[MOBY-dev] moby services deployment
Elise Larsonneur
Elise.Larsonneur at avignon.inra.fr
Fri Jun 4 07:28:58 UTC 2010
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 :
>>
>>
>>
>> <!--
>> ==========================================================
>> ======== -->
>> <!-- Create a wsdd descriptor for given service in 'build/wsdd'
>>
> -->
>
>> <!-- parameter: ${service.name} ... for which service
>>
> -->
>
>> <!-- parameter: ${wsdd.file} ... what file to create
>>
> -->
>
>> <!--
>> ==========================================================
>> ======== -->
>> <target name="create-wsdd" depends="init">
>> <property name="wsdd.template"
>> value="${src.webapps}/standard.wsdd.template"/>
>> <propertycopy property="impl.class" from="service.${service.name}"
>> override="true"/> ----------------------> line "224"
>> <copy file="${wsdd.template}" tofile="${wsdd.file}" overwrite="true"
>> taskname="Create ${service.name}.wsdd">
>> <filterset>
>> <filter token="SERVICE_NAME" value="${service.name}"/>
>> <filter token="IMPL_CLASS" value="${impl.class}"/>
>> </filterset>
>> </copy>
>> </target>
>>
>>
>>
>> I would to know how "${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
>>>
>>>
>> _______________________________________________
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>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>
>
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