mcupak/beacon-of-beacons

Beacon of Beacons.

beacon-of-beacons's Issues

Add unit tests

Not relying on a working internet connection and live beacons, faster and more fine-grained than current integration tests.

List beacons in the client

Add a page providing a list of beacons, their organizations and aggregate flag on a separate page in the client.

Create a Node.js beacon adapter

Beacon development kit for Node.js developers.

Add Cafe Variome beacon

http://beacon.cafevariome.org/ (website)
http://beacon.cafevariome.org/query (API)

Automatic beacon registration

Allow beacons to sign up programmatically provided they implement the API requested by us.

Filter for multiple beacons

We have e.g.:
/rest/responses?chrom=14&pos=106833421&allele=A
/rest/responses?chrom=14&pos=106833421&allele=A&beacon=amplab

We should also have something like:
/rest/responses?chrom=14&pos=106833421&allele=A&beacon=[amplab,kaviar]

Improve timeout handling

Problem description:
BoB server returns a proper HTTP status code when a request to any of the beacons queries times out. The client hangs.

Expected behaviour:
Bob checks for timeouts on a per-beacon basis - if any of the beacons doesn't respond, Bob sets its response to null and the responses of the remaining beacons in query are still delivered properly. The client handles timeouts gracefully.

Update Java BDK to Beacon 0.2 API

Adapter: https://github.com/mcupak/beacon-of-beacons/tree/master/beacon-adapters/beacon-java
Docs: http://mcupak.github.io/beacon-of-beacons/beacons.html#java
API 0.2: https://docs.google.com/document/d/1hFVqmPDKAs2Tacqta98oIPqUOKlHghmuJD8DtYLQFKw/edit?usp=sharing

Change /query and /info endpoints to generate data in the form according to the new API version.

Welcome page

Add an introductory/welcome page for / and /rest contexts.

Cache responses within multi-beacon queries

When querying multiple beacons at once, aggregate beacons can result into the same query being executed multiple times against the same beacon. BoB should resolve beacon dependencies before the query is executed and cache the results to avoid duplicate requests.

Add optional organization attribute to beacons

Add a rest endpoint listing valid reference and chromosome identifiers

Update Node.js BDK to Beacon 0.2 API

Adapter: https://github.com/mcupak/beacon-of-beacons/tree/master/beacon-adapters/beacon-nodejs
Docs: http://mcupak.github.io/beacon-of-beacons/beacons.html#nodejs
API 0.2: https://docs.google.com/document/d/1hFVqmPDKAs2Tacqta98oIPqUOKlHghmuJD8DtYLQFKw/edit?usp=sharing

Change /query and /info endpoints to generate data in the form according to the new API version.

Use 1-based positions

Change 0-based indexing to 1-based as it makes more sense on the genome.

Beacon bundle

Implement a full beacon bundle serving data from VCF files. Probably a beacon with an embedded server and DB monitoring a directory with VCF files.

Fix handling of reference alleles

They should default to "false" response.

Create a Python beacon adapter

Beacon development kit for Python developers.

Migrate the backend away from its current hosting

Improve documentation

Having the documentation in a single README.md is painful to maintain. The docs should be split into multiple pages and hosted separeately (GitHub wiki or GitHub pages).

Usage tracking

Fix logging on the backend so that it works with our hosting, hook up Google Analytics to the frontend.

Add text/plain responses

Implement JAX-RS endpoint providing human-readable plaintext responses.

Get rid of PHP

BoB client is currently dependant on PHP to bypass the limitations of CORS. This has to be improved.

Add beacon from Broad Institute

http://broad-beacon.broadinstitute.org:8090/dev/beacon
http://broad-beacon.broadinstitute.org:8090/dev/beacon/query?chrom=1&pos=13417&allele=CGAGA&ref=hg19

Use allele instead of alt

Rename the query allele tag “ALT” with “ALLELE” or some more specific term. “ALT” implies alternate loci in GRCh assembly.

OAUTH2 support

Implement authentication and authorization support.

Dynamically generated beacon map

Generate beacon map in the client dynamically based on the beacons offered by the backend. This requires the backend to store and expose address/coordinates of the institutions as well as the number of beacons.

Migrate adapters to GA4GH-Beacon-Team

Move adapters to the beacon-quickstarts repo. This includes:

• moving the code while removing the dependencies on bob-parent
• removing the adapters from this repo
• removing the adapters from the docs

Update Python BDK to Beacon 0.2 API

Adapter: https://github.com/mcupak/beacon-of-beacons/tree/master/beacon-adapters/beacon-python
Docs: http://mcupak.github.io/beacon-of-beacons/beacons.html#python
API 0.2: https://docs.google.com/document/d/1hFVqmPDKAs2Tacqta98oIPqUOKlHghmuJD8DtYLQFKw/edit?usp=sharing

Change /query and /info endpoints to generate data in the form according to the new API version.

Rework implementations of beacon-processors

ATM, we have a separate processor for more or less every beacon. The processors should be split to parsers, url constructors and query executors and assigned to beacon entities.

How do I see the list of end points?

I was directed to this site by a collague after noting that his project wasn't shown on the ga4gh.org site as one of the beacon endpoints. He said that it is part of the beacon of beacons end points, but I'm unable to find a list in your code or on the site, as to which end points are queried. This could be useful if I want to present this project to DECIPHER, with the hope of implementing it on the DECIPHER site! =]

Kaviar beacon integration

Add a new beacon:

http://db.systemsbiology.net/kaviar/cgi-pub/beacon

Upgrade to Beacon 0.2 API

Unable to set up the BoB

Order of commands
For Linux: JBOSS_HOME/bin/standalone.sh -c standalone-full.xml
mvn clean install (inside root of the beacon-of-beacon)
cd bob-rest
mvn wildfly:deploy [Runs successfully]
mvn wildfly:undeploy [Throws the following errors]
Please tell me what's wrong.

Thanks!

---

~/Desktop/apps/ga4g/beacon-of-beacons/bob-rest(branch:master) » mvn test -Parq-wildfly-managed -e
[INFO] Error stacktraces are turned on.
[INFO] Scanning for projects...
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] Building bob-rest 1.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO]
[INFO] --- maven-resources-plugin:2.3:resources (default-resources) @ bob-rest ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO]
[INFO] --- maven-compiler-plugin:2.3.2:compile (default-compile) @ bob-rest ---
[INFO] Nothing to compile - all classes are up to date
[INFO]
[INFO] --- maven-resources-plugin:2.3:testResources (default-testResources) @ bob-rest ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO]
[INFO] --- maven-compiler-plugin:2.3.2:testCompile (default-testCompile) @ bob-rest ---
[INFO] Nothing to compile - all classes are up to date
[INFO]
[INFO] --- maven-surefire-plugin:2.10:test (default-test) @ bob-rest ---
[INFO] Surefire report directory: /home/shash/Desktop/apps/ga4g/beacon-of-beacons/bob-rest/target/surefire-reports

---

T E S T S

Running com.dnastack.bob.rest.IcgcResponseTest
log4j:WARN No appenders could be found for logger (org.jboss.logging).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0.653 sec <<< FAILURE!
Running com.dnastack.bob.rest.CuroverseBeaconizerResponseTest
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0.001 sec <<< FAILURE!
Running com.dnastack.bob.rest.AmpLabResponseTest
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0 sec <<< FAILURE!
Running com.dnastack.bob.rest.CafeVariomeResponseTest
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0.001 sec <<< FAILURE!
Running com.dnastack.bob.rest.BobResponseTest
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0.001 sec <<< FAILURE!
Running com.dnastack.bob.rest.EbiResponseTest
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0 sec <<< FAILURE!
Running com.dnastack.bob.rest.BroadInstituteResponseTest
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0 sec <<< FAILURE!
Running com.dnastack.bob.rest.NcbiResponseTest
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0.001 sec <<< FAILURE!
Running com.dnastack.bob.rest.KaviarResponseTest
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0.001 sec <<< FAILURE!
Running com.dnastack.bob.rest.UcscResponseTest
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0 sec <<< FAILURE!
Running com.dnastack.bob.rest.WtsiResponseTest
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0.001 sec <<< FAILURE!
Running com.dnastack.bob.rest.HelpTest
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0 sec <<< FAILURE!
Running com.dnastack.bob.rest.ItemTest
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0 sec <<< FAILURE!
Running com.dnastack.bob.rest.BeaconsTest
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0 sec <<< FAILURE!
Running com.dnastack.bob.rest.BeaconResponsesTest
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0 sec <<< FAILURE!

Results :

Tests in error:
com.dnastack.bob.rest.IcgcResponseTest: The server is already running! Managed containers do not support connecting to running server instances due to the possible harmful effect of connecting to the wrong server. Please stop server before running or change to another type of container.
com.dnastack.bob.rest.CuroverseBeaconizerResponseTest: Arquillian has previously been attempted initialized, but failed. See cause for previous exception
com.dnastack.bob.rest.AmpLabResponseTest: Arquillian has previously been attempted initialized, but failed. See cause for previous exception
com.dnastack.bob.rest.CafeVariomeResponseTest: Arquillian has previously been attempted initialized, but failed. See cause for previous exception
com.dnastack.bob.rest.BobResponseTest: Arquillian has previously been attempted initialized, but failed. See cause for previous exception
com.dnastack.bob.rest.EbiResponseTest: Arquillian has previously been attempted initialized, but failed. See cause for previous exception
com.dnastack.bob.rest.BroadInstituteResponseTest: Arquillian has previously been attempted initialized, but failed. See cause for previous exception
com.dnastack.bob.rest.NcbiResponseTest: Arquillian has previously been attempted initialized, but failed. See cause for previous exception
com.dnastack.bob.rest.KaviarResponseTest: Arquillian has previously been attempted initialized, but failed. See cause for previous exception
com.dnastack.bob.rest.UcscResponseTest: Arquillian has previously been attempted initialized, but failed. See cause for previous exception
com.dnastack.bob.rest.WtsiResponseTest: Arquillian has previously been attempted initialized, but failed. See cause for previous exception
com.dnastack.bob.rest.HelpTest: Arquillian has previously been attempted initialized, but failed. See cause for previous exception
com.dnastack.bob.rest.ItemTest: Arquillian has previously been attempted initialized, but failed. See cause for previous exception
com.dnastack.bob.rest.BeaconsTest: Arquillian has previously been attempted initialized, but failed. See cause for previous exception
com.dnastack.bob.rest.BeaconResponsesTest: Arquillian has previously been attempted initialized, but failed. See cause for previous exception

Tests run: 15, Failures: 0, Errors: 15, Skipped: 0

[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 3.440s
[INFO] Finished at: Sat Mar 07 01:54:12 IST 2015
[INFO] Final Memory: 19M/341M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:2.10:test (default-test) on project bob-rest: There are test failures.
[ERROR]
[ERROR] Please refer to /home/shash/Desktop/apps/ga4g/beacon-of-beacons/bob-rest/target/surefire-reports for the individual test results.
[ERROR] -> [Help 1]
org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:2.10:test (default-test) on project bob-rest: There are test failures.

Please refer to /home/shash/Desktop/apps/ga4g/beacon-of-beacons/bob-rest/target/surefire-reports for the individual test results.
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:213)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:153)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:145)
at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:84)
at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:59)
at org.apache.maven.lifecycle.internal.LifecycleStarter.singleThreadedBuild(LifecycleStarter.java:183)
at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:161)
at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:320)
at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:156)
at org.apache.maven.cli.MavenCli.execute(MavenCli.java:537)
at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:196)
at org.apache.maven.cli.MavenCli.main(MavenCli.java:141)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:289)
at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:229)
at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:415)
at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:356)
Caused by: org.apache.maven.plugin.MojoFailureException: There are test failures.

Please refer to /home/shash/Desktop/apps/ga4g/beacon-of-beacons/bob-rest/target/surefire-reports for the individual test results.
at org.apache.maven.plugin.surefire.SurefireHelper.reportExecution(SurefireHelper.java:87)
at org.apache.maven.plugin.surefire.SurefirePlugin.writeSummary(SurefirePlugin.java:641)
at org.apache.maven.plugin.surefire.SurefirePlugin.handleSummary(SurefirePlugin.java:615)
at org.apache.maven.plugin.surefire.AbstractSurefireMojo.executeAfterPreconditionsChecked(AbstractSurefireMojo.java:137)
at org.apache.maven.plugin.surefire.AbstractSurefireMojo.execute(AbstractSurefireMojo.java:98)
at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:101)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:209)
... 19 more
[ERROR]
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR]
[ERROR] For more information about the errors and possible solutions, please read the following articles:

[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException

Create a Java beacon adapter

Beacon development kit for Java developers.

Migrate the deployment to Wildfly

Both staging and production.

Update to new EBI API

XML API occasionaly returns errors when serializing collections

There seem to be problems with moxy and resteasy-jaxb-provider on Wildfly (everything is working fine on EAP 6).

15:23:38,568 WARN [org.jboss.resteasy.core.ExceptionHandler](default task-3) Failed executing GET /chromosomes: org.jboss.resteasy.plugins.providers.jaxb.JAXBMarshalException: javax.xml.bind.JAXBException:
Exception Description: Class [com.dnastack.bob.dto.ReferenceTo] not found.

• with linked exception:
  [Exception [EclipseLink-50047](Eclipse Persistence Services - 2.6.0.v20140809-296a69f): org.eclipse.persistence.exceptions.JAXBException
  Exception Description: Class [com.dnastack.bob.dto.ReferenceTo] not found.]
  at org.jboss.resteasy.plugins.providers.jaxb.CollectionProvider.writeTo(CollectionProvider.java:288) [resteasy-jaxb-provider-3.0.10.Final.jar:]
  at org.jboss.resteasy.core.interception.AbstractWriterInterceptorContext.writeTo(AbstractWriterInterceptorContext.java:129) [resteasy-jaxrs-3.0.10.Final.jar:]
  at org.jboss.resteasy.core.interception.ServerWriterInterceptorContext.writeTo(ServerWriterInterceptorContext.java:62) [resteasy-jaxrs-3.0.10.Final.jar:]
  at org.jboss.resteasy.core.interception.AbstractWriterInterceptorContext.proceed(AbstractWriterInterceptorContext.java:118) [resteasy-jaxrs-3.0.10.Final.jar:]
  at org.jboss.resteasy.security.doseta.DigitalSigningInterceptor.aroundWriteTo(DigitalSigningInterceptor.java:143) [resteasy-crypto-3.0.10.Final.jar:]
  at org.jboss.resteasy.core.interception.AbstractWriterInterceptorContext.proceed(AbstractWriterInterceptorContext.java:122) [resteasy-jaxrs-3.0.10.Final.jar:]
  at org.jboss.resteasy.plugins.interceptors.encoding.GZIPEncodingInterceptor.aroundWriteTo(GZIPEncodingInterceptor.java:100) [resteasy-jaxrs-3.0.10.Final.jar:]
  at org.jboss.resteasy.core.interception.AbstractWriterInterceptorContext.proceed(AbstractWriterInterceptorContext.java:122) [resteasy-jaxrs-3.0.10.Final.jar:]
  at org.jboss.resteasy.core.ServerResponseWriter.writeNomapResponse(ServerResponseWriter.java:99) [resteasy-jaxrs-3.0.10.Final.jar:]
  at org.jboss.resteasy.core.SynchronousDispatcher.writeResponse(SynchronousDispatcher.java:427) [resteasy-jaxrs-3.0.10.Final.jar:]
  at org.jboss.resteasy.core.SynchronousDispatcher.invoke(SynchronousDispatcher.java:376) [resteasy-jaxrs-3.0.10.Final.jar:]
  at org.jboss.resteasy.core.SynchronousDispatcher.invoke(SynchronousDispatcher.java:179) [resteasy-jaxrs-3.0.10.Final.jar:]
  at org.jboss.resteasy.plugins.server.servlet.ServletContainerDispatcher.service(ServletContainerDispatcher.java:220) [resteasy-jaxrs-3.0.10.Final.jar:]
  at org.jboss.resteasy.plugins.server.servlet.HttpServletDispatcher.service(HttpServletDispatcher.java:56) [resteasy-jaxrs-3.0.10.Final.jar:]
  at org.jboss.resteasy.plugins.server.servlet.HttpServletDispatcher.service(HttpServletDispatcher.java:51) [resteasy-jaxrs-3.0.10.Final.jar:]
  at javax.servlet.http.HttpServlet.service(HttpServlet.java:790) [jboss-servlet-api_3.1_spec-1.0.0.Final.jar:1.0.0.Final]
  at io.undertow.servlet.handlers.ServletHandler.handleRequest(ServletHandler.java:85) [undertow-servlet-1.1.0.Final.jar:1.1.0.Final]
  at io.undertow.servlet.handlers.security.ServletSecurityRoleHandler.handleRequest(ServletSecurityRoleHandler.java:61) [undertow-servlet-1.1.0.Final.jar:1.1.0.Final]
  at io.undertow.servlet.handlers.ServletDispatchingHandler.handleRequest(ServletDispatchingHandler.java:36) [undertow-servlet-1.1.0.Final.jar:1.1.0.Final]
  at org.wildfly.extension.undertow.security.SecurityContextAssociationHandler.handleRequest(SecurityContextAssociationHandler.java:78)
  at io.undertow.server.handlers.PredicateHandler.handleRequest(PredicateHandler.java:43) [undertow-core-1.1.0.Final.jar:1.1.0.Final]
  at io.undertow.servlet.handlers.security.SSLInformationAssociationHandler.handleRequest(SSLInformationAssociationHandler.java:131) [undertow-servlet-1.1.0.Final.jar:1.1.0.Final]
  at io.undertow.servlet.handlers.security.ServletAuthenticationCallHandler.handleRequest(ServletAuthenticationCallHandler.java:56) [undertow-servlet-1.1.0.Final.jar:1.1.0.Final]
  at io.undertow.server.handlers.PredicateHandler.handleRequest(PredicateHandler.java:43) [undertow-core-1.1.0.Final.jar:1.1.0.Final]
  at io.undertow.security.handlers.AbstractConfidentialityHandler.handleRequest(AbstractConfidentialityHandler.java:45) [undertow-core-1.1.0.Final.jar:1.1.0.Final]
  at io.undertow.servlet.handlers.security.ServletConfidentialityConstraintHandler.handleRequest(ServletConfidentialityConstraintHandler.java:63) [undertow-servlet-1.1.0.Final.jar:1.1.0.Final]
  at io.undertow.security.handlers.AuthenticationMechanismsHandler.handleRequest(AuthenticationMechanismsHandler.java:58) [undertow-core-1.1.0.Final.jar:1.1.0.Final]
  at io.undertow.servlet.handlers.security.CachedAuthenticatedSessionHandler.handleRequest(CachedAuthenticatedSessionHandler.java:70) [undertow-servlet-1.1.0.Final.jar:1.1.0.Final]
  at io.undertow.security.handlers.SecurityInitialHandler.handleRequest(SecurityInitialHandler.java:76) [undertow-core-1.1.0.Final.jar:1.1.0.Final]
  at io.undertow.server.handlers.PredicateHandler.handleRequest(PredicateHandler.java:43) [undertow-core-1.1.0.Final.jar:1.1.0.Final]
  at org.wildfly.extension.undertow.security.jacc.JACCContextIdHandler.handleRequest(JACCContextIdHandler.java:61)
  at io.undertow.server.handlers.PredicateHandler.handleRequest(PredicateHandler.java:43) [undertow-core-1.1.0.Final.jar:1.1.0.Final]
  at io.undertow.server.handlers.PredicateHandler.handleRequest(PredicateHandler.java:43) [undertow-core-1.1.0.Final.jar:1.1.0.Final]
  at io.undertow.servlet.handlers.ServletInitialHandler.handleFirstRequest(ServletInitialHandler.java:261) [undertow-servlet-1.1.0.Final.jar:1.1.0.Final]
  at io.undertow.servlet.handlers.ServletInitialHandler.dispatchRequest(ServletInitialHandler.java:247) [undertow-servlet-1.1.0.Final.jar:1.1.0.Final]
  at io.undertow.servlet.handlers.ServletInitialHandler.access$000(ServletInitialHandler.java:76) [undertow-servlet-1.1.0.Final.jar:1.1.0.Final]
  at io.undertow.servlet.handlers.ServletInitialHandler$1.handleRequest(ServletInitialHandler.java:166) [undertow-servlet-1.1.0.Final.jar:1.1.0.Final]
  at io.undertow.server.Connectors.executeRootHandler(Connectors.java:197) [undertow-core-1.1.0.Final.jar:1.1.0.Final]
  at io.undertow.server.HttpServerExchange$1.run(HttpServerExchange.java:759) [undertow-core-1.1.0.Final.jar:1.1.0.Final]
  at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) [rt.jar:1.7.0_51]
  at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) [rt.jar:1.7.0_51]
  at java.lang.Thread.run(Thread.java:744) [rt.jar:1.7.0_51]
  Caused by: javax.xml.bind.JAXBException:
  Exception Description: Class [com.dnastack.bob.dto.ReferenceTo] not found.
• with linked exception:
  [Exception [EclipseLink-50047](Eclipse Persistence Services - 2.6.0.v20140809-296a69f): org.eclipse.persistence.exceptions.JAXBException
  Exception Description: Class [com.dnastack.bob.dto.ReferenceTo] not found.]
  at org.eclipse.persistence.jaxb.JAXBContext$TypeMappingInfoInput.createContextState(JAXBContext.java:1108) [org.eclipse.persistence.moxy-2.6.0-M3.jar:]
  at org.eclipse.persistence.jaxb.JAXBContext.(JAXBContext.java:188) [org.eclipse.persistence.moxy-2.6.0-M3.jar:]
  at org.eclipse.persistence.jaxb.JAXBContextFactory.createContext(JAXBContextFactory.java:165) [org.eclipse.persistence.moxy-2.6.0-M3.jar:]
  at org.eclipse.persistence.jaxb.JAXBContextFactory.createContext(JAXBContextFactory.java:152) [org.eclipse.persistence.moxy-2.6.0-M3.jar:]
  at org.eclipse.persistence.jaxb.JAXBContextFactory.createContext(JAXBContextFactory.java:112) [org.eclipse.persistence.moxy-2.6.0-M3.jar:]
  at org.eclipse.persistence.jaxb.JAXBContextFactory.createContext(JAXBContextFactory.java:102) [org.eclipse.persistence.moxy-2.6.0-M3.jar:]
  at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) [rt.jar:1.7.0_51]
  at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) [rt.jar:1.7.0_51]
  at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) [rt.jar:1.7.0_51]
  at java.lang.reflect.Method.invoke(Method.java:606) [rt.jar:1.7.0_51]
  at javax.xml.bind.ContextFinder.newInstance(ContextFinder.java:211) [jboss-jaxb-api_2.2_spec-1.0.4.Final.jar:1.0.4.Final]
  at javax.xml.bind.ContextFinder.find(ContextFinder.java:349) [jboss-jaxb-api_2.2_spec-1.0.4.Final.jar:1.0.4.Final]
  at javax.xml.bind.JAXBContext.newInstance(JAXBContext.java:618) [jboss-jaxb-api_2.2_spec-1.0.4.Final.jar:1.0.4.Final]
  at org.jboss.resteasy.plugins.providers.jaxb.JAXBContextWrapper.(JAXBContextWrapper.java:88) [resteasy-jaxb-provider-3.0.10.Final.jar:]
  at org.jboss.resteasy.plugins.providers.jaxb.JAXBContextWrapper.(JAXBContextWrapper.java:113) [resteasy-jaxb-provider-3.0.10.Final.jar:]
  at org.jboss.resteasy.plugins.providers.jaxb.XmlJAXBContextFinder.createContextObject(XmlJAXBContextFinder.java:56) [resteasy-jaxb-provider-3.0.10.Final.jar:]
  at org.jboss.resteasy.plugins.providers.jaxb.AbstractJAXBContextFinder.createContext(AbstractJAXBContextFinder.java:150) [resteasy-jaxb-provider-3.0.10.Final.jar:]
  at org.jboss.resteasy.plugins.providers.jaxb.XmlJAXBContextFinder.findCacheContext(XmlJAXBContextFinder.java:72) [resteasy-jaxb-provider-3.0.10.Final.jar:]
  at org.jboss.resteasy.plugins.providers.jaxb.CollectionProvider.writeTo(CollectionProvider.java:252) [resteasy-jaxb-provider-3.0.10.Final.jar:]
  ... 41 more
  Caused by: Exception [EclipseLink-50047](Eclipse Persistence Services - 2.6.0.v20140809-296a69f): org.eclipse.persistence.exceptions.JAXBException
  Exception Description: Class [com.dnastack.bob.dto.ReferenceTo] not found.
  at org.eclipse.persistence.exceptions.JAXBException.classNotFoundException(JAXBException.java:681) [org.eclipse.persistence.core-2.6.0-M3.jar:]
  at org.eclipse.persistence.jaxb.javamodel.reflection.JavaModelImpl.getClass(JavaModelImpl.java:92) [org.eclipse.persistence.moxy-2.6.0-M3.jar:]
  at org.eclipse.persistence.jaxb.javamodel.Helper.getJavaClass(Helper.java:214) [org.eclipse.persistence.moxy-2.6.0-M3.jar:]
  at org.eclipse.persistence.jaxb.compiler.AnnotationsProcessor.processClass(AnnotationsProcessor.java:1319) [org.eclipse.persistence.moxy-2.6.0-M3.jar:]
  at org.eclipse.persistence.jaxb.compiler.AnnotationsProcessor.processAdditionalClasses(AnnotationsProcessor.java:1297) [org.eclipse.persistence.moxy-2.6.0-M3.jar:]
  at org.eclipse.persistence.jaxb.compiler.AnnotationsProcessor.processAdditionalClasses(AnnotationsProcessor.java:1176) [org.eclipse.persistence.moxy-2.6.0-M3.jar:]
  at org.eclipse.persistence.jaxb.compiler.AnnotationsProcessor.postBuildTypeInfo(AnnotationsProcessor.java:771) [org.eclipse.persistence.moxy-2.6.0-M3.jar:]
  at org.eclipse.persistence.jaxb.compiler.AnnotationsProcessor.processClassesAndProperties(AnnotationsProcessor.java:298) [org.eclipse.persistence.moxy-2.6.0-M3.jar:]
  at org.eclipse.persistence.jaxb.compiler.Generator.(Generator.java:156) [org.eclipse.persistence.moxy-2.6.0-M3.jar:]
  at org.eclipse.persistence.jaxb.JAXBContext$TypeMappingInfoInput.createContextState(JAXBContext.java:1104) [org.eclipse.persistence.moxy-2.6.0-M3.jar:]
  ... 59 more

Update DNAstack client

The current version of DNAstack client is not written nicely and needs to be refactored. It should also catch up with the functionality offered by BoB and get included in the repo.

Fix UCSC and AMPlab processors

UCSC and AMPlab tests started failing, probably because the API of those beacons changed. Update BoB to account for these changes.

Add support for LRG coordinates

Based on Marc's parser.

Add UCSC beacons with API v. 0.2

Links:
http://hgwdev-max.soe.ucsc.edu/cgi-bin/beacon2/query
http://hgwdev-max.soe.ucsc.edu/cgi-bin/beacon2/info
http://hgwdev-max.soe.ucsc.edu/cgi-bin/hgBeacon

Admin console

Create UI allowing the administrators to manipulate beacons (CRUD, toggle visibility, aggregate etc.).

Update documentation links

This includes links in:

• BoB client
• http://mcupak.github.io/beacon-of-beacons/

Integrate beacons from Beaconizer

http://webdev.dnastack.com/p/beacon/platinum?chromosome=1&coordinate=10177&allele=AC
http://webdev.dnastack.com/p/beacon/thousandgenomes?chromosome=1&coordinate=10177&allele=AC
http://webdev.dnastack.com/p/beacon/thousandgenomes-phase3?chromosome=1&coordinate=10177&allele=AC

Implement beacon storage

Currently, beacons are pretty much hard-coded. Store them in a DB so that they can be updated during runtime and the changes persist.

Add ICGC beacon

Links:

• https://dcc.icgc.org/ga4gh/beacon
• https://dcc.icgc.org/docs/#!/beacon/query_get_0

Info:
In short, the url follows the documentation on your website with the [BEACON-URL] being https://dcc.icgc.org:443/api/v1/beacon/query

With an optional ‘dataset’ parameter as well.

The beacon follows the v0.2 specification but does not yet implement wildcards/overlap as we are waiting for finalization of the spec to ensure that is implemented properly.

Also note that the only currently supported reference is GRCh37 and the beacon will respond with a JSON object (as required by the v0.2 specification).

Support for anonymous beacons

It should be possible to hide a beacon and expose its result through an aggregation point (essentially a fine-graned bob).

Example: Canadian cancer, US cancer, and UK cancer beacons all queried under a Cancer beacon.

Set proper HTTP status codes

E.g. return 404 if a beacon is not found etc.

Support for specifying genome build

Improve integration tests

The testsuite currently contains a few separate test classes testing different beacons, which involves a lot of redundancy and code duplication.

Normally, this is a kind of problem which could be solved by one of the following:

• parametrized JUnit tests
• JUnit theories
• JUnitParams project

Unfortunaly, all of these require you to use a custom runner, which doesn't work with the Arquillian runner we're using. Figure out a way to run parametrized tests with Arquillian in client mode.