Merge pull request #140 from DiSSCo/PrefillAnnotationClassesWithValues

Prefill annotation classes with values

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 */

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,

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 */
@@ -42,7 +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') {
@@ -182,7 +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
     } = {};
@@ -208,14 +209,33 @@ 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')) {
             return format(new Date, 'yyyy-MM-dd');
         }
     };
 
+    /**
+     * 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 === 'ods:adding' && isArray) {
+            return [CheckForClassDefaultValues(fieldName)];
+        } else if (motivation === 'ods:adding') {
+            return CheckForClassDefaultValues(fieldName) ?? {};
+        }
+    };
+
     /* For each class, add it as a key property to the annotation form fields dictionary */
     classesList.forEach(classProperty => {
         if (!termValue) {
@@ -240,21 +260,32 @@ 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 */
+                formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = DepictClassValues(
+                    classProperty.value.replace(`$`, jsonPath), classFormValues
+                );
+
             } else if (classProperty.value.includes('has') && classProperty.value.at(-3) === 's') {
-                const localClassValues: Dict[] | undefined = 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));
                 }
 
-                formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = classValues ?? localClassValues ?? [];
+                formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = [];
+
+                /* Check if (default) values are present, if so, set form values property with them */
+                formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = DepictClassValues(
+                    classProperty.value.replace(`$`, jsonPath), classValues, true, localClassValues
+                );
             } else {
-                formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, jsonPath))] = {};
+                formValues[FormatFieldNameFromJsonPath(classProperty.value.replace(`$`, 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 */
@@ -271,7 +302,7 @@ 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);
                 }
             });

src/app/utilities/ClassAnnotationUtilities.ts

@@ -0,0 +1,101 @@
+/* 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
+ * @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('$', '').replaceAll("'", '');
+
+    switch (className) {
+        case 'ods:hasAgents': {
+            return ClassAgents();
+        }
+        case 'ods:hasGeoreference': {
+            return ClassGeoreference();
+        }
+        case 'ods:hasIdentifiers': {
+            return ClassIdentifiers(jsonPath);
+        }
+        case 'ods:hasRoles': {
+            return ClassRoles();
+        }
+    };
+};
+
+/**
+ * Function to create a prefilled agent values object
+ * @returns Prefilled agents values array
+ */
+const ClassAgents = () => {
+    /* Construct agent values object */
+    const classValues = {
+        "@id": KeycloakService.GetParsedToken()?.orcid,
+        "@type": 'schema:Person',
+        "schema:identifier": KeycloakService.GetParsedToken()?.orcid,
+        "schema:name": `${KeycloakService.GetParsedToken()?.given_name ?? ''} ${KeycloakService.GetParsedToken()?.family_name ?? ''}`
+    };
+
+    return classValues;
+};
+
+/**
+ * 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 Prefilled identifiers values array
+ */
+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": dctermsIdentifier
+    };
+
+    return classValues;
+};
+
+/**
+ * Function to create a prefilled role values object
+ * @returns Prefilled roles values array
+ */
+const ClassRoles = () => {
+    /* Construct role values object */
+    const classValues = {
+        "@type": '',
+        "schema:roleName": ''
+    };
+
+    return classValues;
+};
+
+export {
+    CheckForClassDefaultValues
+};

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
 };

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']}`;
         }
     };
 

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("'", '"');
                 }
             });
         }

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)
      */

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) {
@@ -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 && {

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