Skip to content

Commit

Permalink
Merge pull request #2782 from mashehu/old-site-new-schema
Browse files Browse the repository at this point in the history 
handle `definitions` and `defs` equally (brute force)
  • Loading branch information
@mashehu
mashehu authored Oct 10, 2024
2 parents 33acd6a + f84ea66 commit aa25569
Show file tree
Hide file tree
Showing 2 changed files with 135 additions and 85 deletions.
155 changes: 83 additions & 72 deletions public_html/assets/js/nf-core-schema-builder.js
View file
Original file line number Diff line number Diff line change
Expand Up @@ -220,10 +220,9 @@ $(function () {
$('.add-group-btn').on('click', function (e) {
var new_id = 'new_group_' + new_group_idx;
var new_title = 'New Group ' + new_group_idx;
if (!schema.hasOwnProperty('definitions')) {
schema['definitions'] = {};
}
while (Object.keys(schema['definitions']).indexOf(new_id) != -1) {
var definitionsKey = schema.hasOwnProperty('definitions') ? 'definitions' : '$defs';
schema[definitionsKey] = schema[definitionsKey] || {};
while (Object.keys(schema[definitionsKey]).indexOf(new_id) != -1) {
new_group_idx += 1;
new_id = 'new_group_' + new_group_idx;
new_title = 'New Group ' + new_group_idx;
Expand All @@ -235,7 +234,7 @@ $(function () {
default: '',
properties: {},
};
schema['definitions'][new_id] = new_group;
schema[definitionsKey][new_id] = new_group;
param_row = $(generate_group_row(new_id, new_group));
param_row.prependTo('#schema-builder').find('.param_id').select();
scroll_to(param_row, 140);
Expand Down Expand Up @@ -349,8 +348,9 @@ $(function () {
} else {
// Do it in a slightly odd way to preserve key order
var new_schema = JSON.parse(JSON.stringify(schema));
var definitionsKey = schema.hasOwnProperty('definitions') ? 'definitions' : '$defs';
new_schema['properties'] = {};
new_schema['definitions'] = {};
new_schema[definitionsKey] = {};
new_schema['allOf'] = [];
// Top-level params
if (schema.hasOwnProperty('properties')) {
Expand All @@ -364,26 +364,26 @@ $(function () {
}
}
// Groups
if (schema.hasOwnProperty('definitions')) {
for (d in schema['definitions']) {
if (schema.hasOwnProperty(definitionsKey)) {
for (d in schema[definitionsKey]) {
// Has the definition ID changed?
var new_d = d;
if (d === id) {
new_d = new_id;
}
new_schema['definitions'][new_d] = schema['definitions'][d];
new_schema['allOf'].push({ $ref: '#/definitions/' + new_d });
new_schema[definitionsKey][new_d] = schema[definitionsKey][d];
new_schema['allOf'].push({ $ref: '#/' + definitionsKey + '/' + new_d });

// Grouped parameters
var new_subschema = JSON.parse(JSON.stringify(schema['definitions'][d]));
new_schema['definitions'][new_d]['properties'] = {};
var new_subschema = JSON.parse(JSON.stringify(schema[definitionsKey][d]));
new_schema[definitionsKey][new_d]['properties'] = {};
if (new_subschema.hasOwnProperty('properties')) {
for (k in new_subschema['properties']) {
var new_k = k;
if (k === id) {
new_k = new_id;
}
new_schema['definitions'][new_d]['properties'][new_k] = new_subschema['properties'][k];
new_schema[definitionsKey][new_d]['properties'][new_k] = new_subschema['properties'][k];
}
}
}
Expand Down Expand Up @@ -589,8 +589,9 @@ $(function () {
function schema_order_change() {
// Don't actually need to know where it landed - just rebuild schema from the DOM
var new_schema = JSON.parse(JSON.stringify(schema));
var definitionsKey = schema.hasOwnProperty('definitions') ? 'definitions' : '$defs';
new_schema['properties'] = {};
new_schema['definitions'] = {};
new_schema[definitionsKey] = {};
new_schema['allOf'] = [];
new_schema['required'] = [];

Expand All @@ -604,17 +605,17 @@ $(function () {

// Groups
if ($(this).hasClass('schema_group_row')) {
new_schema['definitions'][id] = param;
new_schema['definitions'][id]['properties'] = {};
new_schema['definitions'][id]['required'] = [];
new_schema['allOf'].push({ $ref: '#/definitions/' + id });
new_schema[definitionsKey][id] = param;
new_schema[definitionsKey][id]['properties'] = {};
new_schema[definitionsKey][id]['required'] = [];
new_schema['allOf'].push({ $ref: '#/$defs/' + id });
}
// Check if we are inside a group
else if ($(this).parent('.card-body').length) {
var group_id = $(this).parent().data('id');
new_schema['definitions'][group_id]['properties'][id] = param;
new_schema[definitionsKey][group_id]['properties'][id] = param;
if ($(this).find('.param_required').is(':checked')) {
new_schema['definitions'][group_id]['required'].push(id);
new_schema[definitionsKey][group_id]['required'].push(id);
}
}
// Top-level parameters
Expand All @@ -625,17 +626,17 @@ $(function () {
}
}
});
for (k in new_schema['definitions']) {
for (k in new_schema[definitionsKey]) {
// Set group hidden flag, drag + drop helper text
if (new_schema['definitions'][k].hasOwnProperty('properties')) {
if (new_schema[definitionsKey][k].hasOwnProperty('properties')) {
$('.schema_row[data-id="' + k + '"]')
.closest('.schema_group')
.find('.group-drag-drop-help')
.addClass('d-none');
var is_group_hidden = true;
var num_children = 0;
for (child_param_id in new_schema['definitions'][k]['properties']) {
var child_param = new_schema['definitions'][k]['properties'][child_param_id];
for (child_param_id in new_schema[definitionsKey][k]['properties']) {
var child_param = new_schema[definitionsKey][k]['properties'][child_param_id];
if (!child_param['hidden']) {
is_group_hidden = false;
}
Expand Down Expand Up @@ -1029,12 +1030,13 @@ $(function () {
}
}
// Go through groups
for (k in schema['definitions']) {
if (schema['definitions'][k].hasOwnProperty('properties')) {
for (j in schema['definitions'][k]['properties']) {
var definitionsKey = schema.hasOwnProperty('definitions') ? 'definitions' : '$defs';
for (k in schema[definitionsKey]) {
if (schema[definitionsKey][k].hasOwnProperty('properties')) {
for (j in schema[definitionsKey][k]['properties']) {
// Parameter to delete is in a group
if (j === id) {
delete schema['definitions'][k]['properties'][j];
delete schema[definitionsKey][k]['properties'][j];
}
// Group itself is being deleted - move contents of the group
if (k === id) {
Expand All @@ -1045,12 +1047,12 @@ $(function () {
if (!schema.hasOwnProperty('properties')) {
schema['properties'] = {};
}
schema['properties'][j] = schema['definitions'][k]['properties'][j];
schema['properties'][j] = schema[definitionsKey][k]['properties'][j];

// If it is required, set this on the top-level schema object
if (
schema['definitions'][k].hasOwnProperty('required') &&
schema['definitions'][k]['required'].indexOf(j) != -1
schema[definitionsKey][k].hasOwnProperty('required') &&
schema[definitionsKey][k]['required'].indexOf(j) != -1
) {
set_required(j, true);
}
Expand All @@ -1059,11 +1061,11 @@ $(function () {
}
// Delete the group from the schema
if (k === id) {
delete schema['definitions'][k];
delete schema[definitionsKey][k];
// Loop backwards from allOf and remove matching definition
var i = schema['allOf'].length;
while (i--) {
if (schema['allOf'][i]['$ref'] == '#/definitions/' + k) {
if (schema['allOf'][i]['$ref'] == '#/' + definitionsKey + '/' + k) {
schema['allOf'].splice(i, 1);
}
}
Expand Down Expand Up @@ -1252,16 +1254,17 @@ $(function () {
function generate_obj() {
var results = '';
// Groups
for (var id in schema['definitions']) {
if (schema['definitions'][id].hasOwnProperty('properties')) {
var definitionsKey = schema.hasOwnProperty('definitions') ? 'definitions' : '$defs';
for (var id in schema[definitionsKey]) {
if (schema[definitionsKey][id].hasOwnProperty('properties')) {
// Generate child rows
var child_params = '';
for (var child_id in schema['definitions'][id]['properties']) {
if (schema['definitions'][id]['properties'].hasOwnProperty(child_id)) {
child_params += generate_param_row(child_id, schema['definitions'][id]['properties'][child_id]);
for (var child_id in schema[definitionsKey][id]['properties']) {
if (schema[definitionsKey][id]['properties'].hasOwnProperty(child_id)) {
child_params += generate_param_row(child_id, schema[definitionsKey][id]['properties'][child_id]);
}
}
results += generate_group_row(id, schema['definitions'][id], child_params);
results += generate_group_row(id, schema[definitionsKey][id], child_params);
}
}
// Regular rows
Expand Down Expand Up @@ -1321,9 +1324,10 @@ function generate_param_row(id, param) {
}
}
// Lazy, just checking if it's required in any group rather than specifically its own
for (k in schema['definitions']) {
if (schema['definitions'][k].hasOwnProperty('required')) {
if (schema['definitions'][k]['required'].indexOf(id) !== -1) {
var definitionsKey = schema.hasOwnProperty('definitions') ? 'definitions' : '$defs';
for (k in schema[definitionsKey]) {
if (schema[definitionsKey][k].hasOwnProperty('required')) {
if (schema[definitionsKey][k]['required'].indexOf(id) !== -1) {
is_required = true;
}
}
Expand Down Expand Up @@ -1586,6 +1590,7 @@ function init_group_sortable() {
function validate_id(id, old_id) {
var param = false;
var is_object = false;
var definitionsKey = schema.hasOwnProperty('definitions') ? 'definitions' : '$defs';

// Get param if we have the old ID
if (old_id !== undefined) {
Expand All @@ -1609,13 +1614,13 @@ function validate_id(id, old_id) {
num_hits += 1;
}
// Iterate through groups, looking for ID
for (k in schema['definitions']) {
for (k in schema[definitionsKey]) {
// Check that the id is not already a group id
if (k === id) {
num_hits += 1;
}
if (schema['definitions'][k].hasOwnProperty('properties')) {
if (schema['definitions'][k]['properties'].hasOwnProperty(id)) {
if (schema[definitionsKey][k].hasOwnProperty('properties')) {
if (schema[definitionsKey][k]['properties'].hasOwnProperty(id)) {
num_hits += 1;
}
}
Expand Down Expand Up @@ -1715,11 +1720,12 @@ function set_required(id, is_required) {
}
// grouped properties
else {
var definitionsKey = schema.hasOwnProperty('definitions') ? 'definitions' : '$defs';
// Iterate through groups, looking for ID
for (k in schema['definitions']) {
if (schema['definitions'][k].hasOwnProperty('properties')) {
if (schema['definitions'][k]['properties'].hasOwnProperty(id)) {
schema_parent = schema['definitions'][k];
for (k in schema[definitionsKey]) {
if (schema[definitionsKey][k].hasOwnProperty('properties')) {
if (schema[definitionsKey][k]['properties'].hasOwnProperty(id)) {
schema_parent = schema[definitionsKey][k];
}
}
}
Expand Down Expand Up @@ -1750,18 +1756,18 @@ function find_param_in_schema(id) {
if (schema.hasOwnProperty('properties') && schema['properties'].hasOwnProperty(id)) {
return schema['properties'][id];
}

var definitionsKey = schema.hasOwnProperty('definitions') ? 'definitions' : '$defs';
// This ID is itself a group
if (schema.hasOwnProperty('definitions') && schema['definitions'].hasOwnProperty(id)) {
return schema['definitions'][id];
if (schema.hasOwnProperty(definitionsKey) && schema[definitionsKey].hasOwnProperty(id)) {
return schema[definitionsKey][id];
}

// Iterate through groups, looking for ID in groups
for (k in schema['definitions']) {
for (k in schema[definitionsKey]) {
// Check if group
if (schema['definitions'][k].hasOwnProperty('properties')) {
if (schema['definitions'][k]['properties'].hasOwnProperty(id)) {
return schema['definitions'][k]['properties'][id];
if (schema[definitionsKey][k].hasOwnProperty('properties')) {
if (schema[definitionsKey][k]['properties'].hasOwnProperty(id)) {
return schema[definitionsKey][k]['properties'][id];
}
}
}
Expand All @@ -1779,11 +1785,13 @@ function find_param_group(id) {
}

// Iterate through groups, looking for ID
for (k in schema['definitions']) {

var definitionsKey = schema.hasOwnProperty('definitions') ? 'definitions' : '$defs';
for (k in schema[definitionsKey]) {
// Check if group
if (schema['definitions'][k].hasOwnProperty('properties')) {
if (schema['definitions'][k]['properties'].hasOwnProperty(id)) {
return [k, schema['definitions'][k]];
if (schema[definitionsKey][k].hasOwnProperty('properties')) {
if (schema[definitionsKey][k]['properties'].hasOwnProperty(id)) {
return [k, schema[definitionsKey][k]];
}
}
}
Expand All @@ -1795,25 +1803,26 @@ function update_param_in_schema(id, new_param) {
// Given an ID, find the param schema even if it's in a group
// Assumes max one level of nesting and unique IDs everywhere

var definitionsKey = schema.hasOwnProperty('definitions') ? 'definitions' : '$defs';
// Simple case - not in a group
if (schema.hasOwnProperty('properties') && schema['properties'].hasOwnProperty(id)) {
schema['properties'][id] = new_param;
return true;
}

// This ID is itself a group
if (schema.hasOwnProperty('definitions') && schema['definitions'].hasOwnProperty(id)) {
schema['definitions'][id] = new_param;
if (schema.hasOwnProperty(definitionsKey) && schema[definitionsKey].hasOwnProperty(id)) {
schema[definitionsKey][id] = new_param;
return true;
}

// Iterate through groups, looking for ID
if (schema.hasOwnProperty('definitions')) {
for (k in schema['definitions']) {
if (schema.hasOwnProperty(definitionsKey)) {
for (k in schema[definitionsKey]) {
// Check if group
if (schema['definitions'][k].hasOwnProperty('properties')) {
if (schema['definitions'][k]['properties'].hasOwnProperty(id)) {
schema['definitions'][k]['properties'][id] = new_param;
if (schema[definitionsKey][k].hasOwnProperty('properties')) {
if (schema[definitionsKey][k]['properties'].hasOwnProperty(id)) {
schema[definitionsKey][k]['properties'][id] = new_param;
return true;
}
}
Expand All @@ -1826,12 +1835,14 @@ function update_param_in_schema(id, new_param) {
function update_schema_html(schema) {
// Clean up empty keys in schema
schema = clean_empty_schema_keys(schema);
if (schema.hasOwnProperty('definitions') && Object.keys(schema['definitions']).length === 0) {
delete schema['definitions'];

var definitionsKey = schema.hasOwnProperty('definitions') ? 'definitions' : '$defs';
if (schema.hasOwnProperty(definitionsKey) && Object.keys(schema[definitionsKey]).length === 0) {
delete schema[definitionsKey];
}
if (schema.hasOwnProperty('definitions')) {
for (k in schema['definitions']) {
schema['definitions'][k] = clean_empty_schema_keys(schema['definitions'][k]);
if (schema.hasOwnProperty(definitionsKey)) {
for (k in schema[definitionsKey]) {
schema[definitionsKey][k] = clean_empty_schema_keys(schema[definitionsKey][k]);
}
}
// Update in page
Expand Down
Loading

0 comments on commit aa25569

Please sign in to comment.