Merge pull request #49 from SD2E/sbol2

Convert to sbol2

features_to_circuits/features_to_circuits.py

@@ -4,7 +4,7 @@
 import sys
 
 from Bio.Seq import Seq
-from sbol import *
+from sbol2 import *
 from flashtext import KeywordProcessor
 from sequences_to_features import Feature
 from sequences_to_features import FeatureLibrary
@@ -185,6 +185,11 @@ def copy_module_definition(cls, mod_definition, source_doc, sink_doc):
             return sink_doc.getComponentDefinition(mod_definition.identity)
         except RuntimeError:
             definition_copy = mod_definition.copy(sink_doc)
+        except SBOLError as exc:
+            if exc.error_code() == SBOLErrorCode.NOT_FOUND_ERROR:
+                definition_copy = mod_definition.copy(sink_doc)
+            else:
+                raise
 
         for sub_mod in mod_definition.modules:
             sub_mod_definition = source_doc.getModuleDefinition(sub_mod.definition)

sequences_to_features/sequences_to_features.py

@@ -6,9 +6,18 @@
 import json
 
 from Bio.Seq import Seq
-from sbol import *
+from sbol2 import *
 from flashtext import KeywordProcessor
 
+# Set up the not found error for catching
+try:
+    # SBOLError is in the native python module
+    NotFoundError = SBOLError
+except NameError:
+    # The swig wrapper raises RuntimeError on not found
+    NotFoundError = RuntimeError
+
+
 def load_sbol(sbol_file):
     logging.info('Loading %s', sbol_file)
 
@@ -237,9 +246,9 @@ def copy_component_definition(cls, comp_definition, source_doc, sink_doc, import
             else:
                 try:
                     sink_doc.getComponentDefinition(comp_definition.identity)
-                    
+
                     return None
-                except RuntimeError:
+                except NotFoundError:
                     definition_copy = comp_definition.copy(sink_doc)
 
             definition_copy.sequences = list(comp_definition.sequences)
@@ -280,7 +289,7 @@ def copy_component_definition(cls, comp_definition, source_doc, sink_doc, import
             for seq_URI in comp_definition.sequences:
                 try:
                     sink_doc.getSequence(seq_URI)
-                except RuntimeError:
+                except NotFoundError:
                     seq = source_doc.getSequence(seq_URI)
 
                     seq.copy(sink_doc)
@@ -322,6 +331,11 @@ def __create_sub_component(cls, parent_definition, child_definition):
                 sub_comp = parent_definition.components.create('_'.join([child_definition.displayId, str(i)]))
             except RuntimeError:
                 sub_comp = None
+            except SBOLError as exc:
+                if exc.error_code() == SBOLErrorCode.SBOL_ERROR_URI_NOT_UNIQUE:
+                    sub_comp = None
+                else:
+                    raise
 
             if sub_comp is None:
                 i = i + 1
@@ -347,6 +361,11 @@ def __create_sequence_annotation(cls, parent_definition, child_definition, orien
                                                                                   str(i)]))
             except RuntimeError:
                 seq_anno = None
+            except SBOLError as exc:
+                if exc.error_code() == SBOLErrorCode.SBOL_ERROR_URI_NOT_UNIQUE:
+                    seq_anno = None
+                else:
+                    raise
 
             if seq_anno is None:
                 i = i + 1

setup.py

@@ -4,8 +4,9 @@
 
 install_requires = [
     'biopython>=1.7.4',
+    'dnaplotlib>=1.0',
     'flashtext>=2.7',
-    'pysbol>=2.3.1',
+    'sbol2',
     'matplotlib>=1.5.0'
 ]
 

test/test_curation.py

@@ -1,6 +1,6 @@
 import unittest
 import os
-from sbol import *
+from sbol2 import *
 
 from sequences_to_features import *
 from features_to_circuits import *
@@ -167,4 +167,4 @@ def test_curate_nand_circuit(self):
             "Inferred circuit is missing expected sub-circuits: {mi}".format(mi=', '.join(sub_circuit_difference)))
 
 if __name__ == '__main__':
-    unittest.main()
+    unittest.main()