added sources.amt_crefset_language (AMT, AVOF-3171)

OHDSI · Jun 16, 2021 · 3589205 · 3589205
1 parent 107c84a
commit 3589205
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Showing 3 changed files with 22 additions and 3 deletions.
diff --git a/AMT/create_source_tables.sql b/AMT/create_source_tables.sql
@@ -85,6 +85,19 @@ CREATE TABLE SOURCES.AMT_RF2_SS_STRENGTH_REFSET
    VALUE                  VARCHAR(255)
 );
 
+DROP TABLE IF EXISTS SOURCES.AMT_CREFSET_LANGUAGE;
+CREATE TABLE SOURCES.AMT_CREFSET_LANGUAGE
+(
+   ID                         VARCHAR(255),
+   EFFECTIVETIME              VARCHAR(8),
+   ACTIVE                     INT2,
+   MODULEID                   BIGINT,
+   REFSETID                   BIGINT,
+   REFERENCEDCOMPONENTID      BIGINT,
+   ACCEPTABILITYID            BIGINT
+);
+
+CREATE INDEX idx_amt_lang_refid ON SOURCES.AMT_CREFSET_LANGUAGE (REFERENCEDCOMPONENTID);
 CREATE INDEX idx_amt_concept_id ON SOURCES.AMT_SCT2_CONCEPT_FULL_AU (ID);
 CREATE INDEX idx_amt_descr_id ON SOURCES.AMT_FULL_DESCR_DRUG_ONLY (CONCEPTID);
 CREATE INDEX idx_amt_rela_id ON SOURCES.AMT_RF2_FULL_RELATIONSHIPS (ID);

diff --git a/working/packages/load_input_tables/load_input_tables.sql b/working/packages/load_input_tables/load_input_tables.sql
@@ -622,28 +622,32 @@ begin
       analyze sources.ggr_sam;
   when 'AMT' then
       truncate table sources.amt_full_descr_drug_only, sources.amt_sct2_concept_full_au, sources.amt_rf2_full_relationships, sources.amt_rf2_ss_strength_refset,
-      	sources.amt_sct2_rela_full_au;
+      	sources.amt_sct2_rela_full_au, sources.amt_crefset_language;
       drop index sources.idx_amt_concept_id;
       drop index sources.idx_amt_descr_id;
       drop index sources.idx_amt_rela_id;
       drop index sources.idx_amt_rela2_id;
+      drop index sources.idx_amt_lang_refid;
       execute 'COPY sources.amt_full_descr_drug_only FROM '''||pVocabularyPath||'sct2_Description_Full-en-AU_AU.txt'' delimiter E''\t'' csv quote E''\b'' HEADER';
       execute 'COPY sources.amt_sct2_concept_full_au (id,effectivetime,active,moduleid,statusid) FROM '''||pVocabularyPath||'sct2_Concept_Full_AU.txt'' delimiter E''\t'' csv quote E''\b'' HEADER';
       execute 'COPY sources.amt_rf2_full_relationships FROM '''||pVocabularyPath||'sct2_Relationship_Full_AU.txt'' delimiter E''\t'' csv quote E''\b'' HEADER';
       execute 'COPY sources.amt_rf2_ss_strength_refset FROM '''||pVocabularyPath||'der2_ccsRefset_StrengthFull_AU.txt'' delimiter E''\t'' csv quote E''\b'' HEADER';
+      execute 'COPY sources.amt_crefset_language FROM '''||pVocabularyPath||'der2_cRefset_LanguageFull-en-AU_AU.txt'' delimiter E''\t'' csv quote E''\b'' HEADER';
       --execute 'COPY sources.amt_sct2_rela_full_au FROM '''||pVocabularyPath||'sct2_Relationship_Full_AU36.txt'' delimiter E''\t'' csv quote E''\b'' HEADER';
       update sources.amt_sct2_concept_full_au set vocabulary_date=COALESCE(pVocabularyDate,current_date), vocabulary_version=COALESCE(pVocabularyVersion,pVocabularyID||' '||current_date);
 
       create index idx_amt_concept_id on sources.amt_sct2_concept_full_au (id);
       create index idx_amt_descr_id on sources.amt_full_descr_drug_only (conceptid);
       create index idx_amt_rela_id on sources.amt_rf2_full_relationships (id);
       create index idx_amt_rela2_id on sources.amt_sct2_rela_full_au (id);
+      create index idx_amt_lang_refid on sources.amt_crefset_language (referencedcomponentid);
 
       analyze sources.amt_full_descr_drug_only;
       analyze sources.amt_sct2_concept_full_au;
       analyze sources.amt_rf2_full_relationships;
       analyze sources.amt_rf2_ss_strength_refset;
       analyze sources.amt_sct2_rela_full_au;
+      analyze sources.amt_crefset_language;
   when 'ISBT' then
       truncate table sources.isbt_product_desc, sources.isbt_classes, sources.isbt_modifiers, sources.isbt_attribute_values, sources.isbt_attribute_groups, 
       	sources.isbt_categories, sources.isbt_modifier_category_map, sources.isbt_version;

diff --git a/working/packages/vocabulary_download/bash_functions_amt.sql b/working/packages/vocabulary_download/bash_functions_amt.sql
@@ -12,15 +12,17 @@ BEGIN
     unzip -oqj "$2" "SnomedCT_Release_AU1000036_*/RF2Release/Full/Terminology/sct2_Concept_Full_AU1000036_*.txt" -d . && \
     unzip -oqj "$2" "SnomedCT_Release_AU1000036_*/RF2Release/Full/Terminology/sct2_Description_Full-en-AU_AU1000036_*.txt" -d . && \
     unzip -oqj "$2" "SnomedCT_Release_AU1000036_*/RF2Release/Full/Terminology/sct2_Relationship_Full_AU1000036_*.txt" -d . && \
-    unzip -oqj "$2" "SnomedCT_Release_AU1000036_*/RF2Release/Full/Refset/Content/der2_ccsRefset_StrengthFull_AU1000036_*.txt" -d .
+    unzip -oqj "$2" "SnomedCT_Release_AU1000036_*/RF2Release/Full/Refset/Content/der2_ccsRefset_StrengthFull_AU1000036_*.txt" -d . && \
+    unzip -oqj "$2" "SnomedCT_Release_AU1000036_*/RF2Release/Full/Refset/Language/der2_cRefset_LanguageFull-en-AU_AU1000036_*.txt" -d .
 
     #move result to original folder
     cd "$1"
     rm -f *.*
     mv work/sct2_Concept_Full_*.txt "sct2_Concept_Full_AU.txt" && \
     mv work/sct2_Description_Full-en-AU_*.txt "sct2_Description_Full-en-AU_AU.txt" && \
     mv work/sct2_Relationship_Full_*.txt "sct2_Relationship_Full_AU.txt" && \
-    mv work/der2_ccsRefset_StrengthFull_*.txt "der2_ccsRefset_StrengthFull_AU.txt"
+    mv work/der2_ccsRefset_StrengthFull_*.txt "der2_ccsRefset_StrengthFull_AU.txt" && \
+    mv work/der2_cRefset_LanguageFull-en-AU_AU1000036_*.txt "der2_cRefset_LanguageFull-en-AU_AU.txt"
     $BODY$
     LANGUAGE 'plsh'
     SECURITY DEFINER;