Allow to detach a partition from its primary sample

CHANGES.rst

@@ -6,6 +6,7 @@ Changelog
 
 **Added**
 
+- #1420 Allow to detach a partition from its primary sample
 - #1410 Email API
 
 

bika/lims/browser/viewlets/analysisrequest.py

@@ -66,3 +66,10 @@ class RejectedAnalysisRequestViewlet(ViewletBase):
     """Current ANalysis Request was rejected. Display the reasons
     """
     template = ViewPageTemplateFile("templates/rejected_ar_viewlet.pt")
+
+
+class DetachedPartitionViewlet(ViewletBase):
+    """Prints a viewlet that displays the Primary Sample the sample was
+    detached from
+    """
+    template = ViewPageTemplateFile("templates/detached_partition_viewlet.pt")

bika/lims/browser/viewlets/configure.zcml

@@ -160,6 +160,17 @@
     layer="bika.lims.interfaces.IBikaLIMS"
   />
 
+  <!-- Dettached partition viewlet -->
+  <browser:viewlet
+    for="bika.lims.interfaces.IAnalysisRequest"
+    name="bika.lims.detached_partition_viewlet"
+    class=".analysisrequest.DetachedPartitionViewlet"
+    manager="plone.app.layout.viewlets.interfaces.IAboveContent"
+    template="templates/detached_partition_viewlet.pt"
+    permission="zope2.View"
+    layer="bika.lims.interfaces.IBikaLIMS"
+  />
+
   <!-- Secondary Analysis Request viewlet -->
   <browser:viewlet
     for="bika.lims.interfaces.IAnalysisRequestSecondary"

bika/lims/browser/viewlets/templates/detached_partition_viewlet.pt

@@ -0,0 +1,21 @@
+<div tal:omit-tag=""
+     tal:define="primary python: view.context.getDetachedFrom()"
+     tal:condition="python: primary"
+     i18n:domain="senaite.core">
+
+  <div class="visualClear"></div>
+
+  <div id="portal-alert">
+    <div class="portlet-alert-item alert alert-info alert-dismissible">
+      <button type="button" class="close" data-dismiss="alert" aria-label="Close">
+        <span aria-hidden="true">&times;</span>
+      </button>
+      <strong i18n:translate="">Info</strong>
+      <p class="title">
+        <span i18n:translate="">This is a detached partition from Sample </span>
+        <a tal:attributes="href python:primary.absolute_url()"
+           tal:content="python:primary.getId()"></a>
+      </p>
+    </div>
+  </div>
+</div>

bika/lims/content/analysisrequest.py

@@ -1294,6 +1294,20 @@
         ),
     ),
 
+    # The Primary Sample the current sample was detached from
+    ReferenceField(
+        "DetachedFrom",
+        allowed_types=("AnalysisRequest",),
+        relationship="AnalysisRequestDetachedFrom",
+        referenceClass=HoldingReference,
+        mode="rw",
+        read_permission=View,
+        write_permission=ModifyPortalContent,
+        widget=ReferenceWidget(
+            visible=False,
+        )
+    ),
+
     # The Analysis Request the current Analysis Request comes from because of
     # an invalidation of the former
     ReferenceField(

bika/lims/interfaces/__init__.py

@@ -940,6 +940,12 @@ class IReceived(Interface):
     """Marker interface for received objects
     """
 
+
 class IInternalUse(Interface):
     """Marker interface for objects only lab personnel must have access
     """
+
+
+class IDetachedPartition(Interface):
+    """Marker interface for samples that have been detached from its primary
+    """

bika/lims/permissions.py

@@ -106,6 +106,7 @@
 
 # Transition permissions (Analysis Request)
 TransitionCancelAnalysisRequest = "senaite.core: Transition: Cancel Analysis Request"
+TransitionDetachSamplePartition = "senaite.core: Transition: Detach Sample Partition"
 TransitionReinstateAnalysisRequest = "senaite.core: Transition: Reinstate Analysis Request"
 TransitionInvalidate = "senaite.core: Transition Invalidate"
 TransitionPreserveSample = "senaite.core: Transition: Preserve Sample"

bika/lims/permissions.zcml

@@ -78,6 +78,7 @@
 
   # Transition Permissions (Analysis Request)
   <permission id="senaite.core.permissions.TransitionCancelAnalysisRequest" title="senaite.core: Transition: Cancel Analysis Request"/>
+  <permission id="senaite.core.permissions.TransitionDetachSamplePartition" title="senaite.core: Transition: Detach Sample Partition" />
   <permission id="senaite.core.permissions.TransitionReinstateAnalysisRequest" title="senaite.core: Transition: Reinstate Analysis Request"/>
   <permission id="senaite.core.permissions.TransitionInvalidate" title="senaite.core: Transition: Invalidate"/>
   <permission id="senaite.core.permissions.TransitionPreserveSample" title="senaite.core: Transition: Preserve Sample"/>

bika/lims/profiles/default/rolemap.xml

@@ -444,6 +444,11 @@
       <role name="Manager"/>
       <role name="Owner"/>
     </permission>
+    <permission name="senaite.core: Transition: Detach Sample Partition" acquire="False">
+      <role name="LabManager"/>
+      <role name="Manager"/>
+      <role name="LabClerk"/>
+    </permission>
     <permission name="senaite.core: Transition: Reinstate Analysis Request" acquire="False">
       <role name="LabClerk"/>
       <role name="LabManager"/>

bika/lims/profiles/default/workflows/bika_ar_workflow/definition.xml

@@ -20,6 +20,7 @@
   <!-- *** MANAGED PERMISSIONS  *** -->
   <!-- Transitions (governs guards) -->
   <permission>senaite.core: Transition: Cancel Analysis Request</permission>
+  <permission>senaite.core: Transition: Detach Sample Partition</permission>
   <permission>senaite.core: Transition: Reinstate Analysis Request</permission>
   <permission>senaite.core: Transition: Invalidate</permission>
   <permission>senaite.core: Transition: Preserve Sample</permission>
@@ -108,6 +109,7 @@
     <!-- MANAGED PERMISSIONS -->
     <!-- Permissions for Transitions (must match with exit transitions) -->
     <permission-map name="senaite.core: Transition: Cancel Analysis Request" acquired="False"/>
+    <permission-map name="senaite.core: Transition: Detach Sample Partition" acquired="False"/>
     <permission-map name="senaite.core: Transition: Reinstate Analysis Request" acquired="False"/>
     <permission-map name="senaite.core: Transition: Invalidate" acquired="False"/>
     <permission-map name="senaite.core: Transition: Preserve Sample" acquired="False"/>
@@ -194,6 +196,7 @@
     <!-- MANAGED PERMISSIONS -->
     <!-- Permissions for Transitions (must match with exit transitions) -->
     <permission-map name="senaite.core: Transition: Cancel Analysis Request" acquired="True"/>
+    <permission-map name="senaite.core: Transition: Detach Sample Partition" acquired="False"/>
     <permission-map name="senaite.core: Transition: Reinstate Analysis Request" acquired="False"/>
     <permission-map name="senaite.core: Transition: Invalidate" acquired="False"/>
     <permission-map name="senaite.core: Transition: Preserve Sample" acquired="False"/>
@@ -292,6 +295,7 @@
     <!-- MANAGED PERMISSIONS -->
     <!-- Permissions for Transitions (must match with exit transitions) -->
     <permission-map name="senaite.core: Transition: Cancel Analysis Request" acquired="True"/>
+    <permission-map name="senaite.core: Transition: Detach Sample Partition" acquired="False"/>
     <permission-map name="senaite.core: Transition: Reinstate Analysis Request" acquired="False"/>
     <permission-map name="senaite.core: Transition: Invalidate" acquired="False"/>
     <permission-map name="senaite.core: Transition: Preserve Sample" acquired="False"/>
@@ -367,6 +371,7 @@
 
     <!-- TRANSITIONS -->
     <exit-transition transition_id="cancel"/>
+    <exit-transition transition_id="detach" />
     <exit-transition transition_id="receive"/>
     <exit-transition transition_id="submit"/>
     <exit-transition transition_id="reject" />
@@ -385,6 +390,7 @@
     <!-- MANAGED PERMISSIONS -->
     <!-- Permissions for Transitions (must match with exit transitions) -->
     <permission-map name="senaite.core: Transition: Cancel Analysis Request" acquired="True"/>
+    <permission-map name="senaite.core: Transition: Detach Sample Partition" acquired="True"/>
     <permission-map name="senaite.core: Transition: Reinstate Analysis Request" acquired="False"/>
     <permission-map name="senaite.core: Transition: Invalidate" acquired="False"/>
     <permission-map name="senaite.core: Transition: Preserve Sample" acquired="False"/>
@@ -454,6 +460,7 @@
 
     <!-- TRANSITIONS -->
     <exit-transition transition_id="cancel"/>
+    <exit-transition transition_id="detach"/>
     <exit-transition transition_id="prepublish"/>
     <exit-transition transition_id="submit"/>
     <exit-transition transition_id="reject" />
@@ -471,6 +478,7 @@
     <!-- MANAGED PERMISSIONS -->
     <!-- Permissions for Transitions (must match with exit transitions) -->
     <permission-map name="senaite.core: Transition: Cancel Analysis Request" acquired="True"/>
+    <permission-map name="senaite.core: Transition: Detach Sample Partition" acquired="True"/>
     <permission-map name="senaite.core: Transition: Reinstate Analysis Request" acquired="False"/>
     <permission-map name="senaite.core: Transition: Invalidate" acquired="False"/>
     <permission-map name="senaite.core: Transition: Preserve Sample" acquired="False"/>
@@ -626,6 +634,7 @@
     <exit-transition transition_id="retract" />
     <exit-transition transition_id="reject" />
     <exit-transition transition_id="rollback_to_receive" />
+    <exit-transition transition_id="detach" />
     <!-- /TRANSITIONS -->
 
     <permission-map name="Delete objects" acquired="False">
@@ -638,6 +647,7 @@
     <!-- MANAGED PERMISSIONS -->
     <!-- Permissions for Transitions (must match with exit transitions) -->
     <permission-map name="senaite.core: Transition: Cancel Analysis Request" acquired="False"/>
+    <permission-map name="senaite.core: Transition: Detach Sample Partition" acquired="True"/>
     <permission-map name="senaite.core: Transition: Reinstate Analysis Request" acquired="False"/>
     <permission-map name="senaite.core: Transition: Invalidate" acquired="False"/>
     <permission-map name="senaite.core: Transition: Preserve Sample" acquired="False"/>
@@ -714,6 +724,7 @@
     <exit-transition transition_id="cancel"/>
     <exit-transition transition_id="preserve"/>
     <exit-transition transition_id="reject" />
+    <exit-transition transition_id="detach" />
     <!-- /TRANSITIONS -->
 
     <permission-map name="Delete objects" acquired="False">
@@ -726,6 +737,7 @@
     <!-- MANAGED PERMISSIONS -->
     <!-- Permissions for Transitions (must match with exit transitions) -->
     <permission-map name="senaite.core: Transition: Cancel Analysis Request" acquired="True"/>
+    <permission-map name="senaite.core: Transition: Detach Sample Partition" acquired="True"/>
     <permission-map name="senaite.core: Transition: Reinstate Analysis Request" acquired="False"/>
     <permission-map name="senaite.core: Transition: Invalidate" acquired="False"/>
     <permission-map name="senaite.core: Transition: Preserve Sample" acquired="True"/>
@@ -796,6 +808,7 @@
     <exit-transition transition_id="publish" />
     <exit-transition transition_id="invalidate" />
     <exit-transition transition_id="rollback_to_receive" />
+    <exit-transition transition_id="detach" />
     <!-- /TRANSITIONS -->
 
     <permission-map name="Delete objects" acquired="False">
@@ -808,6 +821,7 @@
     <!-- MANAGED PERMISSIONS (partially readonly) -->
     <!-- Permissions for Transitions (must match with exit transitions) -->
     <permission-map name="senaite.core: Transition: Cancel Analysis Request" acquired="False"/>
+    <permission-map name="senaite.core: Transition: Detach Sample Partition" acquired="True"/>
     <permission-map name="senaite.core: Transition: Reinstate Analysis Request" acquired="False"/>
     <permission-map name="senaite.core: Transition: Invalidate" acquired="True"/>
     <permission-map name="senaite.core: Transition: Preserve Sample" acquired="False"/>
@@ -887,6 +901,7 @@
     <!-- MANAGED PERMISSIONS (partially readonly) -->
     <!-- Permissions for Transitions (must match with exit transitions) -->
     <permission-map name="senaite.core: Transition: Cancel Analysis Request" acquired="False"/>
+    <permission-map name="senaite.core: Transition: Detach Sample Partition" acquired="False"/>
     <permission-map name="senaite.core: Transition: Reinstate Analysis Request" acquired="False"/>
     <permission-map name="senaite.core: Transition: Invalidate" acquired="True"/>
     <permission-map name="senaite.core: Transition: Preserve Sample" acquired="False"/>
@@ -962,6 +977,7 @@
     <!-- MANAGED PERMISSIONS (partially readonly) -->
     <!-- Permissions for Transitions (must match with exit transitions) -->
     <permission-map name="senaite.core: Transition: Cancel Analysis Request" acquired="False"/>
+    <permission-map name="senaite.core: Transition: Detach Sample Partition" acquired="False"/>
     <permission-map name="senaite.core: Transition: Reinstate Analysis Request" acquired="False"/>
     <permission-map name="senaite.core: Transition: Invalidate" acquired="False"/>
     <permission-map name="senaite.core: Transition: Preserve Sample" acquired="False"/>
@@ -1036,6 +1052,7 @@
     <!-- MANAGED PERMISSIONS (partially readonly) -->
     <!-- Permissions for Transitions (must match with exit transitions) -->
     <permission-map name="senaite.core: Transition: Cancel Analysis Request" acquired="False"/>
+    <permission-map name="senaite.core: Transition: Detach Sample Partition" acquired="False"/>
     <permission-map name="senaite.core: Transition: Reinstate Analysis Request" acquired="False"/>
     <permission-map name="senaite.core: Transition: Invalidate" acquired="False"/>
     <permission-map name="senaite.core: Transition: Preserve Sample" acquired="False"/>
@@ -1115,6 +1132,7 @@
     <!-- MANAGED PERMISSIONS (partially readonly) -->
     <!-- Permissions for Transitions (must match with exit transitions) -->
     <permission-map name="senaite.core: Transition: Cancel Analysis Request" acquired="False"/>
+    <permission-map name="senaite.core: Transition: Detach Sample Partition" acquired="False"/>
     <permission-map name="senaite.core: Transition: Reinstate Analysis Request" acquired="True"/>
     <permission-map name="senaite.core: Transition: Invalidate" acquired="False"/>
     <permission-map name="senaite.core: Transition: Preserve Sample" acquired="False"/>
@@ -1428,6 +1446,23 @@
     </guard>
   </transition>
 
+  <!-- Transition: Detach
+       This transition only applies to Sample partitions (governed by the guard)
+       and allows the user to detach a given partition from its primary sample.
+       Thus, a detached partition behaves like a Primary Sample and the original
+       primary sample no longer follows the status of the detached partition.
+
+       Note this transition does not have a new state defined, so this
+       transition does not change the current state of the object.
+  -->
+  <transition transition_id="detach" title="Detach" new_state="" trigger="USER"
+              before_script="" after_script="" i18n:attributes="title">
+    <action url="" category="workflow" icon="">Detach</action>
+    <guard>
+      <guard-expression>python:here.guard_handler("detach")</guard-expression>
+      <guard-permission>senaite.core: Transition: Detach Sample Partition</guard-permission>
+    </guard>
+  </transition>
 
   <!-- *** VARIABLES *** -->
 

bika/lims/upgrade/v01_03_002.py

@@ -18,7 +18,10 @@
 # Copyright 2018-2019 by it's authors.
 # Some rights reserved, see README and LICENSE.
 
+from bika.lims import api
 from bika.lims import logger
+from bika.lims.catalog.analysisrequest_catalog import \
+    CATALOG_ANALYSIS_REQUEST_LISTING
 from bika.lims.config import PROJECTNAME as product
 from bika.lims.upgrade import upgradestep
 from bika.lims.upgrade.utils import UpgradeUtils
@@ -43,9 +46,45 @@ def upgrade(tool):
 
     # -------- ADD YOUR STUFF BELOW --------
 
-    # Mixed permissions for transitions in client workflow
-    # https://github.com/senaite/senaite.core/pull/1419
+    # Allow to detach a partition from its primary sample (#1420)
+    setup.runImportStepFromProfile(profile, "rolemap")
+
+    # Mixed permissions for transitions in client workflow (#1419)
+    # Allow to detach a partition from its primary sample (#1420)
     setup.runImportStepFromProfile(profile, "workflow")
 
+    # Allow to detach a partition from its primary sample (#1420)
+    update_partitions_role_mappings(portal)
+
     logger.info("{0} upgraded to version {1}".format(product, version))
     return True
+
+def update_partitions_role_mappings(portal):
+    """Updates the rolemappings for existing partitions that are in a suitable
+     state, so they can be detached from the primary sample they belong to
+    """
+    logger.info("Updating role mappings of partitions ...")
+    wf_tool = api.get_tool("portal_workflow")
+    workflow = wf_tool.getWorkflowById("bika_ar_workflow")
+
+    # States that allow detach transition as defined in workflow definition in
+    # order to query and update role mappings of objects that matter
+    allowed_states = [
+        "to_be_preserved", "sample_due", "sample_received", "to_be_verified",
+        "verified"
+    ]
+    query = dict(portal_type="AnalysisRequest",
+                 isRootAncestor=False,
+                 review_state=allowed_states)
+
+    brains = api.search(query, CATALOG_ANALYSIS_REQUEST_LISTING)
+    total = len(brains)
+    for num, brain in enumerate(brains):
+        if num and num % 100 == 0:
+            logger.info("Updating role mappings of partitions: {}/{}"
+                        .format(num, total))
+        partition = api.get_object(brain)
+        workflow.updateRoleMappingsFor(partition)
+        partition.reindexObjectSecurity()
+
+    logger.info("Updating role mappings of partitions [DONE]")

bika/lims/utils/analysisrequest.py

@@ -405,6 +405,7 @@ def create_partition(analysis_request, request, analyses, sample_type=None,
         "Analyses",
         "Attachment",
         "Client",
+        "DetachedFrom",
         "Profile",
         "Profiles",
         "RejectionReasons",

bika/lims/workflow/analysisrequest/events.py

@@ -20,7 +20,8 @@
 
 from DateTime import DateTime
 from bika.lims import api
-from bika.lims.interfaces import IReceived, IVerified
+from bika.lims.interfaces import IDetachedPartition
+from bika.lims.interfaces import IReceived, IVerified, IAnalysisRequestPartition
 from bika.lims.utils import changeWorkflowState
 from bika.lims.utils.analysisrequest import create_retest
 from bika.lims.workflow import get_prev_status_from_history
@@ -153,3 +154,24 @@ def after_rollback_to_receive(analysis_request):
     """
     if IVerified.providedBy(analysis_request):
         noLongerProvides(analysis_request, IVerified)
+
+
+def after_detach(analysis_request):
+    """Function triggered after "detach" transition is performed
+    """
+    # Unbind the sample from its parent (the primary)
+    parent = analysis_request.getParentAnalysisRequest()
+    analysis_request.setParentAnalysisRequest(None)
+
+    # Assign the primary from which the sample has been detached
+    analysis_request.setDetachedFrom(parent)
+
+    # This sample is no longer a partition
+    noLongerProvides(analysis_request, IAnalysisRequestPartition)
+
+    # And we mark the sample with IDetachedPartition
+    alsoProvides(analysis_request, IDetachedPartition)
+
+    # Reindex both the parent and the detached one
+    analysis_request.reindexObject()
+    parent.reindexObject()