edc-lab

Lab classes

Installation

Get the latest version:

pip install git+https://github.com/botswana-harvard/edc-lab@develop#egg=edc-lab

Add to settings:

INSTALLED_APPS = [
    ...
    'edc_lab.apps.AppConfig',
    ...
]

Configuration

Create aliquots configurations and their relationship:

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')

wb.add_derivatives(pl, bc)

Set up one or more processing profiles:

processing_profile = 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)
processing_profile.add_processes(process_bc, process_pl)

Create one or more panels:

panel = RequisitionPanel(
    name='panel',
    aliquot_type=a,
    processing_profile=processing_profile)

Create a lab profile:

lab_profile = LabProfile(name='lab_profile')
lab_profile.add_panel(panel)

Register the lab_profile with site:

site_labs.register(lab_profile, requisition_model='edc_lab.subjectrequisition')

Usage

Create a requisition model instance:

requisition = SubjectRequisition.objects.create(
    subject_visit=self.subject_visit,
    panel_name=self.panel.name,
    is_drawn=YES)

Pass the requisition to Specimen

specimen = Specimen(requisition=requisition)

Process:

specimen.process()

Aliquots have been created according to the configured processing profile:

>>> specimen.primary_aliquot.identifier
99900GV63F00000201

>>> for aliquot in specimen.aliquots.order_by('count'):
       print(aliquot.aliquot_identifier)
99900GV63F00000201
99900GV63F02013202
99900GV63F02013203
99900GV63F02011604
99900GV63F02011605
99900GV63F02011606
99900GV63F02011607