add input directory

bin/jflow_cli.py

@@ -152,10 +152,12 @@ if __name__ == '__main__':
         gr = workflow.get_execution_graph()
         inputs, components = [], []
         for node in gr.nodes():
-            if Workflow.INPUT_GRAPH_LABEL in gr.node_attributes(node):
+            if Workflow.INPUTFILE_GRAPH_LABEL in gr.node_attributes(node):
+                inputs.append(gr.node_attributes(node)[1])
+            elif Workflow.INPUTFILES_GRAPH_LABEL in gr.node_attributes(node):
+                inputs.append(gr.node_attributes(node)[1])
+            elif Workflow.INPUTDIRECTORY_GRAPH_LABEL in gr.node_attributes(node):
                 inputs.append(gr.node_attributes(node)[1])
-            elif Workflow.INPUTS_GRAPH_LABEL in gr.node_attributes(node):
-                inputs.append(gr.node_attributes(node)[1])    
             elif Workflow.COMPONENT_GRAPH_LABEL in gr.node_attributes(node):
                 components.append(gr.node_attributes(node)[1])
         print "inputs: ", inputs

bin/jflow_server.py

@@ -411,10 +411,12 @@ class JFlowServer (object):
             status = self.jsonify_workflow_status(workflow)
             nodes = []
             for node in g.nodes():
-                if Workflow.INPUT_GRAPH_LABEL in g.node_attributes(node):
-                    nodes.append({"name": node, "display_name": g.node_attributes(node)[1], "type": "input"})
-                elif Workflow.INPUTS_GRAPH_LABEL in g.node_attributes(node):
-                    nodes.append({"name": node, "display_name": g.node_attributes(node)[1], "type": "inputs"})    
+                if Workflow.INPUTFILE_GRAPH_LABEL in g.node_attributes(node):
+                    nodes.append({"name": node, "display_name": g.node_attributes(node)[1], "type": "inputfile"})
+                elif Workflow.INPUTFILES_GRAPH_LABEL in g.node_attributes(node):
+                    nodes.append({"name": node, "display_name": g.node_attributes(node)[1], "type": "inputfiles"})
+                elif Workflow.INPUTDIRECTORY_GRAPH_LABEL in g.node_attributes(node):
+                    nodes.append({"name": node, "display_name": g.node_attributes(node)[1], "type": "inputdirectory"})    
                 elif Workflow.COMPONENT_GRAPH_LABEL in g.node_attributes(node):
                     nodes.append({"name": node, "display_name": g.node_attributes(node)[1], "type": "component"})
             status["nodes"] = nodes

src/jflow/component.py

@@ -68,6 +68,24 @@ class Component(object):
                 outputs[os.path.basename(attribute_value)] = attribute_value
         return outputs
 
+    def add_input_directory(self, name, help, default=None, required=False, flag=None, group="default", 
+                            display_name=None, add_to=None, cmd_format="", argpos=-1):
+        new_param = InputDirectory(name, help, flag=flag, default=default, required=required, group=group, 
+                                   display_name=display_name, cmd_format=cmd_format, argpos=argpos)
+        # store where the parameter is coming from
+        new_param.linkTrace_nameid = self.get_nameid()
+        if issubclass( default.__class__, LinkTraceback ):
+            new_param.parent_linkTrace_nameid = [default.linkTrace_nameid]
+        # if this input should be added to a particular parameter
+        if add_to:
+            try:
+                self.__getattribute__(add_to).add_sub_parameter(new_param)
+            except: pass
+        # otherwise, add it to the class itself
+        else:
+            self.params_order.append(name)
+            self.__setattr__(name, new_param)
+
     def add_input_file(self, name, help, file_format="any", default=None, type="inputfile", 
                        required=False, flag=None, group="default", display_name=None, add_to=None, 
                        cmd_format="", argpos=-1):

src/jflow/parameter.py

@@ -41,6 +41,12 @@ from workflows.formats import *
 INPUTFILE_TYPES = ["inputfile", "localfile", "urlfile", "browsefile"]
 INPUTFILES_TYPES = ["inputfiles", "localfile", "urlfile", "browsefile", "regexpfiles"]
 
+def inputdirectory(directory):
+    if os.path.isdir(directory):
+        return directory
+    else:
+        raise argparse.ArgumentTypeError("'" + directory + "' is not a valid directory!")
+
 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
@@ -50,7 +56,7 @@ def localfile(file):
     if os.path.isfile(file):
         return file
     else:
-        raise argparse.ArgumentTypeError("File '" + file + "' does not exists! Please provide a valid file path!")
+        raise argparse.ArgumentTypeError("'" + file + "' is not a valid file!")
 
 def urlfile(file):
     uri_object = urlparse(file)
@@ -738,6 +744,18 @@ class DateParameter(datetime.datetime, AbstractParameter):
         return (DateParameter, (self.name, self.help, self.default, date, self.choices, self.required,
                  self.flag, self.sub_parameters, self.group, self.display_name), None, None, None)
 
+class InputDirectory(StrParameter, LinkTraceback):
+
+    def __new__(self, name, help, default="", choices=None, required=False, flag=None, 
+                group="default", display_name=None, cmd_format="", argpos=-1):
+        return StrParameter.__new__(self, name, help, flag=flag, default=default, type="inputdirectory", choices=choices, 
+                           required=required, group=group, display_name=display_name, cmd_format=cmd_format, argpos=argpos)
+
+    def __init__(self, name, help, default="", choices=None, required=False, flag=None, 
+                group="default", display_name=None, cmd_format="", argpos=-1):
+        LinkTraceback.__init__(self)
+        StrParameter.__init__(self, name, help, flag=flag, default=default, type="inputdirectory", choices=choices, 
+                           required=required, group=group, display_name=display_name, cmd_format=cmd_format, argpos=argpos)
 
 class AbstractInputFile(AbstractIOFile):
     """

src/jflow/workflow.py

@@ -98,8 +98,9 @@ class Workflow(threading.Thread):
     STATUS_ABORTED = "aborted"
     STATUS_RESETED = "reseted"
     
-    INPUT_GRAPH_LABEL = "input"
-    INPUTS_GRAPH_LABEL = "inputs"
+    INPUTFILE_GRAPH_LABEL = "inputfile"
+    INPUTFILES_GRAPH_LABEL = "inputfiles"
+    INPUTDIRECTORY_GRAPH_LABEL = "inputdirectory"
     COMPONENT_GRAPH_LABEL = "component"
     
     
@@ -154,8 +155,24 @@ class Workflow(threading.Thread):
             if self.stderr is None:
                 self.stderr = self._set_stderr()
             self._serialize()
+            
         self.comp_pckg = self._import_components()
     
+    def add_input_directory(self, name, help, default=None, required=False, flag=None, 
+                            group="default", display_name=None, add_to=None):
+        new_param = InputDirectory(name, help, flag=flag, default=default, 
+                                   required=required, group=group, display_name=display_name)
+        new_param.linkTrace_nameid = name
+        # if this input should be added to a particular parameter
+        if add_to:
+            try:
+                self.__getattribute__(add_to).add_sub_parameter(new_param)
+            except: pass
+        # otherwise, add it to the class itself
+        else:
+            self.params_order.append(name)
+            self.__setattr__(name, new_param)
+    
     def add_input_file(self, name, help, file_format="any", default=None, type="inputfile", 
                        required=False, flag=None, group="default", display_name=None, size_limit="0", add_to=None):
         # check if the size provided is correct
@@ -304,6 +321,12 @@ class Workflow(threading.Thread):
                                    type=parameter.type, choices=parameter.choices, required=parameter.required, flag=parameter.flag, 
                                    group=parameter.group, display_name=parameter.display_name )
             new_param.linkTrace_nameid = parameter.linkTrace_nameid
+        elif parameter.__class__ == InputDirectory:
+            if value == "" : value = None # from GUI
+            new_param = InputDirectory( parameter.name, parameter.help, default=value, choices=parameter.choices, 
+                                        required=parameter.required, flag=parameter.flag, group=parameter.group, 
+                                        display_name=parameter.display_name )
+            new_param.linkTrace_nameid = parameter.linkTrace_nameid
         else:
             raise Exception( "Unknown class '" +  parameter.__class__.__name__ + "' for parameter.")
         return new_param
@@ -345,12 +368,17 @@ class Workflow(threading.Thread):
         for ioparameter in self.__dict__.values():
             if issubclass(ioparameter.__class__, InputFile):
                 gr.add_node(ioparameter.name)
-                gr.add_node_attribute(ioparameter.name, self.INPUT_GRAPH_LABEL)
+                gr.add_node_attribute(ioparameter.name, self.INPUTFILE_GRAPH_LABEL)
                 gr.add_node_attribute(ioparameter.name, ioparameter.display_name)
                 all_nodes[ioparameter.name] = None
             elif issubclass(ioparameter.__class__, InputFileList):
                 gr.add_node(ioparameter.name)
-                gr.add_node_attribute(ioparameter.name, self.INPUTS_GRAPH_LABEL)
+                gr.add_node_attribute(ioparameter.name, self.INPUTFILES_GRAPH_LABEL)
+                gr.add_node_attribute(ioparameter.name, ioparameter.display_name)
+                all_nodes[ioparameter.name] = None
+            elif issubclass(ioparameter.__class__, InputDirectory):
+                gr.add_node(ioparameter.name)
+                gr.add_node_attribute(ioparameter.name, self.INPUTDIRECTORY_GRAPH_LABEL)
                 gr.add_node_attribute(ioparameter.name, ioparameter.display_name)
                 all_nodes[ioparameter.name] = None
         for cpt in self.components:
@@ -360,7 +388,7 @@ class Workflow(threading.Thread):
             all_nodes[cpt.get_nameid()] = None
         for cpt in self.components:
             for ioparameter in cpt.__dict__.values():
-                if issubclass( ioparameter.__class__, InputFile ) or issubclass( ioparameter.__class__, InputFileList):
+                if issubclass( ioparameter.__class__, InputFile ) or issubclass( ioparameter.__class__, InputFileList) or issubclass( ioparameter.__class__, InputDirectory):
                     for parent in ioparameter.parent_linkTrace_nameid:
                         try: gr.add_edge((parent, ioparameter.linkTrace_nameid))
                         except: pass

src/js/cytoscape.js

@@ -13576,7 +13576,7 @@ var cytoscape;
     	  context.lineWidth = tmpLineWidth;
     	  context.font = tmpFont;
       }
-      else if(node._private.data.type == 'input') {
+      else if(node._private.data.type == 'inputfile') {
     	  var tmpLineWidth = context.lineWidth;
     	  context.beginPath();
     	  context.lineWidth = 2;
@@ -13627,7 +13627,7 @@ var cytoscape;
           context.shadowOffsetY = 0;
           context.shadowBlur = 0;
       }
-      else if(node._private.data.type == 'inputs') {
+      else if(node._private.data.type == 'inputfiles') {
     	  var tmpLineWidth = context.lineWidth;
     	  context.beginPath();
     	  context.lineWidth = 2;

src/js/jflow-wfstatus.js

@@ -188,7 +188,7 @@
 		    		}
 		    	}
 		    	for (var i in data.nodes) {
-		    		if(data.nodes[i].type == "input" || data.nodes[i].type == "inputs") {
+		    		if(data.nodes[i].type == "inputfile" || data.nodes[i].type == "inputfiles" || data.nodes[i].type == "inputdirectory") {
 		    			nodes.push({ data: {
 		    				id:   data.nodes[i].name,
 			    			name: data.nodes[i].display_name,