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MRUEDA / Convert-Pheno-0.28 / t / stream.t 

            

              
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#!/usr/bin/env perl
use strict;
use warnings;
use lib ( './lib', '../lib' );
use feature qw(say);
use Data::Dumper;
use File::Temp qw{ tempfile };    # core
#use Test::More tests => 3;
use Test::More qw(no_plan);
use IO::Uncompress::Gunzip;       # core
use File::Compare;
use Convert::Pheno;
my $ohdsi_db = 'share/db/ohdsi.db';
# Test 1
use_ok('Convert::Pheno') or exit;
# Test 2
my $method = 'omop2bff';
{
    my $out = 't/omop2bff/out/individuals_drug_exposure.json.gz';
    my ( undef, $tmp_file ) =
      tempfile( DIR => 't', SUFFIX => ".json.gz", UNLINK => 1 );
    my $convert = Convert::Pheno->new(
        {
            in_file           => undef,
            in_files          => ['t/omop2bff/in/gz/omop_cdm_eunomia.sql.gz'],
            out_file          => $tmp_file,
            redcap_dictionary => undef,
            mapping_file      => undef,
            self_validate_schema => undef,
            schema_file          => 'schema/mapping.json',
            in_textfile          => 1,
            stream               => 1,
            omop_tables          => ['DRUG_EXPOSURE'],
            max_lines_sql        => 2700,
            sep                  => ',',
            test                 => 1,
            search               => 'exact',
            method               => $method
        }
    );
    $convert->$method;
# Does not work with gzipped files
#ok( compare( $out, $tmp_file ) == 0,  qq/$method stream gzipped IO drug_exposure/);
# Open the first file for reading and uncompress it
    my $z1 = new IO::Uncompress::Gunzip $out;
    # Open the second file for reading and uncompress it
    my $z2 = new IO::Uncompress::Gunzip $tmp_file;
    # Read the contents of the first file
    my $content1 = do { local $/; <$z1> };
    # Read the contents of the second file
    my $content2 = do { local $/; <$z2> };
    # Compare the contents of the two files
    is( $content1, $content2, qq/$method stream gzipped IO drug_exposure/ );
    # Close the files
    $z1->close();
    $z2->close();
}
# Test 3
{
    if ( -f $ohdsi_db ) {
        my $out = 't/omop2bff/out/individuals_csv.json.gz';
        my ( undef, $tmp_file ) =
          tempfile( DIR => 't', SUFFIX => ".json.gz", UNLINK => 1 );
        my $convert = Convert::Pheno->new(
            {
                in_file  => undef,
                in_files => [
                    't/omop2bff/in/gz/PERSON.csv.gz',
                    't/omop2bff/in/gz/CONCEPT.csv.gz',
                    't/omop2bff/in/gz/DRUG_EXPOSURE.csv.gz'
                ],
                out_file             => $tmp_file,
                redcap_dictionary    => undef,
                mapping_file         => undef,
                self_validate_schema => undef,
                schema_file          => 'schema/mapping.json',
                in_textfile          => 1,
                ohdsi_db             => 1,
                stream               => 1,
                omop_tables          => [],
                max_lines_sql        => 2700,
                sep                  => "\t",
                test                 => 1,
                search               => 'exact',
                method               => $method
            }
        );
        $convert->$method;
# Does not work with gzipped files
#ok( compare( $out, $tmp_file ) == 0,  qq/$method stream gzipped IO drug_exposure/);
# Open the first file for reading and uncompress it
        my $z1 = new IO::Uncompress::Gunzip $out;
        # Open the second file for reading and uncompress it
        my $z2 = new IO::Uncompress::Gunzip $tmp_file;
        # Read the contents of the first file
        my $content1 = do { local $/; <$z1> };
        # Read the contents of the second file
        my $content2 = do { local $/; <$z2> };
        # Compare the contents of the two files
      SKIP: {
            skip qq{because <$ohdsi_db> is required with <ohdsi_db>}, 1
              unless -f $ohdsi_db;
            is( $content1, $content2, qq/$method stream gzipped IO CSV/ );
        }
        # Close the files
        $z1->close();
        $z2->close();
    }
}