-
-
-
-
-
- {{ uiText.removeToolGroupButton }}
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
\ No newline at end of file
diff --git a/components/column-linking-table.vue b/components/column-linking-table.vue
index 4cffb175..b0311af8 100644
--- a/components/column-linking-table.vue
+++ b/components/column-linking-table.vue
@@ -55,14 +55,14 @@
...mapState([
"colorInfo",
- "columnToCategoryMapping"
+ "columnToCategoryMap"
]),
tableRows() {
return this.getColumnNames.map(column => ({
- category: this.columnToCategoryMapping[column],
+ category: this.columnToCategoryMap[column],
column: column,
description: this.getColumnDescription(column)
}));
@@ -85,7 +85,7 @@
styleTableRow(p_row, p_rowType) {
// Check to see what category has been assigned to this row's column, if any
- const assignedCategory = this.columnToCategoryMapping[p_row.column];
+ const assignedCategory = this.columnToCategoryMap[p_row.column];
return ( null === assignedCategory ) ? "" : this.colorInfo.categoryClasses[assignedCategory];
}
diff --git a/cypress/component/column-linking-table.cy.js b/cypress/component/column-linking-table.cy.js
index 2b1f5d10..5fc41019 100644
--- a/cypress/component/column-linking-table.cy.js
+++ b/cypress/component/column-linking-table.cy.js
@@ -63,7 +63,7 @@ describe("The column-linking-table component", () => {
return "descriptions help";
},
- columnToCategoryMapping: () => {
+ columnToCategoryMap: () => {
return {
diff --git a/cypress/unit/store-getter-getCategoricalOptions.cy.js b/cypress/unit/store-getter-getCategoricalOptions.cy.js
index 7669b490..5e2a6405 100644
--- a/cypress/unit/store-getter-getCategoricalOptions.cy.js
+++ b/cypress/unit/store-getter-getCategoricalOptions.cy.js
@@ -14,7 +14,7 @@ let store = {
]
},
- columnToCategoryMapping: {
+ columnToCategoryMap: {
"column1": "category1"
}
diff --git a/cypress/unit/store-getter-getMappedCategories.cy.js b/cypress/unit/store-getter-getMappedCategories.cy.js
index e6500d3f..191bb8bc 100644
--- a/cypress/unit/store-getter-getMappedCategories.cy.js
+++ b/cypress/unit/store-getter-getMappedCategories.cy.js
@@ -4,7 +4,7 @@ const store = {
state: {
- columnToCategoryMapping: {
+ columnToCategoryMap: {
column1: "category1",
column2: "category2",
diff --git a/cypress/unit/store-getter-getMappedColumns.cy.js b/cypress/unit/store-getter-getMappedColumns.cy.js
index 40278ffe..bd8ccdf7 100644
--- a/cypress/unit/store-getter-getMappedColumns.cy.js
+++ b/cypress/unit/store-getter-getMappedColumns.cy.js
@@ -4,7 +4,7 @@ const store = {
state: {
- columnToCategoryMapping: {
+ columnToCategoryMap: {
"column1": "category1",
"column2": "category2",
diff --git a/cypress/unit/store-getter-getMissingValues.cy.js b/cypress/unit/store-getter-getMissingValues.cy.js
index 443478d0..1de1072e 100644
--- a/cypress/unit/store-getter-getMissingValues.cy.js
+++ b/cypress/unit/store-getter-getMissingValues.cy.js
@@ -5,7 +5,7 @@ const store = {
getters: getters,
state: {
- columnToCategoryMapping: {
+ columnToCategoryMap: {
column1: "category1",
column2: "category1",
diff --git a/cypress/unit/store-getter-getUniqueValues.cy.js b/cypress/unit/store-getter-getUniqueValues.cy.js
index a2e98d23..5858a360 100644
--- a/cypress/unit/store-getter-getUniqueValues.cy.js
+++ b/cypress/unit/store-getter-getUniqueValues.cy.js
@@ -10,7 +10,7 @@ describe("getUniqueValues getter", () => {
state: {
- columnToCategoryMapping: {
+ columnToCategoryMap: {
column1: "Diagnosis",
column2: "Age",
@@ -50,7 +50,7 @@ describe("getUniqueValues getter", () => {
it("Retrieves unique values of a multiple columns", () => {
// Setup
- store.state.columnToCategoryMapping.column2 = "Diagnosis";
+ store.state.columnToCategoryMap.column2 = "Diagnosis";
// Act
const diagnosisUniqueValues = getters.getUniqueValues(store.state)("Diagnosis");
diff --git a/cypress/unit/store-getter-isPageAccessible.cy.js b/cypress/unit/store-getter-isPageAccessible.cy.js
index 582220b5..6c9519d4 100644
--- a/cypress/unit/store-getter-isPageAccessible.cy.js
+++ b/cypress/unit/store-getter-isPageAccessible.cy.js
@@ -11,7 +11,7 @@ describe("isPageAccessible", () => {
annotationCount: 1,
- columnToCategoryMapping: {
+ columnToCategoryMap: {
"column1Name": "Subject ID"
},
@@ -47,13 +47,13 @@ describe("isPageAccessible", () => {
// Setup
let nextPage = "annotation";
- state.columnToCategoryMapping["column2Name"] = "Sex";
+ state.columnToCategoryMap["column2Name"] = "Sex";
// Assert
expect(getters.isPageAccessible(state)(nextPage)).to.be.true;
// Setup
- state.columnToCategoryMapping = {};
+ state.columnToCategoryMap = {};
// Assert
expect(getters.isPageAccessible(state)(nextPage)).to.be.false;
diff --git a/cypress/unit/store-mutation-alterColumnCategoryMapping.cy.js b/cypress/unit/store-mutation-alterColumnCategoryMap.cy.js
similarity index 87%
rename from cypress/unit/store-mutation-alterColumnCategoryMapping.cy.js
rename to cypress/unit/store-mutation-alterColumnCategoryMap.cy.js
index f5071ce9..81de42aa 100644
--- a/cypress/unit/store-mutation-alterColumnCategoryMapping.cy.js
+++ b/cypress/unit/store-mutation-alterColumnCategoryMap.cy.js
@@ -16,7 +16,7 @@ describe("alterColumnCategoryMapping", () => {
state: {
- columnToCategoryMapping : {
+ columnToCategoryMap : {
"column1": "Age",
"column2": null,
@@ -63,7 +63,7 @@ describe("alterColumnCategoryMapping", () => {
mutations.alterColumnCategoryMapping(store.state, { category: "Sex", column: "column3" });
// Assert
- expect(store.state.columnToCategoryMapping.column3).to.equal(null);
+ expect(store.state.columnToCategoryMap.column3).to.equal(null);
});
it("Changes the mapping of column to category if they're not already mapped", () => {
@@ -72,14 +72,14 @@ describe("alterColumnCategoryMapping", () => {
mutations.alterColumnCategoryMapping(store.state, { category: "someCategory", column: "column1" });
// Assert
- expect(store.state.columnToCategoryMapping.column1).to.equal("someCategory");
+ expect(store.state.columnToCategoryMap.column1).to.equal("someCategory");
expect(store.state.dataDictionary.annotated.column1).to.deep.equal(reinitializedAnnotatedColumn);
// Act
mutations.alterColumnCategoryMapping(store.state, { category: "someCategory", column: "column2" });
// Assert
- expect(store.state.columnToCategoryMapping.column2).to.equal("someCategory");
+ expect(store.state.columnToCategoryMap.column2).to.equal("someCategory");
expect(store.state.dataDictionary.annotated.column2).to.deep.equal(reinitializedAnnotatedColumn);
});
});
diff --git a/cypress/unit/store-mutation-initializeColumnToCategoryMap.cy.js b/cypress/unit/store-mutation-initializeColumnToCategoryMap.cy.js
index 2fe7f9ee..d0b7211c 100644
--- a/cypress/unit/store-mutation-initializeColumnToCategoryMap.cy.js
+++ b/cypress/unit/store-mutation-initializeColumnToCategoryMap.cy.js
@@ -9,7 +9,7 @@ describe("initializeColumnToCategoryMap", () => {
// Setup
state = {
- columnToCategoryMapping: {},
+ columnToCategoryMap: {},
dataTable: [
@@ -29,19 +29,19 @@ describe("initializeColumnToCategoryMap", () => {
mutations.initializeColumnToCategoryMap(state, ["column1Name", "column2Name"]);
// Assert
- expect(state.columnToCategoryMapping).to.eql({"column1Name": null, "column2Name": null});
+ expect(state.columnToCategoryMap).to.eql({"column1Name": null, "column2Name": null});
});
it("Make sure that old columns are removed from newly updated map", () => {
// Setup
- state.columnToCategoryMapping["oldColumn1"] = "category1";
- state.columnToCategoryMapping["oldColumn2"] = "category2";
+ state.columnToCategoryMap["oldColumn1"] = "category1";
+ state.columnToCategoryMap["oldColumn2"] = "category2";
// Act
mutations.initializeColumnToCategoryMap(state, ["column1Name", "column2Name"]);
// Assert
- expect(state.columnToCategoryMapping).to.eql({"column1Name": null, "column2Name": null});
+ expect(state.columnToCategoryMap).to.eql({"column1Name": null, "column2Name": null});
});
});
\ No newline at end of file
diff --git a/store/index-old.js b/store/index-old.js
deleted file mode 100644
index 43a203c7..00000000
--- a/store/index-old.js
+++ /dev/null
@@ -1,848 +0,0 @@
-
-// Facilitate Vue reactivity via 'Vue.set' and 'Vue.delete'
-import Vue from "vue";
-
-// Root state - Stores state data
-export const state = () => ({
-
- // Page-related data
-
- currentPage: "home",
-
- columns: [],
-
- pageData: {
-
- home: {
-
- accessible: true,
- fullName: "Home",
- location: "/",
- pageName: "index"
- },
-
- categorization: {
-
- accessible: false,
- fullName: "Categorization",
- location: "categorization",
- pageName: "categorization"
- },
-
- annotation: {
-
- accessible: false,
- fullName: "Annotation",
- location: "annotation",
- pageName: "annotation"
- },
-
- download: {
-
- accessible: false,
- fullName: "Download",
- location: "download",
- pageName: "download"
- }
- },
-
- pageOrder: [
-
- "home",
- "categorization",
- "annotation",
- "download"
- ],
-
- // Data table (i.e. participants.tsv file)
-
- dataTable: {
-
- // List of data table's columns
- columns: [],
-
- // File name of the data table tsv file
- filename: "",
-
- // File type of the original data table file
- fileType: "",
-
- // Participants.tsv file data
- // For format see 'convertTsvLinesToTableData' in index.js
- original: null,
-
- // Version of table data for annotation page
- annotated: null
- },
-
- // Data dictionary (i.e. participants.json)
-
- dataDictionary: {
-
- // File names of the data dictionary json file
- filename: "",
-
- // File type of the original data dictionary file
- fileType: "",
-
- // Original data dictionary file data
- original: null,
-
- // User-amended data dictionary file data
- amended: {}
- },
-
- // Stores table data in format ready for Bootstrap table
- // This is an array of objects. See the mutation
- // 'setupColumnToCategoryMap' for exact format
- columnToCategoryMap: {
-
- },
-
- // Hardcoded list of categories used on the categorization page
- // and possibly elsewhere in the tool
- categories: [],
-
- // This is a computed direct map between current categories and CSS classes
- // See getter 'categoryClasses'
- categoryClasses: null,
-
- // The following fields are only accessed by store methods
-
- // Maps our categories in 'categories' to colors in 'toolColorPalette'
- // (Final class names pending). This way colors can be swappable and
- // rearrangeable for categories.
- categoryToColorMap: {},
-
- // Map of the tools colors to CSS classes containing color (and possibly
- // other style) values. More palettes could be defined here, either out of
- // user preference or if we ever decided to code a light/dark mode feature
- toolColorPalette: {
-
- color1: "category-style-0",
- color2: "category-style-1",
- color3: "category-style-2",
- color4: "category-style-3",
- color5: "category-style-4",
- colorDefault: "category-style-default"
- },
-
- // Annotation page-specific fields
-
- // The string label applied to values designated as "missing values" when the data are annotated.
- missingValueLabel: "missing value",
-
- // Counter for the number of annotations that have been done
- annotationCount: 0,
-
- // Keeps track of textual- and component-related information for the annotation of each category
- // See action nuxtServerInit() for initialization code
- annotationDetails: [],
-
- // Stores a list of (potentially) missing values for each column. This is determined in the missing-values
- // components on the annotation page, and then amended by the user as they see fit
- missingColumnValues: {},
-
- // Keeps track of named assessment tool groups and their associated tools (e.g. columns in the data table)
- toolGroups: {}
-});
-
-// Actions - Call mutations to change state data in order to maintain trace of
-// what component changed state data and when
-export const actions = {
-
- // Initializations
-
- initializeAnnotationDetails(p_context, p_details) {
-
- p_context.commit("setupAnnotationDetails", p_details);
- },
-
- initializeCategories(p_context, p_categories) {
-
- p_context.commit("setupCategories", p_categories);
- },
-
- nuxtServerInit({ commit }) {
-
- // This function is called on Nuxt server startup
-
- // 0. This list is default but we can swap out and reinitialize category
- // data structures by calling store action 'initializeCategories' with
- // a new list of categories
- const categories = [
-
- "Subject ID",
- "Age",
- "Sex",
- "Diagnosis",
- "Assessment Tool"
- ];
-
- // 0. This annotation information is default but we can swap out and reinitialize
- // annotation data structures by calling 'initializeAnnotationDetails' with a new
- // object containing annotation information for each category
- const annotationDetails = [
-
- {
- id: 0,
- category: "Age",
- dataType: "continuous",
- explanation: "This is an explanation for how to annotate age.",
- options: {},
- specializedComponent: "annot-age-values"
- },
- {
- id: 1,
- category: "Sex",
- dataType: "categorical",
- explanation: "This is an explanation for how to annotate sex.",
- options: ["male", "female", "other"],
- specializedComponent: "annot-discrete-choices"
- },
- {
- id: 2,
- category: "Diagnosis",
- dataType: "string",
- explanation: "This is an explanation for how to annotate diagnosis.",
- options: {},
- specializedComponent: "annot-vocabulary"
- }
-
- // NOTE: Assessment tools are now only added to annotationDetails when grouped
- ];
-
- // 1. Setup category-related data structures based on the given categories
- commit("setupCategories", categories);
-
- // 2. Setup annotation-related data structures based on the given categories\
- commit("setupAnnotationDetails", annotationDetails);
-
- // 3. Set the current page as the landing page
- commit("setCurrentPage", "home");
- },
-
- // Tool navigation
-
- // Landing page actions
-
- saveDataDictionary(p_context, p_newFileData) {
-
- // 1. Attempt to transform the string data into JSON if valid data given
- if ( "json" === p_newFileData.fileType ) {
-
- if ( null !== p_newFileData.data )
- p_newFileData.formattedData = JSON.parse(p_newFileData.data);
- }
-
- // 2. Save either an empty object or the JSON dict to state data
- p_context.commit("setDataDictionary", p_newFileData);
- },
-
- saveDataTable(p_context, p_newFileData) {
-
- // 1. Attempt to convert the tsv lines into a dict for each line if valid data given
- if ( "tsv" === p_newFileData.fileType ) {
-
- // 1. Save new table data, formatted for the Vue table element
- if ( null !== p_newFileData.data )
- p_newFileData.formattedData = convertTsvLinesToTableData(p_newFileData.data);
-
- // 2. Save a list of the columns of this new table data
- if ( p_newFileData.formattedData.length > 0 )
- p_newFileData.columns = Object.keys(p_newFileData.formattedData[0]);
- }
-
- // 2. Save either an empty array or array of tsv dictionaries to state data
- p_context.commit("setDataTable", p_newFileData);
- },
-
- // Categorization page actions
-
- alterColumnCategoryRelation(p_context, p_relationData) {
-
- // Category not set or categor is not the same as input category
- if ( null === p_context.state.columnToCategoryMap[p_relationData.column] ||
- p_relationData.category !== p_context.state.columnToCategoryMap[p_relationData.column] ) {
-
- p_context.commit("addColumnCategorization", p_relationData.column, p_relationData.category);
- }
- // Else, category is the same as input category
- else {
-
- p_context.commit("removeColumnCategorization", p_relationData.column);
- }
- },
-
- createToolGroup(p_context, p_toolGroupData) {
-
- p_context.commit("saveToolGroup", p_toolGroupData);
- },
-
- modifyToolGroup(p_context, p_toolGroupData) {
-
- p_context.commit("changeToolGroup", p_toolGroupData);
- },
-
- removeToolGroup(p_context, p_toolGroupData) {
-
- p_context.commit("deleteToolGroup", p_toolGroupData);
- },
-
- // Annotation page actions
-
- revertColumnToOriginal(p_context, p_column) {
-
- // NOTE: Reverts a column of annotated data to its original set of values
- // Currently used when a user decouples a column from a category,
- // but could also have use if an 'Undo Annotation' button is implemented
- // on the annotation page.
-
- // Gather original table column values in row-order
- const originalValues = [];
- for ( let index = 0; index < p_context.state.dataTable.original.length; index++ ){
- originalValues.push(p_context.state.dataTable.original[index][p_column]);
- }
-
- p_context.commit("changeColumnValues", {
-
- column: p_column,
- tableToChange: p_context.state.dataTable.annotated,
- newValues: originalValues
- });
- },
-
- saveMissingColumnValues(p_context, p_missingColumnValues) {
-
- p_context.commit("setMissingColumnValues", p_missingColumnValues);
- }
-};
-
-// Mutations - Change state data, as called by Actions
-export const mutations = {
-
- // Initialization
-
- createColumnToCategoryMap(p_state) {
-
- // Column to category map lists all columns as keys with default value of null
- p_state.columnToCategoryMap =
- Object.fromEntries(p_state.dataTable.columns.map((column) => [column, null]));
- },
-
- setupAnnotationDetails(p_state, p_details) {
-
- p_state.annotationDetails = p_details;
- },
-
- setupCategories(p_state, p_categories) {
-
- // 1. Save the given category list
- p_state.categories = p_categories;
-
- // 2. Get color keys from tool color palette
- const colorKeys = Object.keys(p_state.toolColorPalette);
-
- // 3. Create the category to color map
- let assignedCategories = 0;
- for ( let index = 0; index < p_categories.length &&
- index < colorKeys.length; index++ ) {
-
- // A. Stop when the default color key has been reached
- if ( "colorDefault" === colorKeys[index] )
- break;
-
- // B. Map this category to color key
- p_state.categoryToColorMap[p_categories[index]] = colorKeys[index];
-
- // C. Keep track of how many categories have been assigned color keys
- assignedCategories += 1;
- }
- // D. Issue warning if there are not enough color keys for the given category set
- if ( p_categories.length > assignedCategories ) {
- console.log("WARNING: Not all categories have been assigned color keys!");
- }
-
- // 4. Set up the category to CSS class map
-
- // A. Create a map between category names and color classes
- const mapArray = [];
- for ( let index = 0; index < p_state.categories.length; index++ ) {
-
- const category = p_state.categories[index];
- const colorID = p_state.categoryToColorMap[category];
- const colorClass = p_state.toolColorPalette[colorID];
-
- mapArray.push([category, colorClass]);
- }
-
- // B. Save the new category to class map
- p_state.categoryClasses = Object.fromEntries(mapArray);
- },
-
- // Tool navigation
-
- setCurrentPage(p_state, p_pageName) {
-
- // Set the current page for the layout navbar
- p_state.currentPage = p_pageName;
- },
-
- // Landing page
-
- setDataDictionary(p_state, p_newFileData) {
-
- // 1. Save the new data dictionary to state data
- p_state.dataDictionary.original = p_newFileData.formattedData;
-
- // 2. Save the file name of the data dictionary json file
- p_state.dataDictionary.filename = p_newFileData.filename;
-
- // 3. Save the file type of the new data dictionary
- p_state.dataDictionary.fileType = p_newFileData.fileType;
- },
-
- setDataTable(p_state, p_newFileData) {
-
- // 1. Save the new tsv row dictionary list to state data
- p_state.dataTable.original = p_newFileData.formattedData;
-
- // 2. Save the file name of the tsv file
- p_state.dataTable.filename = p_newFileData.filename;
-
- // 3. Save the file type of the new data table
- p_state.dataTable.fileType = p_newFileData.fileType;
-
- // 4. Save a list of the columns of this data table
- p_state.dataTable.columns = p_newFileData.columns;
-
- // 5. Make the annotated data a copy of the original
- p_state.dataTable.annotated = structuredClone(p_state.dataTable.original);
- },
-
- // Categorization page
-
- addColumnCategorization(p_state, p_column, p_category) {
-
- // Save the categorization-column link in the annotated table
- p_state.columnToCategoryMap[p_column] = p_category;
- },
-
- changeToolGroup(p_state, p_toolGroupData) {
-
- // 1. Remove the old group from the tool group object
- Vue.delete(p_state.toolGroups, p_toolGroupData.previousName);
-
- // 2. Add the new group to the tool group object
- Vue.set(p_state.toolGroups, p_toolGroupData.name, p_toolGroupData.tools);
-
- // 3. Alter the annotation details to reflect this change
- const detailIndex = p_state.annotationDetails.findIndex(
- detail => p_toolGroupData.previousName === detail.groupName);
- p_state.annotationDetails[detailIndex].groupName = p_toolGroupData.name;
- p_state.annotationDetails[detailIndex].tools = p_toolGroupData.tools;
- },
-
- deleteToolGroup(p_state, p_toolGroupData) {
-
- // 1. Remove this tool group from the list
- Vue.delete(p_state.toolGroups, p_toolGroupData.name);
-
- // 2. Remove the toolgroup from the annotation details
- const groupIndex = p_state.annotationDetails.findIndex(detail =>
- p_toolGroupData.name === detail?.groupName);
- p_state.annotationDetails.splice(groupIndex, 1);
- },
-
- removeColumnCategorization(p_state, p_column) {
-
- // Disassociate the column with this category it was linked to
- p_state.columnToCategoryMap[p_column] = null;
- },
-
- deleteToolFromGroup(p_state, p_data) {
-
- // Remove the tool from the given tool group
- p_state.toolGroups[p_data.group].splice(
- p_state.toolGroups[p_data.group].findIndex(element => element === p_data.tool), 1);
- },
-
- saveToolGroup(p_state, p_toolGroupData) {
-
- // 1. Save this group to the tool group map
- // p_state.set(p_state.toolGroups, p_toolGroupData.name, p_toolGroupData.tools);
- Vue.set(p_state.toolGroups, p_toolGroupData.name, [...p_toolGroupData.tools]);
-
- // 2. Add a new assessment tool item to the annotation details list for this tool group
- p_state.annotationDetails.push({
-
- id: p_state.annotationDetails.length,
- category: "Assessment Tool",
- dataType: "string",
- explanation: "This is an explanation for how to annotate assessments.",
- groupName: p_toolGroupData.name,
- options: {},
- specializedComponent: "annot-tool-group",
- tools: p_state.toolGroups[p_toolGroupData.name]
- });
- },
-
- // Annotation page
-
- changeColumnValues(p_state, p_changeInfo) {
-
- // Change the values in the given table's column
- for ( let index = 0; index < p_changeInfo.tableToChange.length; index++ ) {
-
- p_changeInfo.tableToChange[index][p_changeInfo.column] = p_changeInfo.newValues[index];
- }
- },
-
- setAnnotatedDataTable(p_state, p_newTable) {
-
- p_state.dataTable.annotated = p_newTable;
- },
-
- setMissingColumnValues(p_state, p_missingColumnValues) {
-
- // This method merges incoming updated missingColumnValues records with the missingColumnValues
- // object in the store. Because the incoming changes can be incomplete (e.g. only contain updated
- // records of a single column), we cannot just overwrite the store object with them.
- // However, because of how reactivity in Vue works, we can also not simply overwrite the affected columns
- // (i.e. keys) in the object, because that will break reactivity.
- // The below pattern via assign sovles this problem. See here: https://v2.vuejs.org/v2/guide/reactivity.html
-
- const missingColumnKey = Object.keys(p_missingColumnValues)[0];
- if ( 0 === p_missingColumnValues[missingColumnKey].length ) {
- Vue.delete(p_state.missingColumnValues, missingColumnKey);
- } else {
- p_state.missingColumnValues = Object.assign({}, p_state.missingColumnValues, p_missingColumnValues);
- }
- }
-};
-
-// Getters - Give access to state data
-export const getters = {
-
- columnDescription: (p_state) => (p_column) => {
-
- // 0. If we do not have a data dictionary then the column description is undefined (e.g. 'null')
- let columnDescription = null;
-
- // 1. Find the description for this column in the data dictionary
- if ( null !== p_state.dataDictionary.original && Object.keys(p_state.dataDictionary.original).includes(p_column) ) {
-
- // A. Get dictionary's description string for this column
- const dictionaryDescStr = Object.keys(p_state.dataDictionary.original[p_column]).find(
- (key) => key.toLowerCase() === "description");
-
- // B. Get the column description if the description key was found
- if ( dictionaryDescStr ) {
- columnDescription = p_state.dataDictionary.original[p_column][dictionaryDescStr];
- }
- }
-
- return columnDescription;
- },
-
- columns(p_state, p_getters) {
-
- return p_state.dataTable.columns.map(column => ({
-
- name: column,
- description: p_getters.columnDescription(column)
- }));
- },
-
- getColumnsOfCategory: (p_state) => (p_category) => {
-
- // If it exists in the map, retrieve the column(s) assigned this category
- let columns = [];
-
- for ( const column in p_state.columnToCategoryMap ) {
- if ( p_category === p_state.columnToCategoryMap[column] ) {
- columns.push(column);
- }
- }
-
- return columns;
- },
-
- getGroupOfTool: (p_state) => (p_tool) => {
-
- // Look for the group of the given tool
- let toolGroup = null;
- for ( const groupName in p_state.toolGroups ) {
- if ( p_state.toolGroups[groupName].includes(p_tool) ) {
- toolGroup = groupName;
- }
- }
-
- return toolGroup;
- },
-
- getOriginalColumnValue: (p_state) => (p_subjectID, p_column) => {
-
- for ( let index = 0; index < p_state.dataTable.original.length; index++ ) {
-
- if ( p_subjectID === p_state.dataTable.original[index]["participant_id"] ) {
-
- return p_state.dataTable.original[index][p_column];
- }
- }
-
- return null;
- },
-
- isColumnLinkedToCategory: (p_state) => (p_matchData) => {
-
- // Check to see if the given column has been linked to the given category
- return ( p_matchData.category === p_state.columnToCategoryMap[p_matchData.column] );
- },
-
- isDataAnnotated(p_state) {
-
- // 1. Check to see if the annotated data table is different from the original data table
- const tablesAreEqual = p_state.dataTable.original.every((originalTableRow, index) => {
-
- let allValuesEqual = true;
-
- // A. Tables are different if column sizes for rows are different
- if ( Object.keys(originalTableRow).length !== Object.keys(p_state.dataTable.annotated[index]).length ) {
- allValuesEqual = false;
- }
- // B. Or, check to see if values in the respective rows are different
- else {
-
- for ( const column in originalTableRow ) {
- if ( originalTableRow[column] !== p_state.dataTable.annotated[index][column] ) {
- allValuesEqual = false;
- break;
- }
- }
- }
-
- return allValuesEqual;
- });
-
- // Annotation has not occurred if both tables are equal
- return !tablesAreEqual;
- },
-
- isDataDictionaryLoaded(p_state) {
-
- return ( null !== p_state.dataDictionary.original );
- },
-
- isDataTableLoaded(p_state) {
-
- return ( null !== p_state.dataTable.original );
- },
-
- isMissingValue: (p_state) => (p_column, p_value) => {
-
- // Checks if a column-value combination is stored in the missingColumnValues object
- // and returns true if it is, false otherwise
- // if no records are stored for the entire p_column, then also returns false
-
- if ( !Object.keys(p_state.missingColumnValues).includes(p_column) ) {
-
- return false;
- }
-
- return ( p_state.missingColumnValues[p_column].includes(p_value) );
- },
-
- isToolGrouped: (p_state) => (p_column) => {
-
- let foundTool = false;
-
- // Look for tool name in the saved tool groups
- for ( const groupName in p_state.toolGroups ) {
-
- if ( p_state.toolGroups[groupName].includes(p_column) ) {
- foundTool = true;
- break;
- }
- }
-
- return foundTool;
- },
-
- getMissingValuesColumn: (p_state) => (p_column) => {
-
- // For a given column name returns the array of missing values the state knows about
- // or returns null if no missing values are stored for this column name
-
- if ( !Object.keys(p_state.missingColumnValues).includes(p_column) ) {
- return null;
- } else {
- return p_state.missingColumnValues[p_column];
- }
- },
-
- nextPage(p_state) {
-
- let nextPage = "";
-
- switch ( p_state.currentPage ) {
-
- case "home":
- nextPage = "categorization";
- break;
- case "categorization":
- nextPage = "annotation";
- break;
- case "annotation":
- nextPage = "download";
- break;
- }
-
- return nextPage;
- },
-
- pageAccessible: (p_state, p_getters) => (p_pageName) => {
-
- let pageAccessible = false;
-
- switch ( p_pageName ) {
-
- case "home":
-
- // Landing page is always accessible
- pageAccessible = true;
- break;
-
- case "categorization":
-
- // Categorization page is accessible if a data table has been uploaded
- pageAccessible = p_getters.isDataTableLoaded;
-
- break;
-
- case "annotation": {
-
- // 1. Determine if at least one column has been linked to a category
- const linkCount = Object.values(p_state.columnToCategoryMap).filter(
- category => ( null !== category )).length;
- const categorizationStatus = linkCount > 0;
-
- // 2. Determine if all columns assigned the 'Assessment Tool' category have been grouped
- const assessmentToolColumns = [];
- for ( const column in p_state.columnToCategoryMap ) {
- if ( "Assessment Tool" === p_state.columnToCategoryMap[column] ) {
- assessmentToolColumns.push(column);
- }
- }
-
- // 3. Make sure all assessment tool columns are grouped
- for ( const toolGroup in p_state.toolGroups ) {
- for ( const tool of p_state.toolGroups[toolGroup] ) {
- const columnIndex = assessmentToolColumns.indexOf(tool);
- assessmentToolColumns.splice(columnIndex, 1);
- }
- }
- const toolGroupingStatus = ( 0 === assessmentToolColumns.length );
-
- // 4. Make sure one (and only one) column has been categorized as 'Subject ID'
- let subjectIDFound = 0;
- for ( const column in p_state.columnToCategoryMap ) {
- if ( "Subject ID" === p_state.columnToCategoryMap[column] ) {
- subjectIDFound += 1;
- }
- }
- const singleSubjectIDColumn = ( 1 === subjectIDFound );
-
- // Annotation page is only accessible if at least one column has
- // been categorized and all assessment tools have been grouped
- // and if one (and only one) column has been categorized as 'Subject ID'
- pageAccessible = categorizationStatus && toolGroupingStatus && singleSubjectIDColumn;
-
- break;
- }
-
- case "download":
-
- pageAccessible = p_state.annotationCount > 1;
-
- break;
- }
-
- return pageAccessible;
- },
-
- valueDescription: (p_state) => (p_column, p_value) => {
-
- // 0. If we do not have a data dictionary then the value description is undefined (e.g. "")
- let valueDescription = "";
-
- // 1. Find the description for this column's value in the data dictionary
- if ( null !== p_state.dataDictionary.original && Object.keys(p_state.dataDictionary.original).includes(p_column) ) {
-
- // A. Get dictionary's levels string for this column
- const dictionaryLevelsStr = Object.keys(p_state.dataDictionary.original[p_column]).find((key) => key.toLowerCase() === "levels");
-
- // B. Attempt to get the value string in this 'levels' object
- if ( dictionaryLevelsStr ) {
-
- // I. Get the dictionary's value string for this column's value
- const dictionaryValueStr = Object.keys(p_state.dataDictionary.original[p_column][dictionaryLevelsStr]).find(
- (key) => key.toLowerCase() === p_value.toLowerCase());
-
- // II. Get the value description
- if ( dictionaryValueStr ) {
- valueDescription = p_state.dataDictionary.original[p_column][dictionaryLevelsStr][dictionaryValueStr];
- }
- }
- }
-
- return valueDescription;
- }
-};
-
-
-// Action helpers
-function convertTsvLinesToTableData(p_tsvLines){
-
- // 0. Data structure for table will be stored here
- const tsvRowDictArray = [];
-
- // 1. First tsv line contains column headers
- const columnHeaders = p_tsvLines[0];
-
- // 2. Create dictionaries for each tsv row keyed on the column headers
- for ( let index = 1; index < p_tsvLines.length; index++ ){
-
- const tsvRowDict = {};
-
- // A. Loop through the tsv row, matching entries with the tsv column headers
- for ( let index2 = 0; index2 < columnHeaders.length; index2++ ) {
-
- // Skip blank lines
- if ( "" === p_tsvLines[index].join().trim() )
- continue;
-
- // I. Potential warning in case file is malformed.
- // NOTE: Graceful handling of this will be required
- if ( p_tsvLines[index].length !== columnHeaders.length ){
- console.log("WARNING: tsv row " + parseInt(index) + " has different size than tsv header.");
- console.log("Row size: " + parseInt(p_tsvLines[index].length));
- console.log("Row: '" + p_tsvLines[index] + "'");
- console.log("Header fields: " + columnHeaders.length);
- }
-
- // II. Save the field for this row, keyed by the current column header
- tsvRowDict[columnHeaders[index2]] = p_tsvLines[index][index2];
- }
-
- // B. Save the row dictionary
- // NOTE: Conditional here is to account for the possibility of a blank line
- // among the tsv lines input to this function. We may want to readdress this
- // via the Papa parse file input method or just leave as is
- if ( Object.keys(tsvRowDict).length > 0 ) {
- tsvRowDictArray.push(tsvRowDict);
- }
- }
-
- return tsvRowDictArray;
-}
\ No newline at end of file
diff --git a/store/index.js b/store/index.js
index 116425eb..c2d4c853 100644
--- a/store/index.js
+++ b/store/index.js
@@ -71,7 +71,7 @@ export const state = () => ({
}
},
- columnToCategoryMapping: {},
+ columnToCategoryMap: {},
currentPage: "home",
@@ -141,7 +141,7 @@ export const getters = {
// Return the options for this column listed in the current (hardcoded)
// options for each categorical data-based category
- return p_state.categoricalOptions[p_state.columnToCategoryMapping[p_column]] ?? [];
+ return p_state.categoricalOptions[p_state.columnToCategoryMap[p_column]] ?? [];
},
getCategoryNames (p_state) {
@@ -249,7 +249,7 @@ export const getters = {
getMappedCategories: (p_state) => (p_categorySkipList=[]) => {
// 1. Remove unmapped (null) columns and skipped categories
- const currentCategories = Object.values(p_state.columnToCategoryMapping)
+ const currentCategories = Object.values(p_state.columnToCategoryMap)
.filter(category => null !== category && !p_categorySkipList.includes(category));
// 2. Create a set of the unique mapped categories
@@ -262,9 +262,9 @@ export const getters = {
getMappedColumns: (p_state) => (p_category) => {
const mappedColumns = [];
- for ( const column in p_state.columnToCategoryMapping ) {
+ for ( const column in p_state.columnToCategoryMap ) {
- if ( p_category === p_state.columnToCategoryMapping[column] ) {
+ if ( p_category === p_state.columnToCategoryMap[column] ) {
mappedColumns.push(column);
}
@@ -277,9 +277,9 @@ export const getters = {
// 1. Retrieve all columns linked with the given category
const mappedColumns = [];
- for ( const columnName in p_state.columnToCategoryMapping ) {
+ for ( const columnName in p_state.columnToCategoryMap ) {
- if ( p_category === p_state.columnToCategoryMapping[columnName] ) {
+ if ( p_category === p_state.columnToCategoryMap[columnName] ) {
mappedColumns.push(columnName);
}
@@ -334,10 +334,10 @@ export const getters = {
// 1. Construct an object containing a list of unique values for each column
const uniqueValues = {};
- for ( const columnName in p_state.columnToCategoryMapping ) {
+ for ( const columnName in p_state.columnToCategoryMap ) {
// A. Create a new list for values for each column linked to the given category
- if ( p_category === p_state.columnToCategoryMapping[columnName] ) {
+ if ( p_category === p_state.columnToCategoryMap[columnName] ) {
// I. Save unique values for each column
uniqueValues[columnName] = new Set();
@@ -400,12 +400,12 @@ export const getters = {
case "annotation": {
// 1. Make sure one (and only one) column has been categorized as 'Subject ID'
- const singleSubjectIDColumn = ( 1 === Object.values(p_state.columnToCategoryMapping)
+ const singleSubjectIDColumn = ( 1 === Object.values(p_state.columnToCategoryMap)
.filter(category => "Subject ID" === category)
.length );
// 2. Make sure at least one other category other than 'Subject ID' has been linked to a column
- const notOnlySubjectIDCategorized = ( Object.values(p_state.columnToCategoryMapping)
+ const notOnlySubjectIDCategorized = ( Object.values(p_state.columnToCategoryMap)
.filter(category => "Subject ID" !== category &&
null !== category)
.length >= 1 );
@@ -460,15 +460,15 @@ export const mutations = {
*/
alterColumnCategoryMapping(p_state, { category, column }) {
- if ( category === p_state.columnToCategoryMapping[column] ) {
+ if ( category === p_state.columnToCategoryMap[column] ) {
// 1. Unlink the column from the category
- p_state.columnToCategoryMapping[column] = null;
+ p_state.columnToCategoryMap[column] = null;
}
else {
// 1. Link the column to the category
- p_state.columnToCategoryMapping[column] = category;
+ p_state.columnToCategoryMap[column] = category;
}
// 2. Re-initialize the annotated data dictionary column
@@ -499,7 +499,7 @@ export const mutations = {
initializeColumnToCategoryMap(p_state, p_columns) {
// Column to category map lists all columns as keys with default value of null
- p_state.columnToCategoryMapping =
+ p_state.columnToCategoryMap =
Object.fromEntries(p_columns.map((column) => [column, null]));
},