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Introduce NotFoundError for backward and forward compatibility #47

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Introduce NotFoundError for backward and forward compatibility #47

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15 changes: 12 additions & 3 deletions sequences_to_features/sequences_to_features.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,15 @@
from sbol 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)

Expand Down Expand Up @@ -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)
Expand Down Expand Up @@ -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)
Expand Down