Index: trunk/cleanup_gfac.php
===================================================================
--- trunk/cleanup_gfac.php	(revision 25)
+++ trunk/cleanup_gfac.php	(revision 35)
@@ -41,19 +41,10 @@
    write_log( "$me: debug db=$db; requestID=$requestID" );
 
-   $us3_link = mysql_connect( $dbhost, $user, $passwd );
+   $us3_link = mysqli_connect( $dbhost, $user, $passwd, $db );
 
    if ( ! $us3_link )
    {
-      write_log( "$me: could not connect: $dbhost, $user, $passwd" );
-      mail_to_user( "fail", "Internal Error $requestID\nCould not connect to DB" );
-      return( -1 );
-   }
-
-   $result = mysql_select_db( $db, $us3_link );
-
-   if ( ! $result )
-   {
-      write_log( "$me: could not select DB $db" );
-      mail_to_user( "fail", "Internal Error $requestID\n$could not select DB $db" );
+      write_log( "$me: could not connect: $dbhost, $user, $passwd, $db" );
+      mail_to_user( "fail", "Internal Error $requestID\nCould not connect to DB $db" );
       return( -1 );
    }
@@ -62,20 +53,20 @@
    $query  = "SELECT email, investigatorGUID, editXMLFilename FROM HPCAnalysisRequest " .
              "WHERE HPCAnalysisRequestID=$requestID";
-   $result = mysql_query( $query, $us3_link );
+   $result = mysqli_query( $us3_link, $query );
 
    if ( ! $result )
    {
       write_log( "$me: Bad query: $query" );
-      mail_to_user( "fail", "Internal Error $requestID\n$query\n" . mysql_error( $us3_link ) );
-      return( -1 );
-   }
-
-   list( $email_address, $investigatorGUID, $editXMLFilename ) =  mysql_fetch_array( $result );
+      mail_to_user( "fail", "Internal Error $requestID\n$query\n" . mysqli_error( $us3_link ) );
+      return( -1 );
+   }
+
+   list( $email_address, $investigatorGUID, $editXMLFilename ) =  mysqli_fetch_array( $result );
 
    $query  = "SELECT personID FROM people " .
              "WHERE personGUID='$investigatorGUID'";
-   $result = mysql_query( $query, $us3_link );
-
-   list( $personID ) = mysql_fetch_array( $result );
+   $result = mysqli_query( $us3_link, $query );
+
+   list( $personID ) = mysqli_fetch_array( $result );
 
    /*
@@ -90,13 +81,13 @@
              "AND h.HPCAnalysisRequestID=r.HPCAnalysisRequestID";
 
-   $result = mysql_query( $query, $us3_link );
-
-   if ( ! $result )
-   {
-      write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
-      return( -1 );
-   }
-
-   if ( mysql_num_rows( $result ) == 0 )
+   $result = mysqli_query( $us3_link, $query );
+
+   if ( ! $result )
+   {
+      write_log( "$me: Bad query:\n$query\n" . mysqli_error( $us3_link ) );
+      return( -1 );
+   }
+
+   if ( mysqli_num_rows( $result ) == 0 )
    {
       write_log( "$me: US3 Table error - No records for requestID: $requestID" );
@@ -104,5 +95,5 @@
    }
 
-   list( $cluster, $submittime, $queuestatus, $jobtype ) = mysql_fetch_array( $result );
+   list( $cluster, $submittime, $queuestatus, $jobtype ) = mysqli_fetch_array( $result );
 
    // Get the GFAC ID
@@ -110,24 +101,22 @@
             "WHERE HPCAnalysisRequestID=$requestID";
 
-   $result = mysql_query( $query, $us3_link );
+   $result = mysqli_query( $us3_link, $query );
 
    if ( ! $result )
    {
       write_log( "$me: Bad query: $query" );
-      mail_to_user( "fail", "Internal Error $requestID\n$query\n" . mysql_error( $us3_link ) );
-      return( -1 );
-   }
-
-   list( $HPCAnalysisResultID, $gfacID ) = mysql_fetch_array( $result ); 
+      mail_to_user( "fail", "Internal Error $requestID\n$query\n" . mysqli_error( $us3_link ) );
+      return( -1 );
+   }
+
+   list( $HPCAnalysisResultID, $gfacID ) = mysqli_fetch_array( $result ); 
 
    ////////
    // Get data from global GFAC DB and insert it into US3 DB
-   // $gfac_link = mysql_connect( $dbhost, $guser, $gpasswd );
-
-   $result = mysql_select_db( $gDB, $gfac_link );
-
-   if ( ! $result )
-   {
-      write_log( "$me: Could not connect to DB $gDB" );
+   $gfac_link = mysqli_connect( $dbhost, $guser, $gpasswd, $gDB );
+
+   if ( ! $gfac_link )
+   {
+      write_log( "$me: Could not connect to DB $dbhost : $gDB" );
       mail_to_user( "fail", "Internal Error $requestID\nCould not connect to DB $gDB" );
       return( -1 );
@@ -137,5 +126,5 @@
             "WHERE gfacID='$gfacID'";
 
-   $result = mysql_query( $query, $gfac_link );
+   $result = mysqli_query( $gfac_link, $query );
    if ( ! $result )
    {
@@ -145,5 +134,5 @@
    }
 
-   $num_rows = mysql_num_rows( $result );
+   $num_rows = mysqli_num_rows( $result );
    if ( $num_rows == 0 )
    {
@@ -156,5 +145,5 @@
 //}
 
-   list( $status, $cluster, $id ) = mysql_fetch_array( $result );
+   list( $status, $cluster, $id ) = mysqli_fetch_array( $result );
 //write_log( "$me:     db=$db; requestID=$requestID; status=$status; cluster=$cluster" );
 
@@ -176,14 +165,14 @@
             "WHERE gfacID='$gfacID'";
 
-   $result = mysql_query( $query, $gfac_link );
-
-   if ( ! $result )
-   {
-      write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
-      mail_to_user( "fail", "Internal error " . mysql_error( $gfac_link ) );
-      return( -1 );
-   }
-
-   $num_rows = mysql_num_rows( $result );
+   $result = mysqli_query( $gfac_link, $query );
+
+   if ( ! $result )
+   {
+      write_log( "$me: Bad query:\n$query\n" . mysqli_error( $gfac_link ) );
+      mail_to_user( "fail", "Internal error " . mysqli_error( $gfac_link ) );
+      return( -1 );
+   }
+
+   $num_rows = mysqli_num_rows( $result );
    if ( $num_rows == 0 )
    {
@@ -192,5 +181,5 @@
    }
 
-   list( $analysisID, $stderr, $stdout, $tarfile ) = mysql_fetch_array( $result );
+   list( $analysisID, $stderr, $stdout, $tarfile ) = mysqli_fetch_array( $result );
 
    if ( strlen( $tarfile ) > 0 )
@@ -209,10 +198,10 @@
             "WHERE analysisID = $analysisID " .
             "ORDER BY time ";
-   $result = mysql_query( $query, $gfac_link );
+   $result = mysqli_query( $gfac_link, $query );
 
    if ( ! $result )
    {
       // Just log it and continue
-      write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
+      write_log( "$me: Bad query:\n$query\n" . mysqli_error( $gfac_link ) );
    }
 
@@ -226,8 +215,8 @@
    $need_finish = ( $status == 'COMPLETE' );
 
-   if ( mysql_num_rows( $result ) > 0 )
+   if ( mysqli_num_rows( $result ) > 0 )
    {
       $time_msg = time();
-      while ( list( $message, $time ) = mysql_fetch_array( $result ) )
+      while ( list( $message, $time ) = mysqli_fetch_array( $result ) )
       {
 //write_log( "$me: message=$message" );
@@ -263,10 +252,10 @@
             "WHERE analysisID = $analysisID ";
 
-   $result = mysql_query( $query, $gfac_link );
+   $result = mysqli_query( $gfac_link, $query );
 
    if ( ! $result )
    {
       // Just log it and continue
-      write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
+      write_log( "$me: Bad query:\n$query\n" . mysqli_error( $gfac_link ) );
    }
 
@@ -274,13 +263,13 @@
    $query  = "SELECT stdout, stderr, status, queue_msg FROM analysis " .
              "WHERE gfacID='$gfacID' ";
-   $result = mysql_query( $query, $gfac_link );
+   $result = mysqli_query( $gfac_link, $query );
    try
    {
       // What if this is too large?
-      list( $stdout, $stderr, $status, $queue_msg ) = mysql_fetch_array( $result );
+      list( $stdout, $stderr, $status, $queue_msg ) = mysqli_fetch_array( $result );
    }
    catch ( Exception $e )
    {
-      write_log( "$me: stdout + stderr larger than 128M - $gfacID\n" . mysql_error( $gfac_link ) );
+      write_log( "$me: stdout + stderr larger than 128M - $gfacID\n" . mysqli_error( $gfac_link ) );
       // Just go ahead and clean up
    }
@@ -301,10 +290,10 @@
    $query = "DELETE from analysis WHERE gfacID='$gfacID'";
 
-   $result = mysql_query( $query, $gfac_link );
+   $result = mysqli_query( $gfac_link, $query );
 
    if ( ! $result )
    {
       // Just log it and continue
-      write_log( "$me: Bad query:\n$query\n" . mysql_error( $gfac_link ) );
+      write_log( "$me: Bad query:\n$query\n" . mysqli_error( $gfac_link ) );
    }
 write_log( "$me: GFAC DB entry deleted" );
@@ -316,12 +305,12 @@
    $query  = "SELECT HPCAnalysisRequestGUID FROM HPCAnalysisRequest " .
              "WHERE HPCAnalysisRequestID = $requestID ";
-   $result = mysql_query( $query, $us3_link );
+   $result = mysqli_query( $us3_link, $query );
    
    if ( ! $result )
    {
-      write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
+      write_log( "$me: Bad query:\n$query\n" . mysqli_error( $us3_link ) );
    }
    
-   list( $requestGUID ) = mysql_fetch_array( $result );
+   list( $requestGUID ) = mysqli_fetch_array( $result );
    $output_dir = "$submit_dir/$requestGUID";
 write_log( "$me: Output dir determined: $output_dir" );
@@ -334,5 +323,5 @@
    $message_filename = "$output_dir/$db-$requestID-messages.txt";
    file_put_contents( $message_filename, $message_log, FILE_APPEND );
-  // mysql_close( $gfac_link );
+  // mysqli_close( $gfac_link );
 write_log( "$me: *messages.txt written" );
 
@@ -341,14 +330,14 @@
 
    $query = "UPDATE HPCAnalysisResult SET "                              .
-            "stderr='" . mysql_real_escape_string( $stderr, $us3_link ) . "', " .
-            "stdout='" . mysql_real_escape_string( $stdout, $us3_link ) . "' "  .
+            "stderr='" . mysqli_real_escape_string( $us3_link, $stderr ) . "', " .
+            "stdout='" . mysqli_real_escape_string( $us3_link, $stdout ) . "' "  .
             "WHERE HPCAnalysisResultID=$HPCAnalysisResultID";
 
-   $result = mysql_query( $query, $us3_link );
-
-   if ( ! $result )
-   {
-      write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
-      mail_to_user( "fail", "Bad query:\n$query\n" . mysql_error( $us3_link ) );
+   $result = mysqli_query( $us3_link, $query );
+
+   if ( ! $result )
+   {
+      write_log( "$me: Bad query:\n$query\n" . mysqli_error( $us3_link ) );
+      mail_to_user( "fail", "Bad query:\n$query\n" . mysqli_error( $us3_link ) );
       return( -1 );
    }
@@ -442,9 +431,9 @@
                   "mgroupcount = {$otherdata['groupcount']} " .
                   "WHERE HPCAnalysisResultID=$HPCAnalysisResultID";
-         $result = mysql_query( $query, $us3_link );
+         $result = mysqli_query( $us3_link, $query );
 
          if ( ! $result )
          {
-            write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
+            write_log( "$me: Bad query:\n$query\n" . mysqli_error( $us3_link ) );
          }
 
@@ -463,26 +452,30 @@
          $modelGUID  = $noise_data[ 'modelGUID' ];
          $noiseGUID  = $noise_data[ 'noiseGUID' ];
+         $editGUID   = '00000000-0000-0000-0000-000000000000';
+         if ( isset( $model_data[ 'editGUID' ] ) )
+            $editGUID   = $model_data[ 'editGUID' ];
 
          $query = "INSERT INTO noise SET "  .
                   "noiseGUID='$noiseGUID'," .
                   "modelGUID='$modelGUID'," .
-                  "editedDataID=2, "        .
+                  "editedDataID="                .
+                  "(SELECT editedDataID FROM editedData WHERE editGUID='$editGUID')," .
                   "modelID=1, "             .
                   "noiseType='$type',"      .
                   "description='$desc',"    .
-                  "xml='" . mysql_real_escape_string( $xml, $us3_link ) . "'";
+                  "xml='" . mysqli_real_escape_string( $us3_link, $xml ) . "'";
 
          // Add later after all files are processed: editDataID, modelID
 
-         $result = mysql_query( $query, $us3_link );
+         $result = mysqli_query( $us3_link, $query );
 
          if ( ! $result )
          {
-            write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
-            mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) );
+            write_log( "$me: Bad query:\n$query\n" . mysqli_error( $us3_link ) );
+            mail_to_user( "fail", "Internal error\n$query\n" . mysqli_error( $us3_link ) );
             return( -1 );
          }
 
-         $id        = mysql_insert_id( $us3_link );
+         $id        = mysqli_insert_id( $us3_link );
          $file_type = "noise";
          $noiseIDs[] = $id;
@@ -490,5 +483,5 @@
          // Keep track of modelGUIDs for later, when we replace them
          $modelGUIDs[ $id ] = $modelGUID;
-//write_log( "$me:   noise file inserted into DB : id=$id" );
+//write_log( "$me:   noise file inserted into DB : id=$id  modelGUID=$modelGUID" );
          
       }
@@ -512,18 +505,18 @@
                   "mrecsGUID='$mrecGUID'," .
                   "description='$desc',"    .
-                  "xml='" . mysql_real_escape_string( $xml, $us3_link ) . "'";
+                  "xml='" . mysqli_real_escape_string( $us3_link, $xml ) . "'";
 
          // Add later after all files are processed: editDataID, modelID
 
-         $result = mysql_query( $query, $us3_link );
+         $result = mysqli_query( $us3_link, $query );
 
          if ( ! $result )
          {
-            write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
-            mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) );
+            write_log( "$me: Bad query:\n$query\n" . mysqli_error( $us3_link ) );
+            mail_to_user( "fail", "Internal error\n$query\n" . mysqli_error( $us3_link ) );
             return( -1 );
          }
 
-         $id         = mysql_insert_id( $us3_link );
+         $id         = mysqli_insert_id( $us3_link );
          $file_type  = "mrecs";
          $mrecsIDs[] = $id;
@@ -560,16 +553,16 @@
                   "meniscus='$meniscus'," .
                   "variance='$variance'," .
-                  "xml='" . mysql_real_escape_string( $xml, $us3_link ) . "'";
-
-         $result = mysql_query( $query, $us3_link );
+                  "xml='" . mysqli_real_escape_string( $us3_link, $xml ) . "'";
+
+         $result = mysqli_query( $us3_link, $query );
 
          if ( ! $result )
          {
-            write_log( "$me: Bad query:\n$query " . mysql_error( $us3_link ) );
-            mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) );
+            write_log( "$me: Bad query:\n$query " . mysqli_error( $us3_link ) );
+            mail_to_user( "fail", "Internal error\n$query\n" . mysqli_error( $us3_link ) );
             return( -1 );
          }
 
-         $modelID   = mysql_insert_id( $us3_link );
+         $modelID   = mysqli_insert_id( $us3_link );
          $id        = $modelID;
          $file_type = "model";
@@ -577,5 +570,5 @@
          $query = "INSERT INTO modelPerson SET " .
                   "modelID=$modelID, personID=$personID";
-         $result = mysql_query( $query, $us3_link );
+         $result = mysqli_query( $us3_link, $query );
 //write_log( "$me:   model file inserted into DB : id=$id" );
       }
@@ -586,10 +579,10 @@
                "resultID=$id";
 
-      $result = mysql_query( $query, $us3_link );
+      $result = mysqli_query( $us3_link, $query );
 
       if ( ! $result )
       {
-         write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
-         mail_to_user( "fail", "Internal error\n$query\n" . mysql_error( $us3_link ) );
+         write_log( "$me: Bad query:\n$query\n" . mysqli_error( $us3_link ) );
+         mail_to_user( "fail", "Internal error\n$query\n" . mysqli_error( $us3_link ) );
          return( -1 );
       }
@@ -611,10 +604,10 @@
                "WHERE noiseID=$noiseID";
 
-      $result = mysql_query( $query, $us3_link );
+      $result = mysqli_query( $us3_link, $query );
 
       if ( ! $result )
       {
-         write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
-         mail_to_user( "fail", "Bad query\n$query\n" . mysql_error( $us3_link ) );
+         write_log( "$me: Bad query:\n$query\n" . mysqli_error( $us3_link ) );
+         mail_to_user( "fail", "Bad query\n$query\n" . mysqli_error( $us3_link ) );
          return( -1 );
       }
@@ -633,10 +626,10 @@
                "WHERE mrecsID=$mrecsID";
 
-      $result = mysql_query( $query, $us3_link );
+      $result = mysqli_query( $us3_link, $query );
 
       if ( ! $result )
       {
-         write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
-         mail_to_user( "fail", "Bad query\n$query\n" . mysql_error( $us3_link ) );
+         write_log( "$me: Bad query:\n$query\n" . mysqli_error( $us3_link ) );
+         mail_to_user( "fail", "Bad query\n$query\n" . mysqli_error( $us3_link ) );
          return( -1 );
       }
@@ -651,12 +644,12 @@
    $query  = "SELECT HPCAnalysisRequestGUID FROM HPCAnalysisRequest " .
              "WHERE HPCAnalysisRequestID = $requestID ";
-   $result = mysql_query( $query, $us3_link );
-
-   if ( ! $result )
-   {
-      write_log( "$me: Bad query:\n$query\n" . mysql_error( $us3_link ) );
-   }
-
-   list( $requestGUID ) = mysql_fetch_array( $result );
+   $result = mysqli_query( $us3_link, $query );
+
+   if ( ! $result )
+   {
+      write_log( "$me: Bad query:\n$query\n" . mysqli_error( $us3_link ) );
+   }
+
+   list( $requestGUID ) = mysqli_fetch_array( $result );
 
    chdir( "$submit_dir/$requestGUID" );
@@ -669,5 +662,5 @@
    // exec( "rm -rf $gfacID" );
 
-   mysql_close( $us3_link );
+   mysqli_close( $us3_link );
 
    /////////