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From: Martin S. <se...@eb...> - 2005-09-26 13:17:59
|
Peter, How does embossdata work? A user wants to use it ith soaplab and taverna - and it just reports "files was succesfully copied". Is there a way how to get data really back, or they are just copied to a directory? I must admit that I have never used this program over Soaplab. Perhaps it requires some changes in Soaplab launcher (to fetch data from the place where embossdata copies it). Thanks, Martin Marc, I am today (and part of the tomorrow) on email but then I will travelling to Europe and I am not sure how often I will be able to read emails. So bear please with me if I am delayed. Regards, Martin > > > -----Original Message----- > > From: Martin Senger [mailto:se...@eb...] > > Sent: Monday, September 26, 2005 2:38 PM > > To: Marc Logghe > > Cc: soa...@li... > > Subject: Re: [Soaplab-users] Embossdata soaplab service > > > > > When you look at the metadata for the embossdata soaplab > > service you > > > have the possibility to fetch a data file like e.g. 'Cut.index'. > > > However, it is not clear to me how to get to the content of > > that file > > > when you invoke that service within e.g. taverna. > > > > > What program is going to need (to consume) this data? An > > Emboss program? Like another program accessed by Soaplab web srevice? > > Hi Martin, > The purpose is to send the content of Cut.index (a 2 column list of > codon table ids and the corresponding description) to a beanshell script > in Taverna that turns this into a dropdown list. In that way a user > could make a choice based on the description, while the actual value > send to the server is the codon table name. > Cheers and tnx for the prompt reaction, > Marc > > > ------------------------------------------------------- > SF.Net email is sponsored by: > Tame your development challenges with Apache's Geronimo App Server. Download > it for free - -and be entered to win a 42" plasma tv or your very own > Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php > _______________________________________________ > Soaplab-users mailing list > Soa...@li... > https://lists.sourceforge.net/lists/listinfo/soaplab-users > -- Martin Senger email: mar...@gm... skype: martinsenger consulting for: International Rice Research Institute Biometrics and Bioinformatics Unit DAPO BOX 7777, Metro Manila Philippines, phone: +63-2-580-5600 (ext.2324) |
|
From: Martin S. <se...@eb...> - 2005-09-26 12:43:10
|
> When you look at the metadata for the embossdata soaplab service you > have the possibility to fetch a data file like e.g. 'Cut.index'. > However, it is not clear to me how to get to the content of that file > when you invoke that service within e.g. taverna. > What program is going to need (to consume) this data? An Emboss program? Like another program accessed by Soaplab web srevice? Martin -- Martin Senger email: mar...@gm... skype: martinsenger consulting for: International Rice Research Institute Biometrics and Bioinformatics Unit DAPO BOX 7777, Metro Manila Philippines, phone: +63-2-580-5600 (ext.2324) |
|
From: Marc L. <Mar...@DE...> - 2005-09-26 12:42:02
|
> -----Original Message----- > From: Martin Senger [mailto:se...@eb...]=20 > Sent: Monday, September 26, 2005 2:38 PM > To: Marc Logghe > Cc: soa...@li... > Subject: Re: [Soaplab-users] Embossdata soaplab service >=20 > > When you look at the metadata for the embossdata soaplab=20 > service you=20 > > have the possibility to fetch a data file like e.g. 'Cut.index'. > > However, it is not clear to me how to get to the content of=20 > that file=20 > > when you invoke that service within e.g. taverna. > > > What program is going to need (to consume) this data? An=20 > Emboss program? Like another program accessed by Soaplab web srevice? Hi Martin, The purpose is to send the content of Cut.index (a 2 column list of codon table ids and the corresponding description) to a beanshell script in Taverna that turns this into a dropdown list. In that way a user could make a choice based on the description, while the actual value send to the server is the codon table name. Cheers and tnx for the prompt reaction, Marc |
|
From: Marc L. <Mar...@DE...> - 2005-09-26 12:30:01
|
Hi all, When you look at the metadata for the embossdata soaplab service you have the possibility to fetch a data file like e.g. 'Cut.index'. However, it is not clear to me how to get to the content of that file when you invoke that service within e.g. taverna. Any clues ? Thanks, Marc |
|
From: Nandita M. <nan...@ya...> - 2005-07-20 17:40:57
|
hi there, Thanks so much for the input, maybe there is no way to do this but let me just ask in another way. So currently I am using a derived web service say http://industry.ebi.ac.uk/soap/soaplab/edit::seqret::derived. So I get a list of All the set_<name> as well as all get_<name> methods for this derived service by using getInputSpec() as recommended. so i get something like:- set_sequence_direct_data set_osformat set_snucleotide set_sequence_usa .. .. and so on. And now I want to use the following doCall :- String sequence =">PPGLTG\n" + "ACTGCACTCACCGCACCTGGCCAATTTTTGTG.... client.doCall ("set_sequence_direct_data", new Object[] { jobId, sequence}); client.doCall ("set_osformat", new Object[] { jobId, "embl" }); So in the above I have the jobID, set_<name>.And I am fine till here. But is there a way know that set_osformat requires an embl Value and set_sequence_direct_data requires a sequence Value? I wanted to indicate to the user that if he has selected the set_osformat operation, he should input a value for "embl". OR if he has selected set_sequence_direct_data he has to now input a value for "sequence". Thus making it more intuitive for the user , if he has selected a set_<name> operation in a derived web service,I further give him a clue on what value needs to be given as input in the selected set_<name> operation. So for eg. the user wishes to select set_sncuelotide but is confused as to what kind of input value to give the above set operation.Should he give set_snucelotide a sequence ? or something else? I hope the above question makes more sense. I am basically trying to use webservices in Kepler via soaplab and am running into this problem, of being able to provide the user with expected input Values Requirements for the set_<name> operations in a derived service. thank you, nandita. __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com |
|
From: Martin S. <se...@eb...> - 2005-07-20 15:23:23
|
I am sorry not to come back to you sooner. > I am having problems using the ACD filelist command to pass a variable > number of input files to soaplab. > I think that the problem is not on your (ACD) site. But Taverna does not support fully this type of input. This is the situation so far: * In Taverna you can create more 'new inputs' (by clicking several times on the 'new input' button'. And then for each such new input you can either copy and paste its value, or click on 'load' to load it from a file. Such list may be sent to a Soaplab service correctly. I said 'may' because I need to check it because so far nobody was trying to use such kind of input in Taverna for Soaplab services. If it does not then I will fix it in Taverna. * However, the procedure just described above requires manually load each of the input files into Taverna before starting the workflow. And this may not be too user friendly (in case there are many input files). Tom may consider to add a better support in the Taverna GUI for these cases. Summary is that I will try to make the first option working, and you try to communicate with Tom to find how the second option is prioritized :-) Regards, Martin -- Martin Senger EMBL Outstation - Hinxton Se...@EB... European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger |
|
From: Martin S. <se...@eb...> - 2005-07-20 09:04:58
|
Hi, I cannot add much to the Marc's answer. So please feel free to refine or re-phrase your question if you are still in the dark. This is a summary: 1) If you do not use derived services, you need to know parameter names. And there (in the Soaplab's WSDL/API) is a method to get them (together with types) - getInputSpec(). 2) If you use derived services, the WSDL has all parameters and their types defined as individual methods. 3) In both cases, however, there is no way to find which parameters are mutually exclusive, in other words there is no indication about parameter dependencies (typical example in emboss are parameter names 'sequence_direct_data' and 'sequence_usa' - one of them is always mandatory, but it does not make sense to use both of them in the same call). This is a limitation that was never implemented (even though it is still intended to do so sometimes). Regards, Martin -- Martin Senger EMBL Outstation - Hinxton Se...@EB... European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger |
|
From: Marc L. <Mar...@de...> - 2005-07-20 07:55:33
|
Hi Nandita,
In your soaplab distro you should find a little shell script (wrapper to
java AnalysisClient) run/run-analysis.
On the commnand line:
run/run-analysis -ii -name edit::seqret
Result:
Input parameter attributes:
feature
prompt: Use feature information
type: String
send_defaults: false
mandatory: false
default: false
qualifier: feature
firstonly
prompt: Read one sequence and stop
type: String
send_defaults: false
mandatory: false
default: false
qualifier: firstonly
<skip>
This information can also be obtained via the Taverna workbench (I am
not sure what kind of 'users' you are referring to).
HTH,
Marc=20
> -----Original Message-----
> From: soa...@li...=20
> [mailto:soa...@li...] On Behalf=20
> Of Nandita Mangal
> Sent: Wednesday, July 20, 2005 3:39 AM
> To: soa...@li...
> Subject: [Soaplab-users] Getting Parameters Derived Service
>=20
> Hi there,
>=20
> I am trying to use soaplab in order to execute a given web service.=20
> Hence I give the user a set of possible set_<name> methods to=20
> choose from for the given wsdl.
> The user over here has to himself choose the parameters for=20
> the given set_<name> operation. For example
>=20
> in edit::seqret::derived
>=20
> to do client.doCall("set_sequence_direct_data",
> params);
>=20
> the user has to know beforehand what are the exact parameters=20
> for the above operation to be called.i.e set_seq_dir_data=20
> requires a "sequence" param.
>=20
> Is there a way to ease the user of this requirement, of=20
> knowing the exact parameter names & types and can it be=20
> obtained from the wsdl somehow?
> Such that when i instantiate my application, the user is not=20
> only given the names of possible set_<name> operations from=20
> the wsdl but also input params required by the operation such=20
> as sequence in the case of set_sequence_direct_data operation?
>=20
>=20
> thank you so much ,
> nandita.
>=20
>=20
>=20
>=20
> =09
> =09
> __________________________________
> Do you Yahoo!?=20
> Yahoo! Mail - You care about security. So do we.=20
> http://promotions.yahoo.com/new_mail
>=20
>=20
> -------------------------------------------------------
> SF.Net email is sponsored by: Discover Easy Linux Migration Strategies
> from IBM. Find simple to follow Roadmaps, straightforward articles,
> informative Webcasts and more! Get everything you need to get up to
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> _______________________________________________
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> Soa...@li...
> https://lists.sourceforge.net/lists/listinfo/soaplab-users
>=20
|
|
From: Nandita M. <nan...@ya...> - 2005-07-20 01:39:40
|
Hi there,
I am trying to use soaplab in order to execute a given
web service.
Hence I give the user a set of possible set_<name>
methods to choose from for the given wsdl.
The user over here has to himself choose the
parameters for the given set_<name> operation. For
example
in edit::seqret::derived
to do client.doCall("set_sequence_direct_data",
params);
the user has to know beforehand what are the exact
parameters for the above operation to be called.i.e
set_seq_dir_data requires a "sequence" param.
Is there a way to ease the user of this requirement,
of knowing the exact parameter names & types and can
it be obtained from the wsdl somehow?
Such that when i instantiate my application, the user
is not only given the names of possible set_<name>
operations from the wsdl but also input params
required by the operation such as sequence in the case
of set_sequence_direct_data operation?
thank you so much ,
nandita.
__________________________________
Do you Yahoo!?
Yahoo! Mail - You care about security. So do we.
http://promotions.yahoo.com/new_mail
|
|
From: Martin S. <se...@eb...> - 2005-07-18 11:54:17
|
Anders, > I have been trying out the possibility to run an Applab server on a > differnt machine from my Tomcat webserver. > Are you satisfied with the Marc's reply regarding how to run mkre AppLab servers (many thanks, Marc!) - or do you need more details? Cheers, Martin -- Martin Senger EMBL Outstation - Hinxton Se...@EB... European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger |
|
From: Martin S. <se...@eb...> - 2005-07-14 11:15:15
|
Sorry, I am now in the middle of a workshop/meeting - but I will reply to your question later (hopefully) today. Martin -- Martin Senger EMBL Outstation - Hinxton Se...@EB... European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger |
|
From: Andrew E. <a.e...@ci...> - 2005-07-14 10:21:20
|
Hi
I am having problems using the ACD filelist command to pass a variable
number of input files to soaplab.
My ACD file is very simple:
======
appl: bioconductor [
documentation: "Bioconductor example using affy expresso"
version: "1.0"
groups: "Microarrays"
nonemboss: "Y"
executable: affy-expresso.pl
]
filelist: templates [
prompt: "CEL files"
qualifier: "f"
]
outfile: result [
additional:"Y"
prompt: "Normalised affy output"
qualifier: "o"
]
========
Using Taverna I get the following message,
Task failed due to problem invoking soaplab service
....
org.embl.ebi.SoaplabShare.Soaplab.Exception: CONFLICTING_INPUT. templates *
(Parameter: (CORBA related problem) Unknown TypeCode Kind
While the soaplab.log gives me:
| Wrong or incomplete input (in JobAppLab): 1 exception(s)
I may be using Taverna wrongly but with just about every possible
combination of inputs I get the same error. Any clues? Everything works
perfectly with a well-defined number of inputs using ACD infile.
many thanks
Andy Emerson
------------------------
Dr Andrew Emerson
CINECA (High Performance Systems)
via Magnanelli, 6/3
40033 Casalecchio di Reno (BO)-ITALY
tel: +39-051-6171653, fax: +39-051-6132198
e-mail: a.e...@ci...
|
|
From: Martin S. <se...@eb...> - 2005-07-13 13:13:02
|
Hi, I am sorry to be late with an answer to your problem (I was off my office). It seems that you have already solved your problem (my thanks also to Marc for his comments). Neverthelsss, I will try to summarize how CLASSPATH variable is treated in Soaplab. As you noticed, the run-AppLab-server script sets its CLASSPATH from the scratch - so if you have anything in your CLASSPATH (e.g. from your user profile, from .bashrc) it is gone. And it is intentional because otherwise there may be hard-to-find bugs when Soaplab (respectively AppLab) gets mixed versions of various Java packages. And this practice - to clean the CLASSPATH first and then to fill it only with classes needed for a particular java program - is considered a "best practices". That means that - in your case - your script that invokes Java program should first set the full CLASSPATH without expecting anything there. And that's exactly what you did by using option '-classpath' (the same could be reached also by setting and exporting CLASSPATH in your script before calling java). Please let me know if there are still unsolved and new questions. With regards, Martin -- Martin Senger EMBL Outstation - Hinxton Se...@EB... European Bioinformatics Institute Phone: (+44) 1223 494636 Wellcome Trust Genome Campus (Switchboard: 494444) Hinxton Fax : (+44) 1223 494468 Cambridge CB10 1SD United Kingdom http://industry.ebi.ac.uk/~senger |
|
From: Marc L. <Mar...@de...> - 2005-07-06 12:35:15
|
> I have been trying out the possibility to run an Applab=20
> server on a differnt machine from my Tomcat webserver.=20
> However, Tomcat seems to reject the incoming requests due to=20
> security settings. Which Tomcat or Soaplab settings do I=20
> change to fix this? Is there any possibility to get Tomcat to=20
> use a specific user name and password when remote accessing=20
> Tomcat? If not, this means I have to open the Tomcat server=20
> for anonymous remote administration from anywhere, does it not?
>=20
> Would appreciate any help.
Hi Anders,
Suppose you have soaplab running on machine A and you want to wrap a =
soaplab service around a command that can not be run on machine A, but =
only on machine B.=20
This is possible by running AppLab on machine B and saying to soaplab on =
machine A that the service has to be executed on B. This message goes =
via the IOR.
1) Install soaplab on machine B.
2) In Server.cfg set ooc.iiop.host =3D <machine B>
3) In ws/add-services.pl two blocks have to be commented out:
...
# --- where is Axis-in-Tomcat directory
#unless ($opt_x) {
# my $tomcat =3D ($ENV{'CATALINA_HOME'} or $ENV{'TOMCAT_HOME'} or
# die ("Axis-in-Tomcat directory must be specified. Use =
-x <axis-lib>.\n"));
# $opt_x =3D File::Spec->catdir ($tomcat, 'webapps', 'axis', =
'WEB-INF', 'lib');
#}
...
# --- copying derived classes (to Tomcat, and to 'dynalib')
#foreach my $file (glob (File::Spec->catfile ('lib', '*'))) {
# my $in_tomcat =3D File::Spec->catfile ($opt_x, basename ($file));
# die ("File $in_tomcat already exists.\nUse -f to force overwriting: =
add-services -f ...\n")
# if !$opt_f and -e $in_tomcat;
# copy ($file, $in_tomcat) or die "Can't copy $file to $in_tomcat: =
$!\n";
# copy ($file, File::Spec->catdir ($dest_dir, 'dynalib'))
# or die "Can't copy $file to $dest_dir/dynalib: $!\n";
#}
...
4) First of all, you should have deployed the services on machine A, the =
normal way. The distribution file is copied to machine B and added as =
such:
ws/add-services.pl -d ./ /your-distri-file.tar.gz
The most important things here are that the Applications.xml from the =
distribution file is merged to the existing one and that the IOR files =
are created. Now start Applab on machine B in the usual way.
5) Make IOR available to machine A
This can be done in two ways:
5.1) Copy the generated ior file for your service from machine A to =
machine B (in the appropriate folder, /IOR/analyses/)
5.2) Make the machine A ior file for your service available via the web =
(e.g. by creating soft link to /var/analysis-interfaces/IOR/analyses). =
In the server-config.wsdd file of machine A change the line:
<parameter name=3D"applab_factory" =
value=3D"file:/blah/blah/IOR/AppLabFactory.ref"/>
To:
<parameter name=3D"applab_analysis" value=3D"http://machine =
B/link_to/my::service.ior"/>
And, finally restart tomcat.
HTH,
Marc
|
|
From: <and...@bc...> - 2005-07-06 12:12:54
|
Hi, I have been trying out the possibility to run an Applab server on a differnt machine from my Tomcat webserver. However, Tomcat seems to reject the incoming requests due to security settings. Which Tomcat or Soaplab settings do I change to fix this? Is there any possibility to get Tomcat to use a specific user name and password when remote accessing Tomcat? If not, this means I have to open the Tomcat server for anonymous remote administration from anywhere, does it not? Would appreciate any help. Anders -- Anders Lanzén, MSc Programmer Computational Biology Unit Bergen Center for Computational Science http://www.bccs.uib.no phone: +47 5558 4045 email: and...@bc... |
|
From: <an...@ii...> - 2005-07-05 20:40:57
|
Hi, Thanks. I actually managed to solve it just now. The classpath system variable of the user running the Applab-server was overwritten. I actually tried to insert (bashrc) export CLASSPATH=$CLASSPATH:<my_classpath>. However, this did not work (the error message mysteriously gone but nothing at all happening when executing my program instead). What did work is simply java -classpath <my_classpath> <my_program> Should of course have thought about trying that first of all. Cheers, Anders > > I have written a shell script for a custom soaplab ws that > > calls a number of command line tools in sequence, creating > > and reading temporary files as it goes. Some of the calls are > > to java classes available in my classpath. However, these do > > not seem to work (NoClassDefFoundError). It does work when I > > call it directly rather than as a WS. > > > > Is this because the system classpath is not used even from > > the shell? > > How can I fix it? > > Hi Anders, > Hope it makes sense, but I guess you can set the classpath variable in the > profile for the user that runs the applab server. > Another option would be to set it in the run-AppLab-server script directly. > HTH, > Marc > |
|
From: Marc L. <Mar...@de...> - 2005-07-05 20:05:04
|
> I have written a shell script for a custom soaplab ws that=20 > calls a number of command line tools in sequence, creating=20 > and reading temporary files as it goes. Some of the calls are=20 > to java classes available in my classpath. However, these do=20 > not seem to work (NoClassDefFoundError). It does work when I=20 > call it directly rather than as a WS. >=20 > Is this because the system classpath is not used even from=20 > the shell? =20 > How can I fix it? Hi Anders, Hope it makes sense, but I guess you can set the classpath variable in = the profile for the user that runs the applab server. Another option would be to set it in the run-AppLab-server script = directly. HTH, Marc |
|
From: <and...@bc...> - 2005-07-05 16:53:24
|
Hi, I have written a shell script for a custom soaplab ws that calls a number of command line tools in sequence, creating and reading temporary files as it goes. Some of the calls are to java classes available in my classpath. However, these do not seem to work (NoClassDefFoundError). It does work when I call it directly rather than as a WS. Is this because the system classpath is not used even from the shell? How can I fix it? Cheers, Anders -- Anders Lanzén, MSc Programmer Computational Biology Unit Bergen Center for Computational Science http://www.bccs.uib.no phone: +47 5558 4045 email: and...@bc... |
