John Chilton
9ca839fca8
More reworking of job logging.
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Drop now duplicated log message in drmaa, condor, cli, etc.... Have local job runner report which job script it is running - but log it as a job script. For each job runner log the full command-line which includes dependency resolution and not the base version produced directly by the tool and use the old format from the external runners.
2014-05-19 11:02:59 -05:00
John Chilton
b1d39bbfb9
Improved job logging.
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Remove now less useful local runner command-line log statement (still contend it will be valuable for debugging purposes to be able to tweak and rerun the exact script - but point taken :)) . Remove stray statement added in ff4b5fe. Add new logging statement that logs just the base command-line produced by tools for all job runners. Add little note to runners/__init__.py about how to produce an extended command-line logging (with metadata handling, dependencies, and from_work_dir handling).
2014-05-19 10:16:12 -05:00
John Chilton
cb87cf4c27
Merged in jmchilton/galaxy-central-fork-1 (pull request #384 )
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Local Job Runner Enhancements
2014-05-18 21:12:36 -05:00
Greg Von Kuster
9f05fec27c
I meant to make this file a .sample file.
2014-05-17 10:10:23 -04:00
Martin Cech
f599e9b01c
data libraries: permissions UI and API work, library router fixes, security addition for retrieving paginated roles for given dataset
2014-05-16 18:13:26 -04:00
John Chilton
573ce4babe
Update LWR client through LWR changeset f7d15f0.
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Adds new LWR file action type - rewrite - that allows paths to be simply rewritten during paramater replacement or command rewriting.
2014-05-16 16:17:08 -05:00
Greg Von Kuster
60b2e731dc
Add a script for creating a new user and an associated API key to streamline the process of setting up a new local development tool shed.
2014-05-16 17:14:24 -04:00
Daniel Blankenberg
d8566b83f5
Fix for checking dataset access permissions when reruning a tool by job_id.
2014-05-16 15:13:29 -04:00
John Chilton
3c671266e1
A bit more LWR client logging.
2014-05-16 10:24:54 -05:00
John Chilton
82872edc2d
Update LWR client and behavior through LWR changeset 8ea7265.
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LWR now informed of job submission failures in MQ mode so jobs shouldn't sit in queued state forever if job fails to queue remotely. Also small fixes and more logging.
2014-05-16 10:14:52 -05:00
Greg Von Kuster
01f8fd5396
Fix query filters for various Tool Shed "latest revision" grids by making sure revisions have actually been tested by the install and test framework, and not sure prepared the framework's preparation scripts.
2014-05-16 09:48:50 -04:00
John Chilton
551bcc7930
Simplified, truely asynchronous LWR MQ status updates.
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In addition to eliminating some egregious hacks, this reworked functionality should allow any LWR handler process to consume update messages for any job (so LWR jobs don't have to be bound to a particular handler).
2014-05-16 00:57:31 -05:00
John Chilton
f1f95ec988
Correct 'abstract' method definition in AsynchronousJobRunner.
2014-05-16 00:57:31 -05:00
John Chilton
25e9e3019a
Handle LWR failed state in asynchronous MQ updates.
2014-05-16 00:57:31 -05:00
John Chilton
cfb579f527
PEP-8 fixes for JobManager.
2014-05-16 00:57:31 -05:00
John Chilton
634e17d94d
Helper method for creating JobWrappers in JobHandler.
2014-05-16 00:57:31 -05:00
John Chilton
bb11f40b84
Fix for previous commit.
2014-05-15 22:05:04 -05:00
John Chilton
e5d3365f85
Bugfix: LWR - Fix manager name not passed into MQClientManager.
2014-05-15 21:57:54 -05:00
John Chilton
6b58e81a1f
Merge.
2014-05-15 15:58:58 -05:00
John Chilton
4cdc3eb93e
Fix GALAXY_SLOTS calculation for LSF.
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Thanks to Ilya Sytchev for the patch.
2014-05-15 15:58:12 -05:00
Daniel Blankenberg
06df9b5955
Have auto-detect metadata option in library use external set metadata process.
2014-05-15 16:25:44 -04:00
John Chilton
3f1eba59ef
Fix incorrect LWR comment.
2014-05-15 14:59:57 -05:00
John Chilton
f33bb43025
Merged in jmchilton/galaxy-central-fork-1 (pull request #389 )
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Small Column Parameter Enhancements
2014-05-15 13:49:44 -05:00
John Chilton
8e6bcf72c7
Merged in jmchilton/galaxy-central-fork-1 (pull request #387 )
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Recursive Tool Parameter Dictification
2014-05-15 13:43:43 -05:00
John Chilton
d7b4b36756
Change paired collections terminology from left/right to forward/reverse.
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If you have paired datasets in your database they will no longer work - send me an e-mail and I can give you an SQL update statement.
2014-05-15 13:01:36 -05:00
John Chilton
f1a322bc91
Order history.{active,visible}_dataset_collections by hid instead of id.
2014-05-15 12:04:58 -05:00
John Chilton
ededf2451d
PEP-8 fixes for DatasetInterface.copy_datasets.
2014-05-15 12:04:58 -05:00
John Chilton
a376cc7230
Allow 'Copy Datasets' page to copy collections as well.
2014-05-15 12:04:58 -05:00
John Chilton
ae1ea31eec
Bugfix: Copying datasets to existing and new history at same time.
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Previously would give error about set not having an append method.
2014-05-15 12:04:58 -05:00
Greg Von Kuster
2957700246
Refactoring cleanup in the Tool Shed's package installation framework.
2014-05-15 09:59:55 -04:00
John Chilton
bdab215a8d
Bugfix: Yet another bug fix for workflow extraction with collection operations.
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Fail, fail, fail.
2014-05-14 18:25:50 -05:00
John Chilton
d6cea61cc5
Bugfix: Small fix for running workflows with subcollection mapping steps.
2014-05-14 18:25:50 -05:00
Greg Von Kuster
2d5c37a73f
Enhance the galaxy API for the Tool Shed to retrieve the latest installable revision from the Tool Shed from an installed repository, specifying a name and owner. Enhance the ~/scripts/api/install_tool_shed_repositories.py script to allow the changeset_revision to be optional, and if not specified, the latest installable revision will be installed for the repository specified by the name and owner.
2014-05-14 18:13:33 -04:00
Nate Coraor
d18dee991e
Add a config option for controlling the AMQP consumer timeout, catch socket.error and attempt to recover from it.
2014-05-14 16:34:15 -05:00
Daniel Blankenberg
e9391803bb
Fix for setting metadata when uploading directly to a library.
2014-05-14 17:26:41 -04:00
John Chilton
255e77c862
Remove stray log statements in previous commit.
2014-05-14 16:13:32 -05:00
John Chilton
11e0676490
Bugfixes: More bug fixes for extracting collection-y workflows from a history.
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The embarrassment continues...
2014-05-14 16:06:33 -05:00
Nate Coraor
5e32a8ae5b
Correctly handle the case where the AMQP SSL connection param parser gets params=None.
2014-05-14 15:27:28 -05:00
Dave Bouvier
d682e58ad4
Fix missing imports, add self.app in a few more places.
2014-05-14 15:19:48 -04:00
John Chilton
75d47452f9
Merge.
2014-05-14 14:08:56 -05:00
John Chilton
61a28e9b28
Bugfix: Annotation, tags on collections update looking in old location.
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Moved to collection instances instead of collections a little before PR opened.
2014-05-14 14:08:03 -05:00
Greg Von Kuster
e31f73041d
Fix for tool migration manager to use self.app instead of trans.app.
2014-05-14 15:07:30 -04:00
Greg Von Kuster
5b3e02d5c3
Phase 2 of the tool dependency package installation framework rewrite: 1) rename the RecipeManager class to be the StepManager class and add a new TagManager class, both of which are contained in the recipe_manager.py module. 2) Add appropriate new classes for handling recipe tag sets to a new tag_handler.py module. Add a new InstallManager class with functions for installing tool dependencies. Eliminate the use of fabric_util.py and install_util.py.
2014-05-14 14:55:31 -04:00
Martin Cech
37d8aac8cd
data libraries: first take on api for requesting roles(assigned and assignable) for permissions; do not use - needs to be tested on test
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changes to UI, removed modal for dataset details, dissasembled into separate backbone view
2014-05-14 13:53:01 -04:00
Daniel Blankenberg
9b170521ed
Fix for when hours_between_check is defined in ini.
2014-05-14 12:04:47 -04:00
Daniel Blankenberg
3f87380dea
Allow for an arbitrary number of tool_data_table_config_path files to be defined in ini file. Values are comma separated.
2014-05-14 11:52:20 -04:00
John Chilton
486dc41639
Bugfix for updating history dataset collection name.
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Thanks to Bjoern for the bug report.
This attribute had been DatasetCollection in earlier versions of this code and the update code was only partially cut-over to use the new location for name (on HistoryDatasetCollectionAssociation).
2014-05-14 05:26:21 -05:00
John Chilton
c79e4dcc40
Fix duplicated names in on_text when using multiple data inputs.
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Unit tests verifing the fixed, correct behavior included. Bug introduced in e8c84dd715782e7c1d709d8068e6033b835f7f39 as an unintended consequence of duplicating the first dataset in the dictionary of input datasets generated by the tool action code.
Fixes https://trello.com/c/LCEKxImR .
2014-05-13 17:47:57 -05:00
Dannon Baker
48ff27d6e3
Merge from stable.
2014-05-13 17:39:55 -04:00
John Chilton
e536ba727b
Merged in natefoo/galaxy-central (pull request #392 )
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SSL client certificate support for LWR AMQP connections
2014-05-13 15:38:04 -05:00
John Chilton