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 Step(Entity):
"Step, as defined by the genologics API."
_URI = 'steps'
_PREFIX = 'stp'
current_state = StringAttributeDescriptor('current-state')
_reagent_lots = EntityDescriptor('reagent-lots', StepReagentLots)
actions = EntityDescriptor('actions', StepActions)
date_started = StringDescriptor('date-started')
date_completed = StringDescriptor('date-completed')
placements = EntityDescriptor('placements', StepPlacements)
details = EntityDescriptor('details', StepDetails)
step_pools = EntityDescriptor('pools', StepPools)
program_status = EntityDescriptor('program-status', StepProgramStatus)
reagents = EntityDescriptor('reagents', StepReagents)
def advance(self):
self.get()
self.root = self.lims.post(uri="{0}/advance".format(self.uri),
data=self.lims.tostring(
ElementTree.ElementTree(self.root)))
@property
def reagent_lots(self):
return self._reagent_lots.reagent_lots
class ControlType(Entity):
_URI = "controltypes"
_TAG = "control-type"
_PREFIX = 'ctrltp'
name = StringAttributeDescriptor('name')
supplier = StringDescriptor('supplier')
archived = BooleanDescriptor('archived')
single_step = BooleanDescriptor('single_step')
class Protocol(Entity):
"""Protocol, holding ProtocolSteps and protocol-properties"""
_URI = 'configuration/protocols'
_TAG = 'protocol'
name = StringAttributeDescriptor('name')
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 Containertype(Entity):
"Type of container for analyte artifacts."
_TAG = 'container-type'
_URI = 'containertypes'
_PREFIX = 'ctp'
name = StringAttributeDescriptor('name')
calibrant_wells = StringListDescriptor('calibrant-well')
unavailable_wells = StringListDescriptor('unavailable-well')
x_dimension = DimensionDescriptor('x-dimension')
y_dimension = DimensionDescriptor('y-dimension')
class Controltype(Entity):
"""Control sample."""
_URI = 'controltypes'
_TAG = 'control-type'
_PREFIX = 'ctrltp'
name = StringAttributeDescriptor('name')
supplier = StringDescriptor('supplier')
catalogue_number = StringDescriptor('catalogue-number')
website = StringDescriptor('website')
concentration = StringDescriptor('concentration')
archived = BooleanDescriptor('archived')
single_step = BooleanDescriptor('single-step')
class ProtocolStep(Entity):
"""Steps key in the Protocol object"""
_TAG = 'step'
name = StringAttributeDescriptor("name")
type = EntityDescriptor('type', Processtype)
permittedcontainers = NestedStringListDescriptor('container-type',
'container-types')
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 Processtype(Entity):
_TAG = 'process-type'
_URI = 'processtypes'
_PREFIX = 'ptp'
def __init__(self, lims, uri=None, id=None, _create_new=False):
super(Processtype, self).__init__(lims, uri, id, _create_new)
self.parameters = ProcessTypeParametersDescriptor(self)
name = StringAttributeDescriptor('name')
field_definition = EntityListDescriptor('field-definition', Udfconfig)
process_inputs = ProcessTypeProcessInputDescriptor()
process_outputs = ProcessTypeProcessOutputDescriptor()
process_type_attribute = NamedStringDescriptor('process-type-attribute')
@property
def process_input(self):
return self.process_inputs[0]
class ReagentType(Entity):
"""Reagent Type, usually, indexes for sequencing"""
_URI = "reagenttypes"
_TAG = "reagent-type"
_PREFIX = 'rtp'
category = StringDescriptor('reagent-category')
name = StringAttributeDescriptor("name")
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 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 Stage(Entity):
"""Holds Protocol/Workflow"""
name = StringAttributeDescriptor('name')
index = IntegerAttributeDescriptor('index')
protocol = EntityDescriptor('protocol', Protocol)
step = EntityDescriptor('step', ProtocolStep)
class Processtype(Entity):
_TAG = 'process-type'
_URI = 'processtypes'
_PREFIX = 'ptp'
name = StringAttributeDescriptor('name')