- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] f7a6a2: This is an extra hammer swing at #1531 / #1542, wh...
by GitHub 15 Jun '16

15 Jun '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f7a6a2323d188b2eca7ed03d26c59dbcb636b30b https://github.com/galaxyproject/galaxy/commit/f7a6a2323d188b2eca7ed03d26c5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-06-15 (Wed, 15 Jun 2016) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- This is an extra hammer swing at #1531 / #1542, which @rmarenco encountered. He said this resolves it. Commit: 5707954491e90682d5f04f3e631a3e6c8d4fdeb1 https://github.com/galaxyproject/galaxy/commit/5707954491e90682d5f04f3e631a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-06-15 (Wed, 15 Jun 2016) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Try to refresh input_datasets.dataset before accessing creating_job -- this is yet another attempt to resolve this being unavailable at job finish time. Commit: 9d84c0b883c62a5913dfb9e56b895bceedf1690a https://github.com/galaxyproject/galaxy/commit/9d84c0b883c62a5913dfb9e56b89… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-06-15 (Wed, 15 Jun 2016) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Merge pull request #2505 from dannon/bigger_hammer_remi_pja This is an extra hammer swing at #1531 / #1542 Compare: https://github.com/galaxyproject/galaxy/compare/4ef24d6ab8d1...9d84c0b883c6

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[galaxyproject/infrastructure-playbook] 678b59: Lower influxdb memory usage (hopefully)
by GitHub 15 Jun '16

15 Jun '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 678b5913992893dc10db0ef136c0dae07f2418f2 https://github.com/galaxyproject/infrastructure-playbook/commit/678b5913992… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-06-15 (Wed, 15 Jun 2016) Changed paths: M roles/stats/templates/influxdb.conf.j2 Log Message: ----------- Lower influxdb memory usage (hopefully)

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[galaxyproject/usegalaxy-playbook] bd322e: Switch Main to read configs from CVMFS and update.
by GitHub 15 Jun '16

15 Jun '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: bd322e8de6c1650bafcaf7cb1782ffbd647367c4 https://github.com/galaxyproject/usegalaxy-playbook/commit/bd322e8de6c1650b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-06-15 (Wed, 15 Jun 2016) Changed paths: M production/galaxy_version.yml M production/group_vars/galaxyservers.yml Log Message: ----------- Switch Main to read configs from CVMFS and update.

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[galaxyproject/infrastructure-playbook] 803b2d: Upgrade nginx role
by GitHub 15 Jun '16

15 Jun '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 803b2d52d5b0f82a55be7cbd96ca883b76f0fc39 https://github.com/galaxyproject/infrastructure-playbook/commit/803b2d52d5b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-06-15 (Wed, 15 Jun 2016) Changed paths: M roles/galaxyprojectdotorg.nginx/README.md M roles/galaxyprojectdotorg.nginx/meta/.galaxy_install_info M roles/galaxyprojectdotorg.nginx/templates/epel-nginx.conf.j2 Log Message: ----------- Upgrade nginx role Commit: 1ebe7c503bf1fae3ff6989a7de3f83592a37d17f https://github.com/galaxyproject/infrastructure-playbook/commit/1ebe7c503bf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-06-15 (Wed, 15 Jun 2016) Changed paths: M taccenv/host_vars/galaxy04.tacc.utexas.edu.yml M taccenv/inventory M taccenv/playbook.yml A taccenv/templates/nginx/galaxy-installers.j2 Log Message: ----------- Install nginx on TACC cvmfs stratum 0 for Test/Main Galaxy Installer apps Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/f5254387f2…

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[galaxyproject/usegalaxy-playbook] 50a6ca: Allow installer application on database
by GitHub 15 Jun '16

15 Jun '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 50a6ca27b13e8c8d690bda5ab2ac73d49131231b https://github.com/galaxyproject/usegalaxy-playbook/commit/50a6ca27b13e8c8d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-06-15 (Wed, 15 Jun 2016) Changed paths: M common/host_vars/galaxy-db-01.tacc.utexas.edu.yml Log Message: ----------- Allow installer application on database

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[galaxyproject/galaxy] 3680a0: Bump Pulsar client lib version number and add time...
by GitHub 15 Jun '16

15 Jun '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3680a016fdc779b417bf9820d63c4adf164479fc https://github.com/galaxyproject/galaxy/commit/3680a016fdc779b417bf9820d63c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-06-15 (Wed, 15 Jun 2016) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Bump Pulsar client lib version number and add timeout options to Pulsar runner to fix a timeout bug that kills the handlers on usegalaxy.org Commit: f3f0c30106a8adcdb993ec260aff408ca6667407 https://github.com/galaxyproject/galaxy/commit/f3f0c30106a8adcdb993ec260aff… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-06-15 (Wed, 15 Jun 2016) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Merge pull request #2504 from natefoo/pulsar-client-timeout [16.04] Bump Pulsar client lib version number and add timeout options to Pulsar runner Commit: 4ef24d6ab8d172db999fca3759b6699aed1069e6 https://github.com/galaxyproject/galaxy/commit/4ef24d6ab8d172db999fca3759b6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-06-15 (Wed, 15 Jun 2016) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/0fd152c0cc30...4ef24d6ab8d1

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[galaxyproject/galaxy] 3680a0: Bump Pulsar client lib version number and add time...
by GitHub 15 Jun '16

15 Jun '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 3680a016fdc779b417bf9820d63c4adf164479fc https://github.com/galaxyproject/galaxy/commit/3680a016fdc779b417bf9820d63c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-06-15 (Wed, 15 Jun 2016) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Bump Pulsar client lib version number and add timeout options to Pulsar runner to fix a timeout bug that kills the handlers on usegalaxy.org Commit: f3f0c30106a8adcdb993ec260aff408ca6667407 https://github.com/galaxyproject/galaxy/commit/f3f0c30106a8adcdb993ec260aff… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-06-15 (Wed, 15 Jun 2016) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Merge pull request #2504 from natefoo/pulsar-client-timeout [16.04] Bump Pulsar client lib version number and add timeout options to Pulsar runner Compare: https://github.com/galaxyproject/galaxy/compare/37242c8a7cbd...f3f0c30106a8

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[galaxyproject/galaxy] d95e9b: Refactor move_file() method
by GitHub 15 Jun '16

15 Jun '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d95e9b840de5773337c80c612b790571e8229bfc https://github.com/galaxyproject/galaxy/commit/d95e9b840de5773337c80c612b79… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-06-09 (Thu, 09 Jun 2016) Changed paths: M lib/tool_shed/util/basic_util.py Log Message: ----------- Refactor move_file() method Commit: d38936bd8d9b3612dc0718859067e299651e6c86 https://github.com/galaxyproject/galaxy/commit/d38936bd8d9b3612dc0718859067… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-06-09 (Thu, 09 Jun 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Move the whole directory instead of element by element Fix #1947. Commit: 75cdec9b4baa0a003b6516d524c625bb6aaa07bb https://github.com/galaxyproject/galaxy/commit/75cdec9b4baa0a003b6516d524c6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-06-15 (Wed, 15 Jun 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/util/basic_util.py Log Message: ----------- Merge pull request #2479 from nsoranzo/release_16.01_fix_for_1947 [16.01] Fix move_directory_files tool dependency action when new_file_path is on a different filesystem Commit: 37242c8a7cbd4524bb7e585c05548023071c1339 https://github.com/galaxyproject/galaxy/commit/37242c8a7cbd4524bb7e585c0554… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-06-15 (Wed, 15 Jun 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/util/basic_util.py Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Commit: 0fd152c0cc30c5fc00a86bd5020bd0fc91e213fb https://github.com/galaxyproject/galaxy/commit/0fd152c0cc30c5fc00a86bd5020b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-06-15 (Wed, 15 Jun 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/util/basic_util.py Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/dca91dae163f...0fd152c0cc30

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[galaxyproject/galaxy] 16dfca: Merge branch 'release_16.04' of https://github.com...
by GitHub 15 Jun '16

15 Jun '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 16dfca86e69597796e60e604ae410dcf6667291c https://github.com/galaxyproject/galaxy/commit/16dfca86e69597796e60e604ae41… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-04-30 (Sat, 30 Apr 2016) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Merge branch 'release_16.04' of https://github.com/galaxyproject/galaxy into release_16.04 Commit: a27e86786ad031eafcbfeb39ffdadf71d80dcfad https://github.com/galaxyproject/galaxy/commit/a27e86786ad031eafcbfeb39ffda… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-26 (Thu, 26 May 2016) Changed paths: M lib/galaxy/external_services/actions.py M lib/galaxy/external_services/parameters.py M lib/galaxy/external_services/service.py M lib/galaxy/forms/forms.py M lib/galaxy/model/__init__.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/webapps/galaxy/controllers/external_services.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/repository_types/metadata.py M tools/filters/axt_to_lav.py Log Message: ----------- wrap bare str raises with generic Exception() as Pyton 2.7 does not support bare str Commit: fe64a8198bca75f2e535efc7c3813d24810904ab https://github.com/galaxyproject/galaxy/commit/fe64a8198bca75f2e535efc7c381… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-26 (Thu, 26 May 2016) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- fix the mess made with mass edit Commit: 6094990e43f6510833395885d234a2264e7d44f1 https://github.com/galaxyproject/galaxy/commit/6094990e43f6510833395885d234… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-26 (Thu, 26 May 2016) Changed paths: M lib/galaxy/external_services/actions.py M lib/galaxy/external_services/parameters.py M lib/galaxy/external_services/service.py M lib/galaxy/forms/forms.py M lib/galaxy/model/__init__.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/webapps/galaxy/controllers/external_services.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/repository_types/metadata.py M tools/filters/axt_to_lav.py Log Message: ----------- Merge pull request #2424 from martenson/port-exceptionwrap-16.04 [16.04] wrap bare str exceptions Commit: 214e757d81623e9c12d171f3dcfc516c7dcc5e32 https://github.com/galaxyproject/galaxy/commit/214e757d81623e9c12d171f3dcfc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-31 (Tue, 31 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Only scan the last 16 MB of a job's stderr for slurm memory warning messages. Commit: dcb28e095012fef3be769f677fa572f13d4ed88a https://github.com/galaxyproject/galaxy/commit/dcb28e095012fef3be769f677fa5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-31 (Tue, 31 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Fix linting error Commit: ceb825bea8b28c8908c8a719919b9167bedabe55 https://github.com/galaxyproject/galaxy/commit/ceb825bea8b28c8908c8a719919b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-31 (Tue, 31 May 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #2432 from natefoo/job-output-memory-fix [16.04] Only scan the last 16 MB of a job's stderr for slurm memory warning messages Commit: 7cb527ac595591c99401436757168b366f86a526 https://github.com/galaxyproject/galaxy/commit/7cb527ac595591c9940143675716… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-06-02 (Thu, 02 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Overwrite the correct part of stderr - Skip partial line - Seek back to the correct position after readlines() - Use the same approach in __check_memory_limit() Commit: 58f3f5c7dd4c622adce0f18d24a0ee950d1d4dfd https://github.com/galaxyproject/galaxy/commit/58f3f5c7dd4c622adce0f18d24a0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-06-02 (Thu, 02 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #2447 from nsoranzo/release_16.04_fix_for_2432 [16.04] Overwrite the correct part of stderr Commit: 78c866fd34181ecda09488b6d19d2e37f6c69d02 https://github.com/galaxyproject/galaxy/commit/78c866fd34181ecda09488b6d19d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-04 (Sat, 04 Jun 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Relax validation condition Commit: a44f30140990c93aa92b8cb5f0f87b819942b116 https://github.com/galaxyproject/galaxy/commit/a44f30140990c93aa92b8cb5f0f8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-05 (Sun, 05 Jun 2016) Changed paths: M test/unit/tools/test_select_parameters.py Log Message: ----------- Revise contradicting test case, workflow injection through api attempts full validation without available datasets Commit: d9d51d362e8ef3197e01c0440289e60a50ad85e8 https://github.com/galaxyproject/galaxy/commit/d9d51d362e8ef3197e01c0440289… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-06 (Mon, 06 Jun 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add break to interrupt loop Commit: b97c7964457010318b4639e57ca01fd6185269f2 https://github.com/galaxyproject/galaxy/commit/b97c7964457010318b4639e57ca0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-06 (Mon, 06 Jun 2016) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Filter missing inputs when processing data Commit: edca79a0cf4d0e6afceb0f3b3894b6b3a169bd53 https://github.com/galaxyproject/galaxy/commit/edca79a0cf4d0e6afceb0f3b3894… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-06-06 (Mon, 06 Jun 2016) Changed paths: M lib/galaxy/web/security/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Do not encode dict items that start with 'metadata_' in return value of api/tools/create. Resolves #2423, #2137, and https://github.com/galaxyproject/tools-iuc/pull/770. However, this whole act of encoding by key.endswith('_id') is very messy. Commit: 42739c88c80d10742add92f2e3978ed65a295188 https://github.com/galaxyproject/galaxy/commit/42739c88c80d10742add92f2e397… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-06-07 (Tue, 07 Jun 2016) Changed paths: A test-data/biom1_metadata_test.txt A test-data/input_taxonomy.biom1 A test/functional/tools/metadata_biom1.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Add test for failing handling of BIOM1 metadata. Commit: 37a491599257c4045ad9e45ae53d12b9d97be418 https://github.com/galaxyproject/galaxy/commit/37a491599257c4045ad9e45ae53d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-06-07 (Tue, 07 Jun 2016) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Merge pull request #2458 from guerler/fix_process_data [16.04] Filter missing inputs when processing data Commit: 10a3f23de2f8d728780b7c1615e7d4c9afeaeeb2 https://github.com/galaxyproject/galaxy/commit/10a3f23de2f8d728780b7c1615e7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-06-07 (Tue, 07 Jun 2016) Changed paths: M lib/galaxy/web/security/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py A test-data/biom1_metadata_test.txt A test-data/input_taxonomy.biom1 A test/functional/tools/metadata_biom1.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #2459 from blankenberg/metadata-id-fix [16.04] Do not encode dict items that start with 'metadata_' in return value of api/tools/create. Commit: 9e5419f58c2af16d4cc6e8ece79c61f86a38b6cf https://github.com/galaxyproject/galaxy/commit/9e5419f58c2af16d4cc6e8ece79c… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-06-08 (Wed, 08 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Delay import of DrmaaSessionFactory after runner initialization Fix issue #2463, i.e. the regression introduced in #2102 by which Galaxy no longer respects <param id="drmaa_library_path"> in config/job_conf.xml , preventing the use of multiple drmaa runners. Commit: 8983e4304060482426e8f3f2eb072eb0f071ba83 https://github.com/galaxyproject/galaxy/commit/8983e4304060482426e8f3f2eb07… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-06-08 (Wed, 08 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Merge pull request #2466 from nsoranzo/release_16.04_fix_for_2463 [16.04] Delay import of DrmaaSessionFactory after runner initialization Commit: d2be9dc98dbee387bec377a9c89685bb0011c85f https://github.com/galaxyproject/galaxy/commit/d2be9dc98dbee387bec377a9c896… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-08 (Wed, 08 Jun 2016) Changed paths: M templates/webapps/galaxy/workflow/display.mako Log Message: ----------- Prevent missing display to text values in workflow preview Commit: befe35456a606cab03c3119c013c5983323c16e3 https://github.com/galaxyproject/galaxy/commit/befe35456a606cab03c3119c013c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-06-08 (Wed, 08 Jun 2016) Changed paths: M templates/webapps/galaxy/workflow/display.mako Log Message: ----------- Merge pull request #2471 from guerler/fix_workflow_display [16.04] Prevent missing display to text values in workflow preview Commit: 4cd2af860ffc31ee574e6f81c941840ae603efe5 https://github.com/galaxyproject/galaxy/commit/4cd2af860ffc31ee574e6f81c941… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-06-08 (Wed, 08 Jun 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Avoid empty strings when converting values to display text Commit: 04863c833bb1de9c298600be7c2de44d2b6b694b https://github.com/galaxyproject/galaxy/commit/04863c833bb1de9c298600be7c2d… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-06-08 (Wed, 08 Jun 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #2473 from martenson/port-value-to-display [16.04] Avoid empty strings when converting values to display text Commit: 2cf95d8a134bb84cec0408b016e751fc840327c1 https://github.com/galaxyproject/galaxy/commit/2cf95d8a134bb84cec0408b016e7… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-06-08 (Wed, 08 Jun 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M config/galaxy.ini.sample M doc/source/releases/16.01.rst A doc/source/releases/16.04.rst M doc/source/releases/16.04_announce.rst A doc/source/releases/16.07_announce.rst M doc/source/releases/index.rst A lib/galaxy/datatypes/checkers.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/external_services/actions.py M lib/galaxy/external_services/parameters.py M lib/galaxy/external_services/service.py M lib/galaxy/forms/forms.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/managers/histories.py M lib/galaxy/model/__init__.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/util/checkers.py M lib/galaxy/version.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/web/security/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/external_services.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/galaxy/workflow/run.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/repository_types/metadata.py M static/maps/mvc/form/form-input.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-input.js M templates/show_params.mako M templates/webapps/galaxy/data_manager/view_job.mako M templates/webapps/galaxy/workflow/display.mako M templates/webapps/galaxy/workflow/run.mako M templates/webapps/galaxy/workflow/sharing.mako A test-data/biom1_metadata_test.txt A test-data/input_taxonomy.biom1 A test/functional/tools/metadata_biom1.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml M test/unit/managers/test_HistoryManager.py M tools/filters/axt_to_lav.py Log Message: ----------- Merge branch 'release_16.04' of https://github.com/galaxyproject/galaxy into release_16.04 Commit: d95e9b840de5773337c80c612b790571e8229bfc https://github.com/galaxyproject/galaxy/commit/d95e9b840de5773337c80c612b79… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-06-09 (Thu, 09 Jun 2016) Changed paths: M lib/tool_shed/util/basic_util.py Log Message: ----------- Refactor move_file() method Commit: d38936bd8d9b3612dc0718859067e299651e6c86 https://github.com/galaxyproject/galaxy/commit/d38936bd8d9b3612dc0718859067… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-06-09 (Thu, 09 Jun 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Move the whole directory instead of element by element Fix #1947. Commit: 7610f82a421edb422b8ba8f7731a1ae23fb9ac41 https://github.com/galaxyproject/galaxy/commit/7610f82a421edb422b8ba8f7731a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-06-09 (Thu, 09 Jun 2016) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- fix markup for button links on sharing template (ff would fail to generate images) turn of autocomplete Commit: e73e6b3587a98e1537b82283f8935f770648b2e3 https://github.com/galaxyproject/galaxy/commit/e73e6b3587a98e1537b82283f893… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-06-10 (Fri, 10 Jun 2016) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/command_factory.py Log Message: ----------- Allow disabling separating tools commands into their own script. Forcing them there broke Pulsar-on-Windows functionality - this fix is courtesy of @jj-umn. Commit: 7c40c85034d918c50e8b22c1a3eb39746a6e043d https://github.com/galaxyproject/galaxy/commit/7c40c85034d918c50e8b22c1a3eb… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-06-10 (Fri, 10 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Fix for job handlers losing track of jobs when using DRMAA with internalexception_retries or invalidjobexception_retries Commit: 933f42619e2fb2fb518702397aa2f11ea2cfb8e0 https://github.com/galaxyproject/galaxy/commit/933f42619e2fb2fb518702397aa2… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-06-10 (Fri, 10 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Log all failed job status checks Commit: dbbf1edef3d943e13db4e926840061a65742eaab https://github.com/galaxyproject/galaxy/commit/dbbf1edef3d943e13db4e9268400… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-06-10 (Fri, 10 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Merge pull request #2484 from nsoranzo/release_16.01_fix_for_4a024b882f504aded1db32f1ed056f7c9109d218 [16.01] Fix for job handlers losing track of jobs when using DRMAA with internalexception_retries or invalidjobexception_retries Commit: 14844e48eb3869dbb2ecdca29e6069904bac4f28 https://github.com/galaxyproject/galaxy/commit/14844e48eb3869dbb2ecdca29e60… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-06-10 (Fri, 10 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Conflicts: lib/galaxy/jobs/runners/drmaa.py Commit: 574740d0b299d9cd84d9065f4746204f6399d891 https://github.com/galaxyproject/galaxy/commit/574740d0b299d9cd84d9065f4746… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-06-10 (Fri, 10 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Reset exception retries after successful job status check Commit: 08fb160b38fbcd9bcdfd776bb75ae5c92ca002d1 https://github.com/galaxyproject/galaxy/commit/08fb160b38fbcd9bcdfd776bb75a… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-06-10 (Fri, 10 Jun 2016) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- Merge pull request #2481 from martenson/fix-html-sharing [16.04] fix markup for button links on sharing template Commit: 4cf8d691e525142125af56b0627f804eb1bddd7c https://github.com/galaxyproject/galaxy/commit/4cf8d691e525142125af56b0627f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-06-10 (Fri, 10 Jun 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- fix image generation for workflows with missing tools currently this ends up with a server error Commit: fdf9520783ae55795a01e4092b1d6718c5fca5b4 https://github.com/galaxyproject/galaxy/commit/fdf9520783ae55795a01e4092b1d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-06-10 (Fri, 10 Jun 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- drop unnecessary raise and fix capitalization incorporate comments of Bjoern and Nicola Commit: 43694be8647e3d1686b6c4fa80d0300bb9c96d42 https://github.com/galaxyproject/galaxy/commit/43694be8647e3d1686b6c4fa80d0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-06-10 (Fri, 10 Jun 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py M test/unit/tools/test_select_parameters.py Log Message: ----------- Merge pull request #2456 from guerler/fix_building_mode [16.04] Relax validation condition for dynamic parameters Commit: 5245e8a693fc3633762f29a468b84e3487083133 https://github.com/galaxyproject/galaxy/commit/5245e8a693fc3633762f29a468b8… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-06-11 (Sat, 11 Jun 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge pull request #2488 from martenson/wrap-svg-for-missing-tools [16.04] fix image generation for workflows with missing tools Commit: b3a32ac2e19afda605f26f989bf3e16eaa1d27af https://github.com/galaxyproject/galaxy/commit/b3a32ac2e19afda605f26f989bf3… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-06-11 (Sat, 11 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M templates/webapps/galaxy/workflow/sharing.mako M test/unit/tools/test_select_parameters.py Log Message: ----------- Merge branch 'release_16.04' of https://github.com/galaxyproject/galaxy into release_16.04 Commit: 0017b3e9405e5e77904364025889c88cf0991744 https://github.com/galaxyproject/galaxy/commit/0017b3e9405e5e77904364025889… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-06-11 (Sat, 11 Jun 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- add IUC channel to the list Commit: ec0d97327b0bf234021f5a3f5ab261b491baa091 https://github.com/galaxyproject/galaxy/commit/ec0d97327b0bf234021f5a3f5ab2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-06-13 (Mon, 13 Jun 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #2490 from bgruening/iuc_conda_channel [16.04] Add IUC conda channel Commit: 54bffd93ac2a78f248e0d937ae0ea8e1aaafb131 https://github.com/galaxyproject/galaxy/commit/54bffd93ac2a78f248e0d937ae0e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-06-13 (Mon, 13 Jun 2016) Changed paths: M lib/galaxy/jobs/command_factory.py Log Message: ----------- Spelling fix thanks to @nsoranzo. Commit: 6ccfd13ab4e500774a40a54deba949d29f719f2c https://github.com/galaxyproject/galaxy/commit/6ccfd13ab4e500774a40a54deba9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-06-13 (Mon, 13 Jun 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Merge pull request #2487 from nsoranzo/release_16.04_reset_exception_retries [16.04] Reset exception retries after successful job status check Commit: 4bf9955d0333af12d5b6dbdfe4336fda64f5a55e https://github.com/galaxyproject/galaxy/commit/4bf9955d0333af12d5b6dbdfe433… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-06-13 (Mon, 13 Jun 2016) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Backport fac2efc4bd6b2214fa6d17e27b43d26fe4de7d37 to 16.04 to enable functional stats on main. Commit: e1cafd6ab45d385cfa46b16a2c4ab120fc3fde6f https://github.com/galaxyproject/galaxy/commit/e1cafd6ab45d385cfa46b16a2c4a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-06-13 (Mon, 13 Jun 2016) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Add conditional statsd requirement. Wheel is live on wheels.galaxyproject.org. Commit: 2aab4ee72198651a5017d37676853e74edec3b46 https://github.com/galaxyproject/galaxy/commit/2aab4ee72198651a5017d3767685… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-06-13 (Mon, 13 Jun 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/web/framework/middleware/statsd.py Log Message: ----------- More backporting of stats to make it functional on main. Commit: 8ef8522d68ea4d6b6c9a736ec4439306877fff13 https://github.com/galaxyproject/galaxy/commit/8ef8522d68ea4d6b6c9a736ec443… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-06-13 (Mon, 13 Jun 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #2497 from dannon/backport_onion_rearrangement [16.04] Backport of stats fixes/prefix work. Commit: 7d962ee0cb6bcc83033363111d30be375a48a920 https://github.com/galaxyproject/galaxy/commit/7d962ee0cb6bcc83033363111d30… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-06-15 (Wed, 15 Jun 2016) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/command_factory.py Log Message: ----------- Merge pull request #2492 from jmchilton/windows_no_shell [16.04] Allow disabling separating tools commands into their own script. Commit: 75cdec9b4baa0a003b6516d524c625bb6aaa07bb https://github.com/galaxyproject/galaxy/commit/75cdec9b4baa0a003b6516d524c6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-06-15 (Wed, 15 Jun 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/util/basic_util.py Log Message: ----------- Merge pull request #2479 from nsoranzo/release_16.01_fix_for_1947 [16.01] Fix move_directory_files tool dependency action when new_file_path is on a different filesystem Commit: 37242c8a7cbd4524bb7e585c05548023071c1339 https://github.com/galaxyproject/galaxy/commit/37242c8a7cbd4524bb7e585c0554… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-06-15 (Wed, 15 Jun 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/util/basic_util.py Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Commit: 06eeb8bafec6f6262041cabe7b34e57d4e1aaa7c https://github.com/galaxyproject/galaxy/commit/06eeb8bafec6f6262041cabe7b34… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-06-15 (Wed, 15 Jun 2016) Changed paths: M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M lib/galaxy/config.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/external_services/actions.py M lib/galaxy/external_services/parameters.py M lib/galaxy/external_services/service.py M lib/galaxy/forms/forms.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/model/__init__.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/web/security/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/external_services.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/repository_types/metadata.py M lib/tool_shed/util/basic_util.py M templates/webapps/galaxy/workflow/display.mako M templates/webapps/galaxy/workflow/sharing.mako A test-data/biom1_metadata_test.txt A test-data/input_taxonomy.biom1 A test/functional/tools/metadata_biom1.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml M test/unit/tools/test_select_parameters.py M tools/filters/axt_to_lav.py Log Message: ----------- Merge branch 'release_16.04' Compare: https://github.com/galaxyproject/galaxy/compare/5a97b8feac49...06eeb8bafec6

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[galaxyproject/galaxy] d95e9b: Refactor move_file() method
by GitHub 15 Jun '16

15 Jun '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: d95e9b840de5773337c80c612b790571e8229bfc https://github.com/galaxyproject/galaxy/commit/d95e9b840de5773337c80c612b79… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-06-09 (Thu, 09 Jun 2016) Changed paths: M lib/tool_shed/util/basic_util.py Log Message: ----------- Refactor move_file() method Commit: d38936bd8d9b3612dc0718859067e299651e6c86 https://github.com/galaxyproject/galaxy/commit/d38936bd8d9b3612dc0718859067… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-06-09 (Thu, 09 Jun 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Move the whole directory instead of element by element Fix #1947. Commit: 75cdec9b4baa0a003b6516d524c625bb6aaa07bb https://github.com/galaxyproject/galaxy/commit/75cdec9b4baa0a003b6516d524c6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-06-15 (Wed, 15 Jun 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/util/basic_util.py Log Message: ----------- Merge pull request #2479 from nsoranzo/release_16.01_fix_for_1947 [16.01] Fix move_directory_files tool dependency action when new_file_path is on a different filesystem Commit: 37242c8a7cbd4524bb7e585c05548023071c1339 https://github.com/galaxyproject/galaxy/commit/37242c8a7cbd4524bb7e585c0554… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-06-15 (Wed, 15 Jun 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/util/basic_util.py Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Compare: https://github.com/galaxyproject/galaxy/compare/7d962ee0cb6b...37242c8a7cbd

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