix_weird_xml 
[18.09] Fix pretty printing of shed_tool_conf.xml file
 2018-10-23 18:51:15 -04:00
John Chilton 3638378569 Merge pull request #6912 from natefoo/fix-drmaa-job-stop 
[18.09] Fix stopping DRMAA jobs
 2018-10-23 18:43:21 -04:00
Nate Coraor 3f172cc988 Fix job stopping from DRMAA jobs broken in 
a1c58a7088 and improve logging around it.
 2018-10-23 14:32:26 -04:00
Nicola Soranzo ecb56d80a1 Merge branch 'release_18.05' into release_18.09 2018-10-23 14:28:54 +01:00
mvdbeek 57a4e50d8c Fix capsule export in docker testing 
Found this by removing the blank try/except in the previous commit.
This only affects testing when python can't determine the correct
locale and falls back to ASCII.
 2018-10-23 15:23:54 +02:00
mvdbeek a465543260 Drop threading lock and global try/except 
The Lock wasn't actually preventing anything, and I don't think
anything would need ot be protected here. mkdtemp should be thread-safe.

We also remove the try/except Statement. I think it'd be better to
expose any exceptions here instead of producing broken capsules and
logging an exception.
 2018-10-23 15:19:09 +02:00
mvdbeek 8a39f27b3c Fix toolshed tests 2018-10-23 14:51:14 +02:00
John Chilton 1943587034 Merge pull request #6908 from nsoranzo/release_18.09_config_validate 
[18.09] Fix ``make config-validate``
 2018-10-23 08:51:02 -04:00
Nicola Soranzo 4dd2ecb13f Fix `make config-validate` 2018-10-23 12:28:47 +01:00
John Chilton 88b840d2c6 Merge pull request #6893 from martenson/backport-6884 
[18.09] check presence of attribute in addition to value
 2018-10-22 14:58:58 -04:00
mvdbeek 794d1e03be Fix messed up printing of shed_tool_conf.xml file 
This drops xml_to_string from lib/tool_shed/util/xml_util.py
and uses xml_to_string form lib/galaxy/utils/__init__.py.
Also reduces plain string manipulation of xml structures.
Uses xml.dom.minidom to make xml pretty if necessary.
 2018-10-22 20:37:30 +02:00
John Chilton 3411852fed Merge pull request #6885 from mvdbeek/create_in_new_file_path 
[18.05] Create composite file archives in new_file_path instead of TMP
 2018-10-21 15:51:37 -04:00
guerler 46e56417dd Use hasattr instead of relying on value 2018-10-17 15:08:47 -04:00
Dannon 0aca12ce96 Merge pull request #6892 from martenson/security-notes 
[18.09] add discovered tool vulnerabilities to RN
 2018-10-17 13:21:22 -04:00
Martin Cech fa212c3c31 specify which gemini tools were fixed 2018-10-17 11:45:25 -04:00
Martin Cech 9735146f28 add discovered tool vulnerabilities to RN 2018-10-17 10:53:09 -04:00
Nicola Soranzo 89fbe9c934 Merge pull request #6890 from dannon/18.09_release_notes_updates 
[18.09] One last batch of PRs added to RN
 2018-10-17 14:11:02 +01:00
Dannon Baker d19effdf3c One last batch of PRs. 2018-10-17 08:36:33 -04:00
mvdbeek 126ee5fe2b Create composite file archives in new_file_path instead of TMP 2018-10-17 11:06:55 +02:00
Martin Cech d4e2f6d59e Merge pull request #6875 from nsoranzo/release_18.09_fix_commit_changeset 
[18.09] Do not traceback when uploading a TS repo with no changes
 2018-10-15 16:30:18 -04:00
Nicola Soranzo b9a01761b0 Do not traceback when uploading a TS repo with no changes 
Fix the following traceback when executing `planemo shed_update`:

```
galaxy.web.framework.decorators ERROR 2018-10-15 18:07:38,736 [p:30249,w:1,m:0] [uWSGIWorker1Core1] Uncaught exception in exposed API method:
Traceback (most recent call last):
  File "lib/galaxy/web/framework/decorators.py", line 154, in decorator
    rval = func(self, trans, *args, **kwargs)
  File "lib/galaxy/webapps/tool_shed/api/repositories.py", line 1116, in create_changeset_revision
    new_repo_alert
  File "lib/tool_shed/util/repository_content_util.py", line 64, in upload_tar
    undesirable_files_removed)
  File "lib/tool_shed/util/commit_util.py", line 225, in handle_directory_changes
    message=commit_message)
  File "lib/tool_shed/util/hg_util.py", line 65, in commit_changeset
    raise Exception(error_message)
Exception: Error committing '/opt/galaxy/database/community_files/000/repo_1' to repository: Command '['hg', 'commit', '-u', u'earlhaminst', '-m', u'planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest commit 22231ebc4e5e990c61243a3609b3347cf63fa024', '/opt/galaxy/database/community_files/000/repo_1']' returned non-zero exit status 1
Output was:
nothing changed

127.0.0.1 - - [15/Oct/2018:18:07:38 +0100] "POST /api/repositories/adb5f5c93f827949/changeset_revision HTTP/1.1" 500 - "-" "python-requests/2.18.4"
```
 2018-10-15 20:35:04 +01:00
Martin Cech 03073ed124 Merge pull request #6867 from mvdbeek/fix_xlsx_unpacking 
[18.09] Keep xlsx files compressed
 2018-10-15 11:26:35 -04:00
mvdbeek 0c7cc50e73 Only warn about multi-file zips if we don't keep the compressed archive 2018-10-13 17:49:19 +02:00
mvdbeek 8edb7499c8 Keep xlsx files compressed 
Fixes https://github.com/galaxyproject/galaxy/issues/6849
 2018-10-13 17:37:41 +02:00
Marius van den Beek 01f1f1b95f Merge pull request #6858 from jmchilton/fix_metadata_revert 
[18.09] Revert selective metadata flushing - breaks multiple uploads/outputs.
 2018-10-12 15:44:01 +02:00
John Chilton f3da0864b4 Test case for regression #6856. 2018-10-12 09:03:12 -04:00
Marius van den Beek 4805304e0b Merge pull request #6863 from nsoranzo/release_18.09_fix_LocalShell_doctest 
[18.09] Fix ``LocalShell`` doctest
 2018-10-12 14:33:42 +02:00
Nicola Soranzo 19f716de91 Fix `LocalShell` doctest 
Broken in commit 57a1f19b06 .
 2018-10-12 11:48:17 +01:00
Nicola Soranzo d22f652f91 Merge branch 'release_18.05' into release_18.09 2018-10-12 09:44:18 +01:00
Nicola Soranzo a8fa5a1d4a Merge branch 'release_18.01' into release_18.05 2018-10-12 09:43:01 +01:00
Nicola Soranzo 2c14c2afc4 Merge pull request #6859 from martenson/paramiko-update 
[18.09] update paramiko dep
 2018-10-12 01:23:54 +01:00
Martin Cech 20f60a5a44 update paramiko dep 2018-10-11 16:15:00 -04:00
John Chilton d791a2c80f Revert selective metadata flushing - seems to break upload changes. 2018-10-11 16:01:45 -04:00
Nicola Soranzo 9251484e72 Merge pull request #6731 from galaxyproject/18.09_release_notes 
[18.09] 18.09 release notes
 2018-10-11 17:56:33 +01:00