Fix samples w/o active analyses are displayed under "unassigned" filter (senaite#2066)

* Fix samples w/o active analyses are displayed under "unassigned" filter

* Whitespace end of file

* Take partitions into consideration

Co-authored-by: Ramon Bartl <[email protected]>

Author: xispa

CHANGES.rst

@@ -5,6 +5,7 @@ Changelog
 2.3.0 (unreleased)
 ------------------
 
+- #2066 Fix samples w/o active analyses are displayed under "unassigned" filter
 - #2065 Fix "Create Worksheet" modal visible for samples w/o unassigned analyses
 - #2063 Allow to customize email publication template in setup
 - #2062 Fix listing not updated after instrument assignment in Worksheet's view

src/senaite/core/catalog/indexer/sample.py

@@ -10,19 +10,56 @@
 
 @indexer(IAnalysisRequest)
 def assigned_state(instance):
-    """Returns `assigned` or `unassigned` depending on the state of the
-    analyses the analysisrequest contains. Return `unassigned` if the Analysis
-    Request has at least one analysis in `unassigned` state.
-    Otherwise, returns `assigned`
+    """Returns `assigned`, `unassigned` or 'not_applicable' depending on the
+    state of the analyses the analysisrequest contains. Return `unassigned` if
+    the Analysis Request has at least one 'active' analysis in `unassigned`
+    status. Returns 'assigned' if all 'active' analyses of the sample are
+    assigned to a Worksheet. Returns 'not_applicable' if no 'active' analyses
+    for the given sample exist
     """
-    analyses = instance.getAnalyses()
-    if not analyses:
-        return "unassigned"
-    for analysis in analyses:
-        analysis_object = api.get_object(analysis)
-        if not analysis_object.getWorksheet():
+    assigned = False
+    skip_statuses = ["retracted", "rejected", "cancelled"]
+
+    # Retrieve analyses directly from the instance container instead of relying
+    # on ARAnalysesField getter, that performs a catalog query. Reason is, that
+    # we never know if the sample is indexed before the analyses or any other
+    # dependent catalog
+    for analysis in instance.objectValues(spec="Analysis"):
+        status = api.get_review_status(analysis)
+
+        if status == "unassigned":
+            # One unassigned found, no need to go further
             return "unassigned"
-    return "assigned"
+
+        if status in skip_statuses:
+            # Skip "inactive" analyses
+            continue
+
+        if analysis.getWorksheetUID():
+            # At least one analysis with a worksheet assigned
+            assigned = True
+
+    # ARAnalysesField getter returns all the analyses from the sample, those
+    # from partitions included. Since we do not rely on the getter, we need to
+    # manually extract the analyses from the partitions
+    # Pity is, that for the retrieval of partitions we need to rely on
+    # getBackReferences, that is a query against reference_catalog
+    for partition in instance.getDescendants():
+        # Note we call this same index, but for the partition
+        partition_status = assigned_state(partition)()
+        if partition_status == "unassigned":
+            # One of the partitions with unassigned, no need to go further
+            return "unassigned"
+
+        elif partition_status == "assigned":
+            assigned = True
+
+    if assigned:
+        # All "active" analyses assigned to a worksheet
+        return "assigned"
+
+    # Sample without "active" assigned/unassigned analyses
+    return "not_applicable"
 
 
 @indexer(IAnalysisRequest)

src/senaite/core/upgrade/v02_03_000.py

@@ -73,6 +73,7 @@ def upgrade(tool):
     fix_worksheets_analyses(portal)
     fix_cannot_create_partitions(portal)
     fix_interface_interpretation_template(portal)
+    fix_unassigned_samples(portal)
 
     logger.info("{0} upgraded to version {1}".format(product, version))
     return True
@@ -176,3 +177,30 @@ def fix_interface_interpretation_template(portal):
     fti = pt.get("InterpretationTemplate")
     fti.schema = "senaite.core.content.interpretationtemplate.IInterpretationTemplateSchema"
     logger.info("Fix interface for InterpretationTemplate FTI ...")
+
+
+def fix_unassigned_samples(portal):
+    """Reindex the 'assigned_state' index for samples
+    """
+    logger.info("Fix unassigned samples ...")
+    indexes = ["assigned_state"]
+    query = {
+        "portal_type": "AnalysisRequest",
+        "assigned_state": "unassigned",
+    }
+    cat = api.get_tool(SAMPLE_CATALOG)
+    samples = api.search(query, SAMPLE_CATALOG)
+    total = len(samples)
+    for num, sample in enumerate(samples):
+
+        if num and num % 100 == 0:
+            logger.info("Fix unassigned samples {0}/{1}".format(num, total))
+
+        obj = api.get_object(sample)
+        obj_url = api.get_path(sample)
+        cat.catalog_object(obj, obj_url, idxs=indexes, update_metadata=1)
+
+        # Flush the object from memory
+        obj._p_deactivate()  # noqa
+
+    logger.info("Fix unassigned samples ...")