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Handle weird xrefs during loading #327

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merged 2 commits into from
Jul 29, 2021
Merged

Handle weird xrefs during loading #327

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9ce28de
Handle weird xrefs like Gene3D:G3DSA:3.30.920.10
Jul 26, 2021
97ad5a1
missed a spot
Jul 26, 2021
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4 changes: 2 additions & 2 deletions machado/loaders/feature.py
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Original file line number Diff line number Diff line change
Expand Up @@ -425,7 +425,7 @@ def store_bio_searchio_hit(self, searchio_hit: Hit, target: str) -> None:
)

for aux_dbxref in searchio_hit.dbxrefs:
aux_db, aux_term = aux_dbxref.split(":")
aux_db, aux_term = aux_dbxref.split(":", 1)
if aux_db == "GO":
try:
term_db = Db.objects.get(name=aux_db.upper())
Expand Down Expand Up @@ -469,7 +469,7 @@ def store_feature_dbxref(self, feature: str, soterm: str, dbxref: str) -> None:
feature_id = retrieve_feature_id(accession=feature, soterm=soterm)

try:
db_name, dbxref_accession = dbxref.split(":")
db_name, dbxref_accession = dbxref.split(":", 1)
except ValueError:
raise ImportingError(
"Incorrect DBxRef {}. It should have two colon-separated values (eg. DB:DBxREF).".format(
Expand Down
4 changes: 2 additions & 2 deletions machado/loaders/featureattributes.py
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Original file line number Diff line number Diff line change
Expand Up @@ -140,7 +140,7 @@ def process_attributes(self, feature_id: int, attrs: Dict[str, str]) -> None:
terms = attrs[key].split(",")
for term in terms:
try:
aux_db, aux_term = term.split(":")
aux_db, aux_term = term.split(":", 1)
term_db = Db.objects.get(name=aux_db.upper())
dbxref = Dbxref.objects.get(db=term_db, accession=aux_term)
cvterm = Cvterm.objects.get(dbxref=dbxref)
Expand All @@ -161,7 +161,7 @@ def process_attributes(self, feature_id: int, attrs: Dict[str, str]) -> None:
for dbxref in dbxrefs:
# It expects just one dbxref formated as XX:012345
try:
aux_db, aux_dbxref = dbxref.split(":")
aux_db, aux_dbxref = dbxref.split(":", 1)
except ValueError as e:
raise ImportingError("{}: {}".format(dbxref, e))
db, created = Db.objects.get_or_create(name=aux_db.upper())
Expand Down