add import feature to load existing CWL tool content into the model

khillion · khillion · commit 82aa905a3e56 · 2017-05-02T16:52:30.000+02:00
diff --git a/cwlgen/import_cwl.py b/cwlgen/import_cwl.py
@@ -0,0 +1,62 @@
+'''
+Library to handle the manipulation and generation of CWL tool
+'''
+
+#  Import  ------------------------------
+
+# General libraries
+import os
+import argparse
+import sys
+import logging
+
+# External libraries
+import ruamel.yaml as ryaml
+import six
+import cwlgen
+
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
+#  Class(es)  ------------------------------ 
+
+class CWLToolParser(object):
+    """
+    Class to import content from an existing CWL Tool.
+    """
+
+    def _init_tool(self, cwl_dict):
+        """
+        Init tool from existing CWL tool.
+    
+        :param cwl_dict: Full content of CWL file
+        :type cwl_dict: DICT
+        """
+        tool = cwlgen.CommandLineTool(tool_id=cwl_dict.get('id', None),
+                                      base_command=cwl_dict.get('baseCommand', None),
+                                      label=cwl_dict.get('label', None),
+                                      doc=cwl_dict.get('doc', None),
+                                      cwl_version=cwl_dict.get('cwlVersion', None),
+                                      stdin=cwl_dict.get('stdin', None),
+                                      stderr=cwl_dict.get('stderr', None),
+                                      stdout=cwl_dict.get('stdout', None))
+        return tool
+
+    def import_cwl(self, cwl_path):
+        """
+        Load content of cwl into the :class:`cwlgen.CommandLineTool` object.
+    
+        :param cwl_path: Path of the CWL tool to be loaded.
+        :type cwl_path: STRING
+        :return: CWL tool content in cwlgen model.
+        :rtype: :class:`cwlgen.CommandLineTool`
+        """
+        with open(cwl_path) as yaml_file:
+            cwl_dict = ryaml.load(yaml_file, Loader=ryaml.Loader)
+        tool = self._init_tool(cwl_dict)
+        for key in cwl_dict.keys():
+            try:
+                getattr(self, '_load_{}'.format(key))(tool, cwl_dict[key]) 
+            except:
+                logger.warning(key + " is not processed.")
+        return tool
