diff bin/DBSchemaTablesToTextFiles.pl @ 0:4816e4a8ae95 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bin/DBSchemaTablesToTextFiles.pl	Wed Jan 20 09:23:18 2016 -0500
@@ -0,0 +1,470 @@
+#!/usr/bin/perl -w
+#
+# $RCSfile: DBSchemaTablesToTextFiles.pl,v $
+# $Date: 2015/02/28 20:46:19 $
+# $Revision: 1.31 $
+#
+# Author: Manish Sud <[e-mail]>
+#
+# Copyright (C) 2015 Manish Sud. All rights reserved.
+#
+# This file is part of MayaChemTools.
+#
+# MayaChemTools is free software; you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation; either version 3 of the License, or (at your option) any
+# later version.
+#
+# MayaChemTools is distributed in the hope that it will be useful, but without
+# any warranty; without even the implied warranty of merchantability of fitness
+# for a particular purpose.  See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or
+# write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,
+# Boston, MA, 02111-1307, USA.
+#
+
+use strict;
+use FindBin; use lib "$FindBin::Bin/../lib";
+use Getopt::Long;
+use File::Basename;
+use Text::ParseWords;
+use Benchmark;
+use FileUtil;
+use TextUtil;
+use DBUtil;
+
+my($ScriptName, %Options, $StartTime, $EndTime, $TotalTime);
+
+# Autoflush STDOUT
+$| = 1;
+
+# Starting message...
+$ScriptName = basename($0);
+print "\n$ScriptName: Starting...\n\n";
+$StartTime = new Benchmark;
+
+# Get the options and setup script...
+SetupScriptUsage();
+if ($Options{help} || @ARGV < 1) {
+  die GetUsageFromPod("$FindBin::Bin/$ScriptName");
+}
+
+my($DBDriver, $DBHost, $DBName, $DBUser, $DBPassword, $DBMode, $ExportDataLabels, $ExportLOBs, $OutDelim, $OutQuote, $ReplaceNullStr);
+ProcessOptions();
+
+# Connect to database...
+my($DBHandle);
+print "Connecting to $DBDriver:database=$DBName as $DBUser...\n";
+$DBHandle = DBConnect($DBDriver, $DBName, $DBHost, $DBUser, $DBPassword);
+
+# Collect input parameters information...
+print "Checking input parameter(s)...\n";
+my(@DBSchemaNames, @DBTableNames, @DBSQLStatements, @DBTextFiles, $SingleTextFileName);
+RetrieveDBInfo();
+
+if ($Options{numoutfiles} =~ /^single$/i ) {
+  GenerateSingleTextFile();
+}
+else {
+  GenerateMultipleTextFiles();
+}
+print "\nDisconnecting from  $DBDriver:database=$DBName...\n";
+DBDisconnect($DBHandle);
+
+print "$ScriptName:Done...\n\n";
+
+$EndTime = new Benchmark;
+$TotalTime = timediff ($EndTime, $StartTime);
+print "Total time: ", timestr($TotalTime), "\n";
+
+###############################################################################
+
+# Generate multiple text files...
+sub GenerateMultipleTextFiles {
+  my($Index, $TextFile, $SQL);
+  if (@DBTextFiles > 1) {
+    print "Generating text files...\n";
+  }
+ TEXTFILE: for $Index (0 .. $#DBTextFiles) {
+    $TextFile = $DBTextFiles[$Index];
+    $SQL = $DBSQLStatements[$Index];
+
+    if (@DBTextFiles > 1) {
+      print "\nGenerating text file $TextFile...\n";
+    }
+    else {
+      print "Generating text file $TextFile...\n";
+    }
+
+    if (!open TEXTFILE, ">$TextFile") {
+      warn "Warning: Abandoning $TextFile generation: Couldn't open it: $! \n";
+      next TEXTFILE;
+    }
+    print "Processing SQL statement \"$SQL\"...\n";
+
+    if (DBSQLToTextFile($DBHandle, $SQL, \*TEXTFILE, $OutDelim, $OutQuote, $ExportDataLabels, $ExportLOBs, $ReplaceNullStr)) {
+      warn "Warning: Abandoning $TextFile generation...\n";
+      next TEXTFILE;
+    }
+    close TEXTFILE;
+  }
+}
+
+# Generate single text file...
+sub GenerateSingleTextFile {
+  my($Index, $TextFile, $SQL, $SchemaName, $TableName);
+
+  open TEXTFILE, ">$SingleTextFileName" or die "Couldn't open $SingleTextFileName: $! \n";
+  print "Generating text file $SingleTextFileName...\n";
+
+  SQL: for $Index (0 .. $#DBSQLStatements) {
+    $SchemaName = $DBSchemaNames[$Index];
+    $TableName = $DBTableNames[$Index];
+    $SQL = $DBSQLStatements[$Index];
+
+    $TableName = qq($SchemaName.$TableName);
+    $TableName = QuoteAWord($TableName, $OutQuote);
+    print TEXTFILE "\n\n$TableName\n";
+
+    if (DBSQLToTextFile($DBHandle, $SQL, \*TEXTFILE, $OutDelim, $OutQuote, $ExportDataLabels, $ExportLOBs, $ReplaceNullStr)) {
+      warn "Warning: Abandoning table $TableName ...\n";
+      next SQL;
+    }
+  }
+  close TEXTFILE;
+}
+
+# Collect input parameters information...
+sub RetrieveDBInfo {
+  my($FileExt, $UserFileName, $FileDBPrefix);
+
+  # Setup out file ext...
+  $FileExt = ($Options{outdelim} =~ /^tab$/i) ? "tsv" : "csv";
+  $FileDBPrefix = ($DBMode =~ /^exportdata$/i) ? "Export" : "Describe";
+
+  # Get user specified information...
+  $UserFileName = "";
+  if ($Options{root} && (@ARGV == 1)) {
+    my($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($Options{root});
+    if ($RootFileName && $RootFileExt) {
+      $UserFileName = $RootFileName;
+    }
+    else {
+      $UserFileName = $Options{root};
+    }
+  }
+  $SingleTextFileName = "";
+  if ($Options{numoutfiles} =~ /^single$/i) {
+    $SingleTextFileName = $UserFileName ? $UserFileName : ("$FileDBPrefix" . "SchemaTables");
+    $SingleTextFileName .= ".$FileExt";
+  }
+
+  # For each input schema name: collect all the table names, set up appropriate
+  # SQL statements, and output file names...
+  #
+  my($SchemaName, $SQL, $FileName, @SchemaTableNames, $TableName);
+  @DBSchemaNames = ();
+  @DBTableNames = ();
+  @DBSQLStatements = ();
+  @DBTextFiles = ();
+  @SchemaTableNames = ();
+  SCHEMANAME: for $SchemaName (@ARGV) {
+    $SchemaName = ($DBDriver =~ /^(mysql|Oracle)$/i) ? uc($SchemaName) : $SchemaName;
+    if (!(@SchemaTableNames = DBFetchSchemaTableNames($DBDriver, $DBHandle, $SchemaName))) {
+      warn "Warning: Ignoring schema $SchemaName...\n";
+      next SCHEMANAME;
+    }
+    # Prepare SQL statement for each table.
+    for $TableName (@SchemaTableNames) {
+      push @DBSchemaNames, $SchemaName;
+      push @DBTableNames, $TableName;
+      $SQL = ($DBMode =~ /^exportdata$/i) ? DBSetupSelectSQL($DBDriver, $TableName, $SchemaName) : DBSetupDescribeSQL($DBDriver, $TableName, $SchemaName);
+      push @DBSQLStatements, $SQL;
+      if ($Options{numoutfiles} =~ /^multiple$/i) {
+	$FileName = $UserFileName ? ("$UserFileName" . "$TableName") : ("$FileDBPrefix" . "$SchemaName" . "$TableName");
+	$FileName .= ".$FileExt";
+	if (!$Options{overwrite}) {
+	  if (-e $FileName) {
+	    die "Error: The file $FileName already exists.\n";
+	  }
+	}
+	push @DBTextFiles, $FileName;
+      }
+    }
+  }
+}
+
+# Process option values...
+sub ProcessOptions {
+
+  $DBDriver = $Options{dbdriver} ? $Options{dbdriver} : (exists $ENV{DBI_DRIVER} ? $ENV{DBI_DRIVER} : "") ;
+  if ($DBDriver) {
+    if ($DBDriver =~ /^oracle$/i) {
+      $DBDriver = "Oracle";
+    }
+    elsif ($DBDriver =~ /^mysql$/i) {
+      $DBDriver = "mysql";
+    }
+    elsif ($DBDriver =~ /^(Pg|Postgres)$/i) {
+      $DBDriver = "Pg";
+    }
+    else {
+      if ($Options{dbdriver}) {
+	die "Error: The value specified, $DBDriver, for option \"-d --dbdriver\" is not valid. Allowed values: MySQL, Oracle, Postgres or Pg\n";
+      }
+      else {
+	die "Error: The value specified, $DBDriver, using environment variable DBI_DRIVER not valid. Allowed values: MySQL, Oracle, Postgres or Pg\n";
+      }
+    }
+  }
+  else {
+    $DBDriver = "mysql";
+  }
+  $DBHost = $Options{dbhost} ? $Options{dbhost} : (exists $ENV{DBI_HOST} ? $ENV{DBI_HOST} : "127.0.0.1");
+  $DBName = $Options{dbname} ? $Options{dbname} : (exists $ENV{DBI_NAME} ? $ENV{DBI_NAME} : "");
+  if (!$DBName) {
+    if ($DBDriver =~ /^mysql$/i) {
+      $DBName = "mysql";
+    }
+  }
+  $DBUser = $Options{dbusername} ? $Options{dbusername} : (exists $ENV{DBI_USER} ? $ENV{DBI_USER} : "") ;
+  if (!$DBUser) {
+    die "Error: No database username specified. Use \"--dbusername\" option or environment variable DBI_USER to enter a valid value.\n";
+  }
+  $DBPassword = $Options{dbpassword} ? $Options{dbpassword} : (exists $ENV{DBI_PASS} ? $ENV{DBI_PASS} : "") ;
+  if (!$DBPassword) {
+    die "Error: No database password specified. Use \"--dbpassword\" option or environment variable DBI_PASS to enter a valid value.\n";
+  }
+  $DBMode = $Options{mode};
+  $ExportLOBs = ($Options{exportlobs} =~ /^yes$/i) ? 1 : 0;
+  $ExportDataLabels = ($DBMode =~ /^describetable$/i) ? 1 : (($Options{exportdatalabels} =~ /^yes$/i) ? 1 : 0);
+
+  $OutDelim = ($Options{outdelim} =~ /^tab$/i ) ? "\t" : (($Options{outdelim} =~ /^semicolon$/i) ? "\;" : "\,");
+  $OutQuote = ($Options{quote} =~ /^yes$/i) ? 1 : 0;
+
+  $ReplaceNullStr = (defined($Options{replacenullstr}) && length($Options{replacenullstr})) ? $Options{replacenullstr} : "";
+}
+
+# Setup script usage  and retrieve command line arguments specified using various options...
+sub SetupScriptUsage {
+
+  # Retrieve all the options...
+  %Options = ();
+  $Options{mode} = "exportdata";
+  $Options{exportlobs} = "no";
+  $Options{exportdatalabels} = "yes";
+  $Options{numoutfiles} = "single";
+  $Options{outdelim} = "comma";
+  $Options{quote} = "yes";
+
+  if (!GetOptions(\%Options, "dbdriver|d=s", "dbhost=s", "dbname=s", "dbpassword=s", "dbusername=s", "exportdatalabels=s", "exportlobs=s", "help|h", "mode|m=s", "numoutfiles|n=s", "outdelim=s", "overwrite|o", "quote|q=s", "root|r=s", "replacenullstr=s", "workingdir|w=s")) {
+    die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n";
+  }
+  if ($Options{workingdir}) {
+    if (! -d $Options{workingdir}) {
+      die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n";
+    }
+    chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n";
+  }
+  if ($Options{exportdatalabels} !~ /^(yes|no)$/i) {
+    die "Error: The value specified, $Options{exportlobs}, for option \"--exportdatalabels\" is not valid. Allowed values: yes or no\n";
+  }
+  if ($Options{exportlobs} !~ /^(yes|no)$/i) {
+    die "Error: The value specified, $Options{exportlobs}, for option \"--exportlobs\" is not valid. Allowed values: yes or no\n";
+  }
+  if ($Options{numoutfiles} !~ /^(single|multiple)$/i) {
+    die "Error: The value specified, $Options{mode}, for option \"-n --numoutfiles\" is not valid. Allowed values: single or multiple\n";
+  }
+  if ($Options{mode} !~ /^(exportdata|describetable)$/i) {
+    die "Error: The value specified, $Options{mode}, for option \"-m --mode\" is not valid. Allowed values: exportdata or describetable\n";
+  }
+  if ($Options{outdelim} !~ /^(comma|semicolon|tab)$/i) {
+    die "Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n";
+  }
+  if ($Options{quote} !~ /^(yes|no)$/i) {
+    die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: yes or no\n";
+  }
+}
+
+__END__
+
+=head1 NAME
+
+DBSchemaTablesToTextFiles.pl - Export table data from database SchemaName(s) into CSV/TSV text files
+
+=head1 SYNOPSIS
+
+DBSchemaTablesToTextFiles.pl SchemaName(s)...
+
+DBSchemaTablesToTextFiles.pl [B<-d, --dbdriver> mysql | Oracle| Postgres or Pg] [B<--dbhost > hostname]
+[B<--dbname> databasename] [B<--dbpassword> password] [B<--dbusername> username]
+[B<--exportdatalabels> yes | no] [B<--exportlobs> yes | no] [B<-h, --help>]
+[B<-m, --mode> exportdata | describetable] [B<-n, --numoutfilesmode> single | multiple]
+[B<-o, --overwrite>] [B<--outdelim> comma | tab | semicolon]
+[B<-q, --quote> yes | no] [B<-r, --root> rootname] [B<--replacenullstr string>]
+[B<-w --workingdir> dirname] SchemaName(s)...
+
+=head1 DESCRIPTION
+
+Export table data from database SchemaName(s) into CSV/TSV text files. Use B<-n --numoutfiles>
+option to control the number of text files generated for a database schema.
+
+=head1 OPTIONS
+
+=over 4
+
+=item B<-d, --dbdriver> I<mysql | Oracle | Postgres or Pg>
+
+Database driver name. Possible values: I<mysql, Oracle, Postgres or Pg>. Default: I<MySQL> or value of
+environment variable DBI_DRIVER. This script has only been tested with MySQL, Oracle
+and PostgreSQL drivers.
+
+=item B<--dbhost > I<hostname>
+
+Database host name. Default: I<127.0.0.1> for both MySQL and Oracle. For remote
+databases, specify complete remote host domain: I<dbhostname.org> or something
+like it.
+
+=item B<--dbname> I<databasename>
+
+Database name. Default: mysql for MySQL, postgres for PostgreSQL and none for Oracle.
+For connecting to local/remote Oracle databases, this value can be left undefined assuming
+B<--dbhost> is correctly specified.
+
+=item B<--dbpassword> I<password>
+
+Database user password. Default: I<none> and value of environment variable DBI_PASS
+is used for connecting to database.
+
+=item B<--dbusername> I<username>
+
+Database user name. Default: I<none> and value of environment variable DBI_USER is
+used for connecting to database.
+
+=item B<--exportdatalabels> I<yes | no>
+
+This option is mode specific and controls exporting of column data labels during
+exportdata mode. Possible values: I<yes or no>. Default: I<yes>.
+
+=item B<--exportlobs> I<yes | no>
+
+This option is mode specific and controls exporting of CLOB/BLOB or BYTEA data columns during
+exportdata mode. Possible values: I<yes or no>. Default: I<no>.
+
+=item B<-h, --help>
+
+Print this help message.
+
+=item B<-m, --mode> I<exportdata | describetable>
+
+Data selection criterion from database. Possible values: I<exportdata or describetable>.
+Default value: I<exportdata>.
+
+=item B<-n, --numoutfilesmode> I<single | multiple>
+
+Number of CSV/TSV output files to generate: combine output into one file or generate
+a different file for each table in a schema. Possible values: I<single or multiple>. Default:
+I<single>.
+
+In a single output file, data for different tables is separated by a blank line.
+
+Single outfile option in I<exportdata> mode is quite useful for exporting data from all tables
+in specifed schemas to one file which can be used for migrating data to another database
+or simply provide a backup of data; during I<describetable> mode, it provides a means to
+collect information about columns of all schema tables which can help in creation of these
+tables on a different database server.
+
+=item B<-o, --overwrite>
+
+Overwrite existing files.
+
+=item B<--outdelim> I<comma | tab | semicolon>
+
+Output text file delimiter. Possible values: I<comma, tab, or semicolon>.
+Default value: I<comma>
+
+=item B<-q, --quote> I<yes | no>
+
+Put quotes around column values in output text file. Possible values: I<yes or
+no>. Default value: I<yes>.
+
+=item B<-r, --root> I<rootname>
+
+New file name is generated using the root:<Root>.<Ext> and <Root><TableName>.<Ext>
+for I<single> and I<multiple> B<-n --numoutfiles> option values. Default file name for
+I<single> B<-n --numoutfiles> option value: <Mode>SchemaTables.<Ext>. Default file
+names for I<multiple> B<-n --numoutfiles> value: <Mode><SchemaName><TableName>.<Ext>.
+Based on B<-m --mode> option, I<Export> or I<Describe> <Mode> value is used. The csv and tsv
+<Ext> values are used for comma/semicolon, and tab delimited text files respectively. This option is
+ignored for multiple input schema names.
+
+=item B<--replacenullstr> I<string>
+
+Replace NULL or undefined row values with specified value. Default: I<none>.
+
+For importing output text files into MySQL database using "load data local infile '<tablename>.tsv'
+into table <tablename>" command, use I<--raplacenullstr "NULL"> in conjunction with I<--exportdatalabels no>,
+I<--quote no>, and I<--outdelim tab> options: it'll generate files for direct import into MySQL assuming
+tables already exists.
+
+=item B<-w --workingdir> I<dirname>
+
+Location of working directory. Default: current directory.
+
+=back
+
+=head1 EXAMPLES
+
+To export data in all tables from mysql schema on a MySQL server running on a local machine
+using username/password from DBI_USER and DBI_PASS environmental variables, type:
+
+    % DBSchemaTablesToTextFiles.pl mysql
+
+To describe all tables in mysql and test schemas on a MySQL server running on a remote machine
+using explicit username/password and capturing the ouput into a DescribeTables.csv file, type:
+
+    % DBSchemaTablesToTextFiles.pl --dbdriver mysql --dbuser <name>
+      --dbpassword <pasword> --dbname mysql --dbhost
+      <mysqlhostname.org> -r DescribeTable -m describetable
+      -o mysql test
+
+To describe all tables in SCOTT schema in Oracle running on a remote machine using explicit
+username/password and capturing the ouput into a DescribeAllTable.tsv file, type:
+
+    % DBSchemaTablesToTextFiles.pl --dbdriver Oracle --dbuser <name>
+      --dbpassword <pasword> --dbhost <oraclehostname.com>
+      -r DescribeAllTable -m describetable --outdelim tab --quote no
+      -o SCOTT
+
+To export data in all tables in mysql and test schemas on a MySQL server running at a local
+machine using explicit username/password and capturing the data in TSV file for each table with empty
+values substitued with NULL and clob/blob data, type:
+
+    % DBSchemaTablesToTextFiles.pl --dbdriver Oracle --dbuser <name>
+      --dbpassword <pasword> -r ExportTables --outdelim tab --quote no
+      --replacenullstr "NULL" -m exportdata --exportlobs no  --numoutfiles
+      multiple -o user user_info
+
+=head1 AUTHOR
+
+Manish Sud <[e-mail]>
+
+=head1 SEE ALSO
+
+DBSQLToTextFiles.pl, DBTablesToTextFiles.pl
+
+=head1 COPYRIGHT
+
+Copyright (C) 2015 Manish Sud. All rights reserved.
+
+This file is part of MayaChemTools.
+
+MayaChemTools is free software; you can redistribute it and/or modify it under
+the terms of the GNU Lesser General Public License as published by the Free
+Software Foundation; either version 3 of the License, or (at your option)
+any later version.
+
+=cut