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src/main/java/io/anserini/collection/CovidFullTextCollection.java
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| /* | ||
| * Anserini: A Lucene toolkit for replicable information retrieval research | ||
| * | ||
| * Licensed 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.anserini.collection; | ||
|
|
||
| import org.apache.commons.csv.CSVFormat; | ||
| import org.apache.commons.csv.CSVParser; | ||
| import org.apache.commons.csv.CSVRecord; | ||
| import org.apache.logging.log4j.LogManager; | ||
| import org.apache.logging.log4j.Logger; | ||
|
|
||
| import java.io.BufferedReader; | ||
| import java.io.FileInputStream; | ||
| import java.io.IOException; | ||
| import java.io.InputStreamReader; | ||
| import java.nio.file.Files; | ||
| import java.nio.file.Path; | ||
| import java.nio.file.Paths; | ||
| import java.util.Iterator; | ||
| import java.util.NoSuchElementException; | ||
| import java.util.Set; | ||
|
|
||
| /** | ||
| * A document collection for the CORD-19 dataset provided by Semantic Scholar. | ||
| */ | ||
| public class CovidFullTextCollection extends DocumentCollection<CovidFullTextCollection.Document> { | ||
| private static final Logger LOG = LogManager.getLogger(CovidFullTextCollection.class); | ||
|
|
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| public CovidFullTextCollection(Path path){ | ||
| this.path = path; | ||
| this.allowedFileSuffix = Set.of(".csv"); | ||
| } | ||
|
|
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| @Override | ||
| public FileSegment<CovidFullTextCollection.Document> createFileSegment(Path p) throws IOException { | ||
| return new Segment(p); | ||
| } | ||
|
|
||
| /** | ||
| * A file containing a single CSV document. | ||
| */ | ||
| public class Segment extends FileSegment<CovidFullTextCollection.Document> { | ||
| CSVParser csvParser = null; | ||
| private CSVRecord record = null; | ||
| private Iterator<CSVRecord> iterator = null; // iterator for CSV records | ||
|
|
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| public Segment(Path path) throws IOException { | ||
| super(path); | ||
| bufferedReader = new BufferedReader(new InputStreamReader( | ||
| new FileInputStream(path.toString()))); | ||
|
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| csvParser = new CSVParser(bufferedReader, CSVFormat.DEFAULT | ||
| .withFirstRecordAsHeader() | ||
| .withIgnoreHeaderCase() | ||
| .withTrim()); | ||
|
|
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| iterator = csvParser.iterator(); | ||
| if (iterator.hasNext()) { | ||
| record = iterator.next(); | ||
| } | ||
| } | ||
|
|
||
| @Override | ||
| public void readNext() throws NoSuchElementException { | ||
| if (record == null) { | ||
| throw new NoSuchElementException("Record is empty"); | ||
| } else { | ||
| bufferedRecord = new CovidFullTextCollection.Document(record); | ||
| if (iterator.hasNext()) { // if CSV contains more lines, we parse the next record | ||
| record = iterator.next(); | ||
| } else { | ||
| atEOF = true; // there is no more JSON object in the bufferedReader | ||
| } | ||
| } | ||
| } | ||
|
|
||
| @Override | ||
| public void close() { | ||
| super.close(); | ||
| if (csvParser != null) { | ||
| try { | ||
| csvParser.close(); | ||
| } catch (IOException e) { | ||
| // do nothing | ||
| } | ||
| } | ||
| } | ||
| } | ||
|
|
||
| /** | ||
| * A document in a CORD-19 collection. | ||
| */ | ||
| public class Document implements SourceDocument { | ||
| private String id; | ||
| private String content; | ||
| private String raw; | ||
| private CSVRecord record; | ||
|
|
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| public Document(CSVRecord record) { | ||
| id = Long.toString(record.getRecordNumber()); | ||
| content = record.get("title").replace("\n", " "); | ||
| content += record.get("abstract").isEmpty() ? "" : "\n" + record.get("abstract"); | ||
| this.record = record; | ||
|
|
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| String fullTextJson = ""; | ||
| // index full text into raw content | ||
| if (record.get("has_full_text").contains("True")) { | ||
| String[] hashes = record.get("sha").split(";"); | ||
| String fullTextPath = "/" + record.get("full_text_file") + "/" + hashes[hashes.length - 1].strip() + ".json"; | ||
| try { | ||
| fullTextJson = new String(Files.readAllBytes( | ||
| Paths.get(CovidFullTextCollection.this.path.toString() + fullTextPath))); | ||
| } catch (IOException e) { | ||
| LOG.error("Error parsing file at " + fullTextPath); | ||
| raw = record.toString(); | ||
| } | ||
| } | ||
|
|
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| if (!fullTextJson.isEmpty()) { | ||
| content += fullTextJson.isEmpty() ? "" : "\n " + fullTextJson; | ||
| raw = fullTextJson; | ||
| } else { | ||
| raw = record.toString(); | ||
| } | ||
| } | ||
|
|
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| @Override | ||
| public String id() { | ||
| return id; | ||
| } | ||
|
|
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| @Override | ||
| public String content() { | ||
| return content; | ||
| } | ||
|
|
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| @Override | ||
| public boolean indexable() { | ||
| return true; | ||
| } | ||
|
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| public String raw() { | ||
| return raw; | ||
| } | ||
|
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| public CSVRecord record() { | ||
| return record; | ||
| } | ||
| } | ||
| } |
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