From 689243152447213fe2e272149a871288c35e0b9b Mon Sep 17 00:00:00 2001
From: Arne Stabenau <stabenau@sanger.ac.uk>
Date: Wed, 24 Nov 2004 10:05:35 +0000
Subject: [PATCH] not workibng layout for attribute type loading system
---
misc-scripts/attribute_types/attrib_type.txt | 14 +++
.../attribute_types/upload_attributes.pl | 105 ++++++++++++++++++
2 files changed, 119 insertions(+)
create mode 100644 misc-scripts/attribute_types/attrib_type.txt
create mode 100644 misc-scripts/attribute_types/upload_attributes.pl
diff --git a/misc-scripts/attribute_types/attrib_type.txt b/misc-scripts/attribute_types/attrib_type.txt
new file mode 100644
index 0000000000..2071db6229
--- /dev/null
+++ b/misc-scripts/attribute_types/attrib_type.txt
@@ -0,0 +1,14 @@
+# this file is intended to hold all valid attrib_type
+# table entries for all ensembl databases that we release
+#
+# If you use the provided upload script, commentlines and
+# emptry lines should be automatically removed, all
+# other lines should contain tab delimited database entries
+# for the attrib_type table
+
+# each attribute type should be preceeded with a comment that
+# describes its uses.
+
+
+
+
diff --git a/misc-scripts/attribute_types/upload_attributes.pl b/misc-scripts/attribute_types/upload_attributes.pl
new file mode 100644
index 0000000000..2fdbd419b9
--- /dev/null
+++ b/misc-scripts/attribute_types/upload_attributes.pl
@@ -0,0 +1,105 @@
+# Stolen from external db directory this script performs
+# the similar function of uploading all valid attribute types
+# into the attrib_type table of all databases that are going to
+# be released.
+
+
+use strict;
+
+use Getopt::Long;
+use DBI;
+use IO::File;
+use FindBin;
+
+
+my ( $host, $user, $pass, $port,@dbnames, $file, $release_num);
+
+GetOptions( "host=s", \$host,
+ "user=s", \$user,
+ "pass=s", \$pass,
+ "port=i", \$port,
+ "file=s", \$file,
+ "dbnames=s@", \@dbnames,
+ "release_num=i", \$release_num
+ );
+
+$file ||= $FindBin::Bin."/attrib_type.txt";
+usage() if(!$host);
+
+
+
+#release num XOR dbname are required
+usage() if(($release_num && @dbnames) || (!$release_num && !@dbnames));
+my $attribs = read_attrib_file( $file );
+
+$port ||= 3306;
+
+my $dsn = "DBI:mysql:host=$host;port=$port";
+
+my $db = DBI->connect( $dsn, $user, $pass, {RaiseError => 1} );
+
+if($release_num) {
+ @dbnames = map {$_->[0] } @{ $db->selectall_arrayref( "show databases" ) };
+
+ #
+ # filter out all non-core databases
+ #
+ @dbnames = grep {/^[a-zA-Z]+\_[a-zA-Z]+\_(core|est|estgene|vega)\_${release_num}\_\d+[A-Za-z]?$/} @dbnames;
+}
+
+
+#
+# make sure the user wishes to continue
+#
+print STDERR "The following databases will be external_db updated:\n ";
+print join("\n ", @dbnames);
+print "\ncontinue with update (yes/no)> ";
+
+my $input = lc(<STDIN>);
+chomp($input);
+if($input ne 'yes') {
+ print "Attrib_type loading aborted\n";
+ exit();
+}
+
+# if any attrib_types are loaded that are different from
+# the file, a consistency problem is reported and the
+# upload is not done.
+
+# alternatively consistency can be enforceed to a certain degree
+sub check_consistency {
+ my $attribs = shift;
+ my $database_names = shift;
+ my $db = shift;
+
+}
+
+
+
+sub read_attrib_file {
+ my $file = shift;
+ #
+ # read all attrib_type entries from the file
+ #
+ my $fh = IO::File->new();
+ $fh->open($file) or die("could not open input file $file");
+
+ my @rows;
+ my $row;
+ while($row = <$fh>) {
+ chomp($row);
+ next if( /^\S*$/ );
+ next if ( /^\#/ );
+
+ my @a = split(/\t/, $row);
+
+ push @rows, {'attrib_type_id' => $a[0],
+ 'code' => $a[1],
+ 'name' => $a[2],
+ 'description' => $a[3]};
+ }
+ $fh->close();
+ return \@rows;
+}
+
+
--
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