Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 35b7c7788ac439f6ff3ae383aa910545c7ee85ae https://github.com/galaxyproject/galaxy/commit/35b7c7788ac439f6ff3ae383aa910... Author: Carl Eberhard carlfeberhard@gmail.com Date: 2015-04-21 (Tue, 21 Apr 2015)

Changed paths: M lib/galaxy/web/framework/base.py A lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/webapps/galaxy/buildapp.py A test/api/test_api_batch.py A test/casperjs/api-batch-tests.js

Log Message: ----------- API, batch: initial commit

Commit: 5dcc4e8e3a071e979503a0172543876f11984a17 https://github.com/galaxyproject/galaxy/commit/5dcc4e8e3a071e979503a01725438... Author: Carl Eberhard carlfeberhard@gmail.com Date: 2015-04-22 (Wed, 22 Apr 2015)

Changed paths: M lib/galaxy/web/framework/middleware/batch.py M test/api/test_api_batch.py M test/casperjs/api-batch-tests.js

Log Message: ----------- API, batch: handle bad routes

Commit: 09bcb7441c62c890abf799a93411aa9c3b79891e https://github.com/galaxyproject/galaxy/commit/09bcb7441c62c890abf799a93411a... Author: Carl Eberhard carlfeberhard@gmail.com Date: 2015-04-22 (Wed, 22 Apr 2015)

Changed paths: M lib/galaxy/web/framework/middleware/batch.py

Log Message: ----------- API, batch: properly import paste

Commit: 8fb10a5c9a5316552ed3f8f83ecc58592f44b052 https://github.com/galaxyproject/galaxy/commit/8fb10a5c9a5316552ed3f8f83ecc5... Author: Carl Eberhard carlfeberhard@gmail.com Date: 2015-04-22 (Wed, 22 Apr 2015)

Changed paths: M lib/galaxy/web/framework/middleware/batch.py M test/api/test_api_batch.py M test/casperjs/api-batch-tests.js

Log Message: ----------- API, batch: test errored calls

Commit: 1dc0876cdd8a5674cdcea0df506ecc65dc02a5eb https://github.com/galaxyproject/galaxy/commit/1dc0876cdd8a5674cdcea0df506ec... Author: Carl Eberhard carlfeberhard@gmail.com Date: 2015-07-31 (Fri, 31 Jul 2015)

Changed paths: A .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh R .ci/pep8_sources.txt M .gitignore M .travis.yml M CONTRIBUTING.md A CONTRIBUTORS.md M LICENSE.txt M README.rst M client/GruntFile.js M client/README.md M client/bower.json M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.masthead.js R client/galaxy/scripts/galaxy.workflow_editor.canvas.js R client/galaxy/scripts/galaxy.workflows.js M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/libs/handlebars.runtime.js M client/galaxy/scripts/libs/jquery/jquery.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/libs/require.js M client/galaxy/scripts/mvc/collection/collection-model.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/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-section.js M client/galaxy/scripts/mvc/form/form-view.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-panel-annotated.js M client/galaxy/scripts/mvc/history/history-panel-edit.js M client/galaxy/scripts/mvc/history/history-panel.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/list/list-panel.js M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-form-workflow.js M client/galaxy/scripts/mvc/tools/tools-template.js A 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client/package.json A client/toolshed/scripts/mvc/groups/group-detail-view.js A client/toolshed/scripts/mvc/groups/group-list-view.js A client/toolshed/scripts/mvc/groups/group-listrow-view.js A client/toolshed/scripts/mvc/groups/group-model.js A client/toolshed/scripts/toolshed.groups.js M config/auth_conf.xml.sample M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/object_store_conf.xml.sample M config/plugins/interactive_environments/common/templates/ie.mako M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/ipython/config/ipython.xml M config/plugins/interactive_environments/ipython/templates/ipython.mako M config/plugins/interactive_environments/ipython/templates/notebook.ipynb A config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample A config/plugins/interactive_environments/rstudio/config/rstudio.xml A 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config/plugins/visualizations/charts/templates/charts.mako M config/plugins/visualizations/circster/config/circster.xml A config/plugins/visualizations/common/templates/script_entry_point.mako M config/plugins/visualizations/common/templates/visualization_base.mako M config/plugins/visualizations/graphview/config/graphview.xml M config/plugins/visualizations/phyloviz/config/phyloviz.xml M config/plugins/visualizations/scatterplot/config/scatterplot.xml M config/plugins/visualizations/scatterplot/src/scatterplot-display.js M config/plugins/visualizations/scatterplot/static/scatterplot-edit.js M config/plugins/visualizations/sweepster/config/sweepster.xml M config/plugins/visualizations/trackster/config/trackster.xml M config/plugins/visualizations/visualization.dtd M config/tool_conf.xml.sample M config/tool_shed.ini.sample M contrib/nagios/check_galaxy.py M cron/add_manual_builds.py M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M display_applications/ensembl/ensembl_bam.xml M display_applications/ensembl/ensembl_gff.xml M display_applications/ensembl/ensembl_interval_as_bed.xml M display_applications/gbrowse/gbrowse_gff.xml M display_applications/gbrowse/gbrowse_interval_as_bed.xml M display_applications/gbrowse/gbrowse_wig.xml M display_applications/igb/bam.xml M display_applications/igb/bb.xml M display_applications/igb/bed.xml M display_applications/igb/bedgraph.xml M display_applications/igb/bigwig.xml M display_applications/igb/gtf.xml M display_applications/igb/wig.xml M display_applications/igv/bam.xml M display_applications/igv/gff.xml A display_applications/igv/interval_as_bed.xml M display_applications/igv/vcf.xml M display_applications/rviewer/bed.xml M display_applications/rviewer/vcf.xml M doc/patch.py A doc/source/_static/style.css A doc/source/_templates/layout.html A doc/source/api_doc.rst M doc/source/conf.py M doc/source/index.rst R doc/source/lib/fpconst.rst M 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Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into api.batch

Commit: 0b6397ec5c69d73b8b1e6be6e1518b88915e5103 https://github.com/galaxyproject/galaxy/commit/0b6397ec5c69d73b8b1e6be6e1518... Author: carlfeberhard carlfeberhard@gmail.com Date: 2015-12-18 (Fri, 18 Dec 2015)

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Log Message: ----------- Merge remote-tracking branch 'origin/dev' into api.batch

Commit: 69de8d58deda7e1a627e21581e7f14a39e114847 https://github.com/galaxyproject/galaxy/commit/69de8d58deda7e1a627e21581e7f1... Author: carlfeberhard carlfeberhard@gmail.com Date: 2016-02-10 (Wed, 10 Feb 2016)

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tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py M tools/phenotype_association/linkToDavid.xml M tools/stats/aggregate_scores_in_intervals.py M tox.ini

Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into api.batch

Commit: 50b065a50adb4403ecf46f367e8b6960c586777d https://github.com/galaxyproject/galaxy/commit/50b065a50adb4403ecf46f367e8b6... Author: carlfeberhard carlfeberhard@gmail.com Date: 2016-02-17 (Wed, 17 Feb 2016)

Changed paths: M .ci/flake8_blacklist.txt M config/tool_conf.xml.sample M lib/galaxy/datatypes/text.py M lib/galaxy/managers/base.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdas.py A lib/galaxy/managers/hdcas.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/history_contents.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/wrappers.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/workflow/modules.py M templates/show_params.mako A test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M tools/data_source/fetch.py M tools/data_source/genbank.py M tools/data_source/hbvar_filter.py M tools/data_source/import.py M tools/data_source/microbial_import.py M tools/data_source/microbial_import_code.py M tools/filters/axt_to_lav_code.py M tools/filters/bed_to_gff_converter.py M tools/filters/convert_characters.py M tools/filters/gff/gtf_filter_by_attribute_values_list.py M tools/filters/grep.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/lav_to_bed_code.py M tools/filters/mergeCols.py M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.py M tools/filters/sff_extract.py M tools/filters/sorter.py M tools/filters/trimmer.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/filters/uniq.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py M tools/meme/fimo_wrapper.py M tools/metag_tools/blat_wrapper.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/plotting/bar_chart.py R tools/plotting/plot_filter.py R tools/plotting/plotter.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velvetg_wrapper.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/sr_mapping/srma_wrapper.py M tools/sr_mapping/srma_wrapper.xml R tools/validation/fix_errors.py R tools/validation/fix_errors.xml R tools/validation/fix_errors_code.py R tools/validation/validate.py M tools/visualization/LAJ.py M tools/visualization/LAJ_code.py

Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into api.batch

Commit: 7e8537b4697fd6f8b459e3ffe7f6a25ebdddb912 https://github.com/galaxyproject/galaxy/commit/7e8537b4697fd6f8b459e3ffe7f6a... Author: carlfeberhard carlfeberhard@gmail.com Date: 2016-02-17 (Wed, 17 Feb 2016)

Changed paths: M lib/galaxy/web/framework/middleware/batch.py

Log Message: ----------- API, batch: update for newer webob

Commit: b9744906aa4eb020ce84896a735983856d05b482 https://github.com/galaxyproject/galaxy/commit/b9744906aa4eb020ce84896a73598... Author: carlfeberhard carlfeberhard@gmail.com Date: 2016-03-07 (Mon, 07 Mar 2016)

Changed paths: M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/webapps/galaxy/buildapp.py M test/api/test_api_batch.py

Log Message: ----------- API, batch: remove simplejson refs, fix linting errors

Commit: 60936120fb27b1e6242551e55a868bf57793f3f8 https://github.com/galaxyproject/galaxy/commit/60936120fb27b1e6242551e55a868... Author: carlfeberhard carlfeberhard@gmail.com Date: 2016-03-07 (Mon, 07 Mar 2016)

Changed paths: M .ci/flake8_blacklist.txt M .ci/py3_sources.txt M .travis.yml M Makefile M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/popup-menu.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/onload.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/base.less M client/galaxy/style/less/fontawesome/core.less M client/galaxy/style/less/library.less M client/galaxy/style/less/ui/icon-btn.less M client/grunt-tasks/style.js M client/package.json M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/tool_conf.xml.main M create_db.sh M doc/source/project/organization.rst M doc/source/releases/16.01.rst M doc/source/releases/16.01_announce.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/display_applications/application.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/external_services/result_handlers/basic.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/deferred/data_transfer.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/context.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/taggable.py M lib/galaxy/managers/tags.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/metadata.py M lib/galaxy/model/search.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/cwl/__init__.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parameters/sanitize.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/test.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/util/dbkeys.py M lib/galaxy/util/json.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/visualization/data_providers/basic.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/data_providers/registry.py M lib/galaxy/visualization/genomes.py M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/resource_parser.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/form_builder.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/translogger.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/tag.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/api/categories.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/users.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webapps/tool_shed/model/mapping.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/render.py M lib/galaxy/workflow/run.py M lib/galaxy_utils/sequence/fasta.py M lib/galaxy_utils/sequence/fastq.py M lib/pulsar/client/interface.py M lib/pulsar/client/manager.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py M lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py M lib/tool_shed/util/basic_util.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/encoding_util.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_content_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/util/workflow_util.py M manage_db.sh M manage_tools.sh M run_reports.sh M run_tool_shed.sh M scripts/api/common.py M scripts/api/copy_hda_to_library_folder.py M scripts/api/create.py M scripts/api/data_manager_example_execute.py M scripts/api/delete.py M scripts/api/display.py M scripts/api/example_watch_folder.py M scripts/api/form_create_from_xml.py M scripts/api/history_create_history.py M scripts/api/history_delete_history.py M scripts/api/import_library_dataset_to_history.py M scripts/api/import_workflows_from_installed_tool_shed_repository.py M scripts/api/install_tool_shed_repositories.py M scripts/api/library_create_folder.py M scripts/api/library_create_library.py M scripts/api/library_upload_dir.py M scripts/api/library_upload_from_import_dir.py M scripts/api/load_data_with_metadata.py M scripts/api/repair_tool_shed_repository.py M scripts/api/request_type_create_from_xml.py M scripts/api/requests_update_state.py M scripts/api/reset_metadata_on_installed_repositories.py M scripts/api/sample_dataset_update_status.py M scripts/api/sample_update_state.py M scripts/api/search.py M scripts/api/sequencer_configuration_create.py M scripts/api/update.py M scripts/api/upload_to_history.py M scripts/api/workflow_delete.py M scripts/api/workflow_execute.py M scripts/api/workflow_execute_parameters.py M scripts/api/workflow_import.py M scripts/api/workflow_import_from_file_rpark.py M scripts/check_galaxy.py M scripts/check_python.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/update_metadata.py M scripts/create_db.py M scripts/data_libraries/build_lucene_index.py M scripts/data_libraries/build_whoosh_index.py M scripts/db_shell.py M scripts/edam_mapping.py M scripts/extract_dataset_part.py M scripts/functional_tests.py M scripts/galaxy-main M scripts/get_platforms.py M scripts/helper.py M scripts/loc_files/create_all_fasta_loc.py M scripts/manage_db.py M scripts/manage_tools.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/create_nib_seq_loc_file.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/microbes/ncbi_to_ucsc.py M scripts/microbes/util.py M scripts/migrate_tools/migrate_tools.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/paster.py A scripts/patch.sh M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/tool_shed/build_ts_whoosh_index.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/tools/maf/check_loc_file.py M scripts/tools/re_escape_output.py M scripts/transfer.py M scripts/update_shed_config_path.py M static/maps/galaxy.library.js.map M static/maps/layout/masthead.js.map M static/maps/layout/menu.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/library/library-dataset-view.js.map M 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test/tool_shed/functional/test_0140_tool_help_images.py M test/tool_shed/functional/test_0150_prior_installation_required.py M test/tool_shed/functional/test_0160_circular_prior_installation_required.py M test/tool_shed/functional/test_0170_complex_prior_installation_required.py M test/tool_shed/functional/test_0300_reset_all_metadata.py M test/tool_shed/functional/test_0310_hg_push_from_api.py M test/tool_shed/functional/test_0400_repository_component_reviews.py M test/tool_shed/functional/test_0410_repository_component_review_access_control.py M test/tool_shed/functional/test_0420_citable_urls_for_repositories.py M test/tool_shed/functional/test_0430_browse_utilities.py M test/tool_shed/functional/test_0440_deleting_dependency_definitions.py M test/tool_shed/functional/test_0450_skip_tool_tests.py M test/tool_shed/functional/test_0460_upload_to_repository.py M test/tool_shed/functional/test_0470_tool_dependency_repository_type.py M test/tool_shed/functional/test_0480_tool_dependency_xml_verification.py M test/tool_shed/functional/test_0490_export_import_repositories.py M test/tool_shed/functional/test_0500_export_repository_simple_dependency.py M test/tool_shed/functional/test_0510_export_import_repository_complex_dependencies.py M test/tool_shed/functional/test_0520_import_export_circular_dependencies.py M test/tool_shed/functional/test_0530_repository_admin_feature.py A test/tool_shed/functional/test_0540_get_all_metadata_from_api.py M test/tool_shed/functional/test_1000_install_basic_repository.py M test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py M test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py M test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py M test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py M test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py M 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test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py M test/tool_shed/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py M test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py M test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py M test/tool_shed/functional/test_1300_reset_all_metadata.py M test/tool_shed/functional/test_1400_review_migration_stages.py M test/tool_shed/functional/test_1410_update_manager.py M test/tool_shed/functional/test_1420_tool_dependency_environment_inheritance.py M test/tool_shed/functional/test_1430_repair_installed_repository.py M test/tool_shed/functional/test_1440_missing_env_sh_files.py M test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py M test/tool_shed/functional/test_1460_data_managers.py M test/tool_shed/functional/test_1470_updating_installed_repositories.py A test/tool_shed/test_data/0540_files/column_maker/column_maker.tar A test/tool_shed/test_data/0540_files/column_maker/repository_dependencies.xml A test/tool_shed/test_data/0540_files/convert_chars/convert_chars.tar A test/tool_shed/test_data/0540_files/convert_chars/tool_dependencies.xml A test/tool_shed/test_data/0540_files/package_bwa/tool_dependencies.xml M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_job_wrapper.py M test/unit/test_objectstore.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py A test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_parsing.py M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/workflows/test_render.py M tools/data_source/upload.py M tox.ini

Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into api.batch

Commit: 7d5cc9373703a522c38009b16844fae4647a8a54 https://github.com/galaxyproject/galaxy/commit/7d5cc9373703a522c38009b16844f... Author: carlfeberhard carlfeberhard@gmail.com Date: 2016-05-11 (Wed, 11 May 2016)

Changed paths: M .ci/flake8_wrapper.sh M .ci/py3_sources.txt M .gitignore M CONTRIBUTORS.md M Makefile M README.rst R buildbot_setup.sh M client/README.md M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.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-section.js R client/galaxy/scripts/mvc/form/form-select-content.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-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/ui/ui-drilldown.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-options.js A client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/utils/localization.js M client/galaxy/scripts/utils/utils.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/less/base.less M client/galaxy/style/less/library.less M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M client/grunt-tasks/scripts.js M client/grunt-tasks/style.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced A config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M config/plugins/interactive_environments/jupyter/templates/jupyter.mako A config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.scratchbook.yaml M config/plugins/visualizations/charts/static/views/group.js R config/plugins/visualizations/graphview/config/graphview.xml R config/plugins/visualizations/graphview/static/graphview.css R config/plugins/visualizations/graphview/static/graphview.js R config/plugins/visualizations/graphview/static/jquery.rdfquery.core.js R config/plugins/visualizations/graphview/templates/graphview.mako M config/reports.ini.sample M config/tool_data_table_conf.xml.sample M config/tool_shed.ini.sample M contrib/galaxy.debian-init M contrib/galaxy.fedora-init A contrib/galaxy_reports.fedora-init A contrib/galaxy_supervisor.conf A display_applications/biom/biom_simple.xml A display_applications/iobio/bam.xml A display_applications/iobio/vcf.xml M doc/source/admin/framework_dependencies.rst M doc/source/lib/modules.rst R doc/source/lib/pulsar.client.rst R doc/source/lib/pulsar.client.staging.rst R doc/source/lib/pulsar.client.transport.rst R doc/source/lib/pulsar.rst M doc/source/releases/index.rst R install_and_test_tool_shed_repositories.sh M lib/galaxy/app.py M lib/galaxy/config.py A lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml A lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml A lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml A lib/galaxy/datatypes/converters/cml_to_smi_converter.xml A lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml A lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml A lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml A lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml A lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml A lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml A lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml A lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml A lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml A lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml A lib/galaxy/datatypes/converters/mol_to_cml_converter.xml A lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml A lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml A lib/galaxy/datatypes/converters/mol_to_smi_converter.xml A lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py A lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml A lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml A lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml A lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml A lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml A lib/galaxy/datatypes/converters/smi_to_cml_converter.xml A lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml A lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml A lib/galaxy/datatypes/converters/smi_to_mol_converter.xml A lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml A lib/galaxy/datatypes/converters/smi_to_smi_converter.xml M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/display_applications/application.py A lib/galaxy/datatypes/molecules.py A lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/5e5z.pdb A lib/galaxy/datatypes/test/drugbank_drugs.cml A lib/galaxy/datatypes/test/drugbank_drugs.inchi A lib/galaxy/datatypes/test/drugbank_drugs.mol2 A lib/galaxy/datatypes/test/drugbank_drugs.sdf A lib/galaxy/datatypes/test/drugbank_drugs.smi A lib/galaxy/datatypes/test/issue1818.tabular A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.axes A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.filter A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.freq A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.lower.dist A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.map A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.oligos A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.otu A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.pair.dist A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.quan A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.ref.taxonomy A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.sabund A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.shared A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.square.dist A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.axes A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.filter A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.freq A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.lower.dist A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.map A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.oligos A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.otu A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.pair.dist A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.quan A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.ref.taxonomy A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.sabund A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.shared A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.square.dist A lib/galaxy/datatypes/test/q.fps M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh 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/managers/base.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/context.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/history_contents.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/custom_types.py A lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py R lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_paramter_modules.py M lib/galaxy/model/util.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/runtime_actions.py A lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/tools/errors.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/linters/__init__.py M lib/galaxy/tools/linters/citations.py M lib/galaxy/tools/linters/command.py A lib/galaxy/tools/linters/general.py M lib/galaxy/tools/linters/help.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/linters/outputs.py M lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/linters/tests.py R lib/galaxy/tools/linters/top_level.py M lib/galaxy/tools/linters/xml_order.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parameters/wrapped_json.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tools/wrappers.py M lib/galaxy/util/__init__.py R lib/galaxy/util/dictobj.py M lib/galaxy/util/jstree.py M lib/galaxy/util/log/fluent_log.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/util/validation.py M lib/galaxy/version.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/web/proxy/js/package.json M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/metrics.py M lib/galaxy/webapps/galaxy/api/quotas.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/repository_revisions.py M lib/galaxy/webapps/tool_shed/api/users.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webapps/tool_shed/model/mapping.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M lib/galaxy/workflow/scheduling_manager.py R lib/pulsar/__init__.py R lib/pulsar/client/__init__.py R lib/pulsar/client/action_mapper.py R lib/pulsar/client/amqp_exchange.py R lib/pulsar/client/amqp_exchange_factory.py R lib/pulsar/client/client.py R lib/pulsar/client/config_util.py R lib/pulsar/client/decorators.py R lib/pulsar/client/destination.py R lib/pulsar/client/interface.py R lib/pulsar/client/job_directory.py R lib/pulsar/client/manager.py R lib/pulsar/client/object_client.py R lib/pulsar/client/path_mapper.py R lib/pulsar/client/setup_handler.py R lib/pulsar/client/staging/__init__.py R lib/pulsar/client/staging/down.py R lib/pulsar/client/staging/up.py R lib/pulsar/client/transport/__init__.py R lib/pulsar/client/transport/curl.py R lib/pulsar/client/transport/poster.py R lib/pulsar/client/transport/requests.py R lib/pulsar/client/transport/ssh.py R lib/pulsar/client/transport/standard.py R lib/pulsar/client/util.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/repository/relation_builder.py M lib/tool_shed/galaxy_install/dependency_display.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/util.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_registry.py R lib/tool_shed/scripts/api/add_repository_registry_entry.py R lib/tool_shed/scripts/api/common.py R lib/tool_shed/scripts/api/create_categories.py R lib/tool_shed/scripts/api/create_users.py R lib/tool_shed/scripts/api/export.py R lib/tool_shed/scripts/api/get_filtered_repository_revisions.py R lib/tool_shed/scripts/api/import_capsule.py R lib/tool_shed/scripts/api/remove_repository_registry_entry.py R lib/tool_shed/scripts/api/reset_metadata_on_repositories.py R lib/tool_shed/scripts/api/tool_shed_repository_revision_update.py R lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh R lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py R lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py R lib/tool_shed/scripts/bootstrap_tool_shed/parse_run_sh_args.sh R lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml.sample R lib/tool_shed/scripts/check_filesystem_for_empty_tool_dependency_installation_paths.py R lib/tool_shed/scripts/check_repositories_for_functional_tests.py R lib/tool_shed/scripts/check_s3_for_empty_tool_dependency_installation_paths.py R lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py R lib/tool_shed/scripts/clean_up_tool_dependency_directory.py R lib/tool_shed/scripts/deprecate_repositories_without_metadata.py R lib/tool_shed/scripts/show_tool_dependency_installation_dir_contents.py M lib/tool_shed/tool_shed_registry.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/utility_containers/__init__.py M lib/tool_shed/utility_containers/utility_container_manager.py M run.sh M run_reports.sh M run_tests.sh M run_tool_shed.sh M scripts/bootstrap_history.py M scripts/common_startup.sh M scripts/functional_tests.py M scripts/summarize_timings.py A scripts/tool_shed/api/add_repository_registry_entry.py A scripts/tool_shed/api/common.py A scripts/tool_shed/api/create_categories.py A scripts/tool_shed/api/create_users.py A scripts/tool_shed/api/export.py A scripts/tool_shed/api/get_filtered_repository_revisions.py A scripts/tool_shed/api/import_capsule.py A scripts/tool_shed/api/remove_repository_registry_entry.py A scripts/tool_shed/api/reset_metadata_on_repositories.py A scripts/tool_shed/api/tool_shed_repository_revision_update.py A scripts/tool_shed/bootstrap_tool_shed/bootstrap_tool_shed.sh A scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py A scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py A scripts/tool_shed/bootstrap_tool_shed/parse_run_sh_args.sh A scripts/tool_shed/bootstrap_tool_shed/user_info.xml.sample A scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py A scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py A scripts/tool_shed/clean_up_tool_dependency_directory.py A scripts/tool_shed/deprecate_repositories_without_metadata.py A scripts/tool_shed/show_tool_dependency_installation_dir_contents.py M static/maps/layout/masthead.js.map M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/mvc/citation/citation-model.js.map M static/maps/mvc/dataset/dataset-li-edit.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-section.js.map R static/maps/mvc/form/form-select-content.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-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-folderlist-view.js.map M 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Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into api.batch

Commit: 7bfd6410eb8b66a89045e13ca00f6a11572fa9d8 https://github.com/galaxyproject/galaxy/commit/7bfd6410eb8b66a89045e13ca00f6... Author: carlfeberhard carlfeberhard@gmail.com Date: 2016-06-23 (Thu, 23 Jun 2016)

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Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into api.batch

Commit: 6825f4c5f48ebcff0d7ce15e6fc4adc6df5dfc43 https://github.com/galaxyproject/galaxy/commit/6825f4c5f48ebcff0d7ce15e6fc4a... Author: carlfeberhard carlfeberhard@gmail.com Date: 2016-07-14 (Thu, 14 Jul 2016)

Changed paths: M lib/galaxy/web/framework/middleware/batch.py 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 test/api/test_api_batch.py

Log Message: ----------- API, batch: add allowed_list to narrow use

- only allows processing batch calls to the urls that match the regexs in allowed_list controlling/decreasing the scope of the middleware

Commit: 15a686e316a3d47bcc120073dedf1ed659eb0cfa https://github.com/galaxyproject/galaxy/commit/15a686e316a3d47bcc120073dedf1... Author: carlfeberhard carlfeberhard@gmail.com Date: 2016-07-28 (Thu, 28 Jul 2016)

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lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/workflow.py A lib/galaxy/webapps/reports/controllers/history.py A lib/galaxy/webapps/reports/controllers/tools.py M lib/galaxy/webapps/reports/controllers/users.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/render.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/util/shed_util_common.py M run_tests.sh M scripts/api/data_manager_example_execute.py M scripts/api/example_watch_folder.py M scripts/api/form_create_from_xml.py M scripts/api/history_create_history.py M scripts/api/history_delete_history.py M scripts/api/import_library_dataset_to_history.py M scripts/api/import_workflows_from_installed_tool_shed_repository.py M scripts/api/library_create_folder.py M scripts/api/library_create_library.py M scripts/api/library_upload_from_import_dir.py M scripts/api/load_data_with_metadata.py M scripts/api/repair_tool_shed_repository.py M scripts/api/request_type_create_from_xml.py M scripts/api/requests_update_state.py M scripts/api/sample_dataset_update_status.py M scripts/api/sample_update_state.py M scripts/api/search.py M scripts/api/sequencer_configuration_create.py M scripts/api/upload_to_history.py M scripts/api/workflow_delete.py M scripts/api/workflow_execute.py M scripts/api/workflow_import.py M scripts/api/workflow_import_from_file_rpark.py M scripts/bootstrap_history.py M scripts/build_toolbox.py M scripts/check_galaxy.py M scripts/check_python.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py M scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/common_startup.sh A scripts/communication/communication_server.py A scripts/communication/template/communication.css A scripts/communication/template/communication.html A scripts/communication/template/communication.js M scripts/data_libraries/build_whoosh_index.py M scripts/db_shell.py M scripts/drmaa_external_runner.py M scripts/fetch_eggs.py A scripts/grt.py A scripts/grt.yml.sample M scripts/set_dataset_sizes.py M setup.cfg A static/maps/layout/generic-nav-view.js.map M static/maps/layout/menu.js.map M static/maps/layout/page.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/dataset/data.js.map M static/maps/mvc/form/form-data.js.map M 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static/scripts/mvc/history/history-contents.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/tool/tool-template.js M static/scripts/mvc/ui/ui-buttons.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/ui/ui-tabs.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-button.js M static/scripts/mvc/upload/upload-view.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/tracks.js A static/style/base.css M static/style/blue/base.css M templates/admin/impersonate.mako M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/manage_repository.mako M templates/admin/tool_shed_repository/preview_repository.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/base.mako M templates/base/base_panels.mako M templates/ind_share_base.mako M templates/js-app.mako M templates/user/change_password.mako A templates/user/communication_settings.mako M templates/user/index.mako M templates/webapps/galaxy/history/grid.mako A templates/webapps/reports/history_and_dataset_per_user.mako A templates/webapps/reports/history_and_dataset_type.mako A templates/webapps/reports/history_per_user.mako M templates/webapps/reports/index.mako A templates/webapps/reports/tool_error_messages.mako A templates/webapps/reports/tool_execution_time.mako A templates/webapps/reports/tool_execution_time_per_month.mako A templates/webapps/reports/tools_and_job_state.mako A templates/webapps/reports/tools_and_job_state_per_month.mako M templates/webapps/tool_shed/repository/common.mako M 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test/unit/datatypes/dataproviders/test_line_dataproviders.py A test/unit/datatypes/test_data.py 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 test/unit/managers/base.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/test_galaxy_mapping.py M test/unit/tools/test_conda_resolution.py M test/unit/tools/test_toolbox.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.py M tool-data/shared/ucsc/ucsc_build_sites.txt.sample M tools/stats/aggregate_scores_in_intervals.py M tools/stats/gsummary.xml M tox.ini

Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into api.batch

Commit: ff261296673095410eefdcce8c27cf2697c318bc https://github.com/galaxyproject/galaxy/commit/ff261296673095410eefdcce8c27c... Author: carlfeberhard carlfeberhard@gmail.com Date: 2016-07-29 (Fri, 29 Jul 2016)

Changed paths: M lib/galaxy/web/framework/middleware/batch.py M test/api/test_api_batch.py

Log Message: ----------- API, batch: update docs and test, cleanup

Commit: 45c95061d3e76c450cfb6a52e85e84f91927b6dc https://github.com/galaxyproject/galaxy/commit/45c95061d3e76c450cfb6a52e85e8... Author: carlfeberhard carlfeberhard@gmail.com Date: 2016-07-29 (Fri, 29 Jul 2016)

Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py

Log Message: ----------- API, jobs: have create return galactic 501

- Uses MessageException version which can be parsed as 501

Commit: e781aaa2aa6f12b949d301957dddc61f7b1751ac https://github.com/galaxyproject/galaxy/commit/e781aaa2aa6f12b949d301957dddc... Author: carlfeberhard carlfeberhard@gmail.com Date: 2016-08-02 (Tue, 02 Aug 2016)

Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M Makefile M client/bower.json A client/galaxy/scripts/libs/jquery.complexify.js M client/galaxy/scripts/libs/jquery/jquery.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/style/less/base.less M client/grunt-tasks/install-libs.js M client/webpack.config.js M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/base.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/version.py M lib/galaxy/webapps/galaxy/controllers/history.py M run_tests.sh M scripts/bootstrap_history.py M scripts/nosetests.py A static/maps/libs/jquery.complexify.js.map M static/maps/libs/jquery/jquery.js.map M static/maps/libs/raven.js.map M static/maps/mvc/history/options-menu.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 A static/scripts/libs/jquery.complexify.js M static/scripts/libs/jquery/jquery.js M static/scripts/libs/raven.js M static/scripts/mvc/history/options-menu.js M static/style/blue/base.css M templates/user/change_password.mako M templates/user/register.mako M test/unit/tools/test_tool_deps.py

Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into api.batch

Commit: 9de06e1594e8ccff37008bd2700ff4dc38b76f56 https://github.com/galaxyproject/galaxy/commit/9de06e1594e8ccff37008bd2700ff... Author: Dannon Baker dannon.baker@gmail.com Date: 2016-08-23 (Tue, 23 Aug 2016)

Changed paths: M lib/galaxy/web/framework/base.py A lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/buildapp.py A test/api/test_api_batch.py A test/casperjs/api-batch-tests.js

Log Message: ----------- Merge pull request #1768 from carlfeberhard/api.batch

Api batch endpoint

Compare: https://github.com/galaxyproject/galaxy/compare/b16a9403de99...9de06e1594e8