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lib/Convert/Pheno/IO/CSVHandler.pm  view on Meta::CPAN

    my $arg      = shift;
    my $filepath = $arg->{in};
    my $self     = $arg->{self};

# Before resorting to writting this subroutine I performed an exhaustive search on CPAN:
# - Tested MySQL::Dump::Parser::XS but I could not make it work...
# - App-MysqlUtils-0.022 has a CLI utility (mysql-sql-dump-extract-tables)
# - Of course one can always use *nix tools (sed, grep, awk, etc) or other programming languages....
# Anyway, I ended up writting the parser myself...
# The parser is based in reading COPY paragraphs from PostgreSQL dump by using Perl's paragraph mode  $/ = "";
# NB: Each paragraph (TABLE) is loaded into memory. Not great for large files.

    # Define variables that modify what we load
    my $max_lines_sql = $self->{max_lines_sql};
    my @omop_tables   = @{ $self->{omop_tables} };

    # Set record separator to paragraph
    local $/ = "";

#COPY "OMOP_cdm_eunomia".attribute_definition (attribute_definition_id, attribute_name, attribute_description, attribute_type_concept_id, attribute_syntax) FROM stdin;
# ......
# \.

    # Start reading the SQL dump
    my $fh = open_filehandle( $filepath, 'r' );

    # We'll store the data in the hashref $data
    my $data = {};