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

[galaxyproject/galaxy] 563e36: Tool optimization - don't set state to queued twic...
by GitHub 06 Dec '15

06 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 563e363478258cb1d08802e16586c42efe511e6a https://github.com/galaxyproject/galaxy/commit/563e363478258cb1d08802e16586… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/managers/histories.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Tool optimization - don't set state to queued twice. Just keep the dataset in the correct NEW state until it has actually been queued. Addresses FIXME comment added by James 7 years ago in https://github.com/galaxyproject/galaxy/commit/4c3db1af95fb0520960046ae5494…. This behavior feels correct to me, but it does have ramifications in the GUI. I had previously never actually seen a dataset in the "NEW" state. Saves an extra flush per dataset, on sqlite this translates to 50ms per dataset for me. Commit: 0ac7c33522cfeb51b89ec8d14fbb2d716f956450 https://github.com/galaxyproject/galaxy/commit/0ac7c33522cfeb51b89ec8d14fbb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Tool optimization and comment improvement. Commit: 2b8a1423f7e9ae6bdf09571b8992493dc30e035c https://github.com/galaxyproject/galaxy/commit/2b8a1423f7e9ae6bdf09571b8992… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Tool optimization - remove another seemingly needless flush. Saves around a teenth of a second per job. Before: - galaxy.tools.execute DEBUG 2015-12-01 13:00:56,984 Tool [cat1] created job [24] (435.468 ms) - galaxy.tools.execute DEBUG 2015-12-01 13:01:17,296 Tool [cat1] created job [25] (341.687 ms) - galaxy.tools.execute DEBUG 2015-12-01 13:01:32,896 Tool [cat1] created job [26] (354.138 ms) After - - galaxy.tools.execute DEBUG 2015-12-01 12:58:51,154 Tool [cat1] created job [21] (261.932 ms) - galaxy.tools.execute DEBUG 2015-12-01 12:59:11,354 Tool [cat1] created job [22] (278.699 ms) - galaxy.tools.execute DEBUG 2015-12-01 12:59:43,105 Tool [cat1] created job [23] (296.438 ms) Commit: 81799bd3a72b3e704be6c12e89b85eb5bd077428 https://github.com/galaxyproject/galaxy/commit/81799bd3a72b3e704be6c12e89b8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Micro-optimizations for adding many datasets to history... ... during tool execution. Build method once instead of in each function call, use imap instead of map since we don't need a list, remove some duplicated checks. Frankly this is all stuff Python is probably doing anyway - but in case it doesn't and just so the eye doesn't jump to these optimizations again. Timings before and after for a section of tool action execute that includes this additon show that this might have a small effect. Before: - galaxy.tools.actions INFO 2015-12-01 13:11:39,446 Add outputs to history (127.379 ms) - galaxy.tools.actions INFO 2015-12-01 13:12:06,598 Add outputs to history (137.029 ms) - galaxy.tools.actions INFO 2015-12-01 13:12:23,931 Add outputs to history (118.489 ms) After: - galaxy.tools.actions INFO 2015-12-01 13:13:09,999 Add outputs to history (99.456 ms) - galaxy.tools.actions INFO 2015-12-01 13:13:38,573 Add outputs to history (126.131 ms) - galaxy.tools.actions INFO 2015-12-01 13:13:54,538 Add outputs to history (137.643 ms) - galaxy.tools.actions INFO 2015-12-01 13:14:12,516 Add outputs to history (101.451 ms) Commit: bd6a34e279f8d612185fe9d8aa27084efe246e2d https://github.com/galaxyproject/galaxy/commit/bd6a34e279f8d612185fe9d8aa27… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Tool optimization comments for future reference. Including replacing a log statement with a comment. Commit: 59c3acfbf56e14c8f691946932be71b81774de0e https://github.com/galaxyproject/galaxy/commit/59c3acfbf56e14c8f691946932be… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Tool execution optimization - remove another unneeded flush. Flush the job and its output datasets all at the same time in one transaction. Inuitively it makes sense that this should work and the timings seem to improve, triming another quater or third of the submission time per job. Before: - galaxy.tools.execute DEBUG 2015-12-01 12:58:51,154 Tool [cat1] created job [21] (261.932 ms) - galaxy.tools.execute DEBUG 2015-12-01 12:59:11,354 Tool [cat1] created job [22] (278.699 ms) - galaxy.tools.execute DEBUG 2015-12-01 12:59:43,105 Tool [cat1] created job [23] (296.438 ms) After: - galaxy.tools.execute DEBUG 2015-12-01 13:22:00,649 Tool [cat1] created job [39] (265.547 ms) - galaxy.tools.execute DEBUG 2015-12-01 13:22:27,720 Tool [cat1] created job [40] (214.905 ms) - galaxy.tools.execute DEBUG 2015-12-01 13:21:40,225 Tool [cat1] created job [38] (198.936 ms) - galaxy.tools.execute DEBUG 2015-12-01 13:22:44,076 Tool [cat1] created job [41] (213.096 ms) Commit: 3bf466c8f5d554f583dfc2fe8f7b95397278b2d9 https://github.com/galaxyproject/galaxy/commit/3bf466c8f5d554f583dfc2fe8f7b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Micro optimization in tool execute - eliminate repeated trans.app fetch. Commit: e72604be7c0c0a88c6267140b6433fcde88f1d01 https://github.com/galaxyproject/galaxy/commit/e72604be7c0c0a88c6267140b643… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/tools/actions/upload.py Log Message: ----------- Instrument upload action for timing. - Checked and cleanup datasets ~500ms - Create job ~200ms - Persisting ~20 ms Commit: 2c6819cd87520fb43f4ebea96eea5fb151787edb https://github.com/galaxyproject/galaxy/commit/2c6819cd87520fb43f4ebea96eea… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Tool optimization - eliminate repeated role generation. For cat1 with 5 inputs - this shaves about 100 ms off of job execution time. Before: galaxy.tools.execute DEBUG 2015-12-01 15:08:56,745 Tool [cat1] created job [171] (545.776 ms) galaxy.tools.execute DEBUG 2015-12-01 15:08:31,871 Tool [cat1] created job [170] (478.813 ms) After : galaxy.tools.execute DEBUG 2015-12-01 15:07:11,401 Tool [cat1] created job [168] (371.722 ms) galaxy.tools.execute DEBUG 2015-12-01 15:07:42,060 Tool [cat1] created job [169] (333.296 ms) Commit: 836b0dfc1504357b738375b109b22243dd58efe7 https://github.com/galaxyproject/galaxy/commit/836b0dfc1504357b738375b109b2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/tools/execute.py Log Message: ----------- Fix location of timer generation for fairer comparison in next commit. Commit: c14c45be46a4a3b08b3cb0b5132cbbdf151d5100 https://github.com/galaxyproject/galaxy/commit/c14c45be46a4a3b08b3cb0b5132c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/execute.py M test/unit/tools/test_execution.py Log Message: ----------- Further cache user roles across batched tool executions. Commit: 53354c7e361cc769f42c7eae42de0eca1769e9a4 https://github.com/galaxyproject/galaxy/commit/53354c7e361cc769f42c7eae42de… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Fix collection output for less flushing in tool action handle_output. Commit: 4fe36f8d6a151536267e3aeace2414cc148e18e8 https://github.com/galaxyproject/galaxy/commit/4fe36f8d6a151536267e3aeace24… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/managers/histories.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/execute.py M test/unit/tools/test_execution.py Log Message: ----------- Merge pull request #1199 from jmchilton/tool_opts_4 Yet More Tool Execution Optimizations Compare: https://github.com/galaxyproject/galaxy/compare/beb4a67fb0a4...4fe36f8d6a15

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[galaxyproject/galaxy] b55635: Client, upload: fix passing of nginx_upload_path a...
by GitHub 06 Dec '15

06 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b55635f71b7fd3bba8393a3c267408d6dd248f99 https://github.com/galaxyproject/galaxy/commit/b55635f71b7fd3bba8393a3c2674… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M lib/galaxy/managers/configuration.py M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Client, upload: fix passing of nginx_upload_path and ftp_upload_site to upload-view, fix default nginx_upload_path in configuration serializer Commit: beb4a67fb0a4b879b732fd05b35d03019481ea90 https://github.com/galaxyproject/galaxy/commit/beb4a67fb0a4b879b732fd05b35d… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M lib/galaxy/managers/configuration.py M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge pull request #1250 from carlfeberhard/fix.upload Client, upload: fix passing of nginx_upload_path and ftp_upload_site … Compare: https://github.com/galaxyproject/galaxy/compare/91d348a73fd4...beb4a67fb0a4

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[galaxyproject/galaxy] 1fdde2: Refactor generic side workflow editor panel toward...
by GitHub 05 Dec '15

05 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1fdde2cb4d3d685916dc82a8fc846079a8066cd5 https://github.com/galaxyproject/galaxy/commit/1fdde2cb4d3d685916dc82a8fc84… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Refactor generic side workflow editor panel toward backbone. Commit: 91d348a73fd49453c9cde5fb6116c3b230a2f162 https://github.com/galaxyproject/galaxy/commit/91d348a73fd49453c9cde5fb6116… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Merge pull request #1247 from jmchilton/editor_refactor Refactor generic side workflow editor panel toward backbone. Compare: https://github.com/galaxyproject/galaxy/compare/e12179b0160d...91d348a73fd4

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[galaxyproject/galaxy] 4fdea5: Enhance the VTK datatypes to support cell data in ...
by GitHub 05 Dec '15

05 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4fdea55f81756a27bff8ef66b3fe27d4bda36905 https://github.com/galaxyproject/galaxy/commit/4fdea55f81756a27bff8ef66b3fe… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/datatypes/constructive_solid_geometry.py Log Message: ----------- Enhance the VTK datatypes to support cell data in addition to point data. Replaces https://github.com/galaxyproject/galaxy/pull/1189. Commit: 9b085740dfddfcb67f6a2e21a51503cd2ac0741e https://github.com/galaxyproject/galaxy/commit/9b085740dfddfcb67f6a2e21a515… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/jobs/output_checker.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M test/api/test_workflows.py M test/unit/test_galaxy_mapping.py M test/unit/workflows/test_render.py A test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev Commit: d2ce6d4d2b03fc7ad0a40ac4b0194f8636350f52 https://github.com/galaxyproject/galaxy/commit/d2ce6d4d2b03fc7ad0a40ac4b019… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M README.rst M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/graph.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/test.idpDB A lib/galaxy/datatypes/test/test.mz5 A lib/galaxy/datatypes/triples.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/managers/collections.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/execute.py M lib/galaxy/webapps/tool_shed/api/repositories.py M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako A test/functional/tools/create_10.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev Commit: 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static/scripts/mvc/history/history-view-edit-current.js A static/scripts/mvc/history/history-view-edit.js A static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-libraryrow-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/library/library-model.js R static/scripts/mvc/list/list-panel.js A static/scripts/mvc/list/list-view.js A static/scripts/mvc/tag.js R static/scripts/mvc/tags.js A static/scripts/mvc/tool/tools-form-base.js A static/scripts/mvc/tool/tools-form-workflow.js A static/scripts/mvc/tool/tools-form.js A static/scripts/mvc/tool/tools-jobs.js A static/scripts/mvc/tool/tools-template.js A static/scripts/mvc/tool/tools.js R static/scripts/mvc/tools/tools-form-workflow.js R static/scripts/mvc/tools/tools-form.js R static/scripts/mvc/tools/tools-jobs.js R static/scripts/mvc/tools/tools-template.js M static/scripts/mvc/ui/ui-select-ftp.js M static/scripts/mvc/ui/ui-select-library.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-view.js M static/scripts/mvc/user/user-model.js M static/scripts/mvc/visualization/visualization-model.js M static/scripts/mvc/workflow/workflow-connector.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-view-data.js M static/scripts/mvc/workflow/workflow-view.js A static/scripts/onload.js A static/scripts/polyfills.js R static/scripts/rgenetics/checkbox_and_radiobutton.js R static/scripts/rgenetics/helper_functions.js R static/scripts/rgenetics/timer.js M static/scripts/templates/compiled/panel_section.js M static/scripts/templates/compiled/tool_form.js M static/scripts/templates/compiled/tool_link.js M static/scripts/templates/compiled/tool_search.js R static/scripts/tools/rgenetics/checkbox_and_radiobutton.js R 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/api/test_tools.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 M test/unit/tools/test_actions.py M test/unit/tools/test_data_parameters.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev Commit: e12179b0160d242be870b15b8da5a46e294063bf https://github.com/galaxyproject/galaxy/commit/e12179b0160d242be870b15b8da5… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M lib/galaxy/datatypes/constructive_solid_geometry.py Log Message: ----------- Merge pull request #1211 from gregvonkuster/dev Enhance the VTK datatypes to support cell data in addition to point Compare: https://github.com/galaxyproject/galaxy/compare/fef8ce2a762b...e12179b0160d

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[galaxyproject/galaxy] cae457: Fail maxseconds test tool if sleep is interrupted.
by GitHub 05 Dec '15

05 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cae457d8c18ded2abf03a0a6c3fb027735e1b5ef https://github.com/galaxyproject/galaxy/commit/cae457d8c18ded2abf03a0a6c3fb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M test/functional/tools/maxseconds.xml Log Message: ----------- Fail maxseconds test tool if sleep is interrupted. Commit: fef8ce2a762b82480d5f7304c345cc3168e10036 https://github.com/galaxyproject/galaxy/commit/fef8ce2a762b82480d5f7304c345… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M test/functional/tools/maxseconds.xml Log Message: ----------- Merge pull request #1248 from jmchilton/maxseconds_debug_2 Attempt to fix transiently failing tool test on Jenkins Compare: https://github.com/galaxyproject/galaxy/compare/df6470654411...fef8ce2a762b

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[galaxyproject/galaxy] df781d: Fix missing assertion pointed out @nsoranzo.
by GitHub 05 Dec '15

05 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: df781dcc188193ff044a625540dc02961a8c5640 https://github.com/galaxyproject/galaxy/commit/df781dcc188193ff044a625540dc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M test/api/helpers.py Log Message: ----------- Fix missing assertion pointed out @nsoranzo. Lots of other tests would fail if simple uploads aren't working, but it is better to be direct and very explicit about why this particular test is failing. Commit: df6470654411bfa8ce997f932e92b4c2d644c685 https://github.com/galaxyproject/galaxy/commit/df6470654411bfa8ce997f932e92… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M test/api/helpers.py Log Message: ----------- Merge pull request #1237 from jmchilton/test_jobs_fix Fix missing assertion pointed out @nsoranzo. Compare: https://github.com/galaxyproject/galaxy/compare/4d252119fd00...df6470654411

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[galaxyproject/galaxy] e186b6: Fix for getting shed_config_dict when an old/inval...
by GitHub 05 Dec '15

05 Dec '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy 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/f34d70101910...7d4eac1535fc

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[galaxyproject/galaxy] 599440: Fix for workflow progress unit testing.
by GitHub 05 Dec '15

05 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 59944046b7f16d13886928eb6928a7d67446c1e6 https://github.com/galaxyproject/galaxy/commit/59944046b7f16d13886928eb6928… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M test/unit/workflows/test_workflow_progress.py Log Message: ----------- Fix for workflow progress unit testing. Commit: bed421fbc98583fdc00db57d3bb787450766576b https://github.com/galaxyproject/galaxy/commit/bed421fbc98583fdc00db57d3bb7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py Log Message: ----------- Introduce model abstractions for dealing with workflow steps. Three methods to provide higher-level access and reasoning about steps than just a flat array. Commit: da6051922e51ecc43c2f5b973adf5ba2dbf7554b https://github.com/galaxyproject/galaxy/commit/da6051922e51ecc43c2f5b973adf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Unroll input connection logic. Need to extend it downstream and the one-liner is fun but not easy to extend or particularily readable. Commit: d97d8a203c7c09123f7298627ad394d6c96e5b1c https://github.com/galaxyproject/galaxy/commit/d97d8a203c7c09123f7298627ad3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Better error messages in workflow running code. Commit: 296971c5ded17367d2a14a32a072678b727ddf05 https://github.com/galaxyproject/galaxy/commit/296971c5ded17367d2a14a32a072… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Fix typo spotted by @nsoranzo. Commit: 93bfa1992cc23a411e46437547581843c0e7b952 https://github.com/galaxyproject/galaxy/commit/93bfa1992cc23a411e4643754758… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py Log Message: ----------- Make more workflow methods properties. As suggested by @nsoranzo. Commit: 4d252119fd0057b9b9433a4d874784c86f96d42e https://github.com/galaxyproject/galaxy/commit/4d252119fd0057b9b9433a4d8747… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/workflow/run.py M test/unit/workflows/test_workflow_progress.py Log Message: ----------- Merge pull request #1216 from jmchilton/workflow_tweaks_1 More small workflow tweaks. Compare: https://github.com/galaxyproject/galaxy/compare/6126bd0e93e1...4d252119fd00

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[galaxyproject/galaxy] 4a279f: Allow inputs section for Format 2 workflow definit...
by GitHub 05 Dec '15

05 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4a279ffb64576258f2f2755f182430e1ccbacbc2 https://github.com/galaxyproject/galaxy/commit/4a279ffb64576258f2f2755f1824… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py Log Message: ----------- 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. Commit: b0b26e69019162e335ea5a331ab21009c882f0d1 https://github.com/galaxyproject/galaxy/commit/b0b26e69019162e335ea5a331ab2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M test/api/test_workflows.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/main.py Log Message: ----------- Allow specifying Format 2 workflow by path. This will allow importing workflow relative resources in subsequent passes at this. Commit: 70a9f213932947758f9882776140727eb6c0e246 https://github.com/galaxyproject/galaxy/commit/70a9f213932947758f9882776140… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/interface.py Log Message: ----------- 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. Commit: 1bd0a4e9703406223f0e9bfe31df4c801998f400 https://github.com/galaxyproject/galaxy/commit/1bd0a4e9703406223f0e9bfe31df… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py Log Message: ----------- Refactoring and more testing of format 2 workflow implementation code... ... toward more reusable design. Commit: a597e0e8349f33d4d2c642d2e0a74e3da64b156b https://github.com/galaxyproject/galaxy/commit/a597e0e8349f33d4d2c642d2e0a7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py Log Message: ----------- 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>]. Commit: 3d0723c812632a276102748ec6a754bbec0b9d9a https://github.com/galaxyproject/galaxy/commit/3d0723c812632a276102748ec6a7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 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-data.js M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- 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. Commit: 7b3fa824b67c0c7f881a514ae5b6598ede62e14c https://github.com/galaxyproject/galaxy/commit/7b3fa824b67c0c7f881a514ae5b6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M lib/galaxy/managers/workflows.py M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- 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. Commit: cee9d4d1b30633689d8dd5fde715aed528e578a1 https://github.com/galaxyproject/galaxy/commit/cee9d4d1b30633689d8dd5fde715… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: 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-data.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-data.js Log Message: ----------- Grunt the workflow JS. Commit: 40e6932a25f71c240e038e4e6dc9be6a19ff8459 https://github.com/galaxyproject/galaxy/commit/40e6932a25f71c240e038e4e6dc9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M test/api/test_workflows.py M test/api/workflows_format_2/converter.py Log Message: ----------- Fix workflow API tests for workflow output changes. Commit: 6126bd0e93e17c2d9cd6512ec068f806cc9da72d https://github.com/galaxyproject/galaxy/commit/6126bd0e93e17c2d9cd6512ec068… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-12-05 (Sat, 05 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-data.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/managers/workflows.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-data.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-data.js M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/interface.py M test/api/workflows_format_2/main.py M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Merge pull request #1214 from jmchilton/format_2_1 Small enhancements in workflow inputs and outputs Compare: https://github.com/galaxyproject/galaxy/compare/d7f5dbe4ca1b...6126bd0e93e1

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[galaxyproject/galaxy] e9e73f: Remove dated comment.
by GitHub 05 Dec '15

05 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e9e73f4828f7926a1a36654ed48325828992bed3 https://github.com/galaxyproject/galaxy/commit/e9e73f4828f7926a1a36654ed483… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-choice.js Log Message: ----------- Remove dated comment. Commit: c91a2eb33947a64ed8c03115d1de9ccf746cc195 https://github.com/galaxyproject/galaxy/commit/c91a2eb33947a64ed8c03115d1de… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-select-content.js M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/wrappers.py M static/maps/mvc/dataset/dataset-choice.js.map M static/maps/mvc/form/form-select-content.js.map M static/scripts/mvc/form/form-select-content.js M test/api/test_tools.py M test/unit/tools/test_data_parameters.py Log Message: ----------- 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 Commit: 62a26516cd7a3a6d1ad6441dc8d63efafa25d8d0 https://github.com/galaxyproject/galaxy/commit/62a26516cd7a3a6d1ad6441dc8d6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Fix PR #805 for changes in PR #1153. Commit: 17851ba0ea9572f1c387ff1fea1012b7af737855 https://github.com/galaxyproject/galaxy/commit/17851ba0ea9572f1c387ff1fea10… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M test/unit/tools/test_actions.py Log Message: ----------- And fix unit test for b036adcaa166153e544935c12123877c69a7450f. Commit: d7f5dbe4ca1bc0943e3d3edbddd88d1c226ff5e5 https://github.com/galaxyproject/galaxy/commit/d7f5dbe4ca1bc0943e3d3edbddd8… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/form/form-select-content.js M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/wrappers.py M static/maps/mvc/dataset/dataset-choice.js.map M static/maps/mvc/form/form-select-content.js.map M static/scripts/mvc/form/form-select-content.js M test/api/test_tools.py M test/unit/tools/test_actions.py M test/unit/tools/test_data_parameters.py Log Message: ----------- Merge pull request #805 from jmchilton/multi_data_param_enhance Allow multiple collections to be supplied to a multiple data parameter. Compare: https://github.com/galaxyproject/galaxy/compare/b0c1cd7460f1...d7f5dbe4ca1b

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