allow for recordedById to be optional for DarkTaxon sample event reco…

…rds; related to https://github.com/darktaxon/darktaxon/issues/14
bio-guoda · Sep 9, 2024 · c46025e · c46025e
1 parent 26a7896
commit c46025e
Showing 1 changed file with 10 additions and 5 deletions.
diff --git a/preston-taxodros/src/main/java/bio/guoda/preston/cmd/DarkTaxonUtil.java b/preston-taxodros/src/main/java/bio/guoda/preston/cmd/DarkTaxonUtil.java
@@ -29,6 +29,7 @@ public class DarkTaxonUtil {
     public static final String EVENT = "event";
     public static final String PHYSICAL_OBJECT = "physicalobject";
     public static final String PHOTO = "image%2Binner%3Aimage-photo";
+    public static final String GBIF_RECORDED_BY_ID = "http://rs.gbif.org/terms/1.0/recordedByID";
 
     static void appendAlternateIdentifiers(ObjectNode linkRecords, String imageContentId) {
         ZenodoMetaUtil.appendIdentifier(linkRecords, ZenodoMetaUtil.IS_ALTERNATE_IDENTIFIER, imageContentId);
@@ -151,10 +152,8 @@ static ObjectNode toEventDeposit(String jsonString, PublicationDateFactory publi
         addValueAsCustomFieldIfAvailable(zenodoMetadata, ZenodoMetaUtil.FIELD_CUSTOM_DWC_VERBATIM_EVENT_DATE, eventDate);
         addValueAsCustomFieldIfAvailable(zenodoMetadata, ZenodoMetaUtil.FIELD_CUSTOM_DWC_LOCALITY, locality);
         addValueAsCustomFieldIfAvailable(zenodoMetadata, ZenodoMetaUtil.FIELD_CUSTOM_DWC_RECORDED_BY, getValueOrThrow(multimedia, "http://rs.tdwg.org/dwc/terms/recordedBy"));
-        if (multimedia.has(DWC_TERMS_RECORDED_BY_ID) && StringUtils.isNotBlank(multimedia.get(DWC_TERMS_RECORDED_BY_ID).asText())) {
-            addValueAsCustomFieldIfAvailable(zenodoMetadata, ZenodoMetaUtil.FIELD_CUSTOM_DWC_RECORDED_BY_ID, getValueOrThrow(multimedia, DWC_TERMS_RECORDED_BY_ID));
-        }
-        addValueAsCustomFieldIfAvailable(zenodoMetadata, ZenodoMetaUtil.FIELD_CUSTOM_GBIF_DWC_RECORDED_BY_ID, getValueOrThrow(multimedia, "http://rs.tdwg.org/dwc/terms/recordedByID"));
+        addRecordedByIfAvailable(multimedia, zenodoMetadata, DWC_TERMS_RECORDED_BY_ID);
+        addRecordedByIfAvailable(multimedia, zenodoMetadata, GBIF_RECORDED_BY_ID);
         ZenodoMetaUtil.setFilename(zenodoMetadata, "event.json");
         ZenodoMetaUtil.appendIdentifier(zenodoMetadata, ZenodoMetaUtil.IS_ALTERNATE_IDENTIFIER, eventId);
         ZenodoMetaUtil.appendIdentifier(zenodoMetadata, ZenodoMetaUtil.IS_VERSION_OF, ZenodoUtils.getSearchPageForExistingRecords(ctx, Arrays.asList(eventId), EVENT).getIRIString());
@@ -171,6 +170,12 @@ static ObjectNode toEventDeposit(String jsonString, PublicationDateFactory publi
         return ZenodoMetaUtil.wrap(zenodoMetadata);
     }
 
+    private static void addRecordedByIfAvailable(JsonNode multimedia, ObjectNode zenodoMetadata, String fieldName) throws MissingMetadataFieldException {
+        if (multimedia.has(fieldName) && StringUtils.isNotBlank(multimedia.get(fieldName).asText())) {
+            addValueAsCustomFieldIfAvailable(zenodoMetadata, ZenodoMetaUtil.FIELD_CUSTOM_DWC_RECORDED_BY_ID, getValueOrThrow(multimedia, fieldName));
+        }
+    }
+
     private static void addReferences(ObjectNode zenodoMetadata) {
         ZenodoMetaUtil.append(zenodoMetadata, ZenodoMetaUtil.REFERENCES, "Hartop E, Srivathsan A, Ronquist F, Meier R (2022) Towards Large-Scale Integrative Taxonomy (LIT): resolving the data conundrum for dark taxa. Syst Biol 71:1404–1422. https://doi.org/10.1093/sysbio/syac033");
         ZenodoMetaUtil.append(zenodoMetadata, ZenodoMetaUtil.REFERENCES, "Srivathsan, A., Meier, R. (2024). Scalable, Cost-Effective, and Decentralized DNA Barcoding with Oxford Nanopore Sequencing. In: DeSalle, R. (eds) DNA Barcoding. Methods in Molecular Biology, vol 2744. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3581-0_14");
@@ -222,7 +227,7 @@ public static ObjectNode toPhysicalObjectDeposit(String jsonString, PublicationD
 
         if (StringUtils.isBlank(contentId)) {
             contentId = Hasher.calcHashIRI(jsonString, HashType.md5).getIRIString();
-            filename = "event.json";
+            filename = "occurrence.json";
         }
 
         ZenodoMetaUtil.setFilename(zenodoMetadata, filename);