Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: f1348c15c7792af86c507c8b2d8f9121532cfcf5
https://github.com/galaxyproject/galaxy/commit/f1348c15c7792af86c507c8b2d8f…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-11-15 (Wed, 15 Nov 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M client/galaxy/scripts/mvc/workflow/workflow-node.js
M static/maps/mvc/workflow/workflow-forms.js.map
M static/maps/mvc/workflow/workflow-node.js.map
M static/scripts/mvc/workflow/workflow-forms.js
M static/scripts/mvc/workflow/workflow-node.js
Log Message:
-----------
Fix workflow editor output attributes (var shadowing was silently making *everything* the first output attribute...)
Commit: ec7c060a905c66039065ebfc781a0daa617de757
https://github.com/galaxyproject/galaxy/commit/ec7c060a905c66039065ebfc781a…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-11-15 (Wed, 15 Nov 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M static/maps/mvc/workflow/workflow-forms.js.map
Log Message:
-----------
Formatting.
Commit: 5bcd59944d6c5969930bba3c9f4d83b2a82c42c5
https://github.com/galaxyproject/galaxy/commit/5bcd59944d6c5969930bba3c9f4d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-11-15 (Wed, 15 Nov 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M static/maps/mvc/workflow/workflow-forms.js.map
M static/scripts/mvc/workflow/workflow-forms.js
Log Message:
-----------
Unpack options in functions in keeping with previous style here (dunno about this long term though)
Commit: 299ae5c9f5fac0cb701eed3fb30e9ae3b4602bbb
https://github.com/galaxyproject/galaxy/commit/299ae5c9f5fac0cb701eed3fb30e…
Author: Aysam Guerler <aysam.guerler(a)gmail.com>
Date: 2017-11-18 (Sat, 18 Nov 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M client/galaxy/scripts/mvc/workflow/workflow-node.js
M static/maps/mvc/workflow/workflow-forms.js.map
M static/maps/mvc/workflow/workflow-node.js.map
M static/scripts/mvc/workflow/workflow-forms.js
M static/scripts/mvc/workflow/workflow-node.js
Log Message:
-----------
Merge pull request #5021 from dannon/fix-workflow-editor-outputs
Workflow editor outputs fixes
Compare: https://github.com/galaxyproject/galaxy/compare/83e9e07bd596...299ae5c9f5fa
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: a0643e0385c171294d4f57ec2804794df2fcac23
https://github.com/galaxyproject/galaxy/commit/a0643e0385c171294d4f57ec2804…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-11-14 (Tue, 14 Nov 2017)
Changed paths:
M lib/galaxy/managers/collections.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M test/api/test_history_contents.py
Log Message:
-----------
More HDCA copying tests, add option to copy HDAs into new history.
Commit: b5864ad4f74f6f5afe0568c5ed17d75610b9ed87
https://github.com/galaxyproject/galaxy/commit/b5864ad4f74f6f5afe0568c5ed17…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-11-16 (Thu, 16 Nov 2017)
Changed paths:
M lib/galaxy/managers/collections.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M test/api/test_history_contents.py
Log Message:
-----------
Merge pull request #5004 from jmchilton/collection_copy_api
More HDCA copying tests, add option to copy HDAs into new history.
Compare: https://github.com/galaxyproject/galaxy/compare/36dc1560e574...b5864ad4f74f
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 44447ed08940782a4d022cd2dcddbdb2c2813ff4
https://github.com/galaxyproject/galaxy/commit/44447ed08940782a4d022cd2dcdd…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-11-14 (Tue, 14 Nov 2017)
Changed paths:
M test/integration/test_data_manager_table_reload.py
Log Message:
-----------
Use github instead of NCBI for problematic data manager test FASTA.
Seems to be failing many of the integration tool runs I've seen today. I've seen a couple different errors:
```
| File "/tmp/tmpVp6xM0/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/b1bc53e9bbc5/data_manager_fetch_genome_dbkeys_all_fasta/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py", line 312, in download_from_ncbi
| return get_stream_reader(urlopen(url), tmp_dir)
| File "/usr/lib/python2.7/urllib2.py", line 154, in urlopen
| return opener.open(url, data, timeout)
| File "/usr/lib/python2.7/urllib2.py", line 435, in open
| response = meth(req, response)
| File "/usr/lib/python2.7/urllib2.py", line 548, in http_response
| 'http', request, response, code, msg, hdrs)
| File "/usr/lib/python2.7/urllib2.py", line 473, in error
| return self._call_chain(*args)
| File "/usr/lib/python2.7/urllib2.py", line 407, in _call_chain
| result = func(*args)
| File "/usr/lib/python2.7/urllib2.py", line 556, in http_error_default
| raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)
```
and
```
Timed out after 60.25 seconds waiting on state.
-------------------- >> begin captured stdout << ---------------------
Problem in history with id adb5f5c93f827949 - summary of datasets below.
--------------------------------------
| 1 - Create DBKey and Reference Genome (HID - NAME)
| Dataset State:
| queued
| Dataset Blurb:
| queued
| Dataset Info:
| None
| Peek:
| None
| Dataset Job Standard Output:
| None
| Dataset Job Standard Error:
| None
|
--------------------------------------
```
Commit: 36dc1560e574c42550f9450184ae9c44e86459dc
https://github.com/galaxyproject/galaxy/commit/36dc1560e574c42550f9450184ae…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-11-16 (Thu, 16 Nov 2017)
Changed paths:
M test/integration/test_data_manager_table_reload.py
Log Message:
-----------
Merge pull request #5007 from jmchilton/problematic_data_manager
Use github instead of NCBI for problematic data manager test FASTA.
Compare: https://github.com/galaxyproject/galaxy/compare/a9685d3acd4c...36dc1560e574
Branch: refs/heads/release_17.09
Home: https://github.com/galaxyproject/galaxy
Commit: 06e9509d3868c885d41d94e455d7245f4af10156
https://github.com/galaxyproject/galaxy/commit/06e9509d3868c885d41d94e455d7…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-11-13 (Mon, 13 Nov 2017)
Changed paths:
M lib/galaxy/work/context.py
Log Message:
-----------
Allow get_history calls with create=False when evaluation workflows.
No reasons to prevent this I guess - since create means create if a history isn't available not force the creation of a history.
Commit: 5dc2254417667216dab982a4bc375a85d3b55316
https://github.com/galaxyproject/galaxy/commit/5dc2254417667216dab982a4bc37…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2017-11-16 (Thu, 16 Nov 2017)
Changed paths:
M lib/galaxy/work/context.py
Log Message:
-----------
Merge pull request #4997 from jmchilton/allow_create_false_in_work_context
[17.09] Allow get_history calls with create=False when evaluation workflows.
Compare: https://github.com/galaxyproject/galaxy/compare/18467e9b2cec...5dc225441766