Read the configuration from default location when running the trainin…

…g with gradle #131

build.gradle

@@ -65,13 +65,14 @@ dependencies {
     implementation 'org.apache.commons:commons-collections4:4.4'
     implementation 'org.apache.commons:commons-lang3:3.12.0'
     implementation 'commons-logging:commons-logging:1.2'
-    implementation 'commons-io:commons-io:2.6'
+    implementation 'commons-io:commons-io:2.11.0'
     implementation 'commons-pool:commons-pool:1.6'
 
     //Json
-    implementation "com.fasterxml.jackson.core:jackson-core:2.10.1"
-    implementation "com.fasterxml.jackson.core:jackson-databind:2.10.1"
-    implementation "com.fasterxml.jackson.module:jackson-module-afterburner:2.10.1"
+    implementation 'com.fasterxml.jackson.core:jackson-core:2.13.0'
+    implementation 'com.fasterxml.jackson.core:jackson-databind:2.13.0'
+    implementation 'com.fasterxml.jackson.module:jackson-module-afterburner:2.13.0'
+    implementation 'com.fasterxml.jackson.dataformat:jackson-dataformat-yaml:2.13.0'
 
     // measurements
 
@@ -103,8 +104,8 @@ dependencies {
     implementation "net.arnx:jsonic:1.3.10"
 
     // XML
-    implementation 'org.codehaus.woodstox:stax2-api:3.1.4'
-    implementation 'com.fasterxml.woodstox:woodstox-core:5.1.0'
+    implementation 'org.codehaus.woodstox:stax2-api:4.2.1'
+    implementation 'com.fasterxml.woodstox:woodstox-core:6.2.7'
 
 
     // Needed for compatibility with JDK > 8

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

@@ -19,6 +19,7 @@
 import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.apache.commons.lang3.StringUtils.isBlank;
 import static org.grobid.core.engines.QuantitiesModels.QUANTIFIED_OBJECT;
+import static org.grobid.trainer.QuantitiesTrainer.loadConfigurationFromDefaultPath;
 
 public class QuantifiedObjectTrainer extends AbstractTrainer {
     private static final Logger LOGGER = LoggerFactory.getLogger(QuantifiedObjectTrainer.class);
@@ -145,6 +146,7 @@ public int createCRFPPData(File corpusDir, File trainingOutputPath, File evalOut
      */
     public static void main(String[] args) {
         GrobidProperties.getInstance();
+        loadConfigurationFromDefaultPath();
 
         Trainer trainer = new QuantifiedObjectTrainer();
         AbstractTrainer.runSplitTrainingEvaluation(trainer, 0.6);

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

@@ -1,5 +1,9 @@
 package org.grobid.trainer;
 
+import com.fasterxml.jackson.databind.DeserializationFeature;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.dataformat.yaml.YAMLFactory;
+import io.dropwizard.jackson.Jackson;
 import org.apache.commons.io.IOUtils;
 import org.grobid.core.engines.QuantitiesModels;
 import org.grobid.core.exceptions.GrobidException;
@@ -9,11 +13,14 @@
 import org.grobid.core.utilities.OffsetPosition;
 import org.grobid.core.utilities.Pair;
 import org.grobid.core.utilities.UnicodeUtil;
+import org.grobid.service.configuration.GrobidQuantitiesConfiguration;
 import org.grobid.trainer.sax.MeasureAnnotationSaxHandler;
 
 import javax.xml.parsers.SAXParser;
 import javax.xml.parsers.SAXParserFactory;
 import java.io.*;
+import java.nio.file.Path;
+import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -215,8 +222,25 @@ private void addFeatures(List<Pair<String, String>> texts,
      */
     public static void main(String[] args) {
         GrobidProperties.getInstance();
+        loadConfigurationFromDefaultPath();
 
         Trainer trainer = new QuantitiesTrainer();
         AbstractTrainer.runTraining(trainer);
     }
+
+    public static void loadConfigurationFromDefaultPath() {
+        Path configFilePath = Paths.get("resources", "config", "config.yml");
+        ObjectMapper mapper = Jackson.newObjectMapper(new YAMLFactory());
+        mapper.disable(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES);
+
+        try {
+            System.out.println("Reading configuration from default location: "+ configFilePath.toAbsolutePath());
+            GrobidQuantitiesConfiguration configuration = mapper.readValue(configFilePath.toFile(), GrobidQuantitiesConfiguration.class);
+            configuration.getModels().stream().forEach(GrobidProperties::addModel);
+        } catch (Exception e) {
+            System.out.println("Cannot read configuration. To specify the configuration to a custom path, run the training via the JAR file. See java -jar build/lib/*.onjar.jar --help for information.");
+            System.out.println("Exception: " + e);
+            System.exit(-1);
+        }
+    }
 }

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

@@ -21,6 +21,7 @@
 
 import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.apache.commons.lang3.StringUtils.lowerCase;
+import static org.grobid.trainer.QuantitiesTrainer.loadConfigurationFromDefaultPath;
 
 /**
  * Created by lfoppiano on 21.02.16.
@@ -178,6 +179,7 @@ public int createCRFPPData(File corpusDir, File trainingOutputPath, File evalOut
      */
     public static void main(String[] args) {
         GrobidProperties.getInstance();
+        loadConfigurationFromDefaultPath();
 
         Trainer trainer = new UnitTrainer();
         AbstractTrainer.runTraining(trainer);

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

@@ -19,6 +19,7 @@
 import java.util.List;
 
 import static java.nio.charset.StandardCharsets.UTF_8;
+import static org.grobid.trainer.QuantitiesTrainer.loadConfigurationFromDefaultPath;
 
 /**
  * Created by lfoppiano on 21.02.16.
@@ -171,6 +172,7 @@ public boolean accept(File dir, String name) {
      */
     public static void main(String[] args) {
         GrobidProperties.getInstance();
+        loadConfigurationFromDefaultPath();
 
         Trainer trainer = new ValueTrainer();
         AbstractTrainer.runTraining(trainer);