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18642 Commits
Author SHA1 Message Date
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
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
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
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
mvdbeek fc28e0bd83 Use long-form options 2018-10-10 14:56:05 +02:00
mvdbeek 57a1f19b06 Fix slurm cli plugin by avoiding shell=True in subprocess 
Fixes the remaining issue in https://github.com/galaxyproject/galaxy/issues/6831#issuecomment-428097520
 2018-10-10 10:12:18 +02:00
mvdbeek 02410b270d Register job monitor as postfork function 
This should fix https://github.com/galaxyproject/galaxy/issues/6831,
and might fix https://github.com/galaxyproject/galaxy/issues/6261.
 2018-10-08 21:33:20 +02:00
Nicola Soranzo c83c5cb784 Change conda channel priority: conda-forge > bioconda 
xref. https://github.com/bioconda/bioconda-utils/issues/330
 2018-10-08 11:02:23 +01:00
Nicola Soranzo b99fedefa8 Update to latest galaxy-lib 
Includes:
- change channel priority ( https://github.com/galaxyproject/galaxy-lib/pull/132 )
- channel cleanup ( https://github.com/galaxyproject/galaxy-lib/pull/136 )
 2018-10-08 10:08:02 +01:00
John Chilton 98a9c86bad Allow testing tags in input collections. 2018-10-06 09:36:41 -04:00
John Chilton 1c4a4ed8cb Merge remote-tracking branch 'galaxyproject/release_18.05' into release_18.09 2018-10-04 11:43:05 -04:00
John Chilton 4a345b99c3 Fix security problems when extracting untrusted tar files. 
Fixes GX-2018-0006.
 2018-10-04 11:32:52 -04:00
Nate Coraor b7187f0e62 Don't delete referenced Datasets when purging users. 2018-10-01 13:25:13 -04:00
Dannon 1a3e9ae173 Merge pull request #6805 from mvdbeek/gunicorn_run_sh_support 
[18.09] Allow starting Galaxy under gunicorn when using galaxy.ini
 2018-10-01 12:12:59 -04:00
mvdbeek 176364ac80 Move gunicorn to dev-requirements 2018-10-01 18:07:37 +02:00
John Chilton e226edc5ad Merge pull request #6798 from mvdbeek/fix_element_identifier_for_non_multiple_true_mapover_in_conditionals 
[18.09] Fix element identifier for non multiple true mapover in conditionals
 2018-09-30 12:28:21 -04:00
Dannon a47887639d Merge pull request #6803 from mvdbeek/finish_py3_selenium 
[18.09] Fix remaining selenium py3 errors
 2018-09-30 08:28:41 -04:00
mvdbeek 702870c17c Allow starting Galaxy under gunicorn when using galaxy.ini 
and starting Galaxy with `APP_WEBSERVER=gunicorn sh run.sh`.
Additional gunicorn cmdline arguments can be passed using
`GUNICORN_CMD_ARGS`. In a first pass this will allow
running planemo {server, test} under python 3, as Paste
has some problems under python 3:

```
galaxy.web.stack INFO 2018-09-29 22:16:00,216 Galaxy server instance 'main' is running
Traceback (most recent call last):
  File "./scripts/paster.py", line 27, in <module>
    serve.run()
  File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/serve.py", line 1055, in run
    invoke(command, command_name, options, args[1:])
  File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/serve.py", line 1061, in invoke
    exit_code = runner.run(args)
  File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/serve.py", line 226, in run
    result = self.command()
  File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/serve.py", line 676, in command
    serve()
  File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/serve.py", line 653, in serve
    server(app)
  File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/loadwsgi.py", line 232, in server_wrapper
    **context.local_conf)
  File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/loadwsgi.py", line 90, in fix_call
    val = callable(*args, **kw)
  File "/home/travis/.planemo/gx_venv_3_release_18.09/lib/python3.6/site-packages/paste/httpserver.py", line 1353, in server_runner
    for name, value in kwargs.items():
RuntimeError: dictionary changed size during iteration
```

That said gunicorn is a nice pure-python alternative to paste going
forward.
 2018-09-30 13:18:21 +02:00
mvdbeek 2e7adfbee4 Cast to bytestring in md5 function 2018-09-29 15:28:12 +02:00
Dannon Baker f0131eff8b Merge remote-tracking branch 'upstream/release_18.05' into release_18.09 2018-09-29 08:21:52 -04:00
Dannon de794dd905 Merge pull request #6774 from mvdbeek/fix_old_wf_name 
[18.05] Update name of Workflow when updating StoredWorkflow name
 2018-09-29 07:57:54 -04:00
mvdbeek f8d9a9e33a Attempt to recover wrapper datasets 
Otherwise we create new wrappers that lack the element identifier.
 2018-09-29 11:39:07 +02:00
mvdbeek 73f8f3129b Partially fix missing element identifier 
This makes sure that any toplevel `|__identifier__` is passed on
to nested inputs.
 2018-09-29 11:39:07 +02:00
Dannon a29c1e47a7 Merge pull request #6799 from natefoo/better-object-store-logging 
[18.09] Provide a useful exception message for object store exceptions
 2018-09-28 15:40:10 -04:00
Nate Coraor 5bc3b2e16c Provide a useful exception message for object store exceptions. 2018-09-28 14:13:09 -04:00
Dannon Baker 1e7677c3b2 Merge remote-tracking branch 'upstream/release_18.05' into release_18.09 2018-09-28 12:49:17 -04:00
Dannon Baker 9bc37c03b6 Merge remote-tracking branch 'upstream/release_18.01' into release_18.05 2018-09-28 12:48:42 -04:00
Dannon Baker ac46d21ece Merge remote-tracking branch 'upstream/release_17.09' into release_18.01 2018-09-28 12:46:20 -04:00
Dannon Baker 40cecf6ff4 Merge remote-tracking branch 'upstream/release_17.05' into release_17.09 2018-09-28 12:43:36 -04:00
Dannon Baker c4150d2002 Merge remote-tracking branch 'upstream/release_17.01' into release_17.05 2018-09-28 12:38:23 -04:00
Dannon Baker fa7f2a4f5c Merge remote-tracking branch 'upstream/release_16.10' into release_17.01 2018-09-28 12:37:49 -04:00
Dannon Baker 809ae58c52 Merge remote-tracking branch 'upstream/release_16.07' into release_16.10 2018-09-28 12:37:20 -04:00
Dannon Baker 8a1616aaf8 Merge remote-tracking branch 'upstream/release_16.04' into release_16.07 2018-09-28 12:36:48 -04:00
Dannon Baker 482f1ea359 Merge remote-tracking branch 'upstream/release_16.01' into release_16.04 2018-09-28 12:35:30 -04:00
Dannon Baker 814c7f926d Drop unused peek method (this used unencoded ids) 2018-09-28 11:50:18 -04:00
Dannon 29a3b6bbfb Merge pull request #6793 from martenson/fix-sharing-by-link 
[18.09] allow making all datasets within history public, when sharing
 2018-09-28 08:33:03 -04:00
Dannon 5a98515df8 Merge pull request #6789 from mvdbeek/fix_bam_upload 
[18.09] Fix bam upload resulting in 'auto' datatype
 2018-09-28 07:46:22 -04:00
Martin Cech e439902152 show warning to user if some of the items within were not published 2018-09-27 16:50:12 -04:00
Martin Cech b0dff44440 allow making all datasets within history public, when sharing 
this is a one-off operation so notable behavior is that
if you create a new dataset in the shared history, it still
won't be public when there are default permissions set on history
 2018-09-27 16:01:57 -04:00
John Chilton c5a325d015 Merge pull request #6785 from mvdbeek/escape_all_rules 
[18.09] Strip all control characters from rules
 2018-09-27 15:01:45 -04:00
mvdbeek 57fe3a741a Fix metadata spontaneuosly reverting 
Similar to https://github.com/galaxyproject/galaxy/pull/6631/files.
This fixes https://github.com/galaxyproject/galaxy/issues/6769
 2018-09-27 20:31:33 +02:00
Martin Cech f54cba0433 Merge pull request #6782 from dannon/fix-bad-workflow-invocation-merge 
[18.09] Fix __encode_invocation signature
 2018-09-27 12:39:16 -04:00
John Chilton b44379c3d9 Merge pull request #6780 from mvdbeek/visible_extracted_datasets 
[18.09] All extracted datasets should be visible
 2018-09-27 11:54:04 -04:00
mvdbeek becb922dc1 Strip all control characters from rules 
Similar to 366701cfb2, which is valid on its own, but here we just apply it to all rules.
 2018-09-27 16:36:31 +02:00
Dannon Baker da3b6a1566 encode_invocation defers to manager and doesn't require trans passing anymore 2018-09-27 09:47:28 -04:00