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Api node xrefs #241

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Api node xrefs #241

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c5605b5
allow use of other node types for xref
Clare72 Sep 29, 2021
1297312
change to use add_xref method
Clare72 Sep 29, 2021
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22 changes: 10 additions & 12 deletions src/uk/ac/ebi/vfb/neo4j/KB_tools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -354,14 +354,14 @@ def add_fact(self, s, r, o, edge_annotations = None,
match_on=match_on,
safe_label_edge=safe_label_edge)

def add_xref(self, s, xref, stype=''):
def add_xref(self, s, xref, otype=':Site', stype=''):
"""Add an xref axiom"""
# Add regex test for xref
x = xref.split(':')
self.add_annotation_axiom(s=s,
r='hasDbXref',
o=x[0],
otype=':Site',
otype=otype,
stype=stype,
edge_annotations={'accession': x[1]},
match_on='short_form',
Expand Down Expand Up @@ -874,6 +874,7 @@ def add_anatomy_image_set(self,
anatomy_attributes=None,
dbxrefs=None,
dbxref_strings=None,
dbxref_type=':Site',
image_filename='',
match_on='short_form',
orcid='',
Expand All @@ -894,6 +895,7 @@ def add_anatomy_image_set(self,
template: channel ID of the template to which the image is registered
start: Start of range for generation of new accessions
dbxrefs: dict of DB:accession pairs
dbxref_type: type of node for object of hasDbXref relationship, ':Site' by default.
anatomy_attributes: Dict of property:value for anatomy node

hard_fail: Boolean. If True, throw exception for uknown entitise referenced in args"""
Expand Down Expand Up @@ -941,7 +943,7 @@ def add_anatomy_image_set(self,
for db, acc in dbxrefs.items():
self.ec.roll_dbxref_check(db, acc)
if not self.ec.check(hard_fail=hard_fail):
warnings.warn("Load fail: Cross-referenced enties already exist.")
warnings.warn("Load fail: Cross-referenced entities already exist.")
return False

if not self.ec.check(hard_fail=hard_fail):
Expand Down Expand Up @@ -974,15 +976,11 @@ def add_anatomy_image_set(self,

if dbxrefs:
for db, acc in dbxrefs.items():
self.ew.add_annotation_axiom(s=anat_id['short_form'],
r='hasDbXref',
o=db,
stype=':Individual',
otype=':Individual:Site',
match_on='short_form',
edge_annotations={'accession': acc},
safe_label_edge=True
)
self.ew.add_xref(s=anat_id['short_form'],
xref=':'.join([db, acc]),
stype=':Individual',
otype=':Individual' + dbxref_type,
)
if orcid:
self.ew.add_annotation_axiom(s=anat_id['short_form'],
r='contributor',
Expand Down