PHP defines four methods which can execute commands: exec, passthru, shell_exec and system. These methods wait for the script to finish and collect the output generated by that script. However, when a user leaves the page, closes his browser or stops the script, the background script which is executed is also stopped. To prevent this, people tend to use other options like pcntl or cURL. Using these extensions might offer a solution, but for simply starting a script they are much too verbose.

The solution presented is applicable in the situation where you just need to start a script and you don't want users to be able to stop the script after starting. And the solution is....

The function ignore_user_abort().

By putting this function in front of a shell_exec execution, the script still starts the script executed by shell_exec. However, it doesn't care any more if the user aborts the calling script. In my situation, the CLI script updates a status file and a progress file. When running, the status file contains an integer which denotes that the CLI script is running. This prevents the script from being run again while it's already running. Furthermore, the progress file is updated so the progress can be checked by other scripts.

Source

http://stackoverflow.com/questions/265073/php-background-processes

print implode(ArrayFunctions::toString($array))

the array is shown as a tree structure on the screen.

The implementation is as follows:

<?php

class ArrayFunctions {

  public static function toString($array){

    $result = array();

    $depth = 0;

    foreach($array as $k => $v) {
            $show_val = ( is_array($v) ? "" : $v );
 
            // show the indents
            $result []= str_repeat("  ", $depth);
            if($depth == 0) {
                // this is a root node. no parents
                $result []= "O ";
            } elseif(is_array($v)) {
                // this is a normal node. parents and children
                $result []= "+ ";
            } else {
                // this is a leaf node. no children
                $result []= "- ";
            }
 
            // show the actual node
            if ($show_val == "") {
                $result []= "<strong>{$k}</strong>:
";
            }
            else {
                $result []= $k . " (".$show_val.")"."
";
            }
 
            if(is_array($v)) {
                // this is what makes it recursive, rerun for childs
                $temp = self::toTree($v, ($depth+1));
                foreach($temp as $t) {
                    $result []= $t;
                }
            }
        }
        return implode($result);
    }
 
    private static function showtype($show_val) {
        // convert bools to text and quote 'text bools'!
        if (is_string($show_val) &&
           ($show_val == "true" || $show_val == "false")) {
            return "\"{$show_val}\"";
        }
        elseif (is_bool($show_val) && $show_val === true) {
            return "true";
        }
        elseif (is_bool($show_val) && $show_val === false) {
            return "false";
        }
        elseif (is_null($show_val)) {
            return "null";
        }
        else {
            return $show_val;
        }
    }
 
    private static function toTree($pieces, $depth = 0) {
        foreach($pieces as $k => $v) {
            // skip the baseval thingy. Not a real node.
            //if($k == "__base_val") continue;
            // determine the real value of this node.
            $show_val = ( is_array($v) ? "" : $v );
 
            $show_val = self::showtype($show_val);
 
            // show the indents
            $result []= str_repeat("  ", $depth);
            if($depth == 0) {
                // this is a root node. no parents
                $result []= "O ";
            } elseif(is_array($v)) {
                // this is a normal node. parents and children
                $result []= "+ ";
            } else {
                // this is a leaf node. no children
                $result []= "- ";
            }
 
            // show the actual node
            if ($show_val == "") {
                $result []= "<strong>{$k}</strong>:
";
            }
            else {
                $result []= $k . ": <i>{$show_val}</i>
";
            }
 
            if(is_array($v)) {
                // this is what makes it recursive, rerun for childs
                $temp = self::toTree($v, ($depth+1));
                if (is_array($temp)) {
                    foreach($temp as $t) {
                        $result []= $t;
                    }
                }
                else {
                    $result []= $t;
                }
            }
        }
        return $result;
    }
}
?>

It's also available through the download page.

Please note that the code itself is at least 4 years old and there are far better ways to solve some things. I therefore suggest that it is used for studying purposes only. Comments and improvments are very much appreciated.

I was 'fortunate' it wasn't so another task was born: installing YUM on CentOS.For installing, I've found this source to be quite useful. However, I got some warnings because of dependencies. To resolve these dependencies I've upgraded the rpm packages which were denoted by the installer by hand, but the command suggested at the last post in this thread might also work directly.

The names of the most recent rpm packages are listed here. As the rpm packages have circular dependencies one of the packages has to be installed with the --nodeps argument so these dependencies are not taken into account.

Now that all is done it sounds logical. This blogpost is meant for people who want to install PEAR, but are not sure how to do it or about the directories which need to be specified.

Starting install

Log on to your server on the command line (as root). The install acan then be started as follows:

lynx -source http://pear.php.net/go-pear | php

Directories

After some questions (which in 99% of the cases just get the default answer), you'll get the prompt for the directories. After adjustment, my structure looks as follows:

1. Installation prefix ($prefix) : /usr
2. Temporary files directory     : $prefix/temp
3. Binaries directory            : $prefix/bin
4. PHP code directory ($php_dir) : $prefix/share/PEAR
5. Documentation base directory  : $php_dir/docs
6. Data base directory           : $php_dir/data
7. Tests base directory          : $php_dir/tests

Finishing installation

When the installation is done, the config (php.ini) file can automatically be adjusted. Note that you have to restart apache to load this new config.

The full overview

A complete overview from my PEAR install in- and output is given below.

[root@server usr]# lynx -source http://pear.php.net/go-pear | php
Welcome to go-pear!

Go-pear will install the 'pear' command and all the files needed by
it.  This command is your tool for PEAR installation and maintenance.

Go-pear also lets you download and install the following optional PEAR
packages: PEAR_Frontend_Web-beta, PEAR_Frontend_Gtk2, MDB2.

If you wish to abort, press Control-C now, or press Enter to continue:

HTTP proxy (http://user:password@proxy.myhost.com:port), or Enter for none::

Below is a suggested file layout for your new PEAR installation.  To
change individual locations, type the number in front of the
directory.  Type 'all' to change all of them or simply press Enter to
accept these locations.

1. Installation prefix ($prefix) : /usr
2. Temporary files directory     : $prefix/temp
3. Binaries directory            : $prefix/bin
4. PHP code directory ($php_dir) : $prefix/PEAR
5. Documentation base directory  : $php_dir/docs
6. Data base directory           : $php_dir/data
7. Tests base directory          : $php_dir/tests

1-7, 'all' or Enter to continue: 4
PHP code directory ($php_dir) [$prefix/PEAR] : $prefix/share/PEAR

Below is a suggested file layout for your new PEAR installation.  To
change individual locations, type the number in front of the
directory.  Type 'all' to change all of them or simply press Enter to
accept these locations.

1. Installation prefix ($prefix) : /usr
2. Temporary files directory     : $prefix/temp
3. Binaries directory            : $prefix/bin
4. PHP code directory ($php_dir) : $prefix/share/PEAR
5. Documentation base directory  : $php_dir/docs
6. Data base directory           : $php_dir/data
7. Tests base directory          : $php_dir/tests

1-7, 'all' or Enter to continue:
PHP Warning:  putenv(): Safe Mode warning: Cannot set environment variable 'TMPDIR' - it's not in the allowed list in /usr/- on line 1264

The following PEAR packages are bundled with PHP: PEAR_Frontend_Web-beta,
PEAR_Frontend_Gtk2, MDB2.
Would you like to install these as well? [Y/n] : n

Loading zlib: ok

Bootstrapping Installer...................
Bootstrapping PEAR.php............(remote) ok
Bootstrapping Archive/Tar.php............(remote) ok
Bootstrapping Console/Getopt.php............(remote) ok

Extracting installer..................
Downloading package: PEAR.............ok
Downloading package: Structures_Graph....ok

Preparing installer..................
Updating channel "doc.php.net"
Update of Channel "doc.php.net" succeeded
Updating channel "pear.php.net"
Update of Channel "pear.php.net" succeeded
Updating channel "pecl.php.net"
Update of Channel "pecl.php.net" succeeded

Installing selected packages..................
Downloading and installing package: PEAR.............warning: pear/PEAR requires package "pear/Archive_Tar" (recommended version 1.3.3)
warning: pear/PEAR requires package "pear/Structures_Graph" (recommended version 1.0.2)
warning: pear/PEAR requires package "pear/Console_Getopt" (recommended version 1.2.3)
warning: pear/PEAR requires package "pear/XML_Util" (recommended version 1.2.1)
downloading PEAR-1.9.0.tgz ...
Starting to download PEAR-1.9.0.tgz (291,634 bytes)
.............................................................done: 291,634 bytes
install ok: channel://pear.php.net/PEAR-1.9.0
PEAR: Optional feature webinstaller available (PEAR's web-based installer)
PEAR: Optional feature gtkinstaller available (PEAR's PHP-GTK-based installer)
PEAR: Optional feature gtk2installer available (PEAR's PHP-GTK2-based installer)
PEAR: To install optional features use "pear install pear/PEAR#featurename"
Installing bootstrap package: Structures_Graph.......install ok: channel://pear.php.net/Structures_Graph-1.0.3
Downloading and installing package: Archive_Tar-stable.......downloading Archive_Tar-1.3.5.tgz ...
Starting to download Archive_Tar-1.3.5.tgz (17,184 bytes)
...done: 17,184 bytes
install ok: channel://pear.php.net/Archive_Tar-1.3.5
Downloading and installing package: Console_Getopt-stable.......downloading Console_Getopt-1.2.3.tgz ...
Starting to download Console_Getopt-1.2.3.tgz (4,011 bytes)
...done: 4,011 bytes
install ok: channel://pear.php.net/Console_Getopt-1.2.3

******************************************************************************
WARNING!  The include_path defined in the currently used php.ini does not
contain the PEAR PHP directory you just specified:
</usr/share/PEAR>
If the specified directory is also not in the include_path used by
your scripts, you will have problems getting any PEAR packages working.

Would you like to alter php.ini </etc/php.ini>? [Y/n] : Y

php.ini </etc/php.ini> include_path updated.

Current include path           : .:
Configured directory           : /usr/share/PEAR
Currently used php.ini (guess) : /etc/php.ini
Press Enter to continue:

The 'pear' command is now at your service at /usr/bin/pear
[root@server usr]# /etc/init.d/httpd restart
Stopping httpd:                                            [  OK  ]
Starting httpd:                                            [  OK  ]

To Start Plesk

/etc/init.d/psa start

To Stop Plesk

/etc/init.d/psa stop

Upgrade through autoinstaller

/usr/local/psa/admin/bin/autoinstaller

Restart apache

/etc/init.d/httpd restart

Check the running processes.

The first column represents the owner. The second column contains the process id.

Source

ps aux | grep autoinstall

or

ps u

Killing a process

kill -9 [processid]

Backup an RPM database and rebuild it.

source 1

source 2

Remove any stale lock file

/bin/rm -f /var/lib/rpm/__db*

Back up the /var/lib/rpm directory

tar czvf $(hostname).rpmdatabase.tar.gz /var/lib/rpm

If your hostname is linux-server, it will save backup to a file called linux-server.rpmdatabase.tar.gz

Many thanks also go out to 'koor' who helped me at the #plesk IRC channel at FreeNode.

Collision of RPM files (RPM already exists)

When upgrading I encountered a collision of an RPM file which already existed. Because of that the upgrade could not proceed. A solution to that is presented here in the last post. It comes down to:

• Navigating to the folder which holds the rpm file (e.g. cd /root/psa/PSA_8.1.0/dist-rpm-RedHat-el3-i386/base)
• Forcing an update on the RPM. (e.g. rpm -U --force --nodeps psa-8.1.0-rhel3.build81061129.22.i586.rpm)

Running the updater after repairing the file will solve the problem.

SSH connection is refused
I had this problem once. After a little search I found this post. It's brilliant! From Plesk itself you start a cronjob (run it as root user) which (re)starts (or use restart instead of start) the ssh daemon. After that my problem was solved.

Virtual hosts
By default Plesk has a pre-defined 'behavior' of a domain. This includes some settings for PHP like safe mode and open basedir restrictions. By default these settings are stored in a file called 'httpd.include' in the folder

/var/www/vhosts/yourdomain.ext/conf/

You can edit this file to change the behavior of the domain, but changes in this file are just temporary. Once the file is reloaded your changes will be gone.
To permanently make changes you need to create or edit a file called 'vhost.conf' which is located in the same directory. When loading the httpd.include file, the webserver also checks if this vhost.conf file exists and if so, it includes it. How you can create this virtual host file can be found on this page.

PHPUnit

One of the features which I need when starting a new project is a Unittest framework. The two most common are SimpleTest and PHPUnit. SimpleTest can be downloaded and used right away. The PHPUnit manual advises to use PEAR to install PHPUnit. Joshua Doodnauth explains how to activate PEAR and how to install PHPUnit on WampServer. However, as I was running WampServer 2.0i with PHP 5.3, the file go-pear.phar in the PEAR subdirectory was not working correctly. The solution to this is presented here. By executing the command

php -d phar.require_hash=0 go-pear.phar

the problem is solved and PEAR is installed.

After that however, when I tried to get back to Joshua's how-to, the PEAR version was not correct. This site helped me to update PEAR. When PEAR is installed, type

pear channel-update pear.php.net

in the terminal. This will update the PEAR channel. After that, by typing in

pear upgrade PEAR

the PEAR installation will be updated. From that point on PHPUnit can be installed as described at Joshua's blog.

Crontab

A feature which I use pretty often is the crontab. It can schedule and execute scripts at particular moments. A crontab is not provided by WampServer. However, there are external solutions available. One such solutions is nnCron of nnSoft. This is a crontab which can be installed by executing the installer file. The LITE (free) version already provides the desired functionality. The way it works is pretty simple: in the install directory there are batch files startcron.bat and stopcron.bat which allow to start the crontab and stop it. The file cron.tab contains the crontab lines.

N.B. Using WampServer and this Crontab, you can write automated tasks in PHP for executing tasks on your local machine. (Nice!).

Mootools

Today I was unpleasantly surprised that Mootools doesn't work on WampServer. I tried various demo's of AJAX calls, but none of them worked. When I tried one on an online web server it worked directly. So far I haven't been able to find topics about this problem, so any help is appreciated!'

> library(Rserve)
> Rserve(args='--no-save')

Note that the args can be 'save', 'no-save' or 'vanilla'.

Taverna

In Taverna an RShell can be added to the workflow to execute an R script. This script can be edited / defined by right-clicking the node and choosing that particular option.

Currently, when running a workflow in Taverna 2.1 beta2 and R 2.9.2 results in a handshake error. Apparently Rserve uses a newer protocol version than Taverna does.

The whole code file is presented below. For more information you can view my earlier blogpost on K-means clustering.

package actions;
 
import java.awt.Color;
import java.awt.image.BufferedImage;
import java.util.ArrayList;
 
/**
 * This KMeansAction performs a K-means clustering action on a BufferedImage
 * @author Patrick van Kouteren
 *
 */
 
public class KMeansAction {
 
		BufferedImage image_temp;
		boolean not_terminated;
		int loops, changedPixels;
		int[] histogram;
		ArrayList classes;
		int [] lowerbounds;
		public final static int MEAN_BY_MOD = 1;
		public final static int MEAN_BY_SPACE = 2;
		public final static int MEAN_AT_RANDOM = 3;
 
		/**
		 * Controls the actual work:
		 * - Initialization
		 * - Loop until termination condition is met
		 *  + for each pixel: assign pixel to a class such that the distance from the pixel to the mean of that class is minimized
		 *  + for each class: recalculate the means of the class based on pixels belonging to that class
		 * - End loop
		 * @param image
		 * @param bins (k)
		 * @param histogram
		 */
		public KMeansAction(BufferedImage image, int bins, int[]histogram, int initway) {
			this.histogram = histogram;
			lowerbounds = new int[bins];
			initialize(image, bins, initway);
			calculateBounds();
			while (not_terminated) {
				recalculateMeans();
				loops++;
				checkTermination();
				}
			processImage(image, bins);
		}
 
		/**
		 * Set the new color values for the image
		 * @param image
		 */
		private void processImage(BufferedImage image, int bins) {
			int delta = 255 / (bins-1);
			for (int h = 0; h < image.getHeight(); h++){
				for (int w = 0; w < image.getWidth(); w++){
					Color rgb = new Color(image.getRGB(w, h));
					int grey = rgb.getRed();
					for (int i = 0; i classes.get(i).lowerbound && grey < classes.get(i).upperbound) {
							int g = i*delta;
							image_temp.setRGB(w,h,(new Color(g, g, g)).getRGB());
						}
					}
				}
			}
		}
 
		/**
		 * Returns the image created by the processImage method
		 * @return the result image
		 */
		public BufferedImage getResultImage() {
			return image_temp;
		}
 
		/**
		 * Just for fun: returns the number of loops which were needed for getting a stable result
		 * @return number of loops for stable result
		 */
		public int getLoops(){
			return loops;
		}
 
		/**
		 * Initializes the algorithm. Creates k ClusterClasses and puts them into a LinkedList
		 * @param image
		 * @param bins
		 */
		@SuppressWarnings("unchecked")
		private void initialize(BufferedImage image, int bins, int initway){
			image_temp = image;
			loops = 0;
			changedPixels = 0;
			not_terminated = true;
			classes = new ArrayList();
			for (int i = 0; i < bins; i++) {
				ClusterClass cc = new ClusterClass(createMean(initway, bins, i, image));
				classes.add(cc);
			}
 
		}
 
		/**
		 * Controls the calculations of the upper- and lowerbounds of ClusterClasses and sets them
		 *
		 */
		private void calculateBounds() {
			for (int i = 0; i < classes.size(); i++){
				int lb = calculateLowerBound(classes.get(i));
				lowerbounds[i] = lb;
				classes.get(i).setBounds(lb,calculateUpperBound(classes.get(i)) );
				}
		}
 
		/**
		 * Does the actual calculation of the lowerbound
		 * @param ClusterClass
		 * @return Lowerbound
		 */
		private int calculateLowerBound(ClusterClass cc) {
			int cMean = cc.getMean();
			int currentBound = 0;
			for (int i = 0; i< classes.size(); i++) { 					if (cMean > classes.get(i).getMean()) {
						currentBound = Math.max((cMean + classes.get(i).getMean())/2, currentBound);
					}
					else {
					}
				}
			return currentBound;
			}
 
		/**
		 * Does the actual calculation of the upperbound
		 * @param ClusterClass
		 * @return Upperbound
		 */
		private int calculateUpperBound(ClusterClass cc) {
				int cMean = cc.getMean();
				int currentBound = 255;
				for (int i = 0; i< classes.size(); i++) {
						if (cMean < classes.get(i).getMean()) {
							currentBound = Math.min((cMean + classes.get(i).getMean())/2, currentBound);
						}
						else {}
					}
				return currentBound;
				}
 
		/**
		 * Takes care of the recalculation of the means of the ClusterClasses
		 *
		 */
		private void recalculateMeans() {
			for (int i = 0; i= 50) {
				not_terminated = false;
			}
			if (changedPixels <= 300) {
				not_terminated = false;
			}
		}
 
		private void calculateChangedPixels() {
			int changed = 0;
			for (int i = 0; i< lowerbounds[i]) {
					for (int j = c; j lowerbounds[i]) {
					for (int j = lowerbounds[i]; j< image.getHeight(); h++){
					for (int w = 0; w < image.getWidth(); w++){
						pixelindex+=1;
						if (pixelindex % bins == index) {
							Color rgb = new Color(image.getRGB(w, h));
							sum+= rgb.getRed();
							value+=1;
						}
					}}
				return sum/value;
 
			case MEAN_BY_SPACE:
				return (int)(255 / (bins-1) * index);
			case MEAN_AT_RANDOM:
				Double dmean = Math.random() * 255;
				return (int) Math.floor(dmean);
			default:
				return 0;
			}
		}
}

In addition to this, the custom class ClusterClass is defined as:

package actions;
 
/**
 * The ClusterClass is just a class holding the important cluster properties.
 * @author Patrick van Kouteren
 *
 */
 
public class ClusterClass {
	int mean, upperbound, lowerbound;
 
	public ClusterClass(int m) {
		mean = m;
	}
 
	public void setBounds(int lb, int ub) {
		lowerbound = lb;
		upperbound = ub;
	}
 
	public void setMean(int i) {
		mean = i;
	}
 
	public int getMean() {
		return mean;
	}
 
	public int getLowerBound() {
		return lowerbound;
	}
 
	public int getUpperBound() {
		return upperbound;
	}
 
	public void calculateMean(int [] histogram) {
		int tempMean = 0;
		int counter = 0;
		for (int i = lowerbound; i<= upperbound; i++) {
			counter += histogram[i];
			tempMean += histogram[i] * i;
		}
		mean = tempMean / counter;
	}
 
}

The source code might not be completely visible. It can be viewed in a blank screen here. As mentioned in the replies to this post, I forgot to add the ClusterClass. It can be viewed in a blank screen here.

One of the PDFs which should be merged was originally created from Word by a PDF creator which placed its signature in the properties of the PDF document. After removing this signature (in this case opening the PDF with Adobe Illustrator and saving it again) the problem was solved.

Compression and stream

The FPDF / FPDI classes use the input stream of the PDF file to create the concatenated PDF. Setasign remarks that the stream is only used (and altered) in the free version. The paid version should not give such errors. As I've experimented with the free version, I'll treat that one here.

Because of compression, some applications might leave out or mess up the xref property. Although this results in a PDF file which can be opened in a PDF reader, the stream is not according to the 'standards'. In such a case the document markup is 'lost' and applications / scripts using this property cannot handle these files any more.

PDF merging code example

To show how PDF files can be merged by using FPDF and FPDI I've compiled a little example which can be downloaded here. The archive consists of FPDF version 1.6, FPDI version 1.3.1, FPDI_TPL and two sample PDF files which were created with Microsoft Word 2007. The executing script is concat.php. Run this script to concatenate the two sample PDF files together in a new PDF file.

Possible solutions

A paid version of FPDI might be an option, but let's have a look at other possible solutions.

Opening the file and saving it again with a better pdf creator might fix the problem as it reformats the stream which is saved.

Final remarks

When you're creating the source PDF files yourself, watch out which pdf creator you use. Although the visual result might be the same, the stream might not be.