Re: Running PHP 5.2.X on Tomcat 5.5?
On Tue, May 11, 2010 at 7:53 AM, Gregers Blach gregbl...@netscape.net wrote: PHPMyAdmin would be a very nice add-on in order to better support MySQL databases. ...and likely to dig a few security wholes... if you really, really want to go for php, esp. PHPMyAdmin, be sure to configure it to listen on localhost only and tunnel the access via ssh. Furthermore, I'd install httpd, make it listen on localhost only (see above). However, the solution we're having here is: - Use DBVisualizer on the client (pure Java) - make the MySQL listen on local host only - tunnel the access to MySQL via ssh Rgds Gregor -- just because you're paranoid, don't mean they're not after you... gpgp-fp: 79A84FA526807026795E4209D3B3FE028B3170B2 gpgp-key available @ http://pgpkeys.pca.dfn.de:11371 @ http://pgp.mit.edu:11371/ skype:rc46fi - To unsubscribe, e-mail: users-unsubscr...@tomcat.apache.org For additional commands, e-mail: users-h...@tomcat.apache.org
Re: Running PHP 5.2.X on Tomcat 5.5?
Hi all, Thanks for your replies so far. It seems like: 1. No one recommends running PHP on Tomcat. Instead running httpd is recommended. 2. No one is able to provide me with a guide for setting up Tomcat to run PHP. I guess this must be because no one does this... :o) To bad - I really would have liked to see it work. /G -Original Message- From: Gregor Schneider rc4...@googlemail.com To: Tomcat Users List users@tomcat.apache.org Sent: Tue, May 11, 2010 8:59 am Subject: Re: Running PHP 5.2.X on Tomcat 5.5? On Tue, May 11, 2010 at 7:53 AM, Gregers Blach gregbl...@netscape.net wrote: PHPMyAdmin would be a very nice add-on in order to better support MySQL databases. ...and likely to dig a few security wholes... if you really, really want to go for php, esp. PHPMyAdmin, be sure to configure it to listen on localhost only and tunnel the access via ssh. Furthermore, I'd install httpd, make it listen on localhost only (see above). However, the solution we're having here is: - Use DBVisualizer on the client (pure Java) - make the MySQL listen on local host only - tunnel the access to MySQL via ssh Rgds Gregor -- just because you're paranoid, don't mean they're not after you... gpgp-fp: 79A84FA526807026795E4209D3B3FE028B3170B2 gpgp-key available @ http://pgpkeys.pca.dfn.de:11371 @ http://pgp.mit.edu:11371/ skype:rc46fi - To unsubscribe, e-mail: users-unsubscr...@tomcat.apache.org For additional commands, e-mail: users-h...@tomcat.apache.org - To unsubscribe, e-mail: users-unsubscr...@tomcat.apache.org For additional commands, e-mail: users-h...@tomcat.apache.org
Re: Running PHP 5.2.X on Tomcat 5.5?
On Tue, May 11, 2010 at 10:28 AM, Gregers Blach gregbl...@netscape.net wrote: Hi all, 1. No one recommends running PHP on Tomcat. Instead running httpd is recommended. right 2. No one is able to provide me with a guide for setting up Tomcat to run PHP. I guess this must be because no one does this... :o) To bad - I really would have liked to see it work. wrong - it's simply noone likes the idea. btw, googeling for PHP Tomcat would have shown you the following link as 1st hit: http://wiki.apache.org/tomcat/UsingPhp So it is possible, but you might not like what's written there Rgds Gregor -- just because you're paranoid, don't mean they're not after you... gpgp-fp: 79A84FA526807026795E4209D3B3FE028B3170B2 gpgp-key available @ http://pgpkeys.pca.dfn.de:11371 @ http://pgp.mit.edu:11371/ skype:rc46fi - To unsubscribe, e-mail: users-unsubscr...@tomcat.apache.org For additional commands, e-mail: users-h...@tomcat.apache.org
Re: java servlets, jsp and python
I have searched for jython and implemented some examples how to access jython code from java classes (e.g. with the ObjectFactory Pattern). Everything works fine outside the server. But if I create a Dynamic Web Project to access jython code from a java servlet, eclipse cannot find the org.python.util.PythonInterpreter; within my Factory.java I tried to add jython.jar to the class path of the project but it doesn't work. Do I have to configure the tomcat server in a way that it can use jython? On Wed, May 5, 2010 at 6:57 PM, Martin Gainty mgai...@hotmail.com wrote: you can implement a Jython (Python for Java) solution http://www.jython.org/ Martin Gainty __ Verzicht und Vertraulichkeitanmerkung/Note de déni et de confidentialité Diese Nachricht ist vertraulich. Sollten Sie nicht der vorgesehene Empfaenger sein, so bitten wir hoeflich um eine Mitteilung. Jede unbefugte Weiterleitung oder Fertigung einer Kopie ist unzulaessig. Diese Nachricht dient lediglich dem Austausch von Informationen und entfaltet keine rechtliche Bindungswirkung. Aufgrund der leichten Manipulierbarkeit von E-Mails koennen wir keine Haftung fuer den Inhalt uebernehmen. Ce message est confidentiel et peut être privilégié. Si vous n'êtes pas le destinataire prévu, nous te demandons avec bonté que pour satisfaire informez l'expéditeur. N'importe quelle diffusion non autorisée ou la copie de ceci est interdite. Ce message sert à l'information seulement et n'aura pas n'importe quel effet légalement obligatoire. Étant donné que les email peuvent facilement être sujets à la manipulation, nous ne pouvons accepter aucune responsabilité pour le contenu fourni. Date: Wed, 5 May 2010 18:50:40 +0200 Subject: java servlets, jsp and python From: silvio.tscha...@googlemail.com To: users@tomcat.apache.org Hi all, I am new to Web-Programming and maybe my question is trivial. I want to build a dynamic webpage and want to use a python script within a java servlet. Is this possible? I thought that it is only possible to run java code within a servlet. Maybe I havn't understood the architecture right. Could anybody explain me how the web-container would call / interact with python? I haven't found this topic in the documentation. Cheers! _ The New Busy is not the old busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_3
Re: java servlets, jsp and python
how to unsubscribe this mailing list?? On Tue, May 11, 2010 at 4:50 PM, Silvio Tschapke silvio.tscha...@googlemail.com wrote: I have searched for jython and implemented some examples how to access jython code from java classes (e.g. with the ObjectFactory Pattern). Everything works fine outside the server. But if I create a Dynamic Web Project to access jython code from a java servlet, eclipse cannot find the org.python.util.PythonInterpreter; within my Factory.java I tried to add jython.jar to the class path of the project but it doesn't work. Do I have to configure the tomcat server in a way that it can use jython? On Wed, May 5, 2010 at 6:57 PM, Martin Gainty mgai...@hotmail.com wrote: you can implement a Jython (Python for Java) solution http://www.jython.org/ Martin Gainty __ Verzicht und Vertraulichkeitanmerkung/Note de déni et de confidentialité Diese Nachricht ist vertraulich. Sollten Sie nicht der vorgesehene Empfaenger sein, so bitten wir hoeflich um eine Mitteilung. Jede unbefugte Weiterleitung oder Fertigung einer Kopie ist unzulaessig. Diese Nachricht dient lediglich dem Austausch von Informationen und entfaltet keine rechtliche Bindungswirkung. Aufgrund der leichten Manipulierbarkeit von E-Mails koennen wir keine Haftung fuer den Inhalt uebernehmen. Ce message est confidentiel et peut être privilégié. Si vous n'êtes pas le destinataire prévu, nous te demandons avec bonté que pour satisfaire informez l'expéditeur. N'importe quelle diffusion non autorisée ou la copie de ceci est interdite. Ce message sert à l'information seulement et n'aura pas n'importe quel effet légalement obligatoire. Étant donné que les email peuvent facilement être sujets à la manipulation, nous ne pouvons accepter aucune responsabilité pour le contenu fourni. Date: Wed, 5 May 2010 18:50:40 +0200 Subject: java servlets, jsp and python From: silvio.tscha...@googlemail.com To: users@tomcat.apache.org Hi all, I am new to Web-Programming and maybe my question is trivial. I want to build a dynamic webpage and want to use a python script within a java servlet. Is this possible? I thought that it is only possible to run java code within a servlet. Maybe I havn't understood the architecture right. Could anybody explain me how the web-container would call / interact with python? I haven't found this topic in the documentation. Cheers! _ The New Busy is not the old busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_3
Re: java servlets, jsp and python
2010/5/11 anoop singh khimani anoopsinghkhim...@gmail.com: how to unsubscribe this mailing list?? http://tomcat.apache.org/lists.html#tomcat-users 1. Send a short e-mail to users-unsubscr...@tomcat.apache.org Make sure, that the mail has a subject and non-empty body, so that it is not rejected by spam filter. 2. A confirmation will be sent to you. You have to reply to it to complete the unsubscribe process. Best regards, Konstantin Kolinko - To unsubscribe, e-mail: users-unsubscr...@tomcat.apache.org For additional commands, e-mail: users-h...@tomcat.apache.org
RE: java servlets, jsp and python
org.python.util.PythonInterpreter.class is located in jython.jar http://www.jython.org/Project/download.html ping offline if you need further assistance, Martin Gainty __ Verzicht und Vertraulichkeitanmerkung/Note de déni et de confidentialité Diese Nachricht ist vertraulich. Sollten Sie nicht der vorgesehene Empfaenger sein, so bitten wir hoeflich um eine Mitteilung. Jede unbefugte Weiterleitung oder Fertigung einer Kopie ist unzulaessig. Diese Nachricht dient lediglich dem Austausch von Informationen und entfaltet keine rechtliche Bindungswirkung. Aufgrund der leichten Manipulierbarkeit von E-Mails koennen wir keine Haftung fuer den Inhalt uebernehmen. Ce message est confidentiel et peut être privilégié. Si vous n'êtes pas le destinataire prévu, nous te demandons avec bonté que pour satisfaire informez l'expéditeur. N'importe quelle diffusion non autorisée ou la copie de ceci est interdite. Ce message sert à l'information seulement et n'aura pas n'importe quel effet légalement obligatoire. Étant donné que les email peuvent facilement être sujets à la manipulation, nous ne pouvons accepter aucune responsabilité pour le contenu fourni. Date: Tue, 11 May 2010 13:20:02 +0200 Subject: Re: java servlets, jsp and python From: silvio.tscha...@googlemail.com To: users@tomcat.apache.org I have searched for jython and implemented some examples how to access jython code from java classes (e.g. with the ObjectFactory Pattern). Everything works fine outside the server. But if I create a Dynamic Web Project to access jython code from a java servlet, eclipse cannot find the org.python.util.PythonInterpreter; within my Factory.java I tried to add jython.jar to the class path of the project but it doesn't work. Do I have to configure the tomcat server in a way that it can use jython? On Wed, May 5, 2010 at 6:57 PM, Martin Gainty mgai...@hotmail.com wrote: you can implement a Jython (Python for Java) solution http://www.jython.org/ Martin Gainty __ Verzicht und Vertraulichkeitanmerkung/Note de déni et de confidentialité Diese Nachricht ist vertraulich. Sollten Sie nicht der vorgesehene Empfaenger sein, so bitten wir hoeflich um eine Mitteilung. Jede unbefugte Weiterleitung oder Fertigung einer Kopie ist unzulaessig. Diese Nachricht dient lediglich dem Austausch von Informationen und entfaltet keine rechtliche Bindungswirkung. Aufgrund der leichten Manipulierbarkeit von E-Mails koennen wir keine Haftung fuer den Inhalt uebernehmen. Ce message est confidentiel et peut être privilégié. Si vous n'êtes pas le destinataire prévu, nous te demandons avec bonté que pour satisfaire informez l'expéditeur. N'importe quelle diffusion non autorisée ou la copie de ceci est interdite. Ce message sert à l'information seulement et n'aura pas n'importe quel effet légalement obligatoire. Étant donné que les email peuvent facilement être sujets à la manipulation, nous ne pouvons accepter aucune responsabilité pour le contenu fourni. Date: Wed, 5 May 2010 18:50:40 +0200 Subject: java servlets, jsp and python From: silvio.tscha...@googlemail.com To: users@tomcat.apache.org Hi all, I am new to Web-Programming and maybe my question is trivial. I want to build a dynamic webpage and want to use a python script within a java servlet. Is this possible? I thought that it is only possible to run java code within a servlet. Maybe I havn't understood the architecture right. Could anybody explain me how the web-container would call / interact with python? I haven't found this topic in the documentation. Cheers! _ The New Busy is not the old busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_3 _ Hotmail is redefining busy with tools for the New Busy. Get more from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_2
Re: java servlets, jsp and python
On 11/05/2010 13:45, Martin Gainty wrote: ping offline if you need further assistance, No, don't do that. We keep things on-list, so others can benefit from the finding a solution. p Martin Gainty __ Verzicht und Vertraulichkeitanmerkung/Note de déni et de confidentialité Diese Nachricht ist vertraulich. Sollten Sie nicht der vorgesehene Empfaenger sein, so bitten wir hoeflich um eine Mitteilung. Jede unbefugte Weiterleitung oder Fertigung einer Kopie ist unzulaessig. Diese Nachricht dient lediglich dem Austausch von Informationen und entfaltet keine rechtliche Bindungswirkung. Aufgrund der leichten Manipulierbarkeit von E-Mails koennen wir keine Haftung fuer den Inhalt uebernehmen. Ce message est confidentiel et peut être privilégié. Si vous n'êtes pas le destinataire prévu, nous te demandons avec bonté que pour satisfaire informez l'expéditeur. N'importe quelle diffusion non autorisée ou la copie de ceci est interdite. Ce message sert à l'information seulement et n'aura pas n'importe quel effet légalement obligatoire. Étant donné que les email peuvent facilement être sujets à la manipulation, nous ne pouvons accepter aucune responsabilité pour le contenu fourni. Date: Tue, 11 May 2010 13:20:02 +0200 Subject: Re: java servlets, jsp and python From: silvio.tscha...@googlemail.com To: users@tomcat.apache.org I have searched for jython and implemented some examples how to access jython code from java classes (e.g. with the ObjectFactory Pattern). Everything works fine outside the server. But if I create a Dynamic Web Project to access jython code from a java servlet, eclipse cannot find the org.python.util.PythonInterpreter; within my Factory.java I tried to add jython.jar to the class path of the project but it doesn't work. Do I have to configure the tomcat server in a way that it can use jython? On Wed, May 5, 2010 at 6:57 PM, Martin Gainty mgai...@hotmail.com wrote: you can implement a Jython (Python for Java) solution http://www.jython.org/ Martin Gainty __ Verzicht und Vertraulichkeitanmerkung/Note de déni et de confidentialité Diese Nachricht ist vertraulich. Sollten Sie nicht der vorgesehene Empfaenger sein, so bitten wir hoeflich um eine Mitteilung. Jede unbefugte Weiterleitung oder Fertigung einer Kopie ist unzulaessig. Diese Nachricht dient lediglich dem Austausch von Informationen und entfaltet keine rechtliche Bindungswirkung. Aufgrund der leichten Manipulierbarkeit von E-Mails koennen wir keine Haftung fuer den Inhalt uebernehmen. Ce message est confidentiel et peut être privilégié. Si vous n'êtes pas le destinataire prévu, nous te demandons avec bonté que pour satisfaire informez l'expéditeur. N'importe quelle diffusion non autorisée ou la copie de ceci est interdite. Ce message sert à l'information seulement et n'aura pas n'importe quel effet légalement obligatoire. Étant donné que les email peuvent facilement être sujets à la manipulation, nous ne pouvons accepter aucune responsabilité pour le contenu fourni. Date: Wed, 5 May 2010 18:50:40 +0200 Subject: java servlets, jsp and python From: silvio.tscha...@googlemail.com To: users@tomcat.apache.org Hi all, I am new to Web-Programming and maybe my question is trivial. I want to build a dynamic webpage and want to use a python script within a java servlet. Is this possible? I thought that it is only possible to run java code within a servlet. Maybe I havn't understood the architecture right. Could anybody explain me how the web-container would call / interact with python? I haven't found this topic in the documentation. Cheers! _ The New Busy is not the old busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_3 _ Hotmail is redefining busy with tools for the New Busy. Get more from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_2 signature.asc Description: OpenPGP digital signature
snort detecting ICMP traffic, tomcat?
Hi,
I run Snort in a PCI environment. I have just rebuilt Snort and I’m in the
tuning stage.
I have Tomcat 6.0.18 in the PCI environment and it may be initiating ICMP
traffic to external IPs. Here is the alert:
[1:486:5] ICMP Destination Unreachable Communication with Destination Host is
Administratively Prohibited [**] [Classification: Misc activity] [Priority: 3]
{ICMP} 10.10.100.21 - 134.173.121.59
I have read the summary of the rule at http://www.snort.org/search/sid/486?r=1
and understand that no corrective action is necessary but am curious about
this traffic.
Could Tomcat be generating ICMP traffic to an IP accessing the server?
Is this some kind of keep alive?
Thanks,
James
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RE: snort detecting ICMP traffic, tomcat?
From: James R. Marcus [mailto:jmar...@edhance.com] Subject: snort detecting ICMP traffic, tomcat? Could Tomcat be generating ICMP traffic to an IP accessing the server? No. Java is not capable of generating ICMP messages. - Chuck THIS COMMUNICATION MAY CONTAIN CONFIDENTIAL AND/OR OTHERWISE PROPRIETARY MATERIAL and is thus for use only by the intended recipient. If you received this in error, please contact the sender and delete the e-mail and its attachments from all computers. - To unsubscribe, e-mail: users-unsubscr...@tomcat.apache.org For additional commands, e-mail: users-h...@tomcat.apache.org
Re: snort detecting ICMP traffic, tomcat?
On 11/05/2010 15:17, James R. Marcus wrote:
Hi,
I run Snort in a PCI environment. I have just rebuilt Snort and I’m in the
tuning stage.
I have Tomcat 6.0.18 in the PCI environment and it may be initiating ICMP
traffic to external IPs. Here is the alert:
[1:486:5] ICMP Destination Unreachable Communication with Destination Host is
Administratively Prohibited [**] [Classification: Misc activity] [Priority:
3] {ICMP} 10.10.100.21 - 134.173.121.59
I have read the summary of the rule at
http://www.snort.org/search/sid/486?r=1 and understand that no corrective
action is necessary but am curious about this traffic.
Could Tomcat be generating ICMP traffic to an IP accessing the server?
Is this some kind of keep alive?
Please start a new message next time, rather than replying to editing
an existing message. (Which is called thread hijacking).
p
Thanks,
James
-
To unsubscribe, e-mail: users-unsubscr...@tomcat.apache.org
For additional commands, e-mail: users-h...@tomcat.apache.org
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set up tomcat for biopython
Hi all, how do I configure tomcat that it finds the biopython libaries? Biopython is not included in jython.jar (which I have moved into the tomcat/lib folder. Biopython installs itself into the python26/lib/side-packages folder. But how can I tell tomcat about this? There is no python.jar neither a biopython.jar file which I could drop into tomcat/lib. While running my Java Servlet which accesses a Jython module, that should access a Biopython class, this class cannot be found. Thanks for your reply!
Re: set up tomcat for biopython
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Silvio, I'm not familiar with biopython, so... On 5/11/2010 11:36 AM, Silvio Tschapke wrote: how do I configure tomcat that it finds the biopython libaries? Biopython is not included in jython.jar (which I have moved into the tomcat/lib folder. You probably want this JAR file in your webapp's WEB-INF/lib directory, rather than in Tomcat's global lib directory. Biopython installs itself into the python26/lib/side-packages folder. Okay, what files does it put in there? But how can I tell tomcat about this? There is no python.jar neither a biopython.jar file which I could drop into tomcat/lib. So, is biopython a set of binary libraries like .so files? Are you sure that it can be used in general with jython? If so, you probably just have to modify your java.library.path system property. While running my Java Servlet which accesses a Jython module, that should access a Biopython class, this class cannot be found. Can you post the stack trace for the CNFE? - -chris -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (MingW32) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAkvphvUACgkQ9CaO5/Lv0PAMdACgkk4lhyC8eZkbkrh0x6VULbzu nMcAoKKPg0THwapz6qDBLrp+znmnPSPr =gDVj -END PGP SIGNATURE- - To unsubscribe, e-mail: users-unsubscr...@tomcat.apache.org For additional commands, e-mail: users-h...@tomcat.apache.org
Re: Appserver Queues Filling Up
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Ben, On 5/10/2010 4:35 PM, Ben Knight wrote: We are having a Wicket-based Java application deployed in a production server cluster using Apache (2.2.3) with mod_jk (1.2.30) as load balancing component w/ sticky session and Jboss 5 as application container for the Java application. Do you know what version of Tomcat is being used in that version of JBoss? Recently, there have been some problems identified with a few connectors that can cause deadlock at the connector level. Have you looked at a thread dump of your webapp to see what the request processor threads are doing? - -chris -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (MingW32) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAkvpiGAACgkQ9CaO5/Lv0PDfTgCgwHUyW57kRx02K9xn5AsWN41y wZoAnRDiXNuv71fruZE3ejPTWlqA2Jyx =h6dq -END PGP SIGNATURE- - To unsubscribe, e-mail: users-unsubscr...@tomcat.apache.org For additional commands, e-mail: users-h...@tomcat.apache.org
RE: set up tomcat for biopython
i would start here http://sourceforge.net/projects/jython/files/ feel free to ask any questions hth Martin Gainty __ Verzicht und Vertraulichkeitanmerkung/Note de déni et de confidentialité Diese Nachricht ist vertraulich. Sollten Sie nicht der vorgesehene Empfaenger sein, so bitten wir hoeflich um eine Mitteilung. Jede unbefugte Weiterleitung oder Fertigung einer Kopie ist unzulaessig. Diese Nachricht dient lediglich dem Austausch von Informationen und entfaltet keine rechtliche Bindungswirkung. Aufgrund der leichten Manipulierbarkeit von E-Mails koennen wir keine Haftung fuer den Inhalt uebernehmen. Ce message est confidentiel et peut être privilégié. Si vous n'êtes pas le destinataire prévu, nous te demandons avec bonté que pour satisfaire informez l'expéditeur. N'importe quelle diffusion non autorisée ou la copie de ceci est interdite. Ce message sert à l'information seulement et n'aura pas n'importe quel effet légalement obligatoire. Étant donné que les email peuvent facilement être sujets à la manipulation, nous ne pouvons accepter aucune responsabilité pour le contenu fourni. Date: Tue, 11 May 2010 17:36:02 +0200 Subject: set up tomcat for biopython From: silvio.tscha...@googlemail.com To: users@tomcat.apache.org Hi all, how do I configure tomcat that it finds the biopython libaries? Biopython is not included in jython.jar (which I have moved into the tomcat/lib folder. Biopython installs itself into the python26/lib/side-packages folder. But how can I tell tomcat about this? There is no python.jar neither a biopython.jar file which I could drop into tomcat/lib. While running my Java Servlet which accesses a Jython module, that should access a Biopython class, this class cannot be found. Thanks for your reply! _ Hotmail is redefining busy with tools for the New Busy. Get more from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_2
Re: set up tomcat for biopython
First of all, thanks for your reply! On Tue, May 11, 2010 at 6:33 PM, Christopher Schultz ch...@christopherschultz.net wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Silvio, I'm not familiar with biopython, so... On 5/11/2010 11:36 AM, Silvio Tschapke wrote: how do I configure tomcat that it finds the biopython libaries? Biopython is not included in jython.jar (which I have moved into the tomcat/lib folder. You probably want this JAR file in your webapp's WEB-INF/lib directory, rather than in Tomcat's global lib directory. Biopython installs itself into the python26/lib/side-packages folder. Okay, what files does it put in there? There is no jar file. In the side-packages folder it puts a root folder Bio which includes further folders with .py, .pyo, pyc files. But how can I tell tomcat about this? There is no python.jar neither a biopython.jar file which I could drop into tomcat/lib. So, is biopython a set of binary libraries like .so files? Are you sure that it can be used in general with jython? If so, you probably just have to modify your java.library.path system property. I don't understand this. Do I have to tell Tomcat in a configuration file where it has to search for python or the libraries? Biopython works fine with Python outside my webserver. I am not sure if it works with Jython too. But I thought that Jython works fine with Python and Biopython is a subpackage so there shouldn'b be any problem. But I am not sure. When I write a CGI script which I put into the cgi-bin folder of a http server biopython works fine, because there you have to tell the server where it finds python.exe. While running my Java Servlet which accesses a Jython module, that should access a Biopython class, this class cannot be found. Can you post the stack trace for the CNFE? When I call: http://localhost:8080/Test_jee_with_jython/MyServlet I get a HTTP Status 500 error: Apache Tomcat/6.0.26 - Error report Traceback (most recent call last): File C:/Documents and Settings/silvio/My Documents/eclipse_jee_workspace/Test_jee_with_jython/src/jyimplementation/Calculator.py, line 2, in module from Bio import Entrez ImportError: No module named Bio org.python.core.PyException.fillInStackTrace(PyException.java:70) java.lang.Throwable.init(Throwable.java:181) java.lang.Exception.init(Unknown Source) java.lang.RuntimeException.init(Unknown Source) org.python.core.PyException.init(PyException.java:46) org.python.core.PyException.init(PyException.java:43) org.python.core.PyException.init(PyException.java:61) org.python.core.Py.ImportError(Py.java:264) org.python.core.imp.import_first(imp.java:672) org.python.core.imp.import_name(imp.java:756) org.python.core.imp.importName(imp.java:806) org.python.core.ImportFunction.__call__(__builtin__.java:1232) org.python.core.PyObject.__call__(PyObject.java:367) org.python.core.__builtin__.__import__(__builtin__.java:1202) org.python.core.imp.importFromAs(imp.java:884) org.python.core.imp.importFrom(imp.java:860) org.python.pycode._pyx2.f$0(C:/Documents and Settings/silvio/My Documents/eclipse_jee_workspace/Test_jee_with_jython/src/jyimplementation/Calculator.py:7) org.python.pycode._pyx2.call_function(C:/Documents and Settings/silvio/My Documents/eclipse_jee_workspace/Test_jee_with_jython/src/jyimplementation/Calculator.py) org.python.core.PyTableCode.call(PyTableCode.java:165) org.python.core.PyCode.call(PyCode.java:18) org.python.core.Py.runCode(Py.java:1204) org.python.core.__builtin__.execfile_flags(__builtin__.java:541) org.python.util.PythonInterpreter.execfile(PythonInterpreter.java:190) factory.JythonFactory.getJythonObject(JythonFactory.java:21) main.Main.forwardRequest(Main.java:17) servlets.MyServlet.doGet(MyServlet.java:36) javax.servlet.http.HttpServlet.service(HttpServlet.java:617) javax.servlet.http.HttpServlet.service(HttpServlet.java:717) If I change the import command in my jython module from from Bio import Entrez to import Bio.Entrez it doesn't work neither. By the way..what means CNFE? :) - -chris -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (MingW32) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAkvphvUACgkQ9CaO5/Lv0PAMdACgkk4lhyC8eZkbkrh0x6VULbzu nMcAoKKPg0THwapz6qDBLrp+znmnPSPr =gDVj -END PGP SIGNATURE- - To unsubscribe, e-mail: users-unsubscr...@tomcat.apache.org For additional commands, e-mail: users-h...@tomcat.apache.org
Re: set up tomcat for biopython
I took a look at jython and actually I am trying to implement a java servlet which calls a python module with help of jython. But I am not sure how and if I can use Biopython inside my jython modules. On Tue, May 11, 2010 at 6:44 PM, Martin Gainty mgai...@hotmail.com wrote: i would start here http://sourceforge.net/projects/jython/files/ feel free to ask any questions hth Martin Gainty __ Verzicht und Vertraulichkeitanmerkung/Note de déni et de confidentialité Diese Nachricht ist vertraulich. Sollten Sie nicht der vorgesehene Empfaenger sein, so bitten wir hoeflich um eine Mitteilung. Jede unbefugte Weiterleitung oder Fertigung einer Kopie ist unzulaessig. Diese Nachricht dient lediglich dem Austausch von Informationen und entfaltet keine rechtliche Bindungswirkung. Aufgrund der leichten Manipulierbarkeit von E-Mails koennen wir keine Haftung fuer den Inhalt uebernehmen. Ce message est confidentiel et peut être privilégié. Si vous n'êtes pas le destinataire prévu, nous te demandons avec bonté que pour satisfaire informez l'expéditeur. N'importe quelle diffusion non autorisée ou la copie de ceci est interdite. Ce message sert à l'information seulement et n'aura pas n'importe quel effet légalement obligatoire. Étant donné que les email peuvent facilement être sujets à la manipulation, nous ne pouvons accepter aucune responsabilité pour le contenu fourni. Date: Tue, 11 May 2010 17:36:02 +0200 Subject: set up tomcat for biopython From: silvio.tscha...@googlemail.com To: users@tomcat.apache.org Hi all, how do I configure tomcat that it finds the biopython libaries? Biopython is not included in jython.jar (which I have moved into the tomcat/lib folder. Biopython installs itself into the python26/lib/side-packages folder. But how can I tell tomcat about this? There is no python.jar neither a biopython.jar file which I could drop into tomcat/lib. While running my Java Servlet which accesses a Jython module, that should access a Biopython class, this class cannot be found. Thanks for your reply! _ Hotmail is redefining busy with tools for the New Busy. Get more from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_2
Re: set up tomcat for biopython
Silvio Tschapke wrote: I took a look at jython and actually I am trying to implement a java servlet which calls a python module with help of jython. But I am not sure how and if I can use Biopython inside my jython modules. I do not know anything about jython (or python for that matter), but by browsing around I found this, which may give you a clue as to the solution : http://wiki.python.org/jython/UserGuide#embedding-jython Sounds like an interesting animal anyway.. If I understand that thing right, this is a just-in-time compiler that can compile Python programs and modules as Java bytecode, then run it as a servlet. Amazing what smart people can put together nowadays. - To unsubscribe, e-mail: users-unsubscr...@tomcat.apache.org For additional commands, e-mail: users-h...@tomcat.apache.org
Re: set up tomcat for biopython
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Silvio, On 5/11/2010 1:09 PM, Silvio Tschapke wrote: On 5/11/2010 11:36 AM, Silvio Tschapke wrote: how do I configure tomcat that it finds the biopython libaries? Biopython is not included in jython.jar (which I have moved into the tomcat/lib folder. You probably want this JAR file in your webapp's WEB-INF/lib directory, rather than in Tomcat's global lib directory. Biopython installs itself into the python26/lib/side-packages folder. Okay, what files does it put in there? There is no jar file. In the side-packages folder it puts a root folder Bio which includes further folders with .py, .pyo, pyc files. Okay, those are Python scripts, compiled/optimized scripts, and compiled scripts. Nothing in there is directly executable, so you probably don't need to mess with your java.library.path setting. I don't understand this. Do I have to tell Tomcat in a configuration file where it has to search for python or the libraries? Biopython works fine with Python outside my webserver. I am not sure if it works with Jython too. But I thought that Jython works fine with Python and Biopython is a subpackage so there shouldn'b be any problem. But I am not sure. You might want to read a bit more about Jython: it does not give you access to the python environment on the local machine. Instead, it is its own environment. Consider reading http://www.jython.org/docs/tutorial/indexprogress.html If Bio uses direct C-library calls instead of Python functions, you're out of luck for the time being. Your first step would be to determine if Bio will work with Jython: I recommend getting in touch with the Jython folks to help you figure out how to get Bio working with Jython. After that's working, it shouldn't be difficult to move everything into Tomcat. Traceback (most recent call last): File C:/Documents and Settings/silvio/My Documents/eclipse_jee_workspace/Test_jee_with_jython/src/jyimplementation/Calculator.py, line 2, in module from Bio import Entrez ImportError: No module named Bio org.python.core.PyException.fillInStackTrace(PyException.java:70) So, somewhere there must be a place where you can configure where Jython looks for modules. [...] org.python.util.PythonInterpreter.execfile(PythonInterpreter.java:190) factory.JythonFactory.getJythonObject(JythonFactory.java:21) main.Main.forwardRequest(Main.java:17) It looks like before you call execfile(), you might want to make some other calls on either the PythonInterpreter object, or the PySystemState object it's using, which seems to have something to do with locating modules. servlets.MyServlet.doGet(MyServlet.java:36) javax.servlet.http.HttpServlet.service(HttpServlet.java:617) javax.servlet.http.HttpServlet.service(HttpServlet.java:717) If I change the import command in my jython module from from Bio import Entrez to import Bio.Entrez it doesn't work neither. By the way..what means CNFE? :) That's ClassNotFoundException, which is a Java exception. You're not getting that exception, but a different one from the Python interpreter. Don't worry: you gave me what I was looking for. So, it just looks like you need to figure out how to tell Jython that the Bio libraries are under .../lib/side-packages. I think you're going to have to ask the Jython folks. Good luck, - -chris -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (MingW32) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAkvpmNsACgkQ9CaO5/Lv0PAESQCcC4gjP3G9QUM5L7hAnmb1iPlg yOQAnjI8fXrcGPUyl+QJm/DUaf1ocbp+ =v3t/ -END PGP SIGNATURE- - To unsubscribe, e-mail: users-unsubscr...@tomcat.apache.org For additional commands, e-mail: users-h...@tomcat.apache.org
Re: set up tomcat for biopython
Ok, I will try this. Thanks a lot for your help! On Tue, May 11, 2010 at 7:50 PM, Christopher Schultz ch...@christopherschultz.net wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Silvio, On 5/11/2010 1:09 PM, Silvio Tschapke wrote: On 5/11/2010 11:36 AM, Silvio Tschapke wrote: how do I configure tomcat that it finds the biopython libaries? Biopython is not included in jython.jar (which I have moved into the tomcat/lib folder. You probably want this JAR file in your webapp's WEB-INF/lib directory, rather than in Tomcat's global lib directory. Biopython installs itself into the python26/lib/side-packages folder. Okay, what files does it put in there? There is no jar file. In the side-packages folder it puts a root folder Bio which includes further folders with .py, .pyo, pyc files. Okay, those are Python scripts, compiled/optimized scripts, and compiled scripts. Nothing in there is directly executable, so you probably don't need to mess with your java.library.path setting. I don't understand this. Do I have to tell Tomcat in a configuration file where it has to search for python or the libraries? Biopython works fine with Python outside my webserver. I am not sure if it works with Jython too. But I thought that Jython works fine with Python and Biopython is a subpackage so there shouldn'b be any problem. But I am not sure. You might want to read a bit more about Jython: it does not give you access to the python environment on the local machine. Instead, it is its own environment. Consider reading http://www.jython.org/docs/tutorial/indexprogress.html If Bio uses direct C-library calls instead of Python functions, you're out of luck for the time being. Your first step would be to determine if Bio will work with Jython: I recommend getting in touch with the Jython folks to help you figure out how to get Bio working with Jython. After that's working, it shouldn't be difficult to move everything into Tomcat. Traceback (most recent call last): File C:/Documents and Settings/silvio/My Documents/eclipse_jee_workspace/Test_jee_with_jython/src/jyimplementation/Calculator.py, line 2, in module from Bio import Entrez ImportError: No module named Bio org.python.core.PyException.fillInStackTrace(PyException.java:70) So, somewhere there must be a place where you can configure where Jython looks for modules. [...] org.python.util.PythonInterpreter.execfile(PythonInterpreter.java:190) factory.JythonFactory.getJythonObject(JythonFactory.java:21) main.Main.forwardRequest(Main.java:17) It looks like before you call execfile(), you might want to make some other calls on either the PythonInterpreter object, or the PySystemState object it's using, which seems to have something to do with locating modules. servlets.MyServlet.doGet(MyServlet.java:36) javax.servlet.http.HttpServlet.service(HttpServlet.java:617) javax.servlet.http.HttpServlet.service(HttpServlet.java:717) If I change the import command in my jython module from from Bio import Entrez to import Bio.Entrez it doesn't work neither. By the way..what means CNFE? :) That's ClassNotFoundException, which is a Java exception. You're not getting that exception, but a different one from the Python interpreter. Don't worry: you gave me what I was looking for. So, it just looks like you need to figure out how to tell Jython that the Bio libraries are under .../lib/side-packages. I think you're going to have to ask the Jython folks. Good luck, - -chris -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (MingW32) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAkvpmNsACgkQ9CaO5/Lv0PAESQCcC4gjP3G9QUM5L7hAnmb1iPlg yOQAnjI8fXrcGPUyl+QJm/DUaf1ocbp+ =v3t/ -END PGP SIGNATURE- - To unsubscribe, e-mail: users-unsubscr...@tomcat.apache.org For additional commands, e-mail: users-h...@tomcat.apache.org
Re: Tomcat 100% CPU usage after moving from Java 5 to 6
I'm also attempting to track down a cpu usage problem in tomcat. Can someone tell me how to generate thread dumps that includes the cpu= information like the ones Jesse attached? ajp-8009-18 Id=187 in RUNNABLE cpu=242046 ms usr=242015 ms blocked 315 for -1 ms waited 256 for -1 ms When I create a tomcat thread dump using ctrl-break, it does not contain any cpu info: RMI TCP Accept- daemon prio=6 tid=0x26eeda60 nid=0xd58 runnable [0x2712f00 0..0x2712fd68] at java.net.PlainSocketImpl.socketAccept(Native Method) Jesse Klaasse wrote: I am running a production environment for a website (over half a million hits per day), using Tomcat 5.5.20 (I'm stuck to that version due to support restrictions) behind IIS 6 using JK connector 1.2.28, tcnative-1.dll (1.1.19) on Windows Server 2003 R2 Enterprise x64 SP2 (with 16 GB RAM). Until last week, I have been using Sun Java 5. Last week I have upgraded the JDK to Sun Java 6. The system uses a MS SQL Server 2005 database, which resides on another server. That's when things went wrong. At first, all seemed fine (average CPU usage seems lower than when using Java 5), but after an hour or so (30 minutes - 1,5 hour max) after a Tomcat restart, Tomcat's CPU usage jumps to 100% (average CPU usage using Java 5 is around 30-40%, peaks around 60%). I can't really figure out what is causing this. I have retried about 6 restarts (including a complete system reboot), but without any success. When I move back to Java 5, the problems are gone. My Tomcat Java arguments: -Dcatalina.base=D:\tomcat -Dcatalina.home=D:\tomcat -Djava.endorsed.dirs=D:\tomcat\common\endorsed -Djava.io.tmpdir=D:\tomcat\temp -Djavax.sql.DataSource.Factory=org.apache.commons.dbcp.BasicDataSourceFa ctory -Dcom.sun.management.jmxremote -XX:MaxPermSize=512m -Xloggc:D:\logs\gc\tomcat-gc.log -XX:+PrintGCDetails -XX:+UseParNewGC -XX:+UseConcMarkSweepGC -XX:+UseTLAB -XX:+CMSClassUnloadingEnabled -XX:+CMSPermGenSweepingEnabled -Xms4096m -Xmx10240m Some further information which could be important: - I have tried to reproduce the problems on my development environment (using jMeter for generating server load), but without success; - I have created some thread dumps during the 100% CPU periods (attached as a zip file); I would really like to make the move to Java 6, since Java 5's is EOL. Any ideas, anyone? - To unsubscribe, e-mail: users-unsubscr...@tomcat.apache.org For additional commands, e-mail: users-h...@tomcat.apache.org -- View this message in context: http://old.nabble.com/Tomcat-100--CPU-usage-after-moving-from-Java-5-to-6-tp27305110p28527724.html Sent from the Tomcat - User mailing list archive at Nabble.com. - To unsubscribe, e-mail: users-unsubscr...@tomcat.apache.org For additional commands, e-mail: users-h...@tomcat.apache.org
Re: set up tomcat for biopython
Silvio Tschapke wrote: Ok, I will try this. Thanks a lot for your help! On Tue, May 11, 2010 at 7:50 PM, Christopher Schultz ch...@christopherschultz.net wrote: [...] org.python.util.PythonInterpreter.execfile(PythonInterpreter.java:190) factory.JythonFactory.getJythonObject(JythonFactory.java:21) main.Main.forwardRequest(Main.java:17) It looks like before you call execfile(), you might want to make some other calls on either the PythonInterpreter object, or the PySystemState object it's using, which seems to have something to do with locating modules. +1 That is what the link I sent earlier seems to point to also. - To unsubscribe, e-mail: users-unsubscr...@tomcat.apache.org For additional commands, e-mail: users-h...@tomcat.apache.org
RE: Appserver Queues Filling Up
Hey Chris, Thanks for the reply. We have yet to do a thread dump. I was actually waiting for the queues to fill up again to do just that. In the meantime, I have JBoss v. 5.1.0GA and JBoss web v. 2.1.3GA. Which versions of Tomcat have had problems? Thanks Ben -Original Message- From: Christopher Schultz [mailto:ch...@christopherschultz.net] Sent: Tuesday, May 11, 2010 12:40 PM To: Tomcat Users List Subject: Re: Appserver Queues Filling Up -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Ben, On 5/10/2010 4:35 PM, Ben Knight wrote: We are having a Wicket-based Java application deployed in a production server cluster using Apache (2.2.3) with mod_jk (1.2.30) as load balancing component w/ sticky session and Jboss 5 as application container for the Java application. Do you know what version of Tomcat is being used in that version of JBoss? Recently, there have been some problems identified with a few connectors that can cause deadlock at the connector level. Have you looked at a thread dump of your webapp to see what the request processor threads are doing? - -chris -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (MingW32) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAkvpiGAACgkQ9CaO5/Lv0PDfTgCgwHUyW57kRx02K9xn5AsWN41y wZoAnRDiXNuv71fruZE3ejPTWlqA2Jyx =h6dq -END PGP SIGNATURE- - To unsubscribe, e-mail: users-unsubscr...@tomcat.apache.org For additional commands, e-mail: users-h...@tomcat.apache.org - To unsubscribe, e-mail: users-unsubscr...@tomcat.apache.org For additional commands, e-mail: users-h...@tomcat.apache.org
Re: set up tomcat for biopython
Am Dienstag, den 11.05.2010, 17:36 +0200 schrieb Silvio Tschapke: Hi all, how do I configure tomcat that it finds the biopython libaries? Biopython is not included in jython.jar (which I have moved into the tomcat/lib folder. Biopython installs itself into the python26/lib/side-packages folder. If my google-research is correct, you will have to use a branch of bioperl which supports jython: http://github.com/kellrott/biopython If you use this and jython 2.5.1, you will have to set the environment variable JYTHONPATH=$PATH_WHERE_YOU_CHECKEDOUT_BIOPYTHON After that you should be able to run jython in command line and do an import Bio.Entrez without problems. When you have run that command successfully you could go further to try and embed jython with that environment variable into a servlet. Bye Felix Thanks to Chris for providing the link to the jython tutorial :) But how can I tell tomcat about this? There is no python.jar neither a biopython.jar file which I could drop into tomcat/lib. While running my Java Servlet which accesses a Jython module, that should access a Biopython class, this class cannot be found. Thanks for your reply! - To unsubscribe, e-mail: users-unsubscr...@tomcat.apache.org For additional commands, e-mail: users-h...@tomcat.apache.org
error-page exception-type subclasses of RuntimeException are not handled
Tomcat Version: apache-tomcat-6.0.26 JDK: jdk1.6.0_19 OS: Windows XP Service Pack 2 I am using the page-error element in my web.xml with the exception-type element which contains a subclass of RuntimeException. When I subclass RuntimeException the location element which specifies my error-page to land on in the event that exception is raised is not displayed. web.xml snippet: error-page exception-typeorg.lds.lua.directory.exception.LuaSecurityException/exception-type location/error.html/location /error-page Where LuaSecurityException extends RuntimeException When my JAX-RS method throws the LuaSecurityException the error.html is NOT displayed. However, if I change the above configuration to: error-page exception-typejava.lang.RuntimeException/exception-type location/error.html/location /error-page and have my class throw a RuntimeException then the error.html page is displayed. Finally if I change the web.xml to: error-page exception-typejava.lang.Exception/exception-type location/error.html/location /error-page and my jax-rs class throws a LuaSecurityException extends RuntimeException then my error.html is displayed. What I would like to do is: error-page exception-typeorg.lds.lua.directory.exception.LuaSecurityException/exception-type location/error.html/location /error-page That way I can create various RuntimeException subclasses which are appropriate for my application and handle them with specific error pages. Any help would be appreciated. If you need more information please let me know. Bryan _ Hotmail is redefining busy with tools for the New Busy. Get more from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_2
