Fix traceback when retracting an analysis with a detection limit

CHANGES.rst

@@ -4,6 +4,7 @@ Changelog
 2.4.0 (unreleased)
 ------------------
 
+- #2204 Fix traceback when retracting an analysis with a detection limit
 - #2202 Fix detection limit set manually is not displayed on result save
 - #2203 Fix empty date sampled in samples listing when sampling workflow is enabled 
 - #2197 Use portal as relative path for sticker icons

src/bika/lims/content/abstractanalysis.py

@@ -346,14 +346,12 @@ def getLowerDetectionLimit(self):
         """
         if self.isLowerDetectionLimit():
             result = self.getResult()
-            try:
-                # in this case, the result itself is the LDL.
-                return float(result)
-            except (TypeError, ValueError):
-                logger.warn("The result for the analysis %s is a lower "
-                            "detection limit, but not floatable: '%s'. "
-                            "Returnig AS's default LDL." %
-                            (self.id, result))
+            if api.is_floatable(result):
+                return result
+
+            logger.warn("The result for the analysis %s is a lower detection "
+                        "limit, but not floatable: '%s'. Returning AS's "
+                        "default LDL." % (self.id, result))
         return AbstractBaseAnalysis.getLowerDetectionLimit(self)
 
     # Method getUpperDetectionLimit overrides method of class BaseAnalysis
@@ -366,14 +364,12 @@ def getUpperDetectionLimit(self):
         """
         if self.isUpperDetectionLimit():
             result = self.getResult()
-            try:
-                # in this case, the result itself is the LDL.
-                return float(result)
-            except (TypeError, ValueError):
-                logger.warn("The result for the analysis %s is a lower "
-                            "detection limit, but not floatable: '%s'. "
-                            "Returnig AS's default LDL." %
-                            (self.id, result))
+            if api.is_floatable(result):
+                return result
+
+            logger.warn("The result for the analysis %s is an upper detection "
+                        "limit, but not floatable: '%s'. Returning AS's "
+                        "default UDL." % (self.id, result))
         return AbstractBaseAnalysis.getUpperDetectionLimit(self)
 
     @security.public
@@ -479,10 +475,7 @@ def setResult(self, value):
         if val and val[0] in [LDL, UDL]:
             # Strip off the detection limit operand from the result
             operand = val[0]
-
-            # Convert to float-able if possible
-            wo_dl = val.replace(operand, "", 1).strip()
-            val = api.to_float(wo_dl) if api.is_floatable(wo_dl) else val
+            val = val.replace(operand, "", 1).strip()
 
             # Result becomes the detection limit
             selector = self.getDetectionLimitSelector()

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

@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <metadata>
-  <version>2403</version>
+  <version>2405</version>
   <dependencies>
     <dependency>profile-Products.ATContentTypes:base</dependency>
     <dependency>profile-Products.CMFEditions:CMFEditions</dependency>

src/senaite/core/tests/doctests/WorkflowAnalysisRetract.rst

@@ -329,3 +329,79 @@ But the retest does not provide `IRetracted`:
     >>> retest = analysis.getRetest()
     >>> IRetracted.providedBy(retest)
     False
+
+
+Retract an analysis with a result that is a Detection Limit
+...........................................................
+
+Allow the user to manually enter the detection limit as the result:
+
+    >>> Cu.setAllowManualDetectionLimit(True)
+
+Create the sample:
+
+    >>> sample = new_ar([Cu])
+    >>> cu = sample.getAnalyses(full_objects=True)[0]
+    >>> cu.setResult("< 10")
+    >>> success = do_action_for(cu, "submit")
+    >>> cu.getResult()
+    '10'
+
+    >>> cu.getFormattedResult(html=False)
+    '< 10'
+
+    >>> cu.isLowerDetectionLimit()
+    True
+
+    >>> cu.getDetectionLimitOperand()
+    '<'
+
+The Detection Limit is not kept on the retest:
+
+    >>> success = do_action_for(analysis, "retract")
+    >>> retest = analysis.getRetest()
+    >>> retest.getResult()
+    ''
+
+    >>> retest.getFormattedResult(html=False)
+    ''
+
+    >>> retest.isLowerDetectionLimit()
+    False
+
+    >>> retest.getDetectionLimitOperand()
+    ''
+
+Do the same with Upper Detection Limit (UDL):
+
+    >>> sample = new_ar([Cu])
+    >>> cu = sample.getAnalyses(full_objects=True)[0]
+    >>> cu.setResult("> 10")
+    >>> success = do_action_for(cu, "submit")
+    >>> cu.getResult()
+    '10'
+
+    >>> cu.getFormattedResult(html=False)
+    '> 10'
+
+    >>> cu.isUpperDetectionLimit()
+    True
+
+    >>> cu.getDetectionLimitOperand()
+    '>'
+
+The Detection Limit is not kept on the retest:
+
+    >>> success = do_action_for(analysis, "retract")
+    >>> retest = analysis.getRetest()
+    >>> retest.getResult()
+    ''
+
+    >>> retest.getFormattedResult(html=False)
+    ''
+
+    >>> retest.isUpperDetectionLimit()
+    False
+
+    >>> retest.getDetectionLimitOperand()
+    ''

src/senaite/core/tests/test_calculations.py

@@ -354,7 +354,7 @@ def test_analysis_method_calculation(self):
                         or an.isUpperDetectionLimit():
                         operator = an.getDetectionLimitOperand()
                         strres = f['analyses'][key].replace(operator, '')
-                        self.assertEqual(an.getResult(), float(strres))
+                        self.assertEqual(an.getResult(), strres)
                     else:
                         self.assertEqual(an.getResult(), f['analyses'][key])
                 elif key == self.calcservice.getKeyword():

src/senaite/core/upgrade/v02_04_000.py

@@ -19,6 +19,8 @@
 # Some rights reserved, see README and LICENSE.
 
 from bika.lims import api
+from bika.lims import LDL
+from bika.lims import UDL
 from bika.lims.interfaces import IRejected
 from bika.lims.interfaces import IRetracted
 from senaite.core import logger
@@ -137,3 +139,46 @@ def import_typeinfo(tool):
     setup = portal.portal_setup
     setup.runImportStepFromProfile("profile-bika.lims:default", "typeinfo")
     setup.runImportStepFromProfile(profile, "typeinfo")
+
+
+def fix_traceback_retract_dl(tool):
+    """Migrates the values of LDL and UDL of analyses/services to string, as
+    well as results that are DetectionLimit and stored as floats
+    """
+    logger.info("Migrate LDL, UDL and result fields to string ...")
+    cat = api.get_tool("uid_catalog")
+    query = {"portal_type": ["AnalysisService", "Analysis",
+                             "DuplicateAnalysis", "ReferenceAnalysis"]}
+    brains = cat.search(query)
+    total = len(brains)
+
+    for num, brain in enumerate(brains):
+        if num and num % 100 == 0:
+            logger.info("Migrated {0}/{1} LDL/UDL fields".format(num, total))
+
+        obj = api.get_object(brain)
+
+        # Migrate UDL to string
+        field = obj.getField("UpperDetectionLimit")
+        value = field.get(obj)
+        if isinstance(value, (int, float)):
+            field.set(obj, str(value))
+
+        # Migrate LDL to string
+        field = obj.getField("LowerDetectionLimit")
+        value = field.get(obj)
+        if isinstance(value, (int, float)):
+            field.set(obj, str(value))
+
+        # Migrate the result
+        field = obj.getField("Result")
+        if field and obj.getDetectionLimitOperand() in [LDL, UDL]:
+            # The result is the detection limit
+            result = field.get(obj)
+            if isinstance(result, (int, float)):
+                field.set(obj, str(result))
+
+        # Flush the object from memory
+        obj._p_deactivate()
+
+    logger.info("Migrate LDL, UDL and result fields to string [DONE]")

src/senaite/core/upgrade/v02_04_000.zcml

@@ -43,4 +43,14 @@
       handler="senaite.core.upgrade.v02_04_000.import_typeinfo"
       profile="senaite.core:default"/>
 
+  <!-- Fix traceback when retracting an analysis with a detection limit
+       https://github.com/senaite/senaite.core/pull/2204 -->
+  <genericsetup:upgradeStep
+      title="SENAITE CORE 2.4.0: Fix traceback when retracting DL"
+      description="Fix traceback when retracting an analysis with a detection limit"
+      source="2404"
+      destination="2405"
+      handler="senaite.core.upgrade.v02_04_000.fix_traceback_retract_dl"
+      profile="senaite.core:default"/>
+
 </configure>