Fix parsing of JabRef v5.7 study.yml files (#9124)

Author: koppor

CHANGELOG.md

@@ -24,7 +24,8 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We call backup files `.bak` and temporary writing files now `.sav`.
 - JabRef keeps 10 older versions of a `.bib` file in the [user data dir](https://github.com/harawata/appdirs#supported-directories) (instead of a single `.sav` (now: `.bak`) file in the directory of the `.bib` file)
 - We changed the button label from "Return to JabRef" to "Return to library" to better indicate the purpose of the action.
-- We removed "last-search-date" from the SLR feature, because the last-search-date can be deducted from the git logs.
+- We removed "last-search-date" from the SLR feature, because the last-search-date can be deducted from the git logs. [#9116](https://github.com/JabRef/jabref/pull/9116)
+- A user can now add arbitrary data into `study.yml`. JabRef just ignores this data. [#9124](https://github.com/JabRef/jabref/pull/9124)
 - We reworked the External Changes Resolver dialog. [#9021](https://github.com/JabRef/jabref/pull/9021)
 - We reworked the Define study parameters dialog. [#9123](https://github.com/JabRef/jabref/pull/9123)
 

src/main/java/org/jabref/logic/crawler/StudyYamlParser.java

@@ -8,10 +8,8 @@
 import org.jabref.model.study.Study;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
-import com.fasterxml.jackson.databind.SerializationFeature;
 import com.fasterxml.jackson.dataformat.yaml.YAMLFactory;
 import com.fasterxml.jackson.dataformat.yaml.YAMLGenerator;
-import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule;
 
 public class StudyYamlParser {
 
@@ -20,7 +18,6 @@ public class StudyYamlParser {
      */
     public Study parseStudyYamlFile(Path studyYamlFile) throws IOException {
         ObjectMapper yamlMapper = new ObjectMapper(new YAMLFactory());
-        yamlMapper.registerModule(new JavaTimeModule());
         try (InputStream fileInputStream = new FileInputStream(studyYamlFile.toFile())) {
             return yamlMapper.readValue(fileInputStream, Study.class);
         }
@@ -32,8 +29,6 @@ public Study parseStudyYamlFile(Path studyYamlFile) throws IOException {
     public void writeStudyYamlFile(Study study, Path studyYamlFile) throws IOException {
         ObjectMapper yamlMapper = new ObjectMapper(new YAMLFactory().disable(YAMLGenerator.Feature.WRITE_DOC_START_MARKER)
                                                                     .enable(YAMLGenerator.Feature.MINIMIZE_QUOTES));
-        yamlMapper.registerModule(new JavaTimeModule());
-        yamlMapper.disable(SerializationFeature.WRITE_DATES_AS_TIMESTAMPS);
         yamlMapper.writeValue(studyYamlFile.toFile(), study);
     }
 }

src/main/java/org/jabref/model/study/Study.java

@@ -3,6 +3,7 @@
 import java.util.List;
 import java.util.Objects;
 
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import com.fasterxml.jackson.annotation.JsonProperty;
 import com.fasterxml.jackson.annotation.JsonPropertyOrder;
 
@@ -12,6 +13,8 @@
  * This class defines all aspects of a scientific study relevant to the application. It is a proxy for the file based study definition.
  */
 @JsonPropertyOrder({"authors", "title", "research-questions", "queries", "databases"})
+// The user might add arbitrary content to the YAML
+@JsonIgnoreProperties(ignoreUnknown = true)
 public class Study {
     private List<String> authors;
 

src/test/java/org/jabref/logic/crawler/StudyYamlParserTest.java

@@ -18,6 +18,7 @@
 class StudyYamlParserTest {
     @TempDir
     static Path testDirectory;
+
     Study expectedStudy;
 
     @BeforeEach
@@ -48,4 +49,15 @@ public void writeStudyFileSuccessfully() throws Exception {
         Study study = new StudyYamlParser().parseStudyYamlFile(testDirectory.resolve("study.yml"));
         assertEquals(expectedStudy, study);
     }
+
+    @Test
+    public void readsJabRef57StudySuccessfully() throws Exception {
+        // The field "last-search-date" was removed
+        // If the field is "just" removed from the datamodel, one gets following exception:
+        //   com.fasterxml.jackson.databind.exc.UnrecognizedPropertyException: Unrecognized field "last-search-date" (class org.jabref.model.study.Study), not marked as ignorable (5 known properties: "authors", "research-questions", "queries", "title", "databases"])
+        // This tests ensures that this exception does not occur
+        URL studyDefinition = StudyYamlParser.class.getResource("study-jabref-5.7.yml");
+        Study study = new StudyYamlParser().parseStudyYamlFile(Path.of(studyDefinition.toURI()));
+        assertEquals(expectedStudy, study);
+    }
 }

src/test/resources/org/jabref/logic/crawler/study-jabref-5.7.yml

@@ -0,0 +1,17 @@
+authors:
+  - Jab Ref
+title: TestStudyName
+last-search-date: 2020-11-26
+research-questions:
+  - Question1
+  - Question2
+queries:
+  - query: Quantum
+  - query: Cloud Computing
+  - query: '"Software Engineering"'
+databases:
+  - name: Springer
+  - name: ArXiv
+  - name: Medline/PubMed
+  - name: IEEEXplore
+    enabled: false