From 01d230ecb932651d5300f5aabb85237aaf385140 Mon Sep 17 00:00:00 2001
From: Glenn Proctor <gp1@sanger.ac.uk>
Date: Wed, 15 Dec 2004 12:01:33 +0000
Subject: [PATCH] Added support for uploading generated xrefs etc directly.
---
.../xref_mapping/XrefMapper/BasicMapper.pm | 82 ++++++++++++++++---
1 file changed, 71 insertions(+), 11 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
index 02ef511e58..f3bed84d2d 100644
--- a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
@@ -1,6 +1,7 @@
package XrefMapper::BasicMapper;
use strict;
+use Cwd;
use DBI;
use File::Basename;
use IPC::Open3;
@@ -389,12 +390,12 @@ sub fetch_and_dump_seq{
my ($self) = @_;
my $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(-species => $self->species(),
- -dbname => $self->dbname(),
- -host => $self->host(),
- -port => $self->port(),
- -password => $self->password(),
- -user => $self->user(),
- -group => 'core');
+ -dbname => $self->dbname(),
+ -host => $self->host(),
+ -port => $self->port(),
+ -pass => $self->password(),
+ -user => $self->user(),
+ -group => 'core');
#
# store ensembl dna file name and open it
@@ -701,7 +702,7 @@ sub parse_mappings {
my $row = @{$self->dbi()->selectall_arrayref("SELECT MAX(object_xref_id) FROM object_xref")}[0];
my $max_object_xref_id = @{$row}[0];
if (!defined $max_object_xref_id) {
- print "Can't get highest existing object_xref_id, using 1\n)";
+ print "Can't get highest existing object_xref_id, using 1\n";
} else {
print "Maximum existing object_xref_id = $max_object_xref_id\n";
$max_object_xref_id = 1;
@@ -976,7 +977,7 @@ sub dump_core_xrefs {
# create an object_xref linking this (dependent) xref with any objects it maps to
# write to file and add to object_xref_mappings
- if (defined $xref_to_objects{$master_xref_id}) { # XXX check
+ if (defined $xref_to_objects{$master_xref_id}) { # XXX check
my @ensembl_object_ids = keys( %{$xref_to_objects{$master_xref_id}} ); # XXX check
#print "xref $accession has " . scalar(@ensembl_object_ids) . " associated ensembl objects\n";
foreach my $object_id (@ensembl_object_ids) {
@@ -1169,9 +1170,9 @@ sub build_gene_display_xrefs {
-dbname => $self->dbname(),
-host => $self->host(),
-port => $self->port(),
- -password => $self->password(),
- -user => $self->user(),
- -group => 'core');
+ -pass => $self->password(),
+ -user => $self->user(),
+ -group => 'core');
my $ta = $db->get_TranscriptAdaptor();
print "Building gene display_xrefs\n";
@@ -1318,4 +1319,63 @@ sub map_source_to_external_db {
return %source_to_external_db;
}
+# Upload .txt files and execute .sql files.
+
+sub do_upload {
+
+ my ($self, $deleteexisting) = @_;
+
+ # xref.txt etc
+
+ # TODO warn if table not empty
+
+ foreach my $table ("xref", "object_xref", "identity_xref", "external_synonym") {
+
+ my $file = getcwd() . "/" . $table . ".txt";
+ my $sth;
+
+ if ($deleteexisting) {
+
+ $sth = $self->dbi()->prepare("DELETE FROM $table");
+ print "Deleting existing data in $table\n";
+ $sth->execute();
+
+ }
+
+ # don't seem to be able to use prepared statements here
+ $sth = $self->dbi()->prepare("LOAD DATA INFILE \'$file\' INTO TABLE $table");
+ print "Uploading data in $file to $table\n";
+ $sth->execute();
+
+ }
+
+ # gene_display_xref.sql etc
+ foreach my $table ("gene", "transcript") {
+
+ my $file = getcwd() . "/" . $table . "_display_xref.sql";
+ my $sth;
+
+ if ($deleteexisting) {
+
+ $sth = $self->dbi()->prepare("UPDATE $table SET display_xref_id=NULL");
+ print "Setting all existing display_xref_id in $table to NULL\n";
+ $sth->execute();
+
+ }
+
+ # is this nicer than using the mysql client?
+ open(DISPLAY_XREF, $file);
+ while(<DISPLAY_XREF>) {
+
+ $sth = $self->dbi()->prepare($_);
+ print $_;
+ #$sth->execute();
+
+ }
+
+ close(DISPLAY_XREF);
+
+ }
+
+}
1;
--
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