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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...

j35t3r
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0 Answers0