Merge pull request #165 from dictyBase/bug/obo-namespace

Bug/obo namespace
closes #159

Dockerfile.test

@@ -0,0 +1,26 @@
+FROM perl:5.20
+MAINTAINER Siddhartha Basu <siddhartha-basu@northwestern.edu>
+
+ADD https://northwestern.box.com/shared/static/3n0wdp04075oyrnytznn9mzc3k9o92c1.rpm /rpms/
+ADD https://northwestern.box.com/shared/static/o2gd3o70sik5liw43hiomusmu0262auw.rpm /rpms/
+ADD https://northwestern.box.com/shared/static/nsflzsbm2xmcf46z1ybiustosqkdskbb.rpm /rpms/
+
+RUN apt-get update && \
+    apt-get -y install alien libaio1 libdb-dev libexpat1-dev && \
+    mkdir -p /rpms && \
+    alien -i /rpms/*.rpm && \
+    echo '/usr/lib/oracle/11.2/client64/lib' > /etc/ld.so.conf.d/oracle.conf && \
+    echo 'export ORACLE_HOME=/usr/lib/oracle/11.2/client64' > /etc/profile.d/oracle.sh
+
+ENV ORACLE_HOME /usr/lib/oracle/11.2/client64/
+ENV LD_LIBRARY_PATH /usr/lib/oracle/11.2/client64/lib/
+
+ADD cpanfile /tmp/
+RUN cd /tmp \
+    && cpanm -n --quiet --installdeps . \
+    && cpanm -n --quiet DBD::Oracle DBD::Pg Math::Base36 String::CamelCase LWP::Protocol::https \
+    && rm -fr /rpms \
+    && cpanm -n --quiet Child Dist::Zilla
+COPY dist.ini /usr/src/modware/
+WORKDIR /usr/src/modware
+RUN dzil authordeps --missing | cpanm -n --quiet 

lib/Modware/Loader/Ontology.pm

@@ -10,17 +10,18 @@ use SQL::Library;
 use File::Spec::Functions qw/catfile/;
 use Modware::Loader;
 use Modware::Loader::Schema::Temporary;
+use File::Basename;
 
 has 'sqllib' => (
     is      => 'rw',
     isa     => 'SQL::Library',
-    lazy => 1,
+    lazy    => 1,
     default => sub {
         my ($self) = @_;
         my $lib = SQL::Library->new(
             {   lib => catfile(
                     module_dir('Modware::Loader'),
-                    lc ($self->schema->storage->sqlt_type) . '.lib'
+                    lc( $self->schema->storage->sqlt_type ) . '.lib'
                 )
             }
         );
@@ -29,8 +30,8 @@ has 'sqllib' => (
 );
 
 has 'app_instance' => (
-    is      => 'rw',
-    isa     => 'Modware::Load::Command::obo2chado',
+    is  => 'rw',
+    isa => 'Modware::Load::Command::obo2chado',
 );
 
 has 'logger' =>
@@ -68,7 +69,15 @@ has 'ontology' => (
     writer  => 'set_ontology',
     trigger => sub {
         my ( $self, $onto ) = @_;
-        $self->ontology_namespace( $onto->default_namespace || $onto->id );
+        my $namespace
+            = $self->parse_ontology_tag( $self->app_instance->input )
+            || $self->parse_namespace_from_file_path
+            || $onto->default_namespace
+            || $onto->id;
+        $self->app_instance->logger->logdie(
+            "could not parse ontology namespace")
+            if !$namespace;
+        $self->ontology_namespace($namespace);
     }
 );
 
@@ -78,7 +87,7 @@ has '_date_parser' => (
     lazy    => 1,
     default => sub {
         return DateTime::Format::Strptime->new(
-            pattern  => '%d:%m:%Y',
+            pattern  => '%d:%m:%Y%n%H:%M',
             on_error => 'croak'
         );
     }
@@ -89,7 +98,7 @@ has 'create_ontology_hooks' => (
     isa     => 'ArrayRef',
     lazy    => 1,
     default => sub {
-        return [ 'create_synonyms', 'create_comments', 'create_alt_ids'];
+        return [ 'create_synonyms', 'create_comments', 'create_alt_ids' ];
     }
 );
 
@@ -98,10 +107,37 @@ has 'update_ontology_hooks' => (
     isa     => 'ArrayRef',
     lazy    => 1,
     default => sub {
-        return ['update_synonyms', 'update_comments',  'update_alt_ids'];
+        return [ 'update_synonyms', 'update_comments', 'update_alt_ids' ];
     }
 );
 
+sub parse_namespace_from_file_path {
+    my ($self) = @_;
+    my ($namespace)
+        = ( split /\./, basename( $self->app_instance->input ) )[0];
+    return $namespace;
+}
+
+sub parse_ontology_tag {
+    my ( $self, $file ) = @_;
+    my $handler = IO::File->new( $file, "r" )
+        or $self->app_instance->logger->logdie("cannot open file $!");
+    while ( my $line = $handler->getline ) {
+        if ( $line =~ /^\[/ ) {
+            last;
+        }
+        if ( $line =~ /^ontology/ ) {
+            my ($value) = ( ( split /:/, $line ) )[1];
+            $value =~ s/^\s+//;
+            $value =~ s/\s+$//;
+            $handler->close;
+            return $value;
+        }
+    }
+    $handler->close;
+    return;
+}
+
 sub _around_connection {
     my ($self)       = @_;
     my $connect_info = $self->connect_info;

lib/Modware/Loader/Role/Ontology/WithHelper.pm

@@ -73,8 +73,7 @@ sub find_or_create_cvrow {
     if ( $self->has_cvrow($cv) ) {
         return $self->get_cvrow($cv);
     }
-    my $cvrow
-        = $self->schema->resultset('Cv::Cv')
+    my $cvrow = $self->schema->resultset('Cv::Cv')
         ->find_or_create( { name => $cv } );
     $self->set_cvrow( $cv, $cvrow );
     return $cvrow;
@@ -101,8 +100,7 @@ sub find_or_create_cvterm_namespace {
     if ( $self->has_cvterm_row($cvterm) ) {
         return $self->get_cvterm_row($cvterm);
     }
-    my $cvterm_row
-        = $schema->resultset('Cv::Cvterm')
+    my $cvterm_row = $schema->resultset('Cv::Cvterm')
         ->find( { name => $cvterm, 'cv.name' => $cv }, { join => 'cv' } );
     if ($cvterm_row) {
         $self->set_cvterm_row( $cvterm, $cvterm_row );
@@ -150,8 +148,14 @@ sub _normalize_id {
         $accession = $parsed[1];
     }
     else {
-        $db_id = $self->find_or_create_db_id(
-            $self->ontology->default_namespace );
+        my $namespace
+            = $self->ontology->default_namespace
+            || $self->parse_namespace_from_file_path
+            || $self->parse_ontology_tag( $self->app_instance->input );
+        $self->app_instance->logger->logdie(
+            "could not parse default namespace")
+            if !$namespace;
+        $db_id     = $self->find_or_create_db_id($namespace);
         $accession = $id;
     }
     return ( $db_id, $accession );

t/loader/obo2chado-namespace.t

@@ -0,0 +1,55 @@
+use Test::More qw/no_plan/;
+use Test::DatabaseRow;
+use FindBin qw($Bin);
+use Path::Class::Dir;
+use Test::Exception;
+use Test::Chado qw/:all/;
+use Test::Chado::Common qw/:all/;
+use Test::Chado::Cvterm qw/:all/;
+
+my $data_dir    = Path::Class::Dir->new($Bin)->parent->subdir('test_data');
+my $obo_fixture = $data_dir->subdir('preset')->file('cvprop.tar.bz2');
+
+use_ok('Modware::Load');
+
+subtest 'loading of obo file without default namespace' => sub {
+    my $schema = chado_schema( custom_fixture => $obo_fixture );
+    my $dbmanager = get_dbmanager_instance();
+    local $Test::DatabaseRow::dbh = $dbmanager->dbh;
+    my $loader = new_ok('Modware::Load');
+    local @ARGV = (
+        'obo2chado',          '--dsn',
+        $dbmanager->dsn,      '--user',
+        $dbmanager->user,     '--password',
+        $dbmanager->password, '--input',
+        $data_dir->subdir('obo')->file('ro-filter.obo'),
+    );
+    push @ARGV, '--pg_schema', $dbmanager->schema_namespace
+        if $dbmanager->can('schema_namespace');
+
+    lives_ok { $loader->run } "should load ro obo file";
+    has_cv( $schema, 'ro', 'cv namespace should match with ontology tag' );
+    has_dbxref( $schema, 'results_in_morphogenesis_of',
+        'should have dbxref' );
+    has_cvterm(
+        $schema,
+        'results in morphogenesis of',
+        'should have the cvterm'
+    );
+
+    my $sql = <<'SQL';
+    SELECT DBXREF.* from dbxref JOIN DB ON DBXREF.DB_ID=DB.DB_ID
+    WHERE
+    DBXREF.ACCESSION=?
+    AND
+    DB.NAME='ro-filter'
+SQL
+    row_ok(
+        sql         => [$sql, $_],
+        results     => 1,
+        description => 'should have term with db namespace from file path'
+    ) for qw/results_in_morphogenesis_of results_in_development_of results_in_formation_of/;
+
+    drop_schema();
+};
+

t/test_data/obo/dicty_phenotypes.obo

@@ -2,6 +2,7 @@ format-version: 1.2
 date: 27:08:2013 16:37
 saved-by: pfey
 auto-generated-by: OBO-Edit 2.2
+ontology: dphen
 default-namespace: dphen
 remark: cvs version: $Revision: 1.213 $
 

t/test_data/obo/dicty_phenotypes1.198.obo

@@ -2,6 +2,7 @@ format-version: 1.2
 date: 26:09:2012 17:53
 saved-by: pfey
 auto-generated-by: OBO-Edit 2.0
+ontology: dphen
 default-namespace: dphen
 remark: cvs version: $Revision: 1.198 $