Merge branch '1.x' of github.com:senaite/senaite.referral into 2.x

src/senaite/referral/adapters/guards/sample.py

@@ -67,3 +67,14 @@ def guard_invalidate_at_reference(self):
         if not lab_code:
             return False
         return True
+
+    def guard_receive_at_reference(self):
+        """Returns true if current request contains a POST with the
+        'receive_at_reference' action to ensure this transition is not
+        performed manually,
+        """
+        request = api.get_request()
+        lab_code = request.get("lab_code")
+        if not lab_code:
+            return False
+        return True

src/senaite/referral/adapters/listing/samples.py

@@ -103,7 +103,11 @@ def add_review_states(self):
             "id": "shipped",
             "title": _("Referred"),
             "contentFilter": {
-                "review_state": ("shipped", "rejected_at_reference"),
+                "review_state": (
+                    "shipped",
+                    "rejected_at_reference",
+                    "received_at_reference",
+                ),
                 "sort_on": "created",
                 "sort_order": "descending"},
             "transitions": [],

src/senaite/referral/content/inboundsample.py

@@ -125,6 +125,12 @@ class IInboundSampleSchema(model.Schema):
         )
     )
 
+    # TODO 2.x Replace schema.List by senaite.core.schema.UIDReferenceField
+    directives.omitted("services")
+    services = schema.List(
+        title=_(u"label_inboundsample_services", default=u"Services"),
+    )
+
     # TODO 2.x Replace schema.List by senaite.core.schema.UIDReferenceField
     directives.omitted("sample")
     sample = schema.List(
@@ -311,3 +317,21 @@ def getDateRejected(self):
         """Returns the datetime when this inbound sample was rejected or None
         """
         return get_action_date(self, "reject_inbound_sample", default=None)
+
+    def setServices(self, value):
+        """Set the services from the current instance that match with the
+        analyses that were requested by the referring laboratory
+        """
+        set_uids_field_value(self, "services", value)
+
+    def getServices(self):
+        """Returns the services from current instance that match with the
+        analyses that were requested by the referring laboratory
+        """
+        return [api.get_object(uid) for uid in self.getRawServices()]
+
+    def getRawServices(self):
+        """Returns the UIDs of the services from current instance that match
+        with the analyses that were requested by the referring laboratory
+        """
+        return get_uids_field_value(self, "services") or []

src/senaite/referral/jsonapi/outboundsample.py

@@ -33,6 +33,7 @@
 from bika.lims.interfaces import ISubmitted
 from bika.lims.utils import changeWorkflowState
 from bika.lims.workflow import doActionFor
+from senaite.referral import logger
 
 
 @implementer(IPushConsumer)
@@ -65,8 +66,16 @@ def process(self):
                 msg = "No retest found for '%s'" % sample_id
                 raise APIError(500, "ValueError: {}".format(msg))
 
-        # Do not allow to modify the sample if not referred
-        if api.get_review_status(sample) != "shipped":
+        # Do not allow to modify the sample if not received at reference
+        status = api.get_review_status(sample)
+        if status == "shipped":
+            # TODO Do not allow the modification of 'shipped' samples
+            logger.warn("Please upgrade reference instance to latest!!!. The "
+                        "update of samples in 'shipped' statues won't be "
+                        "supported in the near future, but only those in "
+                        "'received_at_reference' status")
+
+        elif status != "received_at_reference":
             # We don't rise an exception here because maybe the sample was
             # updated earlier, but the reference lab got a timeout error and
             # the remote user is now retrying the notification

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

@@ -6,11 +6,10 @@
   dependencies before installing this add-on own profile.
 -->
 <metadata>
-  <version>2003</version>
+  <version>2005</version>
 
   <!-- Be sure to install the following dependencies if not yet installed -->
   <dependencies>
     <dependency>profile-senaite.lims:default</dependency>
   </dependencies>
-
 </metadata>

src/senaite/referral/remotelab.py

@@ -21,7 +21,6 @@
 import math
 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
@@ -191,27 +190,24 @@ def update_analyses(self, sample, timeout=5):
         """
 
         def get_valid_analyses(sample):
-            # Sort by id descending to prioritize newest results if retests
+            # 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 = {
                 "full_objects": True,
+                "getServiceUID": services,
                 "sort_on": "id",
                 "sort_order": "ascending",
             }
 
-            # Exclude old, but valid analyses with same keyword (e.g retests),
+            # 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):
 
-                # Skip analyses for internal use
-                if IInternalUse.providedBy(analysis):
-                    continue
-
-                # Skip hidden, only interested in final results
-                if analysis.getHidden():
-                    continue
-
                 # Skip analyses not in a suitable status
                 if api.get_review_status(analysis) not in valid:
                     continue

src/senaite/referral/setuphandlers.py

@@ -75,12 +75,24 @@
                 "transitions": (
                     "verify",
                     "invalidate_at_reference",
+                    "receive_at_reference",
                     "reject_at_reference",
                     "recall_from_shipment"
                 ),
                 # Sample is read-only
                 "permissions_copy_from":  "invalid",
             },
+            "received_at_reference": {
+                "title": "Received at reference lab",
+                "description": "Sample received at reference laboratory",
+                "transitions": (
+                    "verify",
+                    "reject_at_reference",
+                    "invalidate_at_reference",
+                ),
+                # Sample is read-only
+                "permissions_copy_from":  "invalid",
+            },
             "rejected_at_reference": {
                 "title": "Rejected at reference lab",
                 "description": "Sample rejected at reference laboratory",
@@ -106,6 +118,16 @@
                     "guard_expr": "python:here.guard_handler('ship')",
                 }
             },
+            "receive_at_reference": {
+                "title": "Receive sample (at reference lab)",
+                "new_state": "received_at_reference",
+                "action": "Received at reference lab",
+                "guard": {
+                    "guard_permissions": "",
+                    "guard_roles": "",
+                    "guard_expr": "python:here.guard_handler('receive_at_reference')",
+                }
+            },
             "reject_at_reference": {
                 "title": "Reject sample (at reference lab)",
                 "new_state": "rejected_at_reference",

src/senaite/referral/upgrade/v01_00_000.zcml

@@ -1,7 +1,6 @@
 <configure
     xmlns="http://namespaces.zope.org/zope"
-    xmlns:genericsetup="http://namespaces.zope.org/genericsetup"
-    i18n_domain="senaite.referral">
+    xmlns:genericsetup="http://namespaces.zope.org/genericsetup">
 
   <!-- Setup chunk size for inbound sample reception -->
   <genericsetup:upgradeStep

src/senaite/referral/upgrade/v02_00_000.py

@@ -24,10 +24,12 @@
 from senaite.core.upgrade.utils import UpgradeUtils
 from senaite.referral import logger
 from senaite.referral.catalog import SHIPMENT_CATALOG
+from senaite.referral.catalog import INBOUND_SAMPLE_CATALOG
 from senaite.referral.config import PRODUCT_NAME as product
 from senaite.referral.setuphandlers import setup_ajax_transitions
 from senaite.referral.setuphandlers import setup_workflows
 from senaite.referral.utils import get_sample_types_mapping
+from senaite.referral.utils import get_services_mapping
 
 version = "2.0.0"
 profile = "profile-{0}:default".format(product)
@@ -115,3 +117,47 @@ def setup_invalidate_at_reference(tool):
     setup_workflows(portal)
 
     logger.info("Setup transition 'invalidate_at_reference' [DONE]")
+
+
+def setup_receive_at_reference(tool):
+    logger.info("Setup transition 'receive_at_reference' ...")
+    portal = tool.aq_inner.aq_parent
+
+    # Setup workflows
+    setup_workflows(portal)
+
+    logger.info("Setup transition 'receive_at_reference' [DONE]")
+
+
+def setup_inbound_services(tool):
+    """Updates the inbound samples with the service uids that were requested
+    by the referring laboratory
+    """
+    logger.info("Setup inbound services ...")
+
+    # Get baseline objects mappings
+    services = get_services_mapping()
+
+    query = {
+        "portal_type": "InboundSample",
+        "review_state": "received",
+    }
+    brains = api.search(query, INBOUND_SAMPLE_CATALOG)
+    total = len(brains)
+    for num, brain in enumerate(brains):
+        if num and num % 100 == 0:
+            logger.info("Processed objects: {}/{}".format(num, total))
+
+        obj = api.get_object(brain)
+        if obj.getRawServices():
+            # processed already
+            continue
+
+        # Resolve the service uids that match with the requested analyses
+        keywords = obj.getAnalyses() or []
+        services_uids = map(lambda key: services.get(key), keywords)
+        services_uids = list(filter(api.is_uid, services_uids))
+        obj.setServices(services_uids)
+        obj._p_deactivate()
+
+    logger.info("Setup inbound services [DONE]")

src/senaite/referral/upgrade/v02_00_000.zcml

@@ -3,6 +3,22 @@
     xmlns:genericsetup="http://namespaces.zope.org/genericsetup"
     i18n_domain="senaite.referral">
 
+  <genericsetup:upgradeStep
+      title="SENAITE.REFERRAL 1.0.0: Store service uids in inbound sample"
+      description="Store service uids in inbound sample"
+      source="2004"
+      destination="2005"
+      handler=".v02_00_000.setup_inbound_services"
+      profile="senaite.referral:default"/>
+
+  <genericsetup:upgradeStep
+      title="SENAITE.REFERRAL 1.0.0: New transition: 'Receive at reference'"
+      description="Added the transition 'receive_at_reference'"
+      source="2003"
+      destination="2004"
+      handler=".v02_00_000.setup_receive_at_reference"
+      profile="senaite.referral:default"/>
+
   <genericsetup:upgradeStep
       title="SENAITE.REFERRAL 2.0.0: Invalidate at reference laboratory"
       description="Added the transition 'invalidate_at_reference'"

src/senaite/referral/workflow/__init__.py

@@ -104,11 +104,9 @@ def restore_referred_sample(sample):
     sample.setOutboundShipment(None)
 
     # Transition the sample and analyses to the state before sample was shipped
-    status = api.get_review_status(sample)
-    if status in ["shipped", "rejected_at_reference"]:
-        prev = get_previous_status(sample, before="shipped",
-                                   default="sample_received")
-        changeWorkflowState(sample, SAMPLE_WORKFLOW, prev)
+    previous = get_previous_status(sample, before="shipped")
+    if previous:
+        changeWorkflowState(sample, SAMPLE_WORKFLOW, previous)
 
     # Restore status of referred analyses
     wf_id = ANALYSIS_WORKFLOW

src/senaite/referral/workflow/analysisrequest.py

@@ -58,6 +58,9 @@ def AfterTransitionEventHandler(sample, event): # noqa lowercase
     if event.transition.id == "recall_from_shipment":
         restore_referred_sample(sample)
 
+    if event.transition.id == "receive":
+        after_receive(sample)
+
 
 def after_no_sampling_workflow(sample):
     """Automatically receive and ship samples for which an outbound shipment
@@ -134,6 +137,16 @@ def after_invalidate(sample):
         referring.do_action(sample, "invalidate_at_reference")
 
 
+def after_receive(sample):
+    """Actions to do when receiving a sample
+    """
+    shipment = sample.getInboundShipment()
+    referring = get_remote_lab(shipment)
+    if referring:
+        # notify the referring laboratory
+        referring.do_action(sample, "receive_at_reference")
+
+
 def after_invalidate_at_reference(sample):
     """Actions to do when a sample is invalidated at reference laboratory
     """

src/senaite/referral/workflow/inboundsample/events.py

@@ -81,10 +81,14 @@ def create_sample(inbound_sample):
     if not sample_type_uid:
         raise ValueError("No sample type found for '{}'".format(sample_type))
 
+    # Resolve the service uids that match with the requested analyses
     keywords = inbound_sample.getAnalyses() or []
     services_uids = map(lambda key: services.get(key), keywords)
     services_uids = filter(api.is_uid, services_uids)
 
+    # Update the inbound sample with the service uids
+    inbound_sample.setServices(services_uids)
+
     values = {
         "Client": api.get_uid(client),
         "Contact": None,