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 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 File(Entity):
"File attached to a project or a sample."
attached_to = StringDescriptor('attached-to')
content_location = StringDescriptor('content-location')
original_location = StringDescriptor('original-location')
is_published = BooleanDescriptor('is-published')
class ReagentKit(Entity):
"""Type of Reagent with information about the provider"""
_URI = "reagentkits"
_TAG = "reagent-kit"
_PREFIX = 'kit'
name = StringDescriptor('name')
supplier = StringDescriptor('supplier')
website = StringDescriptor('website')
archived = BooleanDescriptor('archived')
class Instrument(Entity):
"""Lab Instrument
"""
_URI = "instruments"
_TAG = "instrument"
_PREFIX = "inst"
name = StringDescriptor('name')
type = StringDescriptor('type')
serial_number = StringDescriptor('serial-number')
expiry_date = StringDescriptor('expiry-date')
archived = BooleanDescriptor('archived')
class Udfconfig(Entity):
"Instance of field type (cnf namespace)."
_URI = 'configuration/udfs'
name = StringDescriptor('name')
attach_to_name = StringDescriptor('attach-to-name')
attach_to_category = StringDescriptor('attach-to-category')
show_in_lablink = BooleanDescriptor('show-in-lablink')
allow_non_preset_values = BooleanDescriptor('allow-non-preset-values')
first_preset_is_default_value = BooleanDescriptor(
'first-preset-is-default-value')
show_in_tables = BooleanDescriptor('show-in-tables')
is_editable = BooleanDescriptor('is-editable')
is_required = BooleanDescriptor('is-required')
is_deviation = BooleanDescriptor('is-deviation')
is_controlled_vocabulary = BooleanDescriptor('is-controlled-vocabulary')
presets = StringListDescriptor('preset')
class ProcessTypeProcessInput(object):
instance = None
name = None
root = None
tag = ''
artifact_type = StringDescriptor('artifact-type')
display_name = StringDescriptor('display-name')
remove_working_flag = BooleanDescriptor('remove-working-flag')
def __init__(self, pt_instance, node):
self.instance = pt_instance
self.root = node
def get(self):
pass
class ProcessTypeProcessInput(object):
instance = None
name = None
root = None
tag = ''
artifact_type = StringDescriptor('artifact-type')
display_name = StringDescriptor('display-name')
remove_working_flag = BooleanDescriptor('remove-working-flag')
def __init__(self, pt_instance, node):
self.instance = pt_instance
self.root = node
self.lims = pt_instance.lims
def __repr__(self):
return "{0}({1})".format(self.__class__.__name__, self.display_name)
def get(self):
pass
class Artifact(Entity):
"Any process input or output; analyte or file."
_URI = 'artifacts'
_TAG = 'artifact'
_PREFIX = 'art'
name = StringDescriptor('name')
type = StringDescriptor('type')
output_type = StringDescriptor('output-type')
parent_process = EntityDescriptor('parent-process', Process)
volume = StringDescriptor('volume')
concentration = StringDescriptor('concentration')
qc_flag = StringDescriptor('qc-flag')
location = LocationDescriptor('location')
working_flag = BooleanDescriptor('working-flag')
samples = EntityListDescriptor('sample', Sample)
udf = UdfDictionaryDescriptor()
files = EntityListDescriptor(nsmap('file:file'), File)
reagent_labels = ReagentLabelList()
# artifact_flags XXX
# artifact_groups XXX
def input_artifact_list(self):
"""Returns the input artifact ids of the parrent process."""
input_artifact_list = []
try:
for tuple in self.parent_process.input_output_maps:
if tuple[1]['limsid'] == self.id:
input_artifact_list.append(tuple[0]['uri']) # ['limsid'])
except:
pass
return input_artifact_list
def get_state(self):
"Parse out the state value from the URI."
parts = urlparse(self.uri)
params = parse_qs(parts.query)
try:
return params['state'][0]
except (KeyError, IndexError):
return None
@property
def container(self):
"The container where the artifact is located, or None"
try:
return self.location[0]
except:
return None
def stateless(self):
"returns the artefact independently of it's state"
parts = urlparse(self.uri)
if 'state' in parts[4]:
stateless_uri = urlunparse(
[parts[0], parts[1], parts[2], parts[3], '', ''])
return Artifact(self.lims, uri=stateless_uri)
else:
return self
# XXX set_state ?
state = property(get_state)
stateless = property(stateless)
def _get_workflow_stages_and_statuses(self):
self.get()
result = []
rootnode = self.root.find('workflow-stages')
for node in rootnode.findall('workflow-stage'):
result.append((Stage(self.lims, uri=node.attrib['uri']),
node.attrib['status'], node.attrib['name']))
return result
workflow_stages_and_statuses = property(_get_workflow_stages_and_statuses)
