add more metadata related to https://github.com/darktaxon/darktaxon/i…

…ssues/14
bio-guoda · Sep 6, 2024 · 8749291 · 8749291
1 parent 6044c29
commit 8749291
Show file tree

Hide file tree

Showing 5 changed files with 40 additions and 14 deletions.
diff --git a/preston-cmd/src/main/java/bio/guoda/preston/cmd/ZenodoMetaUtil.java b/preston-cmd/src/main/java/bio/guoda/preston/cmd/ZenodoMetaUtil.java
@@ -13,6 +13,7 @@
 
 public class ZenodoMetaUtil {
     public static final String IS_DERIVED_FROM = "isDerivedFrom";
+    public static final String IS_DOCUMENTED_BY = "isDocumentedBy";
     public static final String IS_PART_OF = "isPartOf";
     public static final String REFERENCES = "references";
     public static final String RELATED_IDENTIFIERS = "related_identifiers";
@@ -42,7 +43,8 @@ public class ZenodoMetaUtil {
     public static final String FIELD_CUSTOM_DWC_CLASS = "dwc:class";
     public static final String FIELD_CUSTOM_DWC_ORDER = "dwc:order";
     public static final String FIELD_CUSTOM_AC_RESOURCE_CREATION_TECHNIQUE = "ac:resourceCreationTechnique";
-    public static final String FIELD_CUSTOM_AC_RESOURCE_CAPTURE_DEVICE = "ac:captureDevice";
+    public static final String FIELD_CUSTOM_AC_CAPTURE_DEVICE = "ac:captureDevice";
+    public static final String FIELD_CUSTOM_AC_SUBJECT_PART = "ac:subjectPart";
     public static final String DOI = "doi";
     public static final String IS_ALTERNATE_IDENTIFIER = "isAlternateIdentifier";
     public static final String UPLOAD_TYPE = "upload_type";

diff --git a/preston-taxodros/src/main/java/bio/guoda/preston/cmd/DarkTaxonFileStreamHandler.java b/preston-taxodros/src/main/java/bio/guoda/preston/cmd/DarkTaxonFileStreamHandler.java
@@ -172,15 +172,16 @@ private void populateFileObject(ObjectNode objectNode,
         objectNode.put(IMAGE_CONTENT_ID, imageContentId);
 
         String imageStackId = plateId + "_" + specimenId + "_stacked_" + imageStackNumber;
-        ZenodoMetaUtil.addCustomField(objectNode, ZenodoMetaUtil.FIELD_CUSTOM_AC_RESOURCE_CAPTURE_DEVICE, "digital camera");
+        ZenodoMetaUtil.addCustomField(objectNode, ZenodoMetaUtil.FIELD_CUSTOM_AC_CAPTURE_DEVICE, "digital camera");
         if (StringUtils.equals("stacked", matcher.group("imageAcquisitionMethod"))) {
             idForStack.put(imageStackId, imageContentId);
             ZenodoMetaUtil.addCustomField(objectNode, ZenodoMetaUtil.FIELD_CUSTOM_AC_RESOURCE_CREATION_TECHNIQUE, "focus stacking");
         }
 
 
         String mimeType = "image/tiff";
-        DarkTaxonUtil.populatePhotoDepositMetadata(objectNode, imageFilename, specimenId, imageContentId, mimeType, publicationDateFactory, communities, "Photo of Specimen " + specimenId, "Uploaded by Plazi for the Museum für Naturkunde Berlin.");
+        List<String> creators = Arrays.asList("Museum für Naturkunde Berlin");
+        DarkTaxonUtil.populatePhotoDepositMetadata(objectNode, imageFilename, specimenId, imageContentId, mimeType, publicationDateFactory, communities, "Photo of Specimen " + specimenId, "Uploaded by Plazi for the Museum für Naturkunde Berlin.", creators);
 
         if (StringUtils.equals("RAW", acquisitionMethod)) {
             String imageNumber = matcher.group("imageNumber");

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
@@ -13,6 +13,7 @@
 
 import java.util.Arrays;
 import java.util.List;
+import java.util.stream.Stream;
 
 import static bio.guoda.preston.cmd.ZenodoMetaUtil.PUBLICATION_DATE;
 
@@ -24,7 +25,7 @@ static void appendAlternateIdentifiers(ObjectNode linkRecords, String imageConte
         ZenodoMetaUtil.appendIdentifier(linkRecords, ZenodoMetaUtil.HAS_VERSION, imageContentId);
     }
 
-    public static void populatePhotoDepositMetadata(ObjectNode objectNode, String imageFilename, String specimenId, String imageContentId, String mimeType, PublicationDateFactory publicationDateFactory, List<String> communities, String title, String description) {
+    public static void populatePhotoDepositMetadata(ObjectNode objectNode, String imageFilename, String specimenId, String imageContentId, String mimeType, PublicationDateFactory publicationDateFactory, List<String> communities, String title, String description, List<String> creators) {
         ZenodoMetaUtil.addCustomField(objectNode, ZenodoMetaUtil.FIELD_CUSTOM_DWC_CATALOG_NUMBER, specimenId);
         ZenodoMetaUtil.addCustomField(objectNode, ZenodoMetaUtil.FIELD_CUSTOM_DWC_INSTITUTION_CODE, "MfN");
         ZenodoMetaUtil.addCustomField(objectNode, ZenodoMetaUtil.FIELD_CUSTOM_DWC_MATERIAL_SAMPLE_ID, specimenId);
@@ -33,11 +34,13 @@ public static void populatePhotoDepositMetadata(ObjectNode objectNode, String im
         setDescription(objectNode, description);
         ZenodoMetaUtil.setFilename(objectNode, imageFilename);
         appendAlternateIdentifiers(objectNode, imageContentId);
-        ZenodoMetaUtil.appendIdentifier(objectNode, ZenodoMetaUtil.IS_DERIVED_FROM, StringUtils.startsWith(specimenId, "urn:lsid:") ? specimenId : LSID_PREFIX + specimenId);
+        String specimenLSID = StringUtils.startsWith(specimenId, "urn:lsid:") ? specimenId : LSID_PREFIX + specimenId;
+        ZenodoMetaUtil.appendIdentifier(objectNode, ZenodoMetaUtil.IS_ALTERNATE_IDENTIFIER, specimenLSID + ":" + imageFilename);
+        ZenodoMetaUtil.appendIdentifier(objectNode, ZenodoMetaUtil.IS_DERIVED_FROM, specimenLSID);
         ZenodoMetaUtil.setType(objectNode, mimeType);
         ZenodoMetaUtil.setValue(objectNode, ZenodoMetaUtil.UPLOAD_TYPE, ZenodoMetaUtil.UPLOAD_TYPE_IMAGE);
         ZenodoMetaUtil.setValue(objectNode, ZenodoMetaUtil.IMAGE_TYPE, ZenodoMetaUtil.IMAGE_TYPE_PHOTO);
-        ZenodoMetaUtil.setCreators(objectNode, Arrays.asList("Museum für Naturkunde Berlin"));
+        ZenodoMetaUtil.setCreators(objectNode, creators);
         ZenodoMetaUtil.setValue(objectNode, PUBLICATION_DATE, publicationDateFactory.getPublicationDate());
         ZenodoMetaUtil.setCommunities(objectNode, communities.stream());
     }
@@ -47,8 +50,13 @@ public static void setDescription(ObjectNode objectNode, String description) {
     }
 
     public static ObjectNode toPhotoDeposit(JsonNode multimediaRecord, PublicationDateFactory publicationDateFactory, List<String> communities) {
+        JsonNode format = multimediaRecord.get("http://purl.org/dc/elements/1.1/format");
         JsonNode jsonNode = multimediaRecord.get("http://purl.org/dc/terms/identifier");
         String filename = jsonNode.asText();
+        if (!filename.contains(".")) {
+            filename = filename + "." + StringUtils.lowerCase(format.asText());
+        }
+
         JsonNode specimenReference = multimediaRecord.get("http://rs.tdwg.org/ac/terms/associatedSpecimenReference");
         String specimenId = specimenReference.asText();
         JsonNode hashValue = multimediaRecord.get("http://rs.tdwg.org/ac/terms/hashValue");
@@ -59,13 +67,18 @@ public static ObjectNode toPhotoDeposit(JsonNode multimediaRecord, PublicationDa
             throw new IllegalArgumentException("unsupported content id [" + imageContentId + "]");
         }
 
-        JsonNode format = multimediaRecord.get("http://purl.org/dc/elements/1.1/format");
-
-
         ObjectNode zenodoMetadata = new ObjectMapper().createObjectNode();
 
+        JsonNode tagNode = multimediaRecord.get("http://rs.tdwg.org/ac/terms/tag");
+        if (tagNode != null) {
+            String[] tags = StringUtils.split(tagNode.asText(), "|");
+            Stream.of(tags).forEach(tag -> ZenodoMetaUtil.addKeyword(zenodoMetadata, StringUtils.trim(tag)));
+        }
+
         String title = multimediaRecord.get("http://purl.org/dc/terms/title").asText();
         String description = multimediaRecord.get("http://purl.org/dc/terms/description").asText();
+        JsonNode creatorNode = multimediaRecord.get("http://purl.org/dc/elements/1.1/creator");
+        List<String> creators = Arrays.asList(creatorNode == null ? "Museum für Naturkunde Berlin" : creatorNode.asText());
         populatePhotoDepositMetadata(
                 zenodoMetadata,
                 filename,
@@ -75,12 +88,14 @@ public static ObjectNode toPhotoDeposit(JsonNode multimediaRecord, PublicationDa
                 publicationDateFactory,
                 communities,
                 title,
-                description
+                description, creators
         );
-        ZenodoMetaUtil.addCustomField(zenodoMetadata, ZenodoMetaUtil.FIELD_CUSTOM_AC_RESOURCE_CAPTURE_DEVICE, multimediaRecord.get("http://rs.tdwg.org/ac/terms/captureDevice").asText());
+        ZenodoMetaUtil.appendIdentifier(zenodoMetadata, ZenodoMetaUtil.IS_DOCUMENTED_BY, multimediaRecord.get("http://rs.tdwg.org/ac/terms/hasServiceAccessPoint").asText());
+        ZenodoMetaUtil.addCustomField(zenodoMetadata, ZenodoMetaUtil.FIELD_CUSTOM_AC_SUBJECT_PART, multimediaRecord.get("http://rs.tdwg.org/ac/terms/subjectPart").asText());
+        ZenodoMetaUtil.addCustomField(zenodoMetadata, ZenodoMetaUtil.FIELD_CUSTOM_AC_CAPTURE_DEVICE, multimediaRecord.get("http://rs.tdwg.org/ac/terms/captureDevice").asText());
         ZenodoMetaUtil.addCustomField(zenodoMetadata, ZenodoMetaUtil.FIELD_CUSTOM_AC_RESOURCE_CREATION_TECHNIQUE, multimediaRecord.get("http://rs.tdwg.org/ac/terms/resourceCreationTechnique").asText());
         String[] split = StringUtils.split(specimenId, ":");
-        String catalogNumber = split.length > 0 ? split[split.length-1] : specimenId;
+        String catalogNumber = split.length > 0 ? split[split.length - 1] : specimenId;
         ZenodoMetaUtil.addCustomField(zenodoMetadata, ZenodoMetaUtil.FIELD_CUSTOM_DWC_CATALOG_NUMBER, catalogNumber);
 
         return ZenodoMetaUtil.wrap(zenodoMetadata);

diff --git a/...on/cmd/DarkTaxonRecordTranslatorTest.java → .../guoda/preston/cmd/DarkTaxonUtilTest.java b/...on/cmd/DarkTaxonRecordTranslatorTest.java → .../guoda/preston/cmd/DarkTaxonUtilTest.java
@@ -16,7 +16,7 @@
 import static junit.framework.TestCase.assertNotNull;
 import static org.hamcrest.MatcherAssert.assertThat;
 
-public class DarkTaxonRecordTranslatorTest {
+public class DarkTaxonUtilTest {
 
     @Test
     public void photoDeposit() throws IOException {

diff --git a/preston-taxodros/src/test/resources/bio/guoda/preston/cmd/darktaxon/multimedia-zenodo.json b/preston-taxodros/src/test/resources/bio/guoda/preston/cmd/darktaxon/multimedia-zenodo.json
@@ -1,10 +1,12 @@
 {
   "metadata" : {
+    "keywords" : [ "MfN", "DarkTaxon" ],
     "custom" : {
       "dwc:catalogNumber" : [ "BMT0009388" ],
       "dwc:institutionCode" : [ "MfN" ],
       "dwc:materialSampleID" : [ "urn:lsid:MfN:Ento:BMT0009388" ],
       "ac:associatedSpecimenReference" : [ "urn:lsid:MfN:Ento:BMT0009388" ],
+      "ac:subjectPart" : [ "whole specimen" ],
       "ac:captureDevice" : [ "CAMERA MAKE AND MODEL" ],
       "ac:resourceCreationTechnique" : [ "Focal Stacking" ]
     },
@@ -17,15 +19,21 @@
     }, {
       "relation" : "hasVersion",
       "identifier" : "hash://md5/f052cbac398bf340a620c421bfefa16d"
+    }, {
+      "relation" : "isAlternateIdentifier",
+      "identifier" : "urn:lsid:MfN:Ento:BMT0009388:BMT121_BMT0009388_stacked_01.tiff"
     }, {
       "relation" : "isDerivedFrom",
       "identifier" : "urn:lsid:MfN:Ento:BMT0009388"
+    }, {
+      "relation" : "isDocumentedBy",
+      "identifier" : "https://zenodo.org/search?q=_files.checksum%3A%22md5%3Af052cbac398bf340a620c421bfefa16d%22&f=allversions%3Atrue"
     } ],
     "http://www.w3.org/1999/02/22-rdf-syntax-ns#type" : "image/tiff",
     "upload_type" : "image",
     "image_type" : "photo",
     "creators" : [ {
-      "name" : "Museum für Naturkunde Berlin"
+      "name" : "null"
     } ],
     "publication_date" : "1999-12-31",
     "communities" : [ {