def get(self):
if 'reqType' in self.request.GET:
if self.request.get('reqType') == 'delete':
errorLogsId = int(self.request.get('id'))
errorLogsDb = SBMLImportErrorLogs.get_by_id(errorLogsId)
errorLogsDb.delete()
self.redirect("/importFromSBML")
errorLogsDbQuery = list(
db.GqlQuery("SELECT * FROM SBMLImportErrorLogs WHERE user_id = :1",
self.user.user_id()).run())
errorLogsDbQuery = sorted(
errorLogsDbQuery,
key=lambda x:
(datetime.datetime.strptime(x.date, '%Y-%m-%d-%H-%M-%S')
if hasattr(x, 'date') and x.date != None else datetime.datetime.
now()),
reverse=True)
result = []
for error in errorLogsDbQuery:
modelDb = StochKitModelWrapper.get_by_id(error.modelId)
result.append({
'id': error.key().id(),
'date': error.date,
'fileName': error.fileName,
'modelName': modelDb.name if modelDb else None
})
self.render_response('importFromSBML.html', **{"errors": result})
def deleteModel(handler, model_id):
model = StochKitModelWrapper.get_by_id(model_id)
userID = handler.user.user_id()
if userID != model.user_id:
raise "Error accessing model {0} with user id {1} (model owned by {2})".format(model_id, userID, model.user_id)
model.delete()
def deleteModel(handler, model_id):
model = StochKitModelWrapper.get_by_id(model_id)
userID = handler.user.user_id()
if userID != model.user_id:
raise "Error accessing model {0} with user id {1} (model owned by {2})".format(model_id, userID, model.user_id)
model.delete()
def getModel(handler, model_id):
modelDb = StochKitModelWrapper.get_by_id(int(model_id))
if modelDb == None:
return None
jsonModel = modelDb.toJSON()
jsonModel["ownedByMe"] = modelDb.user_id == handler.user.user_id()
return jsonModel
def getModel(handler, model_id):
modelDb = StochKitModelWrapper.get_by_id(int(model_id))
if modelDb == None:
return None
jsonModel = modelDb.toJSON()
jsonModel["ownedByMe"] = modelDb.user_id == handler.user.user_id()
return jsonModel
def get(self):
if 'id' in self.request.GET:
errorLogsId = int(self.request.get('id'));
errorLogsDb = SBMLImportErrorLogs.get_by_id(errorLogsId)
modelDb = StochKitModelWrapper.get_by_id(errorLogsDb.modelId)
result = { "db" : errorLogsDb,
"modelName" : modelDb.name if modelDb else None }
print result["db"].errors
self.render_response('SBMLErrorLogs.html', **result)
def get(self):
if 'id' in self.request.GET:
errorLogsId = int(self.request.get('id'));
errorLogsDb = SBMLImportErrorLogs.get_by_id(errorLogsId)
modelDb = StochKitModelWrapper.get_by_id(errorLogsDb.modelId)
result = { "db" : errorLogsDb,
"modelName" : modelDb.name if modelDb else None }
print result["db"].errors
self.render_response('SBMLErrorLogs.html', **result)
def get(self):
if self.request.get('reqType') == 'exportToZip':
modelId = int(self.request.get('id'));
model = StochKitModelWrapper.get_by_id(modelId)
try:
if model.zipFileName:
if os.path.exists(model.zipFileName):
os.remove(model.zipFileName)
szip = exportimport.SuperZip(os.path.abspath(os.path.dirname(__file__) + '/../static/tmp/'), preferredName = model.name + "_")
model.zipFileName = szip.getFileName()
szip.addStochKitModel(model)
szip.close()
# Save the updated status
model.put()
relpath = '/' + os.path.relpath(model.zipFileName, os.path.abspath(os.path.dirname(__file__) + '/../'))
self.response.headers['Content-Type'] = 'application/json'
self.response.write(json.dumps({ 'status' : True,
'msg' : 'Model prepared',
'url' : relpath }))
except Exception as e:
traceback.print_exc()
result = {}
result['status'] = False
result['msg'] = 'Error: {0}'.format(e)
self.response.headers['Content-Type'] = 'application/json'
self.response.write(json.dumps(result))
return
#mesheditor.setupMeshes(self)
self.render_response('modelEditor.html')
def get(self):
if self.request.get('reqType') == 'exportToZip':
modelId = int(self.request.get('id'));
model = StochKitModelWrapper.get_by_id(modelId)
try:
if model.zipFileName:
if os.path.exists(model.zipFileName):
os.remove(model.zipFileName)
szip = exportimport.SuperZip(os.path.abspath(os.path.dirname(__file__) + '/../static/tmp/'), preferredName = model.name + "_")
model.zipFileName = szip.getFileName()
szip.addStochKitModel(model)
szip.close()
# Save the updated status
model.put()
relpath = '/' + os.path.relpath(model.zipFileName, os.path.abspath(os.path.dirname(__file__) + '/../'))
self.response.headers['Content-Type'] = 'application/json'
self.response.write(json.dumps({ 'status' : True,
'msg' : 'Model prepared',
'url' : relpath }))
except Exception as e:
traceback.print_exc()
result = {}
result['status'] = False
result['msg'] = 'Error: {0}'.format(e)
self.response.headers['Content-Type'] = 'application/json'
self.response.write(json.dumps(result))
return
#mesheditor.setupMeshes(self)
self.render_response('modelEditor.html')
def get(self):
if 'reqType' in self.request.GET:
if self.request.get('reqType') == 'delete':
errorLogsId = int(self.request.get('id'));
errorLogsDb = SBMLImportErrorLogs.get_by_id(errorLogsId)
errorLogsDb.delete()
self.redirect("/importFromSBML")
errorLogsDbQuery = list(db.GqlQuery("SELECT * FROM SBMLImportErrorLogs WHERE user_id = :1", self.user.user_id()).run())
errorLogsDbQuery = sorted(errorLogsDbQuery, key = lambda x : (datetime.datetime.strptime(x.date, '%Y-%m-%d-%H-%M-%S') if hasattr(x, 'date') and x.date != None else datetime.datetime.now()), reverse = True)
result = []
for error in errorLogsDbQuery:
modelDb = StochKitModelWrapper.get_by_id(error.modelId)
result.append( { 'id' : error.key().id(),
'date' : error.date,
'fileName' : error.fileName,
'modelName' : modelDb.name if modelDb else None } )
self.render_response('importFromSBML.html', **{ "errors" : result })
def createStochKitModelWrapperFromStochKitModel(handler, model, public = False):
species = []
parameters = []
reactions = []
meshWrapperDb = db.GqlQuery("SELECT * FROM MeshWrapper WHERE user_id = :1", handler.user.user_id()).get()
def fixName(name):
if re.match('^[^a-zA-Z_]', name):
name = 'a' + name
return re.sub('[^a-zA-Z0-9_]', '', name)
spatial = {
'initial_conditions' : [],
'mesh_wrapper_id' : meshWrapperDb.key().id(),
'reactions_subdomain_assignments': {},
'species_diffusion_coefficients': {},
'species_subdomain_assignments': {}
}
for specieName, specie in model.listOfSpecies.items():
name = fixName(specie.name)
species.append({ 'name' : name, 'initialCondition' : specie.initial_value })
spatial['species_diffusion_coefficients'][name] = 0.0
spatial['species_subdomain_assignments'][name] = meshWrapperDb.uniqueSubdomains
for parameterName, parameter in model.listOfParameters.items():
parameter.evaluate()
name = fixName(parameter.name)
parameters.append({ 'name' : name, 'value' : parameter.value })
modelType = 'massaction'
for reactionName, reaction in model.listOfReactions.items():
outReaction = {}
reactants = []
products = []
totalReactants = 0
reactantCount = len(reaction.reactants.items())
productCount = len(reaction.products.items())
for reactantName, stoichiometry in reaction.reactants.items():
reactantName = fixName(reactantName)
reactants.append({ 'specie' : reactantName, 'stoichiometry' : stoichiometry })
totalReactants += stoichiometry
for productName, stoichiometry in reaction.products.items():
productName = fixName(productName)
products.append({ 'specie' : productName, 'stoichiometry' : stoichiometry })
if reaction.massaction == True:
outReaction['type'] = 'massaction'
outReaction['rate'] = fixName(reaction.marate.name)
if reactantCount == 0 and productCount == 1:
outReaction['type'] = 'creation'
elif reactantCount == 1 and productCount == 0:
outReaction['type'] = 'destruction'
elif reactantCount == 2 and productCount == 1:
outReaction['type'] = 'merge'
elif reactantCount == 1 and productCount == 1 and totalReactants == 1:
outReaction['type'] = 'change'
elif reactantCount == 1 and productCount == 1 and totalReactants == 2:
outReaction['type'] = 'dimerization'
elif reactantCount == 1 and productCount == 2:
outReaction['type'] = 'split'
elif reactantCount == 2 and productCount == 2:
outReaction['type'] = 'four'
if totalReactants > 2:
raise Exception("Error in Reaction {0}: StochKit mass action reactions cannot have more than 2 total reacting particles. Total stoichiometry for this reaction is {1}".format(reactionName, totalRreactants))
else:
modelType = 'custom'
outReaction['type'] = 'custom'
outReaction['equation'] = reaction.propensity_function
outReaction['reactants'] = reactants
outReaction['products'] = products
outReaction['name'] = fixName(reaction.name)
spatial['reactions_subdomain_assignments'][fixName(reaction.name)] = meshWrapperDb.uniqueSubdomains
reactions.append(outReaction)
names = [modelt['name'] for modelt in ModelManager.getModels(handler)]
modelDb = StochKitModelWrapper()
tmpName = fixName(model.name)
while tmpName in names:
tmpName = fixName(model.name) + '_' + ''.join(random.choice('abcdefghijklmnopqrztuvwxyz') for x in range(3))
name = tmpName
modelDb.user_id = handler.user.user_id()
modelDb.name = name
modelDb.type = modelType
modelDb.species = species
modelDb.parameters = parameters
modelDb.reactions = reactions
modelDb.isSpatial = False
modelDb.units = model.units
modelDb.spatial = spatial
modelDb.zipFileName = None
modelDb.is_public = public
modelDb.put()
return modelDb
def updateModel(handler, jsonModel):
createModel = False
if "id" in jsonModel:
modelWrap = StochKitModelWrapper.get_by_id(jsonModel["id"])
userID = handler.user.user_id()
if userID != modelWrap.user_id:
raise "Error accessing model {0} with user id {1} (model owned by {2})".format(jsonModel["id"], userID, modelWrap.user_id)
else:
createModel = True
modelWrap = StochKitModelWrapper()
if 'isSpatial' not in jsonModel or 'spatial' not in jsonModel:
jsonModel['isSpatial'] = False
jsonModel['spatial'] = { 'subdomains' : [],
'mesh_wrapper_id' : None,
'species_diffusion_coefficients' : {} ,
'species_subdomain_assignments' : {} ,
'reactions_subdomain_assignments' : {},
'initial_conditions' : [] }
# This seems insane
if 'user_id' in jsonModel:
userID = jsonModel['user_id']
else:
userID = handler.user.user_id()
#if "name" not in jsonModel:
# raise Exception("Why is this code here?")
if 'isSpatial' in jsonModel:
modelWrap.isSpatial = jsonModel['isSpatial']
if 'spatial' in jsonModel:
modelWrap.spatial = jsonModel['spatial']
# Make sure we have access to a copy of the mesh (if it exists)
if "mesh_wrapper_id" in modelWrap.spatial and modelWrap.spatial["mesh_wrapper_id"]:
meshDbCurrent = mesheditor.MeshWrapper.get_by_id(modelWrap.spatial["mesh_wrapper_id"])
if createModel:
if meshDbCurrent.user_id != userID:
meshDb = mesheditor.MeshWrapper()
meshDb.user_id = userID
names = [x.name for x in db.Query(mesheditor.MeshWrapper).filter('user_id =', handler.user.user_id()).run()]
tmpName = meshDbCurrent.name
i = 0
while tmpName in names:
tmpName = meshDbCurrent.name + '_' + str(i)
i += 1
meshDb.name = tmpName
meshDb.description = meshDbCurrent.description
meshDb.meshFileId = meshDbCurrent.meshFileId
meshDb.subdomains = meshDbCurrent.subdomains
meshDb.uniqueSubdomains = meshDbCurrent.uniqueSubdomains
meshDb.undeletable = False#meshDbCurrent.undeletable
meshDb.ghost = False
meshDb.put()
modelWrap.spatial["mesh_wrapper_id"] = meshDb.key().id()
else:
meshDbCurrent.ghost = False
meshDbCurrent.put()
# This is maintained here!
modelWrap.subdomains = meshDbCurrent.uniqueSubdomains
if 'is_public' not in jsonModel:
jsonModel['is_public'] = False
modelWrap.user_id = userID
modelWrap.name = jsonModel["name"]
modelWrap.species = jsonModel["species"]
modelWrap.type = jsonModel["type"]
modelWrap.parameters = jsonModel["parameters"]
modelWrap.reactions = jsonModel["reactions"]
#modelWrap.spatial = jsonModel["spatial"]
#modelWrap.isSpatial = jsonModel["isSpatial"]
modelWrap.is_public = jsonModel["is_public"]
modelWrap.units = jsonModel["units"]
return modelWrap.put().id()
def createStochKitModelWrapperFromStochKitModel(handler, model, public = False):
species = []
parameters = []
reactions = []
meshWrapperDb = db.GqlQuery("SELECT * FROM MeshWrapper WHERE user_id = :1", handler.user.user_id()).get()
def fixName(name):
if re.match('^[^a-zA-Z_]', name):
name = 'a' + name
return re.sub('[^a-zA-Z0-9_]', '', name)
spatial = {
'initial_conditions' : [],
'mesh_wrapper_id' : meshWrapperDb.key().id(),
'reactions_subdomain_assignments': {},
'species_diffusion_coefficients': {},
'species_subdomain_assignments': {}
}
for specieName, specie in model.listOfSpecies.items():
name = fixName(specie.name)
species.append({ 'name' : name, 'initialCondition' : specie.initial_value })
spatial['species_diffusion_coefficients'][name] = 0.0
spatial['species_subdomain_assignments'][name] = meshWrapperDb.uniqueSubdomains
for parameterName, parameter in model.listOfParameters.items():
parameter.evaluate()
name = fixName(parameter.name)
parameters.append({ 'name' : name, 'value' : parameter.value })
modelType = 'massaction'
for reactionName, reaction in model.listOfReactions.items():
outReaction = {}
reactants = []
products = []
totalReactants = 0
reactantCount = len(reaction.reactants.items())
productCount = len(reaction.products.items())
for reactantName, stoichiometry in reaction.reactants.items():
reactantName = fixName(reactantName)
reactants.append({ 'specie' : reactantName, 'stoichiometry' : stoichiometry })
totalReactants += stoichiometry
for productName, stoichiometry in reaction.products.items():
productName = fixName(productName)
products.append({ 'specie' : productName, 'stoichiometry' : stoichiometry })
if reaction.massaction == True:
outReaction['type'] = 'massaction'
outReaction['rate'] = fixName(reaction.marate.name)
if reactantCount == 0 and productCount == 1:
outReaction['type'] = 'creation'
elif reactantCount == 1 and productCount == 0:
outReaction['type'] = 'destruction'
elif reactantCount == 2 and productCount == 1:
outReaction['type'] = 'merge'
elif reactantCount == 1 and productCount == 1 and totalReactants == 1:
outReaction['type'] = 'change'
elif reactantCount == 1 and productCount == 1 and totalReactants == 2:
outReaction['type'] = 'dimerization'
elif reactantCount == 1 and productCount == 2:
outReaction['type'] = 'split'
elif reactantCount == 2 and productCount == 2:
outReaction['type'] = 'four'
if totalReactants > 2:
raise Exception("Error in Reaction {0}: StochKit mass action reactions cannot have more than 2 total reacting particles. Total stoichiometry for this reaction is {1}".format(reactionName, totalRreactants))
else:
modelType = 'custom'
outReaction['type'] = 'custom'
outReaction['equation'] = reaction.propensity_function
outReaction['reactants'] = reactants
outReaction['products'] = products
outReaction['name'] = fixName(reaction.name)
spatial['reactions_subdomain_assignments'][fixName(reaction.name)] = meshWrapperDb.uniqueSubdomains
reactions.append(outReaction)
names = [modelt['name'] for modelt in ModelManager.getModels(handler)]
modelDb = StochKitModelWrapper()
tmpName = fixName(model.name)
while tmpName in names:
tmpName = fixName(model.name) + '_' + ''.join(random.choice('abcdefghijklmnopqrztuvwxyz') for x in range(3))
name = tmpName
modelDb.user_id = handler.user.user_id()
modelDb.name = name
modelDb.type = modelType
modelDb.species = species
modelDb.parameters = parameters
modelDb.reactions = reactions
modelDb.isSpatial = False
modelDb.units = model.units
modelDb.spatial = spatial
modelDb.zipFileName = None
modelDb.is_public = public
modelDb.put()
return modelDb
def updateModel(handler, jsonModel):
createModel = False
if "id" in jsonModel:
modelWrap = StochKitModelWrapper.get_by_id(jsonModel["id"])
userID = handler.user.user_id()
if userID != modelWrap.user_id:
raise "Error accessing model {0} with user id {1} (model owned by {2})".format(jsonModel["id"], userID, modelWrap.user_id)
else:
createModel = True
modelWrap = StochKitModelWrapper()
if 'isSpatial' not in jsonModel or 'spatial' not in jsonModel:
jsonModel['isSpatial'] = False
jsonModel['spatial'] = { 'subdomains' : [],
'mesh_wrapper_id' : None,
'species_diffusion_coefficients' : {} ,
'species_subdomain_assignments' : {} ,
'reactions_subdomain_assignments' : {},
'initial_conditions' : [] }
# This seems insane
if 'user_id' in jsonModel:
userID = jsonModel['user_id']
else:
userID = handler.user.user_id()
#if "name" not in jsonModel:
# raise Exception("Why is this code here?")
if 'isSpatial' in jsonModel:
modelWrap.isSpatial = jsonModel['isSpatial']
if 'spatial' in jsonModel:
modelWrap.spatial = jsonModel['spatial']
# Make sure we have access to a copy of the mesh (if it exists)
if "mesh_wrapper_id" in modelWrap.spatial and modelWrap.spatial["mesh_wrapper_id"]:
meshDbCurrent = mesheditor.MeshWrapper.get_by_id(modelWrap.spatial["mesh_wrapper_id"])
if createModel:
if meshDbCurrent.user_id != userID:
meshDb = mesheditor.MeshWrapper()
meshDb.user_id = userID
names = [x.name for x in db.Query(mesheditor.MeshWrapper).filter('user_id =', handler.user.user_id()).run()]
tmpName = meshDbCurrent.name
i = 0
while tmpName in names:
tmpName = meshDbCurrent.name + '_' + str(i)
i += 1
meshDb.name = tmpName
meshDb.description = meshDbCurrent.description
meshDb.meshFileId = meshDbCurrent.meshFileId
meshDb.subdomains = meshDbCurrent.subdomains
meshDb.uniqueSubdomains = meshDbCurrent.uniqueSubdomains
meshDb.undeletable = False#meshDbCurrent.undeletable
meshDb.ghost = False
meshDb.put()
modelWrap.spatial["mesh_wrapper_id"] = meshDb.key().id()
else:
meshDbCurrent.ghost = False
meshDbCurrent.put()
# This is maintained here!
modelWrap.subdomains = meshDbCurrent.uniqueSubdomains
if 'is_public' not in jsonModel:
jsonModel['is_public'] = False
modelWrap.user_id = userID
modelWrap.name = jsonModel["name"]
modelWrap.species = jsonModel["species"]
modelWrap.type = jsonModel["type"]
modelWrap.parameters = jsonModel["parameters"]
modelWrap.reactions = jsonModel["reactions"]
#modelWrap.spatial = jsonModel["spatial"]
#modelWrap.isSpatial = jsonModel["isSpatial"]
modelWrap.is_public = jsonModel["is_public"]
modelWrap.units = jsonModel["units"]
return modelWrap.put().id()
