Remove patient-specific settings, catalogs and objects on uninstall

docs/changelog.rst

@@ -4,6 +4,7 @@ Changelog
 1.6.0 (unreleased)
 ------------------
 
+- #118 Remove patient-specific settings, catalogs and objects on uninstall
 - #131 Fix BehaviorRegistrationNotFound on Patient creation via JSON API
 - #130 Fix cannot search samples by MRN or patient name
 - #127 Add adapter for patient add views

src/senaite/patient/configure.zcml

@@ -69,6 +69,9 @@
   <include package=".subscribers" />
   <include package=".upgrade" />
 
+  <!-- File includes -->
+  <include file="uninstall.zcml"/>
+
   <!-- Default profile -->
   <genericsetup:registerProfile
     name="default"
@@ -89,13 +92,4 @@
     <depends name="workflow"/>
   </genericsetup:importStep>
 
-  <!-- Uninstall profile -->
-  <genericsetup:registerProfile
-    name="uninstall"
-    title="SENAITE PATIENT (uninstall)"
-    directory="profiles/uninstall"
-    description="Uninstalls SENAITE PATIENT"
-    post_handler=".setuphandlers.post_uninstall"
-    provides="Products.GenericSetup.interfaces.EXTENSION" />
-
 </configure>

src/senaite/patient/content/patient.py

@@ -18,12 +18,12 @@
 # Copyright 2020-2025 by it's authors.
 # Some rights reserved, see README and LICENSE.
 
+from datetime import datetime
 from string import Template
 
 from AccessControl import ClassSecurityInfo
 from bika.lims import api
 from bika.lims.api.mail import is_valid_email_address
-from datetime import datetime
 from plone.autoform import directives
 from plone.supermodel import model
 from plone.supermodel.directives import fieldset
@@ -44,7 +44,6 @@
 from senaite.core.z3cform.widgets.phone import PhoneWidgetFactory
 from senaite.patient import api as patient_api
 from senaite.patient import messageFactory as _
-from senaite.patient.catalog import PATIENT_CATALOG
 from senaite.patient.config import GENDERS
 from senaite.patient.config import SEXES
 from senaite.patient.i18n import translate
@@ -459,11 +458,6 @@ def validate_age(data):
 class Patient(Container):
     """Results Interpretation Template content
     """
-
-    # XXX Remove after 1.5.0
-    #     See https://github.com/senaite/senaite.patient/pull/119
-    _catalogs = [PATIENT_CATALOG]
-
     security = ClassSecurityInfo()
 
     @security.protected(permissions.View)

src/senaite/patient/setuphandlers.py

@@ -35,10 +35,6 @@
 
 PROFILE_ID = "profile-{}:default".format(PRODUCT_NAME)
 
-# Maximum threshold in seconds before a transaction.commit takes place
-# Default: 300 (5 minutes)
-MAX_SEC_THRESHOLD = 300
-
 CATALOGS = (
     PatientCatalog,
 )
@@ -218,21 +214,6 @@ def post_install(portal_setup):
     logger.info("{} install handler [DONE]".format(PRODUCT_NAME.upper()))
 
 
-def post_uninstall(portal_setup):
-    """Runs after the last import step of the *uninstall* profile
-    This handler is registered as a *post_handler* in the generic setup profile
-    :param portal_setup: SetupTool
-    """
-    logger.info("{} uninstall handler [BEGIN]".format(PRODUCT_NAME.upper()))
-
-    # https://docs.plone.org/develop/addons/components/genericsetup.html#custom-installer-code-setuphandlers-py
-    profile_id = "profile-{}:uninstall".format(PRODUCT_NAME)
-    context = portal_setup._getImportContext(profile_id)  # noqa
-    portal = context.getSite()  # noqa
-
-    logger.info("{} uninstall handler [DONE]".format(PRODUCT_NAME.upper()))
-
-
 def setup_catalogs(portal):
     """Setup patient catalogs
     """

src/senaite/patient/uninstall.py

@@ -0,0 +1,153 @@
+# -*- coding: utf-8 -*-
+
+from bika.lims import api
+from bika.lims.api import delete
+from plone.registry.interfaces import IRegistry
+from Products.GenericSetup.utils import _resolveDottedName
+from senaite.core.catalog import set_catalogs
+from senaite.patient import logger
+from senaite.patient import PRODUCT_NAME
+from senaite.patient.setuphandlers import CATALOG_MAPPINGS
+from senaite.patient.setuphandlers import CATALOGS
+from senaite.patient.setuphandlers import COLUMNS
+from senaite.patient.setuphandlers import INDEXES
+from zope.component import getUtility
+
+PROFILE_ID = "profile-{}:uninstall".format(PRODUCT_NAME)
+
+TYPES_TO_REMOVE = ["Patient", "PatientFolder"]
+
+
+def pre_uninstall(portal_setup):
+    """Runs before the first import step of the *uninstall* profile
+    This handler is registered as a *pre_handler* in the generic setup profile
+    :param portal_setup: SetupTool
+    """
+    logger.info("%s pre-uninstall handler [BEGIN]" % PRODUCT_NAME.upper())
+
+    context = portal_setup._getImportContext(PROFILE_ID)  # noqa
+    portal = context.getSite()  # noqa
+
+    # Purge product-specific types from navigation bar
+    purge_navigation_types(portal)
+
+    # Purge product-specific objects
+    purge_objects(portal)
+
+    # Purge product-specific catalogs, indexes and metadata
+    purge_catalogs(portal)
+
+    # Purge product-specific records from ID formatting
+    purge_id_formatting(portal)
+
+    logger.info("%s pre-uninstall handler [DONE]" % PRODUCT_NAME.upper())
+
+
+def post_uninstall(portal_setup):
+    """Runs after the last import step of the *uninstall* profile
+    This handler is registered as a *post_handler* in the generic setup profile
+    :param portal_setup: SetupTool
+    """
+    logger.info("%s post-uninstall handler [BEGIN]" % PRODUCT_NAME.upper())
+
+    context = portal_setup._getImportContext(PROFILE_ID)  # noqa
+    portal = context.getSite()  # noqa
+
+    logger.info("%s post-uninstall handler [DONE]" % PRODUCT_NAME.upper())
+
+
+def purge_objects(portal):
+    """Deletes objects that are specific of this product
+    """
+    logger.info("Purge objects ...")
+
+    # Delete patients folder and objects inside
+    patients = portal.get("patients")
+    if patients:
+        logger.info("Removing folder: %s" % api.get_path(patients))
+        delete(patients, check_permissions=False)
+
+    # Delete patient objects left elsewhere (e.g in client folders)
+    uc = api.get_tool("uid_catalog")
+    brains = list(uc(portal_type=TYPES_TO_REMOVE))
+    for brain in brains:
+        try:
+            obj = brain.getObject()
+        except AttributeError:
+            # Object does no longer exist, un-catalog the brain
+            path = api.get_path(brain)
+            # For DXs, uids of uid_catalog are absolute paths to portal root
+            # see plone.app.referencablebehavior.uidcatalog
+            logger.info("Removing stale brain: %s" % path)
+            uc.uncatalog_object(path)
+            continue
+
+        # Delete the patient object
+        path = api.get_path(obj)
+        logger.info("Removing patient: %s" % path)
+        delete(obj, check_permissions=False)
+
+    logger.info("Purge objects [DONE]")
+
+
+def purge_catalogs(portal):
+    """Uninstall catalogs, indexes and columns that are product-specific
+    """
+    logger.info("Purge catalogs ...")
+
+    # Delete product-specific indexes
+    for index_info in INDEXES:
+        cat_id = index_info[0]
+        idx_name = index_info[1]
+        cat = api.get_tool(cat_id)
+        if idx_name in cat.indexes():
+            logger.info("Removing index from %s: %s" % (cat.id, idx_name))
+            cat.delIndex(idx_name)
+
+    # Delete product-specific columns
+    for cat_id, column in COLUMNS:
+        cat = api.get_tool(cat_id)
+        if column not in cat.schema():
+            logger.info("Removing column from %s: %s" % (cat.id, column))
+            cat.delColumn(column)
+
+    # Delete product-specific catalogs
+    for clazz in CATALOGS:
+        module = _resolveDottedName(clazz.__module__)
+        catalog_id = module.CATALOG_ID
+        logger.info("Removing catalog: %s" % catalog_id)
+        portal.manage_delObjects([catalog_id])
+
+    # Clear catalog mappings
+    for portal_type, catalogs in CATALOG_MAPPINGS:
+        logger.info("Flushing catalog mappings for %s" % portal_type)
+        set_catalogs(portal_type, tuple())
+
+    logger.info("Purge catalogs [DONE]")
+
+
+def purge_id_formatting(portal):
+    """Purges ID formatting records that are specific of this product
+    """
+    logger.info("Purge ID formatting ...")
+
+    ids = ["Patient", "MedicalRecordNumber"]
+    records = portal.bika_setup.getIDFormatting()
+    records = filter(lambda rec: rec.get("portal_type") not in ids, records)
+    portal.bika_setup.setIDFormatting(records)
+
+    logger.info("Purge ID formatting [DONE]")
+
+
+def purge_navigation_types(portal):
+    """Purges product-specific types from the navigation menu
+    """
+    logger.info("Purge navigation types ...")
+
+    key = "plone.displayed_types"
+    registry = getUtility(IRegistry)
+    to_display = registry.get(key, ())
+    to_display = filter(lambda ty: ty not in TYPES_TO_REMOVE, to_display)
+    registry[key] = tuple(to_display)
+
+    logger.info("Purge navigation types [DONE]")

src/senaite/patient/uninstall.zcml

@@ -0,0 +1,15 @@
+<configure
+    xmlns="http://namespaces.zope.org/zope"
+    xmlns:genericsetup="http://namespaces.zope.org/genericsetup">
+
+  <!-- Uninstall profile -->
+  <genericsetup:registerProfile
+      name="uninstall"
+      title="SENAITE PATIENT (uninstall)"
+      directory="profiles/uninstall"
+      description="Uninstalls SENAITE PATIENT"
+      pre_handler=".uninstall.pre_uninstall"
+      post_handler=".uninstall.post_uninstall"
+      provides="Products.GenericSetup.interfaces.EXTENSION"/>
+
+</configure>