diff --git a/minerva-core/pom.xml b/minerva-core/pom.xml
index e5e4cfac..4815a330 100644
--- a/minerva-core/pom.xml
+++ b/minerva-core/pom.xml
@@ -54,6 +54,10 @@
apache-jena-libs
pom
+
+ org.apache.jena
+ jena-commonsrdf
+
net.sf.trove4j
trove4j
@@ -73,6 +77,10 @@
org.apache.jena
*
+
+ org.apache.commons
+ commons-rdf-jena
+
diff --git a/minerva-core/src/main/java/org/geneontology/minerva/BlazegraphMolecularModelManager.java b/minerva-core/src/main/java/org/geneontology/minerva/BlazegraphMolecularModelManager.java
index 72241617..7c65c858 100644
--- 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 preSaveFileHandler(OWLOntology model) throws UnknownIdentifierException {
- List allChanges = null;
+ List allChanges = new ArrayList<>();
for (PreFileSaveHandler handler : preFileSaveHandlers) {
List changes = handler.handle(model);
if (changes != null && !changes.isEmpty()) {
- if (allChanges == null) {
- allChanges = new ArrayList(
- 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
index 404cf49c..5c2d4adc 100644
--- 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 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> 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 f = service.submit(() -> {
diff --git a/minerva-core/src/test/resources/validation/should_pass/Test034-cell_differentiation_results_in_acquisition_of_features_of_seam cell.ttl b/minerva-core/src/test/resources/validation/should_pass/Test034-cell_differentiation_results_in_acquisition_of_features_of_seam_cell.ttl
similarity index 100%
rename from minerva-core/src/test/resources/validation/should_pass/Test034-cell_differentiation_results_in_acquisition_of_features_of_seam cell.ttl
rename to minerva-core/src/test/resources/validation/should_pass/Test034-cell_differentiation_results_in_acquisition_of_features_of_seam_cell.ttl
diff --git a/minerva-core/src/test/resources/validation/should_pass/Test035-cell_fate_commitment_results_in_commitment_to_body_wall_muscle cell_from_MS_lineage.ttl b/minerva-core/src/test/resources/validation/should_pass/Test035-cell_fate_commitment_results_in_commitment_to_body_wall_muscle_cell_from_MS_lineage.ttl
similarity index 100%
rename from minerva-core/src/test/resources/validation/should_pass/Test035-cell_fate_commitment_results_in_commitment_to_body_wall_muscle cell_from_MS_lineage.ttl
rename to minerva-core/src/test/resources/validation/should_pass/Test035-cell_fate_commitment_results_in_commitment_to_body_wall_muscle_cell_from_MS_lineage.ttl
diff --git a/pom.xml b/pom.xml
index b76f39c7..ed66035c 100644
--- a/pom.xml
+++ b/pom.xml
@@ -328,6 +328,11 @@
4.9.0
pom
+
+ org.apache.jena
+ jena-commonsrdf
+ 4.9.0
+
net.sf.trove4j
trove4j