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Text of the page (random words):
biomoby a world of data at your fingertips skip to content biomoby a world of data at your fingertips menu what is moby biomoby mailing lists funding agencies and supporters history of moby s moby presentations publications and press who is using biomoby and for what who is using biomoby and for what use moby now biomoby application developers end user biomoby applications developers info biomoby perl tutorial register a moby service connecting to moby central in perl and java extensions and accessories beyond the biomoby core api how to retrieve metadata about moby resources the use of lsid s in biomoby unit tests for moby services create unit tests with dashboard dashboard unit testing unit test specification unit testing services with java unit tests in perl extensions and accessories to the biomoby cor getting the code installing a moby central registry moby constructor clients moby registry clients moby service clients moby tools and toys official code releases setting up a moby central registry taverna moby plugin information taverna support for moby the rdf agent a biomoby tutorial semantic moby moby dashboard as java webstart now available click through to the full blog post for a link andreas groscurth at the max planck institute cologne has made the moby dashboard available as a java webstart app well done andreas dashboard is the most powerful and comprehensive view of the biomoby project allowing you to browse the registry and ontologies add new nodes into the ontology delete un used nodes and register deregister services the added simplicity of having this available through web start will surely make life easier for all mobyers author markw posted on june 12 2008 categories general moby clients moby for java new perl moses panel in dashboard for those developing perl based biomoby services there is a new panel in dashboard the panel is called the perl moses generator and can be used to generate service skeletons for both cgi and soap based biomoby services in addition the panel includes a built in editor with perl syntax highlighting for details start up dashboard and choose help perl moses generator once the perl moses generator panel has been added into view using the settings panel selection further documentation is coming soon please make sure that you are running moses moby version 0 86 or higher author eddie kawas posted on may 16 2008 categories general moby for java news new cpan releases new releases of the moby 1 04 moby client 1 02 and moses moby 0 86 modules are available on cpan view the change log for details on what was fixed and any new functionality author eddie kawas posted on may 16 2008 categories general news jmoby faster access to biomoby registries eddie kawas released a new implementation no api changes of the org biomoby client centralcachedcallsimpl class now getting the contents of the registry using the rdf files when all bugs are fixed it should significantly speed up cache update in dashboard and elsewhere author martin posted on february 21 2008 categories general jmoby using maven major changes in building and using jmoby were introduced during the biohackathlon meeting in japan the changes however are not changes of the jmoby api which means that your own code should continue to work without any changes the main issue is that jmoby uses now the 3rd party libraries form the various maven repositories it fetches them when you compile jmoby or when you use the new ant s task install there is an article about how it is done coming from a different project but using the same principles as in jmoby another issue is that the ant itself is not anymore distributed with jmoby you need to install it separately on your machine author martin posted on february 21 2008 categories general biomoby developers meeting todo list api changes 1 storage of xml lang information in registry is necessary providers should pay attention to which xml lang attribute they send to the registry when they register their service object etc 2 not all sub elements need to be in an object instance document the fact that an element that is missing is different from an element that is blank 3 explicitly say that member articles of an object are allowed to be child types of the registered type we are now promoting a behaviour for member articles that already existed for the parent objects 4 support document style encoding as well as rest as well as the traditional rpc to do s 1 store all incoming registry data as utf 8 mark 2 store the xml lang of the incoming registry entry and reproduce it on output from reg mark 3 support for async services in jmoby core martin inb 4 inb is going to propose using endpoint references as part of async pass references to biiiig data inb 5 everyone look at how to stream data in web services protocol eddyone 6 reorganize jmoby cvs so that tests are in a folder off of root paul 7 mark needs to update commonsubs object parsing code to allow for missing sub tags mark 8 mark needs to document about missing sub tags mark eddie wendy 9 others will look at their parsers to see if they need to be updated everyone 10 mark needs to update commonsubs to allow sub objects to inherit mark eddie wendy 11 classpath template should be added to cvs martin 12 martin is goign to change build process to ant maven martin 13 someone will commit to maven repository need to get permissions on the existing open bio maven repository all java developers 14 java api documentation should either be reduced or shold be split into full and core javadoc etc martin 15 wendy needs to write an introduction to moby document that explains what we mean by object namespace etc and the basic behaviour that we are trying to achieve wendy 16 someone wendy needs to take charge of all documentation and fix it also try to get registry calls in some standard bnf format registry api should be all in one document use xs3p schema documentation generator wendy 17 martin makes a cpan release of moses registry snapshot one day eddie martin 18 mark will explore how feasible it is to register secondary outputs will make api change proposal to list mark 19 releases of moby perl code should be in cpan mark with help from someone who knows 20 methods for testing services at various levels including sample input output in the lsid metadata will become a part of jmoby s api and possibly a panel in dashboard need to know the predicate names for this martin 21 cleanly split perl registry from java stuff eddie 22 andreas continues working on registry synchronization fun fun fun he will propose to the list will take advice from community and decide for himself what he wants to support andreas 23 think about the proper way to attribute e g logo s and state this in the documentation andreas 24 mobycentral needs to generate wsdl consistent with document style encoding mark eddie 25 moby central needs to record the style that a service is provided add new fields to the registerservice findservice input output also the lsid metadata coordinate this with feta mark eddie 26 moby central should somehow support registration of rest style services we decided that post must be supported by any rest service how does this affect wsdl all rest services must be synchronous at the moment mark eddie 27 ivan needs to look into support for async services in rest someday manana inb 28 authentication how should we do it in the various libraries paul java eddie perl 29 paul will jmoby lsid library api implementation to get the metadata from service providers paul 30 can we please make a wsdl xml schema file for moby central eddie author markw posted on june 3 2007 categories general biomoby jmoby developers meeting hour 1 in attendance mark eddie wendy richard ivan andreas paul martin mylah we started with jokes about the danger of having the core moby developers in the same room of a brick hospital built on top of a geological fault issues that come up atrtribution of data to providers set logo should the object ontology have multiple representations for any given concept e g fasta and dna sequence are redundant we need to find a way to encourage object re use we need a rule base to use the seahawk transformation rules rather than registering a new moby object or do we still need to register a new object author markw posted on june 3 2007 categories general monitoring moby usage if we had a referrer that kept track of the previous service that was executed this would go into the service provider logs we could then set up a service pull that moby central could use to gather this information from the logs alternately we could push from the service as it is executed for us as client writers the first step is to ensure that we add the referer header so we gotta do that probably the lsid of the previous service all in all this will give us the ability to make the next most popular choice very visible in our clients filtering out the lesser used services and bringing the cream to the top author markw posted on june 3 2007 categories general day two the future of the moby protocol problem 1 registry we have a problem that the registry is a mishmash of perl and java the resources script is problematic since it is used by moby central to generate the rdf that is passed back from a registerservice call this needs to be perlified the agent is not a web script so that isn t a problem the isalive pinger can be ported to perl but since it uses threads it will run slower in perl than it did in java in any case the entire registry can be written in perl decision write a cpan distribution decision write an installer martin suggests perl hacks book as a must read problem 2 services need to support legacy all 1300 services are currently rpc so we have to keep that we need to add a field in the registry to indicate which style of encoding is being used we prefer document literal wrapped separate field in the database api lsid metadata field called style currently have a field called category which has values moby moby async and unofficially post separate style from category probably a good idea tell wendy that we need to put the async protocol up on the website iff we provide correct wsdl will that make people happier maybe we can provide wsdl in 90 of the cases though not for validation burning issue is that we don t have xml schema why because we allow more specialized objects to be passed into a service and problems with has relationships the world is moving to rdf and rdf also cannot be expressed in xml schema so the political arguments against moby are going to eventually die out one problem is that we pass a full xml document in our soap body if we use document encoding we will need to strip the xml header which has other encoding info that we want to have and the message will have to be parsed twice once by the soap libraries and once by our moby libraries because we don t have an xml schema to give to teh soap libraries to unmarshal the objects and that will give us unacceptable overheads if we move to a rest style then we don t have these problems but we don t get any what advantages of wsdl or soap we can use string encoding and send moby messages exactly as we do now in teh body of a document style soap message no advantages of the soap libraries but also no overhead of double parsing of teh message exactly as we do with the moby xml rpc style right now conclusion inb could you consider asynchronous services support from a rest perspective and suggest a specification conclusion we will support rpc document style and rest services but rest services cannot right now be asynchronous author markw posted on june 3 2007 categories general localization issues support for different languages registry contents should be utf 8 registry code needs to check this and if it isn t utf 8 then either convert it or reject it or save the encoding decision registry converts all incoming xml into utf 8 from services we send data in whatever encoding we want and clients need to be clevererer or parser sax libxml already knows how to deal wtih these things we need to pay more attention to this that was the decision we made to pay more attention languages if the xml lang attribute is defined then it should be maintained and saved in the database and returned when the service description is reconstructed e g for a findservice need to capture the language for object namespace service service instances and secondary parameters author markw posted on june 2 2007 categories general posts pagination page 1 page 2 page 3 next page search for search recent posts moby dashboard as java webstart new perl moses panel in dashboard new cpan releases jmoby faster access to biomoby registries jmoby using maven recent comments archives june 2008 may 2008 february 2008 june 2007 april 2006 categories general moby clients moby for java news meta log in entries feed comments feed wordpress org what is moby biomoby mailing lists funding agencies and supporters history of moby s moby presentations publications and press who is using biomoby and for what who is using biomoby and for what use moby now biomoby application developers end user biomoby applications developers info biomoby perl tutorial register a moby service connecting to moby central in perl and java extensions and accessories beyond the biomoby core api how to retrieve metadata about moby resources the use of lsid s in biomoby unit tests for moby services create unit tests with dashboard dashboard unit testing unit test specification unit testing services with java unit tests in perl extensions and accessories to the biomoby cor getting the code installing a moby central registry moby constructor clients moby registry clients moby service clients moby tools and toys official code releases setting up a moby central registry taverna moby plugin information taverna support for moby the rdf agent a biomoby tutorial semantic moby biomoby proudly 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