Update github actions and JDK 11

.github/workflows/ci-build.yml

@@ -0,0 +1,68 @@
+name: Build unstable
+
+on: [push, workflow_dispatch]
+
+concurrency: 
+  group: gradle
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout grobid home
+      uses: actions/checkout@v4
+      with:
+        repository: kermitt2/grobid
+        ref: 0.8.1
+        path: ./grobid
+    - name: Checkout grobid-ner
+      uses: actions/checkout@v4
+      with:
+        repository: kermitt2/grobid-ner
+        path: ./grobid/grobid-ner
+    - name: Checkout entity-fishing
+      uses: actions/checkout@v4
+      with:
+        path: ./entity-fishing
+    - name: Set up JDK 11
+      uses: actions/setup-java@v4
+      with:
+        java-version: '11'
+        distribution: 'adopt'
+        cache: 'gradle'
+    - name: Build grobid
+      working-directory: grobid
+      run: ./gradlew install -x test
+    - name: Build grobid-ner
+      working-directory: grobid/grobid-ner
+      run: ./gradlew install -x test
+    - name: Install grobid-ner
+      working-directory: grobid/grobid-ner
+      run: ./gradlew copyModels
+    - name: Build entity-fishing with Gradle
+      working-directory: entity-fishing
+      run: ./gradlew build -x test
+
+
+  docker-build:
+    needs: [ build ]
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Create more disk space
+        run: sudo rm -rf /usr/share/dotnet && sudo rm -rf /opt/ghc && sudo rm -rf "/usr/local/share/boost" && sudo rm -rf "$AGENT_TOOLSDIRECTORY"
+      - uses: actions/checkout@v4
+      - name: Build and push
+        id: docker_build
+        uses: mr-smithers-excellent/docker-build-push@v6
+        with:
+          dockerfile: Dockerfile
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+          image: lfoppiano/entity-fishing
+          registry: docker.io
+          pushImage: false
+          tags: latest-develop
+      - name: Image digest
+        run: echo ${{ steps.docker_build.outputs.digest }}

build.gradle

@@ -23,8 +23,8 @@ version = '0.0.6'
 
 description = """entity recognition and disambiguation against Wikidata and Wikipedia in a raw text, partially-annotated text segment, PDF or weighted term vector"""
 
-sourceCompatibility = 1.8
-targetCompatibility = 1.8
+sourceCompatibility = 1.11
+targetCompatibility = 1.11
 
 import org.apache.tools.ant.taskdefs.condition.Os
 
@@ -65,6 +65,10 @@ dependencies {
         exclude(group: 'ch.qos.logback', module: 'logback-classic')
     }
 
+    implementation('ch.qos.logback:logback-classic:1.2.3'){
+        exclude(module: 'com.google.guava:guava')
+    }
+
     implementation 'black.ninia:jep:4.0.2'
     implementation 'org.apache.opennlp:opennlp-tools:1.9.1'
     implementation "joda-time:joda-time:2.9.9"
@@ -76,15 +80,15 @@ dependencies {
     implementation group: 'org.wipo.analysers', name: 'wipo-analysers', version: '0.0.1'
 
     // Apache commons
-    implementation 'org.apache.commons:commons-collections4:4.1'
+    implementation 'org.apache.commons:commons-collections4:4.3'
     implementation 'org.apache.commons:commons-lang3:3.6'
     implementation 'commons-logging:commons-logging:1.2'
     implementation 'commons-io:commons-io:2.7'
     implementation 'commons-pool:commons-pool:1.6'
     implementation group: 'org.apache.httpcomponents', name: 'httpclient', version: '4.5.13'
     implementation group: 'org.apache.httpcomponents', name: 'httpmime', version: '4.5.13'
     implementation group: 'org.apache.commons', name: 'commons-text', version: '1.1'
-    implementation group: 'com.google.guava', name: 'guava', version: '29.0-jre'
+    implementation "com.google.guava:guava:31.0.1-jre"
 
     // json and yaml
     implementation group: 'com.fasterxml.jackson.core', name: 'jackson-core', version: '2.10.1'
@@ -152,7 +156,7 @@ configurations.all {
         force 'xml-apis:xml-apis:1.4.01'
     }
 
-    exclude group: "ch.qos.logback", module: "logback-classic"
+//    exclude group: "ch.qos.logback", module: "logback-classic"
     exclude group: 'org.slf4j', module: "slf4j-log4j12"
     exclude group: 'org.slf4j', module: "slf4j-jdk14"
     exclude group: 'log4j', module: "log4j"
@@ -211,7 +215,7 @@ task(train_corpus, dependsOn: 'classes', type: JavaExec, group: 'training') {
     args getArg('corpus', ''), getArg('lang', 'en')
     jvmArgs '-Djdk.xml.totalEntitySizeLimit=2147480000', '-Djdk.xml.totalEntitySizeLimit=2147480000', '-Xms2g', '-Xmx8g'
     if (JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) {
-        jvmArgs '-Djdk.xml.totalEntitySizeLimit=2147480000', '-Djdk.xml.totalEntitySizeLimit=2147480000', '-Xms2g', '-Xmx8g', "--add-opens", "java.base/java.lang=ALL-UNNAMED", "--add-opens", "java.base/java.nio=ALL-UNNAMED", "--add-opens", "java.base/sun.nio.ch=ALL-UNNAMED", "--add-opens", "java.base/java.text=ALL-UNNAMED", "--add-opens", "java.base/java.net=ALL-UNNAMED", "--add-opens", "java.base/java.lang=ALL-UNNAMED", "--add-opens", "java.base/java.math=ALL-UNNAMED", "--add-opens", "java.base/java.util=ALL-UNNAMED", "--add-opens", "java.base/java.util.concurrent=ALL-UNNAMED" 
+        jvmArgs '-Djdk.xml.totalEntitySizeLimit=2147480000', '-Djdk.xml.totalEntitySizeLimit=2147480000', '-Xms2g', '-Xmx8g', "--add-opens", "java.base/java.lang=ALL-UNNAMED", "--add-opens", "java.base/java.nio=ALL-UNNAMED", "--add-opens", "java.base/sun.nio.ch=ALL-UNNAMED", "--add-opens", "java.base/java.text=ALL-UNNAMED", "--add-opens", "java.base/java.net=ALL-UNNAMED", "--add-opens", "java.base/java.lang=ALL-UNNAMED", "--add-opens", "java.base/java.math=ALL-UNNAMED", "--add-opens", "java.base/java.util=ALL-UNNAMED", "--add-opens", "java.base/java.util.concurrent=ALL-UNNAMED"
     } else {
         jvmArgs '-Djdk.xml.totalEntitySizeLimit=2147480000', '-Djdk.xml.totalEntitySizeLimit=2147480000', '-Xms2g', '-Xmx8g'
     }
@@ -225,7 +229,7 @@ task(evaluation, dependsOn: 'classes', type: JavaExec, group: 'evaluation') {
     classpath = sourceSets.main.runtimeClasspath
     args getArg('corpus', '')
     if (JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) {
-        jvmArgs '--Xms2g', '-Xmx8g', "--add-opens", "--add-opens", "java.base/java.nio=ALL-UNNAMED", "--add-opens", "java.base/sun.nio.ch=ALL-UNNAMED", "--add-opens", "java.base/java.text=ALL-UNNAMED", "--add-opens", "java.base/java.net=ALL-UNNAMED", "--add-opens", "java.base/java.lang=ALL-UNNAMED", "--add-opens", "java.base/java.math=ALL-UNNAMED", "--add-opens", "java.base/java.util=ALL-UNNAMED", "--add-opens", "java.base/java.util.concurrent=ALL-UNNAMED" 
+        jvmArgs '--Xms2g', '-Xmx8g', "--add-opens", "--add-opens", "java.base/java.nio=ALL-UNNAMED", "--add-opens", "java.base/sun.nio.ch=ALL-UNNAMED", "--add-opens", "java.base/java.text=ALL-UNNAMED", "--add-opens", "java.base/java.net=ALL-UNNAMED", "--add-opens", "java.base/java.lang=ALL-UNNAMED", "--add-opens", "java.base/java.math=ALL-UNNAMED", "--add-opens", "java.base/java.util=ALL-UNNAMED", "--add-opens", "java.base/java.util.concurrent=ALL-UNNAMED"
     } else {
         jvmArgs '--Xms2g', '-Xmx8g'
     }
@@ -239,7 +243,7 @@ task(annotatedDataGeneration, dependsOn: 'classes', type: JavaExec, group: 'trai
     classpath = sourceSets.main.runtimeClasspath
     args getArg('corpus', '')
     if (JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) {
-        jvmArgs '--Xms2g', '-Xmx8g', "--add-opens", "--add-opens", "java.base/java.nio=ALL-UNNAMED", "--add-opens", "java.base/sun.nio.ch=ALL-UNNAMED", "--add-opens", "java.base/java.text=ALL-UNNAMED", "--add-opens", "java.base/java.net=ALL-UNNAMED", "--add-opens", "java.base/java.lang=ALL-UNNAMED", "--add-opens", "java.base/java.math=ALL-UNNAMED", "--add-opens", "java.base/java.util=ALL-UNNAMED", "--add-opens", "java.base/java.util.concurrent=ALL-UNNAMED" 
+        jvmArgs '--Xms2g', '-Xmx8g', "--add-opens", "--add-opens", "java.base/java.nio=ALL-UNNAMED", "--add-opens", "java.base/sun.nio.ch=ALL-UNNAMED", "--add-opens", "java.base/java.text=ALL-UNNAMED", "--add-opens", "java.base/java.net=ALL-UNNAMED", "--add-opens", "java.base/java.lang=ALL-UNNAMED", "--add-opens", "java.base/java.math=ALL-UNNAMED", "--add-opens", "java.base/java.util=ALL-UNNAMED", "--add-opens", "java.base/java.util.concurrent=ALL-UNNAMED"
     } else {
         jvmArgs '--Xms2g', '-Xmx8g'
     }
@@ -254,7 +258,7 @@ task(generate_entity_description, dependsOn: 'classes', type: JavaExec, group: '
     classpath = sourceSets.main.runtimeClasspath
     args 'data/embeddings/', getArg('lang', 'en')
     if (JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) {
-        jvmArgs '--Xms2g', '-Xmx8g', "--add-opens", "--add-opens", "java.base/java.nio=ALL-UNNAMED", "--add-opens", "java.base/sun.nio.ch=ALL-UNNAMED", "--add-opens", "java.base/java.text=ALL-UNNAMED", "--add-opens", "java.base/java.net=ALL-UNNAMED", "--add-opens", "java.base/java.lang=ALL-UNNAMED", "--add-opens", "java.base/java.math=ALL-UNNAMED", "--add-opens", "java.base/java.util=ALL-UNNAMED", "--add-opens", "java.base/java.util.concurrent=ALL-UNNAMED" 
+        jvmArgs '--Xms2g', '-Xmx8g', "--add-opens", "--add-opens", "java.base/java.nio=ALL-UNNAMED", "--add-opens", "java.base/sun.nio.ch=ALL-UNNAMED", "--add-opens", "java.base/java.text=ALL-UNNAMED", "--add-opens", "java.base/java.net=ALL-UNNAMED", "--add-opens", "java.base/java.lang=ALL-UNNAMED", "--add-opens", "java.base/java.math=ALL-UNNAMED", "--add-opens", "java.base/java.util=ALL-UNNAMED", "--add-opens", "java.base/java.util.concurrent=ALL-UNNAMED"
     } else {
         jvmArgs '--Xms2g', '-Xmx8g'
     }
@@ -269,7 +273,7 @@ task(quantize_word_embeddings, dependsOn: 'classes', type: JavaExec, group: 'emb
     classpath = sourceSets.main.runtimeClasspath
     args '-i', getArg('i', 'word.embeddings.vec'), '-o', getArg('o', 'word.embeddings.quantized'), '-error', getArg('e', '0.01'), '-hashheader'
     if (JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) {
-        jvmArgs '--Xms2g', '-Xmx8g', "--add-opens", "--add-opens", "java.base/java.nio=ALL-UNNAMED", "--add-opens", "java.base/sun.nio.ch=ALL-UNNAMED", "--add-opens", "java.base/java.text=ALL-UNNAMED", "--add-opens", "java.base/java.net=ALL-UNNAMED", "--add-opens", "java.base/java.lang=ALL-UNNAMED", "--add-opens", "java.base/java.math=ALL-UNNAMED", "--add-opens", "java.base/java.util=ALL-UNNAMED", "--add-opens", "java.base/java.util.concurrent=ALL-UNNAMED" 
+        jvmArgs '--Xms2g', '-Xmx8g', "--add-opens", "--add-opens", "java.base/java.nio=ALL-UNNAMED", "--add-opens", "java.base/sun.nio.ch=ALL-UNNAMED", "--add-opens", "java.base/java.text=ALL-UNNAMED", "--add-opens", "java.base/java.net=ALL-UNNAMED", "--add-opens", "java.base/java.lang=ALL-UNNAMED", "--add-opens", "java.base/java.math=ALL-UNNAMED", "--add-opens", "java.base/java.util=ALL-UNNAMED", "--add-opens", "java.base/java.util.concurrent=ALL-UNNAMED"
     } else {
         jvmArgs '--Xms2g', '-Xmx8g'
     }
@@ -282,7 +286,7 @@ task(generate_entity_embeddings, dependsOn: 'classes', type: JavaExec, group: 'e
     classpath = sourceSets.main.runtimeClasspath
     args '-in', getArg('in', 'entity.description'), '-v', getArg('v', 'word.embeddings.quantized'), '-out', getArg('out', 'entity.embeddings.vec'), '-n', getArg('n', '8')
     if (JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) {
-        jvmArgs '--Xms2g', '-Xmx8g', "--add-opens", "--add-opens", "java.base/java.nio=ALL-UNNAMED", "--add-opens", "java.base/sun.nio.ch=ALL-UNNAMED", "--add-opens", "java.base/java.text=ALL-UNNAMED", "--add-opens", "java.base/java.net=ALL-UNNAMED", "--add-opens", "java.base/java.lang=ALL-UNNAMED", "--add-opens", "java.base/java.math=ALL-UNNAMED", "--add-opens", "java.base/java.util=ALL-UNNAMED", "--add-opens", "java.base/java.util.concurrent=ALL-UNNAMED" 
+        jvmArgs '--Xms2g', '-Xmx8g', "--add-opens", "--add-opens", "java.base/java.nio=ALL-UNNAMED", "--add-opens", "java.base/sun.nio.ch=ALL-UNNAMED", "--add-opens", "java.base/java.text=ALL-UNNAMED", "--add-opens", "java.base/java.net=ALL-UNNAMED", "--add-opens", "java.base/java.lang=ALL-UNNAMED", "--add-opens", "java.base/java.math=ALL-UNNAMED", "--add-opens", "java.base/java.util=ALL-UNNAMED", "--add-opens", "java.base/java.util.concurrent=ALL-UNNAMED"
     } else {
         jvmArgs '--Xms2g', '-Xmx8g'
     }
@@ -295,7 +299,7 @@ task(quantize_entity_embeddings, dependsOn: 'classes', type: JavaExec, group: 'e
     classpath = sourceSets.main.runtimeClasspath
     args '-i', getArg('i', 'entity.embeddings.vec'), '-o', getArg('o', 'entity.embeddings.quantized'), '-error', getArg('e', '0.01'), '-hashheader'
     if (JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) {
-        jvmArgs '--Xms2g', '-Xmx8g', "--add-opens", "--add-opens", "java.base/java.nio=ALL-UNNAMED", "--add-opens", "java.base/sun.nio.ch=ALL-UNNAMED", "--add-opens", "java.base/java.text=ALL-UNNAMED", "--add-opens", "java.base/java.net=ALL-UNNAMED", "--add-opens", "java.base/java.lang=ALL-UNNAMED", "--add-opens", "java.base/java.math=ALL-UNNAMED", "--add-opens", "java.base/java.util=ALL-UNNAMED", "--add-opens", "java.base/java.util.concurrent=ALL-UNNAMED" 
+        jvmArgs '--Xms2g', '-Xmx8g', "--add-opens", "--add-opens", "java.base/java.nio=ALL-UNNAMED", "--add-opens", "java.base/sun.nio.ch=ALL-UNNAMED", "--add-opens", "java.base/java.text=ALL-UNNAMED", "--add-opens", "java.base/java.net=ALL-UNNAMED", "--add-opens", "java.base/java.lang=ALL-UNNAMED", "--add-opens", "java.base/java.math=ALL-UNNAMED", "--add-opens", "java.base/java.util=ALL-UNNAMED", "--add-opens", "java.base/java.util.concurrent=ALL-UNNAMED"
     } else {
         jvmArgs '--Xms2g', '-Xmx8g'
     }
@@ -308,7 +312,7 @@ application {
 
     run {
         if (JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) {
-            jvmArgs "--add-opens", "java.base/java.nio=ALL-UNNAMED", "--add-opens", "java.base/sun.nio.ch=ALL-UNNAMED", "--add-opens", "java.base/java.text=ALL-UNNAMED", "--add-opens", "java.base/java.net=ALL-UNNAMED", "--add-opens", "java.base/java.lang=ALL-UNNAMED", "--add-opens", "java.base/java.math=ALL-UNNAMED", "--add-opens", "java.base/java.util=ALL-UNNAMED", "--add-opens", "java.base/java.util.concurrent=ALL-UNNAMED" 
+            jvmArgs "--add-opens", "java.base/java.nio=ALL-UNNAMED", "--add-opens", "java.base/sun.nio.ch=ALL-UNNAMED", "--add-opens", "java.base/java.text=ALL-UNNAMED", "--add-opens", "java.base/java.net=ALL-UNNAMED", "--add-opens", "java.base/java.lang=ALL-UNNAMED", "--add-opens", "java.base/java.math=ALL-UNNAMED", "--add-opens", "java.base/java.util=ALL-UNNAMED", "--add-opens", "java.base/java.util.concurrent=ALL-UNNAMED"
         }
 
         args = ['server', 'data/config/service.yaml']

doc/build.rst

@@ -6,10 +6,12 @@ Install, build, run, and monitor
 Install, build, and run
 ***********************
 
-*entity-fishing* requires JDK 1.8 or higher. It supports Linux-64. 
+*entity-fishing* requires JDK 1.11 or higher.
+The official supported architecture/OS is Linux-64.
 
-Mac OS environments should work fine, but it is *officially* not supported. 
-Please use a Linux-64 environment for any production works. Below, we make available the up-to-date and full binary index data for Linux-64 architecture.
+Mac OS is not officially supported. Mac OS (Intel) should nevertheless  work fine, but ARM does not work.
+Please use a Linux-64 environment for any production works.
+Below, we make available the up-to-date and full binary index data for Linux-64 architecture.
 
 Running the service requires at least 3GB of RAM for processing text inputs, but more RAM will be exploited if available for speeding up access to the compiled Wikidata and Wikipedia data (including Wikidata statements associated to entities) and for enabling high rate parallel processing. In case PDF are processed, a mimimum of 8GB is required due to additional PDF parsing and structuring requirements. For parallel processing of PDF exploiting multhreading (e.g. 10 parallel threads), 16GB is recommended.