make available browsefile as type

src/jflow/workflow.py

@@ -334,7 +334,7 @@ class Workflow(threading.Thread):
             # handle upload inputs
             try: is_local = os.path.isfile(args[param])
             except: is_local = False
-            if not is_uri and not is_local and kparams[param].type.__name__ == "inputfile":
+            if not is_uri and not is_local and (kparams[param].type.__name__ == "inputfile" or kparams[param].type.__name__ == "browsefile"):
                 if args[param].__class__.__name__ == "list":
                     for i, val in enumerate(args[param]):
                         if args[param][i]:

src/js/jflow-wfform.js

@@ -200,9 +200,9 @@ jQuery.validator.addMethod("exclude_required", function(value, element, options)
 				$this = this;
 
 			// before serializing, all inputs have to be abled, otherwise they are not transmitted
-	    	$("span[id^=inputfile_]").each(function(){
+	    	$("[id^=urlfile_btn_]").each(function(){
 	    		var parts = $(this).attr("id").split("_"),
-					tid = parts.slice(1, parts.lenght).join("_");
+					tid = parts.slice(2, parts.lenght).join("_");
 	    		$("#"+tid).removeAttr('disabled');
 	    		// change the name of the val by the file name with the prefix
 	    		if ($("#"+tid).val()) {
@@ -366,6 +366,14 @@ jQuery.validator.addMethod("exclude_required", function(value, element, options)
 			crule["number"] = true;
 		} else if (param.type == "date") {
 			crule["date"] = true;
+		} else if (param.type == "browsefile") {
+			crule["remote"] = {
+	    			url: server_url + '/validate_field?callback=?',
+	    			type: "post",
+	    			data: {
+	    				type: "str"
+	    			}
+				};
 		} else if (param.type == "inputfile") {
 			crule["remote"] = {
     			url: server_url + '/validate_field?callback=?',
@@ -468,6 +476,12 @@ jQuery.validator.addMethod("exclude_required", function(value, element, options)
 			'      <button id="urlfile_btn_${param.name}" style="display: none;" class="btn" type="button"><i class="icon-search"></i></button>',
 			'    </div>',
 			'  </div>',
+			// if param is a browsefile 			
+			'{{else param.type == "browsefile"}}',
+			'  <div class="input-append">',
+			'    <input id="${param.name}" name="${param.name}" class="${param.group} ${input_size}" type="text" value="${param.default}" disabled>',
+			'    <button id="urlfile_btn_${param.name}" class="btn" type="button"><i class="icon-search"></i></button>',
+			'  </div>',
 			// if param is a boolean 
 			'{{else param.type == "bool"}}',
 			'  <label class="checkbox">',
@@ -542,8 +556,8 @@ jQuery.validator.addMethod("exclude_required", function(value, element, options)
 			'<form method="post" enctype="multipart/form-data" style="display:none;">',
 			'  {{each(gindex, group) workflow.groups}}',
 			'    {{each(index, param) workflow.parameters_per_groups[group]}}',
-			// if param is an inputfile 			
-			'		{{if param.type == "inputfile"}}',
+			// if param is an inputfile or just a browsefile
+			'		{{if param.type == "inputfile" || param.type == "browsefile"}}',
 			'			<input name="browse_${param.name}" id="browse_${param.name}" class="fileupload" type="file">',
 			'		{{/if}}',
 			'    {{/each}}',

workflows/alignment/workflow.properties

@@ -26,8 +26,8 @@ description = align reads against a reference genome
 #      .help: a brief description of what the parameter does
 #      .default [None]: the value produced if the parameter is not provided
 #      .type [str]: the parameter type that should be tested, this can be:
-#          str|int|date|inputfile|urlfile|localfile|bool|... all types defined 
-#          in the types.py package)
+#          str|int|date|inputfile|urlfile|localfile|browsefile|bool|... all types 
+#          defined in the types.py package)
 #      .choices [None]: a container of the allowable values for the parameter
 #      .required [False]: whether or not the command-line option may be omitted
 #      .action [store]: the basic type of action to be taken (store|append)

workflows/types.py

@@ -29,6 +29,11 @@ from jflow.config_reader import JFlowConfigReader
 def date(datestr):
     return datetime.datetime.strptime(datestr, '%d/%m/%Y')
 
+def browsefile(file):
+    # browsefile are not available from command line, considere it as a localfile
+    # from the gui, this will not been tested this way
+    return localfile(file)
+
 def localfile(file):
     if os.path.isfile(file):
         return os.path.abspath(file)