Postgresql loader gives syntax errors

[rjalexa]

Launched sh load_release-postgresql.sh SnomedCT_InternationalRF2_PRODUCTION_20221031T120000Z.zip snomedct FULL

Tables created as desired but then get errors from tmp_loader.sql as follows:

CREATE TABLE
psql:environment-postgresql.sql:273: NOTICE:  table "owlexpressionrefset_f" does not exist, skipping
DROP TABLE
CREATE TABLE
SET
psql:tmp_loader.sql:7: ERROR:  syntax error at or near "-"
LINE 1: -e COPY concept_f
        ^
psql:tmp_loader.sql:11: ERROR:  syntax error at or near "-"
LINE 1: -e 
        ^
psql:tmp_loader.sql:15: ERROR:  syntax error at or near "-"
LINE 1: -e 
        ^
psql:tmp_loader.sql:19: ERROR:  syntax error at or near "-"
LINE 1: -e 
        ^
psql:tmp_loader.sql:23: ERROR:  syntax error at or near "-"
LINE 1: -e 
        ^
psql:tmp_loader.sql:27: ERROR:  syntax error at or near "-"
LINE 1: -e 
        ^
psql:tmp_loader.sql:31: ERROR:  syntax error at or near "-"
LINE 1: -e 
        ^
psql:tmp_loader.sql:35: ERROR:  syntax error at or near "-"
LINE 1: -e 
        ^
psql:tmp_loader.sql:36: ERROR:  syntax error at or near "-"
LINE 1: -e 
        ^

and the content of tmp_loader.sql is:

/* Generated Loader Script */

set schema 'snomedct';

-e COPY concept_f
-e FROM '/Users/bob/Documents/work/@@@ ontologies and misc sources/SNOMED/SNOMEDCT_INT_202210/snomed-database-loader/PostgreSQL/tmp_extracted/sct2_Concept_Full_INT_20221031.txt'
-e WITH (FORMAT csv, HEADER true, DELIMITER E'  ', QUOTE E');
-e 
-e COPY description_f
-e FROM '/Users/bob/Documents/work/@@@ ontologies and misc sources/SNOMED/SNOMEDCT_INT_202210/snomed-database-loader/PostgreSQL/tmp_extracted/sct2_Description_Full-en_INT_20221031.txt'
-e WITH (FORMAT csv, HEADER true, DELIMITER E'  ', QUOTE E');
-e 
-e COPY stated_relationship_f
-e FROM '/Users/bob/Documents/work/@@@ ontologies and misc sources/SNOMED/SNOMEDCT_INT_202210/snomed-database-loader/PostgreSQL/tmp_extracted/sct2_StatedRelationship_Full_INT_20221031.txt'
-e WITH (FORMAT csv, HEADER true, DELIMITER E'  ', QUOTE E');
-e 
-e COPY relationship_f
-e FROM '/Users/bob/Documents/work/@@@ ontologies and misc sources/SNOMED/SNOMEDCT_INT_202210/snomed-database-loader/PostgreSQL/tmp_extracted/sct2_Relationship_Full_INT_20221031.txt'
-e WITH (FORMAT csv, HEADER true, DELIMITER E'  ', QUOTE E');
-e 
-e COPY textdefinition_f
-e FROM '/Users/bob/Documents/work/@@@ ontologies and misc sources/SNOMED/SNOMEDCT_INT_202210/snomed-database-loader/PostgreSQL/tmp_extracted/sct2_TextDefinition_Full-en_INT_20221031.txt'
-e WITH (FORMAT csv, HEADER true, DELIMITER E'  ', QUOTE E');
-e 
-e COPY attributevaluerefset_f
-e FROM '/Users/bob/Documents/work/@@@ ontologies and misc sources/SNOMED/SNOMEDCT_INT_202210/snomed-database-loader/PostgreSQL/tmp_extracted/der2_cRefset_AttributeValueFull_INT_20221031.txt'
-e WITH (FORMAT csv, HEADER true, DELIMITER E'  ', QUOTE E');
-e 
-e COPY langrefset_f
-e FROM '/Users/bob/Documents/work/@@@ ontologies and misc sources/SNOMED/SNOMEDCT_INT_202210/snomed-database-loader/PostgreSQL/tmp_extracted/der2_cRefset_LanguageFull-en_INT_20221031.txt'
-e WITH (FORMAT csv, HEADER true, DELIMITER E'  ', QUOTE E');
-e 
-e COPY associationrefset_f
-e FROM '/Users/bob/Documents/work/@@@ ontologies and misc sources/SNOMED/SNOMEDCT_INT_202210/snomed-database-loader/PostgreSQL/tmp_extracted/der2_cRefset_AssociationFull_INT_20221031.txt'
-e WITH (FORMAT csv, HEADER true, DELIMITER E'  ', QUOTE E');
-e 

[siamchen]

I have no idea where this tmp_loader.sql come from but mate, you need to remove all those -e from the file. Also, it's not right for QUOTE E'. If the single quote has been used as a QUOTE mark, then try to use it as QUOTE E'\''

[pgwilliams]

The -e was coming from the shell script echo commands, which is a flag so that escaped characters are interpreted, so the difference between: echo -e "foo\tbar" which gives foo bar as output and echo "foo\tbar" which gives you that literal string back foo\tbar

I'd be interested to know what OS this was being run on.

[rjalexa]

tmp_loader.sql is generated by the load_release-postgresql.sh script Environment is MacOS 12.6 with zsh Closed since I switched to MySQL out of urgency (and opened a new issue for it regardin transitive closures) Thank you very much for your support

[pgwilliams]

Hmm, maybe I was wrong about the source of the -e problem then, because echo -e behaves as expected when I try it on my Mac under zsh. I'll try it out, but some other time because you said your MySQL issue was more pressing.