Configuration¶

Configuring the system for specimen management¶

To configure the system

define a requisition model
create a lab profile and some tesing panels
add the panels to the lab profile (default panels are in edc_lab_panel)
register the lab profile with the site global.

Define a Requisition model¶

from edc_crf.model_mixins import CrfStatusModelMixin
from edc_lab.model_mixins import RequisitionModelMixin
from edc_model.models import BaseUuidModel


class SubjectRequisition(RequisitionModelMixin, CrfStatusModelMixin, BaseUuidModel):
    class Meta(RequisitionModelMixin.Meta, CrfStatusModelMixin.Meta, BaseUuidModel.Meta):
        pass

Creating a lab profile¶

The first step is to define a lab profile. The lab profile is linked to a single requisition model. The requisition model has a key to the Panel model. The same requisition model is used longitudinally for all requisitions for all panels.

lab_profile = LabProfile(
    name='lab_profile',
    requisition_model='my_app.subjectrequisition')

Building panels to add to the lab profile¶

To build a panel: * define aliqout types; * add aliquots to a processing profile; * add the processing profile a panel

Creating aliquot types¶

Each aliquot listed in a processing profile has enough information to generate a unique aliquot identifier for the type.

# aliquot types
wb = AliquotType(name='whole_blood', alpha_code='WB', numeric_code='02')
bc = AliquotType(name='buffy_coat', alpha_code='BC', numeric_code='16')
pl = AliquotType(name='plasma', alpha_code='PL', numeric_code='32')

Add possible derivatives to an aliquot type:

# in this case, plasma and buffy coat are possible derivatives
wb.add_derivatives(pl, bc)

Set up a processing profile¶

viral_load = ProcessingProfile(
    name='viral_load', aliquot_type=wb)
process_bc = Process(aliquot_type=bc, aliquot_count=4)
process_pl = Process(aliquot_type=pl, aliquot_count=2)
viral_load.add_processes(process_bc, process_pl)

Create a tesing panel that uses the processing profile¶

panel = RequisitionPanel(
    name='Viral Load',
    processing_profile=viral_load)

Adding panels to the lab profile¶

Add the panel (and others) to the lab profile:

lab_profile.add_panel(panel)

Register the lab profile with the site global¶

site_labs.register(lab_profile)