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From: <lis...@ic...> - 2011-07-19 12:18:59
|
Ok problem solved. My program had a load of hidden ^M 's that I didn't see and I just removed them. So yay. Sorry for all the posts. :) > Also I forgot to add that even when I copy this program into the run > directory it doesn't work. But when I run it as a command line tool from > the external directory it works so I know it's set up correctly. Is it > just that it needs a wrapper to run as it calls other executables too? > > > ---------------------------- Original Message ---------------------------- > Subject: Soaplab2 Help > From: lro...@ic... > Date: Tue, July 19, 2011 10:23 am > To: soa...@li... > -------------------------------------------------------------------------- > > Hi I hope that this is alright. I'm quite new to soaplab2 and I'm not sure > what to do about this. Whenever I try to run external programs outside > the run directory I get this error below. Is it cause it's python? Ive > modified the soaplab.properties.template "addtopath.dir" to include this > new path,as suggested in the config guide, but it's still not working. > Any help would be appreciated as I'm stumped. I also just changed the > directory names to make it easier to see. In case this is the problem, I > haven't made the complete acd file yet, im just having a basic layout just > to check if it's set up correctly but when I do that with files in the run > directory it works ok. > > Summary: > Completed: Erroneously > Termination status: -1 > Ended: 2011-Jul-19 10:13:54 (IST) > Report: > Not able to execute an external program: '/i/y/z/program.pl': Cannot run > program "/i/y/z/program.pl" (in directory > "/i/w/l/apache-tomcat-7.0.14/temp/_R_/SANDBOX/[custom.test2]5502098c.13141ac4394._7fff"): > java.io.IOException: error=13, Permission denied > > > > > > |
From: <lis...@ic...> - 2011-07-19 09:54:29
|
Also I forgot to add that even when I copy this program into the run directory it doesn't work. But when I run it as a command line tool from the external directory it works so I know it's set up correctly. Is it just that it needs a wrapper to run as it calls other executables too? ---------------------------- Original Message ---------------------------- Subject: Soaplab2 Help From: lro...@ic... Date: Tue, July 19, 2011 10:23 am To: soa...@li... -------------------------------------------------------------------------- Hi I hope that this is alright. I'm quite new to soaplab2 and I'm not sure what to do about this. Whenever I try to run external programs outside the run directory I get this error below. Is it cause it's python? Ive modified the soaplab.properties.template "addtopath.dir" to include this new path,as suggested in the config guide, but it's still not working. Any help would be appreciated as I'm stumped. I also just changed the directory names to make it easier to see. In case this is the problem, I haven't made the complete acd file yet, im just having a basic layout just to check if it's set up correctly but when I do that with files in the run directory it works ok. Summary: Completed: Erroneously Termination status: -1 Ended: 2011-Jul-19 10:13:54 (IST) Report: Not able to execute an external program: '/i/y/z/program.pl': Cannot run program "/i/y/z/program.pl" (in directory "/i/w/l/apache-tomcat-7.0.14/temp/_R_/SANDBOX/[custom.test2]5502098c.13141ac4394._7fff"): java.io.IOException: error=13, Permission denied |
From: <lis...@ic...> - 2011-07-19 09:54:19
|
Hi I hope that this is alright. I'm quite new to soaplab2 and I'm not sure what to do about this. Whenever I try to run external programs outside the run directory I get this error below. Is it cause it's python? Ive modified the soaplab.properties.template "addtopath.dir" to include this new path,as suggested in the config guide, but it's still not working. Any help would be appreciated as I'm stumped. I also just changed the directory names to make it easier to see. In case this is the problem, I haven't made the complete acd file yet, im just having a basic layout just to check if it's set up correctly but when I do that with files in the run directory it works ok. Summary: Completed: Erroneously Termination status: -1 Ended: 2011-Jul-19 10:13:54 (IST) Report: Not able to execute an external program: '/i/y/z/program.pl': Cannot run program "/i/y/z/program.pl" (in directory "/i/w/l/apache-tomcat-7.0.14/temp/_R_/SANDBOX/[custom.test2]5502098c.13141ac4394._7fff"): java.io.IOException: error=13, Permission denied |
From: Mahmut U. <ul...@eb...> - 2011-03-07 14:27:47
|
Hi Iwe, > I have a few issues with soaplab2. Whenever I make small changes to an > ACD file (I am trying to implement a bunch of our group's scripts in > soaplab to make them available for wide use) I have to rebuild the war > file, and restart the tomcat server. I do this with a shell script. > The problem is this takes about a minute. So every change I make takes > at least a minute to test. Is there maybe a better, faster solution? Instead of using axis1deploy or jaxdeploy targets you can use axis1deployx or jaxdeployx targets that should eliminate the need for restarting the tomcat server (requires Tomcat Web Application Manager). For testing some of your changes you can use soaplab command line client using the 'local' protocol which doesn't require re/building soaplab web application. > Soaplab restart script: > > sudo ant gensowa > sudo ant jaxdeploy > ./tomcat_restart.sh > > Another problem I seem to have is an inconsistency in the list of > services after a restart. The spinet application and Taverna recognize > the new or changed services but the list (/services) is not properly > refreshed. Taverna also does not load the new services correctly > because it can't find them, even though they are in the list. This is probably because you are using 'jaxdeploy' rather than 'axis1deploy', taverna soaplab plugin uses axis1 services. Mahmut |
From: Iwe M. <e.c...@gm...> - 2011-03-07 13:44:56
|
Hello Soaplab team, I have a few issues with soaplab2. Whenever I make small changes to an ACD file (I am trying to implement a bunch of our group's scripts in soaplab to make them available for wide use) I have to rebuild the war file, and restart the tomcat server. I do this with a shell script. The problem is this takes about a minute. So every change I make takes at least a minute to test. Is there maybe a better, faster solution? Soaplab restart script: sudo ant gensowa sudo ant jaxdeploy ./tomcat_restart.sh Another problem I seem to have is an inconsistency in the list of services after a restart. The spinet application and Taverna recognize the new or changed services but the list (/services) is not properly refreshed. Taverna also does not load the new services correctly because it can't find them, even though they are in the list. The error is shown below: Caused by: net.sf.taverna.t2.workflowmodel.processor.activity.ActivityConfigurationException: : Unable to call the get spec method for endpoint : http://localhost:8080/soaplab2-axis/services/benchmark_vis.pyramid Remote exception message The AXIS engine could not find a target service to invoke! targetService is benchmark_vis.pyramid The last problem is that after conversion of some of the ACD files there apparently is a problem with the generated XML. Taverna's log file indicates that with the following error: Caused by: java.lang.IllegalArgumentException: The char '0x1f' after '' is not a valid XML character. I hope this was enough information to help me out a little. Thanks in advance! Greetings, Iwe Muiser -- Iwe EC Muiser Master student NTNU - Department of Cancer Research and Molecular Medicine Bioinformatics & Gene Regulation Group Laboratory Centre, 5th floor. Erling Skjalgssons gt. 1 Trondheim +4594157082 |
From: Martin S. <mar...@gm...> - 2010-11-24 09:47:58
|
Release 2.3.1 is a bug-fix release. Bugs (or missing features) are related to the character encoding of Soaplab2's services inputs and outputs. Details are in the file "docs/ChangeLog" ( http://soaplab.sourceforge.net/soaplab2/ChangeLog). Project main page stays the same: http://soaplab.sourceforge.net/soaplab2/. Many thanks for those who contributed. Feedback and suggestions are again warmly welcome. Cheers, Martin -- Martin Senger email: mar...@gm...,mar...@ka... skype: martinsenger |
From: Martin S. <mar...@gm...> - 2010-08-17 11:05:36
|
Thanks to work of Soaplab2 developers, especially to people from the EBI, I can announce a new Soaplab2 release: Release 2.3.0 is mostly a maintenance release - but it also brings several new features: * Strongly typed services. * Semantically annotated WSDLs. * Changes made to be compliant with the latest EMBOSS package (version 6.3). * More properties to customize Soaplab2 components. * Updated documentation. More details about changes are in the file "docs/ChangeLog". Cheers, Martin -- Martin Senger email: mar...@gm...,mar...@ka... skype: martinsenger |
From: Yuan L. <pp....@ya...> - 2010-08-11 03:45:55
|
Hi Martin, I tried several times and finally it got through! Thanks! It stopped on different jar files but they are all from the same site, biomoby-m2. Yuan ________________________________ From: Martin Senger <mar...@gm...> To: Yuan LUO <pp....@ya...> Cc: soa...@li... Sent: Tue, August 10, 2010 4:15:27 PM Subject: Re: [Soaplab2-dev] installation halt on Maven Hi, Has it stopped on the same place (on the same jar file)? Have you tried Ctrl-C and ant... again several times? I am afraid that all what I can suggest. I did it myself today several times - and sometimes it stopped but on the second try it continued to the end successfully. Martin -- Martin Senger email: mar...@gm...,mar...@ka... skype: martinsenger |
From: Martin S. <mar...@gm...> - 2010-08-10 20:15:36
|
Hi, Has it stopped on the same place (on the same jar file)? Have you tried Ctrl-C and ant... again several times? I am afraid that all what I can suggest. I did it myself today several times - and sometimes it stopped but on the second try it continued to the end successfully. Martin -- Martin Senger email: mar...@gm...,mar...@ka... skype: martinsenger |
From: Yuan L. <pp....@ya...> - 2010-08-10 18:39:52
|
Hi Martin, Thanks for the reply. I am new to the soaplab, and that installation was first try. I can't still get through it. Would it be possible that I get these jar files elsewhere, instead of using Maven to download? Thanks, Yuan ________________________________ From: Martin Senger <mar...@gm...> To: Yuan LUO <pp....@ya...> Cc: soa...@li... Sent: Tue, August 10, 2010 5:29:31 AM Subject: Re: [Soaplab2-dev] installation halt on Maven Hi again, I tried to reproduce your problem - and, indeed, I reproduced it. But then running it again few seconds later, the problem disappeared. I think that the problem is with one of the maven repositories we are using; it is probably a temporary network/access problem. If you have the same problem again, I recommend to backup your whole local maven repository (on Linux, it would be by typing: cd ~; mv .m2 .m2.backup) and try to populate it again (cd soaplab2; ant clean compile). And perhaps to use "ant clean compile" several times until it succeeds - at least, that worked for me. Cheers, Martin -- Martin Senger email: mar...@gm...,mar...@ka... skype: martinsenger |
From: Carsten S. <sch...@el...> - 2010-08-10 10:05:43
|
On 10/08/2010 11:29, Martin Senger wrote: > I tried to reproduce your problem - and, indeed, I reproduced it. But > then running it again few seconds later, the problem disappeared. I > think that the problem is with one of the maven repositories we are > using; it is probably a temporary network/access problem. If you have > the same problem again, I recommend to backup your whole local maven > repository (on Linux, it would be by typing: cd ~; mv .m2 .m2.backup) > and try to populate it again (cd soaplab2; ant clean compile). And > perhaps to use "ant clean compile" several times until it succeeds - at > least, that worked for me. I have had the same problem. My 'solution' was to abort the Maven process with Ctrl-C and restart the installation with ant. This I've had to do a couple of times until all the maven packages could be downloaded. I haven't had the time to investigate the cause, but assume some network problem. Should not be like that though, but interrupting and restarting was the quickest way to go through it for me. Good luck! Carsten |
From: Martin S. <mar...@gm...> - 2010-08-10 09:29:38
|
Hi again, I tried to reproduce your problem - and, indeed, I reproduced it. But then running it again few seconds later, the problem disappeared. I think that the problem is with one of the maven repositories we are using; it is probably a temporary network/access problem. If you have the same problem again, I recommend to backup your whole local maven repository (on Linux, it would be by typing: cd ~; mv .m2 .m2.backup) and try to populate it again (cd soaplab2; ant clean compile). And perhaps to use "ant clean compile" several times until it succeeds - at least, that worked for me. Cheers, Martin -- Martin Senger email: mar...@gm...,mar...@ka... skype: martinsenger |
From: Martin S. <mar...@gm...> - 2010-08-10 07:37:02
|
Hi, It may be that the given Maven repository was not available at the time. I will check on my computer once I get to it (later today) and let you know; meanwhile just try again - you may be lucky this time. Martin -- Martin Senger email: mar...@gm...,mar...@ka... skype: martinsenger |
From: Yuan L. <pp....@ya...> - 2010-08-10 05:09:15
|
Hi, I was installing soaplab2 and it got halt on fetching a Maven library as below. [artifact:dependencies] Downloading: org/codehaus/woodstox/wstx-asl/3.2.3/wstx-asl-3.2.3.pom from biomoby-m2 Anyone please help me. Thanks, Yuan |
From: Martin S. <mar...@gm...> - 2009-06-26 22:12:47
|
Dear Soaplab users, The new version was released. Project: Soaplab (soaplab) Package: soaplab2 Date : 2009-06-26 21:49 Project "Soaplab" ('soaplab') has released the new version of package 'soaplab2'. You can download it from SourceForge.net by following this link: < https://sourceforge.net/project/showfiles.php?group_id=104834&release_id=692718 > or browse Release Notes and ChangeLog by visiting this link: <https://sourceforge.net/project/shownotes.php?release_id=692718> We will appreciate any feedback and bug reports. Cheers, Martin -- Martin Senger email: mar...@gm...,m.s...@cg... skype: martinsenger |
From: Martin S. <mar...@gm...> - 2008-09-09 18:29:04
|
> Ah...is there any way I can get around this? I have an application that > output nine different text files, all with hard-coded names! > > > You have to wrap you script into few lines that can > > map the hard-coded file name into the one given by Soaplab (in your > exanple, > > it was: > > > /home/tc/apache-tomcat-6.0.16/temp/_R_/SANDBOX/[text_to_speech.freetts]_4ca7ea84.11b07436c4e._7ffe/o_output). > > But won't this change every time? Yes, the file name will be different each time, but the parameter name not. What I meant was this: Because your application produces 9 output files, you have to define nine outputs in the ACD file. To each of them, you create a parameter name - any name of your choice; for example: out1, out2, ...out9. Then you write a wrapper that explores the command line create by Soaplab and convert it into your nine hard coded names. For example, Soaplab will produce a command-line like this: wrapper -out1 /home/tc/apache-tomcat..../o_output -out2 /home/tc/.... -out3 blah/blah... and the task of your wrapper is to take the value of the parameter '-out1' (which is /home/tc/apache-tomcat..../o_output) and convert it into a single name that your application expects. And so on, for all -outX parameters. For example, a wrapper in Perl may be like this (just for three hard coded outputs; replace 'echo' by the name of your real program): #!/usr/bin/perl -w # use Getopt::Long; my ($hard1, $hard2, $hard3); GetOptions ("out1=s" => \$hard1, "out2=s" => \$hard2, "out3=s" => \$hard3); exec ('echo', $hard1, $hard2, $hard3); This wrapper changes this input arguments: --out1 value1 --out2 value2 --out3 valu3 into this: value1 value2 value3 A site comment: In order to let Soapab generates a command-line with the 'long' options - the ones started with double dashes, you use in the ACD file the 'option: method', For example: outfile : out1 [ option: "method --&& $$" ... ] But this was just because my example wrapper is using the long options. You can also write an ordinary wrapper that takes only one-letter arguments and, therefore, can use just simple Getopt. An example of such wrapper could be this: use Getopt::Std; our ($opt_a, $opt_b, $opt_c); getopt ('abc'); exec ('echo', $opt_a, $opt_b, $opt_c); converting: -a value1 -b value2 -c value3 into: value1 value2 value3 Cheers, Martin -- Martin Senger email: mar...@gm...,m.s...@cg... skype: martinsenger |
From: Tom C. <tc...@cs...> - 2008-08-29 16:42:18
|
Hi, [bringing up an old thread, original problem now solved...] Martin Senger wrote: > Hi, > > It uses a -dumpAudio flag to output to a file > > No, I am afraid it does not. The dumpAudio is a string, not an outout file. > Soaplab has no idea that the underlying application uses this parameter as > an output file - it just takes its value (e.g. the string 'output.wav' > literally as a command-lien option but it does not do anything else with it. > The only output file the Soaplab sees is the one defined in the 'output' > paremeter (and Soaplab give it its own name). > > If your applicatation has a hard-coded name for the output file, you are out > of luck, at least now. Ah...is there any way I can get around this? I have an application that output nine different text files, all with hard-coded names! > You have to wrap you script into few lines that can > map the hard-coded file name into the one given by Soaplab (in your exanple, > it was: > /home/tc/apache-tomcat-6.0.16/temp/_R_/SANDBOX/[text_to_speech.freetts]_4ca7ea84.11b07436c4e._7ffe/o_output). But won't this change every time? > I think that all your observed problems have the same cause: your > application uses the -dumpAudio parameter for the output file, but Soaplab > consideres the -output parameter as the one for the output. Thanks, Tom |
From: Mahmut U. <ul...@eb...> - 2008-07-18 11:22:07
|
Hi Tom, > With the current version of soaplab2, it is not possible to access the > individual services and their WSDL? I see you can view something at: > > http://<url>/soaplab2/services > > but is it possible to access/specify/deploy WSDL for each individual > soaplab2 service? It is possible to access WSDL files for individual services by specifying the service name on the URL, for example in my local host I can reach seqret's WSDL file using the following URL. http://localhost:8080/soaplab2/services/edit.seqret?wsdl Soaplab2 web applications (using the default jaxws option) has 2 WSDL files shared by all applications/services, both WSDL files can be found under the WEB-INF/wsdl directory in your soaplab2 web application folder. You shouldn't normally change these 2 wsdl files. However you can for example add documentation as the current version unfortunately doesn't have any documentation. If you really want to have a separate WSDL file for one of your services you can copy the Analysis.wsdl file and make your application specific changes on it (should normally be limited to documentation changes, or in the extreme cases you might disable some of the less used methods). You should also update web.xml and sun-jaxws.xml files (found in the WEB-INF folder) to set an endpoint for your service and let jaxws know your new wsdl file. Regards, Mahmut |
From: John S. R. <J.S...@so...> - 2008-07-17 20:54:40
|
I'd be interested to know the answer to this too, so can any replies be on-list, please! Thanks, JohnR. Tom Crick wrote: > Dear all, > > With the current version of soaplab2, it is not possible to access the > individual services and their WSDL? I see you can view something at: > > http://<url>/soaplab2/services > > but is it possible to access/specify/deploy WSDL for each individual > soaplab2 service? > > Thanks, > > Tom > > > -- ---------------------------------------- John S. Robinson, BSc. (Hons) OMII-UK | www.omii.ac.uk School of Electronics & Computer Science University of Southampton, SO17 1BJ, UK J.S...@so... ---------------------------------------- |
From: Tom C. <tc...@cs...> - 2008-07-17 20:26:31
|
Dear all, With the current version of soaplab2, it is not possible to access the individual services and their WSDL? I see you can view something at: http://<url>/soaplab2/services but is it possible to access/specify/deploy WSDL for each individual soaplab2 service? Thanks, Tom -- Tom Crick Mathematical Foundations Group Department of Computer Science University of Bath tc...@cs... http://www.cs.bath.ac.uk/tom/ |
From: Martin S. <mar...@gm...> - 2008-07-10 06:30:55
|
Hi, It uses a -dumpAudio flag to output to a file No, I am afraid it does not. The dumpAudio is a string, not an outout file. Soaplab has no idea that the underlying application uses this parameter as an output file - it just takes its value (e.g. the string 'output.wav' literally as a command-lien option but it does not do anything else with it. The only output file the Soaplab sees is the one defined in the 'output' paremeter (and Soaplab give it its own name). If your applicatation has a hard-coded name for the output file, you are out of luck, at least now. You have to wrap you script into few lines that can map the hard-coded file name into the one given by Soaplab (in your exanple, it was: /home/tc/apache-tomcat-6.0.16/temp/_R_/SANDBOX/[text_to_speech.freetts]_4ca7ea84.11b07436c4e._7ffe/o_output). I think that all your observed problems have the same cause: your application uses the -dumpAudio parameter for the output file, but Soaplab consideres the -output parameter as the one for the output. Cheers, Martin PS. Sorry if I do not reply for your other emails soon - but I will be for next about ten days on my holiday, and I may not be always available on-line. M. -- Martin Senger email: mar...@gm...,m.s...@cg... skype: martinsenger |
From: Tom C. <tc...@cs...> - 2008-07-09 10:15:21
|
Hi, I'm trying to expose a Java program as a web service using soaplab2 (2.1.1), but I am unable to return the wav audio output file that it generates. It uses a -dumpAudio flag to output to a file, otherwise the audio is played on the server (sent to the audio stream - not ideal for a web service). This is how I have encoded the dumpAudio parameter in the ACD file: # -dumpAudio <file> flag string: dump_audio [ qualifier: dumpAudio standard: "Y" default: "output.wav" information: "dump audio to this file (default: output.wav)" comment: defaults comment: "display false" ] it's hidden from the user so will always output to a file. My outfile definition is: outfile: output [ comment: "mimetype audio/x-wav" comment: bindata comment: "make_url yes" ] but when I run the process, it succeeds but I am unable to access output.wav: -------------------------------------- Summary: Completed: Successfully Termination status: 0 Started: 2008-Jul-09 11:08:18 (BST) Ended: 2008-Jul-09 11:08:21 (BST) Duration: 0:00:03.210 Report: Name: text_to_speech.freetts Job ID: [text_to_speech.freetts]_4ca7ea84.11b07436c4e._7ffe Program and parameters: java -jar /opt/freetts-1.2.1/lib/freetts.jar -dumpAudio output.wav -text Hello World! -output /home/tc/apache-tomcat-6.0.16/temp/_R_/SANDBOX/[text_to_speech.freetts]_4ca7ea84.11b07436c4e._7ffe/o_output --- end of parameters Exit: 0 Standard output stream: Wrote synthesized speech to output.wav -------------------------------------- no URL or output is generated, only the "report" and "detailed_status". When I looking in the location above on the server there is the output file, but why is no URL generated? Am I doing something incorrect with the outfile definition? Is it possible to return the file via Spinet? Thanks for your help, Tom -- Tom Crick Mathematical Foundations Group Department of Computer Science University of Bath tc...@cs... http://www.cs.bath.ac.uk/tom/ |
From: Martin S. <mar...@gm...> - 2008-07-03 13:23:57
|
> Can this be done within ACD? The ACD syntax has ability to express parameters/options dependencies. But Soaplab2 (as you correctly pointed out to the "issues" part of the documentation) does not use this syntax, does not implement it. It was always in my ToDo list but never found enough pressure from the users to make it work :-) Martin -- Martin Senger email: mar...@gm...,m.s...@cg... skype: martinsenger |
From: Tom C. <tc...@cs...> - 2008-07-03 10:09:45
|
Hi, I've been using soaplab2 (2.1.1) to expose some solving tools as web services and have been trying to implement dependencies with their command line options e.g. certain options are only valid/available when another option is set. Can this be done within ACD? I saw the issues in the Metadata Guide: http://soaplab.sourceforge.net/soaplab2/MetadataGuide.html#issues and thought this may have answered my question, but wanted to check. Thanks, Tom -- Tom Crick Mathematical Foundations Group Department of Computer Science University of Bath tc...@cs... http://www.cs.bath.ac.uk/tom/ |
From: Martin S. <mar...@gm...> - 2008-05-26 00:54:03
|
Thanks for your enquiry. But I am a bit confused I must admit - because... This is the error message I refer to- > The following error occurred while executing this line: > /home/myhomedir/soaplab2/xmls/maven.xml:48: Can't get > http://apache.hoxt.com/maven/binaries/maven-ant-tasks-2.0.8.jar to > /home/myhomedir/soaplab2/lib/maven-ant-tasks-2.0.8.jar ...in the new Soaplab2 release there is no place where the " http://apache.hoxt.com/"<http://apache.hoxt.com/maven/binaries/maven-ant-tasks-2.0.8.jar>server is used. Or it should not be. It was replaced by the server open-bio (you should see it in xmls/maven.xml - http://biomoby.org/jmoby-jars). The replacement was made because on the new server we can keep the old versions of maven-ant-task library as long as we want. Therefore, I am not sure why you see still the message above... Martin -- Martin Senger email: mar...@gm...,m.s...@cg... skype: martinsenger |