monarch-initiative / scigraph-docker-monarch-data

Build two Docker images with the monarch configs. Uses master HEAD from the SciGraph github repo.

SciGraph-docker-monarch-data

Build two Docker images with the monarch configs. Uses master HEAD from the SciGraph github repo.

!!Deprecated!! See https://github.com/monarch-initiative/scigraph-docker

Need to have docker installed in order to run the build.

Generate the docker images locally:

mvn package

Load the graph:

docker run -v /tmp/graph:/scigraph scigraph-load-monarch

Run the services:

docker run -v /tmp/graph:/scigraph -d -p 9000:9000 --name scigraph-services scigraph-services-monarch

Stop the services:

docker stop scigraph-services

Read logs of the services:

docker logs scigraph-services

Tips, remove all the local images

docker rm $(docker ps -a -q)

docker rmi $(docker images -q)

Enabling the image writers

add that in the /etc/rc.local Xvfb :1 -screen 0 800x600x16 &

and that in the /etc/environment export DISPLAY=:1

scigraph-docker-monarch-data's Issues

expose X11 display from the docker container

ERROR [2016-02-03 23:14:00,620] io.dropwizard.jersey.errors.LoggingExceptionMapper: Error handling a request: 7aa6dd290feef914
! java.awt.HeadlessException:
! No X11 DISPLAY variable was set, but this program performed an operation which requires it.
! at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:204) ~[na:1.8.0_72]
! at java.awt.Window.(Window.java:536) ~[na:1.8.0_72]
! at java.awt.Frame.(Frame.java:420) ~[na:1.8.0_72]
! at java.awt.Frame.(Frame.java:385) ~[na:1.8.0_72]
! at javax.swing.JFrame.(JFrame.java:189) ~[na:1.8.0_72]
! at io.scigraph.services.jersey.writers.ImageWriter.renderImage(ImageWriter.java:155) ~[scigraph-services-1.5-SNAPSHOT.jar:na]
! at io.scigraph.services.jersey.writers.ImageWriter.writeTo(ImageWriter.java:184) ~[scigraph-services-1.5-SNAPSHOT.jar:na]
! at io.scigraph.services.jersey.writers.ImageWriter.writeTo(ImageWriter.java:64) ~[scigraph-services-1.5-SNAPSHOT.jar:na]
! at org.glassfish.jersey.message.internal.WriterInterceptorExecutor$TerminalWriterInterceptor.invokeWriteTo(WriterInterceptorExecutor.java:265) ~[org.glassfish.jersey.core.jersey-common-2.17.jar:na]
! at org.glassfish.jersey.message.internal.WriterInterceptorExecutor$TerminalWriterInterceptor.aroundWriteTo(WriterInterceptorExecutor.java:250) ~[org.glassfish.jersey.core.jersey-common-2.17.jar:na]
! at org.glassfish.jersey.message.internal.WriterInterceptorExecutor.proceed(WriterInterceptorExecutor.java:162) ~[org.glassfish.jersey.core.jersey-common-2.17.jar:na]
! at org.glassfish.jersey.server.internal.JsonWithPaddingInterceptor.aroundWriteTo(JsonWithPaddingInterceptor.java:106) ~[org.glassfish.jersey.core.jersey-server-2.17.jar:na]
! at org.glassfish.jersey.message.internal.WriterInterceptorExecutor.proceed(WriterInterceptorExecutor.java:162) ~[org.glassfish.jersey.core.jersey-common-2.17.jar:na]
! at org.glassfish.jersey.server.internal.MappableExceptionWrapperInterceptor.aroundWriteTo(MappableExceptionWrapperInterceptor.java:86) ~[org.glassfish.jersey.core.jersey-server-2.17.jar:na]
! at org.glassfish.jersey.message.internal.WriterInterceptorExecutor.proceed(WriterInterceptorExecutor.java:162) ~[org.glassfish.jersey.core.jersey-common-2.17.jar:na]
! at org.glassfish.jersey.message.internal.MessageBodyFactory.writeTo(MessageBodyFactory.java:1128) ~[org.glassfish.jersey.core.jersey-common-2.17.jar:na]
! at org.glassfish.jersey.server.ServerRuntime$Responder.writeResponse(ServerRuntime.java:664) ~[org.glassfish.jersey.core.jersey-server-2.17.jar:na]
! at org.glassfish.jersey.server.ServerRuntime$Responder.processResponse(ServerRuntime.java:421) ~[org.glassfish.jersey.core.jersey-server-2.17.jar:na]
! at org.glassfish.jersey.server.ServerRuntime$Responder.process(ServerRuntime.java:411) ~[org.glassfish.jersey.core.jersey-server-2.17.jar:na]
! at org.glassfish.jersey.server.ServerRuntime$2.run(ServerRuntime.java:308) ~[org.glassfish.jersey.core.jersey-server-2.17.jar:na]
! at org.glassfish.jersey.internal.Errors$1.call(Errors.java:271) [org.glassfish.jersey.core.jersey-common-2.17.jar:na]
! at org.glassfish.jersey.internal.Errors$1.call(Errors.java:267) [org.glassfish.jersey.core.jersey-common-2.17.jar:na]
! at org.glassfish.jersey.internal.Errors.process(Errors.java:315) [org.glassfish.jersey.core.jersey-common-2.17.jar:na]
! at org.glassfish.jersey.internal.Errors.process(Errors.java:297) [org.glassfish.jersey.core.jersey-common-2.17.jar:na]
! at org.glassfish.jersey.internal.Errors.process(Errors.java:267) [org.glassfish.jersey.core.jersey-common-2.17.jar:na]
! at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:317) [org.glassfish.jersey.core.jersey-common-2.17.jar:na]
! at org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:288) [org.glassfish.jersey.core.jersey-server-2.17.jar:na]
! at org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:1110) [org.glassfish.jersey.core.jersey-server-2.17.jar:na]
! at org.glassfish.jersey.servlet.WebComponent.service(WebComponent.java:401) [org.glassfish.jersey.containers.jersey-container-servlet-core-2.17.jar:na]
! at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:386) [org.glassfish.jersey.containers.jersey-container-servlet-core-2.17.jar:na]
! at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:335) [org.glassfish.jersey.containers.jersey-container-servlet-core-2.17.jar:na]
! at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:222) [org.glassfish.jersey.containers.jersey-container-servlet-core-2.17.jar:na]
! at io.dropwizard.jetty.NonblockingServletHolder.handle(NonblockingServletHolder.java:49) [io.dropwizard.dropwizard-jetty-0.8.1.jar:0.8.1]
! at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1669) [org.eclipse.jetty.jetty-servlet-9.2.9.v20150224.jar:9.2.9.v20150224]
! at org.eclipse.jetty.servlets.UserAgentFilter.doFilter(UserAgentFilter.java:83) [org.eclipse.jetty.jetty-servlets-9.2.9.v20150224.jar:9.2.9.v20150224]
! at org.eclipse.jetty.servlets.GzipFilter.doFilter(GzipFilter.java:315) [org.eclipse.jetty.jetty-servlets-9.2.9.v20150224.jar:9.2.9.v20150224]
! at io.dropwizard.jetty.BiDiGzipFilter.doFilter(BiDiGzipFilter.java:134) [io.dropwizard.dropwizard-jetty-0.8.1.jar:0.8.1]
! at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1652) [org.eclipse.jetty.jetty-servlet-9.2.9.v20150224.jar:9.2.9.v20150224]
! at io.dropwizard.servlets.ThreadNameFilter.doFilter(ThreadNameFilter.java:29) [io.dropwizard.dropwizard-servlets-0.8.1.jar:0.8.1]
! at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1652) [org.eclipse.jetty.jetty-servlet-9.2.9.v20150224.jar:9.2.9.v20150224]
! at io.dropwizard.jersey.filter.AllowedMethodsFilter.handle(AllowedMethodsFilter.java:44) [io.dropwizard.dropwizard-jersey-0.8.1.jar:0.8.1]
! at io.dropwizard.jersey.filter.AllowedMethodsFilter.doFilter(AllowedMethodsFilter.java:39) [io.dropwizard.dropwizard-jersey-0.8.1.jar:0.8.1]
! at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1652) [org.eclipse.jetty.jetty-servlet-9.2.9.v20150224.jar:9.2.9.v20150224]
! at org.eclipse.jetty.servlets.CrossOriginFilter.handle(CrossOriginFilter.java:259) [org.eclipse.jetty.jetty-servlets-9.2.9.v20150224.jar:9.2.9.v20150224]
! at org.eclipse.jetty.servlets.CrossOriginFilter.doFilter(CrossOriginFilter.java:222) [org.eclipse.jetty.jetty-servlets-9.2.9.v20150224.jar:9.2.9.v20150224]
! at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1652) [org.eclipse.jetty.jetty-servlet-9.2.9.v20150224.jar:9.2.9.v20150224]
! at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:89) [com.google.inject.extensions.guice-servlet-4.0.jar:na]
! at com.google.inject.servlet.ManagedFilterPipeline.dispatch(ManagedFilterPipeline.java:119) [com.google.inject.extensions.guice-servlet-4.0.jar:na]
! at com.google.inject.servlet.GuiceFilter$1.call(GuiceFilter.java:133) [com.google.inject.extensions.guice-servlet-4.0.jar:na]
! at com.google.inject.servlet.GuiceFilter$1.call(GuiceFilter.java:130) [com.google.inject.extensions.guice-servlet-4.0.jar:na]
! at com.google.inject.servlet.GuiceFilter$Context.call(GuiceFilter.java:203) [com.google.inject.extensions.guice-servlet-4.0.jar:na]
! at com.google.inject.servlet.GuiceFilter.doFilter(GuiceFilter.java:130) [com.google.inject.extensions.guice-servlet-4.0.jar:na]
! at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1652) [org.eclipse.jetty.jetty-servlet-9.2.9.v20150224.jar:9.2.9.v20150224]
! at io.scigraph.services.swagger.SwaggerDocUrlFilter.doFilter(SwaggerDocUrlFilter.java:46) [scigraph-services-1.5-SNAPSHOT.jar:na]
! at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1652) [org.eclipse.jetty.jetty-servlet-9.2.9.v20150224.jar:9.2.9..

Cycle in the graph

http://purl.obolibrary.org/obo/DOID_1242 (globe disease)
http://purl.obolibrary.org/obo/DOID_5614 (eye disease)

I tracked down the backward edge in http://purl.obolibrary.org/obo/clo.owl.

    <!-- http://purl.obolibrary.org/obo/DOID_5614 -->

    <owl:Class rdf:about="&obo;DOID_5614">
        <rdfs:label rdf:datatype="&xsd;string">eye disease</rdfs:label>
        <rdfs:subClassOf rdf:resource="&obo;DOID_1242"/>

@cmungall @mbrush @kshefchek

Add versionInfo property to Ontology nodes

Can this be added to the mappedProperties in the yaml?

Then we can get the date that each ontology and data source was ingested in our graph.

    - name: version
        properties:
        - http://www.w3.org/2002/07/owl#versionInfo

Version should not be hardcoded in the docker file

We should be able to build and run from master without modifying the dockerfile.

Package 'oracle-java8-installer' has no installation candidate

Building the DockerFile fails with:

Package 'oracle-java8-installer' has no installation candidate
[exec] The command '/bin/sh -c echo oracle-java8-installer shared/accepted-oracle-license-v1-1 select true | debconf-set-selections &&   add-apt-repository -y ppa:webupd8team/java &&   apt-get update &&   apt-get install -y oracle-java8-installer &&   rm -rf /var/lib/apt/lists/* &&   rm -rf /var/cache/oracle-jdk8-installer' returned a non-zero code: 100
[exec] The command '/bin/sh -c echo oracle-java8-installer shared/accepted-oracle-license-v1-1 select true | debconf-set-selections &&   add-apt-repository -y ppa:webupd8team/java &&   apt-get update &&   apt-get install -y oracle-java8-installer &&   rm -rf /var/lib/apt/lists/* &&   rm -rf /var/cache/oracle-jdk8-installer' returned a non-zero code: 100

We should use the opportunity to clean up the DockerFile and use alpine-jdk