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problem using DBI to COPY FROM STDIN on a Mac

From: Scott Cain <cain(at)cshl(dot)org>
To: pgsql-interfaces(at)postgresql(dot)org
Subject: problem using DBI to COPY FROM STDIN on a Mac
Date: 2004-09-10 14:30:03
Message-ID: 1094826603.1504.119.camel@localhost.localdomain (view raw or flat)
Lists: pgsql-interfaces

I've written a perl script that uses DBD::Pg func calls to do COPY FROM
STDIN.  It does several copies as a single transaction. While this works
fine on my Linux box with Posgresql 7.4.2, it seems to hang while
finishing up the last copy or closing the transaction on my Mac (also
7.4.2).  By 'hang', I mean that the postgres process runs on
indefinitely consuming 90% of the cpu.  The setups are similar; I've
done similar tuning to both databases (though, admittedly, I don't know
as much about doing this for a Mac).  Generally, Postgresql is a little
slower on the Mac, but I haven't had any real problems with it.

Any ideas?  The script is copied below, and the part that does the copy
and commit is at the bottom.

Thanks much,

use strict;
use DBI;
use Chado::LoadDBI;
use Bio::Tools::GFF;
use Getopt::Long;
# parents come before features
# no dbxref_id allowed
# no residues allowed
# reference sequences already in db!
=head1 NAME
                                                                                             - Bulk loads gff3 files into a chado database.
 --gfffile     The file containing GFF3 (optional, can read from stdin)
 --organism    The organism for the data
 --dbname      Database name
 --dbuser      Database user name
 --dbpass      Database password
 --dbhost      Database host
 --dbport      Database port
Note that all of the arguments that begin 'db' can be provided by default
by Bio::GMOD::Config, which was installed when 'make install' was run.
=head2 NOTES
=item The ORGANISM table
This script assumes that the organism table is populated with information
about your organism.  If you are unsure if that is the case, you can
execute this command from the psql command-line:
  select * from organism;
If you do not see your organism listed, execute this command to insert it:
  insert into organism (abbreviation, genus, species, common_name)
                values ('H.sapiens', 'Homo','sapiens','Human');
substituting in the appropriate values for your organism.
=item GFF3
The GFF in the datafile must be version 3 due to its tighter control of
the specification and use of controlled vocabulary.  Accordingly, the names
of feature types must be exactly those in the Sequence Ontology, not the
synonyms and not the accession numbers (SO accession numbers may be
supported in future versions of this script).  There are several caveates
about the GFF3 that will work with this bulk loader:
=item Reference sequences
This loader requires that the reference sequence features be already
loaded into the database (for instance, by using
Future versions of this bulk loader will not have this restriction.
=item Parents/children order
Parents must come before children in the GFF file.
=item Several GFF tags (both reserved and custom) not supported
These include:
=item Dbxref
=item Target
=item Gap
=item Any custom (ie, lowercase-first) tag
=item No sequences
This loader does not load DNA sequences, though chromosome sequences
can be loaded with gmod_load_gff3 when the reference sequence features
are loaded.
=head1 AUTHORS
Allen Day E<lt>allenday(at)ucla(dot)eduE<gt>, Scott Cain E<lt>cain(at)cshl(dot)orgE<gt>
Copyright (c) 2004
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.

if (eval {require Bio::GMOD::Config;
          require Bio::GMOD::DB::Config;
          1;  } ) {
    my $gmod_conf = $ENV{'GMOD_ROOT'} ?
                    Bio::GMOD::Config->new($ENV{'GMOD_ROOT'}) :
    my $db_conf = Bio::GMOD::DB::Config->new($gmod_conf,'default');
    $DBNAME = $db_conf->name();
    $DBUSER = $db_conf->user();
    $DBPASS = $db_conf->password();
    $DBHOST = $db_conf->host();
    $DBPORT = $db_conf->port();
    'organism:s' => \$ORGANISM,
    'gfffile:s'  => \$GFFFILE,
    'dbname:s'   => \$DBNAME,
    'dbuser:s'   => \$DBUSER,
    'dbpass:s'   => \$DBPASS,
    'dbhost:s'   => \$DBHOST,
    'dbport:s'   => \$DBPORT,
) or ( system( 'pod2text', $0 ), exit -1 );;
$ORGANISM ||='human';
$GFFFILE  ||='stdin';  #nobody better name their file 'stdin'
$DBNAME   ||='chado';
$DBPASS   ||='';
$DBHOST   ||='localhost';
$DBPORT   ||='5432';
my %src = ();
my %type = ();
my $pub; # for holding null pub object
my %synonym;
my $gff_source_db;
my %gff_source;
my $source_success = 1; #indicates that GFF_source is in db table
my @tables = (
my %files = (
   feature              => "feature.tmp",
   featureloc           => "featureloc.tmp",
   feature_relationship => "featurerel.tmp",
   featureprop          => "featureprop.tmp",
   feature_cvterm       => "featurecvterm.tmp",
   synonym              => "synonym.tmp",
   feature_synonym      => "featuresynonym.tmp",
   feature_dbxref       => "featuredbxref.tmp",
my %sequences = (
   feature              => "feature_feature_id_seq",
   featureloc           => "featureloc_featureloc_id_seq",
   feature_relationship => "feature_relationship_feature_relationship_id_seq",
   featureprop          => "featureprop_featureprop_id_seq",
   feature_cvterm       => "feature_cvterm_feature_cvterm_id_seq",
   synonym              => "synonym_synonym_id_seq",
   feature_synonym      => "feature_synonym_feature_synonym_id_seq",
   feature_dbxref       => "feature_dbxref_feature_dbxref_id_seq",
my %copystring = (
   feature              => "(feature_id,organism_id,name,uniquename,type_id)",
   featureloc           => "(featureloc_id,feature_id,srcfeature_id,fmin,fmax,strand,phase)",
   feature_relationship => "(feature_relationship_id,subject_id,object_id,type_id)",
   featureprop          => "(featureprop_id,feature_id,type_id,value,rank)",
   feature_cvterm       => "(feature_cvterm_id,feature_id,cvterm_id,pub_id)",
   synonym              => "(synonym_id,name,type_id,synonym_sgml)",
   feature_synonym      => "(feature_synonym_id,synonym_id,feature_id,pub_id)",
   feature_dbxref       => "(feature_dbxref_id,feature_id,dbxref_id)",
my $db = DBI->connect("dbi:Pg:dbname=$DBNAME;port=$DBPORT;host=$DBHOST",
                       $DBUSER,$DBPASS, {AutoCommit => 0});
my $sth = $db->prepare("select nextval('$sequences{feature}')");
my($nextfeature) = $sth->fetchrow_array();
$sth = $db->prepare("select nextval('$sequences{featureloc}')");
my($nextfeatureloc) = $sth->fetchrow_array();
$sth = $db->prepare("select nextval('$sequences{feature_relationship}')");
my($nextfeaturerel) = $sth->fetchrow_array();
$sth = $db->prepare("select nextval('$sequences{featureprop}')");
my($nextfeatureprop) = $sth->fetchrow_array();
$sth = $db->prepare("select nextval('$sequences{feature_cvterm}')");
my($nextfeaturecvterm) = $sth->fetchrow_array();
$sth = $db->prepare("select nextval('$sequences{synonym}')");
my($nextsynonym) = $sth->fetchrow_array();
$sth = $db->prepare("select nextval('$sequences{feature_synonym}')");
my($nextfeaturesynonym) = $sth->fetchrow_array();
$sth = $db->prepare("select nextval('$sequences{feature_dbxref}')");
my($nextfeaturedbxref) = $sth->fetchrow_array();
$sth = $db->prepare("select cvterm_id from cvterm where name = 'part_of'");
my($part_of) = $sth->fetchrow_array();
my($organism) = Chado::Organism->search( common_name => "$ORGANISM" );
$organism or die "organism not found in the database";
open F   ,  ">$files{feature}";
open FLOC,  ">$files{featureloc}";
open FREL,  ">$files{feature_relationship}";
open FPROP, ">$files{featureprop}";
open FCV,   ">$files{feature_cvterm}";
open SYN,   ">$files{synonym}";
open FS,    ">$files{feature_synonym}";
open FDBX,  ">$files{feature_dbxref}";
my $gffio = Bio::Tools::GFF->new(-fh => \*STDIN, -gff_version => 3);
while(my $feature = $gffio->next_feature()){
  my $type = $type{$feature->primary_tag};
    ($type) = Chado::Cvterm->search( name => $feature->primary_tag );
    $type{$feature->primary_tag} = $type->id;
  die "no cvterm for ".$feature->primary_tag unless $type;
  my $src = $src{$feature->seq_id};
    if($feature->seq_id eq '.'){
      $src = '\N';
    } else {
      ($src) = Chado::Feature->search( uniquename => $feature->seq_id )
            || Chado::Feature->search( name => $feature->seq_id );
      if ($src->isa('Class::DBI::Iterator')) {
        my @sources;
        while (my $tmp = $src->next) {
          push @sources, $tmp;
        die "more that one source for ".$feature->seq_id if (@sources>1);
        $src{$feature->seq_id} = $sources[0]->id;
      } else {
        $src{$feature->seq_id} = $src->id;
      $src = $src{$feature->seq_id};
  die "no feature for ".$feature->seq_id unless $src;
    my $pname = undef;
    my($pname) = $feature->get_tag_values('Parent');
    my $parent = $src{$pname};
      ($parent) = Chado::Feature->search( uniquename => $pname )
        || Chado::Feature->search( name => $pname );
      $src{$pname} = $parent->id;
    die "no parent ".$pname unless $parent;
    print FREL join("\t", ($nextfeaturerel,$nextfeature,$parent,$part_of)),"\n";
  my($name) = $feature->has_tag('Name') ? $feature->get_tag_values('Name') : '\N';
  my($uniquename) = $feature->has_tag('ID') ? $feature->get_tag_values('ID') : $nextfeature;
  #my $uniquename = $nextfeature;
  $src{$uniquename} = $nextfeature;
  print F join("\t", ($nextfeature, $organism->id, $name, $uniquename, $type)),"\n";
#need to convert from base to interbase coords
  my $start = $feature->start eq '.' ? '\N' : ($feature->start - 1);
  my $end   = $feature->end   eq '.' ? '\N' : $feature->end;
  my $frame = $feature->frame eq '.' ? '\N' : $feature->frame;
  print FLOC join("\t", ($nextfeatureloc, $nextfeature, $src, $start, $end, $feature->strand, $frame)),"\n";
  if ($feature->has_tag('Note') or $feature->has_tag('note')) {
    my @notes;
    push @notes, $feature->get_tag_values('Note') if $feature->has_tag('Note');
    push @notes, $feature->get_tag_values('note') if $feature->has_tag('note');
    my $rank = 0;
    foreach my $note (@notes) {
      ($type{'Note'}) = Chado::Cvterm->search( name => 'Note')
          unless $type{'Note'};
      print FPROP join("\t",($nextfeatureprop,$nextfeature,$type{'Note'}->id,$note,$rank)),"\n";
  my $source = $feature->source_tag;
  if ( $source_success && $source && $source ne '.') {
    unless ($gff_source_db) {
      ($gff_source_db) = Chado::Db->search({ name => 'GFF_source' });
    if ($gff_source_db) {
      unless ($gff_source{$source}) {
        $gff_source{$source} = Chado::Dbxref->find_or_create( {
            db_id     => $gff_source_db->id,
            accession => $source,
        } );
      my $dbxref_id = $gff_source{$source}->id;
      print FDBX join("\t",($nextfeaturedbxref,$nextfeature,$dbxref_id)),"\n";
    } else {
      $source_success = 0; #geting GFF_source failed, so don't try anymore
  if ($feature->has_tag('Ontology_term')) {
    my @cvterms = $feature->get_tag_values('Ontology_term');
    my %count;
    my @ucvterms = grep {++$count{$_} < 2} @cvterms;
    foreach my $term (@ucvterms) {
      unless ($type{$term}) {
        my ($dbxref) = Chado::Dbxref->search( accession => $term );
        warn "couldn't find $term in dbxref\n" and next unless $dbxref;
        ($type{$term}) = Chado::Cvterm->search( dbxref_id => $dbxref->id );
        warn "couldn't find $term's cvterm_id in cvterm table\n"
          and next unless $type{$term};
      unless ($pub) {
        ($pub) = Chado::Pub->search( miniref => 'null' );
        $pub = $pub->id; #no need to keep whole object when all we want is the id
      print FCV join("\t",($nextfeaturecvterm,$nextfeature,$type{$term}->id,$pub)),"\n";;
  my @aliases;
  if ($feature->has_tag('Alias')) {
    @aliases =   $feature->get_tag_values('Alias');
  if ($name ne '\N') {
    push @aliases, $name;
  #need to unique-ify the list
  my %count;
  my @ualiases = grep {++$count{$_} < 2} @aliases;
  foreach my $alias (@ualiases) {
    unless ($synonym{$alias}) {
      unless ($type{'synonym'}) {
        ($type{'synonym'}) = Chado::Cvterm->search( name => 'synonym' );
        warn "unable to find synonym type in cvterm table"
            and next unless $type{'synonym'};
      print SYN join("\t", ($nextsynonym,$alias,$type{'synonym'}->id,$alias)),"\n";
      unless ($pub) {
        ($pub) = Chado::Pub->search( miniref => 'null' );
        $pub = $pub->id; #no need to keep whole object when all we want is the id
      print FS join("\t", ($nextfeaturesynonym,$nextsynonym,$nextfeature,$pub)),"\n";
#        warn "alias:$alias,name:$name\n";
      $synonym{$alias} = $nextsynonym;
    } else {
      print FS join("\t", ($nextfeaturesynonym,$synonym{$alias},$nextfeature,$pub)),"\n";
#        warn "in seenit, alias:$alias, name:$name\n";
my %nextvalue = (
   "feature"              => $nextfeature,
   "featureloc"           => $nextfeatureloc,
   "feature_relationship" => $nextfeaturerel,
   "featureprop"          => $nextfeatureprop,
   "feature_cvterm"       => $nextfeaturecvterm,
   "synonym"              => $nextsynonym,
   "feature_synonym"      => $nextfeaturesynonym,
   "feature_dbxref"       => $nextfeaturedbxref,
print F    "\\.\n\n";
print FLOC "\\.\n\n";
print FREL "\\.\n\n";
print FPROP "\\.\n\n";
print FCV "\\.\n\n";
print SYN "\\.\n\n";
print FS "\\.\n\n";
print FDBX "\\.\n\n";
close F;
close FLOC;
close FREL;
close FPROP;
close FCV;
close SYN;
close FS;
close FDBX;
foreach my $table (@tables) {
warn "Optimizing database (this may take a while) ...\n";
print STDERR "  (";
foreach (@tables) {
  print STDERR "$_ ";
  $db->do("VACUUM ANALYZE $_");
print STDERR ") Done.\n";
warn "Deleting temporary files\n";
foreach (@tables) {
  unlink $files{$_};
warn "\nWhile this script has made an effort to optimize the database, you\n"
    ."should probably also run VACUUM FULL ANALYZE on the database as well\n";
sub copy_from_stdin {
  my $dbh      = shift;
  my $table    = shift;
  my $fields   = shift;
  my $file     = shift;
  my $sequence = shift;
  my $nextval  = shift;
  warn "Loading data into $table table ...\n";
  my $query = "COPY $table $fields FROM STDIN;";
  my $sth = $dbh->prepare($query);
  open FILE, $file;
  while (<FILE>) {
    $dbh->func($_, 'putline');
  $dbh->func('endcopy');  # no docs on this func--got from google
  close FILE;
  #update the sequence so that later inserts will work
  $dbh->do("SELECT setval('public.$sequence', $nextval) FROM $table");

Scott Cain, Ph. D.                                         cain(at)cshl(dot)org
GMOD Coordinator (                     216-392-3087
Cold Spring Harbor Laboratory

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