Merge pull request #1118 from glatard/master

ENH: a tool to export Nipype interfaces in the Boutiques JSON format (https://github.com/boutiques), importable in CBRAIN.

Author: satra

bin/nipype2boutiques

@@ -0,0 +1,8 @@
+#!/usr/bin/env python
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+import sys
+from nipype.utils.nipype2boutiques import main
+
+if __name__ == '__main__':
+    main(sys.argv)

nipype/utils/nipype2boutiques.py

@@ -0,0 +1,116 @@
+# This tool exports a Nipype interface in the Boutiques (https://github.com/boutiques) JSON format.
+# Boutiques tools can be imported in CBRAIN (https://github.com/aces/cbrain) among other platforms.
+#
+# Limitations:
+#   * optional inputs are ignored because they are not supported in Boutiques.
+#   * inputs with cardinality "Multiple" (InputMultiPath in Nipype) are not supported. Same limitation for the outputs.
+#   * value-templates are wrong when output files are not created in the execution directory (e.g. when a sub-directory is created).
+
+import os
+import argparse
+import inspect
+import sys
+import json
+import tempfile
+
+from nipype.interfaces.base import Interface
+
+def create_tempfile():
+  fileTemp = tempfile.NamedTemporaryFile(delete = False)
+  fileTemp.write("hello")
+  fileTemp.close()
+  return fileTemp.name
+
+def print_inputs(tool_name, module=None, function=None):
+    interface = None
+    if module and function:
+        __import__(module)
+        interface = getattr(sys.modules[module],function)()
+        
+        inputs = interface.input_spec()
+        outputs = interface.output_spec()
+        
+        command_line = "nipype_cmd "+str(module)+" "+tool_name+" "
+        tool_desc = {}
+        tool_desc['name'] = tool_name
+        tool_desc['description'] = "Tool description goes here"
+        
+        tool_inputs = []
+        input_counter = 0
+        tool_outputs = []
+                            
+        for name, spec in sorted(interface.inputs.traits(transient=None).items()):
+
+            #FIXME: optional inputs are not supported yet
+            if not ( hasattr(spec, "mandatory") and spec.mandatory ):
+                continue
+            
+            input = {}
+            input['name'] = name
+            type = spec.full_info(inputs, name, None)
+            if not "an existing file name" in type:
+                type = "String"
+            else:
+                type = "File"            
+            input['type'] = type
+            input['description'] = "\n".join(interface._get_trait_desc(inputs, name, spec))[len(name)+2:].replace("\n\t\t",". ")
+            command_line_key = "["+str(input_counter)+"_"+name.upper()+"]"
+            input_counter += 1
+            input['command-line-key'] = command_line_key
+            input['cardinality'] = "Single"
+            tool_inputs.append(input)
+            
+            if not ( hasattr(spec, "mandatory") and spec.mandatory ): 
+                command_line+= "--%s"%name+" "                        # unreachable code as long as optional inputs are not supported
+                
+            command_line+= command_line_key+" "
+
+            # add value to input so that output names can be generated
+            tempfile_name = create_tempfile()
+            input['tempfile_name'] = tempfile_name
+            if type == "File":
+                setattr(interface.inputs,name,os.path.abspath(tempfile_name))
+            
+        for name,spec in sorted(outputs.traits(transient=None).items()):
+
+            output = {}
+            output['name'] = name
+            output['type'] = "File"
+            output['description'] = "No description provided"
+            output['command-line-key'] = ""
+            output['value-template'] = ""
+            output_value = interface._list_outputs()[name]
+            if output_value != "" and isinstance(output_value,str): # FIXME: this crashes when there are multiple output values.
+                # go find from which input file it was built
+                for input in tool_inputs:
+                    base_file_name = os.path.splitext(os.path.basename(input['tempfile_name']))[0]
+                    if base_file_name in output_value:
+                        output_value = os.path.basename(output_value.replace(base_file_name,input['command-line-key'])) # FIXME: this only works if output is written in the current directory
+                output['value-template'] = os.path.basename(output_value)
+                    
+            output['cardinality'] = "Single"
+            if output['value-template'] != "": # outputs with no templates would certainly crash.
+              tool_outputs.append(output)
+
+        # remove all temporary file names from inputs
+        for input in tool_inputs:
+            del input['tempfile_name']
+            
+        tool_desc['inputs'] = tool_inputs
+        tool_desc['outputs'] = tool_outputs
+        tool_desc['command-line'] = command_line
+        tool_desc['docker-image'] = 'docker.io/robdimsdale/nipype'
+        tool_desc['docker-index'] = 'http://index.docker.io'
+        tool_desc['schema-version'] = '0.1'
+        print json.dumps(tool_desc, indent=4, separators=(',', ': '))
+                        
+def main(argv):
+        
+    parser = argparse.ArgumentParser(description='Nipype Boutiques exporter', prog=argv[0])
+    parser.add_argument("module", type=str, help="Module name")
+    parser.add_argument("interface", type=str, help="Interface name")
+    parsed = parser.parse_args(args=argv[1:3])
+    
+    _, prog = os.path.split(argv[0])
+    interface_parser = argparse.ArgumentParser(description="Run %s"%parsed.interface, prog=" ".join([prog] + argv[1:3]))
+    print_inputs(argv[2],parsed.module, parsed.interface)