Add: queryRetrieveAbstractTemplateElements

KnowledgeCaptureAndDiscovery · Jul 12, 2019 · 422e891 · 422e891
1 parent eaa50b2
commit 422e891
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Showing 4 changed files with 37 additions and 10 deletions.
diff --git a/src/main/java/edu/isi/wings/opmm/ModelUtils.java b/src/main/java/edu/isi/wings/opmm/ModelUtils.java
@@ -10,6 +10,7 @@
 import org.apache.jena.query.QueryFactory;
 import org.apache.jena.query.QuerySolution;
 import org.apache.jena.query.ResultSet;
+import org.apache.jena.rdf.model.Model;
 import org.apache.jena.rdf.model.ModelFactory;
 import org.apache.jena.rdf.model.Resource;
 import org.apache.jena.util.FileManager;
@@ -76,14 +77,13 @@ public static ResultSet queryLocalRepository(String queryIn, OntModel repository
         // Execute the query and obtain results
         QueryExecution qe = QueryExecutionFactory.create(query, repository);
         ResultSet rs =  qe.execSelect();
-        System.out.println(queryIn);
         return rs;
     }
     /**
      * Query an online repository
      * @param queryIn query to specify
      * @param endpointURI URI of the repository
-     * @return 
+     * @return
      */
     public static QuerySolution queryOnlineRepository(String queryIn, String endpointURI){
         Query query = QueryFactory.create(queryIn);
@@ -92,11 +92,21 @@ public static QuerySolution queryOnlineRepository(String queryIn, String endpoin
         ResultSet rs =  qe.execSelect();
         QuerySolution solution = null;
         if(rs.hasNext())
-          solution = rs.next();
+            solution = rs.next();
         qe.close();
         return solution;
     }
-
+
+    public static Model constructOnlineRepository(String queryIn, String endpointURI){
+        Query query = QueryFactory.create(queryIn);
+        // Execute the query and obtain results
+        QueryExecution qe = QueryExecutionFactory.sparqlService(endpointURI, query);
+        Model rs = qe.execConstruct();
+        qe.close();
+        return rs;
+    }
+
+
     /**
      * Function that initializes a model. If the model exists, it empties it.
      * If it doesn't exist (null) it returns a new instance of a model

diff --git a/src/main/java/edu/isi/wings/opmm/QueriesWorkflowTemplateExport.java b/src/main/java/edu/isi/wings/opmm/QueriesWorkflowTemplateExport.java
@@ -49,7 +49,24 @@ public static String queryWINGSTemplateMetadata(){
                 + "OPTIONAL{?m <"+Constants.WINGS_DATA_PROP_LAST_UPDATED_TIME+"> ?time.}}";
         return query;
     }
-
+
+    /**
+     * Query for retrieving the elements of an abstract template from the remote repository
+     */
+    public static String queryRetrieveAbstractTemplateElements(String queryTemplate){
+        String query = "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>" +
+                "CONSTRUCT  {" +
+                "?a ?c ?d" +
+                "}" +
+                "from <urn:x-arq:UnionGraph>" +
+                "WHERE" +
+                "{ " +
+                "  ?a ?b <" + queryTemplate +  ">." +
+                "  ?a ?c ?d" +
+                "  filter not exists {?a a <https://www.opmw.org/ontology/WorkflowTemplate>}" +
+                "}";
+        return query;
+    }
     /**
      * Query to retrieve workflow template steps of a WINGS template
      * @return

diff --git a/src/main/java/edu/isi/wings/opmm/WorkflowExecutionExport.java b/src/main/java/edu/isi/wings/opmm/WorkflowExecutionExport.java
@@ -143,7 +143,6 @@ private String convertExecutionToOPMW(Individual wingsExecution) {
         weInstance.addProperty(opmwModel.createProperty(Constants.OPMW_DATA_PROP_HAS_ORIGINAL_EXECUTION_FILE), wingsExecution.getURI());
         //hasTime, endTime and execution status.
         String queryExecutionMetadata = QueriesWorkflowExecutionExport.getWINGSExecutionMetadata(wingsExecution.getURI());
-        System.out.println("Queries queryExecutionMetadata");
         ResultSet rs = ModelUtils.queryLocalRepository(queryExecutionMetadata, wingsExecutionModel);
         //there is only 1 execution per file
         if (rs.hasNext()) {
@@ -174,7 +173,6 @@ private String convertExecutionToOPMW(Individual wingsExecution) {
 
         //get expanded template loaded in local model (for parameter linking)
         String queryExpandedTemplate = QueriesWorkflowExecutionExport.getWINGSExpandedTemplate();
-        System.out.println("Queries queryExpandedTemplate");
         rs = ModelUtils.queryLocalRepository(queryExpandedTemplate, wingsExecutionModel);
         String expandedTemplateURI = null;
         if (rs.hasNext()) {
@@ -190,7 +188,6 @@ private String convertExecutionToOPMW(Individual wingsExecution) {
 
         //transform all steps and data dependencies (params are in expanded template)
         String queryExecutionStepMetadata = QueriesWorkflowExecutionExport.getWINGSExecutionStepsAndMetadata();
-        System.out.println("Queries queryExecutionStepMedata");
         rs = ModelUtils.queryLocalRepository(queryExecutionStepMetadata, wingsExecutionModel);
         while (rs.hasNext()) {
             QuerySolution qs = rs.next();
@@ -245,7 +242,6 @@ private String convertExecutionToOPMW(Individual wingsExecution) {
 
             //for each step get its i/o (plan)
             String stepVariables = QueriesWorkflowExecutionExport.getWINGSExecutionStepI_O(wingsStep.getURI());
-            System.out.println("Queries step variables");
             ResultSet rsVar = ModelUtils.queryLocalRepository(stepVariables, wingsExecutionModel);
             while (rsVar.hasNext()) {
                 QuerySolution qsVar = rsVar.next();
@@ -286,7 +282,6 @@ private String convertExecutionToOPMW(Individual wingsExecution) {
             //Parameters are specified in the expanded template. The current step is specified with the expanded template URI, same process id.
             String wingsExpandedTempProcessURI = expandedTemplateURI + wingsStep.getLocalName();
             String queryParams = QueriesWorkflowExecutionExport.getWINGSParametersForStep(wingsExpandedTempProcessURI);
-            System.out.println("Queries params variables");
             ResultSet params = ModelUtils.queryLocalRepository(queryParams, concreteTemplateExport.getWingsTemplateModel());
             while (params.hasNext()) {
                 QuerySolution nextP = params.next();

diff --git a/src/main/java/edu/isi/wings/opmm/WorkflowTemplateExport.java b/src/main/java/edu/isi/wings/opmm/WorkflowTemplateExport.java
@@ -4,6 +4,7 @@
 import java.io.UnsupportedEncodingException;
 import java.net.URLEncoder;
 import java.util.Iterator;
+
 import org.apache.jena.datatypes.xsd.XSDDatatype;
 import org.apache.jena.ontology.Individual;
 import org.apache.jena.ontology.OntClass;
@@ -114,6 +115,10 @@ public void transform(){
                 System.out.println("Template " +wingsTemplateName+" has already been published as "+foundTemplateURI.getURI());
                 //no export is necessary
                 transformedTemplate = opmwModel.createClass(Constants.OPMW_WORKFLOW_TEMPLATE).createIndividual(foundTemplateURI.getURI());
+                //            String queryExec = QueriesWorkflowExecutionExport.getOPMWExecutionsWithRunID(wingsExecution.getLocalName());
+                //            QuerySolution solution = ModelUtils.queryOnlineRepository(queryExec, endpointURI);
+                String queryTemplate = QueriesWorkflowTemplateExport.queryRetrieveAbstractTemplateElements(foundTemplateURI.getURI());
+                opmwModel.add(ModelUtils.constructOnlineRepository(queryTemplate, endpointURI));
                 isTemplatePublished = true;
                 return;
             }else{