Merge branch 'dev' into ui_pref_routing

.ci/flake8_blacklist.txt

@@ -5,3 +5,4 @@ database/
 doc/source/conf.py
 eggs/
 lib/galaxy/util/jstree.py
+lib/galaxy/web/proxy/js/node_modules/

client/galaxy/scripts/mvc/grid/grid-view.js

@@ -155,18 +155,6 @@ return Backbone.View.extend({
             });
         });
 
-        // Initialize autocomplete for text inputs in search UI.
-        var t1 = this.$el.find('#input-tags-filter');
-        if (t1.length) {
-            t1.autocomplete(this.grid.history_tag_autocomplete_url,
-                { selectFirst: false, autoFill: false, highlight: false, mustMatch: false });
-        }
-        var t2 = this.$el.find('#input-name-filter');
-        if (t2.length) {
-            t2.autocomplete(this.grid.history_name_autocomplete_url,
-                { selectFirst: false, autoFill: false, highlight: false, mustMatch: false });
-        }
-
         // Initialize standard, advanced search toggles.
         this.$el.find('.advanced-search-toggle').each( function() {
             $(this).off();

config/datatypes_conf.xml.sample

@@ -218,6 +218,7 @@
     <datatype extension="mgf" type="galaxy.datatypes.proteomics:Mgf" display_in_upload="true" />
     <datatype extension="wiff" type="galaxy.datatypes.proteomics:Wiff" display_in_upload="true" />
     <datatype extension="mzxml" type="galaxy.datatypes.proteomics:MzXML" mimetype="application/xml" display_in_upload="true" />
+    <datatype extension="mzdata" type="galaxy.datatypes.proteomics:MzData" mimetype="application/xml" display_in_upload="true" />
     <datatype extension="ms2" type="galaxy.datatypes.proteomics:Ms2" display_in_upload="true" />
     <datatype extension="mzq" type="galaxy.datatypes.proteomics:MzQuantML" mimetype="application/xml" display_in_upload="true" />
     <datatype extension="mz.sqlite" type="galaxy.datatypes.binary:MzSQlite" mimetype="application/octet-stream" display_in_upload="true" />

config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample

@@ -6,7 +6,7 @@
 # appropriate `apt-get/pip install` statements.
 ---
 -
-    image: bgruening/docker-jupyter-notebook:16.01
+    image: bgruening/docker-jupyter-notebook:16.01.1
     description: |
         The Jupyter notebook is the next iteration of IPython, allowing
         analysis in many different languages. This image features the Python,

lib/galaxy/datatypes/proteomics.py

@@ -152,6 +152,14 @@ class MzXML(ProteomicsXml):
     root = "mzXML"
 
 
+class MzData(ProteomicsXml):
+    """mzData data"""
+    edam_format = "format_3245"
+    file_ext = "mzdata"
+    blurb = "mzData Mass Spectrometry data"
+    root = "mzData"
+
+
 class MzIdentML(ProteomicsXml):
     edam_format = "format_3247"
     file_ext = "mzid"

lib/galaxy/visualization/plugins/plugin.py

@@ -274,7 +274,16 @@ def get_api_key():
             render_vars[ 'plugin_path' ] = os.path.abspath( self.path )
 
         if self.config.get( 'plugin_type', 'visualization' ) == "interactive_environment":
-            request = self.INTENV_REQUEST_FACTORY( trans, self )
+            try:
+                request = self.INTENV_REQUEST_FACTORY( trans, self )
+            except:
+                log.exception("IE plugin request handling failed")
+                return trans.fill_template( 'message.mako',
+                    message='Loading the interactive environment failed, please contact the {admin_tag} for assistance'.format(
+                        admin_tag='<a href="mailto:{admin_mail}">Galaxy administrator</a>'.format(
+                            admin_mail=trans.app.config.error_email_to)
+                        if trans.app.config.error_email_to else 'Galaxy administrator'),
+                    status='error')
             render_vars[ "ie_request" ] = request
 
         template_filename = self.config[ 'entry_point' ][ 'file' ]

lib/galaxy/webapps/galaxy/controllers/history.py

@@ -1261,21 +1261,6 @@ def set_accessible_async( self, trans, id=None, accessible=False ):
         return
         # TODO: used in page/editor.mako
 
-    @web.expose
-    def name_autocomplete_data( self, trans, q=None, limit=None, timestamp=None ):
-        """Return autocomplete data for history names"""
-        user = trans.get_user()
-        if not user:
-            return
-
-        ac_data = ""
-        for history in ( trans.sa_session.query( model.History )
-                         .filter_by( user=user )
-                         .filter( func.lower( model.History.name ).like(q.lower() + "%") ) ):
-            ac_data = ac_data + history.name + "\n"
-        return ac_data
-        # TODO: used in grid_base.mako
-
     @web.expose
     @web.require_login( "rename histories" )
     def rename( self, trans, id=None, name=None, **kwd ):

scripts/bootstrap_history.py

@@ -100,15 +100,17 @@
 **Feature3**
   Feature description.
 
-`Github <https://github.com/galaxyproject/galaxy>`__
-===========================================================
+Get Galaxy
+==========
+
+The code lives at `Github <https://github.com/galaxyproject/galaxy>`__ and you should have `Git <https://git-scm.com/>`__ to obtain it.
 
-New Galaxy repository
+To get a new Galaxy repository run:
   .. code-block:: shell
 
       $$ git clone -b release_${release} https://github.com/galaxyproject/galaxy.git
 
-Update of existing Galaxy repository
+To update an existing Galaxy repository run:
   .. code-block:: shell
 
       $$ git checkout release_${release} && git pull --ff-only origin release_${release}

templates/grid_base.mako

@@ -101,7 +101,6 @@
         'cur_page_num'                  : cur_page_num,
         'num_pages'                     : num_pages,
         'num_page_links'                : num_page_links,
-        'history_tag_autocomplete_url'  : url( controller='tag', action='tag_autocomplete_data', item_class=item_class ),
         'status'                        : status,
         'message'                       : util.restore_text(message),
         'global_actions'                : [],