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Author SHA1 Message Date
Nate Coraor 150c17b9e8 Do not explicitly require pexpect. If anyone wants to use the old and 
mostly unused features that depend on it (namely remote sequencer
transfers via scp) they can pip install pexpect.
 2015-09-17 13:56:44 -04:00
John Chilton d717ec833d Merge pull request #698 from bgruening/pip_install 
Use setup.py for Python all installations
 2015-09-17 18:25:45 +01:00
Dannon Baker c74cda3c60 Merge pull request #738 from jmchilton/logging 
Add testing environment variable GALAXY_TEST_LOGGING_CONFIG.
 2015-09-17 13:08:11 -04:00
Bjoern Gruening 4e063e793f add mkdir as safeguard and remove old warning 2015-09-17 17:32:33 +02:00
Aysam Guerler 7c78e01b7d Merge pull request #739 from dannon/rerun_newform 
Swap rerun to use iframe-less Galaxy.display.
 2015-09-17 11:27:55 -04:00
Dannon Baker a7ca9586bb Allow serialization of hdas without 'creating job', though we should probably look into how/why this can ever happen. Seems like there's a bug hidden here somewhere, but this allows the existing functionality to work and pass tests. 2015-09-17 10:52:06 -04:00
John Chilton 4d4e19b379 Merge pull request #736 from dannon/pja_wf_rerun_fix 
Check to make sure a job is actually part of a workflow invocation pr…
 2015-09-17 14:50:07 +01:00
Dannon Baker 3348715971 Add documentation to new API endpoint. 2015-09-17 09:31:56 -04:00
Dannon Baker 5953fb5922 Use tool.to_json optional kwd to parse old job inputs instead of doing it manually. 2015-09-16 14:37:35 -04:00
Dannon Baker c51bfaa51a Flip API endpoint to the jobs API instead of hacking it into the existing tools api. 2015-09-16 14:04:50 -04:00
Nate Coraor 43c13ee162 Merge branch 'release_15.07' into dev 
Conflicts:
	lib/galaxy/model/__init__.py
 2015-09-16 12:02:59 -04:00
Dannon Baker 1a5ef156d9 First pass of updating rerun to use the new modal. Pretty hacky, needs cleanup. 2015-09-16 11:52:38 -04:00
Martin Cech 85552f73f7 Merge pull request #737 from natefoo/job-terminal-update 
[15.07] Don't update the state of terminal jobs
 2015-09-16 11:49:49 -04:00
Nate Coraor d3bd0fa577 Do not change the state of jobs if a state update is received after they 
are set to a terminal state.
 2015-09-16 11:27:48 -04:00
John Chilton bd55650f06 Add testing environment variable GALAXY_TEST_LOGGING_CONFIG. 
Unifies logging through the testing process. Requires adding a Galaxy option to disable its own attempts to configure a different root logger.
 2015-09-16 16:24:53 +01:00
carlfeberhard 1e2adc6b57 Merge pull request #732 from guerler/fix_history_001 
Trigger iframe event for history
 2015-09-15 17:49:37 -04:00
Dannon Baker d3e14ec673 Check to make sure a job is actually part of a workflow invocation prior to attempting to clean other workflow steps. This prevents an error when a 'clean intermediates' type job is remapped. TODO: Perhaps the job should actually be replaced in the workflow invocation as well, but this is a decent defensive check anyway. 2015-09-15 16:55:42 -04:00
Martin Cech 71a1def321 Merge pull request #735 from jmchilton/collection_fix 
Fix for 13ea86753a.
 2015-09-15 16:07:24 -04:00
John Chilton 89b42bf060 Merge pull request #731 from nsoranzo/dev 
Fix more API tests.
 2015-09-15 13:59:00 -04:00
guerler 89cc67baf6 Trigger iframe event for history 2015-09-15 13:32:59 -04:00
Nicola Soranzo 63d1715679 Fix API tests using collection_creates_pair tool. 2015-09-15 17:06:27 +01:00
Nicola Soranzo 3fafbb5e34 Fix more MissingToolException when running "./run_tests.sh -api" without "-with_framework_test_tools". 2015-09-15 16:47:40 +01:00
John Chilton 4671ae8d45 Merge pull request #730 from dannon/pja_wf_rerun_fix 
When rerunning a job w/ remap, reassociate PostJobActions when possib…
 2015-09-15 11:45:26 -04:00
John Chilton 555b6d745d Fix for 13ea86753a. 
Fixes tests and functionality broken with 13ea86753a as spotted by eagle eye @nsoranzo here https://github.com/galaxyproject/galaxy/commit/13ea86753ad778aaaf6e6470a9370190fc2e91a0#commitcomment-13245289.
 2015-09-15 16:03:05 +01:00
Dannon Baker 23051da68c When rerunning a job w/ remap, reassociate PostJobActions when possible to the new job. 2015-09-15 10:18:32 -04:00
Dannon Baker 1ea1da0229 Merge pull request #729 from mr-c/drop-noop-init 
remove no-op __init__ methods from lib/galaxy/datatypes/binary.py
 2015-09-15 07:27:56 -04:00
Michael R. Crusoe 8dadfdcaa0 remove no-op __init__ methods 2015-09-14 17:06:57 -07:00
Eric Rasche 34165913ba Merge pull request #702 from nsoranzo/readme_contributing 
[PROCEDURES] Reorganize content
 2015-09-14 14:45:50 -05:00
Aysam Guerler 08668104e5 Merge pull request #728 from carlfeberhard/fix.galaxy-user 
Fix Galaxy.user to be available when not using 1 require
 2015-09-14 14:35:45 -04:00
John Chilton ba25057922 Merge pull request #694 from erasche/deduplication 
Deduplication PR
 2015-09-14 13:43:56 -04:00
Carl Eberhard 85480e72bf Fix Galaxy.user to be available when not using 1 require 2015-09-14 13:39:15 -04:00
Martin Cech 1ba64709e6 Merge pull request #727 from carlfeberhard/fix.multi-new 
Fix multi-history copy/new to set the history as current
 2015-09-14 11:45:43 -04:00
Carl Eberhard 857755284d Fix multi-history copy/new to set the history as current 2015-09-14 11:37:17 -04:00
Aysam Guerler 2844d8579b Merge pull request #726 from guerler/fix_history_000 
Fix history option flags
 2015-09-14 11:19:11 -04:00
guerler 08fef58438 Fix purge flag in history options 2015-09-14 11:04:54 -04:00
guerler 222d7805e9 Fix history options menu 2015-09-14 10:58:02 -04:00
Martin Cech b51294efba Merge pull request #725 from jmchilton/history_id_entry 
Extend root controller to allow specifying a history id.
 2015-09-14 09:47:11 -04:00
John Chilton 57634f43ea Fix lint problems from merge. 
How did that happen, those pieces of code were largely unrelated. Ekkk...
 2015-09-14 11:21:04 +01:00
John Chilton 17d8e15e4e Merge remote-tracking branch 'erasche/deduplication' into deduplication-merge 
Conflicts:
	lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py
	lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py
 2015-09-14 11:14:42 +01:00
John Chilton 8c2ab4180b Extend root controller to allow specifing a history id. 
It currently allows hoping straight to a given workflow or tool by id, this commit extends that to allow histories as well. Simply add history_id=<history_id> to the query string.
 2015-09-14 09:40:20 +01:00
Björn Grüning 51979deefb Merge pull request #722 from dannon/style_fix 
Fix lint failure in toolshed/admin.
 2015-09-13 22:36:33 +02:00
Dannon Baker 76ad959f16 Fix lint failure in toolshed/admin. 2015-09-13 09:36:20 -04:00
Björn Grüning fef28884fc Merge pull request #720 from nsoranzo/misc_fixes 
Misc fixes
 2015-09-11 21:01:18 +02:00
Nicola Soranzo c01cf85d45 Use __file__ when adding paths to sys.path instead of os.getcwd() . 
Also insert additional paths in position 1 unless strictly necessary.
 2015-09-11 19:05:37 +01:00
Nicola Soranzo cd456e186d Print to stderr when calling sys.exit(1) 2015-09-11 19:05:37 +01:00
Nicola Soranzo 65519718b3 Fix "KeyError: name" error when running "./run_tests.sh -api". 
Example traceback for test/api/test_workflows.py:WorkflowsApiTestCase.test_workflow_run_dynamic_output_collections :

galaxy.web.framework.decorators: ERROR: Uncaught exception in exposed API method:
Traceback (most recent call last):
  File "/opt/galaxy/lib/galaxy/web/framework/decorators.py", line 260, in decorator
    rval = func( self, trans, *args, **kwargs)
  File "/opt/galaxy/lib/galaxy/webapps/galaxy/api/workflows.py", line 182, in create
    return self.__api_import_new_workflow( trans, payload, **kwd )
  File "/opt/galaxy/lib/galaxy/webapps/galaxy/api/workflows.py", line 374, in __api_import_new_workflow
    workflow, missing_tool_tups = self._workflow_from_dict( trans, data, **from_dict_kwds )
  File "/opt/galaxy/lib/galaxy/web/base/controller.py", line 1111, in _workflow_from_dict
    publish=publish
  File "/opt/galaxy/lib/galaxy/managers/workflows.py", line 165, in build_workflow_from_dict
    missing_tool_tup = ( step_dict[ 'tool_id' ], step_dict[ 'name' ], step_dict[ 'tool_version' ] )
KeyError: 'name'
 2015-09-11 19:05:37 +01:00
Nicola Soranzo 760899f9c0 Fix MissingToolException when running "./run_tests.sh -api" without "-with_framework_test_tools". 2015-09-11 19:05:37 +01:00
Nicola Soranzo ed92a12e78 Specify the tool_id of the missing tool when raising MissingToolException. 2015-09-11 19:05:37 +01:00
Nicola Soranzo 63a715f27c Fix Tool Shed test broken with PR #706. 2015-09-11 19:05:37 +01:00
Martin Cech 88abd3451d Merge pull request #719 from natefoo/amqp_ack 
[15.07] Pulsar client: Fix deepcopy() error with copying the errback method from PulsarExchange.
 2015-09-11 13:22:30 -04:00