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update to jdk 11, and grobid 0.8.1 #164

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update to jdk 11, and grobid 0.8.1 #164

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e550ec9
update to jdk 11, and grobid 0.8.1, removed jdk.incubator.foreign
lfoppiano Jul 4, 2024
9aa2c27
add github actions
lfoppiano Jul 4, 2024
98c6918
more sophisticated actions
lfoppiano Jul 4, 2024
66dd67f
minor corrections
lfoppiano Jul 4, 2024
554cecb
typo
lfoppiano Jul 4, 2024
58ee51d
pull the right grobid branch
lfoppiano Jul 4, 2024
c7bef1e
disable tests
lfoppiano Jul 4, 2024
8b73624
typo
lfoppiano Jul 4, 2024
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45 changes: 45 additions & 0 deletions .github/workflows/ci-build.yml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,45 @@
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: release-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
26 changes: 13 additions & 13 deletions build.gradle
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Original file line number Diff line number Diff line change
Expand Up @@ -22,8 +22,8 @@ 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

Expand Down Expand Up @@ -51,11 +51,11 @@ dependencies {
testImplementation group: 'com.googlecode.json-simple', name: 'json-simple', version: '1.1.1'

// GROBID
implementation (group: 'org.grobid', name: 'grobid-core', version: '0.8.0') {
implementation (group: 'org.grobid', name: 'grobid-core', version: '0.8.1') {
//exclude(module: 'log4j-over-slf4j')
exclude(group: 'ch.qos.logback', module: 'logback-classic')
}
implementation (group: 'org.grobid', name: 'grobid-trainer', version: '0.8.0') {
implementation (group: 'org.grobid', name: 'grobid-trainer', version: '0.8.1') {
//exclude(module: 'log4j-over-slf4j')
exclude(group: 'ch.qos.logback', module: 'logback-classic')
}
Expand Down Expand Up @@ -164,7 +164,7 @@ test {

if (JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) {
jvmArgs "--add-opens", "java.base/java.util.stream=ALL-UNNAMED",
"--add-opens", "java.base/java.io=ALL-UNNAMED", "--add-modules", "jdk.incubator.foreign"
"--add-opens", "java.base/java.io=ALL-UNNAMED"
}
}

Expand Down Expand Up @@ -210,7 +210,7 @@ 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-modules", "jdk.incubator.foreign", "--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'
}
Expand All @@ -224,7 +224,7 @@ 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-modules", "jdk.incubator.foreign", "--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'
}
Expand All @@ -238,7 +238,7 @@ 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-modules", "jdk.incubator.foreign", "--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'
}
Expand All @@ -253,7 +253,7 @@ 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-modules", "jdk.incubator.foreign", "--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'
}
Expand All @@ -268,7 +268,7 @@ 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-modules", "jdk.incubator.foreign", "--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'
}
Expand All @@ -281,7 +281,7 @@ 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-modules", "jdk.incubator.foreign", "--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'
}
Expand All @@ -294,7 +294,7 @@ 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-modules", "jdk.incubator.foreign", "--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'
}
Expand All @@ -307,7 +307,7 @@ application {

run {
if (JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) {
jvmArgs "--add-modules", "jdk.incubator.foreign", "--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']
Expand Down