Settings for notification and automatic creation of missing analyses …

…at referring lab (#27)

* Add notify_all_analyses setting

* Add setting for automatic creation of missing tests at referring laboratory

* Use get instead of pop

* Better description for upgrade step

src/senaite/referral/browser/controlpanel.py

@@ -81,6 +81,40 @@ class IReferralControlPanel(Interface):
         required=0,
     )
 
+    notify_all_analyses = schema.Bool(
+        title=_(
+            u"label_referral_notify_all_analyses",
+            u"Notify all analyses to referring laboratory"
+        ),
+        description=_(
+            u"description_referral_notify_all_analyses",
+            u"If selected, the system will send all analyses back to the "
+            u"referring laboratory for results update after verification, "
+            u"those that weren't requested through the shipment included. "
+            u"Otherwise, the system will send notifications back only for "
+            u"those analyses that were initially requested."
+        ),
+        default=False,
+        required=False,
+    )
+
+    create_reference_analyses = schema.Bool(
+        title=_(
+            u"label_referral_create_reference_analyses",
+            u"Create analyses from reference laboratory"
+        ),
+        description=_(
+            u"description_referral_create_reference_analyses",
+            u"If selected, the system will create missing analyses in the "
+            u"referring laboratory when receiving a notification for results "
+            u"update from the reference laboratory. Otherwise, the system "
+            u"will skip results for analyses that do not exist in the "
+            u"referred sample."
+        ),
+        default=False,
+        required=False,
+    )
+
 
 class ReferralControlPanelForm(RegistryEditForm):
     schema = IReferralControlPanel

src/senaite/referral/jsonapi/outboundsample.py

@@ -24,13 +24,16 @@
 
 from senaite.jsonapi.exceptions import APIError
 from senaite.jsonapi.interfaces import IPushConsumer
+from senaite.referral.utils import get_create_reference_analyses
+from senaite.referral.utils import get_services_mapping
 from zope.interface import alsoProvides
 from zope.interface import implementer
 
 from bika.lims import api
 from bika.lims.catalog import CATALOG_ANALYSIS_REQUEST_LISTING
 from bika.lims.interfaces import ISubmitted
 from bika.lims.utils import changeWorkflowState
+from bika.lims.utils.analysis import create_analysis
 from bika.lims.workflow import doActionFor
 from senaite.referral import logger
 
@@ -83,15 +86,37 @@ def process(self):
 
         # TODO Performance - convert to queue task
 
-        # Get the analyses that are in a suitable status grouped by keyword
-        statuses = ["referred", "assigned", "unassigned"]
-        by_keyword = self.get_analyses_by_keyword(sample, statuses)
+        # Get the analyses grouped by keyword
+        by_keyword = self.get_analyses_by_keyword(sample)
+
+        # Allowed statuses
+        statuses = dict.fromkeys(["referred", "assigned", "unassigned"], True)
+
+        # Do we need to create non-existing analyses
+        create_missing = get_create_reference_analyses()
+        services = get_services_mapping() if create_missing else {}
 
         # Update the analyses passed-in
         analysis_records = sample_record.get("analyses")
         for analysis_record in analysis_records:
             keyword = analysis_record.get("keyword")
-            for analysis in by_keyword.get(keyword):
+
+            # pop the analyses to be updated for the given keyword
+            analyses = by_keyword.get(keyword, [])
+            if not analyses:
+                service_uid = services.get(keyword)
+                service = api.get_object(service_uid, default=None)
+                if service:
+                    # create the missing analysis
+                    analyses = [create_analysis(sample, service)]
+
+            for analysis in analyses:
+                # skip if status is not valid
+                status = api.get_review_status(analysis)
+                if not statuses.get(status, False):
+                    continue
+
+                # update the analysis
                 try:
                     self.update_analysis(analysis, analysis_record)
                 except Exception as e:
@@ -100,11 +125,11 @@ def process(self):
 
         return True
 
-    def get_analyses_by_keyword(self, sample, statuses):
+    def get_analyses_by_keyword(self, sample):
         """Returns the analyses of the sample grouped by keyword
         """
         groups = {}
-        analyses = sample.getAnalyses(full_objects=True, review_state=statuses)
+        analyses = sample.getAnalyses(full_objects=True)
         for analysis in analyses:
             keyword = analysis.getKeyword()
             groups.setdefault(keyword, []).append(analysis)

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

@@ -6,7 +6,7 @@
   dependencies before installing this add-on own profile.
 -->
 <metadata>
-  <version>1008</version>
+  <version>1009</version>
 
   <!-- Be sure to install the following dependencies if not yet installed -->
   <dependencies>

src/senaite/referral/remotelab.py

@@ -19,23 +19,22 @@
 # Some rights reserved, see README and LICENSE.
 
 import math
-
-from remotesession import RemoteSession
 from requests.auth import HTTPBasicAuth
 from senaite.core.supermodel import SuperModel
 from senaite.referral import logger
 from senaite.referral.interfaces import IExternalLaboratory
 from senaite.referral.notifications import get_post_base_info
 from senaite.referral.notifications import save_post
 from senaite.referral.utils import get_lab_code
+from senaite.referral.utils import get_notify_all_analyses
 from senaite.referral.utils import get_user_info
 from senaite.referral.utils import is_valid_url
 
 from bika.lims import api
 from bika.lims.interfaces import IAnalysisRequest
-from bika.lims.interfaces import IInternalUse
 from bika.lims.utils import format_supsub
 from bika.lims.utils.analysis import format_uncertainty
+from remotesession import RemoteSession
 
 
 def get_remote_connection(laboratory):
@@ -191,30 +190,32 @@ def update_analyses(self, sample, timeout=5):
         """
 
         def get_valid_analyses(sample):
-            # Get the analyses from current sample that were requested by the
-            # referring laboratory, sorted by id descending to prioritize
-            # newest results if retests
-            inbound_sample = sample.getInboundSample()
-            services = inbound_sample.getRawServices()
-            kwargs = {
+            # Get the analyses to notify about to the reference laboratory,
+            # sorted by id descending to prioritize newest results if retests
+            query = {
                 "full_objects": True,
-                "getServiceUID": services,
                 "sort_on": "id",
                 "sort_order": "ascending",
             }
 
+            notify_all = get_notify_all_analyses()
+            if not notify_all:
+                # only notify about analyses that were requested via shipment
+                inbound_sample = sample.getInboundSample()
+                query["getServiceUID"] = inbound_sample.getRawServices()
+
             # exclude old, but valid analyses with same keyword (e.g retests),
             # cause we want to update the referring lab with the newest result
             analyses = {}
             valid = ["verified", "published"]
-            for analysis in sample.getAnalyses(**kwargs):
+            for analysis in sample.getAnalyses(**query):
 
                 # Skip analyses not in a suitable status
                 if api.get_review_status(analysis) not in valid:
                     continue
 
                 # Skip retested, only interested in final results
-                if analysis.getRetest():
+                if analysis.getRawRetest():
                     continue
 
                 keyword = analysis.getKeyword()

src/senaite/referral/upgrade/v01_00_000.py

@@ -260,3 +260,11 @@ def setup_inbound_services(tool):
         obj._p_deactivate()
 
     logger.info("Setup inbound services [DONE]")
+
+
+def setup_results_notification(tool):
+    logger.info("Setup results notification settings ...")
+    portal = tool.aq_inner.aq_parent
+    setup = portal.portal_setup
+    setup.runImportStepFromProfile(profile, "plone.app.registry")
+    logger.info("Setup results notification settings [DONE]")

src/senaite/referral/upgrade/v01_00_000.zcml

@@ -2,6 +2,14 @@
     xmlns="http://namespaces.zope.org/zope"
     xmlns:genericsetup="http://namespaces.zope.org/genericsetup">
 
+  <genericsetup:upgradeStep
+      title="SENAITE.REFERRAL 1.0.0: Setup results notification settings"
+      description="Setup results notification settings"
+      source="1008"
+      destination="1009"
+      handler=".v01_00_000.setup_results_notification"
+      profile="senaite.referral:default"/>
+
   <genericsetup:upgradeStep
       title="SENAITE.REFERRAL 1.0.0: Store service uids in inbound sample"
       description="Store service uids in inbound sample"

src/senaite/referral/utils.py

@@ -324,3 +324,19 @@ def get_services_mapping():
         services[keyword] = uid
         services[uid] = uid
     return services
+
+
+def get_notify_all_analyses():
+    """Returns whether the system has to send notifications for analyses that
+    weren't initially requested
+    """
+    key = "{}.notify_all_analyses".format(PRODUCT_NAME)
+    return api.get_registry_record(key, default=False)
+
+
+def get_create_reference_analyses():
+    """Returns whether the system has to create analyses if results are
+    notified by reference lab, but the sample does not have them
+    """
+    key = "{}.create_reference_analyses".format(PRODUCT_NAME)
+    return api.get_registry_record(key, default=False)