Labs Last updated: 25 Nov 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 .
Attributes # LabReport # Field Name Type id UUID dbid Integer created DateTime modified DateTime review_mode String junked Boolean requires_signature Boolean assigned_date DateTime patient Patient transmission_type TransmissionType for_test_only Boolean external_id String version Integer requisition_number String review LabReview original_date DateTime date_performed DateTime custom_document_name String originator CanvasUser committer CanvasUser entered_in_error CanvasUser deleted Boolean
LabReview # Field Name Type id UUID dbid Integer created DateTime modified DateTime originator CanvasUser deleted Boolean committer CanvasUser entered_in_error CanvasUser internal_comment String message_to_patient String status String patient Patient patient_communication_method String
LabValue # Field Name Type id UUID dbid Integer created DateTime modified DateTime report LabReport value String units String abnormal_flag String reference_range String low_threshold String high_threshold String comment String observation_status String
LabValueCoding # Field Name Type dbid Integer created DateTime modified DateTime value LabValue code String name String system String
LabOrder # Field Name Type id UUID dbid Integer created DateTime modified DateTime originator CanvasUser deleted Boolean committer CanvasUser entered_in_error CanvasUser patient Patient ontology_lab_partner String comment String requisition_number String is_patient_bill Boolean date_ordered DateTime fasting_status Boolean specimen_collection_type SpecimenCollectionType transmission_type TransmissionType courtesy_copy_type CourtesyCopyType courtesy_copy_number String courtesy_copy_text String parent_order LabOrder healthgorilla_id String manual_processing_status ManualProcessingStatus manual_processing_comment String labcorp_abn_url URL
LabOrderReason # Field Name Type dbid Integer created DateTime modified DateTime originator CanvasUser deleted Boolean committer CanvasUser entered_in_error CanvasUser order LabOrder mode LabReasonMode
Enumeration types # TransmissionType # Value Label F fax H hl7 M manual
SpecimenCollectionType # Value Label L on location P patient service center O other
CourtesyCopyType # Value Label A account F fax P patient
ManualProcessingStatus # Value Label NEEDS_REVIEW Needs Review IN_PROGRESS In Progress PROCESSED Processed FLAGGED Flagged
LabReasonMode # Value Label MO monitor IN investigate SF screen for UNK unknown
LabTestOrderStatus # Value Label NE new SR staged for requisition SE sending SF sending failed PR processing PF processing failed RE received RV reviewed IN inactive
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