Merge pull request #2791 from 4Science/CST-3091

DS-4514 Start new submission by uploading a Bibliographic File (using Live Import)

dspace-api/src/main/java/org/dspace/importer/external/bibtex/service/BibtexImportMetadataSourceServiceImpl.java

@@ -0,0 +1,107 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+
+package org.dspace.importer.external.bibtex.service;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.Reader;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import javax.annotation.Resource;
+
+import org.dspace.importer.external.exception.FileSourceException;
+import org.dspace.importer.external.service.components.AbstractPlainMetadataSource;
+import org.dspace.importer.external.service.components.dto.PlainMetadataKeyValueItem;
+import org.dspace.importer.external.service.components.dto.PlainMetadataSourceDto;
+import org.jbibtex.BibTeXDatabase;
+import org.jbibtex.BibTeXEntry;
+import org.jbibtex.BibTeXParser;
+import org.jbibtex.Key;
+import org.jbibtex.ParseException;
+import org.jbibtex.Value;
+
+/**
+ * Implements a metadata importer for BibTeX files
+ *
+ * @author Pasquale Cavallo (pasquale.cavallo at 4science dot it)
+ */
+public class BibtexImportMetadataSourceServiceImpl extends AbstractPlainMetadataSource {
+
+
+    /**
+     * The string that identifies this import implementation as
+     * MetadataSource implementation
+     *
+     * @return the identifying uri
+     */
+    @Override
+    public String getImportSource() {
+        return "BibTeXMetadataSource";
+    }
+
+    @Override
+    protected List<PlainMetadataSourceDto> readData (InputStream
+        inputStream) throws FileSourceException {
+        List<PlainMetadataSourceDto> list = new ArrayList<>();
+        BibTeXDatabase database;
+        try {
+            database = parseBibTex(inputStream);
+        } catch (IOException | ParseException e) {
+            throw new FileSourceException("Unable to parse file with BibTeX parser");
+        }
+        if (database == null || database.getEntries() == null) {
+            throw new FileSourceException("File results in an empty list of metadata");
+        }
+        if (database.getEntries() != null) {
+            for (Entry<Key, BibTeXEntry> entry : database.getEntries().entrySet()) {
+                PlainMetadataSourceDto item = new PlainMetadataSourceDto();
+                List<PlainMetadataKeyValueItem> keyValues = new ArrayList<>();
+                item.setMetadata(keyValues);
+                PlainMetadataKeyValueItem keyValueItem = new PlainMetadataKeyValueItem();
+                keyValueItem.setKey(entry.getValue().getType().getValue());
+                keyValueItem.setValue(entry.getKey().getValue());
+                keyValues.add(keyValueItem);
+                if (entry.getValue().getFields() != null) {
+                    for (Entry<Key,Value> subentry : entry.getValue().getFields().entrySet()) {
+                        PlainMetadataKeyValueItem innerItem = new PlainMetadataKeyValueItem();
+                        innerItem.setKey(subentry.getKey().getValue());
+                        innerItem.setValue(subentry.getValue().toUserString());
+                        keyValues.add(innerItem);
+                    }
+                }
+                list.add(item);
+            }
+        }
+        return list;
+    }
+
+    private BibTeXDatabase parseBibTex(InputStream inputStream) throws IOException, ParseException {
+        Reader reader = new InputStreamReader(inputStream);
+        BibTeXParser bibtexParser = new BibTeXParser();
+        return bibtexParser.parse(reader);
+    }
+
+
+    /**
+     * Retrieve the MetadataFieldMapping containing the mapping between RecordType
+     * (in this case PlainMetadataSourceDto.class) and Metadata
+     *
+     * @return The configured MetadataFieldMapping
+     */
+    @Override
+    @SuppressWarnings("unchecked")
+    @Resource(name = "bibtexMetadataFieldMap")
+    public void setMetadataFieldMap(@SuppressWarnings("rawtypes") Map metadataFieldMap) {
+        super.setMetadataFieldMap(metadataFieldMap);
+    }
+
+}

dspace-api/src/main/java/org/dspace/importer/external/exception/FileMultipleOccurencesException.java

@@ -0,0 +1,29 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+
+package org.dspace.importer.external.exception;
+
+/**
+ * This exception could be throws when more than one element is found
+ * in a method that works on one only.
+ *
+ * @author Pasquale Cavallo (pasquale.cavallo at 4science dot it)
+ */
+
+public class FileMultipleOccurencesException extends Exception {
+
+    private static final long serialVersionUID = 1222409723339501937L;
+
+    public FileMultipleOccurencesException(String message, Throwable cause) {
+        super(message, cause);
+    }
+
+    public FileMultipleOccurencesException(String message) {
+        super(message);
+    }
+}

dspace-api/src/main/java/org/dspace/importer/external/exception/FileSourceException.java

@@ -0,0 +1,28 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+
+package org.dspace.importer.external.exception;
+
+/**
+ * Represents a problem with the File content: e.g. null input stream, invalid content, ...
+ *
+ * @author Pasquale Cavallo (pasquale.cavallo at 4science dot it)
+ */
+
+public class FileSourceException extends Exception {
+
+    private static final long serialVersionUID = 6895579588455260182L;
+
+    public FileSourceException(String message, Throwable cause) {
+        super(message, cause);
+    }
+
+    public FileSourceException(String message) {
+        super(message);
+    }
+}

dspace-api/src/main/java/org/dspace/importer/external/metadatamapping/AbstractMetadataFieldMapping.java

@@ -117,16 +117,13 @@ public void setMetadataFieldMap(Map<MetadataFieldConfig, MetadataContributor<Rec
     public Collection<MetadatumDTO> resultToDCValueMapping(RecordType record) {
         List<MetadatumDTO> values = new LinkedList<MetadatumDTO>();
 
-
         for (MetadataContributor<RecordType> query : getMetadataFieldMap().values()) {
             try {
                 values.addAll(query.contributeMetadata(record));
             } catch (Exception e) {
                 log.error("Error", e);
             }
-
         }
         return values;
-
     }
 }

dspace-api/src/main/java/org/dspace/importer/external/metadatamapping/contributor/SimpleMetadataContributor.java

@@ -0,0 +1,94 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+
+package org.dspace.importer.external.metadatamapping.contributor;
+
+import java.util.Collection;
+import java.util.LinkedList;
+import java.util.List;
+
+import org.dspace.importer.external.metadatamapping.MetadataFieldConfig;
+import org.dspace.importer.external.metadatamapping.MetadataFieldMapping;
+import org.dspace.importer.external.metadatamapping.MetadatumDTO;
+import org.dspace.importer.external.service.components.dto.PlainMetadataKeyValueItem;
+import org.dspace.importer.external.service.components.dto.PlainMetadataSourceDto;
+
+/**
+ * Metadata contributor that takes an PlainMetadataSourceDto instance and turns it into a
+ * collection of metadatum
+ *
+ * @author Pasquale Cavallo (pasquale.cavallo at 4science dot it)
+ */
+public class SimpleMetadataContributor implements MetadataContributor<PlainMetadataSourceDto> {
+
+    private MetadataFieldConfig field;
+
+    private String key;
+
+    private MetadataFieldMapping<PlainMetadataSourceDto,
+        MetadataContributor<PlainMetadataSourceDto>> metadataFieldMapping;
+
+    public SimpleMetadataContributor(MetadataFieldConfig field, String key) {
+        this.field = field;
+        this.key = key;
+    }
+
+    public SimpleMetadataContributor() { }
+
+    /**
+     * Set the metadataFieldMapping of this SimpleMetadataContributor
+     *
+     * @param metadataFieldMapping the new mapping.
+     */
+    @Override
+    public void setMetadataFieldMapping(
+        MetadataFieldMapping<PlainMetadataSourceDto,
+        MetadataContributor<PlainMetadataSourceDto>> metadataFieldMapping) {
+        this.metadataFieldMapping = metadataFieldMapping;
+    }
+
+    /**
+     * Retrieve the metadata associated with the given object.
+     * It match the key found in PlainMetadataSourceDto instance with the key passed to constructor.
+     * In case of success, new metadatum is constructer (using field elements and PlainMetadataSourceDto value)
+     * and added to the list.
+     *
+     * @param t A class to retrieve metadata and key to match from. t and contained list "metadata" MUST be not null.
+     * @return a collection of import records. Only the identifier of the found records may be put in the record.
+     */
+    @Override
+    public Collection<MetadatumDTO> contributeMetadata(PlainMetadataSourceDto t) {
+        List<MetadatumDTO> values = new LinkedList<>();
+        for (PlainMetadataKeyValueItem metadatum : t.getMetadata()) {
+            if (key.equals(metadatum.getKey())) {
+                MetadatumDTO dcValue = new MetadatumDTO();
+                dcValue.setValue(metadatum.getValue());
+                dcValue.setElement(field.getElement());
+                dcValue.setQualifier(field.getQualifier());
+                dcValue.setSchema(field.getSchema());
+                values.add(dcValue);
+            }
+        }
+        return values;
+    }
+
+    /*
+     * Setter to inject field item
+     */
+    public void setField(MetadataFieldConfig field) {
+        this.field = field;
+    }
+
+    /*
+     * Setter to inject key value
+     */
+    public void setKey(String key) {
+        this.key = key;
+    }
+
+}