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openphacts / Void-Editor2

Open PHACTS VoID Editor v2
http://voideditor.cs.man.ac.uk/
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Should the Docker version be working? #3

Closed randykerber closed 7 years ago

randykerber commented 7 years ago

Tried running this in Docker container and it failed. Maybe it's not ready yet?

I went through all the UI forms to create a void file, then got a VoidValidatorException.

I did make up values for some entries, not sure if that should have mattered.

Here's the error stack dump below (and attached a couple log files I pulled out of the docker container):

logs.zip

message uk.ac.manchester.cs.datadesc.validator.rdftools.VoidValidatorException: The editor created a not valid file - please contact Lefteris.

description The server encountered an internal error that prevented it from fulfilling this request.

exception

javax.servlet.ServletException: uk.ac.manchester.cs.datadesc.validator.rdftools.VoidValidatorException: The editor created a not valid file - please contact Lefteris.
    com.sun.jersey.spi.container.servlet.WebComponent.service(WebComponent.java:420)
    com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:538)
    com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:716)
    javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
    org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
root cause

uk.ac.manchester.cs.datadesc.validator.rdftools.VoidValidatorException: The editor created a not valid file - please contact Lefteris.
    editor.domain.VoidTurtle.validateRDFForOPS(VoidTurtle.java:539)
    editor.domain.VoidTurtle.createVoid(VoidTurtle.java:294)
    editor.service.VoidService.getLocation(VoidService.java:87)
    editor.rest.VoidRestService.getVoidFile(VoidRestService.java:79)
    sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    java.lang.reflect.Method.invoke(Method.java:606)
    com.sun.jersey.spi.container.JavaMethodInvokerFactory$1.invoke(JavaMethodInvokerFactory.java:60)
    com.sun.jersey.server.impl.model.method.dispatch.AbstractResourceMethodDispatchProvider$ResponseOutInvoker._dispatch(AbstractResourceMethodDispatchProvider.java:205)
    com.sun.jersey.server.impl.model.method.dispatch.ResourceJavaMethodDispatcher.dispatch(ResourceJavaMethodDispatcher.java:75)
    com.sun.jersey.server.impl.uri.rules.HttpMethodRule.accept(HttpMethodRule.java:302)
    com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147)
    com.sun.jersey.server.impl.uri.rules.ResourceClassRule.accept(ResourceClassRule.java:108)
    com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147)
    com.sun.jersey.server.impl.uri.rules.RootResourceClassesRule.accept(RootResourceClassesRule.java:84)
    com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1511)
    com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1442)
    com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1391)
    com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1381)
    com.sun.jersey.spi.container.servlet.WebComponent.service(WebComponent.java:416)
    com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:538)
    com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:716)
    javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
    org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
stain commented 7 years ago

I managed to reproduce with the same error. It's probably because I updated the dependencies of the void validator (to avoid a very old SNAPSHOT).

Validation report for: (<http://rdfs.org/ns/void#DatasetDescription>) <file:/usr/local/tomcat/temp/void8854461110473330942.ttl>
     No Errors found!
Validation report for: (<http://rdfs.org/ns/void#Dataset>) <http://www.openphacts.org/d5986e26-9f06-4f1a-9a1a-8f5bab0973e3>
    ERROR: Found: <http://www.openphacts.org/d5986e26-9f06-4f1a-9a1a-8f5bab0973e3> <http://rdfs.org/ns/void#dataDump> <http://example.com/rdf.gz>
        http://example.com/rdf.gz has not been typed, and does not meet the requirements of any known type. 
    Warning: No statements found with predicate: <http://purl.org/dc/terms/subject>
        Please add one or more statement with predicate <http://purl.org/dc/terms/subject> and type A URI.
    Warning: No statements found with predicate: <http://purl.org/pav/previousVersion>
        Please add one or more statement with predicate <http://purl.org/pav/previousVersion> and type  A String
    Warning: No statements found with predicate: <http://purl.org/dc/terms/accuralPeriodicity>
        Please add one or more statement with predicate <http://purl.org/dc/terms/accuralPeriodicity> and type http://vocabularies.bridgedb.org/ops#FrequencyOfChange URI for example: [http://purl.org/cld/freq/weekly, http://purl.org/cld/freq/semiweekly, http://purl.org/cld/freq/continuous, http://purl.org/cld/freq/triennial, http://purl.org/cld/freq/biweekly, http://purl.org/cld/freq/monthly, http://purl.org/cld/freq/threeTimesAWeek, http://purl.org/cld/freq/daily, http://purl.org/cld/freq/annual, http://purl.org/cld/freq/threeTimesAMonth, http://purl.org/cld/freq/semimonthly, http://purl.org/cld/freq/irregular, http://purl.org/cld/freq/bimonthly, http://purl.org/cld/freq/semiannual, http://purl.org/cld/freq/biennial, http://purl.org/cld/freq/threeTimesAYear, http://purl.org/cld/freq/quarterly]
    ERROR: Found: <http://www.openphacts.org/d5986e26-9f06-4f1a-9a1a-8f5bab0973e3> <http://purl.org/pav/derivedFrom> <http://raw.githubusercontent.com/openphacts/ops-platform-setup/2.0.0/void/drugbank_4.1_void.ttl#drugbank-rdf>
        http://raw.githubusercontent.com/openphacts/ops-platform-setup/2.0.0/void/drugbank_4.1_void.ttl#drugbank-rdf has not been typed, and does not meet the requirements of any known type. 
    Warning: No statements found with predicate: <http://rdfs.org/ns/void#exampleResource>
        Please add one or more statement with predicate <http://rdfs.org/ns/void#exampleResource> and type A URI.

@ltatakis - any idea? Do we need to add those things to the form?

ltatakis commented 7 years ago

Hi, @randykerber @stain the dependency of the validator has been removed. Therefore, this shouldn't be an issue anymore. The validator was removed as it was deprecated and not locatable in http://repository.mygrid.org.uk/artifactory/ops see #4 .

ltatakis commented 7 years ago

Closing this issue. Please reopen if you are still having issues.