def get_subject_id(name):
if not name in SUBJECTS_CACHE:
subject = None
try:
subject = Subject.find_one(Q('text', 'eq', name))
except NoResultsFound:
raise Exception('Subject: "{}" not found'.format(name))
else:
SUBJECTS_CACHE[name] = subject._id
return SUBJECTS_CACHE[name]
def get_subject_id(name):
if not name in SUBJECTS_CACHE:
subject = None
try:
subject = Subject.find_one(Q('text', 'eq', name))
except NoResultsFound:
raise Exception('Subject: "{}" not found'.format(name))
else:
SUBJECTS_CACHE[name] = subject._id
return SUBJECTS_CACHE[name]
def migrate_preprint(preprint):
logger.info('Preparint to migrate {}'.format(preprint['_id']))
new_hiers = []
for hier in preprint['subjects']:
leaf = get_leaf(hier)
new_leaf_name = PLOS_TO_BP_MAP[database['plos_subject'].find_one(
{'_id': leaf})['text']]
if new_leaf_name != '<drop>':
new_hiers.append(
Subject.find_one(Q('text', 'eq', new_leaf_name)).hierarchy)
logger.info('Setting subjects on {} to {}'.format(preprint['_id'],
new_hiers))
database['preprintservice'].find_and_modify(
{'_id': preprint['_id']}, {'$set': {
'subjects': new_hiers
}})
def migrate_preprint(preprint):
logger.info('Preparint to migrate {}'.format(preprint['_id']))
new_hiers = []
for hier in preprint['subjects']:
leaf = get_leaf(hier)
new_leaf_name = PLOS_TO_BP_MAP[database['plos_subject'].find_one({'_id': leaf})['text']]
if new_leaf_name != '<drop>':
new_hiers.append(
Subject.find_one(Q('text', 'eq', new_leaf_name)).hierarchy
)
logger.info('Setting subjects on {} to {}'.format(preprint['_id'], new_hiers))
database['preprintservice'].find_and_modify(
{'_id': preprint['_id']},
{'$set':{
'subjects': new_hiers
}}
)
def load_bepress(f_path):
assert Subject.find().count() == 0
logger.info('Loading BePress...')
with open(f_path) as fp:
bpress = json.load(fp)
validate_map_bepress_correctness(set(bpress.keys()))
logger.info('Populating Subjects...')
for text in bpress.keys():
Subject(text=text).save()
assert Subject.find().count() == len(bpress.keys())
logger.info('Setting parents...')
for s in Subject.find():
if bpress[s.text]['lineage']:
s.parents = [Subject.find_one(Q('text', 'eq', bpress[s.text]['lineage'][-1]))]
s.save()
logger.info('Setting children...')
for s in Subject.find():
s.children = Subject.find(Q('parents', 'eq', s))
s.save()
logger.info('Successfully imported BePress taxonomy.')
def load_bepress(f_path):
assert Subject.find().count() == 0
logger.info('Loading BePress...')
with open(f_path) as fp:
bpress = json.load(fp)
validate_map_bepress_correctness(set(bpress.keys()))
logger.info('Populating Subjects...')
for text in bpress.keys():
Subject(text=text).save()
assert Subject.find().count() == len(bpress.keys())
logger.info('Setting parents...')
for s in Subject.find():
if bpress[s.text]['lineage']:
s.parents = [
Subject.find_one(
Q('text', 'eq', bpress[s.text]['lineage'][-1]))
]
s.save()
logger.info('Setting children...')
for s in Subject.find():
s.children = Subject.find(Q('parents', 'eq', s))
s.save()
logger.info('Successfully imported BePress taxonomy.')
