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                "\" is missing."
            );

            $allWantedPresent = 0;
        }
    }
    
    # Next, check whether there are any unrecognised arguments. Just warn about
    # them if so.
    foreach my $argName ( sort keys %{ $argsHash } ) {

        unless( $wantedArgNames{ $argName } ) {

            $logger->warn(
                "Argument \"",
                $argName,
                "\" is not recognised."
            );
        }
    }
    
    # Now return the flag to show whether all wanted arguments are present or
    # not.
    return $allWantedPresent;
}


# REST call running -- common to all the querying functions.
sub _run_rest_call {

    my ( $self, $args ) = @_;

    my $logger = $self->get_log_writer;

    my $userAgent = $self->get_user_agent;

    # Start building the query URL.
    my $url = $self->get_api_base . "/json/";
    
    # If we're passed a minimum percentage of mapped reads, add this to the URL
    # next.
    if( defined( $args->{ "minimum_mapped_reads" } ) ) {

        $url .= $args->{ "minimum_mapped_reads" } . "/";
    }
    
    # Add the function name and argument to the end of the URL.
    $url .= $args->{ "function_name" };

    if( $args->{ "function_argument" } ) {

        $url .= "/" . $args->{ "function_argument" };
    }

    # Run HTTP GET request.
    my $response = $userAgent->get( $url );

    # If the request was successful, return the parsed JSON.
    if( $response->is_success ) {

        return parse_json( $response->decoded_content );
    }
    # Otherwise, log an error and return undef.
    else {
        
        $logger->error(
            "Problem retrieving URL: ",
            $url,
            " . Response from server: ",
            $response->status_line
        );

        return;
    }
}


# Check that the run organism name is allowed. This checks the passed string
# against the keys of the hash stored in the "run_organism_list" attribute.
sub _organism_name_ok {

    my ( $self, $organism, $type ) = @_;

    my $logger = $self->get_log_writer;

    my $organismList = ( $type eq "run" ? $self->get_run_organism_list : $self->get_expression_organism_list );

    if( $organismList->{ $organism } ) {

        return 1;
    }
    else {

        $logger->error(
            "Organism \"",
            $organism,
            "\" is not an allowed organism. Check organisms against the run_organism_list attribute."
        );

        return;
    }
}


=head1 AUTHOR

Maria Keays <mkeays@cpan.org>

The above email should be used for feedback about the Perl module only. All
mail regarding the RNA-seq analysis API itself should be directed to
<rnaseq@ebi.ac.uk>.

=cut

1;