def deleteMongoDocument(self, strDocId, collection=None):
"""
Deletes a document specified by ID.
:param strDocId: Document ID as string. Should be unique.
:returns: 0 if no elements were deleted, 1 if one was deleted.
"""
if not mongo_utils.isObjectId(strDocId):
return 0
return self.deleteMongoDocumentS({"_id": ObjectId(strDocId)},
collection)
def deleteMongoDocument(self, strDocId, collection=None):
"""
Deletes a document specified by ID.
:param strDocId: Document ID as string. Should be unique.
:returns: 0 if no elements were deleted, 1 if one was deleted.
"""
if not mongo_utils.isObjectId(strDocId):
return 0
return self.deleteMongoDocumentS({"_id": ObjectId(strDocId)},
collection)
def __validateDocumentIds(self, documentIds):
"""
:@param documentIds: List of documents containing the annotations.
Raises an exception if documentIds contains an
invalid Id
(Invalid Format, not whenever it exists or not).
:@return: 0 if documentIds is empty.
"""
if not (type(documentIds) is list):
return 0
if (len(documentIds) == 0):
return 0
for docId in documentIds:
if (not mongo_utils.isObjectId(docId)):
logger.logInfo(AnnotationException(3, docId))
raise AnnotationException(3, docId)
return 1
def updateAnnotation(self, jsonDoc, strDocId, storageType=1):
"""
This function updates an annotation.
Currently this only works for annotations in storageType = 1.
@Preconditions:
documentId : A valid storage id. (we don't check that it exists
however). strDocId will be added to the annotation
object as doc_id (or overwrite existing field).
"""
if not mongo_utils.isObjectId(strDocId):
logger.logInfo(AnnotationException(1, strDocId))
raise AnnotationException(1, strDocId)
if (jsonDoc is None):
raise MongoDocumentException(2)
jsonDoc['doc_id'] = strDocId
return self.updateMongoDocument(jsonDoc)
def createAnnotation(self, jsonDoc, strDocId, storageType=1):
"""
This function creates an annotation. Currently this only works for annotations in storageType = 1
@Preconditions:
documentId : A valid storage id. (We don't check that it exists
however). documentId will be added to the annotation
object as doc_id (or overwrite existing field).
For the rest check createMongoDocument(self,jsonDoc,coll).
"""
self.__validateStorageByType(storageType)
if not mongo_utils.isObjectId(strDocId):
logger.logInfo(AnnotationException(1, strDocId))
raise AnnotationException(1, strDocId)
if (jsonDoc is None):
raise MongoDocumentException(2)
jsonDoc['doc_id'] = strDocId
return self.createMongoDocument(jsonDoc,
self.storageCollections[storageType])
def createAnnotationS(self,
jsonBatch,
strDocId,
batchFormat=1,
storageType=1):
"""
Inserts annotations by batch. All annotations must be valid. Raises an
error if there is even a single invalid annotation.
A valid annotation after processing has the following attributes:
:doc_id: Describes the id of the document containing the
annotation. Equals to strDocId.
:@context: A field linking the context of the document.
This field will be automatically created.
_id: A unique id identifying the annotation,
:@param jsonBatch : JSON of the message. See batch format on how this
field is supposed to be structured.
:@param strDocId : Id of the document containing the annotation
:@param storageType : Describes how to store the elements. (Currently can not be changed) Supports: 1,2
:@param batchFormat : Describes the format of the elements to input.
Supports: 0,1
@return: Number of created annotations.
"""
if (not mongo_utils.isObjectId(strDocId)):
logger.logInfo(AnnotationException(1, strDocId))
raise AnnotationException(1, strDocId)
self.__validateStorageByType(storageType)
# We do not support you can not create in all storages.
if (storageType == AnnotationManager.ALL_STORAGE):
logger.logError(AnnotationException(7, storageType))
raise AnnotationException(7, storageType)
# If the batch doesn't have data
if 'data' not in jsonBatch:
return 0
if (batchFormat != AnnotationManager.COMPACT_BATCH_FORMAT and
batchFormat != AnnotationManager.BASIC_BATCH_FORMAT):
logger.logInfo(AnnotationException(5, batchFormat))
raise AnnotationException(5, batchFormat)
batchData = jsonBatch['data']
if (batchFormat == AnnotationManager.COMPACT_BATCH_FORMAT):
if 'common' in jsonBatch:
batchCommon = jsonBatch['common']
# Optimisations later
for anno in batchData:
for common in batchCommon:
anno[common] = batchCommon[common]
for anno in batchData:
# We don't want the client to specify an id.
if '_id' in anno:
del anno["_id"]
if (self.isConnected()):
try:
# make each annotation reference its document
for anno in batchData:
anno['doc_id'] = strDocId
db = self.client[self.mongoDb]
coll = db[self.storageCollections[storageType]]
if (storageType == 1):
# Insert annotations one by one.
nbAnnoToInsert = len(batchData)
nbInserted = len(coll.insert(batchData))
if (nbAnnoToInsert != nbInserted):
# TODO: Delete all annotations if this happens
raise AnnotationException(8, nbInserted, nbAnnoToInsert)
return nbInserted
else: # Batch storage, save as files
fs = gridfs.GridFS(db)
batchDoc = {}
for anno in batchData:
if (batchDoc == {}): # Possible common attributes between annotations.
for attrib in anno:
batchDoc[attrib] = anno[attrib]
# IF an annotation have a different value for an attribute, then the
# common attribute, the common attribute must be deleted.
for attrib in anno:
if (str(attrib) in batchDoc):
if (anno[attrib] != batchDoc[str(attrib)]):
del batchDoc[attrib]
# Add id
anno["id"] = str(ObjectId())
jsonDump = json.dumps(batchData).encode("UTF-8")
annoFileID = fs.put(jsonDump)
nbInserted = len(batchData)
if 'common' in jsonBatch:
batchCommon = jsonBatch['common']
for common in batchCommon:
batchDoc[common] = batchCommon[common]
batchDoc['doc_id'] = str(strDocId)
batchDoc['file_fs_id_batch'] = annoFileID
try:
batch_id = coll.insert(batchDoc)
except Exception as e:
# clean up file info so we dont have garbage in our db
logger.logUnknownError("Annotation Storage Create Annotations", "", e)
fs.delete(annoFileID)
raise MongoDocumentException(0)
return nbInserted
except AnnotationException as e:
logger.logError(e)
raise e
except Exception as e:
logger.logUnknownError("Annotation Storage Create Annotations",
"", e)
raise MongoDocumentException(0)
else:
raise StorageException(1)