Fix merge conflicts

DiSSCo · Sep 18, 2023 · 1f48123 · 1f48123
1 parent 15424d8
commit 1f48123
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Showing 5 changed files with 1 addition and 35 deletions.
diff --git a/pom.xml b/pom.xml
@@ -279,11 +279,6 @@
         <version>1.2.1</version>
         <configuration>
           <sourceDirectory>${basedir}/src/main/resources/json-schema/</sourceDirectory>
-<!--          <sourcePaths>-->
-<!--              <sourcePath>-->
-<!--                  ${basedir}/src/main/resources/json-schema/digital-specimen.json-->
-<!--              </sourcePath>-->
-<!--          </sourcePaths>-->
           <targetPackage>eu.dissco.core.translator.schema</targetPackage>
           <generateBuilders>true</generateBuilders>
           <includeDynamicBuilders>true</includeDynamicBuilders>

diff --git a/src/main/java/eu/dissco/core/translator/service/DwcaService.java b/src/main/java/eu/dissco/core/translator/service/DwcaService.java
@@ -165,7 +165,6 @@ private void processDigitalSpecimen(Collection<ObjectNode> fullRecords)
   private List<DigitalMediaObject> processMedia(String recordId, JsonNode fullDigitalSpecimen,
       String organisationId) throws OrganisationNotRorId {
     var extensions = fullDigitalSpecimen.get(EXTENSIONS);
-    var orgId = termMapper.retrieveFromDWCA(new OrganisationId(), fullDigitalSpecimen);
     if (fullDigitalSpecimen.get(DWC_ASSOCIATED_MEDIA) != null) {
       return publishAssociatedMedia(recordId,
           fullDigitalSpecimen.get(DWC_ASSOCIATED_MEDIA).asText(), organisationId);

diff --git a/src/main/java/eu/dissco/core/translator/terms/specimen/TopicDiscipline.java b/src/main/java/eu/dissco/core/translator/terms/specimen/TopicDiscipline.java
@@ -64,20 +64,6 @@ private static String getDiscipline(String basisOfRecord, String kingdom) {
     }
   }
 
-  @Override
-  public String retrieveFromDWCA(JsonNode unit) {
-    var basisOfRecord = new BasisOfRecord().retrieveFromDWCA(unit);
-    var kingdom = new Kingdom().retrieveFromDWCA(unit);
-    return getCategory(basisOfRecord, kingdom);
-  }
-
-  @Override
-  public String retrieveFromABCD(JsonNode unit) {
-    var basisOfRecord = new BasisOfRecord().retrieveFromABCD(unit);
-    var kingdom = new Kingdom().retrieveFromABCD(unit);
-    return getCategory(basisOfRecord, kingdom);
-  }
-
   @Override
   public String getTerm() {
     return TERM;

diff --git a/src/test/java/eu/dissco/core/translator/repository/MappingRepositoryIT.java b/src/test/java/eu/dissco/core/translator/repository/MappingRepositoryIT.java
@@ -57,7 +57,6 @@ private void givenInsertRecords(String mapping) {
         .set(MAPPING.MAPPING_, JSONB.valueOf(mapping))
         .set(MAPPING.CREATED, Instant.parse("2022-09-16T08:25:01.00Z"))
         .set(MAPPING.CREATOR, "e2befba6-9324-4bb4-9f41-d7dfae4a44b0")
-        .set(MAPPING.SOURCEDATASTANDARD, "dwc")
         .execute();
 
     context.insertInto(SOURCE_SYSTEM)

diff --git a/src/test/java/eu/dissco/core/translator/terms/specimen/TopicDisciplineTest.java b/src/test/java/eu/dissco/core/translator/terms/specimen/TopicDisciplineTest.java
@@ -20,7 +20,7 @@ private static Stream<Arguments> arguments() {
     return Stream.of(
         Arguments.of("FossilSpecimen", null, "Palaeontology"),
         Arguments.of("MeteoriteSpecimen", null, "Astrogeology"),
-        Arguments.of("RockSpecimen", null, "Earth System"),
+        Arguments.of("RockSpecimen", null, "Geology"),
         Arguments.of("PreservedSpecimen", "Animalia", "Zoology"),
         Arguments.of("PreservedSpecimen", "Plantae", "Botany"),
         Arguments.of("PreservedSpecimen", "Bacteria", "Microbiology"),
@@ -44,19 +44,6 @@ void testRetrieveFromDWCA(String basisOfRecord, String kingdom, String expected)
     assertThat(result).isEqualTo(expected);
   }
 
-  private static Stream<Arguments> arguments() {
-    return Stream.of(
-        Arguments.of("FossilSpecimen", null, "Palaeontology"),
-        Arguments.of("MeteoriteSpecimen", null, "Astrogeology"),
-        Arguments.of("RockSpecimen", null, "Geology"),
-        Arguments.of("PreservedSpecimen", "Animalia", "Zoology"),
-        Arguments.of("PreservedSpecimen", "Plantae", "Botany"),
-        Arguments.of("PreservedSpecimen", "Bacteria", "Microbiology"),
-        Arguments.of("PreservedSpecimen", "incertae sedis", "Unclassified"),
-        Arguments.of("Other", null, "Unclassified")
-    );
-  }
-
   @ParameterizedTest
   @MethodSource("arguments")
   void testRetrieveFromABCD(String basisOfRecord, String kingdom, String expected) {