def fmt(x):
if x['op'] == 'i':
op = x['o']
return pymongo.UpdateOne({'_id': op['_id']}, {'$set': op},
upsert=True)
elif x['op'] == 'u':
return pymongo.UpdateOne(x['o2'], x['o'], upsert=True)
elif x['op'] == 'd':
return pymongo.DeleteMany(x['o'])
def removeWithQuery(self, query):
"""
Remove all documents matching a given query from the collection.
For safety reasons, you may not pass an empty query.
Note: this does NOT return a Mongo DeleteResult.
:param query: The search query for documents to delete,
see general MongoDB docs for "find()"
:type query: dict
"""
assert query
self.collection.bulk_write([pymongo.DeleteMany(query)], ordered=False)
def delete_cache(db, collection, cursor, delay):
ids_to_remove = []
files_to_remove = []
for l in cursor:
ids_to_remove.append(l['_id'])
files_to_remove.append((l['bam'], l['bai']))
if len(ids_to_remove) > 0:
requests = [pymongo.DeleteMany({'_id': {'$in': ids_to_remove}})]
result = db[collection].bulk_write(requests)
if len(files_to_remove) > 0:
time.sleep(
delay
) # sleep a little to allow finish any active downloads of selected cached files
for bam, bai in files_to_remove:
try:
os.remove(os.path.join(cache_dir, bam))
os.remove(os.path.join(cache_dir, bai))
except OSError:
pass
def removeWithQuery(self, query):
"""
Remove all documents matching a given query from the collection.
For safety reasons, you may not pass an empty query.
Note: this does NOT return a Mongo DeleteResult.
:param query: The search query for documents to delete,
see general MongoDB docs for "find()"
:type query: dict
"""
if not query:
raise Exception('query must be specified')
attachedQuery = query.copy()
attachedQuery['datafile'] = {'$exists': True}
for element in self.collection.find(attachedQuery):
file = File().load(element['datafile']['fileId'], force=True)
if file:
File().remove(file)
self.collection.bulk_write([pymongo.DeleteMany(query)], ordered=False)
def delete_all_db():
db.bulk_write([pymongo.DeleteMany({})])