galaxy-commits July 2018

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[galaxyproject/galaxy] d8bd5f: Many selenium tests fixes for recent dev changes.
by GitHub 30 Jul '18

30 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d8bd5f4690319374a04d4d4dd2fe179618312fa5 https://github.com/galaxyproject/galaxy/commit/d8bd5f4690319374a04d4d4dd2fe… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-30 (Mon, 30 Jul 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_admin_app.py M test/selenium_tests/test_history_panel_collections.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_published_histories_grid.py Log Message: ----------- Many selenium tests fixes for recent dev changes. Commit: 1d0313c286d4501518a85ecf4361bbc2d7c8c44f https://github.com/galaxyproject/galaxy/commit/1d0313c286d4501518a85ecf4361… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-07-30 (Mon, 30 Jul 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_admin_app.py M test/selenium_tests/test_history_panel_collections.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_published_histories_grid.py Log Message: ----------- Merge pull request #6557 from jmchilton/admin_selenium_fixes Many selenium tests fixes for recent dev changes. Compare: https://github.com/galaxyproject/galaxy/compare/68cb2bb82b60...1d0313c286d4 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] ce4792: Restore log_destination = stdout configuration opt...
by GitHub 30 Jul '18

30 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ce4792e103c43afcb3d50ad3f6252e28365474c4 https://github.com/galaxyproject/galaxy/commit/ce4792e103c43afcb3d50ad3f625… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-30 (Mon, 30 Jul 2018) Changed paths: M lib/galaxy/config.py Log Message: ----------- Restore log_destination = stdout configuration option. Implementation in 17.09 was here https://github.com/galaxyproject/galaxy/blob/release_17.09/lib/galaxy/confi…. This option set to stdout is used by the test framework output Galaxy logs to stdout. As far as I can tell log_destination was removed in 18.01 and the effect was to sort of default to stdout - but when we fixed log_destination for files and backported recently https://github.com/galaxyproject/galaxy/commit/bc95f2563601635cfa1daa686b3d… - test output became written to a file called "stdout". This commit should restore the 17.09 behavior for both files and stdout configuration of this logging. Commit: 68cb2bb82b6023cee3609cc99043a224ef70f44a https://github.com/galaxyproject/galaxy/commit/68cb2bb82b6023cee3609cc99043… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-07-30 (Mon, 30 Jul 2018) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge pull request #6555 from jmchilton/restore_log_destination_stdout Restore log_destination = stdout configuration option. Compare: https://github.com/galaxyproject/galaxy/compare/1a73b1f2adf8...68cb2bb82b60 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 5f19b8: Fix empty handling rule.
by GitHub 30 Jul '18

30 Jul '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 5f19b8752dfd940efd156de1a0c1a4e6e914800b https://github.com/galaxyproject/galaxy/commit/5f19b8752dfd940efd156de1a0c1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-26 (Thu, 26 Jul 2018) Changed paths: M lib/galaxy/util/rules_dsl.py M test/unit/test_rule_utils.py Log Message: ----------- Fix empty handling rule. Commit: 66e74d0e475ef6fd6f6de125b41f9990e274fbfb https://github.com/galaxyproject/galaxy/commit/66e74d0e475ef6fd6f6de125b41f… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-30 (Mon, 30 Jul 2018) Changed paths: M lib/galaxy/util/rules_dsl.py M test/unit/test_rule_utils.py Log Message: ----------- Merge pull request #6542 from jmchilton/1805_fix_empty_handling_rule_on_backend [18.05] Fix "filter empty" rule in Python rule handling framework. Compare: https://github.com/galaxyproject/galaxy/compare/a88bf0a2bee1...66e74d0e475e **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 111b40: Fix linting issue introduced in #6553.
by GitHub 30 Jul '18

30 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 111b40ac37a1fb5cc4746c0987d5d73eb4105d0a https://github.com/galaxyproject/galaxy/commit/111b40ac37a1fb5cc4746c0987d5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-30 (Mon, 30 Jul 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- Fix linting issue introduced in #6553. Commit: 1a73b1f2adf828834a386245d131139fe979b4d2 https://github.com/galaxyproject/galaxy/commit/1a73b1f2adf828834a386245d131… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-30 (Mon, 30 Jul 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- Merge pull request #6554 from jmchilton/fix_lint_ Fix linting issue introduced in #6553. Compare: https://github.com/galaxyproject/galaxy/compare/b829e0cc93b1...1a73b1f2adf8 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] fe5e1f: Integration test for the interaction of nested obj...
by GitHub 30 Jul '18

30 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fe5e1f1686dd60e6357594c4541b894a29f04984 https://github.com/galaxyproject/galaxy/commit/fe5e1f1686dd60e6357594c4541b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-27 (Fri, 27 Jul 2018) Changed paths: M test/base/driver_util.py A test/integration/test_objectstore_jobs.py Log Message: ----------- Integration test for the interaction of nested object stores and jobs. - Test hierarchical store uses its first disk store for new files and not the remaining entries. - Test basic functionality of writing to the distributed object store. - Test all job outputs get placed in the same object store. Commit: b829e0cc93b17842f64d0636a59eec5401753133 https://github.com/galaxyproject/galaxy/commit/b829e0cc93b17842f64d0636a59e… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-30 (Mon, 30 Jul 2018) Changed paths: M test/base/driver_util.py A test/integration/test_objectstore_jobs.py Log Message: ----------- Merge pull request #6546 from jmchilton/objectstore_jobs_test Integration test for the interaction of nested object stores and jobs. Compare: https://github.com/galaxyproject/galaxy/compare/524df1a3b715...b829e0cc93b1 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 06a4c6: Remove the sharing of toolbox in GRT
by GitHub 30 Jul '18

30 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 06a4c603d3b27c4fea948907476a3290acd58690 https://github.com/galaxyproject/galaxy/commit/06a4c603d3b27c4fea948907476a… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-07-30 (Mon, 30 Jul 2018) Changed paths: M scripts/grt/export.py M scripts/grt/grt.yml.sample Log Message: ----------- Remove the sharing of toolbox in GRT This has been broken for a while and was never super useful data to obtain. Fixes #6534 Commit: 524df1a3b71510bcf1c9fe95617627f3bef7a1a7 https://github.com/galaxyproject/galaxy/commit/524df1a3b71510bcf1c9fe956176… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-30 (Mon, 30 Jul 2018) Changed paths: M scripts/grt/export.py M scripts/grt/grt.yml.sample Log Message: ----------- Merge pull request #6553 from erasche/grt-remove-toolbox Remove the sharing of toolbox in GRT Compare: https://github.com/galaxyproject/galaxy/compare/10b17fb48a25...524df1a3b715 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 9794d8: Fix to_dict with io_details=True for tools with co...
by GitHub 26 Jul '18

26 Jul '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 9794d835e507c31d82aa82c79e86998154419980 https://github.com/galaxyproject/galaxy/commit/9794d835e507c31d82aa82c79e86… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-25 (Wed, 25 Jul 2018) Changed paths: M lib/galaxy/tools/parser/output_objects.py M test/api/test_tools.py Log Message: ----------- Fix to_dict with io_details=True for tools with collection outputs. Fixes #6537 and includes a test case. Commit: 0a9010156e30a20d730324807c3e238510f44b77 https://github.com/galaxyproject/galaxy/commit/0a9010156e30a20d730324807c3e… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-07-26 (Thu, 26 Jul 2018) Changed paths: M lib/galaxy/tools/parser/output_objects.py M test/api/test_tools.py Log Message: ----------- Merge pull request #6538 from jmchilton/tool_output_io [18.01] Fix to_dict with io_details=True for tools with collection outputs. Compare: https://github.com/galaxyproject/galaxy/compare/23666c94a22b...0a9010156e30 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 4661b6: Allow invalid optional param values for old tools
by GitHub 26 Jul '18

26 Jul '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 4661b6e8831c2cae86b7d9725431e71bacd22168 https://github.com/galaxyproject/galaxy/commit/4661b6e8831c2cae86b7d9725431… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-02 (Sat, 02 Jun 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Allow invalid optional param values for old tools For tools with profile < 18.09 we return None for provided, but illegal default values. This can happen when referencing columns of an optional dataset for instance, as experienced in https://github.com/galaxyproject/tools-iuc/pull/1842. This used to pass prior to 18.05 because we would always return the value if there were no legal values. This was changed in https://github.com/galaxyproject/galaxy/commit/9febc519944dcfb5c8907b8a302f… where we would only allow this in workflow building mode. Commit: a88bf0a2bee152c859f229c2a017b8a03d96b8d8 https://github.com/galaxyproject/galaxy/commit/a88bf0a2bee152c859f229c2a017… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-26 (Thu, 26 Jul 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #6264 from mvdbeek/allow_optional_and_invalid_parameter_values [18.05] Allow invalid optional param values for tools profile versions < 18.09 Compare: https://github.com/galaxyproject/galaxy/compare/50b34185394c...a88bf0a2bee1 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] f56c0b: Test case for nested collection input to flatten i...
by GitHub 26 Jul '18

26 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f56c0bbac2c9769a69bc03d0092cf2dfc09ceb81 https://github.com/galaxyproject/galaxy/commit/f56c0bbac2c9769a69bc03d0092c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-25 (Wed, 25 Jul 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Test case for nested collection input to flatten in a workflow. Also exercises delayed workflow scheduling because of the dynamic discovery of the input collection. xref #5867 Commit: 10b17fb48a257246a401ce560b371edb41c8237c https://github.com/galaxyproject/galaxy/commit/10b17fb48a257246a401ce560b37… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-26 (Thu, 26 Jul 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Merge pull request #6541 from jmchilton/flatten_bug Test case for nested collection input to flatten in a workflow. Compare: https://github.com/galaxyproject/galaxy/compare/3fd7b87fb96e...10b17fb48a25 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] d06b22: Convert tool parameter XML attribute 'hidden' into...
by GitHub 25 Jul '18

25 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d06b221905cc4eb935939c6a29685c0dff125bf8 https://github.com/galaxyproject/galaxy/commit/d06b221905cc4eb935939c6a2968… Author: Andrey Tovchigrechko <tovchigrechkoa(a)medimmune.com> Date: 2018-07-25 (Wed, 25 Jul 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Convert tool parameter XML attribute 'hidden' into the correct boolean Python type. Previously it was converted into string, and in the logical predicates any non-empty value would always evaluate to True. This fix allows using the 'hidden' attribute in parameterized XML macros with 'true' or 'false' passed as a macros parameter. This in turns allows hiding some form fields (after setting default values) based on choices picked in conditional switches. Commit: 3fd7b87fb96ebb4503f4b8c2c456aaced9a5c482 https://github.com/galaxyproject/galaxy/commit/3fd7b87fb96ebb4503f4b8c2c456… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-25 (Wed, 25 Jul 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #6539 from andreyto/at_hidden_par_conv Convert tool parameter XML attribute 'hidden' into the correct boolean Python type Compare: https://github.com/galaxyproject/galaxy/compare/4955add0a343...3fd7b87fb96e **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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galaxy-commits July 2018