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diff mayachemtools/bin/DBSQLToTextFiles.pl @ 0:73ae111cf86f draft

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author deepakjadmin
date Wed, 20 Jan 2016 11:55:01 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mayachemtools/bin/DBSQLToTextFiles.pl	Wed Jan 20 11:55:01 2016 -0500
@@ -0,0 +1,439 @@
+#!/usr/bin/perl -w
+#
+# $RCSfile: DBSQLToTextFiles.pl,v $
+# $Date: 2015/02/28 20:46:19 $
+# $Revision: 1.32 $
+#
+# Author: Manish Sud <msud@san.rr.com>
+#
+# 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, $ReplaceNullStr);
+ProcessOptions();
+
+# Collect input parameters information...
+print "Checking input parameter(s)...\n";
+my(@DBSQLStatements, @DBTextFiles);
+RetrieveDBInfo();
+
+# Connect to database...
+my($DBHandle);
+print "Connecting to $DBDriver:database=$DBName as $DBUser...\n";
+$DBHandle = DBConnect($DBDriver, $DBName, $DBHost, $DBUser, $DBPassword);
+
+# Generate text files...
+if (@DBTextFiles > 1) {
+  print "Generating text files...\n";
+}
+my($Index, $TextFile, $SQL);
+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 $TextFile...\n";
+  }
+  print "Processing SQL statement \"$SQL\"...\n";
+
+  if (!open TEXTFILE, ">$TextFile") {
+    warn "Warning: Abandoning $TextFile generation: Couldn't open it: $! \n";
+    next TEXTFILE;
+  }
+
+  if (DBSQLToTextFile($DBHandle, $SQL, \*TEXTFILE, $OutDelim, $OutQuote, $ExportDataLabels, $ExportLOBs, $ReplaceNullStr)) {
+    warn "Warning: Abandoning $TextFile generation...\n";
+    next TEXTFILE;
+  }
+  close TEXTFILE;
+}
+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";
+
+###############################################################################
+
+# Collect input parameters information...
+sub RetrieveDBInfo {
+  my($FileExt, $UserFileName);
+
+  # Setup out file ext...
+  $FileExt = ($Options{outdelim} =~ /^tab$/i) ? "tsv" : "csv";
+
+  # Get user specified information...
+  if ($Options{root} && (@ARGV == 1)) {
+    my($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($Options{root});
+    if ($RootFileName && $RootFileExt) {
+      $UserFileName = $RootFileName;
+    }
+    else {
+      $UserFileName = $Options{root};
+    }
+  }
+
+  my($Param, $SQL, $SQLNo, $FileName);
+  # Go over all the input parameters...
+  @DBSQLStatements = ();
+  @DBTextFiles = ();
+  $SQLNo = 0;
+  PARAM: for $Param (@ARGV) {
+    if ($DBMode =~ /^SQLStatement$/i) {
+      $SQLNo++;
+      $SQL = $Param;
+      $FileName = ($Options{root} && (@ARGV == 1)) ? $UserFileName : ("SQLStatement" . "$SQLNo");
+      $FileName .= ".$FileExt";
+      if (!$Options{overwrite}) {
+	if (-e $FileName) {
+	  die "Error: The file $FileName already exists.\n";
+	}
+      }
+      push @DBSQLStatements, $SQL;
+      push @DBTextFiles, $FileName;
+    }
+    elsif ($DBMode =~ /^SQLFile$/i) {
+      # Read SQL file...
+      my($SQLFile) = $Param;
+      if (! -e $Param) {
+	warn "Warning: Ignoring file $SQLFile: It doesn't exist\n";
+	next PARAM;
+      }
+      if (!open SQLFILE, "$SQLFile" ) {
+	warn "Warning: Ignoring file $SQLFile: Couldn't open it: $! \n";
+	next PARAM;
+      }
+      my($Line, $SQLString);
+      $SQLString = "";
+      LINE: while ($Line = GetTextLine(\*SQLFILE)) {
+           # Ignore comments line...
+	if ($Line =~ /^#/ || $Line =~ /^-/) {
+	  next LINE;
+	}
+	$SQLString .= $Line;
+      }
+      close SQLFILE;
+      # Extract select SQL statements...
+      my($SQLFileDir, $SQLFileName, $SQLFileExt) = ParseFileName($SQLFile);
+      my(@SQLSplits) = split "\;", $SQLString;
+      $SQLNo = 0;
+      SQLSPLIT: for $SQL (@SQLSplits) {
+	$SQLNo++;
+	$FileName = ($Options{root} && (@ARGV == 1)) ? ("$UserFileName" . "$SQLNo") : ("$SQLFileName" . "SQLStatement" . "$SQLNo");
+	$FileName .= ".$FileExt";
+	if (!$Options{overwrite}) {
+	  if (-e $FileName) {
+	    die "Error: The file $FileName already exists.\n";
+	  }
+	}
+	push @DBSQLStatements, $SQL;
+	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) {
+      $DBName = "mysql";
+    }
+    elsif ($DBDriver =~ /^pg|Postgres$/i) {
+      $DBName = "postgres";
+    }
+  }
+  $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$/) ? 1 : 0;
+  $ExportDataLabels = ($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} = "SQLStatement";
+  $Options{exportlobs} = "no";
+  $Options{exportdatalabels} = "yes";
+  $Options{outdelim} = "comma";
+  $Options{quote} = "yes";
+
+  if (!GetOptions(\%Options, "dbdriver|d=s", "dbhost=s", "dbname=s", "dbpassword=s", "dbusername=s", "exportdatalabels=s", "exportlobs=s", "help|h",  "mode|m=s", "outdelim=s", "overwrite|o", "quote|q=s", "root|r=s", "replacenullstr=s", "workingdir|w=s")) {
+    die "\nTo get a list of valid options and their values, use \"$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{mode} !~ /^(SQLStatement|SQLFile)$/i) {
+    die "Error: The value specified, $Options{mode}, for option \"-m --mode\" is not valid. Allowed values: SQLStatement or SQLFile\n";
+  }
+  if ($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
+
+DBSQLToTextFiles.pl - Export data from MySQL, Oracle or PostgreSQL database into CSV/TSV text files
+
+=head1 SYNOPSIS
+
+DBSQLToTextFiles.pl SQLFileName(s) | SQLSelectStatement(s)...
+
+DBSQLToTextFiles.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> SQLStatement | SQLFile] [B<-o, --overwrite>] [B<--outdelim> comma | tab | semicolon]
+[B<-q, --quote> yes | no] [B<-r, --root> rootname] [B<--replacenullstr string>]
+[B<-w --workingdir> dirname] SQLFileName(s)  |  SQLSelectStatement(s)...
+
+=head1 DESCRIPTION
+
+Export data from MySQL, Oracle or PostgreSQL database into CSV/TSV text files. Based on B<-m --mode>
+option value, two methods of data selection are availble: in line SQL select statement(s), or
+SQL file name(s) containing SQL select statement(s). All command line parameters must
+correspond to similar mode; mixing of parameters for different modes is not supported.
+
+=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, Oracle and PostgreSQL. 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 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<SQLStatement | SQLFile>
+
+Data selection criterion from database. Two different command line parameter methods
+are available: in line SQL statement(s) specification or file name(s) containing SQL select
+statement(s). This value determines how command line parameters are processed.
+
+Possible values: I<SQLStatement or SQLFile>. Default value: I<SQLStatement>
+
+In SQLFile mode, SQL file contains select statements delimited by I<;>. And the lines starting
+with I<#> or I<-> are ignored.
+
+=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><No>.<Ext>. Default new file
+file names: SQLStatement<No>.<Ext>, or <SQLFileName><StatementNo>.<Ext>.
+The csv and tsv <Ext> values are used for comma/semicolon, and tab delimited
+text files respectively.This option is ignored for multiple input parameters.
+
+=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 all data in user_info table from a MySQL server running on a local machine
+using username/password from DBI_USER and DBI_PASS environmental variables, type:
+
+    % DBSQLToTextFiles.pl -o "select * from user_info"
+
+To describe user table in a MySQL server running on a remote machine using explicit
+username/password and capturing the output into a UserTable.csv file, type:
+
+    % DBSQLToTextFiles.pl --dbdriver mysql --dbuser <name> --dbpassword
+      <pasword> --dbname mysql --dbhost <mysqlhostname.org> -r UserTable
+      -m SQLStatement -o "select * from user_info"
+
+To describe table all_tables in Oracle running on a remote machine using explicit
+username/password and capturing the output into a AllTable.tsv file, type:
+
+    % DBSQLToTextFiles.pl --dbdriver Oracle --dbuser <name> --dbpassword
+      <pasword> --dbhost <oraclehostname.com> -r AllTable -m SQLStatement
+      --outdelim tab --quote no -o "select * from all_tables"
+
+To run all SQL statement in a file sample.sql on a local Oracle host and capturing output
+in a SampleSQL.csv file, type:
+
+    % DBSQLToTextFiles.pl --dbdriver Oracle --dbuser <name> --dbpassword
+      <pasword> -r SampleSQL -m SQLFile -o sample.sql
+
+=head1 AUTHOR
+
+Manish Sud <msud@san.rr.com>
+
+=head1 SEE ALSO
+
+DBSchemaTablesToTextFiles.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