missing fields in queries

[Jiagengjie]

there are some fields such as 20256 (Forced expiratory volume in 1-second (FEV1) Z-score) that cannot be queried via ukbREST. If I do,

 

curl -G -u XXXX

 

 

Then, I got error as:

 

{

  "error_type": "SQL_EXECUTION_ERROR", 

  "message": "(psycopg2.ProgrammingError) syntax error at or near \"\\\"\nLINE 2:             select eid,c20256_\\d+_\\d+\n                                      ^\n [SQL: '\\n            select eid,c20256_\\\\d+_\\\\d+\\n            from all_eids\\n            \\n        ']", 

  "status_code": 400

}

 

So is it possible that ukbREST missed some fields?

Thanks, again.

[Milton Pividori]

While it is possible that you don't have the data-field queried in your dataset, it's not the case in this example.

What's the exact command you are using? Because in the error message I can see that you provided a regular expression with "\d+", but that's not supported in the standard "columns" parameter; you need to use the "ecolumns" parameter for that. Ccheck out the documentation at the wiki (https://github.com/hakyimlab/ukbrest/wiki), the link "Different phenotype query types and output formats".

But again, you don't need to manually query each array to see if the sample has reported a disease (although you can do it, it's easier to use the YAML file).