Merge remote-tracking branch 'upstream/dev' into hashtags

Makefile

@@ -22,14 +22,14 @@ OPEN_RESOURCE=bash -c 'open $$0 || xdg-open $$0'
 SLIDESHOW_TO_PDF?=bash -c 'docker run --rm -v `pwd`:/cwd astefanutti/decktape /cwd/$$0 /cwd/`dirname $$0`/`basename -s .html $$0`.pdf'
 
 all: help
-	@echo "This makefile is primarily used for building Galaxy's JS client. A sensible all target is not yet implemented."
+	@echo "This makefile is used for building Galaxy's JS client, documentation, and drive the release process. A sensible all target is not implemented."
 
-# Building docs requires sphinx and utilities be installed (see issue 3166) as well as pandoc.
-# Run following commands to setup the Python portion of these requirements:
+docs: ## Generate HTML documentation.
+# Run following commands to setup the Python portion of the requirements:
 #   $ ./scripts/common_startup.sh
 #   $ . .venv/bin/activate
-#   $ pip install sphinx sphinx_rtd_theme lxml recommonmark
-docs: ## generate Sphinx HTML documentation, including API docs
+#   $ pip install -r lib/galaxy/dependencies/dev-requirements.txt
+# You also need to install pandoc separately.
 	$(IN_VENV) $(MAKE) -C doc clean
 	$(IN_VENV) $(MAKE) -C doc html
 

client/galaxy/scripts/apps/analysis.js

@@ -95,13 +95,16 @@ window.app = function app( options, bootstrapped ){
             var queryObj = QUERY_STRING.parse( args.pop() );
             args.push( queryObj );
             if( callback ){
-                callback.apply( this, args );
+                if ( this.authenticate( args, name ) ) {
+                    callback.apply( this, args );
+                } else {
+                    this.push( Galaxy.root );
+                }
             }
         },
 
         routes : {
             '(/)' : 'home',
-            // TODO: remove annoying 'root' from root urls
             '(/)root*' : 'home',
             '(/)tours(/)(:tour_id)' : 'show_tours',
             '(/)user(/)' : 'show_user',
@@ -109,6 +112,15 @@ window.app = function app( options, bootstrapped ){
             '(/)custom_builds' : 'show_custom_builds'
         },
 
+        require_login: [
+            'show_user',
+            'show_user_form'
+        ],
+
+        authenticate: function( args, name ) {
+            return ( Galaxy.user && Galaxy.user.id ) || this.require_login.indexOf( name ) == -1;
+        },
+
         show_tours : function( tour_id ){
             if ( tour_id ){
                 Tours.giveTour( tour_id );
@@ -197,4 +209,4 @@ window.app = function app( options, bootstrapped ){
             pushState   : true,
         });
     });
-};
+};

client/galaxy/scripts/mvc/tool/tool-form-composite.js

@@ -151,15 +151,16 @@ define([ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view'
                 if ( step.step_type == 'tool' ) {
                     var data_resolved = true;
                     FormData.visitInputs( step.inputs, function ( input, name, context ) {
+                        var is_runtime_value = input.value && input.value.__class__ == 'RuntimeValue';
                         var is_data_input = ([ 'data', 'data_collection' ]).indexOf( input.type ) != -1;
                         var data_ref = context[ input.data_ref ];
                         input.step_linked && !self._isDataStep( input.step_linked ) && ( data_resolved = false );
                         input.options && ( ( input.options.length == 0 && !data_resolved ) || input.wp_linked ) && ( input.is_workflow = true );
                         data_ref && ( input.is_workflow = ( data_ref.step_linked && !self._isDataStep( data_ref.step_linked ) ) || input.wp_linked );
                         ( is_data_input || ( input.value && input.value.__class__ == 'RuntimeValue' && !input.step_linked ) ) && ( step.collapsed = false );
-                        input.value && input.value.__class__ == 'RuntimeValue' && ( input.value = null );
+                        is_runtime_value && ( input.value = input.default_value );
                         input.flavor = 'workflow';
-                        if ( !is_data_input && input.type !== 'hidden' && !input.wp_linked ) {
+                        if ( !is_runtime_value && !is_data_input && input.type !== 'hidden' && !input.wp_linked ) {
                             if ( input.optional || ( !Utils.isEmpty( input.value ) && input.value !== '' ) ) {
                                 input.collapsible_value = input.value;
                                 input.collapsible_preview = true;

lib/galaxy/dependencies/dev-requirements.txt

@@ -3,3 +3,9 @@ NoseHTML
 twill==0.9.1
 mock
 selenium
+
+# Documentation requirements
+sphinx
+sphinx_rtd_theme
+lxml
+recommonmark

lib/galaxy/dependencies/pinned-requirements.txt

@@ -22,7 +22,7 @@ WebOb==1.4.1
 WebHelpers==1.3
 Mako==1.0.2
 pytz==2015.4
-Babel==2.0
+Babel==2.1.1
 Beaker==1.7.0
 dictobj==0.3.1
 nose==1.3.7

lib/galaxy/objectstore/azure_blob.py

@@ -44,7 +44,6 @@ class AzureBlobObjectStore(ObjectStore):
         self.transfer_progress = 0
         self._parse_config_xml(config_xml)
         self._configure_connection()
-        self.container_lease = self._get_container_lease()
 
         # Clean cache only if value is set in galaxy.ini
         if self.cache_size != -1:
@@ -89,28 +88,6 @@ class AzureBlobObjectStore(ObjectStore):
         self.account = CloudStorageAccount(self.account_name, self.account_key)
         self.service = self.account.create_block_blob_service()
 
-    def _get_container_lease(self):
-        """ Sometimes a handle to a container is not established right away so try
-        it a few times. Raise error is connection is not established. """
-        for i in range(5):
-            try:
-                self.service.break_container_lease(self.container_name)
-                container_lease = self.service.acquire_container_lease(self.container_name)
-                log.debug("Using azure blob store with container '%s'", self.container_name)
-                return container_lease
-            except AzureHttpError:
-                try:
-                    log.debug("container not found, creating azure blob store container with name '%s'", self.container_name)
-                    self.service.create_container(self.container_name)
-                    container_lease = self.service.acquire_container_lease(self.container_name)
-                    return container_lease
-                except AzureHttpError:
-                    log.exception("Could not get container '%s', attempt %s/5", self.container_name, i + 1)
-                    time.sleep(2)
-        # All the attempts have been exhausted and connection was not established,
-        # raise error
-        raise AzureHttpError
-
     def _construct_path(self, obj, base_dir=None, dir_only=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False, **kwargs):
         # extra_dir should never be constructed from provided data but just
         # make sure there are no shenannigans afoot

lib/galaxy/tools/__init__.py

@@ -1835,8 +1835,10 @@ class Tool( object, Dictifiable ):
                     populate_model( input.inputs, group_state, tool_dict[ 'inputs' ], other_values )
                 else:
                     try:
+                        initial_value = input.get_initial_value( request_context, other_values )
                         tool_dict = input.to_dict( request_context, other_values=other_values )
-                        tool_dict[ 'value' ] = input.value_to_basic( state_inputs.get( input.name, input.get_initial_value( request_context, other_values ) ), self.app, use_security=True )
+                        tool_dict[ 'value' ] = input.value_to_basic( state_inputs.get( input.name, initial_value ), self.app, use_security=True )
+                        tool_dict[ 'default_value' ] = input.value_to_basic( initial_value, self.app, use_security=True )
                         tool_dict[ 'text_value' ] = input.value_to_display_text( tool_dict[ 'value' ] )
                     except Exception as e:
                         tool_dict = input.to_dict( request_context )

tox.ini

@@ -8,6 +8,8 @@ whitelist_externals = bash
 deps =
     flake8
     flake8-docstrings
+    # The next dep can be removed when https://gitlab.com/pycqa/flake8-docstrings/issues/19 is fixed
+    pydocstyle<2
 
 [testenv:py33-lint]
 commands = bash .ci/flake8_py3_wrapper.sh
@@ -80,6 +82,8 @@ skip_install = True
 deps =
     flake8
     flake8-docstrings
+    # The next dep can be removed when https://gitlab.com/pycqa/flake8-docstrings/issues/19 is fixed
+    pydocstyle<2
 
 [testenv:py27-lint-docstring-include-list]
 commands = bash .ci/flake8_wrapper_docstrings.sh --include
@@ -88,3 +92,5 @@ skip_install = True
 deps =
     flake8
     flake8-docstrings
+    # The next dep can be removed when https://gitlab.com/pycqa/flake8-docstrings/issues/19 is fixed
+    pydocstyle<2