Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3084e192cb9553f82910aa2cac1187d793b2c5f1 https://github.com/galaxyproject/galaxy/commit/3084e192cb9553f82910aa2cac118... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-05-22 (Mon, 22 May 2017)

Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/managers/collections_util.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/buildapp.py M test/api/test_dataset_collections.py

Log Message: ----------- Add API route for downloading entire collections

Entire collections can now be downloaded as tarballs. I have used the StreamBall class from galaxy.utils, so archives start downloading immediately.

The collection structure is mapped onto a directory struture, where each level of a collection is a directory in the archive. Collections of BAM files are included alongside their .bai indices, and composite datatype are supported as well.

API tests for downloading list, paired and list:paired collections are included.

Currently collection elements that are not in the OK status will be skipped, so we should probably hide the download button if not all collection elements are in a final state.

Commit: 1093b614427f21986068e3fc609099e1573b6c4f https://github.com/galaxyproject/galaxy/commit/1093b614427f21986068e3fc60909... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-05-22 (Mon, 22 May 2017)

Changed paths: M client/galaxy/scripts/mvc/collection/collection-view.js M static/maps/mvc/collection/collection-view.js.map M static/scripts/bundled/admin.bundled.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.map M static/scripts/mvc/collection/collection-view.js

Log Message: ----------- Add download button for collections

Commit: 9db1cc455d48e0b74e3db6b1f39b623297f9b453 https://github.com/galaxyproject/galaxy/commit/9db1cc455d48e0b74e3db6b1f39b6... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-05-22 (Mon, 22 May 2017)

Changed paths: M test/api/test_dataset_collections.py M test/base/populators.py

Log Message: ----------- Fix the API tests for collection downloads

by waiting for the datasets to become ready.

Commit: 7527609e60a7775b705262a1562c969910b65a91 https://github.com/galaxyproject/galaxy/commit/7527609e60a7775b705262a1562c9... Author: mvdbeek m.vandenbeek@gmail.com Date: 2017-05-23 (Tue, 23 May 2017)

Changed paths: M test/api/test_dataset_collections.py

Log Message: ----------- Set assert_ok to true when wiaiting for datasets to become ready

Commit: 00de5b9f9a129805636760f0e0a88cd6cdfc9108 https://github.com/galaxyproject/galaxy/commit/00de5b9f9a129805636760f0e0a88... Author: John Chilton jmchilton@gmail.com Date: 2017-06-05 (Mon, 05 Jun 2017)

Changed paths: M .ci/flake8_lint_include_list.txt M CONTRIBUTORS.md M README.rst M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js A client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/style/less/base.less M client/webpack.config.js M config/job_conf.xml.sample_advanced M contrib/galaxy.debian-init M contrib/galaxy_supervisor.conf M doc/Makefile R doc/patch.py M doc/source/admin/authentication.md M doc/source/admin/special_topics/mulled_containers.rst R doc/source/api/api.rst R doc/source/api/ts_api.rst M doc/source/dev/build_a_job_runner.rst M doc/source/lib/galaxy.actions.rst M doc/source/lib/galaxy.auth.providers.rst M doc/source/lib/galaxy.auth.rst A doc/source/lib/galaxy.containers.rst M doc/source/lib/galaxy.dataset_collections.rst M doc/source/lib/galaxy.dataset_collections.types.rst M doc/source/lib/galaxy.datatypes.converters.rst M doc/source/lib/galaxy.datatypes.dataproviders.rst M doc/source/lib/galaxy.datatypes.display_applications.rst M doc/source/lib/galaxy.datatypes.rst M doc/source/lib/galaxy.datatypes.util.rst M doc/source/lib/galaxy.dependencies.rst M doc/source/lib/galaxy.eggs.rst M doc/source/lib/galaxy.exceptions.rst M doc/source/lib/galaxy.external_services.result_handlers.rst M doc/source/lib/galaxy.external_services.rst M doc/source/lib/galaxy.forms.rst M doc/source/lib/galaxy.jobs.actions.rst M doc/source/lib/galaxy.jobs.deferred.rst M doc/source/lib/galaxy.jobs.metrics.collectl.rst M doc/source/lib/galaxy.jobs.metrics.instrumenters.rst M doc/source/lib/galaxy.jobs.metrics.rst M doc/source/lib/galaxy.jobs.rst M doc/source/lib/galaxy.jobs.runners.rst M doc/source/lib/galaxy.jobs.runners.state_handlers.rst M doc/source/lib/galaxy.jobs.runners.util.cli.job.rst M doc/source/lib/galaxy.jobs.runners.util.cli.rst M doc/source/lib/galaxy.jobs.runners.util.cli.shell.rst M doc/source/lib/galaxy.jobs.runners.util.condor.rst A doc/source/lib/galaxy.jobs.runners.util.drmaa.rst M doc/source/lib/galaxy.jobs.runners.util.job_script.rst M doc/source/lib/galaxy.jobs.runners.util.rst M doc/source/lib/galaxy.jobs.splitters.rst M doc/source/lib/galaxy.managers.rst M doc/source/lib/galaxy.model.migrate.rst M doc/source/lib/galaxy.model.orm.rst M doc/source/lib/galaxy.model.rst M doc/source/lib/galaxy.model.tool_shed_install.migrate.rst M doc/source/lib/galaxy.model.tool_shed_install.rst M doc/source/lib/galaxy.objectstore.rst M doc/source/lib/galaxy.openid.rst M doc/source/lib/galaxy.quota.rst M doc/source/lib/galaxy.rst M doc/source/lib/galaxy.sample_tracking.rst M doc/source/lib/galaxy.security.rst R doc/source/lib/galaxy.tags.rst M doc/source/lib/galaxy.tools.actions.rst A doc/source/lib/galaxy.tools.cwl.rst M doc/source/lib/galaxy.tools.data.rst M doc/source/lib/galaxy.tools.data_manager.rst A doc/source/lib/galaxy.tools.deps.container_resolvers.rst A doc/source/lib/galaxy.tools.deps.mulled.rst M doc/source/lib/galaxy.tools.deps.resolvers.rst M doc/source/lib/galaxy.tools.deps.rst M doc/source/lib/galaxy.tools.filters.rst M doc/source/lib/galaxy.tools.imp_exp.rst M doc/source/lib/galaxy.tools.linters.rst A doc/source/lib/galaxy.tools.locations.rst M doc/source/lib/galaxy.tools.parameters.rst M doc/source/lib/galaxy.tools.parser.rst M doc/source/lib/galaxy.tools.rst M doc/source/lib/galaxy.tools.search.rst M doc/source/lib/galaxy.tools.toolbox.filters.rst M doc/source/lib/galaxy.tools.toolbox.lineages.rst M doc/source/lib/galaxy.tools.toolbox.rst M doc/source/lib/galaxy.tools.util.galaxyops.rst M doc/source/lib/galaxy.tools.util.rst A doc/source/lib/galaxy.tools.verify.asserts.rst A doc/source/lib/galaxy.tools.verify.rst A doc/source/lib/galaxy.tours.rst M doc/source/lib/galaxy.util.backports.rst M doc/source/lib/galaxy.util.log.rst M doc/source/lib/galaxy.util.pastescript.rst M doc/source/lib/galaxy.util.rst M doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst M doc/source/lib/galaxy.visualization.data_providers.rst M doc/source/lib/galaxy.visualization.genome.rst M doc/source/lib/galaxy.visualization.plugins.rst M doc/source/lib/galaxy.visualization.rst M doc/source/lib/galaxy.visualization.tracks.rst M doc/source/lib/galaxy.web.base.controllers.rst M doc/source/lib/galaxy.web.base.rst M doc/source/lib/galaxy.web.framework.helpers.rst M doc/source/lib/galaxy.web.framework.middleware.rst M doc/source/lib/galaxy.web.framework.rst M doc/source/lib/galaxy.web.proxy.rst M doc/source/lib/galaxy.web.rst M doc/source/lib/galaxy.web.security.rst A doc/source/lib/galaxy.web.stack.rst A 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lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml M lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml M lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml M lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml M lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml M lib/galaxy/datatypes/converters/mol_to_cml_converter.xml M lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml M lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml M lib/galaxy/datatypes/converters/mol_to_smi_converter.xml M lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml M lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml M lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml M lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml M lib/galaxy/datatypes/converters/smi_to_cml_converter.xml M lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml M lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml M lib/galaxy/datatypes/converters/smi_to_mol_converter.xml M lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml M lib/galaxy/datatypes/converters/smi_to_smi_converter.xml M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/managers/collections.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/xsd/README.md M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/compression_utils.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/metadata/metadata_generator.py M scripts/bootstrap_history.py M static/maps/layout/menu.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/tool/tool-form-composite.js.map A static/maps/mvc/workflow/workflow-configure-menu.js.map M static/maps/mvc/workflow/workflow.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/layout/menu.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/tool/tool-form-composite.js A static/scripts/mvc/workflow/workflow-configure-menu.js M static/scripts/mvc/workflow/workflow.js M static/style/blue/base.css M static/welcome.html.sample M templates/grid_base.mako R templates/webapps/galaxy/page/list_published.mako R templates/webapps/galaxy/workflow/configure_menu.mako M test/functional/tools/sample_datatypes_conf.xml M test/qunit/test-data/bootstrapped.js M test/qunit/tests/galaxy-app-base.js

Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into download_collection

Commit: 9d1a382f8642959fd157b9695cca52ac056d2d81 https://github.com/galaxyproject/galaxy/commit/9d1a382f8642959fd157b9695cca5... Author: John Chilton jmchilton@gmail.com Date: 2017-06-05 (Mon, 05 Jun 2017)

Changed paths: M client/galaxy/scripts/mvc/collection/collection-view.js M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/managers/collections_util.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/collection/collection-view.js.map M static/scripts/bundled/admin.bundled.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.map M static/scripts/mvc/collection/collection-view.js M test/api/test_dataset_collections.py M test/base/populators.py

Log Message: ----------- Merge pull request #4098 from mvdbeek/download_collection

Add possibility for downloading entire collections

Compare: https://github.com/galaxyproject/galaxy/compare/294c1d115413...9d1a382f8642