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9324 Commits
Author SHA1 Message Date
guerler 5dec24c21e Merge branch 'dev' of https://github.com/galaxyproject/galaxy into library_data_parameter 2015-04-19 22:59:16 -04:00
guerler 27424139a0 Add generic list value wrapper and use it for the library data tool parameter, move wrapper import into parameters 2015-04-19 22:46:45 -04:00
Bjoern Gruening cef67fb4f1 Add command_inject to IE config files. This makes it possible to modify the executed "docker run" command from the config file. 2015-04-18 16:54:34 +02:00
John Chilton b1d3552be4 Add a library_data input test case and small fix. 2015-04-17 14:23:38 -04:00
Dannon Baker e73d90c94e Merge pull request #121 from jmchilton/input_casting 
Improved Cheetah type casting for int/float values.
 2015-04-17 12:10:10 -04:00
guerler ebafd06fea Merge branch 'dev' of https://github.com/galaxyproject/galaxy into library_data_parameter 2015-04-16 20:02:25 -04:00
Dannon Baker 26b766b3bc Merge pull request #125 from jmchilton/md5 
Allow testing tool outputs based on MD5 hashes.
 2015-04-16 16:36:53 -04:00
John Chilton f7ecd1c9d2 Allow testing tool outputs based on MD5 hashes. 
This should not be considered the best practice for most text based files, but for binary files we cannot produce diffs anyway so this is probably better than storing the pointless binary blobs in repositories for instance. In particular Dan and I thought this would be useful for testing index files for data managers.

Includes test tool demonstrating this functionality, run test with

    ./run_tests.sh -framework -id md5sum
 2015-04-16 14:19:36 -04:00
Dannon Baker 1c0d694d47 Swap log string formatting to arg 2015-04-16 14:17:04 -04:00
Dannon Baker 57675eef7b Better logging in scrambler, shows more detailed error when, for example, hardlinked items in tars cause errors 2015-04-16 14:12:23 -04:00
Carl Eberhard f93961c497 Merge testing 2015-04-16 11:09:11 -04:00
Carl Eberhard 5ebe04cfd0 Testing: fix failing unit tests that were recently added 2015-04-16 10:45:24 -04:00
Dannon Baker 1f90dfd86a Merge pull request #115 from guerler/revise_validation 
Revise late validation of tool parameters
 2015-04-16 09:58:14 -04:00
John Chilton 9c1550b36e Improved Cheetah type casting for int/float types. 
Based on idea by @peterjc in a discussion here - http://dev.list.galaxyproject.org/Geting-integer-value-from-InputValueWrapper-in-plugin-xml-file-td4666971.html. With simple test demonstrating new functionality. Run test with

    ./run_tests.sh -framework -id cheetah_casting
 2015-04-16 09:34:08 -04:00
guerler 112409f4e9 Additional fix for genome builds 2015-04-15 17:50:22 -04:00
guerler 4c883d689e Fix genome build and revise drill down parameter 2015-04-15 17:33:22 -04:00
Dannon Baker 4ee3396793 Merge pull request #119 from jmchilton/toolbox_auth 
Stronger toolbox filtering.
 2015-04-15 17:28:33 -04:00
Nate Coraor a4e4e59b5a Merge pull request #117 from jmchilton/detect_errors 
Implement ``detect_errors`` attribute on tool XML.
 2015-04-15 16:43:33 -04:00
John Chilton afcf899f13 Stronger toolbox filtering. 
- Update toolbox filtering rules to also filter on tool.allow_user_access.
 - Use toolbox filtering when listing tools not in the context of panel (so filtered tools are not returned from the API).

See also:

 - https://trello.com/c/jyl0cvFP
 - https://trello.com/c/Sg8D2PBj
 - http://dev.list.galaxyproject.org/Bug-Toolbox-filters-not-applied-in-workflows-td4662879.html

Testing:

The following command will run a superset of relevant tests:

    ./run_tests.sh -u test/unit/tools
 2015-04-15 14:40:50 -04:00
John Chilton 0fe2b601ce Implement detect_errors attribute on XML. 
If present, it can be one of

 - "default", no-op fallback to stdio tags and erroring on standard error output.
 - "exit_code", error if tool exit code is not 0. (The @jmchilton recommendation).
 - "aggressive", error if tool exit code is not 0 or either Exception: or Error: appears in standard error/output. (The @bgruening recommendation).

Refactoring and unit/functional tests to support and demonstrate this.

Run functional test with:

    ./run_tests.sh -framework -id detect_errors_aggressive

Run relevant unit tests:

    nosetests test/unit/tools/test_parsing.py

Updated from original version to reflect comments on pull request #117 - in particular the ``detect_errors`` tag was moved from ``tool`` to ``command``.
 2015-04-15 12:38:35 -04:00
Bjoern Gruening 7f0dede663 add option to pass arbitrary parameters to gem install 2015-04-14 21:10:05 +02:00
guerler 5c8ad19ddb New library data selector for tool form 2015-04-14 02:27:38 -04:00
guerler c0afb6403c Merge branch 'dev' of https://github.com/galaxyproject/galaxy into revise_validation 2015-04-11 03:12:56 -04:00
Martin Cech 0357ac5032 flake8 travis fix 
E127 continuation line over-indented for visual indent
 2015-04-10 21:26:19 -04:00
guerler c1bf66b9b0 Merge branch 'dev' of https://github.com/galaxyproject/galaxy into revise_validation 
Conflicts:
	lib/galaxy/tools/__init__.py
	static/maps/mvc/form/form-view.js.map
	static/scripts/mvc/form/form-view.js
 2015-04-10 19:59:56 -04:00
Nate Coraor cae72a8c69 Merge branch 'release_15.03' into dev 2015-04-10 16:20:25 -04:00
Nate Coraor 0fba80498c Merge pull request #108 from blankenberg/bam_metadat_enhancements 
Reorder BAM metadata to set reference names and lengths before attempting to parse header. Add test.
 2015-04-10 16:13:27 -04:00
Daniel Blankenberg 3d048a80e3 Merge pull request #109 from jmchilton/pulsar_client_apr2015 
Tweaks to the Pulsar job runners handling of async messags.
 2015-04-10 15:53:38 -04:00
John Chilton 647cf55a11 Tweaks to the Pulsar job runners handling of async messags. 
- Report a more appropriate message for responding to "failed" status.
 - Respond to the new "lost" message (https://github.com/galaxyproject/pulsar/commit/61ed774ae6c67e7f0d891999def7233d1572013c).
 - Do not fail "lost" or "failed" jobs that may Galaxy may think have already completed (roughly).
 2015-04-10 15:43:25 -04:00
Nate Coraor 7210e5d46e Move, rather than copy files staged back to Galaxy via the job files 
api. Moving is a rename when the source and destination are on the same
filesystem, which is nearly instantaneous and greatly reduces the
possibility for failure due to mid-copy restarts.
 2015-04-10 15:30:31 -04:00
Nate Coraor 1167c7d724 Enable use of nginx_upload_module for the job files api. 2015-04-10 15:29:18 -04:00
Daniel Blankenberg 56dc50d4fc Reorder BAM metadata to set reference names and lengths before attempting to parse header. pysam will die on parsing headers from e.g. 3unsorted.bam (sorted). 2015-04-10 15:00:27 -04:00
Daniel Blankenberg 91f424a55a Add try/except around BAM metadata pysam actions. 2015-04-10 13:50:11 -04:00
Daniel Blankenberg 34d2564a27 Enhance BAM metadata to include bam_version, sort_order, read_groups, reference_names, reference_lengths, and a dictionary of bam_header. 2015-04-10 13:17:08 -04:00
John Chilton aad36d0776 Rev pulsar client code. 
Updates Pulsar client through https://github.com/galaxyproject/pulsar/commit/f1a9e83674dd98affbed476ba36b3ad07fa5e88b. The most important and substantial change here is a fix for galaxyproject/pulsar#63 provided by @dctrud.
 2015-04-10 12:21:44 -04:00
John Chilton 800e83fef6 Merge pull request #105 from dannon/startup_logfix 
Check to see if toolshed install is actually bound prior to disposing (e...
 2015-04-10 10:36:08 -05:00
Dannon Baker 30c004bd8c Check to see if toolshed install is actually bound prior to disposing (exact same functionality here, but it's less chatty this way, since it might not be bound) 2015-04-10 11:23:46 -04:00
John Chilton e09fc21e6c Merge pull request #104 from guerler/revise_default_values 
Fix default value handling in new tool form
 2015-04-10 07:56:14 -05:00
John Chilton 38b06a704b Merge pull request #35 from guerler/tool_form_section_tag 
Tool form section tag
 2015-04-10 07:52:37 -05:00
guerler 3ff5204801 Fix default tool parameter value handling in current form 2015-04-09 22:44:16 -04:00
guerler e625190219 Fix default value handling in new tool form 2015-04-09 22:18:41 -04:00
John Chilton c983f029cc Merge pull request #8 from jmchilton/argument_name 
Add argument to tool parameters.
 2015-04-09 15:03:05 -05:00
Nicola Soranzo 8254caba54 Update many links which redirect to https. 2015-04-09 20:37:03 +01:00
Dannon Baker 30f0670ade Merge pull request #76 from carlfeberhard/managers 
Managers
 2015-04-09 12:44:19 -04:00
Carl Eberhard 4f78a9aee3 Managers: more travis fixes: missing/misnamed variables 2015-04-09 12:34:07 -04:00
Dannon Baker af7cfadfc4 Merge pull request #99 from jmchilton/travis_enhance_1 
TraivsCI: More comprehensive checks for *very* broken stuff.
 2015-04-09 07:35:08 -04:00
guerler 7f479ff32c WorkflowForm: Use is_workflow instead of is_dynamic for workflow editor 2015-04-09 00:28:37 -04:00
John Chilton 6d49f1ef51 Fix undefined variables in remote_repository_registry_entry. 2015-04-08 23:22:28 -04:00
John Chilton dc256aebf2 Fix tool shed scripts that log without creating a log. 2015-04-08 23:22:28 -04:00
John Chilton 453dde829e Fix unknown name self in tool_shed.scripts.api.export. 2015-04-08 23:22:28 -04:00