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From: John S R. <J.S...@so...> - 2008-11-10 14:15:58
|
On Monday 10 November 2008 14:01:59 Mahmut Uludag wrote:
> Hi,
>
> > I have a few simple scripts wrapped using Soaplab2. Occasionally (about
> > in 1 in 4 invocations, but always immediately after startup, or after a
> > period of innactivity), I get the following exception:
> >
> > AxisFault
> > faultCode:
> > {http://schemas.xmlsoap.org/soap/envelope/}Server.userException
> > faultSubcode:
> > faultString: org.xml.sax.SAXParseException: Premature end of file.
> >
> > I've made my catalina.out available here:
> >
> > http://kraz.omii.ac.uk/~jsr2/catalina.out
>
> looking at the above log file, it is possible that you might have an
> invalid server-config.wsdd file.
>
> It would be useful to check your server-config.wsdd file against the
> following error message recorded in the same log file.
>
> org.xml.sax.SAXParseException: The markup in the document preceding the
> root element must be well-formed.
Hi Mahmut,
Thanks for the quikc response.
xmlwf refports no problems with server-config.wsdd.
As I mentioned, this is an intermittent problem. It's almost as if something
is being uncached after a period of time, and the next call missing the cache
but causing the data to be reloaded so that subsequent calls hit. Does this
sound plausible?
Cheers,
JohnR
--
----------------------------------------
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: Mahmut U. <ul...@eb...> - 2008-11-10 14:02:07
|
Hi,
> I have a few simple scripts wrapped using Soaplab2. Occasionally (about in 1
> in 4 invocations, but always immediately after startup, or after a period of
> innactivity), I get the following exception:
>
> AxisFault
> faultCode: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException
> faultSubcode:
> faultString: org.xml.sax.SAXParseException: Premature end of file.
>
> I've made my catalina.out available here:
>
> http://kraz.omii.ac.uk/~jsr2/catalina.out
looking at the above log file, it is possible that you might have an
invalid server-config.wsdd file.
It would be useful to check your server-config.wsdd file against the
following error message recorded in the same log file.
org.xml.sax.SAXParseException: The markup in the document preceding the root element must be well-formed.
Regards,
Mahmut
|
|
From: John S R. <J.S...@so...> - 2008-11-10 13:37:28
|
Hi,
I have a few simple scripts wrapped using Soaplab2. Occasionally (about in 1
in 4 invocations, but always immediately after startup, or after a period of
innactivity), I get the following exception:
AxisFault
faultCode: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException
faultSubcode:
faultString: org.xml.sax.SAXParseException: Premature end of file.
I've made my catalina.out available here:
http://kraz.omii.ac.uk/~jsr2/catalina.out
Any suggestions would be gratefully received.
Cheers,
JohnR
--
----------------------------------------
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: Sebastien M. <seb...@un...> - 2008-11-05 08:25:30
|
> Hi, > > How to use several help_URL attributes (comment: "help URL") ? > > > No, you cannot have more such attributes. If you really need it, you > would need to create a separate web page with links to other pages, and > use its URL as this attribute. Sorry. > > Martin It worked last week in Taverna, 2 links appeared. I cannot get them now. But a single help link is certainly more portable for most clients. We will do this, most of these pages already exist here. Thanks -- Sébastien Moretti Department of Ecology and Evolution, Biophore, University of Lausanne, CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4221/4056 http://bioinfo.unil.ch/ |
|
From: Martin S. <mar...@gm...> - 2008-11-03 02:14:43
|
Hi, How to use several help_URL attributes (comment: "help URL") ? No, you cannot have more such attributes. If you really need it, you would need to create a separate web page with links to other pages, and use its URL as this attribute. Sorry. Martin -- Martin Senger email: mar...@gm...,m.s...@cg... skype: martinsenger |
|
From: Sebastien M. <Seb...@un...> - 2008-10-31 14:10:14
|
Hi, How to use several help_URL attributes (comment: "help URL") ? If I use several comment: "help URL" lines, only the last one is kept in the XML file. Thanks -- Sébastien Moretti SIB EMBnet, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4056/4221 http://ch.embnet.org/ http://myhits.vital-it.ch/ |
|
From: Sebastien M. <seb...@un...> - 2008-10-27 15:18:33
|
> Hi Sebastien, > > I think I finally understood what Martin meant last Friday. > > ncoils probably reading its input from standard input and for that > reason you provide the '<' sign before the input file. In this case best > solution would probably be defining the input in such a way that Soaplab > knows this so it can feed the input file of ncoils processes using > standard input. One example definition I just tested here looks like as > follows. > > infile: input [ > default:stdin > ] > > Regards, > Mahmut It is perfect. I have not thought to stdin as default. I have just thought to recreate my command line into soaplab directly. Thanks >> Hi, >> >> I have an application which requires that input file is called with the >> < sign: >> >> ncoils -nw < infile >> >> >> It seems that < is problematic for the execution in soaplab2. >> >> How can I pass properly the < sign ? >> >> I have tried <, \< or \\< but everything fails. >> >> Thanks -- Sébastien Moretti Department of Ecology and Evolution, Biophore, University of Lausanne, CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4221/4056 http://bioinfo.unil.ch/ |
|
From: Mahmut U. <ul...@eb...> - 2008-10-27 11:17:02
|
Hi Sebastien,
I think I finally understood what Martin meant last Friday.
ncoils probably reading its input from standard input and for that
reason you provide the '<' sign before the input file. In this case best
solution would probably be defining the input in such a way that Soaplab
knows this so it can feed the input file of ncoils processes using
standard input. One example definition I just tested here looks like as
follows.
infile: input [
default:stdin
]
Regards,
Mahmut
On Fri, 2008-10-24 at 16:07 +0200, Sebastien Moretti wrote:
> Hi,
>
> I have an application which requires that input file is called with the
> < sign:
>
> ncoils -nw < infile
>
>
> It seems that < is problematic for the execution in soaplab2.
>
> How can I pass properly the < sign ?
>
> I have tried <, \< or \\< but everything fails.
>
> Thanks
>
|
|
From: Martin S. <mar...@gm...> - 2008-10-25 12:59:38
|
> I have an application which requires that input file is called with the > < sign: > > ncoils -nw < infile I am not sure that I understand the problem (but perhaps Mahmut's answer already solved this). Where should be the "<" sign? If it should be a fixed part of the command-line, followed by a name of an input file, then Mahmut's answer may be the answer. [I still wonder, however, what kind of application uses the "<" character as an ordinary character on the command-line. :-) ] Martin -- Martin Senger email: mar...@gm...,m.s...@cg... skype: martinsenger |
|
From: Sébastien M. <seb...@un...> - 2008-10-24 19:29:48
|
I will test it. Thanks >> I have an application which requires that input file is called with the >> < sign: >> >> ncoils -nw < infile >> >> >> It seems that < is problematic for the execution in soaplab2. >> >> How can I pass properly the < sign ? >> >> I have tried <, \< or \\< but everything fails. > > Not fully tested but as in the following example if I put the identifier > and the '<' sign inside escaped double quotes Soaplab Substitutor class > stops separating them from each other. > > string: text [ > additional: "Y" > default: "this is a default" > prompt: "An optional string with a default value" > comment: "method \"-text <\" $id" > ] > > Regards, > Mahmut -- Sébastien Moretti SIB EMBnet, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4056/4221 |
|
From: Mahmut U. <ul...@eb...> - 2008-10-24 16:20:34
|
> I have an application which requires that input file is called with the
> < sign:
>
> ncoils -nw < infile
>
>
> It seems that < is problematic for the execution in soaplab2.
>
> How can I pass properly the < sign ?
>
> I have tried <, \< or \\< but everything fails.
Not fully tested but as in the following example if I put the identifier
and the '<' sign inside escaped double quotes Soaplab Substitutor class
stops separating them from each other.
string: text [
additional: "Y"
default: "this is a default"
prompt: "An optional string with a default value"
comment: "method \"-text <\" $id"
]
Regards,
Mahmut
|
|
From: Sebastien M. <Seb...@un...> - 2008-10-24 14:08:09
|
Hi, I have an application which requires that input file is called with the < sign: ncoils -nw < infile It seems that < is problematic for the execution in soaplab2. How can I pass properly the < sign ? I have tried <, \< or \\< but everything fails. Thanks -- Sébastien Moretti SIB EMBnet, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4056/4221 http://ch.embnet.org/ http://myhits.vital-it.ch/ |
|
From: Mahmut U. <ul...@eb...> - 2008-10-23 14:44:42
|
> It seems to be the same case for newcoils, giep (replaced by iep) > applications too. > ACD files available but not in the PATH by default. > > And maybe jaspextract should be hidden because it is used to build the > data for jaspscan. Thanks. These 3 applications have also been disabled. It seems that for emboss we should use the wossname with -gui option to get the list of programs. Mahmut |
|
From: Mahmut U. <ul...@eb...> - 2008-10-23 14:44:27
|
> The same kind of question for seqretsplit. > > It runs completely but fails to create links to output files. > > Should it be disabled ? It is now disabled. I made a record of this as a bug (in my local notebook). It needs some work on the acd2xml parser which I'm not good in. I updated Soaplab ChaneLog file with the EMBOSS applications disabled yesterday and today based on your feedback. Regards, Mahmut |
|
From: Sebastien M. <Seb...@un...> - 2008-10-23 12:49:33
|
>> It seems that primers and prima are always enabled. >> There is no update for them via CVS. > > I forgot to check in the updated emboss.xml file but it is now in CVS. It seems to be the same case for newcoils, giep (replaced by iep) applications too. ACD files available but not in the PATH by default. And maybe jaspextract should be hidden because it is used to build the data for jaspscan. >> And it seems there is an ACD to XML problem for the density application. >> The web service uses -graph as attribute but this one doesn't exist. >> It should be qgraph or dgraph depending on selection for quad or dual >> attributes. >> >> And by default, density doesn't create graph output. >> quad and/or dual have to be used. >> >> Is it a soaplab known problem ? > > Yes. A problem dictated by the current acd2xml parser which assumes only > one graphics output named 'graph'. Alan's updated density.acd and > density.c files fixed the above problem in my local Soaplab > installation. I will update this files too. Thanks > Regards, > Mahmut Best regards, Sébastien -- Sébastien Moretti SIB EMBnet, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4056/4221 http://ch.embnet.org/ http://myhits.vital-it.ch/ |
|
From: Sebastien M. <Seb...@un...> - 2008-10-23 12:49:26
|
>> The same kind of question for seqretsplit. >> >> It runs completely but fails to create links to output files. >> >> Should it be disabled ? > > It is now disabled. I made a record of this as a bug (in my local > notebook). It needs some work on the acd2xml parser which I'm not good > in. > > I updated Soaplab ChaneLog file with the EMBOSS applications disabled > yesterday and today based on your feedback. > > Regards, > Mahmut OK, thanks -- Sébastien Moretti SIB EMBnet, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4056/4221 http://ch.embnet.org/ http://myhits.vital-it.ch/ |
|
From: Mahmut U. <ul...@eb...> - 2008-10-23 10:55:34
|
> It seems that primers and prima are always enabled. > There is no update for them via CVS. I forgot to check in the updated emboss.xml file but it is now in CVS. > And it seems there is an ACD to XML problem for the density application. > The web service uses -graph as attribute but this one doesn't exist. > It should be qgraph or dgraph depending on selection for quad or dual > attributes. > > And by default, density doesn't create graph output. > quad and/or dual have to be used. > > Is it a soaplab known problem ? Yes. A problem dictated by the current acd2xml parser which assumes only one graphics output named 'graph'. Alan's updated density.acd and density.c files fixed the above problem in my local Soaplab installation. Regards, Mahmut |
|
From: Sebastien M. <Seb...@un...> - 2008-10-23 08:53:47
|
>> primers (replaced by eprimer3 !) >> >>> + prima (replaced by eprimer3 ?) > > It looks like, they were even not in EMBOSS-2.8. > > I have disabled these two applications in Soaplab and in the EBI server > as well. > > Mahmut Thanks Mahmut It seems that primers and prima are always enabled. There is no update for them via CVS. And it seems there is an ACD to XML problem for the density application. The web service uses -graph as attribute but this one doesn't exist. It should be qgraph or dgraph depending on selection for quad or dual attributes. And by default, density doesn't create graph output. quad and/or dual have to be used. Is it a soaplab known problem ? Thanks -- Sébastien Moretti SIB EMBnet, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4056/4221 http://ch.embnet.org/ http://myhits.vital-it.ch/ |
|
From: Mahmut U. <ul...@eb...> - 2008-10-22 16:24:14
|
> primers (replaced by eprimer3 !) > > > + prima (replaced by eprimer3 ?) It looks like, they were even not in EMBOSS-2.8. I have disabled these two applications in Soaplab and in the EBI server as well. Mahmut |
|
From: Mahmut U. <ul...@eb...> - 2008-10-22 14:59:57
|
Hi Sebastien, Thank you for pointing these errors in Soaplab and the EBI Soplab server. I have disabled the 'seqretall', 'seqretset', 'seqrettype' and 'complex' programs in Soaplab CVS version and in the EBI Soaplab server. Current acd2xml routine gets the EMBOSS programs list from $emboss_home/share/EMBOSS/acd directory, an alternative is to use the EMBOSS wossname program. I made a note to check why EMBOSS copies these ACD files by default. Regards, Mahmut On Wed, 2008-10-22 at 16:04 +0200, Sebastien Moretti wrote: > Also idem for complex > > > Idem for seqrettype ! > > > > > >> P.S.: seqretallfeat is already disabled ! > >> > >> > >> Hello, > >> > >> It seems that these three software are not available by default |
|
From: Sebastien M. <Seb...@un...> - 2008-10-22 14:54:57
|
+ primers (replaced by eprimer3 !) > + prima (replaced by eprimer3 ?) > >> Also idem for complex >> >>> Idem for seqrettype ! >>> >>> >>>> P.S.: seqretallfeat is already disabled ! >>>> >>>> >>>> Hello, >>>> >>>> It seems that these three software are not available by default in >>>> EMBOSS: >>>> cf. src/ChangeLog >>>> (Since) Version 2.3.0 >>>> >>>> Seqretall, seqretallfeat and seqretset moved to 'make check'. >>>> Seqret has all the functionality of the above. >>>> >>>> >>>> You need to make a 'make check' then to copy manually these programs to >>>> your PATH because 'make install' does not seem to do this. >>>> >>>> >>>> So, ACD files for them are with the other ACD files. >>>> I mean that they become available via soaplab. >>>> But they cannot be run by default. >>>> >>>> It fails for me locally and it is the same from >>>> http://www.ebi.ac.uk/soaplab/ >>>> >>>> >>>> So, should these three programs be disabled in the xmls/emboss.xml >>>> file ? >>>> Else you should add a remark in the Soaplab documentation >>>> (EmbossNotes.html). >>>> >>>> Best regards -- Sébastien Moretti SIB EMBnet, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4056/4221 http://ch.embnet.org/ http://myhits.vital-it.ch/ |
|
From: Sebastien M. <Seb...@un...> - 2008-10-22 14:53:04
|
+ prima (replaced by eprimer3 ?) > Also idem for complex > >> Idem for seqrettype ! >> >> >>> P.S.: seqretallfeat is already disabled ! >>> >>> >>> Hello, >>> >>> It seems that these three software are not available by default in >>> EMBOSS: >>> cf. src/ChangeLog >>> (Since) Version 2.3.0 >>> >>> Seqretall, seqretallfeat and seqretset moved to 'make check'. >>> Seqret has all the functionality of the above. >>> >>> >>> You need to make a 'make check' then to copy manually these programs to >>> your PATH because 'make install' does not seem to do this. >>> >>> >>> So, ACD files for them are with the other ACD files. >>> I mean that they become available via soaplab. >>> But they cannot be run by default. >>> >>> It fails for me locally and it is the same from >>> http://www.ebi.ac.uk/soaplab/ >>> >>> >>> So, should these three programs be disabled in the xmls/emboss.xml >>> file ? >>> Else you should add a remark in the Soaplab documentation >>> (EmbossNotes.html). >>> >>> Best regards -- Sébastien Moretti SIB EMBnet, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4056/4221 http://ch.embnet.org/ http://myhits.vital-it.ch/ |
|
From: Sebastien M. <Seb...@un...> - 2008-10-22 14:05:09
|
Also idem for complex > Idem for seqrettype ! > > >> P.S.: seqretallfeat is already disabled ! >> >> >> Hello, >> >> It seems that these three software are not available by default in >> EMBOSS: >> cf. src/ChangeLog >> (Since) Version 2.3.0 >> >> Seqretall, seqretallfeat and seqretset moved to 'make check'. >> Seqret has all the functionality of the above. >> >> >> You need to make a 'make check' then to copy manually these programs to >> your PATH because 'make install' does not seem to do this. >> >> >> So, ACD files for them are with the other ACD files. >> I mean that they become available via soaplab. >> But they cannot be run by default. >> >> It fails for me locally and it is the same from >> http://www.ebi.ac.uk/soaplab/ >> >> >> So, should these three programs be disabled in the xmls/emboss.xml file ? >> Else you should add a remark in the Soaplab documentation >> (EmbossNotes.html). >> >> Best regards -- Sébastien Moretti SIB EMBnet, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4056/4221 http://ch.embnet.org/ http://myhits.vital-it.ch/ |
|
From: Sebastien M. <Seb...@un...> - 2008-10-22 12:28:08
|
Hello,
It seems that these three software are not available by default in EMBOSS:
cf. src/ChangeLog
(Since) Version 2.3.0
Seqretall, seqretallfeat and seqretset moved to 'make check'.
Seqret has all the functionality of the above.
You need to make a 'make check' then to copy manually these programs to
your PATH because 'make install' does not seem to do this.
So, ACD files for them are with the other ACD files.
I mean that they become available via soaplab.
But they cannot be run by default.
It fails for me locally and it is the same from
http://www.ebi.ac.uk/soaplab/
So, should these three programs be disabled in the xmls/emboss.xml file ?
Else you should add a remark in the Soaplab documentation
(EmbossNotes.html).
Best regards
--
Sébastien Moretti
SIB EMBnet, Quartier Sorge - Genopode
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4056/4221
http://ch.embnet.org/ http://myhits.vital-it.ch/
|
|
From: Sebastien M. <Seb...@un...> - 2008-10-22 12:28:05
|
P.S.: seqretallfeat is already disabled !
Hello,
It seems that these three software are not available by default in EMBOSS:
cf. src/ChangeLog
(Since) Version 2.3.0
Seqretall, seqretallfeat and seqretset moved to 'make check'.
Seqret has all the functionality of the above.
You need to make a 'make check' then to copy manually these programs to
your PATH because 'make install' does not seem to do this.
So, ACD files for them are with the other ACD files.
I mean that they become available via soaplab.
But they cannot be run by default.
It fails for me locally and it is the same from
http://www.ebi.ac.uk/soaplab/
So, should these three programs be disabled in the xmls/emboss.xml file ?
Else you should add a remark in the Soaplab documentation
(EmbossNotes.html).
Best regards
--
Sébastien Moretti
SIB EMBnet, Quartier Sorge - Genopode
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4056/4221
http://ch.embnet.org/ http://myhits.vital-it.ch/
|
