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A modular R2RML suite built on Apache Jena. Featuring a complete domain API built on Jena's polymorphism system, SHACL validation, an R2RML processor with 100% standard conformance based an Jena's ARQ plus common tooling every R2RML project needs.

License: Other

Java 99.55% Makefile 0.21% Shell 0.24%
r2rml apache-jena semantic-web rdb2rdf r2rml-api-jena jena-arq

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r2-rml-toolkit's Issues

Incorrect SPARQL Exprs when joining TriplesMaps with different reference formulations

The TriplesMapProcessorRml incorrectly resolves all expressions against a RefObjectMap's child context .
If the child of a join uses JSON and the parent uses XML then json functions will be applied to the XML data:

[] <http://semweb.mmlab.be/ns/rml#source>  "/data/shared/STOPS.xml" ;
   <https://w3id.org/aksw/norse#rml.output>  ?s2}
BIND(<https://w3id.org/aksw/norse#json.get>(?s2, "stop_id") AS ?jc0)

GitFlow and RPM plugin incompatibility

It seems that this is a conflict between the gitflow and the rpm plugin (or at least the latter's configurations).
Disabling the rpm causes normal termination of mvn gitflow:release-finish.

[ERROR] 
org.apache.maven.plugin.MojoFailureException: SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.

    at com.amashchenko.maven.plugin.gitflow.AbstractGitFlowMojo.executeCommand (AbstractGitFlowMojo.java:963)
    at com.amashchenko.maven.plugin.gitflow.AbstractGitFlowMojo.executeMvnCommand (AbstractGitFlowMojo.java:905)
    at com.amashchenko.maven.plugin.gitflow.AbstractGitFlowMojo.mvnCleanTest (AbstractGitFlowMojo.java:824)

Packages are getting deployed

mvn clean install deploy
results in:

[INFO] rmltk-pkg-deb-cli .................................................................................... FAILURE [  0.527 s]

[ERROR] Failed to execute goal org.apache.maven.plugins:maven-jar-plugin:3.3.0:jar (default-jar) on project rmltk-pkg-deb-cli: You have to use a classifier to attach supplemental artifacts to the project instead of replacing them. -> [Help 1]

The error occasionally appears in other projects, so investigating the culprit for it is worthwhile.
But for this project, packages (debian, rpm, uberjar) should not be deployed in the first place.

Revise model for filters on term maps

The current internal model for RML to SPARQL translation does not handle term maps and their corresponding lateral blocks as first class citizens, such that filters on term maps can not yet be easily translated. A revision of the internal model and the translation procedure is needed:

Example: Given the following term map:

 rr:predicateObjectMap [
      rr:predicate coy:hasAssetId;
      rr:objectMap [
        rml:reference "asset_id";
        rr:datatype xsd:string ;
        norse:rml.filter "?asset_id != ''" ; # filter out empty column
      ]
    ] ;

In the RML-to-SPARQL translation, RML term maps should be be translated to their own SPARQL LATERAL blocks, as sketched below:

  logicalSource
  LATERAL {
        { FILTER(?asset_id != '') BIND(?asset_id AS ?allocatedTermMapVar) }
      UNION
        { ... }
  }

Note, that filters on the logical source just drop bindings of that source, so on that level the current model shouldn't have much problems.

RML to SPARQL should support adding prefixes to sparql queries

There are the following ways forhow this can be handled and appropriate configuration options should be provided:

  • repeat prefixes on every query (gets ugly when many prefixes are involved)
  • only add the prefixes to the beginning of a file containing sparql queries (our parser can handle this, but probably less portable)

For the CLI, in addition it may be worthwhile to add an option that outputs each query to a separate file.

Nexus staging plugin error (probably its version is too old) 

master$ mvn -P release clean install deploy

results in:

[ERROR] Failed to execute goal org.sonatype.plugins:nexus-staging-maven-plugin:1.6.8:deploy (injected-nexus-deploy) on project rmltk-bom: Execution injected-nexus-deploy of goal org.sonatype.plugins:nexus-staging-maven-plugin:1.6.8:deploy failed: An API incompatibility was encountered while executing org.sonatype.plugins:nexus-staging-maven-plugin:1.6.8:deploy: java.lang.ExceptionInInitializerError: null

predicateObjectMap - subject and object are interchanged

In my mapping.ttl I have:

<TradeInValueAdded> a rr:TriplesMap;

    rml:logicalSource [
        rml:source "./trade.csv" ;
        rml:referenceFormulation ql:CSV
    ];

    rr:subjectMap [
        rr:template "https://data.coypu.org/trade/baci/{id}/{i}_{j}_value" ;
        rr:class tiva:ExgrDva
    ];

    rr:predicateObjectMap [
        rr:predicate tiva:hasTrade ;
        rr:objectMap [
            rr:parentTriplesMap <Trades>;
            rr:joinCondition [
                rr:child "id";
                rr:parent "id"
            ]
           ]
    ];

    rr:predicateObjectMap [
        rr:predicate tiva:hasImport ;
        rr:objectMap [
            rr:parentTriplesMap <Countries>;
            rr:joinCondition [
                rr:child "j";
                rr:parent "country_code"
            ]
           ]
    ];

    rr:predicateObjectMap [
        rr:predicate tiva:hasExport;
        rr:objectMap [
            rr:parentTriplesMap <Countries>;
            rr:joinCondition [
                rr:child "i";
                rr:parent "country_code"
            ]
           ]
    ]
    .

and after transforming it to sparql the subject and object are interchanged:

CONSTRUCT 
  { 
    ?v12 <https://schema.coypu.org/vtf#hasTrade> ?v10 .
  }
WHERE
  { SERVICE <https://w3id.org/aksw/norse#rml.source>
      { <https://w3id.org/aksw/norse#rml.source>
                  <http://semweb.mmlab.be/ns/rml#source>  "./trade.csv" ;
                  <http://semweb.mmlab.be/ns/rml#referenceFormulation>  <http://semweb.mmlab.be/ns/ql#CSV> ;
                  <https://w3id.org/aksw/norse#rml.output>  ?s0}
    BIND(encode_for_uri(str(<https://w3id.org/aksw/norse#json.get>(?s0, "id"))) AS ?v2)
    BIND(IRI(concat("https://data.coypu.org/trade/baci/", ?v2)) AS ?v12)
    BIND(IRI(concat("https://data.coypu.org/trade/baci/", ?v2, "/", encode_for_uri(str(<https://w3id.org/aksw/norse#json.get>(?s0, "i"))), "_", encode_for_uri(str(<https://w3id.org/aksw/norse#json.get>(?s0, "j"))), "_value")) AS ?v10)
  }

also after optimizing:

CONSTRUCT 
  { 
    GRAPH ?__g__ 
      { ?__s__ ?__p__ ?__o__ .}
  }
WHERE
  { SELECT  (<urn:x-arq:DefaultGraphNode> AS ?__g__) ?__s__ (<https://schema.coypu.org/vtf#hasTrade> AS ?__p__) ?__o__
    WHERE
      { SELECT DISTINCT  (?m0_v12 AS ?__s__) (?m0_v10 AS ?__o__)
        WHERE
          { SERVICE <https://w3id.org/aksw/norse#rml.source>
              { <https://w3id.org/aksw/norse#rml.source>
                          <http://semweb.mmlab.be/ns/rml#source>  "./trade.csv" ;
                          <http://semweb.mmlab.be/ns/rml#referenceFormulation>  <http://semweb.mmlab.be/ns/ql#CSV> ;
                          <https://w3id.org/aksw/norse#rml.output>  ?s0}
            BIND(encode_for_uri(str(<https://w3id.org/aksw/norse#json.get>(?s0, "id"))) AS ?m0_v2)
            BIND(IRI(concat("https://data.coypu.org/trade/baci/", ?m0_v2)) AS ?m0_v12)
            BIND(IRI(concat("https://data.coypu.org/trade/baci/", ?m0_v2, "/", encode_for_uri(str(<https://w3id.org/aksw/norse#json.get>(?s0, "i"))), "_", encode_for_uri(str(<https://w3id.org/aksw/norse#json.get>(?s0, "j"))), "_value")) AS ?m0_v10)
          }
      }
  }

The data then has the wrong triple:

<https://data.coypu.org/trade/baci/1> <https://schema.coypu.org/vtf#hasTrade> <https://data.coypu.org/trade/baci/1/4_24_value> .

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