class Sample(Entity):
"Customer's sample to be analyzed; associated with a project."
_URI = 'samples'
_PREFIX = 'smp'
name = StringDescriptor('name')
date_received = StringDescriptor('date-received')
date_completed = StringDescriptor('date-completed')
project = EntityDescriptor('project', Project)
submitter = EntityDescriptor('submitter', Researcher)
# artifact: defined below
udf = UdfDictionaryDescriptor()
udt = UdtDictionaryDescriptor()
notes = EntityListDescriptor('note', Note)
files = EntityListDescriptor(nsmap('file:file'), File)
externalids = ExternalidListDescriptor()
# biosource XXX
@classmethod
def create(cls, lims, container, position, **kwargs):
"""Create an instance of Sample from attributes then post it to the LIMS
Udfs can be sent in with the kwarg `udfs`. It should be a dictionary-like.
"""
if not isinstance(container, Container):
raise TypeError('%s is not of type Container' % container)
udfs = kwargs.pop("udfs", None)
instance = super(Sample, cls)._create(lims,
creation_tag='samplecreation',
**kwargs)
location = ElementTree.SubElement(instance.root, 'location')
ElementTree.SubElement(location, 'container', dict(uri=container.uri))
position_element = ElementTree.SubElement(location, 'value')
position_element.text = position
# NOTE: This is a quick fix. I assume that it must be possible to initialize samples
# with UDFs
for key, value in udfs.items():
attrib = {
"name": key,
"xmlns:udf": "http://genologics.com/ri/userdefined",
}
udf = ElementTree.SubElement(instance.root,
'udf:field',
attrib=attrib)
udf.text = value
data = lims.tostring(ElementTree.ElementTree(instance.root))
instance.root = lims.post(uri=lims.get_uri(cls._URI), data=data)
instance._uri = instance.root.attrib['uri']
return instance
class Lab(Entity):
"Lab; container of researchers."
_URI = 'labs'
_PREFIX = 'lab'
name = StringDescriptor('name')
billing_address = StringDictionaryDescriptor('billing-address')
shipping_address = StringDictionaryDescriptor('shipping-address')
udf = UdfDictionaryDescriptor()
udt = UdtDictionaryDescriptor()
externalids = ExternalidListDescriptor()
website = StringDescriptor('website')
class Project(Entity):
"Project concerning a number of samples; associated with a researcher."
_URI = 'projects'
_PREFIX = 'prj'
name = StringDescriptor('name')
open_date = StringDescriptor('open-date')
close_date = StringDescriptor('close-date')
invoice_date = StringDescriptor('invoice-date')
researcher = EntityDescriptor('researcher', Researcher)
udf = UdfDictionaryDescriptor()
udt = UdtDictionaryDescriptor()
files = EntityListDescriptor(nsmap('file:file'), File)
externalids = ExternalidListDescriptor()
class Sample(Entity):
"Customer's sample to be analyzed; associated with a project."
_URI = 'samples'
_TAG = 'sample'
_PREFIX = 'smp'
name = StringDescriptor('name')
date_received = StringDescriptor('date-received')
date_completed = StringDescriptor('date-completed')
project = EntityDescriptor('project', Project)
submitter = EntityDescriptor('submitter', Researcher)
# artifact: defined below
udf = UdfDictionaryDescriptor()
udt = UdtDictionaryDescriptor()
notes = EntityListDescriptor('note', Note)
files = EntityListDescriptor(nsmap('file:file'), File)
externalids = ExternalidListDescriptor()
# biosource XXX
control_type = EntityDescriptor('control-type', Controltype)
@classmethod
def create(cls, lims, container, position, udfs=None, **kwargs):
"""Create an instance of Sample from attributes then post it to the LIMS"""
if udfs is None:
udfs = {}
if not isinstance(container, Container):
raise TypeError('%s is not of type Container' % container)
instance = super(Sample, cls)._create(lims,
creation_tag='samplecreation',
udfs=udfs,
**kwargs)
location = ElementTree.SubElement(instance.root, 'location')
ElementTree.SubElement(location, 'container', dict(uri=container.uri))
position_element = ElementTree.SubElement(location, 'value')
position_element.text = position
data = lims.tostring(ElementTree.ElementTree(instance.root))
instance.root = lims.post(uri=lims.get_uri(cls._URI), data=data)
instance._uri = instance.root.attrib['uri']
return instance
class Researcher(Entity):
"Person; client scientist or lab personnel. Associated with a lab."
_URI = 'researchers'
_PREFIX = 'res'
first_name = StringDescriptor('first-name')
last_name = StringDescriptor('last-name')
phone = StringDescriptor('phone')
fax = StringDescriptor('fax')
email = StringDescriptor('email')
initials = StringDescriptor('initials')
lab = EntityDescriptor('lab', Lab)
udf = UdfDictionaryDescriptor()
udt = UdtDictionaryDescriptor()
externalids = ExternalidListDescriptor()
# credentials XXX
@property
def name(self):
return "%s %s" % (self.first_name, self.last_name)