#1999

Committed 13 May 2026 10:23PM UTC coverage: 70.05% (-0.3%) from 70.334%

Build # #1999

Build Type

Pull #751

github

Committed by

kinow

Commit Message

Last fixes to ease working with the SPARQL queries for a future PR, and more string concatenation removal

Pull Request Pull Request #751: Bump org.springframework.boot:spring-boot-starter-parent from 3.1.4 to 4.1.0-RC1

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120 of 208 new or added lines in 30 files covered. (57.69%)

21 existing lines in 5 files now uncovered.

1691 of 2414 relevant lines covered (70.05%)

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50.51

/src/main/java/org/commonwl/view/cwl/RDFService.java

/*
 * Licensed to the Apache Software Foundation (ASF) under one
 * or more contributor license agreements.  See the NOTICE file
 * distributed with this work for additional information
 * regarding copyright ownership.  The ASF licenses this file
 * to you under the Apache License, Version 2.0 (the
 * "License"); you may not use this file except in compliance
 * with the License.  You may obtain a copy of the License at
 *
 *   http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing,
 * software distributed under the License is distributed on an
 * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
 * KIND, either express or implied.  See the License for the
 * specific language governing permissions and limitations
 * under the License.
 */

package org.commonwl.view.cwl;

import org.apache.commons.io.output.ByteArrayOutputStream;
import org.apache.jena.graph.Node;
import org.apache.jena.graph.NodeFactory;
import org.apache.jena.query.DatasetAccessor;
import org.apache.jena.query.DatasetAccessorFactory;
import org.apache.jena.query.ParameterizedSparqlString;
import org.apache.jena.query.Query;
import org.apache.jena.query.QueryExecution;
import org.apache.jena.query.QueryExecutionFactory;
import org.apache.jena.query.QueryFactory;
import org.apache.jena.query.ResultSet;
import org.apache.jena.query.ResultSetFactory;
import org.apache.jena.rdf.model.Model;
import org.apache.jena.riot.RDFFormat;
import org.apache.jena.web.DatasetGraphAccessorHTTP;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.stereotype.Service;

/** Handles the parsing of CWL RDF files */
@Service
public class RDFService {

  // Context for SPARQL queries
  private final String queryCtx =
      """
          PREFIX cwl: <https://w3id.org/cwl/cwl#>
          PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
          PREFIX sld: <https://w3id.org/cwl/salad#>
          PREFIX dct: <http://purl.org/dc/terms/>
          PREFIX doap: <http://usefulinc.com/ns/doap#>
          PREFIX Workflow: <https://w3id.org/cwl/cwl#Workflow/>
          PREFIX DockerRequirement: <https://w3id.org/cwl/cwl#DockerRequirement/>
          PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
          PREFIX s: <http://schema.org/>""";

  private final String rdfService;

  /**
   * Create the RDFService with configuration
   *
   * @param rdfService The SPARQL endpoint from configuration
   */
  @Autowired
  public RDFService(@Value("${sparql.endpoint}") String rdfService) {
    this.rdfService = rdfService;
  }

  /**
   * Add to ontologies in the triple store
   *
   * @param model The model to be stored
   */
  public void addToOntologies(Model model) {
    DatasetAccessor accessor = DatasetAccessorFactory.createHTTP(rdfService);
    accessor.add("ontologies", model);
  }

  /**
   * Get a model from the triple store in a given format
   *
   * @param graphName The name of the graph for the model
   * @param format The name of the writer (format to be written)
   * @return A byte array representing the model in the given format
   */
  public byte[] getModel(String graphName, String format) {
    DatasetAccessor accessor = DatasetAccessorFactory.createHTTP(rdfService);
    Model model = accessor.getModel(graphName);
    ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
    model.write(outputStream, format);
    return outputStream.toByteArray();
  }

  /**
   * Store a model with triples in the triple store
   *
   * @param graphName The name of the graph to store the model in
   * @param model The model to be stored
   */
  public void storeModel(String graphName, Model model) {
    DatasetGraphAccessorHTTP accessor = new DatasetGraphAccessorHTTP(rdfService);
    accessor.setOutboundSyntax(RDFFormat.TURTLE);
    Node name = NodeFactory.createURI(graphName);
    accessor.httpPut(name, model.getGraph());
  }

  /**
   * Check if a graph exists within the triple store
   *
   * @param graphName The name of the graph
   * @return Whether the graph exists
   */
  public boolean graphExists(String graphName) {
    ParameterizedSparqlString graphQuery = new ParameterizedSparqlString();
    graphQuery.setCommandText("ASK WHERE { GRAPH ?graphName { ?s ?p ?o } }");
    graphQuery.setIri("graphName", graphName);
    Query query = QueryFactory.create(graphQuery.toString());
    try (QueryExecution qexec = QueryExecutionFactory.createServiceRequest(rdfService, query)) {
      return qexec.execAsk();
    }
  }

  /**
   * Check if a property of the ontology exists within the triple store
   *
   * @param ontUri The URI of the property
   * @return Whether the graph exists
   */
  public boolean ontPropertyExists(String ontUri) {
    ParameterizedSparqlString graphQuery = new ParameterizedSparqlString();
    graphQuery.setCommandText(
        """
        PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
        ASK WHERE { GRAPH ?graphName { ?ont rdfs:label ?label } }
        """);
    graphQuery.setIri("ont", ontUri);
    graphQuery.setIri("graphName", rdfService + "ontologies");
    Query query = QueryFactory.create(graphQuery.toString());
    try (QueryExecution qexec = QueryExecutionFactory.createServiceRequest(rdfService, query)) {
      return qexec.execAsk();
    }
  }

  /**
   * Get the label and doc strings for a workflow resource
   *
   * @param workflowURI The URI of the workflow
   * @return Result set with label and doc strings
   */
  public ResultSet getLabelAndDoc(String workflowURI) {
    ParameterizedSparqlString labelQuery = new ParameterizedSparqlString();
    labelQuery.setCommandText(
        queryCtx
            + """
            PREFIX cwl: <https://w3id.org/cwl/cwl#>
            PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
            PREFIX sld: <https://w3id.org/cwl/salad#>
            PREFIX dct: <http://purl.org/dc/terms/>
            PREFIX doap: <http://usefulinc.com/ns/doap#>
            PREFIX Workflow: <https://w3id.org/cwl/cwl#Workflow/>
            PREFIX DockerRequirement: <https://w3id.org/cwl/cwl#DockerRequirement/>
            PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
            PREFIX s: <http://schema.org/>
            SELECT ?label ?doc
            WHERE {
              GRAPH ?wf {
                ?wf rdf:type ?type .
                OPTIONAL { ?wf sld:label|rdfs:label ?label }
                OPTIONAL { ?wf sld:doc|rdfs:comment ?doc }
              }
            }
            """);
    labelQuery.setIri("wf", workflowURI);
    return runQuery(labelQuery);
  }

  /**
   * Get the label for an ontology URL TODO: can be merged with getLabelAndDoc when
   * common-workflow-language/cwltool#427 is resolved
   *
   * @param ontologyURI The format URI for the ontology
   * @return Result set with label and doc strings
   */
  public String getOntLabel(String ontologyURI) {
    ParameterizedSparqlString labelQuery = new ParameterizedSparqlString();
    labelQuery.setCommandText(
        """
            PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\
            SELECT ?label
            WHERE {
              GRAPH ?graphName {
                ?ont rdfs:label ?label
              }
            }
            """);
    labelQuery.setIri("ont", ontologyURI);
    labelQuery.setIri("graphName", rdfService + "ontologies");
    ResultSet result = runQuery(labelQuery);
    if (result.hasNext()) {
      return result.next().get("label").toString();
    }
    return null;
  }

  /**
   * Get the inputs for the workflow in the model
   *
   * @param workflowURI URI of the workflow
   * @return The result set of inputs
   */
  public ResultSet getInputs(String workflowURI) {
    ParameterizedSparqlString inputsQuery = new ParameterizedSparqlString();
    inputsQuery.setCommandText(
        queryCtx
            + """
            PREFIX cwl: <https://w3id.org/cwl/cwl#>
            PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
            PREFIX sld: <https://w3id.org/cwl/salad#>
            PREFIX dct: <http://purl.org/dc/terms/>
            PREFIX doap: <http://usefulinc.com/ns/doap#>
            PREFIX Workflow: <https://w3id.org/cwl/cwl#Workflow/>
            PREFIX DockerRequirement: <https://w3id.org/cwl/cwl#DockerRequirement/>
            PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
            PREFIX s: <http://schema.org/>
            SELECT ?name ?type ?items ?null ?format ?label ?doc
            WHERE {
              GRAPH ?wf {
                ?wf rdf:type cwl:Workflow .
                ?wf cwl:inputs ?name .
                OPTIONAL {
                  {\s
                    ?name sld:type ?type
                    FILTER(?type != sld:null)\s
                    FILTER (!isBlank(?type))
                  } UNION {\s
                    ?name sld:type ?arraytype .
                    ?arraytype sld:type ?type .
                    ?arraytype sld:items ?items\s
                  }
                }
                OPTIONAL {\s
                  ?name sld:type ?null
                  FILTER(?null = sld:null)
                }
                OPTIONAL { ?name cwl:format ?format }
                OPTIONAL { ?name sld:label|rdfs:label ?label }
                OPTIONAL { ?name sld:doc|rdfs:comment ?doc }
              }
            }
            """);
    inputsQuery.setIri("wf", workflowURI);
    return runQuery(inputsQuery);
  }

  /**
   * Get the outputs for the workflow in the model
   *
   * @param workflowURI URI of the workflow
   * @return The result set of outputs
   */
  public ResultSet getOutputs(String workflowURI) {
    ParameterizedSparqlString outputsQuery = new ParameterizedSparqlString();
    outputsQuery.setCommandText(
        queryCtx
            + """
            PREFIX cwl: <https://w3id.org/cwl/cwl#>
            PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
            PREFIX sld: <https://w3id.org/cwl/salad#>
            PREFIX dct: <http://purl.org/dc/terms/>
            PREFIX doap: <http://usefulinc.com/ns/doap#>
            PREFIX Workflow: <https://w3id.org/cwl/cwl#Workflow/>
            PREFIX DockerRequirement: <https://w3id.org/cwl/cwl#DockerRequirement/>
            PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
            PREFIX s: <http://schema.org/>
            SELECT ?name ?type ?items ?null ?format ?label ?doc
            WHERE {
              GRAPH ?wf {
                ?wf rdf:type cwl:Workflow .
                ?wf cwl:outputs ?name .
                OPTIONAL {
                  {\s
                    ?name sld:type ?type
                    FILTER(?type != sld:null)\s
                    FILTER (!isBlank(?type))
                  } UNION {\s
                    ?name sld:type ?arraytype .
                    ?arraytype sld:type ?type .
                    ?arraytype sld:items ?items\s
                  }
                }
                OPTIONAL {\s
                  ?name sld:type ?null
                  FILTER(?null = sld:null)
                }
                OPTIONAL { ?name cwl:format ?format }
                OPTIONAL { ?name sld:label|rdfs:label ?label }
                OPTIONAL { ?name sld:doc|rdfs:comment ?doc }
              }
            }
            """);
    outputsQuery.setIri("wf", workflowURI);
    return runQuery(outputsQuery);
  }

  /**
   * Get the steps for the workflow in the model
   *
   * @param workflowURI URI of the workflow
   * @return The result set of steps
   */
  public ResultSet getSteps(String workflowURI) {
    ParameterizedSparqlString stepQuery = new ParameterizedSparqlString();
    stepQuery.setCommandText(
        queryCtx
            + """
            PREFIX cwl: <https://w3id.org/cwl/cwl#>
            PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
            PREFIX sld: <https://w3id.org/cwl/salad#>
            PREFIX dct: <http://purl.org/dc/terms/>
            PREFIX doap: <http://usefulinc.com/ns/doap#>
            PREFIX Workflow: <https://w3id.org/cwl/cwl#Workflow/>
            PREFIX DockerRequirement: <https://w3id.org/cwl/cwl#DockerRequirement/>
            PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
            PREFIX s: <http://schema.org/>
            SELECT ?step ?run ?runtype ?label ?doc ?stepinput ?default ?src
            WHERE {
              GRAPH ?wf {
                ?wf Workflow:steps ?step .
                ?step cwl:run ?run .
                ?run rdf:type ?runtype .
                OPTIONAL {\s
                    ?step cwl:in ?stepinput .
                    { ?stepinput cwl:source ?src } UNION { ?stepinput cwl:default ?default }
                }
                OPTIONAL { ?run sld:label|rdfs:label ?label }
                OPTIONAL { ?run sld:doc|rdfs:comment ?doc }
              }
            }
            """);
    stepQuery.setIri("wf", workflowURI);
    return runQuery(stepQuery);
  }

  /**
   * Get links between steps for the workflow in the model
   *
   * @param workflowURI URI of the workflow
   * @return The result set of step links
   */
  public ResultSet getStepLinks(String workflowURI) {
    ParameterizedSparqlString linkQuery = new ParameterizedSparqlString();
    linkQuery.setCommandText(
        queryCtx
            + """
            PREFIX cwl: <https://w3id.org/cwl/cwl#>
            PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
            PREFIX sld: <https://w3id.org/cwl/salad#>
            PREFIX dct: <http://purl.org/dc/terms/>
            PREFIX doap: <http://usefulinc.com/ns/doap#>
            PREFIX Workflow: <https://w3id.org/cwl/cwl#Workflow/>
            PREFIX DockerRequirement: <https://w3id.org/cwl/cwl#DockerRequirement/>
            PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
            PREFIX s: <http://schema.org/>
            SELECT ?src ?dest ?default
            WHERE {
              GRAPH ?wf {
                ?wf Workflow:steps ?step .
                ?step cwl:in ?dest .
                { ?dest cwl:source ?src } UNION { ?dest cwl:default ?default }
              }
            }
            """);
    linkQuery.setIri("wf", workflowURI);
    return runQuery(linkQuery);
  }

  /**
   * Get links between steps and outputs for the workflow in the model
   *
   * @param workflowURI URI of the workflow
   * @return The result set of steps
   */
  public ResultSet getOutputLinks(String workflowURI) {
    ParameterizedSparqlString linkQuery = new ParameterizedSparqlString();
    linkQuery.setCommandText(
        queryCtx
            + """
            PREFIX cwl: <https://w3id.org/cwl/cwl#>
            PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
            PREFIX sld: <https://w3id.org/cwl/salad#>
            PREFIX dct: <http://purl.org/dc/terms/>
            PREFIX doap: <http://usefulinc.com/ns/doap#>
            PREFIX Workflow: <https://w3id.org/cwl/cwl#Workflow/>
            PREFIX DockerRequirement: <https://w3id.org/cwl/cwl#DockerRequirement/>
            PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
            PREFIX s: <http://schema.org/>
            SELECT ?src ?dest
            WHERE {
              GRAPH ?wf {
                ?wf rdf:type cwl:Workflow .
                ?wf cwl:outputs ?dest .
                ?dest cwl:outputSource ?src
              }
            }
            """);
    linkQuery.setIri("wf", workflowURI);
    return runQuery(linkQuery);
  }

  /**
   * Gets the docker requirement and pull link for a workflow
   *
   * @param workflowURI URI of the workflow
   * @return Result set of docker hint and pull link
   */
  public ResultSet getDockerLink(String workflowURI) {
    ParameterizedSparqlString dockerQuery = new ParameterizedSparqlString();
    dockerQuery.setCommandText(
        queryCtx
            + """
            PREFIX cwl: <https://w3id.org/cwl/cwl#>
            PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
            PREFIX sld: <https://w3id.org/cwl/salad#>
            PREFIX dct: <http://purl.org/dc/terms/>
            PREFIX doap: <http://usefulinc.com/ns/doap#>
            PREFIX Workflow: <https://w3id.org/cwl/cwl#Workflow/>
            PREFIX DockerRequirement: <https://w3id.org/cwl/cwl#DockerRequirement/>
            PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
            PREFIX s: <http://schema.org/>
            SELECT ?docker ?pull
            WHERE {
              GRAPH ?wf {
                ?wf rdf:type cwl:Workflow .
                { ?wf cwl:requirements ?docker } UNION { ?wf cwl:hints ?docker} .
                ?docker rdf:type cwl:DockerRequirement
                OPTIONAL { ?docker DockerRequirement:dockerPull ?pull }
              }
            }
            """);
    dockerQuery.setIri("wf", workflowURI);
    return runQuery(dockerQuery);
  }

  /**
   * Get authors from schema.org creator fields for a file
   *
   * @param path The path within the Git repository to the file
   * @param fileUri URI of the file
   * @return The result set of step links
   */
  public ResultSet getAuthors(String path, String fileUri) {
    ParameterizedSparqlString linkQuery = new ParameterizedSparqlString();
    linkQuery.setCommandText(
        queryCtx
            + """
            PREFIX cwl: <https://w3id.org/cwl/cwl#>
            PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
            PREFIX sld: <https://w3id.org/cwl/salad#>
            PREFIX dct: <http://purl.org/dc/terms/>
            PREFIX doap: <http://usefulinc.com/ns/doap#>
            PREFIX Workflow: <https://w3id.org/cwl/cwl#Workflow/>
            PREFIX DockerRequirement: <https://w3id.org/cwl/cwl#DockerRequirement/>
            PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
            PREFIX s: <http://schema.org/>
            SELECT ?email ?name ?orcid
            WHERE {
              GRAPH ?graphName {
                ?file s:author|s:contributor|s:creator ?author .
                {
                  ?creator rdf:type s:Person .
                  OPTIONAL { ?author s:email ?email }
                  OPTIONAL { ?author s:name ?name }
                  OPTIONAL { ?author s:id|s:sameAs ?orcid }
                } UNION {
                  ?author rdf:type s:Organization .
                  ?author s:department* ?dept .
                  ?dept s:member ?member
                  OPTIONAL { ?member s:email ?email }
                  OPTIONAL { ?member s:name ?name }
                  OPTIONAL { ?member s:id|s:sameAs ?orcid }
                }
                FILTER(regex(str(?orcid), "^https?://orcid.org/" ))
                FILTER(regex(str(?file), ?wfFilter, "i" ))
              }
            }
            """);
    linkQuery.setLiteral("wfFilter", path + "$");
    linkQuery.setIri("graphName", fileUri);
    return runQuery(linkQuery);
  }

  /**
   * Gets the step name from a full URI
   *
   * @param baseUrl the URL of the workflow
   * @param uri The URI
   * @return The step ID
   */
  public String stepNameFromURI(String baseUrl, String uri) {
    uri = uri.substring(uri.indexOf(baseUrl));
    uri = uri.replace(baseUrl, "");
    uri = uri.replace("#", "/");
    uri = uri.substring(1);
    if (uri.indexOf("/") > 0) {
      return uri.substring(0, uri.indexOf("/"));
    }
    return uri;
  }

  /**
   * Format a default value
   *
   * @param defaultVal The default value
   * @return Default value suitable for a node label
   */
  public String formatDefault(String defaultVal) {
    int lastCaret = defaultVal.indexOf("^^");
    if (lastCaret != -1) {
      return defaultVal.substring(0, lastCaret);
    }
    return "\\\"" + defaultVal + "\\\"";
  }

  /**
   * Convert an RDF type to cwl process
   *
   * @param runtype The string from the RDF
   * @return CWL process the string refers to
   */
  public CWLProcess strToRuntype(String runtype) {
    return switch (runtype) {
      case "https://w3id.org/cwl/cwl#Workflow" -> CWLProcess.WORKFLOW;
      case "https://w3id.org/cwl/cwl#CommandLineTool" -> CWLProcess.COMMANDLINETOOL;
      case "https://w3id.org/cwl/cwl#ExpressionTool" -> CWLProcess.EXPRESSIONTOOL;
      default -> null;
    };
  }

  /**
   * Get the label for the node from its name
   *
   * @param name The name in the form filename#step
   * @return The second part of the name, just the step
   */
  public String labelFromName(String name) {
    name = name.substring(name.indexOf('#') + 1);
    int slashIndex = name.indexOf("/");
    if (slashIndex > 0) {
      name = name.substring(slashIndex + 1);
    }
    return name;
  }

  /**
   * Run a SPARQL query on a given model
   *
   * @param queryString The query to be run
   * @return The result set of the query
   */
  ResultSet runQuery(ParameterizedSparqlString queryString) {
    Query query = QueryFactory.create(queryString.toString());
    try (QueryExecution qexec = QueryExecutionFactory.createServiceRequest(rdfService, query)) {
      return ResultSetFactory.copyResults(qexec.execSelect());
    }
  }

  public ResultSet getLicense(String workflowURI) {
    ParameterizedSparqlString licenseQuery = new ParameterizedSparqlString();
    licenseQuery.setCommandText(
        queryCtx
            + """
            PREFIX cwl: <https://w3id.org/cwl/cwl#>
            PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
            PREFIX sld: <https://w3id.org/cwl/salad#>
            PREFIX dct: <http://purl.org/dc/terms/>
            PREFIX doap: <http://usefulinc.com/ns/doap#>
            PREFIX Workflow: <https://w3id.org/cwl/cwl#Workflow/>
            PREFIX DockerRequirement: <https://w3id.org/cwl/cwl#DockerRequirement/>
            PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
            PREFIX s: <http://schema.org/>
            SELECT ?license\s
            WHERE {
              GRAPH ?wf {
                ?wf rdf:type cwl:Workflow .
                { ?wf s:license ?license }\s
            UNION { ?wf doap:license ?license }\s
            UNION { ?wf dct:license ?license }\s
              }
            }
            """);
    licenseQuery.setIri("wf", workflowURI);
    return runQuery(licenseQuery);
  }
}

1	/*
2	* Licensed to the Apache Software Foundation (ASF) under one
3	* or more contributor license agreements. See the NOTICE file
4	* distributed with this work for additional information
5	* regarding copyright ownership. The ASF licenses this file
6	* to you under the Apache License, Version 2.0 (the
7	* "License"); you may not use this file except in compliance
8	* with the License. You may obtain a copy of the License at
9	*
10	* http://www.apache.org/licenses/LICENSE-2.0
11	*
12	* Unless required by applicable law or agreed to in writing,
13	* software distributed under the License is distributed on an
14	* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
15	* KIND, either express or implied. See the License for the
16	* specific language governing permissions and limitations
17	* under the License.
18	*/
19
20	package org.commonwl.view.cwl;
21
22	import org.apache.commons.io.output.ByteArrayOutputStream;
23	import org.apache.jena.graph.Node;
24	import org.apache.jena.graph.NodeFactory;
25	import org.apache.jena.query.DatasetAccessor;
26	import org.apache.jena.query.DatasetAccessorFactory;
27	import org.apache.jena.query.ParameterizedSparqlString;
28	import org.apache.jena.query.Query;
29	import org.apache.jena.query.QueryExecution;
30	import org.apache.jena.query.QueryExecutionFactory;
31	import org.apache.jena.query.QueryFactory;
32	import org.apache.jena.query.ResultSet;
33	import org.apache.jena.query.ResultSetFactory;
34	import org.apache.jena.rdf.model.Model;
35	import org.apache.jena.riot.RDFFormat;
36	import org.apache.jena.web.DatasetGraphAccessorHTTP;
37	import org.springframework.beans.factory.annotation.Autowired;
38	import org.springframework.beans.factory.annotation.Value;
39	import org.springframework.stereotype.Service;
40
41	/** Handles the parsing of CWL RDF files */
42	@Service
43	public class RDFService {
44
45	// Context for SPARQL queries
46	private final String queryCtx =	1✔
47	"""
48	PREFIX cwl: <https://w3id.org/cwl/cwl#>
49	PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
50	PREFIX sld: <https://w3id.org/cwl/salad#>
51	PREFIX dct: <http://purl.org/dc/terms/>
52	PREFIX doap: <http://usefulinc.com/ns/doap#>
53	PREFIX Workflow: <https://w3id.org/cwl/cwl#Workflow/>
54	PREFIX DockerRequirement: <https://w3id.org/cwl/cwl#DockerRequirement/>
55	PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
56	PREFIX s: <http://schema.org/>""";
57
58	private final String rdfService;
59
60	/**
61	* Create the RDFService with configuration
62	*
63	* @param rdfService The SPARQL endpoint from configuration
64	*/
65	@Autowired
66	public RDFService(@Value("${sparql.endpoint}") String rdfService) {	1✔
67	this.rdfService = rdfService;	1✔
68	}	1✔
69
70	/**
71	* Add to ontologies in the triple store
72	*
73	* @param model The model to be stored
74	*/
75	public void addToOntologies(Model model) {
76	DatasetAccessor accessor = DatasetAccessorFactory.createHTTP(rdfService);	×
77	accessor.add("ontologies", model);	×
78	}	×
79
80	/**
81	* Get a model from the triple store in a given format
82	*
83	* @param graphName The name of the graph for the model
84	* @param format The name of the writer (format to be written)
85	* @return A byte array representing the model in the given format
86	*/
87	public byte[] getModel(String graphName, String format) {
88	DatasetAccessor accessor = DatasetAccessorFactory.createHTTP(rdfService);	×
89	Model model = accessor.getModel(graphName);	×
90	ByteArrayOutputStream outputStream = new ByteArrayOutputStream();	×
91	model.write(outputStream, format);	×
92	return outputStream.toByteArray();	×
93	}
94
95	/**
96	* Store a model with triples in the triple store
97	*
98	* @param graphName The name of the graph to store the model in
99	* @param model The model to be stored
100	*/
101	public void storeModel(String graphName, Model model) {
102	DatasetGraphAccessorHTTP accessor = new DatasetGraphAccessorHTTP(rdfService);	×
103	accessor.setOutboundSyntax(RDFFormat.TURTLE);	×
104	Node name = NodeFactory.createURI(graphName);	×
105	accessor.httpPut(name, model.getGraph());	×
106	}	×
107
108	/**
109	* Check if a graph exists within the triple store
110	*
111	* @param graphName The name of the graph
112	* @return Whether the graph exists
113	*/
114	public boolean graphExists(String graphName) {
115	ParameterizedSparqlString graphQuery = new ParameterizedSparqlString();	×
116	graphQuery.setCommandText("ASK WHERE { GRAPH ?graphName { ?s ?p ?o } }");	×
117	graphQuery.setIri("graphName", graphName);	×
118	Query query = QueryFactory.create(graphQuery.toString());	×
119	try (QueryExecution qexec = QueryExecutionFactory.createServiceRequest(rdfService, query)) {	×
120	return qexec.execAsk();	×
121	}
122	}
123
124	/**
125	* Check if a property of the ontology exists within the triple store
126	*
127	* @param ontUri The URI of the property
128	* @return Whether the graph exists
129	*/
130	public boolean ontPropertyExists(String ontUri) {
131	ParameterizedSparqlString graphQuery = new ParameterizedSparqlString();	×
132	graphQuery.setCommandText(	×
133	"""
134	PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
135	ASK WHERE { GRAPH ?graphName { ?ont rdfs:label ?label } }
136	""");
137	graphQuery.setIri("ont", ontUri);	×
138	graphQuery.setIri("graphName", rdfService + "ontologies");	×
139	Query query = QueryFactory.create(graphQuery.toString());	×
140	try (QueryExecution qexec = QueryExecutionFactory.createServiceRequest(rdfService, query)) {	×
141	return qexec.execAsk();	×
142	}
143	}
144
145	/**
146	* Get the label and doc strings for a workflow resource
147	*
148	* @param workflowURI The URI of the workflow
149	* @return Result set with label and doc strings
150	*/
151	public ResultSet getLabelAndDoc(String workflowURI) {
152	ParameterizedSparqlString labelQuery = new ParameterizedSparqlString();	1✔
153	labelQuery.setCommandText(	1✔
154	queryCtx
155	+ """
156	PREFIX cwl: <https://w3id.org/cwl/cwl#>
157	PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
158	PREFIX sld: <https://w3id.org/cwl/salad#>
159	PREFIX dct: <http://purl.org/dc/terms/>
160	PREFIX doap: <http://usefulinc.com/ns/doap#>
161	PREFIX Workflow: <https://w3id.org/cwl/cwl#Workflow/>
162	PREFIX DockerRequirement: <https://w3id.org/cwl/cwl#DockerRequirement/>
163	PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
164	PREFIX s: <http://schema.org/>
165	SELECT ?label ?doc
166	WHERE {
167	GRAPH ?wf {
168	?wf rdf:type ?type .
169	OPTIONAL { ?wf sld:label\|rdfs:label ?label }
170	OPTIONAL { ?wf sld:doc\|rdfs:comment ?doc }
171	}
172	}
173	""");
174	labelQuery.setIri("wf", workflowURI);	1✔
175	return runQuery(labelQuery);	1✔
176	}
177
178	/**
179	* Get the label for an ontology URL TODO: can be merged with getLabelAndDoc when
180	* common-workflow-language/cwltool#427 is resolved
181	*
182	* @param ontologyURI The format URI for the ontology
183	* @return Result set with label and doc strings
184	*/
185	public String getOntLabel(String ontologyURI) {
186	ParameterizedSparqlString labelQuery = new ParameterizedSparqlString();	×
187	labelQuery.setCommandText(	×
188	"""
189	PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\
190	SELECT ?label
191	WHERE {
192	GRAPH ?graphName {
193	?ont rdfs:label ?label
194	}
195	}
196	""");
197	labelQuery.setIri("ont", ontologyURI);	×
198	labelQuery.setIri("graphName", rdfService + "ontologies");	×
199	ResultSet result = runQuery(labelQuery);	×
200	if (result.hasNext()) {	×
201	return result.next().get("label").toString();	×
202	}
203	return null;	×
204	}
205
206	/**
207	* Get the inputs for the workflow in the model
208	*
209	* @param workflowURI URI of the workflow
210	* @return The result set of inputs
211	*/
212	public ResultSet getInputs(String workflowURI) {
213	ParameterizedSparqlString inputsQuery = new ParameterizedSparqlString();	1✔
214	inputsQuery.setCommandText(	1✔
215	queryCtx
216	+ """
217	PREFIX cwl: <https://w3id.org/cwl/cwl#>
218	PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
219	PREFIX sld: <https://w3id.org/cwl/salad#>
220	PREFIX dct: <http://purl.org/dc/terms/>
221	PREFIX doap: <http://usefulinc.com/ns/doap#>
222	PREFIX Workflow: <https://w3id.org/cwl/cwl#Workflow/>
223	PREFIX DockerRequirement: <https://w3id.org/cwl/cwl#DockerRequirement/>
224	PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
225	PREFIX s: <http://schema.org/>
226	SELECT ?name ?type ?items ?null ?format ?label ?doc
227	WHERE {
228	GRAPH ?wf {
229	?wf rdf:type cwl:Workflow .
230	?wf cwl:inputs ?name .
231	OPTIONAL {
232	{\s
233	?name sld:type ?type
234	FILTER(?type != sld:null)\s
235	FILTER (!isBlank(?type))
236	} UNION {\s
237	?name sld:type ?arraytype .
238	?arraytype sld:type ?type .
239	?arraytype sld:items ?items\s
240	}
241	}
242	OPTIONAL {\s
243	?name sld:type ?null
244	FILTER(?null = sld:null)
245	}
246	OPTIONAL { ?name cwl:format ?format }
247	OPTIONAL { ?name sld:label\|rdfs:label ?label }
248	OPTIONAL { ?name sld:doc\|rdfs:comment ?doc }
249	}
250	}
251	""");
252	inputsQuery.setIri("wf", workflowURI);	1✔
253	return runQuery(inputsQuery);	1✔
254	}
255
256	/**
257	* Get the outputs for the workflow in the model
258	*
259	* @param workflowURI URI of the workflow
260	* @return The result set of outputs
261	*/
262	public ResultSet getOutputs(String workflowURI) {
263	ParameterizedSparqlString outputsQuery = new ParameterizedSparqlString();	1✔
264	outputsQuery.setCommandText(	1✔
265	queryCtx
266	+ """
267	PREFIX cwl: <https://w3id.org/cwl/cwl#>
268	PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
269	PREFIX sld: <https://w3id.org/cwl/salad#>
270	PREFIX dct: <http://purl.org/dc/terms/>
271	PREFIX doap: <http://usefulinc.com/ns/doap#>
272	PREFIX Workflow: <https://w3id.org/cwl/cwl#Workflow/>
273	PREFIX DockerRequirement: <https://w3id.org/cwl/cwl#DockerRequirement/>
274	PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
275	PREFIX s: <http://schema.org/>
276	SELECT ?name ?type ?items ?null ?format ?label ?doc
277	WHERE {
278	GRAPH ?wf {
279	?wf rdf:type cwl:Workflow .
280	?wf cwl:outputs ?name .
281	OPTIONAL {
282	{\s
283	?name sld:type ?type
284	FILTER(?type != sld:null)\s
285	FILTER (!isBlank(?type))
286	} UNION {\s
287	?name sld:type ?arraytype .
288	?arraytype sld:type ?type .
289	?arraytype sld:items ?items\s
290	}
291	}
292	OPTIONAL {\s
293	?name sld:type ?null
294	FILTER(?null = sld:null)
295	}
296	OPTIONAL { ?name cwl:format ?format }
297	OPTIONAL { ?name sld:label\|rdfs:label ?label }
298	OPTIONAL { ?name sld:doc\|rdfs:comment ?doc }
299	}
300	}
301	""");
302	outputsQuery.setIri("wf", workflowURI);	1✔
303	return runQuery(outputsQuery);	1✔
304	}
305
306	/**
307	* Get the steps for the workflow in the model
308	*
309	* @param workflowURI URI of the workflow
310	* @return The result set of steps
311	*/
312	public ResultSet getSteps(String workflowURI) {
313	ParameterizedSparqlString stepQuery = new ParameterizedSparqlString();	1✔
314	stepQuery.setCommandText(	1✔
315	queryCtx
316	+ """
317	PREFIX cwl: <https://w3id.org/cwl/cwl#>
318	PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
319	PREFIX sld: <https://w3id.org/cwl/salad#>
320	PREFIX dct: <http://purl.org/dc/terms/>
321	PREFIX doap: <http://usefulinc.com/ns/doap#>
322	PREFIX Workflow: <https://w3id.org/cwl/cwl#Workflow/>
323	PREFIX DockerRequirement: <https://w3id.org/cwl/cwl#DockerRequirement/>
324	PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
325	PREFIX s: <http://schema.org/>
326	SELECT ?step ?run ?runtype ?label ?doc ?stepinput ?default ?src
327	WHERE {
328	GRAPH ?wf {
329	?wf Workflow:steps ?step .
330	?step cwl:run ?run .
331	?run rdf:type ?runtype .
332	OPTIONAL {\s
333	?step cwl:in ?stepinput .
334	{ ?stepinput cwl:source ?src } UNION { ?stepinput cwl:default ?default }
335	}
336	OPTIONAL { ?run sld:label\|rdfs:label ?label }
337	OPTIONAL { ?run sld:doc\|rdfs:comment ?doc }
338	}
339	}
340	""");
341	stepQuery.setIri("wf", workflowURI);	1✔
342	return runQuery(stepQuery);	1✔
343	}
344
345	/**
346	* Get links between steps for the workflow in the model
347	*
348	* @param workflowURI URI of the workflow
349	* @return The result set of step links
350	*/
351	public ResultSet getStepLinks(String workflowURI) {
352	ParameterizedSparqlString linkQuery = new ParameterizedSparqlString();	1✔
353	linkQuery.setCommandText(	1✔
354	queryCtx
355	+ """
356	PREFIX cwl: <https://w3id.org/cwl/cwl#>
357	PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
358	PREFIX sld: <https://w3id.org/cwl/salad#>
359	PREFIX dct: <http://purl.org/dc/terms/>
360	PREFIX doap: <http://usefulinc.com/ns/doap#>
361	PREFIX Workflow: <https://w3id.org/cwl/cwl#Workflow/>
362	PREFIX DockerRequirement: <https://w3id.org/cwl/cwl#DockerRequirement/>
363	PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
364	PREFIX s: <http://schema.org/>
365	SELECT ?src ?dest ?default
366	WHERE {
367	GRAPH ?wf {
368	?wf Workflow:steps ?step .
369	?step cwl:in ?dest .
370	{ ?dest cwl:source ?src } UNION { ?dest cwl:default ?default }
371	}
372	}
373	""");
374	linkQuery.setIri("wf", workflowURI);	1✔
375	return runQuery(linkQuery);	1✔
376	}
377
378	/**
379	* Get links between steps and outputs for the workflow in the model
380	*
381	* @param workflowURI URI of the workflow
382	* @return The result set of steps
383	*/
384	public ResultSet getOutputLinks(String workflowURI) {
385	ParameterizedSparqlString linkQuery = new ParameterizedSparqlString();	1✔
386	linkQuery.setCommandText(	1✔
387	queryCtx
388	+ """
389	PREFIX cwl: <https://w3id.org/cwl/cwl#>
390	PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
391	PREFIX sld: <https://w3id.org/cwl/salad#>
392	PREFIX dct: <http://purl.org/dc/terms/>
393	PREFIX doap: <http://usefulinc.com/ns/doap#>
394	PREFIX Workflow: <https://w3id.org/cwl/cwl#Workflow/>
395	PREFIX DockerRequirement: <https://w3id.org/cwl/cwl#DockerRequirement/>
396	PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
397	PREFIX s: <http://schema.org/>
398	SELECT ?src ?dest
399	WHERE {
400	GRAPH ?wf {
401	?wf rdf:type cwl:Workflow .
402	?wf cwl:outputs ?dest .
403	?dest cwl:outputSource ?src
404	}
405	}
406	""");
407	linkQuery.setIri("wf", workflowURI);	1✔
408	return runQuery(linkQuery);	1✔
409	}
410
411	/**
412	* Gets the docker requirement and pull link for a workflow
413	*
414	* @param workflowURI URI of the workflow
415	* @return Result set of docker hint and pull link
416	*/
417	public ResultSet getDockerLink(String workflowURI) {
418	ParameterizedSparqlString dockerQuery = new ParameterizedSparqlString();	1✔
419	dockerQuery.setCommandText(	1✔
420	queryCtx
421	+ """
422	PREFIX cwl: <https://w3id.org/cwl/cwl#>
423	PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
424	PREFIX sld: <https://w3id.org/cwl/salad#>
425	PREFIX dct: <http://purl.org/dc/terms/>
426	PREFIX doap: <http://usefulinc.com/ns/doap#>
427	PREFIX Workflow: <https://w3id.org/cwl/cwl#Workflow/>
428	PREFIX DockerRequirement: <https://w3id.org/cwl/cwl#DockerRequirement/>
429	PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
430	PREFIX s: <http://schema.org/>
431	SELECT ?docker ?pull
432	WHERE {
433	GRAPH ?wf {
434	?wf rdf:type cwl:Workflow .
435	{ ?wf cwl:requirements ?docker } UNION { ?wf cwl:hints ?docker} .
436	?docker rdf:type cwl:DockerRequirement
437	OPTIONAL { ?docker DockerRequirement:dockerPull ?pull }
438	}
439	}
440	""");
441	dockerQuery.setIri("wf", workflowURI);	1✔
442	return runQuery(dockerQuery);	1✔
443	}
444
445	/**
446	* Get authors from schema.org creator fields for a file
447	*
448	* @param path The path within the Git repository to the file
449	* @param fileUri URI of the file
450	* @return The result set of step links
451	*/
452	public ResultSet getAuthors(String path, String fileUri) {
453	ParameterizedSparqlString linkQuery = new ParameterizedSparqlString();	×
454	linkQuery.setCommandText(	×
455	queryCtx
456	+ """
457	PREFIX cwl: <https://w3id.org/cwl/cwl#>
458	PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
459	PREFIX sld: <https://w3id.org/cwl/salad#>
460	PREFIX dct: <http://purl.org/dc/terms/>
461	PREFIX doap: <http://usefulinc.com/ns/doap#>
462	PREFIX Workflow: <https://w3id.org/cwl/cwl#Workflow/>
463	PREFIX DockerRequirement: <https://w3id.org/cwl/cwl#DockerRequirement/>
464	PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
465	PREFIX s: <http://schema.org/>
466	SELECT ?email ?name ?orcid
467	WHERE {
468	GRAPH ?graphName {
469	?file s:author\|s:contributor\|s:creator ?author .
470	{
471	?creator rdf:type s:Person .
472	OPTIONAL { ?author s:email ?email }
473	OPTIONAL { ?author s:name ?name }
474	OPTIONAL { ?author s:id\|s:sameAs ?orcid }
475	} UNION {
476	?author rdf:type s:Organization .
477	?author s:department* ?dept .
478	?dept s:member ?member
479	OPTIONAL { ?member s:email ?email }
480	OPTIONAL { ?member s:name ?name }
481	OPTIONAL { ?member s:id\|s:sameAs ?orcid }
482	}
483	FILTER(regex(str(?orcid), "^https?://orcid.org/" ))
484	FILTER(regex(str(?file), ?wfFilter, "i" ))
485	}
486	}
487	""");
488	linkQuery.setLiteral("wfFilter", path + "$");	×
489	linkQuery.setIri("graphName", fileUri);	×
490	return runQuery(linkQuery);	×
491	}
492
493	/**
494	* Gets the step name from a full URI
495	*
496	* @param baseUrl the URL of the workflow
497	* @param uri The URI
498	* @return The step ID
499	*/
500	public String stepNameFromURI(String baseUrl, String uri) {
501	uri = uri.substring(uri.indexOf(baseUrl));	1✔
502	uri = uri.replace(baseUrl, "");	1✔
503	uri = uri.replace("#", "/");	1✔
504	uri = uri.substring(1);	1✔
505	if (uri.indexOf("/") > 0) {	1✔
506	return uri.substring(0, uri.indexOf("/"));	1✔
507	}
508	return uri;	1✔
509	}
510
511	/**
512	* Format a default value
513	*
514	* @param defaultVal The default value
515	* @return Default value suitable for a node label
516	*/
517	public String formatDefault(String defaultVal) {
518	int lastCaret = defaultVal.indexOf("^^");	1✔
519	if (lastCaret != -1) {	1✔
520	return defaultVal.substring(0, lastCaret);	1✔
521	}
522	return "\\\"" + defaultVal + "\\\"";	1✔
523	}
524
525	/**
526	* Convert an RDF type to cwl process
527	*
528	* @param runtype The string from the RDF
529	* @return CWL process the string refers to
530	*/
531	public CWLProcess strToRuntype(String runtype) {
532	return switch (runtype) {	1✔
NEW 533	case "https://w3id.org/cwl/cwl#Workflow" -> CWLProcess.WORKFLOW;	×
534	case "https://w3id.org/cwl/cwl#CommandLineTool" -> CWLProcess.COMMANDLINETOOL;	1✔
NEW 535	case "https://w3id.org/cwl/cwl#ExpressionTool" -> CWLProcess.EXPRESSIONTOOL;	×
NEW 536	default -> null;	×
537	};
538	}
539
540	/**
541	* Get the label for the node from its name
542	*
543	* @param name The name in the form filename#step
544	* @return The second part of the name, just the step
545	*/
546	public String labelFromName(String name) {
547	name = name.substring(name.indexOf('#') + 1);	1✔
548	int slashIndex = name.indexOf("/");	1✔
549	if (slashIndex > 0) {	1✔
550	name = name.substring(slashIndex + 1);	1✔
551	}
552	return name;	1✔
553	}
554
555	/**
556	* Run a SPARQL query on a given model
557	*
558	* @param queryString The query to be run
559	* @return The result set of the query
560	*/
561	ResultSet runQuery(ParameterizedSparqlString queryString) {
562	Query query = QueryFactory.create(queryString.toString());	×
563	try (QueryExecution qexec = QueryExecutionFactory.createServiceRequest(rdfService, query)) {	×
564	return ResultSetFactory.copyResults(qexec.execSelect());	×
565	}
566	}
567
568	public ResultSet getLicense(String workflowURI) {
569	ParameterizedSparqlString licenseQuery = new ParameterizedSparqlString();	×
570	licenseQuery.setCommandText(	×
571	queryCtx
572	+ """
573	PREFIX cwl: <https://w3id.org/cwl/cwl#>
574	PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
575	PREFIX sld: <https://w3id.org/cwl/salad#>
576	PREFIX dct: <http://purl.org/dc/terms/>
577	PREFIX doap: <http://usefulinc.com/ns/doap#>
578	PREFIX Workflow: <https://w3id.org/cwl/cwl#Workflow/>
579	PREFIX DockerRequirement: <https://w3id.org/cwl/cwl#DockerRequirement/>
580	PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
581	PREFIX s: <http://schema.org/>
582	SELECT ?license\s
583	WHERE {
584	GRAPH ?wf {
585	?wf rdf:type cwl:Workflow .
586	{ ?wf s:license ?license }\s
587	UNION { ?wf doap:license ?license }\s
588	UNION { ?wf dct:license ?license }\s
589	}
590	}
591	""");
592	licenseQuery.setIri("wf", workflowURI);	×
593	return runQuery(licenseQuery);	×
594	}
595	}

common-workflow-language / cwlviewer / #1999

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