Dave Bouvier
35bc12d769
Migrate tools from the distribution to the tool shed.
2014-07-28 11:58:52 -04:00
Daniel Blankenberg
b966989a55
1.) Enhance set_metadata scripts to be able to handle metadata declared by tools for both regular declared outputs and new primary output datasets using JSON.
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2.) Enhance collect_primary_datasets to allow tools to provide extra_files.
2014-07-10 12:09:50 -04:00
Dave Bouvier
4e63bc8731
Fetch eggs after initializing sample files, per John Chilton's comment.
2014-06-13 17:32:51 -04:00
Dave Bouvier
8b45411adf
Abstract common startup tasks into scripts/common_startup.sh, which used to be copy_sample_files.sh.
2014-06-13 16:39:59 -04:00
John Chilton
63a4c36770
Add utility for debugging sqlalchemy queries in db_shell.py.
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Should aid in interactively building up queries.
2014-06-10 15:01:38 -05:00
Dave Bouvier
4f2e506042
Enable running the create_users and create_categories scripts via run_tool_shed.sh
2014-05-22 10:59:18 -04:00
Dave Bouvier
a3018feb02
Migrate 22 tools from the distribution to the tool shed.
2014-05-19 13:01:46 -04:00
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
John Chilton
3287af315d
Ensure new_file_path exists before set_metadata.py generates metadata.
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This directory is required to exist but usually unneeded because Galaxy creates this directory on startup. However, when setting metadata remotely with the LWR that remote Galaxy instance may have never been started and this directory may not exist.
2014-05-13 09:29:41 -05:00
Greg Von Kuster
d818047609
Change the name of the current InstallManager to the more appropriate ToolMigrationManager since it handles only tool migrations. This allows for the InstallManager to be used for more general Tool Shed install processes.
2014-05-06 10:34:28 -04:00
John Chilton
3ac17e09f1
Rework test framework testing and tools.
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-framework will still cause just a small set of non-default, non-user facing tools to be tested and exerise various aspects of the tool and test frameworks, but now an argument can be passed in -with_framework_test_tools to allow these tools to be used as part of the normal test framework (i.e. when not using -framework). This serves two purposes - to ensure the feature coverage of existing tests remains high as the tests are migrated out of the distribution and to allow a set of tests to be available for functional (e.g. API tests) that users don't need to see.
2014-04-28 11:48:51 -05:00
Dave Bouvier
5bdb75aa82
Correct usage of "it's" versus "its".
2014-04-17 15:49:32 -04:00
Dave Bouvier
72ce2889cb
Merge in fix from next-stable.
2014-04-14 13:18:47 -04:00
Dave Bouvier
7007f8594c
Fixed tool help image for gops complement.
2014-04-14 13:17:12 -04:00
Dave Bouvier
979f159915
Merge fix from next-stable.
2014-04-14 09:35:00 -04:00
Dave Bouvier
c7e6181c20
Fix issues with tool migration stage 10.
2014-04-14 09:32:41 -04:00
Nicola Soranzo
46641daaa7
Merge galaxy/galaxy-central default branch.
2014-04-11 12:00:39 +02:00
Nicola Soranzo
f73d5fba6c
Fix old wiki links.
2014-04-10 20:00:45 +02:00
Dave Bouvier
7da3f0a6aa
Corrected version for migrated tools.
2014-04-10 13:59:40 -04:00
Dave Bouvier
db12448003
Fixed JAVA_JAR_PATH for realigner_target_creator.
2014-04-04 10:37:52 -04:00
Dave Bouvier
463b50bb1d
Use correct revisions of best_regression_subsets and weightedaverage.
2014-04-03 09:45:51 -04:00
Dave Bouvier
b6af887925
Corrected an error in the analyze_covariates tool shed repository.
2014-04-02 16:05:57 -04:00
Dave Bouvier
83af05b1f2
Migrate 46 tools from the distribution to the tool shed: gatk, gops, regional variation.
2014-04-01 11:04:32 -04:00
Kyle Ellrott
e4f45e04e3
Adding script to generate UUIDs for datasets where the value is null. This is to backfill previously generated records (from now on UUID will be generated during creation)
2014-03-04 15:46:10 -08:00
Dave Bouvier
85add8fc6d
Fix path for bowtie2.
2014-02-20 23:01:05 +00:00
Dave Bouvier
665099efa4
Situations where a migration warning would be incorrectly displayed, and tools with matching filenames would be removed from the tool_conf.xml after running a migration script.
2014-02-19 15:23:45 -05:00
Dannon Baker
7474579310
Swap amqplib for amqp. This was mostly a drop-in replacement, since it's a currently-maintained fork of amqplib, with slight updates to work with amqp 0-9-1.
2014-02-19 14:27:10 -05:00
Daniel Blankenberg
0c945b7c3b
Add a script to check toolshed dependency files for broken/invalid download URLs.
2014-02-17 12:51:34 -05:00
Daniel Blankenberg
ea193ce2e6
Add a very simple example script that uses API to run data managers.
2014-02-10 11:59:58 -05:00
John Chilton
17e935528d
Add example tool with task splitting to tool functional framework tests.
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Enable task splitting in functional tests to test this. Specify tool_dir in samples tool_conf.xml so it doesn't need to be explicitly set in scripts/functional_tests.py.
2014-01-28 14:34:26 -06:00
Dave Bouvier
3ec4601e8d
Fix description for find_diag_hits.
2014-01-27 10:44:24 -05:00
Dave Bouvier
448d9f55eb
Migrate 43 tools from the distribution to the tool shed.
2014-01-27 09:53:14 -05:00
Dave Bouvier
d1114a1b0f
Fix deletion of test methods after tests have been run.
2014-01-16 11:30:25 -05:00
Dannon Baker
e26d6e56c7
Tweaks to scripts/api/common.py to fix JSONDecodeError removal and clean up code.
2014-01-15 09:05:38 -05:00
John Chilton
fb0f7e6fde
Rework workflow functional testing so isn't tested by default...
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Meant to be used with a specific workflow, but nose is picking it up by default when no workflow has been specified.
2014-01-11 22:40:18 -06:00
John Chilton
e62b2ccb56
Implement framework for testing API...
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... if you can call 1 new class a framework. Includes a few test cases to exercise/drive it. These examples include a histories API test (a typical API test) and a general test of the API framework itself (mostly just the run_as functionality).
This includes changes to interactor.py to make it more useful outside the context of tool/workflow testing as well as a tweak to test Galaxy that gets started to allow testing of the run_as feature.
2014-01-10 08:45:36 -06:00
John Chilton
02aeedeef7
Rework key injection logic in test framework.
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Pull logic for how master and user API keys are determinined for testing out of functional_tests.py for reuse elsewhere.
This refactoring will help the creation of an API test framework.
2014-01-10 08:45:36 -06:00
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
Aysam Guerler
b9de337dd3
Merge
2014-01-09 14:06:19 -05:00
Nate Coraor
5a8c6457b9
Fix username argument to PostgreSQL connection in pgcleanup.py
2014-01-09 10:46:01 -05:00
Dave Bouvier
871c301e35
Allow specifying the functional tests' install_database_connection with an environment variable.
2014-01-08 14:50:19 -05:00
Greg Von Kuster
d26d527bc6
Order imports per database_contexts requirements to fix the tool shed's install and test framework.
2014-01-03 10:02:19 -05:00
John Chilton
82787696ef
PEP-8 fixes for set_metadata.py.
2014-01-02 17:50:14 -06:00
John Chilton
7ca5e218fd
Tools now properly migrated into install_database_connection database...
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... this second database is specified.
2013-12-17 11:19:41 -06:00
John Chilton
8f5b10d6d5
Reuse code between scripts/manage_tools.py and lib/galaxy/model/orm/scripts.py
2013-12-17 11:19:41 -06:00
Daniel Blankenberg
3db7688a56
Add Functional Testing support for locally and ToolShed installed Data Managers.
2013-12-10 12:59:29 -05:00
Daniel Blankenberg
20e478f210
Allow ftp for GALAXY_TEST_DB_TEMPLATE and stricter check for protocol URL prefixes.
2013-12-10 11:08:13 -05:00
Daniel Blankenberg
f370e990e0
Fix for using GALAXY_TEST_DB_TEMPLATE with htTp not specified in all lower case.
2013-12-10 10:54:51 -05:00
John Chilton
5e36bde9c8
Rework contribution from pull request #267 to be optional.
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To obtain the behavior (assigning all groups for a given user for each job submission) change the property - 'drmaa_external_runjob_script' from 'scripts/drmaa_external_runner.py' to 'scripts/drmaa_external_runner.py --assign_all_groups'.
Making this optional because my concern is that this could be an expensive operation on some clusters.
2013-12-10 08:26:22 -06:00
Dave Bouvier