add unsio sqlite3 full support

git-svn-id: http://svn.oamp.fr/repos/unsio/trunk@154 ce2cc22f-6084-46ce-a062-084b172ee5dc

CMakeLists.txt

@@ -210,3 +210,14 @@ INSTALL(FILES  ${UNSIO_BINARY_DIR}/../man/man3/unsiof.3 DESTINATION man/man3)
 
 #set (CMAKE_INSTALL_PREFIX $ENV{NEMOBIN})
 INSTALL(PROGRAMS  ${UNSIO_BINARY_DIR}/bin/uns_info DESTINATION bin)
+
+# install sqlite3 database files
+INSTALL(PROGRAMS  ${UNSIO_BINARY_DIR}/../scripts/perl/mains/unsio_sql3_get_info.pl DESTINATION bin)
+INSTALL(PROGRAMS  ${UNSIO_BINARY_DIR}/../scripts/perl/mains/unsio_sql3_update_info.pl DESTINATION bin)
+INSTALL(PROGRAMS  ${UNSIO_BINARY_DIR}/../scripts/perl/mains/unsio_sql3_update_nemorange.pl DESTINATION bin)
+INSTALL(PROGRAMS  ${UNSIO_BINARY_DIR}/../scripts/perl/mains/unsio_sql3_create_db.pl DESTINATION bin)
+
+INSTALL(FILES  ${UNSIO_BINARY_DIR}/../scripts/perl/lib/Tools/Tools.pm DESTINATION scripts/perl/lib/Tools)
+INSTALL(FILES  ${UNSIO_BINARY_DIR}/../scripts/perl/lib/Tools/Sqlite3.pm DESTINATION scripts/perl/lib/Tools)
+INSTALL(FILES  ${UNSIO_BINARY_DIR}/../scripts/sql/create_unsio_db.sql DESTINATION scripts/sql)
+INSTALL(FILES  ${UNSIO_BINARY_DIR}/../scripts/sql/README DESTINATION scripts/sql)

scripts/perl/lib/Tools/Sqlite3.pm

+# -*- Mode: Perl -*-
+#
+# Perl package to manage sqlite3 operations 
+#
+# ============================================================================
+# Copyright Jean-Charles LAMBERT - -2013                                   
+# e-mail:   Jean-Charles.Lambert@oamp.fr                                      
+# address:  Dynamique des galaxies                                            
+#           Laboratoire d'Astrophysique de Marseille                          
+#           Pole de l'Etoile, site de Chateau-Gombert                         
+#           38, rue Frederic Joliot-Curie                                     
+#           13388 Marseille cedex 13 France                                   
+#           CNRS U.M.R 6110                                                   
+# ============================================================================
+#
+package Sqlite3::Sqlite;
+
+use strict;
+use IO::File;
+use Tools::Tools;
+use DBI;
+
+my $db="/pil/programs/DB/simulation.dbl";  # Marseille database
+my $paramfile="$ENV{HOME}/.unsio";
+
+
+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+# create unsio sqlite3 empty table
+sub Sqlite::createUnsioDb()
+{
+    my $class          = shift;
+    my $db             = shift;
+
+# open database
+    my %attr =( PrintWarn=>0,PrintError=>0,RaiseError=>0,Taint=>0);
+
+    my $dbh = DBI->connect( "dbi:SQLite:${db}",,,\%attr ) || die "Cannot connect: $DBI::errstr";
+    if ( $dbh->err()) {
+      printf STDERR "\nUnable to open DATABASE ==> [$db]\n\n";
+      exit();
+    }
+
+    # EPS table
+    my $stmt = qq(CREATE TABLE eps (name text unique, gas real, halo real, disk real, bulge real, stars real););
+    Sqlite->runSqlCommand($dbh,$stmt);
+    # INFO table
+    my $stmt = qq(CREATE TABLE info (name text unique, type text, dir text, base text););
+    Sqlite->runSqlCommand($dbh,$stmt);
+    # NEMORANGE table
+    my $stmt = qq(CREATE TABLE nemorange (name text unique, total text, disk text, 
+                  bulge text, halo text, halo2 text, gas text, bndry text, stars text););
+    Sqlite->runSqlCommand($dbh,$stmt);
+
+$dbh->disconnect();
+    
+}
+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+# create unsio sqlite3 empty table
+sub Sqlite::runSqlCommand() {
+    my $class          = shift;
+    my $dbh            = shift; # DB file handler
+    my $cmd            = shift;
+
+     my $rv = $dbh->do($cmd);
+    if($rv < 0){
+	print $DBI::errstr;
+    } else {
+	print "Sql command successfully commited\n";
+    }
+}
+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+# Return valid unsio sqlite3 database
+sub Sqlite::getValidDb
+{
+    my $class          = shift;
+    my $dbparam        = shift;
+
+    if (defined($dbparam)) {
+	$db = $dbparam;
+    } else {
+	# parse parameter file
+	my (%param,$status)=File->parseParameters($paramfile);
+	#Tools->printKeyValueHash(\%param); # display parameters
+	
+	if (defined ($param{dbname}) ) {
+	    $db = $param{dbname};
+	}
+    }
+    return $db;
+}
+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+# Return Sim information
+#
+sub Sqlite::getAllRef {
+  # parameters
+    my $class          = shift;
+    my $simname        = shift;
+    my $dbparam        = shift;
+
+    my $db = Sqlite->getValidDb($dbparam);
+    die "Unable to open sqlite3 database [$db] ...." if ( ! -f $db );
+
+# open database
+    my %attr =( PrintWarn=>0,PrintError=>0,RaiseError=>0,Taint=>0);
+
+    my $dbh = DBI->connect( "dbi:SQLite:${db}",,,\%attr ) || die "Cannot connect: $DBI::errstr";
+    if ( $dbh->err()) {
+      printf STDERR "\nUnable to open DATABASE ==> [$db]\n\n";
+      exit();
+    }
+    # try Select request
+    #my $sql="select * from info where name=='$simname'";
+    my $sql="select * from info where name like '$simname' ";
+    my $status=$dbh->selectall_hashref($sql,'name');
+
+    if (0) {
+      printf "-------------\n";
+      foreach my $sim ( $status ) {
+	print "sim dir ==> $sim->{dir}\n";
+      }
+      printf "-------------\n";
+    }
+
+    #if (  defined(%$status ) ) {
+    if (  %$status  ) {
+      return %$status;
+    } else {
+      return;
+    }
+}
+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+# Return Sim information
+#
+sub Sqlite::getSimInfo {
+  # parameters
+    my $class          = shift;
+    my $simname        = shift;
+    my $dbparam        = shift;
+
+    my $db = Sqlite->getValidDb($dbparam);
+
+    die "Unable to open sqlite3 database [$db] ...." if ( ! -f $db );
+
+# open database
+    my %attr =( PrintWarn=>0,PrintError=>0,RaiseError=>0,Taint=>0);
+
+    my $dbh = DBI->connect( "dbi:SQLite:${db}",,,\%attr ) || die "Cannot connect: $DBI::errstr";
+    if ( $dbh->err()) {
+      printf STDERR "\nUnable to open DATABASE ==> [$db]\n\n";
+      exit();
+    }
+    # try Select request
+    my $sql="select * from info where name=='$simname'";
+    #my $sql="select * from info";
+    my $status=$dbh->selectrow_hashref($sql);
+
+    if (0) {
+      printf "-------------\n";
+      foreach my $sim ( $status ) {
+	print "sim dir ==> $sim->{dir}\n";
+      }
+      printf "-------------\n";
+    }
+
+    #if (  defined(%$status ) ) {
+    if (  %$status  ) {
+      return %$status;
+    } else {
+      return;
+    }
+}
+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+# Return Sim Eps
+#
+sub Sqlite::getSimEps {
+  # parameters
+    my $class          = shift;
+    my $simname        = shift;
+    my $dbparam        = shift;
+
+    my $db = Sqlite->getValidDb($dbparam);
+    die "Unable to open sqlite3 database [$db] ...." if ( ! -f $db );
+
+# open database
+    my %attr =( PrintWarn=>0,PrintError=>0,RaiseError=>0,Taint=>0);
+
+    my $dbh = DBI->connect( "dbi:SQLite:${db}",,,\%attr ) || die "Cannot connect: $DBI::errstr";
+    if ( $dbh->err()) {
+      printf STDERR "\nUnable to open DATABASE ==> [$db]\n\n";
+      exit();
+    }
+    # try Select request
+    my $sql="select * from eps where name=='$simname'";
+    my $status=$dbh->selectrow_hashref($sql);
+
+    if (0) {
+      printf "-------------\n";
+      foreach my $sim ( $status ) {
+	print "sim dir ==> $sim->{dir}\n";
+      }
+      printf "-------------\n";
+    }
+
+    #if (  defined(%$status ) ) {
+    if (  $status ) {
+      return %$status;
+    } else {
+      return;
+    }
+}
+
+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+# Return Sim Nemo Range
+#
+sub Sqlite::getSimNemoRange {
+  # parameters
+    my $class          = shift;
+    my $simname        = shift;
+    my $dbparam        = shift;
+
+    my $db = Sqlite->getValidDb($dbparam);
+    die "Unable to open sqlite3 database [$db] ...." if ( ! -f $db );
+
+# open database
+    my %attr =( PrintWarn=>0,PrintError=>0,RaiseError=>0,Taint=>0);
+
+    my $dbh = DBI->connect( "dbi:SQLite:${db}",,,\%attr ) || die "Cannot connect: $DBI::errstr";
+    if ( $dbh->err()) {
+      printf STDERR "\nUnable to open DATABASE ==> [$db]\n\n";
+      exit();
+    }
+    # try Select request
+    my $sql="select * from nemorange where name=='$simname'";
+    my $status=$dbh->selectrow_hashref($sql);
+
+    if (0) {
+      printf "-------------\n";
+      foreach my $sim ( $status ) {
+	print "sim dir ==> $sim->{dir}\n";
+      }
+      printf "-------------\n";
+    }
+
+    #if (  defined(%$status ) ) {
+    if (  $status ) {
+      return %$status;
+    } else {
+      return;
+    }
+}
+
+
+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+# Return Snasphots list
+#
+sub Sqlite::getSnapshotsList {
+  # parameters
+    my $class          = shift;
+    my $simname        = shift;
+    my $dbparam        = shift;
+    my $nolog          = shift;
+
+    my $db = Sqlite->getValidDb($dbparam);
+
+    my %res=Sqlite->getSimInfo($simname);
+
+    #if (defined(%res)) {
+    if (%res) {
+      my $simtype=$res{type};
+      #printf STDERR "NOLOG[$nolog]\n";
+      # call the right method
+      $simtype->getSnapshotsList(\%res,$nolog);
+    }
+}
+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+# check if simulation exist and abort if requested                           
+# return simulation's info structure
+sub Sqlite::checkSimAbort {
+  # parameters
+  my $class          = shift;
+  my $name           = shift;
+  my $abort          = shift;
+  
+  # collect information from database
+  my %res=Sqlite->getSimInfo($name);
+  my $status=1;
+  #if ( !defined(%res)) {
+  if ( !(%res)) {
+      $status=0;
+    printf STDERR <<EOF;
+
+  Sorry but the simulation $name does not exist in
+  [$db] database.....
+
+EOF
+    if ($abort) {
+      exit();
+    }
+  }
+   return ($status,%res);
+}

scripts/perl/lib/Tools/Tools.pm

+# -*- Mode: Perl -*-
+#
+# Perl package with useful functions
+#
+#
+# ============================================================================
+# Copyright Jean-Charles LAMBERT - -2013                                   
+# e-mail:   Jean-Charles.Lambert@oamp.fr                                      
+# address:  Dynamique des galaxies                                            
+#           Laboratoire d'Astrophysique de Marseille                          
+#           Pole de l'Etoile, site de Chateau-Gombert                         
+#           38, rue Frederic Joliot-Curie                                     
+#           13388 Marseille cedex 13 France                                   
+#           CNRS U.M.R 6110                                                   
+# ============================================================================
+
+#
+package Tools::Tools;
+
+use strict;
+use IO::File;
+
+# - - - - - - - - - - - - - - - - - - - - - - - - - -
+#
+sub Tools::printUnsioInfo
+{
+    my $class  = shift;
+
+    printf STDERR <<EOF;
+
+  To get information about UNSIO, please visit : 
+  -> http://projets.lam.fr/projects/unsio
+
+  To get information about Unsio Sqlite3 database, please visit :
+  -> http://projets.lam.fr/projects/unsio/wiki/Sqlite3Db
+
+EOF
+}
+# - - - - - - - - - - - - - - - - - - - - - - - - - -
+#
+sub File::readFile
+{
+    my $class  = shift;
+    my $HANDLE = shift;
+    my $line;
+
+    #printf STDERR "In Tools2 [$HANDLE]\n";
+    while ( <$HANDLE> ) {
+	chomp;
+	#printf STDERR ">>> %s\n", $_;
+	return (1,$_); 
+    }
+    return 0;
+}
+
+# - - - - - - - - - - - - - - - - - - - - - - - - - -
+# parse a file with input parameters based on pair "key = value"
+# and fill up the result into an hash table
+sub File::parseParameters
+{
+    my $class  = shift;
+    my $file    = shift;  # input file
+
+    my %param;  # hash structure to store parameter file
+
+    my $FD =  IO::File->new();
+
+    if 	(! $FD->open("<$file")) {
+	warn "Unable to open for reading [$file]";
+	return (%param,0);
+    }
+
+    my $ret=1;
+
+    while ($ret) {
+	my $line;
+	($ret,$line)  = File->readFile($FD);
+	if ($ret) {
+	    my $line2 = (split(/#/,$line))[0]; # skip commented line
+	    if (defined($line2)) {
+		my ($key, $value) = split(/=/,$line2);
+		if ((defined $key) && (defined $value)) {
+		    $key   =~ s/ +//g;   # remove all blank characters
+		    $value =~ s/^\s+//;  # remove leading  blank characters
+		    $value =~ s/\s+$//;  # remove trailing blank characters
+		    #printf STDERR "[$key]/[$value]\n";
+		    $param{$key} = $value;
+		}
+	    }
+	    #my $simname="$tab[0]";  # simulation name
+	}
+    }
+    return (%param,1);
+}
+# - - - - - - - - - - - - - - - - - - - - - - - - - -
+#
+sub Tools::printKeyValueHash
+{
+    my $class = shift;
+    #my %hash  = %{(shift)}; #% hash table given in parameter (copy in local variabl)
+    my $hash  = shift; #% hash table given in parameter (pass by reference)
+
+    #foreach my $kk ( keys((%hash)) ) { #
+    foreach my $kk ( keys(($hash)) ) { #
+	printf STDERR "Key/Value = [$kk/$hash->{$kk}]\n";
+    }
+}
+
+# - - - - - - - - - - - - - - - - - - - - - - - - - -
+#
+sub Tools::run
+{
+    my $class      = shift;
+    my $cmd        = shift;
+    my $notverbose = shift;
+    
+    if (! defined($notverbose)) {
+	print STDERR "Running:\n[$cmd]\n";
+    }
+    system($cmd);
+}
+# - - - - - - - - - - - - - - - - - - - - - - - - - -
+# Guess CPU number 
+# and create hostmpich
+sub guess_cpu_number
+{
+
+    #system("echo `hostname|cut -d. -f1`:$ncpu > hostmpich");
+    my $host=Tools->getMyShortHostname();
+    my $nproc=Tools->getCoresNumber();
+
+    my $hmp="hostmpich";
+    my $HMP = IO::File->new("> $hmp ") ||
+        die "Unable to open for writing [$hmp]";
+    for (my $i=0; $i<${nproc}; ${i}++) {
+	printf $HMP "${host}\n";
+    }
+    $HMP->close();
+        
+    printf "#CPU detected = $nproc\n";
+    return $nproc;
+}
+# - - - - - - - - - - - - - - - - - - - - - - - - - -
+# 
+sub Tools::getCoresNumber {
+  # parameters
+  my $class = shift;
+
+  my $cpu=0;
+  my $FD;
+  if ( open($FD,"cat /proc/cpuinfo | grep processor|wc -l|")) {
+    chomp(my $x=<$FD>);
+    if ( defined $x ) {
+	$cpu=$x;
+    }
+    close ($FD);
+  } else {
+    printf STDERR "In Tools::getCoresNumber, unable to detect #cores..\n";
+  }
+  return $cpu;
+}
+# - - - - - - - - - - - - - - - - - - - - - - - - - -
+1;  # Allways return 1
+
+#

scripts/perl/mains/unsio_sql3_create_db.pl

+#!/usr/bin/perl
+#
+# This script create an empty unsio sqlite3 database
+#
+#
+# ============================================================================
+# Copyright Jean-Charles LAMBERT - -2013                                   
+# e-mail:   Jean-Charles.Lambert@oamp.fr                                      
+# address:  Dynamique des galaxies                                            
+#           Laboratoire d'Astrophysique de Marseille                          
+#           Pole de l'Etoile, site de Chateau-Gombert                         
+#           38, rue Frederic Joliot-Curie                                     
+#           13388 Marseille cedex 13 France                                   
+#           CNRS U.M.R 6110                                                   
+# ============================================================================
+#
+#
+#
+
+BEGIN 
+{ 
+    my $exe=(split(/\//,$0))[-1]; # basename program name
+    my $path=$0;                  # absolute path name
+    $path =~ s/${exe}//g;         # dirname
+    push @INC, "$path/../scripts/perl/lib", "$path/../lib"; # add path to locate modules
+}
+
+# load package
+use strict;                    # must define everything
+use Getopt::Long;
+use Tools::Sqlite3;
+
+
+# -------------------------------------------------------------
+# Main program
+# get exe basename
+my $exe=(split(/\//,$0))[-1];
+
+# setup default input parameter
+my $db; #     = "/pil/programs/DB/simulation.dbl";  # Marseille database
+my $help   = 0; 
+
+GetOptions( 'db=s'        => \$db,
+	    'help!'       => \$help,
+) or die "Incorrect usage!\n";
+
+# check for help
+if( $help  ) {
+    usage();
+    exit();
+}
+# get input parameters not named
+
+if ( @ARGV == 1 ) {
+    chomp ($db  =$ARGV[0]);
+    shift;
+} else {
+# check mandatory parameters
+    die "Option --db not specified.\n" unless defined($db);
+}
+
+Sqlite->createUnsioDb($db);
+printf STDERR "\nUnsio sqlite3 database [$db] has been created ! \n\n";
+
+# ------------------------------------------------------------
+sub usage {
+  
+  printf STDERR <<EOF;
+
+  ========================================================
+  Create an empty unsio sqlite3 database
+  ========================================================
+
+ Usage   : $exe databasename
+ Example : $exe --db=mydb.sql3
+
+EOF
+Tools->printUnsioInfo();
+}
+

scripts/perl/mains/unsio_sql3_get_info.pl

+#!/usr/bin/perl
+#
+# This script update INFO table from an unsio sqlite3 database
+#
+#
+# ============================================================================
+# Copyright Jean-Charles LAMBERT - -2013                                   
+# e-mail:   Jean-Charles.Lambert@oamp.fr                                      
+# address:  Dynamique des galaxies                                            
+#           Laboratoire d'Astrophysique de Marseille                          
+#           Pole de l'Etoile, site de Chateau-Gombert                         
+#           38, rue Frederic Joliot-Curie                                     
+#           13388 Marseille cedex 13 France                                   
+#           CNRS U.M.R 6110                                                   
+# ============================================================================
+#
+#
+#
+
+BEGIN 
+{ 
+    my $exe=(split(/\//,$0))[-1]; # basename program name
+    my $path=$0;                  # absolute path name
+    $path =~ s/${exe}//g;         # dirname
+    push @INC, "$path/../scripts/perl/lib", "$path/../lib"; # add path to locate modules
+}
+
+# load package
+use strict;                    # must define everything
+use Getopt::Long;
+use Tools::Sqlite3;
+
+
+# -------------------------------------------------------------
+# Main program
+# get exe basename
+my $exe=(split(/\//,$0))[-1];
+
+# setup default input parameter
+my $name;
+my $db; #     = "/pil/programs/DB/simulation.dbl";  # Marseille database
+my $help   = 0; 
+
+GetOptions( 'simname=s'   => \$name,
+            'db=s'        => \$db,
+	    'help!'       => \$help,
+) or die "Incorrect usage!\n";
+
+# check for help
+if( $help  ) {
+    usage();
+    exit();
+}
+# get input parameters not named
+if ( @ARGV >= 1) {
+    chomp($name=$ARGV[0]); shift;
+    if ( @ARGV == 1 ) {
+	chomp ($db  =$ARGV[0]);
+	shift;
+    }
+} else {
+# check mandatory parameters
+    die "Option --simname not specified.\n" unless defined($name);
+}
+
+if ($db eq "") {
+    undef $db;
+}
+
+my $db = Sqlite->getValidDb($db);
+
+printf STDERR "simname=[$name] db=[$db]\n";
+
+my %res=Sqlite->getSimInfo($name,$db);
+
+if ((%res)) {
+  printf "dir = $res{dir}\n";
+
+  if (1) {
+    for my $info ( keys %res ) {
+      printf " $info = $res{$info}\n";
+    }
+  }
+}
+
+my %res=Sqlite->getSimEps($name,$db);
+
+if ((%res)) {
+  if (1) {
+    for my $info ( keys %res ) {
+      printf " $info = $res{$info}\n";
+    }
+  }
+}
+
+my %res=Sqlite->getSimNemoRange($name,$db);
+
+if ((%res)) {
+  if (1) {
+    for my $info ( keys %res ) {
+      printf " $info = $res{$info}\n";
+    }
+  }
+}
+
+# ------------------------------------------------------------
+sub usage {
+    my $db = Sqlite->getValidDb($db);
+  printf STDERR <<EOF;
+
+  ========================================================
+  Return from an unsio sqlite3 database simulation file:
+  [$db]
+  all the informations belonging to the simulation\'s name
+  given in parameter.
+  ========================================================
+
+ Usage   : $exe simname [db]