Tweak compare_records to handle inexact but compatible matches.

Author: Peter Amstutz

cwltool/workflow.py

@@ -110,7 +110,7 @@ def can_assign_src_to_sink(src, sink):  # type: (Any, Any) -> bool
         return src == sink
     return False
 
-def _compare_records(rec1, rec2):
+def _compare_records(src, sink):
     """Compare two records, ensuring they have compatible fields.
 
     This handles normalizing record names, which will be relative to workflow
@@ -119,16 +119,17 @@ def _compare_records(rec1, rec2):
     def _rec_fields(rec):
         out = {}
         for field in rec["fields"]:
-            name = field["name"].replace(rec["name"], "")
+            name = shortname(field["name"])
             out[name] = field["type"]
         return out
-    fields1 = _rec_fields(rec1)
-    fields2 = _rec_fields(rec2)
-    for key in set(fields1.keys() + fields2.keys()):
-        if fields1.get(key) != fields2.get(key):
+
+    srcfields = _rec_fields(src)
+    sinkfields = _rec_fields(sink)
+    for key in sinkfields.iterkeys():
+        if not can_assign_src_to_sink(srcfields.get(key, "null"), sinkfields.get(key, "null")) and sinkfields.get(key) is not None:
             _logger.info("Record comparison failure for %s and %s\n"
                          "Did not match fields for %s: %s and %s" %
-                         (rec1["name"], rec2["name"], key, fields1.get(key), fields2.get(key)))
+                         (src["name"], sink["name"], key, srcfields.get(key), sinkfields.get(key)))
             return False
     return True
 

tests/test_examples.py

@@ -169,10 +169,31 @@ def test_typecompare(self):
             {'items': ['int'], 'type': 'array'}))
 
     def test_recordcompare(self):
-        src = {'fields': [{'type': {'items': 'string', 'type': 'array'}, 'name': u'file:///home/chapmanb/drive/work/cwl/test_bcbio_cwl/run_info-cwl-workflow/wf-variantcall.cwl#vc_rec/vc_rec/description'}, {'type': {'items': 'File', 'type': 'array'}, 'name': u'file:///home/chapmanb/drive/work/cwl/test_bcbio_cwl/run_info-cwl-workflow/wf-variantcall.cwl#vc_rec/vc_rec/vrn_file'}], 'type': 'record', 'name': u'file:///home/chapmanb/drive/work/cwl/test_bcbio_cwl/run_info-cwl-workflow/wf-variantcall.cwl#vc_rec/vc_rec'}
-        sink = {'fields': [{'type': {'items': 'string', 'type': 'array'}, 'name': u'file:///home/chapmanb/drive/work/cwl/test_bcbio_cwl/run_info-cwl-workflow/steps/vc_output_record.cwl#vc_rec/vc_rec/description'}, {'type': {'items': 'File', 'type': 'array'}, 'name': u'file:///home/chapmanb/drive/work/cwl/test_bcbio_cwl/run_info-cwl-workflow/steps/vc_output_record.cwl#vc_rec/vc_rec/vrn_file'}], 'type': 'record', 'name': u'file:///home/chapmanb/drive/work/cwl/test_bcbio_cwl/run_info-cwl-workflow/steps/vc_output_record.cwl#vc_rec/vc_rec'}
-        self.assertTrue(cwltool.workflow.can_assign_src_to_sink(src, sink))
+        src = {
+            'fields': [{
+                'type': { 'items': 'string', 'type': 'array' },
+                'name': u'file:///home/chapmanb/drive/work/cwl/test_bcbio_cwl/run_info-cwl-workflow/wf-variantcall.cwl#vc_rec/vc_rec/description'
+            },
+            {
+                'type': { 'items': 'File', 'type': 'array' },
+                'name': u'file:///home/chapmanb/drive/work/cwl/test_bcbio_cwl/run_info-cwl-workflow/wf-variantcall.cwl#vc_rec/vc_rec/vrn_file'
+            }],
+               'type': 'record',
+               'name': u'file:///home/chapmanb/drive/work/cwl/test_bcbio_cwl/run_info-cwl-workflow/wf-variantcall.cwl#vc_rec/vc_rec'
+        }
+        sink = {
+            'fields': [{
+                'type': {'items': 'string', 'type': 'array'},
+                'name': u'file:///home/chapmanb/drive/work/cwl/test_bcbio_cwl/run_info-cwl-workflow/steps/vc_output_record.cwl#vc_rec/vc_rec/description'
+            },
+            {
+                'type': {'items': 'File', 'type': 'array'},
+                'name': u'file:///home/chapmanb/drive/work/cwl/test_bcbio_cwl/run_info-cwl-workflow/steps/vc_output_record.cwl#vc_rec/vc_rec/vrn_file'
+            }],
+            'type': 'record',
+            'name': u'file:///home/chapmanb/drive/work/cwl/test_bcbio_cwl/run_info-cwl-workflow/steps/vc_output_record.cwl#vc_rec/vc_rec'}
 
+        self.assertTrue(cwltool.workflow.can_assign_src_to_sink(src, sink))
 
 
 if __name__ == '__main__':