first component ok

src/jflow/component.py

@@ -19,13 +19,14 @@ import os
 import sys
 import inspect
 import tempfile
+import types
 
 from jflow.workflows_manager import WorkflowsManager
 from jflow.config_reader import JFlowConfigReader
 from jflow.dataset import ArrayList
 from jflow.utils import which
-from jflow.iotypes import DynamicOutput, OutputFile, OutputFileList
-
+from jflow.parameter import *
+from jflow.iotypes import DynamicOutput
 from weaver.util import parse_string_list
 
 
@@ -35,6 +36,7 @@ class Component(object):
         
     def __init__(self):
         self.prefix = "default"
+        self.params_order = []
         self.output_directory = None
         self.config_reader = JFlowConfigReader()
         self.version = self.get_version()
@@ -64,6 +66,62 @@ 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)
+        else:
+            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:
+            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)
+        else:
+            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:
+            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)
+        else:
+            new_param = OutputFile(name, help, default=os.path.join(self.output_directory, basename), 
+                                   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:
+            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/parameter.py

@@ -70,6 +70,17 @@ def inputfile(file):
     else:
         return urlfile(file)
     
+    
+class Formats(object):
+    ANY = "any"
+    BAM = "bam"
+    FASTQ = "fastq"
+    FASTA = "fasta"
+    SFF = "sff"
+    QUAL = "qual"
+    FLOW = "flow"
+    HTML = "html"
+
 
 class MultipleParameters(object):
     def __init__(self, types, required, choices, excludes, default, actions):

workflows/alignment/__init__.py

@@ -30,30 +30,10 @@ class Alignment (Workflow):
         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_multiple_parameter("test", "toto est dnas le gazon", required=True)
-        self.add_parameter("toto", "Whices should be used", required=True, is_list=True, add_to="test")
-        self.add_parameter("tot_2", "Whould be used", type="int", add_to="test")
-        self.add_parameter("rdate", "date be used", type="date", add_to="test")
-        
-        self.add_multiple_parameter("unmulti", "unmulti qui fait chier", required=True, is_list=True)
-        self.add_parameter("a", "Wa", required=True, add_to="unmulti")
-        self.add_parameter("b", "Wb", type="int", add_to="unmulti")
-        self.add_parameter("c", "dc", type="date", add_to="unmulti")
-                
-        #self.add_exclusion_rule("read_1", "read_2")
-        #self.add_exclusion_rule("toto", "tot_2")
 
-    def process(self):
-        
-        print self.read_1
-        print self.read_2
-        print self.reference_genome
-        print self.test
-        print self.unmulti
-        
+    def process(self):        
         # index the reference genome
-        #bwaindex = self.add_component("BWAIndex", [self.args["reference_genome"]])
+        bwaindex = self.add_component("BWAIndex", [self.reference_genome])
         # align reads against indexed genome
         #bwa = self.add_component("BWA", [bwaindex.databank, self.args["read_1"], self.args["read_2"]])
         

workflows/components/bwaindex.py

@@ -19,8 +19,7 @@ import os
 from subprocess import Popen, PIPE
 
 from jflow.component import Component
-from jflow.iotypes import OutputFile, InputFile, Formats
-
+from jflow.parameter import Formats
 from weaver.function import PythonFunction, ShellFunction
 
 
@@ -44,11 +43,11 @@ def bwa_index(exec_path, algorithm, input_fasta, databank, stdout_path, stderr_p
 class BWAIndex (Component):
     
     def define_parameters(self, input_fasta, algorithm="bwtsw"):
-        self.input_fasta = InputFile(input_fasta, Formats.FASTA)
-        self.algorithm = algorithm
-        self.databank = OutputFile(os.path.join(self.output_directory, os.path.basename(input_fasta)))
-        self.stdout = OutputFile(os.path.join(self.output_directory, "bwaindex.stdout"))
-        self.stderr = OutputFile(os.path.join(self.output_directory, "bwaindex.stderr"))
+        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")
         
     def process(self):        
         bwaindex = PythonFunction(bwa_index, cmd_format="{EXE} {ARG} {IN} {OUT}")
@@ -59,4 +58,3 @@ class BWAIndex (Component):
         p = Popen(cmd, stdout=PIPE, stderr=PIPE)
         stdout, stderr = p.communicate()
         return stderr.split()[7]
-    
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