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Merge pull request #58 from EBI-G2P/update/endpoint_lgd_publications
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Update endpoint lgd-publication to support extra data
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@seeta-ramaraju
seeta-ramaraju authored Dec 5, 2024
2 parents aaaf147 + 6ca4ec7 commit 4be0410
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Showing 7 changed files with 342 additions and 91 deletions.
142 changes: 103 additions & 39 deletions gene2phenotype_project/gene2phenotype_app/serializers/locus_genotype_disease.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -163,7 +163,15 @@ def get_variant_type(self, id):
accession = lgd_variant.variant_type_ot.accession

if accession in data and lgd_variant.publication:
# Add pmid to list of publications
data[accession]["publications"].append(lgd_variant.publication.pmid)
# Check the variant inheritance - we group this data for each publication
if(lgd_variant.inherited is True):
data[accession]["inherited"] = lgd_variant.inherited
if(lgd_variant.de_novo is True):
data[accession]["de_novo"] = lgd_variant.de_novo
if(lgd_variant.unknown_inheritance is True):
data[accession]["unknown_inheritance"] = lgd_variant.unknown_inheritance
else:
publication_list = []
if lgd_variant.publication:
Expand Down Expand Up @@ -547,9 +555,9 @@ def update_mechanism(self, lgd_instance, validated_data):
# The mechanism synopsis is optional
cv_synopsis_obj = None
cv_synopsis_support_obj = None
if mechanism_synopsis is not None and mechanism_synopsis.get("name", "") != "":
mechanism_synopsis_value = mechanism_synopsis.get("name")
mechanism_synopsis_support = mechanism_synopsis.get("support")
if mechanism_synopsis and mechanism_synopsis["name"] != "":
mechanism_synopsis_value = mechanism_synopsis["name"]
mechanism_synopsis_support = mechanism_synopsis["support"]

try:
cv_synopsis_obj = CVMolecularMechanism.objects.get(
Expand All @@ -576,11 +584,43 @@ def update_mechanism(self, lgd_instance, validated_data):
is_deleted = 0
)

# Save old molecular mechanism to delete it later
old_mechanism_obj = lgd_instance.molecular_mechanism

# Update LGD record
# The mechanism has to be updated in the locus_genotype_disease before the evidence is added
# Because the evidence is going to be linked to the new lgd.molecular_mechanism
lgd_instance.molecular_mechanism = mechanism_obj
lgd_instance.date_review = datetime.now()
lgd_instance.save()

# Get evidence - the mechanism evidence was validated in the view 'LGDUpdateMechanism'
# Example: {'pmid': '25099252', 'description': 'text', 'evidence_types':
# [{'primary_type': 'Rescue', 'secondary_type': ['Human', 'Patient Cells']}]}
for evidence in mechanism_evidence:
pmid = evidence.get("pmid")
self.update_mechanism_evidence(lgd_instance, mechanism_evidence)

# The old molecular mechanism can be deleted - the deletion is stored in the history table
# As this method only allows to update 'undetermined' mechanisms, there is no evidence to be deleted
old_mechanism_obj.delete()

return lgd_instance

def update_mechanism_evidence(self, lgd_obj, validated_data):
"""
Method to only update the evidence of the LGD molecular mechanism.
'validated_data' example:
"mechanism_evidence": [{
"pmid": "1234",
"description": "This is new evidence for the existing mechanism evidence.",
"evidence_types": [ { "primary_type": "Function",
"secondary_type": [ "Biochemical" ]}
]}]
"""
mechanism_obj = lgd_obj.molecular_mechanism

for evidence in validated_data:
pmid = evidence["pmid"]

# Check if the PMID exists in G2P
# When updating the mechanism the supporting pmid used as evidence
Expand All @@ -591,20 +631,20 @@ def update_mechanism(self, lgd_instance, validated_data):
# TODO: improve in future to insert new pmids + link them to the record
raise serializers.ValidationError({"message": f"pmid '{pmid}' not found in G2P"})

if evidence.get("description") != "":
description = evidence.get("description")
if evidence["description"] != "":
description = evidence["description"]
else:
description = None

evidence_types = evidence.get("evidence_types")
evidence_types = evidence["evidence_types"]
for evidence_type in evidence_types:
# primary_type is the evidence subtype ('rescue')
primary_type = evidence_type.get("primary_type", None)
if not primary_type:
raise serializers.ValidationError({"message": f"Empty evidence subtype"})
primary_type = primary_type.replace(" ", "_").lower()
# secondary_type is the evidence value ('human')
secondary_type = evidence_type.get("secondary_type")
secondary_type = evidence_type["secondary_type"]
for m_type in secondary_type:
try:
cv_evidence_obj = CVMolecularMechanism.objects.get(
Expand All @@ -616,27 +656,28 @@ def update_mechanism(self, lgd_instance, validated_data):
raise serializers.ValidationError({"message": f"Invalid mechanism evidence '{m_type}'"})

# Insert evidence
mechanism_evidence_obj = MolecularMechanismEvidence.objects.create(
try:
mechanism_evidence_obj = MolecularMechanismEvidence.objects.get(
molecular_mechanism = mechanism_obj,
description = description,
publication = publication_obj,
evidence = cv_evidence_obj,
is_deleted = 0
evidence = cv_evidence_obj
)
except MolecularMechanismEvidence.DoesNotExist:
mechanism_evidence_obj = MolecularMechanismEvidence.objects.create(
molecular_mechanism = mechanism_obj,
description = description,
publication = publication_obj,
evidence = cv_evidence_obj,
is_deleted = 0
)
else:
if(mechanism_evidence_obj.is_deleted == 1):
mechanism_evidence_obj.is_deleted = 0
mechanism_evidence_obj.save()

# Save old molecular mechanism to delete it later
old_mechanism_obj = lgd_instance.molecular_mechanism

# Update LGD record
lgd_instance.molecular_mechanism = mechanism_obj
lgd_instance.date_review = datetime.now()
lgd_instance.save()

# The old molecular mechanism can be deleted - the deletion is stored in the history table
# As this method only allows to update 'undetermined' mechanisms, there is no evidence to be deleted
old_mechanism_obj.delete()

return lgd_instance
# Update LGD date_review
lgd_obj.date_review = datetime.now()
lgd_obj.save()

class Meta:
model = LocusGenotypeDisease
Expand Down Expand Up @@ -1083,15 +1124,13 @@ def create(self, validated_data):
# Variants are supposed to be linked to publications
# But if there is no publication then create the object without a pmid
if not publications:
# Check if entry exists in the table
# An unique entry is defined by: lgd, variant_type and publication
try:
lgd_variant_type_obj = LGDVariantType.objects.get(
lgd = lgd,
variant_type_ot = var_type_obj,
inherited = inherited,
de_novo = de_novo,
unknown_inheritance = unknown_inheritance,
publication = None,
is_deleted = 0
publication = None
)
except LGDVariantType.DoesNotExist:
lgd_variant_type_obj = LGDVariantType.objects.create(
Expand All @@ -1102,6 +1141,19 @@ def create(self, validated_data):
unknown_inheritance = unknown_inheritance,
is_deleted = 0
)
else:
# the entry already exists, it probably needs to be updated
# if deleted, set to not deleted
if(lgd_variant_type_obj.is_deleted == 1):
lgd_variant_type_obj.is_deleted = 0
# update inheritance data
if(lgd_variant_type_obj.inherited == 0 and inherited == True):
lgd_variant_type_obj.inherited = 1
if(lgd_variant_type_obj.de_novo == 0 and de_novo == True):
lgd_variant_type_obj.de_novo = 1
if(lgd_variant_type_obj.unknown_inheritance == 0 and unknown_inheritance == True):
lgd_variant_type_obj.unknown_inheritance = 1
lgd_variant_type_obj.save()

# The LGDPhenotypeSummary is created - next step is to create the LGDVariantTypeComment
if(comment != ""):
Expand Down Expand Up @@ -1146,21 +1198,14 @@ def create(self, validated_data):
lgd_variant_type_obj = LGDVariantType.objects.get(
lgd = lgd,
variant_type_ot = var_type_obj,
inherited = inherited,
de_novo = de_novo,
unknown_inheritance = unknown_inheritance,
publication = publication_obj,
is_deleted = 0
publication = publication_obj
)
except LGDVariantType.DoesNotExist:
# Check if LGDVariantType object already exists in db without a publication
try:
lgd_variant_type_obj = LGDVariantType.objects.get(
lgd = lgd,
variant_type_ot = var_type_obj,
inherited = inherited,
de_novo = de_novo,
unknown_inheritance = unknown_inheritance,
publication = None, # no publication attached to entry
is_deleted = 0
)
Expand All @@ -1180,7 +1225,26 @@ def create(self, validated_data):
# LGDVariantType already exists in the db without a publication
# Add publication to existing object
lgd_variant_type_obj.publication = publication_obj
if(lgd_variant_type_obj.inherited == False and inherited == True):
lgd_variant_type_obj.inherited = True
if(lgd_variant_type_obj.de_novo == False and de_novo == True):
lgd_variant_type_obj.de_novo = True
if(lgd_variant_type_obj.unknown_inheritance == False and unknown_inheritance == True):
lgd_variant_type_obj.unknown_inheritance = True
lgd_variant_type_obj.save()
else:
# the entry already exists, it probably needs to be updated
# if deleted, set to not deleted
if(lgd_variant_type_obj.is_deleted == 1):
lgd_variant_type_obj.is_deleted = 0
# update inheritance data
if(lgd_variant_type_obj.inherited == False and inherited == True):
lgd_variant_type_obj.inherited = True
if(lgd_variant_type_obj.de_novo == False and de_novo == True):
lgd_variant_type_obj.de_novo = True
if(lgd_variant_type_obj.unknown_inheritance == False and unknown_inheritance == True):
lgd_variant_type_obj.unknown_inheritance = True
lgd_variant_type_obj.save()

# The LGDPhenotypeSummary is created - next step is to create the LGDVariantTypeComment
if(comment != ""):
Expand Down
2 changes: 1 addition & 1 deletion gene2phenotype_project/gene2phenotype_app/serializers/phenotype.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -131,7 +131,7 @@ class Meta:
class LGDPhenotypeListSerializer(serializers.Serializer):
"""
Serializer to accept a list of phenotypes.
Called by: LocusGenotypeDiseaseAddPhenotypes()
Called by: LocusGenotypeDiseaseAddPhenotypes() and view LGDEditPhenotypes()
"""
phenotypes = LGDPhenotypeSerializer(many=True)

Expand Down
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