dir = Directory(purgeCaches=args.purgeCaches, debug=args.debug, pp=pp)
log.info('Total biobanks: ' + str(dir.getBiobanksCount()))
log.info('Total collections: ' + str(dir.getCollectionsCount()))
if args.negotiator:
contactsToCollections = {}
collectionsToContacts = {}
contactsToEmails = {}
for collection in dir.getCollections():
log.debug("Analyzing collection " + collection['id'])
collectionId = collection['id']
biobankId = dir.getCollectionBiobankId(collection['id'])
biobank = dir.getBiobankById(biobankId)
if 'contact' in collection:
contactId = collection['contact']['id']
contactEmail = collection['contact']['email']
if contactId not in contactsToEmails:
contactsToEmails[contactId] = contactEmail
else:
if (contactsToEmails[contactId] != contactEmail):
log.error(
"Contact mismatch for %s: previously provided <%s>, now provided <%s>"
%
(contactId, contactsToEmails[contactId], contactEmail))
log.debug(" collection %s maps to %s <%s>" %
(collectionId, contactId, contactEmail))
if contactId in contactsToCollections:
contactsToCollections[contactId].append(collectionId)
# Main code
dir = Directory(purgeCaches=args.purgeCaches, debug=args.debug, pp=pp)
log.info('Total biobanks: ' + str(dir.getBiobanksCount()))
log.info('Total collections: ' + str(dir.getCollectionsCount()))
ecraidBSLCollections = []
ecraidPathogenCollections = []
ecraidRelevantBiobankIds = set()
for collection in dir.getCollections():
log.debug("Analyzing collection " + collection['id'])
biobankId = dir.getCollectionBiobankId(collection['id'])
biobank = dir.getBiobankById(biobankId)
biobank_capabilities = []
if 'capabilities' in biobank:
for c in biobank['capabilities']:
biobank_capabilities.append(c['id'])
biobank_covid = []
if 'covid19biobank' in biobank:
for c in biobank['covid19biobank']:
biobank_covid.append(c['id'])
biobank_networks = []
if 'network' in biobank:
for n in biobank['network']:
biobank_networks.append(n['id'])
collection_networks = []
if 'network' in collection: