Multiple analysis specifications

Functional Questions and Answers
1

Hello all,
I’m considering providing Senaite to a labs in Jordan and to actually develop some localized addons, the determining factor for me right now is multiple analysis specifications. Does that exits in the current setup? Can I create multiple reference ranges for an analysis service one for male and one for females for instance?

2

Me interesa este post.
Sufian Ahmad: Valores de referencia (spanish language).
Nosotros contamos con un LIS de desarrollo propio que ha sido escrido en el 2010 (ASP.NET) y en la actualidad estamos tratando de migrar a SENAITE (dado que por política públicas debemos usar software de licencia libre). En el corto plazo no podemos realizar las modificaciones necesarias ya que el rrhh informático se encuentra abocado a otras tareas mas prioritarias.
Si sirve de ayuda puedo colaborar como Product Owner para el desarrollo de esto.
Muchas gracias!

3

Hello @sufrjo,
yes, we integrated dynamic analysis specifications in the upcoming 1.3.3 release

To distinguish different result ranges for male/female patients, you would have to write a custom Dynamic Results Range Adapter as described in the pull request.
Also see the doctest for functional internals: senaite.core/DynamicAnalysisSpec.rst at ab15d24cb73eeb113ce34d8cf2e9d8f05db17afc · senaite/senaite.core · GitHub
Best regards, Ramon

4

Thanks a lot for the help! That is exactly what I’m looking for.

5

Hi @aledeneuquen, if you have senaite.health installed, and therefore you want dynamic specs taking patients sex and age into consideration a Dynamic Results Range Adapter like below might work (haven’t tested):

# -*- coding: utf-8 -*-

from bika.lims.interfaces import IDynamicResultsRange
from zope.interface import implementer

from bika.lims.interfaces.analysis import IRequestAnalysis

marker = object()


@implementer(IDynamicResultsRange)
class DynamicResultsRange(object):

    def __init__(self, analysis):
        self.analysis = analysis

    def __call__(self):
        if not IRequestAnalysis.providedBy(self.analysis):
            # Cannot grab the patient from analyses not assigned to a Sample
            return {}

        # Get the sample's specificaion
        sample = self.analysis.getRequest()
        specification = sample.getSpecification()
        if not specification:
            # No specification, nothing to do
            return {}

        # Dynamic specification
        dyn_spec = specification.getDynamicAnalysisSpec()

        # Get the patient from the sample
        sample = self.analysis.getRequest()
        patient = sample.getField("Patient").get(sample)
        if not patient:
            # No patient assigned for this sample, do nothing
            return {}

        # Patient's age (in years)
        age = patient.getAge()
        # Patient's gender (male/female/dk)
        sex = patient.getGender()

        # Get the dynamic specification for this analysis by keyword
        # We expect the xls to have the columns "keyword", "age" and "sex"
        keyword = self.analysis.getKeyword()
        ranges = dyn_spec.get_by_keyword().get(keyword)
        if not ranges:
            # No ranges defined for this analysis
            return {}

        # Find a match by age and sex
        for range in ranges:
            if range.get("age") == age and range.get("sex") == sex:
                return range

        # No dynamic specification found for this analysis and patient
        return {}

You have to create a Dynamic Analysis Specification in SENAITE and upload an excel with at least the following column headers: keyword, age, sex, min, max.

For instructions on how to add a dynamic results range adapter, please read the links posted by @ramonski above

Hope it helps

6

Just did a write up on the documentation page with the example you have given @xispa:

7

Fantastic!. Thanks @ramonski

8

This has been so helpful, thank you so much!

9

Hi, I’ve followed the instruction that you provide to use dynamic specs but still i didn’t get the out of range mark !