Skip to content

Commit

Permalink
WIP: decoupling the initialization of Toolbar from DataHarmonizer by …
Browse files Browse the repository at this point in the history 
…setting schema outside of the function
  • Loading branch information
@kennethbruskiewicz
kennethbruskiewicz committed Feb 6, 2024
1 parent 7216582 commit 755bc28
Show file tree
Hide file tree
Showing 5 changed files with 10,377 additions and 125 deletions.
3 changes: 1 addition & 2 deletions lib/Toolbar.js
View file
Original file line number Diff line number Diff line change
Expand Up @@ -390,8 +390,6 @@ class Toolbar {
}

// NOTE: (Ken) see dh refactor transcript for a refactored version of loadSelectedTemplate


async loadSelectedTemplate(file = null) {
const loadFromFile = async (file) => {
let schema, template_name;
Expand Down Expand Up @@ -424,6 +422,7 @@ class Toolbar {
let { template_name, schema, exportFormats, languages, schemaClass, columnCoordinates } = loadResult;

// Use the previously coupled dh methods
// change this to use the context instead
this.dh.useSchema(schema, exportFormats, template_name);

if (!languages) languages = await this.dh.getLanguages(template_name);
Expand Down
181 changes: 129 additions & 52 deletions web/index.js
View file
Original file line number Diff line number Diff line change
Expand Up @@ -371,9 +371,21 @@ const main = async function () {

const context = new AppContext(new AppConfig(await getTemplatePath()));


context.initializeTemplate(context.appConfig.template_path)
.then(async (context) => {

const _template = context.template;
const _export_formats = (await context.getExportFormats('grdi'));

// // internationalize
// // TODO: connect to locale of browser!
// // Takes `lang` as argument (unused)
initI18n(( /* lang */ ) => {
$(document).localize();
dhs.forEach(dh => dh.render());
});
context.addTranslationResources(_template, context.getLocaleData());

const classes = (await context.getClasses()).reduce((acc, item) => Object.assign(acc, item), {});

// attributes are the classes which feature 1-M relationships
Expand All @@ -386,6 +398,7 @@ const main = async function () {
// the existence of a container class signifies a 1-M data loading setup with an ID join
if (classes['Container']) {

console.log('branch 1');
console.log('has Container class', classes['Container']);

/* e.g.
Expand Down Expand Up @@ -492,7 +505,7 @@ const main = async function () {
* @returns {Array} An array of slot names.
*/
function findSlotNamesForClass(schema, class_name) {
return Object.keys(schema.classes[class_name].slots)
return !!schema.classes[class_name] && !!schema.classes[class_name].slots ? Object.keys(schema.classes[class_name].slots) : [];
}

/**
Expand All @@ -501,6 +514,53 @@ const main = async function () {
* @returns {Object|null} The schema tree object, or null if no "Container" classes are found.
*/
function buildSchemaTree(schema) {

function updateChildrenAndSharedKeys(data) {
// Use a deep clone to avoid mutating the original object
const result = JSON.parse(JSON.stringify(data));

Object.keys(result).forEach(key => {
const elem = result[key];
(elem.shared_keys || []).forEach(sk => {
if (sk.relation === 'parent' && result[sk.related_concept]) {
const parent = result[sk.related_concept];

// Ensure 'children' array exists
if (!parent.children) {
parent.children = [];
}

// Add key to parent’s 'children' array if not already present
if (!parent.children.includes(key)) {
parent.children.push(key);
}

// Ensure 'shared_keys' array exists
if (!parent.shared_keys) {
parent.shared_keys = [];
}

// Check if reciprocal shared key already exists
const reciprocalExists = parent.shared_keys.some(
rsk => rsk.name === sk.name && rsk.related_concept === key
);

// Add reciprocal shared key if it doesn't exist
if (!reciprocalExists) {
parent.shared_keys.push({
name: sk.name,
related_concept: key,
relation: 'child'
});
}
}
});
});

return result;
}


if (!!!schema.classes["Container"]) return null;

const attributes = schema.classes["Container"].attributes;
Expand All @@ -511,14 +571,16 @@ const main = async function () {

const shared_keys_per_class = findSharedKeys(schema);

return classes.reduce((acc, class_key) => {
const pre_schema_tree = classes.reduce((acc, class_key) => {
acc[class_key] = {
name: class_key,
shared_keys: shared_keys_per_class[class_key],
children: shared_keys_per_class[class_key].map(item => item.range).filter(range => range != class_key) // TODO inefficient
children: shared_keys_per_class[class_key].map(item => item.range).filter(range => range !== class_key && typeof range !== 'undefined') // TODO inefficient
};
return acc;
}, tree_base);

return updateChildrenAndSharedKeys(pre_schema_tree);
};

/**
Expand All @@ -527,14 +589,15 @@ const main = async function () {
* @param {string} cls_key - The starting class key for the visitation.
* @param {Function} callback - The function to perform on each class node.
*/
function visitSchemaTree(schema_tree, cls_key='Container', callback=tap, inc=0) {
if (!schema_tree[cls_key]) return; // Base case: If the class key is not found
callback(schema_tree[cls_key]); // Perform the callback on the current node
function visitSchemaTree(schema_tree, callback=tap, next='Container') {
console.log('visitSchemaTree', schema_tree)
if (!schema_tree[next]) return; // Base case: If the class key is not found
callback(schema_tree[next]); // Perform the callback on the current node

// Recurse on each child node
const children = schema_tree[cls_key].children.filter(el => el);
children.forEach(child_key => {
visitSchemaTree(schema_tree, child_key, callback, inc);
const children = schema_tree[next].children.filter(el => el);
children.forEach(next => {
visitSchemaTree(schema_tree, callback, next);
});
};

Expand All @@ -543,7 +606,7 @@ const main = async function () {
* @param {Object} schema_tree - The schema tree from which to create Data Harmonizers.
* @returns {Object} An object mapping the class names to their respective Data Harmonizer objects.
*/
function makeDataHarmonizersFromSchemaTree(schema_tree) {
function makeDataHarmonizersFromSchemaTree(schema, schema_tree) {

function createDataHarmonizerContainer(dhId, isActive) {
let dhSubroot = document.createElement('div');
Expand Down Expand Up @@ -575,26 +638,35 @@ const main = async function () {
}

let data_harmonizers = {};
Object.entries(schema_tree).forEach(([cls_key, spec], index) => {
const dhId = `data-harmonizer-grid-${index}`;
let dhSubroot = createDataHarmonizerContainer(dhId, index === 0);
dhRoot.appendChild(dhSubroot); // Appending to the parent container

const dhTab = createDataHarmonizerTab(dhId, spec.name, index === 0);
dhTabNav.appendChild(dhTab); // Appending to the tab navigation

data_harmonizers[spec.name] = new DataHarmonizer(dhRoot, {
context: context,
loadingScreenRoot: document.body,
field_filters: findSlotNamesForClass(cls_key) // TODO: Find slot names for filtering
if (!!schema_tree) {
Object.entries(schema_tree).forEach((obj, index) => {
if (obj.length > 0) {
const [cls_key, spec] = obj;
const dhId = `data-harmonizer-grid-${index}`;
let dhSubroot = createDataHarmonizerContainer(dhId, index === 0);
dhRoot.appendChild(dhSubroot); // Appending to the parent container

const dhTab = createDataHarmonizerTab(dhId, spec.name, index === 0);
dhTabNav.appendChild(dhTab); // Appending to the tab navigation

console.log(findSlotNamesForClass(schema, cls_key));

data_harmonizers[spec.name] = new DataHarmonizer(dhRoot, {
context: context,
loadingScreenRoot: document.body,
field_filters: findSlotNamesForClass(schema, cls_key) // TODO: Find slot names for filtering
});
// initialize the data harmonizer
// TODO
data_harmonizers[spec.name].useSchema(schema, _export_formats, 'GRDI_Sample');

}
});
});
}

return data_harmonizers; // Return the created data harmonizers if needed
}

console.log(makeDataHarmonizersFromSchemaTree(buildSchemaTree(schema)));

/**
* Transforms the value of a multivalued column in a Data Harmonizer instance.
* @param {DataHarmonizer} data_harmonizer - The Data Harmonizer instance.
Expand Down Expand Up @@ -666,6 +738,7 @@ const main = async function () {
*/
function attachColumnEditHandler(data_harmonizer, shared_key_name, callback) {
const hot = data_harmonizer.hot;
console.log('attaching column edit handler to ', hot);

// Get the index of the column based on the shared_key_name
const columnIndex = hot.propToCol(shared_key_name);
Expand Down Expand Up @@ -700,6 +773,7 @@ const main = async function () {
* @param {Object} schema_tree_node - The schema tree node containing the shared keys and child references.
*/
function makeSharedKeyHandler(data_harmonizer, schema_tree_node) {
console.log('makeSharedKeyHandler', data_harmonizer);
if (schema_tree_node.shared_keys.length > 0) {
schema_tree_node.shared_keys.forEach((shared_key_name) => {

Expand Down Expand Up @@ -729,43 +803,55 @@ const main = async function () {
* @param {Object} data_harmonizers - An object mapping class names to Data Harmonizer instances.
* @returns {Object} The same object with event handlers attached.
*/
function attachPropagationEventHandlersToDataHarmonizers(data_harmonizers) {
function attachPropagationEventHandlersToDataHarmonizers(data_harmonizers, schema_tree) {
console.log('data_harmonizers', data_harmonizers);
console.log('schema_tree', schema_tree)

visitSchemaTree(schema_tree, (schema_tree_node) => {
// Propagation:
// - If has children with shared_keys, add handler
// - visit children -> lock field from being edited by user (DH methods can modify it)
if (schema_tree_node.children.length > 0) {
makeSharedKeyHandler(data_harmonizers[schema_tree_node.name], schema_tree_node)
if (!schema_tree_node.tree_root) makeSharedKeyHandler(data_harmonizers[schema_tree_node.name], schema_tree_node)
schema_tree_node.children.forEach(child_node_key => {
lockColumnEdits(data_harmonizers[child_node_key], schema_tree_node.shared_column_key);
if (!schema_tree_node.tree_root) lockColumnEdits(data_harmonizers[child_node_key], schema_tree_node.shared_column_key);
});
};
})
return data_harmonizers;
};

function initializeDataHarmonizers(data_harmonizers) {
Object.entries(schema_tree).forEach(([cls_key, spec], index) => {
// // TODO: data harmonizers require initialization code inside of the toolbar to fully render? wut
new Toolbar(dhToolbarRoot, dhs[index], menu, {
context: context,
templatePath: context.appConfig.template_path, // TODO: a default should be loaded before Toolbar is constructed! then take out all loading in "toolbar" to an outside context
releasesURL: 'https: // gi thub.com/cidgoh/pathogen-genomics-package/releases',
getLanguages: context.getLocaleData.bind(context),
getSchema: async (schema) => Template.create(schema).then(result => result.current.schema),
getExportFormats: context.getExportFormats.bind(context),
console.log('data_harmonizers', data_harmonizers);
Object.entries(data_harmonizers).forEach(([cls_key,], index) => {
new Toolbar(dhToolbarRoot, data_harmonizers[cls_key], menu, {
context: context,
templatePath: context.appConfig.template_path, // TODO: a default should be loaded before Toolbar is constructed! then take out all loading in "toolbar" to an outside context
releasesURL: 'https: // gi thub.com/cidgoh/pathogen-genomics-package/releases',
getLanguages: context.getLocaleData.bind(context),
getSchema: async (schema) => Template.create(schema).then(result => result.current.schema),
getExportFormats: context.getExportFormats.bind(context),
});
});
console.log('before attachPropagationEventHandlersToDataHarmonizers');
attachPropagationEventHandlersToDataHarmonizers(data_harmonizers, schema_tree);
return data_harmonizers;
};

const schema_tree = buildSchemaTree(schema);
const data_harmonizers = makeDataHarmonizersFromSchemaTree(schema_tree);
attachPropagationEventHandlersToDataHarmonizers(data_harmonizers);
console.log('before buildSchemaTree');
const schema_tree = buildSchemaTree((await context.getSchema()));
console.log('schema_tree', schema_tree);
console.log('before makeDataHarmonizersFromSchemaTree');
let data_harmonizers = makeDataHarmonizersFromSchemaTree(
(await context.getSchema()),
schema_tree);
// HACK
delete data_harmonizers[undefined];
console.log('before initializeDataHarmonizers');
initializeDataHarmonizers(data_harmonizers);

} else {

console.log('branch 2');
const dh = new DataHarmonizer(dhRoot, {
context: context,
loadingScreenRoot: document.querySelector('body'),
Expand All @@ -785,22 +871,13 @@ const main = async function () {

}

// // internationalize
// // TODO: connect to locale of browser!
// // Takes `lang` as argument (unused)
initI18n(( /* lang */ ) => {
$(document).localize();
dhs.forEach(dh => dh.render());
});
context.addTranslationResources(_template, context.getLocaleData());

new Footer(dhFooterRoot, dhs[0]);

return context;

})
.then(async () => {
// return setTimeout(() => dhs.forEach(dh => dh.showColumnsByNames(dh.field_filters)), 1000);
return setTimeout(() => dhs.forEach(dh => dh.showColumnsByNames(dh.field_filters)), 1000);
});

}
Expand Down
Loading

0 comments on commit 755bc28

Please sign in to comment.