Merge branch 'dev' of https://github.com/galaxyproject/galaxy into po…

…stgresql_datatype

.ci/flake8_lint_include_list.txt

@@ -1,9 +1,6 @@
 client/galaxy/style/source_material/circle.py
 contrib/
-cron/add_manual_builds.py
-cron/cleanup_datasets.py
-cron/parse_builds_3_sites.py
-cron/parse_builds.py
+cron/
 doc/parse_gx_xsd.py
 lib/galaxy/actions/
 lib/galaxy/auth/
@@ -77,6 +74,7 @@ lib/galaxy/visualization/genome/
 lib/galaxy/visualization/genomes.py
 lib/galaxy/visualization/__init__.py
 lib/galaxy/visualization/plugins/__init__.py
+lib/galaxy/visualization/plugins/plugin.py
 lib/galaxy/visualization/plugins/utils.py
 lib/galaxy/visualization/tracks/
 lib/galaxy/web/base/
@@ -152,182 +150,7 @@ lib/log_tempfile.py
 lib/mimeparse.py
 lib/psyco_full.py
 lib/tool_shed/
-scripts/api/common.py
-scripts/api/copy_hda_to_library_folder.py
-scripts/api/create.py
-scripts/api/delete.py
-scripts/api/example_watch_folder.py
-scripts/api/filter_failed_datasets_from_collection.py
-scripts/api/form_create_from_xml.py
-scripts/api/history_create_history.py
-scripts/api/history_delete_history.py
-scripts/api/import_library_dataset_to_history.py
-scripts/api/import_workflows_from_installed_tool_shed_repository.py
-scripts/api/install_tool_shed_repositories.py
-scripts/api/library_create_folder.py
-scripts/api/library_create_library.py
-scripts/api/library_upload_dir.py
-scripts/api/library_upload_from_import_dir.py
-scripts/api/load_data_with_metadata.py
-scripts/api/repair_tool_shed_repository.py
-scripts/api/requests_update_state.py
-scripts/api/request_type_create_from_xml.py
-scripts/api/reset_metadata_on_installed_repositories.py
-scripts/api/sample_dataset_update_status.py
-scripts/api/sample_update_state.py
-scripts/api/sequencer_configuration_create.py
-scripts/api/update.py
-scripts/api/upload_to_history.py
-scripts/api/workflow_delete.py
-scripts/api/workflow_execute_parameters.py
-scripts/api/workflow_execute.py
-scripts/api/workflow_import_from_file_rpark.py
-scripts/api/workflow_import.py
-scripts/auth/
-scripts/bootstrap_history.py
-scripts/build_toolbox.py
-scripts/build_universe_config.py
-scripts/check_galaxy.py
-scripts/check_python.py
-scripts/cleanup_datasets/
-scripts/communication/
-scripts/create_db.py
-scripts/data_libraries/
-scripts/db_shell.py
-scripts/drmaa_external_killer.py
-scripts/drmaa_external_runner.py
-scripts/external_chown_script.py
-scripts/extract_dataset_part.py
-scripts/extract_toolbox_sections.py
-scripts/functional_tests.py
-scripts/get_platforms.py
-scripts/helper.py
-scripts/__init__.py
-scripts/loc_files/
-scripts/manage_db.py
-scripts/manage_tools.py
-scripts/metagenomics/
-scripts/microbes/create_bacteria_loc_file.py
-scripts/microbes/create_bacteria_table.py
-scripts/microbes/create_nib_seq_loc_file.py
-scripts/microbes/get_builds_lengths.py
-scripts/microbes/ncbi_to_ucsc.py
-scripts/microbes/util.py
-scripts/migrate_tools/
-scripts/nosetests.py
-scripts/others/
-scripts/runtime_stats.py
-scripts/secret_decoder_ring.py
-scripts/set_dataset_sizes.py
-scripts/set_user_disk_usage.py
-scripts/sync_reports_config.py
-scripts/tool_shed/api/add_repository_registry_entry.py
-scripts/tool_shed/api/common.py
-scripts/tool_shed/api/create_categories.py
-scripts/tool_shed/api/create_users.py
-scripts/tool_shed/api/import_capsule.py
-scripts/tool_shed/api/remove_repository_registry_entry.py
-scripts/tool_shed/api/reset_metadata_on_repositories.py
-scripts/tool_shed/api/tool_shed_repository_revision_update.py
-scripts/tool_shed/build_ts_whoosh_index.py
-scripts/tool_shed/check_download_urls.py
-scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py
-scripts/tool_shed/clean_up_tool_dependency_directory.py
-scripts/tool_shed/migrate_tools_to_repositories.py
-scripts/tool_shed/show_tool_dependency_installation_dir_contents.py
-scripts/tools/re_escape_output.py
-test/api/__init__.py
-test/api/test_dataset_collections.py
-test/api/test_datasets.py
-test/api/test_framework.py
-test/api/test_history_contents_provenance.py
-test/api/test_jobs.py
-test/api/test_libraries.py
-test/api/test_page_revisions.py
-test/api/test_search.py
-test/api/test_tool_data.py
-test/api/test_tours.py
-test/api/test_workflow_extraction.py
-test/api/test_workflows_from_yaml.py
-test/base/api_asserts.py
-test/base/api.py
-test/base/api_util.py
-test/base/__init__.py
-test/base/instrument.py
-test/base/integration_util.py
-test/base/interactor.py
-test/base/nose_util.py
-test/base/test_logging.py
-test/base/tool_shed_util.py
-test/base/twilltestcase.py
-test/base/workflows_format_2/
-test/casperjs/
-test/functional/database_contexts.py
-test/functional/__init__.py
-test/functional/test_data_managers.py
-test/functional/tool-data/
-test/functional/tools/
-test/integration/
-test/manual/__init__.py
-test/shed_functional/base/common.py
-test/shed_functional/base/__init__.py
-test/shed_functional/functional/
-test/shed_functional/functional_tests.py
-test/shed_functional/__init__.py
-test/unit/dataset_collections/
-test/unit/datatypes/dataproviders/__init__.py
-test/unit/datatypes/dataproviders/test_line_dataproviders.py
-test/unit/datatypes/__init__.py
-test/unit/datatypes/test_data.py
-test/unit/jobs/dynamic_tool_destination/
-test/unit/jobs/__init__.py
-test/unit/jobs/test_command_factory.py
-test/unit/jobs/test_datasets.py
-test/unit/jobs/test_job_configuration.py
-test/unit/jobs/test_job_output_checker.py
-test/unit/jobs/test_mapper.py
-test/unit/jobs/test_rule_helper.py
-test/unit/jobs/test_rules/
-test/unit/jobs/test_runner_params.py
-test/unit/managers/__init__.py
-test/unit/managers/test_CollectionManager.py
-test/unit/managers/test_DatasetManager.py
-test/unit/managers/test_HDAManager.py
-test/unit/managers/test_HDCAManager.py
-test/unit/managers/test_HistoryContentsManager.py
-test/unit/managers/test_UserManager.py
-test/unit/shed_unit/__init__.py
-test/unit/shed_unit/test_fabric_util.py
-test/unit/shed_unit/test_td_common_util.py
-test/unit/test_galaxy_transactions.py
-test/unit/test_lazy_process.py
-test/unit/test_objectstore.py
-test/unit/test_routes.py
-test/unit/test_security_helper.py
-test/unit/test_sockets.py
-test/unit/test_sqlite_utils.py
-test/unit/test_topsort.py
-test/unit/tools/filter_modules/
-test/unit/tools/__init__.py
-test/unit/tools/test_citations.py
-test/unit/tools/test_conda_resolution.py
-test/unit/tools/test_parsing.py
-test/unit/tools/test_select_parameters.py
-test/unit/tools/test_toolbox_filters.py
-test/unit/tools/test_tool_dependency_description.py
-test/unit/tools/test_tool_deps.py
-test/unit/tools/test_tool_external_files.py
-test/unit/tools/test_tool_loader.py
-test/unit/tools/test_tool_panel.py
-test/unit/tools/test_watcher.py
-test/unit/tools/test_wrappers.py
-test/unit/tools_support.py
-test/unit/unittest_utils/
-test/unit/visualizations/__init__.py
-test/unit/visualizations/plugins/__init__.py
-test/unit/web/base/__init__.py
-test/unit/web/framework/__init__.py
-test/unit/web/__init__.py
-test/unit/workflows/
+scripts/
+test/
 tool_list.py
 tools/

client/galaxy/scripts/apps/analysis.js

@@ -15,6 +15,7 @@ var jQuery = require( 'jquery' ),
     Workflows = require( 'mvc/workflow/workflow' ),
     HistoryList = require( 'mvc/history/history-list' ),
     ToolFormComposite = require( 'mvc/tool/tool-form-composite' ),
+    QueryStringParsing = require( 'utils/query-string-parsing' ),
     Utils = require( 'utils/utils' ),
     Ui = require( 'mvc/ui/ui-misc' ),
     DatasetError = require( 'mvc/dataset/dataset-error' ),
@@ -46,8 +47,10 @@ window.app = function app( options, bootstrapped ){
             '(/)workflow(/)' : 'show_workflows',
             '(/)workflow/run(/)' : 'show_run',
             '(/)pages(/)(:action_id)' : 'show_pages',
+            '(/)visualizations(/)edit(/)' : 'show_visualizations_edit',
             '(/)visualizations/(:action_id)' : 'show_visualizations',
             '(/)workflows/list_published(/)' : 'show_workflows_published',
+            '(/)histories(/)rename(/)' : 'show_histories_rename',
             '(/)histories(/)(:action_id)' : 'show_histories',
             '(/)datasets(/)list(/)' : 'show_datasets',
             '(/)workflow/import_workflow' : 'show_import_workflow',
@@ -87,6 +90,10 @@ window.app = function app( options, bootstrapped ){
             this.page.display( new GridShared.View( { action_id: action_id, plural: 'Visualizations', item: 'visualization' } ) );
         },
 
+        show_visualizations_edit : function() {
+            this.page.display( new FormWrapper.View ( { url : 'visualization/edit?id=' + QueryStringParsing.get( 'id' ), redirect: 'visualizations/list' } ) );
+        },
+
         show_workflows_published : function() {
             this.page.display( new GridView( { url_base: Galaxy.root + 'workflow/list_published', dict_format: true } ) );
         },
@@ -95,6 +102,10 @@ window.app = function app( options, bootstrapped ){
             this.page.display( new HistoryList.View( { action_id: action_id } ) );
         },
 
+        show_histories_rename : function() {
+            this.page.display( new FormWrapper.View ( { url : 'history/rename?id=' + QueryStringParsing.get( 'id' ), redirect: 'histories/list' } ) );
+        },
+
         show_datasets : function() {
             this.page.display( new GridView( { url_base: Galaxy.root + 'dataset/list', dict_format: true } ) );
         },