- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 2e288e: Fix attribute error that was missed during refacto...
by GitHub 04 Dec '17

04 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2e288ef60f6a461cbd0bb4c5d82f7e6cee0f9fc8 https://github.com/galaxyproject/galaxy/commit/2e288ef60f6a461cbd0bb4c5d82f… Author: E Rasche <hxr(a)hx42.org> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- Fix attribute error that was missed during refactor Commit: 358cfc14af7c025bcf00d614fafe68ae90ef8437 https://github.com/galaxyproject/galaxy/commit/358cfc14af7c025bcf00d614fafe… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- Merge pull request #5122 from erasche/fix-attr-error Fix attribute error that was missed during refactor of sentry Compare: https://github.com/galaxyproject/galaxy/compare/72ed629c2a33...358cfc14af7c

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[galaxyproject/galaxy] 72aa96: Stricter checks for SDF sniffing
by GitHub 04 Dec '17

04 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 72aa96c7bcc21d333c17dffa5a5623b8b5dc82e4 https://github.com/galaxyproject/galaxy/commit/72aa96c7bcc21d333c17dffa5a56… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-12-02 (Sat, 02 Dec 2017) Changed paths: M lib/galaxy/datatypes/molecules.py Log Message: ----------- Stricter checks for SDF sniffing I had a bunch of protein FASTA files being sniffed as 'sdf'. Also fix https://github.com/galaxyproject/galaxy/issues/4558 . Commit: 95579883de61fb50bf3b309c8ab871b41d0d10ac https://github.com/galaxyproject/galaxy/commit/95579883de61fb50bf3b309c8ab8… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2017-12-02 (Sat, 02 Dec 2017) Changed paths: M lib/galaxy/datatypes/molecules.py A lib/galaxy/datatypes/test/chebi_57262.v3k.mol A lib/galaxy/datatypes/test/github88.v3k.sdf Log Message: ----------- More precise SDF sniffer First check 4th line: if this is conforming, scan up to 10000 lines. Add 2 test files downloaded from: https://github.com/rdkit/rdkit/tree/master/Code/GraphMol/FileParsers/test_d… Commit: c41fc0a4275ad4640a086d9bdf4d6bf3aec8c197 https://github.com/galaxyproject/galaxy/commit/c41fc0a4275ad4640a086d9bdf4d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-02 (Sat, 02 Dec 2017) Changed paths: M lib/galaxy/datatypes/molecules.py A lib/galaxy/datatypes/test/chebi_57262.v3k.mol A lib/galaxy/datatypes/test/github88.v3k.sdf Log Message: ----------- Merge pull request #5118 from mvdbeek/backport_sdf_sniffing_fixes [17.09] Backport stricter checks for SDF sniffing #4729 Commit: d73bb6c6c6b4d7efad56ec46653d11e4542e8f9a https://github.com/galaxyproject/galaxy/commit/d73bb6c6c6b4d7efad56ec46653d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Fix ICM datatype sniffer config Probably a bad merge in https://github.com/galaxyproject/galaxy/pull/5108 Commit: 22aa02f59496f9c10a855a3aac58f785a13124a2 https://github.com/galaxyproject/galaxy/commit/22aa02f59496f9c10a855a3aac58… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #5121 from mvdbeek/fix_icm_datatype_config [17.09] Fix ICM datatype sniffer config Commit: 72ed629c2a333de1adaac6892642e39aba7478c8 https://github.com/galaxyproject/galaxy/commit/72ed629c2a333de1adaac6892642… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge branch 'release_17.09' into dev Conflicts: config/datatypes_conf.xml.sample Compare: https://github.com/galaxyproject/galaxy/compare/7c59b8a33be9...72ed629c2a33

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[galaxyproject/galaxy] d73bb6: Fix ICM datatype sniffer config
by GitHub 04 Dec '17

04 Dec '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: d73bb6c6c6b4d7efad56ec46653d11e4542e8f9a https://github.com/galaxyproject/galaxy/commit/d73bb6c6c6b4d7efad56ec46653d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Fix ICM datatype sniffer config Probably a bad merge in https://github.com/galaxyproject/galaxy/pull/5108 Commit: 22aa02f59496f9c10a855a3aac58f785a13124a2 https://github.com/galaxyproject/galaxy/commit/22aa02f59496f9c10a855a3aac58… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #5121 from mvdbeek/fix_icm_datatype_config [17.09] Fix ICM datatype sniffer config Compare: https://github.com/galaxyproject/galaxy/compare/c41fc0a4275a...22aa02f59496

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[galaxyproject/galaxy] 72aa96: Stricter checks for SDF sniffing
by GitHub 02 Dec '17

02 Dec '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 72aa96c7bcc21d333c17dffa5a5623b8b5dc82e4 https://github.com/galaxyproject/galaxy/commit/72aa96c7bcc21d333c17dffa5a56… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-12-02 (Sat, 02 Dec 2017) Changed paths: M lib/galaxy/datatypes/molecules.py Log Message: ----------- Stricter checks for SDF sniffing I had a bunch of protein FASTA files being sniffed as 'sdf'. Also fix https://github.com/galaxyproject/galaxy/issues/4558 . Commit: 95579883de61fb50bf3b309c8ab871b41d0d10ac https://github.com/galaxyproject/galaxy/commit/95579883de61fb50bf3b309c8ab8… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2017-12-02 (Sat, 02 Dec 2017) Changed paths: M lib/galaxy/datatypes/molecules.py A lib/galaxy/datatypes/test/chebi_57262.v3k.mol A lib/galaxy/datatypes/test/github88.v3k.sdf Log Message: ----------- More precise SDF sniffer First check 4th line: if this is conforming, scan up to 10000 lines. Add 2 test files downloaded from: https://github.com/rdkit/rdkit/tree/master/Code/GraphMol/FileParsers/test_d… Commit: c41fc0a4275ad4640a086d9bdf4d6bf3aec8c197 https://github.com/galaxyproject/galaxy/commit/c41fc0a4275ad4640a086d9bdf4d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-02 (Sat, 02 Dec 2017) Changed paths: M lib/galaxy/datatypes/molecules.py A lib/galaxy/datatypes/test/chebi_57262.v3k.mol A lib/galaxy/datatypes/test/github88.v3k.sdf Log Message: ----------- Merge pull request #5118 from mvdbeek/backport_sdf_sniffing_fixes [17.09] Backport stricter checks for SDF sniffing #4729 Compare: https://github.com/galaxyproject/galaxy/compare/a82d325d1837...c41fc0a4275a

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[galaxyproject/galaxy] 85bf39: change the default ot not add tags based on filena...
by GitHub 01 Dec '17

01 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 85bf398fc33fb7ca230c51b09661176382923796 https://github.com/galaxyproject/galaxy/commit/85bf398fc33fb7ca230c51b09661… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/bundled/library.bundled.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- change the default ot not add tags based on filename this is fairly confusing if you do not expect it and there is no way to revert Commit: 7c59b8a33be920c72eac187ba35d0fdbba0b8e0e https://github.com/galaxyproject/galaxy/commit/7c59b8a33be920c72eac187ba35d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/bundled/library.bundled.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #5115 from martenson/change-libimport-tagdefault change the default to not add tags based on filename Compare: https://github.com/galaxyproject/galaxy/compare/dad11b8ef6d7...7c59b8a33be9

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[galaxyproject/galaxy] 66f57f: Remove external services config file
by GitHub 01 Dec '17

01 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 66f57f51003a7bfa73e44355d901158c06ca9b87 https://github.com/galaxyproject/galaxy/commit/66f57f51003a7bfa73e44355d901… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: R config/external_service_types_conf.xml.sample Log Message: ----------- Remove external services config file Commit: 4fe1b16da89847f99dcbc9b46cac8e088a5cb7f6 https://github.com/galaxyproject/galaxy/commit/4fe1b16da89847f99dcbc9b46cac… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Remove external services from galaxy config Commit: 13dad63cc9d95c43b3dae07c4e0c9bfe4e1fc1a4 https://github.com/galaxyproject/galaxy/commit/13dad63cc9d95c43b3dae07c4e0c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: R external_service_types/454_life_sciences.xml Log Message: ----------- Remove 454 life science Commit: d3f58fde66bb0a3457e4d3e7b9e8a523f782a187 https://github.com/galaxyproject/galaxy/commit/d3f58fde66bb0a3457e4d3e7b9e8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: R external_service_types/applied_biosystems_solid.xml Log Message: ----------- Remove biosystems xml Commit: ebab8f235f5b2c0578fae2739daa046fcd39a564 https://github.com/galaxyproject/galaxy/commit/ebab8f235f5b2c0578fae2739daa… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: R external_service_types/pacific_biosciences_smrt_portal.xml Log Message: ----------- Remove pacific biosciences xml Commit: 223044a91e8595c4ba5e8c809c06f232ffad4dde https://github.com/galaxyproject/galaxy/commit/223044a91e8595c4ba5e8c809c06… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: R external_service_types/simple_unknown_sequencer.xml Log Message: ----------- Remove default wrapper for unkown sequencer Commit: e57b3b83d0e4cf7ff0d91d98156954962bd9f267 https://github.com/galaxyproject/galaxy/commit/e57b3b83d0e4cf7ff0d91d981569… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: M lib/galaxy/app.py Log Message: ----------- Remove sample tracking from config Commit: 5e81fc30cc49512c3911dcfaab61acd13d2f95ad https://github.com/galaxyproject/galaxy/commit/5e81fc30cc49512c3911dcfaab61… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- Remove from config Commit: 65a23a895157f1817349c691369ee9439099a7ed https://github.com/galaxyproject/galaxy/commit/65a23a895157f1817349c691369e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: R lib/galaxy/external_services/__init__.py R lib/galaxy/external_services/actions.py R lib/galaxy/external_services/parameters.py R lib/galaxy/external_services/result_handlers/__init__.py R lib/galaxy/external_services/result_handlers/basic.py R lib/galaxy/external_services/service.py Log Message: ----------- Remove external services from lib Commit: 697eac0be98e006efdc01ac857f545aa767b809d https://github.com/galaxyproject/galaxy/commit/697eac0be98e006efdc01ac857f5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: R lib/galaxy/jobs/deferred/__init__.py R lib/galaxy/jobs/deferred/data_transfer.py R lib/galaxy/jobs/deferred/manual_data_transfer.py R lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py Log Message: ----------- Remove deferred job handler from lib Commit: 7ea7493775f95c1f462e44fd713e92eb819bdd82 https://github.com/galaxyproject/galaxy/commit/7ea7493775f95c1f462e44fd713e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: M lib/galaxy/managers/context.py Log Message: ----------- Remove request types caller from context manager Commit: 10f4d8e9ee16244ac67bebee9fe2c01c5c6c626e https://github.com/galaxyproject/galaxy/commit/10f4d8e9ee16244ac67bebee9fe2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: R lib/galaxy/sample_tracking/__init__.py R lib/galaxy/sample_tracking/data_transfer.py R lib/galaxy/sample_tracking/external_service_types.py R lib/galaxy/sample_tracking/request_types.py R lib/galaxy/sample_tracking/sample.py Log Message: ----------- Remove sample tracking from lib Commit: e8f96a43f6acf668f6c4115c7b8d7b330835ae0e https://github.com/galaxyproject/galaxy/commit/e8f96a43f6acf668f6c4115c7b8d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Remove unused name_autocomplete_data from admin controller Commit: 9444686dbd9f01dfcc6c7a2b2ad0ca1d9d89b595 https://github.com/galaxyproject/galaxy/commit/9444686dbd9f01dfcc6c7a2b2ad0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Remove request details parsing to client in root Commit: 7a2be3b625f8217519f07877687124570206ffed https://github.com/galaxyproject/galaxy/commit/7a2be3b625f8217519f078776871… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: M templates/webapps/galaxy/galaxy.masthead.mako Log Message: ----------- Remove request parsing to masthead mako Commit: b523ed1262530d35e2ff955da63360c6e7965c8c https://github.com/galaxyproject/galaxy/commit/b523ed1262530d35e2ff955da633… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: R templates/webapps/galaxy/external_services/generic_jquery_grid.mako R templates/webapps/galaxy/external_services/generic_json.mako R templates/webapps/galaxy/external_services/json_common.mako Log Message: ----------- Remove external services templates Commit: 7eb9501b430b72bcb6b3c493a0c3678a4133dbbc https://github.com/galaxyproject/galaxy/commit/7eb9501b430b72bcb6b3c493a0c3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-29 (Wed, 29 Nov 2017) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- Remove external service handler from security handler Commit: 3e5ce939dec42dd60e238d136f530a7e2613c588 https://github.com/galaxyproject/galaxy/commit/3e5ce939dec42dd60e238d136f53… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Remove edit template controller Commit: 1443b76c307870968eb3c1401bb8690bcb14111b https://github.com/galaxyproject/galaxy/commit/1443b76c307870968eb3c1401bb8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Remove edit template info controller Commit: 728a64cfa85427e48c18fb4301abbb0d5b27ede9 https://github.com/galaxyproject/galaxy/commit/728a64cfa85427e48c18fb4301ab… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Remove add template controller Commit: ae6bee39bb49d9dcda46fe0916030665b5ff52f4 https://github.com/galaxyproject/galaxy/commit/ae6bee39bb49d9dcda46fe091603… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Remove delete template controller Commit: b7d802f4088251d1755815120b5206785a4f848f https://github.com/galaxyproject/galaxy/commit/b7d802f4088251d1755815120b52… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Remove widget helper Commit: 98dc0ce5aeeff87cc14880026435a6d87008b192 https://github.com/galaxyproject/galaxy/commit/98dc0ce5aeeff87cc14880026435… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Remove empty field helper Commit: 08940a3a5169c9709dc4aafcd54922373e8bfa02 https://github.com/galaxyproject/galaxy/commit/08940a3a5169c9709dc4aafcd549… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Remove widget populator for previous refresh on change handler Commit: 70b094650f84a30a04f880ac94b423566d100514 https://github.com/galaxyproject/galaxy/commit/70b094650f84a30a04f880ac94b4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Remove item retrieval helper Commit: 0051d425917d2fef4f17106adacb12ddf0911b12 https://github.com/galaxyproject/galaxy/commit/0051d425917d2fef4f17106adacb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Remove select field build helper Commit: 3f1dda688376dcfd8e9a09abc275e089fa7d5e2f https://github.com/galaxyproject/galaxy/commit/3f1dda688376dcfd8e9a09abc275… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Remove form filter helper Commit: bbaea8b67cb9cd8ed2ab66120bbef92574629803 https://github.com/galaxyproject/galaxy/commit/bbaea8b67cb9cd8ed2ab66120bbe… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Remove unused form elements from shared controller endpoint Commit: ed1b4e1f432b86bc212478cccfe64daa12d1d6fe https://github.com/galaxyproject/galaxy/commit/ed1b4e1f432b86bc212478cccfe6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Clean up import section in shared controller Commit: 3e8efaf0a83e08d9457f33be61c0d6b648a682dc https://github.com/galaxyproject/galaxy/commit/3e8efaf0a83e08d9457f33be61c0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Remove requests from user keys Commit: fa516635f38f004724bcf6e89ec2b909bab57ad1 https://github.com/galaxyproject/galaxy/commit/fa516635f38f004724bcf6e89ec2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Remove model handlers for tables associated with sample tracking Commit: 5e4b76c422cba4421c39d19e6883c3372bd5b250 https://github.com/galaxyproject/galaxy/commit/5e4b76c422cba4421c39d19e6883… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Remove unused form types Commit: 7c2fab59ee027594cd7a2ee22b5face3a1ac7e09 https://github.com/galaxyproject/galaxy/commit/7c2fab59ee027594cd7a2ee22b5f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Remove unused imports, align comments Commit: 7abb1890594cb411780925bbeae782b19c222e74 https://github.com/galaxyproject/galaxy/commit/7abb1890594cb411780925bbeae7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Remove mapping classes for external services Commit: f305ab724eb4101f7c0a744131d764c39f6c9d52 https://github.com/galaxyproject/galaxy/commit/f305ab724eb4101f7c0a744131d7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Remove external service from mapping Commit: 26163538f314fa32d789ada6df91ecdec475e0f3 https://github.com/galaxyproject/galaxy/commit/26163538f314fa32d789ada6df91… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M .gitignore M Makefile M client/README.md M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/components/Citations.vue A client/galaxy/scripts/components/HistoryImport.vue A client/galaxy/scripts/components/UserAPIKeys.vue R client/galaxy/scripts/components/citations.vue R client/galaxy/scripts/components/history-import.vue R client/galaxy/scripts/components/user_api_keys.vue M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js A client/galaxy/scripts/mvc/history/job-states-model.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/qunit/test.js M client/galaxy/scripts/qunit/tests/form_tests.js R client/galaxy/scripts/qunit/tests/galaxy-app-base.js A client/galaxy/scripts/qunit/tests/galaxy_app_base_tests.js R client/galaxy/scripts/qunit/tests/graph.js A client/galaxy/scripts/qunit/tests/graph_tests.js R client/galaxy/scripts/qunit/tests/hda-base.js A client/galaxy/scripts/qunit/tests/hda_base_tests.js M client/galaxy/scripts/qunit/tests/history_contents_model_tests.js R client/galaxy/scripts/qunit/tests/job-dag.js A client/galaxy/scripts/qunit/tests/job_dag_tests.js R client/galaxy/scripts/qunit/tests/list-of-pairs-collection-creator.js A client/galaxy/scripts/qunit/tests/list_of_pairs_collection_creator_tests.js M client/galaxy/scripts/qunit/tests/masthead_tests.js R client/galaxy/scripts/qunit/tests/metrics-logger.js A client/galaxy/scripts/qunit/tests/metrics_logger_tests.js M client/galaxy/scripts/qunit/tests/modal_tests.js M client/galaxy/scripts/qunit/tests/page_tests.js M client/galaxy/scripts/qunit/tests/popover_tests.js M client/galaxy/scripts/qunit/tests/ui_tests.js M client/galaxy/scripts/qunit/tests/upload_dialog_tests.js R client/galaxy/scripts/qunit/tests/utils_test.js A client/galaxy/scripts/qunit/tests/utils_tests.js M client/galaxy/scripts/qunit/tests/workflow_editor_tests.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/style/less/base.less M client/galaxy/style/less/dataset.less M client/galaxy/style/less/list-item.less M client/gulpfile.js M client/karma.config.js M client/package.json M client/webpack.config.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample M lib/galaxy/config.py M lib/galaxy/dataset_collections/builder.py M lib/galaxy/dataset_collections/matching.py M lib/galaxy/dataset_collections/structure.py M lib/galaxy/dataset_collections/type_description.py M lib/galaxy/datatypes/annotation.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/triples.py 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/jobs/__init__.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/managers/hdcas.py M lib/galaxy/managers/jobs.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0136_collection_and_workflow_state.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/util/image_util.py R lib/galaxy/util/multi_byte.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M scripts/db_shell.py R static/GruntFile.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/adminToolshed.bundled.js R static/scripts/bundled/adminToolshed.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/library.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/viz.bundled.js M static/scripts/bundled/workflow.bundled.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-content-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js A static/scripts/mvc/history/job-states-model.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/tool/tool-form-base.js A static/scripts/packed M static/scripts/viz/trackster.js M static/style/blue/base.css M test/api/test_dataset_collections.py M test/api/test_history_contents.py M test/api/test_tools.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/base/populators.py M test/functional/tools/bibtex.xml M test/functional/tools/collection_creates_dynamic_nested.xml M test/functional/tools/collection_creates_dynamic_nested_fail.xml A test/functional/tools/for_workflows/count_list.xml A test/functional/tools/for_workflows/count_multi_file.xml A test/functional/tools/for_workflows/empty_list.xml A test/functional/tools/output_filter_with_input.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/components.py M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py M test/integration/test_data_manager_table_reload.py R test/integration/test_maximum_worklfow_invocation_duration.py A test/integration/test_workflow_scheduling_options.py M test/selenium_tests/framework.py A test/selenium_tests/test_history_copy_elements.py A test/selenium_tests/test_history_multi_view.py A test/selenium_tests/test_history_panel_collections.py A test/selenium_tests/test_history_panel_pagination.py M test/selenium_tests/test_tool_form.py M test/unit/dataset_collections/test_matching.py M test/unit/workflows/test_workflow_progress.py M tools/data_source/data_source.py M tools/data_source/upload.py Log Message: ----------- Merge branch 'dev' into remove_sample_tracking Commit: dad11b8ef6d7f4e332dff616f6092a759c5aa924 https://github.com/galaxyproject/galaxy/commit/dad11b8ef6d7f4e332dff616f609… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: R config/external_service_types_conf.xml.sample M config/galaxy.ini.sample R external_service_types/454_life_sciences.xml R external_service_types/applied_biosystems_solid.xml R external_service_types/pacific_biosciences_smrt_portal.xml R external_service_types/simple_unknown_sequencer.xml M lib/galaxy/app.py M lib/galaxy/config.py R lib/galaxy/external_services/__init__.py R lib/galaxy/external_services/actions.py R lib/galaxy/external_services/parameters.py R lib/galaxy/external_services/result_handlers/__init__.py R lib/galaxy/external_services/result_handlers/basic.py R lib/galaxy/external_services/service.py R lib/galaxy/jobs/deferred/__init__.py R lib/galaxy/jobs/deferred/data_transfer.py R lib/galaxy/jobs/deferred/manual_data_transfer.py R lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/managers/context.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py R lib/galaxy/sample_tracking/__init__.py R lib/galaxy/sample_tracking/data_transfer.py R lib/galaxy/sample_tracking/external_service_types.py R lib/galaxy/sample_tracking/request_types.py R lib/galaxy/sample_tracking/sample.py M lib/galaxy/security/__init__.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/root.py R templates/webapps/galaxy/external_services/generic_jquery_grid.mako R templates/webapps/galaxy/external_services/generic_json.mako R templates/webapps/galaxy/external_services/json_common.mako M templates/webapps/galaxy/galaxy.masthead.mako Log Message: ----------- Merge pull request #5103 from guerler/remove_sample_tracking Remove sample tracking backend support, preserve data tables Compare: https://github.com/galaxyproject/galaxy/compare/fc18b504be91...dad11b8ef6d7

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[galaxyproject/usegalaxy-playbook] 6ca912: Update Test
by GitHub 01 Dec '17

01 Dec '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 6ca9126f93d03bf7eb9255394e3e80a9668027f1 https://github.com/galaxyproject/usegalaxy-playbook/commit/6ca9126f93d03bf7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Test Commit: eea8722ea758a976f5de601b9b52d0767c65e49f https://github.com/galaxyproject/usegalaxy-playbook/commit/eea8722ea758a976… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M env/main/files/galaxy/galaxy_version.yml Log Message: ----------- Update Main Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/4ae2fa71f5d7...…

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[galaxyproject/galaxy] 06e950: Allow get_history calls with create=False when eva...
by GitHub 01 Dec '17

01 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 06e9509d3868c885d41d94e455d7245f4af10156 https://github.com/galaxyproject/galaxy/commit/06e9509d3868c885d41d94e455d7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-13 (Mon, 13 Nov 2017) Changed paths: M lib/galaxy/work/context.py Log Message: ----------- Allow get_history calls with create=False when evaluation workflows. No reasons to prevent this I guess - since create means create if a history isn't available not force the creation of a history. Commit: 827ac9c0433f581166b5bd06b70a14a39f22ded2 https://github.com/galaxyproject/galaxy/commit/827ac9c0433f581166b5bd06b70a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Do not attempt to visit parameters of invalid conditionals Commit: 1457fa7f937522d4825bb814a927a87b2e363cc8 https://github.com/galaxyproject/galaxy/commit/1457fa7f937522d4825bb814a927… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Check for key/value errors only when testing conditional cases Commit: 75f84bfc476ea94c22a38097d20f694265fcded6 https://github.com/galaxyproject/galaxy/commit/75f84bfc476ea94c22a38097d20f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Add test cases to cover version changes Commit: 9e9edb7e338bcf6a3d4174fc0d8e420a5184ad6b https://github.com/galaxyproject/galaxy/commit/9e9edb7e338bcf6a3d4174fc0d8e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-14 (Tue, 14 Nov 2017) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Remove unnecessary name setting for non-group parameters Commit: 64eced315887f19b7efd6334d4a28f91e8fd6116 https://github.com/galaxyproject/galaxy/commit/64eced315887f19b7efd6334d4a2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Fix comments Commit: de1bd5f5d5af7b9e67180b115407fbc2ccb75a3e https://github.com/galaxyproject/galaxy/commit/de1bd5f5d5af7b9e67180b115407… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-15 (Wed, 15 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/package-lock.json M static/maps/mvc/workflow/workflow-forms.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow-forms.js Log Message: ----------- Fix workflow editor output attributes. Commit: 5dc2254417667216dab982a4bc375a85d3b55316 https://github.com/galaxyproject/galaxy/commit/5dc2254417667216dab982a4bc37… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M lib/galaxy/work/context.py Log Message: ----------- Merge pull request #4997 from jmchilton/allow_create_false_in_work_context [17.09] Allow get_history calls with create=False when evaluation workflows. Commit: 2a0c7114dfafb0c91e3bafb03ae6ff4370ce9ed8 https://github.com/galaxyproject/galaxy/commit/2a0c7114dfafb0c91e3bafb03ae6… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-16 (Thu, 16 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/package-lock.json M static/maps/mvc/workflow/workflow-forms.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow-forms.js Log Message: ----------- Merge pull request #5022 from dannon/workflow_editor_fix_backport [17.09] Fix workflow editor output attributes. Commit: 1cfdf85879213018affc3ec19142e3ebccdb8c40 https://github.com/galaxyproject/galaxy/commit/1cfdf85879213018affc3ec19142… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- add ICM datatype for glimmer Commit: f44175b03c1671e6db11f1b072c3cd704a95fd58 https://github.com/galaxyproject/galaxy/commit/f44175b03c1671e6db11f1b072c3… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- copy paste mistake... Commit: f60a75c285830bff963bd31120f3420e9815dbe2 https://github.com/galaxyproject/galaxy/commit/f60a75c285830bff963bd31120f3… Author: E Rasche <hxr(a)hx42.org> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- extraneous %s Commit: 59e9809585e2322382eaeb7b3e0270485b7e8db0 https://github.com/galaxyproject/galaxy/commit/59e9809585e2322382eaeb7b3e02… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- Merge pull request #5048 from erasche/fix-ufr-6206 Remove extraneous %s in condor logging Commit: a7c8edbaa448805e0211fc75e3888d8426e5fa38 https://github.com/galaxyproject/galaxy/commit/a7c8edbaa448805e0211fc75e388… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-20 (Mon, 20 Nov 2017) Changed paths: M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/wrappers.py M test/api/test_tools.py A test/functional/tools/identifier_in_actions.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Bug fix - expose proper element_identifier in tool action template expansions. (#5049) xref https://github.com/galaxyproject/tools-iuc/commit/f57f1bf4816f212b83c08e0e3… Commit: 0bb7612977a44422acdf9c7d559d555ece1d17da https://github.com/galaxyproject/galaxy/commit/0bb7612977a44422acdf9c7d559d… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2017-11-21 (Tue, 21 Nov 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- don't read too much Commit: 8db4288ab5dcf379a669a5ae6ececc217b3c9da0 https://github.com/galaxyproject/galaxy/commit/8db4288ab5dcf379a669a5ae6ece… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-24 (Fri, 24 Nov 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Fixes galaxy startup when LC_TYPE=UTF-8 on os-x Closes https://github.com/galaxyproject/galaxy/issues/2645. Commit: cbc74f99e462ac3c71dc9bcb2a4c8c735e80170f https://github.com/galaxyproject/galaxy/commit/cbc74f99e462ac3c71dc9bcb2a4c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-24 (Fri, 24 Nov 2017) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py Log Message: ----------- Ignore OSError when chmod'ing integrated_tool_panel_conf.xml This fixes the first error in https://github.com/galaxyproject/galaxy/issues/5031: ``` Exception in thread ToolConfWatcher.thread: Traceback (most recent call last): File "/usr/lib/python2.7/threading.py", line 810, in __bootstrap_inner self.run() File "/usr/lib/python2.7/threading.py", line 763, in run self.__target(*self.__args, **self.__kwargs) File "lib/galaxy/tools/toolbox/watcher.py", line 138, in check self.reload_callback() File "lib/galaxy/webapps/galaxy/config_watchers.py", line 24, in <lambda> self.tool_config_watcher = get_tool_conf_watcher(reload_callback=lambda: reload_toolbox(self.app), tool_cache=self.app.tool_cache) File "lib/galaxy/queue_worker.py", line 92, in reload_toolbox _get_new_toolbox(app) File "lib/galaxy/queue_worker.py", line 111, in _get_new_toolbox new_toolbox = tools.ToolBox(tool_configs, app.config.tool_path, app) File "lib/galaxy/tools/__init__.py", line 226, in __init__ app=app, File "lib/galaxy/tools/toolbox/base.py", line 1061, in __init__ super(BaseGalaxyToolBox, self).__init__(config_filenames, tool_root_dir, app) File "lib/galaxy/tools/toolbox/base.py", line 87, in __init__ self._save_integrated_tool_panel() File "lib/galaxy/tools/toolbox/integrated_panel.py", line 46, in _save_integrated_tool_panel self._write_integrated_tool_panel_config_file() File "lib/galaxy/tools/toolbox/integrated_panel.py", line 106, in _write_integrated_tool_panel_config_file os.chmod(self._integrated_tool_panel_config, 0o644) OSError: [Errno 2] No such file or directory: '/data/users/mvandenb/gx/config/integrated_tool_panel.xml' ``` Commit: adfb623224810a0f383dc4ddf88be4ce51d3aa71 https://github.com/galaxyproject/galaxy/commit/adfb623224810a0f383dc4ddf88b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-24 (Fri, 24 Nov 2017) Changed paths: M lib/galaxy/datatypes/mothur.py Log Message: ----------- Fix metadata setting for Otu datatypes I broke this in https://github.com/galaxyproject/galaxy/pull/4388. I went through the other changes in that PR, and I believe this should be the only error. Figured out through the great detective work of @abernard. Commit: a71d5aa2db41a289b9410b129e6e70652f456593 https://github.com/galaxyproject/galaxy/commit/a71d5aa2db41a289b9410b129e6e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-24 (Fri, 24 Nov 2017) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py Log Message: ----------- Merge pull request #5071 from mvdbeek/installation_fixes [BUG][17.09] Ignore OSError when chmod'ing integrated_tool_panel_conf.xml Commit: f16491cd6506eb0734c415be1e0456faf9c1dd04 https://github.com/galaxyproject/galaxy/commit/f16491cd6506eb0734c415be1e04… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-24 (Fri, 24 Nov 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge pull request #5070 from mvdbeek/docutils_upgrade [BUG][[17.09] Fixes galaxy startup when LC_TYPE=UTF-8 on os-x Commit: a58586f0e4973aa6855142222ed8be124add9ad5 https://github.com/galaxyproject/galaxy/commit/a58586f0e4973aa6855142222ed8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-24 (Fri, 24 Nov 2017) Changed paths: M lib/galaxy/workflow/scheduling_manager.py Log Message: ----------- Cleanup SA objects between workflow invocation scheduling attempts. This would seem to be a fairly serious memory leak in the abstract but I don't have data that it fixes anything. None the less if it gets into dev and the tests seem to pass I'll open a PR to backport it to at least 17.05 and maybe back even more. Commit: ed162d5a69a3fac061f6becf592e737eed678411 https://github.com/galaxyproject/galaxy/commit/ed162d5a69a3fac061f6becf592e… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-11-27 (Mon, 27 Nov 2017) Changed paths: M lib/galaxy/datatypes/mothur.py Log Message: ----------- Merge pull request #5072 from mvdbeek/metadata_investigation [BUG][17.09] Fix metadata setting for Otu datatypes Commit: 385aaf2bd7e2b1c79f4b21f0449aed98fc9d6446 https://github.com/galaxyproject/galaxy/commit/385aaf2bd7e2b1c79f4b21f0449a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-27 (Mon, 27 Nov 2017) Changed paths: M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py Log Message: ----------- Fix exception in admin panel TypeError: Non-hexadecimal digit found File "galaxy/web/framework/middleware/sentry.py", line 40, in __call__ iterable = self.application(environ, start_response) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpexceptions.py", line 640, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/base.py", line 136, in __call__ return self.handle_request(environ, start_response) File "galaxy/web/framework/base.py", line 215, in handle_request body = method(trans, **kwargs) File "galaxy/web/framework/decorators.py", line 98, in decorator return func(self, trans, *args, **kwargs) File "galaxy/webapps/galaxy/controllers/admin_toolshed.py", line 660, in manage_repositories return self.repository_installation_grid(trans, **kwd) File "galaxy/web/framework/helpers/grids.py", line 85, in __call__ query = self.build_initial_query(trans, **kwargs) File "tool_shed/galaxy_install/grids/admin_toolshed_grids.py", line 334, in build_initial_query clause_list.append(self.model_class.table.c.id == trans.security.decode_id(tool_shed_repository_id)) File "galaxy/web/security/__init__.py", line 107, in decode_id return int(id_cipher.decrypt(obj_id.decode('hex')).lstrip("!")) File "encodings/hex_codec.py", line 42, in hex_decode output = binascii.a2b_hex(input) This is due to `tool_shed_repository_ids` being a json dump of a list in certain consitions (noticed this after installing a new repository). Commit: 0493763938ab6146dc383b735a7b3523914c2342 https://github.com/galaxyproject/galaxy/commit/0493763938ab6146dc383b735a7b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- Always fill `message` to avoid KeyError for sentry ERROR_TEMPLATE Commit: f6aedb0d2094256eb7f45ce7fc75f327db5b560c https://github.com/galaxyproject/galaxy/commit/f6aedb0d2094256eb7f45ce7fc75… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #5042 from abretaud/icm_dt [17.09] Add ICM datatype for glimmer Commit: ff3a6b084931f532dbce9a6d82059cda0137e3e3 https://github.com/galaxyproject/galaxy/commit/ff3a6b084931f532dbce9a6d8205… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- Merge pull request #5086 from mvdbeek/sentry_report_fix [17.09] Always fill `message` to avoid KeyError for sentry ERROR_TEMPLATE Commit: 802c943fff711dbeb6105b8b3ece68bf29cdee9e https://github.com/galaxyproject/galaxy/commit/802c943fff711dbeb6105b8b3ece… Author: Eric Rasche <hxr(a)hx42.org> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M lib/galaxy/workflow/scheduling_manager.py Log Message: ----------- Merge pull request #5073 from jmchilton/backport_5045 [17.09] Backport #5045 Commit: e903cb708e2f33bccebf5a0dd89b3bfe13667e03 https://github.com/galaxyproject/galaxy/commit/e903cb708e2f33bccebf5a0dd89b… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Merge pull request #5010 from guerler/fix_pages_workflows [17.09] Do not visit child inputs of invalid conditionals Commit: a82d325d18375797ce8ab53366320f3c9a772ab7 https://github.com/galaxyproject/galaxy/commit/a82d325d18375797ce8ab5336632… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-28 (Tue, 28 Nov 2017) Changed paths: M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py Log Message: ----------- Merge pull request #5079 from mvdbeek/admin_panel_exception_fix [17.09] Fix exception in admin panel Commit: 4dd05fc942988367cd5dd83695321063733f080e https://github.com/galaxyproject/galaxy/commit/4dd05fc942988367cd5dd8369532… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/tools/wrappers.py M lib/galaxy/work/context.py M test/api/test_tools.py A test/functional/tools/identifier_in_actions.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'release_17.09' into dev Commit: fc18b504be91a9f2eeb2ae74d136674ba70df1f6 https://github.com/galaxyproject/galaxy/commit/fc18b504be91a9f2eeb2ae74d136… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/tools/wrappers.py M lib/galaxy/work/context.py M test/api/test_tools.py A test/functional/tools/identifier_in_actions.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #5108 from mvdbeek/merge_forward_17_09 Merge forward 17 09 Compare: https://github.com/galaxyproject/galaxy/compare/e48f0bf319d0...fc18b504be91

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[galaxyproject/galaxy] 48aca7: Update to flake8-import-order 0.16
by GitHub 01 Dec '17

01 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 48aca7dce8608a7288b4613757f9085fad242785 https://github.com/galaxyproject/galaxy/commit/48aca7dce8608a7288b4613757f9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M cron/build_chrom_db.py M lib/galaxy/actions/library.py M lib/galaxy/dependencies/pipfiles/flake8/Pipfile M lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock M lib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt M lib/galaxy/model/migrate/versions/0136_collection_and_workflow_state.py M lib/galaxy/tools/execute.py M lib/galaxy/util/properties.py M lib/galaxy/web/stack/__init__.py M scripts/api/data_manager_example_execute.py M scripts/api/display.py M scripts/microbes/harvest_bacteria.py M test/api/test_api_batch.py M test/api/test_authenticate.py M test/api/test_datatypes.py M test/api/test_histories.py M test/api/test_history_contents.py M test/api/test_jobs.py M test/api/test_pages.py M test/api/test_users.py M test/api/test_visualizations.py M test/api/test_webhooks.py M test/api/test_workflows.py M test/base/integration_util.py M test/functional/test_toolbox.py M test/functional/twilltestcase.py M test/integration/test_local_job_cancellation.py M test/integration/test_workflow_handler_configuration.py M test/integration/test_workflow_scheduling_options.py M test/manual/workflows_scaling.py M test/selenium_tests/framework.py M test/shed_functional/base/test_db_util.py M test/shed_functional/base/twilltestcase.py Log Message: ----------- Update to flake8-import-order 0.16 Commit: e48f0bf319d09c460bd62572f10ce3d7c6b6a168 https://github.com/galaxyproject/galaxy/commit/e48f0bf319d09c460bd62572f10c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-01 (Fri, 01 Dec 2017) Changed paths: M cron/build_chrom_db.py M lib/galaxy/actions/library.py M lib/galaxy/dependencies/pipfiles/flake8/Pipfile M lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock M lib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt M lib/galaxy/model/migrate/versions/0136_collection_and_workflow_state.py M lib/galaxy/tools/execute.py M lib/galaxy/util/properties.py M lib/galaxy/web/stack/__init__.py M scripts/api/data_manager_example_execute.py M scripts/api/display.py M scripts/microbes/harvest_bacteria.py M test/api/test_api_batch.py M test/api/test_authenticate.py M test/api/test_datatypes.py M test/api/test_histories.py M test/api/test_history_contents.py M test/api/test_jobs.py M test/api/test_pages.py M test/api/test_users.py M test/api/test_visualizations.py M test/api/test_webhooks.py M test/api/test_workflows.py M test/base/integration_util.py M test/functional/test_toolbox.py M test/functional/twilltestcase.py M test/integration/test_local_job_cancellation.py M test/integration/test_workflow_handler_configuration.py M test/integration/test_workflow_scheduling_options.py M test/manual/workflows_scaling.py M test/selenium_tests/framework.py M test/shed_functional/base/test_db_util.py M test/shed_functional/base/twilltestcase.py Log Message: ----------- Merge pull request #5110 from nsoranzo/flake8-import-order Update to flake8-import-order 0.16 Compare: https://github.com/galaxyproject/galaxy/compare/dcd7e7809e14...e48f0bf319d0

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[galaxyproject/galaxy] b3271a: Optimize history collection response.
by GitHub 01 Dec '17

01 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b3271a42cb174af5c86bd4e6c32bdcb8cf0c6cab https://github.com/galaxyproject/galaxy/commit/b3271a42cb174af5c86bd4e6c32b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-content-model.js M lib/galaxy/managers/collections_util.py M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Optimize history collection response. Introduce a new collection view type (between view="collection" and view="element") called "element-reference" that fetches the element structure of a collection and enough information to resolve references for leaf datasets but doesn't include details that aren't used in rendering the structure of the collection in the GUI. Prevents transmitting metadata, dataset name (since element identifier is used), info, peek, dbkey, etc.... Backbone and the rest of the infrastructure seems to just work and fills in all remaining details when datasets are actually expanded by users. Optimization mentioned in #3795 - mitigates the issue (hopefully to large degree - but doesn't fix it). Commit: 09c0d2384dbd047a96910f5e6e2daa375b1baf88 https://github.com/galaxyproject/galaxy/commit/09c0d2384dbd047a96910f5e6e2d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-content-model.js M lib/galaxy/managers/collections_util.py M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Limit the number of elements the UX renders/fetches for collections. Fixes #3795 - more or less. Commit: 4b4a6e5a1c0d248ec32f07157ff6ecc3e7364ef3 https://github.com/galaxyproject/galaxy/commit/4b4a6e5a1c0d248ec32f07157ff6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js Log Message: ----------- Instrumentable paging... Commit: 485f64ee38bfeb31601817cac06028c7d043481c https://github.com/galaxyproject/galaxy/commit/485f64ee38bfeb31601817cac060… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml A test/selenium_tests/test_history_panel_pagination.py Log Message: ----------- Selenium testing for pagination of the history panel. Commit: 2a165c9afce58a8428bbdffaa0a5887e57285272 https://github.com/galaxyproject/galaxy/commit/2a165c9afce58a8428bbdffaa0a5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view.js Log Message: ----------- Refactor subtitle of collection display. Commit: 98e5d932f980c0e60f72d6d7184fea145deef3a9 https://github.com/galaxyproject/galaxy/commit/98e5d932f980c0e60f72d6d7184f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/history/hdca-li.js Log Message: ----------- Synchronize logic/code for displaying short collection descriptions. Commit: 37705885db99ed3ae104787730e1d8b04a6f81f4 https://github.com/galaxyproject/galaxy/commit/37705885db99ed3ae104787730e1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/history/history-content-model.js M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_history_panel_collections.py Log Message: ----------- Warn the user if not all collection elements are rendered. With test case. Commit: 345ee9aa9d6dfc6407657786c080accc1f5bad8c https://github.com/galaxyproject/galaxy/commit/345ee9aa9d6dfc6407657786c080… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M test/selenium_tests/test_history_panel_pagination.py Log Message: ----------- Make new Selenium pagination test as flakey - doesn't work consistently on Jenkins. Commit: 94a5cc141dabce5e95044517550a80b2d60e44f6 https://github.com/galaxyproject/galaxy/commit/94a5cc141dabce5e95044517550a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/history-content-model.js M static/scripts/mvc/history/history-contents.js Log Message: ----------- Repack client. Commit: dcd7e7809e144885652a386b3eb14fc59e20deb2 https://github.com/galaxyproject/galaxy/commit/dcd7e7809e144885652a386b3eb1… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js M lib/galaxy/managers/collections_util.py M lib/galaxy/webapps/galaxy/api/history_contents.py M static/scripts/bundled/analysis.bundled.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/history-content-model.js M static/scripts/mvc/history/history-contents.js M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_history_panel_collections.py A test/selenium_tests/test_history_panel_pagination.py Log Message: ----------- Merge pull request #5091 from jmchilton/open_large_collections Render arbitrarily large collections in the UI. Compare: https://github.com/galaxyproject/galaxy/compare/f70e6f5627bc...dcd7e7809e14

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