Cloud ObjectStore

.ci/autopep8.sh

@@ -0,0 +1,2 @@
+exclude=$(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_blacklist.txt | paste -s -d ',' - )
+autopep8 -i -r --exclude $exclude --select E11,E101,E127,E201,E202,E22,E301,E302,E303,E304,E306,E711,W291,W292,W293,W391 ./lib/ ./test/

.ci/flake8_lint_include_list.txt

@@ -79,9 +79,7 @@ lib/galaxy/visualization/__init__.py
 lib/galaxy/visualization/plugins/__init__.py
 lib/galaxy/visualization/plugins/utils.py
 lib/galaxy/visualization/tracks/
-lib/galaxy/web/base/controllers/__init__.py
-lib/galaxy/web/base/__init__.py
-lib/galaxy/web/base/interactive_environments.py
+lib/galaxy/web/base/
 lib/galaxy/web/buildapp.py
 lib/galaxy/web/formatting.py
 lib/galaxy/web/framework/base.py
@@ -96,6 +94,7 @@ lib/galaxy/web/framework/middleware/static.py
 lib/galaxy/web/framework/middleware/statsd.py
 lib/galaxy/web/framework/middleware/translogger.py
 lib/galaxy/web/framework/middleware/xforwardedhost.py
+lib/galaxy/web/framework/webapp.py
 lib/galaxy/web/__init__.py
 lib/galaxy/web/params.py
 lib/galaxy/webapps/galaxy/api/genomes.py
@@ -108,6 +107,7 @@ lib/galaxy/webapps/galaxy/api/roles.py
 lib/galaxy/webapps/galaxy/api/samples.py
 lib/galaxy/webapps/galaxy/api/tools.py
 lib/galaxy/webapps/galaxy/api/tours.py
+lib/galaxy/webapps/galaxy/api/users.py
 lib/galaxy/webapps/galaxy/api/workflows.py
 lib/galaxy/webapps/galaxy/config_watchers.py
 lib/galaxy/webapps/galaxy/controllers/async.py
@@ -190,6 +190,7 @@ 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
@@ -216,6 +217,7 @@ 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

.ci/py3_sources.txt

@@ -27,16 +27,19 @@ lib/galaxy/tools/
 lib/galaxy/tours/
 lib/galaxy/util/
 lib/galaxy/visualization/
+lib/galaxy/web/base/
 lib/galaxy/web/buildapp.py
 lib/galaxy/web/framework/base.py
 lib/galaxy/web/framework/decorators.py
 lib/galaxy/web/framework/__init__.py
 lib/galaxy/web/framework/middleware/error.py
 lib/galaxy/web/framework/middleware/static.py
 lib/galaxy/web/framework/middleware/statsd.py
+lib/galaxy/web/framework/webapp.py
 lib/galaxy/web/__init__.py
 lib/galaxy/webapps/galaxy/api/histories.py
 lib/galaxy/webapps/galaxy/api/tours.py
+lib/galaxy/webapps/galaxy/api/users.py
 lib/galaxy/webapps/galaxy/api/workflows.py
 lib/galaxy/webapps/galaxy/controllers/external_services.py
 lib/galaxy/webapps/galaxy/controllers/search.py
@@ -63,9 +66,11 @@ scripts/check_eggs.py
 scripts/check_galaxy.py
 scripts/check_python.py
 scripts/cleanup_datasets/
+scripts/communication/
 scripts/data_libraries/build_whoosh_index.py
 scripts/db_shell.py
 scripts/drmaa_external_runner.py
+scripts/secret_decoder_ring.py
 test/
 tool_list.py
 tools/

Makefile

@@ -10,6 +10,7 @@ MY_UPSTREAM:=origin
 VENV?=.venv
 # Source virtualenv to execute command (flake8, sphinx, twine, etc...)
 IN_VENV=if [ -f $(VENV)/bin/activate ]; then . $(VENV)/bin/activate; fi;
+CONFIG_MANAGE=$(IN_VENV) python lib/galaxy/webapps/config_manage.py
 PROJECT_URL?=https://github.com/galaxyproject/galaxy
 GRUNT_DOCKER_NAME:=galaxy/client-builder:16.01
 GRUNT_EXEC?=node_modules/grunt-cli/bin/grunt
@@ -52,6 +53,42 @@ open-project: ## open project on github
 lint: ## check style using tox and flake8 for Python 2 and Python 3
 	$(IN_VENV) tox -e py27-lint && tox -e py34-lint
 
+uwsgi-rebuild-validation: ## rebuild uwsgi_config.yml kwalify schema against latest uwsgi master.
+	$(CONFIG_MANAGE) build_uwsgi_yaml
+
+tool-shed-config-validate: ## validate tool shed YAML configuration file
+	$(CONFIG_MANAGE) validate tool_shed
+
+tool-shed-config-lint: ## lint tool shed YAML configuration file
+	$(CONFIG_MANAGE) lint tool_shed
+
+tool-shed-config-convert-dry-run: ## convert old style tool shed ini to yaml (dry run)
+	$(CONFIG_MANAGE) convert tool_shed --dry-run
+
+tool-shed-config-convert: ## convert old style tool shed ini to yaml
+	$(CONFIG_MANAGE) convert tool_shed
+
+tool-shed-config-rebuild-sample: ## Rebuild sample tool shed yaml file from schema
+	$(CONFIG_MANAGE) build_sample_yaml tool_shed --add-comments
+
+reports-config-validate: ## validate reports YAML configuration file
+	$(CONFIG_MANAGE) validate reports
+
+reports-config-convert-dry-run: ## convert old style reports ini to yaml (dry run)
+	$(CONFIG_MANAGE) convert reports --dry-run
+
+reports-config-convert: ## convert old style reports ini to yaml
+	$(CONFIG_MANAGE) convert reports
+
+reports-config-rebuild-sample: ## Rebuild sample reports yaml file from schema
+	$(CONFIG_MANAGE) build_sample_yaml reports --add-comments
+
+reports-config-lint: ## lint reports YAML configuration file
+	$(CONFIG_MANAGE) lint reports
+
+reports-config-rebuild-rst: ## Rebuild sample reports RST docs
+	$(CONFIG_MANAGE) build_rst reports > doc/source/admin/reports_options.rst
+
 release-ensure-upstream: ## Ensure upstream branch for release commands setup
 ifeq (shell git remote -v | grep $(RELEASE_UPSTREAM), )
 	git remote add $(RELEASE_UPSTREAM) [email protected]:galaxyproject/galaxy.git

client/galaxy/scripts/apps/admin.js

@@ -2,16 +2,121 @@ var jQuery = require( 'jquery' ),
     $ = jQuery,
     GalaxyApp = require( 'galaxy' ).GalaxyApp,
     AdminPanel = require( './panels/admin-panel' ),
+    FormWrapper = require( 'mvc/form/form-wrapper' ),
+    GridView = require( 'mvc/grid/grid-view' ),
+    Ui = require( 'mvc/ui/ui-misc' ),
+    QueryStringParsing = require( 'utils/query-string-parsing' ),
+    Router = require( 'layout/router' ),
     Page = require( 'layout/page' );
 
 window.app = function app( options, bootstrapped ){
     window.Galaxy = new GalaxyApp( options, bootstrapped );
     Galaxy.debug( 'admin app' );
-    Galaxy.params = Galaxy.config.params;
-    $(function(){
+
+    /** Routes */
+    var AdminRouter = Router.extend({
+        routes: {
+            '(/)admin(/)users' : 'show_users',
+            '(/)admin(/)roles' : 'show_roles',
+            '(/)admin(/)groups' : 'show_groups',
+            '(/)admin(/)tool_versions' : 'show_tool_versions',
+            '(/)admin(/)quotas' : 'show_quotas',
+            '(/)admin(/)forms(/)(:form_id)' : 'show_forms'
+        },
+
+        authenticate: function( args, name ) {
+            return Galaxy.user && Galaxy.user.id && Galaxy.user.get( 'is_admin' );
+        },
+
+        show_users: function() {
+            this.page.display( new GridView( { url_base: Galaxy.root + 'admin/users_list', url_data: Galaxy.params, dict_format: true } ) );
+        },
+
+        show_roles: function() {
+            this.page.display( new GridView( { url_base: Galaxy.root + 'admin/roles_list', url_data: Galaxy.params, dict_format: true } ) );
+        },
+
+        show_groups: function() {
+            this.page.display( new GridView( { url_base: Galaxy.root + 'admin/groups_list', url_data: Galaxy.params, dict_format: true } ) );
+        },
+
+        show_tool_versions: function() {
+            this.page.display( new GridView( { url_base: Galaxy.root + 'admin/tool_versions_list', url_data: Galaxy.params, dict_format: true } ) );
+        },
+
+        show_quotas: function() {
+            this.page.display( new GridView( { url_base: Galaxy.root + 'admin/quotas_list', url_data: Galaxy.params, dict_format: true } ) );
+        },
+
+        show_forms : function( form_id ) {
+            var id = '?id=' + QueryStringParsing.get( 'id' );
+            var form_defs = {
+                reset_user_password: {
+                    title           : 'Reset passwords',
+                    url             : 'admin/reset_user_password' + id,
+                    icon            : 'fa-user',
+                    submit_title    : 'Save new password',
+                    redirect        : 'admin/users'
+                },
+                manage_roles_and_groups_for_user: {
+                    url             : 'admin/manage_roles_and_groups_for_user' + id,
+                    icon            : 'fa-users',
+                    redirect        : 'admin/users'
+                },
+                manage_users_and_groups_for_role: {
+                    url             : 'admin/manage_users_and_groups_for_role' + id,
+                    redirect        : 'admin/roles'
+                },
+                manage_users_and_roles_for_group: {
+                    url             : 'admin/manage_users_and_roles_for_group' + id,
+                    redirect        : 'admin/groups'
+                },
+                manage_users_and_groups_for_quota: {
+                    url             : 'admin/manage_users_and_groups_for_quota' + id,
+                    redirect        : 'admin/quotas'
+                },
+                create_role: {
+                    url             : 'admin/create_role',
+                    redirect        : 'admin/roles'
+                },
+                create_group: {
+                    url             : 'admin/create_group',
+                    redirect        : 'admin/groups'
+                },
+                create_quota: {
+                    url             : 'admin/create_quota',
+                    redirect        : 'admin/quotas'
+                },
+                rename_role: {
+                    url             : 'admin/rename_role' + id,
+                    redirect        : 'admin/roles'
+                },
+                rename_group: {
+                    url             : 'admin/rename_group' + id,
+                    redirect        : 'admin/groups'
+                },
+                rename_quota: {
+                    url             : 'admin/rename_quota' + id,
+                    redirect        : 'admin/quotas'
+                },
+                edit_quota: {
+                    url             : 'admin/edit_quota' + id,
+                    redirect        : 'admin/quotas'
+                },
+                set_quota_default: {
+                    url             : 'admin/set_quota_default' + id,
+                    redirect        : 'admin/quotas'
+                },
+            };
+            this.page.display( new FormWrapper.View ( form_defs[ form_id ] ) );
+        }
+    });
+
+    $(function() {
         _.extend( options.config, { active_view : 'admin' } );
         Galaxy.page = new Page.View( _.extend( options, {
-            Left : AdminPanel
+            Left    : AdminPanel,
+            Router  : AdminRouter
         } ) );
     });
 };