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From: Sebastien M. <Seb...@un...> - 2008-03-27 09:41:20
|
Hi,
I try to find the right way to create boolean parameters (I mean
parameter name without parameter value) in ACD format.
But they don't appear in the report file when I run the service.
I have two different cases:
-html parameter which can be present or not, depending on user choice.
-def parameter which must be always present
Here is my ACD code:
boolean: html [
additional: "Y"
default: "true"
prompt: "Output format"
information: "Output format, html or not "
outputmodifier: "Y"
]
boolean: def [
default: "true"
comment: "display false"
information: "The 'def' parameter"
]
Do you have any ideas why these parameters are not added on command line
when the application is running ?
Thanks
--
Sébastien Moretti
SIB, Quartier Sorge - Genopode
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4056/4221
|
|
From: Mahmut U. <ul...@eb...> - 2008-03-18 10:37:59
|
Hi Cath, > > I've just tried to install EMBOSS on soaplab2, and it seems sorta > > kinda successful - the EMBOSS services show up in the info-list, and > > they seem to have deployed OK when you look at the list at > > http://myserver.myuni.au:8888/soaplab2-axis/services > > (not real URL) I forgot to say if you don't have special reasons it is better to use the jax-ws services that would make your Soaplab services interoperable with more webservices technologies. If you have decided to use axis services because you want them accessible from Taverna, you might use the Taverna Soaplab plugin which supports both jaxws and axis flavours of Soaplab. http://soaplab.sourceforge.net/soaplab2/TavernaNotes.html The plugin will probably be part of Taverna-2 and replace the so called "Soaplab Scavenger". Regards, Mahmut |
|
From: Mahmut U. <ul...@eb...> - 2008-03-18 10:21:36
|
Hi Cath, > I've just tried to install EMBOSS on soaplab2, and it seems sorta > kinda successful - the EMBOSS services show up in the info-list, and > they seem to have deployed OK when you look at the list at > http://myserver.myuni.au:8888/soaplab2-axis/services > (not real URL) > > However, entering that same URL in a taverna session as a new soaplab > scavenger returns only the original default soaplab list. And the > spinet web page doesn't have them, either. What have I missed? I guess > it must be some config somewhere that I overlooked. > > How can I make taverna see these, and spinet regenerate itself? Spinet > looks like a nifty little testing page, by the way, and I'd like to > use it. >From your description it seems that the services are recognised by Axis but not Soaplab. This should be related to a missing or wrong 'applist' property line in your soaplab.properties file (under your WEB-INF/classes directory of your soaplab2-axis web application). You should have a property definition similar to the following. applist = ${metadata.dir}/EMBOSSApplications.xml Make sure that you have ${metadata.dir} defined correctly above in your properties file. It should normally point to the metadata directory of your soaplab2-axis web application. Regards, Mahmut |
|
From: cajela <ca...@gm...> - 2008-03-18 06:23:23
|
Hi, I've just tried to install EMBOSS on soaplab2, and it seems sorta kinda successful - the EMBOSS services show up in the info-list, and they seem to have deployed OK when you look at the list at http://myserver.myuni.au:8888/soaplab2-axis/services (not real URL) However, entering that same URL in a taverna session as a new soaplab scavenger returns only the original default soaplab list. And the spinet web page doesn't have them, either. What have I missed? I guess it must be some config somewhere that I overlooked. How can I make taverna see these, and spinet regenerate itself? Spinet looks like a nifty little testing page, by the way, and I'd like to use it. cheers Cath -- Cath Lawrence --- cajela at gmail dot com http://thecanberracook.blogspot.com |
|
From: Mahmut U. <ul...@eb...> - 2008-03-14 16:06:14
|
Hi Sebastien, > Is there a simple way to see our ACD files as command lines ? > > I would like to check the command line syntax without running the > application. ExploreParameters tool can be used for this purpose. http://soaplab.sourceforge.net/soaplab2/AdminTools.html#params The following is an example command line that uses this tool. > build/run/run-any-client org.soaplab.admin.ExploreParameters -name gowlab.echo name Kim checked 1 radio b color green -words_ee -words_me Regards, Mahmut |
|
From: Sebastien M. <Seb...@un...> - 2008-03-14 15:08:18
|
Hello, Is there a simple way to see our ACD files as command lines ? I would like to check the command line syntax without running the application. Thanks -- Sébastien Moretti |
|
From: Sebastien M. <Seb...@un...> - 2008-03-13 12:33:24
|
> Hi Sebastian,
>
>> I have two questions about parameter value variable in ACD syntax.
>>
>> First, may I use something like
>> string: seq [
>> standard: "Y" #Mandatory parameter
>> knowntype: "string"
>> minlength: ${min}
>> ...]
>> where min is
>> integer: min [
>> minimum: 14
>> maximum: 26
>> default: 17
>> ...]
>> ?
>
> Although EMBOSS supports the minlength option for the string objects
> current Soaplab doesn't support it. If your command line applications
> are implemented using EMBOSS framework then EMBOSS checks on run-time
> whether the input string lengths have the minimum length specified by
> the minlength option.
>
> You can have something similar to the above example using EMBOSS but you
> should make sure that in the ACD file you define the referenced options
> before the option that refers them. Also instead of curly brackets
> EMBOSS use parenthesis when referring to a variable value.
>
> In summary, current Soaplab doesn't have minlength and maxlength
> validation for String objects but you can do this validation in your
> executable. I don't know whether your Soaplab services are for existing
> applications or you are implementing new applications but if you are
> writing new bioinformatics applications using C/C++ then you may use
> EMBOSS framework to implement them, then you would have this type of
> validation at no extra cost.
>
> Regards,
> Mahmut
OK
I always check this in my application but I wondered if I could check
parameter values before.
Thanks
--
Sébastien Moretti
|
|
From: Mahmut U. <ul...@eb...> - 2008-03-13 12:27:42
|
Hi Sebastian,
> I have two questions about parameter value variable in ACD syntax.
>
> First, may I use something like
> string: seq [
> standard: "Y" #Mandatory parameter
> knowntype: "string"
> minlength: ${min}
> ...]
> where min is
> integer: min [
> minimum: 14
> maximum: 26
> default: 17
> ...]
> ?
Although EMBOSS supports the minlength option for the string objects
current Soaplab doesn't support it. If your command line applications
are implemented using EMBOSS framework then EMBOSS checks on run-time
whether the input string lengths have the minimum length specified by
the minlength option.
You can have something similar to the above example using EMBOSS but you
should make sure that in the ACD file you define the referenced options
before the option that refers them. Also instead of curly brackets
EMBOSS use parenthesis when referring to a variable value.
In summary, current Soaplab doesn't have minlength and maxlength
validation for String objects but you can do this validation in your
executable. I don't know whether your Soaplab services are for existing
applications or you are implementing new applications but if you are
writing new bioinformatics applications using C/C++ then you may use
EMBOSS framework to implement them, then you would have this type of
validation at no extra cost.
Regards,
Mahmut
|
|
From: Sebastien M. <Seb...@un...> - 2008-03-12 16:21:57
|
Hi,
I have two questions about parameter value variable in ACD syntax.
First, may I use something like
string: seq [
standard: "Y" #Mandatory parameter
knowntype: "string"
minlength: ${min}
...]
where min is
integer: min [
minimum: 14
maximum: 26
default: 17
...]
?
Second, I have two dependent parameters, min and max.
I always want min >= max but their range values are overlapping.
So, is there a way to reject query, from ACD syntax, when max > min ?
Thanks
--
Sébastien Moretti
|
|
From: Mahmut U. <ul...@eb...> - 2008-02-12 11:42:38
|
On Tue, 2008-02-12 at 16:46 +0530, Shameer Khadar wrote: > > > If not, my guess is that you are sitting behind a proxy. If that is the > > case you might find a solution here: > > http://ant.apache.org/manual/proxy.html > > I am not able to access this URL : http://ant.apache.org/manual/proxy.html > Are you guys able to access it ? Yes, I can access from the EBI. -- mahmut > I think I should talk to our systems > engineer to know more about the proxy restrictions. > > :) |
|
From: Shameer K. <sh...@nc...> - 2008-02-12 11:38:54
|
> If not, my guess is that you are sitting behind a proxy. If that is the > case you might find a solution here: > http://ant.apache.org/manual/proxy.html I am not able to access this URL : http://ant.apache.org/manual/proxy.html Are you guys able to access it ? I think I should talk to our systems engineer to know more about the proxy restrictions. :) -- K Shameer Lab (# 25) The Computational Biology Group National Centre for Biological Sciences (TIFR) GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India T - 91-080-23666001 EXT - 6251 W - http://www.ncbs.res.in |
|
From: Shameer K. <sh...@nc...> - 2008-02-12 10:48:11
|
Hi, Yes, wget is working after I do an export http_proxy="myproxy:port". wget http://apache.hoxt.com/maven/binaries/maven-ant-tasks-2.0.8.jar --16:16:43-- http://apache.hoxt.com/maven/binaries/maven-ant-tasks-2.0.8.jar => `maven-ant-tasks-2.0.8.jar' Resolving proxy.ncbs.res.in... 192.168.1.1 Connecting to proxy.ncbs.res.in|192.168.1.1|:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 9,80,760 (958K) [text/plain] 100%[====================================>] 9,80,760 --.--K/s 16:16:43 (7.71 MB/s) - `maven-ant-tasks-2.0.8.jar' saved [980760/980760] Without export http_proxy it is not working. I executed same command before building the CVS code as well. > Hi, > Does a wget > http://apache.hoxt.com/maven/binaries/maven-ant-tasks-2.0.8.jar work ? > If not, my guess is that you are sitting behind a proxy. If that is the > case you might find a solution here: > http://ant.apache.org/manual/proxy.html > HTH, > Marc > -- K. Shameer Lab (# 25) The Computational Biology Group National Centre for Biological Sciences (TIFR) GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India T - 91-080-23666001 EXT - 6251 W - http://www.ncbs.res.in |
|
From: Marc L. <Mar...@ab...> - 2008-02-12 10:20:55
|
Hi, Does a wget http://apache.hoxt.com/maven/binaries/maven-ant-tasks-2.0.8.jar work ? If not, my guess is that you are sitting behind a proxy. If that is the case you might find a solution here: http://ant.apache.org/manual/proxy.html HTH, Marc > -----Original Message----- > From: soa...@li... [mailto:soaplab-users- > bo...@li...] On Behalf Of Shameer Khadar > Sent: dinsdag 12 februari 2008 9:44 > To: soa...@li... > Cc: Martin Senger > Subject: Re: [Soaplab-users] CVS Build - Installation problem > > Hi Martin, > > Thanks for your quick reply. I got the code from CVS, I am getting similar > errors. I am on an ubuntu box. I have executed export http_proxy command > to bypass proxy related issues. > > ~/soaplab2$ ant install > Unable to locate tools.jar. Expected to find it in > /usr/lib/j2se/1.4/lib/tools.jar > Buildfile: build.xml > > install: > [welcome] > [welcome] ------------------------------------------ > [welcome] Welcome to the Soaplab2 world. | > [welcome] Project documentation is available from: | > [welcome] http://soaplab.sourceforge.net/soaplab2/ | > [welcome] | > [welcome] ( If you are interested only in Soaplab2 | > [welcome] clients, stop this by Ctrl-C and start | > [welcome] again with 'ant install-clients'. ) | > [welcome] ------------------------------------------ > [welcome] > > [version] > [version] Apache Ant version 1.6.5 compiled on July 5 2006 > [version] Java: 1.4.2-02 > [version] Linux 2.6.20-16-generic > [version] > > check-ant-version: > > bootstrap: > [get] Getting: > http://apache.hoxt.com/maven/binaries/maven-ant-tasks-2.0.8.jar > [get] To: /home/shameer/soaplab2/lib/maven-ant-tasks-2.0.8.jar > [get] Error getting > http://apache.hoxt.com/maven/binaries/maven-ant-tasks-2.0.8.jar to > /home/shameer/soaplab2/lib/maven-ant-tasks-2.0.8.jar > > BUILD FAILED > /home/shameer/soaplab2/xmls/install.xml:32: The following error occurred > while executing this line: > /home/shameer/soaplab2/xmls/maven.xml:48: java.net.ConnectException: > Connection timed out > > Total time: 3 minutes 10 seconds > > > > > > > But I definitely recommend you to go for Soaplab2 - it is a newer, > > recently released, version of Soaplab with much easier deployment, > better > > documentation and much cleaner code. Also the problem you mentioned will > > not happened (because the library that timeout-ed for you is now taken > > from a different place). > > > > -- > K. Shameer > Lab (# 25) The Computational Biology Group > National Centre for Biological Sciences (TIFR) > GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India > T - 91-080-23666001 EXT - 6251 > W - http://www.ncbs.res.in > > > ------------------------------------------------------------------------ - > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > Soaplab-users mailing list > Soa...@li... > https://lists.sourceforge.net/lists/listinfo/soaplab-users |
|
From: Shameer K. <sh...@nc...> - 2008-02-12 09:06:30
|
Hi Martin, Thanks for your quick reply. I got the code from CVS, I am getting similar errors. I am on an ubuntu box. I have executed export http_proxy command to bypass proxy related issues. ~/soaplab2$ ant install Unable to locate tools.jar. Expected to find it in /usr/lib/j2se/1.4/lib/tools.jar Buildfile: build.xml install: [welcome] [welcome] ------------------------------------------ [welcome] Welcome to the Soaplab2 world. | [welcome] Project documentation is available from: | [welcome] http://soaplab.sourceforge.net/soaplab2/ | [welcome] | [welcome] ( If you are interested only in Soaplab2 | [welcome] clients, stop this by Ctrl-C and start | [welcome] again with 'ant install-clients'. ) | [welcome] ------------------------------------------ [welcome] [version] [version] Apache Ant version 1.6.5 compiled on July 5 2006 [version] Java: 1.4.2-02 [version] Linux 2.6.20-16-generic [version] check-ant-version: bootstrap: [get] Getting: http://apache.hoxt.com/maven/binaries/maven-ant-tasks-2.0.8.jar [get] To: /home/shameer/soaplab2/lib/maven-ant-tasks-2.0.8.jar [get] Error getting http://apache.hoxt.com/maven/binaries/maven-ant-tasks-2.0.8.jar to /home/shameer/soaplab2/lib/maven-ant-tasks-2.0.8.jar BUILD FAILED /home/shameer/soaplab2/xmls/install.xml:32: The following error occurred while executing this line: /home/shameer/soaplab2/xmls/maven.xml:48: java.net.ConnectException: Connection timed out Total time: 3 minutes 10 seconds > > But I definitely recommend you to go for Soaplab2 - it is a newer, > recently released, version of Soaplab with much easier deployment, better > documentation and much cleaner code. Also the problem you mentioned will > not happened (because the library that timeout-ed for you is now taken > from a different place). > -- K. Shameer Lab (# 25) The Computational Biology Group National Centre for Biological Sciences (TIFR) GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India T - 91-080-23666001 EXT - 6251 W - http://www.ncbs.res.in |
|
From: Martin S. <mar...@gm...> - 2008-02-12 08:44:19
|
Hi, We have a couple of command line programs developed > in the lab. We are planning to provide them as Web service for public use. > I hope I can use SoapLab to get it done. I hope, too :-) But I definitely recommend you to go for Soaplab2 - it is a newer, recently released, version of Soaplab with much easier deployment, better documentation and much cleaner code. Also the problem you mentioned will not happened (because the library that timeout-ed for you is now taken from a different place). You can find Soaplab2 at http://soaplab.sourceforge.net/soaplab2. Regards, Martin -- Martin Senger email: mar...@gm... skype: martinsenger |
|
From: Shameer K. <sh...@nc...> - 2008-02-12 08:38:57
|
Hi All,
I am new to the list. We have a couple of command line programs developed
in the lab. We are planning to provide them as Web service for public use.
I hope I can use SoapLab to get it done.
I downloaded the source from CVS. When I tried to build it got the
following error.
./build.sh Buildfile: build.xml
gather:
[get] Getting: http://soaplab.sf.net/jar-storage/alltools.jar
[get] Error getting http://soaplab.sf.net/jar-storage/alltools.jar
to /home/shameer/soaplab/lib/alltools.jar
BUILD FAILED
file:/home/shameer/soaplab/build.xml:152: java.net.ConnectException:
Connection timed out
Total time: 3 minutes 10 seconds
Buildfile: build.xml
init:
compile:
BUILD FAILED
file:/home/shameer/soaplab/build.xml:350:
Missing one or more third-party libraries.
Try to run build.sh or build.bat to fetch them from the net.
Total time: 0 seconds
Please Help,
Thanks,
--
K. Shameer
Lab (# 25) The Computational Biology Group
National Centre for Biological Sciences (TIFR)
GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
T - 91-080-23666001 EXT - 6251
W - http://www.ncbs.res.in
|
|
From: Martin S. <mar...@gm...> - 2008-02-05 19:05:35
|
[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 |
|
From: Martin S. <mar...@gm...> - 2007-10-29 05:56:52
|
[ 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 |
|
From: Martin S. <mar...@gm...> - 2007-05-14 11:31:15
|
> I was just wondering if Soaplab would be compatible with the newest > version of Axis, which is Axis2? The new re-incarnation of the soaplab, called Soaplab2, will support (at least the plans are) JAX-WS, Axis2 and because of the backwards compatibility also Axis1. The Soaplab2 is in a quite advanced stage of readiness, we hope to have its first release this summer. Martin -- Martin Senger email: mar...@gm... skype: martinsenger |
|
From: Sirisha G. <si...@my...> - 2007-05-14 11:23:56
|
Hi, I was just wondering if Soaplab would be compatible with the newest version of Axis, which is Axis2? Many thanks, Sirisha This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation. |
|
From: Mahmut U. <ul...@eb...> - 2007-03-06 14:14:24
|
The EBI Soaplap services are back and seem to be healthy after the move to Tomcat 5.5. Regards, Mahmut On Mon, 2007-03-05 at 15:31 +0000, ul...@eb... wrote: > Hi, > > There will be an interrup to the EBI Soaplab services at 2 o'clock > tomorrow afternoon as the services will be moving to a Tomcat 5.5 server. > We hope the interrupt will be short and will email again after the basic > tests pass. > > Regards, > Mahmut |
|
From: <ul...@eb...> - 2007-03-05 15:31:45
|
Hi, There will be an interrup to the EBI Soaplab services at 2 o'clock tomorrow afternoon as the services will be moving to a Tomcat 5.5 server. We hope the interrupt will be short and will email again after the basic tests pass. Regards, Mahmut |
|
From: Mahmut U. <ul...@eb...> - 2007-01-30 16:06:09
|
Hi Tim, > Does emboss-services-2004-06-16.tar.gz work with emboss 4? > Or do I still have to use emboss 2.8.0? The new services tar ball was made available from the following location. ftp://ftp.ebi.ac.uk/pub/software/unix/soaplab/contrib/emboss4.0-services.tar.gz It also includes EMBASSY applications as in EBI Soaplab server for EMBOSS4 (http://www.ebi.ac.uk/soaplab/emboss4). For testing purpose I have installed the tar ball into a local binary Soaplab installation using the Soaplab add-services script. > ws/add-services -f ../emboss-services-2007-01-30.tar.gz All services were then tested using a new test suite derived from the EMBOSS core test suite. The tar ball is for standard Soaplab distributions. If anybody needs I can similarly prepare one for the Peter Ernst version of Soaplab where only the derived services are different. Regards, Mahmut |
|
From: Mahmut U. <ul...@eb...> - 2007-01-25 11:42:51
|
> Does emboss-services-2004-06-16.tar.gz work with emboss 4? > Or do I still have to use emboss 2.8.0? We discussed this in the EMBOSS meeting this week and will soon prepare a release for EMBOSS 4 Soaplab services. Regards, Mahmut |
|
From: Mahmut U. <ul...@eb...> - 2007-01-25 11:42:51
|
Hi Tim, > Is the EBI SOAPLab server for EMBOSS-4.0 applications available to > download so I can install it locally? Not yet. We use it from the CVS version (branch-soaplab-dkfz-1). > http://www.ebi.ac.uk/soaplab/emboss4/index.html > > The link to documentation on the specialized version of soaplab is > broken on the above page. It is now fixed. The poster was prepared by Peter Ernst to summarise his changes to have document style (instead of RPC style) in Soaplab service descriptions. Regards, Mahmut |
