def getProtocols(self, count=100):
"""
Retrieve the Protocols attached to this Labstep Experiment.
Returns
-------
List[:class:`~labstep.entities.experimentProtocol.model.ExperimentProtocol`]
List of the Protocols attached to the Experiment.
Example
-------
::
entity = user.getExperiment(17000)
protocols = entity.getProtocols()
protocols[0].attributes()
"""
from labstep.generic.entity.repository import entityRepository
return entityRepository.getEntities(
self.__user__,
ExperimentProtocol,
count,
{
"is_root": 0,
"experiment_workflow_id": self.id
},
)
def getResourceCategorys(self,
user,
count=100,
search_query=None,
tag_id=None,
extraParams={}):
"""
Retrieve a list of a user's ResourceCategorys on Labstep,
which can be filtered using the parameters:
Parameters
----------
user (obj)
The Labstep user. Must have property
'api_key'. See 'login'.
count (int)
The number of ResourceCategorys to retrieve.
search_query (str)
Search for ResourceCategorys with this 'name'.
tag_id (int)
The id of the Tag to retrieve.
Returns
-------
ResourceCategorys
A list of ResourceCategory objects.
"""
filterParams = {"search_query": search_query, "tag_id": tag_id}
params = {**filterParams, **extraParams, "is_template": 1}
return entityRepository.getEntities(user, ResourceCategory, count,
params)
def getDataFields(self, entity, count=1000, extraParams={}):
params = {}
if isinstance(entity, ExperimentProtocol):
params = {"metadata_thread_id": entity.metadata_thread["id"]}
elif isinstance(entity, Resource):
params = {
"experiment_value_resource_id": entity.id,
"has_value": True
}
elif isinstance(entity, ResourceItem):
params = {
"experiment_value_resource_item_id": entity.id,
"has_value": True
}
return entityRepository.getEntities(entity.__user__,
ExperimentDataField,
count=count,
filterParams={
**params,
**extraParams
})
def getExperimentMaterials(self,
user,
experiment_id,
count=100,
extraParams={}):
params = {'experiment_id': experiment_id, **extraParams}
return entityRepository.getEntities(user, ExperimentMaterial, count,
params)
def getExperimentSignatureRequests(self, user, experiment_id):
params = {
"experiment_workflow_id": experiment_id,
"search": None,
}
return entityRepository.getEntities(user,
ExperimentSignatureRequest,
filterParams=params,
count=100)
def getInvitations(self, user, organization_id, extraParams):
return entityRepository.getEntities(user,
Invitation,
count=None,
filterParams={
'organization_id':
organization_id,
**extraParams
})
def getResourceLocations(
self, user, count=100, search_query=None, tag_id=None, extraParams={}
):
params = {
"group_id": user.activeWorkspace,
"search_query": search_query,
"tag_id": tag_id,
**extraParams,
}
return entityRepository.getEntities(user, ResourceLocation, count, params)
def getCollections(
self, user, count=1000, type=None, search_query=None, extraParams={}
):
types = {
"experiment": "experiment_workflow",
"protocol": "protocol_collection",
None: None,
}
params = {"search_query": search_query, "type": types[type], **extraParams}
return entityRepository.getEntities(user, Collection, count, params)
def getDataFields(self, entity, count=1000, extraParams={}):
if isinstance(entity, ProtocolVersion):
params = {
"metadata_thread_id": entity.metadata_thread["id"]}
return entityRepository.getEntities(
entity.__user__, ProtocolDataField, count=count, filterParams={
**params, **extraParams}
)
def getMetadata(self, entity, count=1000, extraParams={}):
if hasattr(entity, 'metadata_thread') is False:
entity.update()
params = {
"metadata_thread_id": entity.metadata_thread["id"],
**extraParams
}
return entityRepository.getEntities(entity.__user__,
Metadata,
count=count,
filterParams=params)
def getOrganizationUsers(self, organization, count=100, extraParams={}):
params = {
'organization_id': organization.id,
**extraParams,
}
return entityRepository.getEntities(organization.__user__,
OrganizationUser,
count,
filterParams=params)
def getComments(self, entity, count=100, extraParams={}):
if entity.thread is None:
return []
params = {
"parent_thread_id": entity.thread["id"],
"search": None,
**extraParams,
}
return entityRepository.getEntities(entity.__user__, Comment, count,
params)
def getResourceItems(self,
user,
resource_id=None,
count=100,
search_query=None,
extraParams={}):
params = {
"search_query": search_query,
"resource_id": resource_id,
**extraParams,
}
return entityRepository.getEntities(user, ResourceItem, count, params)
def getFiles(self,
user,
count=100,
search_query=None,
file_type=None,
extraParams={}):
params = {
"search_query": search_query,
"filetype": file_type,
**extraParams
}
return entityRepository.getEntities(user, File, count, params)
def getOrderRequests(
self,
user,
count=100,
search_query=None,
tag_id=None,
status=None,
extraParams={},
):
params = {
"group_id": user.activeWorkspace,
"search_query": search_query,
"tag_id": tag_id,
"status": handleKeyword(status),
**extraParams,
}
return entityRepository.getEntities(user, OrderRequest, count, params)
def getAttachedTags(self, entity, count=100):
"""
Retrieve the Tags attached to a Labstep Entity.
Parameters
----------
entity (obj)
The entity to retrieve Tags from.
Returns
-------
tags
List of the tags attached.
"""
key = entity.__entityName__.replace("-", "_") + "_id"
filterParams = {key: entity.id}
return entityRepository.getEntities(entity.__user__,
Tag,
count=count,
filterParams=filterParams)
def getProtocols(
self,
user,
count=100,
search_query=None,
created_at_from=None,
created_at_to=None,
tag_id=None,
collection_id=None,
extraParams={},
):
params = {
"search_query": search_query,
"created_at_from": createdAtFrom(created_at_from),
"created_at_to": createdAtTo(created_at_to),
"tag_id": tag_id,
"folder_id": collection_id,
**extraParams,
}
return entityRepository.getEntities(user, Protocol, count, params)
def getData(self, count=100, search_query=None, extraParams={}):
"""
Retrieve a list of the data sent by an device.
Parameters
----------
count (int)
The total count of data points to return.
search_query (str)
Search for data points by name.
extraParams (dict)
Dictionary of extra filter parameters.
Returns
-------
DeviceData
A list of DeviceData objects.
"""
from labstep.generic.entity.repository import entityRepository
params = {"search_query": search_query,
"device_id": self.id, **extraParams}
return entityRepository.getEntities(self.__user__, DeviceData, count, params)
def getTags(self,
user,
count=1000,
type=None,
search_query=None,
extraParams={}):
"""
Retrieve a list of the user's tags.
Parameters
----------
user (obj)
The Labstep user.
Must have property 'api_key'. See 'login'.
count (int)
The number of Tags to retrieve.
type (str)
Return only tags of a certain type. Options are:
'experiment_workflow', 'protocol_collection',
'resource', 'order_request'.
search_query (str)
Search for Tags with this 'name'.
extraParams (dict)
Dictionary of extra filter parameters.
Returns
-------
tags
A list of tag objects.
"""
params = {
"search_query": search_query,
"type": handleKeyword(type),
**extraParams,
}
return entityRepository.getEntities(user, Tag, count, params)
def getProtocolMaterials(self, user, protocol_id, count=100, extraParams={}):
params = {
'protocol_id': protocol_id,
**extraParams
}
return entityRepository.getEntities(user, ProtocolMaterial, count, params)
def getResources(
self, user, count=100, search_query=None, tag_id=None, extraParams={}
):
params = {"search_query": search_query,
"tag_id": tag_id, **extraParams}
return entityRepository.getEntities(user, Resource, count, params)
def getAttachedCollections(self, entity, count=100):
key = entity.__entityName__.replace("-", "_") + "_id"
filterParams = {key: entity.id, "group_id": entity.__user__.activeWorkspace}
return entityRepository.getEntities(
entity.__user__, Collection, count=count, filterParams=filterParams
)
def getWorkspaces(self, user, count=100, search_query=None, extraParams={}):
params = {"name": search_query, **extraParams}
return entityRepository.getEntities(user, Workspace, count, params)
def getDevices(self, user, count=100, search_query=None, extraParams={}):
params = {"search_query": search_query, **extraParams}
return entityRepository.getEntities(user, Device, count, params)
def getMembers(self, user, workspace_id, count=100, search_query=None, extraParams={}):
params = {"group_id": workspace_id,
"search_query_user": search_query, **extraParams}
return entityRepository.getEntities(user, WorkspaceMember, count, params)
