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

[galaxyproject/galaxy] 08547f: Intermine from Hack
by GitHub 06 Jul '18

06 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 08547faddd42858c072c7eca6f45b7422cd4b710 https://github.com/galaxyproject/galaxy/commit/08547faddd42858c072c7eca6f45… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2018-06-30 (Sat, 30 Jun 2018) Changed paths: M config/datatypes_conf.xml.sample M config/tool_conf.xml.main M config/tool_conf.xml.sample M config/tool_data_table_conf.xml.sample A display_applications/intermine/intermine_simple.xml A tools/data_source/intermine.xml Log Message: ----------- Intermine from Hack Commit: 433d4648706be8902f609a4cba1a0d941acb7a0d https://github.com/galaxyproject/galaxy/commit/433d4648706be8902f609a4cba1a… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M config/tool_conf.xml.sample M tools/data_source/intermine.xml Log Message: ----------- Update InterMine Commit: 5b0088ae43c748edaaccbaa363e0d0c86756a66a https://github.com/galaxyproject/galaxy/commit/5b0088ae43c748edaaccbaa363e0… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M config/tool_conf.xml.sample Log Message: ----------- Update InterMine Commit: 58c68d408f2eec0c787ad176dabb3330a322d582 https://github.com/galaxyproject/galaxy/commit/58c68d408f2eec0c787ad176dabb… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2018-07-06 (Fri, 06 Jul 2018) Changed paths: A tool-data/intermine_simple_display.loc.sample Log Message: ----------- add missing intermine_simple_display.loc.sample Commit: 8df7cafe3ac6d700f2637f0c41d0dfba8a360076 https://github.com/galaxyproject/galaxy/commit/8df7cafe3ac6d700f2637f0c41d0… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-06 (Fri, 06 Jul 2018) Changed paths: M config/datatypes_conf.xml.sample M config/tool_conf.xml.main M config/tool_conf.xml.sample M config/tool_data_table_conf.xml.sample A display_applications/intermine/intermine_simple.xml A tool-data/intermine_simple_display.loc.sample A tools/data_source/intermine.xml Log Message: ----------- Merge pull request #6444 from blankenberg/intermine Intermine Enhancements Compare: https://github.com/galaxyproject/galaxy/compare/0b98e3ed13fe...8df7cafe3ac6 **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] d145d9: Allows DatasetMatcher to use multiple filters
by GitHub 05 Jul '18

05 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d145d9ac92051ecb765d00330a6eb370c6319ac3 https://github.com/galaxyproject/galaxy/commit/d145d9ac92051ecb765d00330a6e… Author: Evan Bolyen <ebolyen(a)gmail.com> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M lib/galaxy/tools/parameters/dataset_matcher.py M test/unit/tools/test_dataset_matcher.py Log Message: ----------- Allows DatasetMatcher to use multiple filters In particular this enables multiple add_value filters to be used with <options>'s option_filter_attribute. Commit: 0b98e3ed13fe24264b8a5037c1c345dd679c26af https://github.com/galaxyproject/galaxy/commit/0b98e3ed13fe24264b8a5037c1c3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/parameters/dataset_matcher.py M test/unit/tools/test_dataset_matcher.py Log Message: ----------- Merge pull request #6443 from ebolyen/multiple_filter_datasetmatcher Allows DatasetMatcher to use multiple filters Compare: https://github.com/galaxyproject/galaxy/compare/e33427a3b790...0b98e3ed13fe **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] 57f5b4: py3: fix workflow extract summary
by GitHub 05 Jul '18

05 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 57f5b42974929d4090429df87aca9973faae869f https://github.com/galaxyproject/galaxy/commit/57f5b42974929d4090429df87aca… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M test/unit/workflows/test_extract_summary.py Log Message: ----------- py3: fix workflow extract summary Commit: af6b572eac2e2571e5f6f0b46945f7f76fce685b https://github.com/galaxyproject/galaxy/commit/af6b572eac2e2571e5f6f0b46945… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M test/unit/tools/test_history_imp_exp.py Log Message: ----------- py3: Fix history/import export Commit: 048f7737dda50c8dc64fc211a5e59c971aa92041 https://github.com/galaxyproject/galaxy/commit/048f7737dda50c8dc64fc211a5e5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Fix job disocvery Commit: c52d1476122adf82b62e6e1045cd7155f34bb9f7 https://github.com/galaxyproject/galaxy/commit/c52d1476122adf82b62e6e1045cd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M test/unit/tools/test_evaluation.py Log Message: ----------- No need to explicitly compare to bytestring Commit: 492ee207e0ac9884178249251f1047181148c458 https://github.com/galaxyproject/galaxy/commit/492ee207e0ac9884178249251f10… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Cast odict.items() and odict.values() to list Commit: b773aedfa7670ee7fe13d43618f956a4bea3d5da https://github.com/galaxyproject/galaxy/commit/b773aedfa7670ee7fe13d43618f9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/jobs/runners/local.py Log Message: ----------- py3: open job script in text mode Commit: c03a86caea4f7cb945a5a8ae539cb7d8ea3ccce8 https://github.com/galaxyproject/galaxy/commit/c03a86caea4f7cb945a5a8ae539c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M test/unit/tools/test_collect_primary_datasets.py Log Message: ----------- py3: fix test_job_param unit test Commit: 3af3591e626ddb7204cb958ef414e1fba203e843 https://github.com/galaxyproject/galaxy/commit/3af3591e626ddb7204cb958ef414… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/jobs/rule_helper.py Log Message: ----------- py3: fix rule-helper Commit: 25b93c78b6d2a68917bd0aad1e27f155f9d5600c https://github.com/galaxyproject/galaxy/commit/25b93c78b6d2a68917bd0aad1e27… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/config.py M test/unit/web/framework/test_webapp.py Log Message: ----------- Fix CORS unit test Commit: 05f8f2063a69e682bc5349933e44d751b2c9e477 https://github.com/galaxyproject/galaxy/commit/05f8f2063a69e682bc5349933e44… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/parser/output_collection_def.py Log Message: ----------- Fix output collection unit test Commit: e649f7876fc7753ec76d356e04992169476d619d https://github.com/galaxyproject/galaxy/commit/e649f7876fc7753ec76d356e0499… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Fix recheck_missing_job_retries by casting retries to integer Commit: 0e9adcca823dc0b0a273486ef3137cc030d54db3 https://github.com/galaxyproject/galaxy/commit/0e9adcca823dc0b0a273486ef313… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/util/rules_dsl.py Log Message: ----------- Fix rules_dsl comparison by converting to key-style sort function Commit: 37e112323ec8b7e17d11921a781b6b49f2bf05a2 https://github.com/galaxyproject/galaxy/commit/37e112323ec8b7e17d11921a781b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/web/security/__init__.py Log Message: ----------- Fix MAXIMUM_ID_SECRET_LENGTH constant Commit: 192633b0b200130b9f718f25c9070deea34981ad https://github.com/galaxyproject/galaxy/commit/192633b0b200130b9f718f25c907… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M .travis.yml Log Message: ----------- Remove py34-unit from allowed failures Commit: 71b9024769d2ba008740e9e071eac46139258987 https://github.com/galaxyproject/galaxy/commit/71b9024769d2ba008740e9e071ea… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/parser/output_collection_def.py Log Message: ----------- Flake8 fix Commit: db10b5b679217c36414dcf2a80189e46ef9cc680 https://github.com/galaxyproject/galaxy/commit/db10b5b679217c36414dcf2a8018… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- py3: Fix has_limit Commit: cde7784606947eb452d1b3c98ca3eaca99b25ea8 https://github.com/galaxyproject/galaxy/commit/cde7784606947eb452d1b3c98ca3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/model/metadata.py M lib/galaxy_ext/metadata/set_metadata.py Log Message: ----------- py3: Fix metadata setting Commit: 84dc5cd02ff0ceab8529cd9e11f825eaed2e3633 https://github.com/galaxyproject/galaxy/commit/84dc5cd02ff0ceab8529cd9e11f8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- py3: Get unicode strings from ElementTree on py3 Commit: c8f720d71c3d14c2e90d5ebcf0fa41d7bb2726b5 https://github.com/galaxyproject/galaxy/commit/c8f720d71c3d14c2e90d5ebcf0fa… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/web/framework/decorators.py Log Message: ----------- py3: don't case payload to bytestring. Doesn't seem to affect py2 either Commit: f29ebb7389a8e695020e11ec4c4c759e89c0a062 https://github.com/galaxyproject/galaxy/commit/f29ebb7389a8e695020e11ec4c4c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- py3: fix generting conda env hash Commit: c16d8531b9948f71d9861692b40a005e7d8c2a21 https://github.com/galaxyproject/galaxy/commit/c16d8531b9948f71d9861692b40a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/parser/output_actions.py Log Message: ----------- py3: fix StringFunctionFilter Commit: 7e29d5d83b55846e0bbe5ec43ced2870b7bb1913 https://github.com/galaxyproject/galaxy/commit/7e29d5d83b55846e0bbe5ec43ced… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M test/unit/test_remote_shell.py Log Message: ----------- py3: fix paramiko shell runner by casting to unicode Commit: 962b1fe176e1120d5a093726d74271fda860884f https://github.com/galaxyproject/galaxy/commit/962b1fe176e1120d5a093726d742… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- py3: fix check_limits Commit: 6bad1027a7b22c833ca241214c93090badc66d37 https://github.com/galaxyproject/galaxy/commit/6bad1027a7b22c833ca241214c93… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/execute.py Log Message: ----------- py3: fix collection mapping over Commit: 9d547dd5e439ea67193e94242b8354b5e6ec1b92 https://github.com/galaxyproject/galaxy/commit/9d547dd5e439ea67193e94242b83… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/web/framework/helpers/grids.py M templates/tagging_common.mako Log Message: ----------- py3: fix 'saved histories' menu Commit: e08c2b347e8e2c625c97f719bc6048e5e956ca9d https://github.com/galaxyproject/galaxy/commit/e08c2b347e8e2c625c97f719bc60… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/triples.py Log Message: ----------- Fix some datatype sniffers and `guess_ext()` doctests Commit: 09e39e90794234ae2cbcc2ea6b747888a5075dcd https://github.com/galaxyproject/galaxy/commit/09e39e90794234ae2cbcc2ea6b74… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- py3: Fix mako template rendering in multiple history view and workflow editor Commit: ea440345facd8c9e1cb6c6636970cacfa0544a6f https://github.com/galaxyproject/galaxy/commit/ea440345facd8c9e1cb6c6636970… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/web/framework/helpers/grids.py M templates/tagging_common.mako Log Message: ----------- py3: fix published workflows grid Commit: 252913b84a4de19d61294790d10ffca93944e520 https://github.com/galaxyproject/galaxy/commit/252913b84a4de19d61294790d10f… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/model/orm/scripts.py Log Message: ----------- Fix SafeConfigParser import for Python 3 Commit: e9f3afa0f3d6451116283a592c680c47a986bbef https://github.com/galaxyproject/galaxy/commit/e9f3afa0f3d6451116283a592c68… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/tool_shed/util/web_util.py Log Message: ----------- py3: fix tool_shed.util.web_util.escape doctest Commit: 7cf76bc66aa9c8b95a74f699a934c4dd81debd57 https://github.com/galaxyproject/galaxy/commit/7cf76bc66aa9c8b95a74f699a934… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- Fix documentation Commit: d5d245ff65841a33c8cb8a32a146a63b14663a7a https://github.com/galaxyproject/galaxy/commit/d5d245ff65841a33c8cb8a32a146… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/jobs/runners/util/job_script/__init__.py Log Message: ----------- py3: Fix job_script writing Commit: 0c3a447f25d74132f5b449cac4c744f57af48198 https://github.com/galaxyproject/galaxy/commit/0c3a447f25d74132f5b449cac4c7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/containers/docker_swarm.py Log Message: ----------- Import docker.types Might fix the last failing unit test? Commit: 84af674f9c84182094803a81091ff932873d80a5 https://github.com/galaxyproject/galaxy/commit/84af674f9c84182094803a81091f… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/web/framework/decorators.py Log Message: ----------- Fix loading workflow in the editor under Python 3 Commit: a177fc6240c90985183807fc141b18e06e436cda https://github.com/galaxyproject/galaxy/commit/a177fc6240c90985183807fc141b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Fix login under Python 3 Commit: b49c4be21c6c090448d899857e53c1fed8be5d5a https://github.com/galaxyproject/galaxy/commit/b49c4be21c6c090448d899857e53… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/model/migrate/versions/0136_collection_and_workflow_state.py M lib/tool_shed/util/readme_util.py Log Message: ----------- Misc Python 3 fixes Commit: d15b6cc7360d3e00780dc1b9ee39353707ba786f https://github.com/galaxyproject/galaxy/commit/d15b6cc7360d3e00780dc1b9ee39… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Code clarifications Commit: e33427a3b79073b1f78a91e848a154f27798ec6c https://github.com/galaxyproject/galaxy/commit/e33427a3b79073b1f78a91e848a1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M .travis.yml M lib/galaxy/config.py M lib/galaxy/containers/docker_swarm.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/triples.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/model/metadata.py M lib/galaxy/model/migrate/versions/0136_collection_and_workflow_state.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/deps/conda_util.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/output_actions.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/util/rules_dsl.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/security/__init__.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/web_util.py M templates/tagging_common.mako M test/unit/test_remote_shell.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_history_imp_exp.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_extract_summary.py Log Message: ----------- Merge pull request #6450 from mvdbeek/py3_workflow_and_tool_unit_fixes Fix all remaining unit tests under Python 3 Compare: https://github.com/galaxyproject/galaxy/compare/9a06474a30cb...e33427a3b790 **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] 0c97d4: GIE static url; https://github.com/galaxyproject/g...
by GitHub 05 Jul '18

05 Jul '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 0c97d4ff5c83318551319524582619656ae848b8 https://github.com/galaxyproject/galaxy/commit/0c97d4ff5c833185513195245826… Author: thobalose <lose.thoba(a)gmail.com> Date: 2018-07-04 (Wed, 04 Jul 2018) Changed paths: M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- GIE static url; https://github.com/galaxyproject/galaxy/issues/6459 Commit: 3fe88a9bfe1b010ca30ffac32e5c4e200398c48e https://github.com/galaxyproject/galaxy/commit/3fe88a9bfe1b010ca30ffac32e5c… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- Merge pull request #6465 from dannon/backport-gie-static-again [18.05] Backport of IE static url fix (to actual 18.05) Compare: https://github.com/galaxyproject/galaxy/compare/39d7cf2eb731...3fe88a9bfe1b **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] 1a2cd7: added daa (diamond alignment) datatype
by GitHub 04 Jul '18

04 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1a2cd725bb303e8db6fa07118f4714b7c0516e60 https://github.com/galaxyproject/galaxy/commit/1a2cd725bb303e8db6fa07118f47… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- added daa (diamond alignment) datatype Commit: 68dc4c26508087829150b8e5c6d3530a47202304 https://github.com/galaxyproject/galaxy/commit/68dc4c26508087829150b8e5c6d3… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- removed try-except and used with Commit: 3b6ab3ecd087786113daa81e8cb0beda9a8eff82 https://github.com/galaxyproject/galaxy/commit/3b6ab3ecd087786113daa81e8cb0… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- shortened code Commit: e636bf00c64354bea8236cbfec81074f19b6a295 https://github.com/galaxyproject/galaxy/commit/e636bf00c64354bea8236cbfec81… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: A lib/galaxy/datatypes/test/diamond.daa Log Message: ----------- added missing test file Commit: a651b6af1ea04041aa4fa4230786e255b5fb954a https://github.com/galaxyproject/galaxy/commit/a651b6af1ea04041aa4fa4230786… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Minor cosmetics on diamond datatypes Commit: 46788b99b2386c165a9edc899d9a0a7fdafaba05 https://github.com/galaxyproject/galaxy/commit/46788b99b2386c165a9edc899d9a… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- added sniffer entry in data_types.conf.sample Commit: 891b8923bfbdd9c51e41f334185589b4ca87280d https://github.com/galaxyproject/galaxy/commit/891b8923bfbdd9c51e41f3341855… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-06-21 (Thu, 21 Jun 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- fixed typo in test this commit introduces also debug output for DAA and DMND snifferes which needs to be removed before merging Commit: 116c7051c9f4cc8e4b36577a3477a1bfcdc4b7d9 https://github.com/galaxyproject/galaxy/commit/116c7051c9f4cc8e4b36577a3477… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- daa detection: fixed typo and removed debug output Commit: 14ef3b8643eb96a98b1f39391c1f385596d1cb42 https://github.com/galaxyproject/galaxy/commit/14ef3b8643eb96a98b1f39391c1f… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M .ci/flake8_blacklist.txt M .travis.yml A client/galaxy/docs/galaxy-buttons.md A client/galaxy/docs/galaxy-forms.md A client/galaxy/docs/galaxy-masthead.md A client/galaxy/docs/galaxy-menus.md A client/galaxy/docs/galaxy-messages.md A client/galaxy/docs/galaxy-panels.md R client/galaxy/docs/galaxy-styles.md A client/galaxy/docs/galaxy-tables.md A client/galaxy/docs/galaxy-tabs.md M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/components/Citations.vue A client/galaxy/scripts/components/DataDialog.vue A client/galaxy/scripts/components/admin/DataTypes.vue M client/galaxy/scripts/galaxy.pages.js A client/galaxy/scripts/layout/data.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/modal.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/job-dag.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/visualization/chart/components/model.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/reports/run_stats.js M client/galaxy/scripts/utils/config.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M client/galaxy/style/scss/galaxy_variables.scss M client/galaxy/style/scss/theme/blue.scss M client/galaxy/style/scss/ui.scss M client/galaxy/style/scss/upload.scss M client/package.json M client/styleguide.config.js M client/webpack.config.js M client/yarn.lock M config/datatypes_conf.xml.sample M config/plugins/visualizations/msa/config/msa.xml M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/converters/bam_to_bai.xml M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/empty.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/dynamic_tool_destination.py R lib/galaxy/jobs/error_level.py M lib/galaxy/jobs/output_checker.py M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/users.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/metadata.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/cwl.py A lib/galaxy/tools/parser/error_level.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/util.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/relabel_from_file.xml M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/util/json.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M scripts/grt/export.py M static/style/blue/base.css R templates/admin/view_datatypes_registry.mako M templates/base/base_panels.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/tool_shed/base_panels.mako M test/api/test_tools.py M test/functional/test_data_managers.py M test/functional/test_toolbox.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/test_bam.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_runner_params.py M test/unit/test_galaxy_mapping.py M test/unit/test_security_helper.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_parsing.py M test/unit/tools/test_tool_dependency_description.py M test/unit/tools/test_tool_deps.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/tempfilecache.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/workflows/test_extract_summary.py M tools/data_source/upload.py Log Message: ----------- Merge branch 'dev' into topic/daa Commit: 9a06474a30cb82122ee6a78c30eca601af9d6578 https://github.com/galaxyproject/galaxy/commit/9a06474a30cb82122ee6a78c30ec… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/diamond.daa Log Message: ----------- Merge pull request #6313 from bernt-matthias/topic/daa added daa (diamond alignment) datatype Compare: https://github.com/galaxyproject/galaxy/compare/1f57706abffb...9a06474a30cb **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] 0c97d4: GIE static url; https://github.com/galaxyproject/g...
by GitHub 04 Jul '18

04 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0c97d4ff5c83318551319524582619656ae848b8 https://github.com/galaxyproject/galaxy/commit/0c97d4ff5c833185513195245826… Author: thobalose <lose.thoba(a)gmail.com> Date: 2018-07-04 (Wed, 04 Jul 2018) Changed paths: M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- GIE static url; https://github.com/galaxyproject/galaxy/issues/6459 Commit: 1f57706abffb933a1e5300f585ed19c1493b39d2 https://github.com/galaxyproject/galaxy/commit/1f57706abffb933a1e5300f585ed… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-07-04 (Wed, 04 Jul 2018) Log Message: ----------- Merge pull request #6464 from dannon/backport-gie-static [18.05] Backport of IE static url fix Compare: https://github.com/galaxyproject/galaxy/compare/6206f706794c...1f57706abffb **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] 7f0684: Fix test_toolbox for python 3
by GitHub 04 Jul '18

04 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7f0684e3d57f248b74ff5d6fd6f9a2537b07d726 https://github.com/galaxyproject/galaxy/commit/7f0684e3d57f248b74ff5d6fd6f9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-04 (Wed, 04 Jul 2018) Changed paths: M test/functional/test_toolbox.py Log Message: ----------- Fix test_toolbox for python 3 Commit: ae9b6057da7a0056191f27511e2a71fd1bd6dac2 https://github.com/galaxyproject/galaxy/commit/ae9b6057da7a0056191f27511e2a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-04 (Wed, 04 Jul 2018) Changed paths: M test/functional/test_data_managers.py Log Message: ----------- Fix test_data_managers for python 3 Commit: 6206f706794c997ae137381eabba7d0d88852c49 https://github.com/galaxyproject/galaxy/commit/6206f706794c997ae137381eabba… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-07-04 (Wed, 04 Jul 2018) Changed paths: M test/functional/test_data_managers.py M test/functional/test_toolbox.py Log Message: ----------- Merge pull request #6463 from mvdbeek/prepare_py3_api_tests Fix test_toolbox for python 3 Compare: https://github.com/galaxyproject/galaxy/compare/d85b65a2e501...6206f706794c **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] 54b6a8: py3: Fix the dynamic tool destination unit test
by GitHub 04 Jul '18

04 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 54b6a8883d9549c0a84204f530332d695676afdb https://github.com/galaxyproject/galaxy/commit/54b6a8883d9549c0a84204f53033… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- py3: Fix the dynamic tool destination unit test Commit: d85b65a2e5011e7187817c7f86db0c1e09a788d5 https://github.com/galaxyproject/galaxy/commit/d85b65a2e5011e7187817c7f86db… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-07-04 (Wed, 04 Jul 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- Merge pull request #6453 from mvdbeek/fix_py3_dtd py3: Fix the dynamic tool destination unit test Compare: https://github.com/galaxyproject/galaxy/compare/37782cf5131e...d85b65a2e501 **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] 5745df: GIE static url; https://github.com/galaxyproject/g...
by GitHub 04 Jul '18

04 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5745df2318d4907fb0fa40bc9032b44db853bca0 https://github.com/galaxyproject/galaxy/commit/5745df2318d4907fb0fa40bc9032… Author: thobalose <lose.thoba(a)gmail.com> Date: 2018-07-03 (Tue, 03 Jul 2018) Changed paths: M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- GIE static url; https://github.com/galaxyproject/galaxy/issues/6459 Commit: 37782cf5131eab2be8c08320bedf8365a475abbc https://github.com/galaxyproject/galaxy/commit/37782cf5131eab2be8c08320bedf… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-04 (Wed, 04 Jul 2018) Changed paths: M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- Merge pull request #6460 from thobalose/ie_static_url GIE static url Compare: https://github.com/galaxyproject/galaxy/compare/fb229c251f74...37782cf5131e **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] 21f42f: fixes test/unit/jobs/test_job_output_checker.py
by GitHub 04 Jul '18

04 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 21f42f5bb6f076b3b318f5f98657929d7f66102b https://github.com/galaxyproject/galaxy/commit/21f42f5bb6f076b3b318f5f98657… Author: caleb <caleb.easterly(a)gmail.com> Date: 2018-07-04 (Wed, 04 Jul 2018) Changed paths: M lib/galaxy/tools/parser/interface.py Log Message: ----------- fixes test/unit/jobs/test_job_output_checker.py Commit: fb0cc8bb1f8a786699f861256d5d25632b50af3f https://github.com/galaxyproject/galaxy/commit/fb0cc8bb1f8a786699f861256d5d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-04 (Wed, 04 Jul 2018) Changed paths: M lib/galaxy/tools/parser/interface.py Log Message: ----------- Use stdioerrorlevel constants to indicate FATAL Commit: 0d59c9cd54d49fad31767f52c07c995ff963ce18 https://github.com/galaxyproject/galaxy/commit/0d59c9cd54d49fad31767f52c07c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-04 (Wed, 04 Jul 2018) Changed paths: R lib/galaxy/jobs/error_level.py M lib/galaxy/jobs/output_checker.py M lib/galaxy/tools/parser/cwl.py A lib/galaxy/tools/parser/error_level.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/util.py M lib/galaxy/tools/parser/xml.py M test/unit/jobs/test_job_output_checker.py Log Message: ----------- Refactor galaxy.jobs.error_level -> galaxy.tools.parser.error_level. Needed after 46170e9bcdcc2eb104ebab72a7afc9b7238bc314 to keep galaxy-lib from importing things outside of galaxy-lib but clearly a good refactoring on its own since it eliminates mid-file imports that were there to prevent circular dependencies from loading Galaxy. Commit: fb229c251f7487215a285967be8b7b331c1d21f2 https://github.com/galaxyproject/galaxy/commit/fb229c251f7487215a285967be8b… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-07-04 (Wed, 04 Jul 2018) Changed paths: R lib/galaxy/jobs/error_level.py M lib/galaxy/jobs/output_checker.py M lib/galaxy/tools/parser/cwl.py A lib/galaxy/tools/parser/error_level.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/util.py M lib/galaxy/tools/parser/xml.py M test/unit/jobs/test_job_output_checker.py Log Message: ----------- Merge pull request #6438 from caleb-easterly/test_job_output_checker_py3 fixes test/unit/jobs/test_job_output_checker.py; strange default? Compare: https://github.com/galaxyproject/galaxy/compare/cc0022d5d1cc...fb229c251f74 **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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