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From: Serge V. <ser...@gm...> - 2007-01-29 23:20:40
|
Hi all, In tutorial\manual you can find examples how to describe a process to consume set of incoming files and produce only one known output file. Is it possible instead of just one predefined output file name to set a selection mask ( *.txt for example ) ? It would be quite useful when a process splits the incoming data file to 0....N files and number and names of output files we do not know. And how can I define a directory as process output ? (any HTML report generator, java compiler, unzip - directory structure quite important as well ) Any tips ? -- sv |
From: Jon B. <jd...@ma...> - 2006-10-11 13:21:41
|
Dear Els, This is a good question. Currently the SGS software uses the Java Simple Argument Parser (JSAP, http://www.martiansoftware.com/jsap/) to parse command-line arguments. As far as I know, JSAP does not allow for flags of the form "-sequence". I will try to find out more from the JSAP developers. In the meantime all I can think of is to create a script that wraps EMBOSS. The script could accept arguments of the form "--sequence" and simply replace them with "-sequence". You would then wrap the script as the Styx Grid Service. Would this be a satisfactory solution? I am sorry that this isn't a very neat way of doing it. Best wishes, Jon On 11/10/06, Els Vanbleu <El...@de...> wrote: > Hallo! > > I have a question concerning Styx Grid Services and writing a > configuration file for command line tools. > > EMBOSS provides a whole bunch of interesting command line tools for > sequence manipulation. However they work, at the command line with > parameters, preceded with solely a single - instead of double --. > > E.g. seqret -sequence <filename> -outseq <outputfile> > > The GridServices currently only accept as attributes for a parameter a > single character flag (-o) or a multiple character longFlag (--outseq). > Can an additional attribute be created to accept the 'inbetween' Flag > (-outseq), i.e. a multiple character flag? > > Or is there any other easy solution to circumvent this problem? > > Thanks in advance! > Greetz > Els Vanbleu > > > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > Jstyx-users mailing list > Jst...@li... > https://lists.sourceforge.net/lists/listinfo/jstyx-users > -- -------------------------------------------------------------- Dr Jon Blower Tel: +44 118 378 5213 (direct line) Technical Director Tel: +44 118 378 8741 (ESSC) Reading e-Science Centre Fax: +44 118 378 6413 ESSC Email: jd...@ma... University of Reading 3 Earley Gate Reading RG6 6AL, UK -------------------------------------------------------------- |
From: Els V. <ElsV@DEVGEN.com> - 2006-10-11 11:45:03
|
Hallo! I have a question concerning Styx Grid Services and writing a configuration file for command line tools. EMBOSS provides a whole bunch of interesting command line tools for sequence manipulation. However they work, at the command line with parameters, preceded with solely a single - instead of double --. E.g. seqret -sequence <filename> -outseq <outputfile> The GridServices currently only accept as attributes for a parameter a single character flag (-o) or a multiple character longFlag (--outseq). Can an additional attribute be created to accept the 'inbetween' Flag (-outseq), i.e. a multiple character flag? =20 Or is there any other easy solution to circumvent this problem?=20 Thanks in advance! Greetz Els Vanbleu |
From: Neateye <nit...@ao...> - 2006-09-26 23:59:51
|
Call out Gouranga be happy Gouranga Gouranga Gouranga! That which brings the highest happiness |
From: Neateye <nit...@ao...> - 2006-09-20 19:32:49
|
Call out Gouranga be happy! Gouranga Gouranga Gouranga That which brings the highest happiness |
From: <MAI...@ma...> - 2006-09-14 15:00:27
|
Failed to deliver to 'js...@tc...' LOCAL module(account js...@tc...) reports: cancelled by the server operator |
From: Jon B. <jd...@ma...> - 2006-05-17 07:18:29
|
I would very much like to see this tested but I don't have an appropriate machine to test it on yet. Has anyone tried this? Assuming it works, yes, we could separate the server and client as you suggest. There are some dependencies that only pertain to the server and some that only pertain to the Styx Grid Services software that is currently bundled with JStyx. This could be refactored so that the client software is as small as possible. I have tested JStyx with Inferno (both with JStyx client/Inferno server and Inferno client/JStyx server) and they interoperate without problems. (At the moment JStyx can't make an authenticated connection to an Inferno server though.) I would therefore be optimistic that JStyx will interoperate with v9fs. Does v9fs support authentication and/or encryption of any kind? Regards, Jon > > If the interoperability of JStyx client with v9fs server is > proven, I would suggest to separate the JStyx client from the > server and to have as few dependent libraries as possible for > the client. > > Best regards, > Tianchao Li > > Tianchao Li wrote: > > >I wonder if anybody has checked the interoperability of JStyx with > >9p2000 (say v9fs), which might include: > >JStyx client - v9fs server > >JStyx server - v9fs client > > > >Best regards, > >Tianchao Li > > |
From: Tianchao Li <li...@in...> - 2006-05-17 05:39:27
|
If the interoperability of JStyx client with v9fs server is proven, I would suggest to separate the JStyx client from the server and to have as few dependent libraries as possible for the client. Best regards, Tianchao Li Tianchao Li wrote: >I wonder if anybody has checked the interoperability of JStyx with >9p2000 (say v9fs), which might include: >JStyx client - v9fs server >JStyx server - v9fs client > >Best regards, >Tianchao Li > > > > >------------------------------------------------------- >Using Tomcat but need to do more? Need to support web services, security? >Get stuff done quickly with pre-integrated technology to make your job easier >Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo >http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 >_______________________________________________ >Jstyx-users mailing list >Jst...@li... >https://lists.sourceforge.net/lists/listinfo/jstyx-users > > > |
From: Tianchao Li <li...@in...> - 2006-05-16 21:58:10
|
I wonder if anybody has checked the interoperability of JStyx with 9p2000 (say v9fs), which might include: JStyx client - v9fs server JStyx server - v9fs client Best regards, Tianchao Li |
From: Jon B. <jd...@ma...> - 2006-05-16 13:03:18
|
> Actually, according to the rules of Styx you should create > directories with read permissions only. Therefore your call: Sorry, I meant to write that you should create directories and open them with the mode OREAD only. Nothing to do with permissions. > -----Original Message----- > From: jst...@li... > [mailto:jst...@li...] On Behalf Of > Jon Blower > Sent: 12 May 2006 12:32 > To: jst...@li... > Subject: RE: [Jstyx-users] Re: question about CStyx.openOrCreate() > > Hi Tianchao, > > Thanks for reporting this so clearly. There is indeed a bug > in the OpenOrCreateCallback class. The fix will be checked > into the SVN repository later, but in the meantime I've > attached the corrected version. > > Actually, according to the rules of Styx you should create > directories with read permissions only. Therefore your call: > > file.openOrCreate(true, StyxUtils.OWRITE); > > will return an error (although in the buggy version it went > into an infinite loop). You should do this: > > file.openOrCreate(true, StyxUtils.OREAD); > > This may seem counter-intuitive but is logical. The > StyxUtils.OREAD is the > *mode* under which the newly-created directory is opened, not the > *permissions* of the directory. It is not legal to write to > directories so it is not legal to open them with mode OWRITE. > You can create new files in the newly-created directory as normal. > > Perhaps I should change the API to something more intuitive... > > Jon > > > > -----Original Message----- > > From: jst...@li... > > [mailto:jst...@li...] On Behalf > Of Tianchao > > Li > > Sent: 11 May 2006 18:54 > > To: jst...@li... > > Subject: [Jstyx-users] Re: question about CStyx.openOrCreate() > > > > The problem only occurs if the first parameter is true (i.e. > > directory) > > > > file.openOrCreate(true, StyxUtils.OWRITE); > > > > Best regards, > > Tianchao Li > > > > On Thu, 2006-05-11 at 12:41 -0400, Tianchao Li wrote: > > > Hi, > > > > > > I have some problem with the correct usage of > CStyx.openOrCreate() > > > method. > > > > > > I have started the following server: > > > import java.io.IOException; > > > > > > import uk.ac.rdg.resc.jstyx.StyxException; > > > import uk.ac.rdg.resc.jstyx.server.DirectoryOnDisk; > > > import uk.ac.rdg.resc.jstyx.server.StyxDirectory; > > > import uk.ac.rdg.resc.jstyx.server.StyxServer; > > > > > > > > > public class TestStyxServer { > > > > > > /** > > > * @param args > > > */ > > > public static void main(String[] args) { > > > > > > StyxDirectory root; > > > try { > > > root = new StyxDirectory("/"); > > > DirectoryOnDisk file = new > > > DirectoryOnDisk("/home/lit/styxfilesystem"); > > > root.addChild(file); > > > new StyxServer(9876, root).start(); > > > } catch (StyxException e) { > > > // TODO Auto-generated catch block > > > e.printStackTrace(); > > > } catch (IOException e) { > > > // TODO Auto-generated catch block > > > e.printStackTrace(); > > > } > > > } > > > > > > } > > > > > > and the following client: > > > > > > import uk.ac.rdg.resc.jstyx.StyxException; > > > import uk.ac.rdg.resc.jstyx.StyxUtils; import > > > uk.ac.rdg.resc.jstyx.client.CStyxFile; > > > import uk.ac.rdg.resc.jstyx.client.StyxConnection; > > > > > > > > > public class TestStyxClient { > > > > > > /** > > > * @param args > > > */ > > > public static void main(String[] args) { > > > StyxConnection conn = new > StyxConnection("localhost", 9876); > > > try > > > { > > > conn.connect(); > > > CStyxFile file = > > conn.getFile("/styxfilesystem/test.txt"); > > > file.openOrCreate(true, StyxUtils.OWRITE); > > > System.out.println(file.getURL()); > > > } > > > catch (StyxException se) > > > { > > > se.printStackTrace(); > > > } > > > finally > > > { > > > conn.close(); > > > } > > > > > > } > > > > > > } > > > > > > The client is blocked at file.openOrCreate(). Or more exactly, the > > > callback.getReply() never returns. > > > > > > public void openOrCreate(boolean isDirectory, int > mode) throws > > > StyxException > > > { > > > StyxReplyCallback callback = new StyxReplyCallback(); > > > this.openOrCreateAsync(isDirectory, mode, callback); > > > // Blocks until the process is complete > > > callback.getReply(); > > > } > > > > > > > > > Is this a bug? > > > > > > Regards, > > > Tianchao Li > > > > > > > > > > > > > > ------------------------------------------------------- > > Using Tomcat but need to do more? Need to support web services, > > security? > > Get stuff done quickly with pre-integrated technology to > make your job > > easier Download IBM WebSphere Application Server > > v.1.0.1 based on Apache Geronimo > > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057& > > dat=121642 > > _______________________________________________ > > Jstyx-users mailing list > > Jst...@li... > > https://lists.sourceforge.net/lists/listinfo/jstyx-users > > > |
From: Jon B. <jd...@ma...> - 2006-05-12 11:32:08
|
Hi Tianchao, Thanks for reporting this so clearly. There is indeed a bug in the OpenOrCreateCallback class. The fix will be checked into the SVN repository later, but in the meantime I've attached the corrected version. Actually, according to the rules of Styx you should create directories with read permissions only. Therefore your call: file.openOrCreate(true, StyxUtils.OWRITE); will return an error (although in the buggy version it went into an infinite loop). You should do this: file.openOrCreate(true, StyxUtils.OREAD); This may seem counter-intuitive but is logical. The StyxUtils.OREAD is the *mode* under which the newly-created directory is opened, not the *permissions* of the directory. It is not legal to write to directories so it is not legal to open them with mode OWRITE. You can create new files in the newly-created directory as normal. Perhaps I should change the API to something more intuitive... Jon > -----Original Message----- > From: jst...@li... > [mailto:jst...@li...] On Behalf Of > Tianchao Li > Sent: 11 May 2006 18:54 > To: jst...@li... > Subject: [Jstyx-users] Re: question about CStyx.openOrCreate() > > The problem only occurs if the first parameter is true (i.e. > directory) > > file.openOrCreate(true, StyxUtils.OWRITE); > > Best regards, > Tianchao Li > > On Thu, 2006-05-11 at 12:41 -0400, Tianchao Li wrote: > > Hi, > > > > I have some problem with the correct usage of CStyx.openOrCreate() > > method. > > > > I have started the following server: > > import java.io.IOException; > > > > import uk.ac.rdg.resc.jstyx.StyxException; > > import uk.ac.rdg.resc.jstyx.server.DirectoryOnDisk; > > import uk.ac.rdg.resc.jstyx.server.StyxDirectory; > > import uk.ac.rdg.resc.jstyx.server.StyxServer; > > > > > > public class TestStyxServer { > > > > /** > > * @param args > > */ > > public static void main(String[] args) { > > > > StyxDirectory root; > > try { > > root = new StyxDirectory("/"); > > DirectoryOnDisk file = new > > DirectoryOnDisk("/home/lit/styxfilesystem"); > > root.addChild(file); > > new StyxServer(9876, root).start(); > > } catch (StyxException e) { > > // TODO Auto-generated catch block > > e.printStackTrace(); > > } catch (IOException e) { > > // TODO Auto-generated catch block > > e.printStackTrace(); > > } > > } > > > > } > > > > and the following client: > > > > import uk.ac.rdg.resc.jstyx.StyxException; > > import uk.ac.rdg.resc.jstyx.StyxUtils; import > > uk.ac.rdg.resc.jstyx.client.CStyxFile; > > import uk.ac.rdg.resc.jstyx.client.StyxConnection; > > > > > > public class TestStyxClient { > > > > /** > > * @param args > > */ > > public static void main(String[] args) { > > StyxConnection conn = new StyxConnection("localhost", 9876); > > try > > { > > conn.connect(); > > CStyxFile file = > conn.getFile("/styxfilesystem/test.txt"); > > file.openOrCreate(true, StyxUtils.OWRITE); > > System.out.println(file.getURL()); > > } > > catch (StyxException se) > > { > > se.printStackTrace(); > > } > > finally > > { > > conn.close(); > > } > > > > } > > > > } > > > > The client is blocked at file.openOrCreate(). Or more exactly, the > > callback.getReply() never returns. > > > > public void openOrCreate(boolean isDirectory, int mode) throws > > StyxException > > { > > StyxReplyCallback callback = new StyxReplyCallback(); > > this.openOrCreateAsync(isDirectory, mode, callback); > > // Blocks until the process is complete > > callback.getReply(); > > } > > > > > > Is this a bug? > > > > Regards, > > Tianchao Li > > > > > > > > ------------------------------------------------------- > Using Tomcat but need to do more? Need to support web > services, security? > Get stuff done quickly with pre-integrated technology to make > your job easier Download IBM WebSphere Application Server > v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057& > dat=121642 > _______________________________________________ > Jstyx-users mailing list > Jst...@li... > https://lists.sourceforge.net/lists/listinfo/jstyx-users > |
From: Tianchao Li <li...@in...> - 2006-05-11 17:58:27
|
The problem only occurs if the first parameter is true (i.e. directory) file.openOrCreate(true, StyxUtils.OWRITE); Best regards, Tianchao Li On Thu, 2006-05-11 at 12:41 -0400, Tianchao Li wrote: > Hi, > > I have some problem with the correct usage of CStyx.openOrCreate() > method. > > I have started the following server: > import java.io.IOException; > > import uk.ac.rdg.resc.jstyx.StyxException; > import uk.ac.rdg.resc.jstyx.server.DirectoryOnDisk; > import uk.ac.rdg.resc.jstyx.server.StyxDirectory; > import uk.ac.rdg.resc.jstyx.server.StyxServer; > > > public class TestStyxServer { > > /** > * @param args > */ > public static void main(String[] args) { > > StyxDirectory root; > try { > root = new StyxDirectory("/"); > DirectoryOnDisk file = new > DirectoryOnDisk("/home/lit/styxfilesystem"); > root.addChild(file); > new StyxServer(9876, root).start(); > } catch (StyxException e) { > // TODO Auto-generated catch block > e.printStackTrace(); > } catch (IOException e) { > // TODO Auto-generated catch block > e.printStackTrace(); > } > } > > } > > and the following client: > > import uk.ac.rdg.resc.jstyx.StyxException; > import uk.ac.rdg.resc.jstyx.StyxUtils; > import uk.ac.rdg.resc.jstyx.client.CStyxFile; > import uk.ac.rdg.resc.jstyx.client.StyxConnection; > > > public class TestStyxClient { > > /** > * @param args > */ > public static void main(String[] args) { > StyxConnection conn = new StyxConnection("localhost", 9876); > try > { > conn.connect(); > CStyxFile file = conn.getFile("/styxfilesystem/test.txt"); > file.openOrCreate(true, StyxUtils.OWRITE); > System.out.println(file.getURL()); > } > catch (StyxException se) > { > se.printStackTrace(); > } > finally > { > conn.close(); > } > > } > > } > > The client is blocked at file.openOrCreate(). Or more exactly, the > callback.getReply() never returns. > > public void openOrCreate(boolean isDirectory, int mode) throws > StyxException > { > StyxReplyCallback callback = new StyxReplyCallback(); > this.openOrCreateAsync(isDirectory, mode, callback); > // Blocks until the process is complete > callback.getReply(); > } > > > Is this a bug? > > Regards, > Tianchao Li > > |
From: Tianchao Li <li...@in...> - 2006-05-11 16:46:18
|
Hi, I have some problem with the correct usage of CStyx.openOrCreate() method. I have started the following server: import java.io.IOException; import uk.ac.rdg.resc.jstyx.StyxException; import uk.ac.rdg.resc.jstyx.server.DirectoryOnDisk; import uk.ac.rdg.resc.jstyx.server.StyxDirectory; import uk.ac.rdg.resc.jstyx.server.StyxServer; public class TestStyxServer { /** * @param args */ public static void main(String[] args) { StyxDirectory root; try { root = new StyxDirectory("/"); DirectoryOnDisk file = new DirectoryOnDisk("/home/lit/styxfilesystem"); root.addChild(file); new StyxServer(9876, root).start(); } catch (StyxException e) { // TODO Auto-generated catch block e.printStackTrace(); } catch (IOException e) { // TODO Auto-generated catch block e.printStackTrace(); } } } and the following client: import uk.ac.rdg.resc.jstyx.StyxException; import uk.ac.rdg.resc.jstyx.StyxUtils; import uk.ac.rdg.resc.jstyx.client.CStyxFile; import uk.ac.rdg.resc.jstyx.client.StyxConnection; public class TestStyxClient { /** * @param args */ public static void main(String[] args) { StyxConnection conn = new StyxConnection("localhost", 9876); try { conn.connect(); CStyxFile file = conn.getFile("/styxfilesystem/test.txt"); file.openOrCreate(true, StyxUtils.OWRITE); System.out.println(file.getURL()); } catch (StyxException se) { se.printStackTrace(); } finally { conn.close(); } } } The client is blocked at file.openOrCreate(). Or more exactly, the callback.getReply() never returns. public void openOrCreate(boolean isDirectory, int mode) throws StyxException { StyxReplyCallback callback = new StyxReplyCallback(); this.openOrCreateAsync(isDirectory, mode, callback); // Blocks until the process is complete callback.getReply(); } Is this a bug? Regards, Tianchao Li |
From: Jon B. <jd...@ma...> - 2006-04-25 09:32:00
|
Hi Tianchao, The version of JStyx (0.3.0-SNAPSHOT) on the Subversion server has a remove() method in the CStyxFile class (as well as other changes). I'm afraid that there are no methods as yet to change owner, group or permissions via CStyxFile. This is because user management is not implemented yet but hopefully will be in the next release. To get the latest version of the JStyx source out of Subversion please check out the code from https://svn.sourceforge.net/svnroot/jstyx/trunk/core. Please post back to the list if you have any further questions. Regards, Jon > -----Original Message----- > From: jst...@li... > [mailto:jst...@li...] On Behalf Of > Tianchao Li > Sent: 25 April 2006 07:18 > To: jst...@li... > Subject: [Jstyx-users] JStyx client API - how do I delete a > file from the client? > > Hi, > I'm trying to use the JStyx, but meet some problems with the > client API > - the CStyxFile provides many methods for accessing, but I do > not find methods for deleting and modifying properties like > owner etc. How can I delete a file/directory and modify properties? > > Regards, > Tianchao Li > > > > ------------------------------------------------------- > Using Tomcat but need to do more? Need to support web > services, security? > Get stuff done quickly with pre-integrated technology to make > your job easier Download IBM WebSphere Application Server > v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057& > dat=121642 > _______________________________________________ > Jstyx-users mailing list > Jst...@li... > https://lists.sourceforge.net/lists/listinfo/jstyx-users > |
From: Tianchao Li <li...@in...> - 2006-04-25 06:18:03
|
Hi, I'm trying to use the JStyx, but meet some problems with the client API - the CStyxFile provides many methods for accessing, but I do not find methods for deleting and modifying properties like owner etc. How can I delete a file/directory and modify properties? Regards, Tianchao Li |
From: Jon B. <jd...@ma...> - 2006-04-04 16:27:32
|
Dear all, The Reading e-Science Centre is very pleased to announce the first public release (version 0.2.0) of the Styx Grid Services (SGS) software. Please see the project website (http://www.resc.rdg.ac.uk/jstyx/sgs) for full details, downloads and documentation. The release also includes the latest version of the JStyx core libraries. The main features of the SGS system are: * Command-line programs can be wrapped and deployed on the Internet as services. * These services can be used *exactly* as if they were local programs. * Services can be composed into workflows with simple shell scripts, making it very easy to create distributed applications. * Data can be streamed directly between services. * Very quick installation procedure. Software is less than 2MB in size and only requires a Java runtime environment, version 1.4.2 and above. If you want to try the software, please follow the tutorial at http://www.resc.rdg.ac.uk/jstyx/sgs/tutorial/. For help and support, please use the project website and the jstyx-users mailing list (http://www.resc.rdg.ac.uk/jstyx/mail-lists.html). Regards, Jon -------------------------------------------------------------- Dr Jon Blower Tel: +44 118 378 5213 (direct line) Technical Director Tel: +44 118 378 8741 (ESSC) Reading e-Science Centre Fax: +44 118 378 6413 ESSC Email: jd...@ma... University of Reading 3 Earley Gate Reading RG6 6AL, UK -------------------------------------------------------------- |
From: <lo...@da...> - 2005-10-30 19:58:13
|
Hello, This may be a bit naive, but is it possible for me to use JStyx to export a filesystem to a Linux kernel (via V9FS protocol)? All the docs I've found imply that Styx is a derivative of V9FS but don't clearly say whether they're compatible. Thanks! Logan Bowers |
From: Jon B. <jd...@ma...> - 2005-02-28 10:33:06
|
Just testing! -- -------------------------------------------------------------- Dr Jon Blower Tel: +44 118 378 5213 (direct line) Technical Director Tel: +44 118 378 8741 (ESSC) Reading e-Science Centre Fax: +44 118 378 6413 ESSC Email: jd...@ma... University of Reading 3 Earley Gate Reading RG6 6AL, UK -------------------------------------------------------------- ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. |