[galaxy-commits] [galaxyproject/galaxy] 9c4310: Remove html builders for tool parameters, strip ru...

GitHub noreply at github.com
Sun Sep 25 23:34:54 EDT 2016


  Branch: refs/heads/dev
  Home:   https://github.com/galaxyproject/galaxy
  Commit: 9c43103630eb8bceb10021b282b8296218c04729
      https://github.com/galaxyproject/galaxy/commit/9c43103630eb8bceb10021b282b8296218c04729
  Author: guerler <aysam.guerler at gmail.com>
  Date:   2016-09-21 (Wed, 21 Sep 2016)

  Changed paths:
    M lib/galaxy/tools/parameters/basic.py
    M templates/webapps/galaxy/workflow/run.mako

  Log Message:
  -----------
  Remove html builders for tool parameters, strip run workflow mako


  Commit: cd93da35c11f9374c5ffd03a44cbf33876dffb29
      https://github.com/galaxyproject/galaxy/commit/cd93da35c11f9374c5ffd03a44cbf33876dffb29
  Author: guerler <aysam.guerler at gmail.com>
  Date:   2016-09-21 (Wed, 21 Sep 2016)

  Changed paths:
    M lib/galaxy/webapps/galaxy/controllers/workflow.py
    R templates/webapps/galaxy/workflow/run_complete.mako

  Log Message:
  -----------
  Remove old run controller


  Commit: 289ac4845ad79cc7ee2079784d31182d3df23027
      https://github.com/galaxyproject/galaxy/commit/289ac4845ad79cc7ee2079784d31182d3df23027
  Author: guerler <aysam.guerler at gmail.com>
  Date:   2016-09-21 (Wed, 21 Sep 2016)

  Changed paths:
    M lib/galaxy/tools/parameters/basic.py

  Log Message:
  -----------
  Remove unused checked list state for booleans


  Commit: 9f6a88a28f968a03301e8a516f10a5322bc77f4e
      https://github.com/galaxyproject/galaxy/commit/9f6a88a28f968a03301e8a516f10a5322bc77f4e
  Author: guerler <aysam.guerler at gmail.com>
  Date:   2016-09-21 (Wed, 21 Sep 2016)

  Changed paths:
    M lib/galaxy/tools/parameters/basic.py

  Log Message:
  -----------
  Remove unused to_dict parameters


  Commit: cd91e3141c7d031b092091ce22345d87b8aa76d2
      https://github.com/galaxyproject/galaxy/commit/cd91e3141c7d031b092091ce22345d87b8aa76d2
  Author: guerler <aysam.guerler at gmail.com>
  Date:   2016-09-21 (Wed, 21 Sep 2016)

  Changed paths:
    M lib/galaxy/tools/parameters/basic.py

  Log Message:
  -----------
  Rename regex parameter, fix spacing


  Commit: b38b9fe2e1663d724651a0c6e1aa78e87acaa43d
      https://github.com/galaxyproject/galaxy/commit/b38b9fe2e1663d724651a0c6e1aa78e87acaa43d
  Author: guerler <aysam.guerler at gmail.com>
  Date:   2016-09-21 (Wed, 21 Sep 2016)

  Changed paths:
    M lib/galaxy/tools/parameters/basic.py

  Log Message:
  -----------
  Remove comment


  Commit: 13f498568c505b24f1b9753aaf158be324542219
      https://github.com/galaxyproject/galaxy/commit/13f498568c505b24f1b9753aaf158be324542219
  Author: guerler <aysam.guerler at gmail.com>
  Date:   2016-09-21 (Wed, 21 Sep 2016)

  Changed paths:
    M lib/galaxy/tools/parameters/basic.py

  Log Message:
  -----------
  Remove unused repeat handling


  Commit: d5ca00d6892874dc7da54be0a45da3cea4acb878
      https://github.com/galaxyproject/galaxy/commit/d5ca00d6892874dc7da54be0a45da3cea4acb878
  Author: guerler <aysam.guerler at gmail.com>
  Date:   2016-09-21 (Wed, 21 Sep 2016)

  Changed paths:
    M lib/galaxy/tools/parameters/basic.py

  Log Message:
  -----------
  Adjust first half of test cases in basic paramter handling


  Commit: 143a3ecffcc8da4469245b40336901f944b531e0
      https://github.com/galaxyproject/galaxy/commit/143a3ecffcc8da4469245b40336901f944b531e0
  Author: guerler <aysam.guerler at gmail.com>
  Date:   2016-09-21 (Wed, 21 Sep 2016)

  Changed paths:
    M lib/galaxy/tools/parameters/basic.py

  Log Message:
  -----------
  Fix test cases


  Commit: adfaa948e9f65c07bf8cf8a67791bb3dd0e30bc6
      https://github.com/galaxyproject/galaxy/commit/adfaa948e9f65c07bf8cf8a67791bb3dd0e30bc6
  Author: guerler <aysam.guerler at gmail.com>
  Date:   2016-09-21 (Wed, 21 Sep 2016)

  Changed paths:
    M lib/galaxy/webapps/galaxy/controllers/workflow.py

  Log Message:
  -----------
  Remove unused imports


  Commit: c61933d1b1c0289735945bf97bf8b1f4bf5e5fc8
      https://github.com/galaxyproject/galaxy/commit/c61933d1b1c0289735945bf97bf8b1f4bf5e5fc8
  Author: guerler <aysam.guerler at gmail.com>
  Date:   2016-09-21 (Wed, 21 Sep 2016)

  Changed paths:
    M lib/galaxy/tools/parameters/basic.py
    M test/unit/tools/test_data_parameters.py
    M test/unit/unittest_utils/galaxy_mock.py

  Log Message:
  -----------
  Fix dataset parameter tests


  Commit: 979bdd44c60d5aab27e472b19afa8dd704ee195a
      https://github.com/galaxyproject/galaxy/commit/979bdd44c60d5aab27e472b19afa8dd704ee195a
  Author: guerler <aysam.guerler at gmail.com>
  Date:   2016-09-21 (Wed, 21 Sep 2016)

  Changed paths:
    M lib/galaxy/tools/parameters/basic.py

  Log Message:
  -----------
  Fix drilldown tests


  Commit: 05923e210c41e0f3a6d14a3bd914356c042f4670
      https://github.com/galaxyproject/galaxy/commit/05923e210c41e0f3a6d14a3bd914356c042f4670
  Author: guerler <aysam.guerler at gmail.com>
  Date:   2016-09-21 (Wed, 21 Sep 2016)

  Changed paths:
    M lib/galaxy/tools/parameters/basic.py

  Log Message:
  -----------
  Undo name change for workflow regex


  Commit: 9863e35368066975fe049adee716c5cabad4c60f
      https://github.com/galaxyproject/galaxy/commit/9863e35368066975fe049adee716c5cabad4c60f
  Author: guerler <aysam.guerler at gmail.com>
  Date:   2016-09-21 (Wed, 21 Sep 2016)

  Changed paths:
    M lib/galaxy/tools/parameters/basic.py
    M lib/galaxy/tools/parameters/grouping.py
    M lib/galaxy/webapps/galaxy/controllers/workflow.py
    M test/unit/tools/test_data_parameters.py

  Log Message:
  -----------
  Attempt to remove value_mapper parsing


  Commit: 29cfd1635879987de9d1efc49d704894454a3ddf
      https://github.com/galaxyproject/galaxy/commit/29cfd1635879987de9d1efc49d704894454a3ddf
  Author: guerler <aysam.guerler at gmail.com>
  Date:   2016-09-21 (Wed, 21 Sep 2016)

  Changed paths:
    M test/unit/tools/test_parameter_parsing.py

  Log Message:
  -----------
  Fix test_parameter_parsing


  Commit: 474c9a26c495ddddeb6ba7c1966de6ae32cedea7
      https://github.com/galaxyproject/galaxy/commit/474c9a26c495ddddeb6ba7c1966de6ae32cedea7
  Author: guerler <aysam.guerler at gmail.com>
  Date:   2016-09-21 (Wed, 21 Sep 2016)

  Changed paths:
    M templates/webapps/tool_shed/repository/tool_form.mako
    M test/unit/tools/test_data_parameters.py

  Log Message:
  -----------
  Fix toolshed tool form preview, import order


  Commit: 6b40607e7917b98c481c4e47ac31d31698ce2660
      https://github.com/galaxyproject/galaxy/commit/6b40607e7917b98c481c4e47ac31d31698ce2660
  Author: guerler <aysam.guerler at gmail.com>
  Date:   2016-09-21 (Wed, 21 Sep 2016)

  Changed paths:
    M lib/galaxy/tools/parameters/basic.py

  Log Message:
  -----------
  Remove debug output


  Commit: 0ef6f7826c621235beef70e8e4c3352d2ab2e2b6
      https://github.com/galaxyproject/galaxy/commit/0ef6f7826c621235beef70e8e4c3352d2ab2e2b6
  Author: guerler <aysam.guerler at gmail.com>
  Date:   2016-09-21 (Wed, 21 Sep 2016)

  Changed paths:
    M lib/galaxy/webapps/galaxy/api/workflows.py
    M templates/webapps/galaxy/workflow/run.mako

  Log Message:
  -----------
  Move controller build endpoint to api


  Commit: 057485b6f6a8c545478907d01bd6ceadfea0d1f6
      https://github.com/galaxyproject/galaxy/commit/057485b6f6a8c545478907d01bd6ceadfea0d1f6
  Author: guerler <aysam.guerler at gmail.com>
  Date:   2016-09-21 (Wed, 21 Sep 2016)

  Changed paths:
    M lib/galaxy/webapps/galaxy/api/workflows.py

  Log Message:
  -----------
  Import exception, fix parameter names


  Commit: a537daa9ed24fe4a4fd7c9e7c54ba30f6de6e156
      https://github.com/galaxyproject/galaxy/commit/a537daa9ed24fe4a4fd7c9e7c54ba30f6de6e156
  Author: guerler <aysam.guerler at gmail.com>
  Date:   2016-09-21 (Wed, 21 Sep 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/tool/tool-form-composite.js
    M lib/galaxy/managers/workflows.py
    M lib/galaxy/webapps/galaxy/api/workflows.py
    M lib/galaxy/webapps/galaxy/controllers/workflow.py
    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
    M static/scripts/bundled/libs.bundled.js.map
    M static/scripts/mvc/tool/tool-form-composite.js
    M templates/webapps/galaxy/workflow/run.mako

  Log Message:
  -----------
  Move run form model builder to workflow data manager


  Commit: b2014fe44ce7b5af42956cf74cd6e75c51a8df0f
      https://github.com/galaxyproject/galaxy/commit/b2014fe44ce7b5af42956cf74cd6e75c51a8df0f
  Author: guerler <aysam.guerler at gmail.com>
  Date:   2016-09-21 (Wed, 21 Sep 2016)

  Changed paths:
    M lib/galaxy/managers/workflows.py

  Log Message:
  -----------
  Disable target history specification for run workflow form


  Commit: 2c79755ba2fb752418d7405efdfdcd46bf14d8a4
      https://github.com/galaxyproject/galaxy/commit/2c79755ba2fb752418d7405efdfdcd46bf14d8a4
  Author: guerler <aysam.guerler at gmail.com>
  Date:   2016-09-21 (Wed, 21 Sep 2016)

  Changed paths:
    M lib/galaxy/managers/workflows.py
    M lib/galaxy/webapps/galaxy/controllers/workflow.py

  Log Message:
  -----------
  Fix stored/workflow handling


  Commit: 667d5e83cb6ccb7b46084b73101cb85cc81dd9fa
      https://github.com/galaxyproject/galaxy/commit/667d5e83cb6ccb7b46084b73101cb85cc81dd9fa
  Author: guerler <aysam.guerler at gmail.com>
  Date:   2016-09-21 (Wed, 21 Sep 2016)

  Changed paths:
    M templates/webapps/tool_shed/repository/tool_form.mako

  Log Message:
  -----------
  Fix value parsing


  Commit: 21b5246c913fbf5ae8361f359e17252718f1f87d
      https://github.com/galaxyproject/galaxy/commit/21b5246c913fbf5ae8361f359e17252718f1f87d
  Author: guerler <aysam.guerler at gmail.com>
  Date:   2016-09-21 (Wed, 21 Sep 2016)

  Changed paths:
    M lib/galaxy/managers/workflows.py

  Log Message:
  -----------
  Remove unused data manager


  Commit: c5d00518fe409d4876c18ceaeeef2ad5b6829385
      https://github.com/galaxyproject/galaxy/commit/c5d00518fe409d4876c18ceaeeef2ad5b6829385
  Author: guerler <aysam.guerler at gmail.com>
  Date:   2016-09-21 (Wed, 21 Sep 2016)

  Changed paths:
    M lib/galaxy/webapps/galaxy/controllers/workflow.py

  Log Message:
  -----------
  Fix error messages


  Commit: 86719ce90e2cb8ee8439b2f4e8a947cc239e1957
      https://github.com/galaxyproject/galaxy/commit/86719ce90e2cb8ee8439b2f4e8a947cc239e1957
  Author: guerler <aysam.guerler at gmail.com>
  Date:   2016-09-21 (Wed, 21 Sep 2016)

  Changed paths:
    M lib/galaxy/managers/workflows.py

  Log Message:
  -----------
  Remove redundant imports


  Commit: 675398c91263eaed37007b76e4856a6d81f888a3
      https://github.com/galaxyproject/galaxy/commit/675398c91263eaed37007b76e4856a6d81f888a3
  Author: guerler <aysam.guerler at gmail.com>
  Date:   2016-09-21 (Wed, 21 Sep 2016)

  Changed paths:
    M lib/galaxy/webapps/galaxy/controllers/workflow.py

  Log Message:
  -----------
  Use message exception to parse errors


  Commit: a0da06d842a6488ee355c0cf37c06f7ffb8ee837
      https://github.com/galaxyproject/galaxy/commit/a0da06d842a6488ee355c0cf37c06f7ffb8ee837
  Author: guerler <aysam.guerler at gmail.com>
  Date:   2016-09-21 (Wed, 21 Sep 2016)

  Changed paths:
    M lib/galaxy/managers/workflows.py

  Log Message:
  -----------
  Revise comment


  Commit: 05b1c988961e9e002e10d4e4cc21f49ff4ab958a
      https://github.com/galaxyproject/galaxy/commit/05b1c988961e9e002e10d4e4cc21f49ff4ab958a
  Author: guerler <aysam.guerler at gmail.com>
  Date:   2016-09-21 (Wed, 21 Sep 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/tool/tool-form-composite.js
    M lib/galaxy/managers/workflows.py
    M static/maps/mvc/tool/tool-form-composite.js.map
    M static/scripts/mvc/tool/tool-form-composite.js

  Log Message:
  -----------
  Add basic step version changes notification


  Commit: 680e34c1adf87e3f6181bc2d6508f3f5ab84c903
      https://github.com/galaxyproject/galaxy/commit/680e34c1adf87e3f6181bc2d6508f3f5ab84c903
  Author: guerler <aysam.guerler at gmail.com>
  Date:   2016-09-21 (Wed, 21 Sep 2016)

  Changed paths:
    M client/galaxy/style/less/ui.less
    M static/style/blue/base.css

  Log Message:
  -----------
  Fix form preview height style


  Commit: 80b5e5da91cdf65b8f06e75a9a6b2c202b94d409
      https://github.com/galaxyproject/galaxy/commit/80b5e5da91cdf65b8f06e75a9a6b2c202b94d409
  Author: guerler <aysam.guerler at gmail.com>
  Date:   2016-09-21 (Wed, 21 Sep 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/tool/tool-form-composite.js
    M client/galaxy/scripts/mvc/ui/ui-portlet.js
    M client/galaxy/style/less/ui.less
    M static/maps/mvc/tool/tool-form-composite.js.map
    M static/maps/mvc/ui/ui-portlet.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-composite.js
    M static/scripts/mvc/ui/ui-portlet.js
    M static/style/blue/base.css

  Log Message:
  -----------
  Remove unused portlet footer


  Commit: 1ab673a4ed5de36db49e24edae821d226040d183
      https://github.com/galaxyproject/galaxy/commit/1ab673a4ed5de36db49e24edae821d226040d183
  Author: guerler <aysam.guerler at gmail.com>
  Date:   2016-09-21 (Wed, 21 Sep 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/ui/ui-select-content.js
    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-select-content.js

  Log Message:
  -----------
  Fix padding distance


  Commit: 9dc412921e5b5446aa4493aca8c7c0105f7d0725
      https://github.com/galaxyproject/galaxy/commit/9dc412921e5b5446aa4493aca8c7c0105f7d0725
  Author: guerler <aysam.guerler at gmail.com>
  Date:   2016-09-21 (Wed, 21 Sep 2016)

  Changed paths:
    M client/galaxy/style/less/ui.less
    M static/style/blue/base.css

  Log Message:
  -----------
  Fix bottom margin


  Commit: 7a736818a6c32615c396a2a18d9ebd884ddccebb
      https://github.com/galaxyproject/galaxy/commit/7a736818a6c32615c396a2a18d9ebd884ddccebb
  Author: guerler <aysam.guerler at gmail.com>
  Date:   2016-09-21 (Wed, 21 Sep 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
    M client/galaxy/scripts/mvc/tool/tool-form.js
    M static/maps/mvc/tool/tool-form-workflow.js.map
    M static/maps/mvc/tool/tool-form.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-workflow.js
    M static/scripts/mvc/tool/tool-form.js
    M test/qunit/tests/form_tests.js

  Log Message:
  -----------
  Avoid inheritance in tool-form view

Avoid inheritance for workflow editor form

Fix test cases


  Commit: 42ebe00c060d6fcbc69fd16973995c33aba48207
      https://github.com/galaxyproject/galaxy/commit/42ebe00c060d6fcbc69fd16973995c33aba48207
  Author: guerler <aysam.guerler at gmail.com>
  Date:   2016-09-23 (Fri, 23 Sep 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/tool/tool-form-base.js
    M client/galaxy/scripts/mvc/tool/tool-form.js
    M static/maps/mvc/tool/tool-form-base.js.map
    M static/maps/mvc/tool/tool-form.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.js

  Log Message:
  -----------
  Add listener to properly clean up deferred form building processes


  Commit: 2cf7b8ee15856626bff5dfad735023a43ace978b
      https://github.com/galaxyproject/galaxy/commit/2cf7b8ee15856626bff5dfad735023a43ace978b
  Author: guerler <aysam.guerler at gmail.com>
  Date:   2016-09-23 (Fri, 23 Sep 2016)

  Changed paths:
    M client/galaxy/scripts/mvc/tool/tool-form-base.js
    M client/galaxy/scripts/utils/utils.js
    M static/maps/mvc/tool/tool-form-base.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/mvc/tool/tool-form-base.js
    M static/scripts/utils/utils.js

  Log Message:
  -----------
  Fix status handling for ajax requests


  Commit: e3346e1d273b277445844e38e9e8d29873b4d619
      https://github.com/galaxyproject/galaxy/commit/e3346e1d273b277445844e38e9e8d29873b4d619
  Author: guerler <aysam.guerler at gmail.com>
  Date:   2016-09-23 (Fri, 23 Sep 2016)

  Changed paths:
    M .gitignore
    M Makefile
    A doc/parse_gx_xsd.py
    A doc/schema_template.md
    M lib/galaxy/webapps/galaxy/controllers/dataset.py
    M lib/galaxy/webapps/tool_shed/api/repositories.py
    M lib/galaxy/webapps/tool_shed/controllers/repository.py
    M lib/galaxy/webapps/tool_shed/model/__init__.py
    M lib/tool_shed/util/metadata_util.py
    M scripts/bootstrap_history.py
    M scripts/tool_shed/build_ts_whoosh_index.py
    M templates/webapps/galaxy/dataset/copy_view.mako
    M test/shed_functional/functional/test_1400_review_migration_stages.py

  Log Message:
  -----------
  Merge branch 'dev' into strip_run_form_mako


  Commit: 7f19ba817c4d8e7d82380bd6fe8d03a7247488f3
      https://github.com/galaxyproject/galaxy/commit/7f19ba817c4d8e7d82380bd6fe8d03a7247488f3
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-25 (Sun, 25 Sep 2016)

  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/tool/tool-form.js
    M client/galaxy/scripts/mvc/ui/ui-portlet.js
    M client/galaxy/scripts/mvc/ui/ui-select-content.js
    M client/galaxy/scripts/utils/utils.js
    M client/galaxy/style/less/ui.less
    M lib/galaxy/managers/workflows.py
    M lib/galaxy/tools/parameters/basic.py
    M lib/galaxy/tools/parameters/grouping.py
    M lib/galaxy/webapps/galaxy/api/workflows.py
    M lib/galaxy/webapps/galaxy/controllers/workflow.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/tool/tool-form.js.map
    M static/maps/mvc/ui/ui-portlet.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/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
    M static/scripts/mvc/ui/ui-portlet.js
    M static/scripts/mvc/ui/ui-select-content.js
    M static/scripts/utils/utils.js
    M static/style/blue/base.css
    M templates/webapps/galaxy/workflow/run.mako
    R templates/webapps/galaxy/workflow/run_complete.mako
    M templates/webapps/tool_shed/repository/tool_form.mako
    M test/qunit/tests/form_tests.js
    M test/unit/tools/test_data_parameters.py
    M test/unit/tools/test_parameter_parsing.py
    M test/unit/unittest_utils/galaxy_mock.py

  Log Message:
  -----------
  Merge pull request #2935 from guerler/strip_run_form_mako

Strip workflow run mako


Compare: https://github.com/galaxyproject/galaxy/compare/cbb957028f0c...7f19ba817c4d


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