From d60f5ae2e3048262ee5b76090ecdb048f7d05573 Mon Sep 17 00:00:00 2001
From: TomDijkema <tom.dijkema@naturalis.nl>
Date: Tue, 10 Dec 2024 16:38:54 +0100
Subject: [PATCH 01/10] Implement basic for prefilling annotation classes

Implement basic for prefilling annotation classes
---
 src/app/Boot.ts                               |  2 +-
 src/app/utilities/AnnotateUtilities.ts        | 14 ++--
 src/app/utilities/ClassAnnotationUtilities.ts | 81 +++++++++++++++++++
 3 files changed, 91 insertions(+), 6 deletions(-)
 create mode 100644 src/app/utilities/ClassAnnotationUtilities.ts

diff --git a/src/app/Boot.ts b/src/app/Boot.ts
index bde58abe..daf6b41a 100644
--- a/src/app/Boot.ts
+++ b/src/app/Boot.ts
@@ -18,7 +18,7 @@ type Callback = (bootState: {
 
 /**
  * Function that runs the application's necessary processes before it can be booted
- * @returns True or false depening on if is has booted
+ * @returns True or false depening on if it has booted
  */
 const Boot = (callback: Callback) => {
     /* Initiate keycloak which will render the root after finishing setting up */
diff --git a/src/app/utilities/AnnotateUtilities.ts b/src/app/utilities/AnnotateUtilities.ts
index 2f63697a..f90491ae 100644
--- a/src/app/utilities/AnnotateUtilities.ts
+++ b/src/app/utilities/AnnotateUtilities.ts
@@ -5,6 +5,7 @@ import jp from 'jsonpath';
 import { cloneDeep, isEmpty, toLower } from 'lodash';
 
 /* Import Utilities */
+import { CheckForClassDefaultValues } from './ClassAnnotationUtilities';
 import { ExtractLowestLevelSchema, ExtractClassesAndTermsFromSchema, MakeJsonPathReadableString } from 'app/utilities/SchemaUtilities';
 
 /* Import Types */
@@ -208,7 +209,7 @@ const GenerateAnnotationFormFieldProperties = async (jsonPath: string, superClas
 
     /**
      * Function to check for a default value for a term
-     * 
+     * @param key The term key to check
      */
     const CheckForTermDefaultValue = (key: string) => {
         if (toLower(key).includes('date')) {
@@ -242,7 +243,7 @@ const GenerateAnnotationFormFieldProperties = async (jsonPath: string, superClas
 
                 formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = classFormValues ?? {};
             } else if (classProperty.value.includes('has') && classProperty.value.at(-3) === 's') {
-                const localClassValues: Dict[] | undefined = classValues ?? [];
+                const localClassValues: Dict[] = classValues ?? [];
 
                 if (!classValues) {
                     const parentFieldName: string = classProperty.value.replace(`$`, jsonPath).split('[').slice(0, -1).join('[');
@@ -252,9 +253,12 @@ const GenerateAnnotationFormFieldProperties = async (jsonPath: string, superClas
                     PushToLocalClassValues(parentValues, childFieldName, (value: Dict) => localClassValues.push(value));
                 }
 
-                formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = classValues ?? localClassValues ?? [];
+                CheckForClassDefaultValues(classProperty.value.replace(`$`, jsonPath));
+
+                formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = classValues ??
+                    (!isEmpty(localClassValues) ? localClassValues : undefined) ?? CheckForClassDefaultValues(classProperty.value.replace(`$`, jsonPath)) ?? [];
             } else {
-                formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = {};
+                formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = CheckForClassDefaultValues(jsonPath) ?? {};
             }
 
             /* For each term of class, add it to the properties array of the corresponding class in the annotation form fields dictionary */
@@ -271,7 +275,7 @@ const GenerateAnnotationFormFieldProperties = async (jsonPath: string, superClas
                 });
 
                 /* Check if the term field needs to be filled with a default value */
-                if (CheckForTermDefaultValue(termOption.key)) {
+                if (CheckForTermDefaultValue(termOption.key) && !(termOption.key in classFormValues)) {
                     classFormValues[termOption.key] = CheckForTermDefaultValue(termOption.key);
                 }
             });
diff --git a/src/app/utilities/ClassAnnotationUtilities.ts b/src/app/utilities/ClassAnnotationUtilities.ts
new file mode 100644
index 00000000..3cb057ca
--- /dev/null
+++ b/src/app/utilities/ClassAnnotationUtilities.ts
@@ -0,0 +1,81 @@
+/* Import Dependencies */
+import KeycloakService from "app/Keycloak";
+
+/* Import Utilities */
+import { FormatFieldNameFromJsonPath } from "./AnnotateUtilities";
+
+
+/* Utilities associated with a class annotation */
+
+
+/**
+ * Function to check for class default values and if present, return them
+ * @param jsonPath The JSON path of the class to check
+ */
+const CheckForClassDefaultValues = (jsonPath: string) => {
+    const className: string = FormatFieldNameFromJsonPath(jsonPath.replaceAll(/\[(\d+)\]/g, '')).split('_').slice(-1)[0].replace('$', '').replaceAll("'", '');
+
+    switch (className) {
+        case 'ods:hasAgents': {
+            return ClassAgents(jsonPath);
+        }
+        case 'ods:hasIdentifiers': {
+            return ClassIdentifiers();
+        }
+        case 'ods:hasRoles': {
+            return ClassRoles();
+        }
+    };
+};
+
+/**
+ * Function to create a prefilled agent values object
+ * @param jsonPath The full provided JSON path
+ * @returns
+ */
+const ClassAgents = (jsonPath: string) => {
+    /* Extract parent class name from JSON path */
+    // const parentClassName: string = FormatFieldNameFromJsonPath(jsonPath.replaceAll(/\[(\d+)\]/g, '')).split('_').slice(-2)[0].replace('$', '').replaceAll("'", '');
+
+    /* Construct agent values object */
+    const classValues = {
+        "@type": 'schema:Person',
+        "schema:name": `${KeycloakService.GetParsedToken()?.given_name ?? ''} ${KeycloakService.GetParsedToken()?.family_name ?? ''}`
+    };
+
+    return classValues;
+};
+
+/**
+ * Function to create a prefilled role values object
+ * @returns 
+ */
+const ClassIdentifiers = () => {
+    /* Construct identifier values object */
+    const classValues = {
+        "@type": '',
+        "dcterms:title": '',
+        "dcterms:identifier": ''
+    };
+
+    return [classValues];
+};
+
+/**
+ * Function to create a prefilled role values object
+ * @param roleForClassName The class name which to create a role for
+ * @returns 
+ */
+const ClassRoles = () => {
+    /* Construct role values object */
+    const classValues = {
+        "@type": '',
+        "schema:roleName": ''
+    };
+
+    return [classValues];
+};
+
+export {
+    CheckForClassDefaultValues
+};
\ No newline at end of file

From 4a2879ceeec7e7ecc7b4cffa0ba8ced7a6b51c90 Mon Sep 17 00:00:00 2001
From: TomDijkema <tom.dijkema@naturalis.nl>
Date: Wed, 11 Dec 2024 09:17:06 +0100
Subject: [PATCH 02/10] Finnish setup for default class values in annotation
 wizard form

Finnish setup for default class values in annotation wizard form
---
 src/app/utilities/AnnotateUtilities.ts        | 29 ++++++++----
 src/app/utilities/ClassAnnotationUtilities.ts | 45 +++++++++++++------
 .../steps/AnnotationFormStep.tsx              |  2 +-
 .../steps/formFields/SelectField.tsx          |  2 +-
 4 files changed, 55 insertions(+), 23 deletions(-)

diff --git a/src/app/utilities/AnnotateUtilities.ts b/src/app/utilities/AnnotateUtilities.ts
index f90491ae..52d9c961 100644
--- a/src/app/utilities/AnnotateUtilities.ts
+++ b/src/app/utilities/AnnotateUtilities.ts
@@ -183,7 +183,7 @@ const FormatJsonPathFromFieldName = (fieldName: string): string => {
  * @param schemaName The name of the base schema
  * @returns The annotation form field properties and their associated form values
  */
-const GenerateAnnotationFormFieldProperties = async (jsonPath: string, superClass: SuperClass, schemaName: string) => {
+const GenerateAnnotationFormFieldProperties = async (jsonPath: string, superClass: SuperClass, schemaName: string, motivation: string) => {
     const annotationFormFieldProperties: {
         [propertyName: string]: AnnotationFormProperty
     } = {};
@@ -241,24 +241,37 @@ const GenerateAnnotationFormFieldProperties = async (jsonPath: string, superClas
                     }
                 });
 
-                formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = classFormValues ?? {};
+                formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = {};
+
+                /* Check if (default) values are present, if so, set form values property with them */
+                if (!isEmpty(classFormValues)) {
+                    formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = classFormValues;
+                } else if (motivation !== 'oa:editing') {
+                    formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = CheckForClassDefaultValues(classProperty.value.replace(`$`, jsonPath)) ?? {};
+                }
             } else if (classProperty.value.includes('has') && classProperty.value.at(-3) === 's') {
-                const localClassValues: Dict[] = classValues ?? [];
+                let localClassValues: Dict[] = classValues ?? [];
 
                 if (!classValues) {
                     const parentFieldName: string = classProperty.value.replace(`$`, jsonPath).split('[').slice(0, -1).join('[');
                     const parentValues: Dict | undefined = jp.value(superClass, parentFieldName);
                     const childFieldName: string = classProperty.value.split('[').pop()?.replace(']', '').replaceAll("'", '') ?? '';
 
-                    PushToLocalClassValues(parentValues, childFieldName, (value: Dict) => localClassValues.push(value));
+                    PushToLocalClassValues(parentValues, childFieldName, (value: Dict) => localClassValues?.push(value));
                 }
 
-                CheckForClassDefaultValues(classProperty.value.replace(`$`, jsonPath));
+                formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = [];
 
-                formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = classValues ??
-                    (!isEmpty(localClassValues) ? localClassValues : undefined) ?? CheckForClassDefaultValues(classProperty.value.replace(`$`, jsonPath)) ?? [];
+                /* Check if (default) values are present, if so, set form values property with them */
+                if (classValues) {
+                    formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = classValues;
+                } else if (!isEmpty(localClassValues)) {
+                    formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = localClassValues;
+                } else if (motivation !== 'oa:editing') {
+                    formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = CheckForClassDefaultValues(classProperty.value.replace(`$`, jsonPath)) ?? [];
+                }
             } else {
-                formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = CheckForClassDefaultValues(jsonPath) ?? {};
+                formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = CheckForClassDefaultValues(classProperty.value.replace(`$`, jsonPath)) ?? {};
             }
 
             /* For each term of class, add it to the properties array of the corresponding class in the annotation form fields dictionary */
diff --git a/src/app/utilities/ClassAnnotationUtilities.ts b/src/app/utilities/ClassAnnotationUtilities.ts
index 3cb057ca..03d8c017 100644
--- a/src/app/utilities/ClassAnnotationUtilities.ts
+++ b/src/app/utilities/ClassAnnotationUtilities.ts
@@ -11,16 +11,20 @@ import { FormatFieldNameFromJsonPath } from "./AnnotateUtilities";
 /**
  * Function to check for class default values and if present, return them
  * @param jsonPath The JSON path of the class to check
+ * @returns Prefilled data array or object depending on provided class
  */
 const CheckForClassDefaultValues = (jsonPath: string) => {
     const className: string = FormatFieldNameFromJsonPath(jsonPath.replaceAll(/\[(\d+)\]/g, '')).split('_').slice(-1)[0].replace('$', '').replaceAll("'", '');
 
     switch (className) {
         case 'ods:hasAgents': {
-            return ClassAgents(jsonPath);
+            return ClassAgents();
+        }
+        case 'ods:hasGeoreference': {
+            return ClassGeoreference();
         }
         case 'ods:hasIdentifiers': {
-            return ClassIdentifiers();
+            return ClassIdentifiers(jsonPath);
         }
         case 'ods:hasRoles': {
             return ClassRoles();
@@ -30,32 +34,48 @@ const CheckForClassDefaultValues = (jsonPath: string) => {
 
 /**
  * Function to create a prefilled agent values object
- * @param jsonPath The full provided JSON path
- * @returns
+ * @returns Prefilled agents values array
  */
-const ClassAgents = (jsonPath: string) => {
-    /* Extract parent class name from JSON path */
-    // const parentClassName: string = FormatFieldNameFromJsonPath(jsonPath.replaceAll(/\[(\d+)\]/g, '')).split('_').slice(-2)[0].replace('$', '').replaceAll("'", '');
-
+const ClassAgents = () => {
     /* Construct agent values object */
     const classValues = {
         "@type": 'schema:Person',
+        "schema:identifier": KeycloakService.GetParsedToken()?.orcid,
         "schema:name": `${KeycloakService.GetParsedToken()?.given_name ?? ''} ${KeycloakService.GetParsedToken()?.family_name ?? ''}`
     };
 
+    return [classValues];
+};
+
+/**
+ * Function to create a prefilled role values object
+ * @returns Prefilled georeferene values object
+ */
+const ClassGeoreference = () => {
+    /* Construct role values object */
+    const classValues = {
+        "@type": 'ods:Georeference'
+    };
+
     return classValues;
 };
 
 /**
  * Function to create a prefilled role values object
- * @returns 
+ * @returns Prefilled identifiers values array
  */
-const ClassIdentifiers = () => {
+const ClassIdentifiers = (jsonPath: string) => {
+    /* Extract parent class name from JSON path */
+    const parentClassName: string = FormatFieldNameFromJsonPath(jsonPath.replaceAll(/\[(\d+)\]/g, '')).split('_').slice(-2)[0].replace('$', '').replaceAll("'", '');
+
+    /* Set parent specific values */
+    const dctermsIdentifier: string = parentClassName === 'ods:hasAgents' ? KeycloakService.GetParsedToken()?.orcid : '';
+
     /* Construct identifier values object */
     const classValues = {
         "@type": '',
         "dcterms:title": '',
-        "dcterms:identifier": ''
+        "dcterms:identifier": dctermsIdentifier
     };
 
     return [classValues];
@@ -63,8 +83,7 @@ const ClassIdentifiers = () => {
 
 /**
  * Function to create a prefilled role values object
- * @param roleForClassName The class name which to create a role for
- * @returns 
+ * @returns Prefilled roles values array
  */
 const ClassRoles = () => {
     /* Construct role values object */
diff --git a/src/components/elements/annotationSidePanel/components/annotationWizard/steps/AnnotationFormStep.tsx b/src/components/elements/annotationSidePanel/components/annotationWizard/steps/AnnotationFormStep.tsx
index e3f8fd97..9df716d9 100644
--- a/src/components/elements/annotationSidePanel/components/annotationWizard/steps/AnnotationFormStep.tsx
+++ b/src/components/elements/annotationSidePanel/components/annotationWizard/steps/AnnotationFormStep.tsx
@@ -94,7 +94,7 @@ const AnnotationFormStep = (props: Props) => {
         }
 
         /* For selected class, get annotation form field properties and their values */
-        GenerateAnnotationFormFieldProperties(jsonPath, localSuperClass, schemaName).then(({ annotationFormFieldProperties, newFormValues }) => {
+        GenerateAnnotationFormFieldProperties(jsonPath, localSuperClass, schemaName, formValues?.motivation).then(({ annotationFormFieldProperties, newFormValues }) => {
             let parentJsonPath: string = '$';
 
             if (annotationTarget?.jsonPath && FormatFieldNameFromJsonPath(annotationTarget.jsonPath).split('_').length > 1) {
diff --git a/src/components/elements/annotationSidePanel/components/annotationWizard/steps/formFields/SelectField.tsx b/src/components/elements/annotationSidePanel/components/annotationWizard/steps/formFields/SelectField.tsx
index 77e63913..21611aaf 100644
--- a/src/components/elements/annotationSidePanel/components/annotationWizard/steps/formFields/SelectField.tsx
+++ b/src/components/elements/annotationSidePanel/components/annotationWizard/steps/formFields/SelectField.tsx
@@ -31,7 +31,7 @@ const SelectField = (props: Props) => {
             <Field name={`annotationValues.${fieldName}`}
                 as="select"
                 value={fieldValue ?? ''}
-                className="w-100 b-grey br-corner mt-1 py-1 px-2"
+                className="w-100 b-grey br-corner mt-1 py-2 px-2"
             >
                 <option value=""
                     disabled

From b9ef6a1109e75de7d87c36465985b598144d6a49 Mon Sep 17 00:00:00 2001
From: TomDijkema <tom.dijkema@naturalis.nl>
Date: Wed, 11 Dec 2024 10:33:41 +0100
Subject: [PATCH 03/10] Fix that not always an array is returned from class
 default values, but is set depending upon the class type

Fix that not always an array is returned from class default values, but is set depending upon the class type
---
 src/app/utilities/AnnotateUtilities.ts        | 2 +-
 src/app/utilities/ClassAnnotationUtilities.ts | 7 ++++---
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/src/app/utilities/AnnotateUtilities.ts b/src/app/utilities/AnnotateUtilities.ts
index 52d9c961..fb5f7f48 100644
--- a/src/app/utilities/AnnotateUtilities.ts
+++ b/src/app/utilities/AnnotateUtilities.ts
@@ -268,7 +268,7 @@ const GenerateAnnotationFormFieldProperties = async (jsonPath: string, superClas
                 } else if (!isEmpty(localClassValues)) {
                     formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = localClassValues;
                 } else if (motivation !== 'oa:editing') {
-                    formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = CheckForClassDefaultValues(classProperty.value.replace(`$`, jsonPath)) ?? [];
+                    formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = [CheckForClassDefaultValues(classProperty.value.replace(`$`, jsonPath))];
                 }
             } else {
                 formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = CheckForClassDefaultValues(classProperty.value.replace(`$`, jsonPath)) ?? {};
diff --git a/src/app/utilities/ClassAnnotationUtilities.ts b/src/app/utilities/ClassAnnotationUtilities.ts
index 03d8c017..2aa81ba9 100644
--- a/src/app/utilities/ClassAnnotationUtilities.ts
+++ b/src/app/utilities/ClassAnnotationUtilities.ts
@@ -39,12 +39,13 @@ const CheckForClassDefaultValues = (jsonPath: string) => {
 const ClassAgents = () => {
     /* Construct agent values object */
     const classValues = {
+        "@id": KeycloakService.GetParsedToken()?.orcid,
         "@type": 'schema:Person',
         "schema:identifier": KeycloakService.GetParsedToken()?.orcid,
         "schema:name": `${KeycloakService.GetParsedToken()?.given_name ?? ''} ${KeycloakService.GetParsedToken()?.family_name ?? ''}`
     };
 
-    return [classValues];
+    return classValues;
 };
 
 /**
@@ -78,7 +79,7 @@ const ClassIdentifiers = (jsonPath: string) => {
         "dcterms:identifier": dctermsIdentifier
     };
 
-    return [classValues];
+    return classValues;
 };
 
 /**
@@ -92,7 +93,7 @@ const ClassRoles = () => {
         "schema:roleName": ''
     };
 
-    return [classValues];
+    return classValues;
 };
 
 export {

From 087fd2812e14b4762223b8685cd98365c6fc440a Mon Sep 17 00:00:00 2001
From: TomDijkema <tom.dijkema@naturalis.nl>
Date: Wed, 11 Dec 2024 10:55:02 +0100
Subject: [PATCH 04/10] Fix footer plugin ending of interval

Fix footer plugin ending of interval
---
 src/components/elements/footer/FooterPlugin.tsx | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/src/components/elements/footer/FooterPlugin.tsx b/src/components/elements/footer/FooterPlugin.tsx
index 77d8c639..21511a6a 100644
--- a/src/components/elements/footer/FooterPlugin.tsx
+++ b/src/components/elements/footer/FooterPlugin.tsx
@@ -14,6 +14,7 @@ const FooterPlugin = () => {
     /* Base variables */
     const [bootPlugin, setBootPlugin] = useState<boolean>(false);
     const [backgroundColor, setBackgroundColor] = useState<string | undefined>();
+    const [explanationInterval, setExplanationInterval] = useState<any>();
     const codeCheck: number[] = [38, 38, 40, 40, 37, 39, 37, 39, 66, 65, 13];
     let pluginCode: number[] = [];
 
@@ -34,6 +35,11 @@ const FooterPlugin = () => {
                 const audioExplanation = new Audio(ExplanationAudio);
 
                 audioExplanation.play();
+
+                audioExplanation.onended = () => {
+                    setBootPlugin(false);
+                    setBackgroundColor(undefined);
+                };
             }
         } else {
             pluginCode = [];
@@ -48,9 +54,11 @@ const FooterPlugin = () => {
     useEffect(() => {
         /* If boot plugin is loaded, start explanation process */
         if (bootPlugin) {
-            setInterval(() => {
-                setBackgroundColor(Math.floor(Math.random()*16777215).toString(16));
-            }, 1250);
+            setExplanationInterval(setInterval(() => {
+                setBackgroundColor(Math.floor(Math.random() * 16777215).toString(16));
+            }, 1250));
+        } else {
+            clearInterval(explanationInterval);
         }
     }, [bootPlugin]);
 

From 7e81c34a35ab134235015dd528ede30030ed75f4 Mon Sep 17 00:00:00 2001
From: TomDijkema <tom.dijkema@naturalis.nl>
Date: Wed, 11 Dec 2024 12:24:51 +0100
Subject: [PATCH 05/10] Update citation on digital specimen overview

Update citation on digital specimen overview
---
 src/app/utilities/AnnotateUtilities.ts        | 51 +++++++++++----
 src/app/utilities/NomenclaturalUtilities.ts   | 11 ++++
 .../components/DigitalSpecimenOverview.tsx    | 62 +++++++++++++++++--
 3 files changed, 107 insertions(+), 17 deletions(-)

diff --git a/src/app/utilities/AnnotateUtilities.ts b/src/app/utilities/AnnotateUtilities.ts
index fb5f7f48..43902a6a 100644
--- a/src/app/utilities/AnnotateUtilities.ts
+++ b/src/app/utilities/AnnotateUtilities.ts
@@ -217,6 +217,25 @@ const GenerateAnnotationFormFieldProperties = async (jsonPath: string, superClas
         }
     };
 
+    /**
+     * Function to depict the values to be set for the class to be annotated
+     * @param fieldName The field name of the class (parsed from JSON path)
+     * @param classValues Possible existing class values from the super class
+     * @param isArray Boolean indicating if the class represents an array
+     * @param localClassValues Possible existing local class values of an annotation
+     */
+    const DepictClassValues = (fieldName: string, classValues: Dict | Dict[] | undefined, isArray?: boolean, localClassValues?: Dict[]) => {
+        if (classValues) {
+            return classValues;
+        } else if (!isEmpty(localClassValues)) {
+            return localClassValues;
+        } else if (motivation !== 'oa:editing' && isArray) {
+            return [CheckForClassDefaultValues(fieldName)];
+        } else if (motivation !== 'oa:editing') {
+            return CheckForClassDefaultValues(fieldName) ?? {};
+        }
+    };
+
     /* For each class, add it as a key property to the annotation form fields dictionary */
     classesList.forEach(classProperty => {
         if (!termValue) {
@@ -244,11 +263,15 @@ const GenerateAnnotationFormFieldProperties = async (jsonPath: string, superClas
                 formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = {};
 
                 /* Check if (default) values are present, if so, set form values property with them */
-                if (!isEmpty(classFormValues)) {
-                    formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = classFormValues;
-                } else if (motivation !== 'oa:editing') {
-                    formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = CheckForClassDefaultValues(classProperty.value.replace(`$`, jsonPath)) ?? {};
-                }
+                // if (!isEmpty(classFormValues)) {
+                //     formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = classFormValues;
+                // } else if (motivation !== 'oa:editing') {
+                //     formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = CheckForClassDefaultValues(classProperty.value.replace(`$`, jsonPath)) ?? {};
+                // }
+                formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = DepictClassValues(
+                    classProperty.value.replace(`$`, jsonPath), classFormValues
+                );
+
             } else if (classProperty.value.includes('has') && classProperty.value.at(-3) === 's') {
                 let localClassValues: Dict[] = classValues ?? [];
 
@@ -263,13 +286,17 @@ const GenerateAnnotationFormFieldProperties = async (jsonPath: string, superClas
                 formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = [];
 
                 /* Check if (default) values are present, if so, set form values property with them */
-                if (classValues) {
-                    formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = classValues;
-                } else if (!isEmpty(localClassValues)) {
-                    formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = localClassValues;
-                } else if (motivation !== 'oa:editing') {
-                    formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = [CheckForClassDefaultValues(classProperty.value.replace(`$`, jsonPath))];
-                }
+                formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = DepictClassValues(
+                    classProperty.value.replace(`$`, jsonPath), classValues, true, localClassValues
+                );
+
+                // if (classValues) {
+                //     formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = classValues;
+                // } else if (!isEmpty(localClassValues)) {
+                //     formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = localClassValues;
+                // } else if (motivation !== 'oa:editing') {
+                //     formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = [CheckForClassDefaultValues(classProperty.value.replace(`$`, jsonPath))];
+                // }
             } else {
                 formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = CheckForClassDefaultValues(classProperty.value.replace(`$`, jsonPath)) ?? {};
             }
diff --git a/src/app/utilities/NomenclaturalUtilities.ts b/src/app/utilities/NomenclaturalUtilities.ts
index aab0aae3..a1d25a83 100644
--- a/src/app/utilities/NomenclaturalUtilities.ts
+++ b/src/app/utilities/NomenclaturalUtilities.ts
@@ -58,6 +58,16 @@ const GetSpecimenNameHTMLLabel = (digitalSpecimen: DigitalSpecimen): string => {
     }
 };
 
+/**
+ * Function to get the scientific name identifier (that leads to COL) of the first accepted identification
+ * @param digitalSpecimen The provided digital specimen
+ */
+const GetSpecimenNameIdentifier = (digitalSpecimen: DigitalSpecimen) => {
+    const acceptedIdentification: Identification | undefined = digitalSpecimen['ods:hasIdentifications']?.find(identification => identification['ods:isVerifiedIdentification']);
+
+    return acceptedIdentification?.['ods:hasTaxonIdentifications']?.[0]["dwc:acceptedNameUsageID"];
+};
+
 /**
  * Function to get the genus HTML label of the first accepted identification within the digital specimen, if not present, provide generic genus string
  * @param digitalSpecimen The provided digital specimen
@@ -74,5 +84,6 @@ export {
     DetermineScientificName,
     DetermineTopicDisciplineIcon,
     GetSpecimenNameHTMLLabel,
+    GetSpecimenNameIdentifier,
     GetSpecimenGenusLabel
 };
\ No newline at end of file
diff --git a/src/components/digitalSpecimen/components/contentBlock/components/DigitalSpecimenOverview.tsx b/src/components/digitalSpecimen/components/contentBlock/components/DigitalSpecimenOverview.tsx
index 32fa8711..a3cbc0fe 100644
--- a/src/components/digitalSpecimen/components/contentBlock/components/DigitalSpecimenOverview.tsx
+++ b/src/components/digitalSpecimen/components/contentBlock/components/DigitalSpecimenOverview.tsx
@@ -5,7 +5,7 @@ import { useState } from 'react';
 import { Row, Col, Card } from 'react-bootstrap';
 
 /* Import Utiltiies */
-import { GetSpecimenNameHTMLLabel } from 'app/utilities/NomenclaturalUtilities';
+import { GetSpecimenNameHTMLLabel, GetSpecimenNameIdentifier } from 'app/utilities/NomenclaturalUtilities';
 
 /* Import Types */
 import { DigitalSpecimen } from 'app/types/DigitalSpecimen';
@@ -74,16 +74,68 @@ const DigitalSpecimenOverview = (props: Props) => {
      * @returns Citation string
      */
     const CraftCitation = (label?: boolean) => {
+        /**
+         * Function to determine the organisation name for the citation string
+         * @returns Organisation name with link
+         */
+        const OrganisationName = () => {
+            return <a href={digitalSpecimen['ods:organisationID']}
+                target="_blank"
+                rel="noreferer"
+                className="tc-accent"
+            >
+                {digitalSpecimen['ods:organisationName'] ?? digitalSpecimen['ods:organisationID']}
+            </a>
+        };
+
+        /**
+         * Function to determine the scientific name for the citation string
+         * @returns Scientific name, with or without link/label
+         */
+        const ScientificName = () => {
+            const scientificNameIdentifier = GetSpecimenNameIdentifier(digitalSpecimen);
+
+            if (scientificNameIdentifier) {
+                return (
+                    <a href={scientificNameIdentifier}
+                        target="_blank"
+                        rel="noreferer"
+                        className="tc-accent"
+                    >
+                        <span dangerouslySetInnerHTML={{ __html: GetSpecimenNameHTMLLabel(digitalSpecimen) }} />
+                    </a>
+                );
+            } else {
+                return <span dangerouslySetInnerHTML={{ __html: (GetSpecimenNameHTMLLabel(digitalSpecimen) ?? digitalSpecimen['ods:specimenName']) }} />;
+            }
+        };
+
         if (label) {
             return (
                 <>
-                    {`Distributed System of Scientific Collections (${new Date().getFullYear()}). `}
-                    <span dangerouslySetInnerHTML={{ __html: GetSpecimenNameHTMLLabel(digitalSpecimen) }} />
-                    {`. ${digitalSpecimen['ods:organisationName'] ? digitalSpecimen['ods:organisationName'] + '.' : ''} [Dataset]. ${digitalSpecimen['@id']}`}
+                    {OrganisationName()}
+                    {` (${new Date().getFullYear()}). `}
+                    {ScientificName()}
+                    {'. '}
+                    <a href="https://ror.org/02wddde16"
+                        target="_blank"
+                        rel="noreferer"
+                        className="tc-accent"
+                    >
+                        Distributed System of Scientific Collections
+                    </a>
+                    {`. [Dataset]. `}
+                    <a href={digitalSpecimen['@id']}
+                        target="_blank"
+                        rel="noreferer"
+                        className="tc-accent"
+                    >
+                        {digitalSpecimen['@id']}
+                    </a>
                 </>
             );
         } else {
-            return `Distributed System of Scientific Collections (${new Date().getFullYear()}). ${digitalSpecimen['ods:specimenName']}. ${digitalSpecimen['ods:organisationName'] ? digitalSpecimen['ods:organisationName'] + '.' : ''} [Dataset]. ${digitalSpecimen['@id']}`;
+            return `${digitalSpecimen['ods:organisationName'] ? digitalSpecimen['ods:organisationName'] + '.' : digitalSpecimen['ods:organisationID'] + '.'} (${new Date().getFullYear()}). ${digitalSpecimen['ods:specimenName']}. Distributed System of Scientific Collections. [Dataset]. ${digitalSpecimen['@id']}`;
         }
     };
 

From a74703217c3ad8b8ba6cd0b5646cac6b12c5fe46 Mon Sep 17 00:00:00 2001
From: TomDijkema <tom.dijkema@naturalis.nl>
Date: Wed, 11 Dec 2024 12:33:23 +0100
Subject: [PATCH 06/10] Sonar Commit

Commit for resolving Sonar Cloud issues
---
 src/app/utilities/AnnotateUtilities.ts | 13 -------------
 1 file changed, 13 deletions(-)

diff --git a/src/app/utilities/AnnotateUtilities.ts b/src/app/utilities/AnnotateUtilities.ts
index 43902a6a..a244eebc 100644
--- a/src/app/utilities/AnnotateUtilities.ts
+++ b/src/app/utilities/AnnotateUtilities.ts
@@ -263,11 +263,6 @@ const GenerateAnnotationFormFieldProperties = async (jsonPath: string, superClas
                 formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = {};
 
                 /* Check if (default) values are present, if so, set form values property with them */
-                // if (!isEmpty(classFormValues)) {
-                //     formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = classFormValues;
-                // } else if (motivation !== 'oa:editing') {
-                //     formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = CheckForClassDefaultValues(classProperty.value.replace(`$`, jsonPath)) ?? {};
-                // }
                 formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = DepictClassValues(
                     classProperty.value.replace(`$`, jsonPath), classFormValues
                 );
@@ -289,14 +284,6 @@ const GenerateAnnotationFormFieldProperties = async (jsonPath: string, superClas
                 formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = DepictClassValues(
                     classProperty.value.replace(`$`, jsonPath), classValues, true, localClassValues
                 );
-
-                // if (classValues) {
-                //     formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = classValues;
-                // } else if (!isEmpty(localClassValues)) {
-                //     formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = localClassValues;
-                // } else if (motivation !== 'oa:editing') {
-                //     formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = [CheckForClassDefaultValues(classProperty.value.replace(`$`, jsonPath))];
-                // }
             } else {
                 formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = CheckForClassDefaultValues(classProperty.value.replace(`$`, jsonPath)) ?? {};
             }

From 2389b576ab349efb6b9f635d6ba6fb371b3e61b0 Mon Sep 17 00:00:00 2001
From: TomDijkema <tom.dijkema@naturalis.nl>
Date: Wed, 11 Dec 2024 14:34:42 +0100
Subject: [PATCH 07/10] Review Commit

Commit addressing review comments
---
 src/app/utilities/AnnotateUtilities.ts | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/app/utilities/AnnotateUtilities.ts b/src/app/utilities/AnnotateUtilities.ts
index a244eebc..ecf2c04d 100644
--- a/src/app/utilities/AnnotateUtilities.ts
+++ b/src/app/utilities/AnnotateUtilities.ts
@@ -229,9 +229,9 @@ const GenerateAnnotationFormFieldProperties = async (jsonPath: string, superClas
             return classValues;
         } else if (!isEmpty(localClassValues)) {
             return localClassValues;
-        } else if (motivation !== 'oa:editing' && isArray) {
+        } else if (motivation === 'ods:adding' && isArray) {
             return [CheckForClassDefaultValues(fieldName)];
-        } else if (motivation !== 'oa:editing') {
+        } else if (motivation === 'ods:adding') {
             return CheckForClassDefaultValues(fieldName) ?? {};
         }
     };

From f16d877d09ee05ce494ef83b0cc6eb7d1f2a7ad5 Mon Sep 17 00:00:00 2001
From: TomDijkema <tom.dijkema@naturalis.nl>
Date: Wed, 11 Dec 2024 15:33:20 +0100
Subject: [PATCH 08/10] Update AnnotationFormStep.tsx

---
 .../components/annotationWizard/steps/AnnotationFormStep.tsx  | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/components/elements/annotationSidePanel/components/annotationWizard/steps/AnnotationFormStep.tsx b/src/components/elements/annotationSidePanel/components/annotationWizard/steps/AnnotationFormStep.tsx
index 9df716d9..cb05ec57 100644
--- a/src/components/elements/annotationSidePanel/components/annotationWizard/steps/AnnotationFormStep.tsx
+++ b/src/components/elements/annotationSidePanel/components/annotationWizard/steps/AnnotationFormStep.tsx
@@ -107,7 +107,9 @@ const AnnotationFormStep = (props: Props) => {
                 annotationValues: {
                     ...newFormValues,
                     ...formValues?.annotationValues,
-                    value: (localAnnotationTarget?.jsonPath !== annotationTarget?.jsonPath) ? newFormValues.value : formValues?.annotationValues.value ?? newFormValues.value
+                    ...(annotationTarget?.type === 'term' && {
+                        value: (localAnnotationTarget?.jsonPath !== annotationTarget?.jsonPath) ? newFormValues.value : formValues?.annotationValues.value ?? newFormValues.value
+                    })
                 },
                 /* Set JSON path and motivation from this checkpoint if editing an annotation */
                 ...(annotationTarget?.annotation && {

From 2420772bb197f25c5459050bda6c3358290142d2 Mon Sep 17 00:00:00 2001
From: TomDijkema <tom.dijkema@naturalis.nl>
Date: Wed, 11 Dec 2024 15:52:08 +0100
Subject: [PATCH 09/10] Fix profile tables content

---
 src/app/Hooks.ts                                               | 2 +-
 .../components/userRecordTables/UserAnnotationRecordsTable.tsx | 3 ++-
 .../components/userRecordTables/UserMasJobRecordsTable.tsx     | 1 -
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/app/Hooks.ts b/src/app/Hooks.ts
index a80f924e..2ed6fbd3 100644
--- a/src/app/Hooks.ts
+++ b/src/app/Hooks.ts
@@ -323,7 +323,7 @@ const usePagination = ({ pageSize, resultKey, params, allowSearchParams = false,
                 const result = await Method({ ...params, pageNumber: pageNumber, pageSize, ...(allowSearchParams && { searchFilters: searchFilters.GetSearchFilters() }) });
 
                 /* Set return data */
-                const records = resultKey ? result[resultKey] : result[Object.keys(result)[0]];
+                const records = resultKey ? result[resultKey] : result;
 
                 setReturnData({
                     records,
diff --git a/src/components/profile/components/userRecordTables/UserAnnotationRecordsTable.tsx b/src/components/profile/components/userRecordTables/UserAnnotationRecordsTable.tsx
index bf462f6f..dc624d5c 100644
--- a/src/components/profile/components/userRecordTables/UserAnnotationRecordsTable.tsx
+++ b/src/components/profile/components/userRecordTables/UserAnnotationRecordsTable.tsx
@@ -34,7 +34,6 @@ const UserAnnotationRecordsTable = () => {
 
     const pagination = usePagination({
         pageSize: 25,
-        resultKey: 'userAnnotations',
         Method: GetCreatorAnnotations
     });
 
@@ -56,6 +55,8 @@ const UserAnnotationRecordsTable = () => {
         });
     });
 
+    console.log(tableData);
+
     return (
         <div className="h-100 d-flex flex-column">
             <Row className="flex-grow-1 overflow-hidden">
diff --git a/src/components/profile/components/userRecordTables/UserMasJobRecordsTable.tsx b/src/components/profile/components/userRecordTables/UserMasJobRecordsTable.tsx
index eef284d2..4a014e10 100644
--- a/src/components/profile/components/userRecordTables/UserMasJobRecordsTable.tsx
+++ b/src/components/profile/components/userRecordTables/UserMasJobRecordsTable.tsx
@@ -35,7 +35,6 @@ const UserMasJobRecordsTable = () => {
 
     const pagination = usePagination({
         pageSize: 25,
-        resultKey: 'userAnnotations',
         Method: GetCreatorMasJobRecords
     });
 

From 6ec74bb91f2087def68fced9d3f8ea56b39fe262 Mon Sep 17 00:00:00 2001
From: TomDijkema <tom.dijkema@naturalis.nl>
Date: Wed, 11 Dec 2024 16:19:49 +0100
Subject: [PATCH 10/10] Fix annotations overview targeting

Fix annotations overview targeting
---
 src/app/utilities/AnnotateUtilities.ts                        | 2 +-
 .../annotationSidePanel/components/AnnotationsOverview.tsx    | 4 ++--
 .../components/annotationWizard/AnnotationWizard.tsx          | 2 ++
 3 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/src/app/utilities/AnnotateUtilities.ts b/src/app/utilities/AnnotateUtilities.ts
index ecf2c04d..f68e426a 100644
--- a/src/app/utilities/AnnotateUtilities.ts
+++ b/src/app/utilities/AnnotateUtilities.ts
@@ -43,7 +43,7 @@ const ConstructAnnotationObject = (params: {
 }): AnnotationTemplate => {
     const { digitalObjectId, digitalObjectType, motivation, annotationTargetType, jsonPath, annotationValues, fragments } = params;
 
-    let localJsonPath: string = jsonPath ?? '';
+    let localJsonPath: string = jsonPath?.replaceAll("'", '"') ?? '';
 
     /* If motivation is adding, check for new index at end of JSON path and remove if it is there */
     if (jsonPath && typeof (jp.parse(jsonPath).at(-1).expression.value) === 'number') {
diff --git a/src/components/elements/annotationSidePanel/components/AnnotationsOverview.tsx b/src/components/elements/annotationSidePanel/components/AnnotationsOverview.tsx
index e3251cce..c5846fde 100644
--- a/src/components/elements/annotationSidePanel/components/AnnotationsOverview.tsx
+++ b/src/components/elements/annotationSidePanel/components/AnnotationsOverview.tsx
@@ -92,9 +92,9 @@ const AnnotationsOverview = (props: Props) => {
         if (jsonPath) {
             filteredSortedAnnotations = filteredSortedAnnotations.filter(annotation => {
                 if (annotation["oa:hasTarget"]["oa:hasSelector"]?.["@type"] === 'ods:ClassSelector') {
-                    return annotation["oa:hasTarget"]["oa:hasSelector"]["ods:class"] === jsonPath;
+                    return annotation["oa:hasTarget"]["oa:hasSelector"]["ods:class"] === jsonPath.replaceAll("'", '"');
                 } else if (annotation["oa:hasTarget"]["oa:hasSelector"]?.["@type"] === 'ods:TermSelector') {
-                    return annotation["oa:hasTarget"]["oa:hasSelector"]["ods:term"] === jsonPath;
+                    return annotation["oa:hasTarget"]["oa:hasSelector"]["ods:term"] === jsonPath.replaceAll("'", '"');
                 }
             });
         }
diff --git a/src/components/elements/annotationSidePanel/components/annotationWizard/AnnotationWizard.tsx b/src/components/elements/annotationSidePanel/components/annotationWizard/AnnotationWizard.tsx
index f0553109..f4f50dc8 100644
--- a/src/components/elements/annotationSidePanel/components/annotationWizard/AnnotationWizard.tsx
+++ b/src/components/elements/annotationSidePanel/components/annotationWizard/AnnotationWizard.tsx
@@ -194,6 +194,8 @@ const AnnotationWizard = (props: Props) => {
         });
     });
 
+    console.log(annotationTarget);
+
     /**
      * Function to set the annotation target based on the user's selection (wizard step one)
      */