/*
* #%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);
}
}
}