January 2018 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] eb506b: Allow map-over when discovering dataset collection...
by GitHub 30 Jan '18

30 Jan '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: eb506b25b9cc02e828442ecb9772cc0d4bcc029b https://github.com/galaxyproject/galaxy/commit/eb506b25b9cc02e828442ecb9772… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-30 (Tue, 30 Jan 2018) Changed paths: M lib/galaxy/dataset_collections/structure.py M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools.py M test/functional/tools/collection_creates_dynamic_list_of_pairs.xml Log Message: ----------- Allow map-over when discovering dataset collections This would affect for example the mapping over of fastq-dump (and all other tools in the sra-toolkit). If one had attempted this previously the discovery phase would fail with: ``` galaxy.tools.parameters.output_collect ERROR 2018-01-30 08:56:46,369 Problem gathering output collection. Traceback (most recent call last): File "/bioinfo/guests/mvandenb/galaxy/lib/galaxy/tools/parameters/output_collect.py", line 169, in collect_dynamic_collections collection File "/bioinfo/guests/mvandenb/galaxy/lib/galaxy/managers/collections.py", line 216, in collection_builder_for return builder.BoundCollectionBuilder(dataset_collection, collection_type_description) File "/bioinfo/guests/mvandenb/galaxy/lib/galaxy/dataset_collections/builder.py", line 84, in __init__ raise Exception("Cannot reset elements of an already populated dataset collection.") Exception: Cannot reset elements of an already populated dataset collection. ``` Instead we force the collection state to be new when we are discovering output collection datasets, which seems reasonable to me. This includes an API testcase that would have failed previously. Commit: cad17b07c36ded48d3f1eaded98f0ea8e9dfd0c6 https://github.com/galaxyproject/galaxy/commit/cad17b07c36ded48d3f1eaded98f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-30 (Tue, 30 Jan 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Revert "Revert extra assertions that are causing unrelated issues to surface." This reverts commit 4925660ab4aa2974c6ac8e94180180bac7db9781. Commit: 54e07568bef2687be10e317cd668d68ba68777bf https://github.com/galaxyproject/galaxy/commit/54e07568bef2687be10e317cd668… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-01-30 (Tue, 30 Jan 2018) Changed paths: M lib/galaxy/dataset_collections/structure.py M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools.py M test/api/test_workflows.py M test/functional/tools/collection_creates_dynamic_list_of_pairs.xml Log Message: ----------- Merge pull request #5413 from mvdbeek/fix_dynamic_collection_output_18_01 Allow map-over when discovering dataset collections Compare: https://github.com/galaxyproject/galaxy/compare/b1c5186e1cb4...54e07568bef2

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[galaxyproject/usegalaxy-playbook] ca3ac7: Update Test Tool Shed
by GitHub 30 Jan '18

30 Jan '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ca3ac7ab5a46ef641346b14569f3446af0976679 https://github.com/galaxyproject/usegalaxy-playbook/commit/ca3ac7ab5a46ef64… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-30 (Tue, 30 Jan 2018) Changed paths: M env/testtoolshed/group_vars/toolshedservers/vars.yml Log Message: ----------- Update Test Tool Shed

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[galaxyproject/galaxy] 889aa2: Conda: pass subprocess arguments as list
by GitHub 26 Jan '18

26 Jan '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 889aa29d02aa54e04a1a31904f1b29b7453c49cf https://github.com/galaxyproject/galaxy/commit/889aa29d02aa54e04a1a31904f1b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-01-26 (Fri, 26 Jan 2018) Changed paths: M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Conda: pass subprocess arguments as list Commit: b8873c65ad8c2b14bf00de2330586e606c232787 https://github.com/galaxyproject/galaxy/commit/b8873c65ad8c2b14bf00de233058… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-01-26 (Fri, 26 Jan 2018) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Install the latest version of conda and conda-build Conda 4.3.33 contains a fix that should solve some conda env creation programs: https://github.com/conda/conda/pull/6766 Also support conda installation on x86 Linux architecture. Commit: b1c5186e1cb496facd4387bb569c231c0c434d13 https://github.com/galaxyproject/galaxy/commit/b1c5186e1cb496facd4387bb569c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-01-26 (Fri, 26 Jan 2018) Changed paths: M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #5397 from nsoranzo/release_18.01_conda_fixes [18.01] Install latest conda and don't use shell=True Compare: https://github.com/galaxyproject/galaxy/compare/17fe5d635afb...b1c5186e1cb4

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[galaxyproject/galaxy] 3b69c6: Merge pull request #5387 from martenson/version-18...
by GitHub 26 Jan '18

26 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3b69c645dab86332c506bd0e510de77d6e7dc215 https://github.com/galaxyproject/galaxy/commit/3b69c645dab86332c506bd0e510d… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #5387 from martenson/version-18.01 [18.01] Update version to 18.01.rc1 Commit: 9c187f0e5a613c925a733f6aeacd7e07f143f25b https://github.com/galaxyproject/galaxy/commit/9c187f0e5a613c925a733f6aeacd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Constrain workflow tool panel entries to those not deleted. Commit: 17fe5d635afb7ccb773370511faee72f11860045 https://github.com/galaxyproject/galaxy/commit/17fe5d635afb7ccb773370511fae… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-26 (Fri, 26 Jan 2018) Log Message: ----------- Merge branch 'release_17.09' into release_18.01 Commit: 28f5aca05695bab1a3608fbbcc93bd3f09c1eb28 https://github.com/galaxyproject/galaxy/commit/28f5aca05695bab1a3608fbbcc93… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-26 (Fri, 26 Jan 2018) Log Message: ----------- Merge branch 'release_18.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/792a07148915...28f5aca05695

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[galaxyproject/galaxy] 9c187f: Constrain workflow tool panel entries to those not...
by GitHub 26 Jan '18

26 Jan '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 9c187f0e5a613c925a733f6aeacd7e07f143f25b https://github.com/galaxyproject/galaxy/commit/9c187f0e5a613c925a733f6aeacd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Constrain workflow tool panel entries to those not deleted. Commit: 17fe5d635afb7ccb773370511faee72f11860045 https://github.com/galaxyproject/galaxy/commit/17fe5d635afb7ccb773370511fae… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-26 (Fri, 26 Jan 2018) Log Message: ----------- Merge branch 'release_17.09' into release_18.01 Compare: https://github.com/galaxyproject/galaxy/compare/3b69c645dab8...17fe5d635afb

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[galaxyproject/galaxy] 74d57c: Fix subworkflow creation
by GitHub 26 Jan '18

26 Jan '18

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 74d57cfc1c0d9d82b6893257438937ba0e37f5af https://github.com/galaxyproject/galaxy/commit/74d57cfc1c0d9d82b68932574389… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-26 (Fri, 26 Jan 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js Log Message: ----------- Fix subworkflow creation This fixes #5396. The problem was that we would override the content_id with an undefined value. Broken in https://github.com/galaxyproject/galaxy/pull/5249. Commit: f589a0cb5b45b5964e654fe7eb1602a13ac1bf57 https://github.com/galaxyproject/galaxy/commit/f589a0cb5b45b5964e654fe7eb16… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-26 (Fri, 26 Jan 2018) Changed paths: M static/maps/mvc/workflow/workflow-node.js.map M static/scripts/mvc/workflow/workflow-node.js Log Message: ----------- Build client Commit: d6fb37071dc4b425763c1e1aeb9b8d404cf111a0 https://github.com/galaxyproject/galaxy/commit/d6fb37071dc4b425763c1e1aeb9b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-26 (Fri, 26 Jan 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M static/maps/mvc/workflow/workflow-node.js.map M static/scripts/mvc/workflow/workflow-node.js Log Message: ----------- Merge pull request #5398 from mvdbeek/subworkflow_creation_fix [17.09] Subworkflow creation fix Compare: https://github.com/galaxyproject/galaxy/compare/b6d0b1492110...d6fb37071dc4

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[galaxyproject/galaxy] 1de0ef: Fix MRO issues
by GitHub 26 Jan '18

26 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1de0ef437b32619a06b23411d26520e89793877b https://github.com/galaxyproject/galaxy/commit/1de0ef437b32619a06b23411d265… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/dictifiable.py M lib/galaxy/util/handlers.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/workflow/scheduling_manager.py M lib/tool_shed/galaxy_install/migrate/common.py M test/unit/jobs/test_mapper.py Log Message: ----------- Fix MRO issues Make Mixins new style classes Commit: d3895db861a003206dce0be833174493923dcc23 https://github.com/galaxyproject/galaxy/commit/d3895db861a003206dce0be83317… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Python3: dict_keys doesn't support indexing Commit: 15cd09d2c5e73e8721c9369bee518d68da3c8e44 https://github.com/galaxyproject/galaxy/commit/15cd09d2c5e73e8721c9369bee51… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Use newer psycopg2 library Commit: 31ec21d89fb91c00f368a46fe071d250a108c26f https://github.com/galaxyproject/galaxy/commit/31ec21d89fb91c00f368a46fe071… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Switch to Cheetah3 Commit: 326f743d3a5582fe6f3c6c78a1f1d7cb6331c9b7 https://github.com/galaxyproject/galaxy/commit/326f743d3a5582fe6f3c6c78a1f1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py Log Message: ----------- Write integrated tool panel xml in one go Commit: fb9ebf980923858a1a4cbeb588d22a2b9820ff9a https://github.com/galaxyproject/galaxy/commit/fb9ebf980923858a1a4cbeb588d2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Switch to Fabric3 for py2/3 support Commit: 00526c9928c3e1fdbdfe0f70d02549b632b82ef7 https://github.com/galaxyproject/galaxy/commit/00526c9928c3e1fdbdfe0f70d025… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/configuration.py Log Message: ----------- Python3 fixes Commit: 973bfbafb980cfd15b545b2b0b4d873440bf1203 https://github.com/galaxyproject/galaxy/commit/973bfbafb980cfd15b545b2b0b4d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/web/security/__init__.py Log Message: ----------- Use Crypto's get_random_bytes instead of rolling our own Commit: fbd33a57e0033a1547c3bf6f9812dd574cdb36d2 https://github.com/galaxyproject/galaxy/commit/fbd33a57e0033a1547c3bf6f9812… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/web/framework/helpers/__init__.py Log Message: ----------- Remove dependency on WebHelpers Workaround babel bug when locale is not set Commit: e87d1aa79d84a08721d76ae2b6cb234351b6356b https://github.com/galaxyproject/galaxy/commit/e87d1aa79d84a08721d76ae2b6cb… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M .ci/jenkins/selenium-compose/run_tests.sh M config/galaxy.yml.sample M config/tool_shed.yml.sample M doc/Makefile M doc/source/admin/galaxy_options.rst M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml M scripts/common_startup.sh M test/manual/launch_and_run.sh Log Message: ----------- More Python3 print function fixes Commit: 6f6a671d36ff4f7ebe258c04aef6155384a4736e https://github.com/galaxyproject/galaxy/commit/6f6a671d36ff4f7ebe258c04aef6… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/security/__init__.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- Make id encoding/decoding py3 compatible Commit: 0ce2d97c4dd65e5b2827c29dfa0aece4e6432666 https://github.com/galaxyproject/galaxy/commit/0ce2d97c4dd65e5b2827c29dfa0a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Create the virtualenv using the python that passed check_python This will make it easier to support Python3. Commit: 792a07148915ccc94d44f415db206e53addb12db https://github.com/galaxyproject/galaxy/commit/792a07148915ccc94d44f415db20… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-01-26 (Fri, 26 Jan 2018) Changed paths: M .ci/jenkins/selenium-compose/run_tests.sh M config/galaxy.yml.sample M config/tool_shed.yml.sample M doc/Makefile M doc/source/admin/galaxy_options.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/configuration.py M lib/galaxy/model/__init__.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/util/dictifiable.py M lib/galaxy/util/handlers.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/security/__init__.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/tool_shed/config_schema.yml M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/workflow/scheduling_manager.py M lib/tool_shed/galaxy_install/migrate/common.py M scripts/common_startup.sh M test/manual/launch_and_run.sh M test/unit/jobs/test_mapper.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- Merge pull request #5359 from mvdbeek/py3_fixes Various Python3 related fixes Compare: https://github.com/galaxyproject/galaxy/compare/046cb8f35956...792a07148915

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[galaxyproject/galaxy]
by GitHub 26 Jan '18

26 Jan '18

Branch: refs/heads/uninstall_repo_fix Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] 9c187f: Constrain workflow tool panel entries to those not...
by GitHub 25 Jan '18

25 Jan '18

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 9c187f0e5a613c925a733f6aeacd7e07f143f25b https://github.com/galaxyproject/galaxy/commit/9c187f0e5a613c925a733f6aeacd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Constrain workflow tool panel entries to those not deleted. Commit: b6d0b1492110d8758a34f412b881977480dd24ad https://github.com/galaxyproject/galaxy/commit/b6d0b1492110d8758a34f412b881… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Merge pull request #5391 from dannon/release_17.09 [17.09] Constrain workflow tool panel entries to those not deleted. Compare: https://github.com/galaxyproject/galaxy/compare/73418ab7875e...b6d0b1492110

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[galaxyproject/usegalaxy-playbook] 978542: Update Test
by GitHub 25 Jan '18

25 Jan '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 9785420ec40314e805df3ea9b1c6c3515da78597 https://github.com/galaxyproject/usegalaxy-playbook/commit/9785420ec40314e8… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Test

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