Update to Gradle, JDK

Dockerfile.dataseer

@@ -125,7 +125,7 @@ RUN rm /opt/grobid/grobid-home/lib/lin-64/jep/libjep.so
 COPY --from=builder /opt/grobid-source/grobid-home/scripts/preload_embeddings.py .
 # embeddings will be loaded when building and running tests
 
-RUN ln -s /opt/grobid /opt/delft
+RUN ln -s /opt/grobid/delft /opt/delft
 
 COPY --from=builder /opt/grobid-source/dataseer-ml /opt/grobid/dataseer-ml
 #COPY --from=builder /root/.m2/repository/org /opt/grobid/dataseer-ml/lib/org

build.gradle

@@ -86,8 +86,8 @@ dependencies {
     //implementation fileTree(dir: new File(rootProject.rootDir, 'lib'), include: localLibs)
 
     //Grobid
-    implementation group: 'org.grobid', name: 'grobid-core', version: '0.7.3'
-    implementation group: 'org.grobid', name: 'grobid-trainer', version: '0.7.3'
+    implementation group: 'org.grobid', name: 'grobid-core', version: '0.8.0'
+    implementation group: 'org.grobid', name: 'grobid-trainer', version: '0.8.0'
 
     implementation group: 'net.arnx', name: 'jsonic', version: '1.3.10'
 
@@ -145,32 +145,22 @@ dependencies {
     testImplementation group: 'org.hamcrest', name: 'hamcrest-all', version: '1.3'
 }
 
-/*configurations {
+configurations {
     implementation.exclude group: "org.slf4j", module: "slf4j-jdk14"
-}*/
+    implementation.exclude group: 'org.slf4j', module: "slf4j-log4j12"
+    implementation.exclude group: 'log4j', module: "log4j"
+}
 
-/*configurations.all {
+configurations.all {
     resolutionStrategy {
         force 'xml-apis:xml-apis:1.4.01'
     }
-}*/
-
-configurations.implementation.setCanBeResolved(true)
 
-configurations.all { 
-    resolutionStrategy {
-        force 'xml-apis:xml-apis:1.4.01'
+    configurations {
+        all*.exclude group: 'org.slf4j', module: "slf4j-log4j12"
+        all*.exclude group: 'log4j', module: "log4j"
+        implementation.setCanBeResolved(true)
     }
-    exclude group: 'org.slf4j', module: "slf4j-log4j12"
-    //exclude group: 'log4j', module: "log4j"
-    exclude group: 'org.slf4j', module: "slf4j-jdk14"
-
-    //if (project.gradle.startParameter.taskNames.contains('run') ||
-    //   project.gradle.startParameter.taskNames.contains('post_process_corpus'))
-    //    exclude group: 'org.slf4j', module: "slf4j-jdk14"
-
-    if (project.gradle.startParameter.taskNames.contains('run'))
-        exclude group: 'org.slf4j', module: "slf4j-jdk14"
 }
 
 // return the default value if the property has not been specified in command line
@@ -250,7 +240,7 @@ test {
 //}
 
 wrapper {
-    gradleVersion "7.1.1"
+    gradleVersion "7.3"
 }
 
 // Custom Tasks
@@ -311,5 +301,28 @@ application {
 
     run {
         args = ['server', 'resources/config/server.yml']
+        if (JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) {
+            jvmArgs "--add-opens", "java.base/java.lang=ALL-UNNAMED"
+        }
+
+        def envPrefix = ""
+        if (System.env.CONDA_PREFIX) {
+            envPrefix = "${System.env.CONDA_PREFIX}"
+        } else if (System.env.VIRTUAL_ENV) {
+            envPrefix = "${System.env.VIRTUAL_ENV}"
+        }
+        def javaLibraryPath = "${System.getProperty('java.library.path')}:"
+
+        if (envPrefix) {
+            def envLibs = "${envPrefix}/lib"
+            def pythonDirectory = file(envLibs).listFiles({ it.toString().contains("/lib/python") } as FileFilter)?.first()
+            def pythonVersion = (pythonDirectory =~ /python([0-9]\.[0-9]+)/)[0][1]
+
+            javaLibraryPath = "${System.getProperty('java.library.path')}:" +
+                    "${envLibs}:" +
+                    "${envLibs}/python${pythonVersion}/site-packages/jep"
+        }
+        println("Running with the java.library.path: ${javaLibraryPath}")
+        systemProperty "java.library.path", javaLibraryPath
     }
 }

gradle/wrapper/gradle-wrapper.properties

@@ -3,4 +3,4 @@ distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-7.1.1-all.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-7.3-all.zip

src/main/java/org/grobid/core/engines/DataseerClassifier.java

@@ -713,7 +713,7 @@ private void enrich(org.w3c.dom.Document doc, Node node) {
                                     JsonNode noDatasetNode = classificationNode.findPath("no_dataset");
                                     JsonNode textNode = classificationNode.findPath("text");
 
-                                    Boolean localResult = new Boolean(false);
+                                    Boolean localResult = Boolean.FALSE;
                                     if ((datasetNode != null) && (!datasetNode.isMissingNode()) &&
                                         (noDatasetNode != null) && (!noDatasetNode.isMissingNode()) ) {
                                         double probDataset = datasetNode.asDouble();
@@ -830,7 +830,7 @@ private void enrich(org.w3c.dom.Document doc, Node node) {
                                             datasetMap.put("dataset-"+dataSetId, Pair.of(bestDataTypeWithProb.getLeft(), null));
                                             dataInstanceMap.put("dataInstance-"+dataSetId, "dataset-"+dataSetId);
                                             dataInstanceScoreMap.put("dataInstance-"+dataSetId, bestDataTypeWithProb.getRight());
-                                            dataInstanceReuseMap.put("dataInstance-"+dataSetId, new Boolean(isReuse));
+                                            dataInstanceReuseMap.put("dataInstance-"+dataSetId, isReuse);
                                             dataSetId++;
 
                                             // we also need to add a dataseer subtype attribute to the parent <div>
@@ -1012,7 +1012,7 @@ private Pair<String, Double> getBestDataType(JsonNode classificationsNode) {
                 bestDataType = className;
             }
         }
-        return Pair.of(bestDataType, new Double(bestProb));
+        return Pair.of(bestDataType, bestProb);
     }
 
     private boolean getReuseInfo(JsonNode classificationsNode) {

src/main/java/org/grobid/core/engines/DataseerParser.java

@@ -114,9 +114,9 @@ public List<Boolean> processing(List<List<LayoutToken>> segments, List<String> s
                     values = line.split(" ");
                 String label = values[values.length-1];
                 if (label.endsWith("no_dataset")) 
-                    result.add(new Boolean(false));
+                    result.add(Boolean.FALSE);
                 else 
-                    result.add(new Boolean(true));
+                    result.add(Boolean.TRUE);
 
                 if (indexMatMetSection == -1 && values[values.length-2].equals("1")) {
                     indexMatMetSection = i;
@@ -145,7 +145,7 @@ public List<Boolean> processing(List<List<LayoutToken>> segments, List<String> s
                 for(int j=indexMatMetSection; j < lines.length; j++) {
                     // set the section to true
                     String line = lines[j].toLowerCase();
-                    result.set(j, new Boolean(true));
+                    result.set(j, Boolean.TRUE);
                     if (j == indexMatMetSection)
                         continue;
 
@@ -163,7 +163,7 @@ public List<Boolean> processing(List<List<LayoutToken>> segments, List<String> s
                         break;
 
                     if (line.indexOf("acknowledgement") != -1 || line.indexOf("funding") != -1 || line.indexOf("conclusion") != -1)  {
-                        result.set(j, new Boolean(false));
+                        result.set(j, Boolean.FALSE);
                         break;
                     }
                 }
@@ -191,7 +191,7 @@ public List<Boolean> processing(List<List<LayoutToken>> segments, List<String> s
                     if (nbDataset > 2) {
                         for(int j=0; j<result.size(); j++) {
                             if (j<indexMatMetSection || j>indexMatMetSection+10)
-                                result.set(j, new Boolean(false));
+                                result.set(j, Boolean.FALSE);
                         }
                     }
                 }

src/main/java/org/grobid/trainer/AnnotatedCorpusGeneratorCSV.java

@@ -202,7 +202,7 @@ public void processXML(String documentPath, String csvPath, String xmlPath) thro
                             if (localSentence.equals(sentence)) {
                                 totalMatchedAnnotations++;
                                 System.out.println("matched sentence!");
-                                solvedAnnotations.add(new Integer(k));
+                                solvedAnnotations.add(k);
                                 // add annotation attributes to the DOM sentence
 
                                 break;
@@ -505,7 +505,7 @@ public void process(String documentPath, String pdfPath, String csvPath, String
                         }
 
                         String sentence = annotation.getContext().trim();
-                        if (sentence.toLowerCase().equals("n/a")) {
+                        if (sentence.equalsIgnoreCase("n/a")) {
                             k++;
                             continue;
                         }
@@ -535,7 +535,7 @@ public void process(String documentPath, String pdfPath, String csvPath, String
 
                                 totalMatchedAnnotations++;
                                 //System.out.println("matched sentence! " + sentence);
-                                solvedAnnotations.add(new Integer(k));
+                                solvedAnnotations.add(k);
 
                                 if (!docMatchedSentences.contains(sentenceSimplified)) {
                                     docMatchedSentences.add(sentenceSimplified);

src/main/java/org/grobid/trainer/DataseerAnnotationSaxHandler.java

@@ -244,7 +244,7 @@ private void writeData(String qName) {
                 }
             }
 
-            nbDatasets.add(new Integer(nb));
+            nbDatasets.add(nb);
             datasetTypes.add(datasetType);
             accumulator.setLength(0);
         }