July 2016 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] fcbaf8: Fix an error with getting the size of an object fr...
by GitHub 28 Jul '16

28 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fcbaf8d17a20b1a910c07d154b690c28689fcb63 https://github.com/galaxyproject/galaxy/commit/fcbaf8d17a20b1a910c07d154b69… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M lib/galaxy/objectstore/azure_blob.py Log Message: ----------- Fix an error with getting the size of an object from Azure. Attempted to future-proof it if the library is fixed. Commit: 05c537e38478ab0c4a674120860b5601f59bbf4a https://github.com/galaxyproject/galaxy/commit/05c537e38478ab0c4a674120860b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M lib/galaxy/objectstore/azure_blob.py Log Message: ----------- Merge pull request #2678 from dannon/azure_followup Fix an error with getting the size of an object from Azure. Attempte… Compare: https://github.com/galaxyproject/galaxy/compare/0066847e0ac1...05c537e38478

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[galaxyproject/galaxy] 4f1228: Limit creation of multitudes of default, empty his...
by GitHub 28 Jul '16

28 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4f1228213886bc9ba2443133ed75936c81e855e9 https://github.com/galaxyproject/galaxy/commit/4f1228213886bc9ba2443133ed75… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Limit creation of multitudes of default, empty histories. This was happening for every new session using remote auth Commit: 0066847e0ac19632c3091ac3148069de3bb3855f https://github.com/galaxyproject/galaxy/commit/0066847e0ac19632c3091ac31480… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Merge pull request #2684 from dannon/remote_auth_many_histories Limit creation of multitudes of default, empty histories. Compare: https://github.com/galaxyproject/galaxy/compare/5c2402f83741...0066847e0ac1

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[galaxyproject/galaxy] 5c79e2: Unpin flake8 in py27-lint-imports* test environmen...
by GitHub 28 Jul '16

28 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5c79e27436446f064674f29bbcd08760a419506f https://github.com/galaxyproject/galaxy/commit/5c79e27436446f064674f29bbcd0… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M tox.ini Log Message: ----------- Unpin flake8 in py27-lint-imports* test environments flake8-import-order 0.9 has been released Commit: ec6e6255c109b5c6a9096fcd281a02e6559dd585 https://github.com/galaxyproject/galaxy/commit/ec6e6255c109b5c6a9096fcd281a… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M .ci/flake8_lint_include_list.txt Log Message: ----------- Extend the list to all files already passing Generated with: find . -path ./.venv -prune -o -path ./.tox -prune -o -path ./eggs -prune -o -path ./database -prune -o -name '*.py' -print0 | sort -z | xargs -0 -L 1 -I '{}' sh -c 'flake8 -qq {} && echo {}' | sed 's|^\./||' > .ci/flake8_lint_include_list.txt followed by some manual editing. Commit: 5c2402f837411972bb534918c4b72891a58a3816 https://github.com/galaxyproject/galaxy/commit/5c2402f837411972bb534918c4b7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M .ci/flake8_lint_include_list.txt M tox.ini Log Message: ----------- Merge pull request #2682 from nsoranzo/flake8-import-order Extend the list of files tested with flake8-import-order to all files already passing Compare: https://github.com/galaxyproject/galaxy/compare/e8f2a74f21e0...5c2402f83741

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[galaxyproject/galaxy] 497817: Break tool parameter help words if necessary
by GitHub 28 Jul '16

28 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4978173e4ed6b76ef4520f6d395788d2c14cf888 https://github.com/galaxyproject/galaxy/commit/4978173e4ed6b76ef4520f6d3957… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Break tool parameter help words if necessary Commit: addc15179744ee01c2f11b198ae4c5f60f25b27d https://github.com/galaxyproject/galaxy/commit/addc15179744ee01c2f11b198ae4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Use word-wrap instead of word-break to apply break-word due to better browser support Commit: e8f2a74f21e034831c562b965e6c0189b719df7e https://github.com/galaxyproject/galaxy/commit/e8f2a74f21e034831c562b965e6c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Merge pull request #2681 from guerler/help_word_break Break tool parameter help words if necessary Compare: https://github.com/galaxyproject/galaxy/compare/c096be04bd53...e8f2a74f21e0

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[galaxyproject/galaxy] 4a8310: Generate metadata in separate conda environment
by GitHub 28 Jul '16

28 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4a831033ed820e3f1220d9d326f8bd8079c390f9 https://github.com/galaxyproject/galaxy/commit/4a831033ed820e3f1220d9d326f8… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Generate metadata in separate conda environment Galaxy supports generating metadata in a separate command (enable beta_tool_command_isolation). This command has its own dependency resolution, that may interfere with thedependency resolution of the actual tool, if the same environment is being used. With this PR we create a new environment when resolving metadata dependencies with conda, that will be active only for metadata generation. Commit: 28da4b6371b23c69d15e7fc59473d4bde5639fde https://github.com/galaxyproject/galaxy/commit/28da4b6371b23c69d15e7fc59473… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Fix whitespace and comma use Commit: f8cf81d73693e5f075b6c9e612244221bbd6e5bb https://github.com/galaxyproject/galaxy/commit/f8cf81d73693e5f075b6c9e61224… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M .ci/flake8_blacklist.txt Log Message: ----------- Ignore .tox directory. Used to be ignored by default w/ flake8 apparently, but not anymore. Commit: f0024d64e15815dcb6c2ac027ed5fb2977651e64 https://github.com/galaxyproject/galaxy/commit/f0024d64e15815dcb6c2ac027ed5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/web/framework/helpers/__init__.py M test/base/driver_util.py Log Message: ----------- Apply @nsoranzo's fix for noqa changes (must end the line, comment comes before it) Commit: 8f978b8957f0cbc7e5d78ca3f3bce9e87e6e8f76 https://github.com/galaxyproject/galaxy/commit/8f978b8957f0cbc7e5d78ca3f3bc… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M .ci/flake8_blacklist.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/web/framework/helpers/__init__.py M test/base/driver_util.py Log Message: ----------- Merge pull request #2662 from jmchilton/backport_2253 [16.04] Backport #2253 as requested by Eagle Eyes Commit: 5d8d932425c879177c40a008a5a2ef3e45020b73 https://github.com/galaxyproject/galaxy/commit/5d8d932425c879177c40a008a5a2… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M tool-data/shared/ucsc/ucsc_build_sites.txt.sample Log Message: ----------- Add hg38 to main for ucsc_build_sites.txt.sample (cherry picked from commit 04b7d11f053e66b14232440e6ff534a62ff26666) Commit: e4ca3bf80fcab185e8ea3502926563707b047236 https://github.com/galaxyproject/galaxy/commit/e4ca3bf80fcab185e8ea35029265… Author: Enis Afgan <afgane(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M tool-data/shared/ucsc/ucsc_build_sites.txt.sample Log Message: ----------- Merge pull request #2673 from blankenberg/ucsc-hg38-display-16.04 [16.04] Add hg38 to main for ucsc_build_sites.txt.sample Commit: c096be04bd53c8184a4c5880c99abe02649e7570 https://github.com/galaxyproject/galaxy/commit/c096be04bd53c8184a4c5880c99a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/fdbaf437c9ba...c096be04bd53

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[galaxyproject/galaxy] 5d8d93: Add hg38 to main for ucsc_build_sites.txt.sample
by GitHub 28 Jul '16

28 Jul '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 5d8d932425c879177c40a008a5a2ef3e45020b73 https://github.com/galaxyproject/galaxy/commit/5d8d932425c879177c40a008a5a2… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M tool-data/shared/ucsc/ucsc_build_sites.txt.sample Log Message: ----------- Add hg38 to main for ucsc_build_sites.txt.sample (cherry picked from commit 04b7d11f053e66b14232440e6ff534a62ff26666) Commit: e4ca3bf80fcab185e8ea3502926563707b047236 https://github.com/galaxyproject/galaxy/commit/e4ca3bf80fcab185e8ea35029265… Author: Enis Afgan <afgane(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M tool-data/shared/ucsc/ucsc_build_sites.txt.sample Log Message: ----------- Merge pull request #2673 from blankenberg/ucsc-hg38-display-16.04 [16.04] Add hg38 to main for ucsc_build_sites.txt.sample Compare: https://github.com/galaxyproject/galaxy/compare/8f978b8957f0...e4ca3bf80fca

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[galaxyproject/galaxy] 8dbc35: Collections should be populated regardless of the ...
by GitHub 28 Jul '16

28 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8dbc35784e209c640f0c010077452f5c32be463c https://github.com/galaxyproject/galaxy/commit/8dbc35784e209c640f0c01007745… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Collections should be populated regardless of the availability of other values Commit: 25fd142667a716775f7230e5e38aadeb3365b9e9 https://github.com/galaxyproject/galaxy/commit/25fd142667a716775f7230e5e38a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Initialize empty other_values dictionary when populating collections Commit: fdbaf437c9bac1c9179347b3bc54093bcdc52ceb https://github.com/galaxyproject/galaxy/commit/fdbaf437c9bac1c9179347b3bc54… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #2672 from guerler/fix_populating_collections Properly populate collections regardless of context values Compare: https://github.com/galaxyproject/galaxy/compare/fed3665fcfa9...fdbaf437c9ba

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[galaxyproject/galaxy] 12a789: Adjust tests for 8cca7be
by GitHub 28 Jul '16

28 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 12a789f3e19c7ac02f9648461cb2cd3dbd2727eb https://github.com/galaxyproject/galaxy/commit/12a789f3e19c7ac02f9648461cb2… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py Log Message: ----------- Adjust tests for 8cca7be Commit: fed3665fcfa96809a00fb4d9b4dfe287123d84f3 https://github.com/galaxyproject/galaxy/commit/fed3665fcfa96809a00fb4d9b4df… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-28 (Thu, 28 Jul 2016) Changed paths: M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py Log Message: ----------- Merge pull request #2680 from mvdbeek/toolshed_test_fixes Fix broken toolshed tests with #2554 Compare: https://github.com/galaxyproject/galaxy/compare/c7caeb3c3959...fed3665fcfa9

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[galaxyproject/galaxy] ea36a6: first commit
by GitHub 28 Jul '16

28 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ea36a627e48d71a5ef3482be36d64b3a57c10235 https://github.com/galaxyproject/galaxy/commit/ea36a627e48d71a5ef3482be36d6… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-18 (Mon, 18 Jul 2016) Changed paths: A lib/galaxy/objectstore/azureObjectStore.py Log Message: ----------- first commit modeled off S3 adapter Commit: 596248ae0f2af5cb1a01dbb8de8f05c572c4bbcb https://github.com/galaxyproject/galaxy/commit/596248ae0f2af5cb1a01dbb8de8f… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-18 (Mon, 18 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/collection/collection-li.js 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/dataset/data.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-contents.js M config/plugins/visualizations/graphviz/config/graphviz.xml M config/plugins/visualizations/graphviz/static/js/graphVis.js M config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js M config/plugins/visualizations/graphviz/templates/graphviz.mako M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/managers/base.py M lib/galaxy/managers/users.py M lib/galaxy/security/validate_user_input.py M lib/galaxy/util/__init__.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/tag.py M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-view-edit.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/dataset/data.js.map M static/maps/mvc/history/hdca-li-edit.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/history/hdca-model.js.map M static/maps/mvc/history/history-contents.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/collection-li.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/dataset/data.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-contents.js M templates/admin/impersonate.mako M templates/ind_share_base.mako M test/api/test_users.py M test/unit/managers/test_UserManager.py M tools/stats/gsummary.xml Log Message: ----------- Merge branch 'dev' into azure-blob-objectstore Commit: c3a074faf044fa21e73ae060e4d5a1872d8b9475 https://github.com/galaxyproject/galaxy/commit/c3a074faf044fa21e73ae060e4d5… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-18 (Mon, 18 Jul 2016) Changed paths: M config/object_store_conf.xml.sample Log Message: ----------- added object_store_conf.xml.sample Commit: b217ecde14d80f211bc550cb56fa4524872e23f9 https://github.com/galaxyproject/galaxy/commit/b217ecde14d80f211bc550cb56fa… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/datatypes/data.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js A test/unit/datatypes/test_data.py Log Message: ----------- Merge remote-tracking branch 'galaxyproject/dev' into azure-blob-objectstore Commit: 0a49f17411dec1235226a8dc0fc7237bc4f6a40a https://github.com/galaxyproject/galaxy/commit/0a49f17411dec1235226a8dc0fc7… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-19 (Tue, 19 Jul 2016) Changed paths: M doc/source/lib/galaxy.objectstore.rst Log Message: ----------- Modified galaxy.objectstore.rst Not sure how RST works — would appreciate some guidance here. Commit: 3a3074134fd0bbdf81c269e127934d1c87b0d8bd https://github.com/galaxyproject/galaxy/commit/3a3074134fd0bbdf81c269e12793… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/objectstore/azureObjectStore.py Log Message: ----------- fixed most lint errors Commit: cb44eb372ef71d856804c3747e0e282e14176702 https://github.com/galaxyproject/galaxy/commit/cb44eb372ef71d856804c3747e0e… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M config/job_conf.xml.sample_advanced A config/tool_destinations.yml.sample M lib/galaxy/config.py M lib/galaxy/datatypes/data.py M lib/galaxy/dependencies/pinned-requirements.txt A lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/mapper.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py M templates/webapps/galaxy/history/grid.mako M test/api/test_workflows.py A test/functional/tools/output_filter_exception_1.xml M test/functional/tools/samples_tool_conf.xml A test/unit/jobs/dynamic_tool_destination/__init__.py A test/unit/jobs/dynamic_tool_destination/data/dest_fail.yml A test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml A test/unit/jobs/dynamic_tool_destination/data/test.empty A test/unit/jobs/dynamic_tool_destination/data/test.fasta A test/unit/jobs/dynamic_tool_destination/data/test1.full A test/unit/jobs/dynamic_tool_destination/data/test3.full A test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml A test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml A test/unit/jobs/dynamic_tool_destination/data/test_users.yml A test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml A test/unit/jobs/dynamic_tool_destination/mockGalaxy.py A test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py A test/unit/jobs/dynamic_tool_destination/ymltests.py M tools/stats/gsummary.xml Log Message: ----------- Merge remote-tracking branch 'galaxyproject/dev' into azure-blob-objectstore Commit: c668baeea5d4106e439ebbb39d406ccc1f4848f2 https://github.com/galaxyproject/galaxy/commit/c668baeea5d4106e439ebbb39d40… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: R lib/galaxy/objectstore/azureObjectStore.py A lib/galaxy/objectstore/azure_blob.py Log Message: ----------- better naming Commit: 8bc8e38b369115d9970586a24626d04b101c6952 https://github.com/galaxyproject/galaxy/commit/8bc8e38b369115d9970586a24626… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/objectstore/azure_blob.py Log Message: ----------- typo Commit: 4fa0c27bf1594a3f46209e3718d55fd7063bbbd9 https://github.com/galaxyproject/galaxy/commit/4fa0c27bf1594a3f46209e3718d5… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/objectstore/azure_blob.py Log Message: ----------- Another lint pass. Commit: 2405f558c8d3abc0cbbe1738208e682d9bc02502 https://github.com/galaxyproject/galaxy/commit/2405f558c8d3abc0cbbe1738208e… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/objectstore/azure_blob.py Log Message: ----------- Oops.. Commit: a2c5e33d021f61b0e2efa95b12fc6a9d3e7ae82e https://github.com/galaxyproject/galaxy/commit/a2c5e33d021f61b0e2efa95b12fc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/objectstore/azure_blob.py Log Message: ----------- Address minor azure objblob lint issues, and one UndefinedObject issue. Commit: ebe83e21bd25c5fc9d4c4f8018401e5967d5cd66 https://github.com/galaxyproject/galaxy/commit/ebe83e21bd25c5fc9d4c4f801840… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/objectstore/azure_blob.py Log Message: ----------- Merge pull request #1 from dannon/minor_azure_tweaks Address minor azure objblob lint issues, and one UndefinedObject issue. Commit: d9d549299171364576e141710637283176fd6dd4 https://github.com/galaxyproject/galaxy/commit/d9d549299171364576e141710637… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M config/object_store_conf.xml.sample Log Message: ----------- more consistent naming. Commit: 4a8a14d8cf593b84cc338062d7361140f8410851 https://github.com/galaxyproject/galaxy/commit/4a8a14d8cf593b84cc338062d736… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Merge remote-tracking branch 'galaxyproject/dev' into azure-blob-objectstore Commit: ca79c905f83aa20be3a598da94ec09919457511a https://github.com/galaxyproject/galaxy/commit/ca79c905f83aa20be3a598da94ec… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/azure_blob.py Log Message: ----------- oops again... Commit: 91081bf2802195f501595bca9a51b38b69c18669 https://github.com/galaxyproject/galaxy/commit/91081bf2802195f501595bca9a51… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- added dependency to azure Commit: 7dcc6374ccf9ce9903cc82f11f146a1f5aefdc87 https://github.com/galaxyproject/galaxy/commit/7dcc6374ccf9ce9903cc82f11f14… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-21 (Thu, 21 Jul 2016) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- oops =) Commit: d36162a389586ffa0d692a446be26c53b1e7741d https://github.com/galaxyproject/galaxy/commit/d36162a389586ffa0d692a446be2… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-22 (Fri, 22 Jul 2016) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- fixes the lint error I think. Commit: e59602fed14e0f7bea81309407e47e600a24a529 https://github.com/galaxyproject/galaxy/commit/e59602fed14e0f7bea81309407e4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- Update check_azure_storage check, read the object store config to detect stores. Commit: 3199217448f7646c660c954c66e989f4a2e224fb https://github.com/galaxyproject/galaxy/commit/3199217448f7646c660c954c66e9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- Remove debug print Commit: 0da66864e491e7b8b1a5454ee12a3db1ba52e9e1 https://github.com/galaxyproject/galaxy/commit/0da66864e491e7b8b1a5454ee12a… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- Merge pull request #2 from dannon/azure-blob-objectstore Fixes azure_blob detection for conditional dependency resolution Commit: 0b1730fe7f94875edf378dec629f692da66c8ad3 https://github.com/galaxyproject/galaxy/commit/0b1730fe7f94875edf378dec629f… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- trying this... Commit: e349aafe047ce0e419634b96c34acef8b60549af https://github.com/galaxyproject/galaxy/commit/e349aafe047ce0e419634b96c34a… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/objectstore/azure_blob.py Log Message: ----------- fix bug. Commit: 4dc8b7d8037defe9b29038ee05ab22b889cd2740 https://github.com/galaxyproject/galaxy/commit/4dc8b7d8037defe9b29038ee05ab… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/objectstore/azure_blob.py Log Message: ----------- clean things up a little... Commit: b4896bc341ab9d40a255c74a7a5fdeb0db37f72a https://github.com/galaxyproject/galaxy/commit/b4896bc341ab9d40a255c74a7a5f… Author: Alexander Lenail <alexander.lenail(a)tufts.edu> Date: 2016-07-26 (Tue, 26 Jul 2016) Changed paths: M lib/galaxy/objectstore/azure_blob.py Log Message: ----------- fix lint Commit: c7caeb3c3959e87e55e791aa4f87de63e71a9032 https://github.com/galaxyproject/galaxy/commit/c7caeb3c3959e87e55e791aa4f87… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M config/object_store_conf.xml.sample M doc/source/lib/galaxy.objectstore.rst M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/objectstore/__init__.py A lib/galaxy/objectstore/azure_blob.py Log Message: ----------- Merge branch 'azure-blob-objectstore' into dev Compare: https://github.com/galaxyproject/galaxy/compare/c4841b352140...c7caeb3c3959

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[galaxyproject/galaxy] 43f800: Modify persistent entry handling for select fields
by GitHub 27 Jul '16

27 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 43f800b56d3002248e42b4145df272a2ad572a7f https://github.com/galaxyproject/galaxy/commit/43f800b56d3002248e42b4145df2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M lib/galaxy/tools/parameters/basic.py M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.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/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Modify persistent entry handling for select fields Commit: 3dcc9adaaffa032e1adb57a42e9054ef8ddfe958 https://github.com/galaxyproject/galaxy/commit/3dcc9adaaffa032e1adb57a42e90… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js M static/maps/mvc/tool/tool-form.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/tool/tool-form.js Log Message: ----------- Improve robustness of error message display on tool execution Commit: b9a02150fef9007391e79521b0712f898ed657b9 https://github.com/galaxyproject/galaxy/commit/b9a02150fef9007391e79521b071… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M static/maps/mvc/ui/ui-select-default.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/ui/ui-select-default.js Log Message: ----------- Filter on the basis of select field values instead of all attributes Commit: c4841b35214083a9cabb51fd816fe7fac3d53684 https://github.com/galaxyproject/galaxy/commit/c4841b35214083a9cabb51fd816f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M lib/galaxy/tools/parameters/basic.py M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.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/tool/tool-form.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Merge pull request #2677 from guerler/update_select Fix dataset selector update when deleting history items Compare: https://github.com/galaxyproject/galaxy/compare/d7a1776a9105...c4841b352140

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