Resolve File Creation Issue With Medline/PubMed (#8552)

* #8455 : Ensure Fetcher Name is converted to a legal file name * #8455 : Modify Test Case * #8455 : Add changelog entry and fix failing tests * #8455 : Fix another failing test * #8455 : Implement test suggestions * #8455 : Format issues * Fixed checkstyle Co-authored-by: Carl Christian Snethlage <50491877+calixtus@users.noreply.github.com>
JabRef · Mar 16, 2022 · 5b27522 · 5b27522
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Showing 6 changed files with 18 additions and 13 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -74,6 +74,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where someone could add a duplicate field in the customize entry type dialog. [#8194](https://github.com/JabRef/jabref/issues/8194)
 - We fixed a typo in the library properties tab: "String constants". There, one can configure [BibTeX string constants](https://docs.jabref.org/advanced/strings).
 - We fixed an issue when writing a non-UTF-8 encoded file: The header is written again. [#8417](https://github.com/JabRef/jabref/issues/8417)
+- We fixed an issue where folder creation during systemic literature review failed due to an illegal fetcher name. [#8552](https://github.com/JabRef/jabref/pull/8552)
 
 ## [5.4] - 2021-12-20
 

diff --git a/src/main/java/org/jabref/logic/crawler/StudyRepository.java b/src/main/java/org/jabref/logic/crawler/StudyRepository.java
@@ -26,6 +26,7 @@
 import org.jabref.logic.importer.SearchBasedFetcher;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.util.OS;
+import org.jabref.logic.util.io.FileNameCleaner;
 import org.jabref.model.database.BibDatabase;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntryTypesManager;
@@ -428,7 +429,7 @@ private void writeResultToFile(Path pathToFile, BibDatabase entries) throws IOEx
     }
 
     private Path getPathToFetcherResultFile(String query, String fetcherName) {
-        return Path.of(repositoryPath.toString(), trimNameAndAddID(query), fetcherName + ".bib");
+        return Path.of(repositoryPath.toString(), trimNameAndAddID(query), FileNameCleaner.cleanFileName(fetcherName) + ".bib");
     }
 
     private Path getPathToQueryResultFile(String query) {

diff --git a/src/test/java/org/jabref/logic/crawler/CrawlerTest.java b/src/test/java/org/jabref/logic/crawler/CrawlerTest.java
@@ -3,6 +3,7 @@
 import java.net.URL;
 import java.nio.file.Files;
 import java.nio.file.Path;
+import java.util.List;
 
 import org.jabref.logic.bibtex.FieldContentFormatterPreferences;
 import org.jabref.logic.citationkeypattern.CitationKeyPatternPreferences;
@@ -51,14 +52,12 @@ public void testWhetherAllFilesAreCreated() throws Exception {
         assertTrue(Files.exists(Path.of(tempRepositoryDirectory.toString(), hashCodeQuantum + " - Quantum")));
         assertTrue(Files.exists(Path.of(tempRepositoryDirectory.toString(), hashCodeCloudComputing + " - Cloud Computing")));
 
-        assertTrue(Files.exists(Path.of(tempRepositoryDirectory.toString(), hashCodeQuantum + " - Quantum", "ArXiv.bib")));
-        assertTrue(Files.exists(Path.of(tempRepositoryDirectory.toString(), hashCodeCloudComputing + " - Cloud Computing", "ArXiv.bib")));
-
-        assertTrue(Files.exists(Path.of(tempRepositoryDirectory.toString(), hashCodeQuantum + " - Quantum", "Springer.bib")));
-        assertTrue(Files.exists(Path.of(tempRepositoryDirectory.toString(), hashCodeCloudComputing + " - Cloud Computing", "Springer.bib")));
-
-        assertTrue(Files.exists(Path.of(tempRepositoryDirectory.toString(), hashCodeQuantum + " - Quantum", "result.bib")));
-        assertTrue(Files.exists(Path.of(tempRepositoryDirectory.toString(), hashCodeCloudComputing + " - Cloud Computing", "result.bib")));
+        List<String> filesToAssert = List.of("ArXiv.bib", "Springer.bib", "result.bib", "Medline_PubMed.bib");
+        filesToAssert.forEach(
+                fileName -> {
+                    assertTrue(Files.exists(Path.of(tempRepositoryDirectory.toString(), hashCodeQuantum + " - Quantum", fileName)));
+                    assertTrue(Files.exists(Path.of(tempRepositoryDirectory.toString(), hashCodeCloudComputing + " - Cloud Computing", fileName)));
+                });
         assertTrue(Files.exists(Path.of(tempRepositoryDirectory.toString(), "studyResult.bib")));
     }
 

diff --git a/src/test/java/org/jabref/logic/crawler/StudyDatabaseToFetcherConverterTest.java b/src/test/java/org/jabref/logic/crawler/StudyDatabaseToFetcherConverterTest.java
@@ -3,6 +3,7 @@
 import java.net.URL;
 import java.nio.file.Path;
 import java.util.List;
+import java.util.stream.Collectors;
 
 import org.jabref.logic.bibtex.FieldContentFormatterPreferences;
 import org.jabref.logic.exporter.SavePreferences;
@@ -58,9 +59,10 @@ public void getActiveFetcherInstances() throws Exception {
         StudyDatabaseToFetcherConverter converter = new StudyDatabaseToFetcherConverter(studyRepository.getActiveLibraryEntries(), importFormatPreferences);
         List<SearchBasedFetcher> result = converter.getActiveFetchers();
 
-        Assertions.assertEquals(2, result.size());
-        Assertions.assertEquals(result.get(0).getName(), "Springer");
-        Assertions.assertEquals(result.get(1).getName(), "ArXiv");
+        Assertions.assertEquals(
+                List.of("Springer", "ArXiv", "Medline/PubMed"),
+                result.stream().map(SearchBasedFetcher::getName).collect(Collectors.toList())
+        );
     }
 
     private void copyTestStudyDefinitionFileIntoDirectory(Path destination) throws Exception {

diff --git a/src/test/java/org/jabref/logic/crawler/StudyYamlParserTest.java b/src/test/java/org/jabref/logic/crawler/StudyYamlParserTest.java
@@ -31,7 +31,8 @@ void setupStudy() throws Exception {
         String studyName = "TestStudyName";
         List<String> researchQuestions = List.of("Question1", "Question2");
         List<StudyQuery> queryEntries = List.of(new StudyQuery("Quantum"), new StudyQuery("Cloud Computing"), new StudyQuery("\"Software Engineering\""));
-        List<StudyDatabase> libraryEntries = List.of(new StudyDatabase("Springer", true), new StudyDatabase("ArXiv", true), new StudyDatabase("IEEEXplore", false));
+        List<StudyDatabase> libraryEntries = List.of(new StudyDatabase("Springer", true), new StudyDatabase("ArXiv", true),
+                new StudyDatabase("Medline/PubMed", true), new StudyDatabase("IEEEXplore", false));
 
         expectedStudy = new Study(authors, studyName, researchQuestions, queryEntries, libraryEntries);
         expectedStudy.setLastSearchDate(LocalDate.parse("2020-11-26"));

diff --git a/src/test/resources/org/jabref/logic/crawler/study.yml b/src/test/resources/org/jabref/logic/crawler/study.yml
@@ -12,5 +12,6 @@ queries:
 databases:
   - name: Springer
   - name: ArXiv
+  - name: Medline/PubMed
   - name: IEEEXplore
     enabled: false