Connect upload front end to upload tool via tools api

lib/galaxy/webapps/galaxy/api/history_contents.py

@@ -214,69 +214,6 @@ class HistoryContentsController( BaseAPIController, UsesHistoryDatasetAssociatio
             trans.sa_session.flush()
             return hda.to_dict()
 
-        # copy from upload
-        if source == 'upload':
-
-            # get upload specific features
-            dbkey = payload.get('dbkey', None)
-            extension = payload.get('extension', None)
-            space_to_tabs = payload.get('space_to_tabs', False)
-        
-            # check for filename
-            if content.filename is None:
-                trans.response.status = 400
-                return "history_contents:create() : The contents parameter needs to contain the uploaded file content."
-            
-            # create a dataset
-            dataset = trans.app.model.Dataset()
-            trans.sa_session.add(dataset)
-            trans.sa_session.flush()
-            
-            # get file destination
-            file_destination = dataset.get_file_name()
-
-            # check if the directory exists
-            dn = os.path.dirname(file_destination)
-            if not os.path.exists(dn):
-                os.makedirs(dn)
-    
-            # get file and directory names
-            fn = os.path.basename(content.filename)
-    
-            # save file locally
-            open(file_destination, 'wb').write(content.file.read())
-            
-            # log
-            log.info ('The file "' + fn + '" was uploaded successfully.')
-            
-            # replace separation with tabs
-            if space_to_tabs:
-                log.info ('Replacing spaces with tabs.')
-                sniff.convert_newlines_sep2tabs(file_destination)
-            
-            # guess extension
-            if extension is None:
-                log.info ('Guessing extension.')
-                extension = sniff.guess_ext(file_destination)
-    
-            # create hda
-            hda = trans.app.model.HistoryDatasetAssociation(dataset = dataset, name = content.filename,
-                    extension = extension, dbkey = dbkey, history = history, sa_session = trans.sa_session)
-    
-            # add status ok
-            hda.state = hda.states.OK
-            
-            # add dataset to history
-            history.add_dataset(hda, genome_build = dbkey)
-            permissions = trans.app.security_agent.history_get_default_permissions( history )
-            trans.app.security_agent.set_all_dataset_permissions( hda.dataset, permissions )
-            
-            # add to session
-            trans.sa_session.add(hda)
-            trans.sa_session.flush()
-
-            # get name
-            return hda.to_dict()
         else:
             # other options
             trans.response.status = 501

static/scripts/galaxy.modal.js

@@ -38,10 +38,12 @@ var GalaxyModal = Backbone.View.extend(
         this.$body.css('max-height', maxHeight);
         
         // fix height if available
-        if (this.options.height < maxHeight)
-            this.$body.css('height', this.options.height);
-        else
-            this.$body.css('height', maxHeight);
+        if (this.options.height) {
+            if (this.options.height < maxHeight)
+                this.$body.css('height', this.options.height);
+            else
+                this.$body.css('height', maxHeight);
+        }
         
         // remove scroll bar
         if (this.options.height)

static/scripts/galaxy.upload.js

@@ -19,9 +19,7 @@ var GalaxyUpload = Backbone.View.extend(
     
     // extension types
     select_extension : {
-        'auto'  : 'Auto-detect',
-        'bed'   : 'bed',
-        'ab1'   : 'ab1'
+        'auto'  : 'Auto-detect'
     },
     
     // states
@@ -134,18 +132,31 @@ var GalaxyUpload = Backbone.View.extend(
     
         // get element
         var it = this.get_upload_item(index);
-        
-        // read in configuration
-        var data = {
-            source          : "upload",
-            space_to_tabs   : it.find('#space_to_tabs').is(':checked'),
-            extension       : it.find('#extension').val()
-        }
-        
-        // configure url
+
+        // get current history
         var current_history = Galaxy.currHistoryPanel.model.get('id');
-        this.uploadbox.configure({url : galaxy_config.root + "api/histories/" + current_history + "/contents"});
         
+        // configure tool
+        this.uploadbox.configure({url : galaxy_config.root + "api/tools/", paramname : "files_0|file_data"});
+        
+        // get
+        var file_type = it.find('#extension').val();
+        var space_to_tabs = it.find('#space_to_tabs').is(':checked');
+        
+        // configure tool
+        tool_input = {};
+        tool_input['dbkey'] = '?';
+        tool_input['file_type'] = file_type;
+        tool_input['files_0|NAME'] = file.name;
+        tool_input['files_0|type'] = 'upload_dataset';
+        tool_input['space_to_tabs'] = space_to_tabs;
+        
+        // setup data
+        data = {};
+        data['history_id'] = current_history;
+        data['tool_id'] = 'upload1';
+        data['inputs'] = JSON.stringify(tool_input);
+                
         // return additional data to be send with file
         return data;
     },