java—是否可以使用sparql和rdf4j批量处理select查询?

ldfqzlk8  于 2021-06-26  发布在  Java
关注(0)|答案(1)|浏览(333)

我正在使用一个相当大的数据集(大约500mio三元组),它存储在graphdb free中,并在本地开发人员机器上运行。
我想用rdf4j对数据集进行一些操作,并且必须或多或少地选择整个数据集。要进行测试,我只需选择所需的元组。代码在第一个一百万元组中运行良好,之后由于graphdb继续分配更多的ram,代码运行速度变得非常慢。
有没有可能对非常大的数据集执行select查询并批量获取它们?
基本上我只想通过一些选定的三元组进行“迭代”,所以不需要使用graphdb中的那么多ram。我可以看到,在查询完成之前,我已经准备好在rdf4j中获取数据,因为它只在大约140万个读取元组时崩溃(heapspaceerror)。不幸的是graphdb并没有释放allready读取元组的内存。我错过什么了吗?
非常感谢你的帮助。
ps.i allready将graphdb的可用堆空间设置为20gb。
rdf4j(java)代码如下所示:

package ch.test;

import org.eclipse.rdf4j.query.*;
import org.eclipse.rdf4j.repository.RepositoryConnection;
import org.eclipse.rdf4j.repository.http.HTTPRepository;

import java.io.File;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import java.nio.file.Files;
import java.nio.file.Paths;

public class RDF2RDF {

    public static void main(String[] args) {
        System.out.println("Running RDF2RDF");

        HTTPRepository sourceRepo = new HTTPRepository("http://localhost:7200/repositories/datatraining");
        try {
            String path = new File("").getAbsolutePath();
            String sparqlCommand= Files.readString(Paths.get(path + "/src/main/resources/sparql/select.sparql"), StandardCharsets.ISO_8859_1);

            int chunkSize = 10000;
            int positionInChunk = 0;
            long loadedTuples = 0;

            RepositoryConnection sourceConnection = sourceRepo.getConnection();
            TupleQuery query = sourceConnection.prepareTupleQuery(sparqlCommand);

            try (TupleQueryResult result = query.evaluate()) {
                for (BindingSet solution:result) {
                    loadedTuples++;
                    positionInChunk++;

                    if (positionInChunk >= chunkSize) {
                        System.out.println("Got " + loadedTuples + " Tuples");
                        positionInChunk = 0;
                    }
                }
            }

        } catch (IOException err) {
            err.printStackTrace();
        }
    }
}

选择.sparql:

PREFIX XXX_meta_schema: <http://schema.XXX.ch/meta/>
PREFIX XXX_post_schema: <http://schema.XXX.ch/post/>
PREFIX XXX_post_tech_schema: <http://schema.XXX.ch/post/tech/>

PREFIX XXX_geo_schema: <http://schema.XXX.ch/geo/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX XXX_raw_schema: <http://schema.XXX.ch/raw/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>

SELECT * WHERE {

    BIND(<http://data.XXX.ch/raw/Table/XXX.csv> as ?table).

    ?row XXX_raw_schema:isDefinedBy ?table.

    ?cellStreetAdress XXX_raw_schema:isDefinedBy ?row;
        XXX_raw_schema:ofColumn <http://data.XXX.ch/raw/Column/Objektadresse>;
        rdf:value ?valueStreetAdress.

    ?cellOrt mobi_raw_schema:isDefinedBy ?row;
        XXX_raw_schema:ofColumn <http://XXX.mobi.ch/raw/Column/Ort>;
        rdf:value ?valueOrt.

    ?cellPlz mobi_raw_schema:isDefinedBy ?row;
        XXX_raw_schema:ofColumn <http://XXX.mobi.ch/raw/Column/PLZ>;
        rdf:value ?valuePLZ.

    BIND (URI(concat("http://data.XXX.ch/post/tech/Adress/", MD5(STR(?cellStreetAdress)))) as ?iri_tech_Adress).
}

我的解决方案是:使用subselect语句,它首先获取所有“行”。

PREFIX mobi_post_schema: <http://schema.mobi.ch/post/>
PREFIX mobi_post_tech_schema: <http://schema.mobi.ch/post/tech/>

PREFIX mobi_geo_schema: <http://schema.mobi.ch/geo/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX mobi_raw_schema: <http://schema.mobi.ch/raw/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>

SELECT * WHERE {

    {
        SELECT ?row WHERE
        {
            BIND(<http://data.mobi.ch/raw/Table/Gebaeudeobjekte_August2020_ARA_Post.csv> as ?table).

            ?row mobi_raw_schema:isDefinedBy ?table.
        }
    }

    ?cellStreetAdress mobi_raw_schema:isDefinedBy ?row;
        mobi_raw_schema:ofColumn <http://data.mobi.ch/raw/Column/Objektadresse>;
        rdf:value ?valueStreetAdress.

    ?cellOrt mobi_raw_schema:isDefinedBy ?row;
        mobi_raw_schema:ofColumn <http://data.mobi.ch/raw/Column/Ort>;
        rdf:value ?valueOrt.

    ?cellPlz mobi_raw_schema:isDefinedBy ?row;
        mobi_raw_schema:ofColumn <http://data.mobi.ch/raw/Column/PLZ>;
        rdf:value ?valuePLZ.

    BIND (URI(concat("http://data.mobi.ch/post/tech/Adress/", MD5(STR(?cellStreetAdress)))) as ?iri_tech_Adress).
}
uurv41yg

uurv41yg1#

我不知道为什么给定的查询会如此昂贵,内存方面的原因,因为graphdb是免费执行的,但是通常很多情况都取决于数据集的形状和大小。当然,首先执行基本上检索整个数据库的查询并不一定是明智之举。
话虽如此,有几件事你可以试试。使用 LIMIT 以及 OFFSET 作为分页机制是一种方法。
您可以尝试的另一种方法是将查询一分为二:一个查询检索您感兴趣的资源的所有标识符,然后对这些标识符进行迭代,并为每个标识符执行一个单独的查询,以获取特定资源的详细信息(属性和关系)。
在你的例子中,你可以在 ?row ,因此您首先要执行一个查询以获取给定表的所有行:

SELECT ?row WHERE {
    VALUES ?table { <http://data.XXX.ch/raw/Table/XXX.csv> }
    ?row XXX_raw_schema:isDefinedBy ?table.
}

然后对结果进行迭代,为 ?row 到检索详细信息的查询中:

SELECT * WHERE {
    VALUES ?row { <http://data.XXX.ch/raw/Table/XXX.csv#row1> }

    ?cellStreetAdress XXX_raw_schema:isDefinedBy ?row;
        XXX_raw_schema:ofColumn <http://data.XXX.ch/raw/Column/Objektadresse>;
        rdf:value ?valueStreetAdress.

    ?cellOrt mobi_raw_schema:isDefinedBy ?row;
        XXX_raw_schema:ofColumn <http://XXX.mobi.ch/raw/Column/Ort>;
        rdf:value ?valueOrt.

    ?cellPlz mobi_raw_schema:isDefinedBy ?row;
        XXX_raw_schema:ofColumn <http://XXX.mobi.ch/raw/Column/PLZ>;
        rdf:value ?valuePLZ.

    BIND (URI(concat("http://data.XXX.ch/post/tech/Adress/", MD5(STR(?cellStreetAdress)))) as ?iri_tech_Adress).
}

在java代码中,类似于:

String sparqlCommand1 = // the query for all rows of the table

// query for details of each row. Value of row will be injected via the API
String sparqlCommand2 = "SELECT * WHERE { \n"
                    + "    ?cellStreetAdress XXX_raw_schema:isDefinedBy ?row;\n"
                    + "        XXX_raw_schema:ofColumn <http://data.XXX.ch/raw/Column/Objektadresse>;\n"
                    + "        rdf:value ?valueStreetAdress.\n"
                    + "    ?cellOrt mobi_raw_schema:isDefinedBy ?row;\n"
                    + "        XXX_raw_schema:ofColumn <http://XXX.mobi.ch/raw/Column/Ort>;\n"
                    + "        rdf:value ?valueOrt.\n"
                    + "    ?cellPlz mobi_raw_schema:isDefinedBy ?row;\n"
                    + "        XXX_raw_schema:ofColumn <http://XXX.mobi.ch/raw/Column/PLZ>;\n"
                    + "        rdf:value ?valuePLZ.\n"
                    + "    BIND (URI(concat(\"http://data.XXX.ch/post/tech/Adress/\", MD5(STR(?cellStreetAdress)))) as ?iri_tech_Adress).\n"
                    + "}";

try(RepositoryConnection sourceConnection = sourceRepo.getConnection()) {
     TupleQuery rowQuery = sourceConnection.prepareTupleQuery(sparqlCommand1);     
     TupleQuery detailsQuery = sourceConnection.prepareTupleQuery(sparqlCommand2);

     try (TupleQueryResult result = rowQuery.evaluate()) {
         for (BindingSet solution: result) {
                // inject the current row identifier
                detailsQuery.setBinding("row", solution.getValue("row"));

                // execute the details query for the row and do something with 
                // the result
                detailsQuery.evaluate().forEach(System.out::println);
         }
     }
}

当然,您会以这种方式进行更多的查询(n+1,其中n是行数),但是每个单独的查询结果只是一个小的块,而且可能更易于graphdb-free(以及您自己的应用程序)管理。

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