galaxy-commits October 2015

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[galaxyproject/galaxy] e9d77a: Attempt to fix transiently failing API tests.
by GitHub 06 Oct '15

06 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e9d77ac763239ccbae43ed553a1ce9541a5b8af3 https://github.com/galaxyproject/galaxy/commit/e9d77ac763239ccbae43ed553a1c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M test/api/helpers.py M test/api/test_jobs.py Log Message: ----------- Attempt to fix transiently failing API tests. - Fix default timeout of wait_on_state api helper. Had the wrong default specified and might fix this failure: https://jenkins.galaxyproject.org/job/docker-api/229/testReport/junit/api.t… - Modify job search test case to allow a little more time between the history being "ok" and the job, in case there is a timing condition if the HDA is committed first and then job. Also improve the test output in case this isn't the problem. Commit: 2b966ca4fae9e7348ac3a17de8d1567ebdacd21d https://github.com/galaxyproject/galaxy/commit/2b966ca4fae9e7348ac3a17de8d1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M test/api/helpers.py M test/api/test_jobs.py Log Message: ----------- Merge pull request #859 from jmchilton/test_fix_2 Attempt to fix more transiently failing API tests. Compare: https://github.com/galaxyproject/galaxy/compare/a2a4ce43ec3f...2b966ca4fae9

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[galaxyproject/galaxy] 84b572: Extend tool API to allow cross product mapping ove...
by GitHub 06 Oct '15

06 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 84b5726ca99bb681b6883bd42093c3a58e036d24 https://github.com/galaxyproject/galaxy/commit/84b5726ca99bb681b6883bd42093… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-18 (Fri, 18 Sep 2015) Changed paths: M lib/galaxy/dataset_collections/matching.py M lib/galaxy/dataset_collections/structure.py M lib/galaxy/dataset_collections/type_description.py M lib/galaxy/tools/parameters/meta.py M test/api/test_tools.py Log Message: ----------- Extend tool API to allow cross product mapping over collections. By default if single data parameters are mapped over by collections, the collections are matched up (e.g. for two collections the items are paired off and two collections of dimension (N) will result in running N jobs and producing an (N) dimensional output for each define output). In the parameter meta value wrapper (where batch mode can be set with the ``batch`` flag), the linked flag is now respected for collection operations. If ``linked`` is ``False``, then the cross product of the inputs will be used to map over the tool. In the above simplest case, this would cause an NxN (``list:list``) collection to be created for each tool output. This operation was previously available for individual datasets, but when supplied a collection it would not create an implicit collection pulling together all the relevant datasets with the correct structure - it would just run the jobs and leave the datasets uncollected. Now a collection with the correct structure and identifiers is created. Limitations: ----------------- This does not enable tool form support but the API for collections matches that for doing cross product operations over sets of individual datasets, so once support is added to the tool form for that collection support should be trivial. Testing: ----------------- The following test case has been extended to now ensure that an implicit collection is created and that it has the right dimensionality/structure and contents. ./run_tests.sh -with_framework_test_tools -api test/api/test_tools.py:ToolsTestCase.test_map_over_two_collections_unlinked Commit: a2a4ce43ec3f7571be12e08a801ea9f21d41f992 https://github.com/galaxyproject/galaxy/commit/a2a4ce43ec3f7571be12e08a801e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M lib/galaxy/dataset_collections/matching.py M lib/galaxy/dataset_collections/structure.py M lib/galaxy/dataset_collections/type_description.py M lib/galaxy/tools/parameters/meta.py M test/api/test_tools.py Log Message: ----------- Merge pull request #743 from jmchilton/cross_product_collection_mapping Extend tool API to allow cross product mapping over collections. Compare: https://github.com/galaxyproject/galaxy/compare/d309535f6871...a2a4ce43ec3f

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[galaxyproject/galaxy] b396b6: concatenate in one VCF some splitted vcfs whith bc...
by GitHub 06 Oct '15

06 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b396b6383bc89a56e6d37b291cc47a2622d02620 https://github.com/galaxyproject/galaxy/commit/b396b6383bc89a56e6d37b291cc4… Author: roalva1 <roalva1(a)gmail.com> Date: 2015-05-04 (Mon, 04 May 2015) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- concatenate in one VCF some splitted vcfs whith bcftools Commit: 9599ab6c3851f72261327d5edf2fa2c6d831254e https://github.com/galaxyproject/galaxy/commit/9599ab6c3851f72261327d5edf2f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Cleanup b396b6383bc89a56e6d37b291cc47a2622d02620 a bit. Use logs instead of print statements, PEP-8 improvements. Commit: 62c7f3ea9a92ab777fc4f7e0995a2db126177e12 https://github.com/galaxyproject/galaxy/commit/62c7f3ea9a92ab777fc4f7e0995a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Merge branch dev into merge-vcf. Conflicts: lib/galaxy/datatypes/tabular.py Commit: 26be140f28483c7de544fb6aeaf342e834664e29 https://github.com/galaxyproject/galaxy/commit/26be140f28483c7de544fb6aeaf3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Cleanup vcf.merge some more based on PR comments. Commit: ef84888863ebf27529c892917191dc232e7e931a https://github.com/galaxyproject/galaxy/commit/ef84888863ebf27529c892917191… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Another vcf.merge fix thanks to @nsoranzo. Commit: 5bb2fcabf4ec493cce5d63601d86c02f01b66e0c https://github.com/galaxyproject/galaxy/commit/5bb2fcabf4ec493cce5d63601d86… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Remove unused commit. Commit: d309535f687125b81f2cf594889d5bdbb803f964 https://github.com/galaxyproject/galaxy/commit/d309535f687125b81f2cf594889d… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Merge pull request #845 from jmchilton/merge-vcf-new Update and cleanup of #209. Compare: https://github.com/galaxyproject/galaxy/compare/903823f2986f...d309535f6871

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[galaxyproject/galaxy] c3ef54: Eliminate LWR from Galaxy.
by GitHub 06 Oct '15

06 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c3ef5467c71e69aa4570613e27bb8bd46d7de4f4 https://github.com/galaxyproject/galaxy/commit/c3ef5467c71e69aa4570613e27bb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: R doc/source/lib/galaxy.jobs.runners.lwr_client.rst R doc/source/lib/galaxy.jobs.runners.lwr_client.staging.rst R doc/source/lib/galaxy.jobs.runners.lwr_client.transport.rst M doc/source/lib/galaxy.jobs.runners.rst M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py R lib/galaxy/jobs/runners/lwr.py R lib/galaxy/jobs/runners/lwr_client/__init__.py R lib/galaxy/jobs/runners/lwr_client/action_mapper.py R lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py R lib/galaxy/jobs/runners/lwr_client/amqp_exchange_factory.py R lib/galaxy/jobs/runners/lwr_client/client.py R lib/galaxy/jobs/runners/lwr_client/config_util.py R lib/galaxy/jobs/runners/lwr_client/decorators.py R lib/galaxy/jobs/runners/lwr_client/destination.py R lib/galaxy/jobs/runners/lwr_client/interface.py R lib/galaxy/jobs/runners/lwr_client/job_directory.py R lib/galaxy/jobs/runners/lwr_client/manager.py R lib/galaxy/jobs/runners/lwr_client/object_client.py R lib/galaxy/jobs/runners/lwr_client/path_mapper.py R lib/galaxy/jobs/runners/lwr_client/setup_handler.py R lib/galaxy/jobs/runners/lwr_client/staging/__init__.py R lib/galaxy/jobs/runners/lwr_client/staging/down.py R lib/galaxy/jobs/runners/lwr_client/staging/up.py R lib/galaxy/jobs/runners/lwr_client/transport/__init__.py R lib/galaxy/jobs/runners/lwr_client/transport/curl.py R lib/galaxy/jobs/runners/lwr_client/transport/standard.py R lib/galaxy/jobs/runners/lwr_client/util.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/wrappers.py Log Message: ----------- Eliminate LWR from Galaxy. Commit: 903823f2986fad624770166a7d31f7936ce1a9f1 https://github.com/galaxyproject/galaxy/commit/903823f2986fad624770166a7d31… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: R doc/source/lib/galaxy.jobs.runners.lwr_client.rst R doc/source/lib/galaxy.jobs.runners.lwr_client.staging.rst R doc/source/lib/galaxy.jobs.runners.lwr_client.transport.rst M doc/source/lib/galaxy.jobs.runners.rst M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py R lib/galaxy/jobs/runners/lwr.py R lib/galaxy/jobs/runners/lwr_client/__init__.py R lib/galaxy/jobs/runners/lwr_client/action_mapper.py R lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py R lib/galaxy/jobs/runners/lwr_client/amqp_exchange_factory.py R lib/galaxy/jobs/runners/lwr_client/client.py R lib/galaxy/jobs/runners/lwr_client/config_util.py R lib/galaxy/jobs/runners/lwr_client/decorators.py R lib/galaxy/jobs/runners/lwr_client/destination.py R lib/galaxy/jobs/runners/lwr_client/interface.py R lib/galaxy/jobs/runners/lwr_client/job_directory.py R lib/galaxy/jobs/runners/lwr_client/manager.py R lib/galaxy/jobs/runners/lwr_client/object_client.py R lib/galaxy/jobs/runners/lwr_client/path_mapper.py R lib/galaxy/jobs/runners/lwr_client/setup_handler.py R lib/galaxy/jobs/runners/lwr_client/staging/__init__.py R lib/galaxy/jobs/runners/lwr_client/staging/down.py R lib/galaxy/jobs/runners/lwr_client/staging/up.py R lib/galaxy/jobs/runners/lwr_client/transport/__init__.py R lib/galaxy/jobs/runners/lwr_client/transport/curl.py R lib/galaxy/jobs/runners/lwr_client/transport/standard.py R lib/galaxy/jobs/runners/lwr_client/util.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/wrappers.py Log Message: ----------- Merge pull request #857 from jmchilton/lwr_remove Eliminate LWR from Galaxy. Compare: https://github.com/galaxyproject/galaxy/compare/920f7950fdb1...903823f2986f

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[galaxyproject/galaxy] 31c89e: UI, Collections: allow expansion to fetch details ...
by GitHub 06 Oct '15

06 Oct '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 31c89ea29c2c504878f336d90dfcf320b873b2ee https://github.com/galaxyproject/galaxy/commit/31c89ea29c2c504878f336d90dfc… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M static/maps/mvc/collection/collection-li-edit.js.map M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/history/hda-li-edit.js.map M static/scripts/mvc/collection/collection-li-edit.js M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/history/hda-li-edit.js Log Message: ----------- UI, Collections: allow expansion to fetch details for DatasetDCEs (assuming they're HDAs); move rerunnable and creating_job fetch to HDAs Commit: 69cd5a98dcda30771ce78118ebd3a934dfb09c65 https://github.com/galaxyproject/galaxy/commit/69cd5a98dcda30771ce78118ebd3… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M static/maps/mvc/collection/collection-li-edit.js.map M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/history/hda-li-edit.js.map M static/scripts/mvc/collection/collection-li-edit.js M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/history/hda-li-edit.js Log Message: ----------- Merge pull request #854 from carlfeberhard/release_15.10 [15.10] UI, Collections: allow expansion to fetch details for DatasetDCEs (as… Compare: https://github.com/galaxyproject/galaxy/compare/cc23adb0a962...69cd5a98dcda

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[galaxyproject/galaxy] fd1fd5: flake8 lib/galaxy/model/migrate/versions/ .
by GitHub 06 Oct '15

06 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fd1fd5e73c1828f79526ac712e3a4d9d5e9afa1c https://github.com/galaxyproject/galaxy/commit/fd1fd5e73c1828f79526ac712e3a… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-10-02 (Fri, 02 Oct 2015) Changed paths: M .ci/flake8_blacklist.txt M lib/galaxy/model/migrate/versions/0001_initial_tables.py M lib/galaxy/model/migrate/versions/0002_metadata_file_table.py M lib/galaxy/model/migrate/versions/0003_security_and_libraries.py M lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py M lib/galaxy/model/migrate/versions/0007_sharing_histories.py M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py M lib/galaxy/model/migrate/versions/0009_request_table.py M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0012_user_address.py M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py M lib/galaxy/model/migrate/versions/0014_pages.py M lib/galaxy/model/migrate/versions/0015_tagging.py M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py M lib/galaxy/model/migrate/versions/0019_request_library_folder.py M lib/galaxy/model/migrate/versions/0020_library_upload_job.py M lib/galaxy/model/migrate/versions/0021_user_prefs.py M lib/galaxy/model/migrate/versions/0022_visualization_tables.py M lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py M lib/galaxy/model/migrate/versions/0025_user_info.py M lib/galaxy/model/migrate/versions/0026_cloud_tables.py M lib/galaxy/model/migrate/versions/0027_request_events.py M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py M lib/galaxy/model/migrate/versions/0029_user_actions.py M lib/galaxy/model/migrate/versions/0030_history_slug_column.py M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py M lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py M lib/galaxy/model/migrate/versions/0037_samples_library.py M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py M lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py M lib/galaxy/model/migrate/versions/0040_page_annotations.py M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py M lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py M lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py M lib/galaxy/model/migrate/versions/0046_post_job_actions.py M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py M lib/galaxy/model/migrate/versions/0049_api_keys_table.py M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py M lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py M lib/galaxy/model/migrate/versions/0053_item_ratings.py M lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py M lib/galaxy/model/migrate/versions/0056_workflow_outputs.py M lib/galaxy/model/migrate/versions/0057_request_notify.py M lib/galaxy/model/migrate/versions/0058_history_import_export.py M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py M lib/galaxy/model/migrate/versions/0060_history_archive_import.py M lib/galaxy/model/migrate/versions/0061_tasks.py M lib/galaxy/model/migrate/versions/0062_user_openid_table.py M lib/galaxy/model/migrate/versions/0063_sequencer_table.py M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py M lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py M lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py M lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py M lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py M lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py M lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py M lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py M lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py M lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py M lib/galaxy/model/migrate/versions/0080_quota_tables.py M lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py M lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py M lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py M lib/galaxy/model/migrate/versions/0085_add_task_info.py M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py M lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py M lib/galaxy/model/migrate/versions/0093_add_job_params_col.py M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py M lib/galaxy/model/migrate/versions/0095_hda_subsets.py M lib/galaxy/model/migrate/versions/0096_openid_provider.py M lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py M lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py M lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py M lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py M lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py M lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py M lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py M lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py M lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py M lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py M lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py M lib/galaxy/model/migrate/versions/0117_add_user_activation.py M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py M lib/galaxy/model/migrate/versions/0119_job_metrics.py M lib/galaxy/model/migrate/versions/0120_dataset_collections.py M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py M lib/galaxy/model/migrate/versions/0124_job_state_history.py M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py M lib/galaxy/model/migrate/versions/0126_password_reset.py M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py M lib/galaxy/model/migrate/versions/0128_session_timeout.py M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py Log Message: ----------- flake8 lib/galaxy/model/migrate/versions/ . Fix 1429 linting errors. Commit: 920f7950fdb10a4df4a237406c680f65e721942b https://github.com/galaxyproject/galaxy/commit/920f7950fdb10a4df4a237406c68… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M .ci/flake8_blacklist.txt M lib/galaxy/model/migrate/versions/0001_initial_tables.py M lib/galaxy/model/migrate/versions/0002_metadata_file_table.py M lib/galaxy/model/migrate/versions/0003_security_and_libraries.py M lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py M lib/galaxy/model/migrate/versions/0007_sharing_histories.py M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py M lib/galaxy/model/migrate/versions/0009_request_table.py M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0012_user_address.py M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py M lib/galaxy/model/migrate/versions/0014_pages.py M lib/galaxy/model/migrate/versions/0015_tagging.py M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py M lib/galaxy/model/migrate/versions/0019_request_library_folder.py M lib/galaxy/model/migrate/versions/0020_library_upload_job.py M lib/galaxy/model/migrate/versions/0021_user_prefs.py M lib/galaxy/model/migrate/versions/0022_visualization_tables.py M lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py M lib/galaxy/model/migrate/versions/0025_user_info.py M lib/galaxy/model/migrate/versions/0026_cloud_tables.py M lib/galaxy/model/migrate/versions/0027_request_events.py M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py M lib/galaxy/model/migrate/versions/0029_user_actions.py M lib/galaxy/model/migrate/versions/0030_history_slug_column.py M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py M lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py M lib/galaxy/model/migrate/versions/0037_samples_library.py M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py M lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py M lib/galaxy/model/migrate/versions/0040_page_annotations.py M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py M lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py M lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py M lib/galaxy/model/migrate/versions/0046_post_job_actions.py M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py M lib/galaxy/model/migrate/versions/0049_api_keys_table.py M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py M lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py M lib/galaxy/model/migrate/versions/0053_item_ratings.py M lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py M lib/galaxy/model/migrate/versions/0056_workflow_outputs.py M lib/galaxy/model/migrate/versions/0057_request_notify.py M lib/galaxy/model/migrate/versions/0058_history_import_export.py M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py M lib/galaxy/model/migrate/versions/0060_history_archive_import.py M lib/galaxy/model/migrate/versions/0061_tasks.py M lib/galaxy/model/migrate/versions/0062_user_openid_table.py M lib/galaxy/model/migrate/versions/0063_sequencer_table.py M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py M lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py M lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py M lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py M lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py M lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py M lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py M lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py M lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py M lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py M lib/galaxy/model/migrate/versions/0080_quota_tables.py M lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py M lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py M lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py M lib/galaxy/model/migrate/versions/0085_add_task_info.py M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py M lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py M lib/galaxy/model/migrate/versions/0093_add_job_params_col.py M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py M lib/galaxy/model/migrate/versions/0095_hda_subsets.py M lib/galaxy/model/migrate/versions/0096_openid_provider.py M lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py M lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py M lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py M lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py M lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py M lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py M lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py M lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py M lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py M lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py M lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py M lib/galaxy/model/migrate/versions/0117_add_user_activation.py M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py M lib/galaxy/model/migrate/versions/0119_job_metrics.py M lib/galaxy/model/migrate/versions/0120_dataset_collections.py M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py M lib/galaxy/model/migrate/versions/0124_job_state_history.py M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py M lib/galaxy/model/migrate/versions/0126_password_reset.py M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py M lib/galaxy/model/migrate/versions/0128_session_timeout.py M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py Log Message: ----------- Merge pull request #832 from nsoranzo/flake8_fixes Flake8 lib/galaxy/model/migrate/versions/ . Compare: https://github.com/galaxyproject/galaxy/compare/c8533f6e3a86...920f7950fdb1

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[galaxyproject/galaxy] 6d3c8a: Do not split parameter of type "text" during funct...
by GitHub 06 Oct '15

06 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6d3c8a8b08367a6063c06b75778b006df596d4e8 https://github.com/galaxyproject/galaxy/commit/6d3c8a8b08367a6063c06b75778b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2015-10-04 (Sun, 04 Oct 2015) Changed paths: M lib/galaxy/tools/test.py Log Message: ----------- Do not split parameter of type "text" during functional tests. Commit: 35dcbc5afb697a663866033372aaefed6912aaa6 https://github.com/galaxyproject/galaxy/commit/35dcbc5afb697a663866033372aa… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M lib/galaxy/tools/test.py Log Message: ----------- Unindent value.type check Commit: c8533f6e3a8602531c438b379c559a8bd9102e25 https://github.com/galaxyproject/galaxy/commit/c8533f6e3a8602531c438b379c55… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M lib/galaxy/tools/test.py Log Message: ----------- Merge pull request #837 from mvdbeek/No_split_text_functional_tests Do not split parameter of type text during functional tests. Compare: https://github.com/galaxyproject/galaxy/compare/fd3cadc371d7...c8533f6e3a86

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[galaxyproject/galaxy] d4fba9: graph visualization added
by GitHub 06 Oct '15

06 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d4fba962310ea8357516526a941df05572fa2a9e https://github.com/galaxyproject/galaxy/commit/d4fba962310ea8357516526a941d… Author: Eteri <eteri(a)eteri-HP-ENVY-Sleekbook-4-PC.(none)> Date: 2015-06-24 (Wed, 24 Jun 2015) Changed paths: A config/plugins/visualizations/graphviz/README.md A config/plugins/visualizations/graphviz/config/graphviz.xml A config/plugins/visualizations/graphviz/static/css/style.css A config/plugins/visualizations/graphviz/static/img/15xvbd5.png A config/plugins/visualizations/graphviz/static/img/lite-blue-check.png A config/plugins/visualizations/graphviz/static/js/collapse.js A config/plugins/visualizations/graphviz/static/js/cytoscape.min.js A config/plugins/visualizations/graphviz/static/js/graphVis.js A config/plugins/visualizations/graphviz/static/js/jquery.qtip.js A config/plugins/visualizations/graphviz/static/js/tip_centerwindow.js A config/plugins/visualizations/graphviz/static/js/tip_followscroll.js A config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js A config/plugins/visualizations/graphviz/static/js/wz_tooltip.js A config/plugins/visualizations/graphviz/templates/graphviz.mako Log Message: ----------- graph visualization added Commit: fd3cadc371d738ae9dfad68988f08c2508790bfd https://github.com/galaxyproject/galaxy/commit/fd3cadc371d738ae9dfad68988f0… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: A config/plugins/visualizations/graphviz/README.md A config/plugins/visualizations/graphviz/config/graphviz.xml A config/plugins/visualizations/graphviz/static/css/style.css A config/plugins/visualizations/graphviz/static/img/15xvbd5.png A config/plugins/visualizations/graphviz/static/img/lite-blue-check.png A config/plugins/visualizations/graphviz/static/js/collapse.js A config/plugins/visualizations/graphviz/static/js/cytoscape.min.js A config/plugins/visualizations/graphviz/static/js/graphVis.js A config/plugins/visualizations/graphviz/static/js/jquery.qtip.js A config/plugins/visualizations/graphviz/static/js/tip_centerwindow.js A config/plugins/visualizations/graphviz/static/js/tip_followscroll.js A config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js A config/plugins/visualizations/graphviz/static/js/wz_tooltip.js A config/plugins/visualizations/graphviz/templates/graphviz.mako Log Message: ----------- Merge pull request #378 from eteriSokhoyan/dev graph visualization added Compare: https://github.com/galaxyproject/galaxy/compare/cc23adb0a962...fd3cadc371d7

1 0

[galaxyproject/galaxy]
by GitHub 06 Oct '15

06 Oct '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy

1 0

[galaxyproject/galaxy] ea2828: Add new run_tests.sh command to mount the external...
by GitHub 06 Oct '15

06 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ea28282b59e286570d6a4fb2c93259f99db0d1df https://github.com/galaxyproject/galaxy/commit/ea28282b59e286570d6a4fb2c932… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M run_tests.sh Log Message: ----------- Add new run_tests.sh command to mount the external tmp directory. This is an attempt to potentially end these "Text file busy" problems on test: https://jenkins.galaxyproject.org/job/docker-api/170/testReport/junit/api.t…. Commit: cc23adb0a962f1c9780b838604718319a0a71888 https://github.com/galaxyproject/galaxy/commit/cc23adb0a962f1c9780b83860471… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #843 from jmchilton/text_file_busy_2 Allow reuse of parent /tmp directory in dockerized testing. Compare: https://github.com/galaxyproject/galaxy/compare/b5b36c0ab184...cc23adb0a962

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