- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 4483f0: Fix ScIdx datatype sniffer
by GitHub 13 Feb '17

13 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 4483f014107d92340573c7113745821e4863c148 https://github.com/galaxyproject/galaxy/commit/4483f014107d92340573c7113745… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-02-13 (Mon, 13 Feb 2017) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Fix ScIdx datatype sniffer Check for EOF before line stripping, otherwise empty or whitespace lines will be considered EOF. Found when uploading a GFF file which was erroneously sniffed as scidx. Commit: 5db0b7681bb60e0671c0d80d06e3d980ef3aab6e https://github.com/galaxyproject/galaxy/commit/5db0b7681bb60e0671c0d80d06e3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-13 (Mon, 13 Feb 2017) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Merge pull request #3602 from nsoranzo/release_17.01_fix_scidx_sniffer Fix ScIdx datatype sniffer Compare: https://github.com/galaxyproject/galaxy/compare/4a22bb902b12...5db0b7681bb6

1 0

[galaxyproject/galaxy] 7e98cd: Update tool XSD for (hopefully deprecated) change_...
by GitHub 13 Feb '17

13 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7e98cde0a9cf62f60b907ed14ee407f6183dee72 https://github.com/galaxyproject/galaxy/commit/7e98cde0a9cf62f60b907ed14ee4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-08 (Wed, 08 Feb 2017) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd A test/functional/tools/output_format_deprecated_when.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Update tool XSD for (hopefully deprecated) change_format syntax. Fixes #3552. Commit: b4b75b276c9d41181e89322754c64abba57cd753 https://github.com/galaxyproject/galaxy/commit/b4b75b276c9d41181e89322754c6… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-02-13 (Mon, 13 Feb 2017) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd A test/functional/tools/output_format_deprecated_when.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3579 from jmchilton/deprecated_change_format_when Update tool XSD for (hopefully deprecated) change_format syntax. Compare: https://github.com/galaxyproject/galaxy/compare/e06f56a61521...b4b75b276c9d

1 0

[galaxyproject/galaxy] 69552b: Fix root location for tool reloader
by GitHub 13 Feb '17

13 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 69552ba63b90604a0d0f0315cad5f42e3344eac5 https://github.com/galaxyproject/galaxy/commit/69552ba63b90604a0d0f0315cad5… 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 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 Log Message: ----------- Fix root location for tool reloader Commit: 4a22bb902b121f91c370b30c64590dd46997a412 https://github.com/galaxyproject/galaxy/commit/4a22bb902b121f91c370b30c6459… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js 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 Log Message: ----------- Merge pull request #3595 from guerler/fix_tool_reload_002 [17.01] Fix root location for tool reloader Commit: e06f56a61521563f1bd17c5ad09df94264d45772 https://github.com/galaxyproject/galaxy/commit/e06f56a61521563f1bd17c5ad09d… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-02-13 (Mon, 13 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js 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 Log Message: ----------- Merge branch 'release_17.01' into dev Conflicts: static/maps/mvc/tool/tool-form-base.js.map static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map static/scripts/mvc/tool/tool-form-base.js Compare: https://github.com/galaxyproject/galaxy/compare/75a17bc31166...e06f56a61521

1 0

[galaxyproject/galaxy] a79ae2: Align architecture slides with training-material r...
by GitHub 13 Feb '17

13 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a79ae2a8c297c1c0f6c0e61271a2ca05ae0aa0f0 https://github.com/galaxyproject/galaxy/commit/a79ae2a8c297c1c0f6c0e61271a2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M CONTRIBUTING.md 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 scripts/slideshow/slideshow_template.html Log Message: ----------- Align architecture slides with training-material remarkjs template. - Copy over the training material style CSS template and add to it only what is needed. - Cleanup style and layout handling in architecture slides markdown. - Update generated images for white background. - Small updates in content to architecture for recent changes (and CONTRIBUTING.md linked to from slides). Commit: d066ae2223ef006a7621ddaa30ecd24ffa2942dd https://github.com/galaxyproject/galaxy/commit/d066ae2223ef006a7621ddaa30ec… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-13 (Mon, 13 Feb 2017) Changed paths: M doc/source/slideshow/architecture/galaxy_architecture.md Log Message: ----------- Link fixes thanks to @nsoranzo. Commit: 75a17bc311662fae24b679a7b41146552f796992 https://github.com/galaxyproject/galaxy/commit/75a17bc311662fae24b679a7b411… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-13 (Mon, 13 Feb 2017) Changed paths: M CONTRIBUTING.md 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 scripts/slideshow/slideshow_template.html Log Message: ----------- Merge pull request #3594 from jmchilton/architecture_touchup Align architecture slides with training-material remarkjs template. Compare: https://github.com/galaxyproject/galaxy/compare/d382537008da...75a17bc31166

1 0

[galaxyproject/galaxy] dc0e9f: Avoid step duplication when ordering steps on the ...
by GitHub 13 Feb '17

13 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: dc0e9fd79eaff575a731409ed7f1771c6cd82b93 https://github.com/galaxyproject/galaxy/commit/dc0e9fd79eaff575a731409ed7f1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M lib/galaxy/workflow/steps.py Log Message: ----------- Avoid step duplication when ordering steps on the fly Commit: d382537008da588b68a86925a42f0828a9e376d8 https://github.com/galaxyproject/galaxy/commit/d382537008da588b68a86925a42f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-13 (Mon, 13 Feb 2017) Changed paths: M lib/galaxy/workflow/steps.py Log Message: ----------- Merge pull request #3590 from guerler/fix_order_steps Avoid step duplication when ordering steps on the fly Compare: https://github.com/galaxyproject/galaxy/compare/9ceaa0d41583...d382537008da

1 0

[galaxyproject/galaxy] 2e7873: Disable transiently failing tour test.
by GitHub 12 Feb '17

12 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2e787394cc0b9ea1a73ba87235faa4f38c1e495e https://github.com/galaxyproject/galaxy/commit/2e787394cc0b9ea1a73ba87235fa… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-12 (Sun, 12 Feb 2017) Changed paths: M test/selenium_tests/test_stock_tours.py Log Message: ----------- Disable transiently failing tour test. See code comment for more information - I am tracking the issue here https://github.com/galaxyproject/galaxy/issues/3598. I think it is important to resolve that test and fix the usability problems with current tours but I'd like to get the Selenium tests stable and testing against new PRs first. Commit: 9ceaa0d41583b66efb1c228755ca4368c0bdb6af https://github.com/galaxyproject/galaxy/commit/9ceaa0d41583b66efb1c228755ca… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-12 (Sun, 12 Feb 2017) Changed paths: M test/selenium_tests/test_stock_tours.py Log Message: ----------- Merge pull request #3599 from jmchilton/disable_galaxy_ui_test Disable transiently failing tour test. Compare: https://github.com/galaxyproject/galaxy/compare/d9b36176a818...9ceaa0d41583

1 0

[galaxyproject/galaxy] 69552b: Fix root location for tool reloader
by GitHub 10 Feb '17

10 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 69552ba63b90604a0d0f0315cad5f42e3344eac5 https://github.com/galaxyproject/galaxy/commit/69552ba63b90604a0d0f0315cad5… 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 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 Log Message: ----------- Fix root location for tool reloader Commit: 4a22bb902b121f91c370b30c64590dd46997a412 https://github.com/galaxyproject/galaxy/commit/4a22bb902b121f91c370b30c6459… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js 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 Log Message: ----------- Merge pull request #3595 from guerler/fix_tool_reload_002 [17.01] Fix root location for tool reloader Compare: https://github.com/galaxyproject/galaxy/compare/087c75e76ff4...4a22bb902b12

1 0

[galaxyproject/galaxy] 0815e6: Add d3_hierarchy subclass
by GitHub 10 Feb '17

10 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0815e6b8813b0ef980cc95ddf08244c44e8fb2e0 https://github.com/galaxyproject/galaxy/commit/0815e6b8813b0ef980cc95ddf082… Author: Jim Johnson <jj(a)umn.edu> Date: 2017-02-08 (Wed, 08 Feb 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Add d3_hierarchy subclass This is to support Unipept API tool and visualization: https://github.com/unipept/unipept-visualizations The unipept visualization would only apply to the d3_hierarchy of json datasets. Commit: d9b36176a8181168f5c4553ead4f9e6545d7e856 https://github.com/galaxyproject/galaxy/commit/d9b36176a8181168f5c4553ead4f… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-02-11 (Sat, 11 Feb 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #3580 from jj-umn/patch-5 Add d3_hierarchy subclass Compare: https://github.com/galaxyproject/galaxy/compare/66a24c8830f5...d9b36176a818

1 0

[galaxyproject/galaxy] 812ad3: Fix transiently failing Selenium upload test.
by GitHub 10 Feb '17

10 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 812ad3af18b087372b31188ac173b7e9238d712b https://github.com/galaxyproject/galaxy/commit/812ad3af18b087372b31188ac173… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M test/selenium_tests/test_uploads.py Log Message: ----------- Fix transiently failing Selenium upload test. Commit: 66a24c8830f5a87579f5e6e4f55c8efbf9073b0f https://github.com/galaxyproject/galaxy/commit/66a24c8830f5a87579f5e6e4f55c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M test/selenium_tests/test_uploads.py Log Message: ----------- Merge pull request #3587 from jmchilton/selenium_fixes Fix transiently failing Selenium upload test. Compare: https://github.com/galaxyproject/galaxy/compare/2ad612349683...66a24c8830f5

1 0

[galaxyproject/galaxy] 1922d5: Increase patience of Galaxy tests throughout.
by GitHub 10 Feb '17

10 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1922d50f903f0c6ad1440d9128a1a23d37cc529c https://github.com/galaxyproject/galaxy/commit/1922d50f903f0c6ad1440d9128a1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-10 (Fri, 10 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: 2ad612349683dd4ab3bde476f9153e90415f0b53 https://github.com/galaxyproject/galaxy/commit/2ad612349683dd4ab3bde476f915… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-10 (Fri, 10 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 #3589 from jmchilton/test_timeout_increases Increase patience of Galaxy tests throughout. Compare: https://github.com/galaxyproject/galaxy/compare/ed52230952a1...2ad612349683

1 0

[galaxyproject/galaxy] a7d05a: Prevent make_html_table() datatype methods from ra...
by GitHub 10 Feb '17

10 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a7d05a47da592e76fd88ed699f034e13e2dba08e https://github.com/galaxyproject/galaxy/commit/a7d05a47da592e76fd88ed699f03… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/tabular.py Log Message: ----------- Prevent make_html_table() datatype methods from raising Exceptions This was preventing the browse of a data library which contained a purged dataset of gg datatype. Also fix import order and Python3 compatibility. Commit: f8dcae95364b79a1612c7a0d04b489d874512aa7 https://github.com/galaxyproject/galaxy/commit/f8dcae95364b79a1612c7a0d04b4… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Remove edam_format for Genbank from config/datatypes_conf.xml.sample This was preventing the loading of the datatype: WARNING 2017-02-10 11:07:05,162 Cannot specify edam_format without setting subclass to True, skipping datatype. Bug introduced in commit c36fbebb443ae5b5263ba6cad6ad36113bb52f44 . Also backport commit 5657a8b809e5938d3d996a77c826811e1176c108 from dev. Commit: 087c75e76ff44cf49eb0b458520d2df4db31e32e https://github.com/galaxyproject/galaxy/commit/087c75e76ff44cf49eb0b458520d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/tabular.py Log Message: ----------- Merge pull request #3585 from nsoranzo/release_17.01_datatypes_fixes [17.01] Two datatypes fixes Commit: ed52230952a1411a39cff3bde7a7ed66e1344f6f https://github.com/galaxyproject/galaxy/commit/ed52230952a1411a39cff3bde7a7… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/tabular.py Log Message: ----------- Merge branch 'release_17.01' into dev Conflicts: config/datatypes_conf.xml.sample Compare: https://github.com/galaxyproject/galaxy/compare/6f5743d052fb...ed52230952a1

1 0

[galaxyproject/galaxy] a7d05a: Prevent make_html_table() datatype methods from ra...
by GitHub 10 Feb '17

10 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: a7d05a47da592e76fd88ed699f034e13e2dba08e https://github.com/galaxyproject/galaxy/commit/a7d05a47da592e76fd88ed699f03… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/tabular.py Log Message: ----------- Prevent make_html_table() datatype methods from raising Exceptions This was preventing the browse of a data library which contained a purged dataset of gg datatype. Also fix import order and Python3 compatibility. Commit: f8dcae95364b79a1612c7a0d04b489d874512aa7 https://github.com/galaxyproject/galaxy/commit/f8dcae95364b79a1612c7a0d04b4… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Remove edam_format for Genbank from config/datatypes_conf.xml.sample This was preventing the loading of the datatype: WARNING 2017-02-10 11:07:05,162 Cannot specify edam_format without setting subclass to True, skipping datatype. Bug introduced in commit c36fbebb443ae5b5263ba6cad6ad36113bb52f44 . Also backport commit 5657a8b809e5938d3d996a77c826811e1176c108 from dev. Commit: 087c75e76ff44cf49eb0b458520d2df4db31e32e https://github.com/galaxyproject/galaxy/commit/087c75e76ff44cf49eb0b458520d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/tabular.py Log Message: ----------- Merge pull request #3585 from nsoranzo/release_17.01_datatypes_fixes [17.01] Two datatypes fixes Compare: https://github.com/galaxyproject/galaxy/compare/884cff33fa04...087c75e76ff4

1 0

[galaxyproject/galaxy] f33098: add option to send API key in header
by GitHub 10 Feb '17

10 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f3309822c856e50c61d94c2e021859342d40c5fb https://github.com/galaxyproject/galaxy/commit/f3309822c856e50c61d94c2e0218… Author: jvolkening <jdv(a)base2bio.com> Date: 2017-02-09 (Thu, 09 Feb 2017) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- add option to send API key in header Commit: 6f5743d052fb4c2ee227d71bf6106f2be9f4428a https://github.com/galaxyproject/galaxy/commit/6f5743d052fb4c2ee227d71bf610… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Merge pull request #3584 from jvolkening/http_header_api_key add option to send API key in header Compare: https://github.com/galaxyproject/galaxy/compare/7d35a029174d...6f5743d052fb

1 0

[galaxyproject/galaxy] f7092b: Clean up Selenium resources better.
by GitHub 09 Feb '17

09 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f7092bd959cfae7f6ee0262a993a2dc5867416e4 https://github.com/galaxyproject/galaxy/commit/f7092bd959cfae7f6ee0262a993a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-09 (Thu, 09 Feb 2017) Changed paths: M .ci/jenkins/selenium/run_tests.sh Log Message: ----------- Clean up Selenium resources better. Commit: 7d35a029174da0e3c8f481c0662139b9a59b3051 https://github.com/galaxyproject/galaxy/commit/7d35a029174da0e3c8f481c06621… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-09 (Thu, 09 Feb 2017) Changed paths: M .ci/jenkins/selenium/run_tests.sh Log Message: ----------- Merge pull request #3583 from jmchilton/selenium_fixes Clean up docker-compose resources better for Selenium tests. Compare: https://github.com/galaxyproject/galaxy/compare/be09b7c2ccf2...7d35a029174d

1 0

[galaxyproject/galaxy] 139bac: Remove broken tour step.
by GitHub 09 Feb '17

09 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 139bacb7d3e507ea56b8c8997e47408db87b5fa3 https://github.com/galaxyproject/galaxy/commit/139bacb7d3e507ea56b8c8997e47… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-08 (Wed, 08 Feb 2017) Changed paths: M config/plugins/tours/core.history.yaml Log Message: ----------- Remove broken tour step. This causes the Selenium tests to fail under various conditions - but legimately so. The referenced target link disappears pretty quickly after the step in the previous click. When I run them in the web browser and this step is "disconnected" and in the center of the screen and as a result it isn't clear what links are being referred to. Commit: be09b7c2ccf2ef861927795c16fb1306ef37ff1a https://github.com/galaxyproject/galaxy/commit/be09b7c2ccf2ef861927795c16fb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-09 (Thu, 09 Feb 2017) Changed paths: M config/plugins/tours/core.history.yaml Log Message: ----------- Merge pull request #3582 from jmchilton/selenium_fixes Remove broken tour step. Compare: https://github.com/galaxyproject/galaxy/compare/ca847e2d588d...be09b7c2ccf2

1 0

[galaxyproject/usegalaxy-playbook] 2e21c5: update submodule
by GitHub 09 Feb '17

09 Feb '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 2e21c55a4645d808ce369104453d38e348f6f6b4 https://github.com/galaxyproject/usegalaxy-playbook/commit/2e21c55a4645d808… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-09 (Thu, 09 Feb 2017) Changed paths: M common_roles Log Message: ----------- update submodule

1 0

[galaxyproject/galaxy] 86a788: Update Nagios check
by GitHub 08 Feb '17

08 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 86a7880e48b81dec9a480600da9f918f7380c3bf https://github.com/galaxyproject/galaxy/commit/86a7880e48b81dec9a480600da9f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-02-07 (Tue, 07 Feb 2017) Changed paths: M contrib/nagios/check_galaxy M contrib/nagios/check_galaxy.py Log Message: ----------- Update Nagios check Commit: ca847e2d588db417bb66664a76ecfdb2105ccc41 https://github.com/galaxyproject/galaxy/commit/ca847e2d588db417bb66664a76ec… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-08 (Wed, 08 Feb 2017) Changed paths: M contrib/nagios/check_galaxy M contrib/nagios/check_galaxy.py Log Message: ----------- Merge pull request #3568 from natefoo/nagios Update Nagios check Compare: https://github.com/galaxyproject/galaxy/compare/ed3062b41de4...ca847e2d588d

1 0

[galaxyproject/galaxy] 3b7890: Set 'deleted' to True when purging a history datas...
by GitHub 08 Feb '17

08 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3b78907fdbbf2f26ea89f4459901e59164a033b7 https://github.com/galaxyproject/galaxy/commit/3b78907fdbbf2f26ea89f4459901… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2017-02-07 (Tue, 07 Feb 2017) Changed paths: M lib/galaxy/managers/deletable.py A lib/galaxy/model/migrate/versions/0134_hda_set_deleted_if_purged.py M test/api/test_history_contents.py M test/unit/managers/test_HDAManager.py Log Message: ----------- Set 'deleted' to True when purging a history dataset association Fix https://github.com/galaxyproject/galaxy/issues/3548 Add API and unit test cases. Add migration to fix misaligned databases. Commit: b215ea1eed127e61421cccb8ff5ddb68963e28ae https://github.com/galaxyproject/galaxy/commit/b215ea1eed127e61421cccb8ff5d… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-02-08 (Wed, 08 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/webapps/galaxy/api/histories.py M test/api/test_histories.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- Sync API history purge with hda implementation Add API and unit test cases. Import order and Python3 fixes. Commit: ed3062b41de47d77974bfae97bac21b2d9806432 https://github.com/galaxyproject/galaxy/commit/ed3062b41de47d77974bfae97bac… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-08 (Wed, 08 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/managers/deletable.py A lib/galaxy/model/migrate/versions/0134_hda_set_deleted_if_purged.py M lib/galaxy/webapps/galaxy/api/histories.py M test/api/test_histories.py M test/api/test_history_contents.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- Merge pull request #3572 from nsoranzo/fix_3548 Set 'deleted' to True when purging a history dataset association Compare: https://github.com/galaxyproject/galaxy/compare/3b3bfad8e0af...ed3062b41de4

1 0

[galaxyproject/galaxy] 012e26: Remove debugging warn statement.
by GitHub 08 Feb '17

08 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 012e261692a2ed8eb3e3c6ca4496b0bd48c99a84 https://github.com/galaxyproject/galaxy/commit/012e261692a2ed8eb3e3c6ca4496… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-06 (Mon, 06 Feb 2017) Changed paths: M lib/galaxy/managers/users.py Log Message: ----------- Remove debugging warn statement. I don't think it was meant to be here. Commit: f2e15588bfad5ad04e4f6530b9b7966e65d138ad https://github.com/galaxyproject/galaxy/commit/f2e15588bfad5ad04e4f6530b9b7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-06 (Mon, 06 Feb 2017) Changed paths: M lib/galaxy/managers/users.py Log Message: ----------- Merge pull request #3566 from jmchilton/1701_user_warn [17.01] Remove debugging warn statement. Commit: 10b743d1d99b0a544002adf57c61a0168ca24e2a https://github.com/galaxyproject/galaxy/commit/10b743d1d99b0a544002adf57c61… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-07 (Tue, 07 Feb 2017) Changed paths: M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Fix default for Pulsar option "dependency_resolution" to match documentation. Commit: 6eb735be8265e0e10d2a5bb7c3845c27dcbff6fb https://github.com/galaxyproject/galaxy/commit/6eb735be8265e0e10d2a5bb7c384… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-07 (Tue, 07 Feb 2017) Changed paths: M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Merge pull request #3575 from jmchilton/pulsar_default_fix [17.01] Fix default for Pulsar option "dependency_resolution" to match documentation. Commit: 561606621cd207c05ec4da33cb7f8c3b9f6f5bfa https://github.com/galaxyproject/galaxy/commit/561606621cd207c05ec4da33cb7f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-07 (Tue, 07 Feb 2017) Changed paths: M doc/source/releases/index.rst Log Message: ----------- Update index.rst Commit: 884cff33fa04915f426f8c24bb53494ff43f0a36 https://github.com/galaxyproject/galaxy/commit/884cff33fa04915f426f8c24bb53… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-02-08 (Wed, 08 Feb 2017) Changed paths: M doc/source/releases/index.rst Log Message: ----------- Merge pull request #3577 from martenson/release-docs-menu [17.01] list new release docs Commit: 3b3bfad8e0af0d07dee1ef379560258aece3f8e6 https://github.com/galaxyproject/galaxy/commit/3b3bfad8e0af0d07dee1ef379560… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-02-08 (Wed, 08 Feb 2017) Changed paths: M doc/source/releases/index.rst M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/managers/users.py Log Message: ----------- Merge branch 'release_17.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/36686199cc71...3b3bfad8e0af

1 0

[galaxyproject/galaxy] 561606: Update index.rst
by GitHub 07 Feb '17

07 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 561606621cd207c05ec4da33cb7f8c3b9f6f5bfa https://github.com/galaxyproject/galaxy/commit/561606621cd207c05ec4da33cb7f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-07 (Tue, 07 Feb 2017) Changed paths: M doc/source/releases/index.rst Log Message: ----------- Update index.rst Commit: 884cff33fa04915f426f8c24bb53494ff43f0a36 https://github.com/galaxyproject/galaxy/commit/884cff33fa04915f426f8c24bb53… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-02-08 (Wed, 08 Feb 2017) Changed paths: M doc/source/releases/index.rst Log Message: ----------- Merge pull request #3577 from martenson/release-docs-menu [17.01] list new release docs Compare: https://github.com/galaxyproject/galaxy/compare/6eb735be8265...884cff33fa04

1 0

[galaxyproject/galaxy] 10b743: Fix default for Pulsar option "dependency_resoluti...
by GitHub 07 Feb '17

07 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 10b743d1d99b0a544002adf57c61a0168ca24e2a https://github.com/galaxyproject/galaxy/commit/10b743d1d99b0a544002adf57c61… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-07 (Tue, 07 Feb 2017) Changed paths: M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Fix default for Pulsar option "dependency_resolution" to match documentation. Commit: 6eb735be8265e0e10d2a5bb7c3845c27dcbff6fb https://github.com/galaxyproject/galaxy/commit/6eb735be8265e0e10d2a5bb7c384… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-07 (Tue, 07 Feb 2017) Changed paths: M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Merge pull request #3575 from jmchilton/pulsar_default_fix [17.01] Fix default for Pulsar option "dependency_resolution" to match documentation. Compare: https://github.com/galaxyproject/galaxy/compare/f2e15588bfad...6eb735be8265

1 0

[galaxyproject/galaxy] 846e76: Update Jupyter IE name to be shorter and consisten...
by GitHub 07 Feb '17

07 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 846e765fa93ebcf33c0acce2ba9a9a49366b6a3a https://github.com/galaxyproject/galaxy/commit/846e765fa93ebcf33c0acce2ba9a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-07 (Tue, 07 Feb 2017) Changed paths: M config/plugins/interactive_environments/jupyter/config/jupyter.xml Log Message: ----------- Update Jupyter IE name to be shorter and consistent with other names. Makes menu entries look correct. Commit: 36686199cc7111cbf17df3ec619a5097048117e3 https://github.com/galaxyproject/galaxy/commit/36686199cc7111cbf17df3ec619a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-07 (Tue, 07 Feb 2017) Changed paths: M config/plugins/interactive_environments/jupyter/config/jupyter.xml Log Message: ----------- Merge pull request #3576 from dannon/jupyter_naming Update Jupyter IE name to be shorter and consistent with other names.… Compare: https://github.com/galaxyproject/galaxy/compare/d302400b99b7...36686199cc71

1 0

[galaxyproject/galaxy] 5ea926: Insert editable title flag for portlets
by GitHub 07 Feb '17

07 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5ea926e4b2b5a70a408780d9fcee1b9b7e4e5e88 https://github.com/galaxyproject/galaxy/commit/5ea926e4b2b5a70a408780d9fcee… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-portlet.js M static/maps/mvc/ui/ui-portlet.js.map M static/scripts/mvc/ui/ui-portlet.js Log Message: ----------- Insert editable title flag for portlets Commit: 6dfc362594c83aa96f6c86acd5d7ee9a84743931 https://github.com/galaxyproject/galaxy/commit/6dfc362594c83aa96f6c86acd5d7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/form/form-view.js.map M static/maps/mvc/ui/ui-portlet.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/form/form-view.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Add optional event handler to edit portlet title text Commit: e96e86644ea924e21611b65e5bf8bfbf0dc23c9d https://github.com/galaxyproject/galaxy/commit/e96e86644ea924e21611b65e5bf8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Display node type icon in portlet header for non-tool modules Commit: 76710c4c7b5030a4cfc89d1a49339a01e0fa1d9c https://github.com/galaxyproject/galaxy/commit/76710c4c7b5030a4cfc89d1a4933… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Disable text editing, leave feature in for future use Commit: 7f391076b22dca78299ff9322c593ff8ea6a7510 https://github.com/galaxyproject/galaxy/commit/7f391076b22dca78299ff9322c59… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Display module type icons for tool modules too Commit: 6e2a0db08272f32abedbbbcb3c3ad06cadaf739b https://github.com/galaxyproject/galaxy/commit/6e2a0db08272f32abedbbbcb3c3a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Use shared portlet style for both module types Commit: 54573f02ebe7d682347e7a9df0a8360b4fad4339 https://github.com/galaxyproject/galaxy/commit/54573f02ebe7d682347e7a9df0a8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/webapps/galaxy/api/workflows.py 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: ----------- Submit label and annotation separate from other inputs to avoid future conflicts Commit: dadd6ee2213a8c1fb4e3954b66a234dc10e81719 https://github.com/galaxyproject/galaxy/commit/dadd6ee2213a8c1fb4e3954b66a2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 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/tool/tool-form.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/webapps/galaxy/api/workflows.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/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/tool/tool-form.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Use underscore to distinguish internal parameters, separate postchange actions Commit: bc51f6f69fc04e07d1c0d3f7c55a15f62e9f337a https://github.com/galaxyproject/galaxy/commit/bc51f6f69fc04e07d1c0d3f7c55a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M client/galaxy/scripts/libs/jquery/jquery.autocomplete.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/ui/autocom_tagging.js M static/maps/libs/jquery/jquery.autocomplete.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/ui/autocom_tagging.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/libs/jquery/jquery.autocomplete.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/ui/autocom_tagging.js Log Message: ----------- Rename custom autocomplete module to avoid interference with original jquery autocomplete, use original version to display datalists Commit: 49e784306ba106b28e3499f054df997cfa3694fa https://github.com/galaxyproject/galaxy/commit/49e784306ba106b28e3499f054df… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Repack scripts Commit: a55038067bde091be7a4edef0c7eda0400c95622 https://github.com/galaxyproject/galaxy/commit/a55038067bde091be7a4edef0c7e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) 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: ----------- Display unfiltered datalist options Commit: e22b4bcbfc465fb46e1cd2dc314e941001ce6164 https://github.com/galaxyproject/galaxy/commit/e22b4bcbfc465fb46e1cd2dc314e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) 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: ----------- Do not attach autocomplete handler if datalist is empty Commit: b3e161a4af6c5059338680591514efea18d553bc https://github.com/galaxyproject/galaxy/commit/b3e161a4af6c5059338680591514… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) 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: ----------- Check datalist length before attaching autocomplete feature Commit: dc5326ce034f6d38955fe0faa7ed6ea7fd2a4977 https://github.com/galaxyproject/galaxy/commit/dc5326ce034f6d38955fe0faa7ed… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) 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: ----------- Use workflow form handler options to parse tool id and version Commit: 20c27075364996898e429936578fdfbcd9abebec https://github.com/galaxyproject/galaxy/commit/20c27075364996898e429936578f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) 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-workflow.js 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-workflow.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-workflow.js Log Message: ----------- Attach onchange handler once, avoid overwrite Commit: e571fce4781ca004c21f8091a46bebaecd6e3bd4 https://github.com/galaxyproject/galaxy/commit/e571fce4781ca004c21f8091a46b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.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.js M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/mvc/tool/tool-form-base.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.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Revise label handling and duplicate check, move save controller to api for proper error response Commit: 37501a5b8475c2c0ef65d6e5dea86cadcd3566bb https://github.com/galaxyproject/galaxy/commit/37501a5b8475c2c0ef65d6e5dea8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Remove debug output Commit: ddf4bad6ffa20df224c724329151e2c810af2c6a https://github.com/galaxyproject/galaxy/commit/ddf4bad6ffa20df224c724329151… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Fix blank line Commit: 6c3b4020200b52352f6a47140a6931456f2755cc https://github.com/galaxyproject/galaxy/commit/6c3b4020200b52352f6a47140a69… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) 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: ----------- Properly attach event handler when user clicks on autocomplete selection Commit: 6c4a4ce3e43af7488f63892420260faab7d9399f https://github.com/galaxyproject/galaxy/commit/6c4a4ce3e43af7488f6389242026… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-14 (Sat, 14 Jan 2017) 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/form/form-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.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 static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.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-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/form/form-input.js M static/scripts/mvc/form/form-section.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-workflow.js M static/scripts/mvc/tool/tool-form.js Log Message: ----------- Revise tool model building to always provide a properly ordered array, augment model handling on front-end Commit: 9c9c4d2d083dc9129ea257a8e0205a4ae89f371b https://github.com/galaxyproject/galaxy/commit/9c9c4d2d083dc9129ea257a8e020… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-15 (Sun, 15 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Fix error display Commit: 3911cb039d46f76f0548d993f4ca932204672bb2 https://github.com/galaxyproject/galaxy/commit/3911cb039d46f76f0548d993f4ca… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/jenkins/selenium/run_galaxy.bash M .ci/py3_sources.txt M README.rst M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/viz/trackster/tracks.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample A config/local_conda_mapping.yml.sample M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/visualizations/csg/templates/csg.mako M config/plugins/visualizations/graphviz/templates/graphviz.mako M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M config/plugins/webhooks/demo/phdcomics/helper/__init__.py M config/plugins/webhooks/demo/phdcomics/static/script.js M doc/schema_template.md M doc/source/admin/webhooks.rst M doc/source/api/guidelines.rst M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/converters/fastqbz2_to_fastq.xml A lib/galaxy/datatypes/converters/fastqcssangerbz2_to_fastqcssanger.xml A lib/galaxy/datatypes/converters/fastqcssangergz_to_fastqcssanger.xml A lib/galaxy/datatypes/converters/fastqgz_to_fastq.xml A lib/galaxy/datatypes/converters/fastqilluminabz2_to_fastqillumina.xml A lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml A lib/galaxy/datatypes/converters/fastqsangerbz2_to_fastqsanger.xml A lib/galaxy/datatypes/converters/fastqsangergz_to_fastqsanger.xml A lib/galaxy/datatypes/converters/fastqsolexabz2_to_fastqsolexa.xml A lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/diamond_db.dmnd M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/model/__init__.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/dependencies.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/conda.py A lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/homebrew.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/deps/views.py M lib/galaxy/tools/errors.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/util/galaxyops/__init__.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/tools/verify/asserts/__init__.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/tools/wrappers.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/object_wrapper.py A lib/galaxy/util/oset.py M lib/galaxy/util/properties.py M lib/galaxy/version.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/util/shed_util_common.py M run.sh M run_tests.sh A scripts/manage_tool_dependencies.py A static/maps/libs/showdown.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/viz/trackster/tracks.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 A static/scripts/libs/showdown.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/viz/trackster/tracks.js M templates/ind_share_base.mako M templates/webapps/galaxy/history/share.mako A test-data/1.fastqsanger.bz2 A test-data/1.fastqsanger.gz M test/api/test_workflows.py M test/docker/README.md M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/docker/base/run_test_wrapper.sh M test/functional/tools/column_param.xml A test/functional/tools/compressed_bz2_fastq_conversion.xml A test/functional/tools/compressed_bz2_fastq_no_conversion.xml A test/functional/tools/compressed_gz_fastq_conversion.xml A test/functional/tools/compressed_gz_fastq_no_conversion.xml A test/functional/tools/explicit_conversion.xml A test/functional/tools/implicit_conversion.xml A test/functional/tools/legacy_r.xml A test/functional/tools/mulled_example_conflict.xml A test/functional/tools/param_text_option.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/navigates_galaxy.py M test/integration/test_resolvers.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_management.py M test/unit/tools/test_tool_deps.py M tools/evolution/add_scores.xml M tools/extract/extract_genomic_dna.xml M tools/filters/pasteWrapper.xml M tools/maf/genebed_maf_to_fasta.xml M tools/maf/interval2maf.xml M tools/maf/interval2maf_pairwise.xml M tools/maf/interval_maf_to_merged_fasta.xml M tools/maf/macros.xml M tools/maf/maf_by_block_number.xml M tools/maf/maf_filter.xml M tools/maf/maf_limit_size.xml M tools/maf/maf_limit_to_species.xml M tools/maf/maf_reverse_complement.xml M tools/maf/maf_split_by_species.xml M tools/maf/maf_stats.xml M tools/maf/maf_thread_for_species.xml M tools/maf/maf_to_bed.xml M tools/maf/maf_to_fasta.xml M tools/maf/maf_to_interval.xml M tools/maf/vcf_to_maf_customtrack.xml M tools/metag_tools/shrimp_color_wrapper.xml M tools/metag_tools/shrimp_wrapper.xml M tools/next_gen_conversion/fastq_gen_conv.xml M tools/plotting/bar_chart.xml M tools/stats/aggregate_binned_scores_in_intervals.xml Log Message: ----------- Merge branch 'dev' into fix_workflow_ui Commit: 5bf7c46eca5c3dbad5c7009f4bb81b48503a6307 https://github.com/galaxyproject/galaxy/commit/5bf7c46eca5c3dbad5c7009f4bb8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-31 (Tue, 31 Jan 2017) Changed paths: M static/maps/mvc/ui/ui-misc.js.map M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Repack scripts Commit: 1bb10da295fdf25855f5140f26bc7a62b278acab https://github.com/galaxyproject/galaxy/commit/1bb10da295fdf25855f5140f26bc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-06 (Mon, 06 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Raise message exception instead of return a dictionary Commit: f264e91cabfd29a8f385f8fbce4c8714b088fa23 https://github.com/galaxyproject/galaxy/commit/f264e91cabfd29a8f385f8fbce4c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-06 (Mon, 06 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/webapps/galaxy/api/workflows.py M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Use update endpoint to store workflows Commit: db47be5ad91bdd9364d5f9525941fd9a7b2c57c0 https://github.com/galaxyproject/galaxy/commit/db47be5ad91bdd9364d5f9525941… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-06 (Mon, 06 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Remove endpoint from routing Commit: 284000c688724f47055a46bab4e8b377224db751 https://github.com/galaxyproject/galaxy/commit/284000c688724f47055a46bab4e8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-06 (Mon, 06 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Remove unused error variable Commit: 5b366642019b4d69d033d916b71b5a85c3767d0f https://github.com/galaxyproject/galaxy/commit/5b366642019b4d69d033d916b71b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-06 (Mon, 06 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M static/maps/mvc/form/form-input.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-input.js M test/qunit/tests/form_tests.js Log Message: ----------- Fix qunit tests Commit: 6a8dc6e26cf92d0c54a35e76c978dba8d6cd9864 https://github.com/galaxyproject/galaxy/commit/6a8dc6e26cf92d0c54a35e76c978… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-07 (Tue, 07 Feb 2017) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/steps.py Log Message: ----------- Evaluate cyclic workflows on the fly when loading the run workflow form Commit: afb024819917535ba4820405c31f00d16224f453 https://github.com/galaxyproject/galaxy/commit/afb024819917535ba4820405c31f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-07 (Tue, 07 Feb 2017) Changed paths: M lib/galaxy/workflow/steps.py Log Message: ----------- Remove blank line Commit: d302400b99b7ae32a2d3f09266b15380b81d83b3 https://github.com/galaxyproject/galaxy/commit/d302400b99b7ae32a2d3f09266b1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-07 (Tue, 07 Feb 2017) Changed paths: M client/galaxy/scripts/libs/jquery/jquery.autocomplete.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.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/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-portlet.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.js M client/galaxy/scripts/ui/autocom_tagging.js M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/steps.py M static/maps/libs/jquery/jquery.autocomplete.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.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/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-portlet.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.js.map M static/maps/ui/autocom_tagging.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/libs/jquery/jquery.autocomplete.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.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/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/ui/autocom_tagging.js M test/qunit/tests/form_tests.js Log Message: ----------- Merge pull request #3407 from guerler/fix_workflow_ui Workflow editor UI touch up Compare: https://github.com/galaxyproject/galaxy/compare/7411aa52fd9c...d302400b99b7

1 0

[galaxyproject/galaxy] 417d11: Avoid stringification of tool state root dictionar...
by GitHub 07 Feb '17

07 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 417d119df9151b0462aa1c802108fa63f46e3f09 https://github.com/galaxyproject/galaxy/commit/417d119df9151b0462aa1c802108… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/workflow/modules.py Log Message: ----------- Avoid stringification of tool state root dictionary Commit: ee6063ec5b88308b2fbc2da9a47c3549f6a5c37b https://github.com/galaxyproject/galaxy/commit/ee6063ec5b88308b2fbc2da9a47c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Adjust export for backward compatibility Commit: fa93c6bbc8449555b1d59dbe9cfaab3ddd3fa45e https://github.com/galaxyproject/galaxy/commit/fa93c6bbc8449555b1d59dbe9cfa… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M templates/webapps/tool_shed/repository/tool_form.mako Log Message: ----------- Remove state handling from tool shed mako Commit: 26a18440304c8b637dc5e0ffe7d3835026087903 https://github.com/galaxyproject/galaxy/commit/26a18440304c8b637dc5e0ffe7d3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-03 (Fri, 03 Feb 2017) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/workflow/modules.py Log Message: ----------- Attempt to use dicts also for module parameter value storage Commit: 6acbafee8a60b03faae9906bfce44d67abfe54b1 https://github.com/galaxyproject/galaxy/commit/6acbafee8a60b03faae9906bfce4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-04 (Sat, 04 Feb 2017) Changed paths: M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Use basic parameter handler to ensure proper text type value decoding Commit: 09f9396eab2c511013c0b637997191bc4f0e74ba https://github.com/galaxyproject/galaxy/commit/09f9396eab2c511013c0b6379971… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-06 (Mon, 06 Feb 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Use number library to identify numeric values Commit: 7411aa52fd9cdaa1874a773fbfd440866f909e65 https://github.com/galaxyproject/galaxy/commit/7411aa52fd9cdaa1874a773fbfd4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-07 (Tue, 07 Feb 2017) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/workflow/modules.py M templates/webapps/tool_shed/repository/tool_form.mako Log Message: ----------- Merge pull request #3522 from guerler/store_step_json_000 Store module step states as nested dictionaries, fix export for backward compatibility Compare: https://github.com/galaxyproject/galaxy/compare/68752b7db0c6...7411aa52fd9c

1 0

[galaxyproject/galaxy] 0d21f6: Consolidate exception logging in db migrations
by GitHub 07 Feb '17

07 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0d21f657ca4115ce3e309394cff8bdb084de6ef3 https://github.com/galaxyproject/galaxy/commit/0d21f657ca4115ce3e309394cff8… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2017-02-07 (Tue, 07 Feb 2017) Changed paths: M lib/galaxy/model/migrate/versions/0003_security_and_libraries.py M lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py M lib/galaxy/model/migrate/versions/0007_sharing_histories.py M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py M lib/galaxy/model/migrate/versions/0009_request_table.py M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0012_user_address.py M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py M lib/galaxy/model/migrate/versions/0014_pages.py M lib/galaxy/model/migrate/versions/0015_tagging.py M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py M lib/galaxy/model/migrate/versions/0019_request_library_folder.py M lib/galaxy/model/migrate/versions/0020_library_upload_job.py M lib/galaxy/model/migrate/versions/0021_user_prefs.py M lib/galaxy/model/migrate/versions/0022_visualization_tables.py M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py M lib/galaxy/model/migrate/versions/0025_user_info.py M lib/galaxy/model/migrate/versions/0027_request_events.py M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py M lib/galaxy/model/migrate/versions/0029_user_actions.py M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py M lib/galaxy/model/migrate/versions/0037_samples_library.py M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py M lib/galaxy/model/migrate/versions/0040_page_annotations.py M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py M lib/galaxy/model/migrate/versions/0046_post_job_actions.py M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py M lib/galaxy/model/migrate/versions/0049_api_keys_table.py M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py M lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py M lib/galaxy/model/migrate/versions/0053_item_ratings.py M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py M lib/galaxy/model/migrate/versions/0057_request_notify.py M lib/galaxy/model/migrate/versions/0058_history_import_export.py M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py M lib/galaxy/model/migrate/versions/0060_history_archive_import.py M lib/galaxy/model/migrate/versions/0062_user_openid_table.py M lib/galaxy/model/migrate/versions/0063_sequencer_table.py M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py M lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py M lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py M lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py M lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py M lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py M lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py M lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py M lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py M lib/galaxy/model/migrate/versions/0080_quota_tables.py M lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py M lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py M lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py M lib/galaxy/model/migrate/versions/0085_add_task_info.py M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py M lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py M lib/galaxy/model/migrate/versions/0093_add_job_params_col.py M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py M lib/galaxy/model/migrate/versions/0095_hda_subsets.py M lib/galaxy/model/migrate/versions/0096_openid_provider.py M lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py M lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py M lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py M lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py M lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py M lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py M lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py M lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py M lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py M lib/galaxy/model/migrate/versions/0117_add_user_activation.py M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py M lib/galaxy/model/migrate/versions/0119_job_metrics.py M lib/galaxy/model/migrate/versions/0120_dataset_collections.py M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py M lib/galaxy/model/migrate/versions/0124_job_state_history.py M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py M lib/galaxy/model/migrate/versions/0126_password_reset.py M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py M lib/galaxy/model/migrate/versions/0128_session_timeout.py M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py M lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py M lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py M lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py Log Message: ----------- Consolidate exception logging in db migrations Also: - align engine_true() and engine_false() methods - remove unused 'now' variables Commit: cb4fbe7a1caba8195ac8ec4965c702a58378f592 https://github.com/galaxyproject/galaxy/commit/cb4fbe7a1caba8195ac8ec4965c7… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2017-02-07 (Tue, 07 Feb 2017) Changed paths: M lib/galaxy/model/migrate/versions/0026_cloud_tables.py M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py M lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py M lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py M lib/galaxy/model/migrate/versions/0057_request_notify.py M lib/galaxy/model/migrate/versions/0063_sequencer_table.py M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py M lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py M lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py M lib/galaxy/model/migrate/versions/0117_add_user_activation.py M lib/galaxy/model/migrate/versions/0120_dataset_collections.py M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py Log Message: ----------- Fix a bunch of database migration bugs Commit: 68752b7db0c6328d1d88e657ad21b2e4312f4401 https://github.com/galaxyproject/galaxy/commit/68752b7db0c6328d1d88e657ad21… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-07 (Tue, 07 Feb 2017) Changed paths: M lib/galaxy/model/migrate/versions/0003_security_and_libraries.py M lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py M lib/galaxy/model/migrate/versions/0007_sharing_histories.py M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py M lib/galaxy/model/migrate/versions/0009_request_table.py M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0012_user_address.py M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py M lib/galaxy/model/migrate/versions/0014_pages.py M lib/galaxy/model/migrate/versions/0015_tagging.py M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py M lib/galaxy/model/migrate/versions/0019_request_library_folder.py M lib/galaxy/model/migrate/versions/0020_library_upload_job.py M lib/galaxy/model/migrate/versions/0021_user_prefs.py M lib/galaxy/model/migrate/versions/0022_visualization_tables.py M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py M lib/galaxy/model/migrate/versions/0025_user_info.py M lib/galaxy/model/migrate/versions/0026_cloud_tables.py M lib/galaxy/model/migrate/versions/0027_request_events.py M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py M lib/galaxy/model/migrate/versions/0029_user_actions.py M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py M lib/galaxy/model/migrate/versions/0037_samples_library.py M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py M lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py M lib/galaxy/model/migrate/versions/0040_page_annotations.py M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py M lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py M lib/galaxy/model/migrate/versions/0046_post_job_actions.py M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py M lib/galaxy/model/migrate/versions/0049_api_keys_table.py M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py M lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py M lib/galaxy/model/migrate/versions/0053_item_ratings.py M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py M lib/galaxy/model/migrate/versions/0057_request_notify.py M lib/galaxy/model/migrate/versions/0058_history_import_export.py M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py M lib/galaxy/model/migrate/versions/0060_history_archive_import.py M lib/galaxy/model/migrate/versions/0062_user_openid_table.py M lib/galaxy/model/migrate/versions/0063_sequencer_table.py M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py M lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py M lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py M lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py M lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py M lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py M lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py M lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py M lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py M lib/galaxy/model/migrate/versions/0080_quota_tables.py M lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py M lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py M lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py M lib/galaxy/model/migrate/versions/0085_add_task_info.py M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py M lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py M lib/galaxy/model/migrate/versions/0093_add_job_params_col.py M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py M lib/galaxy/model/migrate/versions/0095_hda_subsets.py M lib/galaxy/model/migrate/versions/0096_openid_provider.py M lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py M lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py M lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py M lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py M lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py M lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py M lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py M lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py M lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py M lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py M lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py M lib/galaxy/model/migrate/versions/0117_add_user_activation.py M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py M lib/galaxy/model/migrate/versions/0119_job_metrics.py M lib/galaxy/model/migrate/versions/0120_dataset_collections.py M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py M lib/galaxy/model/migrate/versions/0124_job_state_history.py M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py M lib/galaxy/model/migrate/versions/0126_password_reset.py M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py M lib/galaxy/model/migrate/versions/0128_session_timeout.py M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py M lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py M lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py M lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py Log Message: ----------- Merge pull request #3570 from nsoranzo/database_migrations Database migrations: improvements and fixes Compare: https://github.com/galaxyproject/galaxy/compare/27d871f20edc...68752b7db0c6

1 0