fix: update term translations table and sql script to re-new terms

GenomicDataInfrastructure · Apr 16, 2024 · 77a96ed · 77a96ed
1 parent 6ee07de
commit 77a96ed
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Showing 2 changed files with 14 additions and 2 deletions.
diff --git a/ckan/docker-entrypoint.d/common_vocabulary_tags.csv b/ckan/docker-entrypoint.d/common_vocabulary_tags.csv
@@ -1073,4 +1073,11 @@ http://purl.org/zonmw/covid19/10006,regional,en
 http://purl.org/zonmw/generic/10006,other,en
 https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C9245,Invasive Breast Carcinoma,en
 https://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp?code=C0853879,Invasive Breast Carcinoma,en
-http://purl.bioontology.org/ontology/ICD10CM/J96.2,Acute and chronic respiratory failure,en
+http://purl.bioontology.org/ontology/ICD10CM/J96.2,Acute and chronic respiratory failure,en
+access_rights,Access Rights,en
+organization,Catalogues,en
+publisher_name,Publishers,en
+res_format,File Formats,en
+spatial,Spatial Coverage,en
+tags,Keywords,en
+theme,Themes,en
diff --git a/ckan/docker-entrypoint.d/upload_vocabulary.sh b/ckan/docker-entrypoint.d/upload_vocabulary.sh
@@ -12,7 +12,12 @@ psql postgresql://$POSTGRES_USER:$POSTGRES_PASSWORD@$POSTGRES_HOST:5432/$CKAN_DB
       EXISTS(SELECT 1 FROM public.term_translation) as table_not_empty
   \gset
   \if :table_not_empty
-      \echo 'term_translation table is not empty, skipping'
+      \echo 'term_translation table is not empty, updating'
+      create table public.temp (term text, term_translation text, lang_code text);
+      \copy public.temp FROM  '/docker-entrypoint.d/common_vocabulary_tags.csv' WITH (DELIMITER ',', FORMAT CSV, HEADER TRUE);
+      delete from public.term_translation using public.temp where public.term_translation.term = public.temp.term and public.term_translation.term_translation = public.temp.term_translation and public.term_translation.lang_code = public.temp.lang_code;
+      insert into public.term_translation (term, term_translation, lang_code) select term, term_translation, lang_code from public.temp;
+      drop table public.temp;
   \else
       \copy public.term_translation FROM  '/docker-entrypoint.d/common_vocabulary_tags.csv' WITH (DELIMITER ',', FORMAT CSV, HEADER TRUE);
       \echo 'term_translation initialized with common_vocabulary_tags.csv'