I use a docker image (docker pull ubuntu
), I installed postgresql via apt-get and then want to run the following script:
LOAD CSV
FROM 'geneset.csv' (a,b,c,d,e,f,g)
INTO postgresql:///genedb?csv (a,b,c,d,e,f,g)
WITH truncate,
skip header = 1,
fields optionally enclosed by '"',
fields escaped by backslash-quote,
fields terminated by '\t'
SET client_encoding to 'latin1',
work_mem to '80MB',
standard_conforming_strings to 'on'
BEFORE LOAD DO
$$ drop table if exists csv; $$,
$$ create table csv (
a bigint,
b text,
c text,
d text,
e text,
f text,
g text
);
$$;
For executing the script I type into the shell: pgloader csv.load
to execute the code above.
Unfortunately, I always get the warning:
WARNING:
Couldn't re-execute SBCL with proper personality flags (/proc isn't mounted? setuid?)
Trying to continue anyway.
An unhandled error condition has been signalled:
Failed to connect to pgsql at :UNIX (port 5432): The value of CL-POSTGRES::USER is NIL, which is not of type STRING.
;
; compilation unit aborted
; caught 1 fatal ERROR condition
I have already installed apt-get -y install sbcl gcl
but the error does not disappear. Any suggestions to solve that problem? I ve found out that this problem occurs very often on docker images...
Edit:
Can I basically setup a ubuntu 16.04 docker image and install postresql and pdgloader via apt-get? Is my approach ok? I only want to run the database queries locally in the image...