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Update EFO scripts/data to OLS4 #280

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Aug 29, 2023
Merged

Update EFO scripts/data to OLS4 #280

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4 changes: 2 additions & 2 deletions catalog/models.py
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Original file line number Diff line number Diff line change
Expand Up @@ -180,7 +180,7 @@ class Meta:

def parse_api(self):
import requests
response = requests.get('https://www.ebi.ac.uk/ols/api/ontologies/efo/terms?obo_id=%s'%self.id.replace('_', ':'))
response = requests.get(constants.USEFUL_URLS['OLS_ROOT_URL']+'/api/ontologies/efo/terms?obo_id=%s'%self.id.replace('_', ':'))
response = response.json()['_embedded']['terms']
if len(response) == 1:
response = response[0]
Expand Down Expand Up @@ -216,7 +216,7 @@ def display_label(self):
@property
def display_ext_url(self):
if not self.id.startswith('EFO'):
url = 'https://www.ebi.ac.uk/ols/ontologies/efo/terms?iri='+self.url
url = constants.USEFUL_URLS['OLS_ROOT_URL']+'/ontologies/efo/terms?iri='+self.url
else:
url = self.url
return '<a href="%s">%s</a>'%(url, self.id)
Expand Down
1 change: 1 addition & 0 deletions pgs_web/constants.py
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Expand Up @@ -15,6 +15,7 @@
'BAKER_URL' : 'https://baker.edu.au',
'EBI_URL' : 'https://www.ebi.ac.uk',
'HDR_UK_CAM_URL' : 'https://www.hdruk.ac.uk/about-us/our-locations/health-data-research-uk-hdr-uk-cambridge/',
'OLS_ROOT_URL' : 'https://www.ebi.ac.uk/ols4',
'PGS_CONTACT' : 'pgs-info@ebi.ac.uk',
'PGS_FTP_ROOT' : 'ftp://ftp.ebi.ac.uk/pub/databases/spot/pgs',
'PGS_FTP_HTTP_ROOT' : 'https://ftp.ebi.ac.uk/pub/databases/spot/pgs',
Expand Down
8 changes: 4 additions & 4 deletions release/scripts/UpdateEFO.py
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
import requests
from catalog.models import EFOTrait, TraitCategory, EFOTrait_Ontology, Score
#from django.db import connection
from django.db import connections
from pgs_web import constants


class UpdateEFO:
Expand All @@ -18,7 +18,7 @@ class UpdateEFO:
direct_pgs_ids_key = 'direct_pgs_ids'
child_pgs_ids_key = 'child_pgs_ids'

ols_url_root = 'https://www.ebi.ac.uk/ols/api/ontologies/efo'
ols_url_root = constants.USEFUL_URLS['OLS_ROOT_URL']+'/api/ontologies/efo'

categories_info = {
'Biological process': { colour_key: '#BEBADA', parent_key: 'biological process', efo_key: ['GO_0008150'] },
Expand Down Expand Up @@ -104,8 +104,8 @@ def format_data(self, response):

# Mapped terms
new_mapped_terms_string = ''
if 'database_cross_reference' in response['annotation']:
new_mapped_terms = response['annotation']['database_cross_reference']
if 'has_dbxref' in response['annotation']:
new_mapped_terms = response['annotation']['has_dbxref']
if (new_mapped_terms):
new_mapped_terms_string = self.items_separator.join(sorted(new_mapped_terms))
data['mapped_terms'] = new_mapped_terms_string
Expand Down