expose AltoPdf as REST API

grobid-core/src/main/java/org/grobid/core/document/DocumentSource.java

@@ -383,7 +383,9 @@ public File getXmlFile() {
     public void setXmlFile(File xmlFile) {
         this.xmlFile = xmlFile;
     }
-
+    public void setCleanupXml( boolean cleanupXml ){
+        this.cleanupXml=cleanupXml;
+    }
 }
 
 

grobid-service/src/main/java/org/grobid/service/AltoRestService.java

@@ -0,0 +1,45 @@
+package org.grobid.service;
+
+import com.codahale.metrics.annotation.Timed;
+import com.google.inject.Inject;
+import com.google.inject.Singleton;
+import org.glassfish.jersey.media.multipart.FormDataParam;
+
+import org.grobid.service.process.AltoRestProcessFiles;
+
+import javax.ws.rs.*;
+import javax.ws.rs.core.*;
+
+import java.io.InputStream;
+
+
+/**
+ * RESTful service for the GROBID system.
+ *
+ * @author FloZi, Damien, Patrice
+ */
+
+@Timed
+@Singleton
+@Path(GrobidPaths.PATH_PDF_ALTO)
+public class AltoRestService {
+
+    private static final String INPUT = "input";
+
+    @Inject
+    public AltoRestService(){
+
+    }
+
+    @Inject
+    private AltoRestProcessFiles restProcessFiles;
+
+    @Consumes(MediaType.MULTIPART_FORM_DATA)
+    @Produces(MediaType.APPLICATION_XML)
+    @POST
+    public Response processPDFReferenceAlto(@FormDataParam(INPUT) InputStream inputStream) throws Exception {
+
+
+        return restProcessFiles.processPDFReferenceAlto(inputStream);
+    }
+}

grobid-service/src/main/java/org/grobid/service/GrobidPaths.java

@@ -120,6 +120,10 @@ public interface GrobidPaths {
 	 */
 	String PATH_CITATIONS_PATENT_PDF_ANNOTATION = "citationPatentAnnotations";
 
+	/**
+	 * path extension for getting version
+	 */
+	String PATH_PDF_ALTO = "alto";
 	/**
 	 * path extension for processing sha1.
 	 */

grobid-service/src/main/java/org/grobid/service/modules/GrobidServiceModule.java

@@ -5,12 +5,15 @@
 import com.google.inject.Binder;
 import com.google.inject.Provides;
 import com.hubspot.dropwizard.guicier.DropwizardAwareModule;
+
+import org.grobid.service.AltoRestService;
 import org.grobid.service.GrobidRestService;
 import org.grobid.service.GrobidServiceConfiguration;
 import org.grobid.service.exceptions.mapper.GrobidExceptionMapper;
 import org.grobid.service.exceptions.mapper.GrobidExceptionsTranslationUtility;
 import org.grobid.service.exceptions.mapper.GrobidServiceExceptionMapper;
 import org.grobid.service.exceptions.mapper.WebApplicationExceptionMapper;
+import org.grobid.service.process.AltoRestProcessFiles;
 import org.grobid.service.process.GrobidRestProcessFiles;
 import org.grobid.service.process.GrobidRestProcessGeneric;
 import org.grobid.service.process.GrobidRestProcessString;
@@ -38,6 +41,9 @@ public void configure(Binder binder) {
         binder.bind(GrobidExceptionsTranslationUtility.class);
         binder.bind(GrobidExceptionMapper.class);
         binder.bind(WebApplicationExceptionMapper.class);
+        binder.bind(AltoRestService.class);
+        binder.bind(AltoRestProcessFiles.class);
+
     }
 
     @Provides

grobid-service/src/main/java/org/grobid/service/process/AltoRestProcessFiles.java

@@ -0,0 +1,155 @@
+package org.grobid.service.process;
+
+import com.google.inject.Inject;
+import com.google.inject.Singleton;
+import org.grobid.core.document.DocumentSource;
+import org.grobid.core.engines.Engine;
+import org.grobid.core.factory.GrobidPoolingFactory;
+import org.grobid.core.layout.GraphicObject;
+import org.grobid.core.utilities.IOUtilities;
+import org.grobid.service.exceptions.GrobidServiceException;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import javax.ws.rs.core.HttpHeaders;
+import javax.ws.rs.core.MediaType;
+import javax.ws.rs.core.Response;
+import javax.ws.rs.core.Response.Status;
+import java.io.*;
+import java.util.NoSuchElementException;
+
+import org.grobid.core.engines.EngineParsers;
+import org.grobid.core.engines.config.GrobidAnalysisConfig;
+import org.apache.xerces.impl.dv.util.Base64;
+import org.grobid.core.document.Document;
+import java.nio.charset.StandardCharsets;
+import java.util.List;
+import java.util.Base64.*;
+
+import static java.nio.file.Files.readAllBytes;
+import static java.nio.file.Paths.get;
+
+/**
+ * Web services consuming a file
+ */
+@Singleton
+public class AltoRestProcessFiles extends GrobidRestProcessFiles {
+
+    private static final Logger LOGGER = LoggerFactory.getLogger(AltoRestProcessFiles.class);
+
+    @Inject
+    public AltoRestProcessFiles() {
+
+    }
+
+    /**
+     * Uploads the origin PDF, process it and return PDF annotations for references
+     * in JSON.
+     *
+     * @param inputStream the data of origin PDF
+     * @return a response object containing the JSON annotations
+     */
+    public Response processPDFReferenceAlto(final InputStream inputStream) throws Exception {
+        LOGGER.debug(methodLogIn());
+
+        GrobidAnalysisConfig config = new GrobidAnalysisConfig.GrobidAnalysisConfigBuilder().withPreprocessImages(true)
+                .withProcessVectorGraphics(false).build();
+
+        Response response = null;
+        File originFile, xmlFile = null;
+        Engine engine = null;
+        final EngineParsers parsers = new EngineParsers();
+        try {
+            engine = Engine.getEngine(true);
+            // conservative check, if no engine is free in the pool a NoSuchElementException
+            // is normally thrown
+            if (engine == null) {
+                parsers.close();
+                throw new GrobidServiceException("No GROBID engine available", Status.SERVICE_UNAVAILABLE);
+            }
+
+            originFile = IOUtilities.writeInputFile(inputStream);
+            if (originFile == null) {
+                LOGGER.error("The input file cannot be written.");
+                parsers.close();
+                throw new GrobidServiceException("The input file cannot be written.", Status.INTERNAL_SERVER_ERROR);
+            }
+            final DocumentSource docSource = DocumentSource.fromPdf(originFile, -1, -1, true, false, false);
+            xmlFile = docSource.getXmlFile();
+            docSource.setCleanupXml( false);
+            originFile.delete();
+
+            // reading text file into stream, try-with-resources
+            String content = null;
+            try {
+                try (InputStream in = new FileInputStream(xmlFile)) {
+                    final byte[] bytes = new byte[(int) xmlFile.length()];
+
+                    int offset = 0;
+                    while (offset < bytes.length) {
+                        final int result = in.read(bytes, offset, bytes.length - offset);
+                        if (result == -1) {
+                            break;
+                        }
+                        offset += result;
+                    }
+                    content = new String(bytes, StandardCharsets.UTF_8);
+                }
+            } catch (final IOException e) {
+                e.printStackTrace();
+            }
+
+
+            // real pdf document and concat all images no svg to end file with struct
+            // <all><content>alto content <content><images><image name="name"
+            // value="base64"/></images></all>
+            String base64imagesxml = parsers.getSegmentationParser().processing(docSource, config).getImages().stream()
+                    .filter(image -> !image.getFilePath().toString().endsWith(".svg")).map(image -> {
+                        try 
+                        {
+                            LOGGER.debug(" image  string"+ image.getFilePath());
+                            LOGGER.debug(" image  "+ get(image.getFilePath()));
+                            File tempFile = new File(image.getFilePath());
+                            LOGGER.debug(" image Exists "+ tempFile.exists());
+
+                            return "<image name=''" + image.getFilePath().toString() + " value=" + java.util.Base64
+                                    .getEncoder().encodeToString(readAllBytes(get(image.getFilePath()))) + "'/>";
+                        } catch (IOException e) {
+                            LOGGER.error("An unexpected exception occurs to read image  "+ image.getFilePath().toString()+"-"+e);
+                            return " error image "+image.getFilePath().toString();                        }
+                    })
+            .reduce("", String::concat);
+            docSource.setCleanupXml( true);
+            DocumentSource.close(docSource, true, true, true);
+            parsers.close();
+
+
+            //if(base64imagesxml.length()!=0){
+            content = "<all><content>"+ content +"</content><images>"+ base64imagesxml +"<images><all>";
+            //}
+            if (content != null) {
+                response = Response.status(Status.OK).entity(content)
+                        .header(HttpHeaders.CONTENT_TYPE, MediaType.APPLICATION_XML + "; charset=UTF-8").build();
+            }
+            /*} else {
+                response = Response.status(Status.NO_CONTENT).build();
+            }*/
+
+        } catch (final NoSuchElementException nseExp) {
+            LOGGER.error("Could not get an engine from the pool within configured time. Sending service unavailable.");
+            response = Response.status(Status.SERVICE_UNAVAILABLE).build();
+        } catch (final Exception exp) {
+            LOGGER.error("An unexpected exception occurs. ", exp);
+            response = Response.status(Status.INTERNAL_SERVER_ERROR).entity(exp.getMessage()).build();
+        } finally {
+            if (xmlFile != null)
+                IOUtilities.removeTempFile(xmlFile);
+
+            if (engine != null) {
+                GrobidPoolingFactory.returnEngine(engine);
+            }
+        }
+        LOGGER.debug(methodLogOut());
+        return response;
+    }
+}