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Commit Graph
12535 Commits
Author SHA1 Message Date
Gildas Le Corguillé ad8483a7db Update binary.py 2016-08-03 10:47:16 +02:00
lecorguille b16356e490 add a netcdf datatype for metabolomics spectre data 2016-08-03 10:32:15 +02:00
Dannon Baker dd4eabb484 Merge pull request #2654 from carlfeberhard/history.delete_current-id 
History, UI: use id of displayed history in delete
 2016-08-01 14:09:18 -04:00
Nicola Soranzo 5b52b73fbb Datatype classes fixes: wrong file_ext, import order, Python3 
- Specify some classes are abstracts
- Use super() to call superclass methods
- Various simplifications
 2016-07-29 19:29:27 +01:00
carlfeberhard cdab64820c Merge remote-tracking branch 'upstream/dev' into history.delete_current-id 2016-07-29 11:08:45 -04:00
Dannon Baker 9789c116e6 Update version to 16.10.dev 2016-07-28 22:55:39 -04:00
John Chilton 05c537e384 Merge pull request #2678 from dannon/azure_followup 
Fix an error with getting the size of an object from Azure.  Attempte…
 2016-07-28 19:49:52 -04:00
Dannon Baker 4f12282138 Limit creation of multitudes of default, empty histories. This was happening for every new session using remote auth 2016-07-28 11:46:43 -04:00
Dannon Baker fdbaf437c9 Merge pull request #2672 from guerler/fix_populating_collections 
Properly populate collections regardless of context values
 2016-07-28 08:32:13 -04:00
Dannon Baker fcbaf8d17a Fix an error with getting the size of an object from Azure. Attempted to future-proof it if the library is fixed. 2016-07-27 23:07:29 -04:00
Dannon Baker c7caeb3c39 Merge branch 'azure-blob-objectstore' into dev 2016-07-27 23:06:18 -04:00
Dannon Baker c4841b3521 Merge pull request #2677 from guerler/update_select 
Fix dataset selector update when deleting history items
 2016-07-27 18:05:54 -04:00
guerler 43f800b56d Modify persistent entry handling for select fields 2016-07-27 16:23:31 -04:00
Daniel Blankenberg a731ce2e22 Merge pull request #2554 from bxlab/install_via_conda 
Fix bugs in post.
 2016-07-27 15:38:58 -04:00
Marius van den Beek 483b66be27 Address @nsoranzo's review 2016-07-27 22:20:52 +03:00
Marius van den Beek 2a5b043aaf Simplify conda install logic 2016-07-27 21:49:29 +03:00
Nicola Soranzo e625eed9c5 Merge pull request #2158 from martenson/improve-activation 
activation config touch
 2016-07-27 19:13:41 +01:00
Marius van den Beek 06e409ad40 Use continue instead of unused NullDependency 
in Dependency_Manager.find_dep(), and requirement.version instead of
None in Dependency_Manager.find_dep.dependency_shell_commands(). (thanks
@nsoranzo)
 2016-07-27 20:34:45 +03:00
Martin Cech c223ebff6d explicitly disable activation for TS 
because inherited user controller wants the property
 2016-07-27 13:03:53 -04:00
guerler 25fd142667 Initialize empty other_values dictionary when populating collections 2016-07-27 12:58:23 -04:00
guerler 8dbc35784e Collections should be populated regardless of the availability of other values 2016-07-27 12:56:21 -04:00
guerler a9809ca692 Use default job history on build_for_rerun unless specified otherwise 2016-07-27 11:29:54 -04:00
Dannon Baker 28e7f866cb Merge pull request #2576 from abretaud/ldap 
Add python-ldap module to conditional requirements
 2016-07-27 10:10:50 -04:00
Martin Cech b74fd63fef Merge pull request #2664 from dannon/dev_reports 
Reports: new pages and improvements
 2016-07-27 09:21:33 -04:00
Alexander Lenail b4896bc341 fix lint 2016-07-26 18:37:40 -04:00
Alexander Lenail 4dc8b7d803 clean things up a little... 2016-07-26 18:13:49 -04:00
Alexander Lenail e349aafe04 fix bug. 2016-07-26 17:09:49 -04:00
Dannon Baker 8483f2ce8b Fix E731 2016-07-26 17:07:37 -04:00
Alexander Lenail 0b1730fe7f trying this... 2016-07-26 16:48:22 -04:00
guerler 1cdc532ff1 Reduce server sided refresh requests to changes in data associated input fields 2016-07-26 15:25:18 -04:00
Dannon Baker 3d0f5577b1 Merge pull request #2660 from jmchilton/ensure_galaxy_python_for_metadata 
Ensure Galaxy's python binary is used for metadata generation.
 2016-07-26 14:53:57 -04:00
Martin Cech 28a9904707 fix menu items to actually display new templates 
reword certain texts
reorder imports and fix style
remove unnecessary imports
 2016-07-26 13:29:15 -04:00
Martin Cech 12c65d4a63 fix import of and_ operator 2016-07-26 13:29:09 -04:00
John Chilton 7a8d86aa9b Ensure Galaxy's python binary is used for metadata generation. 2016-07-26 13:06:06 -04:00
Dannon Baker 3199217448 Remove debug print 2016-07-26 08:08:55 -04:00
Dannon Baker e59602fed1 Update check_azure_storage check, read the object store config to detect stores. 2016-07-26 08:06:53 -04:00
Marius van den Beek e53a81c40d Fix syntax, return None if dependency not found 2016-07-26 13:32:09 +03:00
Nicola Soranzo 134f988549 Merge pull request #2650 from dannon/flake8_update_tox_default 
Ignore .tox directory.  Used to be ignored by default w/ flake8 appar…
 2016-07-25 19:18:44 +01:00
carlfeberhard 2b4a8557f1 History, UI: use id of displayed history in delete 
- Refactor `delete current` to `delete` and require an id arg.
- Update history options menu to pass the id of the displayed/
current history to the above delete controller endpoint.

This means that the current history panel will delete the history
that's displayed (instead of potentially a different history that's
been set to the current history on the server side).

Note: this isn't an ideal refactoring but should solve the below
issue temporarily until we move more of the session state out of
API.

Closes #894
 2016-07-25 13:32:28 -04:00
Dannon Baker 0deae30285 Remove two unused imports in forms controller. 2016-07-25 11:13:54 -04:00
Dannon Baker 9f2237905b Remove two #noqas and specify __all__ for those modules. Specify many more #noqas to skip the precise relevant exception. 2016-07-25 11:09:15 -04:00
Dannon Baker 10745f252f Apply @nsoranzo's fix for noqa changes (must end the line, comment comes before it) 2016-07-25 10:15:33 -04:00
Marius van den Beek dd8f8f1de0 Fix NullDependency use 
and add default arguments to NullDependency
 2016-07-25 16:32:16 +03:00
Marius van den Beek 6b135c6b1e Drop INDETERMINATE_DEPENDENCY alias 2016-07-25 16:32:16 +03:00
Marius van den Beek 49dee6af10 Flake8 fix 2016-07-25 16:32:16 +03:00
Marius van den Beek c10d1cb172 Remove unused DependencyResolver view from ToolBox 2016-07-25 14:49:51 +03:00
Marius van den Beek b59b797f50 Update INDETERMINATE_DEPENDENCY use to NullDependency instance 2016-07-25 14:45:14 +03:00
zipho 1da80ca3c9 Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev 2016-07-25 11:45:46 +02:00
Marius van den Beek 0b24283395 Use resolver.find_dep to determine dependency status 2016-07-23 18:13:41 +02:00
Marius van den Beek 201863200e Only return requirements of type package (for now) 2016-07-23 02:01:24 +02:00