Java tutorial
/* * #%L * NICTA t3as SNOMED CT service REST client * %% * Copyright (C) 2014 NICTA * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as * published by the Free Software Foundation, either version 3 of the * License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public * License along with this program. If not, see * <http://www.gnu.org/licenses/gpl-3.0.html>. * * Additional permission under GNU GPL version 3 section 7 * * If you modify this Program, or any covered work, by linking or combining * it with H2, GWT, or JavaBeans Activation Framework (JAF) (or a * modified version of those libraries), containing parts covered by the * terms of the H2 License, the GWT Terms, or the Common Development and * Distribution License (CDDL) version 1.0 ,the licensors of this Program * grant you additional permission to convey the resulting work. * #L% */ package org.t3as.snomedct.client.cmdline; import com.beust.jcommander.JCommander; import com.beust.jcommander.Parameter; import com.google.common.base.Charsets; import com.google.common.base.Joiner; import com.google.common.base.Splitter; import com.google.common.io.Files; import org.t3as.metamap.jaxb.Candidate; import org.t3as.metamap.jaxb.Mapping; import org.t3as.metamap.jaxb.Phrase; import org.t3as.metamap.jaxb.SemType; import org.t3as.metamap.jaxb.Utterance; import org.t3as.metamap.options.MetaMapOptions; import org.t3as.snomedct.client.SnomedClient; import org.t3as.snomedct.service.AnalysisRequest; import java.io.File; import java.io.IOException; import java.util.ArrayList; import java.util.Collection; import java.util.List; /** Command line implementation of the SNOMED CT web service client. */ public final class Main { private Main() { } /** Get the relevant options from the command line and invoke the client. */ @SuppressWarnings("MethodNamesDifferingOnlyByCase") public static void main(final String[] args) throws IOException { final Options opts = getOptions(args); // create a web service client final SnomedClient client = new SnomedClient(opts.url); // call the webservice with the text and any passed options if (opts.text.isEmpty()) processFiles(opts, client); else System.out.println(callService(opts.text, opts, client)); } private static void processFiles(final Options opts, final SnomedClient client) throws IOException { // read each file and call the web service for (final File f : opts.files) { final String input = Files.toString(f, Charsets.UTF_8); System.out.printf("%s:\n", f); System.out.println(callService(input, opts, client)); } } private static String callService(final String text, final Options opts, final SnomedClient client) { // create a request final AnalysisRequest request = new AnalysisRequest(text, opts.splitOptions()); // perform the call and get the output final Collection<Utterance> utterances = client.call(request); // turn the output into a human readable string return toString(utterances); } /** * Turn utterances into MetaMap-ish output. * @param utterances Utterances to get data from * @return a MetaMap-ish string meant for printing */ public static String toString(final Collection<Utterance> utterances) { final StringBuilder sb = new StringBuilder(); for (final Utterance u : utterances) { for (final Phrase phrase : u.getPhrases().getPhrase()) { sb.append(String.format("Phrase: %s\n", phrase.getPhraseText())); for (final Mapping mapping : phrase.getMappings().getMapping()) { sb.append(String.format("Score: %s\n", mapping.getMappingScore())); for (final Candidate candidate : mapping.getMappingCandidates().getCandidate()) { final Collection<String> semTypes = new ArrayList<>(); for (final SemType st : candidate.getSemTypes().getSemType()) { semTypes.add(st.getvalue()); } sb.append(String.format(" %-5s %-9s %s %s %s %s\n", candidate.getCandidateScore(), candidate.getCandidateCUI(), candidate.getSnomedId(), candidate.getCandidatePreferred(), semTypes, candidate.getSources().getSource())); } } sb.append("\n"); } } return sb.toString(); } @SuppressWarnings("CallToSystemExit") private static Options getOptions(final String[] args) { final Options opts = new Options(); JCommander jc = null; try { jc = new JCommander(opts, args); } catch (final RuntimeException e) { System.err.println("Could not parse the options: " + e.getMessage()); System.exit(1); } if (opts.showUsage) { jc.usage(); System.exit(0); } if (opts.text.isEmpty() && opts.files.isEmpty()) { System.err.println("Pass either text to analyse or files to read text from."); System.exit(1); } if (!opts.text.isEmpty() && !opts.files.isEmpty()) { System.err.println("Pass either text to analyse or files to read text from, not both."); System.exit(1); } // do nothing unless all files are readable for (final File f : opts.files) { if (!f.canRead()) { System.err.printf("Can not read file '%s'\n", f); System.exit(1); } } return opts; } private static class Options { @Parameter(help = true, names = { "-h", "--help" }, description = "Show this help message.") boolean showUsage; @Parameter(names = "-url", description = "The base URL of the SNOMED web service to access.") String url = SnomedClient.DEFAULT_BASE_URL; @Parameter(names = "-text", description = "The text to analyse for SNOMED CT codes.") String text = ""; @Parameter(names = "-options", description = "Semicolon separated list of options to pass to the SNOMED CT " + "coder - see web service documentation for which ones are " + "supported. To run with no options at all pass an empty string.") String options = Joiner.on("; ").join(MetaMapOptions.DEFAULT_MM_OPTIONS); @Parameter(description = "[files]") Collection<File> files = new ArrayList<>(); List<String> splitOptions() { // split on comma and trim off any surrounding whitespace return Splitter.on(';').omitEmptyStrings().trimResults().splitToList(options); } } }