split all add_* functions to have a clearer api

src/jflow/component.py

@@ -66,14 +66,27 @@ class Component(object):
                 outputs[os.path.basename(attribute_value)] = self._webify_workflow_outputs(web_path, attribute_value)
         return outputs
     
-    def add_input_file(self, name, help, file_format="any", default=None, type="inputfile", required=False, 
-                       flag=None, group="default", display_name=None, is_list=False, add_to=None):
-        if is_list:
-            if default == None: default = []
-            new_param = InputFileList(name, help, flag=flag, file_format=file_format, default=default, 
-                                      type=type, required=required, group=group, display_name=display_name)
+    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):
+        new_param = InputFile(name, help, flag=flag, file_format=file_format, default=default, 
+                              type=type, required=required, group=group, display_name=display_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:
-            new_param = InputFile(name, help, flag=flag, file_format=file_format, default=default, 
+            new_param.component_nameid = self.get_nameid()
+            if default.__class__.__name__ == "OutputFileList" or default.__class__.__name__ == "OutputFile":
+                new_param.parent_component_nameid = default.component_nameid
+            self.params_order.append(name)
+            self.__setattr__(name, new_param)
+
+    def add_input_file_list(self, name, help, file_format="any", default=None, type="inputfile", 
+                            required=False, flag=None, group="default", display_name=None, add_to=None):
+        if default == None: default = []
+        new_param = InputFileList(name, help, flag=flag, file_format=file_format, default=default, 
                                   type=type, required=required, group=group, display_name=display_name)
         # if this input should be added to a particular parameter
         if add_to:
@@ -88,14 +101,24 @@ class Component(object):
             self.params_order.append(name)
             self.__setattr__(name, new_param)
     
-    def add_parameter(self, name, help, default=None, type=types.StringType, choices=None, required=False, 
-                      flag=None, group="default", display_name=None, is_list=False, add_to=None):
-        if is_list:
-            if default == None: default = []
-            new_param = ParameterList(name, help, flag=flag, default=default, type=type, choices=choices, 
-                                      required=required, group=group, display_name=display_name)
+    def add_parameter(self, name, help, default=None, type=types.StringType, choices=None, 
+                      required=False, flag=None, group="default", display_name=None, add_to=None):
+        new_param = Parameter(name, help, flag=flag, default=default, type=type, choices=choices, 
+                              required=required, group=group, display_name=display_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:
-            new_param = Parameter(name, help, flag=flag, default=default, type=type, choices=choices, 
+            self.params_order.append(name)
+            self.__setattr__(name, new_param)
+
+    def add_parameter_list(self, name, help, default=None, type=types.StringType, choices=None, 
+                           required=False, flag=None, group="default", display_name=None, add_to=None):
+        if default == None: default = []
+        new_param = ParameterList(name, help, flag=flag, default=default, type=type, choices=choices, 
                                   required=required, group=group, display_name=display_name)
         # if this input should be added to a particular parameter
         if add_to:
@@ -107,13 +130,24 @@ class Component(object):
             self.params_order.append(name)
             self.__setattr__(name, new_param)
     
-    def add_output_file(self, name, help, file_format="any", pattern='{basename_woext}.out', 
-                        basename=None, group="default", display_name=None, is_list=False, add_to=None):
-        if is_list:
-            new_param = OutputFileList(name, help, default=self.get_outputs(pattern, basename), 
-                                       file_format=file_format, group=group, display_name=display_name)
+    def add_output_file(self, name, help, file_format="any", filename=None, group="default", display_name=None, add_to=None):
+        filename = os.path.basename(filename)
+        new_param = OutputFile(name, help, default=os.path.join(self.output_directory, filename), 
+                               file_format=file_format, group=group, display_name=display_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:
-            new_param = OutputFile(name, help, default=os.path.join(self.output_directory, basename), 
+            new_param.component_nameid = self.get_nameid()
+            self.params_order.append(name)
+            self.__setattr__(name, new_param)
+            
+    def add_output_file_list(self, name, help, file_format="any", pattern='{basename_woext}.out', 
+                             items=None, group="default", display_name=None, add_to=None):
+        new_param = OutputFileList(name, help, default=self.get_outputs(pattern, items), 
                                    file_format=file_format, group=group, display_name=display_name)
         # if this input should be added to a particular parameter
         if add_to:
@@ -125,7 +159,7 @@ class Component(object):
             new_param.component_nameid = self.get_nameid()
             self.params_order.append(name)
             self.__setattr__(name, new_param)
-    
+            
     def _webify_workflow_outputs(self, web_path, path):
         work_dir  = self.config_reader.get_work_directory()
         socket_opt = self.config_reader.get_socket_options()

src/jflow/workflow.py

@@ -104,7 +104,7 @@ class Workflow(threading.Thread):
         self.params_order = []
         self.define_parameters(self.function)
         # add the metadata parameter
-        self.add_parameter("metadata", "Which metadata should be linked to this workflow", is_list=True)
+        self.add_parameter_list("metadata", "Which metadata should be linked to this workflow")
         # if some args are provided, let's fill the parameters
         if args: self._set_parameters(args)
 
@@ -116,14 +116,24 @@ class Workflow(threading.Thread):
                 self.set_stderr()
             self._serialize()
     
-    def add_input_file(self, name, help, file_format="any", default=None, type="inputfile", required=False, 
-                       flag=None, group="default", display_name=None, is_list=False, add_to=None):
-        if is_list:
-            if default == None: default = []
-            new_param = InputFileList(name, help, flag=flag, file_format=file_format, default=default, 
-                                      type=type, required=required, group=group, display_name=display_name)
+    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):
+        new_param = InputFile(name, help, flag=flag, file_format=file_format, default=default, 
+                              type=type, required=required, group=group, display_name=display_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:
-            new_param = InputFile(name, help, flag=flag, file_format=file_format, default=default, 
+            self.params_order.append(name)
+            self.__setattr__(name, new_param)
+            
+    def add_input_file_list(self, name, help, file_format="any", default=None, type="inputfile", 
+                            required=False, flag=None, group="default", display_name=None, add_to=None):
+        if default == None: default = []
+        new_param = InputFileList(name, help, flag=flag, file_format=file_format, default=default, 
                                   type=type, required=required, group=group, display_name=display_name)
         # if this input should be added to a particular parameter
         if add_to:
@@ -134,23 +144,35 @@ class Workflow(threading.Thread):
         else:
             self.params_order.append(name)
             self.__setattr__(name, new_param)
-    
-    def add_multiple_parameter(self, name, help, required=False, flag=None, group="default", display_name=None, is_list=False):
+            
+    def add_multiple_parameter(self, name, help, required=False, flag=None, group="default", display_name=None):
         self.params_order.append(name)
-        if is_list:
-            new_param = MultiParameterList(name, help, flag=flag, required=required, group=group, display_name=display_name)
-        else:
-            new_param = MultiParameter(name, help, flag=flag, required=required, group=group, display_name=display_name)
+        new_param = MultiParameter(name, help, flag=flag, required=required, group=group, display_name=display_name)
+        self.__setattr__(name, new_param)
+
+    def add_multiple_parameter_list(self, name, help, required=False, flag=None, group="default", display_name=None):
+        self.params_order.append(name)
+        new_param = MultiParameterList(name, help, flag=flag, required=required, group=group, display_name=display_name)
         self.__setattr__(name, new_param)
     
-    def add_parameter(self, name, help, default=None, type=types.StringType, choices=None, required=False, 
-                      flag=None, group="default", display_name=None, is_list=False, add_to=None):
-        if is_list:
-            if default == None: default = []
-            new_param = ParameterList(name, help, flag=flag, default=default, type=type, choices=choices, 
-                                      required=required, group=group, display_name=display_name)
+    def add_parameter(self, name, help, default=None, type=types.StringType, choices=None, 
+                      required=False, flag=None, group="default", display_name=None, add_to=None):
+        new_param = Parameter(name, help, flag=flag, default=default, type=type, choices=choices, 
+                              required=required, group=group, display_name=display_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:
-            new_param = Parameter(name, help, flag=flag, default=default, type=type, choices=choices, 
+            self.params_order.append(name)
+            self.__setattr__(name, new_param)
+    
+    def add_parameter_list(self, name, help, default=None, type=types.StringType, choices=None, 
+                           required=False, flag=None, group="default", display_name=None, add_to=None):
+        if default == None: default = []
+        new_param = ParameterList(name, help, flag=flag, default=default, type=type, choices=choices, 
                                   required=required, group=group, display_name=display_name)
         # if this input should be added to a particular parameter
         if add_to:

workflows/alignment/__init__.py

@@ -24,9 +24,9 @@ class Alignment (Workflow):
         return "Align reads against a reference genome"
 
     def define_parameters(self, function="process"):
-        self.add_input_file("read_1", "Which read1 files should be used", required=True, is_list=True)
-        self.add_input_file("read_2", "Which read2 files should be used (if single end, leave empty)", type="localfile", is_list=True)
-        self.add_input_file("reference_genome", "Which genome should the read being align on", required=True, type="localfile")
+        self.add_input_file_list("read_1", "Which read1 files should be used", required=True)
+        self.add_input_file_list("read_2", "Which read2 files should be used (if single end, leave empty)")
+        self.add_input_file("reference_genome", "Which genome should the read being align on", required=True)
 
     def process(self):        
         # index the reference genome

workflows/components/bwa.py

@@ -30,23 +30,23 @@ class BWA (Component):
     
     def define_parameters(self, reference_genome, read1, read2=None, algorithm="aln"):
         self.add_input_file("reference_genome", "Which reference file should be used", default=reference_genome, required=True)
-        self.add_input_file("read1", "Which read1 files should be used", file_format=Formats.FASTQ, default=read1, required=True, is_list=True)
-        self.add_input_file("read2", "Which read2 files should be used", file_format=Formats.FASTQ, default=read2, is_list=True)
+        self.add_input_file_list("read1", "Which read1 files should be used", file_format=Formats.FASTQ, default=read1, required=True)
+        self.add_input_file_list("read2", "Which read2 files should be used", file_format=Formats.FASTQ, default=read2)
         self.add_parameter("algorithm", "Which algorithm should be used to align the reads", default=algorithm, choices=["aln", "bwasw"])
         if algorithm == "aln":
-            self.add_output_file("sai1", "The BWA sai1 file", pattern='{basename_woext}.sai', basename=self.read1, is_list=True)
+            self.add_output_file_list("sai1", "The BWA sai1 file", pattern='{basename_woext}.sai', items=self.read1)
         else: 
             self.sai1 = None
         if read2: 
             if algorithm == "aln":
-                self.add_output_file("sai2", "The BWA sai2 file", pattern='{basename_woext}.sai', basename=self.read2, is_list=True)
+                self.add_output_file_list("sai2", "The BWA sai2 file", pattern='{basename_woext}.sai', items=self.read2)
             else: 
                 self.sai2 = None
-            self.add_output_file("bam_files", "The BWA bam file", pattern='{basename_woext}.bam', basename=[self.read1, self.read2], file_format=Formats.BAM, is_list=True)
+            self.add_output_file_list("bam_files", "The BWA bam file", pattern='{basename_woext}.bam', items=[self.read1, self.read2], file_format=Formats.BAM)
         else:
             self.sai2 = None
-            self.add_output_file("bam_files", "The BWA bam file", pattern='{basename_woext}.bam', basename=self.read1, file_format=Formats.BAM, is_list=True)
-        self.add_output_file("stderr", "The BWA stderr file", basename='bwa.stderr')
+            self.add_output_file_list("bam_files", "The BWA bam file", pattern='{basename_woext}.bam', items=self.read1, file_format=Formats.BAM)
+        self.add_output_file("stderr", "The BWA stderr file", filename='bwa.stderr')
         
     def process(self):        
         if self.algorithm=="bwasw":

workflows/components/bwaindex.py

@@ -45,9 +45,9 @@ class BWAIndex (Component):
     def define_parameters(self, input_fasta, algorithm="bwtsw"):
         self.add_input_file("input_fasta", "Which fasta file should be indexed", file_format=Formats.FASTA, default=input_fasta, required=True)
         self.add_parameter("algorithm", "Which algorithm should be used to index the fasta file", default=algorithm, choices=["bwtsw", "div", "is"])
-        self.add_output_file("databank", "The indexed databank to use with BWA", basename=os.path.basename(input_fasta))
-        self.add_output_file("stdout", "The BWAIndex stdout file", basename="bwaindex.stdout")
-        self.add_output_file("stderr", "The BWAIndex stderr file", basename="bwaindex.stderr")
+        self.add_output_file("databank", "The indexed databank to use with BWA", filename=os.path.basename(input_fasta))
+        self.add_output_file("stdout", "The BWAIndex stdout file", filename="bwaindex.stdout")
+        self.add_output_file("stderr", "The BWAIndex stderr file", filename="bwaindex.stderr")
         
     def process(self):        
         bwaindex = PythonFunction(bwa_index, cmd_format="{EXE} {ARG} {IN} {OUT}")