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LIMS/lab classes for clinicedc/edc projects

Project description

pypi travis coverage

edc-lab

Add to settings:

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

Configuration

Create aliquot types:

# 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``panel`` that uses the processing profile:

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

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

lab_profile = LabProfile(
    name='lab_profile',
    requisition_model='edc_lab.subjectrequisition')
lab_profile.add_panel(panel)

Register the lab_profile with the site global:

site_labs.register(lab_profile)

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'

Project details


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Filename, size & hash SHA256 hash help File type Python version Upload date
edc-lab-0.2.26.macosx-10.13-x86_64.tar.gz (125.7 kB) Copy SHA256 hash SHA256 Source None Sep 23, 2018
edc_lab-0.2.26-py3-none-any.whl (92.9 kB) Copy SHA256 hash SHA256 Wheel py3 Sep 23, 2018

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