From Elise.Larsonneur at avignon.inra.fr Fri Jun 4 03:28:58 2010 From: Elise.Larsonneur at avignon.inra.fr (Elise Larsonneur) Date: Fri, 04 Jun 2010 09:28:58 +0200 Subject: [MOBY-dev] moby services deployment In-Reply-To: <005c01cafdb6$32c44840$984cd8c0$@gmail.com> References: <4BFCE3CE.4060504@avignon.inra.fr> <002401cafcd7$79cb3850$6d61a8f0$@gmail.com> <4BFD31C8.1070008@avignon.inra.fr> <004101cafd9a$f1273570$d375a050$@gmail.com> <4BFE9148.4020800@avignon.inra.fr> <005c01cafdb6$32c44840$984cd8c0$@gmail.com> Message-ID: <4C08AB3A.2090401@avignon.inra.fr> Hi Edward ! We don't manage to deploy services with or without dashboard by applying instructions on Biomoby website (http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/ServiceDevelopment.html) or eusol.net (http://www.eu-sol.net/science/bioinformatics/tutorials/jmoby-step-by-step/writing-biomoby-web-services/copy_of_jmoby-step-by-step-tutorial). The error "Property 'service.jar' is not defined" (deployBuild.xml) is always displayed. Finally, we re-used the deployment arborescence realised two years ago for deployment of the same webservices. And we copied the .class and .java files of the skeletons and implemented webservices into the correct directory (..../tomcat5.5/webapps/axis/WEB-INF/classes). Thanks, Elise. Edward Kawas wrote: > The ant file is meant to help you copy your class files from a specific > location (more about that in the links that I sent you) and creates the > services.jar file for you. If you have to edit the build file then you are > doing something wrong (in the sense that you aren't generating your services > in the manner that MoSeS wishes that you would). > > Eddie > > >> -----Original Message----- >> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- >> bounces at lists.open-bio.org] On Behalf Of Elise Larsonneur >> Sent: Thursday, May 27, 2010 8:36 AM >> To: Core developer announcements >> Subject: Re: [MOBY-dev] moby services deployment >> >> Hi ! >> >> About the initial error : "Property 'service.jar' is not defined" which >> > refers to > >> the next lines in jMoby/xmls/deployBuild.xml file : >> >> >> >> >> > >> > >> > >> >> >> > value="${src.webapps}/standard.wsdd.template"/> >> > override="true"/> ----------------------> line "224" >> > taskname="Create ${service.name}.wsdd"> >> >> >> >> >> >> >> >> >> >> I would to know how "${service.name}" on line "224" can be assigned to >> "jar". >> >> Thanks a lot, >> >> Elise >> >> >> >> Edward Kawas wrote: >> >>> Hi Elise, >>> >>> I cannot replicate your problem, so maybe I can help point you in the >>> > right > >>> direction. >>> >>> [1] >>> http://biomoby.open-bio.org/CVS_CONTENT/moby- >>> >> live/Java/docs/ServiceDevelopme >> >>> nt.html >>> [2] >>> http://biomoby.open-bio.org/CVS_CONTENT/moby- >>> >> live/Java/docs/Moses-generators >> >>> .html >>> [3] >>> http://biomoby.open-bio.org/CVS_CONTENT/moby- >>> >> live/Java/docs/Moses-deploy.htm >> >>> l >>> >>> I think that you may have seen some of these resources, judging by how >>> >> far >> >>> you have gotten, but I think it would be a good idea to read over them. >>> > The > >>> one thing that caught my eye is that when you did 'ant all', lots of >>> unrelated service tasks were executed. If you look at resource [1] and >>> > read > >>> 'Step 1: What is needed' 'ant all' is done from within your service >>> > project > >>> and not from the root moby-live/Java folder. >>> >>> Let me know if this was a good enough push! >>> >>> Thanks, >>> >>> Eddie >>> >>> >>> >>>> -----Original Message----- >>>> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- >>>> bounces at lists.open-bio.org] On Behalf Of Elise Larsonneur >>>> Sent: Wednesday, May 26, 2010 7:36 AM >>>> To: Core developer announcements >>>> Subject: Re: [MOBY-dev] moby services deployment >>>> >>>> Before deploying webservices , I generated datatypes and skeletons in >>>> jMoby with the dashboard. Then, I wrote the implementations of >>>> >> skeletons >> >>>> in another project associated to jMoby. >>>> So, after ant all, ant dashboard, when I launchs the deployment (after >>>> > ant > >>> all) >>> >>> >>>> of these webservices (on remote or local machine) , only the wsdd files >>>> >>>> >>> are >>> >>> >>>> created and the previous error displays. >>>> I used a pattern for implementation class names in the Moses Generator >>>> Panel. >>>> >>>> eclipse console : ant all : >>>> Buildfile: /home/av07/gafl/elarsonneur/workspace/jMoby/build.xml >>>> cleanapi: >>>> clean: >>>> [delete] Deleting directory >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build >>>> checkmaven: >>>> initmaven: >>>> init: >>>> [mkdir] Created dir: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build >>>> [mkdir] Created dir: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes >>>> [mkdir] Created dir: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib >>>> [mkdir] Created dir: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/Clients >>>> [mkdir] Created dir: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/registry_servlets >>>> [mkdir] Created dir: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/run >>>> [mkdir] Created dir: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/others >>>> [mkdir] Created dir: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/test >>>> [mkdir] Created dir: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/core >>>> [mkdir] Created dir: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/coreservice >>>> [mkdir] Created dir: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/central >>>> [mkdir] Created dir: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/model >>>> [mkdir] Created dir: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/modelgui >>>> [mkdir] Created dir: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/generator >>>> [mkdir] Created dir: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/ontology >>>> [mkdir] Created dir: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/visualizers >>>> config: >>>> [copy] Copying 1 file to >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes >>>> [copy] Copying 27 files to >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/run >>>> [copy] Copying 10 files to >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/Clients/help >>>> [copy] Copying 24 files to >>>> >>>> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes/templates >> >>>> [copy] Copying 163 files to >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes >>>> compile: >>>> [javac] Compiling 392 source files to >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes >>>> [javac] Note: >>>> >>>> >> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/serv >> >>>> ices/util/PBERecorder.java >>>> uses or overrides a deprecated API. >>>> [javac] Note: Recompile with -Xlint:deprecation for details. >>>> [javac] Note: Some input files use unchecked or unsafe operations. >>>> [javac] Note: Recompile with -Xlint:unchecked for details. >>>> [javac] Compiling 26 source files to >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/Clients >>>> docs: >>>> [javadoc] Generating Javadoc >>>> [javadoc] Javadoc execution >>>> [javadoc] >>>> >>>> >> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/org/inb/biomob >> >>>> y/central/gui/model/MobyObjectPropertiesTableModel.java:72: >>>> warning - @return tag has no arguments. >>>> [javadoc] 1 warning >>>> jars: >>>> [jar] Building jar: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/jmoby- >>>> >> 1.1.1.jar >> >>>> [jar] Building jar: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/jmoby- >>>> dashboard-1.1.1.jar >>>> rdfagent-init: >>>> [mkdir] Created dir: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent >>>> jar-rdfagent: >>>> [mkdir] Created dir: >>>> >>>> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/temp_lib >> >>>> [copy] Copying 95 files to >>>> >>>> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/temp_lib >> >>>> [delete] Deleting directory >>>> >>>> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/temp_lib >> >>>> [jar] Building jar: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/RDFagent.jar >>>> war: >>>> [mkdir] Created dir: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/webapps/jmoby >>>> [mkdir] Created dir: >>>> >>>> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/webapps/jmoby/cac >> >>>> he >>>> [copy] Copying 1 file to >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/webapps/jmoby >>>> [war] Building war: >>>> >>>> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/webapps/jmoby/jm >> >>>> oby.war >>>> wardist: >>>> [copy] Copying 1 file to >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/docs/dist >>>> bindist-rdfagent: >>>> [delete] Deleting directory >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent >>>> [mkdir] Created dir: >>>> >>>> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent >> >>>> [copy] Copying 96 files to >>>> >>>> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent/li >> >>>> b >>>> [copy] Copying 1 file to >>>> >>>> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent >> >>>> [copy] Copying 1 file to >>>> >>>> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent >> >>>> [copy] Copying 6 files to >>>> >>>> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent >> >>>> [tar] Building tar: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/docs/dist/rdfagent- >>>> >> 2010- >> >>>> 05-26.tar.gz >>>> [zip] Building zip: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/docs/dist/rdfagent- >>>> >> 2010- >> >>>> 05-26.zip >>>> all: >>>> BUILD SUCCESSFUL >>>> >>>> >>>> >>>> ant dashboard : >>>> Buildfile: /home/av07/gafl/elarsonneur/workspace/jMoby/build.xml >>>> checkmaven: >>>> initmaven: >>>> init: >>>> config: >>>> compile: >>>> moses-init: >>>> samples-init: >>>> [mkdir] Created dir: >>>> >>>> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/others/samples/res >> >>>> ources >>>> dashboard-init: >>>> dashboard-config: >>>> [jar] Building jar: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/dashboard- >>>> config.jar >>>> dashboard: >>>> [Dashboard] 144276 [Thread-49] ERROR SimpleAnt - >>>> >>>> >> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:306: >> >>>> The following error occurred while executing this line: >>>> [Dashboard] >>>> >>>> >> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:371: >> >>>> The following error occurred while executing this line: >>>> [Dashboard] >>>> >>>> >> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:224: >> >>>> Property 'service.jar' is not defined. >>>> >>>> >>>> >>>> Dashboard console : >>>> Selected authorities: >>>> avilin05.avignon.inra.fr >>>> >>>> -find-services: >>>> [Services names] >>>> >>>> >> Solstis_getExpDescFromAuthor,Solstis_getTrait,Solstis_getAuthor,Solstis_ge >> >> tExperiment,Solstis_getExpFromDataset,Solstis_getProject,Solstis_getExperi >> >> mentDesc,Solstis_getDatasetDescFromKeyword,Solstis_getFactor,jar,Solstis >> >>>> _getExperimentType,Solstis_getDatasetFromExp >>>> >>>> compile-datatypes: >>>> [javac] Compiling 1796 source files to >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/others/datatypes >>>> >>>> compile-services: >>>> [javac] Compiling 21 source files to >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/others/skeletons >>>> >>>> jar-datatypes: >>>> [jar] Building jar: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/biomoby- >>>> datatypes.jar >>>> >>>> jar-services: >>>> [jar] Building jar: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/biomoby- >>>> skeletons.jar >>>> >>>> deploy-remote: >>>> [mkdir] Created dir: >>>> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services- >>>> >> to- >> >>>> deploy-2010-05-26 >>>> >>>> create-wsdd: >>>> [Create Solstis_getExpDescFromAuthor.wsdd] Copying 1 file to >>>> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services- >>>> >> to- >> >>>> deploy-2010-05-26/deploy-wsdd >>>> >>>> create-wsdd: >>>> [Create Solstis_getTrait.wsdd] Copying 1 file to >>>> >> /tmp/mobyremotedeploy- >> >>>> elarsonneur/null1398203687/moby-services-to-deploy-2010-05- >>>> >> 26/deploy- >> >>>> wsdd >>>> >>>> create-wsdd: >>>> [Create Solstis_getAuthor.wsdd] Copying 1 file to >>>> >> /tmp/mobyremotedeploy- >> >>>> elarsonneur/null1398203687/moby-services-to-deploy-2010-05- >>>> >> 26/deploy- >> >>>> wsdd >>>> >>>> create-wsdd: >>>> [Create Solstis_getExperiment.wsdd] Copying 1 file to >>>> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services- >>>> >> to- >> >>>> deploy-2010-05-26/deploy-wsdd >>>> >>>> create-wsdd: >>>> [Create Solstis_getExpFromDataset.wsdd] Copying 1 file to >>>> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services- >>>> >> to- >> >>>> deploy-2010-05-26/deploy-wsdd >>>> >>>> create-wsdd: >>>> [Create Solstis_getProject.wsdd] Copying 1 file to >>>> >> /tmp/mobyremotedeploy- >> >>>> elarsonneur/null1398203687/moby-services-to-deploy-2010-05- >>>> >> 26/deploy- >> >>>> wsdd >>>> >>>> create-wsdd: >>>> [Create Solstis_getExperimentDesc.wsdd] Copying 1 file to >>>> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services- >>>> >> to- >> >>>> deploy-2010-05-26/deploy-wsdd >>>> >>>> create-wsdd: >>>> [Create Solstis_getDatasetDescFromKeyword.wsdd] Copying 1 file to >>>> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services- >>>> >> to- >> >>>> deploy-2010-05-26/deploy-wsdd >>>> >>>> create-wsdd: >>>> [Create Solstis_getFactor.wsdd] Copying 1 file to >>>> >> /tmp/mobyremotedeploy- >> >>>> elarsonneur/null1398203687/moby-services-to-deploy-2010-05- >>>> >> 26/deploy- >> >>>> wsdd >>>> >>>> BUILD FAILED >>>> >>>> >> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:306: >> >>>> The following error occurred while executing this line: >>>> >>>> >> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:371: >> >>>> The following error occurred while executing this line: >>>> >>>> >> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:224: >> >>>> Property 'service.jar' is not defined. >>>> >>>> >>>> Thanks, >>>> >>>> Elise. >>>> >>>> >>>> >>>> >>>> >>>> >>>> Edward Kawas wrote: >>>> >>>> >>>>> Hi Elise, >>>>> >>>>> Did you make sure to generate the skeletons and their implementations >>>>> >>>>> >>>> first? >>>> >>>> >>>>> Hard to say what the problem is without knowing what you did to get >>>>> >>>>> >>> here. >>> >>> >>>>> Eddie >>>>> >>>>> >>>>> >>>>> >>>>>> -----Original Message----- >>>>>> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- >>>>>> bounces at lists.open-bio.org] On Behalf Of Elise Larsonneur >>>>>> Sent: Wednesday, May 26, 2010 2:03 AM >>>>>> To: moby-dev at lists.open-bio.org >>>>>> Subject: [MOBY-dev] moby services deployment >>>>>> >>>>>> Hi ! >>>>>> >>>>>> When I want to deploy moby services by ant dashboard on remote >>>>>> machine, I meet this problem : >>>>>> >>>>>> The following error occurred while executing this line: >>>>>> >>>>>> >>>>>> >> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:371: >> >>>>>> The following error occurred while executing this line: >>>>>> >>>>>> >>>>>> >> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:224: >> >>>>>> Property 'service.jar' is not defined. >>>>>> >>>>>> What can I do for resolving this problem ? >>>>>> >>>>>> Thanks, >>>>>> >>>>>> Elise Larsonneur >>>>>> Bioinformatics trainee. >>>>>> UR GAFL >>>>>> INRA Avignon >>>>>> France >>>>>> >>>>>> _______________________________________________ >>>>>> MOBY-dev mailing list >>>>>> MOBY-dev at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>>>>> >>>>>> >>>>>> >>>>> _______________________________________________ >>>>> MOBY-dev mailing list >>>>> MOBY-dev at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>>>> >>>>> >>>>> >>>> _______________________________________________ >>>> MOBY-dev mailing list >>>> MOBY-dev at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>>> >>>> >>> _______________________________________________ >>> MOBY-dev mailing list >>> MOBY-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >>> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From Elise.Larsonneur at avignon.inra.fr Fri Jun 4 04:45:32 2010 From: Elise.Larsonneur at avignon.inra.fr (Elise Larsonneur) Date: Fri, 04 Jun 2010 10:45:32 +0200 Subject: [MOBY-dev] moby services deployment In-Reply-To: <005c01cafdb6$32c44840$984cd8c0$@gmail.com> References: <4BFCE3CE.4060504@avignon.inra.fr> <002401cafcd7$79cb3850$6d61a8f0$@gmail.com> <4BFD31C8.1070008@avignon.inra.fr> <004101cafd9a$f1273570$d375a050$@gmail.com> <4BFE9148.4020800@avignon.inra.fr> <005c01cafdb6$32c44840$984cd8c0$@gmail.com> Message-ID: <4C08BD2C.9070902@avignon.inra.fr> Re ! In fact, the problem is that the task *-find-services* (in deployBuil.xml file) find a service called "jar". Where do this task retrieve the service names ? dashboard console with further messages : Selected services: Solstis_getAuthor/avilin05.avignon.inra.fr -find-services: [Services names] *Solstis_getAuthor,jar * <---------------------------------problem : service called "jar" jar-datatypes: [jar] Building jar: /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/biomoby-datatypes.jar deploy-remote: [mkdir] Created dir: /tmp/mobyremotedeploy-elarsonneur/null117677270/moby-services-to-deploy-2010-06-04 create-wsdd: [Value property src.webapps] /home/av07/gafl/elarsonneur/workspace/jMoby/src/webapps/standard.wsdd.template} [Value property impl.class] impl.class [Value property service.service_name] *service.Solstis_getAuthor* [Create Solstis_getAuthor.wsdd] Copying 1 file to /tmp/mobyremotedeploy-elarsonneur/null117677270/moby-services-to-deploy-2010-06-04/deploy-wsdd create-wsdd: [Value property src.webapps] /home/av07/gafl/elarsonneur/workspace/jMoby/src/webapps/standard.wsdd.template} [Value property impl.class] impl.class [Value property service.service_name] *service.jar* BUILD FAILED /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:311: The following error occurred while executing this line: /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:376: The following error occurred while executing this line: /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:229: Property 'service.jar' is not defined. *TARGET -find-services :* - No list of service names found. =============================== Each service that you want to deploy should be defined by a property of the following form (parts in upper-cases should be replaced by the real values): service.SERVICE-NAME = IMPLEMENTATION-CLASS-NAME Each service that you want to undeploy can be defined in the same way (implementation class is not needed), or simpler by creating a property 'services.list' containing a comma-delimited list of names of services to be undeployed. Thanks. Elise Larsonneur. Bioinformatics trainee. UR GAFL INRA Avignon France Edward Kawas wrote: > The ant file is meant to help you copy your class files from a specific > location (more about that in the links that I sent you) and creates the > services.jar file for you. If you have to edit the build file then you are > doing something wrong (in the sense that you aren't generating your services > in the manner that MoSeS wishes that you would). > > Eddie > > From edward.kawas at gmail.com Fri Jun 4 12:56:07 2010 From: edward.kawas at gmail.com (Edward Kawas) Date: Fri, 4 Jun 2010 09:56:07 -0700 Subject: [MOBY-dev] moby services deployment In-Reply-To: <4C08BD2C.9070902@avignon.inra.fr> References: <4BFCE3CE.4060504@avignon.inra.fr> <002401cafcd7$79cb3850$6d61a8f0$@gmail.com> <4BFD31C8.1070008@avignon.inra.fr> <004101cafd9a$f1273570$d375a050$@gmail.com> <4BFE9148.4020800@avignon.inra.fr> <005c01cafdb6$32c44840$984cd8c0$@gmail.com> <4C08BD2C.9070902@avignon.inra.fr> Message-ID: <005b01cb0406$d467fa10$7d37ee30$@gmail.com> Hi Elise, I just tried generating java services with dashboard. I took a clean Ubuntu image, downloaded java 1.6 and Biomoby cvs source code. I built and ran dashboard. I opened the MoSeS generator and selected a service and then proceeded to generate datatypes, followed by generate services. I then hit the deploy button (expecting it to fail because I don't have an instance of tomcat running). I did not see any error about a missing services.jar. Could you please send me a screen shot of your MoSeS panel just before you hit the deploy button? Thanks, Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- > bounces at lists.open-bio.org] On Behalf Of Elise Larsonneur > Sent: Friday, June 04, 2010 1:46 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] moby services deployment > > Re ! > > In fact, the problem is that the task *-find-services* (in deployBuil.xml file) > find a service called "jar". Where do this task retrieve the service names ? > > dashboard console with further messages : > > Selected services: > Solstis_getAuthor/avilin05.avignon.inra.fr > > -find-services: > [Services names] *Solstis_getAuthor,jar * > <---------------------------------problem : service called "jar" > > jar-datatypes: > [jar] Building jar: > /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/biomoby- > datatypes.jar > > deploy-remote: > [mkdir] Created dir: > /tmp/mobyremotedeploy-elarsonneur/null117677270/moby-services-to- > deploy-2010-06-04 > > create-wsdd: > [Value property src.webapps] > /home/av07/gafl/elarsonneur/workspace/jMoby/src/webapps/standard.ws > dd.template} > [Value property impl.class] impl.class > [Value property service.service_name] *service.Solstis_getAuthor* [Create > Solstis_getAuthor.wsdd] Copying 1 file to /tmp/mobyremotedeploy- > elarsonneur/null117677270/moby-services-to-deploy-2010-06-04/deploy- > wsdd > > create-wsdd: > [Value property src.webapps] > /home/av07/gafl/elarsonneur/workspace/jMoby/src/webapps/standard.ws > dd.template} > [Value property impl.class] impl.class > [Value property service.service_name] *service.jar* > > BUILD FAILED > /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:311: > The following error occurred while executing this line: > /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:376: > The following error occurred while executing this line: > /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:229: > Property 'service.jar' is not defined. > > > > *TARGET -find-services :* > > > > > > property="services.list" > delimiter="," > match="service\..*?([^.]+)$" > select="\1" > casesensitive="false" /> > - > > No list of service names found. > =============================== > Each service that you want to deploy should be defined > by a property of the following form (parts in upper-cases should be > replaced by the real values): > service.SERVICE-NAME = IMPLEMENTATION-CLASS-NAME > > Each service that you want to undeploy can be defined in the same > way (implementation class is not needed), or simpler by creating > a property 'services.list' containing a comma-delimited list of > names of services to be undeployed. > > > > > > > Thanks. > > Elise Larsonneur. > > Bioinformatics trainee. > UR GAFL > INRA Avignon > France > > > > > > Edward Kawas wrote: > > The ant file is meant to help you copy your class files from a > > specific location (more about that in the links that I sent you) and > > creates the services.jar file for you. If you have to edit the build > > file then you are doing something wrong (in the sense that you aren't > > generating your services in the manner that MoSeS wishes that you > would). > > > > Eddie > > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From Elise.Larsonneur at avignon.inra.fr Mon Jun 7 04:29:47 2010 From: Elise.Larsonneur at avignon.inra.fr (Elise Larsonneur) Date: Mon, 07 Jun 2010 10:29:47 +0200 Subject: [MOBY-dev] moby services deployment In-Reply-To: <005b01cb0406$d467fa10$7d37ee30$@gmail.com> References: <4BFCE3CE.4060504@avignon.inra.fr> <002401cafcd7$79cb3850$6d61a8f0$@gmail.com> <4BFD31C8.1070008@avignon.inra.fr> <004101cafd9a$f1273570$d375a050$@gmail.com> <4BFE9148.4020800@avignon.inra.fr> <005c01cafdb6$32c44840$984cd8c0$@gmail.com> <4C08BD2C.9070902@avignon.inra.fr> <005b01cb0406$d467fa10$7d37ee30$@gmail.com> Message-ID: <4C0CADFB.4030000@avignon.inra.fr> Hi Eddie ! Here we will found a dashboard image before launching the deployment. The hostname "localhost" and port "8080" gave the same result (service "jar" missing) Thanks. Elise Edward Kawas wrote: > Hi Elise, > > I just tried generating java services with dashboard. I took a clean Ubuntu > image, downloaded java 1.6 and Biomoby cvs source code. I built and ran > dashboard. I opened the MoSeS generator and selected a service and then > proceeded to generate datatypes, followed by generate services. I then hit > the deploy button (expecting it to fail because I don't have an instance of > tomcat running). I did not see any error about a missing services.jar. > > Could you please send me a screen shot of your MoSeS panel just before you > hit the deploy button? > > Thanks, > > Eddie > > >> -----Original Message----- >> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- >> bounces at lists.open-bio.org] On Behalf Of Elise Larsonneur >> Sent: Friday, June 04, 2010 1:46 AM >> To: Core developer announcements >> Subject: Re: [MOBY-dev] moby services deployment >> >> Re ! >> >> In fact, the problem is that the task *-find-services* (in deployBuil.xml >> > file) > >> find a service called "jar". Where do this task retrieve the service names >> > ? > >> dashboard console with further messages : >> >> Selected services: >> Solstis_getAuthor/avilin05.avignon.inra.fr >> >> -find-services: >> [Services names] *Solstis_getAuthor,jar * >> <---------------------------------problem : service called "jar" >> >> jar-datatypes: >> [jar] Building jar: >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/biomoby- >> datatypes.jar >> >> deploy-remote: >> [mkdir] Created dir: >> /tmp/mobyremotedeploy-elarsonneur/null117677270/moby-services-to- >> deploy-2010-06-04 >> >> create-wsdd: >> [Value property src.webapps] >> /home/av07/gafl/elarsonneur/workspace/jMoby/src/webapps/standard.ws >> dd.template} >> [Value property impl.class] impl.class >> [Value property service.service_name] *service.Solstis_getAuthor* [Create >> Solstis_getAuthor.wsdd] Copying 1 file to /tmp/mobyremotedeploy- >> elarsonneur/null117677270/moby-services-to-deploy-2010-06-04/deploy- >> wsdd >> >> create-wsdd: >> [Value property src.webapps] >> /home/av07/gafl/elarsonneur/workspace/jMoby/src/webapps/standard.ws >> dd.template} >> [Value property impl.class] impl.class >> [Value property service.service_name] *service.jar* >> >> BUILD FAILED >> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:311: >> The following error occurred while executing this line: >> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:376: >> The following error occurred while executing this line: >> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:229: >> Property 'service.jar' is not defined. >> >> >> >> *TARGET -find-services :* >> >> > >> > >> > >> >> > property="services.list" >> delimiter="," >> match="service\..*?([^.]+)$" >> select="\1" >> casesensitive="false" /> >> - >> >> No list of service names found. >> =============================== >> Each service that you want to deploy should be defined >> by a property of the following form (parts in upper-cases should be >> replaced by the real values): >> service.SERVICE-NAME = IMPLEMENTATION-CLASS-NAME >> >> Each service that you want to undeploy can be defined in the same >> way (implementation class is not needed), or simpler by creating >> a property 'services.list' containing a comma-delimited list of >> names of services to be undeployed. >> >> >> >> >> >> >> Thanks. >> >> Elise Larsonneur. >> >> Bioinformatics trainee. >> UR GAFL >> INRA Avignon >> France >> >> >> >> >> >> > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -------------- next part -------------- A non-text attachment was scrubbed... Name: dashboard_before_deployment800x600.png Type: image/png Size: 28550 bytes Desc: not available URL: From edward.kawas at gmail.com Mon Jun 7 09:07:51 2010 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 7 Jun 2010 06:07:51 -0700 Subject: [MOBY-dev] moby services deployment In-Reply-To: <4C0CADFB.4030000@avignon.inra.fr> References: <4BFCE3CE.4060504@avignon.inra.fr> <002401cafcd7$79cb3850$6d61a8f0$@gmail.com> <4BFD31C8.1070008@avignon.inra.fr> <004101cafd9a$f1273570$d375a050$@gmail.com> <4BFE9148.4020800@avignon.inra.fr> <005c01cafdb6$32c44840$984cd8c0$@gmail.com> <4C08BD2C.9070902@avignon.inra.fr> <005b01cb0406$d467fa10$7d37ee30$@gmail.com> <4C0CADFB.4030000@avignon.inra.fr> Message-ID: <00d101cb0642$7023e580$506bb080$@gmail.com> Hi Elise, Could you also send me your impl jar as well? Thanks Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- > bounces at lists.open-bio.org] On Behalf Of Elise Larsonneur > Sent: Monday, June 07, 2010 1:30 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] moby services deployment > > Hi Eddie ! > > Here we will found a dashboard image before launching the deployment. > The hostname "localhost" and port "8080" gave the same result (service "jar" > missing) > > Thanks. > > Elise > > > > > Edward Kawas wrote: > > Hi Elise, > > > > I just tried generating java services with dashboard. I took a clean > > Ubuntu image, downloaded java 1.6 and Biomoby cvs source code. I built > > and ran dashboard. I opened the MoSeS generator and selected a service > > and then proceeded to generate datatypes, followed by generate > > services. I then hit the deploy button (expecting it to fail because I > > don't have an instance of tomcat running). I did not see any error about a > missing services.jar. > > > > Could you please send me a screen shot of your MoSeS panel just before > > you hit the deploy button? > > > > Thanks, > > > > Eddie > > > > > >> -----Original Message----- > >> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- > >> bounces at lists.open-bio.org] On Behalf Of Elise Larsonneur > >> Sent: Friday, June 04, 2010 1:46 AM > >> To: Core developer announcements > >> Subject: Re: [MOBY-dev] moby services deployment > >> > >> Re ! > >> > >> In fact, the problem is that the task *-find-services* (in > >> deployBuil.xml > >> > > file) > > > >> find a service called "jar". Where do this task retrieve the service > >> names > >> > > ? > > > >> dashboard console with further messages : > >> > >> Selected services: > >> Solstis_getAuthor/avilin05.avignon.inra.fr > >> > >> -find-services: > >> [Services names] *Solstis_getAuthor,jar * > >> <---------------------------------problem : service called "jar" > >> > >> jar-datatypes: > >> [jar] Building jar: > >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/biomoby- > >> datatypes.jar > >> > >> deploy-remote: > >> [mkdir] Created dir: > >> /tmp/mobyremotedeploy-elarsonneur/null117677270/moby-services-to- > >> deploy-2010-06-04 > >> > >> create-wsdd: > >> [Value property src.webapps] > >> > /home/av07/gafl/elarsonneur/workspace/jMoby/src/webapps/standard.ws > >> dd.template} > >> [Value property impl.class] impl.class [Value property > >> service.service_name] *service.Solstis_getAuthor* [Create > >> Solstis_getAuthor.wsdd] Copying 1 file to /tmp/mobyremotedeploy- > >> elarsonneur/null117677270/moby-services-to-deploy-2010-06-04/deploy- > >> wsdd > >> > >> create-wsdd: > >> [Value property src.webapps] > >> > /home/av07/gafl/elarsonneur/workspace/jMoby/src/webapps/standard.ws > >> dd.template} > >> [Value property impl.class] impl.class [Value property > >> service.service_name] *service.jar* > >> > >> BUILD FAILED > >> > /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:311: > >> The following error occurred while executing this line: > >> > /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:376: > >> The following error occurred while executing this line: > >> > /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:229: > >> Property 'service.jar' is not defined. > >> > >> > >> > >> *TARGET -find-services :* > >> > >> > > > >> > > > >> > > > >> > >> >> property="services.list" > >> delimiter="," > >> match="service\..*?([^.]+)$" > >> select="\1" > >> casesensitive="false" /> > >> - > >> > >> No list of service names found. > >> =============================== > >> Each service that you want to deploy should be defined > >> by a property of the following form (parts in upper-cases should be > >> replaced by the real values): > >> service.SERVICE-NAME = IMPLEMENTATION-CLASS-NAME > >> > >> Each service that you want to undeploy can be defined in the same > >> way (implementation class is not needed), or simpler by creating > >> a property 'services.list' containing a comma-delimited list of > >> names of services to be undeployed. > >> > >> > >> > >> > >> > >> > >> > >> Thanks. > >> > >> Elise Larsonneur. > >> > >> Bioinformatics trainee. > >> UR GAFL > >> INRA Avignon > >> France > >> > >> > >> > >> > >> > >> > > > > _______________________________________________ > > MOBY-dev mailing list > > MOBY-dev at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/moby-dev > > From Elise.Larsonneur at avignon.inra.fr Tue Jun 8 09:33:39 2010 From: Elise.Larsonneur at avignon.inra.fr (Elise Larsonneur) Date: Tue, 08 Jun 2010 15:33:39 +0200 Subject: [MOBY-dev] moby services deployment In-Reply-To: <00d101cb0642$7023e580$506bb080$@gmail.com> References: <4BFCE3CE.4060504@avignon.inra.fr> <002401cafcd7$79cb3850$6d61a8f0$@gmail.com> <4BFD31C8.1070008@avignon.inra.fr> <004101cafd9a$f1273570$d375a050$@gmail.com> <4BFE9148.4020800@avignon.inra.fr> <005c01cafdb6$32c44840$984cd8c0$@gmail.com> <4C08BD2C.9070902@avignon.inra.fr> <005b01cb0406$d467fa10$7d37ee30$@gmail.com> <4C0CADFB.4030000@avignon.inra.fr> <00d101cb0642$7023e580$506bb080$@gmail.com> Message-ID: <4C0E46B3.7000206@avignon.inra.fr> Hi Eddie ! Your corrections in the deployBuild.xml file are OK. The service "jar" didn't appear during the execution of the target -find-services of the deployBuild.xml file. And the deployment is OK. But I noticed an error in the deployBuild.xml file, line 347 : ...... .... Replace TOMACT_WEBAPPS by TOMCAT_WEBAPPS and then the "ant deploy" command can run correctly. Thanks a lot ! Elise. Edward Kawas wrote: > Hi Elise, > > I think that I found the problem. Please cvs update your code (specifically > xmls/deployBuild.xml) and try again. > > Thanks! > > Eddie > > From edward.kawas at gmail.com Tue Jun 8 09:49:46 2010 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 8 Jun 2010 06:49:46 -0700 Subject: [MOBY-dev] moby services deployment In-Reply-To: <4C0E46B3.7000206@avignon.inra.fr> References: <4BFCE3CE.4060504@avignon.inra.fr> <002401cafcd7$79cb3850$6d61a8f0$@gmail.com> <4BFD31C8.1070008@avignon.inra.fr> <004101cafd9a$f1273570$d375a050$@gmail.com> <4BFE9148.4020800@avignon.inra.fr> <005c01cafdb6$32c44840$984cd8c0$@gmail.com> <4C08BD2C.9070902@avignon.inra.fr> <005b01cb0406$d467fa10$7d37ee30$@gmail.com> <4C0CADFB.4030000@avignon.inra.fr> <00d101cb0642$7023e580$506bb080$@gmail.com> <4C0E46B3.7000206@avignon.inra.fr> Message-ID: <001801cb0711$75ca45e0$615ed1a0$@gmail.com> All fixed. Thanks for patience and help! Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- > bounces at lists.open-bio.org] On Behalf Of Elise Larsonneur > Sent: Tuesday, June 08, 2010 6:34 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] moby services deployment > > Hi Eddie ! > > Your corrections in the deployBuild.xml file are OK. The service "jar" > didn't appear during the execution of the target -find-services of the > deployBuild.xml file. And the deployment is OK. > > But I noticed an error in the deployBuild.xml file, line 347 : > > > depends="init,tomcat-init,-find-services,jars,jar-datatypes,jar-services" > description="Create a file helping to deploy services on a different > machine"> ...... > tofile="${result.dir}/build.xml"> > > token="TOMCAT_PORT" value="${cross.tomcat.port}"/> token="TOMCAT_HOST" value="${cross.tomcat.host}"/> token="TOMACT_WEBAPPS" value="${cross.tomcat.webapps}"/> token="AXIS_RELATIVE_PATH" value="${cross.axis.relative.path}"/> > > .... > > > > > Replace TOMACT_WEBAPPS by TOMCAT_WEBAPPS and then the "ant > deploy" > command can run correctly. > > > Thanks a lot ! > > Elise. > > > > Edward Kawas wrote: > > Hi Elise, > > > > I think that I found the problem. Please cvs update your code (specifically > > xmls/deployBuild.xml) and try again. > > > > Thanks! > > > > Eddie > > > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From markw at illuminae.com Wed Jun 9 17:48:30 2010 From: markw at illuminae.com (Mark) Date: Wed, 09 Jun 2010 14:48:30 -0700 Subject: [MOBY-dev] down-time for Moby Central Message-ID: Hi all, we need to schedule a couple of hours down-time for MOBY Central to upgrade memory (and hopefully make it faster and more stable!). Is anyone running an analysis or a workshop in the next few days that we should schedule-around? Please let me know ASAP. Thanks! Mark From markw at illuminae.com Mon Jun 28 14:36:21 2010 From: markw at illuminae.com (Mark) Date: Mon, 28 Jun 2010 11:36:21 -0700 Subject: [MOBY-dev] What to do with the BioMoby website Message-ID: Hi all, As you know, we switched the BioMoby website to Wordpress several years ago. We've just noticed that the WP installation has been compromised, and unfortunately the update to a more secure version of Wordpress is not a trivial process! So... I'm now wondering what we should do with the website. I must admit that I rarely use it - I do look at the interactive map from time-to-time, and the list of papers and software is often useful to refer to... but the bloggy-aspect of the site is something that I simply never use (and it hasn't been updated in quite a while!) From my perspective, the Moby project is "finished", and I have personally moved-on to the newer SADI interoperability framework project (and I hope many Moby'ers will maked this move also!!) so other than archival I have no personal interest in maintaining the current biomoby website, but maybe others do? Does anyone have an interest in any of the biomoby.org website content? If so, please let me know which "bits" are useful/interesting to you and I will create an archive of those pieces on a simple, straightforward set of web pages. Those bits that nobody has an interest in will simply be taken down, I think. We don't have time/manpower at the moment to do a Wordpress upgrade, and having a compromised site on open-bio is not something we can ignore! The biomoby domain, however, is still required as we have a ton of proxying happening via that domain name, so the domain will remain up and running. All we really need to do is take WordPress down, while keeping any useful bits of the Wordpress site available in some simple page-form. Let me know what you all think. Best wishes! Mark P.S. If anyone is interested, we ran the stats the other day - the Moby Central registry hosted in Canada was hit >800,000 times in the past year, and the BioMoby services that we host here were hit almost 1.4 Million times in the past 12 months!! ...so... the project is still pretty active for sure!! From dag at sonsorol.org Mon Jun 28 14:57:46 2010 From: dag at sonsorol.org (Chris Dagdigian) Date: Mon, 28 Jun 2010 14:57:46 -0400 Subject: [MOBY-dev] [MOBY-l] What to do with the BioMoby website In-Reply-To: References: Message-ID: <4C28F0AA.1020706@sonsorol.org> Actually quick update from the sysadmin side here. We were able to regain admin access and it was actually not all that hard to migrate the blog from version 1.5.2 all the way up to wordpress 3.0 Currently we are re-processing 70,000 comments through the akismet spam tester. It's likely that 100% of those comments were spam but since I don't have time to manually review them we decided to pipe them through the spam filter again and see what stays. Anyway since the wordpress 3.0 upgrade went smoothly I think the "what to do" discussion has less urgency. If it would have been a beast to clean up the website then we'd proabably want to talk about relocating it to a less harmful sandbox but that no longer may be necessary. It will take me the rest of the week to see if our box is still compromised and we eventually need to wipe and update the entire system since it's running an ancient version of CentOS but overall I'm feeling OK with leaving the newly updated site as-is -Chris Mark wrote: > Hi all, > > As you know, we switched the BioMoby website to Wordpress several years > ago. We've just noticed that the WP installation has been compromised, > and unfortunately the update to a more secure version of Wordpress is > not a trivial process! > > So... I'm now wondering what we should do with the website. I must admit > that I rarely use it - I do look at the interactive map from > time-to-time, and the list of papers and software is often useful to > refer to... but the bloggy-aspect of the site is something that I simply > never use (and it hasn't been updated in quite a while!) > > From my perspective, the Moby project is "finished", and I have > personally moved-on to the newer SADI interoperability framework project > (and I hope many Moby'ers will maked this move also!!) so other than > archival I have no personal interest in maintaining the current biomoby > website, but maybe others do? > Does anyone have an interest in any of the biomoby.org website content? > If so, please let me know which "bits" are useful/interesting to you and > I will create an archive of those pieces on a simple, straightforward > set of web pages. Those bits that nobody has an interest in will simply > be taken down, I think. We don't have time/manpower at the moment to do > a Wordpress upgrade, and having a compromised site on open-bio is not > something we can ignore! > > The biomoby domain, however, is still required as we have a ton of > proxying happening via that domain name, so the domain will remain up > and running. All we really need to do is take WordPress down, while > keeping any useful bits of the Wordpress site available in some simple > page-form. > > Let me know what you all think. > > Best wishes! > > Mark > > P.S. If anyone is interested, we ran the stats the other day - the Moby > Central registry hosted in Canada was hit >800,000 times in the past > year, and the BioMoby services that we host here were hit almost 1.4 > Million times in the past 12 months!! ...so... the project is still > pretty active for sure!! > _______________________________________________ > moby-l mailing list > moby-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-l From markw at illuminae.com Mon Jun 28 15:30:35 2010 From: markw at illuminae.com (Mark) Date: Mon, 28 Jun 2010 12:30:35 -0700 Subject: [MOBY-dev] [MOBY-l] What to do with the BioMoby website In-Reply-To: <4C28F0AA.1020706@sonsorol.org> References: <4C28F0AA.1020706@sonsorol.org> Message-ID: Oh! Okay then... crisis resolved :-) Chris, you ROCK!! Thank you for all your time and effort!! Mark On Mon, 28 Jun 2010 11:57:46 -0700, Chris Dagdigian wrote: > > Actually quick update from the sysadmin side here. > > We were able to regain admin access and it was actually not all that > hard to migrate the blog from version 1.5.2 all the way up to wordpress > 3.0 > > Currently we are re-processing 70,000 comments through the akismet spam > tester. It's likely that 100% of those comments were spam but since I > don't have time to manually review them we decided to pipe them through > the spam filter again and see what stays. > > Anyway since the wordpress 3.0 upgrade went smoothly I think the "what > to do" discussion has less urgency. If it would have been a beast to > clean up the website then we'd proabably want to talk about relocating > it to a less harmful sandbox but that no longer may be necessary. > > It will take me the rest of the week to see if our box is still > compromised and we eventually need to wipe and update the entire system > since it's running an ancient version of CentOS but overall I'm feeling > OK with leaving the newly updated site as-is > > -Chris > > > > > > Mark wrote: >> Hi all, >> >> As you know, we switched the BioMoby website to Wordpress several years >> ago. We've just noticed that the WP installation has been compromised, >> and unfortunately the update to a more secure version of Wordpress is >> not a trivial process! >> >> So... I'm now wondering what we should do with the website. I must admit >> that I rarely use it - I do look at the interactive map from >> time-to-time, and the list of papers and software is often useful to >> refer to... but the bloggy-aspect of the site is something that I simply >> never use (and it hasn't been updated in quite a while!) >> >> From my perspective, the Moby project is "finished", and I have >> personally moved-on to the newer SADI interoperability framework project >> (and I hope many Moby'ers will maked this move also!!) so other than >> archival I have no personal interest in maintaining the current biomoby >> website, but maybe others do? >> Does anyone have an interest in any of the biomoby.org website content? >> If so, please let me know which "bits" are useful/interesting to you and >> I will create an archive of those pieces on a simple, straightforward >> set of web pages. Those bits that nobody has an interest in will simply >> be taken down, I think. We don't have time/manpower at the moment to do >> a Wordpress upgrade, and having a compromised site on open-bio is not >> something we can ignore! >> >> The biomoby domain, however, is still required as we have a ton of >> proxying happening via that domain name, so the domain will remain up >> and running. All we really need to do is take WordPress down, while >> keeping any useful bits of the Wordpress site available in some simple >> page-form. >> >> Let me know what you all think. >> >> Best wishes! >> >> Mark >> >> P.S. If anyone is interested, we ran the stats the other day - the Moby >> Central registry hosted in Canada was hit >800,000 times in the past >> year, and the BioMoby services that we host here were hit almost 1.4 >> Million times in the past 12 months!! ...so... the project is still >> pretty active for sure!! >> _______________________________________________ >> moby-l mailing list >> moby-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-l > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From markw at illuminae.com Mon Jun 28 15:31:57 2010 From: markw at illuminae.com (Mark) Date: Mon, 28 Jun 2010 12:31:57 -0700 Subject: [MOBY-dev] [MOBY-l] What to do with the BioMoby website In-Reply-To: <4C28F0AA.1020706@sonsorol.org> References: <4C28F0AA.1020706@sonsorol.org> Message-ID: by the way... Eddie just corrected me. The number of hits on MOBY Central registry (800,000) and the number of hits on the Canadian services (1.4M) were in the past TWO months, not the past 12 months. Wow!! The project really IS still going strong! Mark From sneumann at ipb-halle.de Mon Jun 28 17:31:58 2010 From: sneumann at ipb-halle.de (Steffen Neumann) Date: Mon, 28 Jun 2010 23:31:58 +0200 Subject: [MOBY-dev] [MOBY-l] What to do with the BioMoby website In-Reply-To: References: <4C28F0AA.1020706@sonsorol.org> Message-ID: On Mon, 2010-06-28 at 12:31 -0700, Mark wrote: > Wow!! The project really IS still going strong! Yes, I just managed to get a minimalistic Client in R to run. No support for datatypes, but I manage the SOAP request/response :-) Anybody interest can just ask for the snippets. Yours, Steffen -- IPB Halle AG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 http://msbi.bic-gh.de 06120 Halle Tel. +49 (0) 345 5582 - 1470 +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 From schoof at mpiz-koeln.mpg.de Tue Jun 29 04:10:33 2010 From: schoof at mpiz-koeln.mpg.de (Heiko Schoof) Date: Tue, 29 Jun 2010 10:10:33 +0200 Subject: [MOBY-dev] [MOBY-l] What to do with the BioMoby website In-Reply-To: References: <4C28F0AA.1020706@sonsorol.org> Message-ID: <6322376D-3D6A-4905-B89E-133475D03122@mpiz-koeln.mpg.de> Dear Chris, thanks a mill for rescue work! Dear Mark, for us Biomoby is still a core necessity in projects running at least until mid of next year. If anything needs taken care of, let me know; we have just taken your continued Biomoby support for granted but in no way does that mean we'll let Biomoby die silently. You don't even see all our biomoby usage as our EUSOL internal services run off our own registry. Best, Heiko On 28.06.2010, at 21:31, Mark wrote: > by the way... Eddie just corrected me. > > The number of hits on MOBY Central registry (800,000) and the number > of hits on the Canadian services (1.4M) were in the past TWO months, > not the past 12 months. > > Wow!! The project really IS still going strong! > > Mark > _______________________________________________ > moby-l mailing list > moby-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-l From markw at illuminae.com Tue Jun 29 10:32:36 2010 From: markw at illuminae.com (Mark) Date: Tue, 29 Jun 2010 07:32:36 -0700 Subject: [MOBY-dev] [MOBY-l] What to do with the BioMoby website In-Reply-To: <6322376D-3D6A-4905-B89E-133475D03122@mpiz-koeln.mpg.de> References: <4C28F0AA.1020706@sonsorol.org> <6322376D-3D6A-4905-B89E-133475D03122@mpiz-koeln.mpg.de> Message-ID: Hi Heiko, No panic :-) We are not "abandoning" BioMoby any time in the foreseeable future! Certainly the majority of my resources are going into the SADI project rather than the Moby project, but Moby doesn't cost a lot to maintain so there is no pressure at all to shut it down. It was simply a matter of an urgent situation arising with the project website without any hands to look after it properly and quickly, so we were exploring drastic measures. (thanks again, Chris!!!) It would certainly be interesting to know the activity of the project worldwide. Your registry, the INB registry, the IRRI registry, plus our copy of Moby Central... must be close to 1M registry queries per month, I suspect! (do any of you have these statistics?) Not bad for a project that had it's initial funding cut by 70% because the reviewer said "it'll never work" :-) Mark On Tue, 29 Jun 2010 01:10:33 -0700, Heiko Schoof wrote: > Dear Chris, thanks a mill for rescue work! > > Dear Mark, for us Biomoby is still a core necessity in projects > running at least until mid of next year. If anything needs taken care > of, let me know; we have just taken your continued Biomoby support for > granted but in no way does that mean we'll let Biomoby die silently. > > You don't even see all our biomoby usage as our EUSOL internal > services run off our own registry. > > Best, Heiko > > On 28.06.2010, at 21:31, Mark wrote: > >> by the way... Eddie just corrected me. >> >> The number of hits on MOBY Central registry (800,000) and the number >> of hits on the Canadian services (1.4M) were in the past TWO months, >> not the past 12 months. >> >> Wow!! The project really IS still going strong! >> >> Mark >> _______________________________________________ >> moby-l mailing list >> moby-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-l > > _______________________________________________ > moby-l mailing list > moby-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-l From Elise.Larsonneur at avignon.inra.fr Fri Jun 4 07:28:58 2010 From: Elise.Larsonneur at avignon.inra.fr (Elise Larsonneur) Date: Fri, 04 Jun 2010 09:28:58 +0200 Subject: [MOBY-dev] moby services deployment In-Reply-To: <005c01cafdb6$32c44840$984cd8c0$@gmail.com> References: <4BFCE3CE.4060504@avignon.inra.fr> <002401cafcd7$79cb3850$6d61a8f0$@gmail.com> <4BFD31C8.1070008@avignon.inra.fr> <004101cafd9a$f1273570$d375a050$@gmail.com> <4BFE9148.4020800@avignon.inra.fr> <005c01cafdb6$32c44840$984cd8c0$@gmail.com> Message-ID: <4C08AB3A.2090401@avignon.inra.fr> Hi Edward ! We don't manage to deploy services with or without dashboard by applying instructions on Biomoby website (http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/ServiceDevelopment.html) or eusol.net (http://www.eu-sol.net/science/bioinformatics/tutorials/jmoby-step-by-step/writing-biomoby-web-services/copy_of_jmoby-step-by-step-tutorial). The error "Property 'service.jar' is not defined" (deployBuild.xml) is always displayed. Finally, we re-used the deployment arborescence realised two years ago for deployment of the same webservices. And we copied the .class and .java files of the skeletons and implemented webservices into the correct directory (..../tomcat5.5/webapps/axis/WEB-INF/classes). Thanks, Elise. Edward Kawas wrote: > The ant file is meant to help you copy your class files from a specific > location (more about that in the links that I sent you) and creates the > services.jar file for you. If you have to edit the build file then you are > doing something wrong (in the sense that you aren't generating your services > in the manner that MoSeS wishes that you would). > > Eddie > > >> -----Original Message----- >> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- >> bounces at lists.open-bio.org] On Behalf Of Elise Larsonneur >> Sent: Thursday, May 27, 2010 8:36 AM >> To: Core developer announcements >> Subject: Re: [MOBY-dev] moby services deployment >> >> Hi ! >> >> About the initial error : "Property 'service.jar' is not defined" which >> > refers to > >> the next lines in jMoby/xmls/deployBuild.xml file : >> >> >> >> >> > >> > >> > >> >> >> > value="${src.webapps}/standard.wsdd.template"/> >> > override="true"/> ----------------------> line "224" >> > taskname="Create ${service.name}.wsdd"> >> >> >> >> >> >> >> >> >> >> I would to know how "${service.name}" on line "224" can be assigned to >> "jar". >> >> Thanks a lot, >> >> Elise >> >> >> >> Edward Kawas wrote: >> >>> Hi Elise, >>> >>> I cannot replicate your problem, so maybe I can help point you in the >>> > right > >>> direction. >>> >>> [1] >>> http://biomoby.open-bio.org/CVS_CONTENT/moby- >>> >> live/Java/docs/ServiceDevelopme >> >>> nt.html >>> [2] >>> http://biomoby.open-bio.org/CVS_CONTENT/moby- >>> >> live/Java/docs/Moses-generators >> >>> .html >>> [3] >>> http://biomoby.open-bio.org/CVS_CONTENT/moby- >>> >> live/Java/docs/Moses-deploy.htm >> >>> l >>> >>> I think that you may have seen some of these resources, judging by how >>> >> far >> >>> you have gotten, but I think it would be a good idea to read over them. >>> > The > >>> one thing that caught my eye is that when you did 'ant all', lots of >>> unrelated service tasks were executed. If you look at resource [1] and >>> > read > >>> 'Step 1: What is needed' 'ant all' is done from within your service >>> > project > >>> and not from the root moby-live/Java folder. >>> >>> Let me know if this was a good enough push! >>> >>> Thanks, >>> >>> Eddie >>> >>> >>> >>>> -----Original Message----- >>>> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- >>>> bounces at lists.open-bio.org] On Behalf Of Elise Larsonneur >>>> Sent: Wednesday, May 26, 2010 7:36 AM >>>> To: Core developer announcements >>>> Subject: Re: [MOBY-dev] moby services deployment >>>> >>>> Before deploying webservices , I generated datatypes and skeletons in >>>> jMoby with the dashboard. Then, I wrote the implementations of >>>> >> skeletons >> >>>> in another project associated to jMoby. >>>> So, after ant all, ant dashboard, when I launchs the deployment (after >>>> > ant > >>> all) >>> >>> >>>> of these webservices (on remote or local machine) , only the wsdd files >>>> >>>> >>> are >>> >>> >>>> created and the previous error displays. >>>> I used a pattern for implementation class names in the Moses Generator >>>> Panel. >>>> >>>> eclipse console : ant all : >>>> Buildfile: /home/av07/gafl/elarsonneur/workspace/jMoby/build.xml >>>> cleanapi: >>>> clean: >>>> [delete] Deleting directory >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build >>>> checkmaven: >>>> initmaven: >>>> init: >>>> [mkdir] Created dir: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build >>>> [mkdir] Created dir: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes >>>> [mkdir] Created dir: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib >>>> [mkdir] Created dir: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/Clients >>>> [mkdir] Created dir: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/registry_servlets >>>> [mkdir] Created dir: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/run >>>> [mkdir] Created dir: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/others >>>> [mkdir] Created dir: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/test >>>> [mkdir] Created dir: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/core >>>> [mkdir] Created dir: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/coreservice >>>> [mkdir] Created dir: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/central >>>> [mkdir] Created dir: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/model >>>> [mkdir] Created dir: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/modelgui >>>> [mkdir] Created dir: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/generator >>>> [mkdir] Created dir: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/ontology >>>> [mkdir] Created dir: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/visualizers >>>> config: >>>> [copy] Copying 1 file to >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes >>>> [copy] Copying 27 files to >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/run >>>> [copy] Copying 10 files to >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/Clients/help >>>> [copy] Copying 24 files to >>>> >>>> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes/templates >> >>>> [copy] Copying 163 files to >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes >>>> compile: >>>> [javac] Compiling 392 source files to >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes >>>> [javac] Note: >>>> >>>> >> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/serv >> >>>> ices/util/PBERecorder.java >>>> uses or overrides a deprecated API. >>>> [javac] Note: Recompile with -Xlint:deprecation for details. >>>> [javac] Note: Some input files use unchecked or unsafe operations. >>>> [javac] Note: Recompile with -Xlint:unchecked for details. >>>> [javac] Compiling 26 source files to >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/Clients >>>> docs: >>>> [javadoc] Generating Javadoc >>>> [javadoc] Javadoc execution >>>> [javadoc] >>>> >>>> >> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/org/inb/biomob >> >>>> y/central/gui/model/MobyObjectPropertiesTableModel.java:72: >>>> warning - @return tag has no arguments. >>>> [javadoc] 1 warning >>>> jars: >>>> [jar] Building jar: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/jmoby- >>>> >> 1.1.1.jar >> >>>> [jar] Building jar: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/jmoby- >>>> dashboard-1.1.1.jar >>>> rdfagent-init: >>>> [mkdir] Created dir: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent >>>> jar-rdfagent: >>>> [mkdir] Created dir: >>>> >>>> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/temp_lib >> >>>> [copy] Copying 95 files to >>>> >>>> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/temp_lib >> >>>> [delete] Deleting directory >>>> >>>> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/temp_lib >> >>>> [jar] Building jar: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/RDFagent.jar >>>> war: >>>> [mkdir] Created dir: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/webapps/jmoby >>>> [mkdir] Created dir: >>>> >>>> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/webapps/jmoby/cac >> >>>> he >>>> [copy] Copying 1 file to >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/webapps/jmoby >>>> [war] Building war: >>>> >>>> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/webapps/jmoby/jm >> >>>> oby.war >>>> wardist: >>>> [copy] Copying 1 file to >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/docs/dist >>>> bindist-rdfagent: >>>> [delete] Deleting directory >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent >>>> [mkdir] Created dir: >>>> >>>> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent >> >>>> [copy] Copying 96 files to >>>> >>>> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent/li >> >>>> b >>>> [copy] Copying 1 file to >>>> >>>> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent >> >>>> [copy] Copying 1 file to >>>> >>>> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent >> >>>> [copy] Copying 6 files to >>>> >>>> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent >> >>>> [tar] Building tar: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/docs/dist/rdfagent- >>>> >> 2010- >> >>>> 05-26.tar.gz >>>> [zip] Building zip: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/docs/dist/rdfagent- >>>> >> 2010- >> >>>> 05-26.zip >>>> all: >>>> BUILD SUCCESSFUL >>>> >>>> >>>> >>>> ant dashboard : >>>> Buildfile: /home/av07/gafl/elarsonneur/workspace/jMoby/build.xml >>>> checkmaven: >>>> initmaven: >>>> init: >>>> config: >>>> compile: >>>> moses-init: >>>> samples-init: >>>> [mkdir] Created dir: >>>> >>>> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/others/samples/res >> >>>> ources >>>> dashboard-init: >>>> dashboard-config: >>>> [jar] Building jar: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/dashboard- >>>> config.jar >>>> dashboard: >>>> [Dashboard] 144276 [Thread-49] ERROR SimpleAnt - >>>> >>>> >> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:306: >> >>>> The following error occurred while executing this line: >>>> [Dashboard] >>>> >>>> >> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:371: >> >>>> The following error occurred while executing this line: >>>> [Dashboard] >>>> >>>> >> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:224: >> >>>> Property 'service.jar' is not defined. >>>> >>>> >>>> >>>> Dashboard console : >>>> Selected authorities: >>>> avilin05.avignon.inra.fr >>>> >>>> -find-services: >>>> [Services names] >>>> >>>> >> Solstis_getExpDescFromAuthor,Solstis_getTrait,Solstis_getAuthor,Solstis_ge >> >> tExperiment,Solstis_getExpFromDataset,Solstis_getProject,Solstis_getExperi >> >> mentDesc,Solstis_getDatasetDescFromKeyword,Solstis_getFactor,jar,Solstis >> >>>> _getExperimentType,Solstis_getDatasetFromExp >>>> >>>> compile-datatypes: >>>> [javac] Compiling 1796 source files to >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/others/datatypes >>>> >>>> compile-services: >>>> [javac] Compiling 21 source files to >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/others/skeletons >>>> >>>> jar-datatypes: >>>> [jar] Building jar: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/biomoby- >>>> datatypes.jar >>>> >>>> jar-services: >>>> [jar] Building jar: >>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/biomoby- >>>> skeletons.jar >>>> >>>> deploy-remote: >>>> [mkdir] Created dir: >>>> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services- >>>> >> to- >> >>>> deploy-2010-05-26 >>>> >>>> create-wsdd: >>>> [Create Solstis_getExpDescFromAuthor.wsdd] Copying 1 file to >>>> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services- >>>> >> to- >> >>>> deploy-2010-05-26/deploy-wsdd >>>> >>>> create-wsdd: >>>> [Create Solstis_getTrait.wsdd] Copying 1 file to >>>> >> /tmp/mobyremotedeploy- >> >>>> elarsonneur/null1398203687/moby-services-to-deploy-2010-05- >>>> >> 26/deploy- >> >>>> wsdd >>>> >>>> create-wsdd: >>>> [Create Solstis_getAuthor.wsdd] Copying 1 file to >>>> >> /tmp/mobyremotedeploy- >> >>>> elarsonneur/null1398203687/moby-services-to-deploy-2010-05- >>>> >> 26/deploy- >> >>>> wsdd >>>> >>>> create-wsdd: >>>> [Create Solstis_getExperiment.wsdd] Copying 1 file to >>>> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services- >>>> >> to- >> >>>> deploy-2010-05-26/deploy-wsdd >>>> >>>> create-wsdd: >>>> [Create Solstis_getExpFromDataset.wsdd] Copying 1 file to >>>> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services- >>>> >> to- >> >>>> deploy-2010-05-26/deploy-wsdd >>>> >>>> create-wsdd: >>>> [Create Solstis_getProject.wsdd] Copying 1 file to >>>> >> /tmp/mobyremotedeploy- >> >>>> elarsonneur/null1398203687/moby-services-to-deploy-2010-05- >>>> >> 26/deploy- >> >>>> wsdd >>>> >>>> create-wsdd: >>>> [Create Solstis_getExperimentDesc.wsdd] Copying 1 file to >>>> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services- >>>> >> to- >> >>>> deploy-2010-05-26/deploy-wsdd >>>> >>>> create-wsdd: >>>> [Create Solstis_getDatasetDescFromKeyword.wsdd] Copying 1 file to >>>> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services- >>>> >> to- >> >>>> deploy-2010-05-26/deploy-wsdd >>>> >>>> create-wsdd: >>>> [Create Solstis_getFactor.wsdd] Copying 1 file to >>>> >> /tmp/mobyremotedeploy- >> >>>> elarsonneur/null1398203687/moby-services-to-deploy-2010-05- >>>> >> 26/deploy- >> >>>> wsdd >>>> >>>> BUILD FAILED >>>> >>>> >> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:306: >> >>>> The following error occurred while executing this line: >>>> >>>> >> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:371: >> >>>> The following error occurred while executing this line: >>>> >>>> >> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:224: >> >>>> Property 'service.jar' is not defined. >>>> >>>> >>>> Thanks, >>>> >>>> Elise. >>>> >>>> >>>> >>>> >>>> >>>> >>>> Edward Kawas wrote: >>>> >>>> >>>>> Hi Elise, >>>>> >>>>> Did you make sure to generate the skeletons and their implementations >>>>> >>>>> >>>> first? >>>> >>>> >>>>> Hard to say what the problem is without knowing what you did to get >>>>> >>>>> >>> here. >>> >>> >>>>> Eddie >>>>> >>>>> >>>>> >>>>> >>>>>> -----Original Message----- >>>>>> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- >>>>>> bounces at lists.open-bio.org] On Behalf Of Elise Larsonneur >>>>>> Sent: Wednesday, May 26, 2010 2:03 AM >>>>>> To: moby-dev at lists.open-bio.org >>>>>> Subject: [MOBY-dev] moby services deployment >>>>>> >>>>>> Hi ! >>>>>> >>>>>> When I want to deploy moby services by ant dashboard on remote >>>>>> machine, I meet this problem : >>>>>> >>>>>> The following error occurred while executing this line: >>>>>> >>>>>> >>>>>> >> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:371: >> >>>>>> The following error occurred while executing this line: >>>>>> >>>>>> >>>>>> >> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:224: >> >>>>>> Property 'service.jar' is not defined. >>>>>> >>>>>> What can I do for resolving this problem ? >>>>>> >>>>>> Thanks, >>>>>> >>>>>> Elise Larsonneur >>>>>> Bioinformatics trainee. >>>>>> UR GAFL >>>>>> INRA Avignon >>>>>> France >>>>>> >>>>>> _______________________________________________ >>>>>> MOBY-dev mailing list >>>>>> MOBY-dev at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>>>>> >>>>>> >>>>>> >>>>> _______________________________________________ >>>>> MOBY-dev mailing list >>>>> MOBY-dev at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>>>> >>>>> >>>>> >>>> _______________________________________________ >>>> MOBY-dev mailing list >>>> MOBY-dev at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>>> >>>> >>> _______________________________________________ >>> MOBY-dev mailing list >>> MOBY-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >>> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From Elise.Larsonneur at avignon.inra.fr Fri Jun 4 08:45:32 2010 From: Elise.Larsonneur at avignon.inra.fr (Elise Larsonneur) Date: Fri, 04 Jun 2010 10:45:32 +0200 Subject: [MOBY-dev] moby services deployment In-Reply-To: <005c01cafdb6$32c44840$984cd8c0$@gmail.com> References: <4BFCE3CE.4060504@avignon.inra.fr> <002401cafcd7$79cb3850$6d61a8f0$@gmail.com> <4BFD31C8.1070008@avignon.inra.fr> <004101cafd9a$f1273570$d375a050$@gmail.com> <4BFE9148.4020800@avignon.inra.fr> <005c01cafdb6$32c44840$984cd8c0$@gmail.com> Message-ID: <4C08BD2C.9070902@avignon.inra.fr> Re ! In fact, the problem is that the task *-find-services* (in deployBuil.xml file) find a service called "jar". Where do this task retrieve the service names ? dashboard console with further messages : Selected services: Solstis_getAuthor/avilin05.avignon.inra.fr -find-services: [Services names] *Solstis_getAuthor,jar * <---------------------------------problem : service called "jar" jar-datatypes: [jar] Building jar: /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/biomoby-datatypes.jar deploy-remote: [mkdir] Created dir: /tmp/mobyremotedeploy-elarsonneur/null117677270/moby-services-to-deploy-2010-06-04 create-wsdd: [Value property src.webapps] /home/av07/gafl/elarsonneur/workspace/jMoby/src/webapps/standard.wsdd.template} [Value property impl.class] impl.class [Value property service.service_name] *service.Solstis_getAuthor* [Create Solstis_getAuthor.wsdd] Copying 1 file to /tmp/mobyremotedeploy-elarsonneur/null117677270/moby-services-to-deploy-2010-06-04/deploy-wsdd create-wsdd: [Value property src.webapps] /home/av07/gafl/elarsonneur/workspace/jMoby/src/webapps/standard.wsdd.template} [Value property impl.class] impl.class [Value property service.service_name] *service.jar* BUILD FAILED /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:311: The following error occurred while executing this line: /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:376: The following error occurred while executing this line: /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:229: Property 'service.jar' is not defined. *TARGET -find-services :* - No list of service names found. =============================== Each service that you want to deploy should be defined by a property of the following form (parts in upper-cases should be replaced by the real values): service.SERVICE-NAME = IMPLEMENTATION-CLASS-NAME Each service that you want to undeploy can be defined in the same way (implementation class is not needed), or simpler by creating a property 'services.list' containing a comma-delimited list of names of services to be undeployed. Thanks. Elise Larsonneur. Bioinformatics trainee. UR GAFL INRA Avignon France Edward Kawas wrote: > The ant file is meant to help you copy your class files from a specific > location (more about that in the links that I sent you) and creates the > services.jar file for you. If you have to edit the build file then you are > doing something wrong (in the sense that you aren't generating your services > in the manner that MoSeS wishes that you would). > > Eddie > > From edward.kawas at gmail.com Fri Jun 4 16:56:07 2010 From: edward.kawas at gmail.com (Edward Kawas) Date: Fri, 4 Jun 2010 09:56:07 -0700 Subject: [MOBY-dev] moby services deployment In-Reply-To: <4C08BD2C.9070902@avignon.inra.fr> References: <4BFCE3CE.4060504@avignon.inra.fr> <002401cafcd7$79cb3850$6d61a8f0$@gmail.com> <4BFD31C8.1070008@avignon.inra.fr> <004101cafd9a$f1273570$d375a050$@gmail.com> <4BFE9148.4020800@avignon.inra.fr> <005c01cafdb6$32c44840$984cd8c0$@gmail.com> <4C08BD2C.9070902@avignon.inra.fr> Message-ID: <005b01cb0406$d467fa10$7d37ee30$@gmail.com> Hi Elise, I just tried generating java services with dashboard. I took a clean Ubuntu image, downloaded java 1.6 and Biomoby cvs source code. I built and ran dashboard. I opened the MoSeS generator and selected a service and then proceeded to generate datatypes, followed by generate services. I then hit the deploy button (expecting it to fail because I don't have an instance of tomcat running). I did not see any error about a missing services.jar. Could you please send me a screen shot of your MoSeS panel just before you hit the deploy button? Thanks, Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- > bounces at lists.open-bio.org] On Behalf Of Elise Larsonneur > Sent: Friday, June 04, 2010 1:46 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] moby services deployment > > Re ! > > In fact, the problem is that the task *-find-services* (in deployBuil.xml file) > find a service called "jar". Where do this task retrieve the service names ? > > dashboard console with further messages : > > Selected services: > Solstis_getAuthor/avilin05.avignon.inra.fr > > -find-services: > [Services names] *Solstis_getAuthor,jar * > <---------------------------------problem : service called "jar" > > jar-datatypes: > [jar] Building jar: > /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/biomoby- > datatypes.jar > > deploy-remote: > [mkdir] Created dir: > /tmp/mobyremotedeploy-elarsonneur/null117677270/moby-services-to- > deploy-2010-06-04 > > create-wsdd: > [Value property src.webapps] > /home/av07/gafl/elarsonneur/workspace/jMoby/src/webapps/standard.ws > dd.template} > [Value property impl.class] impl.class > [Value property service.service_name] *service.Solstis_getAuthor* [Create > Solstis_getAuthor.wsdd] Copying 1 file to /tmp/mobyremotedeploy- > elarsonneur/null117677270/moby-services-to-deploy-2010-06-04/deploy- > wsdd > > create-wsdd: > [Value property src.webapps] > /home/av07/gafl/elarsonneur/workspace/jMoby/src/webapps/standard.ws > dd.template} > [Value property impl.class] impl.class > [Value property service.service_name] *service.jar* > > BUILD FAILED > /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:311: > The following error occurred while executing this line: > /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:376: > The following error occurred while executing this line: > /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:229: > Property 'service.jar' is not defined. > > > > *TARGET -find-services :* > > > > > > property="services.list" > delimiter="," > match="service\..*?([^.]+)$" > select="\1" > casesensitive="false" /> > - > > No list of service names found. > =============================== > Each service that you want to deploy should be defined > by a property of the following form (parts in upper-cases should be > replaced by the real values): > service.SERVICE-NAME = IMPLEMENTATION-CLASS-NAME > > Each service that you want to undeploy can be defined in the same > way (implementation class is not needed), or simpler by creating > a property 'services.list' containing a comma-delimited list of > names of services to be undeployed. > > > > > > > Thanks. > > Elise Larsonneur. > > Bioinformatics trainee. > UR GAFL > INRA Avignon > France > > > > > > Edward Kawas wrote: > > The ant file is meant to help you copy your class files from a > > specific location (more about that in the links that I sent you) and > > creates the services.jar file for you. If you have to edit the build > > file then you are doing something wrong (in the sense that you aren't > > generating your services in the manner that MoSeS wishes that you > would). > > > > Eddie > > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From Elise.Larsonneur at avignon.inra.fr Mon Jun 7 08:29:47 2010 From: Elise.Larsonneur at avignon.inra.fr (Elise Larsonneur) Date: Mon, 07 Jun 2010 10:29:47 +0200 Subject: [MOBY-dev] moby services deployment In-Reply-To: <005b01cb0406$d467fa10$7d37ee30$@gmail.com> References: <4BFCE3CE.4060504@avignon.inra.fr> <002401cafcd7$79cb3850$6d61a8f0$@gmail.com> <4BFD31C8.1070008@avignon.inra.fr> <004101cafd9a$f1273570$d375a050$@gmail.com> <4BFE9148.4020800@avignon.inra.fr> <005c01cafdb6$32c44840$984cd8c0$@gmail.com> <4C08BD2C.9070902@avignon.inra.fr> <005b01cb0406$d467fa10$7d37ee30$@gmail.com> Message-ID: <4C0CADFB.4030000@avignon.inra.fr> Hi Eddie ! Here we will found a dashboard image before launching the deployment. The hostname "localhost" and port "8080" gave the same result (service "jar" missing) Thanks. Elise Edward Kawas wrote: > Hi Elise, > > I just tried generating java services with dashboard. I took a clean Ubuntu > image, downloaded java 1.6 and Biomoby cvs source code. I built and ran > dashboard. I opened the MoSeS generator and selected a service and then > proceeded to generate datatypes, followed by generate services. I then hit > the deploy button (expecting it to fail because I don't have an instance of > tomcat running). I did not see any error about a missing services.jar. > > Could you please send me a screen shot of your MoSeS panel just before you > hit the deploy button? > > Thanks, > > Eddie > > >> -----Original Message----- >> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- >> bounces at lists.open-bio.org] On Behalf Of Elise Larsonneur >> Sent: Friday, June 04, 2010 1:46 AM >> To: Core developer announcements >> Subject: Re: [MOBY-dev] moby services deployment >> >> Re ! >> >> In fact, the problem is that the task *-find-services* (in deployBuil.xml >> > file) > >> find a service called "jar". Where do this task retrieve the service names >> > ? > >> dashboard console with further messages : >> >> Selected services: >> Solstis_getAuthor/avilin05.avignon.inra.fr >> >> -find-services: >> [Services names] *Solstis_getAuthor,jar * >> <---------------------------------problem : service called "jar" >> >> jar-datatypes: >> [jar] Building jar: >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/biomoby- >> datatypes.jar >> >> deploy-remote: >> [mkdir] Created dir: >> /tmp/mobyremotedeploy-elarsonneur/null117677270/moby-services-to- >> deploy-2010-06-04 >> >> create-wsdd: >> [Value property src.webapps] >> /home/av07/gafl/elarsonneur/workspace/jMoby/src/webapps/standard.ws >> dd.template} >> [Value property impl.class] impl.class >> [Value property service.service_name] *service.Solstis_getAuthor* [Create >> Solstis_getAuthor.wsdd] Copying 1 file to /tmp/mobyremotedeploy- >> elarsonneur/null117677270/moby-services-to-deploy-2010-06-04/deploy- >> wsdd >> >> create-wsdd: >> [Value property src.webapps] >> /home/av07/gafl/elarsonneur/workspace/jMoby/src/webapps/standard.ws >> dd.template} >> [Value property impl.class] impl.class >> [Value property service.service_name] *service.jar* >> >> BUILD FAILED >> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:311: >> The following error occurred while executing this line: >> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:376: >> The following error occurred while executing this line: >> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:229: >> Property 'service.jar' is not defined. >> >> >> >> *TARGET -find-services :* >> >> > >> > >> > >> >> > property="services.list" >> delimiter="," >> match="service\..*?([^.]+)$" >> select="\1" >> casesensitive="false" /> >> - >> >> No list of service names found. >> =============================== >> Each service that you want to deploy should be defined >> by a property of the following form (parts in upper-cases should be >> replaced by the real values): >> service.SERVICE-NAME = IMPLEMENTATION-CLASS-NAME >> >> Each service that you want to undeploy can be defined in the same >> way (implementation class is not needed), or simpler by creating >> a property 'services.list' containing a comma-delimited list of >> names of services to be undeployed. >> >> >> >> >> >> >> Thanks. >> >> Elise Larsonneur. >> >> Bioinformatics trainee. >> UR GAFL >> INRA Avignon >> France >> >> >> >> >> >> > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -------------- next part -------------- A non-text attachment was scrubbed... Name: dashboard_before_deployment800x600.png Type: image/png Size: 28550 bytes Desc: not available URL: From edward.kawas at gmail.com Mon Jun 7 13:07:51 2010 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 7 Jun 2010 06:07:51 -0700 Subject: [MOBY-dev] moby services deployment In-Reply-To: <4C0CADFB.4030000@avignon.inra.fr> References: <4BFCE3CE.4060504@avignon.inra.fr> <002401cafcd7$79cb3850$6d61a8f0$@gmail.com> <4BFD31C8.1070008@avignon.inra.fr> <004101cafd9a$f1273570$d375a050$@gmail.com> <4BFE9148.4020800@avignon.inra.fr> <005c01cafdb6$32c44840$984cd8c0$@gmail.com> <4C08BD2C.9070902@avignon.inra.fr> <005b01cb0406$d467fa10$7d37ee30$@gmail.com> <4C0CADFB.4030000@avignon.inra.fr> Message-ID: <00d101cb0642$7023e580$506bb080$@gmail.com> Hi Elise, Could you also send me your impl jar as well? Thanks Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- > bounces at lists.open-bio.org] On Behalf Of Elise Larsonneur > Sent: Monday, June 07, 2010 1:30 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] moby services deployment > > Hi Eddie ! > > Here we will found a dashboard image before launching the deployment. > The hostname "localhost" and port "8080" gave the same result (service "jar" > missing) > > Thanks. > > Elise > > > > > Edward Kawas wrote: > > Hi Elise, > > > > I just tried generating java services with dashboard. I took a clean > > Ubuntu image, downloaded java 1.6 and Biomoby cvs source code. I built > > and ran dashboard. I opened the MoSeS generator and selected a service > > and then proceeded to generate datatypes, followed by generate > > services. I then hit the deploy button (expecting it to fail because I > > don't have an instance of tomcat running). I did not see any error about a > missing services.jar. > > > > Could you please send me a screen shot of your MoSeS panel just before > > you hit the deploy button? > > > > Thanks, > > > > Eddie > > > > > >> -----Original Message----- > >> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- > >> bounces at lists.open-bio.org] On Behalf Of Elise Larsonneur > >> Sent: Friday, June 04, 2010 1:46 AM > >> To: Core developer announcements > >> Subject: Re: [MOBY-dev] moby services deployment > >> > >> Re ! > >> > >> In fact, the problem is that the task *-find-services* (in > >> deployBuil.xml > >> > > file) > > > >> find a service called "jar". Where do this task retrieve the service > >> names > >> > > ? > > > >> dashboard console with further messages : > >> > >> Selected services: > >> Solstis_getAuthor/avilin05.avignon.inra.fr > >> > >> -find-services: > >> [Services names] *Solstis_getAuthor,jar * > >> <---------------------------------problem : service called "jar" > >> > >> jar-datatypes: > >> [jar] Building jar: > >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/biomoby- > >> datatypes.jar > >> > >> deploy-remote: > >> [mkdir] Created dir: > >> /tmp/mobyremotedeploy-elarsonneur/null117677270/moby-services-to- > >> deploy-2010-06-04 > >> > >> create-wsdd: > >> [Value property src.webapps] > >> > /home/av07/gafl/elarsonneur/workspace/jMoby/src/webapps/standard.ws > >> dd.template} > >> [Value property impl.class] impl.class [Value property > >> service.service_name] *service.Solstis_getAuthor* [Create > >> Solstis_getAuthor.wsdd] Copying 1 file to /tmp/mobyremotedeploy- > >> elarsonneur/null117677270/moby-services-to-deploy-2010-06-04/deploy- > >> wsdd > >> > >> create-wsdd: > >> [Value property src.webapps] > >> > /home/av07/gafl/elarsonneur/workspace/jMoby/src/webapps/standard.ws > >> dd.template} > >> [Value property impl.class] impl.class [Value property > >> service.service_name] *service.jar* > >> > >> BUILD FAILED > >> > /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:311: > >> The following error occurred while executing this line: > >> > /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:376: > >> The following error occurred while executing this line: > >> > /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:229: > >> Property 'service.jar' is not defined. > >> > >> > >> > >> *TARGET -find-services :* > >> > >> > > > >> > > > >> > > > >> > >> >> property="services.list" > >> delimiter="," > >> match="service\..*?([^.]+)$" > >> select="\1" > >> casesensitive="false" /> > >> - > >> > >> No list of service names found. > >> =============================== > >> Each service that you want to deploy should be defined > >> by a property of the following form (parts in upper-cases should be > >> replaced by the real values): > >> service.SERVICE-NAME = IMPLEMENTATION-CLASS-NAME > >> > >> Each service that you want to undeploy can be defined in the same > >> way (implementation class is not needed), or simpler by creating > >> a property 'services.list' containing a comma-delimited list of > >> names of services to be undeployed. > >> > >> > >> > >> > >> > >> > >> > >> Thanks. > >> > >> Elise Larsonneur. > >> > >> Bioinformatics trainee. > >> UR GAFL > >> INRA Avignon > >> France > >> > >> > >> > >> > >> > >> > > > > _______________________________________________ > > MOBY-dev mailing list > > MOBY-dev at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/moby-dev > > From Elise.Larsonneur at avignon.inra.fr Tue Jun 8 13:33:39 2010 From: Elise.Larsonneur at avignon.inra.fr (Elise Larsonneur) Date: Tue, 08 Jun 2010 15:33:39 +0200 Subject: [MOBY-dev] moby services deployment In-Reply-To: <00d101cb0642$7023e580$506bb080$@gmail.com> References: <4BFCE3CE.4060504@avignon.inra.fr> <002401cafcd7$79cb3850$6d61a8f0$@gmail.com> <4BFD31C8.1070008@avignon.inra.fr> <004101cafd9a$f1273570$d375a050$@gmail.com> <4BFE9148.4020800@avignon.inra.fr> <005c01cafdb6$32c44840$984cd8c0$@gmail.com> <4C08BD2C.9070902@avignon.inra.fr> <005b01cb0406$d467fa10$7d37ee30$@gmail.com> <4C0CADFB.4030000@avignon.inra.fr> <00d101cb0642$7023e580$506bb080$@gmail.com> Message-ID: <4C0E46B3.7000206@avignon.inra.fr> Hi Eddie ! Your corrections in the deployBuild.xml file are OK. The service "jar" didn't appear during the execution of the target -find-services of the deployBuild.xml file. And the deployment is OK. But I noticed an error in the deployBuild.xml file, line 347 : ...... .... Replace TOMACT_WEBAPPS by TOMCAT_WEBAPPS and then the "ant deploy" command can run correctly. Thanks a lot ! Elise. Edward Kawas wrote: > Hi Elise, > > I think that I found the problem. Please cvs update your code (specifically > xmls/deployBuild.xml) and try again. > > Thanks! > > Eddie > > From edward.kawas at gmail.com Tue Jun 8 13:49:46 2010 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 8 Jun 2010 06:49:46 -0700 Subject: [MOBY-dev] moby services deployment In-Reply-To: <4C0E46B3.7000206@avignon.inra.fr> References: <4BFCE3CE.4060504@avignon.inra.fr> <002401cafcd7$79cb3850$6d61a8f0$@gmail.com> <4BFD31C8.1070008@avignon.inra.fr> <004101cafd9a$f1273570$d375a050$@gmail.com> <4BFE9148.4020800@avignon.inra.fr> <005c01cafdb6$32c44840$984cd8c0$@gmail.com> <4C08BD2C.9070902@avignon.inra.fr> <005b01cb0406$d467fa10$7d37ee30$@gmail.com> <4C0CADFB.4030000@avignon.inra.fr> <00d101cb0642$7023e580$506bb080$@gmail.com> <4C0E46B3.7000206@avignon.inra.fr> Message-ID: <001801cb0711$75ca45e0$615ed1a0$@gmail.com> All fixed. Thanks for patience and help! Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- > bounces at lists.open-bio.org] On Behalf Of Elise Larsonneur > Sent: Tuesday, June 08, 2010 6:34 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] moby services deployment > > Hi Eddie ! > > Your corrections in the deployBuild.xml file are OK. The service "jar" > didn't appear during the execution of the target -find-services of the > deployBuild.xml file. And the deployment is OK. > > But I noticed an error in the deployBuild.xml file, line 347 : > > > depends="init,tomcat-init,-find-services,jars,jar-datatypes,jar-services" > description="Create a file helping to deploy services on a different > machine"> ...... > tofile="${result.dir}/build.xml"> > > token="TOMCAT_PORT" value="${cross.tomcat.port}"/> token="TOMCAT_HOST" value="${cross.tomcat.host}"/> token="TOMACT_WEBAPPS" value="${cross.tomcat.webapps}"/> token="AXIS_RELATIVE_PATH" value="${cross.axis.relative.path}"/> > > .... > > > > > Replace TOMACT_WEBAPPS by TOMCAT_WEBAPPS and then the "ant > deploy" > command can run correctly. > > > Thanks a lot ! > > Elise. > > > > Edward Kawas wrote: > > Hi Elise, > > > > I think that I found the problem. Please cvs update your code (specifically > > xmls/deployBuild.xml) and try again. > > > > Thanks! > > > > Eddie > > > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From markw at illuminae.com Wed Jun 9 21:48:30 2010 From: markw at illuminae.com (Mark) Date: Wed, 09 Jun 2010 14:48:30 -0700 Subject: [MOBY-dev] down-time for Moby Central Message-ID: Hi all, we need to schedule a couple of hours down-time for MOBY Central to upgrade memory (and hopefully make it faster and more stable!). Is anyone running an analysis or a workshop in the next few days that we should schedule-around? Please let me know ASAP. Thanks! Mark From markw at illuminae.com Mon Jun 28 18:36:21 2010 From: markw at illuminae.com (Mark) Date: Mon, 28 Jun 2010 11:36:21 -0700 Subject: [MOBY-dev] What to do with the BioMoby website Message-ID: Hi all, As you know, we switched the BioMoby website to Wordpress several years ago. We've just noticed that the WP installation has been compromised, and unfortunately the update to a more secure version of Wordpress is not a trivial process! So... I'm now wondering what we should do with the website. I must admit that I rarely use it - I do look at the interactive map from time-to-time, and the list of papers and software is often useful to refer to... but the bloggy-aspect of the site is something that I simply never use (and it hasn't been updated in quite a while!) From my perspective, the Moby project is "finished", and I have personally moved-on to the newer SADI interoperability framework project (and I hope many Moby'ers will maked this move also!!) so other than archival I have no personal interest in maintaining the current biomoby website, but maybe others do? Does anyone have an interest in any of the biomoby.org website content? If so, please let me know which "bits" are useful/interesting to you and I will create an archive of those pieces on a simple, straightforward set of web pages. Those bits that nobody has an interest in will simply be taken down, I think. We don't have time/manpower at the moment to do a Wordpress upgrade, and having a compromised site on open-bio is not something we can ignore! The biomoby domain, however, is still required as we have a ton of proxying happening via that domain name, so the domain will remain up and running. All we really need to do is take WordPress down, while keeping any useful bits of the Wordpress site available in some simple page-form. Let me know what you all think. Best wishes! Mark P.S. If anyone is interested, we ran the stats the other day - the Moby Central registry hosted in Canada was hit >800,000 times in the past year, and the BioMoby services that we host here were hit almost 1.4 Million times in the past 12 months!! ...so... the project is still pretty active for sure!! From dag at sonsorol.org Mon Jun 28 18:57:46 2010 From: dag at sonsorol.org (Chris Dagdigian) Date: Mon, 28 Jun 2010 14:57:46 -0400 Subject: [MOBY-dev] [MOBY-l] What to do with the BioMoby website In-Reply-To: References: Message-ID: <4C28F0AA.1020706@sonsorol.org> Actually quick update from the sysadmin side here. We were able to regain admin access and it was actually not all that hard to migrate the blog from version 1.5.2 all the way up to wordpress 3.0 Currently we are re-processing 70,000 comments through the akismet spam tester. It's likely that 100% of those comments were spam but since I don't have time to manually review them we decided to pipe them through the spam filter again and see what stays. Anyway since the wordpress 3.0 upgrade went smoothly I think the "what to do" discussion has less urgency. If it would have been a beast to clean up the website then we'd proabably want to talk about relocating it to a less harmful sandbox but that no longer may be necessary. It will take me the rest of the week to see if our box is still compromised and we eventually need to wipe and update the entire system since it's running an ancient version of CentOS but overall I'm feeling OK with leaving the newly updated site as-is -Chris Mark wrote: > Hi all, > > As you know, we switched the BioMoby website to Wordpress several years > ago. We've just noticed that the WP installation has been compromised, > and unfortunately the update to a more secure version of Wordpress is > not a trivial process! > > So... I'm now wondering what we should do with the website. I must admit > that I rarely use it - I do look at the interactive map from > time-to-time, and the list of papers and software is often useful to > refer to... but the bloggy-aspect of the site is something that I simply > never use (and it hasn't been updated in quite a while!) > > From my perspective, the Moby project is "finished", and I have > personally moved-on to the newer SADI interoperability framework project > (and I hope many Moby'ers will maked this move also!!) so other than > archival I have no personal interest in maintaining the current biomoby > website, but maybe others do? > Does anyone have an interest in any of the biomoby.org website content? > If so, please let me know which "bits" are useful/interesting to you and > I will create an archive of those pieces on a simple, straightforward > set of web pages. Those bits that nobody has an interest in will simply > be taken down, I think. We don't have time/manpower at the moment to do > a Wordpress upgrade, and having a compromised site on open-bio is not > something we can ignore! > > The biomoby domain, however, is still required as we have a ton of > proxying happening via that domain name, so the domain will remain up > and running. All we really need to do is take WordPress down, while > keeping any useful bits of the Wordpress site available in some simple > page-form. > > Let me know what you all think. > > Best wishes! > > Mark > > P.S. If anyone is interested, we ran the stats the other day - the Moby > Central registry hosted in Canada was hit >800,000 times in the past > year, and the BioMoby services that we host here were hit almost 1.4 > Million times in the past 12 months!! ...so... the project is still > pretty active for sure!! > _______________________________________________ > moby-l mailing list > moby-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-l From markw at illuminae.com Mon Jun 28 19:30:35 2010 From: markw at illuminae.com (Mark) Date: Mon, 28 Jun 2010 12:30:35 -0700 Subject: [MOBY-dev] [MOBY-l] What to do with the BioMoby website In-Reply-To: <4C28F0AA.1020706@sonsorol.org> References: <4C28F0AA.1020706@sonsorol.org> Message-ID: Oh! Okay then... crisis resolved :-) Chris, you ROCK!! Thank you for all your time and effort!! Mark On Mon, 28 Jun 2010 11:57:46 -0700, Chris Dagdigian wrote: > > Actually quick update from the sysadmin side here. > > We were able to regain admin access and it was actually not all that > hard to migrate the blog from version 1.5.2 all the way up to wordpress > 3.0 > > Currently we are re-processing 70,000 comments through the akismet spam > tester. It's likely that 100% of those comments were spam but since I > don't have time to manually review them we decided to pipe them through > the spam filter again and see what stays. > > Anyway since the wordpress 3.0 upgrade went smoothly I think the "what > to do" discussion has less urgency. If it would have been a beast to > clean up the website then we'd proabably want to talk about relocating > it to a less harmful sandbox but that no longer may be necessary. > > It will take me the rest of the week to see if our box is still > compromised and we eventually need to wipe and update the entire system > since it's running an ancient version of CentOS but overall I'm feeling > OK with leaving the newly updated site as-is > > -Chris > > > > > > Mark wrote: >> Hi all, >> >> As you know, we switched the BioMoby website to Wordpress several years >> ago. We've just noticed that the WP installation has been compromised, >> and unfortunately the update to a more secure version of Wordpress is >> not a trivial process! >> >> So... I'm now wondering what we should do with the website. I must admit >> that I rarely use it - I do look at the interactive map from >> time-to-time, and the list of papers and software is often useful to >> refer to... but the bloggy-aspect of the site is something that I simply >> never use (and it hasn't been updated in quite a while!) >> >> From my perspective, the Moby project is "finished", and I have >> personally moved-on to the newer SADI interoperability framework project >> (and I hope many Moby'ers will maked this move also!!) so other than >> archival I have no personal interest in maintaining the current biomoby >> website, but maybe others do? >> Does anyone have an interest in any of the biomoby.org website content? >> If so, please let me know which "bits" are useful/interesting to you and >> I will create an archive of those pieces on a simple, straightforward >> set of web pages. Those bits that nobody has an interest in will simply >> be taken down, I think. We don't have time/manpower at the moment to do >> a Wordpress upgrade, and having a compromised site on open-bio is not >> something we can ignore! >> >> The biomoby domain, however, is still required as we have a ton of >> proxying happening via that domain name, so the domain will remain up >> and running. All we really need to do is take WordPress down, while >> keeping any useful bits of the Wordpress site available in some simple >> page-form. >> >> Let me know what you all think. >> >> Best wishes! >> >> Mark >> >> P.S. If anyone is interested, we ran the stats the other day - the Moby >> Central registry hosted in Canada was hit >800,000 times in the past >> year, and the BioMoby services that we host here were hit almost 1.4 >> Million times in the past 12 months!! ...so... the project is still >> pretty active for sure!! >> _______________________________________________ >> moby-l mailing list >> moby-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-l > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From markw at illuminae.com Mon Jun 28 19:31:57 2010 From: markw at illuminae.com (Mark) Date: Mon, 28 Jun 2010 12:31:57 -0700 Subject: [MOBY-dev] [MOBY-l] What to do with the BioMoby website In-Reply-To: <4C28F0AA.1020706@sonsorol.org> References: <4C28F0AA.1020706@sonsorol.org> Message-ID: by the way... Eddie just corrected me. The number of hits on MOBY Central registry (800,000) and the number of hits on the Canadian services (1.4M) were in the past TWO months, not the past 12 months. Wow!! The project really IS still going strong! Mark From sneumann at ipb-halle.de Mon Jun 28 21:31:58 2010 From: sneumann at ipb-halle.de (Steffen Neumann) Date: Mon, 28 Jun 2010 23:31:58 +0200 Subject: [MOBY-dev] [MOBY-l] What to do with the BioMoby website In-Reply-To: References: <4C28F0AA.1020706@sonsorol.org> Message-ID: On Mon, 2010-06-28 at 12:31 -0700, Mark wrote: > Wow!! The project really IS still going strong! Yes, I just managed to get a minimalistic Client in R to run. No support for datatypes, but I manage the SOAP request/response :-) Anybody interest can just ask for the snippets. Yours, Steffen -- IPB Halle AG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 http://msbi.bic-gh.de 06120 Halle Tel. +49 (0) 345 5582 - 1470 +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 From schoof at mpiz-koeln.mpg.de Tue Jun 29 08:10:33 2010 From: schoof at mpiz-koeln.mpg.de (Heiko Schoof) Date: Tue, 29 Jun 2010 10:10:33 +0200 Subject: [MOBY-dev] [MOBY-l] What to do with the BioMoby website In-Reply-To: References: <4C28F0AA.1020706@sonsorol.org> Message-ID: <6322376D-3D6A-4905-B89E-133475D03122@mpiz-koeln.mpg.de> Dear Chris, thanks a mill for rescue work! Dear Mark, for us Biomoby is still a core necessity in projects running at least until mid of next year. If anything needs taken care of, let me know; we have just taken your continued Biomoby support for granted but in no way does that mean we'll let Biomoby die silently. You don't even see all our biomoby usage as our EUSOL internal services run off our own registry. Best, Heiko On 28.06.2010, at 21:31, Mark wrote: > by the way... Eddie just corrected me. > > The number of hits on MOBY Central registry (800,000) and the number > of hits on the Canadian services (1.4M) were in the past TWO months, > not the past 12 months. > > Wow!! The project really IS still going strong! > > Mark > _______________________________________________ > moby-l mailing list > moby-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-l From markw at illuminae.com Tue Jun 29 14:32:36 2010 From: markw at illuminae.com (Mark) Date: Tue, 29 Jun 2010 07:32:36 -0700 Subject: [MOBY-dev] [MOBY-l] What to do with the BioMoby website In-Reply-To: <6322376D-3D6A-4905-B89E-133475D03122@mpiz-koeln.mpg.de> References: <4C28F0AA.1020706@sonsorol.org> <6322376D-3D6A-4905-B89E-133475D03122@mpiz-koeln.mpg.de> Message-ID: Hi Heiko, No panic :-) We are not "abandoning" BioMoby any time in the foreseeable future! Certainly the majority of my resources are going into the SADI project rather than the Moby project, but Moby doesn't cost a lot to maintain so there is no pressure at all to shut it down. It was simply a matter of an urgent situation arising with the project website without any hands to look after it properly and quickly, so we were exploring drastic measures. (thanks again, Chris!!!) It would certainly be interesting to know the activity of the project worldwide. Your registry, the INB registry, the IRRI registry, plus our copy of Moby Central... must be close to 1M registry queries per month, I suspect! (do any of you have these statistics?) Not bad for a project that had it's initial funding cut by 70% because the reviewer said "it'll never work" :-) Mark On Tue, 29 Jun 2010 01:10:33 -0700, Heiko Schoof wrote: > Dear Chris, thanks a mill for rescue work! > > Dear Mark, for us Biomoby is still a core necessity in projects > running at least until mid of next year. If anything needs taken care > of, let me know; we have just taken your continued Biomoby support for > granted but in no way does that mean we'll let Biomoby die silently. > > You don't even see all our biomoby usage as our EUSOL internal > services run off our own registry. > > Best, Heiko > > On 28.06.2010, at 21:31, Mark wrote: > >> by the way... Eddie just corrected me. >> >> The number of hits on MOBY Central registry (800,000) and the number >> of hits on the Canadian services (1.4M) were in the past TWO months, >> not the past 12 months. >> >> Wow!! The project really IS still going strong! >> >> Mark >> _______________________________________________ >> moby-l mailing list >> moby-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-l > > _______________________________________________ > moby-l mailing list > moby-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-l