flaxsearch/biosolr

A project aiming "to significantly advance the state of the art with regard to indexing and querying biomedical data with freely available open source software"

biosolr's Issues

Solr Hierachical Facet plugin support multiple node ID

example:
{ "id": "1", "node_id": "A", "child_ids": [ "AA"], "name": "NodeA", "label": "nodeA" }
{ "id": "2", "node_id": "B", "child_ids": [ "BB"], "name": "NodeB", "label": "nodeB" }
{ "id": "3", "node_id": "AA", "node_id": "BB", "child_ids": [ ], "name": "NodeAABB", "label": "nodeAABB" }

Unsupported major.minor version 52.0

java -jar swat4ls-webapp-1.0-SNAPSHOT.jar server webapp.yml
Exception in thread "main" java.lang.UnsupportedClassVersionError: uk/co/flax/biosolr/ontology/OntologyApplication : Unsupported major.minor version 52.0
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(ClassLoader.java:800)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:449)
at java.net.URLClassLoader.access$100(URLClassLoader.java:71)
at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:482)

XJoin not working on multi-sharded indexes

The team are using Solr on an instance with replicas, and xjoin does not return any results. It would be great to add this functionality.

empty efu_uri?

If I use a local OWL file, and leave the value for the efu_uri empty. Will the plugin be able to parse the text in the document I send to properly classify the document according to the OWL ontology?

Best.

Theyaa

Example using OWL ontology?

Hi,
Do you have an example/demo using OWL ontology please? what would be the value of the efo_uri field in the documents to be indexed?
@mattflax @tburdett @tomjon
Thanks

Unable to do maven build for Core Annotator Project

While trying to do a MavenBuild for Ontology-Annotator-Core project. I hit with this error

Exception in thread "main" java.lang.NoClassDefFoundError: com/google/common/base/Strings
at org.sonatype.nexus.maven.staging.deploy.DeployLifecycleParticipant.getPluginByGAFromContainer(DeployLifecycleParticipant.java:238)
at org.sonatype.nexus.maven.staging.deploy.DeployLifecycleParticipant.getNexusMavenPluginFromContainer(DeployLifecycleParticipant.java:182)
at org.sonatype.nexus.maven.staging.deploy.DeployLifecycleParticipant.getBuildPluginsNexusMavenPlugin(DeployLifecycleParticipant.java:163)
at org.sonatype.nexus.maven.staging.deploy.DeployLifecycleParticipant.afterProjectsRead(DeployLifecycleParticipant.java:95)
at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:266)
at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:193)
at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:106)
at org.apache.maven.cli.MavenCli.execute(MavenCli.java:863)
at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:288)
at org.apache.maven.cli.MavenCli.main(MavenCli.java:199)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
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: java.lang.ClassNotFoundException: com.google.common.base.Strings
at org.codehaus.plexus.classworlds.strategy.SelfFirstStrategy.loadClass(SelfFirstStrategy.java:50)
at org.codehaus.plexus.classworlds.realm.ClassRealm.unsynchronizedLoadClass(ClassRealm.java:271)
at org.codehaus.plexus.classworlds.realm.ClassRealm.loadClass(ClassRealm.java:247)
at org.codehaus.plexus.classworlds.realm.ClassRealm.loadClass(ClassRealm.java:239)
... 18 more

I tried adding the Guava Jar too in the library and added this entry in POM.xml file-

com.google.guava guava 18

Is there anything else I need to do. Could someone help

phmmer has moved to https

sequence search using phmmer fails I believe because phmmer has moved to https by default. The query returns
"error": {
"msg": "Server returned HTTP response code: 400 for URL: https://www.ebi.ac.uk/Tools/hmmer/search/phmmer",
"trace": "java.io.IOException: Server returned HTTP response code: 400 for URL: https://www.ebi.ac.uk/Tools/hmmer/search/phmmer\n\tat sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1876)\n\tat sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1474)\n\tat sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:254)\n\tat uk.co.flax.biosolr.pdbe.phmmer.PhmmerClient$HttpConnection.getJson(PhmmerClient.java:67)\n\tat uk.co.flax.biosolr.pdbe.phmmer.PhmmerClient$HttpConnection.access$4(PhmmerClient.java:66)\n\tat uk.co.flax.biosolr.pdbe.phmmer.PhmmerClient.getResultsJson(PhmmerClient.java:34)\n\tat uk.co.flax.biosolr.pdbe.phmmer.PhmmerClient.getResults(PhmmerClient.java:21)\n\tat uk.co.flax.biosolr.pdbe.phmmer.PhmmerJob.runJob(PhmmerJob.java:23)\n\tat uk.co.flax.biosolr.pdbe.phmmer.PhmmerXJoinResultsFactory.getResults(PhmmerXJoinResultsFactory.java:70)\n\tat org.apache.solr.search.xjoin.XJoinSearchComponent.prepare(XJoinSearchComponent.java:115)\n\tat org.apache.solr.handler.component.SearchHandler.handleRequestBody(SearchHandler.java:268)\n\tat org.apache.solr.handler.RequestHandlerBase.handleRequest(RequestHandlerBase.java:152)\n\tat org.apache.solr.core.SolrCore.execute(SolrCore.java:2227)\n\tat org.apache.solr.servlet.HttpSolrCall.execute(HttpSolrCall.java:658)\n\tat org.apache.solr.servlet.HttpSolrCall.call(HttpSolrCall.java:464)\n\tat org.apache.solr.servlet.SolrDispatchFilter.doFilter(SolrDispatchFilter.java:303)\n\tat org.apache.solr.servlet.SolrDispatchFilter.doFilter(SolrDispatchFilter.java:254)\n\tat org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1691)\n\tat org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:582)\n\tat org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143)\n\tat org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:548)\n\tat org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:226)\n\tat org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1180)\n\tat org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:512)\n\tat org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:185)\n\tat org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1112)\n\tat org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141)\n\tat org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:213)\n\tat org.eclipse.jetty.server.handler.HandlerCollection.handle(HandlerCollection.java:119)\n\tat org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:134)\n\tat org.eclipse.jetty.server.Server.handle(Server.java:534)\n\tat org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:320)\n\tat org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:251)\n\tat org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:273)\n\tat org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:95)\n\tat org.eclipse.jetty.io.SelectChannelEndPoint$2.run(SelectChannelEndPoint.java:93)\n\tat org.eclipse.jetty.util.thread.strategy.ExecuteProduceConsume.executeProduceConsume(ExecuteProduceConsume.java:303)\n\tat org.eclipse.jetty.util.thread.strategy.ExecuteProduceConsume.produceConsume(ExecuteProduceConsume.java:148)\n\tat org.eclipse.jetty.util.thread.strategy.ExecuteProduceConsume.run(ExecuteProduceConsume.java:136)\n\tat org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:671)\n\tat org.eclipse.jetty.util.thread.QueuedThreadPool$2.run(QueuedThreadPool.java:589)\n\tat java.lang.Thread.run(Thread.java:748)\n",
"code": 500

Is it possible to compile solr ontology update processor in Java 7

I want to integrate your plugins into my system. The reason is to run it in Java 7. Could you confirm me if it could be compiled in Java 7?

Thanks for your support.

pom for xjoin

Would it possible to have a maven pom, or perhaps something equivalent for building the xjoin code?

I was looking at the code under /sequence and seems missing the dependency from package uk.ac.ebi.webservices.axis1.stubs.fasta, and javax.json.

Searching 'mental disorders' do not get 150 results

Hi,

I have tried to test BioSolr.
I have also run to Part Seven: Ontology-powered search.
But I cannot get 150 results with the key words "mental disorders" plus the option "Include child labels". However, I got 5 results with that key words and the option "Include parent labels".

Please see the attached image.

The question is whether you made a mistake in the instruction or the fault comes out my configuration.

Indexing Ontology issue with ElasticSearch

From documentation we see that ontology is added to an existing document as special field of type "Ontology". I try to map an OWL ontology with ver 2.2 of the plugin in the following way:

http://localhost:9200/persone/_mapping/utente

body:

{
"properties": {
"annotation": {
"type": "ontology",
"ontology": {
"ontologyURI": "file:///C:/Users/rezzonicoda/Desktop/Tesi/OntologiaProva/myOntology.owl",
"labelURI": "http://www.w3.org/2000/01/rdf-schema#label",
"synonymURI": "http://www.ebi.ac.uk/efo/alternative_term",
"definitionURI": [
"http://www.ebi.ac.uk/efo/definition",
"http://purl.obolibrary.org/obo/IAO_0000115"
],
"includeIndirect": true,
"includeRelations": true,
"includeParentPaths": false,
"includeParentPathLabels": true
}
}
}
}

and the mapping operation seems to be successfull. But when I try to GET the added properties I can see only the ones that I've added with ES manually. Running this:

curl -XGET 'http://localhost:9200/biosolr/gwas/_search?pretty' -d '{ "_source": ["*"], "fields": ["annotation"], "query": { "match_all": {} } }'

I get this:

{
"took" : 109,
"timed_out" : false,
"_shards" : {
"total" : 5,
"successful" : 5,
"failed" : 0
},
"hits" : {
"total" : 1,
"max_score" : 1.0,
"hits" : [ {
"_index" : "biosolr",
"_type" : "gwas",
"_id" : "AWJS6OE5vH26KX4n0yO3",
"_score" : 1.0,
"_source" : {
"prova" : "Ciao"
}
} ]
}
}

In ElastiSearch log i can see this error

[2018-03-22 16:24:46,474][INFO ][rest.suppressed ] /persone/_mapping/utente Params: {index=persone, type=utente}
[persone] IndexNotFoundException[no such index]

Hoiw I can solve it? Thanks
elasticsearch.log.2018-03-22.txt

Problem with Part Two: indexing some example data

Following instructions in README.md, I am stucking at Part Two for indexing some example data.
Run: curl http://localhost:8983/solr/documents/update --data-binary data/gwas-catalog-annotation-data.csv -H 'Content-type:application/csv'

The error is:

<title>Error 404 Not Found</title>

HTTP ERROR 404
Problem accessing /solr/documents/update. Reason:
    Not Found
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Sample Documents to use with this plugin

Hi,
I am new to using your ontology Solr plugin and I would like to test it with some sample documents to see how it works.

Would you have few sample documents that works with your SPOT-ontology application with the default settings you have there please?

Thanks