diff --git a/misc-scripts/xref_mapping/XrefParser/BaseParser.pm b/misc-scripts/xref_mapping/XrefParser/BaseParser.pm index fb71fd74dcf8c915997fa3abd48e5d7daeaec846..8350bbfc14080c60ffbc5c6d9bbe671652a99c9a 100644 --- a/misc-scripts/xref_mapping/XrefParser/BaseParser.pm +++ b/misc-scripts/xref_mapping/XrefParser/BaseParser.pm @@ -1426,6 +1426,7 @@ sub get_direct_xref{ return undef; } + sub get_xref{ my ($self,$acc,$source) = @_; @@ -1461,12 +1462,28 @@ sub add_xref { sub add_to_xrefs{ my ($self,$master_xref,$acc,$version,$label,$description,$linkage,$source_id,$species_id) = @_; + $master_xref || die( "Need a master_xref_id on which this xref depends" ); + $acc || die( "Need an accession of this dependent xref" ); + $version ||= 0; + $label ||= $acc; + $description ||= undef; + $linkage ||= undef; + $source_id || die( "Need a source_id for this dependent xref" ); + $species_id || die( "Need a species_id for this dependent xref" ); + if(!defined($add_xref_sth)){ - $add_xref_sth = dbi->prepare("INSERT INTO xref (accession,version,label,description,source_id,species_id)". - " VALUES(?,?,?,?,?,?)"); + $add_xref_sth = dbi->prepare(" +INSERT INTO xref + (accession,version,label,description,source_id,species_id) +VALUES + (?,?,?,?,?,?)"); } if(!defined($add_dependent_xref_sth)){ - $add_dependent_xref_sth = dbi->prepare("INSERT INTO dependent_xref VALUES(?,?,?,?)"); + $add_dependent_xref_sth = dbi->prepare(" +INSERT INTO dependent_xref + (master_xref_id,dependent_xref_id,linkage_annotation,linkage_source_id) +VALUES + (?,?,?,?)"); } my $dependent_id = $self->get_xref($acc, $source_id);