- 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 29 Feb '16

29 Feb '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 29 Feb '16

29 Feb '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 29 Feb '16

29 Feb '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 29 Feb '16

29 Feb '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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[galaxyproject/galaxy] 9b4b20: Reduce the use of mutable types in method definiti...
by GitHub 28 Feb '16

28 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9b4b20cb887b290c671c4f2941dfd25c6439b73e https://github.com/galaxyproject/galaxy/commit/9b4b20cb887b290c671c4f2941df… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M test/tool_shed/base/twilltestcase.py Log Message: ----------- Reduce the use of mutable types in method definitions. Commit: 14f58261bd771fe54108efccb081199171d3bd0f https://github.com/galaxyproject/galaxy/commit/14f58261bd771fe54108efccb081… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-02-28 (Sun, 28 Feb 2016) Changed paths: M test/tool_shed/base/twilltestcase.py Log Message: ----------- Merge pull request #1813 from davebx/mutable_types Reduce the use of mutable types in toolshed test framework's method definitions. Compare: https://github.com/galaxyproject/galaxy/compare/db59b9b70368...14f58261bd77

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[galaxyproject/galaxy] 45ac2d: Revert "Switch default job shell back to /bin/sh f...
by GitHub 28 Feb '16

28 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 45ac2de349e0acd64be5e66189c74c9404e2d5da https://github.com/galaxyproject/galaxy/commit/45ac2de349e0acd64be5e66189c7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/util/job_script/__init__.py Log Message: ----------- Revert "Switch default job shell back to /bin/sh for 16.01." This reverts commit 602dc7f6649d96086b85ed0d309eef7c4ed73a13. 16.04 will use bash as the default. Commit: d020522650a9bfc86c22923a01fd5d7c07c65326 https://github.com/galaxyproject/galaxy/commit/d020522650a9bfc86c22923a01fd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M test/functional/tools/samples_tool_conf.xml A test/functional/tools/strict_shell.xml A test/functional/tools/strict_shell_default_off.xml M test/unit/jobs/test_command_factory.py Log Message: ----------- Introduce strict shell command option. Newer tool formats (CWL and YAML just enable this by default), but XML tools can add a strict="true" to the command block to force "set -e" handling on the shell part of tool execution. Run the framework tests verifying the new and older default behavior using the following commands: ``` ./run_tests.sh -framework -id strict_shell_default_off ./run_tests.sh -framework -id strict_shell ``` Commit: b92074e6ff87a19133b4d973577779c4ee6286d7 https://github.com/galaxyproject/galaxy/commit/b92074e6ff87a19133b4d9735777… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M test/unit/tools/test_evaluation.py Log Message: ----------- Implement profile="XX.XX" on tools, better defaults for newer tools. - set -e in tool command scripts. - Disable implicit extra file collection. All dynamic extra file collection requires a <discover_datasets tag. - Disable format="input" - require explicit metadata targets (metadata_source, format_source). - Disable interpreter= - hacky and doesn't work as expected in too many circumstances. Use $__tool_directory__. - Disable $param_file - grepping the command for the string is impercise. If useful we can add flag to match the flag used to produce inputs as a JSON file. - Disable default version of 1.0.0, the IUC has made it clear they prefer all tools have an explicit version. Fixes #1609. Commit: e5d5b16a446d07075378969aafa2a0ff4aa97bbc https://github.com/galaxyproject/galaxy/commit/e5d5b16a446d07075378969aafa2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/util/job_script/__init__.py Log Message: ----------- Simplify pbs runner. Just reuse parent class methods, these are just different ways of executing the same actions essentially. Commit: 0613e038e7292d1648432926e873fba26ba5b23f https://github.com/galaxyproject/galaxy/commit/0613e038e7292d1648432926e873… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M lib/galaxy/jobs/runners/cli.py Log Message: ----------- Remove legacy job support from CLI runner. Commit: 81b5ca564ac7cdd855cb74dad8e98abc83a8efdc https://github.com/galaxyproject/galaxy/commit/81b5ca564ac7cdd855cb74dad8e9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py Log Message: ----------- Make more job options configurable at the destination level. Makes a host of job-related parameters configurable at the destination level instead of the of only at the app level. This solves major problems like allowing the local job runner and the drmma run as real-user runner to operate within in the same environment and provides little conveniences like allowing configuration of cleanup job at the destination level. Commit: 0eab8346b3dd3ee7788c9cdda0f10f8aea4b2726 https://github.com/galaxyproject/galaxy/commit/0eab8346b3dd3ee7788c9cdda0f1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/objectstore/__init__.py M test/unit/test_objectstore.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Rename config.job_working_directory to config.jobs_directory. Commit: a2e31403753c407e7f6966b69b157e32f5f3ef8a https://github.com/galaxyproject/galaxy/commit/a2e31403753c407e7f6966b69b15… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/parameters/output_collect.py M test/unit/jobs/test_command_factory.py Log Message: ----------- Give tool executions a clean working directory. Rather then massively renaming job_directory and job_working_directory, I introduce the concept of the tool execution working directory (tool_working_directory) that is the job working directory + "/working" and that will not be populated with job files. Some legacy cruft in there for the upgrade, things like galaxy.json and dynamic outputs may be in the job working directory or the tool execution working directory. Commit: 9f9a4fbf497241d2de23369a3ca0fdd0ff01fada https://github.com/galaxyproject/galaxy/commit/9f9a4fbf497241d2de23369a3ca0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M lib/galaxy/jobs/command_factory.py Log Message: ----------- Greater resiliency against bad job script commands... ... when building tool execution commands using the command_factory's CommandBuilder. Commit: 57652e5671c5581b3179bc5475c56a4d1283bd62 https://github.com/galaxyproject/galaxy/commit/57652e5671c5581b3179bc5475c5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M lib/galaxy/tools/cwl/__init__.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/parser/cwl.py Log Message: ----------- Updated CWL module for downstream changes and draft 3 support. Commit: 31fc1c608cda3f049e017c0b37c293743336dd7e https://github.com/galaxyproject/galaxy/commit/31fc1c608cda3f049e017c0b37c2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M lib/galaxy/tools/parser/yaml.py Log Message: ----------- Fix YAML jobs for setting tool.description as None. XML tools would set this as '' and there are places it is assumed to be a string. Commit: b8a6302aa8e062962a74d29504afe01dd646373e https://github.com/galaxyproject/galaxy/commit/b8a6302aa8e062962a74d29504af… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M test/unit/tools/test_parsing.py Log Message: ----------- Migrate tool sanitize and refresh options to parser framework. Trying to get everything in there in general and need to disable sanitize for CWL tools downstream using this override point. Commit: f7549f81813ef2b3b19d0f3c071bf147dd5e09bb https://github.com/galaxyproject/galaxy/commit/f7549f81813ef2b3b19d0f3c071b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Cleanup for destination config changes. Commit: e5758ea4e8a9cf4782e76a4228711b69b8dc1650 https://github.com/galaxyproject/galaxy/commit/e5758ea4e8a9cf4782e76a422871… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Rebase into config destinations. Commit: 3b70182877da1c357c2440141d3d602c453eafb2 https://github.com/galaxyproject/galaxy/commit/3b70182877da1c357c2440141d3d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py Log Message: ----------- Improve tool loading problem messages. Include tool paths, IDs, etc... where appropriate. Commit: 2f015881c4416ec7e490a786849b991c9d958f6f https://github.com/galaxyproject/galaxy/commit/2f015881c4416ec7e490a786849b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M test/unit/tools/test_evaluation.py Log Message: ----------- Revise legacy handling Commit: fa27f3c63ce9d82b44077b67f939f35fc7d50a98 https://github.com/galaxyproject/galaxy/commit/fa27f3c63ce9d82b44077b67f939… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M test/unit/tools/test_evaluation.py Log Message: ----------- Add spaces Commit: c34c3a574b208be2f544b469168dce75d88b7f99 https://github.com/galaxyproject/galaxy/commit/c34c3a574b208be2f544b469168d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M test/unit/tools/test_evaluation.py Log Message: ----------- Merge pull request #44 from guerler/revise_tool_profile_000 Revise legacy handling Commit: db59b9b70368e26a3130ead795e9c3166b3cb59b https://github.com/galaxyproject/galaxy/commit/db59b9b70368e26a3130ead795e9… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-02-28 (Sun, 28 Feb 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/cwl/__init__.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M test/functional/tools/samples_tool_conf.xml A test/functional/tools/strict_shell.xml A test/functional/tools/strict_shell_default_off.xml M test/unit/jobs/test_command_factory.py M test/unit/test_objectstore.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_parsing.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Merge pull request #1688 from jmchilton/16.04_jobs Overhaul of Tools and Jobs for 16.04 Compare: https://github.com/galaxyproject/galaxy/compare/da50cf114923...db59b9b70368

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[galaxyproject/usegalaxy-playbook] 49261b: Update Test
by GitHub 26 Feb '16

26 Feb '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 49261bdc3f1a092467fa6ddc620843c75dad98c9 https://github.com/galaxyproject/usegalaxy-playbook/commit/49261bdc3f1a0924… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M stage/group_vars/all.yml Log Message: ----------- Update Test

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[galaxyproject/galaxy] 6d9ac0: Ensure tool.changeset_revision is set...
by GitHub 26 Feb '16

26 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6d9ac081c1fa164382de7a351b90790899636b54 https://github.com/galaxyproject/galaxy/commit/6d9ac081c1fa164382de7a351b90… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Ensure tool.changeset_revision is set... ... in some cases tool.tool_shed will be non-null but changeset_revision will be absent. This is my development instance so it is easy to imagine my database doesn't match my tool panel config. Commit: da50cf114923b241f1e4c6fc1d90f920207170cf https://github.com/galaxyproject/galaxy/commit/da50cf114923b241f1e4c6fc1d90… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #1806 from jmchilton/changeset_problems_fix Ensure tool.changeset_revision is set... Compare: https://github.com/galaxyproject/galaxy/compare/453345c6210f...da50cf114923

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[galaxyproject/galaxy] 1aa1d6: Fix workflow parameters not rendered when tool par...
by GitHub 25 Feb '16

25 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 1aa1d6164a63438b49beb2fd6cc4b80a57bbdb5d https://github.com/galaxyproject/galaxy/commit/1aa1d6164a63438b49beb2fd6cc4… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Fix workflow parameters not rendered when tool parameter wrapped in conditional. Commit: dad1784a087623c990e0b3f05d1c8026f7bd957c https://github.com/galaxyproject/galaxy/commit/dad1784a087623c990e0b3f05d1c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge pull request #1799 from mvdbeek/fix_workflow_parameters_conditional [16.01] Fix workflow parameters not rendered when tool parameter wrapped in conditional. Compare: https://github.com/galaxyproject/galaxy/compare/5546211c0ddd...dad1784a0876

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[galaxyproject/galaxy] bae03b: Port Nicola's fix to dev.
by GitHub 25 Feb '16

25 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bae03bfe3ec41be97dd75e42b40bf730fee5373e https://github.com/galaxyproject/galaxy/commit/bae03bfe3ec41be97dd75e42b40b… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M test/tool_shed/base/twilltestcase.py Log Message: ----------- Port Nicola's fix to dev. Commit: 510543236c472ca1055581952f589762c9cc4dab https://github.com/galaxyproject/galaxy/commit/510543236c472ca1055581952f58… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M test/tool_shed/base/twilltestcase.py Log Message: ----------- Merge #1392's modifications into bae03bfe. Commit: 4383e9f808889bcf62b0417de7254c3d184564a5 https://github.com/galaxyproject/galaxy/commit/4383e9f808889bcf62b0417de725… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M .ci/flake8_blacklist.txt M .ci/py3_sources.txt M .travis.yml M Makefile M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/ui/popup-menu.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/base.less M client/galaxy/style/less/fontawesome/core.less M client/galaxy/style/less/library.less M client/galaxy/style/less/ui/icon-btn.less M config/datatypes_conf.xml.sample M doc/source/releases/16.01.rst M doc/source/releases/16.01_announce.rst M lib/galaxy/config.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/display_applications/application.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/text.py M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/deferred/data_transfer.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/taggable.py M lib/galaxy/managers/tags.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/metadata.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parameters/sanitize.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/test.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/visualization/data_providers/registry.py M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/form_builder.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/translogger.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/tag.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/users.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webapps/tool_shed/model/mapping.py M lib/galaxy/workflow/modules.py M lib/galaxy_utils/sequence/fasta.py M lib/galaxy_utils/sequence/fastq.py M lib/pulsar/client/interface.py M lib/pulsar/client/manager.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py M lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py M lib/tool_shed/util/basic_util.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/encoding_util.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/repository_content_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/util/workflow_util.py M scripts/api/common.py M scripts/api/copy_hda_to_library_folder.py M scripts/api/create.py M scripts/api/data_manager_example_execute.py M scripts/api/delete.py M scripts/api/display.py M scripts/api/example_watch_folder.py M scripts/api/form_create_from_xml.py M scripts/api/history_create_history.py M scripts/api/history_delete_history.py M scripts/api/import_library_dataset_to_history.py M scripts/api/import_workflows_from_installed_tool_shed_repository.py M scripts/api/install_tool_shed_repositories.py M scripts/api/library_create_folder.py M scripts/api/library_create_library.py M scripts/api/library_upload_dir.py M scripts/api/library_upload_from_import_dir.py M scripts/api/load_data_with_metadata.py M scripts/api/repair_tool_shed_repository.py M scripts/api/request_type_create_from_xml.py M scripts/api/requests_update_state.py M scripts/api/reset_metadata_on_installed_repositories.py M scripts/api/sample_dataset_update_status.py M scripts/api/sample_update_state.py M scripts/api/search.py M scripts/api/sequencer_configuration_create.py M scripts/api/update.py M scripts/api/upload_to_history.py M scripts/api/workflow_delete.py M scripts/api/workflow_execute.py M scripts/api/workflow_execute_parameters.py M scripts/api/workflow_import.py M scripts/api/workflow_import_from_file_rpark.py M scripts/check_galaxy.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/update_metadata.py M scripts/create_db.py M scripts/data_libraries/build_lucene_index.py M scripts/data_libraries/build_whoosh_index.py M scripts/db_shell.py M scripts/edam_mapping.py M scripts/extract_dataset_part.py M scripts/functional_tests.py M scripts/galaxy-main M scripts/get_platforms.py M scripts/helper.py M scripts/loc_files/create_all_fasta_loc.py M scripts/manage_db.py M scripts/manage_tools.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/create_nib_seq_loc_file.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/microbes/ncbi_to_ucsc.py M scripts/microbes/util.py M scripts/migrate_tools/migrate_tools.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/paster.py A scripts/patch.sh M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/tool_shed/build_ts_whoosh_index.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/tools/maf/check_loc_file.py M scripts/tools/re_escape_output.py M scripts/transfer.py M scripts/update_shed_config_path.py M static/maps/galaxy.library.js.map M static/maps/layout/masthead.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/ui/popup-menu.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/utils/utils.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/galaxy.library.js M static/scripts/layout/masthead.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/ui/popup-menu.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/utils/utils.js M static/style/blue/base.css M static/style/blue/library.css R templates/admin/requests/select_datasets_to_transfer.mako M templates/admin/tool_shed_repository/common.mako M templates/webapps/galaxy/galaxy.masthead.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/tool_shed/repository/common.mako M test/api/test_tools.py M test/base/twilltestcase.py M test/functional/test_admin_features.py M test/functional/test_data_security.py M test/functional/test_dataset_features.py M test/functional/test_get_data.py M test/functional/test_library_features.py M test/functional/test_library_security.py M test/functional/test_library_templates.py M test/functional/test_metadata_editing.py M test/functional/test_sample_tracking.py M test/functional/test_tags.py M test/functional/test_ucsc_table_browser.py M test/functional/test_user_info.py M test/functional/tools/output_format.xml M test/qunit/tests/masthead_tests.js M test/qunit/tests/workflow_editor_tests.js M test/tool_shed/base/twilltestcase.py M test/tool_shed/functional/test_0000_basic_repository_features.py M test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py M test/tool_shed/functional/test_0020_basic_repository_dependencies.py M test/tool_shed/functional/test_0030_repository_dependency_revisions.py M test/tool_shed/functional/test_0040_repository_circular_dependencies.py M test/tool_shed/functional/test_0050_circular_dependencies_4_levels.py M test/tool_shed/functional/test_0060_workflows.py M test/tool_shed/functional/test_0070_invalid_tool.py M test/tool_shed/functional/test_0080_advanced_circular_dependencies.py M test/tool_shed/functional/test_0090_tool_search.py M test/tool_shed/functional/test_0100_complex_repository_dependencies.py M test/tool_shed/functional/test_0110_invalid_simple_repository_dependencies.py M test/tool_shed/functional/test_0120_simple_repository_dependency_multiple_owners.py M test/tool_shed/functional/test_0130_datatype_converters.py M test/tool_shed/functional/test_0140_tool_help_images.py M test/tool_shed/functional/test_0150_prior_installation_required.py M test/tool_shed/functional/test_0160_circular_prior_installation_required.py M test/tool_shed/functional/test_0170_complex_prior_installation_required.py M test/tool_shed/functional/test_0300_reset_all_metadata.py M test/tool_shed/functional/test_0310_hg_push_from_api.py M test/tool_shed/functional/test_0400_repository_component_reviews.py M test/tool_shed/functional/test_0410_repository_component_review_access_control.py M test/tool_shed/functional/test_0420_citable_urls_for_repositories.py M test/tool_shed/functional/test_0430_browse_utilities.py M test/tool_shed/functional/test_0440_deleting_dependency_definitions.py M test/tool_shed/functional/test_0450_skip_tool_tests.py M test/tool_shed/functional/test_0460_upload_to_repository.py M test/tool_shed/functional/test_0470_tool_dependency_repository_type.py M test/tool_shed/functional/test_0480_tool_dependency_xml_verification.py M test/tool_shed/functional/test_0490_export_import_repositories.py M test/tool_shed/functional/test_0500_export_repository_simple_dependency.py M test/tool_shed/functional/test_0510_export_import_repository_complex_dependencies.py M test/tool_shed/functional/test_0520_import_export_circular_dependencies.py M test/tool_shed/functional/test_0530_repository_admin_feature.py A test/tool_shed/functional/test_0540_get_all_metadata_from_api.py M test/tool_shed/functional/test_1000_install_basic_repository.py M test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py M test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py M test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py M test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py M test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py M test/tool_shed/functional/test_1060_install_repository_with_workflow.py M test/tool_shed/functional/test_1070_invalid_tool.py M test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py R test/tool_shed/functional/test_1085_repository_dependency_handling.py R test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py R test/tool_shed/functional/test_1090_install_tool_from_tool_search.py A test/tool_shed/functional/test_1090_repository_dependency_handling.py R test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py A test/tool_shed/functional/test_1100_install_updated_repository_dependencies.py R test/tool_shed/functional/test_1110_install_repository_with_invalid_repository_dependency.py A test/tool_shed/functional/test_1110_install_tool_from_tool_search.py A test/tool_shed/functional/test_1120_install_repository_with_complex_dependencies.py R test/tool_shed/functional/test_1120_simple_repository_dependency_multiple_owners.py R test/tool_shed/functional/test_1130_datatype_converters.py A test/tool_shed/functional/test_1130_install_repository_with_invalid_repository_dependency.py A test/tool_shed/functional/test_1140_simple_repository_dependency_multiple_owners.py R test/tool_shed/functional/test_1140_tool_help_images.py A test/tool_shed/functional/test_1150_datatype_converters.py R test/tool_shed/functional/test_1150_prior_installation_required.py R test/tool_shed/functional/test_1160_circular_prior_installation_required.py A test/tool_shed/functional/test_1160_tool_help_images.py R test/tool_shed/functional/test_1170_complex_prior_installation_required.py A test/tool_shed/functional/test_1170_prior_installation_required.py A test/tool_shed/functional/test_1180_circular_prior_installation_required.py A test/tool_shed/functional/test_1190_complex_prior_installation_required.py M test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py M test/tool_shed/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py M test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py M test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py M test/tool_shed/functional/test_1300_reset_all_metadata.py M test/tool_shed/functional/test_1400_review_migration_stages.py M test/tool_shed/functional/test_1410_update_manager.py M test/tool_shed/functional/test_1420_tool_dependency_environment_inheritance.py M test/tool_shed/functional/test_1430_repair_installed_repository.py M test/tool_shed/functional/test_1440_missing_env_sh_files.py M test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py M test/tool_shed/functional/test_1460_data_managers.py M test/tool_shed/functional/test_1470_updating_installed_repositories.py A test/tool_shed/test_data/0540_files/column_maker/column_maker.tar A test/tool_shed/test_data/0540_files/column_maker/repository_dependencies.xml A test/tool_shed/test_data/0540_files/convert_chars/convert_chars.tar A test/tool_shed/test_data/0540_files/convert_chars/tool_dependencies.xml A test/tool_shed/test_data/0540_files/package_bwa/tool_dependencies.xml M test/unit/test_objectstore.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_execution.py A test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/unittest_utils/galaxy_mock.py M tox.ini Log Message: ----------- Reintroduce my changes to get_files methods. Commit: 453345c6210fd849f8a832b41b57cb2638ec83ef https://github.com/galaxyproject/galaxy/commit/453345c6210fd849f8a832b41b57… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M test/tool_shed/base/twilltestcase.py Log Message: ----------- Merge pull request #1800 from davebx/fix_ts_tests Port my changes from #1392 Compare: https://github.com/galaxyproject/galaxy/compare/09f597ae4bca...453345c6210f

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[galaxyproject/galaxy] 990c0f: Add changeset_revision to tool attributes, avoid s...
by GitHub 25 Feb '16

25 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 990c0fe5351f560653a54a67f15702b2db88945e https://github.com/galaxyproject/galaxy/commit/990c0fe5351f560653a54a67f157… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Add changeset_revision to tool attributes, avoid self.tool_shed_repository Commit: 09f597ae4bca1ddab775f4238e4c433ab1d65935 https://github.com/galaxyproject/galaxy/commit/09f597ae4bca1ddab775f4238e4c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #1802 from mvdbeek/fix_my_mess Add changeset_revision to tool attributes, avoid self.tool_shed_repos… Compare: https://github.com/galaxyproject/galaxy/compare/93069676e6dd...09f597ae4bca

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[galaxyproject/galaxy] f27ff0: Fix to 9acbfdf: initial fix borked fa-2x, instead ...
by GitHub 25 Feb '16

25 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f27ff0c7ba829a48f9c0eae443baa36cda92cf98 https://github.com/galaxyproject/galaxy/commit/f27ff0c7ba829a48f9c0eae443ba… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M client/galaxy/style/less/base.less M client/galaxy/style/less/fontawesome/core.less M static/style/blue/base.css Log Message: ----------- Fix to 9acbfdf: initial fix borked fa-2x, instead remove second woff loaded due to fa-icon font-family rule by aliasing that to fa Commit: 7a9d4943cd0571f5adebf850b4e167065289700b https://github.com/galaxyproject/galaxy/commit/7a9d4943cd0571f5adebf850b4e1… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M test/tool_shed/base/twilltestcase.py Log Message: ----------- Fix tool shed tests for e4a1d5727805168a9fd15aca1cdd21630ada2bbc . Commit: 15c08d80e4a2c027a01dd8dabc16b802be4c18a1 https://github.com/galaxyproject/galaxy/commit/15c08d80e4a2c027a01dd8dabc16… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M client/galaxy/style/less/base.less M client/galaxy/style/less/fontawesome/core.less M static/style/blue/base.css Log Message: ----------- Merge pull request #1791 from carlfeberhard/release_16.01 [16.01] Fix to 9acbfdf: initial fix borked fa-2x, instead remove second woff … Commit: 5546211c0dddb23bbeae34c0cddbd7ad9cebf6b5 https://github.com/galaxyproject/galaxy/commit/5546211c0dddb23bbeae34c0cddb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M test/tool_shed/base/twilltestcase.py Log Message: ----------- Merge pull request #1798 from nsoranzo/release_16.01_tool_shed_test_fixes [16.01] Fix tool shed tests for e4a1d5727805168a9fd15aca1cdd21630ada2bbc . Commit: 93069676e6dd03af947ccd60e8d0883b64a5ed39 https://github.com/galaxyproject/galaxy/commit/93069676e6dd03af947ccd60e8d0… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M client/galaxy/style/less/base.less M client/galaxy/style/less/fontawesome/core.less 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/style/blue/base.css M test/tool_shed/base/twilltestcase.py Log Message: ----------- Merge branch 'release_16.01' into dev Conflicts: static/style/blue/base.css Compare: https://github.com/galaxyproject/galaxy/compare/94f847b3b247...93069676e6dd

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[galaxyproject/galaxy] 7a9d49: Fix tool shed tests for e4a1d5727805168a9fd15aca1c...
by GitHub 25 Feb '16

25 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 7a9d4943cd0571f5adebf850b4e167065289700b https://github.com/galaxyproject/galaxy/commit/7a9d4943cd0571f5adebf850b4e1… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M test/tool_shed/base/twilltestcase.py Log Message: ----------- Fix tool shed tests for e4a1d5727805168a9fd15aca1cdd21630ada2bbc . Commit: 5546211c0dddb23bbeae34c0cddbd7ad9cebf6b5 https://github.com/galaxyproject/galaxy/commit/5546211c0dddb23bbeae34c0cddb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M test/tool_shed/base/twilltestcase.py Log Message: ----------- Merge pull request #1798 from nsoranzo/release_16.01_tool_shed_test_fixes [16.01] Fix tool shed tests for e4a1d5727805168a9fd15aca1cdd21630ada2bbc . Compare: https://github.com/galaxyproject/galaxy/compare/15c08d80e4a2...5546211c0ddd

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[galaxyproject/galaxy] f27ff0: Fix to 9acbfdf: initial fix borked fa-2x, instead ...
by GitHub 25 Feb '16

25 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: f27ff0c7ba829a48f9c0eae443baa36cda92cf98 https://github.com/galaxyproject/galaxy/commit/f27ff0c7ba829a48f9c0eae443ba… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M client/galaxy/style/less/base.less M client/galaxy/style/less/fontawesome/core.less M static/style/blue/base.css Log Message: ----------- Fix to 9acbfdf: initial fix borked fa-2x, instead remove second woff loaded due to fa-icon font-family rule by aliasing that to fa Commit: 15c08d80e4a2c027a01dd8dabc16b802be4c18a1 https://github.com/galaxyproject/galaxy/commit/15c08d80e4a2c027a01dd8dabc16… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M client/galaxy/style/less/base.less M client/galaxy/style/less/fontawesome/core.less M static/style/blue/base.css Log Message: ----------- Merge pull request #1791 from carlfeberhard/release_16.01 [16.01] Fix to 9acbfdf: initial fix borked fa-2x, instead remove second woff … Compare: https://github.com/galaxyproject/galaxy/compare/5677c2ee4fce...15c08d80e4a2

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[galaxyproject/galaxy] 93348e: Fix the remaining 1334 flake8 errors in scripts/ ....
by GitHub 25 Feb '16

25 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 93348e7199a2e35ee85607b948d2ca4ced951c86 https://github.com/galaxyproject/galaxy/commit/93348e7199a2e35ee85607b948d2… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M .ci/flake8_blacklist.txt M scripts/api/common.py M scripts/api/copy_hda_to_library_folder.py M scripts/api/create.py M scripts/api/data_manager_example_execute.py M scripts/api/delete.py M scripts/api/display.py M scripts/api/example_watch_folder.py M scripts/api/form_create_from_xml.py M scripts/api/history_create_history.py M scripts/api/history_delete_history.py M scripts/api/import_library_dataset_to_history.py M scripts/api/import_workflows_from_installed_tool_shed_repository.py M scripts/api/install_tool_shed_repositories.py M scripts/api/library_create_folder.py M scripts/api/library_create_library.py M scripts/api/library_upload_dir.py M scripts/api/library_upload_from_import_dir.py M scripts/api/load_data_with_metadata.py M scripts/api/repair_tool_shed_repository.py M scripts/api/request_type_create_from_xml.py M scripts/api/requests_update_state.py M scripts/api/reset_metadata_on_installed_repositories.py M scripts/api/sample_dataset_update_status.py M scripts/api/sample_update_state.py M scripts/api/search.py M scripts/api/sequencer_configuration_create.py M scripts/api/update.py M scripts/api/upload_to_history.py M scripts/api/workflow_delete.py M scripts/api/workflow_execute.py M scripts/api/workflow_execute_parameters.py M scripts/api/workflow_import.py M scripts/api/workflow_import_from_file_rpark.py M scripts/check_galaxy.py M scripts/data_libraries/build_lucene_index.py M scripts/data_libraries/build_whoosh_index.py M scripts/galaxy-main M scripts/get_platforms.py M scripts/loc_files/create_all_fasta_loc.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/create_nib_seq_loc_file.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/microbes/ncbi_to_ucsc.py M scripts/microbes/util.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/tools/maf/check_loc_file.py M scripts/tools/re_escape_output.py M scripts/transfer.py Log Message: ----------- Fix the remaining 1334 flake8 errors in scripts/ . Close #391. Commit: 196d174716b54593735ce7ca73d80dc48ed58470 https://github.com/galaxyproject/galaxy/commit/196d174716b54593735ce7ca73d8… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M .ci/py3_sources.txt M scripts/api/common.py M scripts/api/display.py M scripts/api/workflow_execute_parameters.py Log Message: ----------- Python 3 support for 3 files. Commit: d85db9daa6601ab8b1a086d43ea55b46dbe6609a https://github.com/galaxyproject/galaxy/commit/d85db9daa6601ab8b1a086d43ea5… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M scripts/api/copy_hda_to_library_folder.py M scripts/api/create.py M scripts/api/data_manager_example_execute.py M scripts/api/delete.py M scripts/api/display.py M scripts/api/example_watch_folder.py M scripts/api/form_create_from_xml.py M scripts/api/history_create_history.py M scripts/api/history_delete_history.py M scripts/api/import_library_dataset_to_history.py M scripts/api/import_workflows_from_installed_tool_shed_repository.py M scripts/api/install_tool_shed_repositories.py M scripts/api/library_create_folder.py M scripts/api/library_create_library.py M scripts/api/library_upload_from_import_dir.py M scripts/api/load_data_with_metadata.py M scripts/api/repair_tool_shed_repository.py M scripts/api/request_type_create_from_xml.py M scripts/api/requests_update_state.py M scripts/api/reset_metadata_on_installed_repositories.py M scripts/api/sample_dataset_update_status.py M scripts/api/sample_update_state.py M scripts/api/sequencer_configuration_create.py M scripts/api/update.py M scripts/api/workflow_delete.py M scripts/api/workflow_execute.py M scripts/api/workflow_execute_parameters.py M scripts/api/workflow_import.py M scripts/api/workflow_import_from_file_rpark.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/update_metadata.py M scripts/create_db.py M scripts/data_libraries/build_lucene_index.py M scripts/data_libraries/build_whoosh_index.py M scripts/db_shell.py M scripts/edam_mapping.py M scripts/extract_dataset_part.py M scripts/functional_tests.py M scripts/helper.py M scripts/manage_db.py M scripts/manage_tools.py M scripts/migrate_tools/migrate_tools.py M scripts/paster.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/tool_shed/build_ts_whoosh_index.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/transfer.py M scripts/update_shed_config_path.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: 94f847b3b2478d92019237402012a719b1c62c49 https://github.com/galaxyproject/galaxy/commit/94f847b3b2478d92019237402012… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M .ci/flake8_blacklist.txt M .ci/py3_sources.txt M scripts/api/common.py M scripts/api/copy_hda_to_library_folder.py M scripts/api/create.py M scripts/api/data_manager_example_execute.py M scripts/api/delete.py M scripts/api/display.py M scripts/api/example_watch_folder.py M scripts/api/form_create_from_xml.py M scripts/api/history_create_history.py M scripts/api/history_delete_history.py M scripts/api/import_library_dataset_to_history.py M scripts/api/import_workflows_from_installed_tool_shed_repository.py M scripts/api/install_tool_shed_repositories.py M scripts/api/library_create_folder.py M scripts/api/library_create_library.py M scripts/api/library_upload_dir.py M scripts/api/library_upload_from_import_dir.py M scripts/api/load_data_with_metadata.py M scripts/api/repair_tool_shed_repository.py M scripts/api/request_type_create_from_xml.py M scripts/api/requests_update_state.py M scripts/api/reset_metadata_on_installed_repositories.py M scripts/api/sample_dataset_update_status.py M scripts/api/sample_update_state.py M scripts/api/search.py M scripts/api/sequencer_configuration_create.py M scripts/api/update.py M scripts/api/upload_to_history.py M scripts/api/workflow_delete.py M scripts/api/workflow_execute.py M scripts/api/workflow_execute_parameters.py M scripts/api/workflow_import.py M scripts/api/workflow_import_from_file_rpark.py M scripts/check_galaxy.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/update_metadata.py M scripts/create_db.py M scripts/data_libraries/build_lucene_index.py M scripts/data_libraries/build_whoosh_index.py M scripts/db_shell.py M scripts/edam_mapping.py M scripts/extract_dataset_part.py M scripts/functional_tests.py M scripts/galaxy-main M scripts/get_platforms.py M scripts/helper.py M scripts/loc_files/create_all_fasta_loc.py M scripts/manage_db.py M scripts/manage_tools.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/create_nib_seq_loc_file.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/microbes/ncbi_to_ucsc.py M scripts/microbes/util.py M scripts/migrate_tools/migrate_tools.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/paster.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/tool_shed/build_ts_whoosh_index.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/tools/maf/check_loc_file.py M scripts/tools/re_escape_output.py M scripts/transfer.py M scripts/update_shed_config_path.py Log Message: ----------- Merge pull request #1755 from nsoranzo/flake8_fixes Fix the remaining 1334 flake8 errors in scripts/ . Compare: https://github.com/galaxyproject/galaxy/compare/5370f2d1cdb3...94f847b3b247

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[galaxyproject/galaxy] 31096b: Some tweaks to bootstrapping.
by GitHub 25 Feb '16

25 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 31096b7504c3cbd371ac2e482ab949cfea40d53f https://github.com/galaxyproject/galaxy/commit/31096b7504c3cbd371ac2e482ab9… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/users.py M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh M lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py Log Message: ----------- Some tweaks to bootstrapping. Commit: 782fccb8bc3e980ca620e4e9d636d53736ff4518 https://github.com/galaxyproject/galaxy/commit/782fccb8bc3e980ca620e4e9d636… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-19 (Fri, 19 Feb 2016) Changed paths: M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py M lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py Log Message: ----------- Use optparse for python 2.6 compatibility. Commit: 5370f2d1cdb3bb745c5463a803d6d5879b9452c3 https://github.com/galaxyproject/galaxy/commit/5370f2d1cdb3bb745c5463a803d6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/users.py M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py M lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py Log Message: ----------- Merge pull request #1756 from davebx/fix_bootstrap Some tweaks to bootstrapping. Compare: https://github.com/galaxyproject/galaxy/compare/7560677bd964...5370f2d1cdb3

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[galaxyproject/galaxy] 5b515a: Update Makefile for release/point releases
by GitHub 25 Feb '16

25 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5b515a76cd951be8b47ebca7eb6d9f107f1cd5f6 https://github.com/galaxyproject/galaxy/commit/5b515a76cd951be8b47ebca7eb6d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M Makefile Log Message: ----------- Update Makefile for release/point releases Commit: 8943a0f86b6ccf4b90e7063e3d2e952d7265d1f7 https://github.com/galaxyproject/galaxy/commit/8943a0f86b6ccf4b90e7063e3d2e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: A scripts/patch.sh Log Message: ----------- Add the script I used to create security patches Commit: 7560677bd964623cbbc322f34d29f527c53b65cb https://github.com/galaxyproject/galaxy/commit/7560677bd964623cbbc322f34d29… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M Makefile A scripts/patch.sh Log Message: ----------- Merge pull request #1793 from natefoo/make-release Update makefile and add the script I used to apply security patches for 16.01 Compare: https://github.com/galaxyproject/galaxy/compare/4f73c4b5f8a5...7560677bd964

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[galaxyproject/galaxy] d21cc8: Tests for some of the 16.01 security vulnerabiliti...
by GitHub 25 Feb '16

25 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d21cc83fc21024f97cc723e872f77c4f5fefb86b https://github.com/galaxyproject/galaxy/commit/d21cc83fc21024f97cc723e872f7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M test/unit/test_objectstore.py A test/unit/tools/test_history_imp_exp.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Tests for some of the 16.01 security vulnerabilities Commit: 4f73c4b5f8a5bdd1f4f2d3eaa4e3bc3e3b208208 https://github.com/galaxyproject/galaxy/commit/4f73c4b5f8a5bdd1f4f2d3eaa4e3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M test/unit/test_objectstore.py A test/unit/tools/test_history_imp_exp.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Merge pull request #1794 from natefoo/16.01-security-tests Tests for some of the 16.01 security vulnerabilities Compare: https://github.com/galaxyproject/galaxy/compare/70a96dd79e4e...4f73c4b5f8a5

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[galaxyproject/galaxy] 06e52c: Drop python2.6 (deprecated, will not be supported ...
by GitHub 25 Feb '16

25 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 06e52c0129581f7ed4691bc6790eb2418c20c366 https://github.com/galaxyproject/galaxy/commit/06e52c0129581f7ed4691bc6790e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-23 (Tue, 23 Feb 2016) Changed paths: M .travis.yml M tox.ini Log Message: ----------- Drop python2.6 (deprecated, will not be supported in 16.04) from testing. Commit: 70a96dd79e4e3479def3e9072d6d0e5076357fc8 https://github.com/galaxyproject/galaxy/commit/70a96dd79e4e3479def3e9072d6d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M .travis.yml M tox.ini Log Message: ----------- Merge pull request #1785 from dannon/26_deprecated Drop python2.6 (deprecated, will not be supported in 16.04) from test… Compare: https://github.com/galaxyproject/galaxy/compare/874540e9120d...70a96dd79e4e

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