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eu.interedition.collatex.tools.JsonProcessor Maven / Gradle / Ivy
/*
* Copyright (c) 2015 The Interedition Development Group.
*
* This file is part of CollateX.
*
* CollateX 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.
*
* CollateX 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 CollateX. If not, see Gregor Middell
*/
public class JsonProcessor {
public static SimpleCollation read(InputStream inputStream) throws IOException {
try (JsonReader reader = Json.createReader(inputStream)) {
final JsonStructure collationNode = reader.read();
if (collationNode.getValueType() != JsonValue.ValueType.OBJECT) {
throw new IOException("Expecting JSON object");
}
final JsonObject collationObject = (JsonObject) collationNode;
JsonArray witnessesNode;
try {
witnessesNode = collationObject.getJsonArray("witnesses");
} catch (ClassCastException e) {
throw new IOException("Expecting 'witnesses' array");
}
final List witnesses = new ArrayList<>(witnessesNode.size());
for (JsonValue witnessNode : witnessesNode) {
if (witnessNode.getValueType() != JsonValue.ValueType.OBJECT) {
throw new IOException("Expecting witness object");
}
final JsonObject witnessObject = (JsonObject) witnessNode;
final String witnessId;
try {
witnessId = witnessObject.getString("id").trim();
} catch (ClassCastException e) {
throw new IOException("Expected textual witness 'id'");
}
if (witnessId.length() == 0) {
throw new IOException("Empty witness 'id' encountered");
}
final SimpleWitness witness = new SimpleWitness(witnessId);
if (witnesses.contains(witness)) {
throw new IOException(String.format("Duplicate sigil for witness '%s", witness));
}
final JsonValue contentNode = witnessObject.get("content");
final JsonValue tokensNode = witnessObject.get("tokens");
if (contentNode == null && tokensNode == null) {
throw new IOException(String.format("Expected either 'tokens' or 'content' field in witness \"%s\"", witness));
}
if (tokensNode != null) {
if (tokensNode.getValueType() != JsonValue.ValueType.ARRAY) {
throw new IOException(String.format("Expected 'tokens' array in witness \"%s\"", witness));
}
final JsonArray tokensArray = (JsonArray) tokensNode;
final List tokens = new ArrayList<>(tokensArray.size());
for (JsonValue tokenNode : tokensArray) {
if (tokenNode.getValueType() != JsonValue.ValueType.OBJECT) {
throw new IOException(String.format("Expected token object in 'tokens' field in witness \"%s\"", witness));
}
final JsonObject tokenObject = (JsonObject) tokenNode;
String tokenContent;
try {
tokenContent = tokenObject.getString("t");
} catch (ClassCastException | NullPointerException e) {
throw new IOException(String.format("Expected textual token content field 't' in witness \"%s\"", witness));
}
String normalizedTokenContent;
if (tokenObject.containsKey("n")) {
try {
normalizedTokenContent = tokenObject.getString("n");
} catch (ClassCastException e) {
throw new IOException(String.format("Expected textual normalized token content in witness \"%s\"", witness));
}
} else {
normalizedTokenContent = SimpleWitness.TOKEN_NORMALIZER.apply(tokenContent);
}
if (normalizedTokenContent == null || normalizedTokenContent.length() == 0) {
throw new IOException(String.format("Empty token encountered in witness \"%s\"", witness));
}
tokens.add(new Token(witness, tokenContent, normalizedTokenContent, tokenObject));
}
witness.setTokens(tokens);
} else {
if (contentNode.getValueType() != JsonValue.ValueType.STRING) {
throw new IOException(String.format("Expected 'content' text field in witness \"%s\"", witness));
}
witness.setTokenContents(
SimplePatternTokenizer.BY_WS_OR_PUNCT.apply(((JsonString) contentNode).getString()),
SimpleTokenNormalizers.LC_TRIM_WS
);
}
witnesses.add(witness);
}
if (witnesses.isEmpty()) {
throw new IOException("No witnesses in collation");
}
Comparator tokenComparator = null;
final JsonValue tokenComparatorNode = collationObject.get("tokenComparator");
if (tokenComparatorNode != null && tokenComparatorNode.getValueType() == JsonValue.ValueType.OBJECT) {
final JsonObject tokenComparatorObject = (JsonObject) tokenComparatorNode;
try {
if ("levenshtein".equals(tokenComparatorObject.getString("type"))) {
final int configuredDistance = tokenComparatorObject.getInt("distance", 0);
tokenComparator = new EditDistanceTokenComparator(configuredDistance == 0 ? 1 : configuredDistance);
}
} catch (ClassCastException e) {
// ignored
}
}
if (tokenComparator == null) {
tokenComparator = new EqualityTokenComparator();
}
CollationAlgorithm collationAlgorithm = null;
final JsonValue collationAlgorithmNode = collationObject.get("algorithm");
if (collationAlgorithmNode != null && collationAlgorithmNode.getValueType() == JsonValue.ValueType.STRING) {
final String collationAlgorithmValue = ((JsonString) collationAlgorithmNode).getString();
if ("needleman-wunsch".equalsIgnoreCase(collationAlgorithmValue)) {
collationAlgorithm = CollationAlgorithmFactory.needlemanWunsch(tokenComparator);
} else if ("gst".equalsIgnoreCase(collationAlgorithmValue)) {
collationAlgorithm = CollationAlgorithmFactory.greedyStringTiling(tokenComparator, 2);
} else if ("medite".equalsIgnoreCase(collationAlgorithmValue)) {
collationAlgorithm = CollationAlgorithmFactory.medite(tokenComparator, SimpleToken.TOKEN_MATCH_EVALUATOR);
}
}
if (collationAlgorithm == null) {
collationAlgorithm = CollationAlgorithmFactory.dekker(tokenComparator);
}
boolean joined = true;
try {
joined = collationObject.getBoolean("joined", true);
} catch (ClassCastException e) {
// ignored
}
if (collationAlgorithm instanceof InspectableCollationAlgorithm) {
boolean mergeTranspositions = true;
try {
mergeTranspositions = collationObject.getBoolean("transpositions", true);
} catch (ClassCastException e) {
// ignored
}
((InspectableCollationAlgorithm) collationAlgorithm).setMergeTranspositions(mergeTranspositions);
}
return new SimpleCollation(witnesses, collationAlgorithm, joined);
}
}
public static void write(VariantGraph graph, OutputStream outputStream) throws IOException {
try (final JsonGenerator jgen = Json.createGenerator(outputStream)) {
write(jgen, graph);
}
}
public static void write(VariantGraph graph, PrintWriter writer) throws IOException {
try (final JsonGenerator jgen = Json.createGenerator(writer)) {
write(jgen, graph);
}
}
protected static void write(JsonGenerator jgen, VariantGraph graph) {
ParallelSegmentationApparatus.generate(VariantGraphRanking.of(graph), new ParallelSegmentationApparatus.GeneratorCallback() {
@Override
public void start() {
jgen.writeStartObject();
jgen.writeStartArray("witnesses");
graph.witnesses().stream().sorted(Witness.SIGIL_COMPARATOR).map(Witness::getSigil).forEach(jgen::write);
jgen.writeEnd();
jgen.writeStartArray("table");
}
@Override
public void segment(SortedMap> contents) {
jgen.writeStartArray();
contents.values().stream().forEach(tokens -> {
jgen.writeStartArray();
StreamSupport.stream(Spliterators.spliteratorUnknownSize(tokens.iterator(), Spliterator.NONNULL | Spliterator.IMMUTABLE), false)
.filter(t -> t instanceof SimpleToken)
.map(t -> (SimpleToken) t)
.sorted()
.forEach(t -> {
if (t instanceof Token) {
jgen.write(((Token) t).getJsonNode());
} else {
jgen.write(t.getContent());
}
});
jgen.writeEnd();
});
jgen.writeEnd();
}
@Override
public void end() {
jgen.writeEnd();
jgen.writeEnd();
}
});
}
public static class Token extends SimpleToken {
private final JsonObject jsonNode;
public Token(SimpleWitness witness, String content, String normalized, JsonObject jsonNode) {
super(witness, content, normalized);
this.jsonNode = jsonNode;
}
public JsonObject getJsonNode() {
return jsonNode;
}
}
private JsonProcessor() {
}
}
