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JS linting round 3: fix remaining no-undef findings #1588 #1589

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55 changes: 55 additions & 0 deletions eslint.config.mjs
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Original file line number Diff line number Diff line change
Expand Up @@ -45,17 +45,72 @@ export default [
loadNodeData: "readonly", // analysis.js
getGridAndEditorWindow: "readonly", // analysis.js
lockNodeField: "readonly", // analysis.js
replaceEditorWindow: "readonly", // analysis.js
loadGridAndEditorForNode: "readonly", // analysis.js
analysisVariable: "readonly", // analysis.js
addAnalysisVariableButton: "readonly", // analysis.js
_getAnalysisWindow: "readonly", // analysis.js
createJSEvent: "readonly", // analysis.js
addVariantTag: "readonly", // analysis.js
removeVariantTag: "readonly", // analysis.js
hideLoadingOverlay: "readonly", // analysis.js
getAnalysisWindow: "readonly", // grid.js
createIgvUrl: "readonly", // grid.js (typeof-guarded use in vc_links.js)
deleteNodesFromDOM: "readonly", // analysis_nodes.js
unselectActive: "readonly", // analysis_nodes.js
addNodesToDOM: "readonly", // analysis_nodes.js
attatchAnalysisNodeConnections: "readonly", // analysis_nodes.js
checkAndMarkDirtyNodes: "readonly", // analysis_nodes.js
getNode: "readonly", // analysis_nodes.js
loggedOutHandler: "readonly", // analysis_nodes.js
createSampleNode: "readonly", // samplenode.js
createTrioNode: "readonly", // pedigree_node.js
createQuadNode: "readonly", // pedigree_node.js
venn2: "readonly", // venn_intersect.js
venn_select: "readonly", // venn_intersect.js
getValue: "readonly", // global.js
removeItemFromArray: "readonly", // global.js
checkLoggedIn: "readonly", // global.js
convertTimestamp: "readonly", // global.js
JS_DATE_FORMAT_SECONDS: "readonly", // global.js
JS_DATE_FORMAT_SCIENTIFIC: "readonly", // global.js
loadAjaxBlock: "readonly", // global.js
formatJson: "readonly", // global.js
createTimestampDom: "readonly", // global.js
setupModalAnimationForWebTesting: "readonly", // global.js
EncodeQueryData: "readonly", // global.js
deleteItemClickHandler: "readonly", // global.js
createModal: "readonly", // global.js
highlightTextAsDom: "readonly", // global.js
limitLengthSpan: "readonly", // global.js
DataTableDefinition: "readonly", // datatable_definition.js
VCTable: "readonly", // vc_form.js
Flags: "readonly", // flags.js
VCLinks: "readonly", // vc_links.js
// cross-execution state in fragment-loaded files: these scripts are
// re-executed on AJAX load, so the state must stay a plain assignment
// (a top-level let/const would throw on re-execution)
seen_igv_error: "writable", // grid.js
RAISED_GET_ANALYSIS_WINDOW_JS_ERROR: "writable", // grid.js
VENN_TOGGLE_WIDGET_CLASS: "writable", // venn_intersect.js, read by analysis_nodes.js
venn_id: "writable", // venn_intersect.js
freq: "writable", // cached_generated_files.js
// globals injected by Django templates (inline <script> blocks)
ANALYSIS_ID: "readonly", // analysis.html
ANALYSIS_SETTINGS: "readonly", // analysis_settings_node_counts_tab.html
ANALYSIS_TAGS_NODE_ID: "readonly", // analysis.html
NODE_HELP: "readonly", // analysis.html
messagePoller: "readonly", // analysis.html
analysisNodeVariables: "readonly", // analysis.html
saveSettingsOnResize: "writable", // analysis.html, assigned in analysis.js
secondWindow: "writable", // analysis.html, assigned in analysis.js
panelResizeTimeout: "writable", // analysis.html, assigned in analysis.js
panelResizeUpdateDelay: "readonly", // analysis.html
variantTags: "readonly", // analysis.html
loadInitialGridEditor: "readonly", // analysis.html
registerComponent: "readonly", // analysis_editor_and_grid.html
EDITOR: "readonly", // analysis_editor_and_grid.html
reloadNodes: "readonly", // analysis_settings.html
},
},
rules: {
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2 changes: 1 addition & 1 deletion variantgrid/static_files/default_static/js/analysis_nodes.js
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Expand Up @@ -178,7 +178,7 @@ function setupHideInvalidConnectionsOnDrag() {
const endpoint = getEndpoint(id, 'target');
if (endpoint) {
for (let i=0 ; i<endpoint.connections.length ; ++i) {
source = endpoint.connections[i].sourceId;
const source = endpoint.connections[i].sourceId;
ancestors = ancestors.concat(getAncestors(source));
}
}
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2 changes: 1 addition & 1 deletion variantgrid/static_files/default_static/js/citations.js
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Expand Up @@ -145,7 +145,7 @@ const CitationsManager = (function() {
if (!citation.error) {
$('<a>', {'class':'d-block', 'data-toggle':'ajax-modal', 'data-href':Urls.view_citation_detail(citation.id), 'data-title': prettyId, 'text':'Show Detail'}).appendTo(citDom);
} else {
$('<p>', {class: 'abstract', text: citation.abstract && citation.abstract.length ? citation.abstract : 'Could not fetch abstract'}).appendTo(detailContainer);
$('<p>', {class: 'abstract', text: citation.abstract && citation.abstract.length ? citation.abstract : 'Could not fetch abstract'}).appendTo(citDom);
}
return citDom;
},
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4 changes: 2 additions & 2 deletions variantgrid/static_files/default_static/js/datatable_definition.js
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Expand Up @@ -433,7 +433,7 @@ TableFormat.list_codes = (data, type, row) => {
}
const elements = [];
let isFirst = true;
for (value of data) {
for (const value of data) {
if (!isFirst) {
elements.push(", ");
}
Expand Down Expand Up @@ -579,7 +579,7 @@ TableFormat.combine = function(formatters, settings, data, type, columns) {
part = eval(formatter)(data[index], type, columns);
}
if (settings.separator) {
dom.append($(separator));
dom.append($(settings.separator));
dom.append(part);
} else {
dom.append($('<div>', {'html': part}));
Expand Down
14 changes: 7 additions & 7 deletions variantgrid/static_files/default_static/js/flags.js
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Expand Up @@ -148,7 +148,7 @@ const Flags = (function () {
});
},
raisableFlags() {
flagTypes = this.flagTypes().filter(ft => {
const flagTypes = this.flagTypes().filter(ft => {
const userPermission = this.user_permission;
const requiredPermission = ft.raise_permission;
return userPermission >= requiredPermission;
Expand Down Expand Up @@ -340,7 +340,7 @@ const Flags = (function () {
}
this.setPosting();

sendParams = {
const sendParams = {
comment: comment || null,
};
if (resolution) {
Expand Down Expand Up @@ -402,7 +402,7 @@ const Flags = (function () {

updateComments() {
// fixme, don't re-render comments already rendered
shouldScroll = (isScrolledToBottom(this.scrollablePanel) && !this.firstUpdate) || this.justPosted;
const shouldScroll = (isScrolledToBottom(this.scrollablePanel) && !this.firstUpdate) || this.justPosted;

let lastEntry = this.lastEntry;
let reachedStart = lastEntry == null;
Expand Down Expand Up @@ -721,7 +721,7 @@ const Flags = (function () {
} else {
this.applyActiveContent(new FlagCollectionSummaryContent(this.collection, this));
}
modalDialog = modalContent.modal({focus:true, show:true});
const modalDialog = modalContent.modal({focus:true, show:true});
if (params.triggerDom) {
$(params.triggerDom).LoadingOverlay('hide');
}
Expand Down Expand Up @@ -940,7 +940,7 @@ const Flags = (function () {

if (this.data && this.data.transcript) {
const transcript = this.data.transcript;
parts = /^([_A-Z0-9]+)(?:[.]([0-9]+))?$/i;
const parts = /^([_A-Z0-9]+)(?:[.]([0-9]+))?$/i;
const match = parts.exec(transcript);
if (match) {
let transcriptUrl = null;
Expand Down Expand Up @@ -1052,7 +1052,7 @@ const Flags = (function () {

let timestamp = moment(this.created * 1000).format('DD-MMM-YYYY');
if (lastEntry) {
oldTimestamp = moment(lastEntry.created * 1000).format('DD-MMM-YYYY');
const oldTimestamp = moment(lastEntry.created * 1000).format('DD-MMM-YYYY');
if (oldTimestamp === timestamp) {
timestamp = null;
}
Expand Down Expand Up @@ -1081,7 +1081,7 @@ const Flags = (function () {
}

const actionCommentDom = $('<div>', { class: 'action-text' }).appendTo(content);
action = this.action();
const action = this.action();

if (params.includeTitle) {
$('<div>', {
Expand Down
8 changes: 4 additions & 4 deletions variantgrid/static_files/default_static/js/panel_app.js
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Expand Up @@ -4,19 +4,19 @@ function getEvidenceHover(geneSymbol, evidence, confidence) {
container.append(geneTitle);
const modeOfInheritance = evidence["mode_of_inheritance"];
if (modeOfInheritance) {
mohDiv = $("<div />").append("<b>Mode of inheritance</b> " + modeOfInheritance);
const mohDiv = $("<div />").append("<b>Mode of inheritance</b> " + modeOfInheritance);
container.append(mohDiv);
}
const penetrance = evidence["penetrance"];
if (penetrance) {
penetranceDiv = $("<div />").append("<b>Penetrance</b> " + penetrance);
const penetranceDiv = $("<div />").append("<b>Penetrance</b> " + penetrance);
container.append(penetranceDiv);
}

const evidences = evidence["evidence"];
if (evidences) {
container.append($("<h3 />").text("Sources"));
evidencesUl = $("<ul />");
const evidencesUl = $("<ul />");
for (let i=0 ; i<evidences.length ; ++i) {
evidencesUl.append($("<li />").text(evidences[i]));
}
Expand All @@ -26,7 +26,7 @@ function getEvidenceHover(geneSymbol, evidence, confidence) {
const phenotypes = evidence["phenotypes"];
if (phenotypes) {
container.append($("<h3 />").text("Phenotypes"));
phenotypesUl = $("<ul />");
const phenotypesUl = $("<ul />");
for (let i=0 ; i<phenotypes.length ; ++i) {
phenotypesUl.append($("<li />").text(phenotypes[i]));
}
Expand Down
4 changes: 2 additions & 2 deletions variantgrid/static_files/default_static/js/samplenode.js
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@@ -1,5 +1,5 @@
SIDE_LENGTH = 60;
DEFAULT_SHADOW_COLOR = "#aaa";
const SIDE_LENGTH = 60;
const DEFAULT_SHADOW_COLOR = "#aaa";


function maleSVG(svg, sideLength) {
Expand Down
4 changes: 2 additions & 2 deletions variantgrid/static_files/default_static/js/vc_diff.js
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Expand Up @@ -305,7 +305,7 @@ const Diff = (function() {
}
let content = null;

clinSigText = [];
const clinSigText = [];

const clin_sig_key = this.eKeys.key(SpecialEKeys.CLINICAL_SIGNIFICANCE);
const clin_sig = clin_sig_key.prettyValue((v.clinical_significance || {}).value);
Expand Down Expand Up @@ -532,7 +532,7 @@ const Diff = (function() {
diffBreakdown.push(`${hasBlank} <span style="color:#888;font-size:smaller">x</span> <span style="color:#888">blank</span>`);
}
}
valueCounts = Object.values(uniqueValues);
const valueCounts = Object.values(uniqueValues);
valueCounts.sort((vc1,vc2) => {
if (vc1.count !== vc2.count) {
return vc1.count - vc2.count;
Expand Down
11 changes: 3 additions & 8 deletions variantgrid/static_files/default_static/js/vc_form.js
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Expand Up @@ -59,6 +59,7 @@ const VCForm = (function() {
let jShareButtons = null;

let eKeys = null;
let eKeysBase = null;
let vcLinks = null;

const VCForm = function() {};
Expand Down Expand Up @@ -672,12 +673,6 @@ const VCForm = (function() {

$(`#label-${error.key}`).prepend(inlineError);

switch (error.severity) {
case 'error': icon = '<i class="fas fa-exclamation-circle text-danger"></i>'; break;
case 'warning': icon = '<i class="fas fa-exclamation-triangle text-warning"></i>'; break;
case 'info': icon = '<i class="fas fa-info-circle text-primary"></i>'; break;
}

const listItem = $('<a>', {class: 'list-group-item list-group-item-action', target: '_blank', click: () => {
jFilterBox.val('#' + eKey.key);
jFilterBox.keyup();
Expand Down Expand Up @@ -1043,7 +1038,7 @@ const VCForm = (function() {
},

cHGVS() {
vc_value = this.value(SpecialEKeys.C_HGVS);
const vc_value = this.value(SpecialEKeys.C_HGVS);
if (vc_value) {
return vc_value;
}
Expand Down Expand Up @@ -1576,7 +1571,7 @@ const VCForm = (function() {
])
);
} else {
descriptionSpan = eKey.description ? EKeys.fixDescription(eKey.description) : $('<i>', {text:'No help is provided for this field'});
const descriptionSpan = eKey.description ? EKeys.fixDescription(eKey.description) : $('<i>', {text:'No help is provided for this field'});
if (this.isEditMode()) {
if (eKey.hide === true) {
descriptionSpan.append($('<br/><br/><i>This field is not shown by default for your lab.</i>'));
Expand Down
2 changes: 1 addition & 1 deletion variantgrid/static_files/default_static/js/vc_links.js
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Expand Up @@ -55,7 +55,7 @@ const VCLink = (function() {

})();

EMPTY_LINK = new VCLink({
const EMPTY_LINK = new VCLink({
text: null,
href: null,
missing: true,
Expand Down
12 changes: 6 additions & 6 deletions variantgrid/static_files/default_static/js/venn_intersect.js
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Expand Up @@ -9,20 +9,20 @@ function venn_select(selector, venn_flag) {
}

function vennAddToggleCallbacks(selector, callback) {
get_venn_flag = function() {
const get_venn_flag = function() {
let venn_flag = 0;
$('.' + VENN_TOGGLE_WIDGET_CLASS, selector).each(function() {
const widget = d3.select(this);
toggled = widget.attr("toggled");
const toggled = widget.attr("toggled");
if (toggled == "true") {
venn_flag |= widget.attr("venn_bit");
}
});
return venn_flag;
};
toggleColor = function() {
const toggleColor = function() {
toggleSelect(d3.select(this));
venn_flag = get_venn_flag();
const venn_flag = get_venn_flag();
callback(venn_flag);
};

Expand All @@ -34,7 +34,7 @@ function vennAddToggleCallbacks(selector, callback) {

// Either set to value (if provided) or toggle (if not)
function toggleSelect(select, value) {
toggled = value;
let toggled = value;
if (toggled == null) {
toggled = select.attr('toggled');
toggled = toggled != "true";
Expand Down Expand Up @@ -122,7 +122,7 @@ function venn2(selector, w, h) {


function venn3(selector, w, h) {
radius = w * 0.3;
const radius = w * 0.3;

const svg = d3.select(selector).append("svg:svg")
.attr("width", w)
Expand Down