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Author SHA1 Message Date
John Chilton 09a68adb1e Add another API test verifying validation of workflow substitions. 
A little different because it targets a different tool, validation, and is inside a repeat.
 2015-12-10 00:06:54 +00:00
John Chilton 133e5f2e24 Various small API testing fixes/improvements. 2015-12-10 00:06:53 +00:00
Björn Grüning 4d252119fd Merge pull request #1216 from jmchilton/workflow_tweaks_1 
More small workflow tweaks.
 2015-12-05 21:38:34 +01:00
Björn Grüning 6126bd0e93 Merge pull request #1214 from jmchilton/format_2_1 
Small enhancements in workflow inputs and outputs
 2015-12-05 21:37:50 +01:00
Björn Grüning d7f5dbe4ca Merge pull request #805 from jmchilton/multi_data_param_enhance 
Allow multiple collections to be supplied to a multiple data parameter.
 2015-12-05 20:09:10 +01:00
Martin Cech b0c1cd7460 Merge pull request #1243 from jmchilton/maxseconds_debug 
Improved logging related tool test timeouts.
 2015-12-05 00:29:27 -05:00
Martin Cech f7a2acdcab Merge pull request #1246 from jmchilton/test-commons 
Fix up merge issue with double underscore shim.
 2015-12-05 00:28:38 -05:00
John Chilton 9f8eb465e7 Merge pull request #1144 from carlfeberhard/webpack 
Webpack
 2015-12-04 20:21:36 -05:00
John Chilton 17851ba0ea And fix unit test for b036adcaa166153e544935c12123877c69a7450f. 2015-12-04 20:41:22 +00:00
John Chilton 62a26516cd Fix PR #805 for changes in PR #1153. 2015-12-04 20:41:22 +00:00
John Chilton c91a2eb339 Multi data parameter improvements. 
Allow multiple collections to be fed to a multi data parameter in one reduction step. Fixes #750 and will really simplify certain classes of tools.

Rebased original with fixes for rerun of such reductions.

Manually tested workflow execution and everything seems fine. The workflow editor already thought this was possible, so that is another bug corrected by this enhancement.

To run the associated API test, execute the following command:

./run_tests.sh -with_framework_test_tools -api test/api/test_tools.py:ToolsTestCase.test_reduce_multiple_lists_on_multi_data

Conflicts:
	static/maps/mvc/dataset/dataset-choice.js.map
	static/maps/mvc/form/form-select-content.js.map
	static/scripts/mvc/form/form-select-content.js
 2015-12-04 20:41:21 +00:00
John Chilton e9e73f4828 Remove dated comment. 2015-12-04 20:40:29 +00:00
John Chilton 40e6932a25 Fix workflow API tests for workflow output changes. 2015-12-04 20:37:37 +00:00
John Chilton cee9d4d1b3 Grunt the workflow JS. 2015-12-04 20:37:35 +00:00
John Chilton 7b3fa824b6 Update worklfow editor representation of workflow outputs. 
Modified this for the workflow export representation but this needed to be updated for the workflow editor because they shared some code in the manager. This was going to be needed downstream when I add labels and uuids to workflow outputs anyway.
 2015-12-04 20:36:18 +00:00
John Chilton 3d0723c812 JS Model abstractions for dealing workflow outputs. 
Need to modify how these are represented so I want the logic centralized in the model... also the logic should be centralized in the model.
 2015-12-04 20:36:16 +00:00
John Chilton a597e0e834 Implement workflow outputs for format 2 workflow definitions. 
Copy CWL style of specifying a outputs specification block at the top-level of the workflow specification and within that use the "source" attribute to specify the output. Reuse the specification used by "$link"s to describe this output - namely <label_or_order_index>[#<output_name=output>].
 2015-12-04 20:34:57 +00:00
John Chilton 1bd0a4e970 Refactoring and more testing of format 2 workflow implementation code... 
... toward more reusable design.
 2015-12-04 20:34:57 +00:00
John Chilton 70a9f21393 Update workflow format 2 code with infrastructure for nesting runnables. 
In downstream work this is used for subworkflows and nested tools. Not sure which of these would potentially hit main line Galaxy first so setting this all up in its own commit.
 2015-12-04 20:34:57 +00:00
John Chilton b0b26e6901 Allow specifying Format 2 workflow by path. 
This will allow importing workflow relative resources in subsequent passes at this.
 2015-12-04 20:34:56 +00:00
John Chilton 4a279ffb64 Allow inputs section for Format 2 workflow definitions. 
Arguably a more natural way to define inputs, regardless it allows more CWL-like input definitions for workflows.
 2015-12-04 20:34:56 +00:00
John Chilton 0924891e31 Fix up merge issue with double underscore shim. 2015-12-04 20:33:01 +00:00
carlfeberhard 9e8068f367 (merge dev) 2015-12-04 13:17:29 -05:00
Nate Coraor 3e8b58c5aa Merge branch 'release_15.10' into dev 2015-12-04 13:15:49 -05:00
Martin Cech 736bf3ce84 Merge pull request #1234 from natefoo/pulsar-missing-param 
[15.10] Add the missing "amqp_ack_republish_time" param for the Pulsar runner
 2015-12-04 13:11:19 -05:00
Martin Cech 5675617178 Merge pull request #985 from erasche/nicer-history-menu 
Add icons and reorganise history menu
 2015-12-04 12:57:42 -05:00
Eric Rasche 198cb7c9a1 Fix rebase issue 2015-12-04 11:51:17 -06:00
John Chilton 4d396a6945 Merge pull request #1221 from pvanheus/env-modules-resolve 
Add documentation and extra options to Environment Modules resolver
 2015-12-04 12:47:13 -05:00
Eric Rasche 9bd2712c5d Just going to clobber everything 2015-12-04 11:46:27 -06:00
Eric Rasche 42b6da8755 Comment out debugging 2015-12-04 11:46:00 -06:00
Eric Rasche 564f12c50f Remove icons 2015-12-04 11:46:00 -06:00
Eric Rasche 1cc57b1eb2 Add icons and reorganise history menu 2015-12-04 11:46:00 -06:00
Martin Cech 4289cf3ab2 Merge pull request #1235 from blankenberg/typo_dev 
Minor docstring typo
 2015-12-04 12:17:58 -05:00
Daniel Blankenberg 0eb87f911c Minor docstring typo 2015-12-04 12:15:44 -05:00
Nate Coraor 107de0e1d7 Add the missing "amqp_ack_republish_time" param for the Pulsar runner 
(it's available in the Pulsar client lib).
 2015-12-04 11:35:42 -05:00
Martin Cech 905471e32f Merge pull request #1226 from jmchilton/jobs_api_test_fix 
Wait on jobs and history in certain API test cases.
 2015-12-04 11:33:35 -05:00
carlfeberhard 5c87d07e0f Merge pull request #1233 from jmchilton/underscore_shim 
Fix qunit shim to match base_panels.mako shim.
 2015-12-04 11:29:17 -05:00
John Chilton 74f7b90036 Merge pull request #1230 from openlangrid/dev 
Replacement should be applied only to first occurrence.
 2015-12-04 11:11:56 -05:00
John Chilton bab7ae0998 Improved logging related tool test timeouts. 
There are transient failures of maxseconds.xml's tool test on Jenkins that I can't reproduce locally, hopefully improved logging will help.

https://jenkins.galaxyproject.org/job/docker-framework/1309/testReport/junit/functional.test_toolbox/TestForTool_maxseconds/test_tool_000000/
 2015-12-04 16:06:01 +00:00
Nate Coraor 600338dac7 Merge pull request #1231 from nsoranzo/dev_tests_conditional_wheels 
Export GALAXY_TEST_DBURI as GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION before installing wheels.
 2015-12-04 10:40:08 -05:00
carlfeberhard f40d4fc178 Webpack: re-add show_welcome_with_login config option (lost due to merge/gitignore?); remove root/index.mako 2015-12-04 10:18:51 -05:00
John Chilton 93bfa1992c Make more workflow methods properties. 
As suggested by @nsoranzo.
 2015-12-04 15:08:56 +00:00
John Chilton fcabc5242c Merge pull request #1160 from Christian-B/unlinked_dependencies 
Allowed for capitalised package names such as R
 2015-12-04 09:15:23 -05:00
John Chilton 296971c5de Fix typo spotted by @nsoranzo. 2015-12-04 13:48:36 +00:00
Nicola Soranzo 0c8a738a35 Export GALAXY_TEST_DBURI as GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION before installing wheels. Fix #1205. 
As test/docker/base/run_test_wrapper.sh does.
 2015-12-04 11:39:36 +00:00
John Chilton f969eabf26 Fix qunit shim to match base_panels.mako shim. 
QUnit tests of things with underscore require statements would not work without this change.
 2015-12-04 11:24:43 +00:00
Nicola Soranzo 11c46f4f35 Merge branch 'master' into dev 2015-12-04 09:37:28 +00:00
Takao Nakaguchi 102eeef2d7 Replacement should be applied only to first occurrence. 2015-12-04 01:28:23 +00:00
Eric Rasche e76933b557 Merge pull request #1229 from martenson/remove-readthecdocs-badge 
replace the readthedocs badge,
 2015-12-03 16:56:03 -06:00
Martin Cech 6735c9dece replace the readthedocs badge, 
we cannot use it until https://github.com/rtfd/readthedocs.org/issues/1767 is resolved
 2015-12-03 17:11:52 -05:00