Resolve version incompatibilities among commons-rdf, shexjava, and jena.

geneontology · Jul 18, 2024 · 8b11272 · 8b11272
1 parent c7426ed
commit 8b11272
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Showing 6 changed files with 26 additions and 15 deletions.
diff --git a/minerva-core/pom.xml b/minerva-core/pom.xml
@@ -54,6 +54,10 @@
             <artifactId>apache-jena-libs</artifactId>
             <type>pom</type>
         </dependency>
+        <dependency>
+            <groupId>org.apache.jena</groupId>
+            <artifactId>jena-commonsrdf</artifactId>
+        </dependency>
         <dependency>
             <groupId>net.sf.trove4j</groupId>
             <artifactId>trove4j</artifactId>
@@ -73,6 +77,10 @@
                     <groupId>org.apache.jena</groupId>
                     <artifactId>*</artifactId>
                 </exclusion>
+                <exclusion>  <!-- declare the exclusion here -->
+                    <groupId>org.apache.commons</groupId>
+                    <artifactId>commons-rdf-jena</artifactId>
+                </exclusion>
             </exclusions>
         </dependency>
         <dependency>

diff --git a/minerva-core/src/main/java/org/geneontology/minerva/BlazegraphMolecularModelManager.java b/minerva-core/src/main/java/org/geneontology/minerva/BlazegraphMolecularModelManager.java
@@ -7,8 +7,6 @@
 import info.aduna.iteration.Iterations;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.lang3.StringUtils;
-import org.apache.commons.rdf.jena.JenaGraph;
-import org.apache.commons.rdf.jena.JenaRDF;
 import org.apache.jena.graph.Graph;
 import org.apache.jena.shex.ShapeMap;
 import org.apache.jena.shex.ShexReport;
@@ -243,14 +241,10 @@ private void writeModelToDatabase(OWLOntology model, IRI modelId) throws Reposit
     }
 
     private List<OWLOntologyChange> preSaveFileHandler(OWLOntology model) throws UnknownIdentifierException {
-        List<OWLOntologyChange> allChanges = null;
+        List<OWLOntologyChange> allChanges = new ArrayList<>();
         for (PreFileSaveHandler handler : preFileSaveHandlers) {
             List<OWLOntologyChange> changes = handler.handle(model);
             if (changes != null && !changes.isEmpty()) {
-                if (allChanges == null) {
-                    allChanges = new ArrayList<OWLOntologyChange>(
-                            changes.size());
-                }
                 allChanges.addAll(changes);
             }
         }

diff --git a/minerva-core/src/main/java/org/geneontology/minerva/validation/ShexValidator.java b/minerva-core/src/main/java/org/geneontology/minerva/validation/ShexValidator.java
@@ -14,13 +14,15 @@
 import fr.inria.lille.shexjava.validation.Status;
 import fr.inria.lille.shexjava.validation.Typing;
 import org.apache.commons.lang3.StringUtils;
-import org.apache.commons.rdf.api.RDF;
-import org.apache.commons.rdf.api.RDFTerm;
-import org.apache.commons.rdf.jena.JenaGraph;
-import org.apache.commons.rdf.jena.JenaRDF;
+import org.apache.commons.rdf.api.*;
 import org.apache.commons.rdf.simple.SimpleRDF;
+import org.apache.jena.commonsrdf.JenaCommonsRDF;
+import org.apache.jena.commonsrdf.JenaRDF;
+import org.apache.jena.commonsrdf.impl.JenaGraph;
 import org.apache.jena.query.*;
 import org.apache.jena.rdf.model.*;
+import org.apache.jena.rdf.model.Literal;
+import org.apache.jena.sys.JenaSystem;
 import org.apache.log4j.Logger;
 import org.geneontology.minerva.BlazegraphOntologyManager;
 import org.geneontology.minerva.curie.CurieHandler;
@@ -34,7 +36,9 @@
 import java.util.HashSet;
 import java.util.Map;
 import java.util.Set;
+import java.util.UUID;
 import java.util.concurrent.*;
+import java.util.stream.Stream;
 
 /**
  * @author bgood
@@ -67,6 +71,7 @@ public ShexValidator(File shex_schema_file, File shex_map_file, BlazegraphOntolo
     }
 
     public void init(File shex_schema_file, File shex_map_file, BlazegraphOntologyManager go_lego, CurieHandler curieHandler_) throws Exception {
+        JenaSystem.init();
         schema = GenParser.parseSchema(shex_schema_file.toPath());
         GoQueryMap = makeGoQueryMap(shex_map_file.getAbsolutePath());
         //tbox_reasoner = tbox_reasoner_;
@@ -115,9 +120,8 @@ public static Map<String, String> makeGoQueryMap(String shapemap_file) throws IO
     public ShexValidationReport runShapeMapValidation(Model test_model) {
         boolean explain = true;
         ShexValidationReport r = new ShexValidationReport();
-        JenaRDF jr = new JenaRDF();
         //this shex implementation likes to use the commons JenaRDF interface, nothing exciting here
-        JenaGraph shexy_graph = jr.asGraph(test_model);
+        Graph shexy_graph = JenaCommonsRDF.fromJena(test_model.getGraph());
         boolean all_good = true;
         try {
             Typing all_typed = runRefineWithTimeout(shexy_graph);
@@ -251,7 +255,7 @@ public ShexValidationReport runShapeMapValidationWithRecursiveSingleNodeValidati
         ShexValidationReport r = new ShexValidationReport();
         JenaRDF jr = new JenaRDF();
         //this shex implementation likes to use the commons JenaRDF interface, nothing exciting here
-        JenaGraph shexy_graph = jr.asGraph(test_model);
+        Graph shexy_graph = JenaCommonsRDF.fromJena(test_model.getGraph());
         //recursive only checks the focus node against the chosen shape.
         RecursiveValidationWithMemorization shex_model_validator = new RecursiveValidationWithMemorization(schema, shexy_graph);
         //for each shape in the query map (e.g. MF, BP, CC, etc.)
@@ -391,7 +395,7 @@ private Map<Resource, Set<String>> getShapesToTestForEachResource(Model test_mod
         return node_s_shapes;
     }
 
-    private Typing runRefineWithTimeout(JenaGraph shexy_graph) {
+    private Typing runRefineWithTimeout(Graph shexy_graph) {
         final ExecutorService service = Executors.newSingleThreadExecutor();
         try {
             final Future<Typing> f = service.submit(() -> {

diff --git a/..._acquisition_of_features_of_seam cell.ttl → ..._acquisition_of_features_of_seam_cell.ttl b/..._acquisition_of_features_of_seam cell.ttl → ..._acquisition_of_features_of_seam_cell.ttl
diff --git a/...body_wall_muscle cell_from_MS_lineage.ttl → ...body_wall_muscle_cell_from_MS_lineage.ttl b/...body_wall_muscle cell_from_MS_lineage.ttl → ...body_wall_muscle_cell_from_MS_lineage.ttl
diff --git a/pom.xml b/pom.xml
@@ -328,6 +328,11 @@
                 <version>4.9.0</version>
                 <type>pom</type>
             </dependency>
+            <dependency>
+                <groupId>org.apache.jena</groupId>
+                <artifactId>jena-commonsrdf</artifactId>
+                <version>4.9.0</version>
+            </dependency>
             <dependency>
                 <groupId>net.sf.trove4j</groupId>
                 <artifactId>trove4j</artifactId>