From senger at ebi.ac.uk Mon Jan 10 07:00:04 2005 From: senger at ebi.ac.uk (Martin Senger) Date: Mon Jan 10 06:56:58 2005 Subject: [MOBY-dev] MOBY Central now breaks Java In-Reply-To: <41C1E0CA.4040307@cbr.nrc.ca> Message-ID: Hi all, Is this still an issue? Should I change anything in the CentralImpl? My today test, however, does not indicate any problems: bagheera:~/moby-live/Java> build/run/run-testing-central retrieveServiceNames OK retrieveServiceProviders OK retrieveServiceTypes OK retrieveNamespaces OK retrieveObjectNames OK registerServiceType OK registerNamespace - 1 OK registerNamespace - 2 OK registerDataType - 1 OK registerDataType - 3 OK registerDataType - 2 OK getDataTypeDefinition - 2 OK registerService OK deregisterService OK deregisterDataType - 2 OK deregisterDataType - 3 OK deregisterDataType - 1 OK deregisterNamespace - 2 OK deregisterNamespace - 1 OK deregisterServiceType OK With regards, 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 ywong at infobiogen.fr Tue Jan 11 09:28:30 2005 From: ywong at infobiogen.fr (ywong@infobiogen.fr) Date: Tue Jan 11 09:25:05 2005 Subject: [MOBY-dev] bioMoby Python, dynamic typing and multithreading (client side) Message-ID: <33443.195.221.101.193.1105453710.squirrel@195.221.101.193> Hello and Happy new year ^O^ I have made some modifications on the API of bioMoby Python (however, I haven't commited the changes yet as I have to review the documentation) The modifications are: -Multithreading on the client side of service execution (no need to wait the end of the execution of a service before invoking another, it is useful when you have different services to query at the same time (as an HTTP transaction is rather slow, we can use that time to send other queries) The syntax would look like this: firstService=Service(wsdl) firstService.start(mobyQueries, timeout=50) secondService=Service(wsdl) secondService.start(mobyQueries, timeout=50) thirdService=Service(wsdl) thirdService.start(mobyQueries, timeout=50) firstService.join() secondService.join() thirdService.join() A property in Service class will allow user to manipulate directly the thread object which will enable rendez-vous techniques, locks, and so on... Webservices are already slow, if we can send several queries at different services at the same time, it won't be a luxury I believe... -Use of Python's ability for dynamic typing to build classes from scratch (even methods!): No need of moby2python to generate classes from bioMoby definition. It is now the job of mobyUnmarshaller. from bioMoby import mobyUnmarshaller um=MobyUnmarshaller() r=um.loads() r will contain a generated python instance of a Class with attributes generated from the XML (only attributes, partial deserialization) for serialization: m=MobyMarshaller() m.dumps(a Python Object) an example: a=(1,2,3,4,5) m.dumps(a) '12345' It also works for objects: class DNASequence(object): def __init__(self, sequence): self.SequenceString=sequence self.Length=len(sequence) seq=DNASequence("ACGTAGCATGCTAGCTAGCTAGCATGCT") m.dumps(seq) 28ACGTAGCATGCTAGCTAGCTAGCATGCT From ywong at infobiogen.fr Tue Jan 11 12:38:08 2005 From: ywong at infobiogen.fr (ywong@infobiogen.fr) Date: Tue Jan 11 12:34:36 2005 Subject: [MOBY-dev] questions about gbrowse-moby Message-ID: <34407.195.221.101.193.1105465088.squirrel@195.221.101.193> After some implementations of webservices in Python, I've noticed that I was able to query moby services normally, but when I used gbrowse_moby to query Python webservices, it wasn't successful at all. My Python API send a string to query services, these services all return results: *** Outgoing HTTP headers ********************************************** POST /webservices/predotar.py HTTP/1.0 Host: genoplante-info.infobiogen.fr User-agent: SOAPpy 0.11.4 (http://pywebsvcs.sf.net) Content-type: text/xml; charset="UTF-8" Content-length: 2248 SOAPAction: "http://biomoby.org/#predotarP" ************************************************************************ *** Outgoing SOAP ******************************************************

<?xml version="1.0" encoding="UTF-8"?><moby:MOBY xmlns:moby="http://www.biomoby.org/moby"><moby:mobyContent><moby:mobyData moby:queryID='query'><moby:Simple><moby:AminoAcidSequence ><moby:Integer moby:articleName="Length" >1256</moby:Integer><moby:String moby:articleName="SequenceString" >MGLGCGTSIAHEPPMVKCMVMYNGQSSWDMFSPWLVGGDEQPVNMIFEPMRAVTIISNNTPGMVFSGCWPDRYTHENVVGDRFKIINCKFPHQCNNVGAALCCDIRIDSHEGDQDKDEGWQYFEFCHMHAQNNVIWPQQHFGDWNWMWHKQNPKEMCMSRYCEWNKCVWTMGHPCSVRMYGIRLSSNVCSRQAEPAVQNSRGPSETPKEPIHYEGSSNRYGVHKGVSLMNWGNSCMNVINPGTCFIARADNNATVKDWMEPHHAAKLCVCAWQQRSYENAFEKHRAQIGKGSWSSAKMKGRKGNGGQSLMFCSCYHLDTPESMSTTYHIKFCPGLHAMQWRNDEWLSRGWNATKTKDPPFQWNKNVTKHAVEFRKGGTWSTKATEYWGKSHKEWGHNNHPHYVLDWAGCHFCAMESERDWPVQNKRCNQTLHCMDENLNPHITIILWWVWAWCVFYESCPNIEQKVCDKTRHIVLQQCDEDHYVACHHALWMKLWLMAVMHPLHFRYNLGNLTCPMIATMDLEFCHYMWQMYDYKRIYKYDVRNVIAKWGWEMKIQLFTSAHEFPSPMSTAQDKPPMMGSSAVEIWYHPVLYTMYVNISNPNHQHGNGSFEAEVAPPFHKYTSYNSHTRVLITPAYYEFQRLKEPFEHWDWSEPGPYSNITGPYVIALSPCPNEIEVCSKSNQHKTQEIMFMRHIGGLEWGVMYIYWNSWVGRWHWFDPQEGVRNNICNDLVKNPHFYDNAVPVNVQQHRKARICNNMNVKCRCENMPDIMEGHSTIPGLYHEQEFTGEIIHAENECANQVKSLGWVLMWQYPVPEPTEEKPAKSAWLGNGACPPPSRYCMYPNPNPKYPMTACCEHMQEYRRAIHRWNRLNEHKADLTFTEVPVVRRIPVVMSHDGHDCEDICMMRIIADMDRGQWWRHDTWPFYWSSLKEAVFKDKWCPEENCQLLFHEISKEVQKRLPNSKCTRTIPRTNESRHAQWRHGWH! NRINSFKTPRQIDQFIIPYYMERMKCPTVPLHCQPVWWFQRSEDCKYDDVKTNEVKMVQGYTMCRMYYSMHIGSLFDYETVALNWSKWMGKLDRYHYSNGFEYDTTHRFATQEVGNQEAHEPHRHFCLAFHSAEDMNRDCHTRYGMGLKIADYETYCVTIWHYNHVKHAGISVFKSTEKSNFIGDPSHIERQIGMRISTVTGECGDPHKVMQSPEPAGRWKFLMFKTHCKKAYLCNSNITFQDQYMHFIKEFVWMREFFNIILDCVPLTPW</moby:String></moby:AminoAcidSequence></moby:Simple></moby:mobyData></moby:mobyContent></moby:MOBY>

************************************************************************ here one of the response my service give: *** Incoming HTTP headers ********************************************** HTTP/1.? 200 Date: Tue, 11 Jan 2005 17:31:49 GMT Server: Apache Content-Length: 1441 Connection: close Content-Type: text/xml; charset="utf-8" ************************************************************************ *** Incoming SOAP ******************************************************

<?xml version="1.0" encoding="UTF-8"?><moby:MOBY xmlns:moby="http://www.biomoby.org/moby"><moby:mobyContent><moby:mobyData moby:queryID='query'><moby:Simple><moby:PredotarP_result moby:namespace="" moby:id="" moby:articleName=""><moby:Float moby:namespace="" moby:id="" moby:articleName="ER_Score">0.01</moby:Float><moby:Float moby:namespace="" moby:id="" moby:articleName="MIT_Score">0.01</moby:Float><moby:Float moby:namespace="" moby:id="" moby:articleName="None_Score">0.96</moby:Float><moby:Float moby:namespace="" moby:id="" moby:articleName="P_Score">0.03</moby:Float><moby:String moby:namespace="" moby:id="" moby:articleName="Prediction"><![CDATA[none]]></moby:String></moby:PredotarP_result></moby:Simple></moby:mobyData></moby:mobyContent></moby:MOBY>

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From ywong at infobiogen.fr Thu Jan 13 09:58:08 2005 From: ywong at infobiogen.fr (ywong@infobiogen.fr) Date: Thu Jan 13 09:54:29 2005 Subject: [moby] [MOBY-dev] questions about gbrowse-moby In-Reply-To: References: Message-ID: <33655.195.221.101.193.1105628288.squirrel@195.221.101.193> I used the Perl API to query test_python_echo, bad luck, no results... I used the debugYourService script to trace execution. I send the trace. AFAIK the script give results except when I query my service! Now I am almost clueless... The most astonishing fact is that apparently, it receives the answer but doesn't seems able to deserialize the content ?! I hope it can help, next week I'll put the test_python_echo webservice on the public webserver (then you'll be able to test by yourself). > Hi, > For this service it is normal as it is a service on my personal > webserver which is offline most of the time. > > I send you the captured frames of the answer, maybe this will help. On > my side, I'll do some testing using the moby Perl API (As gbrowse_moby > uses it to query services) maybe this will help me to find what's wrong > with my service... > > ------------------------------------------------------------- > NetCourrier, votre bureau virtuel sur Internet : Mail, Agenda, Clubs, > Toolbar... > Web/Wap : www.netcourrier.com > T?l?phone/Fax : 08 92 69 00 21 (0,34 ? TTC/min) > Minitel: 3615 NETCOURRIER (0,16 ? TTC/min) > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev@biomoby.org > http://www.biomoby.org/mailman/listinfo/moby-dev > -------------- next part -------------- SOAP::Transport::new: () SOAP::Serializer::new: () SOAP::Deserializer::new: () SOAP::Parser::new: () SOAP::Lite::new: () SOAP::Transport::HTTP::Client::new: () SOAP::Lite::call: () SOAP::Serializer::envelope: () SOAP::Serializer::envelope: findService 0 moby test_python_echo 0 0 SOAP::Data::new: () SOAP::Data::new: () SOAP::Data::new: () SOAP::Data::new: () SOAP::Data::new: () SOAP::Transport::HTTP::Client::send_receive: HTTP::Request=HASH(0x871f07c) SOAP::Transport::HTTP::Client::send_receive: POST http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral.pl HTTP/1.1 Accept: text/xml Accept: multipart/* Content-Length: 776 Content-Type: text/xml; charset=utf-8 SOAPAction: "http://mobycentral.cbr.nrc.ca/MOBY/Central#findService"

<findService> <authoritative>0</authoritative> <Category>moby</Category> <serviceName>test_python_echo</serviceName> <expandObjects>0</expandObjects> <expandServices>0</expandServices> </findService>

SOAP::Transport::HTTP::Client::send_receive: HTTP::Response=HASH(0x882e784) SOAP::Transport::HTTP::Client::send_receive: HTTP/1.1 200 OK Connection: close Date: Thu, 13 Jan 2005 14:42:47 GMT Server: Apache/1.3.29 (Unix) mod_perl/1.29 Content-Length: 1428 Content-Type: text/xml; charset=utf-8 Client-Date: Thu, 13 Jan 2005 14:42:38 GMT Client-Peer: 198.166.4.151:80 Client-Response-Num: 1 SOAPServer: SOAP::Lite/Perl/0.60

<Services> <Service authURI='test.test.test' serviceName='test_python_echo'> <serviceType>Retrieval</serviceType> <authoritative>1</authoritative> <Category>moby</Category> <Description> Don't use it, this service is here for testing Python webservice </Description> <contactEmail>gpsupport@infobiogen.fr</contactEmail> <signatureURL></signatureURL> <URL>http://192.168.101.23/cgi-bin/echo.py</URL> <Input> <Simple articleName=''> <objectType>Object</objectType> <Namespace>Global_Keyword</Namespace> </Simple> </Input> <Output> <Simple articleName=''> <objectType>Object</objectType> <Namespace>Global_Keyword</Namespace> </Simple> </Output> <secondaryArticles> </secondaryArticles> </Service> </Services>

SOAP::Deserializer::deserialize: () SOAP::Parser::decode: () SOAP::SOM::new: () SOAP::Lite::call: () SOAP::Serializer::envelope: () SOAP::Serializer::envelope: retrieveService Retrieval 1 moby Don't use it, this service is here for testing Python webservice gpsupport@infobiogen.fr http://192.168.101.23/cgi-bin/echo.py Object Global_Keyword Object Global_Keyword SOAP::Data::new: () SOAP::Data::new: () SOAP::Data::DESTROY: () SOAP::Data::DESTROY: () SOAP::Data::DESTROY: () SOAP::Data::DESTROY: () SOAP::Data::DESTROY: () SOAP::Data::new: () SOAP::Data::new: () SOAP::Data::new: () SOAP::Transport::HTTP::Client::send_receive: HTTP::Request=HASH(0x8881624) SOAP::Transport::HTTP::Client::send_receive: POST http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral.pl HTTP/1.1 Accept: text/xml Accept: multipart/* Content-Length: 1408 Content-Type: text/xml; charset=utf-8 SOAPAction: "http://mobycentral.cbr.nrc.ca/MOBY/Central#retrieveService"

<retrieveService> <Service authURI="test.test.test" serviceName="test_python_echo"> <serviceType>Retrieval</serviceType> <authoritative>1</authoritative> <Category>moby</Category> <Description> Don't use it, this service is here for testing Python webservice </Description> <contactEmail>gpsupport@infobiogen.fr</contactEmail> <signatureURL/> <URL>http://192.168.101.23/cgi-bin/echo.py</URL> <Input> <Simple articleName=""> <objectType>Object</objectType> <Namespace>Global_Keyword</Namespace> </Simple> </Input> <Output> <Simple articleName=""> <objectType>Object</objectType> <Namespace>Global_Keyword</Namespace> </Simple> </Output> <secondaryArticles> </secondaryArticles> </Service> </retrieveService>

SOAP::Transport::HTTP::Client::send_receive: HTTP::Response=HASH(0x8881768) SOAP::Transport::HTTP::Client::send_receive: HTTP/1.1 200 OK Connection: close Date: Thu, 13 Jan 2005 14:42:47 GMT Server: Apache/1.3.29 (Unix) mod_perl/1.29 Content-Length: 2810 Content-Type: text/xml; charset=utf-8 Client-Date: Thu, 13 Jan 2005 14:42:38 GMT Client-Peer: 198.166.4.151:80 Client-Response-Num: 1 SOAPServer: SOAP::Lite/Perl/0.60