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Commit cc88db72 authored by Patrick Meidl's avatar Patrick Meidl
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committing intermediate state of module before rewriting it to use lightweight... 

committing intermediate state of module before rewriting it to use lightweight feature object for caching
parent d3383f5d
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modules/Bio/EnsEMBL/IdMapping/Cache.pm
+ 83
− 66
View file @ cc88db72
......@@ -89,14 +89,17 @@ sub new {
sub cache_file_exists {
my $self = shift;
my $type = shift;
throw("You must provide a cache type (old|new).") unless $type;
my $cache_path = $self->cache_path;
my $cache_path = $self->cache_path($type);
if (-s $cache_path) {
$self->logger->log("Cache file exists. Will read cache from $cache_path.\n");
$self->logger->log("Cache file found. Will read from $cache_path.\n", 1);
return(1);
} else {
$self->logger->log("No cache file found. Will have to build cache from db.\n");
$self->logger->log("No cache file found. Will build cache from db.\n", 1);
return(0);
}
}
......@@ -104,98 +107,71 @@ sub cache_file_exists {
sub cache_path {
my $self = shift;
my $type = shift;
unless ($self->{'_cache_path'}) {
$self->{'_cache_path'} = ($self->conf->param('dumppath') || '.').'/'.
($self->conf->param('cachefile') || 'object_cache.ser');
}
throw("You must provide a cache type (old|new).") unless $type;
return $self->{'_cache_path'};
my $cache_path = ($self->conf->param('dumppath') || '.')."/$type.".
($self->conf->param('cachefile') || 'object_cache.ser');
return $cache_path;
}
sub write_to_file {
my $self = shift;
my $type = shift;
throw("You must provide a cache type (old|new).") unless $type;
# create dump directory if it doesn't exist
if (my $dump_path = $self->conf->param('dumppath')) {
unless (-d $dump_path) {
$self->logger->log("Cache directory $dump_path doesn't exist. Will create it.\n");
$self->logger->log("Cache directory $dump_path doesn't exist. Will create it.\n", 1);
system("mkdir -p $dump_path") == 0 or
throw("Unable to create directory $dump_path.\n");
}
}
my $cache_path = $self->cache_path;
my $cache_path = $self->cache_path($type);
$self->logger->log("Will dump to $cache_path.\n");
$self->logger->log_stamped("Dumping cache...\n");
$self->logger->log("Will dump to $cache_path.\n", 1);
$self->logger->log_stamped("Dumping cache...\n", 1);
eval { nstore($self->{'_cache'}, $cache_path) };
eval { nstore($self->{'_cache'}->{$type}, $cache_path) };
if ($@) {
throw("Unable to store $cache_path: $@\n");
}
my $size = -s $cache_path;
$size = parse_bytes($size);
$self->logger->log_stamped("Done (cache file is $size).\n");
$self->logger->log_stamped("Done (cache file is $size).\n", 1);
}
sub read_from_file {
my $self = shift;
my $type = shift;
throw("You must provide a cache type (old|new).") unless $type;
my $cache_path = $self->cache_path;
my $cache_path = $self->cache_path($type);
unless (-s $cache_path) {
throw("No valid cache file found at $cache_path.");
}
eval { $self->{'_cache'} = retrieve($cache_path); };
$self->logger->log("Reading cache from $cache_path...\n");
eval { $self->{'_cache'}->{$type} = retrieve($cache_path); };
if ($@) {
throw("Unable to retrieve cache: $@");
}
$self->logger->log_stamped("Done.\n");
return $self->{'_cache'};
return $self->{'_cache'}->{$type};
}
=head2
Arg[1] :
Example :
Description :
Return type :
Exceptions :
Caller :
Status :
=cut
sub build_cache {
my $self = shift;
# connect to db
my $old_dba = $self->get_DBAdaptor('old');
my $new_dba = $self->get_DBAdaptor('new');
#
# old database
#
$self->logger->log_stamped("Loading from old database...\n");
# fetch genes
my $old_genes = $self->fetch_genes($old_dba);
# fetch transcripts, translations and exons and build caches
$self->build_cache_from_genes('old', $old_genes);
#
# new database
#
}
sub fetch_genes {
my $self = shift;
my $dba = shift;
......@@ -213,11 +189,11 @@ sub fetch_genes {
# fetch genes, depending on filters to apply
#
my @all_genes = ();
my @genes = ();
my $genes = [];
if ($self->conf->param('chromosomes')) {
# filter by chromosome
$self->logger->log("Filtering by chromosome: ", 2);
$self->logger->log("Filtering by chromosome: ", 3);
foreach my $chr ($self->conf->param('chromosomes')) {
$self->logger->log("$chr ");
......@@ -228,7 +204,7 @@ sub fetch_genes {
} elsif ($self->conf->param('region')) {
# filter by region (specific slice)
$self->logger->log("Filtering by region: ".$self->conf->param('region')."\n", 2);
$self->logger->log("Filtering by region: ".$self->conf->param('region')."\n", 3);
my $slice = $sa->fetch_by_name($self->conf->param('region'));
@all_genes = @{ $slice->get_all_Genes(undef, undef, 1) };
......@@ -240,22 +216,22 @@ sub fetch_genes {
# filter by biotype
if ($self->conf->param('biotypes')) {
$self->logger->log("Filtering by biotype: ", 2);
$self->logger->log("Filtering by biotype: ", 3);
foreach my $biotype ($self->conf->param('biotypes')) {
$self->logger->log("$biotype ");
push @genes, grep { $_->biotype eq $biotype } @all_genes;
push @$genes, grep { $_->biotype eq $biotype } @all_genes;
}
$self->logger->log("\n");
} else {
@genes = @all_genes;
$genes = \@all_genes;
}
$self->logger->log_stamped("Done loading ".scalar(@genes)." genes.\n\n", 1);
$self->logger->log_stamped("Done loading ".scalar(@$genes)." genes.\n\n", 1);
return \@genes;
return $genes;
}
......@@ -273,10 +249,13 @@ sub build_cache_from_genes {
my $num_genes = scalar(@$genes);
$self->logger->init_progressbar('index_genes', $num_genes);
#use Data::Dumper;
#$Data::Dumper::Indent = 1;
foreach my $gene (@$genes) {
#$self->logger->log_progressbar('index_genes', ++$i, 2);
$self->logger->log_progress($num_genes, ++$i, 20, 2, 1);
$self->logger->log_progress($num_genes, ++$i, 20, 3, 1);
# build gene caches
$self->add($type, 'genes_by_id', $gene->dbID, $gene);
$self->add($type, 'genes_by_stable_id', $gene->stable_id, $gene);
......@@ -308,10 +287,38 @@ sub build_cache_from_genes {
}
}
$self->logger->log_stamped("Done building the index:\n", 1);
foreach my $gene (@$genes) {
#
# delete all unwanted data from objects
#
$gene->adaptor(undef);
$gene->analysis(undef);
$gene->display_xref(undef);
$gene->slice->adaptor(undef);
$gene->slice->coord_system->adaptor(undef);
foreach my $tr (@{ $gene->get_all_Transcripts }) {
$tr->adaptor(undef);
$tr->display_xref(undef);
$tr->analysis(undef);
if (my $tl = $tr->translation) {
$tl->adaptor(undef);
}
foreach my $exon (@{ $tr->get_all_Exons }) {
$exon->adaptor(undef);
$exon->analysis(undef);
}
}
#warn Data::Dumper::Dumper($gene) if ($i < 2);;
}
$self->logger->log_stamped("Done building the index:\n", 2);
foreach my $name (qw(genes transcripts translations exons)) {
my $num = scalar(keys %{ $self->get_by_name('old', "${name}_by_id") });
$self->logger->log(sprintf("%12.0f %-20s\n", $num, $name), 2);
my $num = scalar(keys %{ $self->get_by_name($type, "${name}_by_id") });
$self->logger->log(sprintf("%12.0f %-20s\n", $num, $name), 3);
}
$self->logger->log("\n");
}
......@@ -374,6 +381,16 @@ sub get_by_name {
}
sub flush_by_type {
my $self = shift;
my $type = shift;
throw("You must provide a cache type (old|new).") unless $type;
undef $self->{'_cache'}->{$type};
}
sub get_DBAdaptor {
my $self = shift;
my $prefix = shift;
......
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