New sample fields: Diagnosis, Additional Notes, Case Status, Case Outcome

docs/changelog.rst

@@ -4,6 +4,7 @@ Changelog
 1.1.0 (unreleased)
 ------------------
 
+- #5 New sample fields: Diagnosis, Additional Notes, Case Status, Case Outcome
 
 1.0.1 (2024-01-16)
 ------------------

src/senaite/diagnosis/__init__.py

@@ -26,6 +26,7 @@
 from config import PRODUCT_NAME
 
 messageFactory = MessageFactory(PRODUCT_NAME)
+_ = messageFactory
 logger = logging.getLogger(PRODUCT_NAME)
 
 

src/senaite/diagnosis/configure.zcml

@@ -22,6 +22,7 @@
   <include package=".patches"/>
   <include package=".subscribers"/>
   <include package=".upgrade"/>
+  <include package=".vocabularies"/>
 
   <!-- Default profile -->
   <genericsetup:registerProfile

src/senaite/diagnosis/content/analysisrequest.py

@@ -20,16 +20,26 @@
 
 from archetypes.schemaextender.interfaces import IBrowserLayerAwareExtender
 from archetypes.schemaextender.interfaces import ISchemaExtender
+from bika.lims.browser.widgets import SelectionWidget
 from bika.lims.interfaces import IAnalysisRequest
+from Products.Archetypes.Widget import TextAreaWidget
 from Products.CMFCore.permissions import View
 from senaite.core.browser.widgets import DateTimeWidget
 from senaite.core.browser.widgets import ReferenceWidget
 from senaite.core.catalog import SETUP_CATALOG
 from senaite.diagnosis import messageFactory as _
 from senaite.diagnosis import permissions
 from senaite.diagnosis.content.fields import ExtDateTimeField
+from senaite.diagnosis.content.fields import ExtStringField
+from senaite.diagnosis.content.fields import ExtTextField
 from senaite.diagnosis.content.fields import ExtUIDReferenceField
 from senaite.diagnosis.interfaces import ISenaiteDiagnosisLayer
+from senaite.diagnosis.permissions import FieldEditAdditionalNotes
+from senaite.diagnosis.permissions import FieldEditCaseOutcome
+from senaite.diagnosis.permissions import FieldEditCaseStatus
+from senaite.diagnosis.permissions import FieldEditDiagnosis
+from senaite.diagnosis.vocabularies.case import CASE_OUTCOMES_VOCABULARY_ID
+from senaite.diagnosis.vocabularies.case import CASE_STATUSES_VOCABULARY_ID
 from zope.component import adapter
 from zope.interface import implementer
 
@@ -170,6 +180,96 @@
         )
     ),
 
+    ExtTextField(
+        "Diagnosis",
+        read_permission=View,
+        write_permission=FieldEditDiagnosis,
+        widget=TextAreaWidget(
+            label=_(
+                u"label_sample_diagnosis",
+                default=u"Diagnosis",
+            ),
+            description=_(
+                u"description_sample_diagnosis",
+                default=u"Assessment or identification of the disease, "
+                        u"condition, or injury affecting the patient, based "
+                        u"on observed signs and reported symptoms",
+            ),
+            render_own_label=True,
+            visible={
+                "add": "edit",
+            },
+            rows=4,
+        )
+    ),
+
+    ExtTextField(
+        "AdditionalNotes",
+        read_permission=View,
+        write_permission=FieldEditAdditionalNotes,
+        widget=TextAreaWidget(
+            label=_(
+                u"label_sample_additional_notes",
+                default=u"Additional notes",
+            ),
+            description=_(
+                u"description_sample_additional_notes",
+                default=u"Additional details about the patient's condition or "
+                        u"other relevant information that may assist with "
+                        u"diagnosis and interpretation",
+            ),
+            render_own_label=True,
+            visible={
+                "add": "edit",
+            },
+            rows=4,
+        )
+    ),
+
+    ExtStringField(
+        "CaseStatus",
+        read_permission=View,
+        write_permission=FieldEditCaseStatus,
+        vocabulary_factory=CASE_STATUSES_VOCABULARY_ID,
+        widget=SelectionWidget(
+            label=_(
+                u"label_sample_case_status",
+                default=u"Case status",
+            ),
+            description=_(
+                u"description_sample_case_status",
+                default=u"Classification of the case based on its context or "
+                        u"investigation type"
+            ),
+            format="select",
+            visible={
+                "add": "edit",
+            },
+        )
+    ),
+
+    ExtStringField(
+        "CaseOutcome",
+        read_permission=View,
+        write_permission=FieldEditCaseOutcome,
+        vocabulary_factory=CASE_OUTCOMES_VOCABULARY_ID,
+        widget=SelectionWidget(
+            label=_(
+                u"label_sample_case_outcome",
+                default=u"Case outcome",
+            ),
+            description=_(
+                u"description_sample_case_outcome",
+                default=u"Result of the case based on the patient's condition "
+                        u"or treatment outcome"
+            ),
+            format="select",
+            visible={
+                "add": "edit",
+            },
+        )
+    ),
+
 ]
 
 

src/senaite/diagnosis/content/fields.py

@@ -18,11 +18,22 @@
 # Copyright 2022-2024 by it's authors.
 # Some rights reserved, see README and LICENSE.
 
-from archetypes.schemaextender.field import ExtensionField
+from archetypes.schemaextender.field import ExtensionField as ATExtensionField
 from bika.lims.browser.fields import UIDReferenceField
+from Products.Archetypes.Field import StringField
+from Products.Archetypes.public import TextField
 from senaite.core.browser.fields.datetime import DateTimeField
 
 
+class ExtensionField(ATExtensionField):
+    """Mix-in class to make Archetypes fields not depend on generated accessors
+    and mutators, and use AnnotationStorage by default
+    """
+
+    def __init__(self, *args, **kwargs):
+        super(ExtensionField, self).__init__(*args, **kwargs)
+
+
 class ExtUIDReferenceField(ExtensionField, UIDReferenceField):
     """Field Extender of core's UIDReferenceField for AT types
     """
@@ -31,3 +42,13 @@ class ExtUIDReferenceField(ExtensionField, UIDReferenceField):
 class ExtDateTimeField(ExtensionField, DateTimeField):
     """Field extender of core's DateTimeField
     """
+
+
+class ExtStringField(ExtensionField, StringField):
+    """Field extender of StringField
+    """
+
+
+class ExtTextField(ExtensionField, TextField):
+    """Extended Text Field
+    """

src/senaite/diagnosis/patches/content/analysisrequest.py

@@ -94,3 +94,51 @@ def setEtiologicAgents(self, value):  # noqa camelcase
     """Sets the etiologic agents to the sample
     """
     self.getField("EtiologicAgents").set(self, value)
+
+
+def getDiagnosis(self):  # noqa camelcase
+    """Returns the determined diagnosis
+    """
+    return self.getField("Diagnosis").get(self)
+
+
+def setDiagnosis(self, value):  # noqa camelcase
+    """Sets the determined diagnosis
+    """
+    self.getField("Diagnosis").set(self, value)
+
+
+def getAdditionalNotes(self):  # noqa camelcase
+    """Returns the additional information provided for this sample
+    """
+    return self.getField("AdditionalNotes").get(self)
+
+
+def setAdditionalNotes(self, value):  # noqa camelcase
+    """Sets the additional information provided for this sample
+    """
+    self.getField("AdditionalNotes").set(self, value)
+
+
+def getCaseStatus(self):  # noqa camelcase
+    """Returns the case status of this sample
+    """
+    return self.getField("CaseStatus").get(self)
+
+
+def setCaseStatus(self, value):  # noqa camelcase
+    """Sets the case status for this sample
+    """
+    self.getField("CaseStatus").set(self, value)
+
+
+def getCaseOutcome(self):  # noqa camelcase
+    """Returns the case outcome of this sample
+    """
+    return self.getField("CaseOutcome").get(self)
+
+
+def setCaseOutcome(self, value):  # noqa camelcase
+    """Sets the case outcome for this sample
+    """
+    self.getField("CaseOutcome").set(self, value)

src/senaite/diagnosis/patches/content/analysisrequest.zcml

@@ -81,4 +81,52 @@
       ignoreOriginal="True"
       replacement=".analysisrequest.setEtiologicAgents" />
 
+  <monkey:patch
+      class="bika.lims.content.analysisrequest.AnalysisRequest"
+      original="getDiagnosis"
+      ignoreOriginal="True"
+      replacement=".analysisrequest.getDiagnosis" />
+
+  <monkey:patch
+      class="bika.lims.content.analysisrequest.AnalysisRequest"
+      original="setDiagnosis"
+      ignoreOriginal="True"
+      replacement=".analysisrequest.setDiagnosis" />
+
+  <monkey:patch
+      class="bika.lims.content.analysisrequest.AnalysisRequest"
+      original="getAdditionalNotes"
+      ignoreOriginal="True"
+      replacement=".analysisrequest.getAdditionalNotes" />
+
+  <monkey:patch
+      class="bika.lims.content.analysisrequest.AnalysisRequest"
+      original="setAdditionalNotes"
+      ignoreOriginal="True"
+      replacement=".analysisrequest.setAdditionalNotes" />
+
+  <monkey:patch
+      class="bika.lims.content.analysisrequest.AnalysisRequest"
+      original="getCaseStatus"
+      ignoreOriginal="True"
+      replacement=".analysisrequest.getCaseStatus" />
+
+  <monkey:patch
+      class="bika.lims.content.analysisrequest.AnalysisRequest"
+      original="setCaseStatus"
+      ignoreOriginal="True"
+      replacement=".analysisrequest.setCaseStatus" />
+
+  <monkey:patch
+      class="bika.lims.content.analysisrequest.AnalysisRequest"
+      original="getCaseOutcome"
+      ignoreOriginal="True"
+      replacement=".analysisrequest.getCaseOutcome" />
+
+  <monkey:patch
+      class="bika.lims.content.analysisrequest.AnalysisRequest"
+      original="setCaseOutcome"
+      ignoreOriginal="True"
+      replacement=".analysisrequest.setCaseOutcome" />
+
 </configure>

src/senaite/diagnosis/permissions.py

@@ -23,3 +23,7 @@
 FieldEditEtiologicAgents = "senaite.diagnosis: Field: Edit Etiologic Agents"
 FieldEditDiseases = "senaite.diagnosis: Field: Edit Diseases"
 FieldEditSymptoms = "senaite.diagnosis: Field: Edit Symptoms"
+FieldEditDiagnosis = "senaite.diagnosis: Field: Edit Diagnosis"
+FieldEditAdditionalNotes = "senaite.diagnosis: Field: Edit Additional Notes"
+FieldEditCaseStatus = "senaite.diagnosis: Field: Edit Case Status"
+FieldEditCaseOutcome = "senaite.diagnosis: Field: Edit Case Outcome"

src/senaite/diagnosis/permissions.zcml

@@ -8,5 +8,9 @@
   <permission id="senaite.diagnosis.permissions.FieldEditDiseases" title="senaite.diagnosis: Field: Edit Diseases"/>
   <permission id="senaite.diagnosis.permissions.FieldEditEtiologicAgents" title="senaite.diagnosis: Field: Edit Etiologic Agents"/>
   <permission id="senaite.diagnosis.permissions.FieldEditSymptoms" title="senaite.diagnosis: Field: Edit Symptoms"/>
+  <permission id="senaite.diagnosis.permissions.FieldEditDiagnosis" title="senaite.diagnosis: Field: Edit Diagnosis"/>
+  <permission id="senaite.diagnosis.permissions.FieldEditAdditionalNotes" title="senaite.diagnosis: Field: Edit Additional Notes"/>
+  <permission id="senaite.diagnosis.permissions.FieldEditCaseStatus" title="senaite.diagnosis: Field: Edit Case Status"/>
+  <permission id="senaite.diagnosis.permissions.FieldEditCaseOutcome" title="senaite.diagnosis: Field: Edit Case Outcome"/>
 
 </configure>

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

@@ -6,7 +6,7 @@
   dependencies before installing this add-on own profile.
 -->
 <metadata>
-  <version>1100</version>
+  <version>1101</version>
 
   <!-- Be sure to install the following dependencies if not yet installed -->
   <dependencies>

src/senaite/diagnosis/profiles/default/rolemap.xml

@@ -34,6 +34,30 @@
       <role name="Manager"/>
       <role name="Client"/>
     </permission>
+    <permission name="senaite.diagnosis: Field: Edit Diagnosis" acquire="False">
+      <role name="LabClerk"/>
+      <role name="LabManager"/>
+      <role name="Manager"/>
+      <role name="Client"/>
+    </permission>
+    <permission name="senaite.diagnosis: Field: Edit Additional Notes" acquire="False">
+      <role name="LabClerk"/>
+      <role name="LabManager"/>
+      <role name="Manager"/>
+      <role name="Client"/>
+    </permission>
+    <permission name="senaite.diagnosis: Field: Edit Case Status" acquire="False">
+      <role name="LabClerk"/>
+      <role name="LabManager"/>
+      <role name="Manager"/>
+      <role name="Client"/>
+    </permission>
+    <permission name="senaite.diagnosis: Field: Edit Case Outcome" acquire="False">
+      <role name="LabClerk"/>
+      <role name="LabManager"/>
+      <role name="Manager"/>
+      <role name="Client"/>
+    </permission>
 
   </permissions>