From 621369050968f970dcba3c3fa43d2609e5391337 Mon Sep 17 00:00:00 2001
From: Arman Jahanpour <77515879+rmanaem@users.noreply.github.com>
Date: Thu, 12 Dec 2024 16:20:15 -0500
Subject: [PATCH 1/3] [MNT] Removed `FromInt` age transformation (#829)

* Removed `FromInt` transformation

* Updated relevant component test

* Addressed PR comment
---
 .../good/ds003653_participant_annotated_1698934398962.json | 4 ++--
 cypress/unit/store-getter-getContinousJsonOutput.cy.js     | 5 -----
 cypress/unit/store-getter-getTransformOptions.cy.js        | 7 +------
 store/index.js                                             | 6 ------
 4 files changed, 3 insertions(+), 19 deletions(-)

diff --git a/cypress/fixtures/examples/good/ds003653_participant_annotated_1698934398962.json b/cypress/fixtures/examples/good/ds003653_participant_annotated_1698934398962.json
index df085cbd..cb9c98aa 100644
--- a/cypress/fixtures/examples/good/ds003653_participant_annotated_1698934398962.json
+++ b/cypress/fixtures/examples/good/ds003653_participant_annotated_1698934398962.json
@@ -16,8 +16,8 @@
                 "TermURL": "nb:Age"
             },
             "Transformation": {
-                "Label": "integer value",
-                "TermURL": "nb:FromInt"
+                "Label": "float value",
+                "TermURL": "nb:FromFloat"
             },
             "MissingValues": []
         },
diff --git a/cypress/unit/store-getter-getContinousJsonOutput.cy.js b/cypress/unit/store-getter-getContinousJsonOutput.cy.js
index 6579a596..1eed7b71 100644
--- a/cypress/unit/store-getter-getContinousJsonOutput.cy.js
+++ b/cypress/unit/store-getter-getContinousJsonOutput.cy.js
@@ -44,11 +44,6 @@ let store = {
                 Label: "float value",
                 TermURL: "nb:FromFloat"
             },
-            int: {
-
-                Label: "integer value",
-                TermURL: "nb:FromInt"
-            },
             iso8601: {
 
                 Label: "period of time defined according to the ISO8601 standard",
diff --git a/cypress/unit/store-getter-getTransformOptions.cy.js b/cypress/unit/store-getter-getTransformOptions.cy.js
index 47afca9a..90ee7488 100644
--- a/cypress/unit/store-getter-getTransformOptions.cy.js
+++ b/cypress/unit/store-getter-getTransformOptions.cy.js
@@ -30,11 +30,6 @@ let store = {
                 Label: "float value"
             },
 
-            int: {
-                TermURL: "nb:FromInt",
-                Label: "integer value"
-            },
-
             iso8601: {
                 TermURL: "nb:FromISO8601",
                 Label: "period of time defined according to the ISO8601 standard"
@@ -52,7 +47,7 @@ describe("getTransformOptions", () => {
 
         // Assert
         expect(options).to.deep.equal([
-            "bounded", "euro", "float", "int", "iso8601"
+            "bounded", "euro", "float", "iso8601"
         ]);
     });
 });
\ No newline at end of file
diff --git a/store/index.js b/store/index.js
index b0e6b732..b682d4c9 100644
--- a/store/index.js
+++ b/store/index.js
@@ -137,12 +137,6 @@ export const state = () => ({
             TermURL: "nb:FromFloat"
         },
 
-        int: {
-
-            Label: "integer value",
-            TermURL: "nb:FromInt"
-        },
-
         iso8601: {
 
             Label: "period of time defined according to the ISO8601 standard",

From fe3f035bba21bbb8b5e423a3ba3354281cce9c44 Mon Sep 17 00:00:00 2001
From: Arman Jahanpour <77515879+rmanaem@users.noreply.github.com>
Date: Thu, 12 Dec 2024 16:33:29 -0500
Subject: [PATCH 2/3] [ENH] Made requirement of age annotation more prominent
 (#830)

* Removed `FromInt` transformation

* Updated relevant component test

* Made requirement of age annotation more prominent

* Addressed PR comment

* Addressed PR comment
---
 pages/download.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pages/download.vue b/pages/download.vue
index e3a84cac..7bd3d667 100644
--- a/pages/download.vue
+++ b/pages/download.vue
@@ -9,7 +9,7 @@
                     There are incomplete annotations for columns that were mapped to variables.
                     You can go back and complete these annotations before you download the .json data dictionary.
                     <br /><br />
-                    The following columns are missing annotations:
+                    The following columns have incomplete annotations:
                     <ul v-for="column in incompleteAnnotations" :key="column">
                         <li>{{ column }}</li>
                     </ul>

From b578fd79cfdef34d386aed89dcf526f4ebbdf8c0 Mon Sep 17 00:00:00 2001
From: Arman Jahanpour <77515879+rmanaem@users.noreply.github.com>
Date: Thu, 12 Dec 2024 17:23:29 -0500
Subject: [PATCH 3/3] [ENH] Implemented `Annotate Another Dataset` button
 (#832)

* Removed `FromInt` transformation

* Updated relevant component test

* Made requirement of age annotation more prominent

* Implemented `filterOptions` function

* Implemented `filterOptions` function

* Implemented `Annotate Another Dataset` button

* Addressed requested changes
---
 components/annot-categorical.vue       | 25 +++++++++++++++++++++++++
 components/annot-continuous-values.vue |  2 +-
 components/category-toolgroup.vue      | 26 ++++++++++++++++++++++++++
 cypress.config.js                      |  3 ++-
 pages/download.vue                     | 21 +++++++++++++++++++--
 store/index.js                         | 20 +++++++++++++++++---
 6 files changed, 90 insertions(+), 7 deletions(-)

diff --git a/components/annot-categorical.vue b/components/annot-categorical.vue
index d4d78335..8f9ec7a2 100644
--- a/components/annot-categorical.vue
+++ b/components/annot-categorical.vue
@@ -26,6 +26,7 @@
 
                         <v-select
                             :data-cy="'categoricalSelector' + '_' + row.index"
+                            :filter-by="filterOptions"
                             :options="getCategoricalOptions(row.item['columnName'])"
                             :reduce="term => term.identifier"
                             :value="getSelectedCategoricalOption(row.item['columnName'], row.item['rawValue'])"
@@ -150,7 +151,31 @@
                 "selectCategoricalOption",
                 "updateAnnotationCount"
             ]),
+            filterOptions(option, label, search) {
+                if (!label || search[0].toLowerCase() !== label[0].toLowerCase()) {
+                    return false;
+                }
+
+                let labelIndex = 1;
+                for (let searchIndex = 1; searchIndex < search.length; searchIndex++) {
+                    const searchChar = search[searchIndex].toLowerCase();
+                    let matchFound = false;
+
+                    while (labelIndex < label.length) {
+                        if (label[labelIndex].toLowerCase() === searchChar) {
+                            matchFound = true;
+                            labelIndex++;
+                            break;
+                        }
+                        labelIndex++;
+                    }
 
+                    if (!matchFound) {
+                        return false;
+                    }
+                }
+                return true;
+            },
             selectOptionAndUpdate(p_optionValue, p_columnName, p_rawValue) {
 
                 // 1. Set the categoricla option for this value in the store
diff --git a/components/annot-continuous-values.vue b/components/annot-continuous-values.vue
index 7e0f0048..e55935e4 100644
--- a/components/annot-continuous-values.vue
+++ b/components/annot-continuous-values.vue
@@ -86,7 +86,7 @@
                     instructions: "Review the age harmonization",
                     missingValueButton: "Mark as missing",
                     saveButton: "Save Annotation",
-                    dropDownExplanationText: "Please select the format of age values in this column"
+                    dropDownExplanationText: "Please select the format of age values in this column*"
                 }
             };
         },
diff --git a/components/category-toolgroup.vue b/components/category-toolgroup.vue
index 4f91d262..b64663a2 100644
--- a/components/category-toolgroup.vue
+++ b/components/category-toolgroup.vue
@@ -5,6 +5,7 @@
                 <b-row>
                     <v-select
                         v-if="tableRows.length > 0"
+                        :filter-by="filterOptions"
                         placeholder="Select an assessment tool"
                         data-cy="toolgroup-select"
                         :options="toolTerms"
@@ -84,6 +85,31 @@
                 "createAssessmentTool",
                 "alterColumnToToolMapping"
             ]),
+            filterOptions(option, label, search) {
+                if (!label || search[0].toLowerCase() !== label[0].toLowerCase()) {
+                    return false;
+                }
+
+                let labelIndex = 1;
+                for (let searchIndex = 1; searchIndex < search.length; searchIndex++) {
+                    const searchChar = search[searchIndex].toLowerCase();
+                    let matchFound = false;
+
+                    while (labelIndex < label.length) {
+                        if (label[labelIndex].toLowerCase() === searchChar) {
+                            matchFound = true;
+                            labelIndex++;
+                            break;
+                        }
+                        labelIndex++;
+                    }
+
+                    if (!matchFound) {
+                        return false;
+                    }
+                }
+                return true;
+            },
             selectTool(selectedTool) {
                 if ( selectedTool !== null ) {
                     this.createAssessmentTool({
diff --git a/cypress.config.js b/cypress.config.js
index f25f21be..53de9698 100644
--- a/cypress.config.js
+++ b/cypress.config.js
@@ -33,7 +33,8 @@ module.exports = defineConfig({
     },
 
     component: {
-
+        viewportHeight: 1080,
+        viewportWidth: 1920,
         devServer: {
 
             bundler: "webpack",
diff --git a/pages/download.vue b/pages/download.vue
index 7bd3d667..f002e41f 100644
--- a/pages/download.vue
+++ b/pages/download.vue
@@ -79,13 +79,21 @@
             </b-col>
 
         </b-row>
+        <b-row align-h="center">
+            <b-col cols="3">
+                <b-button
+                    @click="restartAnnotation">
+                    {{ uiText.restartButton }}
+                </b-button>
+            </b-col>
+        </b-row>
 
     </div>
 
 </template>
 
 <script>
-    import { mapState, mapGetters, mapActions } from "vuex";
+    import { mapState, mapGetters, mapActions, mapMutations } from "vuex";
     import { saveAs } from "file-saver";
     import Ajv from "ajv";
     import jsonSchema from "@/assets/neurobagel_data_dictionary.schema.json";
@@ -113,7 +121,8 @@
                 // Text for UI elements
                 uiText: {
 
-                    downloadButton: "Download Annotated Data"
+                    downloadButton: "Download Annotated Data",
+                    restartButton: "Annotate Another Dataset"
                 },
 
                 incompleteAnnotations: [],
@@ -163,10 +172,18 @@
         },
 
         methods: {
+            ...mapMutations([
+                "resetState"
+            ]),
+
             ...mapActions([
                 "navigateToPage"
             ]),
 
+            restartAnnotation() {
+                this.resetState();
+                this.navigateToPage("home");
+            },
             formatJson(p_jsonData) {
                 if (p_jsonData) {
                     return JSON.stringify(p_jsonData, null, this.jsonSpacing);
diff --git a/store/index.js b/store/index.js
index b682d4c9..f5e33e19 100644
--- a/store/index.js
+++ b/store/index.js
@@ -4,7 +4,9 @@ import Vue from "vue";
 import toolTerms from "~/static/toolTerms.json";
 import diagnosisTerms from "~/static/diagnosisTerms.json";
 
-export const state = () => ({
+// The default state of the store
+function getDefaultState() {
+    return {
 
     // Keeps track of number of annotations made in current run;
     // > 0 annotations allows access to the download page
@@ -151,7 +153,10 @@ export const state = () => ({
       })),
 
     columnToToolMap: {}
-});
+};
+}
+
+export const state = () => getDefaultState();
 
 export const getters = {
 
@@ -936,5 +941,14 @@ export const mutations = {
 
         // 2. Save the updated annotation in the store
         p_state.annotationCount = count;
-    }
+    },
+
+    resetState(p_state) {
+        const initialState = getDefaultState();
+        Object.keys(p_state).forEach((key) => {
+          if (Object.prototype.hasOwnProperty.call(initialState, key)) {
+            Vue.set(p_state, key, initialState[key]);
+          }
+        });
+      }
 };