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Merge pull request #2914 from 4Science/D4CRIS-960
DS-4514 Additional Providers - Start new submission by uploading a Bibliographic File (using Live Import)
This commit is contained in:
Tim Donohue
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/**
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* The contents of this file are subject to the license and copyright
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* detailed in the LICENSE and NOTICE files at the root of the source
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* tree and available online at
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*
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* http://www.dspace.org/license/
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*/
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package org.dspace.importer.external.csv.service;
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import java.io.IOException;
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import java.io.InputStream;
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import java.io.InputStreamReader;
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import java.nio.charset.StandardCharsets;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.Map;
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import au.com.bytecode.opencsv.CSVReader;
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import org.dspace.importer.external.exception.FileSourceException;
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import org.dspace.importer.external.metadatamapping.MetadataFieldConfig;
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import org.dspace.importer.external.metadatamapping.contributor.MetadataContributor;
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import org.dspace.importer.external.service.components.AbstractPlainMetadataSource;
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import org.dspace.importer.external.service.components.MetadataSource;
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import org.dspace.importer.external.service.components.dto.PlainMetadataKeyValueItem;
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import org.dspace.importer.external.service.components.dto.PlainMetadataSourceDto;
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/**
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* This class is an implementation of {@link MetadataSource} which extends {@link AbstractPlainMetadataSource}
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* in order to parse "character separated" files like csv, tsv, etc using the Live Import framework.
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*
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* @author Pasquale Cavallo
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*
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*/
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public class CharacterSeparatedImportMetadataSourceServiceImpl extends AbstractPlainMetadataSource {
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private char separator = ',';
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private char escapeCharacter = '"';
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private Integer skipLines = 1;
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private String importSource = "CsvMetadataSource";
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/**
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* Set the number of lines to skip at the start of the file. This method is suitable,
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* for example, to skip file headers.
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*
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* @param skipLines number of the line at the start of the file to skip.
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*/
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public void setSkipLines(Integer skipLines) {
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this.skipLines = skipLines;
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}
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/**
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*
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* @return the number of the lines to skip
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*/
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public Integer getSkipLines() {
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return skipLines;
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}
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/**
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* Method to inject the separator
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* This must be the ASCII integer
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* related to the char.
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* In example, 9 for tab, 44 for comma
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*/
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public void setSeparator(char separator) {
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this.separator = separator;
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}
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@Override
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public String getImportSource() {
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return importSource;
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}
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/**
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* Method to set the name of the source
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*/
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public void setImportSource(String importSource) {
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this.importSource = importSource;
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}
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/**
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* Method to inject the escape character. This must be the ASCII integer
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* related to the char.
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* In example, 9 for tab, 44 for comma
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*
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*/
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public void setEscapeCharacter(char escapeCharacter) {
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this.escapeCharacter = escapeCharacter;
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}
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/**
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* The method process any kind of "character separated" files, like CSV, TSV, and so on.
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* It return a List of PlainMetadataSourceDto.
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* Using the superclass methods AbstractPlainMetadataSource.getRecord(s), any of this
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* element will then be converted in an {@link org.dspace.importer.external.datamodel.ImportRecord}.
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* Columns will be identified by their position, zero based notation.
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* Separator character and escape character MUST be defined at class level. Number of lines to skip (headers)
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* could also be defined in the field skipLines.
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*
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* @param InputStream The inputStream of the file
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* @return A list of PlainMetadataSourceDto
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* @throws FileSourceException if, for any reason, the file is not parsable
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*/
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@Override
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protected List<PlainMetadataSourceDto> readData(InputStream inputStream) throws FileSourceException {
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List<PlainMetadataSourceDto> plainMetadataList = new ArrayList<>();
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try (CSVReader csvReader = new CSVReader(new InputStreamReader(inputStream, StandardCharsets.UTF_8),
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separator, escapeCharacter);) {
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// read all row
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List<String[]> lines = csvReader.readAll();
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int listSize = lines == null ? 0 : lines.size();
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int count = skipLines;
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// iterate over row (skipping the first skipLines)
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while (count < listSize) {
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String [] items = lines.get(count);
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List<PlainMetadataKeyValueItem> keyValueList = new ArrayList<>();
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if (items != null) {
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int size = items.length;
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int index = 0;
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//iterate over column in the selected row
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while (index < size) {
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//create key/value item for the specifics row/column
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PlainMetadataKeyValueItem keyValueItem = new PlainMetadataKeyValueItem();
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keyValueItem.setKey(String.valueOf(index));
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keyValueItem.setValue(items[index]);
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keyValueList.add(keyValueItem);
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index++;
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}
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//save all column key/value for the given row
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PlainMetadataSourceDto dto = new PlainMetadataSourceDto();
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dto.setMetadata(keyValueList);
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plainMetadataList.add(dto);
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}
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count++;
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}
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} catch (IOException e) {
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throw new FileSourceException("Error reading file", e);
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}
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return plainMetadataList;
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}
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@Override
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public void setMetadataFieldMap(Map<MetadataFieldConfig,
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MetadataContributor<PlainMetadataSourceDto>> metadataFieldMap) {
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super.setMetadataFieldMap(metadataFieldMap);
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}
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}
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@@ -0,0 +1,140 @@
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/**
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* The contents of this file are subject to the license and copyright
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* detailed in the LICENSE and NOTICE files at the root of the source
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* tree and available online at
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*
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* http://www.dspace.org/license/
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*/
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package org.dspace.importer.external.endnote.service;
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import java.io.BufferedReader;
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import java.io.IOException;
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import java.io.InputStream;
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import java.io.InputStreamReader;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.Map;
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import java.util.regex.Matcher;
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import java.util.regex.Pattern;
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import org.dspace.importer.external.exception.FileSourceException;
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import org.dspace.importer.external.metadatamapping.MetadataFieldConfig;
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import org.dspace.importer.external.metadatamapping.contributor.MetadataContributor;
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import org.dspace.importer.external.service.components.AbstractPlainMetadataSource;
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import org.dspace.importer.external.service.components.dto.PlainMetadataKeyValueItem;
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import org.dspace.importer.external.service.components.dto.PlainMetadataSourceDto;
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/**
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* Implements a metadata importer for Endnote files
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*
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* @author Pasquale Cavallo (pasquale.cavallo at 4science dot it)
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*/
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public class EndnoteImportMetadataSourceServiceImpl extends AbstractPlainMetadataSource {
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@Override
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public String getImportSource() {
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return "EndnoteMetadataSource";
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}
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/**
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* This method map the data present in the inputStream, then return a list PlainMetadataSourceDto.
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* Any PlainMetadataSourceDto will be used to create a single {@link org.dspace.importer.external.datamodel.ImportRecord}
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*
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* @param inputStream the inputStream of the Endnote file
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* @return List of {@link org.dspace.importer.external.service.components.dto.PlainMetadataSourceDto}
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* @throws FileSourceException
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* @see org.dspace.importer.external.service.components.AbstractPlainMetadataSource
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*/
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@Override
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protected List<PlainMetadataSourceDto> readData(InputStream fileInpuStream) throws FileSourceException {
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List<PlainMetadataSourceDto> list = new ArrayList<>();
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try {
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// row start from 3, because the first 2 (FN and VR) will be removed by tokenize
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int lineForDebug = 3;
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List<PlainMetadataKeyValueItem> tokenized = tokenize(fileInpuStream);
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List<PlainMetadataKeyValueItem> tmpList = new ArrayList<>();
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// iterate over key/value pairs, create a new PlainMetadataSourceDto on "ER" rows (which means "new record)
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// and stop on EF (end of file).
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for (PlainMetadataKeyValueItem item : tokenized) {
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if (item.getKey() == null || item.getKey().isEmpty()) {
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throw new FileSourceException("Null or empty key expected on line "
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+ lineForDebug + ". Keys cannot be null nor empty");
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}
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if ("EF".equals(item.getKey())) {
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// end of file
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break;
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}
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if ("ER".equals(item.getKey())) {
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// new ImportRecord start from here (ER is a content delimiter)
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// save the previous, then create a new one
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PlainMetadataSourceDto dto = new PlainMetadataSourceDto();
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dto.setMetadata(new ArrayList<>(tmpList));
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list.add(dto);
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tmpList = new ArrayList<>();
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} else {
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if (item.getValue() == null || item.getValue().isEmpty()) {
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throw new FileSourceException("Null or empty value expected on line "
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+ lineForDebug + ". Value expected");
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}
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tmpList.add(item);
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}
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lineForDebug++;
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}
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} catch (Exception e) {
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throw new FileSourceException("Error reading file", e);
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}
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return list;
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}
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/**
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* This method iterate over file rows, split content in a list of key/value items through RexExp
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* and save the content sequentially.
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* Key "FN" and "VR", which is a preamble in Endnote, will be checked but not saved.
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*
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* @param fileInpuStream the inputStream of the Endnote file
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* @return A list of key/value items which map the file's row sequentially
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* @throws IOException
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* @throws FileSourceException
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*/
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private List<PlainMetadataKeyValueItem> tokenize(InputStream fileInpuStream)
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throws IOException, FileSourceException {
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BufferedReader reader = new BufferedReader(new InputStreamReader(fileInpuStream));
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String line;
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line = reader.readLine();
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// FN and VR works as preamble, just check and skip them
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if (line == null || !line.startsWith("FN")) {
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throw new FileSourceException("Invalid endNote file");
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}
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line = reader.readLine();
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if (line == null || !line.startsWith("VR")) {
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throw new FileSourceException("Invalid endNote file");
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}
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// split any row into first part ^[A-Z]{2} used as key (the meaning of the data)
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// and second part ?(.*) used as value (the data)
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Pattern pattern = Pattern.compile("(^[A-Z]{2}) ?(.*)$");
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List<PlainMetadataKeyValueItem> list = new ArrayList<PlainMetadataKeyValueItem>();
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while ((line = reader.readLine()) != null) {
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line = line.trim();
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// skip empty lines
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if (line.isEmpty() || line.equals("")) {
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continue;
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}
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Matcher matcher = pattern.matcher(line);
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if (matcher.matches()) {
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PlainMetadataKeyValueItem item = new PlainMetadataKeyValueItem();
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item.setKey(matcher.group(1));
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item.setValue(matcher.group(2));
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list.add(item);
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}
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}
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return list;
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}
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@Override
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public void setMetadataFieldMap(Map<MetadataFieldConfig,
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MetadataContributor<PlainMetadataSourceDto>> metadataFieldMap) {
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super.setMetadataFieldMap(metadataFieldMap);
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}
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}
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@@ -0,0 +1,108 @@
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/**
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* The contents of this file are subject to the license and copyright
|
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* detailed in the LICENSE and NOTICE files at the root of the source
|
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* tree and available online at
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*
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* http://www.dspace.org/license/
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*/
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package org.dspace.importer.external.metadatamapping.contributor;
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import java.io.IOException;
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import java.io.StringReader;
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import java.util.Collection;
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import java.util.LinkedList;
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import java.util.List;
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import au.com.bytecode.opencsv.CSVReader;
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import org.dspace.importer.external.metadatamapping.MetadatumDTO;
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import org.dspace.importer.external.service.components.dto.PlainMetadataKeyValueItem;
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import org.dspace.importer.external.service.components.dto.PlainMetadataSourceDto;
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/**
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* This class implements functionalities to handle common situation regarding plain metadata.
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* In some scenario, like csv or tsv, the format don't allow lists.
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* We can use this MetadataContribut to parse a given plain metadata and split it into
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* related list, based on the delimiter. No escape character is present.
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* Default values are comma (,) for delimiter, and double quote (") for escape character
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*
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* @author Pasquale Cavallo (pasquale.cavallo at 4science dot it)
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*
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*/
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public class EnhancedSimpleMetadataContributor extends SimpleMetadataContributor {
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private char delimiter = ',';
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private char escape = '"';
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/**
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* This method could be used to set the delimiter used during parse
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* If no delimiter is set, comma will be used
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*/
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public void setDelimiter(char delimiter) {
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this.delimiter = delimiter;
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}
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/**
|
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* This method could be used to get the delimiter used in this class
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*/
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||||
public char getDelimiter() {
|
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return delimiter;
|
||||
}
|
||||
|
||||
/**
|
||||
* Method to inject the escape character.
|
||||
* This must be the ASCII integer
|
||||
* related to the char.
|
||||
* In example, 9 for tab, 44 for comma
|
||||
* If no escape is set, double quote will be used
|
||||
*/
|
||||
public void setEscape(char escape) {
|
||||
this.escape = escape;
|
||||
}
|
||||
|
||||
/**
|
||||
* Method to get the escape character.
|
||||
*
|
||||
*/
|
||||
public char getEscape() {
|
||||
return escape;
|
||||
}
|
||||
|
||||
@Override
|
||||
public Collection<MetadatumDTO> contributeMetadata(PlainMetadataSourceDto t) {
|
||||
Collection<MetadatumDTO> values = null;
|
||||
values = new LinkedList<>();
|
||||
for (PlainMetadataKeyValueItem metadatum : t.getMetadata()) {
|
||||
if (getKey().equals(metadatum.getKey())) {
|
||||
String[] splitted = splitToRecord(metadatum.getValue());
|
||||
for (String value : splitted) {
|
||||
MetadatumDTO dcValue = new MetadatumDTO();
|
||||
dcValue.setValue(value);
|
||||
dcValue.setElement(getField().getElement());
|
||||
dcValue.setQualifier(getField().getQualifier());
|
||||
dcValue.setSchema(getField().getSchema());
|
||||
values.add(dcValue);
|
||||
}
|
||||
}
|
||||
}
|
||||
return values;
|
||||
}
|
||||
|
||||
private String[] splitToRecord(String value) {
|
||||
List<String[]> rows;
|
||||
// For example, list of author must be: Author 1, author 2, author 3
|
||||
// if author name contains comma, is important to escape its in
|
||||
// this way: Author 1, \"Author 2, something\", Author 3
|
||||
try (CSVReader csvReader = new CSVReader(new StringReader(value),
|
||||
delimiter, escape);) {
|
||||
rows = csvReader.readAll();
|
||||
} catch (IOException e) {
|
||||
//fallback, use the inpu as value
|
||||
return new String[] { value };
|
||||
}
|
||||
//must be one row
|
||||
return rows.get(0);
|
||||
}
|
||||
|
||||
}
|
||||
@@ -0,0 +1,139 @@
|
||||
/**
|
||||
* 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.ArrayList;
|
||||
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;
|
||||
|
||||
/**
|
||||
* This Contributor is helpful to avoid the limit of the Live Import Framework.
|
||||
* In Live Import, one dc schema/element/qualifier could be associate with one and
|
||||
* only one MetadataContributor, because the map they're saved in use dc entity as key.
|
||||
*
|
||||
* In fact, in this implementation we use the MetadataFieldConfig present in this MultipleMetadataContributor
|
||||
* contributor, but the data (values of the dc metadatum) will be loaded using any of the contributor defined
|
||||
* in the List metadatumContributors, by iterating over them.
|
||||
*
|
||||
* @see org.dspace.importer.external.metadatamapping.AbstractMetadataFieldMapping<RecordType>
|
||||
*
|
||||
* @author Pasquale Cavallo (pasquale.cavallo at 4science dot it)
|
||||
*
|
||||
*/
|
||||
public class MultipleMetadataContributor<T> implements MetadataContributor<T> {
|
||||
|
||||
private MetadataFieldConfig field;
|
||||
|
||||
private List<MetadataContributor> metadatumContributors;
|
||||
|
||||
/**
|
||||
* Empty constructor
|
||||
*/
|
||||
public MultipleMetadataContributor() {
|
||||
}
|
||||
|
||||
/**
|
||||
* @param field {@link org.dspace.importer.external.metadatamapping.MetadataFieldConfig} used in
|
||||
* mapping
|
||||
* @param metadatumContributors A list of MetadataContributor
|
||||
*/
|
||||
public MultipleMetadataContributor(MetadataFieldConfig field, List<MetadataContributor> metadatumContributors) {
|
||||
this.field = field;
|
||||
this.metadatumContributors = (LinkedList<MetadataContributor>) metadatumContributors;
|
||||
}
|
||||
|
||||
/**
|
||||
* Set the metadatafieldMapping used in the transforming of a record to actual metadata
|
||||
*
|
||||
* @param metadataFieldMapping the new mapping.
|
||||
*/
|
||||
@Override
|
||||
public void setMetadataFieldMapping(MetadataFieldMapping<T, MetadataContributor<T>> metadataFieldMapping) {
|
||||
for (MetadataContributor metadatumContributor : metadatumContributors) {
|
||||
metadatumContributor.setMetadataFieldMapping(metadataFieldMapping);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* a separate Metadatum object is created for each index of Metadatum returned from the calls to
|
||||
* MetadatumContributor.contributeMetadata(t) for each MetadatumContributor in the metadatumContributors list.
|
||||
* All of them have as dc schema/element/qualifier the values defined in MetadataFieldConfig.
|
||||
*
|
||||
* @param t the object we are trying to translate
|
||||
* @return a collection of metadata got from each MetadataContributor
|
||||
*/
|
||||
@Override
|
||||
public Collection<MetadatumDTO> contributeMetadata(T t) {
|
||||
Collection<MetadatumDTO> values = new ArrayList<>();
|
||||
for (MetadataContributor metadatumContributor : metadatumContributors) {
|
||||
Collection<MetadatumDTO> metadata = metadatumContributor.contributeMetadata(t);
|
||||
values.addAll(metadata);
|
||||
}
|
||||
changeDC(values);
|
||||
return values;
|
||||
}
|
||||
|
||||
/**
|
||||
* This method does the trick of this implementation.
|
||||
* It changes the DC schema/element/qualifier of the given Metadatum into
|
||||
* the ones present in this contributor.
|
||||
* In this way, the contributors in metadatumContributors could have any dc values,
|
||||
* because this method remap them all.
|
||||
*
|
||||
* @param the list of metadata we want to remap
|
||||
*/
|
||||
private void changeDC(Collection<MetadatumDTO> values) {
|
||||
for (MetadatumDTO dto : values) {
|
||||
dto.setElement(field.getElement());
|
||||
dto.setQualifier(field.getQualifier());
|
||||
dto.setSchema(field.getSchema());
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Return the MetadataFieldConfig used while retrieving MetadatumDTO
|
||||
*
|
||||
* @return MetadataFieldConfig
|
||||
*/
|
||||
public MetadataFieldConfig getField() {
|
||||
return field;
|
||||
}
|
||||
|
||||
/**
|
||||
* Setting the MetadataFieldConfig
|
||||
*
|
||||
* @param field MetadataFieldConfig used while retrieving MetadatumDTO
|
||||
*/
|
||||
public void setField(MetadataFieldConfig field) {
|
||||
this.field = field;
|
||||
}
|
||||
|
||||
/**
|
||||
* Return the List of MetadataContributor objects set to this class
|
||||
*
|
||||
* @return metadatumContributors, list of MetadataContributor
|
||||
*/
|
||||
public List<MetadataContributor> getMetadatumContributors() {
|
||||
return metadatumContributors;
|
||||
}
|
||||
|
||||
/**
|
||||
* Set the List of MetadataContributor objects set to this class
|
||||
*
|
||||
* @param metadatumContributors A list of MetadatumContributor classes
|
||||
*/
|
||||
public void setMetadatumContributors(List<MetadataContributor> metadatumContributors) {
|
||||
this.metadatumContributors = metadatumContributors;
|
||||
}
|
||||
}
|
||||
@@ -77,18 +77,33 @@ public class SimpleMetadataContributor implements MetadataContributor<PlainMetad
|
||||
return values;
|
||||
}
|
||||
|
||||
/*
|
||||
* Setter to inject field item
|
||||
/**
|
||||
* Method to inject field item
|
||||
*
|
||||
* @param field the {@link MetadataFieldConfig} to use in this contributor
|
||||
*/
|
||||
public void setField(MetadataFieldConfig field) {
|
||||
this.field = field;
|
||||
}
|
||||
|
||||
/*
|
||||
* Setter to inject key value
|
||||
/**
|
||||
* Method to inject key value
|
||||
*/
|
||||
public void setKey(String key) {
|
||||
this.key = key;
|
||||
}
|
||||
|
||||
/**
|
||||
* Method to retrieve field item
|
||||
*/
|
||||
public String getKey() {
|
||||
return key;
|
||||
}
|
||||
|
||||
/**
|
||||
* Method to retrieve the {@link MetadataFieldConfig} used in this contributor
|
||||
*/
|
||||
public MetadataFieldConfig getField() {
|
||||
return field;
|
||||
}
|
||||
}
|
||||
|
||||
@@ -44,6 +44,7 @@ import org.jaxen.JaxenException;
|
||||
* Implements a data source for querying PubMed Central
|
||||
*
|
||||
* @author Roeland Dillen (roeland at atmire dot com)
|
||||
* @author Pasquale Cavallo (pasquale.cavallo at 4science dot it)
|
||||
*/
|
||||
public class PubmedImportMetadataSourceServiceImpl extends AbstractImportMetadataSourceService<OMElement>
|
||||
implements QuerySource, FileSource {
|
||||
|
||||
@@ -0,0 +1,141 @@
|
||||
/**
|
||||
* 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.ris.service;
|
||||
|
||||
import java.io.BufferedReader;
|
||||
import java.io.InputStream;
|
||||
import java.io.InputStreamReader;
|
||||
import java.util.ArrayList;
|
||||
import java.util.Iterator;
|
||||
import java.util.LinkedList;
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
import java.util.regex.Matcher;
|
||||
import java.util.regex.Pattern;
|
||||
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;
|
||||
|
||||
/**
|
||||
* Implements a metadata importer for RIS files
|
||||
* Implementations insprider by BTE DataLoader {@link https://github.com/EKT/Biblio-Transformation-Engine/blob/master/bte-io/src/main/java/gr/ekt/bteio/loaders/RISDataLoader.java}
|
||||
*
|
||||
* @author Pasquale Cavallo (pasquale.cavallo at 4science dot it)
|
||||
*/
|
||||
public class RisImportMetadataSourceServiceImpl extends AbstractPlainMetadataSource {
|
||||
|
||||
@Override
|
||||
public String getImportSource() {
|
||||
return "RISMetadataSource";
|
||||
}
|
||||
|
||||
@Override
|
||||
protected List<PlainMetadataSourceDto> readData(InputStream inputStream) throws FileSourceException {
|
||||
return aggregateData(inputStream);
|
||||
}
|
||||
|
||||
/**
|
||||
* This method map the data present in the inputStream, then return a list PlainMetadataSourceDto.
|
||||
* Any PlainMetadataSourceDto will be used to create a single {@link org.dspace.importer.external.datamodel.ImportRecord}
|
||||
*
|
||||
* @see org.dspace.importer.external.service.components.AbstractPlainMetadataSource
|
||||
*
|
||||
* @param inputStream the inputStream of the RIS file
|
||||
* @return List of {@link org.dspace.importer.external.service.components.dto.PlainMetadataSourceDto}
|
||||
* @throws FileSourceException
|
||||
*/
|
||||
private List<PlainMetadataSourceDto> aggregateData(InputStream inputStream) throws FileSourceException {
|
||||
List<PlainMetadataSourceDto> metadata = new ArrayList<>();
|
||||
//map any line of the field to a key/value pair
|
||||
List<PlainMetadataKeyValueItem> notAggregatedItems = notAggregatedData(inputStream);
|
||||
List<PlainMetadataKeyValueItem> aggregatedTmpList = null;
|
||||
Iterator<PlainMetadataKeyValueItem> itr = notAggregatedItems.iterator();
|
||||
// iterate over the list of key/value items
|
||||
// create a new PlainMetadataSourceDto (which map and ImportRecord)
|
||||
// any times the key is "TY" (content separator in RIS)
|
||||
while (itr.hasNext()) {
|
||||
PlainMetadataKeyValueItem item = itr.next();
|
||||
if ("TY".equals(item.getKey())) {
|
||||
if (aggregatedTmpList != null) {
|
||||
PlainMetadataSourceDto dto = new PlainMetadataSourceDto();
|
||||
dto.setMetadata(new ArrayList<>(aggregatedTmpList));
|
||||
metadata.add(dto);
|
||||
}
|
||||
aggregatedTmpList = new ArrayList<>();
|
||||
aggregatedTmpList.add(item);
|
||||
} else {
|
||||
if (aggregatedTmpList != null) {
|
||||
aggregatedTmpList.add(item);
|
||||
// save last iteration metadata
|
||||
if (!itr.hasNext()) {
|
||||
PlainMetadataSourceDto dto = new PlainMetadataSourceDto();
|
||||
dto.setMetadata(new ArrayList<>(aggregatedTmpList));
|
||||
metadata.add(dto);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
return metadata;
|
||||
}
|
||||
|
||||
/**
|
||||
* This method transform any row of the RIS file into a PlainMetadataKeyValueItem,
|
||||
* splitting the row sequentially through a RegExp without take care of the means of the data.
|
||||
* In this way, all entries present in the file are mapped in the resulting list.
|
||||
*
|
||||
* @param inputStream the inputStrem of the file
|
||||
* @return A list
|
||||
* @throws FileSourceException
|
||||
*/
|
||||
private List<PlainMetadataKeyValueItem> notAggregatedData(InputStream inputStream) throws FileSourceException {
|
||||
LinkedList<PlainMetadataKeyValueItem> items = new LinkedList<>();
|
||||
BufferedReader reader;
|
||||
try {
|
||||
reader = new BufferedReader(new InputStreamReader(inputStream, "UTF-8"));
|
||||
String line;
|
||||
while ((line = reader.readLine()) != null) {
|
||||
if (line.isEmpty() || line.equals("") || line.matches("^\\s*$")) {
|
||||
continue;
|
||||
}
|
||||
//match valid RIS entry
|
||||
Pattern risPattern = Pattern.compile("^([A-Z][A-Z0-9]) - (.*)$");
|
||||
Matcher risMatcher = risPattern.matcher(line);
|
||||
if (risMatcher.matches()) {
|
||||
PlainMetadataKeyValueItem keyValueItem = new PlainMetadataKeyValueItem();
|
||||
keyValueItem.setValue(risMatcher.group(2));
|
||||
keyValueItem.setKey(risMatcher.group(1));
|
||||
items.add(keyValueItem);
|
||||
} else {
|
||||
if (!items.isEmpty()) {
|
||||
items.getLast().setValue(items.getLast().getValue().concat(line));
|
||||
}
|
||||
}
|
||||
}
|
||||
} catch (Exception e) {
|
||||
throw new FileSourceException("Cannot parse RIS file", e);
|
||||
}
|
||||
return items;
|
||||
}
|
||||
|
||||
/**
|
||||
* Retrieve the MetadataFieldMapping containing the mapping between RecordType
|
||||
* (in this case PlainMetadataSourceDto.class) and Metadata
|
||||
*
|
||||
* @return The configured MetadataFieldMapping
|
||||
*/
|
||||
@Override
|
||||
@SuppressWarnings("unchecked")
|
||||
@Resource(name = "risMetadataFieldMap")
|
||||
public void setMetadataFieldMap(@SuppressWarnings("rawtypes") Map metadataFieldMap) {
|
||||
super.setMetadataFieldMap(metadataFieldMap);
|
||||
}
|
||||
|
||||
}
|
||||
@@ -22,6 +22,11 @@ import org.dspace.importer.external.exception.FileSourceException;
|
||||
*/
|
||||
public interface FileSource extends MetadataSource {
|
||||
|
||||
/**
|
||||
* Get the file extensions (xml, csv, txt, ...) supported by the FileSource
|
||||
*/
|
||||
public List<String> getSupportedExtensions();
|
||||
|
||||
/**
|
||||
* Return a list of ImportRecord constructed from input file.
|
||||
*
|
||||
@@ -62,9 +67,4 @@ public interface FileSource extends MetadataSource {
|
||||
return false;
|
||||
}
|
||||
|
||||
/**
|
||||
* Get the file extensions (xml, csv, txt, ...) supported by the FileSource implementation
|
||||
*/
|
||||
public List<String> getSupportedExtensions();
|
||||
|
||||
}
|
||||
|
||||
@@ -26,13 +26,15 @@
|
||||
Will result in using the PubmedImportService for the lookup step
|
||||
Omitting this property will default to searching over all configured ImportService implementations
|
||||
-->
|
||||
|
||||
<bean id="importService" class="org.dspace.importer.external.service.ImportService" scope="singleton"
|
||||
lazy-init="false" autowire="byType" destroy-method="destroy">
|
||||
<bean id="importService" class="org.dspace.importer.external.service.ImportService" lazy-init="false" autowire="byType" destroy-method="destroy">
|
||||
<property name="importSources">
|
||||
<list>
|
||||
<ref bean="PubmedImportService"></ref>
|
||||
<ref bean="BibtexImportService"></ref>
|
||||
<ref bean="pubmedImportService" />
|
||||
<ref bean="bibtexImportService" />
|
||||
<ref bean="risImportService" />
|
||||
<ref bean="csvImportService" />
|
||||
<ref bean="tsvImportService" />
|
||||
<ref bean="endnoteImportService" />
|
||||
</list>
|
||||
</property>
|
||||
</bean>
|
||||
@@ -47,9 +49,9 @@
|
||||
</bean>
|
||||
|
||||
|
||||
<bean id="PubmedImportService"
|
||||
class="org.dspace.importer.external.pubmed.service.PubmedImportMetadataSourceServiceImpl" scope="singleton">
|
||||
<property name="metadataFieldMapping" ref="PubmedMetadataFieldMapping"/>
|
||||
<bean id="pubmedImportService"
|
||||
class="org.dspace.importer.external.pubmed.service.PubmedImportMetadataSourceServiceImpl">
|
||||
<property name="metadataFieldMapping" ref="pubmedMetadataFieldMapping"/>
|
||||
<property name="baseAddress" value="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/"/>
|
||||
<property name="generateQueryForItem" ref="pubmedService"></property>
|
||||
<property name="supportedExtensions">
|
||||
@@ -60,12 +62,21 @@
|
||||
</bean>
|
||||
|
||||
|
||||
<bean id="PubmedMetadataFieldMapping"
|
||||
<bean id="pubmedMetadataFieldMapping"
|
||||
class="org.dspace.importer.external.pubmed.metadatamapping.PubmedFieldMapping">
|
||||
</bean>
|
||||
|
||||
<bean id="BibtexImportService"
|
||||
class="org.dspace.importer.external.bibtex.service.BibtexImportMetadataSourceServiceImpl" scope="singleton">
|
||||
<bean id="risImportService"
|
||||
class="org.dspace.importer.external.ris.service.RisImportMetadataSourceServiceImpl">
|
||||
<property name="supportedExtensions">
|
||||
<list>
|
||||
<value>ris</value>
|
||||
</list>
|
||||
</property>
|
||||
</bean>
|
||||
|
||||
<bean id="bibtexImportService"
|
||||
class="org.dspace.importer.external.bibtex.service.BibtexImportMetadataSourceServiceImpl">
|
||||
<property name="supportedExtensions">
|
||||
<list>
|
||||
<value>bib</value>
|
||||
@@ -74,6 +85,42 @@
|
||||
</property>
|
||||
</bean>
|
||||
|
||||
<bean id="csvImportService"
|
||||
class="org.dspace.importer.external.csv.service.CharacterSeparatedImportMetadataSourceServiceImpl">
|
||||
<property name="metadataFieldMap" ref="csvMetadataFieldMap"></property>
|
||||
<property name="skipLines" value="1" />
|
||||
<property name="supportedExtensions">
|
||||
<list>
|
||||
<value>csv</value>
|
||||
</list>
|
||||
</property>
|
||||
</bean>
|
||||
|
||||
<bean id="tsvImportService"
|
||||
class="org.dspace.importer.external.csv.service.CharacterSeparatedImportMetadataSourceServiceImpl">
|
||||
<property name="importSource" value="TsvMetadataSource" />
|
||||
<property name="separator" value="\u0009" />
|
||||
<property name="skipLines" value="1" />
|
||||
<property name="metadataFieldMap" ref="tsvMetadataFieldMap" />
|
||||
<property name="supportedExtensions">
|
||||
<list>
|
||||
<value>tsv</value>
|
||||
</list>
|
||||
</property>
|
||||
</bean>
|
||||
|
||||
<bean id="endnoteImportService"
|
||||
class="org.dspace.importer.external.endnote.service.EndnoteImportMetadataSourceServiceImpl">
|
||||
<property name="metadataFieldMap" ref="endnoteMetadataFieldMap"></property>
|
||||
<property name="supportedExtensions">
|
||||
<list>
|
||||
<value>enl</value>
|
||||
<value>enw</value>
|
||||
</list>
|
||||
</property>
|
||||
</bean>
|
||||
|
||||
|
||||
<!-- Metadatafield used to check against if it's already imported or not during the JSONLookupSearcher-->
|
||||
<bean id="lookupID" class="org.dspace.importer.external.metadatamapping.MetadataFieldConfig">
|
||||
<constructor-arg value="dc.identifier.other"/>
|
||||
|
||||
@@ -385,6 +385,9 @@ public class WorkspaceItemRestRepository extends DSpaceRestRepository<WorkspaceI
|
||||
records.add(record);
|
||||
break;
|
||||
}
|
||||
} catch (Exception e) {
|
||||
log.error("Error processing data", e);
|
||||
throw e;
|
||||
} finally {
|
||||
file.delete();
|
||||
}
|
||||
|
||||
@@ -872,7 +872,7 @@ public class WorkspaceItemRestRepositoryIT extends AbstractControllerIntegration
|
||||
*
|
||||
* @throws Exception
|
||||
*/
|
||||
public void createSingleWorkspaceItemFromFileWithOneEntryTest() throws Exception {
|
||||
public void createSingleWorkspaceItemFromBibtexFileWithOneEntryTest() throws Exception {
|
||||
context.turnOffAuthorisationSystem();
|
||||
|
||||
//** GIVEN **
|
||||
@@ -898,7 +898,9 @@ public class WorkspaceItemRestRepositoryIT extends AbstractControllerIntegration
|
||||
|
||||
context.restoreAuthSystemState();
|
||||
|
||||
AtomicReference<List<Integer>> idRef = new AtomicReference<>();
|
||||
String authToken = getAuthToken(eperson.getEmail(), password);
|
||||
try {
|
||||
// create a workspaceitem from a single bibliographic entry file explicitly in the default collection (col1)
|
||||
getClient(authToken).perform(fileUpload("/api/submission/workspaceitems")
|
||||
.file(bibtexFile))
|
||||
@@ -915,10 +917,19 @@ public class WorkspaceItemRestRepositoryIT extends AbstractControllerIntegration
|
||||
+ ".metadata['dc.title'][0].value",
|
||||
is("bibtex-test.bib")))
|
||||
.andExpect(
|
||||
jsonPath("$._embedded.workspaceitems[*]._embedded.upload").doesNotExist());
|
||||
;
|
||||
jsonPath("$._embedded.workspaceitems[*]._embedded.upload").doesNotExist())
|
||||
.andDo(result -> idRef.set(read(result.getResponse().getContentAsString(),
|
||||
"$._embedded.workspaceitems[*].id")));
|
||||
} finally {
|
||||
if (idRef != null && idRef.get() != null) {
|
||||
for (int i : idRef.get()) {
|
||||
WorkspaceItemBuilder.deleteWorkspaceItem(i);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// create a workspaceitem from a single bibliographic entry file explicitly in the col2
|
||||
try {
|
||||
getClient(authToken).perform(fileUpload("/api/submission/workspaceitems")
|
||||
.file(bibtexFile)
|
||||
.param("owningCollection", col2.getID().toString()))
|
||||
@@ -934,12 +945,522 @@ public class WorkspaceItemRestRepositoryIT extends AbstractControllerIntegration
|
||||
+ ".files[0].metadata['dc.title'][0].value",
|
||||
is("bibtex-test.bib")))
|
||||
.andExpect(
|
||||
jsonPath("$._embedded.workspaceitems[*]._embedded.upload").doesNotExist());
|
||||
|
||||
jsonPath("$._embedded.workspaceitems[*]._embedded.upload").doesNotExist())
|
||||
.andDo(result -> idRef.set(read(result.getResponse().getContentAsString(),
|
||||
"$._embedded.workspaceitems[*].id")));
|
||||
} finally {
|
||||
if (idRef != null && idRef.get() != null) {
|
||||
for (int i : idRef.get()) {
|
||||
WorkspaceItemBuilder.deleteWorkspaceItem(i);
|
||||
}
|
||||
}
|
||||
}
|
||||
bibtex.close();
|
||||
}
|
||||
|
||||
@Test
|
||||
/**
|
||||
* Test the creation of workspaceitems POSTing to the resource collection endpoint a csv file
|
||||
*
|
||||
* @throws Exception
|
||||
*/
|
||||
public void createSingleWorkspaceItemFromCSVWithOneEntryTest() throws Exception {
|
||||
context.turnOffAuthorisationSystem();
|
||||
|
||||
//** GIVEN **
|
||||
//1. A community-collection structure with one parent community with sub-community and two collections.
|
||||
parentCommunity = CommunityBuilder.createCommunity(context)
|
||||
.withName("Parent Community")
|
||||
.build();
|
||||
Community child1 = CommunityBuilder.createSubCommunity(context, parentCommunity)
|
||||
.withName("Sub Community")
|
||||
.build();
|
||||
Collection col1 = CollectionBuilder.createCollection(context, child1)
|
||||
.withName("Collection 1")
|
||||
.withSubmitterGroup(eperson)
|
||||
.build();
|
||||
Collection col2 = CollectionBuilder.createCollection(context, child1)
|
||||
.withName("Collection 2")
|
||||
.withSubmitterGroup(eperson)
|
||||
.build();
|
||||
|
||||
InputStream csv = getClass().getResourceAsStream("csv-test.csv");
|
||||
final MockMultipartFile csvFile = new MockMultipartFile("file", "/local/path/csv-test.csv",
|
||||
"text/csv", csv);
|
||||
|
||||
context.restoreAuthSystemState();
|
||||
|
||||
String authToken = getAuthToken(eperson.getEmail(), password);
|
||||
// create workspaceitems in the default collection (col1)
|
||||
AtomicReference<List<Integer>> idRef = new AtomicReference<>();
|
||||
try {
|
||||
getClient(authToken).perform(fileUpload("/api/submission/workspaceitems")
|
||||
.file(csvFile))
|
||||
// create should return 200, 201 (created) is better for single resource
|
||||
.andExpect(status().isOk())
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.traditionalpageone['dc.title'][0].value",
|
||||
is("My Article")))
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.traditionalpageone"
|
||||
+ "['dc.contributor.author'][0].value",
|
||||
is("Nobody")))
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.traditionalpageone"
|
||||
+ "['dc.date.issued'][0].value",
|
||||
is("2006")))
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.traditionalpageone"
|
||||
+ "['dc.identifier.issn'][0].value",
|
||||
is("Mock ISSN")))
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.traditionalpageone['dc.type'][0].value",
|
||||
is("Mock subtype")))
|
||||
.andExpect(
|
||||
jsonPath("$._embedded.workspaceitems[0]._embedded.collection.id", is(col1.getID().toString())))
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.upload.files[0]"
|
||||
+ ".metadata['dc.source'][0].value",
|
||||
is("/local/path/csv-test.csv")))
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.upload.files[0]"
|
||||
+ ".metadata['dc.title'][0].value",
|
||||
is("csv-test.csv")))
|
||||
.andExpect(
|
||||
jsonPath("$._embedded.workspaceitems[*]._embedded.upload").doesNotExist())
|
||||
.andDo(result -> idRef.set(read(result.getResponse().getContentAsString(),
|
||||
"$._embedded.workspaceitems[*].id")));
|
||||
} finally {
|
||||
if (idRef != null && idRef.get() != null) {
|
||||
for (int i : idRef.get()) {
|
||||
WorkspaceItemBuilder.deleteWorkspaceItem(i);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// create workspaceitems explicitly in the col2
|
||||
try {
|
||||
getClient(authToken).perform(fileUpload("/api/submission/workspaceitems")
|
||||
.file(csvFile)
|
||||
.param("owningCollection", col2.getID().toString()))
|
||||
.andExpect(status().isOk())
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.traditionalpageone"
|
||||
+ "['dc.title'][0].value",
|
||||
is("My Article")))
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.traditionalpageone"
|
||||
+ "['dc.contributor.author'][0].value",
|
||||
is("Nobody")))
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.traditionalpageone"
|
||||
+ "['dc.date.issued'][0].value",
|
||||
is("2006")))
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.traditionalpageone"
|
||||
+ "['dc.identifier.issn'][0].value",
|
||||
is("Mock ISSN")))
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.traditionalpageone['dc.type'][0].value",
|
||||
is("Mock subtype")))
|
||||
.andExpect(
|
||||
jsonPath("$._embedded.workspaceitems[0]._embedded.collection.id", is(col2.getID().toString())))
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.upload.files[0]"
|
||||
+ ".metadata['dc.source'][0].value",
|
||||
is("/local/path/csv-test.csv")))
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.upload"
|
||||
+ ".files[0].metadata['dc.title'][0].value",
|
||||
is("csv-test.csv")))
|
||||
.andExpect(
|
||||
jsonPath("$._embedded.workspaceitems[*]._embedded.upload").doesNotExist())
|
||||
.andDo(result -> idRef.set(read(result.getResponse().getContentAsString(),
|
||||
"$._embedded.workspaceitems[*].id")));
|
||||
} finally {
|
||||
if (idRef != null && idRef.get() != null) {
|
||||
for (int i : idRef.get()) {
|
||||
WorkspaceItemBuilder.deleteWorkspaceItem(i);
|
||||
}
|
||||
}
|
||||
}
|
||||
csv.close();
|
||||
}
|
||||
|
||||
@Test
|
||||
/**
|
||||
* Test the creation of workspaceitems POSTing to the resource collection endpoint a csv file
|
||||
* with some missing data
|
||||
*
|
||||
* @throws Exception
|
||||
*/
|
||||
public void createSingleWorkspaceItemFromCSVWithOneEntryAndMissingDataTest() throws Exception {
|
||||
context.turnOffAuthorisationSystem();
|
||||
|
||||
//** GIVEN **
|
||||
//1. A community-collection structure with one parent community with sub-community and two collections.
|
||||
parentCommunity = CommunityBuilder.createCommunity(context)
|
||||
.withName("Parent Community")
|
||||
.build();
|
||||
Community child1 = CommunityBuilder.createSubCommunity(context, parentCommunity)
|
||||
.withName("Sub Community")
|
||||
.build();
|
||||
Collection col1 = CollectionBuilder.createCollection(context, child1)
|
||||
.withName("Collection 1")
|
||||
.withSubmitterGroup(eperson)
|
||||
.build();
|
||||
Collection col2 = CollectionBuilder.createCollection(context, child1)
|
||||
.withName("Collection 2")
|
||||
.withSubmitterGroup(eperson)
|
||||
.build();
|
||||
|
||||
InputStream csv = getClass().getResourceAsStream("csv-missing-field-test.csv");
|
||||
final MockMultipartFile csvFile = new MockMultipartFile("file", "/local/path/csv-missing-field-test.csv",
|
||||
"text/csv", csv);
|
||||
|
||||
context.restoreAuthSystemState();
|
||||
|
||||
String authToken = getAuthToken(eperson.getEmail(), password);
|
||||
AtomicReference<List<Integer>> idRef = new AtomicReference<>();
|
||||
// create workspaceitems in the default collection (col1)
|
||||
|
||||
try {
|
||||
getClient(authToken).perform(fileUpload("/api/submission/workspaceitems")
|
||||
.file(csvFile))
|
||||
// create should return 200, 201 (created) is better for single resource
|
||||
.andExpect(status().isOk())
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.traditionalpageone['dc.title'][0].value",
|
||||
is("My Article")))
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.traditionalpageone"
|
||||
+ "['dc.contributor.author'][0].value",
|
||||
is("Nobody")))
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.traditionalpageone"
|
||||
+ "['dc.contributor.author'][1].value",
|
||||
is("Try escape, in item")))
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.traditionalpageone"
|
||||
+ "['dc.date.issued'][0].value").isEmpty())
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.traditionalpageone"
|
||||
+ "['dc.identifier.issn'][0].value",
|
||||
is("Mock ISSN")))
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.traditionalpageone['dc.type'][0].value"
|
||||
).doesNotExist())
|
||||
.andExpect(
|
||||
jsonPath("$._embedded.workspaceitems[0]._embedded.collection.id", is(col1.getID().toString())))
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.upload.files[0]"
|
||||
+ ".metadata['dc.source'][0].value",
|
||||
is("/local/path/csv-missing-field-test.csv")))
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.upload.files[0]"
|
||||
+ ".metadata['dc.title'][0].value",
|
||||
is("csv-missing-field-test.csv")))
|
||||
.andExpect(
|
||||
jsonPath("$._embedded.workspaceitems[*]._embedded.upload").doesNotExist())
|
||||
.andDo(result -> idRef.set(read(result.getResponse().getContentAsString(),
|
||||
"$._embedded.workspaceitems[*].id")));
|
||||
} finally {
|
||||
if (idRef != null && idRef.get() != null) {
|
||||
for (int i : idRef.get()) {
|
||||
WorkspaceItemBuilder.deleteWorkspaceItem(i);
|
||||
}
|
||||
}
|
||||
}
|
||||
csv.close();
|
||||
}
|
||||
|
||||
@Test
|
||||
/**
|
||||
* Test the creation of workspaceitems POSTing to the resource collection endpoint a tsv file
|
||||
*
|
||||
* @throws Exception
|
||||
*/
|
||||
public void createSingleWorkspaceItemFromTSVWithOneEntryTest() throws Exception {
|
||||
context.turnOffAuthorisationSystem();
|
||||
|
||||
//** GIVEN **
|
||||
//1. A community-collection structure with one parent community with sub-community and two collections.
|
||||
parentCommunity = CommunityBuilder.createCommunity(context)
|
||||
.withName("Parent Community")
|
||||
.build();
|
||||
Community child1 = CommunityBuilder.createSubCommunity(context, parentCommunity)
|
||||
.withName("Sub Community")
|
||||
.build();
|
||||
Collection col1 = CollectionBuilder.createCollection(context, child1)
|
||||
.withName("Collection 1")
|
||||
.withSubmitterGroup(eperson)
|
||||
.build();
|
||||
Collection col2 = CollectionBuilder.createCollection(context, child1)
|
||||
.withName("Collection 2")
|
||||
.withSubmitterGroup(eperson)
|
||||
.build();
|
||||
|
||||
InputStream tsv = getClass().getResourceAsStream("tsv-test.tsv");
|
||||
final MockMultipartFile tsvFile = new MockMultipartFile("file", "/local/path/tsv-test.tsv",
|
||||
"text/tsv", tsv);
|
||||
|
||||
context.restoreAuthSystemState();
|
||||
|
||||
String authToken = getAuthToken(eperson.getEmail(), password);
|
||||
AtomicReference<List<Integer>> idRef = new AtomicReference<>();
|
||||
|
||||
// create workspaceitems in the default collection (col1)
|
||||
try {
|
||||
getClient(authToken).perform(fileUpload("/api/submission/workspaceitems")
|
||||
.file(tsvFile))
|
||||
// create should return 200, 201 (created) is better for single resource
|
||||
.andExpect(status().isOk())
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.traditionalpageone['dc.title'][0].value",
|
||||
is("My Article")))
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.traditionalpageone"
|
||||
+ "['dc.contributor.author'][0].value",
|
||||
is("Nobody")))
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.traditionalpageone"
|
||||
+ "['dc.date.issued'][0].value",
|
||||
is("2006")))
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.traditionalpageone"
|
||||
+ "['dc.identifier.issn'][0].value",
|
||||
is("Mock ISSN")))
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.traditionalpageone['dc.type'][0].value",
|
||||
is("Mock subtype")))
|
||||
.andExpect(
|
||||
jsonPath("$._embedded.workspaceitems[0]._embedded.collection.id", is(col1.getID().toString())))
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.upload.files[0]"
|
||||
+ ".metadata['dc.source'][0].value",
|
||||
is("/local/path/tsv-test.tsv")))
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.upload.files[0]"
|
||||
+ ".metadata['dc.title'][0].value",
|
||||
is("tsv-test.tsv")))
|
||||
.andExpect(
|
||||
jsonPath("$._embedded.workspaceitems[*]._embedded.upload").doesNotExist())
|
||||
.andDo(result -> idRef.set(read(result.getResponse().getContentAsString(),
|
||||
"$._embedded.workspaceitems[*].id")));
|
||||
} finally {
|
||||
if (idRef != null && idRef.get() != null) {
|
||||
for (int i : idRef.get()) {
|
||||
WorkspaceItemBuilder.deleteWorkspaceItem(i);
|
||||
}
|
||||
}
|
||||
}
|
||||
tsv.close();
|
||||
}
|
||||
|
||||
@Test
|
||||
/**
|
||||
* Test the creation of workspaceitems POSTing to the resource collection endpoint a ris file
|
||||
*
|
||||
* @throws Exception
|
||||
*/
|
||||
public void createSingleWorkspaceItemFromRISWithOneEntryTest() throws Exception {
|
||||
context.turnOffAuthorisationSystem();
|
||||
|
||||
//** GIVEN **
|
||||
//1. A community-collection structure with one parent community with sub-community and two collections.
|
||||
parentCommunity = CommunityBuilder.createCommunity(context)
|
||||
.withName("Parent Community")
|
||||
.build();
|
||||
Community child1 = CommunityBuilder.createSubCommunity(context, parentCommunity)
|
||||
.withName("Sub Community")
|
||||
.build();
|
||||
Collection col1 = CollectionBuilder.createCollection(context, child1)
|
||||
.withName("Collection 1")
|
||||
.withSubmitterGroup(eperson)
|
||||
.build();
|
||||
Collection col2 = CollectionBuilder.createCollection(context, child1)
|
||||
.withName("Collection 2")
|
||||
.withSubmitterGroup(eperson)
|
||||
.build();
|
||||
|
||||
InputStream ris = getClass().getResourceAsStream("ris-test.ris");
|
||||
final MockMultipartFile tsvFile = new MockMultipartFile("file", "/local/path/ris-test.ris",
|
||||
"text/ris", ris);
|
||||
|
||||
context.restoreAuthSystemState();
|
||||
|
||||
String authToken = getAuthToken(eperson.getEmail(), password);
|
||||
AtomicReference<List<Integer>> idRef = new AtomicReference<>();
|
||||
|
||||
// create workspaceitems in the default collection (col1)
|
||||
try {
|
||||
getClient(authToken).perform(fileUpload("/api/submission/workspaceitems")
|
||||
.file(tsvFile))
|
||||
// create should return 200, 201 (created) is better for single resource
|
||||
.andExpect(status().isOk())
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.traditionalpageone['dc.title'][0].value",
|
||||
is("Challenge–Response Identification")))
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.traditionalpageone['dc.title'][1].value",
|
||||
is("Challenge–Response Identification second title")))
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.traditionalpageone"
|
||||
+ "['dc.contributor.author'][0].value",
|
||||
is("Just, Mike")))
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.traditionalpageone"
|
||||
+ "['dc.date.issued'][0].value",
|
||||
is("2005")))
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.traditionalpageone"
|
||||
+ "['dc.identifier.issn'][0].value",
|
||||
is("978-0-387-23483-0")))
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.traditionalpageone['dc.type'][0].value",
|
||||
is("Mock subtype")))
|
||||
.andExpect(
|
||||
jsonPath("$._embedded.workspaceitems[0]._embedded.collection.id", is(col1.getID().toString())))
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.upload.files[0]"
|
||||
+ ".metadata['dc.source'][0].value",
|
||||
is("/local/path/ris-test.ris")))
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.upload.files[0]"
|
||||
+ ".metadata['dc.title'][0].value",
|
||||
is("ris-test.ris")))
|
||||
.andExpect(
|
||||
jsonPath("$._embedded.workspaceitems[*]._embedded.upload").doesNotExist())
|
||||
.andDo(result -> idRef.set(read(result.getResponse().getContentAsString(),
|
||||
"$._embedded.workspaceitems[*].id")));
|
||||
} finally {
|
||||
if (idRef != null && idRef.get() != null) {
|
||||
for (int i : idRef.get()) {
|
||||
WorkspaceItemBuilder.deleteWorkspaceItem(i);
|
||||
}
|
||||
}
|
||||
}
|
||||
ris.close();
|
||||
}
|
||||
|
||||
@Test
|
||||
/**
|
||||
* Test the creation of workspaceitems POSTing to the resource collection endpoint an endnote file
|
||||
*
|
||||
* @throws Exception
|
||||
*/
|
||||
public void createSingleWorkspaceItemFromEndnoteWithOneEntryTest() throws Exception {
|
||||
context.turnOffAuthorisationSystem();
|
||||
|
||||
//** GIVEN **
|
||||
//1. A community-collection structure with one parent community with sub-community and two collections.
|
||||
parentCommunity = CommunityBuilder.createCommunity(context)
|
||||
.withName("Parent Community")
|
||||
.build();
|
||||
Community child1 = CommunityBuilder.createSubCommunity(context, parentCommunity)
|
||||
.withName("Sub Community")
|
||||
.build();
|
||||
Collection col1 = CollectionBuilder.createCollection(context, child1)
|
||||
.withName("Collection 1")
|
||||
.withSubmitterGroup(eperson)
|
||||
.build();
|
||||
Collection col2 = CollectionBuilder.createCollection(context, child1)
|
||||
.withName("Collection 2")
|
||||
.withSubmitterGroup(eperson)
|
||||
.build();
|
||||
|
||||
InputStream endnote = getClass().getResourceAsStream("endnote-test.enw");
|
||||
final MockMultipartFile endnoteFile = new MockMultipartFile("file", "/local/path/endnote-test.enw",
|
||||
"text/endnote", endnote);
|
||||
|
||||
context.restoreAuthSystemState();
|
||||
|
||||
String authToken = getAuthToken(eperson.getEmail(), password);
|
||||
AtomicReference<List<Integer>> idRef = new AtomicReference<>();
|
||||
// create workspaceitems in the default collection (col1)
|
||||
try {
|
||||
getClient(authToken).perform(fileUpload("/api/submission/workspaceitems")
|
||||
.file(endnoteFile))
|
||||
// create should return 200, 201 (created) is better for single resource
|
||||
.andExpect(status().isOk())
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.traditionalpageone['dc.title'][0].value",
|
||||
is("My Title")))
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.traditionalpageone"
|
||||
+ "['dc.contributor.author'][0].value",
|
||||
is("Author 1")))
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.traditionalpageone"
|
||||
+ "['dc.contributor.author'][1].value",
|
||||
is("Author 2")))
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.traditionalpageone"
|
||||
+ "['dc.date.issued'][0].value",
|
||||
is("2005")))
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.traditionalpagetwo"
|
||||
+ "['dc.description.abstract'][0].value",
|
||||
is("This is my abstract")))
|
||||
.andExpect(
|
||||
jsonPath("$._embedded.workspaceitems[0]._embedded.collection.id", is(col1.getID().toString())))
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.upload.files[0]"
|
||||
+ ".metadata['dc.source'][0].value",
|
||||
is("/local/path/endnote-test.enw")))
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.upload.files[0]"
|
||||
+ ".metadata['dc.title'][0].value",
|
||||
is("endnote-test.enw")))
|
||||
.andExpect(
|
||||
jsonPath("$._embedded.workspaceitems[*]._embedded.upload").doesNotExist())
|
||||
.andDo(result -> idRef.set(read(result.getResponse().getContentAsString(),
|
||||
"$._embedded.workspaceitems[*].id")));
|
||||
} finally {
|
||||
if (idRef != null && idRef.get() != null) {
|
||||
for (int i : idRef.get()) {
|
||||
WorkspaceItemBuilder.deleteWorkspaceItem(i);
|
||||
}
|
||||
}
|
||||
}
|
||||
endnote.close();
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
/**
|
||||
* Test the creation of workspaceitems POSTing to the resource collection endpoint a csv file
|
||||
* with some missing data and inner tab in field (those have to be read as list)
|
||||
*
|
||||
* @throws Exception
|
||||
*/
|
||||
public void createSingleWorkspaceItemFromTSVWithOneEntryAndMissingDataTest() throws Exception {
|
||||
context.turnOffAuthorisationSystem();
|
||||
|
||||
//** GIVEN **
|
||||
//1. A community-collection structure with one parent community with sub-community and two collections.
|
||||
parentCommunity = CommunityBuilder.createCommunity(context)
|
||||
.withName("Parent Community")
|
||||
.build();
|
||||
Community child1 = CommunityBuilder.createSubCommunity(context, parentCommunity)
|
||||
.withName("Sub Community")
|
||||
.build();
|
||||
Collection col1 = CollectionBuilder.createCollection(context, child1)
|
||||
.withName("Collection 1")
|
||||
.withSubmitterGroup(eperson)
|
||||
.build();
|
||||
Collection col2 = CollectionBuilder.createCollection(context, child1)
|
||||
.withName("Collection 2")
|
||||
.withSubmitterGroup(eperson)
|
||||
.build();
|
||||
|
||||
InputStream tsv = getClass().getResourceAsStream("tsv-missing-field-test.tsv");
|
||||
final MockMultipartFile csvFile = new MockMultipartFile("file", "/local/path/tsv-missing-field-test.tsv",
|
||||
"text/tsv", tsv);
|
||||
|
||||
context.restoreAuthSystemState();
|
||||
|
||||
String authToken = getAuthToken(eperson.getEmail(), password);
|
||||
AtomicReference<List<Integer>> idRef = new AtomicReference<>();
|
||||
|
||||
// create workspaceitems in the default collection (col1)
|
||||
try {
|
||||
getClient(authToken).perform(fileUpload("/api/submission/workspaceitems")
|
||||
.file(csvFile))
|
||||
// create should return 200, 201 (created) is better for single resource
|
||||
.andExpect(status().isOk())
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.traditionalpageone['dc.title'][0].value",
|
||||
is("My Article")))
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.traditionalpageone"
|
||||
+ "['dc.contributor.author'][0].value",
|
||||
is("Nobody")))
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.traditionalpageone"
|
||||
+ "['dc.contributor.author'][1].value",
|
||||
is("Try escape \t\t\tin \t\titem")))
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.traditionalpageone"
|
||||
+ "['dc.date.issued'][0].value").isEmpty())
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.traditionalpageone"
|
||||
+ "['dc.identifier.issn'][0].value",
|
||||
is("Mock ISSN")))
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.traditionalpageone['dc.type'][0].value"
|
||||
).doesNotExist())
|
||||
.andExpect(
|
||||
jsonPath("$._embedded.workspaceitems[0]._embedded.collection.id", is(col1.getID().toString())))
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.upload.files[0]"
|
||||
+ ".metadata['dc.source'][0].value",
|
||||
is("/local/path/tsv-missing-field-test.tsv")))
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.upload.files[0]"
|
||||
+ ".metadata['dc.title'][0].value",
|
||||
is("tsv-missing-field-test.tsv")))
|
||||
.andExpect(
|
||||
jsonPath("$._embedded.workspaceitems[*]._embedded.upload").doesNotExist())
|
||||
.andDo(result -> idRef.set(read(result.getResponse().getContentAsString(),
|
||||
"$._embedded.workspaceitems[*].id")));
|
||||
} finally {
|
||||
if (idRef != null && idRef.get() != null) {
|
||||
for (int i : idRef.get()) {
|
||||
WorkspaceItemBuilder.deleteWorkspaceItem(i);
|
||||
}
|
||||
}
|
||||
}
|
||||
tsv.close();
|
||||
}
|
||||
|
||||
@Test
|
||||
/**
|
||||
@@ -977,7 +1498,10 @@ public class WorkspaceItemRestRepositoryIT extends AbstractControllerIntegration
|
||||
context.restoreAuthSystemState();
|
||||
|
||||
String authToken = getAuthToken(eperson.getEmail(), password);
|
||||
AtomicReference<List<Integer>> idRef = new AtomicReference<>();
|
||||
|
||||
// create a workspaceitem from a single bibliographic entry file explicitly in the default collection (col1)
|
||||
try {
|
||||
getClient(authToken).perform(fileUpload("/api/submission/workspaceitems")
|
||||
.file(bibtexFile).file(pubmedFile))
|
||||
// create should return 200, 201 (created) is better for single resource
|
||||
@@ -999,9 +1523,19 @@ public class WorkspaceItemRestRepositoryIT extends AbstractControllerIntegration
|
||||
is("/local/path/pubmed-test.xml")))
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.upload.files[1]"
|
||||
+ ".metadata['dc.title'][0].value",
|
||||
is("pubmed-test.xml")));
|
||||
is("pubmed-test.xml")))
|
||||
.andDo(result -> idRef.set(read(result.getResponse().getContentAsString(),
|
||||
"$._embedded.workspaceitems[*].id")));
|
||||
} finally {
|
||||
if (idRef != null && idRef.get() != null) {
|
||||
for (int i : idRef.get()) {
|
||||
WorkspaceItemBuilder.deleteWorkspaceItem(i);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// create a workspaceitem from a single bibliographic entry file explicitly in the col2
|
||||
try {
|
||||
getClient(authToken).perform(fileUpload("/api/submission/workspaceitems")
|
||||
.file(bibtexFile).file(pubmedFile)
|
||||
.param("owningCollection", col2.getID().toString()))
|
||||
@@ -1023,7 +1557,16 @@ public class WorkspaceItemRestRepositoryIT extends AbstractControllerIntegration
|
||||
is("/local/path/pubmed-test.xml")))
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.upload.files[1]"
|
||||
+ ".metadata['dc.title'][0].value",
|
||||
is("pubmed-test.xml")));
|
||||
is("pubmed-test.xml")))
|
||||
.andDo(result -> idRef.set(read(result.getResponse().getContentAsString(),
|
||||
"$._embedded.workspaceitems[*].id")));
|
||||
} finally {
|
||||
if (idRef != null && idRef.get() != null) {
|
||||
for (int i : idRef.get()) {
|
||||
WorkspaceItemBuilder.deleteWorkspaceItem(i);
|
||||
}
|
||||
}
|
||||
}
|
||||
bibtex.close();
|
||||
xmlIS.close();
|
||||
}
|
||||
@@ -1063,6 +1606,7 @@ public class WorkspaceItemRestRepositoryIT extends AbstractControllerIntegration
|
||||
context.restoreAuthSystemState();
|
||||
|
||||
String authToken = getAuthToken(eperson.getEmail(), password);
|
||||
|
||||
// create a workspaceitem from a single bibliographic entry file explicitly in the default collection (col1)
|
||||
getClient(authToken).perform(fileUpload("/api/submission/workspaceitems")
|
||||
.file(bibtexFile))
|
||||
@@ -1105,7 +1649,10 @@ public class WorkspaceItemRestRepositoryIT extends AbstractControllerIntegration
|
||||
context.restoreAuthSystemState();
|
||||
|
||||
String authToken = getAuthToken(eperson.getEmail(), password);
|
||||
AtomicReference<List<Integer>> idRef = new AtomicReference<>();
|
||||
|
||||
// create a workspaceitem from a single bibliographic entry file explicitly in the default collection (col1)
|
||||
try {
|
||||
getClient(authToken).perform(fileUpload("/api/submission/workspaceitems")
|
||||
.file(pubmedFile))
|
||||
.andExpect(status().isOk())
|
||||
@@ -1123,9 +1670,20 @@ public class WorkspaceItemRestRepositoryIT extends AbstractControllerIntegration
|
||||
is("/local/path/pubmed-test.xml")))
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.upload.files[0]"
|
||||
+ ".metadata['dc.title'][0].value",
|
||||
is("pubmed-test.xml")));
|
||||
is("pubmed-test.xml")))
|
||||
.andDo(result -> idRef.set(read(result.getResponse().getContentAsString(),
|
||||
"$._embedded.workspaceitems[*].id")));
|
||||
} finally {
|
||||
if (idRef != null && idRef.get() != null) {
|
||||
for (int i : idRef.get()) {
|
||||
WorkspaceItemBuilder.deleteWorkspaceItem(i);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
// create a workspaceitem from a single bibliographic entry file explicitly in the col2
|
||||
try {
|
||||
getClient(authToken).perform(fileUpload("/api/submission/workspaceitems")
|
||||
.file(pubmedFile)
|
||||
.param("owningCollection", col2.getID().toString()))
|
||||
@@ -1142,8 +1700,16 @@ public class WorkspaceItemRestRepositoryIT extends AbstractControllerIntegration
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.upload.files[0].metadata['dc.source'][0].value",
|
||||
is("/local/path/pubmed-test.xml")))
|
||||
.andExpect(jsonPath("$._embedded.workspaceitems[0].sections.upload.files[0].metadata['dc.title'][0].value",
|
||||
is("pubmed-test.xml")));
|
||||
|
||||
is("pubmed-test.xml")))
|
||||
.andDo(result -> idRef.set(read(result.getResponse().getContentAsString(),
|
||||
"$._embedded.workspaceitems[*].id")));
|
||||
} finally {
|
||||
if (idRef != null && idRef.get() != null) {
|
||||
for (int i : idRef.get()) {
|
||||
WorkspaceItemBuilder.deleteWorkspaceItem(i);
|
||||
}
|
||||
}
|
||||
}
|
||||
xmlIS.close();
|
||||
}
|
||||
|
||||
@@ -1177,10 +1743,10 @@ public class WorkspaceItemRestRepositoryIT extends AbstractControllerIntegration
|
||||
|
||||
context.restoreAuthSystemState();
|
||||
|
||||
// bulk create a workspaceitem
|
||||
// create a workspaceitem
|
||||
getClient(authToken).perform(fileUpload("/api/submission/workspaceitems")
|
||||
.file(pdfFile))
|
||||
// bulk create should return 200, 201 (created) is better for single resource
|
||||
// create should return 200, 201 (created) is better for single resource
|
||||
.andExpect(status().isOk())
|
||||
//FIXME it will be nice to setup a mock grobid server for end to end testing
|
||||
// no metadata for now
|
||||
|
||||
@@ -0,0 +1,2 @@
|
||||
Title,Author,Year,Journal,Abstract,ISSN,Type
|
||||
My Article,"Nobody, \"Try escape, in item\"",,My Journal,"This is my abstract, i use comma to check escape works fine",Mock ISSN
|
||||
|
Can't render this file because it contains an unexpected character in line 2 and column 22.
|
@@ -0,0 +1,2 @@
|
||||
Title,Author,Year,Journal,Abstract,ISSN,Type
|
||||
My Article,Nobody,2006,My Journal,"This is my abstract, i use comma to check escape works fine",Mock ISSN,Mock subtype
|
||||
|
@@ -0,0 +1,10 @@
|
||||
FN
|
||||
VR
|
||||
SO My Journal
|
||||
PY 2005
|
||||
AB This is my abstract
|
||||
AU Author 1
|
||||
AU Author 2
|
||||
TI My Title
|
||||
ER
|
||||
EF
|
||||
@@ -0,0 +1,20 @@
|
||||
TY - CHAP
|
||||
AU - Just, Mike
|
||||
ED - van Tilborg, Henk C. A.
|
||||
PY - 2005
|
||||
DA - 2005//
|
||||
TI - Challenge–Response Identification
|
||||
T1 - Challenge–Response Identification second title
|
||||
BT - Encyclopedia of Cryptography and Security
|
||||
SP - 73
|
||||
EP - 74
|
||||
PB - Springer US
|
||||
CY - Boston, MA
|
||||
SN - 978-0-387-23483-0
|
||||
SO - My Journal
|
||||
UR - https://doi.org/10.1007/0-387-23483-7_56
|
||||
DO - 10.1007/0-387-23483-7_56
|
||||
ID - Just2005
|
||||
PT - Mock subtype
|
||||
AB - This is the abstract
|
||||
ER -
|
||||
@@ -0,0 +1,2 @@
|
||||
Title Author Year Journal Abstract ISSN Type
|
||||
My Article "Nobody, \"Try escape in item\"" My Journal "This is my abstract, i use tab to check escape works fine" Mock ISSN
|
||||
|
Can't render this file because it contains an unexpected character in line 2 and column 22.
|
@@ -0,0 +1,2 @@
|
||||
Title Author Year Journal Abstract ISSN Type
|
||||
My Article Nobody 2006 My Journal "This is my abstract i'm using use tab to check escape works fine" Mock ISSN Mock subtype
|
||||
|
Can't render this file because it has a wrong number of fields in line 2.
|
@@ -17,58 +17,36 @@
|
||||
only matters here for postprocessing of the value. The mapped MetadatumContributor has full control over
|
||||
what metadatafield is generated.
|
||||
</description>
|
||||
<entry key-ref="bibtex.dc.title" value-ref="bibtexTitleContrib" />
|
||||
<entry key-ref="bibtex.dc.authors" value-ref="bibtexAuthorsContrib" />
|
||||
<entry key-ref="bibtex.dc.journal" value-ref="bibtexJournalContrib" />
|
||||
<entry key-ref="bibtex.dc.issued" value-ref="bibtexIssuedContrib" />
|
||||
<entry key-ref="bibtex.dc.jissn" value-ref="bibtexJissnContrib" />
|
||||
<entry key-ref="dcTitle" value-ref="bibtexTitleContrib" />
|
||||
<entry key-ref="dcAuthors" value-ref="bibtexAuthorsContrib" />
|
||||
<entry key-ref="dcJournal" value-ref="bibtexJournalContrib" />
|
||||
<entry key-ref="dcIssued" value-ref="bibtexIssuedContrib" />
|
||||
<entry key-ref="dcJissn" value-ref="bibtexJissnContrib" />
|
||||
</util:map>
|
||||
|
||||
<bean id="bibtexJissnContrib" class="org.dspace.importer.external.metadatamapping.contributor.SimpleMetadataContributor">
|
||||
<property name="field" ref="bibtex.dc.jissn"/>
|
||||
<property name="field" ref="dcJissn"/>
|
||||
<property name="key" value="ISSN" />
|
||||
</bean>
|
||||
|
||||
<bean id="bibtexIssuedContrib" class="org.dspace.importer.external.metadatamapping.contributor.SimpleMetadataContributor">
|
||||
<property name="field" ref="bibtex.dc.issued"/>
|
||||
<property name="field" ref="dcIssued"/>
|
||||
<property name="key" value="year" />
|
||||
</bean>
|
||||
|
||||
<bean id="bibtexJournalContrib" class="org.dspace.importer.external.metadatamapping.contributor.SimpleMetadataContributor">
|
||||
<property name="field" ref="bibtex.dc.journal"/>
|
||||
<property name="field" ref="dcJournal"/>
|
||||
<property name="key" value="journal" />
|
||||
</bean>
|
||||
|
||||
<bean id="bibtexAuthorsContrib" class="org.dspace.importer.external.metadatamapping.contributor.SimpleMetadataContributor">
|
||||
<property name="field" ref="bibtex.dc.authors"/>
|
||||
<property name="field" ref="dcAuthors"/>
|
||||
<property name="key" value="author" />
|
||||
</bean>
|
||||
|
||||
<bean id="bibtexTitleContrib" class="org.dspace.importer.external.metadatamapping.contributor.SimpleMetadataContributor">
|
||||
<property name="field" ref="bibtex.dc.title"/>
|
||||
<property name="field" ref="dcTitle"/>
|
||||
<property name="key" value="title" />
|
||||
</bean>
|
||||
|
||||
|
||||
|
||||
<bean id="bibtex.dc.jissn" class="org.dspace.importer.external.metadatamapping.MetadataFieldConfig">
|
||||
<constructor-arg value="dc.identifier.issn"/>
|
||||
</bean>
|
||||
|
||||
<bean id="bibtex.dc.issued" class="org.dspace.importer.external.metadatamapping.MetadataFieldConfig">
|
||||
<constructor-arg value="dc.date.issued"/>
|
||||
</bean>
|
||||
|
||||
<bean id="bibtex.dc.journal" class="org.dspace.importer.external.metadatamapping.MetadataFieldConfig">
|
||||
<constructor-arg value="dc.source"/>
|
||||
</bean>
|
||||
|
||||
<bean id="bibtex.dc.authors" class="org.dspace.importer.external.metadatamapping.MetadataFieldConfig">
|
||||
<constructor-arg value="dc.contributor.author"/>
|
||||
</bean>
|
||||
|
||||
<bean id="bibtex.dc.title" class="org.dspace.importer.external.metadatamapping.MetadataFieldConfig">
|
||||
<constructor-arg value="dc.title"/>
|
||||
</bean>
|
||||
|
||||
</beans>
|
||||
80
dspace/config/spring/api/characterseparated-integration.xml
Normal file
80
dspace/config/spring/api/characterseparated-integration.xml
Normal file
@@ -0,0 +1,80 @@
|
||||
<beans xmlns="http://www.springframework.org/schema/beans"
|
||||
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
||||
xmlns:context="http://www.springframework.org/schema/context"
|
||||
xmlns:util="http://www.springframework.org/schema/util"
|
||||
xsi:schemaLocation="http://www.springframework.org/schema/beans
|
||||
http://www.springframework.org/schema/beans/spring-beans-2.5.xsd
|
||||
http://www.springframework.org/schema/context
|
||||
http://www.springframework.org/schema/context/spring-context-2.5.xsd http://www.springframework.org/schema/util http://www.springframework.org/schema/util/spring-util.xsd"
|
||||
default-autowire-candidates="*Service,*DAO,javax.sql.DataSource">
|
||||
|
||||
<context:annotation-config/>
|
||||
<!-- allows us to use spring annotations in beans -->
|
||||
|
||||
<util:map id="csvMetadataFieldMap" key-type="org.dspace.importer.external.metadatamapping.MetadataFieldConfig"
|
||||
value-type="org.dspace.importer.external.metadatamapping.contributor.MetadataContributor">
|
||||
<description>Defines which metadatum is mapped on which metadatum. Note that while the key must be unique it
|
||||
only matters here for postprocessing of the value. The mapped MetadatumContributor has full control over
|
||||
what metadatafield is generated.
|
||||
</description>
|
||||
<entry key-ref="dcTitle" value-ref="charSepTitleContrib" />
|
||||
<entry key-ref="dcAuthors" value-ref="charSepAuthorsContrib" />
|
||||
<entry key-ref="dcIssued" value-ref="charSepDateContrib" />
|
||||
<entry key-ref="dcJournal" value-ref="charSepJournalContrib" />
|
||||
<entry key-ref="dcAbstract" value-ref="charSepAbstractContrib" />
|
||||
<entry key-ref="dcJissn" value-ref="charSepJissnContrib" />
|
||||
<entry key-ref="dcSubtype" value-ref="charSepTypeContrib" />
|
||||
</util:map>
|
||||
|
||||
<util:map id="tsvMetadataFieldMap" key-type="org.dspace.importer.external.metadatamapping.MetadataFieldConfig"
|
||||
value-type="org.dspace.importer.external.metadatamapping.contributor.MetadataContributor">
|
||||
<description>Defines which metadatum is mapped on which metadatum. Note that while the key must be unique it
|
||||
only matters here for postprocessing of the value. The mapped MetadatumContributor has full control over
|
||||
what metadatafield is generated.
|
||||
</description>
|
||||
<entry key-ref="dcTitle" value-ref="charSepTitleContrib" />
|
||||
<entry key-ref="dcAuthors" value-ref="charSepAuthorsContrib" />
|
||||
<entry key-ref="dcIssued" value-ref="charSepDateContrib" />
|
||||
<entry key-ref="dcJournal" value-ref="charSepJournalContrib" />
|
||||
<entry key-ref="dcAbstract" value-ref="charSepAbstractContrib" />
|
||||
<entry key-ref="dcJissn" value-ref="charSepJissnContrib" />
|
||||
<entry key-ref="dcSubtype" value-ref="charSepTypeContrib" />
|
||||
</util:map>
|
||||
|
||||
|
||||
<bean id="charSepTitleContrib" class="org.dspace.importer.external.metadatamapping.contributor.SimpleMetadataContributor">
|
||||
<property name="field" ref="dcTitle"/>
|
||||
<property name="key" value="0" />
|
||||
</bean>
|
||||
|
||||
<bean id="charSepAuthorsContrib" class="org.dspace.importer.external.metadatamapping.contributor.EnhancedSimpleMetadataContributor">
|
||||
<property name="field" ref="dcAuthors"/>
|
||||
<property name="key" value="1" />
|
||||
</bean>
|
||||
|
||||
<bean id="charSepDateContrib" class="org.dspace.importer.external.metadatamapping.contributor.SimpleMetadataContributor">
|
||||
<property name="field" ref="dcIssued"/>
|
||||
<property name="key" value="2" />
|
||||
</bean>
|
||||
|
||||
<bean id="charSepJournalContrib" class="org.dspace.importer.external.metadatamapping.contributor.SimpleMetadataContributor">
|
||||
<property name="field" ref="dcJournal"/>
|
||||
<property name="key" value="3" />
|
||||
</bean>
|
||||
|
||||
<bean id="charSepAbstractContrib" class="org.dspace.importer.external.metadatamapping.contributor.SimpleMetadataContributor">
|
||||
<property name="field" ref="dcAbstract"/>
|
||||
<property name="key" value="4" />
|
||||
</bean>
|
||||
|
||||
<bean id="charSepJissnContrib" class="org.dspace.importer.external.metadatamapping.contributor.SimpleMetadataContributor">
|
||||
<property name="field" ref="dcJissn"/>
|
||||
<property name="key" value="5" />
|
||||
</bean>
|
||||
|
||||
<bean id="charSepTypeContrib" class="org.dspace.importer.external.metadatamapping.contributor.SimpleMetadataContributor">
|
||||
<property name="field" ref="dcSubtype"/>
|
||||
<property name="key" value="6" />
|
||||
</bean>
|
||||
|
||||
</beans>
|
||||
59
dspace/config/spring/api/dublicore-metadata-mapper.xml
Normal file
59
dspace/config/spring/api/dublicore-metadata-mapper.xml
Normal file
@@ -0,0 +1,59 @@
|
||||
<beans xmlns="http://www.springframework.org/schema/beans"
|
||||
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
||||
xmlns:context="http://www.springframework.org/schema/context"
|
||||
xsi:schemaLocation="http://www.springframework.org/schema/beans
|
||||
http://www.springframework.org/schema/beans/spring-beans-2.5.xsd
|
||||
http://www.springframework.org/schema/context
|
||||
http://www.springframework.org/schema/context/spring-context-2.5.xsd http://www.springframework.org/schema/util http://www.springframework.org/schema/util/spring-util.xsd"
|
||||
default-autowire-candidates="*Service,*DAO,javax.sql.DataSource">
|
||||
|
||||
|
||||
<bean id="dcJissn" class="org.dspace.importer.external.metadatamapping.MetadataFieldConfig">
|
||||
<constructor-arg value="dc.identifier.issn"/>
|
||||
</bean>
|
||||
<bean id="dcPisbn" class="org.dspace.importer.external.metadatamapping.MetadataFieldConfig">
|
||||
<constructor-arg value="dc.identifier.isbn"/>
|
||||
</bean>
|
||||
<bean id="dcIssued" class="org.dspace.importer.external.metadatamapping.MetadataFieldConfig">
|
||||
<constructor-arg value="dc.date.issued"/>
|
||||
</bean>
|
||||
<bean id="dcLanguage" class="org.dspace.importer.external.metadatamapping.MetadataFieldConfig">
|
||||
<constructor-arg value="dc.language.iso"/>
|
||||
</bean>
|
||||
<bean id="dcSubtype" class="org.dspace.importer.external.metadatamapping.MetadataFieldConfig">
|
||||
<constructor-arg value="dc.type"/>
|
||||
</bean>
|
||||
<bean id="dcJournal" class="org.dspace.importer.external.metadatamapping.MetadataFieldConfig">
|
||||
<constructor-arg value="dc.source"/>
|
||||
</bean>
|
||||
<bean id="dcTitle" class="org.dspace.importer.external.metadatamapping.MetadataFieldConfig">
|
||||
<constructor-arg value="dc.title"/>
|
||||
</bean>
|
||||
<bean id="dcAuthors" class="org.dspace.importer.external.metadatamapping.MetadataFieldConfig">
|
||||
<constructor-arg value="dc.contributor.author"/>
|
||||
</bean>
|
||||
<bean id="dcEditors" class="org.dspace.importer.external.metadatamapping.MetadataFieldConfig">
|
||||
<constructor-arg value="dc.contributor.editor"/>
|
||||
</bean>
|
||||
<bean id="dcTranslators" class="org.dspace.importer.external.metadatamapping.MetadataFieldConfig">
|
||||
<constructor-arg value="dc.contributor.other"/>
|
||||
</bean>
|
||||
<bean id="dcChairs" class="org.dspace.importer.external.metadatamapping.MetadataFieldConfig">
|
||||
<constructor-arg value="dc.contributor.other"/>
|
||||
</bean>
|
||||
<bean id="dcAbstract" class="org.dspace.importer.external.metadatamapping.MetadataFieldConfig">
|
||||
<constructor-arg value="dc.description.abstract"/>
|
||||
</bean>
|
||||
<bean id="dcAllKeyword" class="org.dspace.importer.external.metadatamapping.MetadataFieldConfig">
|
||||
<constructor-arg value="dc.subject"/>
|
||||
</bean>
|
||||
<bean id="dcArxivCategory" class="org.dspace.importer.external.metadatamapping.MetadataFieldConfig">
|
||||
<constructor-arg value="dc.subject"/>
|
||||
</bean>
|
||||
<bean id="dcDoi" class="org.dspace.importer.external.metadatamapping.MetadataFieldConfig">
|
||||
<constructor-arg value="dc.identifier"/>
|
||||
</bean>
|
||||
<bean id="dcPublisher" class="org.dspace.importer.external.metadatamapping.MetadataFieldConfig">
|
||||
<constructor-arg value="dc.publisher"/>
|
||||
</bean>
|
||||
</beans>
|
||||
52
dspace/config/spring/api/endnote-integration.xml
Normal file
52
dspace/config/spring/api/endnote-integration.xml
Normal file
@@ -0,0 +1,52 @@
|
||||
<beans xmlns="http://www.springframework.org/schema/beans"
|
||||
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
||||
xmlns:context="http://www.springframework.org/schema/context"
|
||||
xmlns:util="http://www.springframework.org/schema/util"
|
||||
xsi:schemaLocation="http://www.springframework.org/schema/beans
|
||||
http://www.springframework.org/schema/beans/spring-beans-2.5.xsd
|
||||
http://www.springframework.org/schema/context
|
||||
http://www.springframework.org/schema/context/spring-context-2.5.xsd http://www.springframework.org/schema/util http://www.springframework.org/schema/util/spring-util.xsd"
|
||||
default-autowire-candidates="*Service,*DAO,javax.sql.DataSource">
|
||||
|
||||
<context:annotation-config/>
|
||||
<!-- allows us to use spring annotations in beans -->
|
||||
|
||||
<util:map id="endnoteMetadataFieldMap" key-type="org.dspace.importer.external.metadatamapping.MetadataFieldConfig"
|
||||
value-type="org.dspace.importer.external.metadatamapping.contributor.MetadataContributor">
|
||||
<description>Defines which metadatum is mapped on which metadatum. Note that while the key must be unique it
|
||||
only matters here for postprocessing of the value. The mapped MetadatumContributor has full control over
|
||||
what metadatafield is generated.
|
||||
</description>
|
||||
<entry key-ref="dcTitle" value-ref="endnoteTitleContrib" />
|
||||
<entry key-ref="dcAuthors" value-ref="endnoteAuthorsContrib" />
|
||||
<entry key-ref="dcAbstract" value-ref="endnoteAbstractContrib" />
|
||||
<entry key-ref="dcIssued" value-ref="endnoteIssuedContrib" />
|
||||
<entry key-ref="dcJournal" value-ref="endnoteJournalContrib" />
|
||||
</util:map>
|
||||
|
||||
<bean id="endnoteJournalContrib" class="org.dspace.importer.external.metadatamapping.contributor.SimpleMetadataContributor">
|
||||
<property name="field" ref="dcJournal"/>
|
||||
<property name="key" value="SO" />
|
||||
</bean>
|
||||
|
||||
<bean id="endnoteIssuedContrib" class="org.dspace.importer.external.metadatamapping.contributor.SimpleMetadataContributor">
|
||||
<property name="field" ref="dcIssued"/>
|
||||
<property name="key" value="PY" />
|
||||
</bean>
|
||||
|
||||
<bean id="endnoteAbstractContrib" class="org.dspace.importer.external.metadatamapping.contributor.SimpleMetadataContributor">
|
||||
<property name="field" ref="dcAbstract"/>
|
||||
<property name="key" value="AB" />
|
||||
</bean>
|
||||
|
||||
<bean id="endnoteAuthorsContrib" class="org.dspace.importer.external.metadatamapping.contributor.SimpleMetadataContributor">
|
||||
<property name="field" ref="dcAuthors"/>
|
||||
<property name="key" value="AU" />
|
||||
</bean>
|
||||
|
||||
<bean id="endnoteTitleContrib" class="org.dspace.importer.external.metadatamapping.contributor.SimpleMetadataContributor">
|
||||
<property name="field" ref="dcTitle"/>
|
||||
<property name="key" value="TI" />
|
||||
</bean>
|
||||
|
||||
</beans>
|
||||
77
dspace/config/spring/api/ris-integration.xml
Normal file
77
dspace/config/spring/api/ris-integration.xml
Normal file
@@ -0,0 +1,77 @@
|
||||
<beans xmlns="http://www.springframework.org/schema/beans"
|
||||
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
||||
xmlns:context="http://www.springframework.org/schema/context"
|
||||
xmlns:util="http://www.springframework.org/schema/util"
|
||||
xsi:schemaLocation="http://www.springframework.org/schema/beans
|
||||
http://www.springframework.org/schema/beans/spring-beans-2.5.xsd
|
||||
http://www.springframework.org/schema/context
|
||||
http://www.springframework.org/schema/context/spring-context-2.5.xsd http://www.springframework.org/schema/util http://www.springframework.org/schema/util/spring-util.xsd"
|
||||
default-autowire-candidates="*Service,*DAO,javax.sql.DataSource">
|
||||
|
||||
<context:annotation-config/>
|
||||
<!-- allows us to use spring annotations in beans -->
|
||||
|
||||
<util:map id="risMetadataFieldMap" key-type="org.dspace.importer.external.metadatamapping.MetadataFieldConfig"
|
||||
value-type="org.dspace.importer.external.metadatamapping.contributor.MetadataContributor">
|
||||
<description>Defines which metadatum is mapped on which metadatum. Note that while the key must be unique it
|
||||
only matters here for postprocessing of the value. The mapped MetadatumContributor has full control over
|
||||
what metadatafield is generated.
|
||||
</description>
|
||||
<entry key-ref="dcTitle" value-ref="risTitleContrib" />
|
||||
<entry key-ref="dcAuthors" value-ref="risAuthorContrib" />
|
||||
<entry key-ref="dcJournal" value-ref="risSourceContrib" />
|
||||
<entry key-ref="dcIssued" value-ref="risDateContrib" />
|
||||
<entry key-ref="dcJissn" value-ref="risISSNContrib" />
|
||||
<entry key-ref="dcSubtype" value-ref="risTypeContrib" />
|
||||
<entry key-ref="dcAbstract" value-ref="risAbstractContrib" />
|
||||
</util:map>
|
||||
|
||||
|
||||
<bean id="risTitleContrib" class="org.dspace.importer.external.metadatamapping.contributor.MultipleMetadataContributor">
|
||||
<property name="field" ref="dcTitle"/>
|
||||
<property name="metadatumContributors" ref="risTitleContribList" />
|
||||
</bean>
|
||||
|
||||
<util:list id="risTitleContribList">
|
||||
<bean id="risTitleContribTI" class="org.dspace.importer.external.metadatamapping.contributor.SimpleMetadataContributor">
|
||||
<property name="field" ref="dcTitle"/>
|
||||
<property name="key" value="TI" />
|
||||
</bean>
|
||||
<bean id="risTitleContribT1" class="org.dspace.importer.external.metadatamapping.contributor.SimpleMetadataContributor">
|
||||
<property name="field" ref="dcTitle"/>
|
||||
<property name="key" value="T1" />
|
||||
</bean>
|
||||
</util:list>
|
||||
|
||||
<bean id="risAuthorContrib" class="org.dspace.importer.external.metadatamapping.contributor.SimpleMetadataContributor">
|
||||
<property name="field" ref="dcAuthors"/>
|
||||
<property name="key" value="AU" />
|
||||
</bean>
|
||||
|
||||
<bean id="risSourceContrib" class="org.dspace.importer.external.metadatamapping.contributor.SimpleMetadataContributor">
|
||||
<property name="field" ref="dcJournal"/>
|
||||
<property name="key" value="SO" />
|
||||
</bean>
|
||||
|
||||
|
||||
<bean id="risDateContrib" class="org.dspace.importer.external.metadatamapping.contributor.SimpleMetadataContributor">
|
||||
<property name="field" ref="dcIssued"/>
|
||||
<property name="key" value="PY" />
|
||||
</bean>
|
||||
|
||||
<bean id="risISSNContrib" class="org.dspace.importer.external.metadatamapping.contributor.SimpleMetadataContributor">
|
||||
<property name="field" ref="dcJissn"/>
|
||||
<property name="key" value="SN" />
|
||||
</bean>
|
||||
|
||||
<bean id="risTypeContrib" class="org.dspace.importer.external.metadatamapping.contributor.SimpleMetadataContributor">
|
||||
<property name="field" ref="dcSubtype"/>
|
||||
<property name="key" value="PT" />
|
||||
</bean>
|
||||
|
||||
<bean id="risAbstractContrib" class="org.dspace.importer.external.metadatamapping.contributor.SimpleMetadataContributor">
|
||||
<property name="field" ref="dcAbstract"/>
|
||||
<property name="key" value="AB" />
|
||||
</bean>
|
||||
|
||||
</beans>
|
||||
Reference in New Issue
Block a user