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Commit 098e418e authored by AndiMajore's avatar AndiMajore
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renamed uniprot_ac to uniprot

parent 2bfce28d
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......@@ -15,4 +15,4 @@ CELERY_BROKER_URL=redis://redis:6379/0
FLOWER_PORT=8888
FLOWER_BASIC_AUTH=drugstone:test
GT_THREADS=2
DB_UPDATE_ON_START=1
\ No newline at end of file
DB_UPDATE_ON_START=0
\ No newline at end of file
......@@ -226,7 +226,7 @@ class DataLoader:
# @staticmethod
# def load_pdis_disgenet() -> pd.DataFrame:
# """Loads the DisGeNET PDis associations with UniprotAC Numbers and Mondo IDs
# """Loads the DisGeNET PDis associations with Uniprot Numbers and Mondo IDs
#
# Returns:
# pd.DataFrame: columns "protein_name", "disorder_name" and "score"
......
......@@ -301,6 +301,8 @@ def is_licenced_drdi_source(source):
def remove_old_pdi_data(new_datasets, licenced):
if new_datasets is None:
return
for dataset in new_datasets:
print("Deleting all except "+str(dataset))
try:
......@@ -316,6 +318,8 @@ def remove_old_pdi_data(new_datasets, licenced):
def remove_old_ppi_data(new_datasets, licenced):
if new_datasets is None:
return
for dataset in new_datasets:
print("Deleting all except " + str(dataset))
try:
......@@ -331,6 +335,8 @@ def remove_old_ppi_data(new_datasets, licenced):
def remove_old_pdis_data(new_datasets, licenced):
if new_datasets is None:
return
for dataset in new_datasets:
print("Deleting all except " + str(dataset))
try:
......@@ -346,6 +352,8 @@ def remove_old_pdis_data(new_datasets, licenced):
def remove_old_drdi_data(new_datasets, licenced):
if new_datasets is None:
return
for dataset in new_datasets:
print("Deleting all except " + str(dataset))
try:
......
......@@ -30,7 +30,7 @@ class DrDisDatasetSerializer(serializers.ModelSerializer):
class ProteinNodeSerializer(serializers.ModelSerializer):
drugstone_id = serializers.SerializerMethodField()
uniprot_ac = serializers.SerializerMethodField()
uniprot = serializers.SerializerMethodField()
symbol = serializers.SerializerMethodField()
ensg = serializers.SerializerMethodField()
entrez = serializers.SerializerMethodField()
......@@ -38,7 +38,7 @@ class ProteinNodeSerializer(serializers.ModelSerializer):
def get_drugstone_id(self, obj):
return [f'p{obj.id}']
def get_uniprot_ac(self, obj):
def get_uniprot(self, obj):
return [obj.uniprot_code]
def get_symbol(self, obj):
......@@ -61,19 +61,19 @@ class ProteinNodeSerializer(serializers.ModelSerializer):
class Meta:
model = Protein
fields = ['drugstone_id', 'uniprot_ac', 'symbol', 'protein_name', 'entrez', 'ensg']
fields = ['drugstone_id', 'uniprot', 'symbol', 'protein_name', 'entrez', 'ensg']
class ProteinSerializer(serializers.ModelSerializer):
drugstone_id = serializers.SerializerMethodField()
uniprot_ac = serializers.SerializerMethodField()
uniprot = serializers.SerializerMethodField()
symbol = serializers.SerializerMethodField()
ensg = serializers.SerializerMethodField()
def get_drugstone_id(self, obj):
return f'p{obj.id}'
def get_uniprot_ac(self, obj):
def get_uniprot(self, obj):
return obj.uniprot_code
def get_symbol(self, obj):
......@@ -93,7 +93,7 @@ class ProteinSerializer(serializers.ModelSerializer):
class Meta:
model = Protein
fields = ['drugstone_id', 'uniprot_ac', 'symbol', 'protein_name', 'entrez', 'ensg']
fields = ['drugstone_id', 'uniprot', 'symbol', 'protein_name', 'entrez', 'ensg']
class DrugSerializer(serializers.ModelSerializer):
......
......@@ -30,7 +30,7 @@ def query_proteins_by_identifier(node_ids: Set[str], identifier: str) -> Tuple[L
protein_attribute = 'symbol'
q_list = map(lambda n: Q(gene__iexact=n), node_ids)
elif identifier == 'uniprot':
protein_attribute = 'uniprot_ac'
protein_attribute = 'uniprot'
q_list = map(lambda n: Q(uniprot_code__iexact=n), node_ids)
elif identifier == 'ensg' or identifier == 'ensembl':
protein_attribute = 'ensg'
......@@ -66,7 +66,7 @@ def query_proteins_by_identifier(node_ids: Set[str], identifier: str) -> Tuple[L
def get_protein_ids(id_space, proteins):
if (id_space == 'uniprot'):
return [p['uniprot_ac'] for p in proteins]
return [p['uniprot'] for p in proteins]
if (id_space == 'ensg' or id_space == 'ensembl'):
return [p['ensg'] for p in proteins]
if (id_space == 'symbol'):
......
......@@ -368,7 +368,7 @@ def result_view(request) -> Response:
if 'drugstoneType' in detail and detail['drugstoneType'] == 'protein':
detail['symbol'] = list(set(detail['symbol']))
detail['entrez'] = list(set(detail['entrez']))
detail['uniprot_ac'] = list(set(detail['uniprot_ac']))
detail['uniprot'] = list(set(detail['uniprot']))
if 'ensg' in detail:
detail['ensg'] = list(set(detail['ensg']))
......@@ -420,7 +420,7 @@ def result_view(request) -> Response:
for i in proteins:
new_i = {
'id': i['id'],
'uniprot_ac': i['uniprot_ac'] if 'uniprot_ac' in i else [],
'uniprot': i['uniprot'] if 'uniprot' in i else [],
'gene': i['symbol'] if 'symbol' in i else [],
'name': i['protein_name'] if 'protein_name' in i else [],
'ensembl': i['ensg'] if 'ensg' in i else [],
......
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