Labs

Last updated: 3 Oct 2024

Introduction #

The LabReport, LabValue and LabReview models represent diagnostic clinical laboratory results.

Basic Usage #

To retrieve a LabReport model by id, use the objects.get method on the model. For example:

from canvas_sdk.v1.data.lab import LabReport

lab_report = LabReport.objects.get(id="bcd287b7-8b04-4540-a1ea-6529eb576565")

Filtering #

To retrieve the LabValue instances that are associated with the LabReport, you can either call the values on the LabReport instance:

from canvas_sdk.v1.data.lab import LabReport

lab_report = LabReport.objects.get(id="bcd287b7-8b04-4540-a1ea-6529eb576565")
lab_values = lab_report.values.all()

Or query the LabValue model and pass the report argument:

from canvas_sdk.v1.data.lab import LabReport, LabValue

lab_report = LabReport.objects.get(id="bcd287b7-8b04-4540-a1ea-6529eb576565")
lab_values = LabValue.objects.filter(lab_report=lab_report)

Additionally, codings for lab values can be attained by querying the LabValueCoding model. To retrieve the codings associated with a LabValue, you can call codings on the LabValue instance:

from logger import log
from canvas_sdk.v1.data.lab import LabReport, LabValue

lab_report = LabReport.objects.get(id="bcd287b7-8b04-4540-a1ea-6529eb576565")
lab_values = LabValue.objects.filter(lab_report=lab_report)
for value in lab_values:
    log.info(value.codings.all())

Or query the LabValueCoding model directly:

from logger import log
from canvas_sdk.v1.data.lab import LabReport, LabValue, LabValueCoding

lab_report = LabReport.objects.get(id="bcd287b7-8b04-4540-a1ea-6529eb576565")
lab_values = LabValue.objects.filter(lab_report=lab_report)
for value in lab_values:
    lab_value_codings = LabValueCoding.objects.filter(value=value)
    log.info(lab_value_codings)

To query all lab reports for a particular patient, the patient argument can be used:

from logger import log
from canvas_sdk.v1.data.lab import LabReport
from canvas_sdk.v1.data.patient import Patient

patient = Patient.objects.get(id="6cbc40b408294a5f9b41f57ba1b2b487")
lab_report = LabReport.objects.filter(patient=patient)

Example #

A common plugin use case may be for a plugin to run every time a new Lab Report is created in Canvas. The following plugin code will run every time a new Lab Report is created and log the patient it is for, along with the values and codings from the report’s results:

from canvas_sdk.events import EventType
from canvas_sdk.protocols import BaseProtocol
from logger import log

from canvas_sdk.v1.data.lab import LabReport


class Protocol(BaseProtocol):
    RESPONDS_TO = EventType.Name(EventType.LAB_REPORT_CREATED)

    def compute(self):
        lab_report = LabReport.objects.select_related("patient").get(id=self.target)
        if lab_report.patient:
            log.info(f"{lab_report.patient.first_name} {lab_report.patient.last_name}")
        for value in lab_report.values.all():
            log.info(f"{value.value} {value.units}")
            for coding in value.codings.all():
                log.info(coding.system)
                log.info(coding.name)
                log.info(coding.code)
        return []

Each value and coding are instances of LabValue and LabValueCoding, respectively. To view the fields available for each of these models, they are available in the Canvas SDK open source repository.