Add two parameters in ConceptAncestorCore() and pManualConceptAncestor()

working/packages/vocabulary_pack/ConceptAncestorCore.sql

@@ -1,4 +1,9 @@
-CREATE OR REPLACE FUNCTION vocabulary_pack.ConceptAncestorCore (pVocabularies TEXT, pDebugLoops BOOLEAN)
+CREATE OR REPLACE FUNCTION vocabulary_pack.ConceptAncestorCore (
+    pVocabularies TEXT, 
+    pDebugLoops BOOLEAN, 
+    pIncludeNonStandard BOOLEAN DEFAULT FALSE,
+    pIncludeInvalidReason BOOLEAN DEFAULT FALSE
+)
 RETURNS VOID AS
 $BODY$
 	/*
@@ -38,13 +43,13 @@ BEGIN
 	JOIN relationship s ON s.relationship_id = r.relationship_id
 		AND s.defines_ancestry = 1
 	JOIN concept c1 ON c1.concept_id = r.concept_id_1
-		AND c1.invalid_reason IS NULL
+		AND (pIncludeInvalidReason OR c1.invalid_reason IS NULL)
 		AND (
 			c1.vocabulary_id = ANY (iVocabularies)
 			OR iVocabularies IS NULL
 			)
 	JOIN concept c2 ON c2.concept_id = r.concept_id_2
-		AND c2.invalid_reason IS NULL
+		AND (pIncludeInvalidReason OR c2.invalid_reason IS NULL)
 		AND (
 			c2.vocabulary_id = ANY (iVocabularies)
 			OR iVocabularies IS NULL
@@ -84,12 +89,12 @@ BEGIN
 					ca.levels_of_separation,
 					ARRAY [descendant_concept_id] AS full_path
 				FROM temporary_ca_base$ ca
-				WHERE EXISTS (
+				WHERE (pIncludeNonStandard OR EXISTS (
 						SELECT 1
 						FROM concept c_int
 						WHERE c_int.concept_id = ca.ancestor_concept_id
 							AND c_int.standard_concept IS NOT NULL --remove non-standard records in ancestor_concept_id
-						)
+						))
 					AND ca.ancestor_concept_id > cRecord.ancestor_concept_id_min
 					AND ca.ancestor_concept_id <= cRecord.ancestor_concept_id_max
 
@@ -120,23 +125,27 @@ BEGIN
 			hc.descendant_concept_id;
 	END LOOP;
 
-	--remove non-standard records in descendant_concept_id
-	DELETE
-	FROM temporary_ca$ ca
-	USING concept c
-	WHERE c.standard_concept IS NULL
-		AND c.concept_id = ca.descendant_concept_id;
-
+    IF NOT pIncludeNonStandard THEN
+        --remove non-standard records in descendant_concept_id
+        DELETE
+        FROM temporary_ca$ ca
+        USING concept c
+        WHERE c.standard_concept IS NULL
+            AND c.concept_id = ca.descendant_concept_id;
+    END IF;
+
 	IF pDebugLoops THEN
 		--in debug mode we preserve the temporary_ca$ for future use 
 		RETURN;
 	END IF;
 
-	PERFORM FROM temporary_ca$ ca WHERE ca.ancestor_concept_id=ca.descendant_concept_id LIMIT 1;
-	IF FOUND THEN
-		--loops found, e.g. code1 'Subsumes' code2 'Subsumes' code1, which leads to the creation of an code1-code1 chain
-		RAISE EXCEPTION $$Loops in the ancestor were found, please run SELECT vocabulary_pack.GetAncestorLoops(pVocabularies=>'%'); For view chains you can also use SELECT * FROM vocabulary_pack.GetAncestorPath_in_DEV(ancestor_id, descendant_id)$$, pVocabularies;
-	END IF;
+    IF NOT (pIncludeNonStandard OR pIncludeInvalidReason) THEN 
+        PERFORM FROM temporary_ca$ ca WHERE ca.ancestor_concept_id=ca.descendant_concept_id LIMIT 1;
+        IF FOUND THEN
+            --loops found, e.g. code1 'Subsumes' code2 'Subsumes' code1, which leads to the creation of an code1-code1 chain
+            RAISE EXCEPTION $$Loops in the ancestor were found, please run SELECT vocabulary_pack.GetAncestorLoops(pVocabularies=>'%'); For view chains you can also use SELECT * FROM vocabulary_pack.GetAncestorPath_in_DEV(ancestor_id, descendant_id)$$, pVocabularies;
+        END IF;
+    END IF;
 
 	--Add connections to self for those vocabs having at least one concept in the concept_relationship table
 	INSERT INTO temporary_ca$
@@ -149,10 +158,10 @@ BEGIN
 			SELECT c_int.vocabulary_id
 			FROM concept_relationship cr_int
 			JOIN concept c_int ON c_int.concept_id = cr_int.concept_id_1
-			WHERE cr_int.invalid_reason IS NULL
+			WHERE r_int.invalid_reason IS NULL
 			)
-		AND c.invalid_reason IS NULL
-		AND c.standard_concept IS NOT NULL;
+		AND (pIncludeInvalidReason OR c.invalid_reason IS NULL)
+		AND (pIncludeNonStandard OR c.standard_concept IS NOT NULL);
 
 	CREATE INDEX idx_tmp_ca$ ON temporary_ca$ (ancestor_concept_id, descendant_concept_id) INCLUDE (min_levels_of_separation, max_levels_of_separation) WITH (FILLFACTOR=100);
 	ANALYZE temporary_ca$;

working/packages/vocabulary_pack/pManualConceptAncestor.sql

@@ -1,4 +1,8 @@
-CREATE OR REPLACE FUNCTION vocabulary_pack.pManualConceptAncestor (pVocabularies TEXT)
+CREATE OR REPLACE FUNCTION vocabulary_pack.pManualConceptAncestor (
+    pVocabularies TEXT, 
+    pIncludeNonStandard BOOLEAN DEFAULT FALSE,
+    pIncludeInvalidReason BOOLEAN DEFAULT FALSE
+)
 RETURNS VOID AS
 $BODY$
 	/*
@@ -17,10 +21,18 @@ DECLARE
 	cStartTime TIMESTAMP:=CLOCK_TIMESTAMP();
 	cWorkTime NUMERIC;
 BEGIN
-	PERFORM vocabulary_pack.ConceptAncestorCore(pVocabularies, FALSE);
+	PERFORM vocabulary_pack.ConceptAncestorCore(pVocabularies, FALSE, pIncludeNonStandard, pIncludeInvalidReason);
 
 	cWorkTime:=ROUND((EXTRACT(EPOCH FROM CLOCK_TIMESTAMP()-cStartTime)/60)::NUMERIC,1);
-	PERFORM devv5.SendMailHTML (iSmallCA_emails, 'Manual concept ancestor in '||UPPER(CURRENT_SCHEMA)||' [ok]', 'Manual concept ancestor in '||UPPER(CURRENT_SCHEMA)||' completed'||crlf||'Execution time: '||cWorkTime||' min');
+	PERFORM devv5.SendMailHTML (
+        iSmallCA_emails, 
+        'Manual concept ancestor in '||UPPER(CURRENT_SCHEMA)||' [ok]', 
+        'Manual concept ancestor in '||UPPER(CURRENT_SCHEMA)||' completed'||crlf||
+        CASE WHEN pIncludeNonStandard THEN 'incliding non-standard concepts' ELSE '' END||crlf||
+        CASE WHEN pIncludeInvalidReason THEN 'including invalid reason ' ELSE '' END||crlf||
+        'Execution time: '||cWorkTime||' min'
+
+    );
 
 	EXCEPTION WHEN OTHERS THEN
 		GET STACKED DIAGNOSTICS cRet = PG_EXCEPTION_CONTEXT, cRet2 = PG_EXCEPTION_DETAIL;