November 2015 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/infrastructure-playbook] 910371: Update common_roles
by GitHub 04 Nov '15

04 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 910371e63e950a4c737c0a6ddb67af72786556a9 https://github.com/galaxyproject/infrastructure-playbook/commit/910371e63e9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-04 (Wed, 04 Nov 2015) Changed paths: M common_roles Log Message: ----------- Update common_roles Commit: 9ccfe62f803c62f03fe66cbda8fbb7356133a91d https://github.com/galaxyproject/infrastructure-playbook/commit/9ccfe62f803… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-04 (Wed, 04 Nov 2015) Changed paths: A galaxyenv/host_vars/mjolnir0.galaxyproject.org.yml M galaxyenv/inventory A galaxyenv/secret_host_vars/mjolnir0.galaxyproject.org.yml M playbook.yml Log Message: ----------- Add mjolnir0, a starforge builder Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/cf8a746f22…

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[galaxyproject/galaxy] 4fc500: Fixes broken env-var declarations for tools with w...
by GitHub 04 Nov '15

04 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4fc500a5c9eaddbb1cb1ae420fe2b2c19d206446 https://github.com/galaxyproject/galaxy/commit/4fc500a5c9eaddbb1cb1ae420fe2… Author: youri <y.hoogstrate(a)erasmusmc.nl> Date: 2015-11-04 (Wed, 04 Nov 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Fixes broken env-var declarations for tools with weird chars in their name Commit: 8c0b9468a20ad20530ad290136fab351fca306d3 https://github.com/galaxyproject/galaxy/commit/8c0b9468a20ad20530ad290136fa… Author: youri <y.hoogstrate(a)erasmusmc.nl> Date: 2015-11-04 (Wed, 04 Nov 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Replacement of dots Commit: afa65f4d9a3684f4870815709e852927e34bfdb9 https://github.com/galaxyproject/galaxy/commit/afa65f4d9a3684f4870815709e85… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-11-04 (Wed, 04 Nov 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #1028 from yhoogstrate/step_handler_fix Fixes broken env-var declarations for tools with weird chars in their… Compare: https://github.com/galaxyproject/galaxy/compare/1649570e7806...afa65f4d9a36

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[galaxyproject/galaxy] 0fe684: Fix upload button style
by GitHub 04 Nov '15

04 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0fe684c688a86a0f8398191e66794f22adf5cf5d https://github.com/galaxyproject/galaxy/commit/0fe684c688a86a0f8398191e6679… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-04 (Wed, 04 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/upload-button.js.map M static/scripts/mvc/upload/upload-button.js M static/style/blue/base.css Log Message: ----------- Fix upload button style More fixes Commit: 1649570e7806315a235b4e9799a74e6e3e16887f https://github.com/galaxyproject/galaxy/commit/1649570e7806315a235b4e9799a7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-04 (Wed, 04 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/upload-button.js.map M static/scripts/mvc/upload/upload-button.js M static/style/blue/base.css Log Message: ----------- Rebuild client styles, merge. Compare: https://github.com/galaxyproject/galaxy/compare/4d05a5a3ed02...1649570e7806

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[galaxyproject/galaxy] 5c56ec: Fix style of labels in grids
by GitHub 04 Nov '15

04 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5c56ec8bc7ef580259982d5b775b468622464e57 https://github.com/galaxyproject/galaxy/commit/5c56ec8bc7ef580259982d5b775b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-04 (Wed, 04 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/style/less/base.less M static/maps/mvc/grid/grid-template.js.map M static/scripts/mvc/grid/grid-template.js M static/style/blue/base.css Log Message: ----------- Fix style of labels in grids Fix styles Pack styles Commit: 4d05a5a3ed029abca962288ca997823c52a46bcc https://github.com/galaxyproject/galaxy/commit/4d05a5a3ed029abca962288ca997… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-04 (Wed, 04 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/style/less/base.less M static/maps/mvc/grid/grid-template.js.map M static/scripts/mvc/grid/grid-template.js M static/style/blue/base.css Log Message: ----------- Merge pull request #1027 from guerler/fix_grids_000 Fix style of menu button labels in grids Compare: https://github.com/galaxyproject/galaxy/compare/53ee0f0a8913...4d05a5a3ed02

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[galaxyproject/galaxy] 5c7dd7: Refactor test dataset populator for reuse on jobs ...
by GitHub 03 Nov '15

03 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5c7dd75fd0d8ee6edce98e277e7ef6215f85f92c https://github.com/galaxyproject/galaxy/commit/5c7dd75fd0d8ee6edce98e277e7e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-02 (Mon, 02 Nov 2015) Changed paths: M test/api/helpers.py Log Message: ----------- Refactor test dataset populator for reuse on jobs without outputs. Commit: ac0cfbd2e32944d0f71eda877d1e8767a86d7cb3 https://github.com/galaxyproject/galaxy/commit/ac0cfbd2e32944d0f71eda877d1e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-02 (Mon, 02 Nov 2015) Changed paths: M run.sh Log Message: ----------- Add a quick shortcut for starting Galaxy with development tools. Start Galaxy using GALAXY_RUN_WITH_TEST_TOOLS=1 run.sh Enables beta tool formats (e.g. YAML, and CWL downstream), beta workflow modules, and the suite of Galaxy test tools used by testing framework. Commit: 53ee0f0a8913585e54d6ca59da79130196d31164 https://github.com/galaxyproject/galaxy/commit/53ee0f0a8913585e54d6ca59da79… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-03 (Tue, 03 Nov 2015) Changed paths: M run.sh M test/api/helpers.py Log Message: ----------- Merge pull request #1014 from jmchilton/cwl_util Two Small Tweaks from CWL Branch Compare: https://github.com/galaxyproject/galaxy/compare/593cb4074b5f...53ee0f0a8913

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[galaxyproject/galaxy] 2e21e0: Insert promises
by GitHub 03 Nov '15

03 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2e21e027b0b47b18ca7b1aac68d89ccbd16f2d2c https://github.com/galaxyproject/galaxy/commit/2e21e027b0b47b18ca7b1aac68d8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-02 (Mon, 02 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/utils/deferred.js M config/plugins/visualizations/charts/static/build-app.js M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js M config/plugins/visualizations/charts/static/charts/tools.js M config/plugins/visualizations/charts/static/views/group.js M config/plugins/visualizations/charts/static/views/viewport.js M static/maps/mvc/tools/tools-form-base.js.map M static/maps/utils/deferred.js.map M static/scripts/mvc/tools/tools-form-base.js M static/scripts/utils/deferred.js Log Message: ----------- Insert promises Revision Revise deferred class to use promises Update charts Fix comment Use resolve and reject properly Fix comments Fix comments Fix comments Fix comment Improve naming/comments Remove unnecessary queue handler Fix naming Commit: f1f5efe703cc25a63426fa5cf709ab410e19652f https://github.com/galaxyproject/galaxy/commit/f1f5efe703cc25a63426fa5cf709… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-02 (Mon, 02 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/app/app-view.js M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/app/app-view.js.map M static/scripts/mvc/app/app-analysis.js Log Message: ----------- Fix display call Fix config Fix naming Commit: cc4e8e4a34aa8ffdaa6fc357c226164571fd384d https://github.com/galaxyproject/galaxy/commit/cc4e8e4a34aa8ffdaa6fc357c226… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-02 (Mon, 02 Nov 2015) Changed paths: M .ci/flake8_blacklist.txt M .gitignore M client/galaxy/scripts/mvc/app/app-analysis.js A client/galaxy/scripts/mvc/app/app-login.js M client/galaxy/scripts/mvc/app/app-view.js M client/galaxy/style/less/base.less M doc/source/lib/galaxy.auth.providers.rst M doc/source/lib/galaxy.datatypes.rst A doc/source/lib/galaxy.dependencies.rst M doc/source/lib/galaxy.eggs.rst M doc/source/lib/galaxy.jobs.runners.rst M doc/source/lib/galaxy.rst M doc/source/lib/galaxy.tools.deps.resolvers.rst M doc/source/lib/galaxy.web.framework.middleware.rst M doc/source/lib/galaxy.webapps.galaxy.controllers.rst M doc/source/lib/galaxy.webapps.reports.controllers.rst M doc/source/lib/galaxy.webapps.rst M doc/source/lib/galaxy.webapps.tool_shed.api.rst M doc/source/lib/modules.rst R doc/source/lib/pkg_resources.rst M lib/galaxy/jobs/metrics/instrumenters/collectl.py A lib/galaxy/jobs/runners/util/drmaa/__init__.py A lib/galaxy/jobs/runners/util/retry.py A lib/galaxy/jobs/runners/util/sudo.py M lib/galaxy/managers/configuration.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/deps/dockerfiles.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/lint.py A lib/galaxy/tools/lint_util.py M lib/galaxy/tools/linters/command.py M lib/galaxy/tools/linters/help.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/linters/outputs.py A lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/linters/tests.py M lib/galaxy/tools/linters/top_level.py A lib/galaxy/tools/linters/xml_order.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/util/xml_macros.py M lib/galaxy/web/framework/webapp.py M lib/pulsar/client/transport/curl.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M scripts/tools/maf/check_loc_file.py M static/maps/galaxy.library.js.map M static/maps/mvc/app/app-analysis.js.map A static/maps/mvc/app/app-login.js.map M static/maps/mvc/app/app-view.js.map M static/scripts/galaxy.library.js M static/scripts/mvc/app/app-analysis.js A static/scripts/mvc/app/app-login.js M static/scripts/mvc/app/app-view.js M static/style/blue/base.css M static/welcome.html.sample M tools/data_source/data_source.py M tools/evolution/add_scores.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.py M tools/filters/axt_to_concat_fasta.py M tools/filters/axt_to_fasta.py M tools/filters/axt_to_lav.py M tools/filters/catWrapper.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/sort_gtf.py M tools/filters/gff_to_bed_converter.py M tools/filters/lav_to_bed.py M tools/filters/secure_hash_message_digest.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/maf/interval2maf.py M tools/maf/interval2maf.xml M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_split_by_species.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed_code.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/vcf_to_maf_customtrack.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into revise_promise_000 Commit: 142db64fb3ba6d694007485da8b64803db762309 https://github.com/galaxyproject/galaxy/commit/142db64fb3ba6d694007485da8b6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-03 (Tue, 03 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M static/maps/mvc/app/app-analysis.js.map M static/scripts/mvc/app/app-analysis.js Log Message: ----------- Use remove instead of empty if iframe is shown Commit: 593cb4074b5fc2d58685bae8831c621c16831e53 https://github.com/galaxyproject/galaxy/commit/593cb4074b5fc2d58685bae8831c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-03 (Tue, 03 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/app/app-view.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/utils/deferred.js M config/plugins/visualizations/charts/static/build-app.js M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js M config/plugins/visualizations/charts/static/charts/tools.js M config/plugins/visualizations/charts/static/views/group.js M config/plugins/visualizations/charts/static/views/viewport.js M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/app/app-view.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/utils/deferred.js.map M static/scripts/mvc/app/app-analysis.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/utils/deferred.js Log Message: ----------- Merge pull request #1018 from guerler/revise_promise_000 Revise deferred queue, use jQuery promises Compare: https://github.com/galaxyproject/galaxy/compare/86648d23e2fe...593cb4074b5f

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[galaxyproject/galaxy] a9ac91: Client logging: adapt metrics logger for optional ...
by GitHub 03 Nov '15

03 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a9ac9193c1bda03d45df7afd9aefec9898cf684b https://github.com/galaxyproject/galaxy/commit/a9ac9193c1bda03d45df7afd9aef… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-29 (Thu, 29 Oct 2015) Changed paths: M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/utils/add-logging.js M static/maps/galaxy-app-base.js.map M static/maps/utils/add-logging.js.map M static/scripts/galaxy-app-base.js M static/scripts/mvc/base-mvc.js M static/scripts/utils/add-logging.js M templates/galaxy_client_app.mako Log Message: ----------- Client logging: adapt metrics logger for optional debug logging Commit: d96fc60e1f84606a33f5b86a915bc9768a2eaa4e https://github.com/galaxyproject/galaxy/commit/d96fc60e1f84606a33f5b86a915b… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-29 (Thu, 29 Oct 2015) Changed paths: M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/utils/metrics-logger.js M static/maps/galaxy-app-base.js.map M static/maps/mvc/base-mvc.js.map M static/maps/utils/metrics-logger.js.map M static/scripts/galaxy-app-base.js M static/scripts/mvc/base-mvc.js M static/scripts/utils/metrics-logger.js Log Message: ----------- Client logging: allow focusing on one or more namespaces, add function to more easily namespace loggers Commit: 945f3690038fbe744465eb34074447c307aa467e https://github.com/galaxyproject/galaxy/commit/945f3690038fbe744465eb340744… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-29 (Thu, 29 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js 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-panel.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/dataset/dataset-choice.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/dataset/dataset-list.js M client/galaxy/scripts/mvc/dataset/dataset-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-panel.js M client/galaxy/scripts/mvc/history/history-structure-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/job/job-model.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-panel.js M client/galaxy/scripts/mvc/tags.js M client/galaxy/scripts/mvc/user/user-model.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M static/maps/mvc/citation/citation-model.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-panel.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/collection/pair-collection-creator.js.map M static/maps/mvc/dataset/dataset-choice.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/dataset/dataset-list.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/history/history-content-model.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-panel.js.map M static/maps/mvc/history/history-structure-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/job/job-model.js.map M static/maps/mvc/list/list-item.js.map M static/maps/mvc/list/list-panel.js.map M static/maps/mvc/tags.js.map M static/maps/mvc/user/user-model.js.map M static/maps/mvc/user/user-quotameter.js.map M static/maps/mvc/visualization/visualization-model.js.map M static/scripts/mvc/citation/citation-model.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-panel.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/dataset/dataset-list.js M static/scripts/mvc/dataset/dataset-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-panel.js M static/scripts/mvc/history/history-structure-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/list/list-item.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/user/user-model.js M static/scripts/mvc/user/user-quotameter.js Log Message: ----------- Client logging: namespace current loggables Commit: b75150ade7aad1a3e8e3b120e1f4a6d9f0929a23 https://github.com/galaxyproject/galaxy/commit/b75150ade7aad1a3e8e3b120e1f4… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-30 (Fri, 30 Oct 2015) Changed paths: M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-structure-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/user/user-model.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/utils/add-logging.js M client/galaxy/scripts/utils/metrics-logger.js M static/maps/galaxy-app-base.js.map M static/maps/mvc/base-mvc.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-structure-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/user/user-model.js.map M static/maps/mvc/user/user-quotameter.js.map M static/maps/utils/add-logging.js.map M static/maps/utils/metrics-logger.js.map M static/scripts/galaxy-app-base.js M static/scripts/mvc/base-mvc.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-structure-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/user/user-model.js M static/scripts/mvc/user/user-quotameter.js M static/scripts/utils/add-logging.js M static/scripts/utils/metrics-logger.js Log Message: ----------- Client logging: remove 'namespaced', allow 'log' to be added in the standard way (now that browsers are compat with this), simplify interface in the Galaxy object Commit: 0a8ea970030f9d7e106f9e55405af5d40929edd2 https://github.com/galaxyproject/galaxy/commit/0a8ea970030f9d7e106f9e55405a… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-30 (Fri, 30 Oct 2015) Changed paths: M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into logging: attempting to fix qunit failures Commit: b67601f74c9a0fa1dd07764dc8a4c4b0f70f512b https://github.com/galaxyproject/galaxy/commit/b67601f74c9a0fa1dd07764dc8a4… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-30 (Fri, 30 Oct 2015) Changed paths: M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/utils/add-logging.js M static/maps/galaxy-app-base.js.map M static/maps/galaxy.library.js.map M static/maps/utils/add-logging.js.map M static/scripts/galaxy-app-base.js M static/scripts/galaxy.library.js M static/scripts/utils/add-logging.js M test/qunit/tests/galaxy-app-base.js Log Message: ----------- Client logging: move logger assignment into Galaxy object, both Galaxy.user and all LoggableMixins will now respond to debugging, properly localize error messages Commit: 86648d23e2fe34893728c859c2559836eb55c752 https://github.com/galaxyproject/galaxy/commit/86648d23e2fe34893728c859c255… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-03 (Tue, 03 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js 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-panel.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/dataset/dataset-choice.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/dataset/dataset-list.js M client/galaxy/scripts/mvc/dataset/dataset-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-panel.js M client/galaxy/scripts/mvc/history/history-structure-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/job/job-model.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-panel.js M client/galaxy/scripts/mvc/tags.js M client/galaxy/scripts/mvc/user/user-model.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/utils/add-logging.js M client/galaxy/scripts/utils/metrics-logger.js M static/maps/galaxy-app-base.js.map M static/maps/mvc/base-mvc.js.map M static/maps/mvc/citation/citation-model.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-panel.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/collection/pair-collection-creator.js.map M static/maps/mvc/dataset/dataset-choice.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/dataset/dataset-list.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/history/history-content-model.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-panel.js.map M static/maps/mvc/history/history-structure-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/job/job-model.js.map M static/maps/mvc/list/list-item.js.map M static/maps/mvc/list/list-panel.js.map M static/maps/mvc/tags.js.map M static/maps/mvc/user/user-model.js.map M static/maps/mvc/user/user-quotameter.js.map M static/maps/mvc/visualization/visualization-model.js.map M static/maps/utils/add-logging.js.map M static/maps/utils/metrics-logger.js.map M static/scripts/galaxy-app-base.js M static/scripts/mvc/base-mvc.js M static/scripts/mvc/citation/citation-model.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-panel.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/dataset/dataset-list.js M static/scripts/mvc/dataset/dataset-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-panel.js M static/scripts/mvc/history/history-structure-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/list/list-item.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/user/user-model.js M static/scripts/mvc/user/user-quotameter.js M static/scripts/utils/add-logging.js M static/scripts/utils/metrics-logger.js M templates/galaxy_client_app.mako M test/qunit/tests/galaxy-app-base.js Log Message: ----------- Merge pull request #1011 from carlfeberhard/logging Client side logging Compare: https://github.com/galaxyproject/galaxy/compare/9fd0bd1cc112...86648d23e2fe

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[galaxyproject/galaxy] 9e0973: Labels for individual tools in tool panel.
by GitHub 03 Nov '15

03 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9e0973d7203ba36d5f3f37357d6cea6e603ba465 https://github.com/galaxyproject/galaxy/commit/9e0973d7203ba36d5f3f37357d6c… Author: James Taylor <james(a)jamestaylor.org> Date: 2015-10-31 (Sat, 31 Oct 2015) Changed paths: M client/galaxy/scripts/templates/compiled/tool_link.js M client/galaxy/scripts/templates/tool_link.handlebars M client/galaxy/style/less/base.less M client/galaxy/style/less/bootstrap.less M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M static/maps/galaxy.library.js.map M static/maps/templates/compiled/tool_link.js.map M static/scripts/galaxy.library.js M static/scripts/templates/compiled/tool_link.js M static/style/blue/base.css Log Message: ----------- Labels for individual tools in tool panel. Allow one or more labels to be attached to a tool in the tool panel. These will be rendered to the right of the tool's link using the boostrap label style. Styles for specific labels can be defined in CSS, specific colored labels for "new" and "beta" are defined. Commit: f920dec0c277e8301bf8392d638757a70a441dc7 https://github.com/galaxyproject/galaxy/commit/f920dec0c277e8301bf8392d6387… Author: James Taylor <james(a)jamestaylor.org> Date: 2015-10-31 (Sat, 31 Oct 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/search/__init__.py Log Message: ----------- Make toolbox searchable by tool labels. Commit: 9fd0bd1cc112811b10a9a16ae47bf76eef6eaaff https://github.com/galaxyproject/galaxy/commit/9fd0bd1cc112811b10a9a16ae47b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-03 (Tue, 03 Nov 2015) Changed paths: M client/galaxy/scripts/templates/compiled/tool_link.js M client/galaxy/scripts/templates/tool_link.handlebars M client/galaxy/style/less/base.less M client/galaxy/style/less/bootstrap.less M lib/galaxy/tools/__init__.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/toolbox/base.py M static/maps/templates/compiled/tool_link.js.map M static/scripts/templates/compiled/tool_link.js M static/style/blue/base.css Log Message: ----------- Manual merge and rebuild due to conflict. Compare: https://github.com/galaxyproject/galaxy/compare/269ed53fcdc6...9fd0bd1cc112

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[galaxyproject/galaxy] a0f65d: Apply stricter flake8 rules for the directories sh...
by GitHub 03 Nov '15

03 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a0f65d02866a463f9bdbf94919208212a9e441d0 https://github.com/galaxyproject/galaxy/commit/a0f65d02866a463f9bdbf9491920… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-10-30 (Fri, 30 Oct 2015) Changed paths: M .ci/flake8_wrapper.sh Log Message: ----------- Apply stricter flake8 rules for the directories shared with Pulsar Commit: 269ed53fcdc68854a35a995c6793435d45f9d0e3 https://github.com/galaxyproject/galaxy/commit/269ed53fcdc68854a35a995c6793… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-03 (Tue, 03 Nov 2015) Changed paths: M .ci/flake8_wrapper.sh Log Message: ----------- Merge pull request #1010 from nsoranzo/flake8_fixes Apply stricter flake8 rules for the directories shared with Pulsar Compare: https://github.com/galaxyproject/galaxy/compare/c78898932dac...269ed53fcdc6

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[galaxyproject/galaxy] 0e6033: Replace remaining print statements with log.*
by GitHub 03 Nov '15

03 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0e60332f449609a43a49b7d33ec64bf53663befd https://github.com/galaxyproject/galaxy/commit/0e60332f449609a43a49b7d33ec6… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-29 (Thu, 29 Oct 2015) Changed paths: M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/model/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/reports/app.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/hg_util.py Log Message: ----------- Replace remaining print statements with log.* Commit: 5396426609b334c4fb68eb1a04baf3426e957033 https://github.com/galaxyproject/galaxy/commit/5396426609b334c4fb68eb1a04ba… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-30 (Fri, 30 Oct 2015) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/tool_shed/app.py M lib/tool_shed/galaxy_install/tool_migration_manager.py Log Message: ----------- Fix flake8 errors, @nsoranzo Commit: c78898932dac835f07515cd291aeab37b4eb1b0c https://github.com/galaxyproject/galaxy/commit/c78898932dac835f07515cd291ae… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-03 (Tue, 03 Nov 2015) Changed paths: M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/model/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/reports/app.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/hg_util.py Log Message: ----------- Merge pull request #1009 from erasche/print-logging Replace remaining print statements with log.* Compare: https://github.com/galaxyproject/galaxy/compare/99319f59c887...c78898932dac

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