From bmg at sfu.ca Wed Mar 2 15:17:02 2005 From: bmg at sfu.ca (Benjamin Good) Date: Wed Mar 2 15:15:18 2005 Subject: [MOBY-l] perl example service code Message-ID: <42261F3E.6060206@sfu.ca> Would it be possible to post a complete example of a perl service that uses the new API? The example everyone still seems to be using from Ken Steube relies on some deprecated methods and produces services that don't seem to work with clients built from jMoby. (I think this is because we do not send moby:queryInput tags in the request). As people continue to find and use the old demo (despite the removal of the link) and get confused, a fresh demo would be very helpful for our beginners. Thanks -Ben From bmg at sfu.ca Wed Mar 2 16:41:41 2005 From: bmg at sfu.ca (Benjamin Good) Date: Wed Mar 2 16:38:59 2005 Subject: [MOBY-l] perl example service code In-Reply-To: <42261F3E.6060206@sfu.ca> References: <42261F3E.6060206@sfu.ca> Message-ID: <42263315.90401@sfu.ca> Scratch that, the example is there, I was just blind.. http://www.biomoby.org/twiki/bin/view/Moby/MobySByExamplePerlEdition though more wouldn't hurt! -Ben Benjamin Good wrote: > Would it be possible to post a complete example of a perl service that > uses the new API? > The example everyone still seems to be using from Ken Steube relies on > some deprecated methods and produces services that don't seem to work > with clients built from jMoby. (I think this is because we do not > send moby:queryInput tags in the request). > > As people continue to find and use the old demo (despite the removal > of the link) and get confused, a fresh demo would be very helpful for > our beginners. > > Thanks > -Ben > _______________________________________________ > moby-l mailing list > moby-l@biomoby.org > http://biomoby.org/mailman/listinfo/moby-l > > From mlangill at sfu.ca Wed Mar 2 19:06:01 2005 From: mlangill at sfu.ca (Morgan Langille) Date: Wed Mar 2 19:01:59 2005 Subject: [MOBY-l] Boolean object Message-ID: <1109808361.4212.16.camel@moosehead.mrl.ubc.ca> I was thinking that it would be nice to have a boolean moby object. It could be a sub-object of Integer (Boolean ISA Integer) that should only contain 1 (true) or 0 (false). Of course there is no way to constrain this but it seems useful to have this. Does anyone have any suggestions on if/how a boolean object should be made? Morgan Langille From tmo at ebi.ac.uk Wed Mar 2 19:16:44 2005 From: tmo at ebi.ac.uk (Tom Oinn) Date: Wed Mar 2 19:12:27 2005 Subject: [MOBY-l] Boolean object In-Reply-To: <1109808361.4212.16.camel@moosehead.mrl.ubc.ca> References: <1109808361.4212.16.camel@moosehead.mrl.ubc.ca> Message-ID: <4226576C.6030001@ebi.ac.uk> Morgan Langille wrote: > I was thinking that it would be nice to have a boolean moby object. It > could be a sub-object of Integer (Boolean ISA Integer) that should only > contain 1 (true) or 0 (false). Of course there is no way to constrain > this but it seems useful to have this. Does anyone have any suggestions > on if/how a boolean object should be made? Surely 'Boolean ISA Integer' translates to 'all operations that can consume an integer can consume a boolean' which is clearly wrong, at least from my perspective. You might implement a boolean as an enumeration but it shouldn't look like that in the ontology. I would be very surprised (as a user) if I asked what I could do with a boolean operator and got multiplication as an answer... Tom -- No virus found in this outgoing message. Checked by AVG Anti-Virus. Version: 7.0.300 / Virus Database: 266.5.1 - Release Date: 2/27/2005 From mlangill at sfu.ca Wed Mar 2 19:32:04 2005 From: mlangill at sfu.ca (Morgan Langille) Date: Wed Mar 2 19:28:06 2005 Subject: [MOBY-l] Boolean object In-Reply-To: <4226576C.6030001@ebi.ac.uk> References: <1109808361.4212.16.camel@moosehead.mrl.ubc.ca> <4226576C.6030001@ebi.ac.uk> Message-ID: <1109809924.4212.25.camel@moosehead.mrl.ubc.ca> On Wed, 2005-03-02 at 16:16, Tom Oinn wrote: > Morgan Langille wrote: > > I was thinking that it would be nice to have a boolean moby object. It > > could be a sub-object of Integer (Boolean ISA Integer) that should only > > contain 1 (true) or 0 (false). Of course there is no way to constrain > > this but it seems useful to have this. Does anyone have any suggestions > > on if/how a boolean object should be made? > > Surely 'Boolean ISA Integer' translates to 'all operations that can > consume an integer can consume a boolean' which is clearly wrong, at > least from my perspective. You might implement a boolean as an > enumeration but it shouldn't look like that in the ontology. I would be > very surprised (as a user) if I asked what I could do with a boolean > operator and got multiplication as an answer... > > Tom > You are right. So how could I make a boolean object? Here are a couple of ideas. 1) Boolean could be a primitive sub-object of Object, but that would require some major changes because the current API would not recognize Boolean as a primitive object and skip over contents of the object. OR 2) Boolean could contain an Integer or String or both (Boolean ISA Object, Boolean HASA String and/or Boolean HASA Integer) This would be a much easier solution then making a primitive Boolean object, but is not really as correct. Morgan From gordonp at ucalgary.ca Wed Mar 2 20:26:26 2005 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed Mar 2 20:21:23 2005 Subject: [MOBY-l] Boolean object In-Reply-To: <1109808361.4212.16.camel@moosehead.mrl.ubc.ca> References: <1109808361.4212.16.camel@moosehead.mrl.ubc.ca> Message-ID: <422667C2.30308@ucalgary.ca> I'd make boolean a primitive and adjust the APIs, it's really an oversight that this wasn't in there before. This is a natural progression for the Java API, as boolean is a primitive in Java. This avoids many potential headaches of boolean misuse in conditionals and arithmetic as are found in C/C++ (no dig intended, I love those languages). Morgan Langille wrote: >I was thinking that it would be nice to have a boolean moby object. It >could be a sub-object of Integer (Boolean ISA Integer) that should only >contain 1 (true) or 0 (false). Of course there is no way to constrain >this but it seems useful to have this. Does anyone have any suggestions >on if/how a boolean object should be made? > >Morgan Langille >_______________________________________________ >moby-l mailing list >moby-l@biomoby.org >http://biomoby.org/mailman/listinfo/moby-l > > > From markw at illuminae.com Wed Mar 2 20:32:52 2005 From: markw at illuminae.com (markw@illuminae.com) Date: Wed Mar 2 20:27:48 2005 Subject: [MOBY-l] Boolean object In-Reply-To: <422667C2.30308@ucalgary.ca> References: <1109808361.4212.16.camel@moosehead.mrl.ubc.ca> <422667C2.30308@ucalgary.ca> Message-ID: <1109813572.42266944a39c2@webmail.illuminae.com> Quoting Paul Gordon : > I'd make boolean a primitive and adjust the APIs, it's really an > oversight that this wasn't in there before. I agree 100%. It should be a primitive (inherit from Object)... but I don't think we need to adjust the API in any way to accomodate this. It is interesting to think what it means to have a namespace and ID on a boolean, though :-) gi|163483 = yes! M From bmg at sfu.ca Wed Mar 2 20:48:05 2005 From: bmg at sfu.ca (Benjamin Good) Date: Wed Mar 2 20:45:16 2005 Subject: [MOBY-l] Boolean object In-Reply-To: <1109813572.42266944a39c2@webmail.illuminae.com> References: <1109808361.4212.16.camel@moosehead.mrl.ubc.ca> <422667C2.30308@ucalgary.ca> <1109813572.42266944a39c2@webmail.illuminae.com> Message-ID: <42266CD5.7000107@sfu.ca> I am confused, I thought an Object was not a primitive "The value of the Object element is ignored */with the exception of/* the Classes representing primitives (e.g. Integer, Float, String, etc.; discussed in the Class Ontology section below). For example, in the following object this has no value the text "this has no value" is ignored by both client and service." For this to work it seems like we would have to officially declare Boolean as a primitive and adapt the API accordingly. Otherwise code for displaying/manipulating Objects (at least like what Eddie and I have been working on) won't work properly because it won't try to look for the text value of the new Boolean object. Neh??? -Ben markw@illuminae.com wrote: >Quoting Paul Gordon : > > > >>I'd make boolean a primitive and adjust the APIs, it's really an >>oversight that this wasn't in there before. >> >> > >I agree 100%. It should be a primitive (inherit from Object)... but I don't >think we need to adjust the API in any way to accomodate this. > >It is interesting to think what it means to have a namespace and ID on a >boolean, though :-) > >gi|163483 = yes! > > >M > > > >_______________________________________________ >moby-l mailing list >moby-l@biomoby.org >http://biomoby.org/mailman/listinfo/moby-l > > > > From markw at illuminae.com Wed Mar 2 22:01:24 2005 From: markw at illuminae.com (markw@illuminae.com) Date: Wed Mar 2 21:56:25 2005 Subject: [MOBY-l] Boolean object In-Reply-To: <42266CD5.7000107@sfu.ca> References: <1109808361.4212.16.camel@moosehead.mrl.ubc.ca> <422667C2.30308@ucalgary.ca> <1109813572.42266944a39c2@webmail.illuminae.com> <42266CD5.7000107@sfu.ca> Message-ID: <1109818884.42267e04afd35@webmail.illuminae.com> Sorry - you are right, of course. I'm multi-tasking and hadn't seen that issue in my quick think about the problem. Thanks for your clear headed advice! It wouldn't take much to update the API, I suspect. I'll think about it when I get home. Greetings from sweltering Australia! M Quoting Benjamin Good : > I am confused, I thought an Object was not a primitive > > "The value of the Object element is ignored */with the exception of/* > the Classes representing primitives (e.g. Integer, Float, String, etc.; > discussed in the Class Ontology > > section below). For example, in the following object > > this has no > value > > the text "this has no value" is ignored by both client and service." > > For this to work it seems like we would have to officially declare > Boolean as a primitive and adapt the API accordingly. Otherwise code > for displaying/manipulating Objects (at least like what Eddie and I have > been working on) won't work properly because it won't try to look for > the text value of the new Boolean object. > > Neh??? > > -Ben > > markw@illuminae.com wrote: > > >Quoting Paul Gordon : > > > > > > > >>I'd make boolean a primitive and adjust the APIs, it's really an > >>oversight that this wasn't in there before. > >> > >> > > > >I agree 100%. It should be a primitive (inherit from Object)... but I don't > >think we need to adjust the API in any way to accomodate this. > > > >It is interesting to think what it means to have a namespace and ID on a > >boolean, though :-) > > > >gi|163483 = yes! > > > > > >M > > > > > > > >_______________________________________________ > >moby-l mailing list > >moby-l@biomoby.org > >http://biomoby.org/mailman/listinfo/moby-l > > > > > > > > > > From gordonp at ucalgary.ca Thu Mar 3 11:44:39 2005 From: gordonp at ucalgary.ca (Paul Gordon) Date: Thu Mar 3 11:39:49 2005 Subject: [MOBY-l] Boolean object In-Reply-To: <1109818884.42267e04afd35@webmail.illuminae.com> References: <1109808361.4212.16.camel@moosehead.mrl.ubc.ca> <422667C2.30308@ucalgary.ca> <1109813572.42266944a39c2@webmail.illuminae.com> <42266CD5.7000107@sfu.ca> <1109818884.42267e04afd35@webmail.illuminae.com> Message-ID: <42273EF7.2060502@ucalgary.ca> May I suggest that the boolean primitive have the one of the values "true" or "false", not "0" or "1". This would alleve any confusion with integers, is more human readable, and is valid since "0" and "1" in Boolean logic are only arbitrary symbols in a lattice system (i.e. it is the union, intersection and negation functions that define the logic, not the symbols used). markw@illuminae.com wrote: >Sorry - you are right, of course. I'm multi-tasking and hadn't seen that issue >in my quick think about the problem. > >Thanks for your clear headed advice! > >It wouldn't take much to update the API, I suspect. I'll think about it when I >get home. > >Greetings from sweltering Australia! > >M > > > >Quoting Benjamin Good : > > > >>I am confused, I thought an Object was not a primitive >> >>"The value of the Object element is ignored */with the exception of/* >>the Classes representing primitives (e.g. Integer, Float, String, etc.; >>discussed in the Class Ontology >> >>section below). For example, in the following object >> >> this has no >>value >> >>the text "this has no value" is ignored by both client and service." >> >>For this to work it seems like we would have to officially declare >>Boolean as a primitive and adapt the API accordingly. Otherwise code >>for displaying/manipulating Objects (at least like what Eddie and I have >>been working on) won't work properly because it won't try to look for >>the text value of the new Boolean object. >> >>Neh??? >> >>-Ben >> >>markw@illuminae.com wrote: >> >> >> >>>Quoting Paul Gordon : >>> >>> >>> >>> >>> >>>>I'd make boolean a primitive and adjust the APIs, it's really an >>>>oversight that this wasn't in there before. >>>> >>>> >>>> >>>> >>>I agree 100%. It should be a primitive (inherit from Object)... but I don't >>>think we need to adjust the API in any way to accomodate this. >>> >>>It is interesting to think what it means to have a namespace and ID on a >>>boolean, though :-) >>> >>>gi|163483 = yes! >>> >>> >>>M >>> >>> >>> >>>_______________________________________________ >>>moby-l mailing list >>>moby-l@biomoby.org >>>http://biomoby.org/mailman/listinfo/moby-l >>> >>> >>> >>> >>> >>> >> >> > > > > > From gss at ncgr.org Thu Mar 3 12:58:09 2005 From: gss at ncgr.org (Gary Schiltz) Date: Thu Mar 3 12:52:56 2005 Subject: [MOBY-l] Boolean object In-Reply-To: <42273EF7.2060502@ucalgary.ca> References: <1109808361.4212.16.camel@moosehead.mrl.ubc.ca> <422667C2.30308@ucalgary.ca> <1109813572.42266944a39c2@webmail.illuminae.com> <42266CD5.7000107@sfu.ca> <1109818884.42267e04afd35@webmail.illuminae.com> <42273EF7.2060502@ucalgary.ca> Message-ID: <42275031.2010402@ncgr.org> I think I'm in Paul's camp here, although I notice that the W3C recommendation on XML Schema allows true, false, 1, and 0 as valid lexical values for booleans (see www.w3.org/TR/xmlschema-2/#boolean). But then, they say that the "canonical representation" for booleans is true and false. I am still confused as to the difference between the lexical and canonical representations. // Gary Paul Gordon wrote: > May I suggest that the boolean primitive have the one of the values > "true" or "false", not "0" or "1". This would alleve any confusion > with integers, is more human readable, and is valid since "0" and "1" > in Boolean logic are only arbitrary symbols in a lattice system (i.e. > it is the union, intersection and negation functions that define the > logic, not the symbols used). From gordonp at ucalgary.ca Thu Mar 3 14:31:48 2005 From: gordonp at ucalgary.ca (Paul Gordon) Date: Thu Mar 3 14:27:00 2005 Subject: [MOBY-l] Boolean object In-Reply-To: <42275031.2010402@ncgr.org> References: <1109808361.4212.16.camel@moosehead.mrl.ubc.ca> <422667C2.30308@ucalgary.ca> <1109813572.42266944a39c2@webmail.illuminae.com> <42266CD5.7000107@sfu.ca> <1109818884.42267e04afd35@webmail.illuminae.com> <42273EF7.2060502@ucalgary.ca> <42275031.2010402@ncgr.org> Message-ID: <42276624.70104@ucalgary.ca> Wikipedia to the rescue! :-) http://en.wikipedia.org/wiki/Canonical#Computer_science In CS, "canonical" is more like "best-practice convention" than canonical in the religous or mathematical sense. "true" and "false" are "best-practice" lexical representations for booleans. Of course, since MOBY's lexical and semantic rules stand alone (though they could be *expressed* in XMLSchema, DTDs, Relax-NG, etc.), there is no requirement to allow 0 and 1 as valid values. I realize that I'm being pedantic, but I think that giving people choices on how to express such a simple notion brings unneeded (albeit minor) complexity to the API. My $0.02 :-) P.S. One advatange of 0/1 is that it is not specific to English. But given that the entire MOBY API is in English anyway... Gary Schiltz wrote: > I think I'm in Paul's camp here, although I notice that the W3C > recommendation on XML Schema allows true, false, 1, and 0 as valid > lexical values for booleans (see www.w3.org/TR/xmlschema-2/#boolean). > But then, they say that the "canonical representation" for booleans is > true and false. I am still confused as to the difference between the > lexical and canonical representations. > > // Gary > > Paul Gordon wrote: > >> May I suggest that the boolean primitive have the one of the values >> "true" or "false", not "0" or "1". This would alleve any confusion >> with integers, is more human readable, and is valid since "0" and "1" >> in Boolean logic are only arbitrary symbols in a lattice system (i.e. >> it is the union, intersection and negation functions that define the >> logic, not the symbols used). > > > _______________________________________________ > moby-l mailing list > moby-l@biomoby.org > http://biomoby.org/mailman/listinfo/moby-l > From Pieter.Neerincx at wur.nl Mon Mar 7 06:48:14 2005 From: Pieter.Neerincx at wur.nl (Neerincx, Pieter) Date: Mon Mar 7 06:42:55 2005 Subject: [MOBY-l] Perl API: conversion of node content to and from XML Message-ID: <5F9035D8A446C84C903301CCD5FC8DB43F786E@salte0010.wurnet.nl> Hi all, I'm pretty new to BioMOBY and have a question about the Perl API. I have some problems with extracting text data from objects like for example the String object. I have something like this: some text & more text The plain text contains for example "&" which has a special meaning in XML. Therefore I have to encode it using "&". If I use the getNodeContentWithArticle sub from CommonSubs.pm it serializes the data resulting in raw XML. Hence the result contains the "&" still encoded as "&". The same thing happens with encoded quotes. If I would be using the extractRawContent sub that would make sense to me. Off course I can convert the encoded stuff from and to raw XML manually, but wouldn't it be nicer if the API would take care of that? Or am I missing something here and is there a good reason the have for example the getNodeContentWithArticle sub return raw XML? If I change the code like this: sub getNodeContentWithArticle { ### lot's of other stuff ... ### # Using ->toString results in raw XML and will # not map encoded chars like '&' back to '&'. # Fetching node content using -> data will. #$resp .= $_->toString; $resp .= $_->data; ### lot's of other stuff ... ### } decoding the raw XML is taken care of by the API. Any feedback would be appriciated. Regards, Pieter Neerincx From mwilkinson at mrl.ubc.ca Mon Mar 7 12:40:04 2005 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Mon Mar 7 11:31:26 2005 Subject: [MOBY-l] Registration for the May 7/8 BioMOBY meeting in Vancouver Message-ID: <1110217204.3898.418.camel@mobycentral.icapture.ubc.ca> Hi all, I've set up a CGI form for registration. Please submit your registration ASAP so that I can complete the budget for the meeting. I will be doing my best to supplement your room and food from my grant so that your travel will be the primary expense to you. http://biomoby.org/cgi-bin/register.cgi Cheers! See you all in Vancouver! Mark -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From mwilkinson at mrl.ubc.ca Mon Mar 7 23:38:25 2005 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Mon Mar 7 23:32:38 2005 Subject: [moby] [MOBY-l] Perl API: conversion of node content to and from XML In-Reply-To: <5F9035D8A446C84C903301CCD5FC8DB43F786E@salte0010.wurnet.nl> References: <5F9035D8A446C84C903301CCD5FC8DB43F786E@salte0010.wurnet.nl> Message-ID: <1110256704.6742.14.camel@mobycentral.icapture.ubc.ca> Thanks for the fix! It is now committed to the CVS - let me know if it still causes problems. Cheers! M On Mon, 2005-03-07 at 03:48, Neerincx, Pieter wrote: > Hi all, > > I'm pretty new to BioMOBY and have a question about the Perl API. I have some problems with extracting text data from objects like for example the String object. I have something like this: > > some text & more text > > The plain text contains for example "&" which has a special meaning in XML. Therefore I have to encode it using "&". If I use the getNodeContentWithArticle sub from CommonSubs.pm it serializes the data resulting in raw XML. Hence the result contains the "&" still encoded as "&". The same thing happens with encoded quotes. If I would be using the extractRawContent sub that would make sense to me. Off course I can convert the encoded stuff from and to raw XML manually, but wouldn't it be nicer if the API would take care of that? Or am I missing something here and is there a good reason the have for example the getNodeContentWithArticle sub return raw XML? > > If I change the code like this: > > sub getNodeContentWithArticle { > > ### lot's of other stuff ... ### > > # Using ->toString results in raw XML and will > # not map encoded chars like '&' back to '&'. > # Fetching node content using -> data will. > #$resp .= $_->toString; > $resp .= $_->data; > > ### lot's of other stuff ... ### > > } > > decoding the raw XML is taken care of by the API. Any feedback would be appriciated. > > Regards, > > Pieter Neerincx > > _______________________________________________ > moby-l mailing list > moby-l@biomoby.org > http://biomoby.org/mailman/listinfo/moby-l -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From ismael at lcc.uma.es Fri Mar 11 03:54:54 2005 From: ismael at lcc.uma.es (Ismael Navas) Date: Fri Mar 11 03:49:35 2005 Subject: [MOBY-l] Taverna Parser Message-ID: <20050311085147.4D46138CE8@sol10.lcc.uma.es> Hello, I'm working with the parser for Taverna from Java, and I've obtained a object of the Processor class that access to a BioMOBY service, but I don't know how to access to several values of this Processor (mobyEndpoint,serviceName and authorityName) that are into the element biomobywsdl. Do somebody know how to access from Java to these elements? Thanks in advance, Ismael Navas. From senger at ebi.ac.uk Fri Mar 11 04:04:47 2005 From: senger at ebi.ac.uk (Martin Senger) Date: Fri Mar 11 04:09:20 2005 Subject: [MOBY-l] Taverna Parser In-Reply-To: <20050311085147.4D46138CE8@sol10.lcc.uma.es> Message-ID: Hi, > I'm working with the parser for Taverna from Java > Could you clarify please what parser you are referring to? Do you mean the part of Taverna (the BioMoby plug-in in Taverna code), or some outside-Taverna parser? Thanks, Martin -- Martin Senger EMBL Outstation - Hinxton Senger@EBI.ac.uk 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 mark.fiers at wur.nl Fri Mar 11 03:00:38 2005 From: mark.fiers at wur.nl (Mark Fiers) Date: Fri Mar 11 10:16:56 2005 Subject: [MOBY-l] a (fixed?) problem with biomoby python Message-ID: <42315026.40905@wur.nl> LS We've ran into some problems with the latest biomoby python version from cvs. executing this script: ########################################################################## from bioMoby import * m = MobyMarshaller() um = MobyUnmarshaller() g = BasicGFFSequenceFeature.MobyBasicGFFSequenceFeature( id='2', Reference='SEQa', Source='pipeline', Method='something', Start=1, Stop=44, Strand='-', Frame='3', Score=33.3, articleName='Gene', Column9_tag_value=[ Multi_key_value_pair.MobyMulti_key_value_pair( articleName="Column9_tag_value", Key='mobytstings', Value=['1','2','3']) ]) mo = m.dumps(MobyContent({'test' : [g]})) print mo.replace('<',"\n<") m2 = um.loads(mo) print str(m2).replace('<',"\n<") ########################################################################## returns a biomoby string with all features I entered, but all of these are empty. Upon looking at the source code, it appears that the features are not parsed out because of a case mismatch. The xml contains, for example,: 33.3 but the from_moby function looks for a float with the name "score". If I change this in the function, everything works again. I had to change it also for the Multi_key_value_pair, but the GenericSequence was working ok. Attached are the fixed BasicGFFSequenceFeature and Multi_key_value_pair. but there are many more in the ontology which are broken. Or is there a more generic way in which this can be fixed? Cheers Mark Fiers From tmo at ebi.ac.uk Fri Mar 11 17:47:20 2005 From: tmo at ebi.ac.uk (Tom Oinn) Date: Fri Mar 11 17:41:51 2005 Subject: [MOBY-l] Taverna Parser In-Reply-To: References: Message-ID: <42321FF8.9080105@ebi.ac.uk> Martin Senger wrote: > Hi, > >>I'm working with the parser for Taverna from Java >> > > Could you clarify please what parser you are referring to? Do you mean > the part of Taverna (the BioMoby plug-in in Taverna code), or some > outside-Taverna parser? Ismael - I believe you're working with the BiomobyProcessor class in Taverna? If so there are get and set methods for these properties, you should be able to see the source here : http://cvs.sourceforge.net/viewcvs.py/taverna/taverna1.0/src/org/embl/ebi/escience/scuflworkers/biomoby/BiomobyProcessor.java?rev=1.13&view=markup If that isn't enough I'm sure Martin can answer any further questions as this is his code :) Cheers, Tom From mwilkinson at mrl.ubc.ca Tue Mar 15 19:09:37 2005 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Tue Mar 15 19:02:32 2005 Subject: [MOBY-l] REGISATRATION CALL #2 MOBY-DIC meeting Message-ID: <1110931777.3201.18.camel@mobycentral.icapture.ubc.ca> Hi all, Just re-pinging everyone who wants to come to Vancouver for the MOBY DIC meeting in May (7/8). PLEASE REGISTER AS SOON AS POSSIBLE at: http://www.biomoby.org/cgi-bin/register.cgi I am pretty sure now that I will be able to cover 100% of your housing costs, and probably some of the meal costs as well. I'm still working out the final budget, but I do need to know how many people are coming before I can come up with the final number. My current guesstimate is that the registration fees (to cover your room for up to three nights, and breakfast + lunch on the two meeting days) will be about CAD$200. I will try to bring that even lower if I can! Cheers! Mark -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From p.lord at cs.man.ac.uk Tue Mar 22 09:45:12 2005 From: p.lord at cs.man.ac.uk (Phillip Lord) Date: Tue Mar 22 09:41:52 2005 Subject: [MOBY-l] Re: Ant tasks (was: [MOBY-dev] Java packages conversation) In-Reply-To: References: Message-ID: >>>>> "Martin" == Martin Senger writes: Martin> I have not find a way how to pass to an Ant target Martin> parameters from the Ant's command-line (let me know please Martin> if anybody knows how to do it). You can set ant properties using -D properties as command line arguments to the JVM. I normally use properties files like so... myself. Cheers Phil From senger at ebi.ac.uk Tue Mar 22 10:09:03 2005 From: senger at ebi.ac.uk (Martin Senger) Date: Tue Mar 22 10:05:03 2005 Subject: [MOBY-l] Re: Ant tasks (was: [MOBY-dev] Java packages conversation) In-Reply-To: Message-ID: > You can set ant properties using -D properties as command line > arguments to the JVM. > That's what I used in my example - but as an inconvenient way (and unfortunately the only one, I still think). What I was asking about is the (non-existent, I think) possibility to say, e.g.: ant my_target - -my param1 -your param2 Martin -- Martin Senger EMBL Outstation - Hinxton Senger@EBI.ac.uk 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 p.lord at cs.man.ac.uk Tue Mar 22 10:20:44 2005 From: p.lord at cs.man.ac.uk (Phillip Lord) Date: Tue Mar 22 10:19:17 2005 Subject: [MOBY-l] Re: Ant tasks (was: [MOBY-dev] Java packages conversation) In-Reply-To: References: Message-ID: >>>>> "Martin" == Martin Senger writes: >> You can set ant properties using -D properties as command line >> arguments to the JVM. >> Martin> That's what I used in my example Yes, I realised that after I sent it, when I read your second email. Martin> but as an inconvenient way (and unfortunately the only one, Martin> I still think). What I was asking about is the Martin> (non-existent, I think) possibility to say, e.g.: Martin> ant my_target - -my param1 -your param2 Only with a wrapper script as far as I know. More of a pain than it's worth. You could try popping up a fill in gui... Phil From p.lord at cs.man.ac.uk Tue Mar 22 10:19:26 2005 From: p.lord at cs.man.ac.uk (Phillip Lord) Date: Tue Mar 22 10:22:26 2005 Subject: [MOBY-l] Re: Ant tasks (was: [MOBY-dev] Java packages conversation) In-Reply-To: References: Message-ID: -- Phillip Lord, Phone: +44 (0) 161 275 0683 PostDoctoral Research Associate, Email: p.lord@cs.man.ac.uk (preferred) School of Computer Science : p.lord@russet.org.uk Kilburn Building http://www.cs.man.ac.uk/~phillord University of Manchester http://www.russet.org.uk Oxford Road Manchester M13 9PL From senger at ebi.ac.uk Tue Mar 22 11:15:51 2005 From: senger at ebi.ac.uk (Martin Senger) Date: Tue Mar 22 11:11:20 2005 Subject: [MOBY-l] Re: Ant tasks (was: [MOBY-dev] Java packagesconversation) In-Reply-To: <200503221529.j2MFTXF07870@mail.lion-ag.de> Message-ID: > Maybe I miss something, but I think there is not much difference of > "ant my_target - -my param1 -your param2" to "ant my_target > -Dproperty=value" and then to reference it as ${property} in your ANT > script. > I think it is, that's all :-) Martin -- Martin Senger EMBL Outstation - Hinxton Senger@EBI.ac.uk 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 mwilkinson at mrl.ubc.ca Wed Mar 23 11:05:45 2005 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Wed Mar 23 10:58:20 2005 Subject: [MOBY-l] mobycentral revived Message-ID: <1111593945.22484.18.camel@mobycentral.icapture.ubc.ca> Hi all, sorry about that - I was in post-surgery with my cat when it went down and I never got back on-line until this AM. MOBY Central is a bit flaky at the moment, and we can't figure out why. It is a rather sudden flakyness that doesn't seem to correspond to any particular change we have made. The Apache error logs fill up with segfaults within a couple of hours and that crashes the system as the amount of available memory goes to zero. MySQL seems to be having a similar problem (it was mysql that had crashed last night). This all seems to point to a physical memory error, but we can't detect one... It may be time to get a new machine for MOBY :-) Anyway, I'll keep an eye on it throughout the day. I have turned apache's error logging to "critical" to reduce teh number of error messages, so hopefully we'll have longer availability between crashes. Sorry about this! M -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From mwilkinson at mrl.ubc.ca Wed Mar 23 11:53:44 2005 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Wed Mar 23 11:44:29 2005 Subject: [MOBY-l] recompiling Apache Message-ID: <1111596824.22717.28.camel@mobycentral.icapture.ubc.ca> Hi everyone, I've just found a posting that suggests that there is a conflict between expat and apache. Expat is the XML parser that I believe is part of libxml2 which is what is used by XML::LibXML - the new libraries that are doing the XML parsing for MOBY Central. I will need to recompile Apache to fix this problem (if it is the problem...), so you might notice mobycentral going up and down over the next 48 hours as I play with it, but I will try to limit my testing to the test instance of the server so that it doesn't disturb anyone too badly. Sorry for the flakyness! M (this doesn't explain the crash of mysql... but it might just have been a coincidence...) -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From mwilkinson at mrl.ubc.ca Wed Mar 23 15:43:07 2005 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Wed Mar 23 15:34:11 2005 Subject: [MOBY-l] Cut-off for MOBY-DIC registration: March 31, 2005. Message-ID: <1111610587.24448.12.camel@mobycentral.icapture.ubc.ca> Hi all, Particularly pinging the S-MOBY crew, the CSHL crew, the Brisbane crew, and anyone from myGrid or GO who wants to spend a few days away from the dull Manchester/Hinxton rain lapping up the sun in Lotus Land :-) If you have not registered yet, go to: http://biomoby.org/cgi-bin/register.cgi In order to make a budget and book the catering I have to set a cut-off date for the MOBY DIC meeting registration. March 31st will be the last date for attendees who want to take advantage of the substantially discounted registration supplement from my Genome Canada grant, after which you will be responsible for paying your own room and board. So... if you haven't already registered... get on y'r horse! :-) If you aren't sure if you have registered, go to http://biomoby.org/regisrations.txt I will make the final budget on the 1st of April and then will be able to let you know exactly what the registration fees will be (including 3 nights and breakfast/lunch and coffee breaks for the the meeting days). I'm still expecting this to be under $200, probably well under that number. Cheers all! M -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From senger at ebi.ac.uk Wed Mar 23 19:09:24 2005 From: senger at ebi.ac.uk (Martin Senger) Date: Wed Mar 23 19:05:52 2005 Subject: [MOBY-l] Re: [MOBY-dev] recompiling Apache In-Reply-To: <1111596824.22717.28.camel@mobycentral.icapture.ubc.ca> Message-ID: > I've just found a posting that suggests that there is a conflict between > expat and apache. Expat is the XML parser that I believe is part of > libxml2 > FYI, I do not know about libxml12 but I know that Expat is a base part for XML::Parser. I wish you luck with finding the cause of problems. Martin -- Martin Senger EMBL Outstation - Hinxton Senger@EBI.ac.uk 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 markw at illuminae.com Wed Mar 23 21:40:40 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Wed Mar 23 21:34:55 2005 Subject: [MOBY-l] Re: [MOBY-dev] recompiling Apache In-Reply-To: References: Message-ID: <424228A8.5040507@illuminae.com> It seems to have settled down a bit now. All I did was install a newer version of DBI! There's still a segfault in the error log that happened some time in the past 6 hours, but that is better than the several dozen per hour that were happening a few days ago :-) I'll keep an eye on it, but for now it seems somewhat stable (touch wood!) M Martin Senger wrote: >>I've just found a posting that suggests that there is a conflict between >>expat and apache. Expat is the XML parser that I believe is part of >>libxml2 >> >> >> > FYI, I do not know about libxml12 but I know that Expat is a base part >for XML::Parser. > > I wish you luck with finding the cause of problems. > Martin > > > From ismael at lcc.uma.es Mon Mar 28 09:07:52 2005 From: ismael at lcc.uma.es (Ismael Navas) Date: Mon Mar 28 09:03:38 2005 Subject: [MOBY-l] Taverna Parser In-Reply-To: Message-ID: <20050328140430.59EF838CE8@sol10.lcc.uma.es> Hello, I've Developer a tool that makes use of the Taverna parser, in order to read and use Taverna workflows, and this tool runs correctly in windows. However, when I've tried to run it in Linux, it doesn't work. First I had problems with the classpath, so I've changed ';' for ':' in classpath definition, but now I obtain this error: java -classpath .:./lib/mysql-connector-java-3.0.10-stable-bin.jar:./lib/taverna-1.0.jar:./l ib/dom4j-1.5.jar:./lib/log4j-1.2.8.jar:./lib/martj.jar:./lib/jmoby.jar:./lib /axis-nightly-11.01.05.jar:./lib/jaxrpc-nightly-11.01.05.jar:./lib/commons-l ogging-1.0.4.jar:./lib/commons-discovery-0.2.jar:./lib/saaj-nightly-11.01.05 .jar:./lib/jdom-1.0.jar TavernaINB.LoadWorkflow 91 HomologySearchAndPhylogeneticStudy.xml java.lang.NoClassDefFoundError at org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread.run(XScuflParser.ja va:438) java.lang.NoClassDefFoundError at org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread.run(XScuflParser.ja va:438) java.lang.NoClassDefFoundError at org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread.run(XScuflParser.ja va:438) java.lang.InternalError: Can't connect to X11 window server using ':0.0' as the value of the DISPLAY variable. at sun.awt.X11GraphicsEnvironment.initDisplay(Native Method) at sun.awt.X11GraphicsEnvironment.(X11GraphicsEnvironment.java:134) at java.lang.Class.forName0(Native Method) at java.lang.Class.forName(Class.java:141) at java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment(GraphicsEnvironment .java:62) at sun.awt.motif.MToolkit.(MToolkit.java:81) at java.lang.Class.forName0(Native Method) at java.lang.Class.forName(Class.java:141) at java.awt.Toolkit$2.run(Toolkit.java:748) at java.security.AccessController.doPrivileged(Native Method) at java.awt.Toolkit.getDefaultToolkit(Toolkit.java:739) at javax.swing.ImageIcon.(ImageIcon.java:119) at javax.swing.ImageIcon.(ImageIcon.java:138) at org.embl.ebi.escience.scuflworkers.ProcessorHelper.(ProcessorHelper. java:85) at org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread.run(XScuflParser.ja va:438) java.lang.NoClassDefFoundError at org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread.run(XScuflParser.ja va:438) org.embl.ebi.escience.scufl.UnknownProcessorException: Unable to locate processor with name 'Create_moby_data' at org.embl.ebi.escience.scufl.ScuflModel.locateProcessor(ScuflModel.java:528) at org.embl.ebi.escience.scufl.ScuflModel.locatePortOrCreate(ScuflModel.java:49 9) at org.embl.ebi.escience.scufl.DataConstraint.(DataConstraint.java:32) at org.embl.ebi.escience.scufl.parser.XScuflParser.populate(XScuflParser.java:3 61) at org.embl.ebi.escience.scufl.parser.XScuflParser.populate(XScuflParser.java:1 47) at TavernaINB.LoadWorkflow.loadWorkflow(LoadWorkflow.java:194) at TavernaINB.LoadWorkflow.load(LoadWorkflow.java:437) at TavernaINB.LoadWorkflow.main(LoadWorkflow.java:471) Could somebody help me? Thanks, Ismael Navas -----Mensaje original----- De: Martin Senger [mailto:senger@ebi.ac.uk] Enviado el: viernes, 11 de marzo de 2005 10:05 Para: Ismael Navas CC: moby-l@biomoby.org Asunto: Re: [MOBY-l] Taverna Parser Hi, > I'm working with the parser for Taverna from Java > Could you clarify please what parser you are referring to? Do you mean the part of Taverna (the BioMoby plug-in in Taverna code), or some outside-Taverna parser? Thanks, Martin -- Martin Senger EMBL Outstation - Hinxton Senger@EBI.ac.uk 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 tmo at ebi.ac.uk Mon Mar 28 09:31:16 2005 From: tmo at ebi.ac.uk (Tom Oinn) Date: Mon Mar 28 09:26:02 2005 Subject: [MOBY-l] Taverna Parser In-Reply-To: <20050328140430.59EF838CE8@sol10.lcc.uma.es> References: <20050328140430.59EF838CE8@sol10.lcc.uma.es> Message-ID: <42481534.3070908@ebi.ac.uk> Ismael, This is a standard problem with running Java on a machine with no display configured - when Java creates a Graphics context (such as when loading an icon image, which is where I think the problem is occuring) it attempts to connect to an X server on unix like platforms. There are several generic workarounds. 1) Use a more recent version of java - they fixed this a while back, you might be using quite an old version? 2) Use something like the XVFB device, produces a virtual frame buffer which Java can then connect to to get font metrics etc. A search for 'headless java' will produce more information, I don't know any more detail than this though. Cheers, Tom Ismael Navas wrote: > Hello, > > I've Developer a tool that makes use of the Taverna parser, in order to read > and use Taverna workflows, and this tool runs correctly in windows. However, > when I've tried to run it in Linux, it doesn't work. First I had problems > with the classpath, so I've changed ';' for ':' in classpath definition, but > now I obtain this error: > > java -classpath > .:./lib/mysql-connector-java-3.0.10-stable-bin.jar:./lib/taverna-1.0.jar:./l > ib/dom4j-1.5.jar:./lib/log4j-1.2.8.jar:./lib/martj.jar:./lib/jmoby.jar:./lib > /axis-nightly-11.01.05.jar:./lib/jaxrpc-nightly-11.01.05.jar:./lib/commons-l > ogging-1.0.4.jar:./lib/commons-discovery-0.2.jar:./lib/saaj-nightly-11.01.05 > .jar:./lib/jdom-1.0.jar TavernaINB.LoadWorkflow 91 > HomologySearchAndPhylogeneticStudy.xml > java.lang.NoClassDefFoundError > at > org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread.run(XScuflParser.ja > va:438) > java.lang.NoClassDefFoundError > at > org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread.run(XScuflParser.ja > va:438) > java.lang.NoClassDefFoundError > at > org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread.run(XScuflParser.ja > va:438) > java.lang.InternalError: Can't connect to X11 window server using ':0.0' as > the value of the DISPLAY variable. > at sun.awt.X11GraphicsEnvironment.initDisplay(Native Method) > at > sun.awt.X11GraphicsEnvironment.(X11GraphicsEnvironment.java:134) > at java.lang.Class.forName0(Native Method) > at java.lang.Class.forName(Class.java:141) > at > java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment(GraphicsEnvironment > .java:62) > at sun.awt.motif.MToolkit.(MToolkit.java:81) > at java.lang.Class.forName0(Native Method) > at java.lang.Class.forName(Class.java:141) > at java.awt.Toolkit$2.run(Toolkit.java:748) > at java.security.AccessController.doPrivileged(Native Method) > at java.awt.Toolkit.getDefaultToolkit(Toolkit.java:739) > at javax.swing.ImageIcon.(ImageIcon.java:119) > at javax.swing.ImageIcon.(ImageIcon.java:138) > at > org.embl.ebi.escience.scuflworkers.ProcessorHelper.(ProcessorHelper. > java:85) > at > org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread.run(XScuflParser.ja > va:438) > java.lang.NoClassDefFoundError > at > org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread.run(XScuflParser.ja > va:438) > org.embl.ebi.escience.scufl.UnknownProcessorException: Unable to locate > processor with name 'Create_moby_data' > at > org.embl.ebi.escience.scufl.ScuflModel.locateProcessor(ScuflModel.java:528) > at > org.embl.ebi.escience.scufl.ScuflModel.locatePortOrCreate(ScuflModel.java:49 > 9) > at > org.embl.ebi.escience.scufl.DataConstraint.(DataConstraint.java:32) > at > org.embl.ebi.escience.scufl.parser.XScuflParser.populate(XScuflParser.java:3 > 61) > at > org.embl.ebi.escience.scufl.parser.XScuflParser.populate(XScuflParser.java:1 > 47) > at TavernaINB.LoadWorkflow.loadWorkflow(LoadWorkflow.java:194) > at TavernaINB.LoadWorkflow.load(LoadWorkflow.java:437) > at TavernaINB.LoadWorkflow.main(LoadWorkflow.java:471) > > Could somebody help me? > > Thanks, > Ismael Navas > > > -----Mensaje original----- > De: Martin Senger [mailto:senger@ebi.ac.uk] > Enviado el: viernes, 11 de marzo de 2005 10:05 > Para: Ismael Navas > CC: moby-l@biomoby.org > Asunto: Re: [MOBY-l] Taverna Parser > > Hi, > >>I'm working with the parser for Taverna from Java >> > > Could you clarify please what parser you are referring to? Do you mean > the part of Taverna (the BioMoby plug-in in Taverna code), or some > outside-Taverna parser? > > Thanks, > Martin > From jmfernandez at cnb.uam.es Mon Mar 28 08:51:32 2005 From: jmfernandez at cnb.uam.es (=?ISO-8859-1?Q?Jos=E9_Mar=EDa_Fern=E1ndez_Gonz=E1lez?=) Date: Mon Mar 28 09:47:08 2005 Subject: [MOBY-l] Taverna Parser In-Reply-To: <42481534.3070908@ebi.ac.uk> References: <20050328140430.59EF838CE8@sol10.lcc.uma.es> <42481534.3070908@ebi.ac.uk> Message-ID: <42480BE4.3060308@cnb.uam.es> Hi everybody, the easiest way to run java 1.4.x in a headless environment is using the system property java.awt.headless: java -Djava.awt.headless=true ... Best regards, Jos? Mar?a Tom Oinn wrote: > Ismael, > > This is a standard problem with running Java on a machine with no > display configured - when Java creates a Graphics context (such as when > loading an icon image, which is where I think the problem is occuring) > it attempts to connect to an X server on unix like platforms. There are > several generic workarounds. > > 1) Use a more recent version of java - they fixed this a while back, you > might be using quite an old version? > > 2) Use something like the XVFB device, produces a virtual frame buffer > which Java can then connect to to get font metrics etc. > > A search for 'headless java' will produce more information, I don't know > any more detail than this though. > > Cheers, > > Tom > > Ismael Navas wrote: > >> Hello, >> >> I've Developer a tool that makes use of the Taverna parser, in order >> to read >> and use Taverna workflows, and this tool runs correctly in windows. >> However, >> when I've tried to run it in Linux, it doesn't work. First I had problems >> with the classpath, so I've changed ';' for ':' in classpath >> definition, but >> now I obtain this error: >> >> java -classpath >> .:./lib/mysql-connector-java-3.0.10-stable-bin.jar:./lib/taverna-1.0.jar:./l >> >> ib/dom4j-1.5.jar:./lib/log4j-1.2.8.jar:./lib/martj.jar:./lib/jmoby.jar:./lib >> >> /axis-nightly-11.01.05.jar:./lib/jaxrpc-nightly-11.01.05.jar:./lib/commons-l >> >> ogging-1.0.4.jar:./lib/commons-discovery-0.2.jar:./lib/saaj-nightly-11.01.05 >> >> .jar:./lib/jdom-1.0.jar TavernaINB.LoadWorkflow 91 >> HomologySearchAndPhylogeneticStudy.xml java.lang.NoClassDefFoundError >> at >> org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread.run(XScuflParser.ja >> >> va:438) >> java.lang.NoClassDefFoundError >> at >> org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread.run(XScuflParser.ja >> >> va:438) >> java.lang.NoClassDefFoundError >> at >> org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread.run(XScuflParser.ja >> >> va:438) >> java.lang.InternalError: Can't connect to X11 window server using >> ':0.0' as >> the value of the DISPLAY variable. >> at sun.awt.X11GraphicsEnvironment.initDisplay(Native Method) >> at >> sun.awt.X11GraphicsEnvironment.(X11GraphicsEnvironment.java:134) >> at java.lang.Class.forName0(Native Method) >> at java.lang.Class.forName(Class.java:141) >> at >> java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment(GraphicsEnvironment >> >> .java:62) >> at sun.awt.motif.MToolkit.(MToolkit.java:81) >> at java.lang.Class.forName0(Native Method) >> at java.lang.Class.forName(Class.java:141) >> at java.awt.Toolkit$2.run(Toolkit.java:748) >> at java.security.AccessController.doPrivileged(Native Method) >> at java.awt.Toolkit.getDefaultToolkit(Toolkit.java:739) >> at javax.swing.ImageIcon.(ImageIcon.java:119) >> at javax.swing.ImageIcon.(ImageIcon.java:138) >> at >> org.embl.ebi.escience.scuflworkers.ProcessorHelper.(ProcessorHelper. >> >> java:85) >> at >> org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread.run(XScuflParser.ja >> >> va:438) >> java.lang.NoClassDefFoundError >> at >> org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread.run(XScuflParser.ja >> >> va:438) >> org.embl.ebi.escience.scufl.UnknownProcessorException: Unable to locate >> processor with name 'Create_moby_data' >> at >> org.embl.ebi.escience.scufl.ScuflModel.locateProcessor(ScuflModel.java:528) >> >> at >> org.embl.ebi.escience.scufl.ScuflModel.locatePortOrCreate(ScuflModel.java:49 >> >> 9) >> at >> org.embl.ebi.escience.scufl.DataConstraint.(DataConstraint.java:32) >> at >> org.embl.ebi.escience.scufl.parser.XScuflParser.populate(XScuflParser.java:3 >> >> 61) >> at >> org.embl.ebi.escience.scufl.parser.XScuflParser.populate(XScuflParser.java:1 >> >> 47) >> at TavernaINB.LoadWorkflow.loadWorkflow(LoadWorkflow.java:194) >> at TavernaINB.LoadWorkflow.load(LoadWorkflow.java:437) >> at TavernaINB.LoadWorkflow.main(LoadWorkflow.java:471) >> >> Could somebody help me? >> >> Thanks, >> Ismael Navas >> >> >> -----Mensaje original----- >> De: Martin Senger [mailto:senger@ebi.ac.uk] Enviado el: viernes, 11 de >> marzo de 2005 10:05 >> Para: Ismael Navas >> CC: moby-l@biomoby.org >> Asunto: Re: [MOBY-l] Taverna Parser >> >> Hi, >> >>> I'm working with the parser for Taverna from Java >>> >> >> Could you clarify please what parser you are referring to? Do you mean >> the part of Taverna (the BioMoby plug-in in Taverna code), or some >> outside-Taverna parser? >> >> Thanks, >> Martin >> > > _______________________________________________ > moby-l mailing list > moby-l@biomoby.org > http://biomoby.org/mailman/listinfo/moby-l > > -- Jos? Mar?a Fern?ndez Gonz?lez e-mail: jmfernandez@cnb.uam.es Tlfn: (+34) 91 585 54 50 Fax: (+34) 91 585 45 06 Grupo de Dise?o de Proteinas Protein Design Group Centro Nacional de Biotecnolog?a National Center of Biotechnology C.P.: 28049 Zip Code: 28049 C/. Darwin n? 3 (Campus Cantoblanco, U. Aut?noma), Madrid (Spain) From p.lord at cs.man.ac.uk Wed Mar 30 08:08:18 2005 From: p.lord at cs.man.ac.uk (Phillip Lord) Date: Wed Mar 30 08:08:03 2005 Subject: [MOBY-l] The Eighth Annual Bio-Ontologies Meeting Call for Submissions (second mailing) Message-ID: The Eighth Annual Bio-Ontologies Meeting Call for Submissions ============================================================= Key Information =============== Organisers: Robert Stevens(1), Phillip Lord(1), Robin McEntire(2), and James.A.Butler(2) (1) School of Computer Science, University of Manchester (2) GlaxoSmithKline Website: http://bio-ontologies.man.ac.uk Location: Detroit, Michigan Submission Deadline: 29th April Main Conference: http://www.iscb.org/ismb2005 General Information =================== The Bio-Ontologies workshop has been a satellite meeting to the annual ISMB conference since 1998, and is now operated as a Special Interest Group at the ISMB Conference. Bio-Ontologies is well established as one of the key meetings for dissemination of latest information and research on ontologies in the life sciences and has drawn the key researchers in the field. Ontologies provide a mechanism for organising, sharing and reconciling data. Within recent years there has been a great deal of interest in the use of ontologies within bioinformatics, particularly in providing computationally accessible annotation, or standard data models for complex data for microarray or pathway information. Meetings such as last years workshop and SOFG have made it clear that there are many important uses of ontologies and a clear realisation of the importance of implementing mechanisms for integrating source ontologies rather than duplicating effort or causing confusion by extending a given ontology to include everything. However, with the increase in scope and use of ontologies within bioinformatics, issues of scalability, expressivity and best practices for modelling are becoming more important. We are particularly interested, therefore, in work involving multiple source ontologies, and which cut across the different levels of granularity implicit within biological systems. BioOntologies is an informal workshop. Submissions will be reviewed by the programme committee. A number of talks will be invited for ***full publication*** as papers in Comparative and Functional Genomics (see http://www3.interscience.wiley.com/cgi-bin/jissue/109860809 for last years papers) Submissions =========== Submission We invite submissions to this years Bio-Ontologies. Suitable topics include but are not restricted to: * Biological Applications of Ontologies. * Reports on Newly Developed or Existing Bio-Ontologies. * Tools for Developing Ontologies. * Use of Semantic Web technologies in BioInformatics * The implications of Bio-Ontologies or the Semantic Web for the drug discovery process * Current Research In Ontology Languages and its implication for Bio-Ontologies This year, for the first time, we would like to have a number of short software or ontology demonstrations, showing new or existing tools for building or using ontologies, or describing the design of ontologies. Submissions for these demonstrations are particularly encouraged. Submission Instructions ======================= Submissions are limited to 2 pages. Please submit using word using the templates available at http://bio-ontologies.man.ac.uk/submissions.html. Alternatively, submissions may be as a text file. Submissions should be emailed to bio-ont-sig@cs.man.ac.uk. We will acknowledge within a day or two. Bio-Ontologies is an informal meeting. Abstracts are reviewed by the programme committee. All accepted abstracts will be published by the organisers on their web site and in the main programme booklet. By submitting your paper, you consent to this publication. Authors of abstracts accepted for full publication as long (8 page) papers in Comparative and Functional Genomics will be notified following the meeting, for publication around October. Full details will be given later. Authors will be informed of acceptance within a few days of the submission deadline. -- Phillip Lord, Phone: +44 (0) 161 275 0683 PostDoctoral Research Associate, Email: p.lord@cs.man.ac.uk (preferred) School of Computer Science : p.lord@russet.org.uk Kilburn Building http://www.cs.man.ac.uk/~phillord University of Manchester http://www.russet.org.uk Oxford Road Manchester M13 9PL From mwilkinson at mrl.ubc.ca Wed Mar 30 17:48:40 2005 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Wed Mar 30 17:37:16 2005 Subject: [MOBY-l] LSID's are running again :-) Message-ID: <1112222920.3843.123.camel@mobycentral.icapture.ubc.ca> Hi all, The LSID resolver for MOBY LSID's is up and running again thanks to Eddie and with help and advice from Stephen Evanchik@IBM. I've also written a little CGI form that will resolve a MOBY LSID to the screen for viewing. This is available under the "Cool Tools" link from the MOBY homepage. Cheers all! M (reminder - just one more day to register for the MOBY meeting at a discount rate!!) -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From bmg at sfu.ca Thu Mar 31 19:41:37 2005 From: bmg at sfu.ca (Benjamin Good) Date: Thu Mar 31 19:42:24 2005 Subject: [MOBY-l] Re: [MOBY-dev] moby data and parameters In-Reply-To: <424C8F56.7080701@bcgsc.bc.ca> References: <424C8F56.7080701@bcgsc.bc.ca> Message-ID: <424C98C1.7070601@sfu.ca> Hi Stephen, You have an example of a collection of two GenericSequence objects (which could be either DNA or AA) in the Parser java file I sent you. So, yep, its a collection. Here is the (already java Stringified!) example. String xmlString2 = ""+ " "+ " "+ ""+ " "+ " "+ " "+ " "+ " 214 "+ " putative SUPERMAN-like C2H2 zinc finger transcription factor "+ "MKRTHLASFSNRDKTQEEEGEDGNGDNRVIMNHYKNYEAGLIPWPPKNYTCSFCRREFRSAQALGGHMNVHRRDRAKLRQIPSWLFEPHHHTPIANPNPNFSSSSSSSTTTAHLEPSLTNQRSKTTPFPSARFDLLDSTTSYGGLMMDREKNKSNVCSREIKKSAIDACHSVRCEISRGDLMNKKDDQVMGLELGMSLRNPNQVLDLELRLGYL"+ " "+ " "+ " "+ " "+ " "+ " "+ "1777 "+ "superman protein "+ "MERSNSIELRNSFYGRARTSPWSYGDYDNCQQDHDYLLGFSWPPRSYTCSFCKREFRSAQALGGHMNVHRRDRARLRLQQSPSSSSTPSPPYPNPNYSYSTMANSPPPHHSPLTLFPTLSPPSSPRYRAGLIRSLSPKSKHTPENACKTKKSSLLVEAGEATRFTSKDACKILRNDEIISLELEIGLINESEQDLDLELRLGFA"+ ""+ ""+ ""+ ""; For the return datatype, I think you might actually want to define the "parameters" as children (ie has/hasa) of your Chinook-service-list-datatype and then send back a collection of these datatypes. Maybe send a proposed example of this new datatype? -Ben Stephen Montgomery wrote: > hi - > > does anyone have an example of a xml input where more than one dna > sequence is coming down the wire. is this a collection? > > also, for a registered return data type we want to attach some > parameters (corresponding to the application that is going to be > run). is there a java example out there of doing this? > > all the best, > > stephen > > ps ben and i had an awesome crash coding session yesterday. set-up > the plan, built the supports, now we just need to execute the vision. > rock on. > _______________________________________________ > MOBY-dev mailing list > MOBY-dev@biomoby.org > http://www.biomoby.org/mailman/listinfo/moby-dev > > From bmg at sfu.ca Thu Mar 31 19:58:46 2005 From: bmg at sfu.ca (Benjamin Good) Date: Thu Mar 31 19:59:29 2005 Subject: [MOBY-l] Re: [MOBY-dev] moby data and parameters In-Reply-To: <424C8F56.7080701@bcgsc.bc.ca> References: <424C8F56.7080701@bcgsc.bc.ca> Message-ID: <424C9CC6.6090404@sfu.ca> For a potentially non-moby bioinformatics service discovered using Chinook (inside moby), what about an object like this? ChinookService isa object hasa String articleName "location" hasa String articleName "name" hasa String articleName "version" hasa String articleName "MobyXMLData-input" with secondary articles... has Float articleName "FloatParam??" has String articleName "StringParam??" See here for details about how you ~should compose objects http://www.biomoby.org/twiki/bin//view/Moby/MobySAPI -ben Stephen Montgomery wrote: > hi - > > does anyone have an example of a xml input where more than one dna > sequence is coming down the wire. is this a collection? > > also, for a registered return data type we want to attach some > parameters (corresponding to the application that is going to be > run). is there a java example out there of doing this? > > all the best, > > stephen > > ps ben and i had an awesome crash coding session yesterday. set-up > the plan, built the supports, now we just need to execute the vision. > rock on. > _______________________________________________ > MOBY-dev mailing list > MOBY-dev@biomoby.org > http://www.biomoby.org/mailman/listinfo/moby-dev > > From bmg at sfu.ca Thu Mar 31 20:08:24 2005 From: bmg at sfu.ca (Benjamin Good) Date: Thu Mar 31 20:09:23 2005 Subject: [MOBY-l] secondary articles Message-ID: <424C9F08.8030507@sfu.ca> When you decide on a datatype, go ahead and register it so we can check it out - don't forget you can use bioinfo.icapture.ubc.ca instead of mobycentral (since it is problematic right now). I sent an email with details on this one yesterday. I believe the secondary articles are not part of the DataType registration phenomenon, but rather the service registration. So you can say I am a service that accepts DNASequence object with secondary data bla bla bla. The basic jMoby structure for registration is to build an example instance of the thing (MobyService or MobyDataType for example) and then call CentralImpl to register it (or deregister it). There are methods within the MobyService and MobyDataType classes for specifying whatever you need. -Ben From wangch at cpsc.ucalgary.ca Wed Mar 30 18:59:24 2005 From: wangch at cpsc.ucalgary.ca (Chunyan Wang) Date: Mon Aug 15 11:28:33 2005 Subject: [MOBY-l] How to register the service to Moby References: <1112222920.3843.123.camel@mobycentral.icapture.ubc.ca> Message-ID: <424B3E8B.5070607@cpsc.ucalgary.ca> Hi All, I am new to Moby. I followed the Fasta example service to create our svervice. How do I register our service to Moby Centrol? could Anyone let me know about? Thanks, Joyce Mark Wilkinson wrote: >Hi all, > >The LSID resolver for MOBY LSID's is up and running again thanks to >Eddie and with help and advice from Stephen Evanchik@IBM. > >I've also written a little CGI form that will resolve a MOBY LSID to the >screen for viewing. This is available under the "Cool Tools" link from >the MOBY homepage. > >Cheers all! > >M > >(reminder - just one more day to register for the MOBY meeting at a >discount rate!!) > > > > From daniel.schulz at lionbioscience.com Tue Mar 22 10:24:37 2005 From: daniel.schulz at lionbioscience.com (schulz) Date: Mon Aug 15 11:28:51 2005 Subject: [MOBY-l] Re: Ant tasks (was: [MOBY-dev] Java packagesconversation) Message-ID: <200503221529.j2MFTXF07870@mail.lion-ag.de> Hi, >> You can set ant properties using -D properties as command line >> arguments to the JVM. >> > That's what I used in my example - but as an inconvenient way (and > unfortunately the only one, I still think). What I was asking about is the > (non-existent, I think) possibility to say, e.g.: > > ant my_target - -my param1 -your param2 Maybe I miss something, but I think there is not much difference of "ant my_target - -my param1 -your param2" to "ant my_target -Dproperty=value" and then to reference it as ${property} in your ANT script. Best, Daniel From bmg at sfu.ca Wed Mar 2 15:17:02 2005 From: bmg at sfu.ca (Benjamin Good) Date: Wed, 02 Mar 2005 12:17:02 -0800 Subject: [MOBY-l] perl example service code Message-ID: <42261F3E.6060206@sfu.ca> Would it be possible to post a complete example of a perl service that uses the new API? The example everyone still seems to be using from Ken Steube relies on some deprecated methods and produces services that don't seem to work with clients built from jMoby. (I think this is because we do not send moby:queryInput tags in the request). As people continue to find and use the old demo (despite the removal of the link) and get confused, a fresh demo would be very helpful for our beginners. Thanks -Ben From bmg at sfu.ca Wed Mar 2 16:41:41 2005 From: bmg at sfu.ca (Benjamin Good) Date: Wed, 02 Mar 2005 13:41:41 -0800 Subject: [MOBY-l] perl example service code In-Reply-To: <42261F3E.6060206@sfu.ca> References: <42261F3E.6060206@sfu.ca> Message-ID: <42263315.90401@sfu.ca> Scratch that, the example is there, I was just blind.. http://www.biomoby.org/twiki/bin/view/Moby/MobySByExamplePerlEdition though more wouldn't hurt! -Ben Benjamin Good wrote: > Would it be possible to post a complete example of a perl service that > uses the new API? > The example everyone still seems to be using from Ken Steube relies on > some deprecated methods and produces services that don't seem to work > with clients built from jMoby. (I think this is because we do not > send moby:queryInput tags in the request). > > As people continue to find and use the old demo (despite the removal > of the link) and get confused, a fresh demo would be very helpful for > our beginners. > > Thanks > -Ben > _______________________________________________ > moby-l mailing list > moby-l at biomoby.org > http://biomoby.org/mailman/listinfo/moby-l > > From mlangill at sfu.ca Wed Mar 2 19:06:01 2005 From: mlangill at sfu.ca (Morgan Langille) Date: Wed, 02 Mar 2005 16:06:01 -0800 Subject: [MOBY-l] Boolean object Message-ID: <1109808361.4212.16.camel@moosehead.mrl.ubc.ca> I was thinking that it would be nice to have a boolean moby object. It could be a sub-object of Integer (Boolean ISA Integer) that should only contain 1 (true) or 0 (false). Of course there is no way to constrain this but it seems useful to have this. Does anyone have any suggestions on if/how a boolean object should be made? Morgan Langille From tmo at ebi.ac.uk Wed Mar 2 19:16:44 2005 From: tmo at ebi.ac.uk (Tom Oinn) Date: Thu, 03 Mar 2005 00:16:44 +0000 Subject: [MOBY-l] Boolean object In-Reply-To: <1109808361.4212.16.camel@moosehead.mrl.ubc.ca> References: <1109808361.4212.16.camel@moosehead.mrl.ubc.ca> Message-ID: <4226576C.6030001@ebi.ac.uk> Morgan Langille wrote: > I was thinking that it would be nice to have a boolean moby object. It > could be a sub-object of Integer (Boolean ISA Integer) that should only > contain 1 (true) or 0 (false). Of course there is no way to constrain > this but it seems useful to have this. Does anyone have any suggestions > on if/how a boolean object should be made? Surely 'Boolean ISA Integer' translates to 'all operations that can consume an integer can consume a boolean' which is clearly wrong, at least from my perspective. You might implement a boolean as an enumeration but it shouldn't look like that in the ontology. I would be very surprised (as a user) if I asked what I could do with a boolean operator and got multiplication as an answer... Tom -- No virus found in this outgoing message. Checked by AVG Anti-Virus. Version: 7.0.300 / Virus Database: 266.5.1 - Release Date: 2/27/2005 From mlangill at sfu.ca Wed Mar 2 19:32:04 2005 From: mlangill at sfu.ca (Morgan Langille) Date: Wed, 02 Mar 2005 16:32:04 -0800 Subject: [MOBY-l] Boolean object In-Reply-To: <4226576C.6030001@ebi.ac.uk> References: <1109808361.4212.16.camel@moosehead.mrl.ubc.ca> <4226576C.6030001@ebi.ac.uk> Message-ID: <1109809924.4212.25.camel@moosehead.mrl.ubc.ca> On Wed, 2005-03-02 at 16:16, Tom Oinn wrote: > Morgan Langille wrote: > > I was thinking that it would be nice to have a boolean moby object. It > > could be a sub-object of Integer (Boolean ISA Integer) that should only > > contain 1 (true) or 0 (false). Of course there is no way to constrain > > this but it seems useful to have this. Does anyone have any suggestions > > on if/how a boolean object should be made? > > Surely 'Boolean ISA Integer' translates to 'all operations that can > consume an integer can consume a boolean' which is clearly wrong, at > least from my perspective. You might implement a boolean as an > enumeration but it shouldn't look like that in the ontology. I would be > very surprised (as a user) if I asked what I could do with a boolean > operator and got multiplication as an answer... > > Tom > You are right. So how could I make a boolean object? Here are a couple of ideas. 1) Boolean could be a primitive sub-object of Object, but that would require some major changes because the current API would not recognize Boolean as a primitive object and skip over contents of the object. OR 2) Boolean could contain an Integer or String or both (Boolean ISA Object, Boolean HASA String and/or Boolean HASA Integer) This would be a much easier solution then making a primitive Boolean object, but is not really as correct. Morgan From gordonp at ucalgary.ca Wed Mar 2 20:26:26 2005 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 02 Mar 2005 18:26:26 -0700 Subject: [MOBY-l] Boolean object In-Reply-To: <1109808361.4212.16.camel@moosehead.mrl.ubc.ca> References: <1109808361.4212.16.camel@moosehead.mrl.ubc.ca> Message-ID: <422667C2.30308@ucalgary.ca> I'd make boolean a primitive and adjust the APIs, it's really an oversight that this wasn't in there before. This is a natural progression for the Java API, as boolean is a primitive in Java. This avoids many potential headaches of boolean misuse in conditionals and arithmetic as are found in C/C++ (no dig intended, I love those languages). Morgan Langille wrote: >I was thinking that it would be nice to have a boolean moby object. It >could be a sub-object of Integer (Boolean ISA Integer) that should only >contain 1 (true) or 0 (false). Of course there is no way to constrain >this but it seems useful to have this. Does anyone have any suggestions >on if/how a boolean object should be made? > >Morgan Langille >_______________________________________________ >moby-l mailing list >moby-l at biomoby.org >http://biomoby.org/mailman/listinfo/moby-l > > > From markw at illuminae.com Wed Mar 2 20:32:52 2005 From: markw at illuminae.com (markw@illuminae.com) Date: Wed, 2 Mar 2005 20:32:52 -0500 Subject: [MOBY-l] Boolean object In-Reply-To: <422667C2.30308@ucalgary.ca> References: <1109808361.4212.16.camel@moosehead.mrl.ubc.ca> <422667C2.30308@ucalgary.ca> Message-ID: <1109813572.42266944a39c2@webmail.illuminae.com> Quoting Paul Gordon : > I'd make boolean a primitive and adjust the APIs, it's really an > oversight that this wasn't in there before. I agree 100%. It should be a primitive (inherit from Object)... but I don't think we need to adjust the API in any way to accomodate this. It is interesting to think what it means to have a namespace and ID on a boolean, though :-) gi|163483 = yes! M From bmg at sfu.ca Wed Mar 2 20:48:05 2005 From: bmg at sfu.ca (Benjamin Good) Date: Wed, 02 Mar 2005 17:48:05 -0800 Subject: [MOBY-l] Boolean object In-Reply-To: <1109813572.42266944a39c2@webmail.illuminae.com> References: <1109808361.4212.16.camel@moosehead.mrl.ubc.ca> <422667C2.30308@ucalgary.ca> <1109813572.42266944a39c2@webmail.illuminae.com> Message-ID: <42266CD5.7000107@sfu.ca> I am confused, I thought an Object was not a primitive "The value of the Object element is ignored */with the exception of/* the Classes representing primitives (e.g. Integer, Float, String, etc.; discussed in the Class Ontology section below). For example, in the following object this has no value the text "this has no value" is ignored by both client and service." For this to work it seems like we would have to officially declare Boolean as a primitive and adapt the API accordingly. Otherwise code for displaying/manipulating Objects (at least like what Eddie and I have been working on) won't work properly because it won't try to look for the text value of the new Boolean object. Neh??? -Ben markw at illuminae.com wrote: >Quoting Paul Gordon : > > > >>I'd make boolean a primitive and adjust the APIs, it's really an >>oversight that this wasn't in there before. >> >> > >I agree 100%. It should be a primitive (inherit from Object)... but I don't >think we need to adjust the API in any way to accomodate this. > >It is interesting to think what it means to have a namespace and ID on a >boolean, though :-) > >gi|163483 = yes! > > >M > > > >_______________________________________________ >moby-l mailing list >moby-l at biomoby.org >http://biomoby.org/mailman/listinfo/moby-l > > > > From markw at illuminae.com Wed Mar 2 22:01:24 2005 From: markw at illuminae.com (markw@illuminae.com) Date: Wed, 2 Mar 2005 22:01:24 -0500 Subject: [MOBY-l] Boolean object In-Reply-To: <42266CD5.7000107@sfu.ca> References: <1109808361.4212.16.camel@moosehead.mrl.ubc.ca> <422667C2.30308@ucalgary.ca> <1109813572.42266944a39c2@webmail.illuminae.com> <42266CD5.7000107@sfu.ca> Message-ID: <1109818884.42267e04afd35@webmail.illuminae.com> Sorry - you are right, of course. I'm multi-tasking and hadn't seen that issue in my quick think about the problem. Thanks for your clear headed advice! It wouldn't take much to update the API, I suspect. I'll think about it when I get home. Greetings from sweltering Australia! M Quoting Benjamin Good : > I am confused, I thought an Object was not a primitive > > "The value of the Object element is ignored */with the exception of/* > the Classes representing primitives (e.g. Integer, Float, String, etc.; > discussed in the Class Ontology > > section below). For example, in the following object > > this has no > value > > the text "this has no value" is ignored by both client and service." > > For this to work it seems like we would have to officially declare > Boolean as a primitive and adapt the API accordingly. Otherwise code > for displaying/manipulating Objects (at least like what Eddie and I have > been working on) won't work properly because it won't try to look for > the text value of the new Boolean object. > > Neh??? > > -Ben > > markw at illuminae.com wrote: > > >Quoting Paul Gordon : > > > > > > > >>I'd make boolean a primitive and adjust the APIs, it's really an > >>oversight that this wasn't in there before. > >> > >> > > > >I agree 100%. It should be a primitive (inherit from Object)... but I don't > >think we need to adjust the API in any way to accomodate this. > > > >It is interesting to think what it means to have a namespace and ID on a > >boolean, though :-) > > > >gi|163483 = yes! > > > > > >M > > > > > > > >_______________________________________________ > >moby-l mailing list > >moby-l at biomoby.org > >http://biomoby.org/mailman/listinfo/moby-l > > > > > > > > > > From gordonp at ucalgary.ca Thu Mar 3 11:44:39 2005 From: gordonp at ucalgary.ca (Paul Gordon) Date: Thu, 03 Mar 2005 09:44:39 -0700 Subject: [MOBY-l] Boolean object In-Reply-To: <1109818884.42267e04afd35@webmail.illuminae.com> References: <1109808361.4212.16.camel@moosehead.mrl.ubc.ca> <422667C2.30308@ucalgary.ca> <1109813572.42266944a39c2@webmail.illuminae.com> <42266CD5.7000107@sfu.ca> <1109818884.42267e04afd35@webmail.illuminae.com> Message-ID: <42273EF7.2060502@ucalgary.ca> May I suggest that the boolean primitive have the one of the values "true" or "false", not "0" or "1". This would alleve any confusion with integers, is more human readable, and is valid since "0" and "1" in Boolean logic are only arbitrary symbols in a lattice system (i.e. it is the union, intersection and negation functions that define the logic, not the symbols used). markw at illuminae.com wrote: >Sorry - you are right, of course. I'm multi-tasking and hadn't seen that issue >in my quick think about the problem. > >Thanks for your clear headed advice! > >It wouldn't take much to update the API, I suspect. I'll think about it when I >get home. > >Greetings from sweltering Australia! > >M > > > >Quoting Benjamin Good : > > > >>I am confused, I thought an Object was not a primitive >> >>"The value of the Object element is ignored */with the exception of/* >>the Classes representing primitives (e.g. Integer, Float, String, etc.; >>discussed in the Class Ontology >> >>section below). For example, in the following object >> >> this has no >>value >> >>the text "this has no value" is ignored by both client and service." >> >>For this to work it seems like we would have to officially declare >>Boolean as a primitive and adapt the API accordingly. Otherwise code >>for displaying/manipulating Objects (at least like what Eddie and I have >>been working on) won't work properly because it won't try to look for >>the text value of the new Boolean object. >> >>Neh??? >> >>-Ben >> >>markw at illuminae.com wrote: >> >> >> >>>Quoting Paul Gordon : >>> >>> >>> >>> >>> >>>>I'd make boolean a primitive and adjust the APIs, it's really an >>>>oversight that this wasn't in there before. >>>> >>>> >>>> >>>> >>>I agree 100%. It should be a primitive (inherit from Object)... but I don't >>>think we need to adjust the API in any way to accomodate this. >>> >>>It is interesting to think what it means to have a namespace and ID on a >>>boolean, though :-) >>> >>>gi|163483 = yes! >>> >>> >>>M >>> >>> >>> >>>_______________________________________________ >>>moby-l mailing list >>>moby-l at biomoby.org >>>http://biomoby.org/mailman/listinfo/moby-l >>> >>> >>> >>> >>> >>> >> >> > > > > > From gss at ncgr.org Thu Mar 3 12:58:09 2005 From: gss at ncgr.org (Gary Schiltz) Date: Thu, 03 Mar 2005 10:58:09 -0700 Subject: [MOBY-l] Boolean object In-Reply-To: <42273EF7.2060502@ucalgary.ca> References: <1109808361.4212.16.camel@moosehead.mrl.ubc.ca> <422667C2.30308@ucalgary.ca> <1109813572.42266944a39c2@webmail.illuminae.com> <42266CD5.7000107@sfu.ca> <1109818884.42267e04afd35@webmail.illuminae.com> <42273EF7.2060502@ucalgary.ca> Message-ID: <42275031.2010402@ncgr.org> I think I'm in Paul's camp here, although I notice that the W3C recommendation on XML Schema allows true, false, 1, and 0 as valid lexical values for booleans (see www.w3.org/TR/xmlschema-2/#boolean). But then, they say that the "canonical representation" for booleans is true and false. I am still confused as to the difference between the lexical and canonical representations. // Gary Paul Gordon wrote: > May I suggest that the boolean primitive have the one of the values > "true" or "false", not "0" or "1". This would alleve any confusion > with integers, is more human readable, and is valid since "0" and "1" > in Boolean logic are only arbitrary symbols in a lattice system (i.e. > it is the union, intersection and negation functions that define the > logic, not the symbols used). From gordonp at ucalgary.ca Thu Mar 3 14:31:48 2005 From: gordonp at ucalgary.ca (Paul Gordon) Date: Thu, 03 Mar 2005 12:31:48 -0700 Subject: [MOBY-l] Boolean object In-Reply-To: <42275031.2010402@ncgr.org> References: <1109808361.4212.16.camel@moosehead.mrl.ubc.ca> <422667C2.30308@ucalgary.ca> <1109813572.42266944a39c2@webmail.illuminae.com> <42266CD5.7000107@sfu.ca> <1109818884.42267e04afd35@webmail.illuminae.com> <42273EF7.2060502@ucalgary.ca> <42275031.2010402@ncgr.org> Message-ID: <42276624.70104@ucalgary.ca> Wikipedia to the rescue! :-) http://en.wikipedia.org/wiki/Canonical#Computer_science In CS, "canonical" is more like "best-practice convention" than canonical in the religous or mathematical sense. "true" and "false" are "best-practice" lexical representations for booleans. Of course, since MOBY's lexical and semantic rules stand alone (though they could be *expressed* in XMLSchema, DTDs, Relax-NG, etc.), there is no requirement to allow 0 and 1 as valid values. I realize that I'm being pedantic, but I think that giving people choices on how to express such a simple notion brings unneeded (albeit minor) complexity to the API. My $0.02 :-) P.S. One advatange of 0/1 is that it is not specific to English. But given that the entire MOBY API is in English anyway... Gary Schiltz wrote: > I think I'm in Paul's camp here, although I notice that the W3C > recommendation on XML Schema allows true, false, 1, and 0 as valid > lexical values for booleans (see www.w3.org/TR/xmlschema-2/#boolean). > But then, they say that the "canonical representation" for booleans is > true and false. I am still confused as to the difference between the > lexical and canonical representations. > > // Gary > > Paul Gordon wrote: > >> May I suggest that the boolean primitive have the one of the values >> "true" or "false", not "0" or "1". This would alleve any confusion >> with integers, is more human readable, and is valid since "0" and "1" >> in Boolean logic are only arbitrary symbols in a lattice system (i.e. >> it is the union, intersection and negation functions that define the >> logic, not the symbols used). > > > _______________________________________________ > moby-l mailing list > moby-l at biomoby.org > http://biomoby.org/mailman/listinfo/moby-l > From Pieter.Neerincx at wur.nl Mon Mar 7 06:48:14 2005 From: Pieter.Neerincx at wur.nl (Neerincx, Pieter) Date: Mon, 7 Mar 2005 12:48:14 +0100 Subject: [MOBY-l] Perl API: conversion of node content to and from XML Message-ID: <5F9035D8A446C84C903301CCD5FC8DB43F786E@salte0010.wurnet.nl> Hi all, I'm pretty new to BioMOBY and have a question about the Perl API. I have some problems with extracting text data from objects like for example the String object. I have something like this: some text & more text The plain text contains for example "&" which has a special meaning in XML. Therefore I have to encode it using "&". If I use the getNodeContentWithArticle sub from CommonSubs.pm it serializes the data resulting in raw XML. Hence the result contains the "&" still encoded as "&". The same thing happens with encoded quotes. If I would be using the extractRawContent sub that would make sense to me. Off course I can convert the encoded stuff from and to raw XML manually, but wouldn't it be nicer if the API would take care of that? Or am I missing something here and is there a good reason the have for example the getNodeContentWithArticle sub return raw XML? If I change the code like this: sub getNodeContentWithArticle { ### lot's of other stuff ... ### # Using ->toString results in raw XML and will # not map encoded chars like '&' back to '&'. # Fetching node content using -> data will. #$resp .= $_->toString; $resp .= $_->data; ### lot's of other stuff ... ### } decoding the raw XML is taken care of by the API. Any feedback would be appriciated. Regards, Pieter Neerincx From mwilkinson at mrl.ubc.ca Mon Mar 7 12:40:04 2005 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Mon, 07 Mar 2005 09:40:04 -0800 Subject: [MOBY-l] Registration for the May 7/8 BioMOBY meeting in Vancouver Message-ID: <1110217204.3898.418.camel@mobycentral.icapture.ubc.ca> Hi all, I've set up a CGI form for registration. Please submit your registration ASAP so that I can complete the budget for the meeting. I will be doing my best to supplement your room and food from my grant so that your travel will be the primary expense to you. http://biomoby.org/cgi-bin/register.cgi Cheers! See you all in Vancouver! Mark -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From mwilkinson at mrl.ubc.ca Mon Mar 7 23:38:25 2005 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Mon, 07 Mar 2005 20:38:25 -0800 Subject: [moby] [MOBY-l] Perl API: conversion of node content to and from XML In-Reply-To: <5F9035D8A446C84C903301CCD5FC8DB43F786E@salte0010.wurnet.nl> References: <5F9035D8A446C84C903301CCD5FC8DB43F786E@salte0010.wurnet.nl> Message-ID: <1110256704.6742.14.camel@mobycentral.icapture.ubc.ca> Thanks for the fix! It is now committed to the CVS - let me know if it still causes problems. Cheers! M On Mon, 2005-03-07 at 03:48, Neerincx, Pieter wrote: > Hi all, > > I'm pretty new to BioMOBY and have a question about the Perl API. I have some problems with extracting text data from objects like for example the String object. I have something like this: > > some text & more text > > The plain text contains for example "&" which has a special meaning in XML. Therefore I have to encode it using "&". If I use the getNodeContentWithArticle sub from CommonSubs.pm it serializes the data resulting in raw XML. Hence the result contains the "&" still encoded as "&". The same thing happens with encoded quotes. If I would be using the extractRawContent sub that would make sense to me. Off course I can convert the encoded stuff from and to raw XML manually, but wouldn't it be nicer if the API would take care of that? Or am I missing something here and is there a good reason the have for example the getNodeContentWithArticle sub return raw XML? > > If I change the code like this: > > sub getNodeContentWithArticle { > > ### lot's of other stuff ... ### > > # Using ->toString results in raw XML and will > # not map encoded chars like '&' back to '&'. > # Fetching node content using -> data will. > #$resp .= $_->toString; > $resp .= $_->data; > > ### lot's of other stuff ... ### > > } > > decoding the raw XML is taken care of by the API. Any feedback would be appriciated. > > Regards, > > Pieter Neerincx > > _______________________________________________ > moby-l mailing list > moby-l at biomoby.org > http://biomoby.org/mailman/listinfo/moby-l -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From ismael at lcc.uma.es Fri Mar 11 03:54:54 2005 From: ismael at lcc.uma.es (Ismael Navas) Date: Fri, 11 Mar 2005 09:54:54 +0100 Subject: [MOBY-l] Taverna Parser Message-ID: <20050311085147.4D46138CE8@sol10.lcc.uma.es> Hello, I'm working with the parser for Taverna from Java, and I've obtained a object of the Processor class that access to a BioMOBY service, but I don't know how to access to several values of this Processor (mobyEndpoint,serviceName and authorityName) that are into the element biomobywsdl. Do somebody know how to access from Java to these elements? Thanks in advance, Ismael Navas. From senger at ebi.ac.uk Fri Mar 11 04:04:47 2005 From: senger at ebi.ac.uk (Martin Senger) Date: Fri, 11 Mar 2005 09:04:47 +0000 (GMT) Subject: [MOBY-l] Taverna Parser In-Reply-To: <20050311085147.4D46138CE8@sol10.lcc.uma.es> Message-ID: Hi, > I'm working with the parser for Taverna from Java > Could you clarify please what parser you are referring to? Do you mean the part of Taverna (the BioMoby plug-in in Taverna code), or some outside-Taverna parser? Thanks, Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk 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 mark.fiers at wur.nl Fri Mar 11 03:00:38 2005 From: mark.fiers at wur.nl (Mark Fiers) Date: Fri, 11 Mar 2005 09:00:38 +0100 Subject: [MOBY-l] a (fixed?) problem with biomoby python Message-ID: <42315026.40905@wur.nl> LS We've ran into some problems with the latest biomoby python version from cvs. executing this script: ########################################################################## from bioMoby import * m = MobyMarshaller() um = MobyUnmarshaller() g = BasicGFFSequenceFeature.MobyBasicGFFSequenceFeature( id='2', Reference='SEQa', Source='pipeline', Method='something', Start=1, Stop=44, Strand='-', Frame='3', Score=33.3, articleName='Gene', Column9_tag_value=[ Multi_key_value_pair.MobyMulti_key_value_pair( articleName="Column9_tag_value", Key='mobytstings', Value=['1','2','3']) ]) mo = m.dumps(MobyContent({'test' : [g]})) print mo.replace('<',"\n<") m2 = um.loads(mo) print str(m2).replace('<',"\n<") ########################################################################## returns a biomoby string with all features I entered, but all of these are empty. Upon looking at the source code, it appears that the features are not parsed out because of a case mismatch. The xml contains, for example,: 33.3 but the from_moby function looks for a float with the name "score". If I change this in the function, everything works again. I had to change it also for the Multi_key_value_pair, but the GenericSequence was working ok. Attached are the fixed BasicGFFSequenceFeature and Multi_key_value_pair. but there are many more in the ontology which are broken. Or is there a more generic way in which this can be fixed? Cheers Mark Fiers From tmo at ebi.ac.uk Fri Mar 11 17:47:20 2005 From: tmo at ebi.ac.uk (Tom Oinn) Date: Fri, 11 Mar 2005 22:47:20 +0000 Subject: [MOBY-l] Taverna Parser In-Reply-To: References: Message-ID: <42321FF8.9080105@ebi.ac.uk> Martin Senger wrote: > Hi, > >>I'm working with the parser for Taverna from Java >> > > Could you clarify please what parser you are referring to? Do you mean > the part of Taverna (the BioMoby plug-in in Taverna code), or some > outside-Taverna parser? Ismael - I believe you're working with the BiomobyProcessor class in Taverna? If so there are get and set methods for these properties, you should be able to see the source here : http://cvs.sourceforge.net/viewcvs.py/taverna/taverna1.0/src/org/embl/ebi/escience/scuflworkers/biomoby/BiomobyProcessor.java?rev=1.13&view=markup If that isn't enough I'm sure Martin can answer any further questions as this is his code :) Cheers, Tom From mwilkinson at mrl.ubc.ca Tue Mar 15 19:09:37 2005 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Tue, 15 Mar 2005 16:09:37 -0800 Subject: [MOBY-l] REGISATRATION CALL #2 MOBY-DIC meeting Message-ID: <1110931777.3201.18.camel@mobycentral.icapture.ubc.ca> Hi all, Just re-pinging everyone who wants to come to Vancouver for the MOBY DIC meeting in May (7/8). PLEASE REGISTER AS SOON AS POSSIBLE at: http://www.biomoby.org/cgi-bin/register.cgi I am pretty sure now that I will be able to cover 100% of your housing costs, and probably some of the meal costs as well. I'm still working out the final budget, but I do need to know how many people are coming before I can come up with the final number. My current guesstimate is that the registration fees (to cover your room for up to three nights, and breakfast + lunch on the two meeting days) will be about CAD$200. I will try to bring that even lower if I can! Cheers! Mark -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From p.lord at cs.man.ac.uk Tue Mar 22 09:45:12 2005 From: p.lord at cs.man.ac.uk (Phillip Lord) Date: 22 Mar 2005 14:45:12 +0000 Subject: [MOBY-l] Re: Ant tasks (was: [MOBY-dev] Java packages conversation) In-Reply-To: References: Message-ID: >>>>> "Martin" == Martin Senger writes: Martin> I have not find a way how to pass to an Ant target Martin> parameters from the Ant's command-line (let me know please Martin> if anybody knows how to do it). You can set ant properties using -D properties as command line arguments to the JVM. I normally use properties files like so... myself. Cheers Phil From senger at ebi.ac.uk Tue Mar 22 10:09:03 2005 From: senger at ebi.ac.uk (Martin Senger) Date: Tue, 22 Mar 2005 15:09:03 +0000 (GMT) Subject: [MOBY-l] Re: Ant tasks (was: [MOBY-dev] Java packages conversation) In-Reply-To: Message-ID: > You can set ant properties using -D properties as command line > arguments to the JVM. > That's what I used in my example - but as an inconvenient way (and unfortunately the only one, I still think). What I was asking about is the (non-existent, I think) possibility to say, e.g.: ant my_target - -my param1 -your param2 Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk 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 p.lord at cs.man.ac.uk Tue Mar 22 10:20:44 2005 From: p.lord at cs.man.ac.uk (Phillip Lord) Date: 22 Mar 2005 15:20:44 +0000 Subject: [MOBY-l] Re: Ant tasks (was: [MOBY-dev] Java packages conversation) In-Reply-To: References: Message-ID: >>>>> "Martin" == Martin Senger writes: >> You can set ant properties using -D properties as command line >> arguments to the JVM. >> Martin> That's what I used in my example Yes, I realised that after I sent it, when I read your second email. Martin> but as an inconvenient way (and unfortunately the only one, Martin> I still think). What I was asking about is the Martin> (non-existent, I think) possibility to say, e.g.: Martin> ant my_target - -my param1 -your param2 Only with a wrapper script as far as I know. More of a pain than it's worth. You could try popping up a fill in gui... Phil From p.lord at cs.man.ac.uk Tue Mar 22 10:19:26 2005 From: p.lord at cs.man.ac.uk (Phillip Lord) Date: 22 Mar 2005 15:19:26 +0000 Subject: [MOBY-l] Re: Ant tasks (was: [MOBY-dev] Java packages conversation) In-Reply-To: References: Message-ID: -- Phillip Lord, Phone: +44 (0) 161 275 0683 PostDoctoral Research Associate, Email: p.lord at cs.man.ac.uk (preferred) School of Computer Science : p.lord at russet.org.uk Kilburn Building http://www.cs.man.ac.uk/~phillord University of Manchester http://www.russet.org.uk Oxford Road Manchester M13 9PL From senger at ebi.ac.uk Tue Mar 22 11:15:51 2005 From: senger at ebi.ac.uk (Martin Senger) Date: Tue, 22 Mar 2005 16:15:51 +0000 (GMT) Subject: [MOBY-l] Re: Ant tasks (was: [MOBY-dev] Java packagesconversation) In-Reply-To: <200503221529.j2MFTXF07870@mail.lion-ag.de> Message-ID: > Maybe I miss something, but I think there is not much difference of > "ant my_target - -my param1 -your param2" to "ant my_target > -Dproperty=value" and then to reference it as ${property} in your ANT > script. > I think it is, that's all :-) Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk 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 mwilkinson at mrl.ubc.ca Wed Mar 23 11:05:45 2005 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Wed, 23 Mar 2005 08:05:45 -0800 Subject: [MOBY-l] mobycentral revived Message-ID: <1111593945.22484.18.camel@mobycentral.icapture.ubc.ca> Hi all, sorry about that - I was in post-surgery with my cat when it went down and I never got back on-line until this AM. MOBY Central is a bit flaky at the moment, and we can't figure out why. It is a rather sudden flakyness that doesn't seem to correspond to any particular change we have made. The Apache error logs fill up with segfaults within a couple of hours and that crashes the system as the amount of available memory goes to zero. MySQL seems to be having a similar problem (it was mysql that had crashed last night). This all seems to point to a physical memory error, but we can't detect one... It may be time to get a new machine for MOBY :-) Anyway, I'll keep an eye on it throughout the day. I have turned apache's error logging to "critical" to reduce teh number of error messages, so hopefully we'll have longer availability between crashes. Sorry about this! M -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From mwilkinson at mrl.ubc.ca Wed Mar 23 11:53:44 2005 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Wed, 23 Mar 2005 08:53:44 -0800 Subject: [MOBY-l] recompiling Apache Message-ID: <1111596824.22717.28.camel@mobycentral.icapture.ubc.ca> Hi everyone, I've just found a posting that suggests that there is a conflict between expat and apache. Expat is the XML parser that I believe is part of libxml2 which is what is used by XML::LibXML - the new libraries that are doing the XML parsing for MOBY Central. I will need to recompile Apache to fix this problem (if it is the problem...), so you might notice mobycentral going up and down over the next 48 hours as I play with it, but I will try to limit my testing to the test instance of the server so that it doesn't disturb anyone too badly. Sorry for the flakyness! M (this doesn't explain the crash of mysql... but it might just have been a coincidence...) -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From mwilkinson at mrl.ubc.ca Wed Mar 23 15:43:07 2005 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Wed, 23 Mar 2005 12:43:07 -0800 Subject: [MOBY-l] Cut-off for MOBY-DIC registration: March 31, 2005. Message-ID: <1111610587.24448.12.camel@mobycentral.icapture.ubc.ca> Hi all, Particularly pinging the S-MOBY crew, the CSHL crew, the Brisbane crew, and anyone from myGrid or GO who wants to spend a few days away from the dull Manchester/Hinxton rain lapping up the sun in Lotus Land :-) If you have not registered yet, go to: http://biomoby.org/cgi-bin/register.cgi In order to make a budget and book the catering I have to set a cut-off date for the MOBY DIC meeting registration. March 31st will be the last date for attendees who want to take advantage of the substantially discounted registration supplement from my Genome Canada grant, after which you will be responsible for paying your own room and board. So... if you haven't already registered... get on y'r horse! :-) If you aren't sure if you have registered, go to http://biomoby.org/regisrations.txt I will make the final budget on the 1st of April and then will be able to let you know exactly what the registration fees will be (including 3 nights and breakfast/lunch and coffee breaks for the the meeting days). I'm still expecting this to be under $200, probably well under that number. Cheers all! M -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From senger at ebi.ac.uk Wed Mar 23 19:09:24 2005 From: senger at ebi.ac.uk (Martin Senger) Date: Thu, 24 Mar 2005 00:09:24 +0000 (GMT) Subject: [MOBY-l] Re: [MOBY-dev] recompiling Apache In-Reply-To: <1111596824.22717.28.camel@mobycentral.icapture.ubc.ca> Message-ID: > I've just found a posting that suggests that there is a conflict between > expat and apache. Expat is the XML parser that I believe is part of > libxml2 > FYI, I do not know about libxml12 but I know that Expat is a base part for XML::Parser. I wish you luck with finding the cause of problems. Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk 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 markw at illuminae.com Wed Mar 23 21:40:40 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 23 Mar 2005 18:40:40 -0800 Subject: [MOBY-l] Re: [MOBY-dev] recompiling Apache In-Reply-To: References: Message-ID: <424228A8.5040507@illuminae.com> It seems to have settled down a bit now. All I did was install a newer version of DBI! There's still a segfault in the error log that happened some time in the past 6 hours, but that is better than the several dozen per hour that were happening a few days ago :-) I'll keep an eye on it, but for now it seems somewhat stable (touch wood!) M Martin Senger wrote: >>I've just found a posting that suggests that there is a conflict between >>expat and apache. Expat is the XML parser that I believe is part of >>libxml2 >> >> >> > FYI, I do not know about libxml12 but I know that Expat is a base part >for XML::Parser. > > I wish you luck with finding the cause of problems. > Martin > > > From ismael at lcc.uma.es Mon Mar 28 09:07:52 2005 From: ismael at lcc.uma.es (Ismael Navas) Date: Mon, 28 Mar 2005 16:07:52 +0200 Subject: [MOBY-l] Taverna Parser In-Reply-To: Message-ID: <20050328140430.59EF838CE8@sol10.lcc.uma.es> Hello, I've Developer a tool that makes use of the Taverna parser, in order to read and use Taverna workflows, and this tool runs correctly in windows. However, when I've tried to run it in Linux, it doesn't work. First I had problems with the classpath, so I've changed ';' for ':' in classpath definition, but now I obtain this error: java -classpath .:./lib/mysql-connector-java-3.0.10-stable-bin.jar:./lib/taverna-1.0.jar:./l ib/dom4j-1.5.jar:./lib/log4j-1.2.8.jar:./lib/martj.jar:./lib/jmoby.jar:./lib /axis-nightly-11.01.05.jar:./lib/jaxrpc-nightly-11.01.05.jar:./lib/commons-l ogging-1.0.4.jar:./lib/commons-discovery-0.2.jar:./lib/saaj-nightly-11.01.05 .jar:./lib/jdom-1.0.jar TavernaINB.LoadWorkflow 91 HomologySearchAndPhylogeneticStudy.xml java.lang.NoClassDefFoundError at org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread.run(XScuflParser.ja va:438) java.lang.NoClassDefFoundError at org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread.run(XScuflParser.ja va:438) java.lang.NoClassDefFoundError at org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread.run(XScuflParser.ja va:438) java.lang.InternalError: Can't connect to X11 window server using ':0.0' as the value of the DISPLAY variable. at sun.awt.X11GraphicsEnvironment.initDisplay(Native Method) at sun.awt.X11GraphicsEnvironment.(X11GraphicsEnvironment.java:134) at java.lang.Class.forName0(Native Method) at java.lang.Class.forName(Class.java:141) at java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment(GraphicsEnvironment .java:62) at sun.awt.motif.MToolkit.(MToolkit.java:81) at java.lang.Class.forName0(Native Method) at java.lang.Class.forName(Class.java:141) at java.awt.Toolkit$2.run(Toolkit.java:748) at java.security.AccessController.doPrivileged(Native Method) at java.awt.Toolkit.getDefaultToolkit(Toolkit.java:739) at javax.swing.ImageIcon.(ImageIcon.java:119) at javax.swing.ImageIcon.(ImageIcon.java:138) at org.embl.ebi.escience.scuflworkers.ProcessorHelper.(ProcessorHelper. java:85) at org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread.run(XScuflParser.ja va:438) java.lang.NoClassDefFoundError at org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread.run(XScuflParser.ja va:438) org.embl.ebi.escience.scufl.UnknownProcessorException: Unable to locate processor with name 'Create_moby_data' at org.embl.ebi.escience.scufl.ScuflModel.locateProcessor(ScuflModel.java:528) at org.embl.ebi.escience.scufl.ScuflModel.locatePortOrCreate(ScuflModel.java:49 9) at org.embl.ebi.escience.scufl.DataConstraint.(DataConstraint.java:32) at org.embl.ebi.escience.scufl.parser.XScuflParser.populate(XScuflParser.java:3 61) at org.embl.ebi.escience.scufl.parser.XScuflParser.populate(XScuflParser.java:1 47) at TavernaINB.LoadWorkflow.loadWorkflow(LoadWorkflow.java:194) at TavernaINB.LoadWorkflow.load(LoadWorkflow.java:437) at TavernaINB.LoadWorkflow.main(LoadWorkflow.java:471) Could somebody help me? Thanks, Ismael Navas -----Mensaje original----- De: Martin Senger [mailto:senger at ebi.ac.uk] Enviado el: viernes, 11 de marzo de 2005 10:05 Para: Ismael Navas CC: moby-l at biomoby.org Asunto: Re: [MOBY-l] Taverna Parser Hi, > I'm working with the parser for Taverna from Java > Could you clarify please what parser you are referring to? Do you mean the part of Taverna (the BioMoby plug-in in Taverna code), or some outside-Taverna parser? Thanks, Martin -- Martin Senger EMBL Outstation - Hinxton Senger at EBI.ac.uk 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 tmo at ebi.ac.uk Mon Mar 28 09:31:16 2005 From: tmo at ebi.ac.uk (Tom Oinn) Date: Mon, 28 Mar 2005 15:31:16 +0100 Subject: [MOBY-l] Taverna Parser In-Reply-To: <20050328140430.59EF838CE8@sol10.lcc.uma.es> References: <20050328140430.59EF838CE8@sol10.lcc.uma.es> Message-ID: <42481534.3070908@ebi.ac.uk> Ismael, This is a standard problem with running Java on a machine with no display configured - when Java creates a Graphics context (such as when loading an icon image, which is where I think the problem is occuring) it attempts to connect to an X server on unix like platforms. There are several generic workarounds. 1) Use a more recent version of java - they fixed this a while back, you might be using quite an old version? 2) Use something like the XVFB device, produces a virtual frame buffer which Java can then connect to to get font metrics etc. A search for 'headless java' will produce more information, I don't know any more detail than this though. Cheers, Tom Ismael Navas wrote: > Hello, > > I've Developer a tool that makes use of the Taverna parser, in order to read > and use Taverna workflows, and this tool runs correctly in windows. However, > when I've tried to run it in Linux, it doesn't work. First I had problems > with the classpath, so I've changed ';' for ':' in classpath definition, but > now I obtain this error: > > java -classpath > .:./lib/mysql-connector-java-3.0.10-stable-bin.jar:./lib/taverna-1.0.jar:./l > ib/dom4j-1.5.jar:./lib/log4j-1.2.8.jar:./lib/martj.jar:./lib/jmoby.jar:./lib > /axis-nightly-11.01.05.jar:./lib/jaxrpc-nightly-11.01.05.jar:./lib/commons-l > ogging-1.0.4.jar:./lib/commons-discovery-0.2.jar:./lib/saaj-nightly-11.01.05 > .jar:./lib/jdom-1.0.jar TavernaINB.LoadWorkflow 91 > HomologySearchAndPhylogeneticStudy.xml > java.lang.NoClassDefFoundError > at > org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread.run(XScuflParser.ja > va:438) > java.lang.NoClassDefFoundError > at > org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread.run(XScuflParser.ja > va:438) > java.lang.NoClassDefFoundError > at > org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread.run(XScuflParser.ja > va:438) > java.lang.InternalError: Can't connect to X11 window server using ':0.0' as > the value of the DISPLAY variable. > at sun.awt.X11GraphicsEnvironment.initDisplay(Native Method) > at > sun.awt.X11GraphicsEnvironment.(X11GraphicsEnvironment.java:134) > at java.lang.Class.forName0(Native Method) > at java.lang.Class.forName(Class.java:141) > at > java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment(GraphicsEnvironment > .java:62) > at sun.awt.motif.MToolkit.(MToolkit.java:81) > at java.lang.Class.forName0(Native Method) > at java.lang.Class.forName(Class.java:141) > at java.awt.Toolkit$2.run(Toolkit.java:748) > at java.security.AccessController.doPrivileged(Native Method) > at java.awt.Toolkit.getDefaultToolkit(Toolkit.java:739) > at javax.swing.ImageIcon.(ImageIcon.java:119) > at javax.swing.ImageIcon.(ImageIcon.java:138) > at > org.embl.ebi.escience.scuflworkers.ProcessorHelper.(ProcessorHelper. > java:85) > at > org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread.run(XScuflParser.ja > va:438) > java.lang.NoClassDefFoundError > at > org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread.run(XScuflParser.ja > va:438) > org.embl.ebi.escience.scufl.UnknownProcessorException: Unable to locate > processor with name 'Create_moby_data' > at > org.embl.ebi.escience.scufl.ScuflModel.locateProcessor(ScuflModel.java:528) > at > org.embl.ebi.escience.scufl.ScuflModel.locatePortOrCreate(ScuflModel.java:49 > 9) > at > org.embl.ebi.escience.scufl.DataConstraint.(DataConstraint.java:32) > at > org.embl.ebi.escience.scufl.parser.XScuflParser.populate(XScuflParser.java:3 > 61) > at > org.embl.ebi.escience.scufl.parser.XScuflParser.populate(XScuflParser.java:1 > 47) > at TavernaINB.LoadWorkflow.loadWorkflow(LoadWorkflow.java:194) > at TavernaINB.LoadWorkflow.load(LoadWorkflow.java:437) > at TavernaINB.LoadWorkflow.main(LoadWorkflow.java:471) > > Could somebody help me? > > Thanks, > Ismael Navas > > > -----Mensaje original----- > De: Martin Senger [mailto:senger at ebi.ac.uk] > Enviado el: viernes, 11 de marzo de 2005 10:05 > Para: Ismael Navas > CC: moby-l at biomoby.org > Asunto: Re: [MOBY-l] Taverna Parser > > Hi, > >>I'm working with the parser for Taverna from Java >> > > Could you clarify please what parser you are referring to? Do you mean > the part of Taverna (the BioMoby plug-in in Taverna code), or some > outside-Taverna parser? > > Thanks, > Martin > From jmfernandez at cnb.uam.es Mon Mar 28 08:51:32 2005 From: jmfernandez at cnb.uam.es (=?ISO-8859-1?Q?Jos=E9_Mar=EDa_Fern=E1ndez_Gonz=E1lez?=) Date: Mon, 28 Mar 2005 15:51:32 +0200 Subject: [MOBY-l] Taverna Parser In-Reply-To: <42481534.3070908@ebi.ac.uk> References: <20050328140430.59EF838CE8@sol10.lcc.uma.es> <42481534.3070908@ebi.ac.uk> Message-ID: <42480BE4.3060308@cnb.uam.es> Hi everybody, the easiest way to run java 1.4.x in a headless environment is using the system property java.awt.headless: java -Djava.awt.headless=true ... Best regards, Jos? Mar?a Tom Oinn wrote: > Ismael, > > This is a standard problem with running Java on a machine with no > display configured - when Java creates a Graphics context (such as when > loading an icon image, which is where I think the problem is occuring) > it attempts to connect to an X server on unix like platforms. There are > several generic workarounds. > > 1) Use a more recent version of java - they fixed this a while back, you > might be using quite an old version? > > 2) Use something like the XVFB device, produces a virtual frame buffer > which Java can then connect to to get font metrics etc. > > A search for 'headless java' will produce more information, I don't know > any more detail than this though. > > Cheers, > > Tom > > Ismael Navas wrote: > >> Hello, >> >> I've Developer a tool that makes use of the Taverna parser, in order >> to read >> and use Taverna workflows, and this tool runs correctly in windows. >> However, >> when I've tried to run it in Linux, it doesn't work. First I had problems >> with the classpath, so I've changed ';' for ':' in classpath >> definition, but >> now I obtain this error: >> >> java -classpath >> .:./lib/mysql-connector-java-3.0.10-stable-bin.jar:./lib/taverna-1.0.jar:./l >> >> ib/dom4j-1.5.jar:./lib/log4j-1.2.8.jar:./lib/martj.jar:./lib/jmoby.jar:./lib >> >> /axis-nightly-11.01.05.jar:./lib/jaxrpc-nightly-11.01.05.jar:./lib/commons-l >> >> ogging-1.0.4.jar:./lib/commons-discovery-0.2.jar:./lib/saaj-nightly-11.01.05 >> >> .jar:./lib/jdom-1.0.jar TavernaINB.LoadWorkflow 91 >> HomologySearchAndPhylogeneticStudy.xml java.lang.NoClassDefFoundError >> at >> org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread.run(XScuflParser.ja >> >> va:438) >> java.lang.NoClassDefFoundError >> at >> org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread.run(XScuflParser.ja >> >> va:438) >> java.lang.NoClassDefFoundError >> at >> org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread.run(XScuflParser.ja >> >> va:438) >> java.lang.InternalError: Can't connect to X11 window server using >> ':0.0' as >> the value of the DISPLAY variable. >> at sun.awt.X11GraphicsEnvironment.initDisplay(Native Method) >> at >> sun.awt.X11GraphicsEnvironment.(X11GraphicsEnvironment.java:134) >> at java.lang.Class.forName0(Native Method) >> at java.lang.Class.forName(Class.java:141) >> at >> java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment(GraphicsEnvironment >> >> .java:62) >> at sun.awt.motif.MToolkit.(MToolkit.java:81) >> at java.lang.Class.forName0(Native Method) >> at java.lang.Class.forName(Class.java:141) >> at java.awt.Toolkit$2.run(Toolkit.java:748) >> at java.security.AccessController.doPrivileged(Native Method) >> at java.awt.Toolkit.getDefaultToolkit(Toolkit.java:739) >> at javax.swing.ImageIcon.(ImageIcon.java:119) >> at javax.swing.ImageIcon.(ImageIcon.java:138) >> at >> org.embl.ebi.escience.scuflworkers.ProcessorHelper.(ProcessorHelper. >> >> java:85) >> at >> org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread.run(XScuflParser.ja >> >> va:438) >> java.lang.NoClassDefFoundError >> at >> org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread.run(XScuflParser.ja >> >> va:438) >> org.embl.ebi.escience.scufl.UnknownProcessorException: Unable to locate >> processor with name 'Create_moby_data' >> at >> org.embl.ebi.escience.scufl.ScuflModel.locateProcessor(ScuflModel.java:528) >> >> at >> org.embl.ebi.escience.scufl.ScuflModel.locatePortOrCreate(ScuflModel.java:49 >> >> 9) >> at >> org.embl.ebi.escience.scufl.DataConstraint.(DataConstraint.java:32) >> at >> org.embl.ebi.escience.scufl.parser.XScuflParser.populate(XScuflParser.java:3 >> >> 61) >> at >> org.embl.ebi.escience.scufl.parser.XScuflParser.populate(XScuflParser.java:1 >> >> 47) >> at TavernaINB.LoadWorkflow.loadWorkflow(LoadWorkflow.java:194) >> at TavernaINB.LoadWorkflow.load(LoadWorkflow.java:437) >> at TavernaINB.LoadWorkflow.main(LoadWorkflow.java:471) >> >> Could somebody help me? >> >> Thanks, >> Ismael Navas >> >> >> -----Mensaje original----- >> De: Martin Senger [mailto:senger at ebi.ac.uk] Enviado el: viernes, 11 de >> marzo de 2005 10:05 >> Para: Ismael Navas >> CC: moby-l at biomoby.org >> Asunto: Re: [MOBY-l] Taverna Parser >> >> Hi, >> >>> I'm working with the parser for Taverna from Java >>> >> >> Could you clarify please what parser you are referring to? Do you mean >> the part of Taverna (the BioMoby plug-in in Taverna code), or some >> outside-Taverna parser? >> >> Thanks, >> Martin >> > > _______________________________________________ > moby-l mailing list > moby-l at biomoby.org > http://biomoby.org/mailman/listinfo/moby-l > > -- Jos? Mar?a Fern?ndez Gonz?lez e-mail: jmfernandez at cnb.uam.es Tlfn: (+34) 91 585 54 50 Fax: (+34) 91 585 45 06 Grupo de Dise?o de Proteinas Protein Design Group Centro Nacional de Biotecnolog?a National Center of Biotechnology C.P.: 28049 Zip Code: 28049 C/. Darwin n? 3 (Campus Cantoblanco, U. Aut?noma), Madrid (Spain) From p.lord at cs.man.ac.uk Wed Mar 30 08:08:18 2005 From: p.lord at cs.man.ac.uk (Phillip Lord) Date: 30 Mar 2005 14:08:18 +0100 Subject: [MOBY-l] The Eighth Annual Bio-Ontologies Meeting Call for Submissions (second mailing) Message-ID: The Eighth Annual Bio-Ontologies Meeting Call for Submissions ============================================================= Key Information =============== Organisers: Robert Stevens(1), Phillip Lord(1), Robin McEntire(2), and James.A.Butler(2) (1) School of Computer Science, University of Manchester (2) GlaxoSmithKline Website: http://bio-ontologies.man.ac.uk Location: Detroit, Michigan Submission Deadline: 29th April Main Conference: http://www.iscb.org/ismb2005 General Information =================== The Bio-Ontologies workshop has been a satellite meeting to the annual ISMB conference since 1998, and is now operated as a Special Interest Group at the ISMB Conference. Bio-Ontologies is well established as one of the key meetings for dissemination of latest information and research on ontologies in the life sciences and has drawn the key researchers in the field. Ontologies provide a mechanism for organising, sharing and reconciling data. Within recent years there has been a great deal of interest in the use of ontologies within bioinformatics, particularly in providing computationally accessible annotation, or standard data models for complex data for microarray or pathway information. Meetings such as last years workshop and SOFG have made it clear that there are many important uses of ontologies and a clear realisation of the importance of implementing mechanisms for integrating source ontologies rather than duplicating effort or causing confusion by extending a given ontology to include everything. However, with the increase in scope and use of ontologies within bioinformatics, issues of scalability, expressivity and best practices for modelling are becoming more important. We are particularly interested, therefore, in work involving multiple source ontologies, and which cut across the different levels of granularity implicit within biological systems. BioOntologies is an informal workshop. Submissions will be reviewed by the programme committee. A number of talks will be invited for ***full publication*** as papers in Comparative and Functional Genomics (see http://www3.interscience.wiley.com/cgi-bin/jissue/109860809 for last years papers) Submissions =========== Submission We invite submissions to this years Bio-Ontologies. Suitable topics include but are not restricted to: * Biological Applications of Ontologies. * Reports on Newly Developed or Existing Bio-Ontologies. * Tools for Developing Ontologies. * Use of Semantic Web technologies in BioInformatics * The implications of Bio-Ontologies or the Semantic Web for the drug discovery process * Current Research In Ontology Languages and its implication for Bio-Ontologies This year, for the first time, we would like to have a number of short software or ontology demonstrations, showing new or existing tools for building or using ontologies, or describing the design of ontologies. Submissions for these demonstrations are particularly encouraged. Submission Instructions ======================= Submissions are limited to 2 pages. Please submit using word using the templates available at http://bio-ontologies.man.ac.uk/submissions.html. Alternatively, submissions may be as a text file. Submissions should be emailed to bio-ont-sig at cs.man.ac.uk. We will acknowledge within a day or two. Bio-Ontologies is an informal meeting. Abstracts are reviewed by the programme committee. All accepted abstracts will be published by the organisers on their web site and in the main programme booklet. By submitting your paper, you consent to this publication. Authors of abstracts accepted for full publication as long (8 page) papers in Comparative and Functional Genomics will be notified following the meeting, for publication around October. Full details will be given later. Authors will be informed of acceptance within a few days of the submission deadline. -- Phillip Lord, Phone: +44 (0) 161 275 0683 PostDoctoral Research Associate, Email: p.lord at cs.man.ac.uk (preferred) School of Computer Science : p.lord at russet.org.uk Kilburn Building http://www.cs.man.ac.uk/~phillord University of Manchester http://www.russet.org.uk Oxford Road Manchester M13 9PL From mwilkinson at mrl.ubc.ca Wed Mar 30 17:48:40 2005 From: mwilkinson at mrl.ubc.ca (Mark Wilkinson) Date: Wed, 30 Mar 2005 14:48:40 -0800 Subject: [MOBY-l] LSID's are running again :-) Message-ID: <1112222920.3843.123.camel@mobycentral.icapture.ubc.ca> Hi all, The LSID resolver for MOBY LSID's is up and running again thanks to Eddie and with help and advice from Stephen Evanchik at IBM. I've also written a little CGI form that will resolve a MOBY LSID to the screen for viewing. This is available under the "Cool Tools" link from the MOBY homepage. Cheers all! M (reminder - just one more day to register for the MOBY meeting at a discount rate!!) -- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical Genetics, UBC, Canada From bmg at sfu.ca Thu Mar 31 19:41:37 2005 From: bmg at sfu.ca (Benjamin Good) Date: Thu, 31 Mar 2005 16:41:37 -0800 Subject: [MOBY-l] Re: [MOBY-dev] moby data and parameters In-Reply-To: <424C8F56.7080701@bcgsc.bc.ca> References: <424C8F56.7080701@bcgsc.bc.ca> Message-ID: <424C98C1.7070601@sfu.ca> Hi Stephen, You have an example of a collection of two GenericSequence objects (which could be either DNA or AA) in the Parser java file I sent you. So, yep, its a collection. Here is the (already java Stringified!) example. String xmlString2 = ""+ " "+ " "+ ""+ " "+ " "+ " "+ " "+ " 214 "+ " putative SUPERMAN-like C2H2 zinc finger transcription factor "+ "MKRTHLASFSNRDKTQEEEGEDGNGDNRVIMNHYKNYEAGLIPWPPKNYTCSFCRREFRSAQALGGHMNVHRRDRAKLRQIPSWLFEPHHHTPIANPNPNFSSSSSSSTTTAHLEPSLTNQRSKTTPFPSARFDLLDSTTSYGGLMMDREKNKSNVCSREIKKSAIDACHSVRCEISRGDLMNKKDDQVMGLELGMSLRNPNQVLDLELRLGYL"+ " "+ " "+ " "+ " "+ " "+ " "+ "1777 "+ "superman protein "+ "MERSNSIELRNSFYGRARTSPWSYGDYDNCQQDHDYLLGFSWPPRSYTCSFCKREFRSAQALGGHMNVHRRDRARLRLQQSPSSSSTPSPPYPNPNYSYSTMANSPPPHHSPLTLFPTLSPPSSPRYRAGLIRSLSPKSKHTPENACKTKKSSLLVEAGEATRFTSKDACKILRNDEIISLELEIGLINESEQDLDLELRLGFA"+ ""+ ""+ ""+ ""; For the return datatype, I think you might actually want to define the "parameters" as children (ie has/hasa) of your Chinook-service-list-datatype and then send back a collection of these datatypes. Maybe send a proposed example of this new datatype? -Ben Stephen Montgomery wrote: > hi - > > does anyone have an example of a xml input where more than one dna > sequence is coming down the wire. is this a collection? > > also, for a registered return data type we want to attach some > parameters (corresponding to the application that is going to be > run). is there a java example out there of doing this? > > all the best, > > stephen > > ps ben and i had an awesome crash coding session yesterday. set-up > the plan, built the supports, now we just need to execute the vision. > rock on. > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://www.biomoby.org/mailman/listinfo/moby-dev > > From bmg at sfu.ca Thu Mar 31 19:58:46 2005 From: bmg at sfu.ca (Benjamin Good) Date: Thu, 31 Mar 2005 16:58:46 -0800 Subject: [MOBY-l] Re: [MOBY-dev] moby data and parameters In-Reply-To: <424C8F56.7080701@bcgsc.bc.ca> References: <424C8F56.7080701@bcgsc.bc.ca> Message-ID: <424C9CC6.6090404@sfu.ca> For a potentially non-moby bioinformatics service discovered using Chinook (inside moby), what about an object like this? ChinookService isa object hasa String articleName "location" hasa String articleName "name" hasa String articleName "version" hasa String articleName "MobyXMLData-input" with secondary articles... has Float articleName "FloatParam??" has String articleName "StringParam??" See here for details about how you ~should compose objects http://www.biomoby.org/twiki/bin//view/Moby/MobySAPI -ben Stephen Montgomery wrote: > hi - > > does anyone have an example of a xml input where more than one dna > sequence is coming down the wire. is this a collection? > > also, for a registered return data type we want to attach some > parameters (corresponding to the application that is going to be > run). is there a java example out there of doing this? > > all the best, > > stephen > > ps ben and i had an awesome crash coding session yesterday. set-up > the plan, built the supports, now we just need to execute the vision. > rock on. > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://www.biomoby.org/mailman/listinfo/moby-dev > > From bmg at sfu.ca Thu Mar 31 20:08:24 2005 From: bmg at sfu.ca (Benjamin Good) Date: Thu, 31 Mar 2005 17:08:24 -0800 Subject: [MOBY-l] secondary articles Message-ID: <424C9F08.8030507@sfu.ca> When you decide on a datatype, go ahead and register it so we can check it out - don't forget you can use bioinfo.icapture.ubc.ca instead of mobycentral (since it is problematic right now). I sent an email with details on this one yesterday. I believe the secondary articles are not part of the DataType registration phenomenon, but rather the service registration. So you can say I am a service that accepts DNASequence object with secondary data bla bla bla. The basic jMoby structure for registration is to build an example instance of the thing (MobyService or MobyDataType for example) and then call CentralImpl to register it (or deregister it). There are methods within the MobyService and MobyDataType classes for specifying whatever you need. -Ben From wangch at cpsc.ucalgary.ca Wed Mar 30 18:59:24 2005 From: wangch at cpsc.ucalgary.ca (Chunyan Wang) Date: Wed, 30 Mar 2005 23:59:24 -0000 Subject: [MOBY-l] How to register the service to Moby References: <1112222920.3843.123.camel@mobycentral.icapture.ubc.ca> Message-ID: <424B3E8B.5070607@cpsc.ucalgary.ca> Hi All, I am new to Moby. I followed the Fasta example service to create our svervice. How do I register our service to Moby Centrol? could Anyone let me know about? Thanks, Joyce Mark Wilkinson wrote: >Hi all, > >The LSID resolver for MOBY LSID's is up and running again thanks to >Eddie and with help and advice from Stephen Evanchik at IBM. > >I've also written a little CGI form that will resolve a MOBY LSID to the >screen for viewing. This is available under the "Cool Tools" link from >the MOBY homepage. > >Cheers all! > >M > >(reminder - just one more day to register for the MOBY meeting at a >discount rate!!) > > > > From daniel.schulz at lionbioscience.com Tue Mar 22 10:24:37 2005 From: daniel.schulz at lionbioscience.com (schulz) Date: Tue, 22 Mar 2005 15:24:37 -0000 Subject: [MOBY-l] Re: Ant tasks (was: [MOBY-dev] Java packagesconversation) Message-ID: <200503221529.j2MFTXF07870@mail.lion-ag.de> Hi, >> You can set ant properties using -D properties as command line >> arguments to the JVM. >> > That's what I used in my example - but as an inconvenient way (and > unfortunately the only one, I still think). What I was asking about is the > (non-existent, I think) possibility to say, e.g.: > > ant my_target - -my param1 -your param2 Maybe I miss something, but I think there is not much difference of "ant my_target - -my param1 -your param2" to "ant my_target -Dproperty=value" and then to reference it as ${property} in your ANT script. Best, Daniel