- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] bc33f9: Fix upload tool routing
by GitHub 01 Mar '16

01 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bc33f9b182df89f78679d15e71269000d6d35c5f https://github.com/galaxyproject/galaxy/commit/bc33f9b182df89f78679d15e7126… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Fix upload tool routing Commit: a01ff73c7b0d5d15f34929de3f0e48366c34a79f https://github.com/galaxyproject/galaxy/commit/a01ff73c7b0d5d15f34929de3f0e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge pull request #1827 from guerler/fix_upload_link_000 Fix upload tool routing Compare: https://github.com/galaxyproject/galaxy/compare/763fb112904f...a01ff73c7b0d

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[galaxyproject/galaxy] e122bb: Annotate make targets
by GitHub 01 Mar '16

01 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e122bb8f5dd8120f155fcd0b3be87e836663d4a0 https://github.com/galaxyproject/galaxy/commit/e122bb8f5dd8120f155fcd0b3be8… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M Makefile Log Message: ----------- Annotate make targets Saw this cute trick http://marmelab.com/blog/2016/02/29/auto-documented-makefile.html and figured it wouldn't be too hard to do here as well. Produces a nice help text for commands Commit: a034238c8cb75db1ce165366e87498f48a4a38f6 https://github.com/galaxyproject/galaxy/commit/a034238c8cb75db1ce165366e874… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M Makefile Log Message: ----------- Silence expr warning Commit: b9c8d5beb48dbd71f1cfedd39afb75eb5ceb569e https://github.com/galaxyproject/galaxy/commit/b9c8d5beb48dbd71f1cfedd39afb… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M Makefile Log Message: ----------- Duplicate @jxtx's fix Commit: 763fb112904f51a0a646c0e951d5b759083832db https://github.com/galaxyproject/galaxy/commit/763fb112904f51a0a646c0e951d5… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M Makefile Log Message: ----------- Merge pull request #1824 from erasche/makefile-help Makefile help target + formatting Compare: https://github.com/galaxyproject/galaxy/compare/e730af5a27bc...763fb112904f

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[galaxyproject/galaxy] 340024: This silences logging when display whitelist isn't...
by GitHub 01 Mar '16

01 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 34002458f432ea83ba510bcc25100753f80d4430 https://github.com/galaxyproject/galaxy/commit/34002458f432ea83ba510bcc2510… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-19 (Fri, 19 Feb 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- This silences logging when display whitelist isn't explicitly defined and the default file doesn't exist. Explicit usage still logs a failure. Commit: 9dc1d56dabf5630d1dbd8b2eacb3c2cf62d5b773 https://github.com/galaxyproject/galaxy/commit/9dc1d56dabf5630d1dbd8b2eacb3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M lib/galaxy/app.py M lib/galaxy/config.py Log Message: ----------- Only attempt to read/load sanitize_whitelist_file when starting an actual galaxy application. Commit: e730af5a27bc1fd41231986d8a35e9581b34988b https://github.com/galaxyproject/galaxy/commit/e730af5a27bc1fd41231986d8a35… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M lib/galaxy/app.py M lib/galaxy/config.py Log Message: ----------- Merge pull request #1819 from dannon/whitelist_reloading_logging Whitelist logging tweaks Compare: https://github.com/galaxyproject/galaxy/compare/e43c2ef5dea0...e730af5a27bc

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[galaxyproject/galaxy] 865f2d: Fix create/manage db scripts to respect GALAXY_VIR...
by GitHub 01 Mar '16

01 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 865f2d49bd04b636552002cd0e4830f2dbad5c75 https://github.com/galaxyproject/galaxy/commit/865f2d49bd04b636552002cd0e48… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M create_db.sh M manage_db.sh Log Message: ----------- Fix create/manage db scripts to respect GALAXY_VIRTUAL_ENV. Commit: 50bc127a3b55432884ed6350bee3e0ea67beb95f https://github.com/galaxyproject/galaxy/commit/50bc127a3b55432884ed6350bee3… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-03-01 (Tue, 01 Mar 2016) Changed paths: M create_db.sh M manage_db.sh Log Message: ----------- Merge pull request #1820 from jmchilton/db_script_fixes [16.01] Fix create/manage db scripts to respect GALAXY_VIRTUAL_ENV. Compare: https://github.com/galaxyproject/galaxy/compare/fa8beb225004...50bc127a3b55

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[galaxyproject/usegalaxy-playbook] 137e8b: update MTS
by GitHub 01 Mar '16

01 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 137e8b34960321b9b9608897813dccf1bf724c6d https://github.com/galaxyproject/usegalaxy-playbook/commit/137e8b34960321b9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M production/group_vars/toolshedservers.yml Log Message: ----------- update MTS

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[galaxyproject/galaxy] 5bc55f: Add js for mako based masthead
by GitHub 01 Mar '16

01 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 5bc55f9fa2fd6af9142df644bf82e830b56f9ce4 https://github.com/galaxyproject/galaxy/commit/5bc55f9fa2fd6af9142df644bf82… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M templates/webapps/tool_shed/base_panels.mako Log Message: ----------- Add js for mako based masthead Commit: 281f5b734610963b437b72837e7b71cebbb3c5bd https://github.com/galaxyproject/galaxy/commit/281f5b734610963b437b72837e7b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/ui/popup-menu.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/style/less/base.less M client/galaxy/style/less/fontawesome/core.less M client/galaxy/style/less/ui/icon-btn.less M doc/source/releases/16.01.rst M doc/source/releases/16.01_announce.rst M lib/galaxy/config.py M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/version.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/encoding_util.py M lib/tool_shed/util/repository_content_util.py M lib/tool_shed/util/shed_util_common.py M static/maps/mvc/ui/popup-menu.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/popup-menu.js M static/scripts/mvc/workflow/workflow-terminals.js M static/style/blue/base.css R templates/admin/requests/select_datasets_to_transfer.mako M templates/admin/tool_shed_repository/common.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/requests/common/common.mako M templates/webapps/galaxy/requests/common/view_request_history.mako M templates/webapps/galaxy/requests/common/view_sample_datasets.mako M templates/webapps/galaxy/workflow/run.mako M templates/webapps/tool_shed/repository/common.mako M test/functional/tools/output_format.xml M test/qunit/tests/workflow_editor_tests.js M test/tool_shed/base/twilltestcase.py M test/unit/jobs/test_job_wrapper.py M test/unit/tools_support.py Log Message: ----------- Merge branch 'release_16.01' of https://github.com/galaxyproject/galaxy into release_16.01 Commit: fa8beb225004d27da24065f8f633c7917b5be942 https://github.com/galaxyproject/galaxy/commit/fa8beb225004d27da24065f8f633… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M templates/webapps/tool_shed/base_panels.mako Log Message: ----------- Merge pull request #1823 from martenson/port-masthead-fix [16.01] Port masthead fix Compare: https://github.com/galaxyproject/galaxy/compare/47c93180708e...fa8beb225004

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[galaxyproject/galaxy] aeb008: Implement dataset empty input validator.
by GitHub 01 Mar '16

01 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: aeb008ca43621bb87a58675764ab04eaa24b5608 https://github.com/galaxyproject/galaxy/commit/aeb008ca43621bb87a58675764ab… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M lib/galaxy/tools/parameters/validation.py M test/api/test_tools.py A test/functional/tools/empty_output.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/validation_empty_dataset.xml Log Message: ----------- Implement dataset empty input validator. Commit: e43c2ef5dea09864bf59339c738f0b32b85d8ef5 https://github.com/galaxyproject/galaxy/commit/e43c2ef5dea09864bf59339c738f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M lib/galaxy/tools/parameters/validation.py M test/api/test_tools.py A test/functional/tools/empty_output.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/validation_empty_dataset.xml Log Message: ----------- Merge pull request #1808 from jmchilton/empty_dataset Implement dataset empty input validator. Compare: https://github.com/galaxyproject/galaxy/compare/052187b80cd8...e43c2ef5dea0

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[galaxyproject/galaxy] c78451: Initial swap from svgfig to svgwrite, more or less...
by GitHub 01 Mar '16

01 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c78451f1bd0487109591cf81740c1d5a10f3d2ae https://github.com/galaxyproject/galaxy/commit/c78451f1bd0487109591cf81740c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/render.py Log Message: ----------- Initial swap from svgfig to svgwrite, more or less drop-in replacement of the same rendering approach and look/feel. Commit: 0db0655b10ad47631b636300635e87530b057d94 https://github.com/galaxyproject/galaxy/commit/0db0655b10ad47631b636300635e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Both uses need to .tostring() the canvas, not just the first one. Commit: 872bcbc4ead7694583c5d398dc799f862aff8a0a https://github.com/galaxyproject/galaxy/commit/872bcbc4ead7694583c5d398dc79… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Arrow aesthetics, simplification; some magic number replacement. Commit: f7c41623ae9abaacaf30044954f48e8ab858d1ed https://github.com/galaxyproject/galaxy/commit/f7c41623ae9abaacaf30044954f4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Add svgwrite wheel. Commit: 6f72338b449c9f92ca8a58e42f898716b0edcc74 https://github.com/galaxyproject/galaxy/commit/6f72338b449c9f92ca8a58e42f89… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M lib/galaxy/dependencies/pinned-hashed-requirements.txt Log Message: ----------- Remove svgfig and add svgwrite hash from pinned reqs. Commit: 4dce3e35d75fdf94938b70a56d28ace806c907b8 https://github.com/galaxyproject/galaxy/commit/4dce3e35d75fdf94938b70a56d28… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M lib/tool_shed/util/workflow_util.py M test/unit/workflows/test_render.py Log Message: ----------- Toolshed/test swaps from standalone_xml to tostring Commit: c4350b4ab9e3e367f0101109b6db404d32ab0eb9 https://github.com/galaxyproject/galaxy/commit/c4350b4ab9e3e367f0101109b6db… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Font styling/sizing to match original behavior. Commit: 052187b80cd8f11d72bea4aa18f15ee94aad56cb https://github.com/galaxyproject/galaxy/commit/052187b80cd8f11d72bea4aa18f1… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/render.py M lib/tool_shed/util/workflow_util.py M test/unit/workflows/test_render.py Log Message: ----------- Merge pull request #1747 from dannon/svg_lib_swap Swapping from svgfig to svgwrite Compare: https://github.com/galaxyproject/galaxy/compare/1019f7b40fcb...052187b80cd8

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[galaxyproject/galaxy] 0dac0c: Refactor workflow loading.
by GitHub 29 Feb '16

29 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0dac0c207757cf160901df387214dcfc56016469 https://github.com/galaxyproject/galaxy/commit/0dac0c207757cf160901df387214… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-15 (Mon, 15 Feb 2016) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py Log Message: ----------- Refactor workflow loading. Remove even more duplication between updating and creating workflows. A few new test cases to verify errors under certain conditions. Commit: 92d978dd9d9b15bab7b3852787c2ce094880f97d https://github.com/galaxyproject/galaxy/commit/92d978dd9d9b15bab7b3852787c2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-16 (Tue, 16 Feb 2016) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Eliminate from_editor param to simplify workflow manager... ... slightly. Commit: 1019f7b40fcb916c96dc62dafeee8bffeb44f33a https://github.com/galaxyproject/galaxy/commit/1019f7b40fcb916c96dc62dafeee… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #1735 from jmchilton/more_wf_loading_dup Refactor workflow loading. Compare: https://github.com/galaxyproject/galaxy/compare/14f58261bd77...1019f7b40fcb

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[galaxyproject/galaxy] 56076d: Disable command isolation for Pulsar...
by GitHub 28 Feb '16

28 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 56076db848459cb1da39b04dc635538ff013d3a9 https://github.com/galaxyproject/galaxy/commit/56076db848459cb1da39b04dc635… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Disable command isolation for Pulsar... ... it builds its own job script - no need to have Galaxy do this isolation on the Galaxy end. The more Pulsar can handle the better. Commit: cb19630bd4e04b21653a2cb9848e888805dfabcc https://github.com/galaxyproject/galaxy/commit/cb19630bd4e04b21653a2cb9848e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M test/unit/jobs/test_job_wrapper.py M test/unit/tools_support.py Log Message: ----------- Fix unit tests for 56076db848459cb1da39b04dc635538ff013d3a9 Commit: 47c93180708eb138c1fa0393cd18b24d27249359 https://github.com/galaxyproject/galaxy/commit/47c93180708eb138c1fa0393cd18… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-02-28 (Sun, 28 Feb 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/pulsar.py M test/unit/jobs/test_job_wrapper.py M test/unit/tools_support.py Log Message: ----------- Merge pull request #1812 from jmchilton/pulsar_16.01_fixes [16.01] Disable command isolation for Pulsar... Compare: https://github.com/galaxyproject/galaxy/compare/dad1784a0876...47c93180708e

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