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Commit cbfefbe1 authored by Ian Longden's avatar Ian Longden
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deleteexisting will only delete the sources which are being updated

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misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
+ 100
− 26
View file @ cbfefbe1
......@@ -48,6 +48,8 @@ my %source_to_external_db;
my %xrefs_written;
my %object_xrefs_written;
my %failed_xref_mappings;
my %updated_source;
=head2 new
Description: Constructor for BasicMapper.
......@@ -1028,6 +1030,9 @@ sub dump_triage_data() {
if (!$xrefs_written{$xref_id}) {
$xrefs_written{$xref_id} = 1;
my $external_db_id = $source_to_external_db{$source_id};
if(!defined($updated_source{$external_db_id})){
$self->cleanup_sources_file($external_db_id);
}
print XREF ($xref_id+$xref_id_offset) . "\t" . $external_db_id . "\t" . $accession . "\t" . $label . "\t" . $version . "\t" . $description . "\n";
if(defined($failed_xref_mappings{$xref_id})){
my ($ensembl_id,$type,$q_perc,$t_perc,$q_cut,$t_cut) = split(/\|/,$failed_xref_mappings{$xref_id});
......@@ -1080,6 +1085,9 @@ sub dump_orphan_xrefs() {
my $external_db_id = $source_to_external_db{$source_id};
if ($external_db_id) { # skip "unknown" sources
if (!$xrefs_written{$xref_id}) {
if(!defined($updated_source{$external_db_id})){
$self->cleanup_sources_file($external_db_id);
}
print XREF ($xref_id+$xref_id_offset) . "\t" . $external_db_id . "\t" . $accession . "\t" . $label . "\t" . $version . "\t" . $description . "\n";
$xrefs_written{$xref_id} = 1;
......@@ -1155,6 +1163,9 @@ sub dump_direct_xrefs {
if ($ensembl_internal_id) {
if (!$xrefs_written{$xref_id}) {
if(!defined($updated_source{$external_db_id})){
$self->cleanup_sources_file($external_db_id);
}
print XREF ($xref_id+$xref_id_offset) . "\t" . $external_db_id . "\t" . $accession . "\t" . $label . "\t" . $version . "\t" . $description . "\n";
$xrefs_written{$xref_id} = 1;
}
......@@ -1177,6 +1188,9 @@ sub dump_direct_xrefs {
if ($stable_id =~ /$pat/) {
if (!$xrefs_written{$xref_id}) {
if(!defined($updated_source{$external_db_id})){
$self->cleanup_sources_file($external_db_id);
}
print XREF ($xref_id+$xref_id_offset) . "\t" . $external_db_id . "\t" . $accession . "\t" . $label . "\t" . $version . "\t" . $description . "\n";
$xrefs_written{$xref_id} = 1;
}
......@@ -1413,6 +1427,9 @@ sub dump_core_xrefs {
if (!$xrefs_written{$xref_id}) {
my $external_db_id = $source_to_external_db{$source_id};
if ($external_db_id) { # skip "unknown" sources
if(!defined($updated_source{$external_db_id})){
$self->cleanup_sources_file($external_db_id);
}
print XREF ($xref_id+$xref_id_offset) . "\t" . $external_db_id . "\t" . $accession . "\t" . $label . "\t" . $version . "\t" . $description . "\n";
$xrefs_written{$xref_id} = 1;
$source_ids{$source_id} = $source_id;
......@@ -1439,6 +1456,9 @@ sub dump_core_xrefs {
$label = $accession if (!$label);
if (!$xrefs_written{$xref_id}) {
if(!defined($updated_source{$external_db_id})){
$self->cleanup_sources_file($external_db_id);
}
print XREF ($xref_id+$xref_id_offset) . "\t" . $external_db_id . "\t" . $accession . "\t" . $label . "\t" . $version . "\t" . $description . "\tDEPENDENT\n";
$xrefs_written{$xref_id} = 1;
$source_ids{$source_id} = $source_id;
......@@ -1928,6 +1948,41 @@ sub map_source_to_external_db {
return %source_to_external_db;
}
sub cleanup_sources_file{
my ($self,$id) = @_;
$updated_source{$id} =1;
my $dir = $self->core->dir();
open (DEL, ">>$dir/cleanup.sql") || die "Could not open $dir/cleanup.sql\n";
print DEL "DELETE external_synonym ";
print DEL "FROM external_synonym, xref ";
print DEL "WHERE external_synonym.xref_id = xref.xref_id ";
print DEL "AND xref.external_db_id = $id\n";
print DEL "DELETE identity_xref ";
print DEL "FROM identity_xref, object_xref, xref ";
print DEL "WHERE identity_xref.object_xref_id = object_xref.object_xref_id ";
print DEL "AND object_xref.xref_id = xref.xref_id ";
print DEL "AND xref.external_db_id = $id \n";
print DEL "DELETE object_xref ";
print DEL "FROM object_xref, xref ";
print DEL "WHERE object_xref.xref_id = xref.xref_id ";
print DEL "AND xref.external_db_id = $id\n";
print DEL "DELETE FROM xref WHERE xref.external_db_id = $id \n";
close DEL;
}
# Upload .txt files and execute .sql files.
sub do_upload {
......@@ -1938,7 +1993,46 @@ sub do_upload {
my $core_db = $ensembl->dbc;
# xref.txt etc
# TODO warn if table not empty
if(defined($self->delete_existing())){
my $file = $ensembl->dir() . "/cleanup.sql";
open(CLEAN,"<$file") || die "could not open $file for reading \n";
while(<CLEAN>){
chomp;
my $sth = $core_db->prepare($_);
$sth->execute() or die "Couldn't execute statement: " . $sth->errstr;
}
close CLEAN;
#
# used execute to make getting errors easier.
# my $str = "mysql -u" .$core_db->username() ." -p" . $core_db->password() . " -h " . $core_db->host() ." -P " . $core_db->port() . " " .$core_db->dbname() . " < $file";
# system $str;
foreach my $table ("go_xref", "interpro") {
my $sth = $core_db->prepare("DELETE FROM $table");
print "Deleting existing data in $table\n";
$sth->execute();
}
# gene_display_xref.sql etc
foreach my $table ("gene", "transcript") {
my $sth = $core_db->prepare("UPDATE $table SET display_xref_id=NULL");
print "Setting all existing display_xref_id in $table to null\n";
$sth->execute();
}
# gene descriptions
my $sth = $core_db->prepare("UPDATE gene SET description=NULL");
print "Setting all existing descriptions in gene table to null\n";
$sth->execute();
}
foreach my $table ("xref", "object_xref", "identity_xref", "external_synonym", "go_xref", "interpro") {
......@@ -1981,33 +2075,12 @@ sub do_upload {
sub delete_existing {
my $self = shift;
my $ensembl = $self->core;
my $core_db = $ensembl->dbc;
# xref.txt etc
foreach my $table ("xref", "object_xref", "identity_xref", "external_synonym", "go_xref", "interpro") {
my $sth = $core_db->prepare("DELETE FROM $table");
print "Deleting existing data in $table\n";
$sth->execute();
}
# gene_display_xref.sql etc
foreach my $table ("gene", "transcript") {
my $sth = $core_db->prepare("UPDATE $table SET display_xref_id=NULL");
print "Setting all existing display_xref_id in $table to null\n";
$sth->execute();
my ($self, $arg) = @_;
}
(defined $arg) &&
($self->{_delete_existing} = $arg );
return $self->{_delete_existing};
# gene descriptions
my $sth = $core_db->prepare("UPDATE gene SET description=NULL");
print "Setting all existing descriptions in gene table to null\n";
$sth->execute();
}
......@@ -2141,6 +2214,7 @@ sub filter_by_regexp {
foreach my $regexp (@$regexps) {
$str =~ s/$regexp//ig;
$str =~ s/\"//ig;
}
return $str;
......
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