Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1aa8eb980aac5503a6cf585241fe974899922557 https://github.com/galaxyproject/galaxy/commit/1aa8eb980aac5503a6cf585241fe9... Author: Dave Bouvier dave@bx.psu.edu Date: 2016-04-04 (Mon, 04 Apr 2016)

Changed paths: M lib/tool_shed/util/metadata_util.py

Log Message: ----------- Attempted fix for server error on repo preview.

This should handle cases where the database record specifies a repository dependency, but the repository in question (and its downloadable changeset) has been updated since the dependency was created.

Commit: ad929f231076706167cd88274bcf7c074e74fac4 https://github.com/galaxyproject/galaxy/commit/ad929f231076706167cd88274bcf7... Author: Dave Bouvier dave@bx.psu.edu Date: 2016-04-05 (Tue, 05 Apr 2016)

Changed paths: A test/shed_functional/functional/test_0550_metadata_updated_dependencies.py A test/shed_functional/test_data/0550_files/filtering_1.0.tgz A test/shed_functional/test_data/0550_files/package_freebayes_1_0550.tgz A test/shed_functional/test_data/0550_files/package_freebayes_2_0550.tgz A test/shed_functional/test_data/0550_files/package_samtools_1_0550.tgz A test/shed_functional/test_data/0550_files/package_samtools_2_0550.tgz A test/shed_functional/test_data/0550_files/temp/tool_dependencies.xml

Log Message: ----------- Add test for server error with updated repository.

Commit: 8c3f458bca948fc5efda027a4e09b8b5b8289276 https://github.com/galaxyproject/galaxy/commit/8c3f458bca948fc5efda027a4e09b... Author: Dave Bouvier dave@bx.psu.edu Date: 2016-04-06 (Wed, 06 Apr 2016)

Changed paths: M test/shed_functional/functional/test_0550_metadata_updated_dependencies.py

Log Message: ----------- Correct docs and names.

Commit: f4993b782679096f2576e749b146c76b45397314 https://github.com/galaxyproject/galaxy/commit/f4993b782679096f2576e749b146c... Author: Dave Bouvier dave@bx.psu.edu Date: 2016-04-06 (Wed, 06 Apr 2016)

Changed paths: M test/shed_functional/functional/test_0550_metadata_updated_dependencies.py

Log Message: ----------- Fix one more travis error.

Commit: 78e2eef2fcb4bcc51f26307ee351a3c5a679c300 https://github.com/galaxyproject/galaxy/commit/78e2eef2fcb4bcc51f26307ee351a... Author: Dave Bouvier dave@bx.psu.edu Date: 2016-04-06 (Wed, 06 Apr 2016)

Changed paths: M test/shed_functional/functional/test_0550_metadata_updated_dependencies.py

Log Message: ----------- Fix another travis error that escaped my notice.

Commit: d8b0add9c20bf6aee7c96d1c6106178cbf72cb3d https://github.com/galaxyproject/galaxy/commit/d8b0add9c20bf6aee7c96d1c61061... Author: Dave Bouvier dave@bx.psu.edu Date: 2016-04-14 (Thu, 14 Apr 2016)

Changed paths: M .ci/py3_sources.txt M .gitignore M Makefile R buildbot_setup.sh M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/style/less/base.less 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/tool_data_table_conf.xml.sample M contrib/galaxy.debian-init A contrib/galaxy_supervisor.conf A display_applications/biom/biom_simple.xml R install_and_test_tool_shed_repositories.sh M lib/galaxy/config.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/issue1818.tabular 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/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/managers/configuration.py M lib/galaxy/model/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/tools/errors.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/util/__init__.py M lib/galaxy/util/log/fluent_log.py M lib/galaxy/version.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/proxy/__init__.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.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/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/workflow/modules.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/util/shed_util_common.py M run_tests.sh M run_tool_shed.sh M scripts/bootstrap_history.py M scripts/functional_tests.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/menu.js.map M static/maps/mvc/tool/tool-form-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/tool/tool-form-workflow.js M static/style/blue/base.css M templates/sharing_base.mako M templates/webapps/galaxy/admin/index.mako A templates/webapps/galaxy/visualization/gie.mako R templates/webapps/galaxy/workflow/export.mako M templates/webapps/galaxy/workflow/list.mako M templates/webapps/galaxy/workflow/run.mako M templates/webapps/galaxy/workflow/sharing.mako M templates/webapps/tool_shed/repository/view_changeset.mako M test/base/driver_util.py A test/base/integration_util.py M test/casperjs/casperjs_runner.py A test/integration/__init__.py A test/integration/embedded_pulsar_job_conf.xml A test/integration/test_pulsar_embedded.py M test/shed_functional/base/twilltestcase.py M test/unit/jobs/test_command_factory.py M test/unit/tools/test_conda_resolution.py A tool-data/biom_simple_display.loc.sample

Log Message: ----------- Merge branch 'dev' of git://github.com/galaxyproject/galaxy into api_install_bugfixes

Commit: afa353b6fd00eb0ecf1d4bac9d64751537cae12a https://github.com/galaxyproject/galaxy/commit/afa353b6fd00eb0ecf1d4bac9d647... Author: Dave Bouvier dave@bx.psu.edu Date: 2016-04-15 (Fri, 15 Apr 2016)

Changed paths: M lib/tool_shed/util/shed_util_common.py M test/shed_functional/functional/test_0540_get_all_metadata_from_api.py

Log Message: ----------- Return current changeset if it is latest.

Commit: d35d6a707f3b265b10b859714deec793ecf31a53 https://github.com/galaxyproject/galaxy/commit/d35d6a707f3b265b10b859714deec... Author: Dave Bouvier dave@bx.psu.edu Date: 2016-04-15 (Fri, 15 Apr 2016)

Changed paths: M lib/tool_shed/util/shed_util_common.py

Log Message: ----------- Update documentation.

Commit: 4c126af1b0137fad228f0254dab45b6bec8fb9da https://github.com/galaxyproject/galaxy/commit/4c126af1b0137fad228f0254dab45... Author: Dave Bouvier dave@bx.psu.edu Date: 2016-04-15 (Fri, 15 Apr 2016)

Changed paths: M lib/galaxy/webapps/tool_shed/api/repository_revisions.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/repository/relation_builder.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py

Log Message: ----------- Ensure legacy behavior remains unaltered.

Per to the logic change in shed_util_common.get_next_downloadable_changeset_revision, this commit modifies some conditionals to check whether it previously would have returned None.

Commit: e1b167b312385df2a02fb5c7d4c4c464e3733bd7 https://github.com/galaxyproject/galaxy/commit/e1b167b312385df2a02fb5c7d4c4c... Author: Dave Bouvier dave@bx.psu.edu Date: 2016-04-15 (Fri, 15 Apr 2016)

Changed paths: M lib/galaxy/webapps/tool_shed/api/repository_revisions.py

Log Message: ----------- Remove extra else statement.

Commit: 50757a13baf060601b681795403ba503a8897ede https://github.com/galaxyproject/galaxy/commit/50757a13baf060601b681795403ba... Author: Dave Bouvier dave@bx.psu.edu Date: 2016-04-15 (Fri, 15 Apr 2016)

Changed paths: M lib/tool_shed/util/metadata_util.py

Log Message: ----------- Fix test 0550.

Commit: c79d057ca459586f4a01d50158d36530d0cbb163 https://github.com/galaxyproject/galaxy/commit/c79d057ca459586f4a01d50158d36... Author: Martin Cech cech.marten@gmail.com Date: 2016-04-20 (Wed, 20 Apr 2016)

Changed paths: M lib/galaxy/webapps/tool_shed/api/repository_revisions.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/dependencies/repository/relation_builder.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py M test/shed_functional/functional/test_0540_get_all_metadata_from_api.py A test/shed_functional/functional/test_0550_metadata_updated_dependencies.py A test/shed_functional/test_data/0550_files/filtering_1.0.tgz A test/shed_functional/test_data/0550_files/package_freebayes_1_0550.tgz A test/shed_functional/test_data/0550_files/package_freebayes_2_0550.tgz A test/shed_functional/test_data/0550_files/package_samtools_1_0550.tgz A test/shed_functional/test_data/0550_files/package_samtools_2_0550.tgz A test/shed_functional/test_data/0550_files/temp/tool_dependencies.xml

Log Message: ----------- Merge pull request #2079 from davebx/api_install_bugfixes

Attempted fix for server error on repo preview.

Compare: https://github.com/galaxyproject/galaxy/compare/9b5fdbf9a497...c79d057ca459