- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 148c11: Adjust interface to basic.py.
by GitHub 16 Dec '15

16 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 148c11f403674d133bb0301ce2fc01ef108c38bd https://github.com/galaxyproject/galaxy/commit/148c11f403674d133bb0301ce2fc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Adjust interface to basic.py. Commit: 9f68003438cac76a223e84756b0584d7530df239 https://github.com/galaxyproject/galaxy/commit/9f68003438cac76a223e84756b05… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Revise checking for workflow parameters in tooling code. - Use verbose and higher level abstractions. - Tighten up checks (use re.match instead of search when appropriate, replace startwith.("$") with more robust regex matches). Commit: 7687ed7fad52ef69002a2f985fcf682999068f00 https://github.com/galaxyproject/galaxy/commit/7687ed7fad52ef69002a2f985fcf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Tighten workflow parameter check. a440813e37941d050ac503a0898dcf00c5f1b4fe always skipped validation of text/int/float values if they looked like they were workflow parameters. This restricts that check to just occurring when coming from the workflow editor tool form. Commit: fafa72dde200b05954d038902e317c8fe0d302bd https://github.com/galaxyproject/galaxy/commit/fafa72dde200b05954d038902e31… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Slightly tighten up relaxed validation of workflow paramters. Don't allow mid-parameter placement of values for integers, floats, etc... (e.g. 10${param}). This is enforced other places as well. Commit: 9dad7f76c41845e23d07a8583950d41e4b60b3cf https://github.com/galaxyproject/galaxy/commit/9dad7f76c41845e23d07a8583950… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix another instance of using _allow_workflow_parameters_in_context. As recommended by @nsoranzo. Commit: 7b11ebc52e30e6613e1b94c6db0db6bda70a5255 https://github.com/galaxyproject/galaxy/commit/7b11ebc52e30e6613e1b94c6db0d… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-12-16 (Wed, 16 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #1319 from jmchilton/workflow_validation_2 More tightening up of parameter validation during workflow stuff. Compare: https://github.com/galaxyproject/galaxy/compare/d5cddaf7cc4f...7b11ebc52e30

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[galaxyproject/usegalaxy-playbook] aa5b1b: Remove trello card creator. Redirect to GH issues...
by GitHub 15 Dec '15

15 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: aa5b1bc855fadaa8121ee98b3d00e9d1b73c7305 https://github.com/galaxyproject/usegalaxy-playbook/commit/aa5b1bc855fadaa8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: R app_infrastructure.yml M common/inventory R roles/trello_card_creator/handlers/main.yml R roles/trello_card_creator/tasks/main.yml R roles/trello_card_creator/templates/trello_card_creator.ini.j2 M templates/nginx/galaxyproject.j2 Log Message: ----------- Remove trello card creator. Redirect to GH issues.

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[galaxyproject/usegalaxy-playbook] c52ccb: Update interactive_environments role
by GitHub 15 Dec '15

15 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c52ccbe9d8525be4f9e97dce03a879e2b2b30b25 https://github.com/galaxyproject/usegalaxy-playbook/commit/c52ccbe9d8525be4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M roles/galaxyprojectdotorg.interactive_environments/README.md M roles/galaxyprojectdotorg.interactive_environments/meta/.galaxy_install_info M roles/galaxyprojectdotorg.interactive_environments/tasks/extract_component.yml M roles/galaxyprojectdotorg.interactive_environments/tasks/synchronize_components.yml Log Message: ----------- Update interactive_environments role Commit: b3c4a0b0ec0d965eee356d333d0cd18feace8408 https://github.com/galaxyproject/usegalaxy-playbook/commit/b3c4a0b0ec0d965e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M templates/supervisor/toolshed.conf.j2 Log Message: ----------- Merge branch 'master' of github.com:galaxyproject/usegalaxy-playbook Commit: 3edc4c9d17ff2467937943b5c180d9d87985018f https://github.com/galaxyproject/usegalaxy-playbook/commit/3edc4c9d17ff2467… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M stage/files/interactive_environments/plugins/.ansible_ie_role_current_version M stage/files/interactive_environments/proxy/.ansible_ie_role_current_version M stage/group_vars/all.yml Log Message: ----------- Update Test Commit: 15facabe5f7c0dbc6c80ae093a56fc837ee5bacd https://github.com/galaxyproject/usegalaxy-playbook/commit/15facabe5f7c0dbc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M files/galaxy/test.galaxyproject.org/config/job_resource_params_conf.xml M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Resource changes for Anton Commit: ffa181b7f4f422cf0a01e8fc9b1534fc15431cf7 https://github.com/galaxyproject/usegalaxy-playbook/commit/ffa181b7f4f422cf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml Log Message: ----------- Mutable configs on Test Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/b4841230c39d...…

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[galaxyproject/galaxy] 74be6f: Fix for creating workflow outputs on initial workf...
by GitHub 15 Dec '15

15 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 74be6f54cd1868f663dc89609c90a28c0db8214f https://github.com/galaxyproject/galaxy/commit/74be6f54cd1868f663dc89609c90… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Fix for creating workflow outputs on initial workflow upload. Commit: d5cddaf7cc4fa734cb738521167e854393e5d380 https://github.com/galaxyproject/galaxy/commit/d5cddaf7cc4fa734cb738521167e… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #1330 from jmchilton/failing_test Fix for creating workflow outputs on initial workflow upload. Compare: https://github.com/galaxyproject/galaxy/compare/bb0c1366f723...d5cddaf7cc4f

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[galaxyproject/galaxy] b3e3b3: Update Kombu and AMQP wheels to fix problems with ...
by GitHub 15 Dec '15

15 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b3e3b359aec1bce3d7ee4a23289d96318f5b0af3 https://github.com/galaxyproject/galaxy/commit/b3e3b359aec1bce3d7ee4a23289d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Update Kombu and AMQP wheels to fix problems with El Capitan's System Integrity Protection Commit: bb0c1366f723b8236872d05da4c553a53d1aedc7 https://github.com/galaxyproject/galaxy/commit/bb0c1366f723b8236872d05da4c5… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Merge pull request #1327 from natefoo/kombu-el-cap-wheels Update Kombu and AMQP wheels to fix problems with El Capitan's System Integrity Protection Compare: https://github.com/galaxyproject/galaxy/compare/86632afdd3b7...bb0c1366f723

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[galaxyproject/galaxy] 31f174: Add enhancements to the Galaxy repository install ...
by GitHub 15 Dec '15

15 Dec '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 31f174a4254e5cc4c85747a76c3908b0170cf358 https://github.com/galaxyproject/galaxy/commit/31f174a4254e5cc4c85747a76c39… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Add enhancements to the Galaxy repository install process to cleanly handle the case described here: https://github.com/galaxyproject/galaxy/issues/667. Specifically, the following scenario is now cleanly handled: Example use case: In a toolshed I have a repository of a tool, say package_new_gene_db_1_2_3, and in revision 1 it depends on package_sqlite_1_0_0: package_new_gene_db_1_2_3 package_sqlite_1_0_0 At some point in time I discover that postgres is a better solution for my gene database, and I upload revision 2: package_new_gene_db_1_2_3 package_postgres__2_0_0 And I remove the dependecy of sqlite. If I go to my galaxy instance and I remove revision 1 and install revision 2, the installation is cleanly handled with theis PR. It should be noted that this enhancement could adversely impact reproducibility if best practices are not followed with regard to defining package dependencies. Since it is now cleanly possible to eliminate dependencies over time, best practices must be followed to ensure that elimination of a dependency does not affect the output of a tool that uses the underlying hierarchy of packages. Commit: a23e644a9cd7ab64f0fa56314ae5ec2b5a768f7a https://github.com/galaxyproject/galaxy/commit/a23e644a9cd7ab64f0fa56314ae5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge pull request #1329 from martenson/release_15.10 [15.10] Add enhancements to the Galaxy repository install process Compare: https://github.com/galaxyproject/galaxy/compare/c48965ffcc5d...a23e644a9cd7

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[galaxyproject/galaxy] f95300: Fix typo causing the option "Link files instead of...
by GitHub 15 Dec '15

15 Dec '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: f953005f72310279fe69a0deb0b9adef973bf6da https://github.com/galaxyproject/galaxy/commit/f953005f72310279fe69a0deb0b9… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- Fix typo causing the option "Link files instead of copying" to be ignored. When uploading folders with the new data library interface. Commit: c48965ffcc5d35877f00dcf1941317cf23c3d4f4 https://github.com/galaxyproject/galaxy/commit/c48965ffcc5d35877f00dcf19413… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- Merge pull request #1326 from nsoranzo/release_15.10_link_data_only [15.10] Fix typo causing the option "Link files instead of copying" to be ignored. Compare: https://github.com/galaxyproject/galaxy/compare/989f961fb635...c48965ffcc5d

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[galaxyproject/usegalaxy-playbook] b48412: Fix the manual hackery employed by
by GitHub 15 Dec '15

15 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b4841230c39de5e87136d371a9a7366b8055689d https://github.com/galaxyproject/usegalaxy-playbook/commit/b4841230c39de5e8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M templates/supervisor/toolshed.conf.j2 Log Message: ----------- Fix the manual hackery employed by 0db21fc8feab6ff45a5346e307f8d178c7fdeef2 by using uwsgi's -H/--home/--virtualenv/--venv/--pyhome

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[galaxyproject/infrastructure-playbook] 633d58: Give radegast the "lite" env and minor related imp...
by GitHub 15 Dec '15

15 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 633d582b88ebc48ce23884a30a8ad47d97b0ef03 https://github.com/galaxyproject/infrastructure-playbook/commit/633d582b88e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M galaxyenv/inventory R roles/nfs/defaults/main.yml M roles/nfs/tasks/main.yml A roles/nfs/vars/debian_8.yml A roles/nfs/vars/default.yml Log Message: ----------- Give radegast the "lite" env and minor related improvements to the nfs role

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[galaxyproject/galaxy] 58911e: Remove worklfow casperjs API test.
by GitHub 15 Dec '15

15 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 58911edbfb5aa6e858addd9452e90d6ed389b0d2 https://github.com/galaxyproject/galaxy/commit/58911edbfb5aa6e858addd9452e9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: R test/casperjs/api-workflow-tests.js M test/casperjs/casperjs_runner.py Log Message: ----------- Remove worklfow casperjs API test. It has good and more updated coverage in the Python API testing framework. Commit: 86632afdd3b7f2dbfed47671779818835a075496 https://github.com/galaxyproject/galaxy/commit/86632afdd3b7f2dbfed476717798… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: R test/casperjs/api-workflow-tests.js M test/casperjs/casperjs_runner.py Log Message: ----------- Merge pull request #1316 from jmchilton/remove_casper_api_tests Remove worklfow casperjs API test. Compare: https://github.com/galaxyproject/galaxy/compare/b2a3684f03e4...86632afdd3b7

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[galaxyproject/galaxy] 7f7010: Remove left over packed scripts.
by GitHub 15 Dec '15

15 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7f7010dbd96b4b9ce494ba320b853e6441162f5e https://github.com/galaxyproject/galaxy/commit/7f7010dbd96b4b9ce494ba320b85… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: R static/scripts/mvc/collection/paired-collection-creator.js R static/scripts/mvc/history/history-panel.js R static/scripts/mvc/upload/upload-row.js R static/scripts/mvc/workflow/workflow.js Log Message: ----------- Remove left over packed scripts. The source files have been deleted. Commit: b2a3684f03e42d3743d02f4d4f039d429bf5e235 https://github.com/galaxyproject/galaxy/commit/b2a3684f03e42d3743d02f4d4f03… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: R static/scripts/mvc/collection/paired-collection-creator.js R static/scripts/mvc/history/history-panel.js R static/scripts/mvc/upload/upload-row.js R static/scripts/mvc/workflow/workflow.js Log Message: ----------- Merge pull request #1323 from jmchilton/fix_deleted_static Remove left over packed scripts. Compare: https://github.com/galaxyproject/galaxy/compare/cc67557df848...b2a3684f03e4

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[galaxyproject/galaxy] 8e2db2: Fix workflow output step entries
by GitHub 15 Dec '15

15 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8e2db2944cbd546fa0f6f6cb46bf78d470ab31c8 https://github.com/galaxyproject/galaxy/commit/8e2db2944cbd546fa0f6f6cb46bf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Fix workflow output step entries Commit: cc67557df8483899e7058f2047607d0e5339c4eb https://github.com/galaxyproject/galaxy/commit/cc67557df8483899e7058f204760… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #1322 from guerler/fix_workflow_outputs Fix workflow output step entries Compare: https://github.com/galaxyproject/galaxy/compare/19cb62660a37...cc67557df848

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[galaxyproject/galaxy] ce5793: Show a more user-friendly error when the webserver...
by GitHub 15 Dec '15

15 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ce57930342c2a4f7eb672f95dc0b19c93c2322f8 https://github.com/galaxyproject/galaxy/commit/ce57930342c2a4f7eb672f95dc0b… Author: shane <shane(a)shanedowling.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/config.py Log Message: ----------- Show a more user-friendly error when the webserver port is blocked Commit: a42328f0002955295cfb70bc6e16fcf83e42ad82 https://github.com/galaxyproject/galaxy/commit/a42328f0002955295cfb70bc6e16… Author: shane <shane(a)shanedowling.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/config.py Log Message: ----------- Removing unnecessary line Commit: c14bb93a60dba72db34996cadcf20ee0e19a7f19 https://github.com/galaxyproject/galaxy/commit/c14bb93a60dba72db34996cadcf2… Author: shane <shane(a)shanedowling.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/config.py Log Message: ----------- Tidying code for linter Commit: 541231bb1723b2aac3fede7f45ca0455ca954894 https://github.com/galaxyproject/galaxy/commit/541231bb1723b2aac3fede7f45ca… Author: shane <shane(a)shanedowling.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/config.py M lib/galaxy/util/pastescript/serve.py Log Message: ----------- Config-based port checker has been removed and adding in an exception checker for paste response Commit: 19cb62660a3779a6333696ec645f7fcee3db5bc5 https://github.com/galaxyproject/galaxy/commit/19cb62660a3779a6333696ec645f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/util/pastescript/serve.py Log Message: ----------- Merge pull request #1320 from shano/dev Show a more user-friendly error when the webserver port is blocked Compare: https://github.com/galaxyproject/galaxy/compare/4c3dfc7cd471...19cb62660a37

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[galaxyproject/galaxy] 2acdbe: UI, Citations: fix citation-model's import of bibt...
by GitHub 15 Dec '15

15 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2acdbe54f76312cb748693e018d2d505cf95c3a2 https://github.com/galaxyproject/galaxy/commit/2acdbe54f76312cb748693e018d2… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M static/maps/mvc/citation/citation-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/citation/citation-model.js M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- UI, Citations: fix citation-model's import of bibtex to use *either* commonjs or global Commit: 4c3dfc7cd471181edc406724ca8f039e6b2a83d1 https://github.com/galaxyproject/galaxy/commit/4c3dfc7cd471181edc406724ca8f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M static/maps/mvc/citation/citation-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/citation/citation-model.js M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge pull request #1321 from carlfeberhard/fix.citations UI, Citations: fix citation-model's import of bibtex to use *either* … Compare: https://github.com/galaxyproject/galaxy/compare/5bf926bf3ec1...4c3dfc7cd471

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[galaxyproject/infrastructure-playbook] c767b4: Modified authorized users
by GitHub 14 Dec '15

14 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: c767b40a2d3641c5736e8dd7fd706dbeb2b6d987 https://github.com/galaxyproject/infrastructure-playbook/commit/c767b40a2d3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M galaxyenv/secret_host_vars/orval.galaxyproject.org.yml Log Message: ----------- Modified authorized users

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[galaxyproject/galaxy] 886f6d: Improved validation of tools during workflow execu...
by GitHub 14 Dec '15

14 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 886f6d2d707a9b4e2a80b0aaa89157e1137415ad https://github.com/galaxyproject/galaxy/commit/886f6d2d707a9b4e2a80b0aaa891… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/execute.py M test/api/test_workflows.py Log Message: ----------- Improved validation of tools during workflow execution. Do a more complete validation of everything after workflow parameters have been replaced and inputs connected up. Attempt 2 at the idea in https://github.com/galaxyproject/galaxy/pull/1284. Commit: cdd9ca16f0a38ffab5fe54d559fc4bb4e4a7a37d https://github.com/galaxyproject/galaxy/commit/cdd9ca16f0a38ffab5fe54d559fc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/execute.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py Log Message: ----------- Don't silently swallow job creation problems when running workflows. Commit: ce787adff93dafb950341243f3951221cadfc813 https://github.com/galaxyproject/galaxy/commit/ce787adff93dafb950341243f395… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix bug related to collection reductions state. Commit: 5bf926bf3ec19933c0ef82e51c919c0595bfc741 https://github.com/galaxyproject/galaxy/commit/5bf926bf3ec19933c0ef82e51c91… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #1302 from jmchilton/workflow_validation_1 Improved validation of tools during workflow execution. Compare: https://github.com/galaxyproject/galaxy/compare/e838b0330096...5bf926bf3ec1

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[galaxyproject/galaxy] 458766: Add run workflow tool form
by GitHub 14 Dec '15

14 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 458766b00f05a2d46c834d461e59201796ff0358 https://github.com/galaxyproject/galaxy/commit/458766b00f05a2d46c834d461e59… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/form/form-view.js A client/galaxy/scripts/mvc/tool/tool-form-base.js A client/galaxy/scripts/mvc/tool/tool-form-composite.js A client/galaxy/scripts/mvc/tool/tool-form-workflow.js A client/galaxy/scripts/mvc/tool/tool-form.js A client/galaxy/scripts/mvc/tool/tool-template.js M client/galaxy/scripts/mvc/tools.js R client/galaxy/scripts/mvc/tools/tools-form-base.js R client/galaxy/scripts/mvc/tools/tools-form-workflow.js R client/galaxy/scripts/mvc/tools/tools-form.js R client/galaxy/scripts/mvc/tools/tools-jobs.js R client/galaxy/scripts/mvc/tools/tools-template.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/galaxy_bootstrap/variables.less M client/galaxy/style/less/ui.less M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/webapps/galaxy/api/workflows.py M static/maps/galaxy-app-base.js.map M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/form/form-view.js.map A static/maps/mvc/tool/tool-form-base.js.map A static/maps/mvc/tool/tool-form-composite.js.map A static/maps/mvc/tool/tool-form-workflow.js.map A static/maps/mvc/tool/tool-form.js.map A static/maps/mvc/tool/tool-template.js.map M static/maps/mvc/tools.js.map R static/maps/mvc/tools/tools-form-base.js.map R static/maps/mvc/tools/tools-form-workflow.js.map R static/maps/mvc/tools/tools-form.js.map R static/maps/mvc/tools/tools-jobs.js.map R static/maps/mvc/tools/tools-template.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-portlet.js.map M static/maps/mvc/ui/ui-slider.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/utils/utils.js.map M static/scripts/mvc/app/app-analysis.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/form/form-view.js A static/scripts/mvc/tool/tool-form-base.js A static/scripts/mvc/tool/tool-form-composite.js A static/scripts/mvc/tool/tool-form-workflow.js A static/scripts/mvc/tool/tool-form.js A static/scripts/mvc/tool/tool-template.js M static/scripts/mvc/tools.js R static/scripts/mvc/tools/tools-form-base.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-misc.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-slider.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/utils/utils.js M static/style/blue/base.css M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Add run workflow tool form Move styles to css Improve handling of numeric workflow parameters Commit: 9f7dff740f0133d6ba66abe067fb2edeb7a6b705 https://github.com/galaxyproject/galaxy/commit/9f7dff740f0133d6ba66abe067fb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M static/maps/mvc/tool/tool-form-workflow.js.map M static/scripts/mvc/tool/tool-form-workflow.js Log Message: ----------- Revise is_workflow setting Commit: 0770d8d988b20e36c2178d906bd05c6471018edf https://github.com/galaxyproject/galaxy/commit/0770d8d988b20e36c2178d906bd0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/webapps/galaxy/api/workflows.py M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/mvc/tool/tool-form-base.js M templates/webapps/galaxy/workflow/editor_tool_form.mako M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Revise workflow mode flag handling Fix comment Commit: 28715a5bca299933c69859559d5b88b381b6c998 https://github.com/galaxyproject/galaxy/commit/28715a5bca299933c69859559d5b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/style/less/ui.less M lib/galaxy/tools/__init__.py M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/tool/tool-form-composite.js M static/style/blue/base.css Log Message: ----------- Add runtime modification switch Commit: 2f31a3cbcd087f26caa9b8754920a6dddb924b30 https://github.com/galaxyproject/galaxy/commit/2f31a3cbcd087f26caa9b8754920… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form-workflow.js Log Message: ----------- Cleanup collapsible handling Commit: 3017c61f380c8caa722ff04d11e2e3d37ca56b1c https://github.com/galaxyproject/galaxy/commit/3017c61f380c8caa722ff04d11e2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Fix step order Commit: 98e738d6f0cb2faae1c304a889baaa66b10df953 https://github.com/galaxyproject/galaxy/commit/98e738d6f0cb2faae1c304a889ba… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Show pja info inside form portlet Improve readability Commit: aa90e346dd4e10850482e38c7331864bef50f007 https://github.com/galaxyproject/galaxy/commit/aa90e346dd4e10850482e38c7331… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-02 (Wed, 02 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tool-form.js M lib/galaxy/tools/parameters/basic.py M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/tool/tool-form.js.map M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/tool/tool-form.js Log Message: ----------- Revise form base Fix style Commit: a8a4480d5c7e92e0f121eefd66357f5504c4cb26 https://github.com/galaxyproject/galaxy/commit/a8a4480d5c7e92e0f121eefd6635… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/style/less/ui.less M config/plugins/visualizations/charts/static/build-app.js M config/plugins/visualizations/charts/static/library/ui-table-form.js M config/plugins/visualizations/charts/static/views/editor.js M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/dataset_matcher.py M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/style/blue/base.css M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Fix dataset matching Commit: ac79cf191c0a0588cdaf45b5075a2494bf097f57 https://github.com/galaxyproject/galaxy/commit/ac79cf191c0a0588cdaf45b5075a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/style/less/ui.less M static/maps/mvc/form/form-input.js.map M static/scripts/mvc/form/form-input.js M static/style/blue/base.css Log Message: ----------- Fix style naming Commit: 4dc134d43bfa415cf3d1b77475dc0d4a3efb05b1 https://github.com/galaxyproject/galaxy/commit/4dc134d43bfa415cf3d1b77475dc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M .gitignore M README.rst M client/GruntFile.js A client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/apps/history-panel.js A client/galaxy/scripts/apps/login.js A client/galaxy/scripts/apps/tool-panel.js R client/galaxy/scripts/base.js R client/galaxy/scripts/galaxy-app-base.js R client/galaxy/scripts/galaxy.autocom_tagging.js R client/galaxy/scripts/galaxy.base.js R client/galaxy/scripts/galaxy.frame.js A client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.library.js R client/galaxy/scripts/galaxy.masthead.js R 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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 templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako M test/api/helpers.py M test/api/test_jobs.py M test/api/test_tools.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py A test/api/workflows_format_2/README.txt A test/api/workflows_format_2/__init__.py A test/api/workflows_format_2/converter.py A test/api/workflows_format_2/interface.py A test/api/workflows_format_2/main.py R test/api/yaml_to_workflow.py M test/base/twilltestcase.py M test/casperjs/api-history-permission-tests.js M test/casperjs/spaceghost.js A test/functional/tools/cheetah_problem_syntax_error.xml A test/functional/tools/cheetah_problem_unbound_var.xml A test/functional/tools/cheetah_problem_unbound_var_input.xml A test/functional/tools/collection_type_source.xml A test/functional/tools/create_10.xml A test/functional/tools/maxseconds.xml A test/functional/tools/output_format_collection.xml M test/functional/tools/samples_tool_conf.xml M test/functional/tools/simple_constructs.yml M test/qunit/package.json 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/test_galaxy_mapping.py M test/unit/tools/test_actions.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_parsing.py M test/unit/tools/test_tool_loader.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 git://github.com/galaxyproject/galaxy into run_workflow_form_004 Commit: 8e5b8016c6684e2364ba14b9061b0d5a2d218eb1 https://github.com/galaxyproject/galaxy/commit/8e5b8016c6684e2364ba14b9061b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: R client/galaxy/scripts/mvc/app/app-analysis.js R static/maps/mvc/app/app-analysis.js.map Log Message: ----------- Remove files Commit: 7e5069baff533ba61fef3f8f6fc46ecab565a9c6 https://github.com/galaxyproject/galaxy/commit/7e5069baff533ba61fef3f8f6fc4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: R client/galaxy/scripts/mvc/tool/tools-form-base.js R client/galaxy/scripts/mvc/tool/tools-form-workflow.js R client/galaxy/scripts/mvc/tool/tools-form.js R client/galaxy/scripts/mvc/tool/tools-jobs.js R client/galaxy/scripts/mvc/tool/tools-template.js R static/maps/mvc/tool/tools-form-base.js.map R static/maps/mvc/tool/tools-form-workflow.js.map R static/maps/mvc/tool/tools-form.js.map R static/maps/mvc/tool/tools-jobs.js.map R static/maps/mvc/tool/tools-template.js.map R static/maps/mvc/tools/tools-form-base.js.map R static/scripts/mvc/tool/tools-form-base.js R static/scripts/mvc/tool/tools-form-workflow.js R static/scripts/mvc/tool/tools-form.js R static/scripts/mvc/tool/tools-jobs.js R static/scripts/mvc/tool/tools-template.js R static/scripts/mvc/tools/tools-form-base.js Log Message: ----------- Remove files Commit: 0f9cb1478f81d512d4232b42cf490b8022b3a420 https://github.com/galaxyproject/galaxy/commit/0f9cb1478f81d512d4232b42cf49… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M static/style/blue/base.css Log Message: ----------- Repack files Commit: e29f7155c479365ede4a69513e729fa1bc67c369 https://github.com/galaxyproject/galaxy/commit/e29f7155c479365ede4a69513e72… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: R static/maps/mvc/tools.js.map R static/scripts/mvc/app/app-analysis.js R static/scripts/mvc/tools.js Log Message: ----------- Remove files Commit: 6820b29d3b867b452205c275f274449fb55c8119 https://github.com/galaxyproject/galaxy/commit/6820b29d3b867b452205c275f274… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/datatypes/constructive_solid_geometry.py M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js M test/api/helpers.py M test/functional/tools/maxseconds.xml Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into run_workflow_form_004 Commit: ab651fa89c0e24d637daa8bd5716b3932532c6a3 https://github.com/galaxyproject/galaxy/commit/ab651fa89c0e24d637daa8bd5716… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tool-form.js M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/tool/tool-form.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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/tool/tool-form.js M static/scripts/utils/utils.js Log Message: ----------- Fix url, lint and packing Catch missing history, fix failing api test Commit: 00452e1b8aecd3ed2fc4c06262f451c9efafa1c6 https://github.com/galaxyproject/galaxy/commit/00452e1b8aecd3ed2fc4c06262f4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add more specific error message for workflow parameters Commit: a951d34c703a239ac00c780025a9657bc7101b0b https://github.com/galaxyproject/galaxy/commit/a951d34c703a239ac00c780025a9… Author: guerler <aysam.guerler(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: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into run_workflow_form_004 Commit: 8c6d530a661842a56fbb8800856237582701fc56 https://github.com/galaxyproject/galaxy/commit/8c6d530a661842a56fbb88008562… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-07 (Mon, 07 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M lib/galaxy/managers/histories.py M lib/galaxy/managers/workflows.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 lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/workflow/modules.py M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/mvc/tool/tool-form-base.js M templates/ind_share_base.mako M templates/webapps/galaxy/history/share.mako M test/unit/tools/test_execution.py Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into run_workflow_form_004 Commit: 485e8ef8f22330bce5a402c5b4bb0182ce5b180c https://github.com/galaxyproject/galaxy/commit/485e8ef8f22330bce5a402c5b4bb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-07 (Mon, 07 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js M static/maps/mvc/form/form-section.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-section.js Log Message: ----------- Add fallback for missing section and repeat title Commit: 2b63427e965837eb29df54e5918cf8f84004f534 https://github.com/galaxyproject/galaxy/commit/2b63427e965837eb29df54e5918c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/dynamic_options.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Handle late validated dataset references Commit: 636e9900ba5e82c37a26fee84f56872c9413bd1b https://github.com/galaxyproject/galaxy/commit/636e9900ba5e82c37a26fee84f56… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Improve handling of unspecified workflow editor values Commit: 9a4c8343701c676ccf996cbbaa864f12135bac5b https://github.com/galaxyproject/galaxy/commit/9a4c8343701c676ccf996cbbaa86… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-drilldown.js M client/galaxy/style/less/ui.less M static/maps/mvc/ui/ui-drilldown.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-drilldown.js M static/style/blue/base.css Log Message: ----------- Use fa icons for drill down expansion Commit: c61a5529b4c788580d2c3615c7dab2386a9b8e4e https://github.com/galaxyproject/galaxy/commit/c61a5529b4c788580d2c3615c7da… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: A .ci/check_controller.sh A .ci/check_mako.sh A Makefile A client/.docker-build.sh A client/Dockerfile M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/polyfills.js M client/galaxy/style/less/ui.less M config/dependency_resolvers_conf.xml.sample M config/reports.ini.sample M config/tool_shed.ini.sample A doc/source/admin/dependency_resolvers.rst M doc/source/admin/index.rst M doc/source/dev/faq.rst M lib/galaxy/datatypes/text.py M lib/galaxy/managers/base.py M lib/galaxy/managers/users.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/migrate/check.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/util/tool_dependency_util.py M lib/tool_shed/util/workflow_util.py M run_tests.sh M static/maps/mvc/base-mvc.js.map M static/maps/mvc/citation/citation-model.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/polyfills.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/base-mvc.js M static/scripts/mvc/citation/citation-model.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/polyfills.js M static/style/blue/base.css R templates/webapps/galaxy/history/options.mako M templates/webapps/galaxy/workflow/editor_generic_form.mako M test/api/test_tools.py M test/api/test_workflows.py M test/api/workflows_format_2/converter.py M test/base/interactor.py M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh M test/qunit/tests/workflow_editor_tests.js M test/tool_shed/functional/test_1460_data_managers.py M test/unit/managers/test_UserManager.py M test/unit/tools/test_tool_deps.py M test/unit/workflows/test_modules.py M tox.ini Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into run_workflow_form_004 Commit: b8d7cf035df49f2fda9291b91eadf59fd48bfdd0 https://github.com/galaxyproject/galaxy/commit/b8d7cf035df49f2fda9291b91ead… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M config/galaxy.ini.sample M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Add config setting, disable by default Commit: 42edfca679f204aa7e69a6c3df6dc14c8118e22c https://github.com/galaxyproject/galaxy/commit/42edfca679f204aa7e69a6c3df6d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/tools/__init__.py M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Repack, refix section validation Commit: 10fff14ce5ba6952f21da10c81a31ceda397a666 https://github.com/galaxyproject/galaxy/commit/10fff14ce5ba6952f21da10c81a3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Fix missing wf parameter issue in classic form Commit: 57bc4660cf4e21ebe8b73035095e021e4f298680 https://github.com/galaxyproject/galaxy/commit/57bc4660cf4e21ebe8b73035095e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix workflow parameter validation Commit: 3108ba5c01ded7b0209685f57ab231c2cfe92938 https://github.com/galaxyproject/galaxy/commit/3108ba5c01ded7b0209685f57ab2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Ensure that text fields only display text Commit: a440813e37941d050ac503a0898dcf00c5f1b4fe https://github.com/galaxyproject/galaxy/commit/a440813e37941d050ac503a0898d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add workflow_mode flag to validation Commit: e838b03300964615bc2144ceeb9ba785cf5f7a7d https://github.com/galaxyproject/galaxy/commit/e838b03300964615bc2144ceeb9b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/form/form-view.js A client/galaxy/scripts/mvc/tool/tool-form-base.js A client/galaxy/scripts/mvc/tool/tool-form-composite.js A client/galaxy/scripts/mvc/tool/tool-form-workflow.js A client/galaxy/scripts/mvc/tool/tool-form.js A client/galaxy/scripts/mvc/tool/tool-template.js R client/galaxy/scripts/mvc/tool/tools-form-base.js R client/galaxy/scripts/mvc/tool/tools-form-workflow.js R client/galaxy/scripts/mvc/tool/tools-form.js R client/galaxy/scripts/mvc/tool/tools-jobs.js R client/galaxy/scripts/mvc/tool/tools-template.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/ui/ui-drilldown.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/ui.less M config/galaxy.ini.sample M config/plugins/visualizations/charts/static/build-app.js M config/plugins/visualizations/charts/static/library/ui-table-form.js M config/plugins/visualizations/charts/static/views/editor.js M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/webapps/galaxy/api/workflows.py A static/maps/galaxy-app-base.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/form/form-view.js.map A static/maps/mvc/tool/tool-form-base.js.map A static/maps/mvc/tool/tool-form-composite.js.map A static/maps/mvc/tool/tool-form-workflow.js.map A static/maps/mvc/tool/tool-form.js.map A static/maps/mvc/tool/tool-template.js.map R static/maps/mvc/tool/tools-form-base.js.map R static/maps/mvc/tool/tools-form-workflow.js.map R static/maps/mvc/tool/tools-form.js.map R static/maps/mvc/tool/tools-jobs.js.map R static/maps/mvc/tool/tools-template.js.map M 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static/scripts/mvc/tool/tool-form-base.js A static/scripts/mvc/tool/tool-form-composite.js A static/scripts/mvc/tool/tool-form-workflow.js A static/scripts/mvc/tool/tool-form.js A static/scripts/mvc/tool/tool-template.js R static/scripts/mvc/tool/tools-form-base.js R static/scripts/mvc/tool/tools-form-workflow.js R static/scripts/mvc/tool/tools-form.js R static/scripts/mvc/tool/tools-jobs.js R static/scripts/mvc/tool/tools-template.js M static/scripts/mvc/tool/tools.js R static/scripts/mvc/tools.js R static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/ui/ui-drilldown.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-slider.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/utils/utils.js M static/style/blue/base.css M templates/webapps/galaxy/workflow/editor_tool_form.mako M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge pull request #1249 from guerler/run_workflow_form_004 Run workflow form Compare: https://github.com/galaxyproject/galaxy/compare/0fce226b96f9...e838b0330096

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[galaxyproject/galaxy] 1931bd: lazy load metadata to speed up history loading
by GitHub 14 Dec '15

14 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1931bd59077f97946a1af6daa93bc920fceee58e https://github.com/galaxyproject/galaxy/commit/1931bd59077f97946a1af6daa93b… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2015-11-26 (Thu, 26 Nov 2015) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- lazy load metadata to speed up history loading Commit: 7d4f0d82de328ffb763737c067fc9332b61534e9 https://github.com/galaxyproject/galaxy/commit/7d4f0d82de328ffb763737c067fc… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2015-11-26 (Thu, 26 Nov 2015) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- fix indentation Commit: 52078baf99ed2aadae4b30f6b71ae00aecba521a https://github.com/galaxyproject/galaxy/commit/52078baf99ed2aadae4b30f6b71a… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M lib/galaxy/model/custom_types.py Log Message: ----------- don't load or overwrite a value with a not-yet-loaded value (i.e. None) Commit: 27e43e8907a5fb529cdf36175a6ffe04de762379 https://github.com/galaxyproject/galaxy/commit/27e43e8907a5fb529cdf36175a6f… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M lib/galaxy/datatypes/metadata.py Log Message: ----------- Load deferred column before pickling dataset instance Commit: 0fce226b96f98bf3393935602e0b5e9a8762bc4e https://github.com/galaxyproject/galaxy/commit/0fce226b96f98bf3393935602e0b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/datatypes/metadata.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/mapping.py Log Message: ----------- Merge pull request #1179 from abretaud/defer_metadata Lazy load HDA/LDDA metadata to speed up history loading Compare: https://github.com/galaxyproject/galaxy/compare/dd429b640ffe...0fce226b96f9

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[galaxyproject/galaxy] f14b38: UI, list of pairs collection creator: prevent vice...
by GitHub 14 Dec '15

14 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f14b38124bc08c228bfce30f27d1815d7dd27c0b https://github.com/galaxyproject/galaxy/commit/f14b38124bc08c228bfce30f27d1… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/list-of-pairs-collection-creator.js Log Message: ----------- UI, list of pairs collection creator: prevent vice-versa pair duplication by removing paired dataset from both temp lists during auto pairing Commit: c1ce8ef0ce074271c9ba7a9a1718258482cca69f https://github.com/galaxyproject/galaxy/commit/c1ce8ef0ce074271c9ba7a9a1718… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/list-of-pairs-collection-creator.js Log Message: ----------- UI, list of pairs collection creator: improve auto-pair error message to be more beginner friendly(?) Commit: dd429b640ffeb656a1fd61b49e88db890e7743cf https://github.com/galaxyproject/galaxy/commit/dd429b640ffeb656a1fd61b49e88… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/list-of-pairs-collection-creator.js Log Message: ----------- Merge pull request #1310 from carlfeberhard/fix.lop-creator UI, list of pairs creator: properly remove datasets from the filtered lists when pairing Compare: https://github.com/galaxyproject/galaxy/compare/812343d8ccc1...dd429b640ffe

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[galaxyproject/galaxy] 195928: Include link to toolshed repository, and make sure...
by GitHub 14 Dec '15

14 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1959288637bf8c4f11da70df5cd5558c1bc1099a https://github.com/galaxyproject/galaxy/commit/1959288637bf8c4f11da70df5cd5… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/workflow/modules.py Log Message: ----------- Include link to toolshed repository, and make sure upgrade message is not overwritten by tool_version changes. Commit: c143748e62e976fa3a43a721ed49bdbdc78ea980 https://github.com/galaxyproject/galaxy/commit/c143748e62e976fa3a43a721ed49… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Better formatting of workflow warning message. Commit: cd61cdc51b387d6cfb7905307c669e17111ab96d https://github.com/galaxyproject/galaxy/commit/cd61cdc51b387d6cfb7905307c66… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Add back tool id to pass unit tests. Commit: b633c949c875788d5bba9ae0126882b3439d7f7e https://github.com/galaxyproject/galaxy/commit/b633c949c875788d5bba9ae01268… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Mention tool id as hover text on version changes. Commit: 812343d8ccc10a77bab58287178cceb64ad9cb39 https://github.com/galaxyproject/galaxy/commit/812343d8ccc10a77bab58287178c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #1286 from mvdbeek/cross_toolshed_tool_fetching Include link to old and new toolshed repository, and make sure upgrade message is… Compare: https://github.com/galaxyproject/galaxy/compare/a7e60eae2c27...812343d8ccc1

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[galaxyproject/galaxy] 6c9a82: Fix for Section upgrade messages.
by GitHub 12 Dec '15

12 Dec '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 6c9a82e142c5bf70ae4612f094b8d0c89e3fd2f3 https://github.com/galaxyproject/galaxy/commit/6c9a82e142c5bf70ae4612f094b8… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix for Section upgrade messages. Commit: 2c0ad432f8485cb40719adfa8ecbbf1a342afd03 https://github.com/galaxyproject/galaxy/commit/2c0ad432f8485cb40719adfa8ecb… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Use test param label instead of param label in conditional upgrade missing message. Commit: 989f961fb6351d1f63374b4fc40429c1e897b1e2 https://github.com/galaxyproject/galaxy/commit/989f961fb6351d1f63374b4fc404… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #1218 from blankenberg/rerunfix_15.10 [15.10] Fix for Section and conditional upgrade messages. Compare: https://github.com/galaxyproject/galaxy/compare/66146ad5d0e1...989f961fb635

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[galaxyproject/galaxy] ce6cd0: Enforce metrics related to moving toward modern cl...
by GitHub 11 Dec '15

11 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ce6cd03f6c7f020a8127025c49224f1bb920bc18 https://github.com/galaxyproject/galaxy/commit/ce6cd03f6c7f020a8127025c4922… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: A .ci/check_controller.sh A .ci/check_mako.sh M tox.ini Log Message: ----------- Enforce metrics related to moving toward modern client infrastructure. Having a CI enforced blacklist and then a whitelist of files failing to meet style guidelines (as well as expanding list of rules enforced) may have helped create incentive to rework Galaxy toward a more compliant and uniform Python styling. We briefly discussed the possibility of doing this with other team code base objectives on a conference call - in particular to help the transition toward replacing all of the web controllers with API controllers and eliminating the use of Python mako files for rendering web content and replacing it with client side templates. To do this I have created two rough metrics - the number of lines of web controller code in the Galaxy app and the number of mako files in the templates directory. The hope is that people feel ... compelled to lower these numbers. While these metrics are admittedly rough, they do also encourage de-duplication of mako templates and transition of API code into managers (in addition to elimination of functions) both of these secondary incentives are also good things and should be project objectives. Commit: a7e60eae2c2721e7d4377112b7aaceb8424fd3da https://github.com/galaxyproject/galaxy/commit/a7e60eae2c2721e7d4377112b7aa… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: A .ci/check_controller.sh A .ci/check_mako.sh M tox.ini Log Message: ----------- Merge pull request #1292 from jmchilton/client_incentives Enforce metrics related to moving toward modern client infrastructure. Compare: https://github.com/galaxyproject/galaxy/compare/eb4b8e716d26...a7e60eae2c27

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[galaxyproject/galaxy] 760c2b: Properly show and label hidden datasets on rerurn
by GitHub 11 Dec '15

11 Dec '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 760c2b56bee664f2f874e2cc26d2129858da1bb1 https://github.com/galaxyproject/galaxy/commit/760c2b56bee664f2f874e2cc26d2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Properly show and label hidden datasets on rerurn Commit: 66146ad5d0e17e35b6eee50699b0261422835000 https://github.com/galaxyproject/galaxy/commit/66146ad5d0e17e35b6eee50699b0… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #1305 from guerler/fix_workflow_rerun_001 [15.10] Properly show and label hidden datasets on workflow reruns Compare: https://github.com/galaxyproject/galaxy/compare/6a47d2d3a7f2...66146ad5d0e1

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[galaxyproject/galaxy] 1aafc4: Dead sendmail_path vars, this is unused in favor o...
by GitHub 11 Dec '15

11 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1aafc489356d4ad62a00b82f1b0679d66f037be4 https://github.com/galaxyproject/galaxy/commit/1aafc489356d4ad62a00b82f1b06… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M config/reports.ini.sample M config/tool_shed.ini.sample M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- Dead sendmail_path vars, this is unused in favor of smtp (as of a long time ago) Commit: c0b349306f17ed924a5673fab465d105d2cfdaf2 https://github.com/galaxyproject/galaxy/commit/c0b349306f17ed924a5673fab465… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M config/tool_shed.ini.sample M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- Add smtp_ssl option to toolshed mailing capabilities, update .sample to include the smtp auth/ssl. Commit: eb4b8e716d26897e58c78c08e9a2d62a770604f5 https://github.com/galaxyproject/galaxy/commit/eb4b8e716d26897e58c78c08e9a2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M config/reports.ini.sample M config/tool_shed.ini.sample M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- Merge pull request #1299 from dannon/mail_fixes Minor mail config cleanup Compare: https://github.com/galaxyproject/galaxy/compare/6580d5129386...eb4b8e716d26

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[galaxyproject/galaxy] 48064c: * Clarify comment in XML
by GitHub 11 Dec '15

11 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 48064cc20352d3e38f985769ba5b2eeb66f051a8 https://github.com/galaxyproject/galaxy/commit/48064cc20352d3e38f985769ba5b… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2015-12-07 (Mon, 07 Dec 2015) Changed paths: M config/dependency_resolvers_conf.xml.sample Log Message: ----------- * Clarify comment in XML Commit: e40fbe5374f906139f8be7a3ceb001f049a6b244 https://github.com/galaxyproject/galaxy/commit/e40fbe5374f906139f8be7a3ceb0… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M config/dependency_resolvers_conf.xml.sample A doc/source/admin/dependency_resolvers.rst M doc/source/admin/index.rst Log Message: ----------- * Add comment about base_path in sample config * Add documentation on dependency resolvers Commit: 584d886b5ee68257921dff24c4dbe0a2dbb0c00c https://github.com/galaxyproject/galaxy/commit/584d886b5ee68257921dff24c4db… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M doc/source/admin/dependency_resolvers.rst M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/modules.py Log Message: ----------- * Mention modulepath attribute in dependency resolver docs * Use modulepath in both environment modules resolvers * Export MODULEPATH in generated shell command * Add logging for operation of dependency resolvers Commit: 035f1b5d663841fa61d32ba79e1b43553dab4fab https://github.com/galaxyproject/galaxy/commit/035f1b5d663841fa61d32ba79e1b… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M doc/source/admin/dependency_resolvers.rst M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/modules.py M test/unit/tools/test_tool_deps.py Log Message: ----------- * Incorporate documentation fixes from nsoranzo * Replace {} and .format with %s and % to preserve Python 2.6 compatibility * Add a modulepath= paranter to the fake resolver (Bunch object) used to test the modules dependency resolver Commit: 2b90ca9b0e23715bd7a03614fa989bcf540f73e9 https://github.com/galaxyproject/galaxy/commit/2b90ca9b0e23715bd7a03614fa98… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- * Replaced incorrect %b with %s Commit: 73b6fb23db300501c9124c61c90d73d2c28dc7a4 https://github.com/galaxyproject/galaxy/commit/73b6fb23db300501c9124c61c90d… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M doc/source/admin/dependency_resolvers.rst Log Message: ----------- * Replaced all references to "version number" with "version string" Commit: 6580d5129386ab5b8634583c5378dfc340ed2800 https://github.com/galaxyproject/galaxy/commit/6580d5129386ab5b8634583c5378… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M config/dependency_resolvers_conf.xml.sample A doc/source/admin/dependency_resolvers.rst M doc/source/admin/index.rst M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/modules.py M test/unit/tools/test_tool_deps.py Log Message: ----------- Merge pull request #1296 from pvanheus/env-modules-resolve Documentation for dependency resolvers Compare: https://github.com/galaxyproject/galaxy/compare/bca004eff860...6580d5129386

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