Purge stale metadata and indexes from analysis catalog

CHANGES.rst

@@ -4,6 +4,7 @@ Changelog
 2.0.0rc3 (unreleased)
 ---------------------
 
+- #1724 Purge stale metadata and indexes from analysis catalog
 - #1720 Fix UnicodeDecodeError for Instrument Import Log View
 - #1719 Service/Method/Calculation relationship handling
 - #1717 Port workflow definitions to senaite namespace

src/bika/lims/browser/worksheet/views/results.py

@@ -176,9 +176,8 @@ def checkInstrumentsValidity(self):
         invalid = []
         ans = self.context.getAnalyses()
         for an in ans:
-            valid = an.isInstrumentValid()
-            if not valid:
-                instrument = an.getInstrument()
+            instrument = an.getInstrument()
+            if instrument and not instrument.isValid():
                 inv = "%s (%s)" % (
                     safe_unicode(an.Title()), safe_unicode(instrument.Title()))
                 if inv not in invalid:

src/bika/lims/catalog/analysis_catalog.py

@@ -36,7 +36,6 @@
 # Defining the indexes for this catalog
 _indexes_dict = {
     "sortable_title": "FieldIndex",
-    "getParentUID": "FieldIndex",
     "getDueDate": "DateIndex",
     "getDateReceived": "DateIndex",
     "getResultCaptureDate": "DateIndex",
@@ -50,17 +49,13 @@
     "getCategoryUID": "FieldIndex",
     "getPointOfCapture": "FieldIndex",
     "getSampleTypeUID": "FieldIndex",
-    # TODO Index "getSamplePointUID" is only used in reports/selection_macros
-    "getSamplePointUID": "FieldIndex",
     "getReferenceAnalysesGroupID": "FieldIndex",
-    "getMethodUID": "FieldIndex",
     "getInstrumentUID": "FieldIndex",
     "getWorksheetUID": "FieldIndex",
     "getOriginalReflexedAnalysisUID": "FieldIndex",
     "getPrioritySortkey": "FieldIndex",
     "getAncestorsUIDs": "KeywordIndex",
     "isSampleReceived": "BooleanIndex",
-    "isRetest": "BooleanIndex",
 }
 # Defining the columns for this catalog
 _columns_list = [
@@ -69,13 +64,10 @@
     "getResultCaptureDate",
     "getParentURL",
     "getRequestURL",
-    "getParentTitle",
-    "getParentUID",
     "getClientTitle",
     "getClientURL",
     "getRequestTitle",
     "getResult",
-    "getCalculationUID",
     "getUnit",
     "getKeyword",
     "getCategoryTitle",
@@ -86,12 +78,9 @@
     "getReferenceResults",
     # Used in duplicated analysis objects
     "getAnalysisPortalType",
-    "isInstrumentValid",
     # Columns from method
-    "getMethodUID",
     "getMethodTitle",
     "getMethodURL",
-    "getAllowedMethodUIDs",
     "getAnalyst",
     "getAnalystName",
     "getNumberOfRequiredVerifications",
@@ -106,9 +95,6 @@
     # defined as a service metacolumn instead of an analysis one
     "getResultOptions",
     "getServiceUID",
-    "getInstrumentEntryOfResults",
-    "getAllowedInstrumentUIDs",
-    "getInstrumentUID",
     "getSampleTypeUID",
     "getClientOrderNumber",
     "getDateReceived",

src/bika/lims/catalog/analysisrequest_catalog.py

@@ -86,8 +86,6 @@
     "getContactFullName",
     "getSampleTypeUID",
     "getSampleTypeTitle",
-    # TODO Index "getSamplePointUID" is only used in reports/selection_macros
-    "getSamplePointUID",
     "getSamplePointTitle",
     "getStorageLocationUID",
     "getStorageLocationTitle",

src/bika/lims/content/abstractanalysis.py

@@ -675,18 +675,6 @@ def getLateness(self):
         """
         return -self.getEarliness()
 
-    @security.public
-    def isInstrumentValid(self):
-        """Checks if the instrument selected for this analysis is valid.
-        Returns false if an out-of-date or uncalibrated instrument is
-        assigned.
-        :return: True if the Analysis has no instrument assigned or is valid
-        :rtype: bool
-        """
-        if self.getInstrument():
-            return self.getInstrument().isValid()
-        return True
-
     @security.public
     def isInstrumentAllowed(self, instrument):
         """Checks if the specified instrument can be set for this analysis,
@@ -696,7 +684,7 @@ def isInstrumentAllowed(self, instrument):
         :rtype: bool
         """
         uid = api.get_uid(instrument)
-        return uid in self.getAllowedInstrumentUIDs()
+        return uid in map(api.get_uid, self.getAllowedInstruments())
 
     @security.public
     def isMethodAllowed(self, method):
@@ -707,7 +695,7 @@ def isMethodAllowed(self, method):
         :rtype: bool
         """
         uid = api.get_uid(method)
-        return uid in self.getAllowedMethodUIDs()
+        return uid in map(api.get_uid, self.getAllowedMethods())
 
     @security.public
     def getAllowedMethods(self):
@@ -724,15 +712,6 @@ def getAllowedMethods(self):
         # get the available methods of the service
         return service.getMethods()
 
-    @security.public
-    def getAllowedMethodUIDs(self):
-        """Used to populate getAllowedMethodUIDs metadata. Delegates to
-        method getAllowedMethods() for the retrieval of the methods allowed.
-        :return: A list with the UIDs of the methods allowed for this analysis
-        :rtype: list of strings
-        """
-        return map(api.get_uid, self.getAllowedMethods())
-
     @security.public
     def getAllowedInstruments(self):
         """Returns the allowed instruments from the service
@@ -745,15 +724,6 @@ def getAllowedInstruments(self):
             return []
         return service.getInstruments()
 
-    @security.public
-    def getAllowedInstrumentUIDs(self):
-        """Used to populate getAllowedInstrumentUIDs metadata. Delegates to
-        getAllowedInstruments() for the retrieval of the instruments allowed.
-        :return: List of instruments' UIDs allowed for this analysis
-        :rtype: list of strings
-        """
-        return map(api.get_uid, self.getAllowedInstruments())
-
     @security.public
     def getExponentialFormatPrecision(self, result=None):
         """ Returns the precision for the Analysis Service and result
@@ -1039,15 +1009,6 @@ def getStartProcessDate(self):
         """
         return self.created()
 
-    @security.public
-    def getParentUID(self):
-        """This method is used to populate catalog values
-        This function returns the analysis' parent UID
-        """
-        parent = self.aq_parent
-        if parent:
-            return parent.UID()
-
     @security.public
     def getParentURL(self):
         """This method is used to populate catalog values
@@ -1088,16 +1049,6 @@ def getWorksheet(self):
                 % self.getId())
         return worksheet[0]
 
-    @security.public
-    def getInstrumentValid(self):
-        """Used to populate catalog values. Delegates to isInstrumentValid()
-        Returns false if an out-of-date or uncalibrated instrument is
-        assigned.
-        :return: True if the Analysis has no instrument assigned or is valid
-        :rtype: bool
-        """
-        return self.isInstrumentValid()
-
     @security.public
     def remove_duplicates(self, ws):
         """When this analysis is unassigned from a worksheet, this function

src/bika/lims/content/abstractbaseanalysis.py

@@ -898,14 +898,6 @@ def _getNumberOfRequiredVerificationsVocabulary(self):
         items = [(-1, bsval), (1, '1'), (2, '2'), (3, '3'), (4, '4')]
         return IntDisplayList(list(items))
 
-    @security.public
-    def getInstrumentEntryOfResults(self):
-        """XXX: ALWAYS ALLOW INSTRUMENT RESULTS
-
-        TODO: Remove if refactored
-        """
-        return True
-
     @security.public
     def getMethodTitle(self):
         """This is used to populate catalog values

src/bika/lims/content/abstractroutineanalysis.py

@@ -247,14 +247,6 @@ def getSamplePoint(self):
             return request.getSamplePoint()
         return None
 
-    @security.public
-    def getSamplePointUID(self):
-        """Used to populate catalog values.
-        """
-        sample_point = self.getSamplePoint()
-        if sample_point:
-            return api.get_uid(sample_point)
-
     @security.public
     def getDueDate(self):
         """Used to populate getDueDate index and metadata.
@@ -354,14 +346,6 @@ def getCalculation(self):
             return None
         return calculation
 
-    @security.public
-    def getCalculationUID(self):
-        """Used to populate catalog values
-        """
-        calculation = self.getCalculation()
-        if calculation:
-            return calculation.UID()
-
     @security.public
     def getDependents(self, with_retests=False, recursive=False):
         """

src/bika/lims/workflow/duplicateanalysis/events.py

@@ -101,7 +101,7 @@ def after_retract(duplicate_analysis):
     worksheet.setAnalyses(worksheet.getAnalyses() + [retest, ])
 
     # Reindex
-    retest.reindexObject(idxs=["getAnalyst", "getWorksheetUID", "isRetest",
+    retest.reindexObject(idxs=["getAnalyst", "getWorksheetUID",
                                "getReferenceAnalysesGroupID"])
     worksheet.reindexObject(idxs=["getAnalysesUIDs"])
 

src/bika/lims/workflow/indexes.py

@@ -41,7 +41,6 @@
             "getAnalyst",
             "getDueDate",
             "getInstrumentUID",
-            "getMethodUID",
             "getResultCaptureDate",
         ],
         "unassign": [
@@ -62,7 +61,6 @@
             "getAnalyst",
             "getDueDate",
             "getInstrumentUID",
-            "getMethodUID",
             "getResultCaptureDate",
         ],
         "unassign": None,
@@ -79,7 +77,6 @@
             "getAnalyst",
             "getDueDate",
             "getInstrumentUID",
-            "getMethodUID",
             "getResultCaptureDate",
             "review_state",
         ],

src/senaite/core/tests/doctests/WorksheetApplyTemplate.rst

@@ -786,7 +786,6 @@ Re-assign the worksheet template:
 
 The worksheet now contains the two analyses:
 
-    >>> worksheet.applyWorksheetTemplate(method_template)
     >>> ws_analyses = worksheet.getAnalyses()
     >>> len(ws_analyses)
     2

src/senaite/core/upgrade/v02_00_000.py

@@ -79,12 +79,30 @@
     (SETUP_CATALOG, "department_id", "KeywordIndex"),
 ]
 
+INDEXES_TO_REMOVE = [
+    # List of tuples (catalog_name, index_name)
+    (CATALOG_ANALYSIS_LISTING, "getMethodUID"),
+    (CATALOG_ANALYSIS_LISTING, "isRetest"),
+    (CATALOG_ANALYSIS_LISTING, "getSamplePointUID"),
+    (CATALOG_ANALYSIS_LISTING, "getParentUID"),
+]
+
 METADATA_TO_REMOVE = [
     # Only used in Analyses listing and it's behavior is bizarre, probably
     # because is a dict and requires special care with ZODB
     (CATALOG_ANALYSIS_LISTING, "getInterimFields"),
     # No longer used, see https://github.com/senaite/senaite.core/pull/1709/
-    (CATALOG_ANALYSIS_LISTING, "getAttachmentUIDs")
+    (CATALOG_ANALYSIS_LISTING, "getAttachmentUIDs"),
+    (CATALOG_ANALYSIS_LISTING, "getInstrumentEntryOfResults"),
+    (CATALOG_ANALYSIS_LISTING, "getCalculationUID"),
+    (CATALOG_ANALYSIS_LISTING, "getAllowedInstrumentUIDs"),
+    (CATALOG_ANALYSIS_LISTING, "getMethodUID"),
+    (CATALOG_ANALYSIS_LISTING, "getAllowedMethodUIDs"),
+    (CATALOG_ANALYSIS_LISTING, "getInstrumentUID"),
+    (CATALOG_ANALYSIS_REQUEST_LISTING, "getSamplePointUID"),
+    (CATALOG_ANALYSIS_LISTING, "getParentUID"),
+    (CATALOG_ANALYSIS_LISTING, "getParentTitle"),
+    (CATALOG_ANALYSIS_LISTING, "isInstrumentValid"),
 ]
 
 STALE_WORKFLOW_DEFINITIONS = [
@@ -177,6 +195,9 @@ def upgrade(tool):
     remove_supplyorder_typeinfo(portal)
     remove_supplyorder_workflow(portal)
 
+    # Remove stale indexes
+    remove_stale_indexes(portal)
+
     # Remove stale metadata
     remove_stale_metadata(portal)
 
@@ -497,6 +518,24 @@ def del_metadata(catalog_id, column):
     catalog.delColumn(column)
 
 
+def remove_stale_indexes(portal):
+    logger.info("Removing stale indexes ...")
+    for catalog_id, index_name in INDEXES_TO_REMOVE:
+        del_index(portal, catalog_id, index_name)
+    logger.info("Removing stale indexes ... [DONE]")
+
+
+def del_index(portal, catalog_id, index_name):
+    logger.info("Removing '{}' index from '{}' ..."
+                .format(index_name, catalog_id))
+    catalog = api.get_tool(catalog_id)
+    if index_name not in catalog.indexes():
+        logger.info("Index '{}' not in catalog '{}' [SKIP]"
+                    .format(index_name, catalog_id))
+        return
+    catalog.delIndex(index_name)
+
+
 def remove_at_portal_types(portal):
     """Remove AT portal type information
     """