fix and ignore tests

build.gradle

@@ -112,7 +112,7 @@ dependencies {
     implementation 'com.sun.xml.bind:jaxb-core:4.0.1'
     implementation 'com.sun.xml.bind:jaxb-impl:4.0.1'
     implementation 'com.fasterxml.jackson.datatype:jackson-datatype-guava:2.13.4'
-    
+
     //Grobid-quantities
     implementation 'tech.units:indriya:2.1.3'
     implementation group: 'si.uom', name: 'si-units', version: '2.1'
@@ -326,7 +326,7 @@ publishing {
     }
 }
 
-def conf = new org.yaml.snakeyaml.Yaml().load( new File("resources/config/config.yml").newInputStream() )
+def conf = new org.yaml.snakeyaml.Yaml().load(new File("resources/config/config.yml").newInputStream())
 def grobidHome = conf.grobidHome.replace("\$", "").replace('{', "").replace("GROBID_HOME:- ", "").replace("}", "")
 if (grobidHome.startsWith("../")) {
     grobidHome = "${rootProject.rootDir}/${grobidHome}"

src/test/java/org/grobid/core/engines/CRFBasedLinkerIntegrationTest.java

@@ -8,17 +8,24 @@
 import org.grobid.core.data.document.RawPassage;
 import org.grobid.core.data.document.TextPassage;
 import org.grobid.core.data.document.Span;
+import org.grobid.core.data.normalization.UnitNormalizer;
 import org.grobid.core.engines.linking.CRFBasedLinker;
 import org.grobid.core.layout.LayoutToken;
 import org.grobid.core.main.LibraryLoader;
+import org.grobid.core.utilities.GrobidConfig;
 import org.grobid.core.utilities.client.ChemDataExtractorClient;
 import org.grobid.core.utilities.GrobidProperties;
 import org.grobid.core.utilities.client.StructureIdentificationModuleClient;
+import org.grobid.service.configuration.GrobidQuantitiesConfiguration;
 import org.grobid.service.configuration.GrobidSuperconductorsConfiguration;
 import org.junit.Before;
+import org.junit.BeforeClass;
 import org.junit.Ignore;
 import org.junit.Test;
+import org.powermock.reflect.Whitebox;
 
+import java.io.IOException;
+import java.lang.reflect.Field;
 import java.util.*;
 import java.util.stream.Collectors;
 
@@ -29,24 +36,38 @@
 import static org.hamcrest.collection.IsCollectionWithSize.hasSize;
 import static org.hamcrest.MatcherAssert.assertThat;
 
+@Ignore("This has been decommissioned")
 public class CRFBasedLinkerIntegrationTest {
 
     private CRFBasedLinker target;
     private ModuleEngine moduleEngine;
     private ChemDataExtractorClient mockChemdataExtractorClient;
     private StructureIdentificationModuleClient mockSpaceGroupsClient;
 
-
-    @Before
-    public void setUp() throws Exception {
+    public static void initEngineForTests() throws IOException, IllegalAccessException {
         ObjectMapper mapper = new ObjectMapper(new YAMLFactory());
-        
+
         // https://stackoverflow.com/questions/14853324/can-not-find-deserialize-for-non-concrete-collection-type
         mapper.registerModule(new GuavaModule());
-        GrobidSuperconductorsConfiguration configuration = mapper.readValue(this.getClass().getResourceAsStream("config-test.yml"), GrobidSuperconductorsConfiguration.class);
+        GrobidSuperconductorsConfiguration configuration = mapper.readValue(RuleBasedLinker.class.getResourceAsStream("config-test.yml"), GrobidSuperconductorsConfiguration.class);
         configuration.getModels().stream().forEach(GrobidProperties::addModel);
+        GrobidProperties.getInstance();
+        Field modelMap = Whitebox.getField(GrobidProperties.class, "modelMap");
+
+        Map<String, GrobidConfig.ModelParameters> newModelMap = (Map<String, GrobidConfig.ModelParameters>) modelMap.get(new HashMap<>());
+        newModelMap.entrySet().stream()
+            .forEach(entry -> {
+                entry.getValue().engine = "wapiti";
+            });
+        Whitebox.setInternalState(GrobidProperties.class, "modelMap", newModelMap);
+//        GrobidProperties.getDistinctModels().stream().forEach(model -> model);
         LibraryLoader.load();
-
+    }
+
+    @Before
+    public void setUp() throws Exception {
+        initEngineForTests();
+
         target = new CRFBasedLinker();
         mockChemdataExtractorClient = EasyMock.createMock(ChemDataExtractorClient.class);
         mockSpaceGroupsClient = EasyMock.createMock(StructureIdentificationModuleClient.class);
@@ -55,37 +76,36 @@ public void setUp() throws Exception {
     }
 
     @Test
-    @Ignore()
     public void testRealCase_shouldExtract1Link() throws Exception {
         String input = "MgB 2 was discovered to be a superconductor in 2001, and it has a remarkably high critical temperature (T c ) around 40 K with a simple hexagonal structure.";
         List<LayoutToken> layoutTokens = DeepAnalyzer.getInstance().tokenizeWithLayoutToken(input);
 
         EasyMock.expect(mockChemdataExtractorClient.processBulk(EasyMock.anyObject())).andReturn(Arrays.asList(new ArrayList<>()));
         EasyMock.expect(mockSpaceGroupsClient.extractStructuresMulti(EasyMock.anyObject())).andReturn(new ArrayList<>());
         EasyMock.replay(mockChemdataExtractorClient, mockSpaceGroupsClient);
-        
+
         List<TextPassage> passages = moduleEngine.process(Arrays.asList(new RawPassage(layoutTokens)), true);
-        
+
         assertThat(passages, hasSize(1));
-        
+
         TextPassage passage = passages.get(0);
         List<Span> annotations = passage.getSpans();
         assertThat(annotations, hasSize(4));
-        
+
         //set the annotations linkable 
         annotations
             .stream()
             .filter(l -> l.getType().equals(SUPERCONDUCTORS_TC_VALUE_LABEL) || l.getType().equals(SUPERCONDUCTORS_MATERIAL_LABEL))
             .forEach(l -> l.setLinkable(true));
-        
+
         target.process(layoutTokens, annotations, CRFBasedLinker.getInstance().MATERIAL_TCVALUE_ID);
-        
+
         List<Span> linkedEntities = annotations.stream().filter(l -> isNotEmpty(l.getLinks())).collect(Collectors.toList());
         assertThat(linkedEntities, hasSize(2));
 
         assertThat(linkedEntities.get(0).getText(), is("MgB 2"));
         assertThat(linkedEntities.get(0).getLinks().get(0).getTargetText(), is("40 K"));
-        
+
         EasyMock.verify(mockChemdataExtractorClient, mockSpaceGroupsClient);
     }
 
@@ -102,7 +122,7 @@ public void testRealCase_shouldRecogniseOneLink() throws Exception {
 
         List<TextPassage> paragraphs = moduleEngine.process(Arrays.asList(new RawPassage(layoutTokens)), true);
         assertThat(paragraphs, hasSize(1));
-        
+
         TextPassage paragraph = paragraphs.get(0);
         List<Span> annotations = paragraph.getSpans();
         assertThat(annotations, hasSize(annotations.size()));
@@ -133,14 +153,14 @@ public void testRealCase_shouldNotLink() throws Exception {
         EasyMock.expect(mockChemdataExtractorClient.processBulk(EasyMock.anyObject())).andReturn(Arrays.asList(new ArrayList<>()));
         EasyMock.expect(mockSpaceGroupsClient.extractStructuresMulti(EasyMock.anyObject())).andReturn(new ArrayList<>());
         EasyMock.replay(mockChemdataExtractorClient, mockSpaceGroupsClient);
-        
+
         List<TextPassage> paragraphs = moduleEngine.process(Arrays.asList(new RawPassage(layoutTokens)), true);
         assertThat(paragraphs, hasSize(1));
 
         TextPassage paragraph = paragraphs.get(0);
         List<Span> annotations = paragraph.getSpans();
-        
-        
+
+
         target.process(layoutTokens, annotations, CRFBasedLinker.MATERIAL_TCVALUE_ID);
 
         List<Span> linkedEntities = annotations.stream().filter(l -> isNotEmpty(l.getLinks())).collect(Collectors.toList());
@@ -204,7 +224,7 @@ public void testRealCase_shouldExtract1Links_2() throws Exception {
         List<Span> linkedEntities = processedSpans.stream()
             .filter(l -> isNotEmpty(l.getLinks()) && l.getType().equals(SUPERCONDUCTORS_MATERIAL_LABEL))
             .collect(Collectors.toList());
-        
+
         assertThat(linkedEntities, hasSize(1));
 
         EasyMock.verify(mockChemdataExtractorClient, mockSpaceGroupsClient);
@@ -218,7 +238,7 @@ public void testRealCase_shouldExtract0Links_3() throws Exception {
         EasyMock.expect(mockChemdataExtractorClient.processBulk(EasyMock.anyObject())).andReturn(Arrays.asList(new ArrayList<>()));
         EasyMock.expect(mockSpaceGroupsClient.extractStructuresMulti(EasyMock.anyObject())).andReturn(new ArrayList<>());
         EasyMock.replay(mockChemdataExtractorClient, mockSpaceGroupsClient);
-        
+
         List<TextPassage> paragraphs = moduleEngine.process(Collections.singletonList(new RawPassage(layoutTokens)), true);
         assertThat(paragraphs, hasSize(1));
 

src/test/java/org/grobid/core/engines/CRFBasedLinkerTest.java

@@ -33,6 +33,7 @@
 import static org.hamcrest.collection.IsCollectionWithSize.hasSize;
 import static org.hamcrest.MatcherAssert.assertThat;
 
+@Ignore("Decommissioned")
 @RunWith(PowerMockRunner.class)
 @PrepareForTest(Lexicon.class)
 public class CRFBasedLinkerTest {

src/test/java/org/grobid/core/engines/GrobidPDFEngineStaticMockTest.java

@@ -17,6 +17,7 @@
 import java.util.List;
 
 import static org.easymock.EasyMock.*;
+import static org.grobid.core.engines.CRFBasedLinkerIntegrationTest.initEngineForTests;
 import static org.hamcrest.CoreMatchers.is;
 import static org.hamcrest.MatcherAssert.assertThat;
 import static org.hamcrest.collection.IsCollectionWithSize.hasSize;
@@ -32,6 +33,7 @@ public class GrobidPDFEngineStaticMockTest {
 
     @BeforeClass
     public static void before() throws Exception {
+        initEngineForTests();
         GrobidConfig.ModelParameters modelParameters = new GrobidConfig.ModelParameters();
         modelParameters.name = "bao";
         GrobidProperties.addModel(modelParameters);

src/test/java/org/grobid/core/engines/SentenceSegmenterIntegrationTest.java

@@ -12,6 +12,7 @@
 import java.util.List;
 import java.util.stream.Collectors;
 
+import static org.grobid.core.engines.CRFBasedLinkerIntegrationTest.initEngineForTests;
 import static org.hamcrest.MatcherAssert.assertThat;
 import static org.hamcrest.collection.IsCollectionWithSize.hasSize;
 import static org.hamcrest.core.Is.is;
@@ -22,7 +23,7 @@ public class SentenceSegmenterIntegrationTest {
 
     @Before
     public void setUp() throws Exception {
-        LibraryLoader.load();
+        initEngineForTests();
         target = new SentenceSegmenter();
     }
 

src/test/java/org/grobid/core/engines/SuperconductorsParserTest.java

@@ -28,6 +28,7 @@
 import java.util.stream.Collectors;
 import java.util.stream.IntStream;
 
+import static org.grobid.core.engines.CRFBasedLinkerIntegrationTest.initEngineForTests;
 import static org.grobid.core.engines.SuperconductorsParser.NONE_CHEMSPOT_TYPE;
 import static org.grobid.core.utilities.GrobidTestUtils.getWapitiResult;
 import static org.hamcrest.CoreMatchers.is;

src/test/java/org/grobid/trainer/stax/handler/AnnotationValuesTEIStaxHandlerIntegrationTest.java

@@ -27,7 +27,7 @@ public class AnnotationValuesTEIStaxHandlerIntegrationTest {
 
     @Before
     public void setUp() throws Exception {
-        LibraryLoader.load();
+//        LibraryLoader.load();
     }