ncbi-entrez-direct 7.40.20170928+ds-1 / usr / bin / einfo

#!/usr/bin/perl -w
# Detect whether to run einfo.epub or edirect -info.

use strict;

my $usage = <<EOF;
USAGE: einfo [<epub einfo options>] <filename>
 -or-  einfo [<NCBI Entrez Direct einfo options>]

per, respectively,

    einfo.epub -h (or man einfo.epub)
    edirect -info -help (or man einfo)
EOF

if ( !@ARGV  ||  ! -x '/usr/bin/einfo.epub' ) {
    ExecNCBI();
} elsif (grep /--?help/, @ARGV) {
    print $usage;
    exit 0;
}

my $epub_flags = 'qvdp';
my $epub_keys  = 't';

my %ncbi_supported = (
    'db'          => 's',
    'dbs'         => undef,
    'fields'      => undef,
    'links'       => undef,
    'email'       => 's',
    'tool'        => 's',
    'help'        => undef,
    'silent'      => undef,
    'verbose'     => undef,
    'debug'       => undef,
    'log'         => undef,
    'http'        => 's',
    'https'       => 's',
    'alias'       => 's',
    'base'        => 's');

my %ncbi_abbrev = ();
{
    my @names = sort keys %ncbi_supported;
    unshift @names, '';
    push @names, '';
    my $i;
    my $j;
    for ($i = 1;  $i + 1 < @names;  ++$i) {
        my $name      = $names[$i];
        my $prev_name = $names[$i - 1];
        my $next_name = $names[$i + 1];
        for ($j = 1;  $j < length($name);  ++$j) {
            my $abbrev = substr($name, 0, $j);
            if ($abbrev ne substr($prev_name, 0, $j)
                &&  $abbrev ne substr($next_name, 0, $j)) {
                $ncbi_abbrev{$abbrev} = $name;
            }
        }
    }
}

my @epub_red_flags;
my @epub_yellow_flags;
my $epub_value_expected;
my $epub_query;
my @ncbi_red_flags;
my @ncbi_yellow_flags;
my $ncbi_value_expected;

for (@ARGV) {
    if (/^-\d+$/  ||  !/^-/) {
        if ( !defined $epub_value_expected ) {
            if (defined $epub_query) {
                push @epub_red_flags, "$epub_query $_";
            }
            $epub_query = $_;
        }
        if ( !defined $ncbi_value_expected ) {
            push @ncbi_red_flags, $_;
        }
        undef $epub_value_expected;
        undef $ncbi_value_expected;
    } else {
        my $epub_type;
        if (defined $epub_value_expected) {
            push @epub_red_flags, "$epub_value_expected $_";
            $epub_type = 'nominal-value';
            undef $epub_value_expected;
        } elsif (/^-[ho]$/  ||  /^-[$epub_flags]*(?:[$epub_keys].+)?$/) {
            $epub_type = 'flag';
        } elsif (/^-[$epub_flags]*([$epub_keys])$/) {
            $epub_type = 'key';
            $epub_value_expected = "-$1";
        } else {
            $epub_type = 'invalid';
            push @epub_red_flags, $_;
        }

        my $ncbi_type;
        if (defined $ncbi_value_expected) {
            push @ncbi_red_flags, "$ncbi_value_expected $_";
            $ncbi_type = 'nominal-value';
            undef $ncbi_value_expected;
        } elsif (/^--?([^=]+)(=.*)?/) {
            my $base = lc($1);
            my $has_value = defined $2;
            if (exists $ncbi_abbrev{$base}) {
                $base = $ncbi_abbrev{$base};
                push @ncbi_yellow_flags, $_;
            }
            if ( !exists $ncbi_supported{$base}
                 ||  ($has_value  &&  !defined $ncbi_supported{$base})) {
                $ncbi_type = 'invalid';
                push @ncbi_red_flags, $_;
            } else {
                if (lc($1) eq $base  &&  $1 =~ /[A-Z]/) {
                    # Worry about capitalization only if otherwise OK
                    push @ncbi_yellow_flags, $_;
                }
                if (defined $ncbi_supported{$base}  &&  !$has_value) {
                    $ncbi_type = 'key';
                    $ncbi_value_expected = $_;
                } else {
                    $ncbi_type = 'flag';
                }
            }
        } else {
            $ncbi_type = 'invalid';
            push @ncbi_red_flags, $_;
        }

        if ($epub_type =~ /^[fk]/  &&  $ncbi_type =~ /^[fk]/) {
            # Could technically be valid for einfo.epub, but far likelier
            # to have been intended for edirect -info.
            push @epub_yellow_flags, $_;
        }
    }
}

if ( !defined $epub_query ) {
    push @epub_red_flags, "no filename";
}
if (defined $epub_value_expected) {
    push @epub_red_flags, "$epub_value_expected with no value";
}
if (defined $ncbi_value_expected) {
    push @ncbi_red_flags, "$ncbi_value_expected with no value";
}

my $epub_red  = @epub_red_flags;
my $epub_ylw  = @epub_yellow_flags;
my $ncbi_red   = @ncbi_red_flags;
my $ncbi_ylw   = @ncbi_yellow_flags;

if ($epub_red  &&  !$ncbi_red) {
    # clear-cut, even if there happen to be NCBI yellow flags
    ExecNCBI();
} elsif ($ncbi_red  &&  !$epub_red) {
    ExecEpub();
}

my $epub_misgivings = "EPUB misgivings ($epub_red major, $epub_ylw minor):";
my $ncbi_misgivings  = "NCBI misgivings ($ncbi_red major, $ncbi_ylw minor):";

for (@epub_red_flags) {
    $epub_misgivings .= "\n  $_ (major)";
}
for (@epub_yellow_flags) {
    $epub_misgivings .= "\n  $_ (minor)";
}
for (@ncbi_red_flags) {
    $ncbi_misgivings .= "\n  $_ (major)";
}
for (@ncbi_yellow_flags) {
    $ncbi_misgivings .= "\n  $_ (minor)";
}

if ($ncbi_red > $epub_red
    ||  ($ncbi_red == $epub_red  &&  $ncbi_ylw > $epub_ylw)) {
    if ($epub_red  ||  $epub_ylw) {
        warn <<EOF;
Launching EPUB einfo rather than NCBI einfo despite misgivings,
due to more severe misgivings about NCBI syntax compatibility.  If you
meant to run NCBI einfo, please explicitly run it via edirect -info.
$ncbi_misgivings
$epub_misgivings
EOF
    }
    ExecEpub();
}

if ($epub_red > $ncbi_red
    ||  ($epub_red == $ncbi_red  &&  $epub_ylw > $ncbi_ylw)) {
    if ($ncbi_red  ||  $ncbi_ylw) {
        warn <<EOF;
Launching NCBI einfo rather than EPUB einfo despite misgivings,
due to more severe misgivings about EPUB syntax compatibility.  If you
meant to run EPUB einfo, please explicitly run it via einfo.epub.
$epub_misgivings
$ncbi_misgivings
EOF
    }
    ExecNCBI();
}

if ($epub_red) {
    die <<EOF;
Usage equally bad for both EPUB einfo and NCBI einfo.  Please double
check your usage or explicitly run einfo.epub or edirect -info.
$epub_misgivings
$ncbi_misgivings

$usage
EOF
} elsif ($epub_ylw) {
    die <<EOF;
Usage equally suspect (but still technically valid, at least to first
approximation) for both EPUB einfo and NCBI einfo.  Please double
check your usage or explicitly run einfo.epub or edirect -info.
$epub_misgivings
$ncbi_misgivings

$usage
EOF
} else {
    die <<EOF;
Usage apparently valid (at least to first approximation) for both
EPUB einfo and NCBI einfo.  Please disambiguate your usage or
explicitly run einfo.epub or edirect -info.
EOF
}

sub ExecEpub
{
    # exec {'/usr/bin/einfo.epub'} ('/usr/bin/einfo', @ARGV);
    exec('/usr/bin/einfo.epub', @ARGV);
}
sub ExecNCBI
{
    exec('/usr/bin/edirect', '-info', @ARGV);
}