Dynamic Analysis Specifications

[ramonski]

Description of the issue/feature this PR addresses

This PR adds the ability to link dynamic analysis specifications to the standard analysis specifications.

It is primarily meant to provide the basis for this requested functionality:
https://community.senaite.org/t/age-and-gender-based-specifications-in-senaite-health/102

Current behavior before PR

Analysis Specifications (Result Ranges) can be defined per Sample Type.
If different ranges are needed for Methods, Sample Points, Sample Conditions etc., different Analysis Specifications need to be created.

Desired behavior after PR is merged

An Excel file can be uploaded to a "Dynamic Analysis Specification" object.
This object can be linked to a common Analysis Specification for a given Sample Type.
In the Excel file the columns are used to match the values per row against the values of the Analysis or the Analysis Request. If all values match, the given result range will be used.

Example

Given is an Excel with the following minimal set of columns:

Keyword	Method	min	max
H2O	Method-1	1	2
H2O	Method-2	3	4

This Excel is uploaded to an Dynamic Analysis Specification object, which is linked to an Analysis Specification for the Sample Type "Water".

A new "Water" Sample is created with an containing H2O sample to be tested with Method-2.
The results range selected will be [3;4]

Supported Results Range columns

The following column names have to be chosen to define a valid results range:

warn_min, min, min_operator, warn_max, max, max_operator, error

Defining a custom Dynamic Results Range Adapter

Sometimes it is needed to define more complex matches, e.g. to match the Gender or Age of a Patient to find a specification. In that case, it is supported to define a custom Adapter like this:

<configure
    xmlns="http://namespaces.zope.org/zope">

  <!-- Dynamic Results Range Adapter
       Looked up in `abstractroutineanalysis.getResultsRange` -->
  <adapter
      for="my.lims.interfaces.IRoutineAnalysis"
      factory=".dynamicresultsrange.DynamicResultsRange"
      provides="bika.lims.interfaces.IDynamicResultsRange"
      />

  <class class="bika.lims.content.analysis.Analysis">
    <implements interface="my.lims.interfaces.IRoutineAnalysis" />
  </class>

</configure>

Contents of dynamicresultsrange.py:

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

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

marker = object()


@implementer(IDynamicResultsRange)
class DynamicResultsRange(object):
    """Default Dynamic Results Range Adapter

    Matches all columns against the Analysis field values with the same names.
    """

    def __init__(self, analysis):
        self.analysis = analysis
        self.analysisrequest = analysis.getRequest()
        self.specification = self.analysisrequest.getSpecification()
        self.dynamicspec = None
        if self.specification:
            self.dynamicspec = self.specification.getDynamicAnalysisSpec()

    def __call__(self):
        # calculate a dynamic analysis specification for `self.analysis`

--
I confirm I have tested this PR thoroughly and coded it according to PEP8
and Plone's Python styleguide standards.

[shamut]

Great functionality, this will make analysis specifications much easier to configure, manage and generally work with

Kudos

[xispa]

Good stuff