From cc88db72dca0a0ba5b01f8e8630ebfaf6f16ba9f Mon Sep 17 00:00:00 2001
From: Patrick Meidl <pm2@sanger.ac.uk>
Date: Wed, 19 Jul 2006 10:05:38 +0000
Subject: [PATCH] committing intermediate state of module before rewriting it
to use lightweight feature object for caching
---
modules/Bio/EnsEMBL/IdMapping/Cache.pm | 149 ++++++++++++++-----------
1 file changed, 83 insertions(+), 66 deletions(-)
diff --git a/modules/Bio/EnsEMBL/IdMapping/Cache.pm b/modules/Bio/EnsEMBL/IdMapping/Cache.pm
index 6c45749100..82ea0d28da 100644
--- a/modules/Bio/EnsEMBL/IdMapping/Cache.pm
+++ b/modules/Bio/EnsEMBL/IdMapping/Cache.pm
@@ -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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