Fix #10498 Create Fetcher and Transformer for ScholarArchive

CHANGELOG.md

@@ -13,6 +13,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 - We added a dropdown menu to let users change the reference library during AUX file import. [#10472](https://github.com/JabRef/jabref/issues/10472)
 - We added a button to let users reset the cite command to the default value. [#10569](https://github.com/JabRef/jabref/issues/10569)
+- We added [scholar.archive.org](https://scholar.archive.org/) as a new fetcher. [#10498](https://github.com/JabRef/jabref/issues/10498)
 
 ### Changed
 

src/main/java/org/jabref/logic/importer/WebFetchers.java

@@ -37,6 +37,7 @@
 import org.jabref.logic.importer.fetcher.OpenAccessDoi;
 import org.jabref.logic.importer.fetcher.ResearchGate;
 import org.jabref.logic.importer.fetcher.RfcFetcher;
+import org.jabref.logic.importer.fetcher.ScholarArchiveFetcher;
 import org.jabref.logic.importer.fetcher.ScienceDirect;
 import org.jabref.logic.importer.fetcher.SemanticScholar;
 import org.jabref.logic.importer.fetcher.SpringerFetcher;
@@ -126,6 +127,7 @@ public static SortedSet<SearchBasedFetcher> getSearchBasedFetchers(ImportFormatP
  set.add(new ResearchGate(importFormatPreferences));
  set.add(new BiodiversityLibrary(importerPreferences));
  set.add(new LOBIDFetcher(importerPreferences));
+ set.add(new ScholarArchiveFetcher());
  return set;
  }
 

src/main/java/org/jabref/logic/importer/fetcher/ScholarArchiveFetcher.java

@@ -0,0 +1,158 @@
+package org.jabref.logic.importer.fetcher;
+
+import java.net.MalformedURLException;
+import java.net.URISyntaxException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Optional;
+import java.util.stream.IntStream;
+
+import org.jabref.logic.importer.FetcherException;
+import org.jabref.logic.importer.PagedSearchBasedParserFetcher;
+import org.jabref.logic.importer.ParseException;
+import org.jabref.logic.importer.Parser;
+import org.jabref.logic.importer.fetcher.transformers.ScholarArchiveQueryTransformer;
+import org.jabref.logic.importer.util.JsonReader;
+import org.jabref.logic.net.URLDownload;
+import org.jabref.model.entry.AuthorList;
+import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.field.StandardField;
+import org.jabref.model.entry.types.EntryType;
+import org.jabref.model.entry.types.StandardEntryType;
+
+import jakarta.ws.rs.core.MediaType;
+import kong.unirest.json.JSONArray;
+import kong.unirest.json.JSONException;
+import kong.unirest.json.JSONObject;
+import org.apache.http.client.utils.URIBuilder;
+import org.apache.lucene.queryparser.flexible.core.nodes.QueryNode;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+public class ScholarArchiveFetcher implements PagedSearchBasedParserFetcher {
+
+ public static final String FETCHER_NAME = "ScholarArchive";
+
+ private static final Logger LOGGER = LoggerFactory.getLogger(ScholarArchiveFetcher.class);
+
+ private static final String API_URL = "https://scholar.archive.org/search";
+
+ /**
+ * Gets the query URL by luceneQuery and pageNumber.
+ *
+ * @param luceneQuery the search query
+ * @param pageNumber the number of the page indexed from 0
+ * @return URL
+ */
+ @Override
+ public URL getURLForQuery(QueryNode luceneQuery, int pageNumber) throws URISyntaxException, MalformedURLException, FetcherException {
+ URIBuilder uriBuilder = new URIBuilder(API_URL);
+ uriBuilder.addParameter("q", new ScholarArchiveQueryTransformer().transformLuceneQuery(luceneQuery).orElse(""));
+ uriBuilder.addParameter("from", String.valueOf(getPageSize() * pageNumber));
+ uriBuilder.addParameter("size", String.valueOf(getPageSize()));
+ uriBuilder.addParameter("format", "json");
+
+ LOGGER.debug("using URL for search {}", uriBuilder.build());
+ return uriBuilder.build().toURL();
+ }
+
+ @Override
+ public URLDownload getUrlDownload(URL url) {
+ URLDownload download = new URLDownload(url);
+ download.addHeader("Accept", MediaType.APPLICATION_JSON);
+ return download;
+ }
+
+ /**
+ * Gets the list of BibEntry by given Json response from scholar archive fetcher API
+ *
+ * @return Parser, list of BibEntry
+ */
+ @Override
+ public Parser getParser() {
+ return inputStream -> {
+ JSONObject response = JsonReader.toJsonObject(inputStream);
+ List<BibEntry> entries = new ArrayList<>();
+ if (response.has("results")) {
+ JSONArray results = response.getJSONArray("results");
+ for (int i = 0; i < results.length(); i++) {
+ JSONObject jsonEntry = results.getJSONObject(i);
+ BibEntry entry = parseJSONtoBibtex(jsonEntry);
+ entries.add(entry);
+ }
+ }
+
+ return entries;
+ };
+ }
+
+ @Override
+ public String getName() {
+ return FETCHER_NAME;
+ }
+
+ private BibEntry parseJSONtoBibtex(JSONObject jsonEntry) throws ParseException {
+ try {
+ BibEntry entry = new BibEntry();
+ EntryType entryType = StandardEntryType.InCollection;
+ JSONObject biblio = jsonEntry.optJSONObject("biblio");
+
+ JSONArray abstracts = jsonEntry.getJSONArray("abstracts");
+ String foundAbstract = IntStream.range(0, abstracts.length())
+ .mapToObj(abstracts::getJSONObject)
+ .map(object -> object.optString("body"))
+ .findFirst().orElse("");
+
+ String url = Optional.ofNullable(jsonEntry.optJSONObject("fulltext")).map(fullText -> fullText.optString("access_url")).orElse("");
+
+ // publication type
+ String type = biblio.optString("release_type");
+ entry.setField(StandardField.TYPE, type);
+ if (type.toLowerCase().contains("book")) {
+ entryType = StandardEntryType.Book;
+ } else if (type.toLowerCase().contains("article")) {
+ entryType = StandardEntryType.Article;
+ }
+ entry.setType(entryType);
+
+ entry.setField(StandardField.TITLE, biblio.optString("title"));
+ entry.setField(StandardField.JOURNAL, biblio.optString("container_name"));
+ entry.setField(StandardField.DOI, biblio.optString("doi"));
+ entry.setField(StandardField.ISSUE, biblio.optString("issue"));
+ entry.setField(StandardField.LANGUAGE, biblio.optString("lang_code"));
+ entry.setField(StandardField.PUBLISHER, biblio.optString("publisher"));
+
+ entry.setField(StandardField.YEAR, String.valueOf(biblio.optInt("release_year")));
+ entry.setField(StandardField.VOLUME, String.valueOf(biblio.optInt("volume_int")));
+ entry.setField(StandardField.ABSTRACT, foundAbstract);
+ entry.setField(StandardField.URL, url);
+
+ String dateString = biblio.optString("date");
+ entry.setField(StandardField.DATE, dateString);
+
+ // Authors are in contrib_names
+ if (biblio.has("contrib_names")) {
+ JSONArray authors = biblio.getJSONArray("contrib_names");
+ List<String> authorList = new ArrayList<>();
+ for (int i = 0; i < authors.length(); i++) {
+ authorList.add(authors.getString(i));
+ }
+ AuthorList parsedAuthors = AuthorList.parse(String.join(" and ", authorList));
+ entry.setField(StandardField.AUTHOR, parsedAuthors.getAsLastFirstNamesWithAnd(false));
+ }
+
+ if (biblio.has("issns")) {
+ JSONArray issn = biblio.getJSONArray("issns");
+ List<String> issnList = new ArrayList<>();
+ for (int i = 0; i < issn.length(); i++) {
+ issnList.add(issn.getString(i));
+ }
+ entry.setField(StandardField.ISSN, String.join(" ", issnList));
+ }
+ return entry;
+ } catch (JSONException exception) {
+ throw new ParseException("ScholarArchive API JSON format has changed", exception);
+ }
+ }
+}

src/main/java/org/jabref/logic/importer/fetcher/transformers/ScholarArchiveQueryTransformer.java

@@ -0,0 +1,71 @@
+package org.jabref.logic.importer.fetcher.transformers;
+
+/**
+ * This class extends the AbstractQueryTransformer to provide specific implementations
+ * for transforming standard queries into ones suitable for the Scholar Archive's unique format.
+ */
+public class ScholarArchiveQueryTransformer extends AbstractQueryTransformer {
+
+ @Override
+ protected String getLogicalAndOperator() {
+ return " AND ";
+ }
+
+ @Override
+ protected String getLogicalOrOperator() {
+ return " OR ";
+ }
+
+ @Override
+ protected String getLogicalNotOperator() {
+ return "NOT ";
+ }
+
+ @Override
+ protected String handleAuthor(String author) {
+ return createKeyValuePair("contrib_names", author);
+ }
+
+ @Override
+ protected String handleTitle(String title) {
+ return createKeyValuePair("title", title);
+ }
+
+ @Override
+ protected String handleJournal(String journalTitle) {
+ return createKeyValuePair("container_name", journalTitle);
+ }
+
+ /**
+ * Handles the year query by formatting it specifically for a range search in the Scholar Archive.
+ * This method is for an exact year match.
+ *
+ * @param year the publication year to be searched in the Scholar Archive.
+ * @return A string query segment formatted for the year search.
+ */
+ @Override
+ protected String handleYear(String year) {
+ return "publication.startDate:[" + year + " TO " + year + "]";
+ }
+
+ /**
+ * Handles a year range query, transforming it for the Scholar Archive's query format.
+ * If only a start year is provided, the range will extend to the current year.
+ *
+ * @param yearRange the range of years to be searched in the Scholar Archive, usually in the format "startYear-endYear".
+ * @return A string query segment formatted for the year range search.
+ */
+ @Override
+ protected String handleYearRange(String yearRange) {
+ parseYearRange(yearRange);
+ if (endYear == Integer.MAX_VALUE) {
+ // If no specific end year is set, it assumes the range extends to the current year.
+ return yearRange;
+ }
+ return "publication.startDate:[" + startYear + " TO " + endYear + "]";
+ }
+}
+
+
+
+

src/test/java/org/jabref/gui/slr/ManageStudyDefinitionViewModelTest.java

@@ -51,6 +51,7 @@ public void emptyStudyConstructorFillsDatabasesCorrectly() {
  new StudyCatalogItem("Medline/PubMed", false),
  new StudyCatalogItem("ResearchGate", false),
  new StudyCatalogItem("SAO/NASA ADS", false),
+ new StudyCatalogItem("ScholarArchive", false),
  new StudyCatalogItem("SemanticScholar", false),
  new StudyCatalogItem("Springer", true),
  new StudyCatalogItem("zbMATH", false)
@@ -59,21 +60,7 @@ public void emptyStudyConstructorFillsDatabasesCorrectly() {
 
  @Test
  public void studyConstructorFillsDatabasesCorrectly(@TempDir Path tempDir) {
- List<StudyDatabase> databases = List.of(
- new StudyDatabase("ACM Portal", true));
- Study study = new Study(
- List.of("Name"),
- "title",
- List.of("Q1"),
- List.of(),
- databases
- );
- ManageStudyDefinitionViewModel manageStudyDefinitionViewModel = new ManageStudyDefinitionViewModel(
- study,
- tempDir,
- importFormatPreferences,
- importerPreferences,
- dialogService);
+ ManageStudyDefinitionViewModel manageStudyDefinitionViewModel = getManageStudyDefinitionViewModel(tempDir);
  assertEquals(List.of(
  new StudyCatalogItem("ACM Portal", true),
  new StudyCatalogItem("ArXiv", false),
@@ -92,9 +79,28 @@ public void studyConstructorFillsDatabasesCorrectly(@TempDir Path tempDir) {
  new StudyCatalogItem("Medline/PubMed", false),
  new StudyCatalogItem("ResearchGate", false),
  new StudyCatalogItem("SAO/NASA ADS", false),
+ new StudyCatalogItem("ScholarArchive", false),
  new StudyCatalogItem("SemanticScholar", false),
  new StudyCatalogItem("Springer", false),
  new StudyCatalogItem("zbMATH", false)
  ), manageStudyDefinitionViewModel.getCatalogs());
  }
+
+ private ManageStudyDefinitionViewModel getManageStudyDefinitionViewModel(Path tempDir) {
+ List<StudyDatabase> databases = List.of(
+ new StudyDatabase("ACM Portal", true));
+ Study study = new Study(
+ List.of("Name"),
+ "title",
+ List.of("Q1"),
+ List.of(),
+ databases
+ );
+ return new ManageStudyDefinitionViewModel(
+ study,
+ tempDir,
+ importFormatPreferences,
+ importerPreferences,
+ dialogService);
+ }
 }

src/test/java/org/jabref/logic/importer/fetcher/ScholarArchiveFetcherTest.java

@@ -0,0 +1,51 @@
+package org.jabref.logic.importer.fetcher;
+
+import java.util.List;
+
+import org.jabref.logic.importer.FetcherException;
+import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.field.StandardField;
+import org.jabref.model.entry.types.StandardEntryType;
+import org.jabref.testutils.category.FetcherTest;
+
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+
+@FetcherTest
+public class ScholarArchiveFetcherTest {
+ private ScholarArchiveFetcher fetcher;
+ private BibEntry bibEntry;
+
+ @BeforeEach
+ public void setUp() {
+ fetcher = new ScholarArchiveFetcher();
+ bibEntry = new BibEntry(StandardEntryType.InCollection)
+ .withField(StandardField.TITLE, "Query expansion using associated queries")
+ .withField(StandardField.AUTHOR, "Billerbeck, Bodo and Scholer, Falk and Williams, Hugh E. and Zobel, Justin")
+ .withField(StandardField.VOLUME, "0")
+ .withField(StandardField.DOI, "10.1145/956863.956866")
+ .withField(StandardField.JOURNAL, "Proceedings of the twelfth international conference on Information and knowledge management - CIKM '03")
+ .withField(StandardField.PUBLISHER, "ACM Press")
+ .withField(StandardField.TYPE, "paper-conference")
+ .withField(StandardField.YEAR, "2003")
+ .withField(StandardField.URL, "https://web.archive.org/web/20170810164449/http://goanna.cs.rmit.edu.au/~jz/fulltext/cikm03.pdf");
+ }
+
+ @Test
+ public void getNameReturnsCorrectName() {
+ assertEquals("ScholarArchive", fetcher.getName());
+ }
+
+ @Test
+ public void performSearchReturnsExpectedResults() throws FetcherException {
+ List<BibEntry> fetchedEntries = fetcher.performSearch("query");
+ fetchedEntries.forEach(entry -> entry.clearField(StandardField.ABSTRACT));
+ assertTrue(fetchedEntries.contains(bibEntry), "Found the following entries " + fetchedEntries);
+ }
+}
+
+
+