class Role(Entity):
"""Clarity Role, hosting permissions"""
name = StringDescriptor('name')
researchers = NestedEntityListDescriptor('researcher', Researcher,
'researchers')
permissions = NestedEntityListDescriptor('permission', Permission,
'permissions')
class Workflow(Entity):
""" Workflow, introduced in 3.5"""
_URI = "configuration/workflows"
_TAG = "workflow"
name = StringAttributeDescriptor("name")
status = StringAttributeDescriptor("status")
protocols = NestedEntityListDescriptor('protocol', Protocol, 'protocols')
stages = NestedEntityListDescriptor('stage', Stage, 'stages')
class Queue(Entity):
"""Queue of a given step"""
_URI = "queues"
_TAG = "queue"
_PREFIX = "que"
artifacts = NestedEntityListDescriptor("artifact", Artifact, "artifacts")
class Protocol(Entity):
"""Protocol, holding ProtocolSteps and protocol-properties"""
_URI = 'configuration/protocols'
_TAG = 'protocol'
steps = NestedEntityListDescriptor('step', ProtocolStep, 'steps')
properties = NestedAttributeListDescriptor('protocol-property',
'protocol-properties')
class Automation(Entity):
"""Automation, holding Automation configurations"""
_URI = 'configuration/automations'
_TAG = 'automation'
process_types = NestedEntityListDescriptor('process-type', Processtype,
'process-types')
string = NestedStringDescriptor('string')
name = StringAttributeDescriptor('name')
context = NestedStringDescriptor('context')
class ProtocolStep(Entity):
"""Steps key in the Protocol object"""
_TAG = 'step'
name = StringAttributeDescriptor("name")
type = EntityDescriptor('process-type', Processtype)
permittedcontainers = NestedStringListDescriptor('container-type',
'permitted-containers')
permitted_control_types = NestedEntityListDescriptor(
'control-type', ControlType, 'permitted-control-types')
required_reagent_kits = NestedEntityListDescriptor(
'reagent-kit', ReagentKit, 'required-reagent-kits')
queue_fields = NestedAttributeListDescriptor('queue-field', 'queue-fields')
step_fields = NestedAttributeListDescriptor('step-field', 'step-fields')
sample_fields = NestedAttributeListDescriptor('sample-field',
'sample-fields')
step_properties = NestedAttributeListDescriptor('step-property',
'step-properties')
epp_triggers = NestedAttributeListDescriptor('epp-trigger', 'epp-triggers')
class StepReagentLots(Entity):
reagent_lots = NestedEntityListDescriptor('reagent-lot', ReagentLot,
'reagent-lots')
super(ReagentType, self).__init__(lims, uri, id)
assert self.uri is not None
self.root = lims.get(self.uri)
self.sequence = None
for t in self.root.findall('special-type'):
if t.attrib.get("name") == "Index":
for child in t.findall("attribute"):
if child.attrib.get("name") == "Sequence":
self.sequence = child.attrib.get("value")
class Queue(Entity):
"""Queue of a given step. Will recursively get all the pages of artifacts, and therefore, can be quite slow to load"""
_URI = "queues"
_TAG = "queue"
_PREFIX = "que"
artifacts = MultiPageNestedEntityListDescriptor("artifact", Artifact,
"artifacts")
Sample.artifact = EntityDescriptor('artifact', Artifact)
StepActions.step = EntityDescriptor('step', Step)
Stage.workflow = EntityDescriptor('workflow', Workflow)
Artifact.workflow_stages = NestedEntityListDescriptor('workflow-stage', Stage,
'workflow-stages')
Step.configuration = EntityDescriptor('configuration', ProtocolStep)
StepProgramStatus.configuration = EntityDescriptor('configuration',
ProtocolStep)
Researcher.roles = NestedEntityListDescriptor('role', Role, 'credentials')
category = StringDescriptor('reagent-category')
def __init__(self, lims, uri=None, id=None):
super(ReagentType, self).__init__(lims, uri, id)
assert self.uri is not None
self.root = lims.get(self.uri)
self.sequence = None
for t in self.root.findall('special-type'):
if t.attrib.get("name") == "Index":
for child in t.findall("attribute"):
if child.attrib.get("name") == "Sequence":
self.sequence = child.attrib.get("value")
class Queue(Entity):
"""Queue of a given step"""
_URI = "queues"
_TAG = "queue"
_PREFIX = "que"
artifacts = NestedEntityListDescriptor("artifact", Artifact, "artifacts")
Sample.artifact = EntityDescriptor('artifact', Artifact)
StepActions.step = EntityDescriptor('step', Step)
Stage.workflow = EntityDescriptor('workflow', Workflow)
Artifact.workflow_stages = NestedEntityListDescriptor('workflow-stage', Stage,
'workflow-stages')
Step.configuration = EntityDescriptor('configuration', ProtocolStep)