Re-ordered AddFreshMAPSTO() and DeprecateWrongMAPSTO() due to bug OHDSI@

dff9f24
mgurley · Oct 11, 2019 · bd7e13f · bd7e13f
1 parent afc3ddf
commit bd7e13f
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Showing 29 changed files with 126 additions and 138 deletions.
diff --git a/ATC/load_stage.sql b/ATC/load_stage.sql
@@ -1642,16 +1642,16 @@ BEGIN
 	PERFORM VOCABULARY_PACK.CheckReplacementMappings();
 END $_$;
 
--- 19. Deprecate 'Maps to' mappings to deprecated and upgraded concepts
+-- 19. Add mapping from deprecated to fresh concepts
 DO $_$
 BEGIN
-	PERFORM VOCABULARY_PACK.DeprecateWrongMAPSTO();
+	PERFORM VOCABULARY_PACK.AddFreshMAPSTO();
 END $_$;
 
--- 20. Add mapping from deprecated to fresh concepts
+-- 20. Deprecate 'Maps to' mappings to deprecated and upgraded concepts
 DO $_$
 BEGIN
-	PERFORM VOCABULARY_PACK.AddFreshMAPSTO();
+	PERFORM VOCABULARY_PACK.DeprecateWrongMAPSTO();
 END $_$;
 
 -- 21. DELETE ambiguous 'Maps to' mappings

diff --git a/CIEL/load_stage.sql b/CIEL/load_stage.sql
@@ -664,16 +664,16 @@ BEGIN
 	PERFORM VOCABULARY_PACK.CheckReplacementMappings();
 END $_$;
 
---8. Deprecate 'Maps to' mappings to deprecated and upgraded concepts
+--8. Add mapping from deprecated to fresh concepts
 DO $_$
 BEGIN
-	PERFORM VOCABULARY_PACK.DeprecateWrongMAPSTO();
+	PERFORM VOCABULARY_PACK.AddFreshMAPSTO();
 END $_$;
 
---9. Add mapping from deprecated to fresh concepts
+--9. Deprecate 'Maps to' mappings to deprecated and upgraded concepts
 DO $_$
 BEGIN
-	PERFORM VOCABULARY_PACK.AddFreshMAPSTO();
+	PERFORM VOCABULARY_PACK.DeprecateWrongMAPSTO();
 END $_$;
 
 --10. Delete ambiguous 'Maps to' mappings

diff --git a/CPT4/load_stage.sql b/CPT4/load_stage.sql
@@ -635,16 +635,16 @@ BEGIN
 	PERFORM VOCABULARY_PACK.CheckReplacementMappings();
 END $_$;
 
---14. Deprecate 'Maps to' mappings to deprecated and upgraded concepts
+--14. Add mapping from deprecated to fresh concepts
 DO $_$
 BEGIN
-	PERFORM VOCABULARY_PACK.DeprecateWrongMAPSTO();
+	PERFORM VOCABULARY_PACK.AddFreshMAPSTO();
 END $_$;
 
---15. Add mapping from deprecated to fresh concepts
+--15. Deprecate 'Maps to' mappings to deprecated and upgraded concepts
 DO $_$
 BEGIN
-	PERFORM VOCABULARY_PACK.AddFreshMAPSTO();
+	PERFORM VOCABULARY_PACK.DeprecateWrongMAPSTO();
 END $_$;
 
 --16. Delete ambiguous 'Maps to' mappings

diff --git a/GCN_SEQNO/load_stage.sql b/GCN_SEQNO/load_stage.sql
@@ -93,16 +93,16 @@ JOIN SOURCES.rxnconso rxn ON rxn.rxcui = gcn.rxcui
 WHERE gcn.sab = 'NDDF'
 	AND gcn.tty = 'CDC';
 
---5. Deprecate 'Maps to' mappings to deprecated and upgraded concepts
+--5. Add mapping from deprecated to fresh concepts
 DO $_$
 BEGIN
-	PERFORM VOCABULARY_PACK.DeprecateWrongMAPSTO();
+	PERFORM VOCABULARY_PACK.AddFreshMAPSTO();
 END $_$;
 
---6. Add mapping from deprecated to fresh concepts
+--6. Deprecate 'Maps to' mappings to deprecated and upgraded concepts
 DO $_$
 BEGIN
-	PERFORM VOCABULARY_PACK.AddFreshMAPSTO();
+	PERFORM VOCABULARY_PACK.DeprecateWrongMAPSTO();
 END $_$;
 
 --7. Delete ambiguous 'Maps to' mappings

diff --git a/GPI/load_stage.sql b/GPI/load_stage.sql
@@ -201,16 +201,16 @@ FROM (
 	) AS s0
 WHERE TRIM(concept_name) IS NOT NULL;
 
---6. Deprecate 'Maps to' mappings to deprecated and upgraded concepts
+--6. Add mapping from deprecated to fresh concepts
 DO $_$
 BEGIN
-	PERFORM VOCABULARY_PACK.DeprecateWrongMAPSTO();
+	PERFORM VOCABULARY_PACK.AddFreshMAPSTO();
 END $_$;
 
---7. Add mapping from deprecated to fresh concepts
+--7. Deprecate 'Maps to' mappings to deprecated and upgraded concepts
 DO $_$
 BEGIN
-	PERFORM VOCABULARY_PACK.AddFreshMAPSTO();
+	PERFORM VOCABULARY_PACK.DeprecateWrongMAPSTO();
 END $_$;
 
 --8. Delete ambiguous 'Maps to' mappings

diff --git a/Gemscript/final_part.sql b/Gemscript/final_part.sql
@@ -143,17 +143,17 @@ BEGIN
 END $_$;
 /
 
--- Deprecate 'Maps to' mappings to deprecated and upgraded concepts
+-- Add mapping from deprecated to fresh concepts, and also from non-standard to standard concepts
 DO $_$
 BEGIN
-	PERFORM VOCABULARY_PACK.DeprecateWrongMAPSTO();
+	PERFORM VOCABULARY_PACK.AddFreshMAPSTO();
 END $_$;
 /
 
--- Add mapping from deprecated to fresh concepts, and also from non-standard to standard concepts
+-- Deprecate 'Maps to' mappings to deprecated and upgraded concepts
 DO $_$
 BEGIN
-	PERFORM VOCABULARY_PACK.AddFreshMAPSTO();
+	PERFORM VOCABULARY_PACK.DeprecateWrongMAPSTO();
 END $_$;
 /
 

diff --git a/Gemscript/final_rxE_version.sql b/Gemscript/final_rxE_version.sql
@@ -82,17 +82,17 @@ BEGIN
 END $_$;
 /
 
--- Deprecate 'Maps to' mappings to deprecated and upgraded concepts
+-- Add mapping from deprecated to fresh concepts, and also from non-standard to standard concepts
 DO $_$
 BEGIN
-	PERFORM VOCABULARY_PACK.DeprecateWrongMAPSTO();
+	PERFORM VOCABULARY_PACK.AddFreshMAPSTO();
 END $_$;
 /
 
--- Add mapping from deprecated to fresh concepts, and also from non-standard to standard concepts
+-- Deprecate 'Maps to' mappings to deprecated and upgraded concepts
 DO $_$
 BEGIN
-	PERFORM VOCABULARY_PACK.AddFreshMAPSTO();
+	PERFORM VOCABULARY_PACK.DeprecateWrongMAPSTO();
 END $_$;
 /
 

diff --git a/Gemscript/load_stage.sql b/Gemscript/load_stage.sql
@@ -206,17 +206,17 @@ BEGIN
 END $_$;
 /
 
--- Deprecate 'Maps to' mappings to deprecated and upgraded concepts
+-- Add mapping from deprecated to fresh concepts, and also from non-standard to standard concepts
 DO $_$
 BEGIN
-	PERFORM VOCABULARY_PACK.DeprecateWrongMAPSTO();
+	PERFORM VOCABULARY_PACK.AddFreshMAPSTO();
 END $_$;
 /
 
--- Add mapping from deprecated to fresh concepts, and also from non-standard to standard concepts
+-- Deprecate 'Maps to' mappings to deprecated and upgraded concepts
 DO $_$
 BEGIN
-	PERFORM VOCABULARY_PACK.AddFreshMAPSTO();
+	PERFORM VOCABULARY_PACK.DeprecateWrongMAPSTO();
 END $_$;
 /
 

diff --git a/HCPCS/load_stage.sql b/HCPCS/load_stage.sql
@@ -1642,16 +1642,16 @@ BEGIN
 	PERFORM VOCABULARY_PACK.CheckReplacementMappings();
 END $_$;
 
---15. Deprecate 'Maps to' mappings to deprecated and upgraded concepts
+--15. Add mapping from deprecated to fresh concepts
 DO $_$
 BEGIN
-	PERFORM VOCABULARY_PACK.DeprecateWrongMAPSTO();
+	PERFORM VOCABULARY_PACK.AddFreshMAPSTO();
 END $_$;
 
---16. Add mapping from deprecated to fresh concepts
+--16. Deprecate 'Maps to' mappings to deprecated and upgraded concepts
 DO $_$
 BEGIN
-	PERFORM VOCABULARY_PACK.AddFreshMAPSTO();
+	PERFORM VOCABULARY_PACK.DeprecateWrongMAPSTO();
 END $_$;
 
 --17. Delete ambiguous 'Maps to' mappings

diff --git a/ICD10/load_stage.sql b/ICD10/load_stage.sql
@@ -294,16 +294,16 @@ BEGIN
 	PERFORM VOCABULARY_PACK.CheckReplacementMappings();
 END $_$;
 
---8. Deprecate 'Maps to' mappings to deprecated and upgraded concepts
+--8. Add mapping from deprecated to fresh concepts
 DO $_$
 BEGIN
-	PERFORM VOCABULARY_PACK.DeprecateWrongMAPSTO();
+	PERFORM VOCABULARY_PACK.AddFreshMAPSTO();
 END $_$;
 
---9. Add mapping from deprecated to fresh concepts
+--9. Deprecate 'Maps to' mappings to deprecated and upgraded concepts
 DO $_$
 BEGIN
-	PERFORM VOCABULARY_PACK.AddFreshMAPSTO();
+	PERFORM VOCABULARY_PACK.DeprecateWrongMAPSTO();
 END $_$;
 
 --10. Delete ambiguous 'Maps to' mappings

diff --git a/ICD10CM/load_stage.sql b/ICD10CM/load_stage.sql
@@ -84,16 +84,16 @@ BEGIN
 	PERFORM VOCABULARY_PACK.CheckReplacementMappings();
 END $_$;
 
---6. Deprecate 'Maps to' mappings to deprecated and upgraded concepts
+--6. Add mapping from deprecated to fresh concepts
 DO $_$
 BEGIN
-	PERFORM VOCABULARY_PACK.DeprecateWrongMAPSTO();
+	PERFORM VOCABULARY_PACK.AddFreshMAPSTO();
 END $_$;
 
---7. Add mapping from deprecated to fresh concepts
+--7. Deprecate 'Maps to' mappings to deprecated and upgraded concepts
 DO $_$
 BEGIN
-	PERFORM VOCABULARY_PACK.AddFreshMAPSTO();
+	PERFORM VOCABULARY_PACK.DeprecateWrongMAPSTO();
 END $_$;
 
 --8. Delete ambiguous 'Maps to' mappings

diff --git a/ICD10PCS/load_stage.sql b/ICD10PCS/load_stage.sql
@@ -184,16 +184,16 @@ BEGIN
 	PERFORM VOCABULARY_PACK.CheckReplacementMappings();
 END $_$;
 
---9. Deprecate 'Maps to' mappings to deprecated and upgraded concepts
+--9. Add mapping from deprecated to fresh concepts
 DO $_$
 BEGIN
-	PERFORM VOCABULARY_PACK.DeprecateWrongMAPSTO();
+	PERFORM VOCABULARY_PACK.AddFreshMAPSTO();
 END $_$;
 
---10. Add mapping from deprecated to fresh concepts
+--10. Deprecate 'Maps to' mappings to deprecated and upgraded concepts
 DO $_$
 BEGIN
-	PERFORM VOCABULARY_PACK.AddFreshMAPSTO();
+	PERFORM VOCABULARY_PACK.DeprecateWrongMAPSTO();
 END $_$;
 
 --11. Delete ambiguous 'Maps to' mappings

diff --git a/ICD9CM/load_stage.sql b/ICD9CM/load_stage.sql
@@ -273,16 +273,16 @@ BEGIN
 	PERFORM VOCABULARY_PACK.CheckReplacementMappings();
 END $_$;
 
---11. Deprecate 'Maps to' mappings to deprecated and upgraded concepts
+--11. Add mapping from deprecated to fresh concepts
 DO $_$
 BEGIN
-	PERFORM VOCABULARY_PACK.DeprecateWrongMAPSTO();
+	PERFORM VOCABULARY_PACK.AddFreshMAPSTO();
 END $_$;
 
---12. Add mapping from deprecated to fresh concepts
+--12. Deprecate 'Maps to' mappings to deprecated and upgraded concepts
 DO $_$
 BEGIN
-	PERFORM VOCABULARY_PACK.AddFreshMAPSTO();
+	PERFORM VOCABULARY_PACK.DeprecateWrongMAPSTO();
 END $_$;
 
 --13. Delete ambiguous 'Maps to' mappings

diff --git a/ICD9Proc/load_stage.sql b/ICD9Proc/load_stage.sql
@@ -159,16 +159,16 @@ BEGIN
 	PERFORM VOCABULARY_PACK.CheckReplacementMappings();
 END $_$;
 
---9. Deprecate 'Maps to' mappings to deprecated and updated concepts
+--9. Delete ambiguous 'Maps to' mappings
 DO $_$
 BEGIN
-	PERFORM VOCABULARY_PACK.DeprecateWrongMAPSTO();
+	PERFORM VOCABULARY_PACK.DeleteAmbiguousMAPSTO();
 END $_$;
 
---10. Delete ambiguous 'Maps to' mappings
+--10. Deprecate 'Maps to' mappings to deprecated and updated concepts
 DO $_$
 BEGIN
-	PERFORM VOCABULARY_PACK.DeleteAmbiguousMAPSTO();
+	PERFORM VOCABULARY_PACK.DeprecateWrongMAPSTO();
 END $_$;
 
 --11. Add "Is a" relationship from ICD9Proc descendants (or their standard SNOMED equivalents) to ICD9Proc  ancestors  (or their standard SNOMED equivalents), using ICD9Proc code similarity, to the CONCEPT_RELATIONSHIP_STAGE

diff --git a/Indication/load_stage.sql b/Indication/load_stage.sql
@@ -247,16 +247,16 @@ BEGIN
 	PERFORM VOCABULARY_PACK.CheckReplacementMappings();
 END $_$;
 
---6. Deprecate 'Maps to' mappings to deprecated and upgraded concepts
+--6. Add mapping from deprecated to fresh concepts
 DO $_$
 BEGIN
-	PERFORM VOCABULARY_PACK.DeprecateWrongMAPSTO();
+	PERFORM VOCABULARY_PACK.AddFreshMAPSTO();
 END $_$;
 
---7. Add mapping from deprecated to fresh concepts
+--7. Deprecate 'Maps to' mappings to deprecated and upgraded concepts
 DO $_$
 BEGIN
-	PERFORM VOCABULARY_PACK.AddFreshMAPSTO();
+	PERFORM VOCABULARY_PACK.DeprecateWrongMAPSTO();
 END $_$;
 
 --8. Delete ambiguous 'Maps to' mappings

diff --git a/LOINC/load_stage.sql b/LOINC/load_stage.sql
@@ -892,16 +892,16 @@ BEGIN
 	PERFORM VOCABULARY_PACK.CheckReplacementMappings();
 END $_$;
 
---22. Deprecate 'Maps to' mappings to deprecated and upgraded concepts
+--22. Add mapping from deprecated to fresh concepts
 DO $_$
 BEGIN
-	PERFORM VOCABULARY_PACK.DeprecateWrongMAPSTO();
+	PERFORM VOCABULARY_PACK.AddFreshMAPSTO();
 END $_$;
 
---23. Add mapping from deprecated to fresh concepts
+--23. Deprecate 'Maps to' mappings to deprecated and upgraded concepts
 DO $_$
 BEGIN
-	PERFORM VOCABULARY_PACK.AddFreshMAPSTO();
+	PERFORM VOCABULARY_PACK.DeprecateWrongMAPSTO();
 END $_$;
 
 --24. Delete ambiguous 'Maps to' mappings

diff --git a/MeSH/load_stage.sql b/MeSH/load_stage.sql
@@ -290,16 +290,16 @@ JOIN SOURCES.mrconso u ON u.code = c.concept_code
 	AND u.suppress = 'N'
 	AND u.lat = 'ENG';
 
---6. Deprecate 'Maps to' mappings to deprecated and upgraded concepts
+--6. Add mapping from deprecated to fresh concepts
 DO $_$
 BEGIN
-	PERFORM VOCABULARY_PACK.DeprecateWrongMAPSTO();
+	PERFORM VOCABULARY_PACK.AddFreshMAPSTO();
 END $_$;
 
---7. Add mapping from deprecated to fresh concepts
+--7. Deprecate 'Maps to' mappings to deprecated and upgraded concepts
 DO $_$
 BEGIN
-	PERFORM VOCABULARY_PACK.AddFreshMAPSTO();
+	PERFORM VOCABULARY_PACK.DeprecateWrongMAPSTO();
 END $_$;
 
 --8. Delete ambiguous 'Maps to' mappings

diff --git a/MedDRA/load_stage.sql b/MedDRA/load_stage.sql
@@ -411,16 +411,16 @@ BEGIN
 	PERFORM VOCABULARY_PACK.CheckReplacementMappings();
 END $_$;
 
---10. Deprecate 'Maps to' mappings to deprecated and upgraded concepts
+--10. Add mapping from deprecated to fresh concepts
 DO $_$
 BEGIN
-	PERFORM VOCABULARY_PACK.DeprecateWrongMAPSTO();
+	PERFORM VOCABULARY_PACK.AddFreshMAPSTO();
 END $_$;
 
---11. Add mapping from deprecated to fresh concepts
+--11. Deprecate 'Maps to' mappings to deprecated and upgraded concepts
 DO $_$
 BEGIN
-	PERFORM VOCABULARY_PACK.AddFreshMAPSTO();
+	PERFORM VOCABULARY_PACK.DeprecateWrongMAPSTO();
 END $_$;
 
 --12. Delete ambiguous 'Maps to' mappings