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globalbioticinteractions / nomer

maps identifiers and names to other identifiers and names
GNU General Public License v3.0
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http://graph.openbiodiv.net/repositories/OpenBiodiv2020 does not appear to respond to queries #113

Closed jhpoelen closed 2 years ago

jhpoelen commented 2 years ago

hi @mdmtrv or pensoft colleagues ,

I noticed that some of my OpenBiodiv integration tests failed today for some reason. They succeeded previously.

Any idea why queries like the ones below are available to produce results against endpoint http://graph.openbiodiv.net/repositories/OpenBiodiv2020 ? 

PREFIX prism: <http://prismstandard.org/namespaces/basic/2.0/>
PREFIX doco: <http://purl.org/spar/doco/>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
select ?name ?rank ?id ?kingdom ?phylum ?class ?order ?family ?genus ?specificEpithet where { {
    BIND(<http://openbiodiv.net/6A54156A-BE5C-44D7-A9E3-3902DA4CCFAC> AS ?id). 
     ?id <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://openbiodiv.net/TaxonomicNameUsage>.
      OPTIONAL { ?taxon <http://rs.tdwg.org/dwc/terms/specificEpithet> ?specificEpithet.}
      OPTIONAL { ?taxon <http://rs.tdwg.org/dwc/terms/genus> ?genus.}
      OPTIONAL { ?taxon <http://rs.tdwg.org/dwc/terms/family> ?family.}
      OPTIONAL { ?taxon <http://rs.tdwg.org/dwc/terms/order> ?order. }
      OPTIONAL { ?taxon <http://rs.tdwg.org/dwc/terms/class> ?class. }
      OPTIONAL { ?taxon <http://rs.tdwg.org/dwc/terms/phylum> ?phylum.}
      OPTIONAL { ?taxon <http://rs.tdwg.org/dwc/terms/kingdom> ?kingdom.}
    { ?id <http://proton.semanticweb.org/protonkm#mentions> ?taxon.
      ?taxon <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://openbiodiv.net/ScientificName>.
      OPTIONAL { ?taxon <http://rs.tdwg.org/dwc/terms/verbatimTaxonRank> ?rank.}
      ?taxon <http://www.w3.org/2000/01/rdf-schema#label> ?name.
   }    UNION
    { ?id <http://proton.semanticweb.org/protonkm#mentions> ?btaxon.
      ?btaxon <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://openbiodiv.net/ScientificName>.
      ?btaxon <http://openbiodiv.net/hasGbifTaxon> ?taxon.
      OPTIONAL { ?taxon <http://rs.tdwg.org/dwc/terms/taxonRank> ?rank.}
      ?btaxon <http://www.w3.org/2000/01/rdf-schema#label> ?name.
   }  } }]

    at org.globalbioticinteractions.util.SparqlClientImpl.query(SparqlClientImpl.java:27)
    at org.globalbioticinteractions.nomer.util.OpenBiodivUtil.doLookup(OpenBiodivUtil.java:58)
    at org.globalbioticinteractions.nomer.util.OpenBiodivUtil.retrieveTaxonHierarchyById(OpenBiodivUtil.java:21)
    at org.globalbioticinteractions.nomer.util.OpenBiodivUtilTest.retrieveTaxonSpecies(OpenBiodivUtilTest.java:40)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
    at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
    at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
    at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
    at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
    at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
    at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
    at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
    at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
    at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
    at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
    at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
    at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
    at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
    at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
    at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
    at org.junit.runner.JUnitCore.run(JUnitCore.java:137)
    at com.intellij.junit4.JUnit4IdeaTestRunner.startRunnerWithArgs(JUnit4IdeaTestRunner.java:68)
    at com.intellij.rt.execution.junit.IdeaTestRunner$Repeater.startRunnerWithArgs(IdeaTestRunner.java:47)
    at com.intellij.rt.execution.junit.JUnitStarter.prepareStreamsAndStart(JUnitStarter.java:242)
    at com.intellij.rt.execution.junit.JUnitStarter.main(JUnitStarter.java:70)
Caused by: java.io.IOException: failed to get [http://graph.openbiodiv.net/repositories/OpenBiodiv2020?query=PREFIX%20fabio:%20%3Chttp://purl.org/spar/fabio/%3E%0APREFIX%20prism:%20%3Chttp://prismstandard.org/namespaces/basic/2.0/%3E%0APREFIX%20doco:%20%3Chttp://purl.org/spar/doco/%3E%0APREFIX%20dc:%20%3Chttp://purl.org/dc/elements/1.1/%3E%0Aselect%20?name%20?rank%20?id%20?kingdom%20?phylum%20?class%20?order%20?family%20?genus%20?specificEpithet%20where%20%7B%20%7B%0A%20%20%20%20BIND(%3Chttp://openbiodiv.net/6A54156A-BE5C-44D7-A9E3-3902DA4CCFAC%3E%20AS%20?id).%20%0A%20%20%20%20%20?id%20%3Chttp://www.w3.org/1999/02/22-rdf-syntax-ns%23type%3E%20%3Chttp://openbiodiv.net/TaxonomicNameUsage%3E.%0A%20%20%20%20%20%20OPTIONAL%20%7B%20?taxon%20%3Chttp://rs.tdwg.org/dwc/terms/specificEpithet%3E%20?specificEpithet.%7D%0A%20%20%20%20%20%20OPTIONAL%20%7B%20?taxon%20%3Chttp://rs.tdwg.org/dwc/terms/genus%3E%20?genus.%7D%0A%20%20%20%20%20%20OPTIONAL%20%7B%20?taxon%20%3Chttp://rs.tdwg.org/dwc/terms/family%3E%20?family.%7D%0A%20%20%20%20%20%20OPTIONAL%20%7B%20?taxon%20%3Chttp://rs.tdwg.org/dwc/terms/order%3E%20?order.%20%7D%0A%20%20%20%20%20%20OPTIONAL%20%7B%20?taxon%20%3Chttp://rs.tdwg.org/dwc/terms/class%3E%20?class.%20%7D%0A%20%20%20%20%20%20OPTIONAL%20%7B%20?taxon%20%3Chttp://rs.tdwg.org/dwc/terms/phylum%3E%20?phylum.%7D%0A%20%20%20%20%20%20OPTIONAL%20%7B%20?taxon%20%3Chttp://rs.tdwg.org/dwc/terms/kingdom%3E%20?kingdom.%7D%0A%20%20%20%20%7B%20?id%20%3Chttp://proton.semanticweb.org/protonkm%23mentions%3E%20?taxon.%0A%20%20%20%20%20%20?taxon%20%3Chttp://www.w3.org/1999/02/22-rdf-syntax-ns%23type%3E%20%3Chttp://openbiodiv.net/ScientificName%3E.%0A%20%20%20%20%20%20OPTIONAL%20%7B%20?taxon%20%3Chttp://rs.tdwg.org/dwc/terms/verbatimTaxonRank%3E%20?rank.%7D%0A%20%20%20%20%20%20?taxon%20%3Chttp://www.w3.org/2000/01/rdf-schema%23label%3E%20?name.%0A%20%20%20%7D%20%20%20%20UNION%0A%20%20%20%20%7B%20?id%20%3Chttp://proton.semanticweb.org/protonkm%23mentions%3E%20?btaxon.%0A%20%20%20%20%20%20?btaxon%20%3Chttp://www.w3.org/1999/02/22-rdf-syntax-ns%23type%3E%20%3Chttp://openbiodiv.net/ScientificName%3E.%0A%20%20%20%20%20%20?btaxon%20%3Chttp://openbiodiv.net/hasGbifTaxon%3E%20?taxon.%0A%20%20%20%20%20%20OPTIONAL%20%7B%20?taxon%20%3Chttp://rs.tdwg.org/dwc/terms/taxonRank%3E%20?rank.%7D%0A%20%20%20%20%20%20?btaxon%20%3Chttp://www.w3.org/2000/01/rdf-schema%23label%3E%20?name.%0A%20%20%20%7D%20%20%7D%20%7D]
    at org.eol.globi.util.HttpUtil.executeAndRelease(HttpUtil.java:130)
    at org.eol.globi.util.HttpUtil.executeAndRelease(HttpUtil.java:123)
    at org.globalbioticinteractions.nomer.util.OpenBiodivUtilTest.lambda$getResourceServiceTest$0(OpenBiodivUtilTest.java:69)
    at org.globalbioticinteractions.util.SparqlClientImpl.query(SparqlClientImpl.java:25)
    ... 28 more
Caused by: org.apache.http.conn.ConnectTimeoutException: Connect to graph.openbiodiv.net:80 [graph.openbiodiv.net/84.21.205.131] failed: connect timed out
    at org.apache.http.impl.conn.DefaultHttpClientConnectionOperator.connect(DefaultHttpClientConnectionOperator.java:151)
    at org.apache.http.impl.conn.PoolingHttpClientConnectionManager.connect(PoolingHttpClientConnectionManager.java:376)
    at org.apache.http.impl.execchain.MainClientExec.establishRoute(MainClientExec.java:393)
    at org.apache.http.impl.execchain.MainClientExec.execute(MainClientExec.java:236)
    at org.apache.http.impl.execchain.ProtocolExec.execute(ProtocolExec.java:186)
    at org.apache.http.impl.execchain.RetryExec.execute(RetryExec.java:89)
    at org.apache.http.impl.execchain.RedirectExec.execute(RedirectExec.java:110)
    at org.apache.http.impl.client.InternalHttpClient.doExecute(InternalHttpClient.java:185)
    at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:72)
    at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:221)
    at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:165)
    at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:140)
    at org.eol.globi.util.HttpUtil.executeAndRelease(HttpUtil.java:128)
    ... 31 more
Caused by: java.net.SocketTimeoutException: connect timed out
    at java.net.PlainSocketImpl.socketConnect(Native Method)
    at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
    at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
    at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
    at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
    at java.net.Socket.connect(Socket.java:607)
    at org.apache.http.conn.socket.PlainConnectionSocketFactory.connectSocket(PlainConnectionSocketFactory.java:75)
    at org.apache.http.impl.conn.DefaultHttpClientConnectionOperator.connect(DefaultHttpClientConnectionOperator.java:142)
    ... 43 more
jhpoelen commented 2 years ago

Looks like the openbiodiv sparql endpoint is up and running again.