def updateMongoDocument(self, jsonDoc, collection=None):
# Note for now: We just create a new document. Reason: Simpler
"""
Updates an existing document, by replacing it with new contents.
This function only validates the presence of the required fields.
:Preconditions (Otherwise exception is thrown):
* isConnected must be true,
* required fields must be present
:param jsonDoc: Document as a JSON document. The document needs to contain a valid id.
:return : If the document to be updated is found, returns the id of the document. If it can not be found, raises an exception.
Document content returned (mandatory). Other user fields may be present:
::
{
_id: Document id as a string
@context: Context describing the format of the document
}
"""
if not collection:
collection = self.mongoCollection
if self.isConnected():
if jsonDoc is None:
raise MongoDocumentException(2)
if '_id' in jsonDoc:
doWithId = self.getMongoDocument(jsonDoc['_id'])
if doWithId is None:
# ID cannot be found
logger.logInfo(MongoDocumentException(5, jsonDoc['_id']))
raise MongoDocumentException(5, jsonDoc['_id'])
else:
logger.logInfo(MongoDocumentException(5, ""))
raise MongoDocumentException(5, "")
mongo_utils.changeDocIdToMongoId(jsonDoc)
try:
db = self.client[self.mongoDb]
coll = db[collection]
doc_id = coll.save(jsonDoc)
return str(doc_id)
except Exception as e:
logger.logUnknownError("Annotation Storage Update Document",
"", e)
raise MongoDocumentException(0)
else:
raise StorageException(1)
def updateMongoDocument(self, jsonDoc, collection=None):
# Note for now: We just create a new document. Reason: Simpler
"""
Updates an existing document, by replacing it with new contents.
This function only validates the presence of the required fields.
:Preconditions (Otherwise exception is thrown):
* isConnected must be true,
* required fields must be present
:param jsonDoc: Document as a JSON document. The document needs to contain a valid id.
:return : If the document to be updated is found, returns the id of the document. If it can not be found, raises an exception.
Document content returned (mandatory). Other user fields may be present:
::
{
_id: Document id as a string
@context: Context describing the format of the document
}
"""
if not collection:
collection = self.mongoCollection
if self.isConnected():
if jsonDoc is None:
raise MongoDocumentException(2)
if '_id' in jsonDoc:
doWithId = self.getMongoDocument(jsonDoc['_id'])
if doWithId is None:
# ID cannot be found
logger.logInfo(MongoDocumentException(5, jsonDoc['_id']))
raise MongoDocumentException(5, jsonDoc['_id'])
else:
logger.logInfo(MongoDocumentException(5, ""))
raise MongoDocumentException(5, "")
mongo_utils.changeDocIdToMongoId(jsonDoc)
try:
db = self.client[self.mongoDb]
coll = db[collection]
doc_id = coll.save(jsonDoc)
return str(doc_id)
except Exception as e:
logger.logUnknownError("Annotation Storage Update Document",
"", e)
raise MongoDocumentException(0)
else:
raise StorageException(1)
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)