Add dataset ID to history entries

Fix some minor bugs around history

devops/girder/plugins/AnnotationPlugin/upenncontrast_annotation/server/api/annotation.py

@@ -3,17 +3,49 @@
 from girder.api.rest import Resource, loadmodel
 from girder.constants import AccessType
 from girder.exceptions import AccessException, RestException
-from ..helpers.proxiedModel import recordable
+from ..helpers.proxiedModel import recordable, cacheBodyJson
 from ..models.annotation import Annotation as AnnotationModel
 
+from bson.objectid import ObjectId
+
+
+# Helper functions to get dataset ID for recordable endpoints
+
+def getDatasetIdFromAnnotationInBody(self: 'Annotation', *args, **kwargs):
+ annotation = self.getBodyJson()
+ return annotation['datasetId']
+
+def getDatasetIdFromAnnotationListInBody(self: 'Annotation', *args, **kwargs):
+ annotations = self.getBodyJson()
+ if len(annotations) <= 0:
+ return None
+ else:
+ return annotations[0]['datasetId']
+
+def getDatasetIdFromLoadedAnnotation(self: 'Annotation', *args, **kwargs):
+ annotation = kwargs['upenn_annotation']
+ return annotation['datasetId']
+
+def getDatasetIdFromAnnotationIdListInBody(self: 'Annotation', *args, **kwargs):
+ annotationStringIds = self.getBodyJson()
+ query = {
+ '_id': { '$in': [ObjectId(stringId) for stringId in annotationStringIds] },
+ }
+ cursor = self._annotationModel.findWithPermissions(query, user=self.getCurrentUser(), level=AccessType.READ, limit=1)
+ annotation = next(cursor, None)
+ if annotation is None:
+ return None
+ else:
+ return annotation['datasetId']
+
 
 class Annotation(Resource):
 
  def __init__(self):
  super().__init__()
  self.resourceName = 'upenn_annotation'
 
- self._annotationModel = AnnotationModel()
+ self._annotationModel: AnnotationModel = AnnotationModel()
 
  self.route('DELETE', (':id',), self.delete)
  self.route('GET', (':id',), self.get)
@@ -31,18 +63,20 @@ def __init__(self):
  # TODO(performance): use objectId whenever possible
  # TODO: error handling and documentation
 
+ @cacheBodyJson
  @access.user
  @describeRoute(Description("Create a new annotation").param('body', 'Annotation Object', paramType='body'))
- @recordable('Create an annotation')
+ @recordable('Create an annotation', getDatasetIdFromAnnotationInBody)
  def create(self, params):
  currentUser = self.getCurrentUser()
  if not currentUser:
  raise AccessException('User not found', 'currentUser')
  return self._annotationModel.create(currentUser, self.getBodyJson())
 
+ @cacheBodyJson
  @access.user
  @describeRoute(Description("Create multiple new annotations").param('body', 'Annotation Object List', paramType='body'))
- @recordable('Create multiple annotations')
+ @recordable('Create multiple annotations', getDatasetIdFromAnnotationListInBody)
  def createMultiple(self, params):
  currentUser = self.getCurrentUser()
  if not currentUser:
@@ -53,14 +87,15 @@ def createMultiple(self, params):
  .errorResponse('Write access was denied for the annotation.', 403))
  @access.user
  @loadmodel(model='upenn_annotation', plugin='upenncontrast_annotation', level=AccessType.WRITE)
- @recordable('Delete an annotation')
+ @recordable('Delete an annotation', getDatasetIdFromLoadedAnnotation)
  def delete(self, upenn_annotation, params):
  self._annotationModel.delete(upenn_annotation)
 
+ @cacheBodyJson
  @access.user
  @describeRoute(Description("Delete all annotations in the id list")
  .param('body', 'A list of all annotation ids to delete.', paramType='body'))
- @recordable('Delete multiple annotations')
+ @recordable('Delete multiple annotations', getDatasetIdFromAnnotationIdListInBody)
  def deleteMultiple(self, params):
  stringIds = [stringId for stringId in self.getBodyJson()]
  self._annotationModel.deleteMultiple(stringIds)
@@ -74,7 +109,7 @@ def deleteMultiple(self, params):
  .errorResponse("Validation Error: JSON doesn't follow schema."))
  @access.user
  @loadmodel(model='upenn_annotation', plugin='upenncontrast_annotation', level=AccessType.WRITE)
- @recordable('Update an annotation')
+ @recordable('Update an annotation', getDatasetIdFromLoadedAnnotation)
  def update(self, upenn_annotation, params):
  upenn_annotation.update(self.getBodyJson())
  self._annotationModel.update(upenn_annotation)

devops/girder/plugins/AnnotationPlugin/upenncontrast_annotation/server/api/connections.py

@@ -3,8 +3,52 @@
 from girder.api.rest import Resource, loadmodel
 from girder.constants import AccessType
 from girder.exceptions import AccessException
-from ..helpers.proxiedModel import recordable
+from ..helpers.proxiedModel import recordable, cacheBodyJson
 from ..models.connections import AnnotationConnection as ConnectionModel
+from ..models.annotation import Annotation as AnnotationModel
+
+from bson.objectid import ObjectId
+
+
+# Helper functions to get dataset ID for recordable endpoints
+
+def getDatasetIdFromConnectionInBody(self: 'AnnotationConnection', *args, **kwargs):
+ connection = self.getBodyJson()
+ return connection['datasetId']
+
+def getDatasetIdFromConnectionListInBody(self: 'AnnotationConnection', *args, **kwargs):
+ connections = self.getBodyJson()
+ if len(connections) <= 0:
+ return None
+ else:
+ return connections[0]['datasetId']
+
+def getDatasetIdFromLoadedConnection(self: 'AnnotationConnection', *args, **kwargs):
+ connection = kwargs['annotation_connection']
+ return connection['datasetId']
+
+def getDatasetIdFromConnectionIdListInBody(self: 'AnnotationConnection', *args, **kwargs):
+ connectionStringIds = self.getBodyJson()
+ query = {
+ '_id': { '$in': [ObjectId(stringId) for stringId in connectionStringIds] },
+ }
+ cursor = self._connectionModel.findWithPermissions(query, user=self.getCurrentUser(), level=AccessType.READ, limit=1)
+ connection = next(cursor, None)
+ if connection is None:
+ return None
+ else:
+ return connection['datasetId']
+
+def getDatasetIdFromInfoInBody(self: 'AnnotationConnection', *args, **kwargs):
+ info = self.getBodyJson()
+ annotationsIdsToConnect = info['annotationsIds']
+ annotationModel: AnnotationModel = AnnotationModel()
+ for stringId in annotationsIdsToConnect:
+ id = ObjectId(stringId)
+ annotation = annotationModel.getAnnotationById(id, self.getCurrentUser())
+ if annotation is not None:
+ return annotation['datasetId']
+ return None
 
 
 class AnnotationConnection(Resource):
@@ -13,7 +57,7 @@ def __init__(self):
  super().__init__()
  self.resourceName = 'annotation_connection'
 
- self._connectionModel = ConnectionModel()
+ self._connectionModel: ConnectionModel = ConnectionModel()
 
  self.route('DELETE', (':id',), self.delete)
  self.route('GET', (':id',), self.get)
@@ -29,18 +73,20 @@ def __init__(self):
  # TODO: creation date, update date, creatorId
  # TODO: error handling and documentation
 
+ @cacheBodyJson
  @access.user
  @describeRoute(Description("Create a new connection").param('body', 'Connection Object', paramType='body'))
- @recordable('Create a connection')
+ @recordable('Create a connection', getDatasetIdFromConnectionInBody)
  def create(self, params):
  currentUser = self.getCurrentUser()
  if not currentUser:
  raise AccessException('User not found', 'currentUser')
  return self._connectionModel.create(currentUser, self.getBodyJson())
 
+ @cacheBodyJson
  @access.user
  @describeRoute(Description("Create multiple new connections").param('body', 'Connection Object List', paramType='body'))
- @recordable('Create multiple connections')
+ @recordable('Create multiple connections', getDatasetIdFromConnectionListInBody)
  def multipleCreate(self, params):
  currentUser = self.getCurrentUser()
  if not currentUser:
@@ -51,14 +97,15 @@ def multipleCreate(self, params):
  .errorResponse('Write access was denied for the connection.', 403))
  @access.user
  @loadmodel(model='annotation_connection', plugin='upenncontrast_annotation', level=AccessType.WRITE)
- @recordable('Delete a connection')
+ @recordable('Delete a connection', getDatasetIdFromLoadedConnection)
  def delete(self, annotation_connection, params):
  self._connectionModel.remove(annotation_connection)
-
+
+ @cacheBodyJson
  @access.user
  @describeRoute(Description("Delete all annotation connections in the id list")
  .param('body', 'A list of all annotation connection ids to delete.', paramType='body'))
- @recordable('Delete multiple connections')
+ @recordable('Delete multiple connections', getDatasetIdFromConnectionIdListInBody)
  def deleteMultiple(self, params):
  stringIds = [stringId for stringId in self.getBodyJson()]
  self._connectionModel.deleteMultiple(stringIds)
@@ -72,7 +119,7 @@ def deleteMultiple(self, params):
  .errorResponse("Validation Error: JSON doesn't follow schema."))
  @access.user
  @loadmodel(model='annotation_connection', plugin='upenncontrast_annotation', level=AccessType.WRITE)
- @recordable('Update a connection')
+ @recordable('Update a connection', getDatasetIdFromLoadedConnection)
  def update(self, connection, params):
  connection.update(self.getBodyJson())
  self._connectionModel.update(connection)
@@ -115,9 +162,10 @@ def get(self, annotation_connection):
  return annotation_connection
 
 
+ @cacheBodyJson
  @access.user
  @describeRoute(Description("Create connections between annotations").param('body', 'Connection Object', paramType='body'))
- @recordable('Create connections with nearest')
+ @recordable('Create connections with nearest', getDatasetIdFromInfoInBody)
  def connectToNearest(self, params):
  currentUser = self.getCurrentUser()
  if not currentUser:

devops/girder/plugins/AnnotationPlugin/upenncontrast_annotation/server/api/history.py

@@ -1,42 +1,54 @@
 from girder.api import access
 from girder.api.describe import Description, describeRoute
 from girder.api.rest import Resource
-from girder.constants import SortDir, AccessType
-from girder.exceptions import AccessException
+from girder.exceptions import AccessException, RestException
 from ..models.history import History as HistoryModel
+from bson.objectid import ObjectId
 
 class History(Resource):
 
  def __init__(self):
  super().__init__()
  self.resourceName = 'history'
 
- self._historyModel = HistoryModel()
+ self._historyModel: HistoryModel = HistoryModel()
 
  self.route('GET', (), self.find)
  self.route('PUT', ('undo',), self.undo)
  self.route('PUT', ('redo',), self.redo)
 
  @access.user
- @describeRoute(Description("Get last history actions for the user, from the most recent to the oldest"))
+ @describeRoute(Description("Get last history actions for the user, from the most recent to the oldest")
+ .param('datasetId', 'The dataset in which are the history entries', required=True))
  def find(self, params):
  user = self.getCurrentUser()
  if user is None:
  raise AccessException('You must be logged in.')
- return self._historyModel.getLastEntries(user)
+ if 'datasetId' not in params:
+ raise RestException(code=400, message='Dataset ID is missing')
+ datasetId = ObjectId(params['datasetId'])
+ return self._historyModel.getLastEntries(user, datasetId)
 
  @access.user
- @describeRoute(Description("Undo the last history entry which hasn't been undone"))
+ @describeRoute(Description("Undo the last history entry which hasn't been undone")
+ .param('datasetId', 'The dataset in which undo should be done', required=True))
  def undo(self, params):
  user = self.getCurrentUser()
  if user is None:
  raise AccessException('You must be logged in.')
- return self._historyModel.undo(user)
+ if 'datasetId' not in params:
+ raise RestException(code=400, message='Dataset ID is missing')
+ datasetId = ObjectId(params['datasetId'])
+ return self._historyModel.undo(user, datasetId)
 
  @access.user
- @describeRoute(Description("Redo the last history entry which has been undone"))
+ @describeRoute(Description("Redo the last history entry which has been undone")
+ .param('datasetId', 'The dataset in which redo should be done', required=True))
  def redo(self, params):
  user = self.getCurrentUser()
  if user is None:
  raise AccessException('You must be logged in.')
- self._historyModel.redo(user)
+ if 'datasetId' not in params:
+ raise RestException(code=400, message='Dataset ID is missing')
+ datasetId = ObjectId(params['datasetId'])
+ self._historyModel.redo(user, datasetId)