From a08d8ceea95a7cc77f875ce671b2b0b195944a5a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20K=C5=99emen?= <petr.kremen@biomax.com>
Date: Thu, 3 Nov 2022 15:10:35 +0100
Subject: [PATCH 1/2] [#1070] downgrading SnakeYml to 1.31

---
 robot-core/pom.xml                            |  2 +-
 .../obolibrary/robot/ReportOperationTest.java | 54 +++++++++++++++++--
 2 files changed, 50 insertions(+), 6 deletions(-)

diff --git a/robot-core/pom.xml b/robot-core/pom.xml
index 25534bd99..5b01797e1 100644
--- a/robot-core/pom.xml
+++ b/robot-core/pom.xml
@@ -183,7 +183,7 @@
     <dependency>
       <groupId>org.yaml</groupId>
       <artifactId>snakeyaml</artifactId>
-      <version>1.32</version>
+      <version>1.31</version>
     </dependency>
     <dependency>
       <groupId>com.opencsv</groupId>
diff --git a/robot-core/src/test/java/org/obolibrary/robot/ReportOperationTest.java b/robot-core/src/test/java/org/obolibrary/robot/ReportOperationTest.java
index c968b8665..72ad223ad 100644
--- a/robot-core/src/test/java/org/obolibrary/robot/ReportOperationTest.java
+++ b/robot-core/src/test/java/org/obolibrary/robot/ReportOperationTest.java
@@ -1,18 +1,26 @@
 package org.obolibrary.robot;
 
-import java.io.*;
-import java.nio.charset.Charset;
-import java.nio.charset.StandardCharsets;
-import java.util.Collections;
 import org.apache.commons.io.IOUtils;
 import org.junit.Assert;
 import org.junit.Test;
-import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.model.*;
 import org.yaml.snakeyaml.error.YAMLException;
 
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.InputStream;
+import java.net.URI;
+import java.nio.charset.Charset;
+import java.nio.charset.StandardCharsets;
+import java.util.Collections;
+
 /** Tests for the ReportOperation. */
 public class ReportOperationTest extends CoreTest {
 
+  private static final String oboInOwl = "http://www.geneontology.org/formats/oboInOwl#";
+  private static final String obo = "http://purl.obolibrary.org/obo/";
+
   /** Test report produces correct JSON. */
   @Test
   public void testReportProducesValidJson() throws Exception {
@@ -45,4 +53,40 @@ private void testReportProducesCorrectOutput(String extension) throws Exception
       Assert.fail();
     }
   }
+
+  private OWLOntology generateOntologyWithLotsOfViolations() throws OWLOntologyCreationException {
+    final OWLOntologyManager m = OWLManager.createOWLOntologyManager();
+    final OWLDataFactory f = m.getOWLDataFactory();
+    final OWLOntology o = m.createOntology(IRI.create(URI.create("https://example.org/o")));
+
+    final OWLAnnotationProperty pLabel = f.getRDFSLabel();
+    final OWLAnnotationProperty pHasExactSynonym = f.getOWLAnnotationProperty(IRI.create(oboInOwl + "hasExactSynonym"));
+    final OWLAnnotationProperty pHasRelatedSynonym = f.getOWLAnnotationProperty(IRI.create(oboInOwl + "hasRelatedSynonym"));
+    final OWLAnnotationProperty pIAO_0000115 = f.getOWLAnnotationProperty(IRI.create(obo + "IAO_0000115"));
+
+    for (int i = 0; i < 5000; i++) {
+      final IRI iriC = IRI.create("https://example.org/o/a" + i);
+      m.addAxiom(o, f.getOWLAnnotationAssertionAxiom(pLabel, iriC, f.getOWLLiteral(" X\tX")));
+      m.addAxiom(o, f.getOWLAnnotationAssertionAxiom(pLabel, iriC, f.getOWLLiteral("obsolete X\tX")));
+      m.addAxiom(o, f.getOWLAnnotationAssertionAxiom(pHasExactSynonym, iriC, f.getOWLLiteral(" X\tX")));
+      m.addAxiom(o, f.getOWLAnnotationAssertionAxiom(pHasRelatedSynonym, iriC, f.getOWLLiteral(" X\tX")));
+      m.addAxiom(o, f.getOWLAnnotationAssertionAxiom(pIAO_0000115, iriC, f.getOWLLiteral("x")));
+    }
+    return o;
+  }
+
+  // disabling, as the test takes a few minutes to run
+  // @Test
+  public void testReportProducesCorrectOutput() throws Exception {
+    try {
+      final IOHelper iohelper = new IOHelper();
+      final File outputFile =
+        File.createTempFile("1070-codepoint-defaults-output", ".json");
+      final OWLOntology o = generateOntologyWithLotsOfViolations();
+      ReportOperation.report(o, iohelper, outputFile.toString(), Collections.emptyMap());
+    } catch (YAMLException e) {
+      e.printStackTrace();
+      Assert.fail();
+    }
+  }
 }

From 8fc7cc230530ba1fdf494f9d4d3f6e90ccb94640 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Petr=20K=C5=99emen?= <petr.kremen@biomax.com>
Date: Thu, 3 Nov 2022 15:12:23 +0100
Subject: [PATCH 2/2] [#1070] changelog updated

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index cf8004ddf..b01190fcf 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## [Unreleased]
+- Downgrade SnakeYaml to 1.31 [#1070]
 
 ## [1.9.1] - 2022-10-28