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Merge branch 'hotfix-release-0.0011'
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@cybersiddhu
cybersiddhu committed Mar 28, 2011
2 parents 7241074 + c6cf13a commit 88773f6
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Showing 7 changed files with 260 additions and 157 deletions.
8 changes: 6 additions & 2 deletions Build.PL
View file
Expand Up @@ -66,7 +66,7 @@ my $build = Modware::Build->new(
profile => { type => ':s' },
superuser => { type => ':s' },
superpassword => { type => ':s' },
loader => { type => ':s', default => 'preset' },
loader => { type => ':s' },
name => { type => ':s', default => 'custom' },
profile => { type => ':s', default => 'fallback' },
load_fixture => { type => '!', default => 1 },
Expand All @@ -77,7 +77,7 @@ my $build = Modware::Build->new(
db_config => { default => $db_config, type => ':s' },
file_config => { default => $file_config, type => ':s' },
fixture_config => { default => $fixture_config, type => ':s' },
preset => { default => 1, type => '!' },
preset => { type => '!' },
append_path => {
default => catfile( 't', 'data', 'preset' ),
type => ':s'
Expand All @@ -95,6 +95,10 @@ $build->args( 'preset_file',
catdir( $build->base_dir, 't', 'data', 'preset.tar.gz' ) );
$build->args( 'tmp_dir', catdir( 't', 'tmp' ) );
$build->args( 'config' => 'custom' );
if ( !$build->args('loader') ) {
$build->args( 'loader' => 'preset' );
$build->args( 'preset' => 1 );
}
$build->create_build_script;

1;
Expand Down
195 changes: 93 additions & 102 deletions bin/ontology/gaf2chado.pl
View file
Expand Up @@ -114,11 +114,6 @@ sub is_from_pubmed {
return $id if $id =~ /^PMID/;
}

sub is_from_dicty {
my ( $self, $id ) = @_;
return $id if $id =~ /^PUB/;
}

sub get_anno_ref_records {
my ( $self, $anno ) = @_;
my @ids;
Expand All @@ -130,23 +125,6 @@ sub get_anno_ref_records {

}

sub get_anno_dicty_records {
my ( $self, $anno ) = @_;
my @ids;
for my $xref ( @{ $anno->provenance->xrefs } ) {
my ( $db, $id ) = $self->parse_id( $xref->id );
push @ids, $db eq 'dictyBase_REF' ? 'PUB' . $id : $id;
}
return @ids;

}

sub normalize_dicty_id {
my ( $self, $id ) = @_;
$id =~ s/^PUB//;
$id;
}

sub get_db_pub_records {
my ( $self, $row ) = @_;
my $fcp_rs = $row->feature_cvterm_pubs;
Expand Down Expand Up @@ -198,8 +176,6 @@ package GAFManager;
},
handles => {
'is_from_pubmed' => 'is_from_pubmed',
'is_from_dicty' => 'is_from_dicty',
'normalize_dicty_id' => 'normalize_dicty_id',
'has_idspace' => 'has_idspace',
'chado' => 'chado',
'parse_id' => 'parse_id',
Expand Down Expand Up @@ -317,6 +293,19 @@ package GAFManager;
}
);

has '_rev_evcode_cache' => (
is => 'rw',
isa => 'HashRef',
traits => [qw/Hash/],
default => sub { {} },
handles => {
'_rev_add_to_evcode_cache' => 'set',
'_clean_rev_evcode_cache' => 'clear',
'_has_rev_evcode_in_cache' => 'defined',
'_get_rev_evcode_from_cache' => 'get'
}
);

has 'digest_cache' => (
is => 'rw',
isa => 'HashRef',
Expand Down Expand Up @@ -507,29 +496,6 @@ sub find_annotation {
$self->set_rank_in_digest_cache( $digest, 0 );
return;

# -- Get from database
# my @type_ids_from_db = = map {
# $_->feature_cvtermprops(
# { 'cv.name' => { -like => 'evidence_code%' } },
# { join => { 'type' => 'cv' } } )->first->type_id
# }
# grep { $_->pub->uniquename eq $id } $rs->all;
#
# # -- from the graph
# my @type_ids_from_graph
# = map { $self->get_evcode_from_cache($_) }
# map { $self->parse_evcode( $_->evidence ) } grep {
# ( $_->provenance->id eq $anno->provenance->id )
# and ( $_->gene->id eq $anno->gene->id )
# and ( $evcode ne $self->parse_evcode( $_->evidence ) )
# } @{ $self->graph->get_annotations_by_target( $anno->target->id ) };
#
# if ( @from_graph > 1 and @evcodes )
# { ## -- will always have the self annotation
# my @db_records = $rank_count += $#from_graph;
# }
# return GAFRow->new( rank => $rank_count ) if $rank_rount;
# return;
}

sub find_dicty_annotation {
Expand Down Expand Up @@ -562,12 +528,8 @@ sub find_dicty_annotation {
{ join => { 'type' => 'cv' } } )->first;

if ( $evrow->type->cvterm_id == $evcode_id ) {
my $db_id
= $self->is_from_dicty( $row->pub->uniquename )
? $self->normalize_dicty_id( $row->pub->uniquename )
: $row->pub->uniquename;
return GAFRank->new( row => $row )
if $id eq $db_id;
if $id eq $row->pub->pub_id;
}
}
}
Expand All @@ -588,29 +550,6 @@ sub find_dicty_annotation {
$self->set_rank_in_digest_cache( $digest, 0 );
return;

# -- Get from database
# my @type_ids_from_db = = map {
# $_->feature_cvtermprops(
# { 'cv.name' => { -like => 'evidence_code%' } },
# { join => { 'type' => 'cv' } } )->first->type_id
# }
# grep { $_->pub->uniquename eq $id } $rs->all;
#
# # -- from the graph
# my @type_ids_from_graph
# = map { $self->get_evcode_from_cache($_) }
# map { $self->parse_evcode( $_->evidence ) } grep {
# ( $_->provenance->id eq $anno->provenance->id )
# and ( $_->gene->id eq $anno->gene->id )
# and ( $evcode ne $self->parse_evcode( $_->evidence ) )
# } @{ $self->graph->get_annotations_by_target( $anno->target->id ) };
#
# if ( @from_graph > 1 and @evcodes )
# { ## -- will always have the self annotation
# my @db_records = $rank_count += $#from_graph;
# }
# return GAFRow->new( rank => $rank_count ) if $rank_rount;
# return;
}

sub keep_state_in_cache {
Expand Down Expand Up @@ -771,10 +710,8 @@ sub process_dicty_annotation {

my $reference = $anno->provenance->id;
my ( $db, $ref_id ) = $self->parse_id($reference);
$ref_id = 'PUB' . $ref_id if $db eq 'dictyBase_REF';

my $pub_row = $self->chado->resultset('Pub::Pub')
->find( { uniquename => $ref_id } );
my $pub_row
= $self->chado->resultset('Pub::Pub')->find( { pub_id => $ref_id } );
if ( !$pub_row ) {
$self->skipped_message("$reference Not found");
return;
Expand All @@ -785,10 +722,8 @@ sub process_dicty_annotation {
XREF:
for my $xref ( @{ $anno->provenance->xrefs } ) {
my ( $db, $ref_id ) = $self->parse_id( $xref->id );
$ref_id = 'PUB' . $ref_id if $db eq 'dictyBase_REF';

my $pub_row = $self->chado->resultset('Pub::Pub')
->find( { uniquename => $ref_id } );
->find( { pub_id => $ref_id } );
if ($pub_row) {
$self->insert_to_feature_cvterm_pubs(
{ 'pub_id' => $pub_row->pub_id } );
Expand Down Expand Up @@ -866,9 +801,9 @@ sub process_dicty_annotation {
}

## -- extra qualifiers
my $qual = [ grep { $_->id ne 'not' } $anno->qualifier_list ];
my $qual = $anno->qualifier_list;
if ( defined $qual ) {
for my $entry (@$qual) {
for my $entry ( grep { $_->id ne 'not' } @$qual ) {
$self->add_to_insert_feature_cvtermprops(
{ type_id => $self->find_or_create_cvterm_id(
cv => $self->extra_cv,
Expand All @@ -880,7 +815,6 @@ sub process_dicty_annotation {
}
);
}

}
return 1;
}
Expand Down Expand Up @@ -937,7 +871,12 @@ sub _preload_evcode_cache {
},
{ join => [ { 'type' => 'cv' } ] }
);
$self->add_to_evcode_cache( $_->synonym_, $_ ) for $syn_rs->all;

for my $syn ( $syn_rs->all ) {
$self->add_to_evcode_cache( $syn->synonym_, $syn );
$self->_rev_add_to_evcode_cache( $syn->cvterm->cvterm_id,
$syn->synonym_ );
}
}

1;
Expand All @@ -964,7 +903,11 @@ sub _preload_evcode_cache {
},
{ join => [ { 'type' => 'cv' } ] }
);
$self->add_to_evcode_cache( $_->synonym, $_ ) for $syn_rs->all;
for my $syn ( $syn_rs->all ) {
$self->add_to_evcode_cache( $syn->synonym, $syn );
$self->_rev_add_to_evcode_cache( $syn->cvterm->cvterm_id,
$syn->synonym );
}
}

1;
Expand All @@ -980,6 +923,11 @@ package GAFLoader;
use Set::Object;
use DateTime::Format::Strptime;

has 'logger' => (
is => 'rw',
isa => 'Object',
);

has 'manager' => (
is => 'rw',
isa => 'GAFManager'
Expand Down Expand Up @@ -1015,23 +963,66 @@ package GAFLoader;
sub store_cache {
my ( $self, $cache ) = @_;
my $chado = $self->chado;
my $index;
try {
$chado->txn_do(
sub {

#$chado->resultset( $self->resultset )->populate($cache);
for my $i ( 0 .. $#$cache ) {
$index = $i;
for my $i ( 0 .. $#$cache ) {
try {
$chado->txn_do(
sub {
$chado->resultset( $self->resultset )
->create( $cache->[$i] );
}
);
}
catch {
carp "error in inserting $_\n Data dump ", Dumper $cache->[$i],
"\n";
$self->logger->fatal("error in inserting $_");
$self->logger->fatal( Dumper $cache->[$i] );

## -- reporting the error
my $error_str = $self->_get_error_string( $cache->[$i] );
$self->logger->error("Not loaded:\t$error_str");

};
}
}

sub _get_error_string {
my ( $self, $data_str ) = @_;
my $chado = $self->chado;

my ( $gene_id, $goid, $reference_id, $evcode );
$gene_id
= $chado->resultset('Sequence::Feature')
->find( { feature_id => $data_str->{feature_id} } )
->dbxref->accession;

$goid
= 'GO:'
. $chado->resultset('Cv::Cvterm')
->find( { cvterm_id => $data_str->{cvterm_id} } )->dbxref->accession;

my $pub = $chado->resultset('Pub::Pub')
->find( { pub_id => $data_str->{pub_id} } );
if ( $pub->pubplace =~ /pubmed/i ) {
$reference_id = 'PMID:' . $pub->uniquename;
}
else {
$reference_id = 'REF:' . $data_str->{pub_id};
}

for my $props ( @{ $data_str->{feature_cvtermprops} } ) {
if ( $props->{value} =~ /^\d{1}$/ ) {
if ( $self->manager->_has_rev_evcode_in_cache( $props->{type_id} )
)
{
$evcode = $self->manager->_get_rev_evcode_from_cache(
$props->{type_id} );
last;
}
);
}
}
catch {
croak $_, "\t", Dumper $cache->[$index];
};
return sprintf "%s\t%s\t%s\t%s\n", $gene_id, $goid, $reference_id,
$evcode;
}

sub dicty_update {
Expand Down Expand Up @@ -1072,8 +1063,7 @@ sub dicty_update {
$self->update_qualifier($row);

## -- all annotation secondary references
my $anno_ref_rec
= Set::Object->new( $self->get_anno_dicty_records($anno) );
my $anno_ref_rec = Set::Object->new( $self->get_anno_ref_records($anno) );

## -- database records that are stored through feature_cvterm_dbxref
my $db_rec = Set::Object->new( $self->get_db_records($row) );
Expand Down Expand Up @@ -1243,7 +1233,7 @@ sub update_qualifier {

my $anno = $self->manager->annotation;
my $qual = [ grep { $_->id ne 'not' } $anno->qualifier_list ];
if ( defined $qual ) {
if ( defined $qual ) {
my $anno_qual = Set::Object->new( [ map { $_->id } @$qual ] );
my $db_qual = Set::Object->new( $self->manager->get_db_qual($row) );
if ( $db_qual->members ) {
Expand Down Expand Up @@ -1370,6 +1360,7 @@ package main;
my $loader = GAFLoader->new( manager => $manager );
$loader->helper($helper);
$loader->resultset('Sequence::FeatureCvterm');
$loader->logger($logger);

# -- evidence ontology loaded
if ( !$manager->evcodes_in_cache ) {
Expand Down

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