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

[galaxyproject/galaxy] b11002: Don't iterate over unused key.
by GitHub 08 Dec '15

08 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b11002bef32d83b058e3495f96695c8dc12cb91b https://github.com/galaxyproject/galaxy/commit/b11002bef32d83b058e3495f9669… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M test/api/workflows_format_2/converter.py Log Message: ----------- Don't iterate over unused key. Thanks to @bgruening. Commit: 2aa7f04364e10e46c655de636925883a43698694 https://github.com/galaxyproject/galaxy/commit/2aa7f04364e10e46c655de636925… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M test/api/workflows_format_2/converter.py Log Message: ----------- Replace __rip_value with dict.pop. Thanks @bgruening. Commit: 98249058e85d8133748519ac59ebed96a28a77ac https://github.com/galaxyproject/galaxy/commit/98249058e85d8133748519ac59eb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Cleanup error message. Thanks @bgruening. Commit: f17a6c996a060f68bc8a250effa23f60b96b44a7 https://github.com/galaxyproject/galaxy/commit/f17a6c996a060f68bc8a250effa2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/web/base/controller.py Log Message: ----------- Synchronize decoding ids across base controller and manager base. To ensure we have the same kind of exception thrown in both cases. Commit: f6d26c9ee6f148fd033d1b070c2dbe8c69b08fa8 https://github.com/galaxyproject/galaxy/commit/f6d26c9ee6f148fd033d1b070c2d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py M test/unit/workflows/test_modules.py Log Message: ----------- Small refactor making workflow views and modules tad more generic. - Reduce duplication between initializing generic modules and tool modules. - Switch tool_id to content_id as variable names throughout the client. - Rename get_tool_id to get_content_id on workflow modules. - Add some minimal documentation to the workflow module about get_content_id. Downstream in the subworkflow commit I switch the over-the-wire communication to use content_id instead of tool_id also and use content_ids to refer to workflow ids in subworkflow moduls. Commit: 73bfbf016347f764a0747ad7c6d138c74b6f519d https://github.com/galaxyproject/galaxy/commit/73bfbf016347f764a0747ad7c6d1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Refactor some workflow API code into workflows manager. This allows for reuse outside of the API controller, such as loading subworkflows downstream. Commit: f92220a74f216d937dc5b147472261d154779512 https://github.com/galaxyproject/galaxy/commit/f92220a74f216d937dc5b1474722… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Allow workflow outputs on non-tool steps. Commit: d18c75ceb875632f9e68a74ebeb88389262d6fa8 https://github.com/galaxyproject/galaxy/commit/d18c75ceb875632f9e68a74ebeb8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor_generic_form.mako Log Message: ----------- Bring gneric and tool module styles into alignment in workflow editor. Commit: d7ac52f6bb61fe360198f91310a3e22076183d7b https://github.com/galaxyproject/galaxy/commit/d7ac52f6bb61fe360198f91310a3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Add icons to existing workflow steps in workflow editor. Tools have an icon there. Commit: e3161b4671e9fb19a47c7f341e3fb46617111a9e https://github.com/galaxyproject/galaxy/commit/e3161b4671e9fb19a47c7f341e3f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor_generic_form.mako M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Add support for workflow step labels in editor. - If a step has a label, display it in the step editor side panel title. - Allow clicking the title to change the label. - Display the label (if set) as the workflow node box title. - Add icon to workflow node since the title might not be related to type anymore. - Enforce unique labels accross the workflow in the editor. - Qunit test cases for some of this behavior and other recent changes. Commit: ef0b6cc459a40227db2e63ee709e9dd5d8fd37c6 https://github.com/galaxyproject/galaxy/commit/ef0b6cc459a40227db2e63ee709e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-07 (Mon, 07 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- show notifications as Toasts and not like JS alerts (bleh) Commit: 4a9dad9f14b94df14b52f41466c9e66dbbfb0556 https://github.com/galaxyproject/galaxy/commit/4a9dad9f14b94df14b52f41466c9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-07 (Mon, 07 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Merge pull request #12 from martenson/labels_toastr show notifications as Toasts and not like JS alerts (bleh) Commit: 3f8950628c3e31d9e2abe0b4f4a360c035133b8e https://github.com/galaxyproject/galaxy/commit/3f8950628c3e31d9e2abe0b4f4a3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor_generic_form.mako Log Message: ----------- Workflow label UI refinement. - Escape workflow labels in mako. - Handle unlabelling steps properly (restore original node name to node and editor form titles). Commit: fe1c9dd2931fb8efccb98fb1646c3e1063b0ab52 https://github.com/galaxyproject/galaxy/commit/fe1c9dd2931fb8efccb98fb1646c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/managers/base.py M lib/galaxy/managers/workflows.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor_generic_form.mako M test/api/workflows_format_2/converter.py M test/qunit/tests/workflow_editor_tests.js M test/unit/workflows/test_modules.py Log Message: ----------- Merge pull request #1251 from jmchilton/workflow_labels_2 Workflow Editor UI for Step Labels Compare: https://github.com/galaxyproject/galaxy/compare/0e5d42f3d67e...fe1c9dd2931f

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[galaxyproject/galaxy] 5ff098: UI, Citations: fix require of bibtex parser
by GitHub 08 Dec '15

08 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5ff09896f7d4ee5208f2f39ca16a7846690af229 https://github.com/galaxyproject/galaxy/commit/5ff09896f7d4ee5208f2f39ca16a… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M static/maps/mvc/citation/citation-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/citation/citation-model.js Log Message: ----------- UI, Citations: fix require of bibtex parser Commit: 6ba86d89bc9d2b6b45dddb13d8dc79a4e2c395a0 https://github.com/galaxyproject/galaxy/commit/6ba86d89bc9d2b6b45dddb13d8dc… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M static/maps/mvc/citation/citation-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/citation/citation-model.js Log Message: ----------- UI, Citations: don't create new BibtexParser, remove debugging Commit: 0e5d42f3d67e5f75dea4abe78909539df3716f1e https://github.com/galaxyproject/galaxy/commit/0e5d42f3d67e5f75dea4abe78909… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M static/maps/mvc/citation/citation-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/citation/citation-model.js Log Message: ----------- Merge pull request #1261 from carlfeberhard/fix.citations UI, Citations: fix require of bibtex parser Compare: https://github.com/galaxyproject/galaxy/compare/bcf8ddfbd0a9...0e5d42f3d67e

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[galaxyproject/galaxy] 833459: Fixes for dataset 'cleanup'/association linking wh...
by GitHub 08 Dec '15

08 Dec '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 8334593de11e915389b1da58c3b5db26121c7bef https://github.com/galaxyproject/galaxy/commit/8334593de11e915389b1da58c3b5… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/workflow/extract.py Log Message: ----------- Fixes for dataset 'cleanup'/association linking when extracting workflows from a history. Commit: 2be17071f35bb5db2298883aff107134a53701d1 https://github.com/galaxyproject/galaxy/commit/2be17071f35bb5db2298883aff10… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M lib/galaxy/workflow/extract.py Log Message: ----------- Merge pull request #1228 from blankenberg/wf_extrac_15.10 [15.10] Fixes for dataset 'cleanup'/association linking when extracting workflows from a history. Compare: https://github.com/galaxyproject/galaxy/compare/94b049926d84...2be17071f35b

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[galaxyproject/galaxy] 41a56e: Fix list collection creator being cutoff by restor...
by GitHub 08 Dec '15

08 Dec '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 41a56ead749bd25c6bc46107201b0e62bb65af9a https://github.com/galaxyproject/galaxy/commit/41a56ead749bd25c6bc46107201b… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-07 (Mon, 07 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M static/maps/mvc/collection/list-collection-creator.js.map M static/scripts/mvc/collection/list-collection-creator.js Log Message: ----------- Fix list collection creator being cutoff by restoring height: 100% Commit: 94b049926d844a8aa54017b6d7a9983b94203316 https://github.com/galaxyproject/galaxy/commit/94b049926d844a8aa54017b6d7a9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M static/maps/mvc/collection/list-collection-creator.js.map M static/scripts/mvc/collection/list-collection-creator.js Log Message: ----------- Merge pull request #1258 from carlfeberhard/release_15.10 [15.10] Fix list collection creator being cutoff by restoring height: 100% Compare: https://github.com/galaxyproject/galaxy/compare/7d4eac1535fc...94b049926d84

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[galaxyproject/usegalaxy-playbook] 082bb6: update Main
by GitHub 07 Dec '15

07 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 082bb67d5aa95a845016ffbc76c6f8c17e9f3e34 https://github.com/galaxyproject/usegalaxy-playbook/commit/082bb67d5aa95a84… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-07 (Mon, 07 Dec 2015) Changed paths: M production/group_vars/all.yml Log Message: ----------- update Main

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[galaxyproject/galaxy] f08d51: Use fixed path to sync like in dev.
by GitHub 07 Dec '15

07 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f08d518aa0bfee1ba3d3da1cca410eee77446534 https://github.com/galaxyproject/galaxy/commit/f08d518aa0bfee1ba3d3da1cca41… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Use fixed path to sync like in dev. It keeps picking up something else on my PATH and breaking my tests when I switch to release_15.10. Commit: f34d70101910dcdd6d699dc1f8688f69ea6d97cf https://github.com/galaxyproject/galaxy/commit/f34d70101910dcdd6d699dc1f868… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Merge pull request #1242 from jmchilton/sync_path [15.10] Use fixed path to sync like in dev. Commit: e186b6a0cfeada4d7852d4661530dec30f73685f https://github.com/galaxyproject/galaxy/commit/e186b6a0cfeada4d7852d4661530… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py Log Message: ----------- Fix for getting shed_config_dict when an old/invalid shed_config_filename has been stored. Fixes issue updating repositories that have had shed_tool_conf.xml changed since installation. Commit: 7d4eac1535fcdc46bea5e407ca74902128dbee18 https://github.com/galaxyproject/galaxy/commit/7d4eac1535fcdc46bea5e407ca74… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py Log Message: ----------- Merge pull request #1245 from blankenberg/shed_update_moved_config [15.10] Fix for getting shed_config_dict when an old/invalid shed_config_filename has been stored. Commit: bcf8ddfbd0a966fd3d6fad157f8ca87702e9c61a https://github.com/galaxyproject/galaxy/commit/bcf8ddfbd0a966fd3d6fad157f8c… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-07 (Mon, 07 Dec 2015) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py Log Message: ----------- Merge branch 'master' into dev Conflicts: lib/galaxy/jobs/runners/__init__.py Compare: https://github.com/galaxyproject/galaxy/compare/01a919ce6a7c...bcf8ddfbd0a9

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[galaxyproject/galaxy] f08d51: Use fixed path to sync like in dev.
by GitHub 07 Dec '15

07 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: f08d518aa0bfee1ba3d3da1cca410eee77446534 https://github.com/galaxyproject/galaxy/commit/f08d518aa0bfee1ba3d3da1cca41… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Use fixed path to sync like in dev. It keeps picking up something else on my PATH and breaking my tests when I switch to release_15.10. Commit: 107de0e1d77200dbd8ac6bc94359f424a25ebca8 https://github.com/galaxyproject/galaxy/commit/107de0e1d77200dbd8ac6bc94359… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Add the missing "amqp_ack_republish_time" param for the Pulsar runner (it's available in the Pulsar client lib). Commit: 736bf3ce843daef3af1fef10ed8441c5ebe65603 https://github.com/galaxyproject/galaxy/commit/736bf3ce843daef3af1fef10ed84… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Merge pull request #1234 from natefoo/pulsar-missing-param [15.10] Add the missing "amqp_ack_republish_time" param for the Pulsar runner Commit: f34d70101910dcdd6d699dc1f8688f69ea6d97cf https://github.com/galaxyproject/galaxy/commit/f34d70101910dcdd6d699dc1f868… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Merge pull request #1242 from jmchilton/sync_path [15.10] Use fixed path to sync like in dev. Commit: e186b6a0cfeada4d7852d4661530dec30f73685f https://github.com/galaxyproject/galaxy/commit/e186b6a0cfeada4d7852d4661530… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py Log Message: ----------- Fix for getting shed_config_dict when an old/invalid shed_config_filename has been stored. Fixes issue updating repositories that have had shed_tool_conf.xml changed since installation. Commit: 7d4eac1535fcdc46bea5e407ca74902128dbee18 https://github.com/galaxyproject/galaxy/commit/7d4eac1535fcdc46bea5e407ca74… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py Log Message: ----------- Merge pull request #1245 from blankenberg/shed_update_moved_config [15.10] Fix for getting shed_config_dict when an old/invalid shed_config_filename has been stored. Compare: https://github.com/galaxyproject/galaxy/compare/516b079ab97d...7d4eac1535fc

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[galaxyproject/galaxy] 732b57: Do not mess with galaxy_config_file, if provided.
by GitHub 07 Dec '15

07 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 732b5722ae7c668634185209171fa55288e19985 https://github.com/galaxyproject/galaxy/commit/732b5722ae7c668634185209171f… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/tool_shed/galaxy_install/migrate/check.py Log Message: ----------- Do not mess with galaxy_config_file, if provided. Commit: 01a919ce6a7cc29556e257fd0af46f5071310748 https://github.com/galaxyproject/galaxy/commit/01a919ce6a7cc29556e257fd0af4… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-07 (Mon, 07 Dec 2015) Changed paths: M lib/tool_shed/galaxy_install/migrate/check.py Log Message: ----------- Merge pull request #1253 from nsoranzo/dev_verify_tools Tool migration: do not mess with galaxy_config_file, if provided. Compare: https://github.com/galaxyproject/galaxy/compare/371125bc870a...01a919ce6a7c

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[galaxyproject/galaxy] 71b27b: Select2 for sharing
by GitHub 06 Dec '15

06 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 71b27b0f018c6bc3997099137ff2c80ca088981d https://github.com/galaxyproject/galaxy/commit/71b27b0f018c6bc3997099137ff2… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-11-16 (Mon, 16 Nov 2015) Changed paths: M templates/ind_share_base.mako Log Message: ----------- Select2 for sharing This adjusts the default 'share' template to use the select2/exposed user list implemented in 60ad9e934b3e4c50389a624a28578aa9fc326f32. As previously, if the email list is not exposed then you may still enter an email address manually. If usernames are exposed but not emails (e.g. public galaxies) we currently just hide those results even if searches match. Fixes #977 Commit: 86bb4aeaca80b9fbf98ef89f92c1ce2a5bfc6208 https://github.com/galaxyproject/galaxy/commit/86bb4aeaca80b9fbf98ef89f92c1… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-11-16 (Mon, 16 Nov 2015) Changed paths: M templates/webapps/galaxy/history/share.mako Log Message: ----------- Patch other share implementation to handle case of undefined emails more gracefully Commit: 944df4a5647a71304bab12185b708b4bb28da049 https://github.com/galaxyproject/galaxy/commit/944df4a5647a71304bab12185b70… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-11-16 (Mon, 16 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py M templates/ind_share_base.mako M templates/webapps/galaxy/history/share.mako Log Message: ----------- Followup to #1109, #1110, add f_any to user API Commit: 9516b7179d541953ebaea4061300440d02f11bb7 https://github.com/galaxyproject/galaxy/commit/9516b7179d541953ebaea4061300… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-11-17 (Tue, 17 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Documented API call Commit: 371125bc870a29371fba8656d3c93538a50a63ab https://github.com/galaxyproject/galaxy/commit/371125bc870a29371fba8656d3c9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py M templates/ind_share_base.mako M templates/webapps/galaxy/history/share.mako Log Message: ----------- Merge pull request #1111 from erasche/user-search-name Add search on username/any for API calls to user, use Select2 for sharing workflows/pages/histories Compare: https://github.com/galaxyproject/galaxy/compare/3a023f4cae6b...371125bc870a

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[galaxyproject/galaxy] d0a011: Enable lookup of tools from other tool sheds.
by GitHub 06 Dec '15

06 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d0a011675323ba7e8deba588ae0ae6ed9c23f0fe https://github.com/galaxyproject/galaxy/commit/d0a011675323ba7e8deba588ae0a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Enable lookup of tools from other tool sheds. Commit: c040a18b4b164e58a45d1c4f6da65f1eacf18ed5 https://github.com/galaxyproject/galaxy/commit/c040a18b4b164e58a45d1c4f6da6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Modify get_tool() directly instead of using decorator. Commit: 2d168a2c07798ab736676a1eb865ae6976b48464 https://github.com/galaxyproject/galaxy/commit/2d168a2c07798ab736676a1eb865… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Remove whitespaces in blank line. Commit: 1be4f85404c75be364cb20b3c460ea3f51c4dae2 https://github.com/galaxyproject/galaxy/commit/1be4f85404c75be364cb20b3c460… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form-base.js M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/workflow/modules.py M static/maps/mvc/tools/tools-form-base.js.map M static/scripts/mvc/tools/tools-form-base.js Log Message: ----------- Add messages inform users of changes in the tool_id. Commit: 4f1359a0a6d703c8a40b6bb015e89d991d97570e https://github.com/galaxyproject/galaxy/commit/4f1359a0a6d703c8a40b6bb015e8… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M .gitignore A client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/apps/history-panel.js A client/galaxy/scripts/apps/login.js A client/galaxy/scripts/apps/tool-panel.js R client/galaxy/scripts/base.js R client/galaxy/scripts/galaxy-app-base.js R client/galaxy/scripts/galaxy.autocom_tagging.js R client/galaxy/scripts/galaxy.base.js R client/galaxy/scripts/galaxy.frame.js A client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.library.js R client/galaxy/scripts/galaxy.masthead.js R client/galaxy/scripts/galaxy.menu.js M client/galaxy/scripts/galaxy.pages.js R client/galaxy/scripts/galaxy.panels.js R client/galaxy/scripts/galaxy.tools.js R client/galaxy/scripts/galaxy.ui.scrollPanel.js A client/galaxy/scripts/layout/masthead.js A 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static/scripts/tools/rgenetics/helper_functions.js R static/scripts/tools/rgenetics/timer.js A static/scripts/ui/autocom_tagging.js A static/scripts/ui/editable-text.js A static/scripts/ui/popupmenu.js A static/scripts/ui/scroll-panel.js A static/scripts/utils/async-save-text.js M static/scripts/utils/localization.js M static/scripts/utils/query-string-parsing.js M static/scripts/utils/utils.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/trackster/util.js M static/scripts/viz/visualization.js M static/style/blue/base.css R static/style/blue/galaxy.frame.masthead.css M templates/base.mako M templates/base/base_panels.mako M templates/display_base.mako M templates/galaxy_client_app.mako M templates/grid_base.mako A templates/js-app.mako M templates/refresh_frames.mako M templates/tagging_common.mako M templates/user/logout.mako M templates/webapps/galaxy/dataset/display.mako M templates/webapps/galaxy/dataset/edit_attributes.mako M templates/webapps/galaxy/dataset/tabular_chunked.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/history/view_multiple.mako M templates/webapps/galaxy/library/common/ldda_edit_info.mako M templates/webapps/galaxy/library/common/move_library_item.mako M templates/webapps/galaxy/library/common/upload.mako M templates/webapps/galaxy/page/editor.mako M templates/webapps/galaxy/requests/common/create_request.mako M templates/webapps/galaxy/requests/common/find_samples.mako R templates/webapps/galaxy/root/index.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/display_in_frame.mako M templates/webapps/galaxy/visualization/sweepster.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/galaxy/workflow/run.mako M test/api/helpers.py M test/api/test_jobs.py M test/base/twilltestcase.py M test/casperjs/api-history-permission-tests.js M test/casperjs/spaceghost.js M test/qunit/test-app.js M test/qunit/test-common.js M test/qunit/test-data/bootstrapped.js M test/qunit/tests/galaxy-app-base.js M test/qunit/tests/workflow_editor_tests.js M test/tool_shed/test_data/1440_files/complex_dependency/tool_dependencies.xml Log Message: ----------- Merge branch 'dev' of github.com:galaxyproject/galaxy into cross_toolshed_tool_fetching Commit: 77f034019b93bdd539a495a89318bcb1e51b3993 https://github.com/galaxyproject/galaxy/commit/77f034019b93bdd539a495a89318… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Fix failing api test Commit: 3a023f4cae6b9b6b25c1d389b9ba2ad7223cb24a https://github.com/galaxyproject/galaxy/commit/3a023f4cae6b9b6b25c1d389b9ba… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tool/tools-form-base.js M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/workflow/modules.py M static/maps/mvc/tools/tools-form-base.js.map M static/scripts/mvc/tools/tools-form-base.js Log Message: ----------- Merge pull request #818 from mvdbeek/cross_toolshed_tool_fetching Look up installed tools from different toolshed(s) Compare: https://github.com/galaxyproject/galaxy/compare/4fe36f8d6a15...3a023f4cae6b

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