galaxy-commits February 2017

galaxy-commits@lists.galaxyproject.org

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133 discussions

[galaxyproject/usegalaxy-playbook] 9789e1: Main mutable configs
by GitHub 21 Feb '17

21 Feb '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 9789e124fbd5589656799028e31a6a6fae0ef43d https://github.com/galaxyproject/usegalaxy-playbook/commit/9789e124fbd55896… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_data_manager_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml Log Message: ----------- Main mutable configs

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[galaxyproject/galaxy]
by GitHub 21 Feb '17

21 Feb '17

Branch: refs/heads/revert-3572-fix_3548 Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/usegalaxy-playbook] 975b26: Use per-job temporary directories (in the job work...
by GitHub 21 Feb '17

21 Feb '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 975b269a91bf8e7de721d91595dc94df5afa8f94 https://github.com/galaxyproject/usegalaxy-playbook/commit/975b269a91bf8e7d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M production/group_vars/galaxyservers.yml M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Use per-job temporary directories (in the job working dir) on Main. Also switch the new_file_path to /galaxy-repl/main/scratch2 temporarily while /galaxy-repl/main/scratch is cleaning.

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[galaxyproject/usegalaxy-playbook] 5187d5: Switch Main to use build_sites.yml and upstream da...
by GitHub 21 Feb '17

21 Feb '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 5187d5de7e15e6cb5f375f34e9473c606e6973e8 https://github.com/galaxyproject/usegalaxy-playbook/commit/5187d5de7e15e6cb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M production/group_vars/galaxyservers.yml A templates/galaxy/usegalaxy.org/config/build_sites.yml.j2 R templates/galaxy/usegalaxy.org/config/datatypes_conf.xml.j2 Log Message: ----------- Switch Main to use build_sites.yml and upstream datatypes_conf.xml.sample

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[galaxyproject/usegalaxy-playbook] 255409: Test mutable configs
by GitHub 21 Feb '17

21 Feb '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 255409268f66823cb91a31a4458c3c5059419c30 https://github.com/galaxyproject/usegalaxy-playbook/commit/255409268f66823c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml Log Message: ----------- Test mutable configs

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[galaxyproject/usegalaxy-playbook] 36bb20: Switch Test to use build_sites.yml and upstream da...
by GitHub 21 Feb '17

21 Feb '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 36bb20ed9a45d752d50147df7d155d2196c6ab6b https://github.com/galaxyproject/usegalaxy-playbook/commit/36bb20ed9a45d752… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M stage/group_vars/galaxyservers.yml A templates/galaxy/test.galaxyproject.org/config/build_sites.yml.j2 R templates/galaxy/test.galaxyproject.org/config/datatypes_conf.xml.j2 M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Switch Test to use build_sites.yml and upstream datatypes_conf.xml.sample. Also switch Test to use per-job $TEMP/$TMPDIR.

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[galaxyproject/galaxy] 027875: Increase patience of Galaxy tests throughout.
by GitHub 21 Feb '17

21 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 0278753d0e2db921cd7d3f55cef483defff5cdb9 https://github.com/galaxyproject/galaxy/commit/0278753d0e2db921cd7d3f55cef4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M test/api/test_tools.py M test/api/test_workflow_extraction.py M test/base/populators.py M test/selenium_tests/framework.py Log Message: ----------- Increase patience of Galaxy tests throughout. This should help reduce various API and Selenium transient failures. Commit: caf57c6f3e21eb38e3331d1a1dd44f2cd5b68dc2 https://github.com/galaxyproject/galaxy/commit/caf57c6f3e21eb38e3331d1a1dd4… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M test/api/test_tools.py M test/api/test_workflow_extraction.py M test/base/populators.py M test/selenium_tests/framework.py Log Message: ----------- Merge pull request #3637 from jmchilton/backport_3589 [17.01] Backport #3589 Compare: https://github.com/galaxyproject/galaxy/compare/09c08d1f61f9...caf57c6f3e21

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[galaxyproject/galaxy] 07a92f: Remove tool_model usage from client
by GitHub 21 Feb '17

21 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 07a92fd3ef084a6d7cbe27199d281e534e35cec1 https://github.com/galaxyproject/galaxy/commit/07a92fd3ef084a6d7cbe27199d28… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-09 (Thu, 09 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M lib/galaxy/webapps/galaxy/api/workflows.py M static/maps/mvc/tool/tool-form-workflow.js.map M static/scripts/mvc/tool/tool-form-workflow.js Log Message: ----------- Remove tool_model usage from client Commit: 171655930aa44227d6b88709aac638dea77a6cd0 https://github.com/galaxyproject/galaxy/commit/171655930aa44227d6b88709aac6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-09 (Thu, 09 Feb 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- Move populate state to parameter handling module Commit: 3e3eb4d1397effc8b46c913bb80f3c02773ac506 https://github.com/galaxyproject/galaxy/commit/3e3eb4d1397effc8b46c913bb80f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-09 (Thu, 09 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M static/maps/mvc/tool/tool-form-workflow.js.map M static/scripts/mvc/tool/tool-form-workflow.js Log Message: ----------- Unify build_module handler Commit: 62d42f711e26e0ab176041ce9a552d1af1290f1a https://github.com/galaxyproject/galaxy/commit/62d42f711e26e0ab176041ce9a55… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-09 (Thu, 09 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Parse payload directly to from_dict handler, handle tool specific attributes in corresponding module wrapper Commit: d27e0570cb0b372288114498fa1ad26a1f5df188 https://github.com/galaxyproject/galaxy/commit/d27e0570cb0b372288114498fa1a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/workflow/modules.py M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Remove name handling field from workflow module forms Commit: 1858e43d46355be344c0fab9e61a2e5a57dc8947 https://github.com/galaxyproject/galaxy/commit/1858e43d46355be344c0fab9e61a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.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/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Unify handling/parsing of label and fixed module name to build title in workflow run form Commit: d484355832a1c6518d38326ef4fbb526423c0e34 https://github.com/galaxyproject/galaxy/commit/d484355832a1c6518d38326ef4fb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Provide attributes to front-end, build title on client side Commit: b9f1e29eaf32cda146fea2b102157489a639ea51 https://github.com/galaxyproject/galaxy/commit/b9f1e29eaf32cda146fea2b10215… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Remove redundant label handling from subworkflows Commit: 7ac954f757d2485ae7543db15f400dca0b94fdf3 https://github.com/galaxyproject/galaxy/commit/7ac954f757d2485ae7543db15f40… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/workflow/run_request.py M lib/tool_shed/util/workflow_util.py Log Message: ----------- Strip name handler Commit: 11f9e1863f9616d58fc00a22526f71b2bca7b880 https://github.com/galaxyproject/galaxy/commit/11f9e1863f9616d58fc00a22526f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix label and annotation handling for subworkflows Commit: c6c210a4fa47d0fc47306d30b9dbf40589f68cd8 https://github.com/galaxyproject/galaxy/commit/c6c210a4fa47d0fc47306d30b9db… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M lib/galaxy/workflow/run_request.py Log Message: ----------- Remove uncommented code block from request builder Commit: eb95131ab3a03a3675c3e6d6db23caca524b3da6 https://github.com/galaxyproject/galaxy/commit/eb95131ab3a03a3675c3e6d6db23… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Export label instead of name for description export Commit: d298c1c0da5871105898166ca72dd224f7897fc6 https://github.com/galaxyproject/galaxy/commit/d298c1c0da5871105898166ca72d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-11 (Sat, 11 Feb 2017) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Fix lint issues Commit: 047c833db79fef8daa25ddf022f85d2ef9386d63 https://github.com/galaxyproject/galaxy/commit/047c833db79fef8daa25ddf022f8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-11 (Sat, 11 Feb 2017) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run_request.py Log Message: ----------- Align subworkflow handling, fix run request through input name Commit: dfa1ddacb93acf341b71148114450c993379adc1 https://github.com/galaxyproject/galaxy/commit/dfa1ddacb93acf341b7114811445… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Restore legacy name handling for backward compatibility Commit: 93f190dd0518005f195960333895b645556860cd https://github.com/galaxyproject/galaxy/commit/93f190dd0518005f195960333895… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Restore previous export behavior Commit: c4491b2d834cdbb61cf009d57c1d3f1086bcfbdb https://github.com/galaxyproject/galaxy/commit/c4491b2d834cdbb61cf009d57c1d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Fix quotes Commit: 79c24066b444b7bd7a85f0ec2ccdd4b131c4da9e https://github.com/galaxyproject/galaxy/commit/79c24066b444b7bd7a85f0ec2ccd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/jenkins/selenium/run_tests.sh M .ci/py3_sources.txt M CONTRIBUTING.md M client/galaxy/scripts/mvc/tool/tool-form-base.js M config/datatypes_conf.xml.sample M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml M contrib/nagios/check_galaxy M contrib/nagios/check_galaxy.py M doc/source/slideshow/architecture/galaxy_architecture.md M doc/source/slideshow/architecture/images/hda_dataset.plantuml.svg M doc/source/slideshow/architecture/images/hda_hdca.plantuml.svg M doc/source/slideshow/architecture/images/objectstore.plantuml.svg M doc/source/slideshow/architecture/images/plantuml_options.txt M doc/source/slideshow/architecture/images/server_client.plantuml.svg M doc/source/slideshow/architecture/images/server_client_old.plantuml.svg M doc/source/slideshow/architecture/images/webapp.plantuml.svg M doc/source/slideshow/architecture/style.css M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/workflow/steps.py M scripts/slideshow/slideshow_template.html M static/maps/mvc/tool/tool-form-base.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/tool/tool-form-base.js M templates/admin/reload_tool.mako M test/api/test_tools.py M test/api/test_workflow_extraction.py M test/base/populators.py A test/functional/tools/output_format_deprecated_when.xml M test/functional/tools/samples_tool_conf.xml M test/selenium_tests/framework.py M test/selenium_tests/test_stock_tours.py M test/selenium_tests/test_uploads.py Log Message: ----------- Merge branch 'dev' into unify_name_label Commit: 1cb8a5da38006cace8c48966a5326b2d3747c574 https://github.com/galaxyproject/galaxy/commit/1cb8a5da38006cace8c48966a532… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Fix import order Commit: 6330f6051790b7d86bdd5674697163efc3c2a0f0 https://github.com/galaxyproject/galaxy/commit/6330f6051790b7d86bdd56746971… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-quotameter.js M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/mvc/user/user-quotameter.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-quotameter.js Log Message: ----------- Merge branch 'dev' into unify_name_label Commit: dcda376c9ca68742eb58efe6f3438d4d6c5f834f https://github.com/galaxyproject/galaxy/commit/dcda376c9ca68742eb58efe6f343… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Restore subworkflow behavior, no need for modifications anymore Commit: 5cd05161413b73c5eb6ea7393b78cafd213409b9 https://github.com/galaxyproject/galaxy/commit/5cd05161413b73c5eb6ea7393b78… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/model/mapping.py M lib/galaxy/model/orm/engine_factory.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/mvc/user/user-quotameter.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-quotameter.js M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge branch 'dev' into unify_name_label Commit: 678a8627984852ea4282f6a25bf8c5176783c7c3 https://github.com/galaxyproject/galaxy/commit/678a8627984852ea4282f6a25bf8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/run_request.py Log Message: ----------- Fix Commit: 7ad46c22694ac7b58acdaefca59ca82cca328f25 https://github.com/galaxyproject/galaxy/commit/7ad46c22694ac7b58acdaefca59c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py Log Message: ----------- Fix subworkflow caller Commit: c75671484058bc5c0cec8f07dda081cff7c0eb57 https://github.com/galaxyproject/galaxy/commit/c75671484058bc5c0cec8f07dda0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Properly initialize subworkflow parameter Commit: 841cbfd9c7bf1efe2c10bbbff59da22ce67e800c https://github.com/galaxyproject/galaxy/commit/841cbfd9c7bf1efe2c10bbbff59d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/workflow/modules.py M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Fix content id parsing, through error if subworkflow could not be found Commit: 4610da47863c9ca9c5eb092bfd031f32c6984b96 https://github.com/galaxyproject/galaxy/commit/4610da47863c9ca9c5eb092bfd03… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix style Commit: f548af88076b11d33e3a24b50102108a076df1b4 https://github.com/galaxyproject/galaxy/commit/f548af88076b11d33e3a24b50102… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Add test case for state populating Commit: 8557c32034c9723dc110719b26082312dde1a998 https://github.com/galaxyproject/galaxy/commit/8557c32034c9723dc110719b2608… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-20 (Mon, 20 Feb 2017) 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 sanitization Commit: cdb15f63925e9879744ae38e5e140e5eb9cc6c19 https://github.com/galaxyproject/galaxy/commit/cdb15f63925e9879744ae38e5e14… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: 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/workflow/workflow-view.js M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run_request.py M lib/tool_shed/util/workflow_util.py 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/workflow/workflow-view.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/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/workflow/workflow-view.js Log Message: ----------- Merge pull request #3593 from guerler/unify_name_label Introduce label and annotation attributes to subworkflows, fix annotation display, unify module form update handler Compare: https://github.com/galaxyproject/galaxy/compare/430ac221baea...cdb15f63925e

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[galaxyproject/galaxy] f1f6bf: Fix annotation display for data inputs
by GitHub 21 Feb '17

21 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: f1f6bf6c3a765e05f8a2dc2b127ee480a485b42e https://github.com/galaxyproject/galaxy/commit/f1f6bf6c3a765e05f8a2dc2b127e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-20 (Mon, 20 Feb 2017) 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 annotation display for data inputs Commit: 09c08d1f61f93ec7973cab1d2cd24532d20e3bb7 https://github.com/galaxyproject/galaxy/commit/09c08d1f61f93ec7973cab1d2cd2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) 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: ----------- Merge pull request #3636 from guerler/fix_annotation [17.01] Fix annotation display for data inputs Compare: https://github.com/galaxyproject/galaxy/compare/493cf2816134...09c08d1f61f9

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[galaxyproject/galaxy] ab6ae4: Cancel existing delayed updates when changing page...
by GitHub 21 Feb '17

21 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: ab6ae42c7a7d76b3fbf024edbbdec407b7b1f490 https://github.com/galaxyproject/galaxy/commit/ab6ae42c7a7d76b3fbf024edbbde… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-view.js M static/maps/mvc/history/history-view.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/history/history-view.js Log Message: ----------- Cancel existing delayed updates when changing pages in the history. Commit: f155a9420a23241c6dc7e404ce487c803a911726 https://github.com/galaxyproject/galaxy/commit/f155a9420a23241c6dc7e404ce48… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-17 (Fri, 17 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.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/base/controlled-fetch-collection.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M tools/filters/random_lines_two_pass.py Log Message: ----------- temp Commit: ce264f9542df6d4ba779309fb8e7822c6f351f2e https://github.com/galaxyproject/galaxy/commit/ce264f9542df6d4ba779309fb8e7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-20 (Mon, 20 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/options-menu.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/history/options-menu.js Log Message: ----------- Reimplement *old* method for unhide/delete-all-hidden using a temporary web controller endpoint. Commit: a3a7e1001cc0ffa985fd7e987c7190f2d74492ff https://github.com/galaxyproject/galaxy/commit/a3a7e1001cc0ffa985fd7e987c71… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-20 (Mon, 20 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.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/base/controlled-fetch-collection.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M tools/filters/random_lines_two_pass.py Log Message: ----------- Strip stashed-yet-merged debug detritus from history UI fixes. Commit: bf602a8add58289900fa64cc5c1163c0721f1d10 https://github.com/galaxyproject/galaxy/commit/bf602a8add58289900fa64cc5c11… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-20 (Mon, 20 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Yet more debugging cruft. This is why we have reviews. Commit: 493cf2816134562188ba009e8bf04ffbcc18a2ac https://github.com/galaxyproject/galaxy/commit/493cf2816134562188ba009e8bf0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/options-menu.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/options-menu.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/history/history-model.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/options-menu.js Log Message: ----------- Merge pull request #3621 from dannon/fix-paginated-history-updates [17.01] History Fixes Compare: https://github.com/galaxyproject/galaxy/compare/f6cc1dcf077f...493cf2816134

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