use Zenodo supported [isDerivedFrom] instead of [wasDerivedFrom] and …

…[isInformedBy]; related to https://github.com/darktaxon/darktaxon/issues/5
bio-guoda · Jul 30, 2024 · 5c52912 · 5c52912
1 parent ef787c6
commit 5c52912
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Showing 2 changed files with 7 additions and 9 deletions.
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
@@ -101,11 +101,11 @@ public boolean handle(IRI version, InputStream is) throws ContentStreamException
                     ZenodoMetaUtil.appendIdentifier(linkRecords, ZenodoMetaUtil.IS_ALTERNATE_IDENTIFIER, imageContentId);
                     ArrayNode arrayNode = new ObjectMapper().createArrayNode();
                     entry.getValue().forEach(arrayNode::add);
-                    linkRecords.set(ZenodoMetaUtil.WAS_DERIVED_FROM, arrayNode);
+                    linkRecords.set(ZenodoMetaUtil.IS_DERIVED_FROM, arrayNode);
 
                     List<String> rawImages = entry.getValue();
                     for (String rawImage : rawImages) {
-                        ZenodoMetaUtil.appendIdentifier(linkRecords, ZenodoMetaUtil.WAS_DERIVED_FROM, rawImage);
+                        ZenodoMetaUtil.appendIdentifier(linkRecords, ZenodoMetaUtil.IS_DERIVED_FROM, rawImage);
                     }
                     setDescription(linkRecords);
                     writeZenodoMetadata(foundAtLeastOne, linkRecords);
@@ -196,8 +196,8 @@ private void setOriginReference(String iriString, int lineStart, int lineFinish,
                 ? "-" + "L" + lineFinish
                 : "";
         String value = (StringUtils.isBlank(suffix) && lineStart == -1) ? iriString : ("line:" + iriString + "!/L" + lineStart + suffix);
-        ZenodoMetaUtil.setValue(objectNode, ZenodoMetaUtil.WAS_INFORMED_BY, value);
-        ZenodoMetaUtil.appendIdentifier(objectNode, ZenodoMetaUtil.WAS_INFORMED_BY, "https://linker.bio/" + value);
+        ZenodoMetaUtil.setValue(objectNode, ZenodoMetaUtil.IS_DERIVED_FROM, value);
+        ZenodoMetaUtil.appendIdentifier(objectNode, ZenodoMetaUtil.IS_DERIVED_FROM, "https://linker.bio/" + value);
         ZenodoMetaUtil.append(objectNode, 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 " +
                 "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");
 

diff --git a/preston-taxodros/src/test/java/bio/guoda/preston/cmd/DarkTaxonFileExtractorTest.java b/preston-taxodros/src/test/java/bio/guoda/preston/cmd/DarkTaxonFileExtractorTest.java
@@ -86,7 +86,7 @@ public InputStream get(IRI key) {
 
         assertDescription(taxonNode);
 
-        assertThat(taxonNode.get("http://www.w3.org/ns/prov#wasInformedBy").asText(), is("line:hash://sha256/856ecd48436bb220a80f0a746f94abd7c4ea47cb61d946286f7e25cf0ec69dc1!/L9"));
+        assertThat(taxonNode.get("isDerivedFrom").asText(), is("line:hash://sha256/856ecd48436bb220a80f0a746f94abd7c4ea47cb61d946286f7e25cf0ec69dc1!/L9"));
         assertThat(taxonNode.get("darktaxon:plateId").asText(), is("BMT121"));
         assertThat(taxonNode.get("darktaxon:specimenId").asText(), is("BMT0009397"));
         assertThat(taxonNode.get("darktaxon:imageFilepath").asText(), is("BMT121/BMT0009397/BMT121_BMT0009397_RAW_Data_01/BMT121_BMT0009397_RAW_01_01.tiff"));
@@ -102,7 +102,7 @@ public InputStream get(IRI key) {
 
         assertDescription(taxonNode);
 
-        assertThat(taxonNode.get("http://www.w3.org/ns/prov#wasInformedBy").asText(), is("line:hash://sha256/856ecd48436bb220a80f0a746f94abd7c4ea47cb61d946286f7e25cf0ec69dc1!/L78"));
+        assertThat(taxonNode.get("isDerivedFrom").asText(), is("line:hash://sha256/856ecd48436bb220a80f0a746f94abd7c4ea47cb61d946286f7e25cf0ec69dc1!/L78"));
         assertThat(taxonNode.get("title").asText(), is("Photo of Specimen BMT0009392"));
         assertThat(taxonNode.get("darktaxon:plateId").asText(), is("BMT121"));
         assertThat(taxonNode.get("darktaxon:specimenId").asText(), is("BMT0009392"));
@@ -119,9 +119,7 @@ public InputStream get(IRI key) {
 
         assertDescription(taxonNode);
 
-        assertThat(taxonNode.get("http://www.w3.org/ns/prov#wasInformedBy").asText(), is("hash://sha256/856ecd48436bb220a80f0a746f94abd7c4ea47cb61d946286f7e25cf0ec69dc1"));
-
-        JsonNode jsonNode = taxonNode.get("http://www.w3.org/ns/prov#wasDerivedFrom");
+        JsonNode jsonNode = taxonNode.get("isDerivedFrom");
         assertThat(jsonNode.isArray(), is(true));
 
         ArrayNode arrayNode = (ArrayNode) jsonNode;