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Merge pull request #276 from geneontology/performance-go_shapes199
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Performance go shapes199
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@kltm
kltm committed Feb 11, 2020
2 parents 516aa56 + 7b7f285 commit 0254300
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Showing 2 changed files with 48 additions and 31 deletions.
2 changes: 0 additions & 2 deletions minerva-cli/src/main/java/org/geneontology/minerva/cli/CommandLineInterface.java
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Original file line number Diff line number Diff line change
Expand Up @@ -91,8 +91,6 @@ public class CommandLineInterface {
private static final Logger LOGGER = Logger.getLogger(CommandLineInterface.class);

public static void main(String[] args) throws Exception {
ShexSchema schema = GenParser.parseSchema(new File("/Users/benjamingood/GitHub/GO_Shapes/shapes/go-cam-shapes.shex").toPath());


reportSystemParams();
Options main_options = new Options();
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77 changes: 48 additions & 29 deletions minerva-core/src/main/java/org/geneontology/minerva/validation/ShexValidator.java
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Original file line number Diff line number Diff line change
Expand Up @@ -51,6 +51,7 @@
import fr.inria.lille.shexjava.schema.abstrsynt.TCProperty;
import fr.inria.lille.shexjava.schema.abstrsynt.TripleConstraint;
import fr.inria.lille.shexjava.schema.abstrsynt.TripleExpr;
import fr.inria.lille.shexjava.schema.abstrsynt.TripleExprRef;
import fr.inria.lille.shexjava.schema.parsing.GenParser;
import fr.inria.lille.shexjava.util.Pair;
import fr.inria.lille.shexjava.validation.RecursiveValidation;
Expand Down Expand Up @@ -174,7 +175,7 @@ public ShexValidationReport runShapeMapValidation(Model test_model, boolean stre
shapes.removeAll(shapes_to_remove);
node_s_shapes.put(node, shapes);
}

for(Resource focus_node_resource : node_s_shapes.keySet()) {
Set<String> shape_nodes = node_s_shapes.get(focus_node_resource);
for(String shapelabel : shape_nodes) {
Expand Down Expand Up @@ -272,42 +273,46 @@ public Set<ShexViolation> checkForExtraProperties(Resource node_r, Model model,
Set<ShexViolation> violations = new HashSet<ShexViolation>();
Set<String> allowed_properties = this.shape_expected_property_ranges.get(shape_label).keySet();
Set<String> actual_properties = new HashSet<String>();
Map<String, String> prop_value = new HashMap<String, String>(); //don't really care if there are multiple values, one will do.
Map<String, RDFNode> prop_value = new HashMap<String, RDFNode>(); //don't really care if there are multiple values, one will do.
String sparql = "select distinct ?prop ?value where{ <"+node_r.getURI()+"> ?prop ?value }";
QueryExecution qe = QueryExecutionFactory.create(sparql, model);
ResultSet results = qe.execSelect();
while (results.hasNext()) {
QuerySolution qs = results.next();
Resource prop = qs.getResource("prop");
RDFNode value = qs.get("value");
String v = "value";
if(value.isResource()) {
v = value.asResource().getURI();
}else if(value.isLiteral()) {
v = value.asLiteral().getString();
}
actual_properties.add(prop.getURI());
prop_value.put(prop.getURI(), v);
prop_value.put(prop.getURI(), value);
}
qe.close();
actual_properties.removeAll(allowed_properties);
if(!actual_properties.isEmpty()) {
ShexViolation extra = new ShexViolation(getCurie(node_r.getURI()));
Set<ShexExplanation> explanations = new HashSet<ShexExplanation>();
for(String prop : actual_properties) {
String value = prop_value.get(prop);
String value = "value";
boolean value_is_uri = false;
if(prop_value.get(prop).isResource()) {
value = prop_value.get(prop).asResource().getURI();
value_is_uri = true;
}else if(prop_value.get(prop).isLiteral()) {
value = prop_value.get(prop).asLiteral().getString();
}
ShexExplanation extra_explain = new ShexExplanation();
extra_explain.setShape(getCurie(shape_label.stringValue()));
String object = value;
Set<String> intended_range_shapes = new HashSet<String>();
//For this CLOSED test, no shape fits in intended. Any use of the property here would be incorrect.
intended_range_shapes.add("owl:Nothing");
Set<String> node_types = getNodeTypes(model, node_r.getURI());
Set<String> object_types = getNodeTypes(model, value);
Set<String> object_types = null;
//TODO consider here. extra info but not really meaningful - anything in the range would be wrong.
Set<String> matched_range_shapes = getAllMatchedShapes(value, shex_model_validator);
Set<String> matched_range_shapes = null;
if(value_is_uri) {
object_types = getNodeTypes(model, value);
matched_range_shapes = getAllMatchedShapes(value, shex_model_validator);
}
String report_prop = getCurie(prop);
ShexConstraint c = new ShexConstraint(object, report_prop, intended_range_shapes, node_types, object_types);
ShexConstraint c = new ShexConstraint(value, report_prop, intended_range_shapes, node_types, object_types);
c.setMatched_range_shapes(matched_range_shapes);
Set<ShexConstraint> cs = new HashSet<ShexConstraint>();
cs.add(c);
Expand Down Expand Up @@ -390,6 +395,7 @@ public Model enrichSuperClasses(Model model) {
}

public Set<String> getNodeTypes(Model model, String node_uri) {

String getOntTerms =
"PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> "
+ "PREFIX owl: <http://www.w3.org/2002/07/owl#> "
Expand All @@ -414,6 +420,7 @@ public Set<String> getNodeTypes(Model model, String node_uri) {
}
qe.close();
} catch(QueryParseException e){
LOGGER.error(getOntTerms);
e.printStackTrace();
}

Expand Down Expand Up @@ -482,21 +489,30 @@ private Set<ShexConstraint> getUnmetConstraints(Resource focus_node, String shap
}
}
if(!good) {
String object = obj.toString();
Set<String> object_types = getNodeTypes(model, object);
String property = prop.toString();
object = getCurie(object);
property = getCurie(property);
Set<String> expected = new HashSet<String>();
for(String e : expected_property_ranges.get(prop_uri)) {
String curie_e = getCurie(e);
expected.add(curie_e);
}
ShexConstraint constraint = new ShexConstraint(object, property, expected, node_types, object_types);
//return all shapes that are matched by this node for explanation
Set<String> obj_matched_shapes = getAllMatchedShapes(range_obj, shex_model_validator);
constraint.setMatched_range_shapes(obj_matched_shapes);
unmet_constraints.add(constraint);
if(obj.isURIResource()) {
String object = obj.toString();
Set<String> object_types = getNodeTypes(model, obj.toString());

String property = prop.toString();
object = getCurie(object);
property = getCurie(property);
Set<String> expected = new HashSet<String>();
for(String e : expected_property_ranges.get(prop_uri)) {
String curie_e = getCurie(e);
expected.add(curie_e);
}
ShexConstraint constraint = new ShexConstraint(object, property, expected, node_types, object_types);
//return all shapes that are matched by this node for explanation
Set<String> obj_matched_shapes = getAllMatchedShapes(range_obj, shex_model_validator);
constraint.setMatched_range_shapes(obj_matched_shapes);
unmet_constraints.add(constraint);
}else {
ShexConstraint constraint = new ShexConstraint(obj.toString(), getCurie(prop.toString()), null, node_types, null);
//return all shapes that are matched by this node for explanation
Set<String> obj_matched_shapes = getAllMatchedShapes(range_obj, shex_model_validator);
constraint.setMatched_range_shapes(obj_matched_shapes);
unmet_constraints.add(constraint);
}
}
}
}
Expand Down Expand Up @@ -609,6 +625,9 @@ public Map<String, Set<String>> getPropertyRangeMap(TripleExpr texp, Map<String,
rep.getCardinality().toString();
TripleExpr t = rep.getSubExpression();
prop_range = getPropertyRangeMap(t, prop_range);
}else if(texp instanceof TripleExprRef) {
TripleExprRef ref = (TripleExprRef)texp;
prop_range = getPropertyRangeMap(ref.getTripleExp(), prop_range);
}
else {
System.out.println("\tlost again here on "+texp);
Expand Down

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