September 2015 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 857755: Fix multi-history copy/new to set the history as c...
by GitHub 14 Sep '15

14 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 857755284db6ba2c6a773e01050222ba9748e616 https://github.com/galaxyproject/galaxy/commit/857755284db6ba2c6a773e010502… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-09-14 (Mon, 14 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M static/maps/mvc/history/history-model.js.map M static/scripts/mvc/history/history-model.js Log Message: ----------- Fix multi-history copy/new to set the history as current Commit: 1ba64709e668f08ce757606a784aec19f7a840d1 https://github.com/galaxyproject/galaxy/commit/1ba64709e668f08ce757606a784a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-14 (Mon, 14 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M static/maps/mvc/history/history-model.js.map M static/scripts/mvc/history/history-model.js Log Message: ----------- Merge pull request #727 from carlfeberhard/fix.multi-new Fix multi-history copy/new to set the history as current Compare: https://github.com/galaxyproject/galaxy/compare/2844d8579b5e...1ba64709e668

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[galaxyproject/galaxy] 222d78: Fix history options menu
by GitHub 14 Sep '15

14 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 222d7805e9a36b5d9b1e31377f1fb35f3405f084 https://github.com/galaxyproject/galaxy/commit/222d7805e9a36b5d9b1e31377f1f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-14 (Mon, 14 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M static/maps/mvc/app/app-analysis.js.map M static/scripts/mvc/app/app-analysis.js Log Message: ----------- Fix history options menu Commit: 08fef5843894317b791559e7dc2aa54bb720aed3 https://github.com/galaxyproject/galaxy/commit/08fef5843894317b791559e7dc2a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-14 (Mon, 14 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M static/maps/mvc/app/app-analysis.js.map M static/scripts/mvc/app/app-analysis.js Log Message: ----------- Fix purge flag in history options Commit: 2844d8579b5e84c81b22a662ca4d1211f96f39d3 https://github.com/galaxyproject/galaxy/commit/2844d8579b5e84c81b22a662ca4d… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2015-09-14 (Mon, 14 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M static/maps/mvc/app/app-analysis.js.map M static/scripts/mvc/app/app-analysis.js Log Message: ----------- Merge pull request #726 from guerler/fix_history_000 Fix history option flags Compare: https://github.com/galaxyproject/galaxy/compare/b51294efba3b...2844d8579b5e

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[galaxyproject/galaxy] 8c2ab4: Extend root controller to allow specifing a histor...
by GitHub 14 Sep '15

14 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8c2ab4180b218c3cffcf5c739ccbe4d22c52edaa https://github.com/galaxyproject/galaxy/commit/8c2ab4180b218c3cffcf5c739ccb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-14 (Mon, 14 Sep 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- 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. Commit: b51294efba3ba018bab6b7f5d9234196f7712adc https://github.com/galaxyproject/galaxy/commit/b51294efba3ba018bab6b7f5d923… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-14 (Mon, 14 Sep 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge pull request #725 from jmchilton/history_id_entry Extend root controller to allow specifying a history id. Compare: https://github.com/galaxyproject/galaxy/compare/51979deefbd9...b51294efba3b

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[galaxyproject/galaxy] 76ad95: Fix lint failure in toolshed/admin.
by GitHub 13 Sep '15

13 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 76ad959f16e0f30a8e306056ab8042ba8512b9a9 https://github.com/galaxyproject/galaxy/commit/76ad959f16e0f30a8e306056ab80… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-13 (Sun, 13 Sep 2015) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/admin.py Log Message: ----------- Fix lint failure in toolshed/admin. Commit: 51979deefbd98858987d7c93495743300845c90c https://github.com/galaxyproject/galaxy/commit/51979deefbd98858987d7c934957… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-09-13 (Sun, 13 Sep 2015) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/admin.py Log Message: ----------- Merge pull request #722 from dannon/style_fix Fix lint failure in toolshed/admin. Compare: https://github.com/galaxyproject/galaxy/compare/fef28884fc6f...51979deefbd9

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[galaxyproject/usegalaxy-playbook] 41bc8a: Update Test Galaxy and Pulsar
by GitHub 11 Sep '15

11 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 41bc8a7d80e99b1c405a72254729a223e4a625b9 https://github.com/galaxyproject/usegalaxy-playbook/commit/41bc8a7d80e99b1c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M stage/group_vars/all.yml M stage/group_vars/pulsarservers.yml Log Message: ----------- Update Test Galaxy and Pulsar

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[galaxyproject/galaxy] 63a715: Fix Tool Shed test broken with PR #706.
by GitHub 11 Sep '15

11 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 63a715f27c5ee31de6bdd0cd4222b309b3f2ce23 https://github.com/galaxyproject/galaxy/commit/63a715f27c5ee31de6bdd0cd4222… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M test/tool_shed/functional/test_1140_tool_help_images.py Log Message: ----------- Fix Tool Shed test broken with PR #706. Commit: ed92a12e78dad1d7290fde30b23768b613e68232 https://github.com/galaxyproject/galaxy/commit/ed92a12e78dad1d7290fde30b237… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Specify the tool_id of the missing tool when raising MissingToolException. Commit: 760899f9c0ce717df4e6c789e36693973d048c7d https://github.com/galaxyproject/galaxy/commit/760899f9c0ce717df4e6c789e366… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M test/api/test_workflows.py Log Message: ----------- Fix MissingToolException when running "./run_tests.sh -api" without "-with_framework_test_tools". Commit: 65519718b37a0a08c802c131b92ca0335a0b7eda https://github.com/galaxyproject/galaxy/commit/65519718b37a0a08c802c131b92c… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M test/api/yaml_to_workflow.py Log Message: ----------- 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' Commit: cd456e186dc1ba6f51e3cafb0c54d6b1f1651817 https://github.com/galaxyproject/galaxy/commit/cd456e186dc1ba6f51e3cafb0c54… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M cron/add_manual_builds.py M cron/build_chrom_db.py M cron/cleanup_datasets.py M scripts/check_galaxy.py Log Message: ----------- Print to stderr when calling sys.exit(1) Commit: c01cf85d450a83c4f235ba488b84d2c7a60c4209 https://github.com/galaxyproject/galaxy/commit/c01cf85d450a83c4f235ba488b84… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M doc/source/conf.py M lib/galaxy/main.py M lib/galaxy_ext/metadata/set_metadata.py M test/base/tool_shed_util.py M test/install_and_test_tool_shed_repositories/base/util.py M test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py M test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py M test/manual/workflows_scaling.py M test/tool_shed/functional_tests.py M test/unit/unittest_utils/utility.py Log Message: ----------- Use __file__ when adding paths to sys.path instead of os.getcwd() . Also insert additional paths in position 1 unless strictly necessary. Commit: fef28884fc6f46efb01816c9466667840947f372 https://github.com/galaxyproject/galaxy/commit/fef28884fc6f46efb01816c94666… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M cron/add_manual_builds.py M cron/build_chrom_db.py M cron/cleanup_datasets.py M doc/source/conf.py M lib/galaxy/main.py M lib/galaxy/workflow/modules.py M lib/galaxy_ext/metadata/set_metadata.py M scripts/check_galaxy.py M test/api/test_workflows.py M test/api/yaml_to_workflow.py M test/base/tool_shed_util.py M test/install_and_test_tool_shed_repositories/base/util.py M test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py M test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py M test/manual/workflows_scaling.py M test/tool_shed/functional/test_1140_tool_help_images.py M test/tool_shed/functional_tests.py M test/unit/unittest_utils/utility.py Log Message: ----------- Merge pull request #720 from nsoranzo/misc_fixes Misc fixes Compare: https://github.com/galaxyproject/galaxy/compare/36809cd6f37f...fef28884fc6f

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[galaxyproject/galaxy] 819c7d: Pulsar client: Fix deepcopy() error with copying t...
by GitHub 11 Sep '15

11 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 819c7dce408f35f69457cd92803c63cf3efca0c4 https://github.com/galaxyproject/galaxy/commit/819c7dce408f35f69457cd92803c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M lib/pulsar/client/amqp_exchange.py Log Message: ----------- Pulsar client: Fix deepcopy() error with copying the errback method from PulsarExchange. Commit: 36809cd6f37f65e9b571a0eb3e663419930e5871 https://github.com/galaxyproject/galaxy/commit/36809cd6f37f65e9b571a0eb3e66… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M lib/pulsar/client/amqp_exchange.py Log Message: ----------- Merge branch 'amqp_ack' into test Compare: https://github.com/galaxyproject/galaxy/compare/91799c3891fe...36809cd6f37f

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[galaxyproject/galaxy] 819c7d: Pulsar client: Fix deepcopy() error with copying t...
by GitHub 11 Sep '15

11 Sep '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: 819c7dce408f35f69457cd92803c63cf3efca0c4 https://github.com/galaxyproject/galaxy/commit/819c7dce408f35f69457cd92803c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M lib/pulsar/client/amqp_exchange.py Log Message: ----------- Pulsar client: Fix deepcopy() error with copying the errback method from PulsarExchange. Commit: 88abd3451d1b8cb7161fde7559684d5378dc76fc https://github.com/galaxyproject/galaxy/commit/88abd3451d1b8cb7161fde755968… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M lib/pulsar/client/amqp_exchange.py Log Message: ----------- Merge pull request #719 from natefoo/amqp_ack [15.07] Pulsar client: Fix deepcopy() error with copying the errback method from PulsarExchange. Compare: https://github.com/galaxyproject/galaxy/compare/358dc4071462...88abd3451d1b

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[galaxyproject/galaxy] d41c13: Fix for logging in using OpenID when the OpenID is...
by GitHub 11 Sep '15

11 Sep '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: d41c137e2d6b4d9871bb25c5162745dda36e2f31 https://github.com/galaxyproject/galaxy/commit/d41c137e2d6b4d9871bb25c51627… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M templates/user/login.mako Log Message: ----------- Fix for logging in using OpenID when the OpenID isn't associated with a user yet. (cherry picked from commit 451196e4d39800995d7b1ea1f69b177294c3c632) Commit: 358dc4071462347dacecd1f6ec125d650b261db0 https://github.com/galaxyproject/galaxy/commit/358dc4071462347dacecd1f6ec12… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M templates/user/login.mako Log Message: ----------- Merge pull request #718 from blankenberg/openid_15.07 [15.07] Fix for logging in using OpenID when the OpenID isn't associated with a user yet. Compare: https://github.com/galaxyproject/galaxy/compare/16fb094f1a10...358dc4071462

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[galaxyproject/usegalaxy-playbook] 6a7350: Fix secret vars path for updating Galaxy on Pulsar...
by GitHub 11 Sep '15

11 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 6a73502f1c8ace9f721427ef6f0c24e59fe33ae3 https://github.com/galaxyproject/usegalaxy-playbook/commit/6a73502f1c8ace9f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M galaxy.yml Log Message: ----------- Fix secret vars path for updating Galaxy on Pulsar servers

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