[mart-dev] Accessing SOAP services from a local biomart installation

://mygrid.ncl.ac.uk:9002/biomart/martwsdl Why am I not seeing anything here? Is there some extra step in the installation that I would need to do in order to install the web services aspect? Any help would be most appreciated. Thanks :) -- Thanks, Allyson :) Allyson Lister Research Associate Centre

Re: [mart-dev] Accessing SOAP services from a local biomart installation

the release-0_7 branch. If you look in the cgi-bin folder inside biomart-perl and don't see martsoap.pl etc. present there, then you probably don't have the 0.7 branch checked out. cheers, Richard Allyson Lister wrote: Hi all, I've made a local biomart installation, and have started with just

Re: [mart-dev] Accessing SOAP services from a local biomart installation

the checked out branch in the output under the 'Existing Tags' sections. cheers, Richard Allyson Lister wrote: Hi Richard, Thanks for the quick reply. I do have release 0.7 (sorry I forgot to mention that in the original post), but I'm sure I checked out from the head/trunk

[mart-dev] Biomart WSDL

context, or should I find some sort of workaround just for me? Thanks again! -- Thanks, Allyson :) Allyson Lister Research Associate Centre for Integrated Systems Biology for Ageing and Nutrition Newcastle University http://www.cisban.ac.uk School of Computing Science Newcastle University Newcastle

Re: [mart-dev] Biomart WSDL

/ -- Thanks, Allyson :) Allyson Lister Research Associate Centre for Integrated Systems Biology for Ageing and Nutrition Newcastle University http://www.cisban.ac.uk School of Computing Science Newcastle University Newcastle upon Tyne, NE1 7RU

[mart-dev] Accessing biomart.org WSDL from Java CXF client

) at org.apache.cxf.jaxws.JaxWsClientProxy.invoke(JaxWsClientProxy.java:177) ... 28 more Process finished with exit code 255 -- Thanks, Allyson :) Allyson Lister Research Associate Centre for Integrated Systems Biology for Ageing and Nutrition Newcastle University http://www.cisban.ac.uk School of Computing Science

[mart-dev] Re: Accessing biomart.org WSDL from Java CXF client

) at org.apache.cxf.frontend.ClientProxy.invokeSync(ClientProxy.java:73) at org.apache.cxf.jaxws.JaxWsClientProxy.invoke(JaxWsClientProxy.java:177) ... 28 more Process finished with exit code 255 -- Thanks, Allyson :) Allyson Lister Research Associate Centre for Integrated Systems Biology for Ageing and Nutrition Newcastle

[mart-dev] SOAP::Lite required in local biomart install if want to use SOAP

to install it via cpan or similar if you don't already have it in order to get your local SOAP services working. :) -- Thanks, Allyson :) Allyson Lister Research Associate Centre for Integrated Systems Biology for Ageing and Nutrition Newcastle University http://www.cisban.ac.uk School

Re: [mart-dev] Biomart WSDL

...@oicr.on.ca On 09/01/09 2:43 AM, Allyson Lister a.l.lis...@newcastle.ac.uk wrote: Hi all, Thanks for all the tips - I agree that modifying the XSD would seem to be the best long-term fix. Otherwise, I'll have a look into some JAXB modifications, like the one already suggested. There's

Re: [mart-dev] SOAP::Lite required in local biomart install if want to use SOAP

Allyson Lister wrote: Hi all, One other thing that was causing me problems in my *local* biomart installation was traced, ultimately, from a HTTP 500 error via the apache logs to a lack of the SOAP::Lite perl module. Just a note for everyone out there, as it seems the config script doesn't

Re: [mart-dev] Expected XML response from SOAP service does not start with XML

Just one modification of this email: 2009/1/10 Allyson Lister a.l.lis...@newcastle.ac.uk Whereas the biomart service returns: Status: 200 OK [...] The above should read: Whereas the biomart service returns: HTTP/1.1 200 OK [...] [newline] Status: 200 OK [...]

Re: [mart-dev] Expected XML response from SOAP service does not start with XML

and restart your apache, the extra headers will be gone, you dont need to write a custom parser anymore. Cheers Syed Allyson Lister wrote: Just one modification of this email: 2009/1/10 Allyson Lister a.l.lis...@newcastle.ac.uk mailto: a.l.lis...@newcastle.ac.uk Whereas the biomart

Re: [mart-dev] Expected XML response from SOAP service does not start with XML

:) cheers Syed Richard Holland wrote: in which case, ignore my last email :) :) cheers, Richard Allyson Lister wrote: Hi Syed, Thanks very much! Now my soap calls are working perfectly. Thanks again! :) allyson 2009/1/10 Syed Haider s...@ebi.ac.uk mailto:s...@ebi.ac.uk

Re: [mart-dev] Ensembl and biomart release numbers from the Web services

://myhits.vital-it.ch/ -- Allyson Lister http://lurena.vox.com CISBAN, http://www.cisban.ac.uk Newcastle University

[mart-dev] reaction result in reactome.org not matched in query in biomart.org

= stableidentifier_identifier / Attribute name = reaction_db_id / Attribute name = _displayname / Attribute name = species__displayname / /Dataset /Query Thanks, Allyson -- Allyson Lister http://lurena.vox.com CISBAN, http

[mart-dev] Re: Fwd: interpreting GO IDs

-- Forwarded message -- From: *Allyson Lister* allyson.lur...@googlemail.com mailto: allyson.lur...@googlemail.com Date: 2009/1/16 Subject: interpreting GO IDs To: mart-dev@ebi.ac.uk mailto:mart-dev@ebi.ac.uk mart-dev@ebi.ac.ukmailto: mart-dev@ebi.ac.uk Not sure if this made

[mart-dev] Re: Fwd: interpreting GO IDs

. If you retrieve the complete results set, that will be the same in terms of first three columns. Please try that and let me know if that explains... Cheers Syed Allyson Lister wrote: Hi Syed, I'm not sure that is the reason, because even though the GO IDs *seem* identical, the GO

[mart-dev] SOAP service not returning the same result as MartView

, when martview says there are 50. I am confused! Martview says the query has 50 results, and provides those results. MartSoap says there are 66 (or 2!) but cannot display any of those results. Please let me know what I'm doing wrong! -- Allyson Lister http://lurena.vox.com CISBAN, http

[mart-dev] Re: Fwd: interpreting GO IDs

and comprehensive version of UNIPROT is about to be released (Jie cc'ed here can point you to the test site too). Also, I guess the attributes you are interested in can be retrieved from Ensembl too, please try that. Thanks Syed Allyson Lister wrote: Hi Syed, I guess I'm still

[mart-dev] Re: Fwd: interpreting GO IDs

...@googlemail.com] *On Behalf Of *Allyson Lister *Sent:* 26 January 2009 09:19 *To:* Syed Haider *Cc:* mart-dev@ebi.ac.uk; Jie Luo *Subject:* Re: Fwd: interpreting GO IDs Hi Syed, Jie, I will try Ensembl, but I would be very interested in the new Uniprot mart - I had no way of knowing

Re: [mart-dev] SOAP service not returning the same result as MartView

the result set with all the GO IDs against the said gene names. Unfortunately, I cant be of any help on your Soap client why its misbehaving, somebody from list please Hope this helps a bit, Syed Allyson Lister wrote: Hi all, I've tried to recreate a simple query done in biomart.org

Re: [mart-dev] SOAP service not returning the same result as MartView

2009/1/26 Damian Smedley dam...@ebi.ac.uk Allyson Lister wrote: Hi Syed, I think there are two points here: 1. There is a bug with biomart, irrespective of how you query against it (soapUI, martview, Apache CXF). You've shown it in the previous email you sent: the response

Re: [mart-dev] SOAP service not returning the same result as MartView

is saying the response will be? Thanks very much! :) Allyson 2009/1/26 Allyson Lister a.l.lis...@newcastle.ac.uk 1. The soap client I'm using is NOT one I've written - it is autogenerated, via Apache CXF (a freely-available, widely-used SOAP app). Therefore *anyone* who may wish

Re: [mart-dev] SOAP service not returning the same result as MartView

Hi Syed, Tom, I'll address both of you in one email :) See inline for comments. 2009/1/28 Syed Haider s...@ebi.ac.uk Hi Tom, Allyson Lister wrote: Hi all, Just bumping up the bit of my previous email (below) that hasn't had a response yet. Does anyone have any ideas on this one? How