Dannon Baker
c1558e8205
One more simplejson/json fix that slipped through the merge.
2014-01-10 07:42:58 -05:00
Dannon Baker
a40457ab09
Merge.
2014-01-10 07:40:02 -05:00
Dannon Baker
559ecb4ec8
Remove dependency on simplejson; convert everything over to using the json module in the python standard library.
2014-01-10 07:29:05 -05:00
Greg Von Kuster
3014265a07
Tool Shed API fixes and code cleanup.
2014-01-09 15:59:18 -05:00
Nate Coraor
3091ce1584
Log native spec on drmaa job submission.
2014-01-09 13:27:47 -05:00
Nate Coraor
93cdf33174
Merged in natefoo/galaxy-central (pull request #290 )
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Configurable terminal job state, Slurm enhancements
2014-01-09 12:01:19 -05:00
Greg Von Kuster
7d261866bd
Eliminate unnecessary RepositoryMetadata.to_dict() method in the tool shed.
2014-01-08 21:25:19 -05:00
Greg Von Kuster
6cc918bbb5
Filter out deprecated repositories when resetting metadata on repositories in the tool shed - resetting metadata on deprecated repositories is essential only for ensuring reproducibility.
2014-01-08 16:26:51 -05:00
Greg Von Kuster
d3640c6bcf
Fix for pruning content from the tool shed's repository dependencies container.
2014-01-08 15:27:25 -05:00
Martin Cech
f92f01a264
js data libraries refactor, tweaks, logging removal
2014-01-08 13:54:38 -05:00
Dave Bouvier
d780c1e99f
When a push is received in the hg controller, update the repository on disk after the push is complete.
2014-01-08 12:27:14 -05:00
Dave Bouvier
7c6fd53a49
Fix error when time_last_tested has a None value.
2014-01-08 12:20:41 -05:00
Greg Von Kuster
adf813800a
Retain and display more errors if they occurred during repository creation and population when importing a repository capsule into a tool shed.
2014-01-08 10:10:05 -05:00
Greg Von Kuster
3f92caaf6b
Fix for retrieving repository dependency information for a repository changeset revision via the Tool Shed's API.
2014-01-08 09:46:33 -05:00
Greg Von Kuster
d61e9b0347
Fixes for comparing datetime values in the tool shed's install and test framework.
2014-01-08 09:25:17 -05:00
Greg Von Kuster
58943fb241
Don't map the time_last_tested column in the tool shed API.
2014-01-07 21:37:17 -05:00
Greg Von Kuster
0a2863a01f
When exporting a repository and dependency hierarchy from the tool shed, always make sure the primary repository entry is ordered last in the manifest.
2014-01-07 16:55:59 -05:00
Martin Cech
299886a2cc
extensive logging for folder_contents API datasets
2014-01-07 16:08:20 -05:00
Carl Eberhard
853311907b
Merged in jmchilton/galaxy-central-fork-1 (pull request #289 )
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Move history contents filtering logic into model.
2014-01-07 15:48:55 -05:00
Nate Coraor
1889852e8f
Add a Slurm runner (subclassed from the drmaa runner), adds some logic for
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determining/reporting the reason of job failure and requeuing jobs that failed
due to node failure.
2014-01-07 15:23:11 -05:00
Nate Coraor
4a024b882f
Make job terminal state logic somewhat configurable via runner params, update
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DRMAA runner plugin changes for configurable terminal state handling. Also
allow the drmaa plugin to read the drmaa library path from job_conf.xml rather
than the $DRMAA_LIBRARY_PATH environment variable.
2014-01-07 15:21:50 -05:00
Nate Coraor
458df6faf2
Allow runners plugins to accept params, provide some simple load-time validation logic for params.
2014-01-07 15:18:11 -05:00
Nate Coraor
0fa7f79dec
Allow handlers to control which runner plugins they will load.
2014-01-07 15:13:01 -05:00
Dannon Baker
f4194d306b
Update to PR285, use datetime.isoformat() instead of str(). Left in stringifying bit (commented) for future reference.
2014-01-07 14:41:53 -05:00
Dannon Baker
c154ed4091
Merged in kellrott/galaxy-central/search (pull request #285 )
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Make to_dict method stringify non-JSONable objects
2014-01-07 14:32:27 -05:00
Dannon Baker
b6b78e5b05
Remove redundant run_as_users check.
2014-01-07 14:25:11 -05:00
Dannon Baker
e253b930b7
Merged in jmchilton/galaxy-central-fork-1 (pull request #288 )
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If master_api_key set, allow it to run_as if any user can run_as.
2014-01-07 14:24:11 -05:00
Martin Cech
ce7cd66c16
galaxy.modal refactoring; API documentation; folders API refactoring and implementation; libraries API refactoring
2014-01-07 13:52:04 -05:00
Dannon Baker
ba49e34798
Update cloudlaunch default AMI
2014-01-07 09:47:37 -05:00
Greg Von Kuster
7aefa6879a
Enhance the tool shed's install and test framework to populate and store information about the installation of each repository dependency in addition to the repository itself. This changeset also include miscellaneous typo fixes and code cleanup.
2014-01-06 16:30:27 -05:00
Carl Eberhard
3fd49bc195
History view: replace mako gen. w/ js panel, allow importing to include deleted datasets (by using import when deleted datasets are visible); The original view page is still (temporarily) accessible by altering the url to history/original_view
2014-01-06 13:49:20 -05:00
Greg Von Kuster
603f868f7a
Set a repository and its dependent repositories created from a capsule to be defined as installable only if its creation resulted in no errors.
2014-01-04 19:25:43 -05:00
John Chilton
4d22d5fe02
If master_api_key set, allow it to run_as if any user can run_as.
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If no master_api_key set no change in behavior, if api_allow_run_as is empty no change in behavior (i.e. run_as will not work with master_api_key if no api_allow_run_as users are configured - as to not increase attack surface for these Galaxy instances).
This changeset contains no tests, but pull request #278 included functional tests for these changes (as well as original behavior) which passed.
2014-01-03 22:04:36 -06:00
John Chilton
edf064101f
Fix history contents ordering broken with previous changeset.
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Add stronger test cases, though these are still insufficient to exercise the error. The only way I was able to get the history contents to come out misordered was to use postgres. Nonetheless, using postgres this now orders datasets properly.
2014-01-03 21:58:13 -06:00
John Chilton
e3757343d0
Backout of Backout of 714f5b1 for now.
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... or would that be back-into 714f5b1?
714f5b1 - Move history contents filtering logic into model.
Filtering for deleted, visible, and ids with ORM should prevent loading unneeded objects into memory (a history with 1000 items and 5 visible will now only cause 5 items to be loaded instead of 1000 just to filter out 5). Simplifies history_contents API logic somewhat, allows easier 'unit' testing (included), and provides a clearer entry point for additional 'showing' additional contents types (read dataset collections).
2014-01-03 21:58:12 -06:00
Martin Cech
1c5408ab0c
fix for bug with hid starting at 2 instead of 1, introduced by myself at 2bb7df0
2014-01-03 16:01:54 -05:00
Greg Von Kuster
c40b2b88fa
Raise an exception if attempting to install a repository into Galaxy that contains an invalid repository dependency definition (implying a bug in the Tool Shed framework).
2014-01-03 14:21:29 -05:00
Nate Coraor
ce49bfce9b
Allow changing the header for remote user.
2014-01-03 11:41:19 -05:00
John Chilton
4dd09b8452
Adjust GALAXY_SLOTS in local.py for pre-bash shells.
2014-01-02 17:50:15 -06:00
John Chilton
6740335dca
Fix version output redirection for pre-bash shells.
2014-01-02 17:50:15 -06:00
John Chilton
3122393fb7
PEP-8 fixes task runner.
2014-01-02 17:50:13 -06:00
John Chilton
b5431104d0
PEP-8 fixes for jobs/__init__.py
2014-01-02 17:50:12 -06:00
John Chilton
30ad7c826f
PEP-8 fixes for local job runner.
2014-01-02 17:50:12 -06:00
John Chilton
ca672b2f68
Fix bug in from_work_dir location checking...
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... would only be exhibited if using LWR + 'remote_metadata'.
2014-01-02 17:50:11 -06:00
John Chilton
a4a01b3d93
Update LWR client through LWR changeset 8ef5299.
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This encompasses numerous individual LWR changesets. The largest of these changes include extensions to:
- Enable LWR client to work in a fashion where remote paths are precalculated and used during job input evaluation instead of having these inputs rewritten after the fact. (Galaxy + LWR runner require significant modifications to enable this - found in subsequent changesets). https://bitbucket.org/jmchilton/lwr/commits/a06587ff0544f3a09cf221057be1b9107021a9fb .
- Allow staging or arbitrary paths (not restricted to job files such as inputs, working directory files, configs, etc...). https://bitbucket.org/jmchilton/lwr/commits/63981e79696337399edb42be5614bc7218cdf95f .
- Vast improvements to extra_files_path handling - before it only worked for one level of input extra_files_path - now works with arbitrary nesting of inputs and outputs. https://bitbucket.org/jmchilton/lwr/commits/b5e8c4dffc3a04639550e01f3f44ac3138cc6079 , https://bitbucket.org/jmchilton/lwr/commits/ab5bc61f6e0c9e11748436bd61aa1f6cba05f293 .
- Handle tools with version_command defined (LWR servers running on *nix systems only). https://bitbucket.org/jmchilton/lwr/commits/a3b43baa1aa6a8167a4e8cbb195d2a966b6527eb .
- Allow restircting path mapping to specific input types (input, tool, config, workdir, output, output_workdir, *default* (all previous), unstructured (new for arbitrary files), and *any* (*default* + unstructured). https://bitbucket.org/jmchilton/lwr/commits/27e678d47846c2fdf5792d0c64167d15c3abfecc
As well as several major refactorings to break improve the LWR client code structure
- Break up stager.py into smaller modules - https://bitbucket.org/jmchilton/lwr/commits/d0efda40b2c92100161ca7f825cb754d6b914db5
- Refactor complex method __download_results into class with smaller helper methods - https://bitbucket.org/jmchilton/lwr/commits/45fd16e52579c273eea5f52948ca57a1b19daa51
- Introduce higher level abstrction for staging actions - https://bitbucket.org/jmchilton/lwr/commits/35ea7e2fa88714aff5a38f0e0a55e3fdbcfbe779 .
2014-01-02 17:50:11 -06:00
John Chilton
dda63a54e6
Refactor JobRunner's in_directory out into galaxy.util for reuse.
2014-01-02 17:50:10 -06:00
John Chilton
d0ec446ab9
Fix LWR exit code handling.
2014-01-02 17:50:10 -06:00
Greg Von Kuster
8fd8656c8c
A bit of code cleanup and enhanced logging for the tool shed's install and test framework.
2014-01-02 16:39:46 -05:00
Kyle Ellrott
f73b1009f9
Fix to 'stringify' datetime object that was getting passed from to_dict LibraryFolder and into JSON converter.
2014-01-02 11:51:31 -08:00
Martin Cech
a36ed7aa16
removed manual setting of ‘200’ response code because it causes httpexception module errors
2014-01-02 11:25:02 -05:00
Dannon Baker