From 7710b7d50a464631205283bf325ae11add27033e Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@renci.org>
Date: Wed, 19 Jun 2024 00:14:28 -0400
Subject: [PATCH 1/3] Updated dwc:basisOfRecord to basisOfRecord.

That's what the publication says we should use. I think we previously
had dwc: prefixes everywhere, but we didn't notice that this was still
around for basisOfRecord until just now.
---
 src/wrappers/SpecimenWrapper.js | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/wrappers/SpecimenWrapper.js b/src/wrappers/SpecimenWrapper.js
index ce8ab8f..5103391 100644
--- a/src/wrappers/SpecimenWrapper.js
+++ b/src/wrappers/SpecimenWrapper.js
@@ -10,8 +10,8 @@ const { PhyxCacheManager } = require('../utils/PhyxCacheManager');
  *
  * - TaxonomicUnitWrapper.TYPE_SPECIMEN: A specimen.
  *    - Based on http://rs.tdwg.org/dwc/terms/Occurrence
- *    - Should have a dwc:occurrenceID with the occurrence identifier.
- *    - Should have a dwc:basisOfRecord to indicate what sort of occurrence this is.
+ *    - Should have a occurrenceID with the occurrence identifier.
+ *    - Should have a basisOfRecord to indicate what sort of occurrence this is.
  *
  * Since TaxonNameWrapper follows the TDWG ontology, we'd love to do the same for
  * SpecimenWrapper, but unfortunately the TaxonOccurrence ontology has been deprecated
@@ -38,7 +38,7 @@ class SpecimenWrapper {
     const normalizedSpecimen = {
       '@type': SpecimenWrapper.TYPE_SPECIMEN,
       label: wrapped.label,
-      'dwc:basisOfRecord': wrapped.basisOfRecord,
+      basisOfRecord: wrapped.basisOfRecord,
       occurrenceID: wrapped.occurrenceID,
       catalogNumber: wrapped.catalogNumber,
       institutionCode: wrapped.institutionCode,
@@ -62,7 +62,7 @@ class SpecimenWrapper {
     // Prepare the specimen.
     const specimen = {
       '@type': SpecimenWrapper.TYPE_SPECIMEN,
-      'dwc:basisOfRecord': basisOfRecord,
+      basisOfRecord: basisOfRecord,
       occurrenceID: occurID,
     };
 
@@ -185,7 +185,7 @@ class SpecimenWrapper {
    * Return the basis of record, if one is present.
    */
   get basisOfRecord() {
-    if (has(this.specimen, 'dwc:basisOfRecord')) return this.specimen['dwc:basisOfRecord'];
+    if (has(this.specimen, 'basisOfRecord')) return this.specimen.basisOfRecord;
     return undefined;
   }
 
@@ -194,7 +194,7 @@ class SpecimenWrapper {
    * recommended values.
    */
   set basisOfRecord(bor) {
-    this.specimen['dwc:basisOfRecord'] = bor;
+    this.specimen.basisOfRecord = bor;
   }
 
   /** Return this specimen as a taxon concept if it contains taxon name information. */

From afc7f9b669b9b6a631f4658f6aebc64ea01dd6ee Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@renci.org>
Date: Wed, 19 Jun 2024 00:29:16 -0400
Subject: [PATCH 2/3] Minor fixes.

---
 src/wrappers/SpecimenWrapper.js | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/wrappers/SpecimenWrapper.js b/src/wrappers/SpecimenWrapper.js
index 5103391..a919804 100644
--- a/src/wrappers/SpecimenWrapper.js
+++ b/src/wrappers/SpecimenWrapper.js
@@ -57,12 +57,12 @@ class SpecimenWrapper {
   static fromOccurrenceID(occurrenceID, basisOfRecord = 'PreservedSpecimen') {
     // Copy the occurrence ID so we can truncate it if necessary.
     let occurID = occurrenceID;
-    if (occurID.startsWith('urn:catalog:')) occurID = occurID.substr(12);
+    if (occurID.startsWith('urn:catalog:')) occurID = occurID.substring(12);
 
     // Prepare the specimen.
     const specimen = {
       '@type': SpecimenWrapper.TYPE_SPECIMEN,
-      basisOfRecord: basisOfRecord,
+      basisOfRecord,
       occurrenceID: occurID,
     };
 

From fac126971aca9a32db6b9c708b06e88e9047e721 Mon Sep 17 00:00:00 2001
From: Gaurav Vaidya <gaurav@renci.org>
Date: Wed, 19 Jun 2024 00:31:55 -0400
Subject: [PATCH 3/3] Updated tests.

---
 test/specimens.js | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/test/specimens.js b/test/specimens.js
index 5ef11b5..027c209 100644
--- a/test/specimens.js
+++ b/test/specimens.js
@@ -24,7 +24,7 @@ describe('SpecimenWrapper', function () {
     it('should be able to extract an occurenceID and catalogNumber from simple specimen IDs', function () {
       const wrapper = new phyx.SpecimenWrapper({
         occurrenceID: 'Wall 2527, Fiji (uc)',
-        'dwc:basisOfRecord': 'PreservedSpecimen',
+        basisOfRecord: 'PreservedSpecimen',
       });
       expect(wrapper.occurrenceID).to.equal('Wall 2527, Fiji (uc)');
       expect(wrapper.catalogNumber).to.equal('Wall 2527, Fiji (uc)');
@@ -33,7 +33,7 @@ describe('SpecimenWrapper', function () {
     it('should extract institutionCode and catalogNumber from a institutionCode:catalogNumber combination', function () {
       const wrapper = new phyx.SpecimenWrapper({
         occurrenceID: 'FMNH:PR 2081',
-        'dwc:basisOfRecord': 'PreservedSpecimen',
+        basisOfRecord: 'PreservedSpecimen',
       });
       expect(wrapper.occurrenceID).to.equal('FMNH:PR 2081');
       expect(wrapper.institutionCode).to.equal('FMNH');
@@ -80,7 +80,7 @@ describe('SpecimenWrapper', function () {
       expect(specimen.institutionCode).to.equal('FMNH');
       expect(specimen.collectionCode).to.equal('PR');
       expect(specimen.catalogNumber).to.equal('2081');
-      expect(specimen['dwc:basisOfRecord']).to.equal('PreservedSpecimen');
+      expect(specimen.basisOfRecord).to.equal('PreservedSpecimen');
     });
   });
 });