Merge pull request #94 from senaite/fix-empty-spaces

Fix Patient Medical Record must be unique error when MRN has leading/traling whitespaces

src/senaite/patient/browser/widgets/temporaryidentifier.py

@@ -48,7 +48,7 @@ def process_form(self, instance, field, form, empty_marker=None,
 
         value = {
             "temporary": temporary,
-            "value": identifier,
+            "value": identifier.strip(),
             "value_auto": autogenerated,
         }
         return value, {}

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

@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <metadata>
-  <version>1415</version>
+  <version>1416</version>
   <dependencies>
     <dependency>profile-senaite.lims:default</dependency>
   </dependencies>

src/senaite/patient/upgrade/v01_04_000.py

@@ -552,3 +552,56 @@ def allow_searches_by_patient_in_samples(tool):
     cat = api.get_tool(SAMPLE_CATALOG)
     cat.reindexIndex(["listing_searchable_text"], None, ZLogHandler())
     logger.info("Allowing searches by patient in samples [DONE]")
+
+
+def remove_whitespaces_mrn(tool):
+    """Resets the date of birth from samples
+    """
+    logger.info("Removing lead and trailing whitespaces from MRN ...")
+
+    uc = api.get_tool("uid_catalog")
+    brains = uc(portal_type="AnalysisRequest")
+    total = len(brains)
+
+    for num, brain in enumerate(brains):
+        if num and num % 100 == 0:
+            logger.info("Migrated {0}/{1} fields".format(num, total))
+
+        if num and num % 1000 == 0:
+            # reduce memory size of the transaction
+            transaction.savepoint()
+
+        try:
+            obj = api.get_object(brain)
+        except AttributeError:
+            uncatalog_brain(brain)
+            continue
+
+        if not obj:
+            continue
+
+        mrn = obj.getField("MedicalRecordNumber").get(obj)
+        if not mrn:
+            # Flush the object from memory
+            obj._p_deactivate()
+            continue
+
+        value = mrn.get("value")
+        if not value:
+            # Flush the object from memory
+            obj._p_deactivate()
+            continue
+
+        stripped = value.strip()
+        if stripped == value:
+            obj._p_deactivate()
+            continue
+
+        # Reset the value
+        mrn["value"] = stripped
+        obj.getField("MedicalRecordNumber").set(obj, mrn)
+        # reindex so indexes and columns are updated in accordance
+        obj.reindexObject()
+        obj._p_deactivate()
+
+    logger.info("Removing lead and trailing whitespaces from MRN [DONE]")

src/senaite/patient/upgrade/v01_04_000.zcml

@@ -2,6 +2,20 @@
     xmlns="http://namespaces.zope.org/zope"
     xmlns:genericsetup="http://namespaces.zope.org/genericsetup">
 
+  <!-- 1416: Allow searches by patient in samples -->
+  <genericsetup:upgradeStep
+      title="Remove lead and trailing whitespaces from MRN"
+      description="
+        This upgrade step walks through all samples and removes trailing and
+        leading whitespaces from Medical Record Number fields. This is
+        necessary because when creating a Patient object, the MRN is
+        automatically stripped in setMRN function, although is left without
+        changes in AnalysisRequest."
+      source="1415"
+      destination="1416"
+      handler=".v01_04_000.remove_whitespaces_mrn"
+      profile="senaite.patient:default"/>
+
   <!-- 1415: Allow searches by patient in samples -->
   <genericsetup:upgradeStep
       title="SENAITE PATIENT 1.4.0: Allow patient searches in samples"