/*
* Licensed to the Apache Software Foundation (ASF) under one or more
* contributor license agreements. See the NOTICE file distributed with
* this work for additional information regarding copyright ownership.
* The ASF licenses this file to You under the Apache License, Version 2.0
* (the "License"); you may not use this file except in compliance with
* the License. You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.apache.tika.parser.isatab;
import java.io.IOException;
import java.io.InputStream;
import java.io.Reader;
import java.util.Arrays;
import java.util.HashMap;
import java.util.Iterator;
import java.util.Locale;
import java.util.Map;
import org.apache.commons.csv.CSVFormat;
import org.apache.commons.csv.CSVParser;
import org.apache.commons.csv.CSVRecord;
import org.apache.commons.io.input.CloseShieldInputStream;
import org.apache.tika.config.TikaConfig;
import org.apache.tika.detect.AutoDetectReader;
import org.apache.tika.exception.TikaException;
import org.apache.tika.io.TikaInputStream;
import org.apache.tika.metadata.Metadata;
import org.apache.tika.parser.ParseContext;
import org.apache.tika.sax.XHTMLContentHandler;
import org.xml.sax.SAXException;
public class ISATabUtils {
/**
* INVESTIGATION
*/
// Investigation section.
private static final String[] sections = {
"ONTOLOGY SOURCE REFERENCE",
"INVESTIGATION",
"INVESTIGATION PUBLICATIONS",
"INVESTIGATION CONTACTS"
};
// STUDY section (inside the Study section)
private static final String studySectionField = "STUDY";
// Study File Name (inside the STUDY section)
private static final String studyFileNameField = "Study File Name";
public static void parseInvestigation(InputStream stream, XHTMLContentHandler handler, Metadata metadata, ParseContext context, String studyFileName) throws IOException, TikaException, SAXException {
TikaConfig tikaConfig = context.get(TikaConfig.class);
if (tikaConfig == null) {
tikaConfig = TikaConfig.getDefaultConfig();
}
// Automatically detect the character encoding
try (AutoDetectReader reader = new AutoDetectReader(new CloseShieldInputStream(stream),
metadata, tikaConfig.getEncodingDetector())) {
extractMetadata(reader, metadata, studyFileName);
}
}
public static void parseInvestigation(InputStream stream, XHTMLContentHandler handler, Metadata metadata, ParseContext context) throws IOException, TikaException, SAXException {
parseInvestigation(stream, handler, metadata, context, null);
}
public static void parseStudy(InputStream stream, XHTMLContentHandler xhtml, Metadata metadata, ParseContext context) throws IOException, TikaException, SAXException {
TikaInputStream tis = TikaInputStream.get(stream);
// Automatically detect the character encoding
TikaConfig tikaConfig = context.get(TikaConfig.class);
if (tikaConfig == null) {
tikaConfig = TikaConfig.getDefaultConfig();
}
try (AutoDetectReader reader = new AutoDetectReader(new CloseShieldInputStream(tis),
metadata, tikaConfig.getEncodingDetector());
CSVParser csvParser = new CSVParser(reader, CSVFormat.TDF)) {
Iterator<CSVRecord> iterator = csvParser.iterator();
xhtml.startElement("table");
xhtml.startElement("thead");
if (iterator.hasNext()) {
CSVRecord record = iterator.next();
for (int i = 0; i < record.size(); i++) {
xhtml.startElement("th");
xhtml.characters(record.get(i));
xhtml.endElement("th");
}
}
xhtml.endElement("thead");
xhtml.startElement("tbody");
while (iterator.hasNext()) {
CSVRecord record = iterator.next();
xhtml.startElement("tr");
for (int j = 0; j < record.size(); j++) {
xhtml.startElement("td");
xhtml.characters(record.get(j));
xhtml.endElement("td");
}
xhtml.endElement("tr");
}
xhtml.endElement("tbody");
xhtml.endElement("table");
}
}
public static void parseAssay(InputStream stream, XHTMLContentHandler xhtml, Metadata metadata, ParseContext context) throws IOException, TikaException, SAXException {
TikaInputStream tis = TikaInputStream.get(stream);
// Automatically detect the character encoding
TikaConfig tikaConfig = context.get(TikaConfig.class);
if (tikaConfig == null) {
tikaConfig = TikaConfig.getDefaultConfig();
}
try (AutoDetectReader reader = new AutoDetectReader(new CloseShieldInputStream(tis),
metadata, tikaConfig.getEncodingDetector());
CSVParser csvParser = new CSVParser(reader, CSVFormat.TDF)) {
xhtml.startElement("table");
Iterator<CSVRecord> iterator = csvParser.iterator();
xhtml.startElement("thead");
if (iterator.hasNext()) {
CSVRecord record = iterator.next();
for (int i = 0; i < record.size(); i++) {
xhtml.startElement("th");
xhtml.characters(record.get(i));
xhtml.endElement("th");
}
}
xhtml.endElement("thead");
xhtml.startElement("tbody");
while (iterator.hasNext()) {
CSVRecord record = iterator.next();
xhtml.startElement("tr");
for (int j = 0; j < record.size(); j++) {
xhtml.startElement("td");
xhtml.characters(record.get(j));
xhtml.endElement("td");
}
xhtml.endElement("tr");
}
xhtml.endElement("tbody");
xhtml.endElement("table");
}
}
private static void extractMetadata(Reader reader, Metadata metadata, String studyFileName) throws IOException {
boolean investigationSection = false;
boolean studySection = false;
boolean studyTarget = false;
Map<String, String> map = new HashMap<String, String>();
try (CSVParser csvParser = new CSVParser(reader, CSVFormat.TDF)) {
Iterator<CSVRecord> iterator = csvParser.iterator();
while (iterator.hasNext()) {
CSVRecord record = iterator.next();
String field = record.get(0);
if ((field.toUpperCase(Locale.ENGLISH).equals(field)) && (record.size() == 1)) {
investigationSection = Arrays.asList(sections).contains(field);
studySection = (studyFileName != null) && (field.equals(studySectionField));
} else {
if (investigationSection) {
addMetadata(field, record, metadata);
} else if (studySection) {
if (studyTarget) {
break;
}
String value = record.get(1);
map.put(field, value);
studyTarget = (field.equals(studyFileNameField)) && (value.equals(studyFileName));
if (studyTarget) {
mapStudyToMetadata(map, metadata);
studySection = false;
}
} else if (studyTarget) {
addMetadata(field, record, metadata);
}
}
}
} catch (IOException ioe) {
throw ioe;
}
}
private static void addMetadata(String field, CSVRecord record, Metadata metadata) {
if ((record ==null) || (record.size() <= 1)) {
return;
}
for (int i = 1; i < record.size(); i++) {
metadata.add(field, record.get(i));
}
}
private static void mapStudyToMetadata(Map<String, String> map, Metadata metadata) {
for (Map.Entry<String, String> entry : map.entrySet()) {
metadata.add(entry.getKey(), entry.getValue());
}
}
}