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From: cajela <ca...@gm...> - 2008-05-26 00:38:55
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Hi Martin et al, Thanks for the announcement. I assume this also includes the file formerly at http://apache.hoxt.com/maven/binaries/maven-ant-tasks-2.0.8.jar? I see it's now 2.0.9 up on that page. I discovered this when I tried a rebuild. (I was tweaking my emboss install as spinet was failing to see the database info, but that's another thing). May I suggest that you amend the error message from the build to indicate that it's a probably an update issue? Or perhaps maintain the old version for a month or two? 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 thanks, Cath 2008/5/17 Martin Senger <mar...@gm...>: > FYI... > Martin > > ---------- Forwarded message ---------- > From: SourceForge.net <no...@so...> > Date: Sat, May 17, 2008 at 12:00 AM > Subject: [SourceForge.net Release] soaplab : soaplab2 > To: no...@so... > > > Project: Soaplab (soaplab) > Package: soaplab2 > Date : 2008-05-16 23:00 > > 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=599721 >> > or browse Release Notes and ChangeLog by visiting this link: > <https://sourceforge.net/project/shownotes.php?release_id=599721> -- Cath Lawrence --- cajela at gmail dot com http://thecanberracook.blogspot.com |
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From: Martin S. <mar...@gm...> - 2008-05-16 23:09:29
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FYI... Martin ---------- Forwarded message ---------- From: SourceForge.net <no...@so...> Date: Sat, May 17, 2008 at 12:00 AM Subject: [SourceForge.net Release] soaplab : soaplab2 To: no...@so... Project: Soaplab (soaplab) Package: soaplab2 Date : 2008-05-16 23:00 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=599721 > or browse Release Notes and ChangeLog by visiting this link: <https://sourceforge.net/project/shownotes.php?release_id=599721> -- Martin Senger email: mar...@gm...,m.s...@cg... skype: martinsenger |
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From: Martin S. <mar...@gm...> - 2008-02-05 19:05:35
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[Sorry for the cross-posting] The first non-beta release of Soaplab2 is out. The very enhanced documentation (e.g. finally, there is a documentation how to create metadata for Soaplab2 services) is available at http://soaplab.sourceforge.net/soaplab2/. I would like to use this opportunity to thank everybody for helping us to find bugs and for inspiring us about the new features. The most cordial thanks go to Mahmut Uludag from EBI who updated significantly the Taverna plug-in for Soaplab (both 1 and 2) and who significantly contributed to the stability of the Soaplab2 code. Please feel welcome to send us your comments and bug reports. Cheers, Martin -- Martin Senger email: mar...@gm... skype: martinsenger |
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From: Martin S. <mar...@gm...> - 2007-10-29 05:56:52
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[ I apologize for the cross-posting ] In the early hours of the Monday morning, after last "fixes" that took the whole night :-) I can announce, finally, a release of the completely re-written Soaplab - Soaplab2. Some features are still missing (it is a beta, after all) but the main functionality should be there. Please have a look at http://soaplab.sourceforge.net/soaplab2. As usual: without your feedback and suggestions, it will be hard to improve it. With regards, Martin Senger Mahmut Uludag -- Martin Senger email: mar...@gm... skype: martinsenger |
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From: Cyber W. <kas...@ya...> - 2007-08-19 15:13:54
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Dear all=0AI want to deploy cat web service enable and can invoke from Tave= rna=0AIf in shell prompt we type=0A$ cat > test.txt=0Aaaaaaaaaaaaaaaaaaaaaa= aaa <return>=0Abbbbbbbbbbbbbbbbbbbbbbbb <return>=0Acccccccccccccccccccccccc= ccc <ctrl-d>=0AHow to decribe it in ACD file? and I want to enter input fro= m Taverna=0A=0AThanks,=0AKasikrit=0A=0A=0A=0A=0A=0A=0A=0A =0A________= ___________________________________________________________________________= _=0AYahoo! oneSearch: Finally, mobile search =0Athat gives answers, not web= links. =0Ahttp://mobile.yahoo.com/mobileweb/onesearch?refer=3D1ONXIC |
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From: Martin S. <mar...@gm...> - 2006-12-05 17:36:04
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Hi everybody, Just a note that last month the work on Soaplab2 really started. It does not do much yet, but it has already clearly defined architecture that helps with extensions. The architecture is part of the Developer Guide. The code is in a new module 'soaplab2'. Please check: http://soaplab.sourceforge.net/soaplab2/ Regards, Martin -- Martin Senger email: mar...@gm... skype: martinsenger |
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From: Mahmut U. <ul...@eb...> - 2006-09-04 11:22:17
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Hi, I just wanted to say that "Too many open files" problem and most of the important memory leaks in AppLab has been fixed. The leaks were generally due to unnecessary references to some important objects such as input objects or the worker thread objects. Also there was a Java File object referenced by one of the frequently used classes (embl.ebi.AppLabServer.Data). Now we use an "isFile" attribute in this class and open new Files only when it is necessary and closing it afterwards. The modifications has been checked in to EBI CVS Server cvsebi.ebi.ac.uk, repository path /ebi/cvs/public, module AppLab-dev. Eclipse profiling tool was very useful in finding the memory leaks, especially its ability to show references to individual objects. Regards, Mahmut |
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From: Martin S. <mar...@gm...> - 2006-08-23 16:23:40
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> When do you plan to start checking in Soaplab-2 into the CVS server on > sourceforge.net? When I am back from South America (a week after September 21). Martin -- Martin Senger email: mar...@gm... skype: martinsenger |
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From: Mahmut U. <ul...@eb...> - 2006-08-23 16:12:00
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When do you plan to start checking in Soaplab-2 into the CVS server on sourceforge.net? M. On Wed, 2006-08-23 at 12:55 -0300, Martin Senger wrote: > > We didn't hear recently about Soaplab version 2. Are you > working on it? > > Yes, I am. The main month to finish it will be October. > Martin |
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From: Martin S. <mar...@gm...> - 2006-08-23 15:56:03
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> We didn't hear recently about Soaplab version 2. Are you working on it? Yes, I am. The main month to finish it will be October. Martin -- Martin Senger email: mar...@gm... skype: martinsenger |
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From: Mahmut U. <ul...@eb...> - 2006-08-23 13:31:52
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Hi Martin, > If there is anything that I can help with let me know please. Thank you for your help offer. I will ask your help when I need it. Recently we have installed new services for EMBOSS-4 into the EBI Soaplab server. http://www.ebi.ac.uk/soaplab/emboss4/ Before recommending people to use it we are working to minimise the memory leaks in the Soaplab server. We didn't hear recently about Soaplab version 2. Are you working on it? Regards, Mahmut |
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From: Martin S. <se...@eb...> - 2006-06-23 13:47:28
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> Martin, is it correct that also Soaplab-2 will still have both flavours of > services? Derived and Non-derived? > Yes, I think so. > (Btw., I opt for some other naming of the flavours, e.g. untyped/typed, > simple/verbose, etc.) > Good point. M. -- Martin Senger email: mar...@gm... skype: martinsenger |
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From: Peter E. <p....@dk...> - 2006-06-23 13:44:06
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On Fri, 23 Jun 2006, Mahmut Uludag wrote: > "... unable to call the get spec method for endpoint ... " > > This is due to fact that this version of derived Soaplab services also > missing the getInputSpec operation. This should be due to the fact that > we have this information already in the WSDL's. Currently, Taverna's Soaplab scavenger does not use the derived services; only the non-derived services in Soaplab. (Endpoints without ".derived") Taverna also does not use WSDL for Soaplab. Taverna uses the "AnalysisFactory" service, to get a list of Soaplab services. Then, it uses the getInputSpec() and getResultSpec() methods on a particular service (non-derived), to retrieve further information about that service. (compare with: http://taverna.cvs.sourceforge.net/taverna/taverna1.0/src/org/embl/ebi/escience/scuflworkers/soaplab/) You are right, in the derived services, getInputSpec() and getResultSpec() are not necessary, because this information is already in the WSDL. Martin, is it correct that also Soaplab-2 will still have both flavours of services? Derived and Non-derived? (Btw., I opt for some other naming of the flavours, e.g. untyped/typed, simple/verbose, etc.) Kind regards, Peter |
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From: Mahmut U. <ul...@eb...> - 2006-06-23 08:49:09
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On Thu, 2006-06-22 at 18:58 +0200, Peter Ernst wrote: > On Thu, 22 Jun 2006, Mahmut Uludag wrote: > > > It seems that due to this problem new Soaplab services are not > > recognised by the Soaplab scavenger in Taverna. However individual > > services are properly recognised by the WSDL scavenger. Do you know > > which tools are generally used by the clients of your services? > > What error messages do you get? "... unable to call the get spec method for endpoint ... " This is due to fact that this version of derived Soaplab services also missing the getInputSpec operation. This should be due to the fact that we have this information already in the WSDL's. > I did not test, if the services work from Taverna or not. > Probably, it will not work with the DKFZ installation, because there, only > the derived services are deployed, and I assume, that Taverna is not using > them. The services seems to be ok with the standard WSDL scavanger in Taverna. The only problem with using them, users would need to add WSDL's of the individual services to their workbenches, for the services they find interesting. Mahmut |
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From: Mahmut U. <ul...@eb...> - 2006-06-23 08:24:21
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On Thu, 2006-06-22 at 17:49 +0100, Martin Senger wrote: > > It seems that due to this problem new Soaplab services are not > > recognised by the Soaplab scavenger in Taverna. > > > I doubt it. Soaplab scavenger does not use WSDL's (at least it did not > when I last checked it out). That's right, Soaplab scavenger does not use WSDL's. It is my fault; when I got an error, instead of investigating the error message I just thought the error should be related to the broken WSDL links. Mahmut |
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From: Peter E. <p....@dk...> - 2006-06-22 17:06:11
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On Thu, 22 Jun 2006, Peter Ernst wrote: > I did not test, if the services work from Taverna or not. > Probably, it will not work with the DKFZ installation, because there, only > the derived services are deployed, and I assume, that Taverna is not using > them. Yes, indeed. In Taverna, right-mouse-click->invoke revealed: error with endpoint: http://..../display::showdb (no .derived). Peter |
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From: Peter E. <p....@dk...> - 2006-06-22 16:59:22
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On Thu, 22 Jun 2006, Mahmut Uludag wrote: > It seems that due to this problem new Soaplab services are not > recognised by the Soaplab scavenger in Taverna. However individual > services are properly recognised by the WSDL scavenger. Do you know > which tools are generally used by the clients of your services? What error messages do you get? I get: "could not find a target service to invoke! targetService is GowlabFactory" Yes, I did not deploy the GowlabFactory. But this does not seem to be a problem because, the services do appear in Taverna's Available Services listing. (Because it can contact the AnalysisFactory service) I did not test, if the services work from Taverna or not. Probably, it will not work with the DKFZ installation, because there, only the derived services are deployed, and I assume, that Taverna is not using them. Regards, Peter |
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From: Martin S. <se...@eb...> - 2006-06-22 16:49:55
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> It seems that due to this problem new Soaplab services are not > recognised by the Soaplab scavenger in Taverna. > I doubt it. Soaplab scavenger does not use WSDL's (at least it did not when I last checked it out). Martin -- Martin Senger email: mar...@gm... skype: martinsenger |
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From: Mahmut U. <ul...@eb...> - 2006-06-22 16:11:35
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Hi Peter, > This is a bug in the Axis service/servlet, that creates the list of all > deployed services. > > When I remember correctly, this happens when <enpointURL> is used in the > deployment descriptor. Axis shoud just use the given URL, but instead adds > the service name. (Therefore it appears twice) It seems that due to this problem new Soaplab services are not recognised by the Soaplab scavenger in Taverna. However individual services are properly recognised by the WSDL scavenger. Do you know which tools are generally used by the clients of your services? Kind regards, Mahmut |
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From: Peter E. <p....@dk...> - 2006-06-22 15:23:51
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On Thu, 22 Jun 2006, Mahmut Uludag wrote: > It seems that links to WSDL files for the Soaplab derived services > generated by the patched version of Soaplab is broken, because all the > links have the service name twice. > > Do you think these duplicate names are result of a problem in the new > generation mechanism? or is this a bug in Axis? This is a bug in the Axis service/servlet, that creates the list of all deployed services. When I remember correctly, this happens when <enpointURL> is used in the deployment descriptor. Axis shoud just use the given URL, but instead adds the service name. (Therefore it appears twice) If you specify only the directory in <endpointURL> (without the service name), I assume that the links in the service listing will get right, but then the links in the WSDL file (pointing to the endpoint) will be wrong. In the current setup, the links in the listing are wrong, but the links in the WSDL files are correct. In the depolyment template at http://soaplab.cvs.sourceforge.net/soaplab/soaplab/src/etc/templates/applab/DerivedAnalysis.wsdd.template?revision=1.1.2.1&view=markup&pathrev=branch-soaplab-dkfz-1 the endpointURL is set at the end, and the name in the service's attributes. I assume the problem disappears if endpointURL is not used. But at DKFZ it is necessary (proxy). Kind regards, Peter |
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From: Mahmut U. <ul...@eb...> - 2006-06-22 13:57:17
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Hi Peter, It seems that links to WSDL files for the Soaplab derived services generated by the patched version of Soaplab is broken, because all the links have the service name twice. I have this problem in my local Soaplab installation but checked that your Axis services page has also the same problem. http://www.dkfz-heidelberg.de/menu/tomcat/as If the duplicate names are manually removed from the URLs then the WSDLs are retrieved correctly. Do you think these duplicate names are result of a problem in the new generation mechanism? or is this a bug in Axis? Regards, Mahmut |
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From: Peter E. <P....@dk...> - 2006-06-02 17:37:32
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For an overview, about the dkfz-1 branch in Soaplab, I uploaded a small poster to the Soaplab web site: http://soaplab.sourceforge.net/soaplab2/dev-doc/Soaplab_in_branch-dkfz-1.pdf A change-log, describing the differences between the soaplab-branch-dkfz-1 and the MAIN branch can be found here: http://soaplab.cvs.sourceforge.net/soaplab/soaplab/ChangeLog.branch-dkfz-1?view=markup&pathrev=branch-soaplab-dkfz-1 Kind regards, Peter On Wed, 31 May 2006, Martin Senger wrote: > > Do we plan to have a Soaplab2 branch on the Soaplab CVS repository? or > > soaplab-dkfz-1 branch will be used for the Soaplab2 development? > > There will be a new CVS module (not a branch) in the Soaplab > sourceforge CVS repository, called Soaplab2. I will re-use there what > Peter put, so far, into a branch in the current Soaplab. |
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From: Peter E. <P....@dk...> - 2006-06-02 15:16:34
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On Fri, 2 Jun 2006, Mahmut Uludag wrote: > I didn't understand how you generated the XML schema. Was it generated > by a program or was it hand coded? It was generated. I sent the generator to Jon last week in a private email. It is really just a hack, but I attach it here, too. > Actually I can see some common points between your work and Jon's work > on acdtools. Is there any plan to consolidate the two. Yes, I think so. Because Jon is now working on this issue, he wrote me, that he is considering to reuse parts of the schema and the generator. Regards, Peter |
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From: Peter E. <P....@dk...> - 2006-06-02 14:58:56
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Hello Mahmut, thank you for the link. On Fri, 2 Jun 2006, Mahmut Uludag wrote: > http://www-128.ibm.com/developerworks/webservices/library/ws-whichwsdl/ > > The main advantage of the rpc/encoded style is that the WSDL is as > straightforward as it's possible for a WSDL to be. :-)) Well, not really a strong point. The referenced web page claims this "strength" also for rpc/literal: "The WSDL is still about as straightforward as it is possible for WSDL to be." And below, they weaken these strenghts by saying about document/literal: "The WSDL is getting a bit more complicated. This is a very minor weakness, however, since WSDL is not meant to be read by humans." I can accept the phrase "getting a bit more complicated", when talking about "read by humans". However, I don't think that document style is more difficult to create by machines (here: Soaplab) and more difficult to read by machines (here: Soaplab clients). > > Does rpc/rpc provide features, missing in document/literal but > > necessary or good to have in Soaplab? > > Using rpc/encoded style it is possible to reference the same object in > more than one place by using the href and the id attributes, so avoiding > duplication of data in some cases. This is indeed the best point for rpc-style. Kind regards, Peter |
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From: Mahmut U. <ul...@eb...> - 2006-06-02 14:53:23
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Hi Peter, > I attach to this mail a XML schema, I generated from Emboss for use in > Soaplab. I didn't understand how you generated the XML schema. Was it generated by a program or was it hand coded? Actually I can see some common points between your work and Jon's work on acdtools. Is there any plan to consolidate the two. Regards, Mahmut |
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