Java tutorial
/* * 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()); } } }