Hello, I am new to OHDSI and am trying to create an instance of the CDM with the POSTGRES control files.
After the first 2 steps:
- Create an empty schema.
- Execute the script
OMOP CDM postgresql ddl.txtto create the tables and fields.
I attempted to load the Standardized Vocabularies (v5.0 13-MAR-20) into the corresponding tables by following the statements in “VocabImport/OMOP CDM vocabulary load - PostgreSQL.sql”:
COPY DRUG_STRENGTH FROM ‘C:\CDMV5VOCAB\DRUG_STRENGTH.csv’ WITH DELIMITER E’\t’ CSV HEADER QUOTE E’\b’ ;
COPY CONCEPT FROM ‘C:\CDMV5VOCAB\CONCEPT.csv’ WITH DELIMITER E’\t’ CSV HEADER QUOTE E’\b’ ;
COPY CONCEPT_RELATIONSHIP FROM ‘C:\CDMV5VOCAB\CONCEPT_RELATIONSHIP.csv’ WITH DELIMITER E’\t’ CSV HEADER QUOTE E’\b’ ;
COPY CONCEPT_ANCESTOR FROM ‘C:\CDMV5VOCAB\CONCEPT_ANCESTOR.csv’ WITH DELIMITER E’\t’ CSV HEADER QUOTE E’\b’ ;
COPY CONCEPT_SYNONYM FROM ‘C:\CDMV5VOCAB\CONCEPT_SYNONYM.csv’ WITH DELIMITER E’\t’ CSV HEADER QUOTE E’\b’ ;
COPY VOCABULARY FROM ‘C:\CDMV5VOCAB\VOCABULARY.csv’ WITH DELIMITER E’\t’ CSV HEADER QUOTE E’\b’ ;
COPY RELATIONSHIP FROM ‘C:\CDMV5VOCAB\RELATIONSHIP.csv’ WITH DELIMITER E’\t’ CSV HEADER QUOTE E’\b’ ;
COPY CONCEPT_CLASS FROM ‘C:\CDMV5VOCAB\CONCEPT_CLASS.csv’ WITH DELIMITER E’\t’ CSV HEADER QUOTE E’\b’ ;
COPY DOMAIN FROM ‘C:\CDMV5VOCAB\DOMAIN.csv’ WITH DELIMITER E’\t’ CSV HEADER QUOTE E’\b’ ;
However, the commands for CONCEPT and CONCEPT_SYNONYM fail due to lack of delimiters in certain rows of those tables’ CSV files. This results in the process trying to load multiple columns of a row’s data under a single column. Thus, an error message like “Value too long for varchar(255)” appears.
It’s a little difficult to view these files in Excel, perhaps due to their size, but as far as I can tell, the delimiters (tabs) are there.
Is this due to something on my end, or have others had this issue with v5.0 13-MAR-20?