search

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"
Apache License 2.0
77 stars 26 forks source link

phmmer has moved to https #10

Open otienoanyango opened 6 years ago

otienoanyango commented 6 years ago

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