Allow to flag patients as deceased (#98)

* Added deceased field to Patient content type

* Add deceased index

* Added deceased filter in patients listing

* Changelog

* Localize death dagger symbol

* Reuse function translate from core

* Better spelling

---------

Co-authored-by: Ramon Bartl <rb@ridingbytes.com>

docs/changelog.rst

@@ -4,6 +4,8 @@ Changelog
 1.5.0 (unreleased)
 ------------------
 
+- #98 Allow to flag patients as deceased
+
 
 1.4.0 (2023-01-10)
 ------------------

src/senaite/patient/browser/patientfolder.py

@@ -20,14 +20,13 @@
 
 import collections
 from bika.lims import api
-from bika.lims import senaiteMessageFactory as _
 from bika.lims.interfaces import IClient
 from bika.lims.utils import get_email_link
 from bika.lims.utils import get_image
 from bika.lims.utils import get_link
 from senaite.app.listing.view import ListingView
 from senaite.core.api import dtime
-from senaite.patient import messageFactory as _sp
+from senaite.patient import messageFactory as _
 from senaite.patient.api import to_identifier_type_name
 from senaite.patient.api import tuplify_identifiers
 from senaite.patient.catalog import PATIENT_CATALOG
@@ -67,7 +66,7 @@ def __init__(self, context, request):
         self.icon = "{}/{}".format(
             self.portal_url, "senaite_theme/icon/patientfolder")
 
-        self.title = _sp("Patients")
+        self.title = _("Patients")
         self.description = self.context.Description()
         self.show_select_column = True
         self.pagesize = 25
@@ -110,6 +109,11 @@ def __init__(self, context, request):
                 "title": _("Inactive"),
                 "contentFilter": {'is_active': False},
                 "columns": self.columns.keys(),
+            }, {
+                "id": "deceased",
+                "title": _("Deceased"),
+                "contentFilter": {'patient_deceased': True},
+                "columns": self.columns.keys(),
             }, {
                 "id": "all",
                 "title": _("All"),
@@ -159,7 +163,7 @@ def folderitem(self, obj, item, index):
         mrn = obj.getMRN()
         if not mrn:
             item["before"]["mrn"] = get_image("info", width=16)
-            mrn = t(_sp("mrn_not_defined", default="Not defined"))
+            mrn = t(_("mrn_not_defined", default="Not defined"))
 
         item["mrn"] = self.to_utf8(mrn)
         item["replace"]["mrn"] = get_link(url, value=mrn)
@@ -170,11 +174,19 @@ def folderitem(self, obj, item, index):
             self.get_identifier_tags(identifiers))
 
         # Fullname
-        fullname = obj.getFullname()
-        if fullname:
-            fullname = api.safe_unicode(fullname).encode("utf8")
-            item["fullname"] = fullname
-            item["replace"]["fullname"] = get_link(url, value=fullname)
+        fullname_nd = t(_("fullname_not_defined", default="Not defined"))
+        fullname = obj.getFullname() or fullname_nd
+        fullname = api.safe_unicode(fullname).encode("utf8")
+        item["fullname"] = fullname
+
+        # Death dagger
+        if obj.getDeceased():
+            fullname = t(_(
+                "patient_fullname_deceased_html",
+                default="${fullname} <sup>&dagger;</sup>",
+                mapping={"fullname": fullname}
+            ))
+        item["replace"]["fullname"] = get_link(url, value=fullname)
 
         # Email
         email = obj.getEmail()

src/senaite/patient/catalog/indexer/configure.zcml

@@ -22,5 +22,6 @@
   <adapter name="patient_fullname" factory=".patient.patient_fullname" />
   <adapter name="patient_searchable_text" factory=".patient.patient_searchable_text" />
   <adapter name="patient_searchable_mrn" factory=".patient.patient_searchable_mrn" />
+  <adapter name="patient_deceased" factory=".patient.patient_deceased" />
 
 </configure>

src/senaite/patient/catalog/indexer/patient.py

@@ -100,6 +100,13 @@ def patient_birthdate(instance):
     return birthdate
 
 
+@indexer(IPatient)
+def patient_deceased(instance):
+    """Index deceased
+    """
+    return instance.getDeceased()
+
+
 @indexer(IPatient)
 def patient_searchable_text(instance):
     """Index for searchable text queries

src/senaite/patient/catalog/patient_catalog.py

@@ -42,6 +42,7 @@
     ("patient_birthdate", "", "DateIndex"),
     ("patient_searchable_text", "", "ZCTextIndex"),
     ("patient_searchable_mrn", "", "ZCTextIndex"),
+    ("patient_deceased", "", "BooleanIndex"),
 ]
 
 COLUMNS = BASE_COLUMNS + [

src/senaite/patient/content/patient.py

@@ -304,6 +304,17 @@ class IPatientSchema(model.Schema):
         required=False,
     )
 
+    deceased = schema.Bool(
+        title=_(
+            u"label_patient_deceased",
+            default=u"Deceased"),
+        description=_(
+            u"description_patient_deceased",
+            default=u"Select this option if the patient is deceased"),
+        required=False,
+        default=False,
+    )
+
     @invariant
     def validate_mrn(data):
         """Checks if the patient MRN # is unique
@@ -732,3 +743,17 @@ def getFormattedAddress(self, atype=PHYSICAL_ADDRESS):
             output = Template(address_format).safe_substitute(record)
             output = filter(None, output.split(", "))
             return ", ".join(output)
+
+    @security.protected(permissions.View)
+    def getDeceased(self):
+        """Returns whether the patient is deceased
+        """
+        accessor = self.accessor("deceased")
+        return accessor(self)
+
+    @security.protected(permissions.ModifyPortalContent)
+    def setDeceased(self, value):
+        """Set if the patient deceased
+        """
+        mutator = self.mutator("deceased")
+        return mutator(self, value)

src/senaite/patient/i18n.py

@@ -18,22 +18,11 @@
 # Copyright 2020-2024 by it's authors.
 # Some rights reserved, see README and LICENSE.
 
-from bika.lims import api
+from senaite.core.i18n import translate as core_translate
 
 
 def translate(msgid, **kwargs):
     """Translate any zope i18n msgid returned from MessageFactory
     """
-    msgid = api.safe_unicode(msgid)
-
-    # XX: If the msgid is from type `Message`, Zope's i18n translate tool gives
-    #     priority `Message.domain` over the domain passed through kwargs
     domain = kwargs.pop("domain", "senaite.patient")
-    params = {
-        "domain": getattr(msgid, "domain", domain),
-        "context": api.get_request(),
-    }
-    params.update(kwargs)
-
-    ts = api.get_tool("translation_service")
-    return ts.translate(msgid, **params)
+    return core_translate(msgid, domain=domain, **kwargs)

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

@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <metadata>
-  <version>1500</version>
+  <version>1501</version>
   <dependencies>
     <dependency>profile-senaite.lims:default</dependency>
   </dependencies>

src/senaite/patient/upgrade/v01_05_000.py

@@ -22,6 +22,7 @@
 from senaite.core.upgrade.utils import UpgradeUtils
 from senaite.patient import logger
 from senaite.patient.config import PRODUCT_NAME
+from senaite.patient.setuphandlers import setup_catalogs
 
 version = "1.5.0"
 profile = "profile-{0}:default".format(PRODUCT_NAME)
@@ -46,3 +47,15 @@ def upgrade(tool):
 
     logger.info("{0} upgraded to version {1}".format(PRODUCT_NAME, version))
     return True
+
+
+def upgrade_catalog_indexes(tool):
+    """Reinstall controlpanel registry
+
+    :param tool: portal_setup tool
+    """
+    logger.info("Upgrade catalog indexes ...")
+    portal = tool.aq_inner.aq_parent
+    # setup patient catalog to add new indexes
+    setup_catalogs(portal)
+    logger.info("Upgrade catalog indexes [DONE]")

src/senaite/patient/upgrade/v01_05_000.zcml

@@ -2,6 +2,18 @@
     xmlns="http://namespaces.zope.org/zope"
     xmlns:genericsetup="http://namespaces.zope.org/genericsetup">
 
+  <!-- 1501: Allow to flag patients as deceased -->
+  <genericsetup:upgradeStep
+      title="Allow to flag patients as deceased"
+      description="
+        This upgrade step adds the field Deceased for patient content type, as
+        well as a new index 'patient_deceased' to allows to filter deceased
+        patients in patients listing."
+      source="1500"
+      destination="1501"
+      handler=".v01_05_000.upgrade_catalog_indexes"
+      profile="senaite.patient:default"/>
+
   <genericsetup:upgradeStep
       title="Upgrade to SENAITE.PATIENT 1.5.0"
       source="1416"