[galaxy-commits] [galaxyproject/galaxy] 2b97a6: History manager: prototype history contents as a s...

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2b97a654558c95aa3ebfee4d9521c59212e67d09 https://github.com/galaxyproject/galaxy/commit/2b97a654558c95aa3ebfee4d9521c... Author: Carl Eberhard <carlfeberhard@gmail.com> Date: 2015-07-27 (Mon, 27 Jul 2015) Changed paths: M lib/galaxy/managers/containers.py M lib/galaxy/managers/histories.py A lib/galaxy/managers/history_contents.py A test/unit/managers/test_HistoryContentsManager.py Log Message: ----------- History manager: prototype history contents as a separate manager - one that is a facade over the common/shared interfaces of the contained classes Commit: 7aace6dee0ddad8c0325b6ccc681f5b62035acb5 https://github.com/galaxyproject/galaxy/commit/7aace6dee0ddad8c0325b6ccc681f... Author: Carl Eberhard <carlfeberhard@gmail.com> Date: 2015-07-27 (Mon, 27 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/history/history-panel.js M client/galaxy/scripts/mvc/list/list-panel.js M lib/galaxy/managers/histories.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/web/framework/base.py M static/maps/mvc/history/history-panel.js.map M static/maps/mvc/list/list-panel.js.map M static/scripts/mvc/history/history-panel.js M static/scripts/mvc/list/list-panel.js Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into managers.history-contents Commit: c9a5ce7c28ef778fb68ce714806ee0e4cc5a16b3 https://github.com/galaxyproject/galaxy/commit/c9a5ce7c28ef778fb68ce714806ee... Author: Carl Eberhard <carlfeberhard@gmail.com> Date: 2015-07-27 (Mon, 27 Jul 2015) Changed paths: M lib/galaxy/managers/containers.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/history_contents.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- History contents: remove HistoryAsContainer mixin Commit: 2c03d5330f0a45bb00c042b5553fa4fab9c3768b https://github.com/galaxyproject/galaxy/commit/2c03d5330f0a45bb00c042b5553fa... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: A .ci/check_controller.sh A .ci/check_mako.sh M .ci/flake8_blacklist.txt A .ci/flake8_py3_wrapper.sh M .ci/flake8_wrapper.sh A .ci/py3_sources.txt M .gitignore A CODE_OF_CONDUCT.md M CONTRIBUTING.md M CONTRIBUTORS.md A Makefile M README.rst A client/.docker-build.sh A client/Dockerfile M client/GruntFile.js M client/README.md M client/bower.json A client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/apps/history-panel.js A client/galaxy/scripts/apps/login.js A client/galaxy/scripts/apps/tool-panel.js R client/galaxy/scripts/base.js R client/galaxy/scripts/galaxy-app-base.js R client/galaxy/scripts/galaxy.autocom_tagging.js R client/galaxy/scripts/galaxy.base.js R client/galaxy/scripts/galaxy.frame.js A client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.library.js R client/galaxy/scripts/galaxy.masthead.js R client/galaxy/scripts/galaxy.menu.js M client/galaxy/scripts/galaxy.pages.js R client/galaxy/scripts/galaxy.panels.js R client/galaxy/scripts/galaxy.tools.js R client/galaxy/scripts/galaxy.ui.scrollPanel.js A client/galaxy/scripts/layout/masthead.js A client/galaxy/scripts/layout/menu.js A client/galaxy/scripts/layout/modal.js A client/galaxy/scripts/layout/page.js A client/galaxy/scripts/layout/panel.js A client/galaxy/scripts/layout/scratchbook.js R client/galaxy/scripts/libs/IE/IE7.js R client/galaxy/scripts/libs/IE/IE8.js R client/galaxy/scripts/libs/IE/blank.gif R client/galaxy/scripts/libs/IE/excanvas.js R client/galaxy/scripts/libs/IE/ie7-recalc.js A client/galaxy/scripts/libs/backbone.js R client/galaxy/scripts/libs/backbone/backbone.js M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/libs/farbtastic.js A client/galaxy/scripts/libs/jquery.sparklines.js M client/galaxy/scripts/libs/jquery/jqtouch.js M client/galaxy/scripts/libs/jquery/jquery.dynatree.js M client/galaxy/scripts/libs/jquery/select2.js M 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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/sr_mapping/bfast_wrapper.xml M tools/sr_mapping/fastq_statistics.xml M tools/sr_mapping/mosaik.xml M tools/sr_mapping/srma_wrapper.xml M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tools/visualization/LAJ.xml M tox.ini Log Message: ----------- Merge remote-tracking branch 'origin/dev' into managers.history-contents Commit: 9aa977eda3fe236207908f7b3607af0bda9d8e82 https://github.com/galaxyproject/galaxy/commit/9aa977eda3fe236207908f7b3607a... 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Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-01-12 (Tue, 12 Jan 2016) Changed paths: M lib/galaxy/managers/history_contents.py M test/unit/managers/test_HistoryContentsManager.py Log Message: ----------- History contents manager: fix tests Commit: 8e4d3845fdc6c535912d5cbca85646b367890362 https://github.com/galaxyproject/galaxy/commit/8e4d3845fdc6c535912d5cbca8564... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/managers/containers.py M lib/galaxy/managers/history_contents.py M test/unit/managers/test_HistoryContentsManager.py Log Message: ----------- History contents manager: (an attempt to) clarify/simplify/clean up, re-implement default_order_by and respect it Commit: 28b8816f46d4619b396a13deb21f15135b020b7b https://github.com/galaxyproject/galaxy/commit/28b8816f46d4619b396a13deb21f1... 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Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M lib/galaxy/managers/containers.py M lib/galaxy/managers/history_contents.py M test/unit/managers/test_HistoryContentsManager.py Log Message: ----------- History contents manager: add tests, fix order_by defaulting, clarify filter getter name Commit: ee2c3cb82a410afeb33d5f21a2b05dbaab5d8f8f https://github.com/galaxyproject/galaxy/commit/ee2c3cb82a410afeb33d5f21a2b05... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M .gitignore M client/GruntFile.js M client/README.md M client/bower.json M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/layout/menu.js R client/galaxy/scripts/libs/handlebars.runtime.js M client/galaxy/scripts/mvc/base-mvc.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-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.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/dataset/states.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hda-model.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/hdca-model.js M client/galaxy/scripts/mvc/history/history-content-model.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-structure-view.js M client/galaxy/scripts/mvc/history/history-view-annotated.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/job-dag.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/mvc/user/user-model.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/onload.js R client/galaxy/scripts/templates/compiled/panel_section.js R client/galaxy/scripts/templates/compiled/tool_form.js R client/galaxy/scripts/templates/compiled/tool_link.js R client/galaxy/scripts/templates/compiled/tool_search.js R client/galaxy/scripts/templates/panel_section.handlebars R client/galaxy/scripts/templates/tool_form.handlebars R client/galaxy/scripts/templates/tool_link.handlebars R client/galaxy/scripts/templates/tool_search.handlebars M client/galaxy/style/less/base.less A client/galaxy/style/less/tour.less M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M client/grunt-tasks/install-libs.js M client/grunt-tasks/style.js R client/grunt-tasks/templates.js A client/grunt-tasks/webpack.js M client/package.json M client/webpack.config.js M config/galaxy.ini.sample A config/plugins/tours/core.scratchbook.yaml R config/plugins/visualizations/charts/static/build-app.js M config/plugins/visualizations/scatterplot/Gruntfile.js M config/plugins/visualizations/scatterplot/package.json R config/plugins/visualizations/scatterplot/src/handlebars/chartcontrol.handlebars R config/plugins/visualizations/scatterplot/src/handlebars/datacontrol.handlebars R config/plugins/visualizations/scatterplot/src/handlebars/editor.handlebars M config/plugins/visualizations/scatterplot/src/scatterplot-config-editor.js M config/plugins/visualizations/scatterplot/static/scatterplot-edit.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M lib/galaxy/config.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt 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/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/model/custom_types.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/output_actions.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/test.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/tools/wrappers.py M lib/galaxy/util/__init__.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/visualization/genomes.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/openid_manager.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/user.py M requirements.txt M run.sh M run_tests.sh M scripts/binary_compatibility.py M scripts/common_startup.sh M setup.cfg M static/maps/layout/menu.js.map R static/maps/libs/handlebars.runtime.js.map M static/maps/mvc/base-mvc.js.map M static/maps/mvc/collection/collection-li-edit.js.map 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/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-edit.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/dataset/states.js.map M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/history/hda-li-edit.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hda-model.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-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-structure-view.js.map M static/maps/mvc/history/history-view-annotated.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/job-dag.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/list/list-item.js.map M static/maps/mvc/list/list-view.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/tool/tools.js.map M static/maps/mvc/ui/ui-list.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/upload/upload-settings.js.map M static/maps/mvc/user/user-model.js.map M static/maps/mvc/user/user-quotameter.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/onload.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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/menu.js R static/scripts/libs/handlebars.runtime.js M static/scripts/mvc/base-mvc.js M static/scripts/mvc/collection/collection-li-edit.js 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/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-edit.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/dataset/states.js M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/history/hda-li-edit.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hda-model.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/history/hdca-model.js M static/scripts/mvc/history/history-content-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-structure-view.js M static/scripts/mvc/history/history-view-annotated.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/job-dag.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/list/list-item.js M static/scripts/mvc/list/list-view.js M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/tool/tools.js M static/scripts/mvc/ui/ui-list.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/upload-settings.js M static/scripts/mvc/user/user-model.js M static/scripts/mvc/user/user-quotameter.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/onload.js R static/scripts/templates/compiled/panel_section.js R static/scripts/templates/compiled/tool_form.js R static/scripts/templates/compiled/tool_link.js R static/scripts/templates/compiled/tool_search.js M static/style/blue/base.css M templates/base/base_panels.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/visualization/sweepster.mako M templates/webapps/tool_shed/base_panels.mako M test/api/helpers.py M test/api/test_workflows.py M test/api/workflows_format_2/interface.py M test/api/workflows_format_2/main.py M test/casperjs/casperjs_runner.py M test/functional/test_toolbox.py M test/functional/tools/output_action_change_format.xml M test/qunit/tests/masthead_tests.js A test/qunit/tests/ui_tests.html A test/qunit/tests/ui_tests.js M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_runner_local.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_execution.py M test/unit/unittest_utils/galaxy_mock.py A test/unit/web/framework/__init__.py A test/unit/web/framework/test_webapp.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into managers.history-contents Commit: 8ab1607b556b872ccedc6411790786f0a1b5db42 https://github.com/galaxyproject/galaxy/commit/8ab1607b556b872ccedc641179078... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M test/unit/managers/test_HistoryManager.py Log Message: ----------- Testing: remove unused imports in test_HistoryManager Commit: 48f45cb1853877f78eb917121c0da4fc7dc51c15 https://github.com/galaxyproject/galaxy/commit/48f45cb1853877f78eb917121c0da... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M test/unit/managers/test_HistoryContentsManager.py Log Message: ----------- Testing: remove egg import from test_HistoryContentsManager Commit: a162f91447dc47f89df42246ce313de1e27acd35 https://github.com/galaxyproject/galaxy/commit/a162f91447dc47f89df42246ce313... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-01-22 (Fri, 22 Jan 2016) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/managers/containers.py M lib/galaxy/managers/histories.py A lib/galaxy/managers/history_contents.py A test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- Merge pull request #1490 from carlfeberhard/managers.history-contents An attempt to add limit/offset to history contents Compare: https://github.com/galaxyproject/galaxy/compare/0f52600583e4...a162f91447dc