- galaxy-commits - lists.galaxyproject.org

[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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[galaxyproject/galaxy] dd6b64: Use cached database identity to avoid certain DB r...
by GitHub 25 Jul '18

25 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: dd6b6436c845752c50d0f376300bcbadf8ea196e https://github.com/galaxyproject/galaxy/commit/dd6b6436c845752c50d0f376300b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-23 (Mon, 23 Jul 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/web/framework/webapp.py M test/unit/test_galaxy_mapping.py Log Message: ----------- Use cached database identity to avoid certain DB requests when creating jobs. When creating thousands of jobs for large database transactions - previously Galaxy would query the database thousands of times for the same history id, user id, and session id. Commit: 43a0482f1ca4b5e48d1ec576ff0c4875bae87fe3 https://github.com/galaxyproject/galaxy/commit/43a0482f1ca4b5e48d1ec576ff0c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-25 (Wed, 25 Jul 2018) Changed paths: M lib/galaxy/model/__init__.py M test/unit/test_galaxy_mapping.py Log Message: ----------- Minor (comment-only) wording tweaks. Commit: 4955add0a343bd0b1b09a3cde11d9ffc8621baf9 https://github.com/galaxyproject/galaxy/commit/4955add0a343bd0b1b09a3cde11d… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-25 (Wed, 25 Jul 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/web/framework/webapp.py M test/unit/test_galaxy_mapping.py Log Message: ----------- Merge pull request #6524 from jmchilton/cached_identity Use cached database identity to avoid many DB requests when creating jobs. Compare: https://github.com/galaxyproject/galaxy/compare/b0b12e470699...4955add0a343 **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] 63c2ff: Implement simple history copy unit tests.
by GitHub 25 Jul '18

25 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 63c2ffd3bae58fc4d37edf6149b79cf51de8a37c https://github.com/galaxyproject/galaxy/commit/63c2ffd3bae58fc4d37edf6149b7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-24 (Tue, 24 Jul 2018) Changed paths: A test/unit/test_model_copy.py Log Message: ----------- Implement simple history copy unit tests. Commit: fe3e284bf9d17c2274cfac8b80b3c11b5e52297b https://github.com/galaxyproject/galaxy/commit/fe3e284bf9d17c2274cfac8b80b3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-24 (Tue, 24 Jul 2018) Changed paths: M lib/galaxy/managers/hdcas.py M lib/galaxy/model/__init__.py M lib/galaxy/model/item_attrs.py M lib/galaxy/model/mapping.py M test/unit/test_galaxy_mapping.py Log Message: ----------- Fix HDCA annotations. Backend for these simply did not work. Commit: 9780d069c8646fb4f02de848d62159680d95ae79 https://github.com/galaxyproject/galaxy/commit/9780d069c8646fb4f02de848d621… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-24 (Tue, 24 Jul 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/metadata.py Log Message: ----------- Optimized dataset copying during histories. Use only one unqualified flush to prevent constant repeated invalidation off all SA just to get a single ID for a new object. For a simple history with 10 datasets - this reduces the copy() time in testing from 260 ms to 70ms. Some random times: Before optimization: 10 datasets - with a MetadataFile metadata parameter history copied (390.457 ms) history copied (398.501 ms) history copied (360.997 ms) 10 datasets - without a MetadataFile metadata parameter history copied (291.972 ms) history copied (276.479 ms) history copied (272.323 ms) 10 datasets - with a MetadataFile metadata parameter history copied (230.171 ms) history copied (218.215 ms) history copied (226.205 ms) 10 datasets - without a MetadataFile metadata parameter history copied (66.360 ms) history copied (70.126 ms) history copied (65.166 ms) Commit: b0b12e4706999ddce317769b660e4d9a32a8a2bb https://github.com/galaxyproject/galaxy/commit/b0b12e4706999ddce317769b660e… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-25 (Wed, 25 Jul 2018) Changed paths: M lib/galaxy/managers/hdcas.py M lib/galaxy/model/__init__.py M lib/galaxy/model/item_attrs.py M lib/galaxy/model/mapping.py M lib/galaxy/model/metadata.py M test/unit/test_galaxy_mapping.py A test/unit/test_model_copy.py Log Message: ----------- Merge pull request #6531 from jmchilton/history_copy_opts Optimizations for history copying. Compare: https://github.com/galaxyproject/galaxy/compare/f1ab39a0a01a...b0b12e470699 **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] 4d8b13: Handle pasted content in fetch API.
by GitHub 25 Jul '18

25 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4d8b13d0e54f31679b9adcd58a045f01efee3f30 https://github.com/galaxyproject/galaxy/commit/4d8b13d0e54f31679b9adcd58a04… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-23 (Mon, 23 Jul 2018) Changed paths: M lib/galaxy/tools/data_fetch.py M test/api/test_tools.py M test/base/populators.py Log Message: ----------- Handle pasted content in fetch API. Unlike upload 1.0, use different 'src' types to distinguish between URLs and pasted content - in the abstract this is better because it is more structured and practically this allows 'pasting' spreadsheets that start with URLs for instance (that is sometimes useful). Commit: f1ab39a0a01a4faaef215a3b914ebf31e430513b https://github.com/galaxyproject/galaxy/commit/f1ab39a0a01a4faaef215a3b914e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-25 (Wed, 25 Jul 2018) Changed paths: M lib/galaxy/tools/data_fetch.py M test/api/test_tools.py M test/base/populators.py Log Message: ----------- Merge pull request #6523 from jmchilton/fetch_api_pasted Handle pasted content in fetch API. Compare: https://github.com/galaxyproject/galaxy/compare/84159d37cc44...f1ab39a0a01a **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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