galaxy-commits February 2016

galaxy-commits@lists.galaxyproject.org

2 participants
135 discussions

[galaxyproject/galaxy] 1aa1d6: Fix workflow parameters not rendered when tool par...
by GitHub 26 Feb '16

26 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 1aa1d6164a63438b49beb2fd6cc4b80a57bbdb5d https://github.com/galaxyproject/galaxy/commit/1aa1d6164a63438b49beb2fd6cc4… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Fix workflow parameters not rendered when tool parameter wrapped in conditional. Commit: dad1784a087623c990e0b3f05d1c8026f7bd957c https://github.com/galaxyproject/galaxy/commit/dad1784a087623c990e0b3f05d1c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge pull request #1799 from mvdbeek/fix_workflow_parameters_conditional [16.01] Fix workflow parameters not rendered when tool parameter wrapped in conditional. Compare: https://github.com/galaxyproject/galaxy/compare/5546211c0ddd...dad1784a0876

1 0

[galaxyproject/galaxy] bae03b: Port Nicola's fix to dev.
by GitHub 26 Feb '16

26 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bae03bfe3ec41be97dd75e42b40bf730fee5373e https://github.com/galaxyproject/galaxy/commit/bae03bfe3ec41be97dd75e42b40b… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M test/tool_shed/base/twilltestcase.py Log Message: ----------- Port Nicola's fix to dev. Commit: 510543236c472ca1055581952f589762c9cc4dab https://github.com/galaxyproject/galaxy/commit/510543236c472ca1055581952f58… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M test/tool_shed/base/twilltestcase.py Log Message: ----------- Merge #1392's modifications into bae03bfe. Commit: 4383e9f808889bcf62b0417de7254c3d184564a5 https://github.com/galaxyproject/galaxy/commit/4383e9f808889bcf62b0417de725… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M .ci/flake8_blacklist.txt M .ci/py3_sources.txt M .travis.yml M Makefile 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/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/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 config/datatypes_conf.xml.sample M doc/source/releases/16.01.rst M doc/source/releases/16.01_announce.rst 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/text.py M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/deferred/data_transfer.py M lib/galaxy/managers/configuration.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/metadata.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/imp_exp/__init__.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/output_collection_def.py M lib/galaxy/tools/test.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/visualization/data_providers/registry.py M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/plugin.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/tools.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/api/workflows.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/tag.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/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/modules.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/tool_dependencies/recipe/env_file_builder.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.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/repository_content_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 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/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/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 static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/ui/popup-menu.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/utils/utils.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/galaxy.library.js M static/scripts/layout/masthead.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/ui/popup-menu.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/utils/utils.js M static/style/blue/base.css M static/style/blue/library.css R templates/admin/requests/select_datasets_to_transfer.mako M templates/admin/tool_shed_repository/common.mako M templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/requests/common/common.mako M templates/webapps/galaxy/requests/common/view_request_history.mako M templates/webapps/galaxy/requests/common/view_sample_datasets.mako M templates/webapps/tool_shed/repository/common.mako M test/api/test_tools.py M test/base/twilltestcase.py M test/functional/test_admin_features.py M test/functional/test_data_security.py M test/functional/test_dataset_features.py M test/functional/test_get_data.py M test/functional/test_library_features.py M test/functional/test_library_security.py M test/functional/test_library_templates.py M test/functional/test_metadata_editing.py M test/functional/test_sample_tracking.py M test/functional/test_tags.py M test/functional/test_ucsc_table_browser.py M test/functional/test_user_info.py M test/functional/tools/output_format.xml M test/qunit/tests/masthead_tests.js M test/qunit/tests/workflow_editor_tests.js M test/tool_shed/base/twilltestcase.py M test/tool_shed/functional/test_0000_basic_repository_features.py M test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py M test/tool_shed/functional/test_0020_basic_repository_dependencies.py M test/tool_shed/functional/test_0030_repository_dependency_revisions.py M test/tool_shed/functional/test_0040_repository_circular_dependencies.py M test/tool_shed/functional/test_0050_circular_dependencies_4_levels.py M test/tool_shed/functional/test_0060_workflows.py M test/tool_shed/functional/test_0070_invalid_tool.py M test/tool_shed/functional/test_0080_advanced_circular_dependencies.py M test/tool_shed/functional/test_0090_tool_search.py M test/tool_shed/functional/test_0100_complex_repository_dependencies.py M test/tool_shed/functional/test_0110_invalid_simple_repository_dependencies.py M test/tool_shed/functional/test_0120_simple_repository_dependency_multiple_owners.py M test/tool_shed/functional/test_0130_datatype_converters.py M 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 test/tool_shed/functional/test_1060_install_repository_with_workflow.py M test/tool_shed/functional/test_1070_invalid_tool.py M test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py R test/tool_shed/functional/test_1085_repository_dependency_handling.py R test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py R test/tool_shed/functional/test_1090_install_tool_from_tool_search.py A test/tool_shed/functional/test_1090_repository_dependency_handling.py R test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py A test/tool_shed/functional/test_1100_install_updated_repository_dependencies.py R test/tool_shed/functional/test_1110_install_repository_with_invalid_repository_dependency.py A test/tool_shed/functional/test_1110_install_tool_from_tool_search.py A test/tool_shed/functional/test_1120_install_repository_with_complex_dependencies.py R test/tool_shed/functional/test_1120_simple_repository_dependency_multiple_owners.py R test/tool_shed/functional/test_1130_datatype_converters.py A test/tool_shed/functional/test_1130_install_repository_with_invalid_repository_dependency.py A test/tool_shed/functional/test_1140_simple_repository_dependency_multiple_owners.py R test/tool_shed/functional/test_1140_tool_help_images.py A test/tool_shed/functional/test_1150_datatype_converters.py R test/tool_shed/functional/test_1150_prior_installation_required.py R test/tool_shed/functional/test_1160_circular_prior_installation_required.py A test/tool_shed/functional/test_1160_tool_help_images.py R test/tool_shed/functional/test_1170_complex_prior_installation_required.py A test/tool_shed/functional/test_1170_prior_installation_required.py A test/tool_shed/functional/test_1180_circular_prior_installation_required.py A test/tool_shed/functional/test_1190_complex_prior_installation_required.py M 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/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_execution.py A test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/unittest_utils/galaxy_mock.py M tox.ini Log Message: ----------- Reintroduce my changes to get_files methods. Commit: 453345c6210fd849f8a832b41b57cb2638ec83ef https://github.com/galaxyproject/galaxy/commit/453345c6210fd849f8a832b41b57… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M test/tool_shed/base/twilltestcase.py Log Message: ----------- Merge pull request #1800 from davebx/fix_ts_tests Port my changes from #1392 Compare: https://github.com/galaxyproject/galaxy/compare/09f597ae4bca...453345c6210f

1 0

[galaxyproject/galaxy] 990c0f: Add changeset_revision to tool attributes, avoid s...
by GitHub 26 Feb '16

26 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 990c0fe5351f560653a54a67f15702b2db88945e https://github.com/galaxyproject/galaxy/commit/990c0fe5351f560653a54a67f157… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Add changeset_revision to tool attributes, avoid self.tool_shed_repository Commit: 09f597ae4bca1ddab775f4238e4c433ab1d65935 https://github.com/galaxyproject/galaxy/commit/09f597ae4bca1ddab775f4238e4c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #1802 from mvdbeek/fix_my_mess Add changeset_revision to tool attributes, avoid self.tool_shed_repos… Compare: https://github.com/galaxyproject/galaxy/compare/93069676e6dd...09f597ae4bca

1 0

[galaxyproject/galaxy] f27ff0: Fix to 9acbfdf: initial fix borked fa-2x, instead ...
by GitHub 25 Feb '16

25 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f27ff0c7ba829a48f9c0eae443baa36cda92cf98 https://github.com/galaxyproject/galaxy/commit/f27ff0c7ba829a48f9c0eae443ba… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M client/galaxy/style/less/base.less M client/galaxy/style/less/fontawesome/core.less M static/style/blue/base.css Log Message: ----------- Fix to 9acbfdf: initial fix borked fa-2x, instead remove second woff loaded due to fa-icon font-family rule by aliasing that to fa Commit: 7a9d4943cd0571f5adebf850b4e167065289700b https://github.com/galaxyproject/galaxy/commit/7a9d4943cd0571f5adebf850b4e1… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M test/tool_shed/base/twilltestcase.py Log Message: ----------- Fix tool shed tests for e4a1d5727805168a9fd15aca1cdd21630ada2bbc . Commit: 15c08d80e4a2c027a01dd8dabc16b802be4c18a1 https://github.com/galaxyproject/galaxy/commit/15c08d80e4a2c027a01dd8dabc16… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M client/galaxy/style/less/base.less M client/galaxy/style/less/fontawesome/core.less M static/style/blue/base.css Log Message: ----------- Merge pull request #1791 from carlfeberhard/release_16.01 [16.01] Fix to 9acbfdf: initial fix borked fa-2x, instead remove second woff … Commit: 5546211c0dddb23bbeae34c0cddbd7ad9cebf6b5 https://github.com/galaxyproject/galaxy/commit/5546211c0dddb23bbeae34c0cddb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M test/tool_shed/base/twilltestcase.py Log Message: ----------- Merge pull request #1798 from nsoranzo/release_16.01_tool_shed_test_fixes [16.01] Fix tool shed tests for e4a1d5727805168a9fd15aca1cdd21630ada2bbc . Commit: 93069676e6dd03af947ccd60e8d0883b64a5ed39 https://github.com/galaxyproject/galaxy/commit/93069676e6dd03af947ccd60e8d0… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M client/galaxy/style/less/base.less M client/galaxy/style/less/fontawesome/core.less 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/style/blue/base.css M test/tool_shed/base/twilltestcase.py Log Message: ----------- Merge branch 'release_16.01' into dev Conflicts: static/style/blue/base.css Compare: https://github.com/galaxyproject/galaxy/compare/94f847b3b247...93069676e6dd

1 0

[galaxyproject/galaxy] 7a9d49: Fix tool shed tests for e4a1d5727805168a9fd15aca1c...
by GitHub 25 Feb '16

25 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 7a9d4943cd0571f5adebf850b4e167065289700b https://github.com/galaxyproject/galaxy/commit/7a9d4943cd0571f5adebf850b4e1… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M test/tool_shed/base/twilltestcase.py Log Message: ----------- Fix tool shed tests for e4a1d5727805168a9fd15aca1cdd21630ada2bbc . Commit: 5546211c0dddb23bbeae34c0cddbd7ad9cebf6b5 https://github.com/galaxyproject/galaxy/commit/5546211c0dddb23bbeae34c0cddb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M test/tool_shed/base/twilltestcase.py Log Message: ----------- Merge pull request #1798 from nsoranzo/release_16.01_tool_shed_test_fixes [16.01] Fix tool shed tests for e4a1d5727805168a9fd15aca1cdd21630ada2bbc . Compare: https://github.com/galaxyproject/galaxy/compare/15c08d80e4a2...5546211c0ddd

1 0

[galaxyproject/galaxy] f27ff0: Fix to 9acbfdf: initial fix borked fa-2x, instead ...
by GitHub 25 Feb '16

25 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: f27ff0c7ba829a48f9c0eae443baa36cda92cf98 https://github.com/galaxyproject/galaxy/commit/f27ff0c7ba829a48f9c0eae443ba… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M client/galaxy/style/less/base.less M client/galaxy/style/less/fontawesome/core.less M static/style/blue/base.css Log Message: ----------- Fix to 9acbfdf: initial fix borked fa-2x, instead remove second woff loaded due to fa-icon font-family rule by aliasing that to fa Commit: 15c08d80e4a2c027a01dd8dabc16b802be4c18a1 https://github.com/galaxyproject/galaxy/commit/15c08d80e4a2c027a01dd8dabc16… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M client/galaxy/style/less/base.less M client/galaxy/style/less/fontawesome/core.less M static/style/blue/base.css Log Message: ----------- Merge pull request #1791 from carlfeberhard/release_16.01 [16.01] Fix to 9acbfdf: initial fix borked fa-2x, instead remove second woff … Compare: https://github.com/galaxyproject/galaxy/compare/5677c2ee4fce...15c08d80e4a2

1 0

[galaxyproject/galaxy] 93348e: Fix the remaining 1334 flake8 errors in scripts/ ....
by GitHub 25 Feb '16

25 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 93348e7199a2e35ee85607b948d2ca4ced951c86 https://github.com/galaxyproject/galaxy/commit/93348e7199a2e35ee85607b948d2… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M .ci/flake8_blacklist.txt 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/data_libraries/build_lucene_index.py M scripts/data_libraries/build_whoosh_index.py M scripts/galaxy-main M scripts/get_platforms.py M scripts/loc_files/create_all_fasta_loc.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/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.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 Log Message: ----------- Fix the remaining 1334 flake8 errors in scripts/ . Close #391. Commit: 196d174716b54593735ce7ca73d80dc48ed58470 https://github.com/galaxyproject/galaxy/commit/196d174716b54593735ce7ca73d8… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M .ci/py3_sources.txt M scripts/api/common.py M scripts/api/display.py M scripts/api/workflow_execute_parameters.py Log Message: ----------- Python 3 support for 3 files. Commit: d85db9daa6601ab8b1a086d43ea55b46dbe6609a https://github.com/galaxyproject/galaxy/commit/d85db9daa6601ab8b1a086d43ea5… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: 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_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/sequencer_configuration_create.py M scripts/api/update.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/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/helper.py M scripts/manage_db.py M scripts/manage_tools.py M scripts/migrate_tools/migrate_tools.py M scripts/paster.py 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/migrate_tools_to_repositories.py M scripts/transfer.py M scripts/update_shed_config_path.py Log Message: ----------- Use __file__ when adding paths to sys.path instead of os.getcwd() . Also insert additional paths in position 1 unless strictly necessary. Commit: 94f847b3b2478d92019237402012a719b1c62c49 https://github.com/galaxyproject/galaxy/commit/94f847b3b2478d92019237402012… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M .ci/flake8_blacklist.txt M .ci/py3_sources.txt 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/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 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 Log Message: ----------- Merge pull request #1755 from nsoranzo/flake8_fixes Fix the remaining 1334 flake8 errors in scripts/ . Compare: https://github.com/galaxyproject/galaxy/compare/5370f2d1cdb3...94f847b3b247

1 0

[galaxyproject/galaxy] 31096b: Some tweaks to bootstrapping.
by GitHub 25 Feb '16

25 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 31096b7504c3cbd371ac2e482ab949cfea40d53f https://github.com/galaxyproject/galaxy/commit/31096b7504c3cbd371ac2e482ab9… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-18 (Thu, 18 Feb 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/users.py M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh M lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py Log Message: ----------- Some tweaks to bootstrapping. Commit: 782fccb8bc3e980ca620e4e9d636d53736ff4518 https://github.com/galaxyproject/galaxy/commit/782fccb8bc3e980ca620e4e9d636… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-19 (Fri, 19 Feb 2016) Changed paths: 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 Log Message: ----------- Use optparse for python 2.6 compatibility. Commit: 5370f2d1cdb3bb745c5463a803d6d5879b9452c3 https://github.com/galaxyproject/galaxy/commit/5370f2d1cdb3bb745c5463a803d6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/users.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 Log Message: ----------- Merge pull request #1756 from davebx/fix_bootstrap Some tweaks to bootstrapping. Compare: https://github.com/galaxyproject/galaxy/compare/7560677bd964...5370f2d1cdb3

1 0

[galaxyproject/galaxy] 5b515a: Update Makefile for release/point releases
by GitHub 25 Feb '16

25 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5b515a76cd951be8b47ebca7eb6d9f107f1cd5f6 https://github.com/galaxyproject/galaxy/commit/5b515a76cd951be8b47ebca7eb6d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M Makefile Log Message: ----------- Update Makefile for release/point releases Commit: 8943a0f86b6ccf4b90e7063e3d2e952d7265d1f7 https://github.com/galaxyproject/galaxy/commit/8943a0f86b6ccf4b90e7063e3d2e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: A scripts/patch.sh Log Message: ----------- Add the script I used to create security patches Commit: 7560677bd964623cbbc322f34d29f527c53b65cb https://github.com/galaxyproject/galaxy/commit/7560677bd964623cbbc322f34d29… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M Makefile A scripts/patch.sh Log Message: ----------- Merge pull request #1793 from natefoo/make-release Update makefile and add the script I used to apply security patches for 16.01 Compare: https://github.com/galaxyproject/galaxy/compare/4f73c4b5f8a5...7560677bd964

1 0

[galaxyproject/galaxy] d21cc8: Tests for some of the 16.01 security vulnerabiliti...
by GitHub 25 Feb '16

25 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d21cc83fc21024f97cc723e872f77c4f5fefb86b https://github.com/galaxyproject/galaxy/commit/d21cc83fc21024f97cc723e872f7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M test/unit/test_objectstore.py A test/unit/tools/test_history_imp_exp.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Tests for some of the 16.01 security vulnerabilities Commit: 4f73c4b5f8a5bdd1f4f2d3eaa4e3bc3e3b208208 https://github.com/galaxyproject/galaxy/commit/4f73c4b5f8a5bdd1f4f2d3eaa4e3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M test/unit/test_objectstore.py A test/unit/tools/test_history_imp_exp.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Merge pull request #1794 from natefoo/16.01-security-tests Tests for some of the 16.01 security vulnerabilities Compare: https://github.com/galaxyproject/galaxy/compare/70a96dd79e4e...4f73c4b5f8a5

1 0

Jump to page:

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

galaxy-commits February 2016