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Allow skipping ShEx in --validate-go-cams when --shex is omitted #422

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merged 1 commit into from
Nov 8, 2021
Merged

Allow skipping ShEx in --validate-go-cams when --shex is omitted #422

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10 changes: 5 additions & 5 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 @@ -920,13 +920,13 @@ else if(!model_iris.add(modeluri)) {
// TODO Auto-generated catch block
e1.printStackTrace();
}

if(checkShex) {
if(checkShex) {
shex.setActive(true);
}else {
shex.setActive(false);
}
shex.setActive(true);
}else {
shex.setActive(false);
}

//shex validator is ready, now build the inference provider (which provides access to the shex validator and provides inferences useful for shex)
String reasonerOpt = "arachne";
LOGGER.info("Building OWL inference provider: "+reasonerOpt);
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4 changes: 2 additions & 2 deletions minerva-core/src/main/java/org/geneontology/minerva/validation/ShexValidationReport.java
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Expand Up @@ -36,8 +36,8 @@ public class ShexValidationReport extends ModelValidationReport{
/**
*
*/
public ShexValidationReport(String id, Model model) {
super(id, tracker, rulefile);
public ShexValidationReport() {
super(null, tracker, rulefile);
}

public String getAsText() {
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4 changes: 2 additions & 2 deletions minerva-core/src/main/java/org/geneontology/minerva/validation/ShexValidator.java
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Expand Up @@ -148,7 +148,7 @@ public static Map<String, String> makeGoQueryMap(String shapemap_file) throws IO

public ShexValidationReport runShapeMapValidation(Model test_model) {
boolean explain = true;
ShexValidationReport r = new ShexValidationReport(null, test_model);
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);
Expand Down Expand Up @@ -282,7 +282,7 @@ public Violation getTimeoutViolation(String node, String shapelabel) {


public ShexValidationReport runShapeMapValidationWithRecursiveSingleNodeValidation(Model test_model, boolean stream_output) throws Exception {
ShexValidationReport r = new ShexValidationReport(null, test_model);
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);
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2 changes: 1 addition & 1 deletion ...server/src/main/java/org/geneontology/minerva/server/inferences/MapInferenceProvider.java
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Expand Up @@ -79,7 +79,7 @@ public static InferenceProvider create(OWLReasoner r, OWLOntology ont, MinervaSh
reasoner_validation.addViolation(i_v);
}
//shex
ShexValidationReport shex_validation = null;
ShexValidationReport shex_validation = new ShexValidationReport();
if(shex.isActive()) {
//generate an RDF model
Model model = JenaOwlTool.getJenaModel(ont);
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