Merge branch '2.x' into fix-2d-csv-interface

CHANGES.rst

@@ -5,6 +5,7 @@ Changelog
 ------------------
 
 - #2689 Fix 2-Dimensional CSV import interface
+- #2682 Added Limit of Quantification (LOQ) for services and analyses
 - #2687 Remove legacy and obsolete rejection.js
 - #2685 Fix missing default instrument import template
 - #2684 Fix Traceback for unicode titled instruments

src/bika/lims/content/abstractbaseanalysis.py

@@ -175,37 +175,98 @@
     )
 )
 
-# If the value is below this limit, it means that the measurement lacks
-# accuracy and this will be shown in manage_results and also on the final
-# report.
 LowerDetectionLimit = StringField(
     "LowerDetectionLimit",
-    schemata="Analysis",
+    schemata="Limits",
+    default="0.0",
+    validators=("lower_limit_of_detection_validator",),
+    widget=DecimalWidget(
+        label=_(
+            u"label_analysis_lower_limit_of_detection_title",
+            default=u"Lower Limit of Detection (LLOD)"
+        ),
+        description=_(
+            u"label_analysis_lower_limit_of_detection_description",
+            default=u"The Lower Limit of Detection (LLOD) is the lowest "
+                    u"concentration of a parameter that can be reliably "
+                    u"detected by a specified testing methodology with a "
+                    u"defined level of confidence. Results below this "
+                    u"threshold are typically reported as '< LLOD' (or 'Not "
+                    u"Detected'), indicating that the parameter's "
+                    u"concentration, if present, is below the detection "
+                    u"capability of the method at a reliable level."
+        )
+    )
+)
+
+LowerLimitOfQuantification = StringField(
+    "LowerLimitOfQuantification",
+    schemata="Limits",
     default="0.0",
+    validators=("lower_limit_of_quantification_validator",),
+    widget=DecimalWidget(
+        label=_(
+            u"label_analysis_lower_limit_of_quantification_title",
+            default=u"Lower Limit Of Quantification (LLOQ)"
+        ),
+        description=_(
+            u"label_analysis_lower_limit_of_quantification_description",
+            default=u"The Lower Limit of Quantification (LLOQ) is the lowest "
+                    u"concentration of a parameter that can be reliably and "
+                    u"accurately measured using the specified testing "
+                    u"methodology, with acceptable levels of precision and "
+                    u"accuracy. Results below this value cannot be quantified "
+                    u"with confidence and are typically reported as '< LOQ' "
+                    u"(or 'Detected but < LOQ'), indicating that while the "
+                    u"parameter may be present, its exact concentration "
+                    u"cannot be determined reliably."
+        )
+    )
+)
+
+UpperLimitOfQuantification = StringField(
+    "UpperLimitOfQuantification",
+    schemata="Limits",
+    default="1000000000.0",
+    validators=("upper_limit_of_quantification_validator",),
     widget=DecimalWidget(
-        label=_("Lower Detection Limit (LDL)"),
+        label=_(
+            u"label_analysis_upper_limit_of_quantification_title",
+            default=u"Upper Limit Of Quantification (ULOQ)"),
         description=_(
-            "The Lower Detection Limit is the lowest value to which the "
-            "measured parameter can be measured using the specified testing "
-            "methodology. Results entered which are less than this value will "
-            "be reported as < LDL")
+            u"label_analysis_upper_limit_of_quantification_description",
+            default=u"The Upper Limit of Quantification (ULOQ) is the highest "
+                    u"concentration of a parameter that can be reliably and "
+                    u"accurately measured using the specified testing "
+                    u"methodology, with acceptable levels of precision and "
+                    u"accuracy. Results above this value cannot be quantified "
+                    u"with confidence and are typically reported as '> ULOQ', "
+                    u"indicating that its exact concentration cannot be "
+                    u"determined reliably."
+        )
     )
 )
 
-# If the value is above this limit, it means that the measurement lacks
-# accuracy and this will be shown in manage_results and also on the final
-# report.
 UpperDetectionLimit = StringField(
     "UpperDetectionLimit",
-    schemata="Analysis",
+    schemata="Limits",
     default="1000000000.0",
     widget=DecimalWidget(
-        label=_("Upper Detection Limit (UDL)"),
+        label=_(
+            u"label_analysis_upper_limit_of_detection_title",
+            default=u"Upper Limit of Detection (ULOD)"),
         description=_(
-            "The Upper Detection Limit is the highest value to which the "
-            "measured parameter can be measured using the specified testing "
-            "methodology. Results entered which are greater than this value "
-            "will be reported as > UDL")
+            u"label_analysis_upper_limit_of_detection_description",
+            default=u"The Upper Limit of Detection (ULOD) is the highest "
+                    u"concentration of a parameter that can be reliably "
+                    u"measured using a specified testing methodology. Beyond "
+                    u"this limit, results may no longer be accurate or valid "
+                    u"due to instrument saturation or methodological "
+                    u"limitations. Results exceeding this threshold are "
+                    u"typically reported as '> ULOD', indicating that the "
+                    u"parameter's concentration is above the reliable "
+                    u"detection range of the method."
+        )
     )
 )
 
@@ -230,7 +291,7 @@
 # displayed in the results table.
 DetectionLimitSelector = BooleanField(
     'DetectionLimitSelector',
-    schemata="Analysis",
+    schemata="Limits",
     default=False,
     widget=BooleanWidget(
         label=_("Display a Detection Limit selector"),
@@ -249,7 +310,7 @@
 # further information.
 AllowManualDetectionLimit = BooleanField(
     'AllowManualDetectionLimit',
-    schemata="Analysis",
+    schemata="Limits",
     default=False,
     widget=BooleanWidget(
         label=_("Allow Manual Detection Limit input"),
@@ -804,6 +865,8 @@
     Precision,
     ExponentialFormatPrecision,
     LowerDetectionLimit,
+    LowerLimitOfQuantification,
+    UpperLimitOfQuantification,
     UpperDetectionLimit,
     DetectionLimitSelector,
     AllowManualDetectionLimit,
@@ -962,6 +1025,24 @@ def getUpperDetectionLimit(self):
             value = value.rstrip("0").rstrip(".")
         return value
 
+    @security.public
+    def setLowerLimitOfQuantification(self, value):
+        """Sets the Lower Limit of Quantification (LLOQ) and ensures its value
+        is stored as a string without exponential notation and with whole
+        fraction preserved
+        """
+        value = api.float_to_string(value)
+        self.getField("LowerLimitOfQuantification").set(self, value)
+
+    @security.public
+    def setUpperLimitOfQuantification(self, value):
+        """Sets the Upper Limit of Quantification (ULOW) and ensures its value
+        is stored as a string without exponential notation and with whole
+        fraction preserved
+        """
+        value = api.float_to_string(value)
+        self.getField("UpperLimitOfQuantification").set(self, value)
+
     @security.public
     def isSelfVerificationEnabled(self):
         """Returns if the user that submitted a result for this analysis must

src/bika/lims/utils/analysis.py

@@ -237,10 +237,23 @@ def format_uncertainty(analysis, decimalmark=".", sciformat=1):
                   By default 1
     :returns: the formatted uncertainty
     """
-    try:
-        result = float(analysis.getResult())
-    except (ValueError, TypeError):
-        pass
+    if not api.is_floatable(analysis.getResult()):
+        # do not display uncertainty, result is not floatable
+        return ""
+
+    if analysis.isOutsideTheQuantifiableRange():
+        # Displaying uncertainty for results outside the quantifiable range is
+        # not meaningful because the Lower Limit of Quantification (LLOQ) and
+        # Upper Limit of Quantification (ULOQ) define the range within which
+        # a parameter can be reliably and accurately measured. Results outside
+        # this range are prone to significant variability and may be
+        # indistinguishable from background noise or method imprecision.
+        # As such, any numeric value reported outside the quantifiable range
+        # lacks the reliability required for meaningful interpretation.
+        # It is important to note that the quantifiable range is always nested
+        # within the detection range, which is defined by the Lower Limit of
+        # Detection (LLOD) and Upper Limit of Detection (ULOD).
+        return ""
 
     uncertainty = analysis.getUncertainty()
     if api.to_float(uncertainty, default=-1) < 0:
@@ -260,7 +273,7 @@ def format_uncertainty(analysis, decimalmark=".", sciformat=1):
         precision = uncertainty[::-1].find(".")
 
     if precision == -1:
-        precision = analysis.getPrecision(result)
+        precision = analysis.getPrecision()
 
     # Scientific notation?
     # Get the default precision for scientific notation
@@ -276,7 +289,7 @@ def format_uncertainty(analysis, decimalmark=".", sciformat=1):
     return formatDecimalMark(formatted, decimalmark)
 
 
-def format_numeric_result(analysis, result, decimalmark='.', sciformat=1):
+def format_numeric_result(analysis, decimalmark='.', sciformat=1):
     """
     Returns the formatted number part of a results value.  This is
     responsible for deciding the precision, and notation of numeric
@@ -332,6 +345,7 @@ def format_numeric_result(analysis, result, decimalmark='.', sciformat=1):
     :result: should be a string to preserve the decimal precision.
     :returns: the formatted result as string
     """
+    result = analysis.getResult()
     try:
         result = float(result)
     except ValueError:
@@ -344,7 +358,7 @@ def format_numeric_result(analysis, result, decimalmark='.', sciformat=1):
     # Scientific notation?
     # Get the default precision for scientific notation
     threshold = analysis.getExponentialFormatPrecision()
-    precision = analysis.getPrecision(result)
+    precision = analysis.getPrecision()
     formatted = _format_decimal_or_sci(result, precision, threshold, sciformat)
     return formatDecimalMark(formatted, decimalmark)
 

src/bika/lims/validators.py

@@ -28,13 +28,13 @@
 from bika.lims import logger
 from bika.lims.api import APIError
 from bika.lims.catalog import SETUP_CATALOG
-from senaite.core.i18n import translate as _t
 from bika.lims.utils import to_utf8
 from Products.CMFCore.utils import getToolByName
 from Products.CMFPlone.utils import safe_unicode
 from Products.validation import validation
 from Products.validation.interfaces.IValidator import IValidator
 from Products.ZCTextIndex.ParseTree import ParseError
+from senaite.core.i18n import translate as _t
 from zope.interface import implements
 
 
@@ -501,8 +501,13 @@ def __call__(self, value, *args, **kwargs):
                     })
                 return to_utf8(translate(msg))
 
-        # Allow to use Wildcards, LDL and UDL values in calculations
-        allowedwds = ["LDL", "UDL", "BELOWLDL", "ABOVEUDL"]
+        # Allow to use Wildcards, LDL, UDL and LLOQ values in calculations
+        allowedwds = [
+            "LDL", "BELOWLDL",
+            "UDL", "ABOVEUDL",
+            "LOQ", "LLOQ", "BELOWLOQ", "BELOWLLOQ",
+            "ULOQ", "ABOVEULOQ",
+        ]
         keysandwildcards = re.compile(r"\[([^\]]+)\]").findall(value)
         keysandwildcards = [k for k in keysandwildcards if "." in k]
         keysandwildcards = [k.split(".", 1) for k in keysandwildcards]
@@ -1456,3 +1461,90 @@ def validate_record(self, record):
 
 
 validation.register(ServiceConditionsValidator())
+
+
+class LowerLimitOfDetectionValidator(object):
+    """Validates that the Lower Limit of Detection (LLOD) is lower than or
+    equal to the Lower Limit of Quantification (LLOQ)
+    """
+    implements(IValidator)
+    name = "lower_limit_of_detection_validator"
+
+    def __call__(self, value, **kwargs):
+        instance = kwargs["instance"]
+        field_name = kwargs["field"].getName()
+
+        # get the value (or fallback to field's default)
+        default = instance.getField(field_name).getDefault(instance)
+        llod = api.to_float(value, default)
+
+        form = kwargs["REQUEST"].form
+        lloq = form.get("LowerLimitOfQuantification", None)
+        lloq = api.to_float(lloq, llod)
+        if llod > lloq:
+            return _t(_(
+                u"validator_llod_above_lloq",
+                default=u"The Lower Limit of Detection (LLOD) cannot be "
+                        u"greater than the Lower Limit of Quantification "
+                        u"(LLOQ)."
+            ))
+
+
+class LowerLimitOfQuantificationValidator(object):
+    """Validates that the Lower Limit of Quantification (LLOQ) is lower than
+    the Upper Limit of Quantification (ULOQ)
+    """
+    implements(IValidator)
+    name = "lower_limit_of_quantification_validator"
+
+    def __call__(self, value, **kwargs):
+        instance = kwargs["instance"]
+        field_name = kwargs["field"].getName()
+
+        # get the value (or fallback to field's default)
+        default = instance.getField(field_name).getDefault(instance)
+        lloq = api.to_float(value, default)
+
+        # compare with the lower limit of detection
+        form = kwargs["REQUEST"].form
+        uloq = form.get("UpperLimitOfQuantification", None)
+        uloq = api.to_float(uloq, lloq)
+        if lloq >= uloq:
+            return _t(_(
+                u"validator_lloq_above_uloq",
+                default=u"The Lower Limit of Quantification (LLOQ) cannot be "
+                        u"greater than or equal to the Upper Limit of "
+                        u"Quantification (ULOQ)."
+            ))
+
+
+class UpperLimitOfQuantificationValidator(object):
+    """Validates that the Upper Limit of Quantification (ULOD) is lower than
+    or equal to the Upper Limit of Detection (ULOD)
+    """
+    implements(IValidator)
+    name = "upper_limit_of_quantification_validator"
+
+    def __call__(self, value, **kwargs):
+        instance = kwargs["instance"]
+        field_name = kwargs["field"].getName()
+
+        # get the value (or fallback to field's default)
+        default = instance.getField(field_name).getDefault(instance)
+        uloq = api.to_float(value, default)
+
+        # compare with the lower limit of detection
+        form = kwargs["REQUEST"].form
+        ulod = form.get("UpperDetectionLimit", None)
+        ulod = api.to_float(ulod, uloq)
+        if uloq > ulod:
+            return _t(_(
+                u"validator_uloq_above_ulod",
+                default=u"The Upper Limit of Quantification (LLOQ) cannot be "
+                        u"greater than the Upper Limit of Detection (ULOD)."
+            ))
+
+
+validation.register(LowerLimitOfDetectionValidator())
+validation.register(LowerLimitOfQuantificationValidator())
+validation.register(UpperLimitOfQuantificationValidator())

src/senaite/core/profiles/default/metadata.xml

@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <metadata>
-  <version>2658</version>
+  <version>2659</version>
   <dependencies>
     <dependency>profile-Products.ATContentTypes:base</dependency>
     <dependency>profile-Products.CMFEditions:CMFEditions</dependency>