Question

This is the original question（这是第二部分）。

我正在使用HyperGraphQL基于EBI-RDF sparql endpoint查询this tutorial。

当我执行此GraphQL查询以检索GO_0044727的父母时：

{
  Class_GET_BY_ID(uris:[
    "http://purl.obolibrary.org/obo/GO_0044727"]) {
    id
    label
    subClassOf {
      id
      label
      subClassOf {
        id
        label
        subClassOf {  # <--- 4th sub level
          id
          label
        }
      }
    }
  }
}

我没有结果：

{
  "extensions": {},
  "data": {
    "@context": {
      "_type": "@type",
      "_id": "@id",
      "label": "http://www.w3.org/2000/01/rdf-schema#label",
      "id": "http://www.geneontology.org/formats/oboInOwl#id",
      "Class_GET_BY_ID": "http://hypergraphql.org/query/Class_GET_BY_ID",
      "subClassOf": "http://www.w3.org/2000/01/rdf-schema#subClassOf"
    },
    "Class_GET_BY_ID": []
  },
  "errors": []
}

在日志中，我得到了错误：

java.util.concurrent.ExecutionException: org.apache.jena.query.QueryException: Endpoint returned Content-Type: text/html which is not rcognized for SELECT queries
    at java.util.concurrent.FutureTask.report(FutureTask.java:122)
    at java.util.concurrent.FutureTask.get(FutureTask.java:192)
    at org.hypergraphql.datafetching.services.SPARQLEndpointService.iterateFutureResults(SPARQLEndpointService.java:86)
    at org.hypergraphql.datafetching.services.SPARQLEndpointService.executeQuery(SPARQLEndpointService.java:69)
    at org.hypergraphql.datafetching.ExecutionTreeNode.generateTreeModel(ExecutionTreeNode.java:357)
    at org.hypergraphql.datafetching.FetchingExecution.call(FetchingExecution.java:21)
    at org.hypergraphql.datafetching.FetchingExecution.call(FetchingExecution.java:8)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)
Caused by: org.apache.jena.query.QueryException: Endpoint returned Content-Type: text/html which is not rcognized for SELECT queries
    at org.apache.jena.sparql.engine.http.QueryEngineHTTP.execResultSetInner(QueryEngineHTTP.java:377)
    at org.apache.jena.sparql.engine.http.QueryEngineHTTP.execSelect(QueryEngineHTTP.java:344)
    at org.hypergraphql.datafetching.SPARQLEndpointExecution.call(SPARQLEndpointExecution.java:81)
    at org.hypergraphql.datafetching.SPARQLEndpointExecution.call(SPARQLEndpointExecution.java:33)
    ... 4 more

根据上面的GraphQL查询生成的SPARQL查询：

SELECT * 
WHERE { 
    GRAPH <http://rdf.ebi.ac.uk/dataset/go> { 
        VALUES ?x_1 { <http://purl.obolibrary.org/obo/GO_0044727> } 
        ?x_1 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Class> . 
        OPTIONAL { 
            ?x_1 <http://www.w3.org/2000/01/rdf-schema#subClassOf> ?x_1_1 .?x_1_1 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Class> . 
            OPTIONAL { ?x_1_1 <http://www.w3.org/2000/01/rdf-schema#label> ?x_1_1_1 . }  
                OPTIONAL { ?x_1_1 <http://www.w3.org/2000/01/rdf-schema#subClassOf> ?x_1_1_2 .?x_1_1_2 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Class> . 
                OPTIONAL { ?x_1_1_2 <http://www.geneontology.org/formats/oboInOwl#id> ?x_1_1_2_1 . }  
                OPTIONAL { 
                    ?x_1_1_2 <http://www.w3.org/2000/01/rdf-schema#subClassOf> ?x_1_1_2_2 .?x_1_1_2_2 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Class> . 
                    OPTIONAL { ?x_1_1_2_2 <http://www.w3.org/2000/01/rdf-schema#label> ?x_1_1_2_2_1 . }  
                    OPTIONAL { ?x_1_1_2_2 <http://www.geneontology.org/formats/oboInOwl#id> ?x_1_1_2_2_2 . }  
                }  
                OPTIONAL { ?x_1_1_2 <http://www.w3.org/2000/01/rdf-schema#label> ?x_1_1_2_3 . }  
            }  
            OPTIONAL { ?x_1_1 <http://www.geneontology.org/formats/oboInOwl#id> ?x_1_1_3 . }  
        }  
        OPTIONAL { ?x_1 <http://www.w3.org/2000/01/rdf-schema#label> ?x_1_2 . }  
        OPTIONAL { ?x_1 <http://www.geneontology.org/formats/oboInOwl#id> ?x_1_3 . }  
    }  
}

我通过在?force文件（行：config.json）中添加"url": "http://www.ebi.ac.uk/rdf/services/sparql?force"来尝试@AKSW回答here，但是没有用。

我认为查询时间可能太长，但是当我tested the query时，它没有给出任何错误。

Answer 1

我发现的唯一解决方案是使用local RDF file查询基因本体：

我下载了go.owl文件。

使用Ontology Converter将其转换为Turtle。

 java -jar ont-converter.jar -i go.owl -o go_ont.ttl -of ttl -v

配置的HyperGraphQL：

goconfig.json文件：

{
    "name": "go-hgql",
    "schema": "schemas/goschema.graphql",
    "server": {
        "port": 8082,
        "graphql": "/graphql",
        "graphiql": "/graphiql"
    },
    "services": [
        {
            "id": "go-local",
            "type": "LocalModelSPARQLService",
            "filepath": "go_ont.ttl",  # <----- the TTL file
            "filetype": "TTL"
        }
    ]
}

goschema.graphql：

type __Context {
    Class:          _@href(iri: "http://www.w3.org/2002/07/owl#Class")
    id:             _@href(iri: "http://www.geneontology.org/formats/oboInOwl#id")
    label:          _@href(iri: "http://www.w3.org/2000/01/rdf-schema#label")
    subClassOf:     _@href(iri: "http://www.w3.org/2000/01/rdf-schema#subClassOf")
}

type Class @service(id:"go-local") {
    id: [String] @service(id:"go-local")
    label: [String] @service(id:"go-local")
    subClassOf: [Class] @service(id:"go-local")
}

使用配置文件启动HyperGraphQL：

java -jar build/libs/hypergraphql-1.0.3-exe.jar --config hgql/config/goconfig.json

然后执行查询，一切顺利，没有问题，我可以根据需要添加任意多个子级别。

返回的端点Content-Type：text / html，SELECT查询无法识别

1 个答案: