Maj jflow and fix editable popup on click

bin/jflow_server.py

@@ -202,7 +202,11 @@ class JFlowServer (object):
                     action = "MiltipleAppendAction"
                 else:
                     action = param.action
-                hash_param = {"help": param.help,
+                try:
+                    cparam_help = param.global_help
+                except:
+                    cparam_help = param.help
+                hash_param = {"help": cparam_help,
                               "required": param.required,
                               "default": param.default,
                               "choices": param.choices,
@@ -233,7 +237,7 @@ class JFlowServer (object):
                               "type": sub_param.get_type(),
                               "name": param.name + JFlowServer.MULTIPLE_TYPE_SPLITER + sub_param.flag,
                               "display_name": sub_param.display_name,
-                              "group": param.group})
+                              "group": sub_param.group})
                         if hash_param["sub_parameters"][-1]["type"] == "date":
                             hash_param["sub_parameters"][-1]["format"] = self.jflow_config_reader.get_date_format()
                             if hash_param["sub_parameters"][-1]["format"] == '%d/%m/%Y':
@@ -262,6 +266,20 @@ class JFlowServer (object):
     def run_workflow(self, **kwargs):
         try:
             kwargs_modified = {}
+            
+            # handle MultiParameterList
+            multi_sub_params = {}
+            for key in kwargs.keys():
+                parts = key.split(JFlowServer.MULTIPLE_TYPE_SPLITER)
+                if len(parts) == 3:
+                    if not kwargs_modified.has_key(parts[0]):
+                        kwargs_modified[parts[0]] = []
+                        multi_sub_params[parts[0]] = {}
+                    if multi_sub_params[parts[0]].has_key(parts[2]):
+                        multi_sub_params[parts[0]][parts[2]].append((parts[1], kwargs[key].encode('utf8')))
+                    else:
+                        multi_sub_params[parts[0]][parts[2]] = [(parts[1], kwargs[key].encode('utf8'))]
+            
             for key in kwargs.keys():
                 parts = key.split(JFlowServer.MULTIPLE_TYPE_SPLITER)
                 # split append values
@@ -277,9 +295,13 @@ class JFlowServer (object):
                         kwargs_modified[parts[0]].append((parts[1], new_values))
                     else:
                         kwargs_modified[parts[0]] = [(parts[1], new_values)]
-                # if this is a MultiParameterList
-                # TODO: du cote interface faire qq chose du genre: key.sub_key.1 ... donc si len == 3 
-                # l'objectif etant d'avoir une structure de type: [[(sub_key1: val), (sub_key2: val)], [(sub_key1: val2), (sub_key2: val2)]]
+                                    
+            # handle MultiParameterList
+            for param in multi_sub_params:
+                kwargs_modified[param] = []
+                for sub_param in multi_sub_params[param]:
+                    kwargs_modified[param].append(multi_sub_params[param][sub_param])
+
             workflow = self.wfmanager.run_workflow(kwargs_modified["workflow_class"], kwargs_modified)
             return { "status" : 0, "content" : self.jsonify_workflow_status(workflow, True) }
         except Exception as err:

src/ng6/ng6workflow.py

@@ -132,7 +132,7 @@ class NG6Workflow (BasicNG6Workflow):
         self.add_parameter("sample_id", "The uniq identifier of the sample", add_to = "input_sample")
         self.add_parameter("sample_name", "A descriptive name for the sample", add_to = "input_sample")
         self.add_parameter("sample_description", "A brief description of the sample", add_to = "input_sample")
-        self.add_parameter("type", "Read orientation and type", choices = Sample.AVAILABLE_TYPES, add_to = "input_sample")
+        self.add_parameter("type", "Read orientation and type", choices = Sample.AVAILABLE_TYPES, default='se', add_to = "input_sample")
         self.add_parameter("insert_size", "Insert size for paired end reads", type = int, add_to = "input_sample")
         self.add_parameter("species", "Species related to this sample", add_to = "input_sample")
         self.add_parameter_list("metadata", "Add metadata to the sample", type=samplemetadata  ,add_to = "input_sample")

ui/nG6/pi1/class.tx_nG6_pi1.php

@@ -77,8 +77,10 @@ class tx_nG6_pi1 extends tslib_pibase {
 			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/bootstrap-datepicker.js"></script>	
 			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/bootstrap3-wysihtml5.all.min.js"></script>
 			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/dataTables.bootstrap.js"></script>
-			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/cytoscape.js"></script>
+			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/cytoscape-2.3.7.js"></script>
 			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/cytoscape.js-panzoom.js"></script>
+			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/dagre.js"></script>
+			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/ZeroClipboard.min.js"></script>
 			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/typeahead.bundle.js"></script>
 			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/handsontable.full.min.js"></script>
 			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jflow-activewf.js"></script>

ui/nG6/pi6/class.tx_nG6_pi6.php

@@ -67,8 +67,10 @@ class tx_nG6_pi6 extends tslib_pibase {
 			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.dataTables.min.js"></script>
 			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/bootstrap.min.js"></script>
 			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/dataTables.bootstrap.js"></script>
-			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/cytoscape.js"></script>
+			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/cytoscape-2.3.7.js"></script>
 			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/cytoscape.js-panzoom.js"></script>
+			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/dagre.js"></script>
+			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/ZeroClipboard.min.js"></script>
 			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/typeahead.bundle.js"></script>
 			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/handsontable.full.min.js"></script>
 			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jflow-activewf.js"></script>

ui/nG6/res/css/jflow.css

@@ -185,6 +185,11 @@ animation-delay:1.3s;
 transform:rotate(-135deg);
 }
 
+.handsontable .htDimmed{
+color:#777;
+background-color:#F7F7F9;
+}
+
 @-moz-keyframes fadeG{
 0%{
 background-color:#000000}

ui/nG6/res/js/jflow-wfstatus.js

@@ -221,22 +221,6 @@
 			    	$this.$element.find("#wfstatus_error_location").text( data.errors["location"] );
 			    	$this.$element.find("#wfstatus_error_panel").show();
 		    	}
-
-		    	var layoptions = {
-		    			name: 'breadthfejofijefirst',
-		    			  fit: true, // whether to fit the viewport to the graph
-		    			  directed: true, // whether the tree is directed downwards (or edges can point in any direction if false)
-		    			  padding: 30, // padding on fit
-		    			  circle: false, // put depths in concentric circles if true, put depths top down if false
-		    			  boundingBox: undefined, // constrain layout bounds; { x1, y1, x2, y2 } or { x1, y1, w, h }
-		    			  avoidOverlap: true, // prevents node overlap, may overflow boundingBox if not enough space
-		    			  roots: undefined, // the roots of the trees
-		    			  maximalAdjustments: 0, // how many times to try to position the nodes in a maximal way (i.e. no backtracking)
-		    			  animate: false, // whether to transition the node positions
-		    			  animationDuration: 500, // duration of animation in ms if enabled
-		    			  ready: undefined, // callback on layoutready
-		    			  stop: undefined // callback on layoutstop*/
-		    	};
 		    	
 		    	$('#cytoscape_panel').cytoscape({
 		    		  style: cytoscape.stylesheet()
@@ -284,19 +268,23 @@
 			    		  edges: edges
 		    		  },
 		    		  layout: {
-		    			  name: 'breadthfirst',
-		    			  fit: true, // whether to fit the viewport to the graph
-		    			  directed: true, // whether the tree is directed downwards (or edges can point in any direction if false)
-		    			  padding: 30, // padding on fit
-		    			  circle: false, // put depths in concentric circles if true, put depths top down if false
-		    			  boundingBox: undefined, // constrain layout bounds; { x1, y1, x2, y2 } or { x1, y1, w, h }
-		    			  avoidOverlap: true, // prevents node overlap, may overflow boundingBox if not enough space
-		    			  roots: undefined, // the roots of the trees
-		    			  maximalAdjustments: 0, // how many times to try to position the nodes in a maximal way (i.e. no backtracking)
+		    			  name: 'dagre',
+
+		    			  // dagre algo options, uses default value on undefined
+		    			  nodeSep: undefined, // the separation between adjacent nodes in the same rank
+		    			  edgeSep: undefined, // the separation between adjacent edges in the same rank
+		    			  rankSep: undefined, // the separation between adjacent nodes in the same rank
+		    			  rankDir: 'LR', // 'TB' for top to bottom flow, 'LR' for left to right
+		    			  minLen: function( edge ){ return 1; }, // number of ranks to keep between the source and target of the edge
+		    			  
+		    			  // general layout options
+		    			  fit: true, // whether to fit to viewport
+		    			  padding: 30, // fit padding
 		    			  animate: false, // whether to transition the node positions
 		    			  animationDuration: 500, // duration of animation in ms if enabled
-		    			  ready: undefined, // callback on layoutready
-		    			  stop: undefined // callback on layoutstop
+		    			  boundingBox: undefined, // constrain layout bounds; { x1, y1, x2, y2 } or { x1, y1, w, h }
+		    			  ready: function(){}, // on layoutready
+		    			  stop: function(){} // on layoutstop
 		    		  },
 		    		  ready: function(){
 		    		    window.cy = this;

ui/nG6/res/js/tx_nG6_pi1.js

@@ -1407,15 +1407,15 @@ function showEditableFromTD(e) {
 }
 
 function initEditableFields() {
-    $('span.editable > a').click(function() {
-    	$('td.editable').unbind('click', showEditableFromTD);
-    });
     $('span.editable').editable({
     	toggle: 'manual',
     	display: function(value) {
     		if ($(this).html().indexOf('<a') == 0) {
     			var newlink = $($(this).html()).html(value);
         		$(this).html(newlink);
+        		$(this).find('a').click(function() {
+        	    	$('td.editable').unbind('click', showEditableFromTD);
+        	    });
     		} else {
     			$(this).html(value);
     		}