ENSCORESW-371: annotation extensions commited back from branch into head

modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm

@@ -776,6 +776,49 @@ sub _store_object_xref_mapping {
             $sth->bind_param( 3, $linkage_type,  SQL_VARCHAR );
             $sth->execute();
         } #end foreach
+        
+        $sth = $self->prepare( "
+             INSERT ignore INTO associated_xref
+                SET object_xref_id = ?,
+                    xref_id = ?,
+                    source_xref_id = ?,
+                    condition_type = ?,
+                    associated_group_id = ?,
+                    rank = ? " );
+        
+        my $annotext = $dbEntry->get_all_associated_xrefs();
+        foreach my $ax_group (sort keys %{ $annotext }) {
+          my $group = $annotext->{$ax_group};
+          my $gsth = $self->prepare( " 
+                  INSERT INTO associated_group 
+                    SET description = ?;" );
+          $sth->bind_param( 1, $ax_group,     SQL_INTEGER );
+          $gsth->execute();
+          my $associatedGid = $self->last_insert_id();
+          
+          foreach my $ax_rank (sort keys %{ $group }) {
+            my @ax = @{ $group->{$ax_rank} };
+            
+            my $associatedXid = undef;
+            my $sourceXid = undef;
+            
+            $ax[0]->is_stored( $self->dbc ) || $self->store($ax[0]);
+            $associatedXid = $ax[0]->dbID;
+            $ax[1]->is_stored( $self->dbc ) || $self->store($ax[1]);
+            $sourceXid = $ax[1]->dbID;
+            
+            if (!defined $associatedXid || !defined $sourceXid) {
+              next;
+            }
+            $sth->bind_param( 1, $object_xref_id,     SQL_INTEGER );
+            $sth->bind_param( 2, $associatedXid,      SQL_INTEGER );
+            $sth->bind_param( 3, $sourceXid,          SQL_INTEGER );
+            $sth->bind_param( 4, $ax[2],              SQL_VARCHAR );
+            $sth->bind_param( 5, $associatedGid,      SQL_VARCHAR );
+            $sth->bind_param( 6, $ax_rank,            SQL_INTEGER );
+            $sth->execute();
+          }
+        } #end foreach
       } #end elsif
     } # end if ($object_xref_id)
     return $object_xref_id;
@@ -1178,6 +1221,11 @@ sub remove_from_object {
   $sth->bind_param(1,$ox_id,SQL_INTEGER);
   $sth->execute();
   $sth->finish();
+  
+  $sth = $self->prepare("DELETE FROM associated_xref WHERE object_xref_id = ?");
+  $sth->bind_param(1,$ox_id,SQL_INTEGER);
+  $sth->execute();
+  $sth->finish();
 
   $sth = $self->prepare("DELETE FROM identity_xref WHERE object_xref_id = ?");
   $sth->bind_param(1,$ox_id,SQL_INTEGER);
@@ -1247,11 +1295,15 @@ sub _fetch_by_object_type {
            idt.cigar_line, idt.score, idt.evalue, oxr.analysis_id,
            gx.linkage_type,
            xref.info_type, xref.info_text, exDB.type, gx.source_xref_id,
-           oxr.linkage_annotation, xref.description
+           oxr.linkage_annotation, xref.description,
+           ax.xref_id, ax.source_xref_id, ax.condition_type, 
+           ax.associated_group_id, ax.rank
     FROM   (xref xref, external_db exDB, object_xref oxr)
     LEFT JOIN external_synonym es on es.xref_id = xref.xref_id
     LEFT JOIN identity_xref idt on idt.object_xref_id = oxr.object_xref_id
     LEFT JOIN ontology_xref gx on gx.object_xref_id = oxr.object_xref_id
+    LEFT JOIN associated_xref ax ON ax.object_xref_id = oxr.object_xref_id
+    LEFT JOIN associated_group ag ON ax.associated_group_id = ag.associated_group_id
     WHERE  xref.xref_id = oxr.xref_id
       AND  xref.external_db_id = exDB.external_db_id
       AND  oxr.ensembl_id = ?
@@ -1284,32 +1336,39 @@ SSQL
   $sth->bind_param( 2, $ensType, SQL_VARCHAR );
   $sth->execute();
 
-  my ( %seen, %linkage_types, %synonyms );
+  my ( %seen, %linkage_types, %synonyms, %associated_xrefs );
 
   my $max_rows = 1000;
 
   while ( my $rowcache = $sth->fetchall_arrayref( undef, $max_rows ) ) {
     while ( my $arrRef = shift( @{$rowcache} ) ) {
-      my ( $refID,                  $dbprimaryId,
-           $displayid,              $version,
+      my ( $refID,                     $dbprimaryId,
+           $displayid,                 $version,
            $priority,
-           $dbname,                 $release,
-           $exDB_status,            $exDB_db_display_name,
-           $exDB_secondary_db_name, $exDB_secondary_db_table,
-           $objid,                  $synonym,
-           $xrefid,                 $ensemblid,
-           $xref_start,             $xref_end,
-           $ensembl_start,          $ensembl_end,
-           $cigar_line,             $score,
-           $evalue,                 $analysis_id,
-           $linkage_type,           $info_type,
-           $info_text,              $type,
-           $source_xref_id,         $link_annotation,
-	   $description
+           $dbname,                    $release,
+           $exDB_status,               $exDB_db_display_name,
+           $exDB_secondary_db_name,    $exDB_secondary_db_table,
+           $objid,                     $synonym,
+           $xrefid,                    $ensemblid,
+           $xref_start,                $xref_end,
+           $ensembl_start,             $ensembl_end,
+           $cigar_line,                $score,
+           $evalue,                    $analysis_id,
+           $linkage_type,              $info_type,
+           $info_text,                 $type,
+           $source_xref_id,            $link_annotation,
+           $description,               $associated_xref_id,
+           $source_associated_xref_id, $condition_type,
+           $associate_group_id,        $associate_group_rank
       ) = @$arrRef;
 
       my $linkage_key =
         ( $linkage_type || '' ) . ( $source_xref_id || '' );
+      
+      my $associated_key =
+        ( $condition_type || '' )
+        . ( $source_associated_xref_id || '' )
+        . ( $associated_xref_id || '' );
 
 
       my $analysis = undef;
@@ -1341,6 +1400,8 @@ SSQL
       # original). Since there is at most one identity_xref row per
       # xref, this is easy enough; all the 'extra' bits are synonyms.
       my $source_xref;
+      my $associated_xref;
+      my $source_associated_xref;
       if ( !$seen{$refID} ) {
 	
 	my $exDB;
@@ -1364,6 +1425,20 @@ SSQL
                               : undef );
           $exDB->add_linkage_type( $linkage_type, $source_xref || () );
           $linkage_types{$refID}->{$linkage_key} = 1;
+          
+          # Add associated Xref annotations to the OntologyXref entry.
+          if ( defined $associated_xref_id && $associated_xref_id ne "" ) {
+            $exDB = Bio::EnsEMBL::OntologyXref->new_fast( \%obj_hash );
+            $associated_xref = ( defined($associated_xref_id)
+                                ? $self->fetch_by_dbID($associated_xref_id)
+                                : undef );
+            $source_associated_xref = ( defined($source_associated_xref_id)
+                                ? $self->fetch_by_dbID($source_associated_xref_id)
+                                : undef );
+            if ( defined($associated_xref) ) {
+              $exDB->add_linked_associated_xref( $associated_xref, $source_associated_xref, $condition_type || '', $associate_group_id, $associate_group_rank );
+            }
+          }
 
         } else {
           $exDB = Bio::EnsEMBL::DBEntry->new_fast( \%obj_hash );
@@ -1400,6 +1475,24 @@ SSQL
           ->add_linkage_type( $linkage_type, $source_xref || () );
         $linkage_types{$refID}->{$linkage_key} = 1;
       }
+      
+      if (    defined($associated_xref_id)
+           && $associated_xref_id ne ""
+           && !$associated_xrefs{$refID}->{$associated_key} )
+      {
+        $associated_xref = ( defined($associated_xref_id)
+                            ? $self->fetch_by_dbID($associated_xref_id)
+                            : undef );
+        $source_associated_xref = ( defined($source_associated_xref_id)
+                                ? $self->fetch_by_dbID($source_associated_xref_id)
+                                : undef );
+        if ( defined($associated_xref) ) {
+          $seen{$refID}->add_linked_associated_xref( $associated_xref, $source_associated_xref, $condition_type || '', $associate_group_id, $associate_group_rank );
+        }
+        
+        $linkage_types{$refID}->{$linkage_key} = 1;
+      }
+      
     } ## end while ( my $arrRef = shift...
   } ## end while ( my $rowcache = $sth...
 

modules/Bio/EnsEMBL/OntologyXref.pm

@@ -176,4 +176,335 @@ sub flush_linkage_types {
   $self->{'linkage_types'} = [];
 }
 
+
+=head2 add_associated_xref
+
+  Arg [1]    : Bio::EnsEMBL::DBEntry $associated_xref
+               or an Array of Bio::EnsEMBL::DBEntry for compound annotations
+  Arg [2]    : Bio::EnsEMBL::DBEntry $source_dbentry
+  Arg [3]    : string $condition_type or an Array of string $condition_types
+               matching the order of Arg[1] for compound queries.
+  Arg [4]    : (optional) Integer $group id for compound annotations.
+  Arg [5]    : (optional) Integer $rank order for a term within a compound annotation.
+  Example    : $ontology_xref->add_associated_xref(
+                                  $associated_xref,
+                                  $source_dbentry,
+                                  'with',
+                                  42,
+                                  5);
+  Description: Associates a linkage type and source DBEntry with
+               this ontology_xref
+  Returntype : none
+  Exceptions : thrown if $linkage_type argument not supplied or
+               the optional DBEntry is not a DBEntry object.
+  Caller     : DBEntryAdaptor
+  Status     : Experimantal
+
+=cut
+
+sub add_associated_xref {
+  my ( $self, $associated_xref, $source_dbentry, $condition_type, $group, $rank ) = @_;
+  if ( ref($associated_xref) eq 'ARRAY' )
+  {
+    foreach my $e ( @{ $associated_xref } ) {
+      if ( !$e->isa('Bio::EnsEMBL::DBEntry') ) {
+        $self->throw("associated_xref must be a Bio::EnsEMBL::DBEntry or an 
+                  Array of Bio::EnsEMBL::DBEntry objects.");
+      }
+    }
+  } elsif ( defined($associated_xref)
+       && !$associated_xref->isa('Bio::EnsEMBL::DBEntry') )
+  {
+    $self->throw("associated_xref must be a Bio::EnsEMBL::DBEntry or an Array
+                  of Bio::EnsEMBL::DBEntry objects.");
+  }
+  
+  if ( defined($source_dbentry)
+       && !$source_dbentry->isa('Bio::EnsEMBL::DBEntry') )
+  {
+    $self->throw("source_dbentry must be a Bio::EnsEMBL::DBEntry");
+  }
+  
+  if ( !defined $condition_type ) {
+      $self->throw("condition must be a string");
+  }
+  
+  if (!defined $group) {
+    $group = 1 + scalar keys %{ $self->{'associated_xref'} };
+  }
+  
+  if (!defined $rank) {
+    #$rank = 0;
+    $rank = 1 + scalar keys %{ $self->{'associated_xref'}->{ $group } };
+  }
+
+  $self->{'associated_xref'} ||= {};
+
+  $self->{'associated_xref'}->{ $group }->{$rank} = 
+    [ $associated_xref, $source_dbentry, $condition_type ];
+}
+
+
+=head2 add_linked_associated_xref
+
+  Arg [1]    : Bio::EnsEMBL::DBEntry $associated_xref
+               or an Array of Bio::EnsEMBL::DBEntry for compound annotations
+  Arg [2]    : Bio::EnsEMBL::DBEntry $source_dbentry
+  Arg [3]    : string $condition_type or an Array of string $condition_types
+               matching the order of Arg[1] for compound queries.
+  Arg [4]    : Integer $group id.
+  Arg [5]    : Integer $rank id.
+  Example    : $ontology_xref->add_associated_xref(
+                                  $associated_xref,
+                                  $source_dbentry,
+                                  'with',
+                                  42,
+                                  5);
+  Description: Associates a linkage type and source DBEntry with this
+               ontology_xref that have come from the same annotation source
+  Returntype : none
+  Exceptions : thrown if $linkage_type argument not supplied or
+               the optional DBEntry is not a DBEntry object.
+  Caller     : DBEntryAdaptor
+  Status     : Experimantal
+
+=cut
+
+sub add_linked_associated_xref {
+  my ( $self, $associated_xref, $source_dbentry, $condition_type, $associate_group_id, $associate_group_rank ) = @_;
+  
+  if ( !defined($associated_xref) )
+  {
+    $self->throw("associated_xref must be a Bio::EnsEMBL::DBEntry or an Array
+                  of Bio::EnsEMBL::DBEntry objects.");
+  }
+  
+  if ( defined($associated_xref)
+       && !$associated_xref->isa('Bio::EnsEMBL::DBEntry') )
+  {
+    $self->throw("associated_xref must be a Bio::EnsEMBL::DBEntry or an Array
+                  of Bio::EnsEMBL::DBEntry objects.");
+  }
+  
+  if ( defined($source_dbentry)
+       && !$source_dbentry->isa('Bio::EnsEMBL::DBEntry') )
+  {
+    $self->throw("source_dbentry must be a Bio::EnsEMBL::DBEntry");
+  }
+  
+  if ( !defined $condition_type ) {
+      $self->throw("condition must be a string");
+  }
+  
+  if ( !defined $associate_group_id )
+  {
+    $self->throw("$associate_group_id must be an integer");
+  }
+  
+  if ( !defined $associate_group_rank )
+  {
+    $self->throw("$associate_group_rank must be an integer");
+  }
+  
+#  print "\t" . $associate_group_id;
+#  print "\t" . $associate_group_rank;
+#  print "\t|" . defined($associated_xref) . '|';
+#  #print "\t" . defined($associated_xref->primary_id);
+#  print "\t" . $associated_xref->primary_id;# . ' (' . $associated_xref->display_id . ')';
+#  print "\t" . $source_dbentry->primary_id;
+#  print "\t" . $condition_type . "\n"; 
+  
+  my $associated_xref_array = {};
+  my $matching_link = 0;
+  
+  my $load_postion = 0;
+  if ( !defined $self->{'associated_xref'} ) {
+    $associated_xref_array->{$associate_group_id}->{$associate_group_rank} = [
+      $associated_xref,
+      $source_dbentry,
+      $condition_type
+    ];
+    $load_postion = 1;
+  } else {
+    $associated_xref_array = $self->{'associated_xref'};
+    
+    if (!defined $associated_xref_array->{$associate_group_id} ) {
+      $associated_xref_array->{$associate_group_id}->{$associate_group_rank} = [
+        $associated_xref,
+        $source_dbentry,
+        $condition_type
+      ];
+      $load_postion = 2;
+    } else {
+      my $already_loaded = 0;
+      foreach my $rank ( keys %{$associated_xref_array->{$associate_group_id}} ) {
+        my @ax_gr_set = @{ $associated_xref_array->{$associate_group_id}->{$rank} };
+        if (
+          $ax_gr_set[0]->primary_id eq $associated_xref->primary_id && 
+          $ax_gr_set[1]->primary_id eq $source_dbentry->primary_id &&
+          $ax_gr_set[2] eq $condition_type
+        ) {
+          $already_loaded = 1;
+          $load_postion = 4;
+          #last;
+        }
+      }
+      if ( !$already_loaded ) {
+        if (!defined $associated_xref_array->{$associate_group_id}->{$associate_group_rank} ) {
+          $associated_xref_array->{$associate_group_id}->{$associate_group_rank} = [
+            $associated_xref,
+            $source_dbentry,
+            $condition_type
+          ];
+          $load_postion = 5;
+        } else {
+          $associated_xref_array->{$associate_group_id}->{scalar keys %{ $associated_xref_array->{$associate_group_id} }} = [
+            $associated_xref,
+            $source_dbentry,
+            $condition_type
+          ];
+          $load_postion = 3;
+        }
+      }
+    }
+  }
+  $self->{'associated_xref'} = $associated_xref_array;
+#  print "\t\tLoaded at " . $load_postion . "\n";
+#  if ($associate_group_id == 28792 || $associate_group_id == 28793) {
+#    print Data::Dumper->Dumper([$self->{'associated_xref'}]);
+#  }
+}
+
+
+=head2 get_all_associated_xrefs
+
+  Arg [1]    : none
+  Example    :
+
+    foreach ( @{ $ontology_xref->get_all_associated_xref() } ) {
+      print "evidence: $_->[0] via $_->[1]->display_id";
+    }
+
+  Description: Retrieves a list of associated-DBEntry/source-DBEntry/condition
+               sets associated with this ontology_xref
+  Returntype : listref of listrefs
+  Exceptions : none
+  Caller     : geneview? general.
+  Status     : Experimental
+
+=cut
+
+sub get_all_associated_xrefs {
+  my ($self) = @_;
+
+  return $self->{'associated_xref'} || {};
+}
+
+=head2 get_extensions
+  Arg [1]    : none
+  Example    :
+
+    use Data::Dumper;
+    print Dumper @{ $ontology_xref->get_extensions_for_web() }
+    
+  Returns    :
+    $VAR1 = {
+              'source' => '<a href="<Link to CiteXplore>">11937031</a>',
+              'evidence' => 'IDA',
+              'description' => '<strong>has_direct_input</strong> 
+                   <a href="http://www.pombase.org/spombe/result/SPBC32F12.09">
+                     SPBC32F12.09
+                   </a>'
+            };
+
+  Description: Retrieves a list of associated-DBEntry/source-DBEntry/condition
+               sets associated with this ontology_xref and formats them ready
+               for web display in a group per row fashion.
+               The accessions for ontologies are linkable. Extra links need to
+               be added for each distinct database that is reference. 
+  Returntype : listref of hashrefs
+  Exceptions : none
+  Caller     : 
+  Status     : Experimental
+=cut
+sub get_extensions {
+  my ($self) = @_;
+  
+  if ( !defined $self->{'associated_xref'} ) {
+    return [];
+  }
+  
+  my @annotExtRows = ();
+  
+  my %external_urls = (
+    'GO'     => 'http://www.ebi.ac.uk/ego/GTerm?id=',
+    'GO_REF' => 'http://www.geneontology.org/cgi-bin/references.cgi#',
+    'SO'     => 'http://www.sequenceontology.org/miso/current_cvs/term/',
+    #'MOD'    => 'href=mod',
+    'PomBase' => 'http://www.pombase.org/spombe/result/',
+    'PomBase_Systematic_ID' => 'http://www.pombase.org/spombe/result/',
+    'PUBMED' => 'http://europepmc.org/abstract/MED/'
+  );
+  
+  foreach my $groupId (keys %{ $self->{'associated_xref'} } ) {
+    my $description = '';
+    my $evidence    = '';
+    my $source      = '';
+    
+    foreach my $rank ( keys %{ $self->{'associated_xref'}->{$groupId} } ) {
+      if ( $self->{'associated_xref'}->{$groupId}->{$rank}->[2]
+           eq 'evidence' ) {
+        if ( exists $external_urls{$self->{'associated_xref'}->{$groupId}->{$rank}->[0]->dbname} ) {
+          $evidence = '<a href="' . $external_urls{$self->{'associated_xref'}->{$groupId}->{$rank}->[0]->dbname}
+                    . $self->{'associated_xref'}->{$groupId}->{$rank}->[0]->primary_id . '">'
+                    . $self->{'associated_xref'}->{$groupId}->{$rank}->[0]->display_id
+                    . '</a>';
+        } else {
+          $evidence = $self->{'associated_xref'}->{$groupId}->{$rank}->[0]->display_id;
+        }
+      } else {
+        if (length $description > 0) {
+          $description .= ', ';
+        }
+        $description .= '<strong>' . $self->{'associated_xref'}->{$groupId}->{$rank}->[2] . '</strong> ';
+        
+        if (exists $external_urls{$self->{'associated_xref'}->{$groupId}->{$rank}->[0]->dbname} ) {
+          $description .= '<a href="' . $external_urls{$self->{'associated_xref'}->{$groupId}->{$rank}->[0]->dbname}
+                        . $self->{'associated_xref'}->{$groupId}->{$rank}->[0]->primary_id . '">'
+                        . $self->{'associated_xref'}->{$groupId}->{$rank}->[0]->display_id
+                        . '</a>';
+        } else {
+          $description .= $self->{'associated_xref'}->{$groupId}->{$rank}->[0]->display_id;
+        }
+        
+        
+      }
+      
+      if ( !undef $external_urls{$self->{'associated_xref'}->{$groupId}->{$rank}->[1]} ) {
+        if ( exists $external_urls{$self->{'associated_xref'}->{$groupId}->{$rank}->[1]->dbname} ) {
+          $source = '<a href="' . $external_urls{$self->{'associated_xref'}->{$groupId}->{$rank}->[1]->dbname}
+                  . $self->{'associated_xref'}->{$groupId}->{$rank}->[1]->primary_id . '">';
+          if ( $self->{'associated_xref'}->{$groupId}->{$rank}->[1]->dbname ne 'GO_REF' ) {
+            $source .= 'PMC:';
+          }
+          $source .= $self->{'associated_xref'}->{$groupId}->{$rank}->[1]->display_id . '</a>';
+        } elsif ($self->{'associated_xref'}->{$groupId}->{$rank}->[1]->display_id eq 'PMPB:0') {
+          $source = '';
+        } else {
+          $source = $self->{'associated_xref'}->{$groupId}->{$rank}->[1]->display_id;
+        }
+      }
+    }
+    
+    if ($evidence ne '' and $description ne '') {
+      my %row =  ('description' => $description,
+                  'evidence'    => $evidence,
+                  'source'      => $source);
+      push @annotExtRows, (\%row);
+    }
+  }
+  
+  return \@annotExtRows;
+}
+
 1;