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/*
* 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 io.uhndata.cards.vocabularies.internal;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.Reader;
import java.nio.charset.StandardCharsets;
import java.util.Collection;
import java.util.Collections;
import java.util.LinkedHashMap;
import java.util.LinkedHashSet;
import java.util.Map;
import java.util.function.Consumer;
import org.osgi.service.component.annotations.Component;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import io.uhndata.cards.vocabularies.spi.SourceParser;
import io.uhndata.cards.vocabularies.spi.VocabularyDescription;
import io.uhndata.cards.vocabularies.spi.VocabularyIndexException;
import io.uhndata.cards.vocabularies.spi.VocabularyTermSource;
/**
* Parser for vocabulary sources in the OBO format.
*
* @version $Id: 78fd45d83ccd942e2c19f92cf98f89b219daa1a1 $
*/
@Component(
service = SourceParser.class,
name = "SourceParser.OBO")
@SuppressWarnings("checkstyle:ClassDataAbstractionCoupling")
public class OboParser implements SourceParser
{
/** Marks the start of a new Frame. */
private static final String FRAME_MARKER = "^\\[[a-zA-Z]+\\]$";
/** Marks the start of a new Term Frame. */
private static final String TERM_MARKER = "[Term]";
/**
* Regex pattern for separating the tag and its value from a line: an optional even number of backslashes, followed
* by a colon, and optional whitespace.
*/
private static final String FIELD_NAME_VALUE_SEPARATOR = "(? crtTerm = new InheritableThreadLocal<>();
/** Holds all the terms parsed so far. */
private InheritableThreadLocal> data = new InheritableThreadLocal<>();
/** Logger object used to handle thrown errors. */
private Logger logger = LoggerFactory.getLogger(this.getClass());
@Override
public boolean canParse(String format)
{
return "OBO".equalsIgnoreCase(format);
}
@Override
public void parse(
final File source,
final VocabularyDescription vocabularyDescription,
final Consumer consumer) throws IOException, VocabularyIndexException
{
try {
this.data.set(new LinkedHashMap<>());
readLines(source);
propagateAncestors();
consumeData(consumer);
this.data.remove();
} catch (IOException ex) {
this.logger.error("IOException: {}", ex.getMessage());
}
}
/**
* Read the source file and populate the data variable.
*
* @param source the file containing the vocabulary source in OBO format
* @throws IOException if reading the source file fails
*/
private void readLines(final File source) throws IOException
{
// Start by examining a new term
this.crtTerm.set(new TermData());
try (ConcatenatingLineReader br =
new ConcatenatingLineReader(new InputStreamReader(new FileInputStream(source), StandardCharsets.UTF_8))) {
String line;
// Used to skip over the header and non-Term frames
// Initially false, since at the start of the file is the header
boolean isTerm = false;
while ((line = br.readLine()) != null) {
if (line.trim().matches(FRAME_MARKER)) {
// We just encountered the start of a new frame
if (isTerm) {
// If the previous frame was a Term, store it
storeCrtTerm();
}
// Non-Term frames must be ignored, only Terms are recorded
isTerm = line.trim().equalsIgnoreCase(TERM_MARKER);
continue;
}
if (isTerm) {
// Inside a Term, process its values
String[] pieces = line.split(FIELD_NAME_VALUE_SEPARATOR, 2);
if (pieces.length != 2) {
continue;
}
loadField(pieces[0], pieces[1]);
}
}
// Also store the last term parsed when the end of the file is encountered
if (isTerm) {
storeCrtTerm();
}
}
}
/**
* Store the current term data and set up a new TermData instance to record the next term.
*/
private void storeCrtTerm()
{
// Only terms with a valid identifier can be stored
TermData termToProcess = this.crtTerm.get();
if (termToProcess.getId() != null) {
// Multiple frames can describe the same term, we must combine them into one
TermData existing = this.data.get().get(termToProcess.getId());
if (existing == null) {
this.data.get().put(termToProcess.getId(), termToProcess);
} else {
existing.getAllProperties().putAll(termToProcess.getAllProperties());
}
}
this.crtTerm.set(new TermData());
}
/**
* Process a field ("name = value" pair) by extracting only the actual value, ignoring trailing modifiers, dbxrefs,
* and comments, as well as synonym categories.
*
* @param name the name of the property
* @param value the raw value, which may be a simple unquoted or quoted value, or a value with additional trailing
* modifiers, comments, and other tags
*/
private void loadField(String name, String value)
{
this.crtTerm.get().addTo(process(name), process(value));
}
/**
* Process a raw value read from the OBO file to extract only the real value, ignoring trailing modifiers, comments,
* and xref lists, removing quotes if needed, and unescaping special escape sequences.
*
* @param rawValue the value as present in the input file
* @return the processed value, with any trailing bits removed, unquoted, and unescaped
*/
private String process(final String rawValue)
{
String realValue = rawValue;
// If the string was quoted, then trailing modifiers and comments don't need to be trimmed from within
final boolean wasQuoted = rawValue.startsWith("\"");
// If the value is quoted, only keep the part inside the quotes.
// - must match from the start: ^
// - must start with a quote: \"
// - start a capture: (
// - any characters: .*
// - lazy matching, capture the shortest match to avoid capturing between two distinct quoted strings): ?
// (now going backwards from the last closing bracket)
// - end the capture: )
// - which may be proceded by an even number of backslashes, including none: (?:\\\\\\\\)*
// -- two backslashes: \\
// -- escaped as part of the regexp: \\\\
// -- escaped again as part of a java string: \\\\\\\\
// -- in a non-capturing group: (?:\\\\\\\\)
// -- repeated any number of times, including 0: (?:\\\\\\\\)*
// - not preceded by another backslash, which would make it an odd number of backslashes: (? findAncestors(String termID)
{
TermData term = this.data.get().get(termID);
if (term == null) {
// Unknown parent
return Collections.emptySet();
}
// If the ancestors for this node have already been determined, return them as a list of IDs.
if (term.hasKey(TermData.TERM_CATEGORY_FIELD_NAME)) {
return term.getAllValues(TermData.TERM_CATEGORY_FIELD_NAME);
} else {
Collection parents;
// If the node has Parents, it definitely has Ancestors but they have not yet been determined.
if (term.hasKey(TermData.PARENT_FIELD_NAME)) {
parents = term.getAllValues(TermData.PARENT_FIELD_NAME);
} else {
// Else we have reached the root node which has no parents.
parents = Collections.emptySet();
}
Collection ancestors = new LinkedHashSet<>(parents);
// Take the Union of the ancestors IDs of all parent nodes and the IDs of parents.
for (String parent : parents) {
ancestors.addAll(findAncestors(parent));
}
// This Union is set as the current node's ancestors.
term.addTo(TermData.TERM_CATEGORY_FIELD_NAME, ancestors);
// Return Union
return ancestors;
}
}
/**
* Recursively computes ancestors from the parents for all terms.
*/
private void propagateAncestors()
{
for (String id : this.data.get().keySet()) {
findAncestors(id);
}
}
/**
* Creates a new VocabularyTermSource object from the parsed Term and passes it to the consumer function.
*
* @param consumer method that will store the parsed term
*/
private void consumeData(final Consumer consumer)
{
String[] typeString = {};
for (String id : this.data.get().keySet()) {
TermData term = this.data.get().get(id);
consumer.accept(new VocabularyTermSource(
term.getId(),
term.getLabel(),
term.getAllValues(TermData.PARENT_FIELD_NAME).toArray(typeString),
term.getAllValues(TermData.TERM_CATEGORY_FIELD_NAME).toArray(typeString),
term.getAllProperties()));
}
}
/**
* A buffered line reader that concatenates split lines into one. In other words, whenever a real line ends with an
* unescaped backslash, the backslash is removed and the following line is appended.
*
* @version $Id: 78fd45d83ccd942e2c19f92cf98f89b219daa1a1 $
*/
private static final class ConcatenatingLineReader extends BufferedReader
{
ConcatenatingLineReader(Reader in)
{
super(in);
}
@Override
public String readLine() throws IOException
{
String line = super.readLine();
StringBuilder concatenatedLine = new StringBuilder();
boolean firstLineIsNull = true;
while (line != null
&& line.toString().matches(".*((?
