Hemonc refresh

mgurley · Sep 6, 2022 · 1c6afb4 · 1c6afb4
1 parent 28cb86b
commit 1c6afb4
Show file tree

Hide file tree

Showing 2 changed files with 9 additions and 3 deletions.
diff --git a/HemOnc/load_stage.sql b/HemOnc/load_stage.sql
@@ -385,6 +385,14 @@ JOIN concept_stage cs ON cs.concept_code = css.synonym_concept_code
 	-- 15704 has empty name, typo, I suppose
 	AND css.synonym_name IS NOT NULL;
 
+
+--11,1 Working with manual synonyms
+DO $_$
+BEGIN
+	PERFORM VOCABULARY_PACK.ProcessManualSynonyms();
+END $_$;
+
+
 --12. Replace 'Was replaced by' to 'Concept replaced by' (need to tell Jeremy)
 UPDATE concept_relationship_stage
 SET relationship_id = 'Concept replaced by'

diff --git a/HemOnc/manual_work/readme_manual_tables.md b/HemOnc/manual_work/readme_manual_tables.md
@@ -16,7 +16,7 @@ FROM concept_manual
 ORDER BY vocabulary_id, concept_code, invalid_reason, valid_start_date, valid_end_date, concept_name`
 
 2.Extract the following csv file into the concept_synonym_manual table:
-
+https://docs.google.com/spreadsheets/d/17C887UjOZxPPJ0_H58AUU7mFuEq2wVD_EHQLpW2vth8/edit#gid=0
 `SELECT synonym_name,
        synonym_concept_code,
        synonym_vocabulary_id,
@@ -36,5 +36,3 @@ ORDER BY synonym_vocabulary_id, synonym_concept_code, language_concept_id, synon
 FROM concept_relationship_manual
 ORDER BY vocabulary_id_1, vocabulary_id_2, relationship_id, concept_code_1, concept_code_2, invalid_reason, valid_start_date, valid_end_date
 ;`
-
-