From bfa51d99f8f8a52a4d96913605edf189f93d0b07 Mon Sep 17 00:00:00 2001
From: Graham McVicker <mcvicker@sanger.ac.uk>
Date: Fri, 20 Dec 2002 14:00:06 +0000
Subject: [PATCH] *** empty log message ***
---
modules/Bio/EnsEMBL/Utils/CreateTable.pm | 131 -------------
.../EnsEMBL/Utils/ExportProgramTemplate.txt | 125 -------------
.../Bio/EnsEMBL/Utils/ExportProgramWriter.pm | 57 ------
modules/Bio/EnsEMBL/Utils/SchemaTool.pl | 176 ------------------
4 files changed, 489 deletions(-)
delete mode 100644 modules/Bio/EnsEMBL/Utils/CreateTable.pm
delete mode 100644 modules/Bio/EnsEMBL/Utils/ExportProgramTemplate.txt
delete mode 100644 modules/Bio/EnsEMBL/Utils/ExportProgramWriter.pm
delete mode 100755 modules/Bio/EnsEMBL/Utils/SchemaTool.pl
diff --git a/modules/Bio/EnsEMBL/Utils/CreateTable.pm b/modules/Bio/EnsEMBL/Utils/CreateTable.pm
deleted file mode 100644
index 53566139bf..0000000000
--- a/modules/Bio/EnsEMBL/Utils/CreateTable.pm
+++ /dev/null
@@ -1,131 +0,0 @@
-package CreateTable;
-
-sub new {
- my $self = bless {};
- return $self;
-}
-
-sub get_table_name {
- my $this = shift;
- return $this->{'table_name'};
-}
-
-sub set_table_name {
- my $this = shift;
- $this->{'table_name'} = shift;
-}
-
-
-sub get_create_statement {
- my $this = shift;
- return $this->{'create_statement'};
-}
-
-# returns array by reference
-sub get_fields{
- my $this = shift;
- return $this->{'fields'};
-}
-
-# pass array by reference
-sub set_fields{
- my $this = shift;
- #my $tmp_fieds = shift;
- $this->{'fields'} = shift;
-}
-
-
-sub to_string {
- my $this = shift;
- return "CreateTable[" . $this->get_table_name() . ", " . $this->get_create_statement() . ", (" . scalar(@{$this->get_fields()}) . ")" . join(",", @{$this->get_fields()}) . "]";
-}
-
-
-sub equals {
- my $this=shift;
- my $other= shift;
-
- # check names same
- if ( $this->get_table_name() ne $other->get_table_name() ) {return 0;}
-
- # extract fields in order to compare them
- my @this_fields = @{$this->get_fields()};
- my @other_fields = @{$other->get_fields()};
- #print "THIS " . $this->get_table_name() . "\t" . scalar(@this_fields) . " --> " . join(":", @this_fields) . "\n";
- #print "OTHER " . $other->get_table_name() . "\t" . scalar(@other_fields) . " --> " . join(":", @other_fields)."\n";
-
- my $this_fields_len = scalar(@this_fields);
- my $other_fields_len = scalar(@other_fields);
- #check same number of fields
- if ( $this_fields_len != $other_fields_len ) {return 0;}
-
- #check same field names
- for (my $i=0; $i<$this_fields_len; ++$i) {
- if (@this_fields[$i] ne @other_fields[$i]) { return 0; }
- }
-
- return 1;
-}
-
-
-
-# Module function which returns 0 if no entry corresponding to
-# $table_name is found, otherwise returns a corresponding CreateTable
-# instance.
-
-sub create_from_string {
- my $table_name;
- my $string;
-
- my @fields;
- my $create_statement;
-
- my @complete_fields;
- my $field_index;
-
- #shift;
- ($table_name, $string) = @_;
-
- # extract the sql create table statement
- $string =~ /(create\s+table\s+$table_name\s*\(([^;]*\))\s*\)\s*;)/sig;
- $create_statement = $1;
- my $tmp_fields = $2;
- # remove all (...) sections because these can contain commas which would break our mechanism for sliptting fields at commas
- $tmp_fields =~ s/\([^\)]*\)//g;
- @complete_fields = split(",", $tmp_fields);
- @fields = [];
- $field_index = 0;
- for (my $i=0; $i<scalar(@complete_fields); ++$i) {
- @complete_fields[$i] =~ /^\s*(\w+)\s/;
- my $row = $1;
- unless ($row =~/PRIMARY/i || $row=~/KEY/i || $row=~/UNIQUE/i || $row=~/^\s*$/) {@fields[$field_index++] = $row;}
- }
-
- if ( !$create_statement || $create_statement eq "" ) {return 0;}
- else {
- my $v = CreateTable::new();
- $v->{'create_statement'} = $create_statement;
- $v->{'table_name'} = $table_name;
- $v->{'fields'} = \@fields;
- return $v;
- }
-}
-
-
-
-
-
-# returns array of all tables specified in schema string
-sub create_all_from_string {
- (my $schema) = @_;
-
- my @create_tables;
- my $i = 0;
- while($schema =~ m/(create\s*table\s*(\w+)\s*\(([^;]*\))\s*\)\s*;)/sig) {
- my $create_table = CreateTable::create_from_string($2, $1);
- @create_tables[$i++] = $create_table;
- }
- return @create_tables; # return by copying
-}
-
-1;
diff --git a/modules/Bio/EnsEMBL/Utils/ExportProgramTemplate.txt b/modules/Bio/EnsEMBL/Utils/ExportProgramTemplate.txt
deleted file mode 100644
index f703a65572..0000000000
--- a/modules/Bio/EnsEMBL/Utils/ExportProgramTemplate.txt
+++ /dev/null
@@ -1,125 +0,0 @@
-package PACKAGE_LABEL;
-
-# Fields are read from the database in the order specified in
-# @selection_list, they can then be modified, after loading, in the
-# function modify_loaded_values() before being written to a file.
-
-# If the fields to be read are different to that list in #
-# @selection_list then edit the list. Similarly if the values need #
-# modifying before being saved change modify_loaded_values().
-
-use DBI;
-use strict;
-use Getopt::Long;
-
-# @row is a global array used to hold row of data read from data
-# base.It can be modified in modify_loaded_values() before writing to
-# file as tab separated fields.
-
-my @row;
-my $verbose;
-
-
-# *********************************************************************
-# INPUT PARAMETERS
-#
-my $old_tables="OLD_TABLE_NAME";
-my $where="";
-INPUT_ARRAY
-# *********************************************************************
-
-# *********************************************************************
-# MODIFY VALUES LOADED IN BEFORE WRITING TO FILE
-sub modify_loaded_values {
- @row[0] = ensembl_id_to_int(@row[0]);
-}
-# *********************************************************************
-
-
-# *********************************************************************
-# TARGET SQL DATABASE TABLE
-#OUTPUT_TABLE_CREATE_STATEMENT
-# *********************************************************************
-
-
-
-main();
-
-
-sub main {
- # Handle command line params
- my $num_rows;
- my $all;
-
- GetOptions("num_rows:i" => \$num_rows,
- "all" => \$all,
- "verbose" => \$verbose);
-
- my $limit = ($num_rows) ? "limit $num_rows" : "limit 10";
- my $limit = ($all) ? "" : $limit;
-
- my $file_contents = export($old_tables, CONNECTION_STRING, USER, PASSWORD, $limit);
-
- # Write the export program to a file.
- open(OUTHANDLE, ">OUT_FILE_PATH");
- print OUTHANDLE $file_contents;
- close(OUTHANDLE);
-
- if ($verbose) {print $file_contents;}
-
-}
-
-
-sub ensembl_id_to_int {
- my $old_id = shift;
- $old_id =~ /[\D|0]*(\d*)/;
- return $1;
-}
-
-sub chr_name_to_int {
- (my $v) = @_;
- $v =~ s/chr//; # remove chr from string
- if ($v eq "x" || $v eq "X") {$v = 23} # map chr X to 23
- elsif ($v eq "y" || $v eq "Y") {$v = 24; } # map chr Y to 24
- return $v;
-}
-
-sub export {
- ( my $table,
- my $connection_string,
- my $user,
- my $password,
- my $limit ) = @_;
-
- my $db_old = DBI->connect ($connection_string, $user, $password);
- if (!$db_old) {
- print "Error connecting to old database; $DBI::errstr\n";
- exit 1;
- }
-
- # Construct the list of values to retrieve.
- my $selection_list;
- $selection_list = join(", ", @selection_list);
-
- # Get the old format data
- my $cmd = "select $selection_list from $table $where $limit";
- if ($verbose) {print "SQL query : " . $cmd . "\n";}
- $db_old->prepare($cmd);
-
- my $sth_old = $db_old->prepare($cmd);
- $sth_old->execute;
-
- my $export_program = "";
- while ((@row) = $sth_old->fetchrow_array) {
- modify_loaded_values();
- $export_program .= join("\t", @row) . "\n";
- }
-
- $sth_old->finish();
- $db_old->disconnect();
-
- return $export_program;
-}
-
-
-1;
diff --git a/modules/Bio/EnsEMBL/Utils/ExportProgramWriter.pm b/modules/Bio/EnsEMBL/Utils/ExportProgramWriter.pm
deleted file mode 100644
index f4e52e2042..0000000000
--- a/modules/Bio/EnsEMBL/Utils/ExportProgramWriter.pm
+++ /dev/null
@@ -1,57 +0,0 @@
-package ExportProgramWriter;
-
-use CreateTable;
-
-sub create_export_program {
- (my $package_label,
- my $new_create_table,
- my $old_create_table) = @_;
-
- my $new_table_name = $new_create_table->get_table_name();
- my $old_table_name = $old_create_table->get_table_name();
-
- my $template;
- open(TEMPLATE, "ExportProgramTemplate.txt") || die "can not open file: $!";;
- while(<TEMPLATE>) {
- $template .= $_;
- }
-
- my @old_fields = @{$old_create_table->get_fields()};
- my $old_fields = join(", ", @old_fields);
-
- my @new_fields = @{$new_create_table->get_fields()};
- my $new_fields = join(", ", @new_fields);
- my $new_table_create_statement = $new_create_table->get_create_statement();
-
-
- my $old_max = scalar(@old_fields);
- my $new_max = scalar(@new_fields);
- my $max = ($old_max>$new_max) ? $old_max : $new_max;
-
- my $mapping = ($old_max!=$new_max) ? "# WARNING INCOMPATIBLE NUMBER OF FIELDS\n": "\n";
- $mapping .= "my \@selection_list;\n";
- for (my $i=0; $i<$max; ++$i) {
- my $old_field = @old_fields[$i];
- my $new_field = @new_fields[$i];
- my $too_many = ($i>=$new_max) ? "**WARNNING TOO MANY OLD FIELDS**" : "";
- my $hide = ($i>=$new_max) ? "#" : "";
- $mapping .= "$hide\@selection_list[$i] \t= \"" . $old_field . "\"; # $new_field $too_many\n";
- }
-
- # search and replace KEYWORDS in template
- my $filename = $new_table_name . ".txt";
- $template=~ s/OUT_FILE_PATH/$filename/s;
- $template=~ s/OLD_TABLE_NAME/$old_table_name/s;
- $template=~ s/NEW_TABLE_CREATE_STATEMENT/$new_table_create_statement/s;
- $template=~ s/INPUT_ARRAY/$mapping/s;
- $template=~ s/CONNECTION_STRING/"DBI:mysql:homo_sapiens_core_110:ensrv3:3306",/s;
- $template=~ s/USER/"ensro"/s;
- $template=~ s/PASSWORD/""/s;
- my $table_statment = $new_table_create_statement;
- $table_statment =~ s/^|\n/\n#/gs;
- $template=~ s/OUTPUT_TABLE_CREATE_STATEMENT/$table_statment/s;
-
- return $template;
-}
-
-1;
diff --git a/modules/Bio/EnsEMBL/Utils/SchemaTool.pl b/modules/Bio/EnsEMBL/Utils/SchemaTool.pl
deleted file mode 100755
index 7ec8123f0b..0000000000
--- a/modules/Bio/EnsEMBL/Utils/SchemaTool.pl
+++ /dev/null
@@ -1,176 +0,0 @@
-#!/usr/bin/env perl
-
-# Command line front end to ExportProgramWriter.pm.
-#
-# Use --help for help.
-
-use ExportProgramWriter;
-use Carp;
-use Getopt::Long;
-
-# Command line param variables. e.g. --newtable value stored in $newtable
-my $verbose;
-my $help;
-my $outdir;
-my $newtable;
-my $oldtable;
-my $print;
-
-# Created during compare_two_schema()
-my @unchanged = [];
-my @changed = [];
-my @novel = [];
-
-
-main();
-
-sub main {
- GetOptions(
- "verbose" => \$verbose,
- "help" => \$help,
- "outdir:s" => \$outdir,
- "newtable:s" => \$newtable,
- "oldtable:s" => \$oldtable,
- "print" => \$print
- );
-
- if (scalar($help || @ARGV)==0) {
- print "usage: $0 <--print> <--verbose> <--newtable NEW_TABLE_NAME <--oldtable OLD_TABLE_NAME>> <--outdir OUTPUT_DIR> new_schema_filename old_schema_filename \n";
- print "usage: $0 --help\n";
- exit 1;
-
- }
-
- elsif ($newtable) {
- if ( !$oldtable ) { $oldtable = $newtable; }
- create_specific_export_program($newtable, @ARGV[0], $oldtable, @ARGV[1]);
- }
-
- elsif (scalar(@ARGV)==2) {
- compare_two_schemas(@ARGV[1], @ARGV[0]);
- if ( !$print ) {
- create_many_export_programs("Creating export program for Changed table : ", @changed);
- create_many_export_programs("Creating export program for Novel table : ", @novel);
- }
- }
-
-
-}
-
-
-sub file_to_string {
- (my $filename) = @_;
- my $str = "";
- open(INFILE, $filename)|| confess "cannot open \"$filename\": $!";
- $str = join("", <INFILE>);
- close(INFILE);
- return $str;
-}
-
-
-sub save {
- (my $package_name,
- my $new_create_table,
- my $old_create_table) =@_;
-
- my $filename = $package_name;
- $filename =~ s/::/\//g;
- $filename .= ".pm";
- $filename = $outdir . "/" . $filename;
-
- open(OUTFILE, ">" . $filename) || die "failed to open file $filename : $!";
- print OUTFILE ExportProgramWriter::create_export_program($package_name,
- $new_create_table,
- $old_create_table);
- close(OUTFILE);
-}
-
-
-sub create_many_export_programs {
- (my $description, my @new_old_pairs) = @_;
-
- foreach $pair (@new_old_pairs) {
- my $new_create_table = @{$pair}[0];
- my $old_create_table = @{$pair}[1];
- my $package_name = ucfirst($new_create_table->get_table_name());
- if ($verbose) {print $description . $new_create_table->get_table_name() . "\n"};
- save($package_name, $new_create_table, $old_create_table);
- }
-}
-
-
-sub create_specific_export_program {
- ( my $new_table_name,
- my $new_schema_file,
- my $old_table_name,
- my $old_schema_file, ) = @_;
-
- my $package_name = ucfirst($new_table_name);
-
- my $new_schema = file_to_string($new_schema_file);
- my $old_schema = file_to_string($old_schema_file);
-
- my $new_create_table = CreateTable::create_from_string($new_table_name, $new_schema);
- my $old_create_table = CreateTable::create_from_string($old_table_name, $old_schema);
- if ($old_create_table==0) {
- $old_create_table = CreateTable::new();
- }
- save($package_name, $new_create_table, $old_create_table);
-}
-
-
-
-sub compare_two_schemas {
- (my $new_schema_filename, my $old_schema_filename) = @_;
-
- # Read in new schema file and create CreateTable objects for each..
-
- my $new_schema = file_to_string($new_schema_filename);
- my $old_schema = file_to_string($old_schema_filename);
- my @create_tables = CreateTable::create_all_from_string($new_schema);
-
- # Identify different tables.
- my $len = scalar(@create_tables);
-
- my $unchanged_index = 0;
- my $changed_index = 0;
- my $novel_index = 0;
-
- my $empty_create_table = CreateTable::new();
- $empty_create_table->set_table_name("****UNKNOWN*****");
- my @empty = [];
- $empty_create_table->set_fields(\@empty);
-
- print "EMPTY TABLE : " . $empty_create_table->to_string() . "\n";
-
- for(my $i=0; $i<$len; ++$i) {
- # look for a correspondingly named table in the old file
- my $new_create_table = @create_tables[$i];
- my $new_table_name = $new_create_table->get_table_name();
- my $equivalent_old_create_table = CreateTable::create_from_string( $new_table_name, $old_schema);
-
- if ( $verbose ) {print "$i/$len " . $new_create_table->get_table_name() . " ";}
-
- if ( !$equivalent_old_create_table ) {
- #@novel[$novel_index++] = $new_create_table;
- @novel[$novel_index++] = ([$new_create_table, $empty_create_table]);
- if ( $verbose ) {print "UNKOWN\n";}
- }
- elsif ( $new_create_table->equals($equivalent_old_create_table) ) {
- #@unchanged[$unchanged_index++] = $new_create_table;
- @unchanged[$unchanged_index++] = ([$new_create_table, $equivalent_old_create_table]);
- if ( $verbose ) {print "SAME\n" . join(",", @{$new_create_table->get_fields()}) . "\n" . join(",", @{$equivalent_old_create_table->get_fields()}) . "\n";}
- }
- else {
- #@changed[$changed_index++] = $new_create_table;
- @changed[$changed_index++] = ([$new_create_table, $equivalent_old_create_table]);
- if ( $verbose ) {print "CHANGED\n" . join(",", @{$new_create_table->get_fields()}) . "\n" . join(",", @{$equivalent_old_create_table->get_fields()}) . "\n";}
- }
- }
-
- print "Unchanged : " . scalar(@unchanged) ."\n";
- print "Changed : " . scalar(@changed) ."\n";
- print "Novel : " . scalar(@novel) ."\n";
-
-
-}
--
GitLab