loadAseqsJson.pl

#!/usr/bin/perl

use strict;
use warnings;
use JSON;

use FindBin '$Bin';
use lib "$Bin";
use Common;


my $usage = <<USAGE;
Usage: $0 <database json>

  <database json> should consist of an entire json object per line

  Loads into the aseqs collection.

USAGE

my $g_File = shift or die $usage;

my $g_colFlag = "aseqs";
GetOptions("col=s", \$g_colFlag);

my $aseqs = &Common::aseqs($g_colFlag);

#my $fh = &Common::openFileOrGzFile($g_File);

&Common::startTicker(10000);
my $count = 0;
open(FH,"|/usr/bin/tac $g_File");
while (<FH>) {
    my $json = $_;
#print("hey");
#    my $son = substr($json,23);
#    print($son);
#    $json = $son;
    #my $aseq = from_json(substr($json,23));
    my $aseq = from_json(substr($_,23));
    #print("$aseq->{_id}\n");
    if ($aseqs->find_one({_id => $aseq->{_id}})) {
        #print("$aseq->{_id}\n");
	
	#print($count++);
        # This assumes that the $aseq->{x}->{gi} is the most recent gi
	# list and will overwrite any pre-existing ones.
	#my %set = (
	#    'x.gi' => $aseq->{x}->{gi}
	#);
	#$aseqs->update({_id => $aseq->{_id}}, {'$set' => \%set});
	&Common::tick();
	next;
    }
    else {
    print("$count\t$aseq->{_id}\n________________________\n");
    $count++;
    #print($aseq); 
    my $hasUndoneData = index($aseq->{_s}, '-') != -1;
    if ($hasUndoneData) { $aseq->{$Common::paddingKey} =
    $Common::padding{basic}->{buffer}; }

    $aseqs->insert($aseq);
    &Common::removePadding($aseqs, $aseq->{_id});
    &Common::tick();
    }
}