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tissueExpressionBAR.js
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tissueExpressionBAR.js
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/* eslint-disable prefer-destructuring */
//= =========================== Alexander Sullivan =============================
//
// Purpose: Generates eFP tissue expression data
//
//= ============================================================================
/** Stroke data of compendiums that have already been called */
const existingStrokeData = {};
window.existingStrokeData = existingStrokeData;
/**
* Add details to an SVG or SVG-subunit including: hover and outline
* @param {String} elementID Which SVG or SVG-subunit is being found and edited
*/
function addTissueMetadata(elementID) {
// Adjusting for BioticStressPseudomonassyringae's half leaf:
if (elementID.includes("Half_Leaf_Pseudomonas_syringae")) {
elementID += "_outline";
}
// Retrieve document objects:
let svgDoc;
let svgPart;
let svgPartChildren;
if (document.getElementById(createSVGExpressionData.svgObjectName)) {
svgDoc = document.getElementById(createSVGExpressionData.svgObjectName);
svgPart = svgDoc.getElementById(elementID);
svgPartChildren = svgPart.childNodes;
}
/** Increase stroke width within SVG by (multiplied) this much */
const increaseStrokeWidthBy = 2.25;
// Storing stroke widths
let existingStrokeWidth;
let existingStrokeColour;
if (svgDoc && svgPart) {
if (svgPart.getAttribute("stroke-width")) {
existingStrokeWidth = svgPart.getAttribute("stroke-width");
if (svgPart.getAttribute("stroke")) {
existingStrokeColour = svgPart.getAttribute("stroke");
}
} else if (svgPartChildren.length > 0) {
for (const svgChildPart of svgPartChildren) {
if (svgChildPart.nodeName === "path") {
if (svgChildPart.getAttribute("stroke-width")) {
existingStrokeWidth = svgChildPart.getAttribute("stroke-width");
}
if (svgChildPart.getAttribute("stroke")) {
existingStrokeColour = svgChildPart.getAttribute("stroke");
}
}
}
}
if (!existingStrokeData[elementID]) {
existingStrokeData[elementID] = {};
existingStrokeData[elementID].strokeWidth = existingStrokeWidth;
existingStrokeData[elementID].strokeColour = existingStrokeColour;
existingStrokeData[elementID].addedMetadata = false;
}
// Making stroke width thicker
if (svgDoc.getElementById(elementID) && !existingStrokeData[elementID].addedMetadata) {
existingStrokeData[elementID].addedMetadata = true;
const strokeElement = svgDoc.getElementById(elementID);
// Create hover title box
if (strokeElement.getBoundingClientRect()) {
/** Title box's text */
const titleText = svgPart.getElementsByTagName("title")?.[0]?.textContent;
/** Title box's x-coordinate */
const boxLeft = strokeElement.getBoundingClientRect().right;
/** Title box's y-coordinate */
const boxTop = strokeElement.getBoundingClientRect().bottom;
// If all the data is available, add the title box
if (titleText && boxLeft && boxTop) {
ePlantPlantEFPChangeTitlePosition(true, boxLeft, boxTop, titleText);
} else {
// Fail-safe, hide title box
ePlantPlantEFPChangeTitlePosition(false);
}
} else {
// Fail-safe, hide title box
ePlantPlantEFPChangeTitlePosition(false);
}
existingStrokeWidth = Number(existingStrokeWidth);
let newStrokeWidth = existingStrokeWidth * increaseStrokeWidthBy;
const maxStrokeWidth = increaseStrokeWidthBy;
const minStrokeWidth = increaseStrokeWidthBy / 2;
if (newStrokeWidth > maxStrokeWidth && maxStrokeWidth > existingStrokeWidth) {
newStrokeWidth = maxStrokeWidth;
} else if (newStrokeWidth < minStrokeWidth && minStrokeWidth > existingStrokeWidth) {
newStrokeWidth = minStrokeWidth;
} else if (newStrokeWidth === 0) {
newStrokeWidth = increaseStrokeWidthBy;
} else if (!newStrokeWidth) {
newStrokeWidth = minStrokeWidth;
}
/** Boolean to determine if metadata has been added already */
let addedHoverMetadata = false;
if (strokeElement.getAttribute("stroke-width")) {
svgDoc.getElementById(elementID).setAttribute("stroke-width", newStrokeWidth);
svgDoc.getElementById(elementID).setAttribute("stroke", "#000");
addedHoverMetadata = true;
} else if (svgPartChildren && svgPartChildren.length > 0) {
for (const svgChildPart of svgPartChildren) {
if (svgChildPart.nodeName === "path" && svgChildPart.getAttribute("stroke-width")) {
svgChildPart.setAttribute("stroke-width", newStrokeWidth);
if (svgChildPart.getAttribute("stroke")) {
svgChildPart.setAttribute("stroke", "#000");
}
addedHoverMetadata = true;
}
}
}
if (!addedHoverMetadata) {
svgDoc.getElementById(elementID).setAttribute("stroke-width", newStrokeWidth);
svgDoc.getElementById(elementID).setAttribute("stroke", "#000");
}
}
}
}
/**
* Remove details to an SVG or SVG-subunit including: hover and outline
* @param {String} elementID Which SVG or SVG-subunit is being found and edited
*/
function removeTissueMetadata(elementID) {
// Adjusting for BioticStressPseudomonassyringae's half leaf:
if (elementID.includes("Half_Leaf_Pseudomonas_syringae")) {
elementID += "_outline";
}
/** A fallback stroke width for the SVG if one is not already pre-determined */
const fallbackStrokeWidth = 1;
/** A fallback stroke colour (black) for the SVG if one is not already pre-determined */
const fallbackStrokeColour = "#000"; // Black
// Retrieve document objects:
let svgDoc;
let svgPart;
let svgPartChildren;
if (document.getElementById(createSVGExpressionData.svgObjectName)) {
svgDoc = document.getElementById(createSVGExpressionData.svgObjectName);
svgPart = svgDoc.getElementById(elementID);
svgPartChildren = svgPart.childNodes;
}
// If existing stroke data exists, then proceed
if (existingStrokeData[elementID] && existingStrokeData[elementID].addedMetadata) {
existingStrokeData[elementID].addedMetadata = false;
if (svgPart && svgPart.getAttribute("stroke-width")) {
if (Number(existingStrokeData[elementID].strokeWidth) >= 0) {
svgDoc
.getElementById(elementID)
.setAttribute("stroke-width", existingStrokeData[elementID].strokeWidth);
} else if (!existingStrokeData[elementID].strokeWidth) {
svgDoc.getElementById(elementID).removeAttribute("stroke-width");
} else {
svgDoc.getElementById(elementID).setAttribute("stroke-width", fallbackStrokeWidth);
}
if (svgPart.getAttribute("stroke")) {
if (existingStrokeData[elementID].strokeColour) {
svgDoc.getElementById(elementID).setAttribute("stroke", existingStrokeData[elementID].strokeColour);
} else {
svgDoc.getElementById(elementID).setAttribute("stroke", fallbackStrokeColour);
}
}
} else if (svgPartChildren.length > 0) {
for (const svgChildPart of svgPartChildren) {
if (svgChildPart.nodeName === "path") {
if (svgChildPart.getAttribute("stroke-width")) {
if (Number(existingStrokeData[elementID].strokeWidth) >= 0) {
svgChildPart.setAttribute("stroke-width", existingStrokeData[elementID].strokeWidth);
} else if (!existingStrokeData[elementID].strokeWidth) {
svgDoc.getElementById(elementID).removeAttribute("stroke-width");
} else {
svgChildPart.setAttribute("stroke-width", fallbackStrokeWidth);
}
}
if (svgChildPart.getAttribute("stroke")) {
if (existingStrokeData[elementID].strokeColour) {
svgChildPart.setAttribute("stroke", existingStrokeData[elementID].strokeColour);
} else {
svgChildPart.setAttribute("stroke", fallbackStrokeColour);
}
}
}
}
} else {
svgPart.setAttribute("stroke-width", fallbackStrokeWidth);
svgPart.setAttribute("stroke", fallbackStrokeColour);
}
}
// Hide title box
ePlantPlantEFPChangeTitlePosition(false);
}
/**
* General debounce function for the ePlant Plant eFP and its tissue metadata
* @param {Function} func Function to be debounced
* @param {Number} wait Time to wait before executing the function
* @returns {Function} The debounced function
* @example <caption>Example usage of the debounce function where the function is debounced for 250ms and prevents that function from being called again during that weight time</caption>
* debounceTissueMetadata(functionToBeDebounced, 250);
* // returns functionToBeDebounced (after 250ms)
*/
function debounceTissueMetadata(func, wait) {
let timeout;
// eslint-disable-next-line func-names
return function (...args) {
const context = this;
clearTimeout(timeout);
timeout = setTimeout(() => func.apply(context, args), wait);
};
}
/**
* Create and display the ePlant Plant eFP's hover title box
* @param {Boolean} display Whether to display [true] or hide [false, default] the title box
* @param {Number | String} x The x-coordinate of the element being hovered over
* @param {Number | String} y The y-coordinate of the element being hovered over
* @param {String} textContent The text to be displayed in the title box
* @param {String} domID The ID of the title box DOM element
*/
function ePlantPlantEFPChangeTitlePosition(
display = false,
x = 0,
y = 0,
textContent = "",
domID = "ePlant-hover-title-box",
) {
/** DOM of the title box element */
const domElm = document.getElementById(domID);
if (domElm) {
if (!display) {
// Hide title box
domElm.style.display = "none";
} else {
// Display title box
domElm.style.display = "block";
domElm.style.left = `${x}px`;
domElm.style.top = `${y}px`;
domElm.textContent = textContent;
}
}
}
/** ePlant Plant's eFP mouse event data */
const ePlantPlantEFPHandleMouseEventData = {
/** Whether mouse events can occur [true] or not [false, default] */
start: false,
/** Cache last mouse position to calculate next position on drag */
cacheMousePos: { x: null, y: null },
/** Initial height of the SVG */
startHeight: null,
/** How much the SVG has been zoomed in by */
zoomLevel: 1,
};
/**
* Handle mouse events to drag the SVG compendium
* @param {String} domID DOM ID of the SVG container
* @param {String} type What type of event is happening: 'down' to initiate drag, 'move' to drag, 'up' to end drag
* @param {Event} e Mouse event object
* @param {Number} moveBy How much the SVG has been moved by
*/
// eslint-disable-next-line no-unused-vars
function ePlantPlantEFPHandleMouseEvent(domID, type, e, moveBy = 1.5) {
/** SVG document */
const svgElement = domID.firstElementChild;
// If SVG is not loaded, then return
if (svgElement?.viewBox?.baseVal) {
// If the SVG is not yet been cached, then cache it
if (!ePlantPlantEFPHandleMouseEventData.startHeight) {
ePlantPlantEFPHandleMouseEventData.startHeight = svgElement.viewBox.baseVal.height;
}
// Determine if SVG should be draggable or not
if (
type === "down" &&
!ePlantPlantEFPHandleMouseEventData.start &&
window.getSelection() &&
window.getSelection().isCollapsed
) {
// Prevent highlighting of text when dragging
e.preventDefault();
// Cache the mouse position and begin dragging
ePlantPlantEFPHandleMouseEventData.start = true;
ePlantPlantEFPHandleMouseEventData.cacheMousePos = { x: e.clientX, y: e.clientY };
}
// If the SVG is being dragged, then drag it
if (type === "move" && ePlantPlantEFPHandleMouseEventData.start) {
// Prevent highlighting of text when dragging
e.preventDefault();
/** How much the SVG will be dragged */
const moveByValue = svgElement.viewBox.baseVal.height
? window.innerHeight / svgElement.viewBox.baseVal.height / moveBy
: moveBy;
// Calculate the new position of the SVG
/** New X position of SVG */
const xDiff = -(e.clientX - ePlantPlantEFPHandleMouseEventData.cacheMousePos.x) / moveByValue;
/** New Y position of SVG */
const yDiff = -(e.clientY - ePlantPlantEFPHandleMouseEventData.cacheMousePos.y) / moveByValue;
// Find boundaries of the SVG so it does not leave viewpoint
/** Default boundaries for SVG viewpoint */
const defaultScaleBoundaries = 0.95;
/** Boundaries to scale the SVG's viewpoint on the X axis */
let scaleBoundariesX = svgElement.height.baseVal.value
? (defaultScaleBoundaries * 100 - svgElement.height.baseVal.value / svgElement.viewBox.baseVal.height) /
100
: (defaultScaleBoundaries * 100 - window.innerHeight / svgElement.viewBox.baseVal.height) / 100;
// Should be between 0 and 1
if (scaleBoundariesX <= 0 || scaleBoundariesX >= 1) {
scaleBoundariesX = defaultScaleBoundaries;
}
/** Boundaries to scale the SVG's viewpoint on the Y axis */
let scaleBoundariesY = svgElement.width.baseVal.value
? (defaultScaleBoundaries * 100 - svgElement.width.baseVal.value / svgElement.viewBox.baseVal.width) /
100
: (defaultScaleBoundaries * 100 - window.innerWidth / svgElement.viewBox.baseVal.height) / 100;
// Should be between 0 and 1
if (scaleBoundariesY <= 0 || scaleBoundariesY >= 1) {
scaleBoundariesY = defaultScaleBoundaries;
}
/** Current zoom level on the SVG compendium */
const zoomLevel =
1 / ePlantPlantEFPHandleMouseEventData.zoomLevel === 1
? defaultScaleBoundaries
: 1 / ePlantPlantEFPHandleMouseEventData.zoomLevel;
/** Boundaries to scale the SVG's viewpoint on the X axis */
const xBoundaries = svgElement.viewBox.baseVal.width * scaleBoundariesX * zoomLevel;
/** Boundaries for the X axis on the right side of the SVG compendium's viewpoint */
const xRightBoundaries = svgElement.viewBox.baseVal.width * scaleBoundariesX;
/** Boundaries to scale the SVG's viewpoint on the Y axis */
const yBoundaries = svgElement.viewBox.baseVal.height * scaleBoundariesY;
/** Upper boundaries to scale the SVG's viewpoint on the Y axis */
const yUpperBoundaries = yBoundaries * zoomLevel;
// Cache mouse position
ePlantPlantEFPHandleMouseEventData.cacheMousePos = { x: e.clientX, y: e.clientY };
// If SVG's Y position within viewpoint, then move it
if (
svgElement.viewBox.baseVal.y + yDiff <= yUpperBoundaries &&
svgElement.viewBox.baseVal.y + yDiff >= -yBoundaries
) {
svgElement.viewBox.baseVal.y += yDiff;
} else {
// If SVG's Y position is outside viewpoint, then move it to the top or bottom
svgElement.viewBox.baseVal.y =
svgElement.viewBox.baseVal.y + yDiff > 0 ? yUpperBoundaries : -yBoundaries;
}
// If SVG's X position within viewpoint, then move it
if (
svgElement.viewBox.baseVal.x + xDiff <= xBoundaries &&
svgElement.viewBox.baseVal.x + xDiff >= -xRightBoundaries
) {
svgElement.viewBox.baseVal.x += xDiff;
} else {
// If SVG's X position is outside viewpoint, then move it to the left or right
svgElement.viewBox.baseVal.x =
svgElement.viewBox.baseVal.x + xDiff > 0 ? xBoundaries : -xRightBoundaries;
}
}
}
// End dragging
if (type === "up") {
ePlantPlantEFPHandleMouseEventData.start = false;
}
}
/**
* Handle zooming of SVG
* @param {String} domID DOM ID of the SVG container
* @param {Event} e Mouse event object
* @param {Number} changeBy How much the SVG has been moved by
*/
// eslint-disable-next-line no-unused-vars
function ePlantPlantEFPHandleMouseWheel(domID, e, changeBy = 3) {
/** SVG document */
const svgElement = domID.firstElementChild;
/** SVG viewpoint */
const baseValues = svgElement.viewBox.baseVal;
/** If should zoom in [true] or out [false] */
const up = e.deltaY > 0;
/** How much the zoom will zoom in by */
const changeByValue = ePlantPlantEFPHandleMouseEventData.startHeight
? window.innerHeight / ePlantPlantEFPHandleMouseEventData.startHeight / changeBy
: changeBy;
if (
window.getSelection() &&
window.getSelection().isCollapsed &&
baseValues &&
e.deltaY &&
ePlantPlantEFPHandleMouseEventData.start
) {
// Prevent scrolling window
e.preventDefault();
if (up) {
svgElement.viewBox.baseVal.width = baseValues.width * changeByValue;
svgElement.viewBox.baseVal.height = baseValues.height * changeByValue;
ePlantPlantEFPHandleMouseEventData.zoomLevel *= changeByValue;
} else {
svgElement.viewBox.baseVal.width = baseValues.width / changeByValue;
svgElement.viewBox.baseVal.height = baseValues.height / changeByValue;
ePlantPlantEFPHandleMouseEventData.zoomLevel /= changeByValue;
}
}
}
/**
* Create and retrieve expression data in an SVG format
*/
class CreateSVGExpressionData {
constructor() {
// callPlantEFP
this.eFPObjects = {};
// loadSampleData
this.sampleData = {};
this.sampleOptions = [];
this.sampleReadableName = {};
// Top expression data
this.topExpressionValues = {};
this.expressionValues = {};
this.topExpressionOptions = ["Microarray", "RNA-seq"];
// Local storage grabbed
this.localStorageTop = false;
this.localStorageSample = {};
// Local for this class
this.desiredDOMid = "";
/** Markup for the visualization container */
// eslint-disable-next-line no-unused-expressions
this.appendSVG;
// createSVGValues
this.clickList = [];
this.svgValues = {};
this.svgMax = 0;
this.svgMin = 0;
this.svgMaxAverage = 0;
this.svgMaxAverageSample = "";
this.svgMinAverage = 0;
this.svgMinAverageSample = "";
// Store object name:
this.svgObjectName = "";
/** SVG DOM container's height styling */
this.svgContainerHeight = "95vh";
}
/**
* Verify that the locus being called is valid
* IMPORTANT: The current script only works for Arabidopsis thaliana
* TODO: Add support for other languages. Fill list of loci patterns can be found within GAIA's tools (accessible only to BAR developer at the moment)
* @param {String} locus The AGI ID (example: AT3G24650 or AT3G24650.1)
* @returns {Boolean} If locus is valid [true] or not [false, default]
*/
// eslint-disable-next-line class-methods-use-this
verifyLoci(locus) {
// Check if locus is a string
if (typeof locus === "string") {
/** Arabidopsis thaliana locus pattern */
const arabidopsisThalianaPattern = `^[A][T][MC0-9][G][0-9]{5}[.][0-9]{1,2}$|^[A][T][MC0-9][G][0-9]{5}$`;
/** Reg Exp for the locus pattern */
const regexPattern = new RegExp(arabidopsisThalianaPattern, "i");
// If match, then return true, else return false
return Boolean(locus.trim().match(regexPattern));
}
return false;
}
/**
* Create and generate an SVG based on the desired tissue expression locus
* @param {String} locus The AGI ID (example: AT3G24650)
* @param {String} desiredDOMid The desired DOM location or if kept empty, would not replace any DOM elements and just create the related HTML DOM elements within appendSVG
* @param {String} svgName Name of the SVG file without the .svg at the end. Default is set to "default", when left this value, the highest expression value (if any) is chosen and if not, then Abiotic Stress is.
* @param {Boolean} includeDropdownAll true = include a html dropdown/select of all available SVGs/samples, false = don't
* @param {String | Number} containerHeight The height of the SVG container, default is 95vh
*/
generateSVG(
locus = "AT3G24650",
desiredDOMid = undefined,
svgName = "default",
includeDropdownAll = true,
containerHeight = undefined,
) {
if (this.verifyLoci(locus.trim())) {
// Reset variables:
this.svgValues = {};
this.svgMax = undefined;
this.svgMin = undefined;
this.svgMaxAverage = undefined;
this.svgMaxAverageSample = undefined;
this.svgMinAverage = undefined;
this.svgMinAverageSample = undefined;
this.includeDropdownAll = includeDropdownAll;
if (this.clickList.includes(svgName) === false) {
this.clickList.push(svgName);
}
if (containerHeight && typeof containerHeight === "string") {
this.svgContainerHeight = containerHeight.toString();
} else if (containerHeight && typeof containerHeight === "number") {
this.svgContainerHeight = `${containerHeight.toString()}px`;
}
// Initiate scripts
this.desiredDOMid = desiredDOMid;
this.#retrieveTopExpressionValues(svgName, locus.trim().toUpperCase());
} else {
console.error(`Invalid locus: ${locus.trim()}`);
}
}
/**
* Retrieve information about the top expression values for a specific locus
* @param {String} svgName Name of the SVG file without the .svg at the end
* @param {String} locus The AGI ID (example: AT3G24650)
*/
async #retrieveTopExpressionValues(svgName, locus = "AT3G24650") {
let completedFetches = 0;
let localStorageTopExpressionValues = localStorage.getItem("bar_eplant-top-expression-values");
let fetchData = true;
if (!this.localStorageTop) {
if (localStorageTopExpressionValues) {
localStorageTopExpressionValues = JSON.parse(localStorageTopExpressionValues);
// Check if week passed expiration
if (
localStorageTopExpressionValues.expiry &&
new Date().getTime() - localStorageTopExpressionValues.expiry <= 7 * 24 * 60 * 60 * 1000
) {
fetchData = false;
} else if (localStorageTopExpressionValues[locus]) {
fetchData = false;
}
this.topExpressionValues = {
...this.topExpressionValues,
...localStorageTopExpressionValues,
};
this.localStorageTop = true;
}
}
if (this.topExpressionValues[locus]) {
fetchData = false;
}
// If never been called before
if (fetchData) {
for (const topMethod of this.topExpressionOptions) {
const url = `https://bar.utoronto.ca/expression_max_api/max_average?method=${topMethod}`;
const sendHeaders = "application/json";
let postSend = {
loci: [locus.toUpperCase()],
method: topMethod,
};
postSend = JSON.stringify(postSend);
const methods = { mode: "cors" };
methods.method = "POST";
if (sendHeaders) {
methods.headers = {};
methods.headers["Content-type"] = sendHeaders;
}
methods.body = postSend;
// eslint-disable-next-line no-await-in-loop
await fetch(url, methods)
// eslint-disable-next-line no-loop-func
.then(async (response) => {
if (response.status === 200) {
await response.text().then(async (data) => {
let responseData;
if (data.length > 0) {
responseData = JSON.parse(data);
} else {
responseData = {};
}
let topMethodUsed;
const urlQuery = url.split("=");
if (urlQuery.length > 1) {
topMethodUsed = urlQuery[1];
}
if (topMethodUsed && responseData && responseData.wasSuccessful === true) {
if (responseData.maxAverage) {
const tempTopExpressionData = {};
tempTopExpressionData[topMethodUsed] = {};
tempTopExpressionData[topMethodUsed].maxAverage =
responseData.maxAverage[locus.toUpperCase()];
if (responseData.standardDeviation) {
tempTopExpressionData[topMethodUsed].standardDeviation =
responseData.standardDeviation[locus.toUpperCase()];
}
if (responseData.sample) {
tempTopExpressionData[topMethodUsed].sample =
responseData.sample[locus.toUpperCase()];
}
if (responseData.compendium) {
tempTopExpressionData[topMethodUsed].compendium =
responseData.compendium[locus.toUpperCase()];
}
if (!this.topExpressionValues) {
this.topExpressionValues = {};
}
this.topExpressionValues[locus] = {
...this.topExpressionValues[locus],
...tempTopExpressionData,
};
}
}
completedFetches += 1;
if (completedFetches === this.topExpressionOptions.length) {
// Update local storage:
// Add to local storage as well:
if (!localStorageTopExpressionValues || fetchData) {
localStorageTopExpressionValues = {};
localStorageTopExpressionValues[locus] = {
...this.topExpressionValues[locus],
};
localStorageTopExpressionValues.expiry = new Date().getTime();
} else {
localStorageTopExpressionValues[locus] = {
...this.topExpressionValues[locus],
};
}
// Ensure that local storage has no more than 10 entries
if (
localStorageTopExpressionValues &&
Object.keys(localStorageTopExpressionValues).length > 10
) {
// Remove the first entry if not the one we just added and not 'expiry'
for (const key in localStorageTopExpressionValues) {
if (key !== locus && key !== "expiry") {
delete localStorageTopExpressionValues[key];
break;
}
}
}
if (localStorageTopExpressionValues) {
localStorage.setItem(
"bar_eplant-top-expression-values",
JSON.stringify(localStorageTopExpressionValues),
);
this.localStorageTop = true;
}
await this.#loadSampleData(svgName, locus);
}
});
} else if (response.status !== 200) {
completedFetches += 1;
if (completedFetches === this.topExpressionOptions.length) {
await this.#loadSampleData(svgName, locus);
}
console.error(
`fetch error - Status Code: ${response.status}, fetch-url: ${response.url}, document-url: ${window.location.href}`,
);
}
})
// eslint-disable-next-line no-loop-func
.catch(async (err) => {
completedFetches += 1;
if (completedFetches === this.topExpressionOptions.length) {
await this.#loadSampleData(svgName, locus);
}
console.error(err);
});
}
} else if (Object.keys(this.topExpressionValues[locus]).length > 0) {
await this.#loadSampleData(svgName, locus);
} else if (Object.keys(localStorageTopExpressionValues[locus]).length > 0) {
if (!this.topExpressionValues) {
this.topExpressionValues = {};
}
this.topExpressionValues[locus] = localStorageTopExpressionValues[locus];
await this.#loadSampleData(svgName, locus);
}
}
/**
* Calls and stores the sample Data for the SVG, SVG's subunits, datasource and it's name-values
* @param {String} svgName Name of the SVG file without the .svg at the end
* @param {String} locus The AGI ID (example: AT3G24650)
*/
async #loadSampleData(svgName, locus) {
if (Object.keys(this.sampleData).length === 0) {
/** Whether to fetch the sample data container from GitHub (true, default) or not */
let fetchFromGitHub = true;
/** Browser's local storage for the sample data, if exists */
let localStoredSampleData = localStorage?.getItem("bar_eplant-sample-data-storage");
// If the local storage exists, see if it's expired (1 week) to fetch from GitHub or use the local storage data
if (localStoredSampleData) {
// Convert to JSON
localStoredSampleData = JSON.parse(localStoredSampleData);
// If a week has passed since the last time the data was stored
if (
localStoredSampleData.expiry &&
localStoredSampleData.data &&
new Date().getTime() - localStoredSampleData.expiry <= 7 * 24 * 60 * 60 * 1000
) {
// Has not expire, use this data
fetchFromGitHub = false;
this.sampleData = localStoredSampleData.data;
}
}
if (fetchFromGitHub) {
/** GitHub's URL for the sample data container */
const url =
"https://raw.githubusercontent.com/BioAnalyticResource/ePlant_Plant_eFP/master/data/SampleData.min.json";
/** Fetch methods */
const methods = { mode: "cors" };
await fetch(url, methods)
.then(async (response) => {
if (response.status === 200) {
await response.text().then(async (data) => {
/** Response data */
const res = data.length > 0 ? JSON.parse(data) : {};
// Store response
this.sampleData = res;
// Store into local storage
const sampleDataStorage = {
data: res,
expiry: new Date().getTime(),
};
localStorage.setItem(
"bar_eplant-sample-data-storage",
JSON.stringify(sampleDataStorage),
);
});
} else if (response.status !== 200) {
console.error(
`fetch error - Status Code: ${response.status}, fetch-url: ${response.url}, document-url: ${window.location.href}`,
);
}
})
.catch(async (err) => {
console.error(err);
});
}
// Setup and retrieve information about the target SVG and locus
await this.#retrieveSampleData(svgName, locus);
} else if (Object.keys(this.sampleData).length > 0) {
await this.#retrieveSampleData(svgName, locus);
}
}
/**
* Retrieves the sample information relating to an SVG for a specific set of data
* @param {String} svgName Name of the SVG file without the .svg at the end
* @param {String} locus The AGI ID (example: AT3G24650)
*/
async #retrieveSampleData(svgName, locus) {
// Check if svgName contains .svg
if (svgName.substring(-4) === ".svg") {
svgName = svgName.substring(0, svgName.length - 4);
}
if (this.sampleOptions.length === 0) {
for (const [key, value] of Object.entries(this.sampleData)) {
this.sampleOptions.push(key);
this.sampleReadableName[value.name] = key;
}
}
// Create variables that will be used in #retrieveSampleData
const sampleDataKeys = Object.keys(this.sampleData); // All possible SVGs
let sampleDB = ""; // The sample's datasource
let sampleIDList = []; // List of all of the sample's IDs
let sampleSubunits = []; // List of SVG's subunits
await this.#processLocalStorageEFPObjectData();
// Check if valid SVG
if (!sampleDataKeys.includes(svgName) && this.topExpressionValues[locus]) {
// Determine max expression value to default too
let maxExpressionValue = 0;
let maxExpressionCompendium;
for (const [, value] of Object.entries(this.topExpressionValues[locus])) {
if (value.compendium && value.compendium[1] && sampleDataKeys.includes(value.compendium[1])) {
if (value.maxAverage && value.maxAverage[1] && value.maxAverage[1] > maxExpressionValue) {
maxExpressionValue = value.maxAverage[1];
maxExpressionCompendium = value.compendium[1];
}
}
}
if (maxExpressionCompendium) {
svgName = maxExpressionCompendium;
} else {
svgName = "AbioticStress";
}
}
// If still default, load in Abiotic Stress
if (svgName === "default") {
svgName = "AbioticStress";
}
// Create variables for parsing
const sampleInfo = this.sampleData[svgName];
let sampleOptions;
if (sampleInfo && sampleInfo.sample) {
sampleOptions = sampleInfo.sample;
}
if (sampleInfo && sampleInfo.db) {
sampleDB = sampleInfo.db;
}
// If a database is available for this SVG, then find sample ID information
if (sampleDB !== undefined) {
sampleSubunits = Object.keys(sampleInfo.sample);
sampleIDList = [];
for (const sample of sampleSubunits) {
sampleIDList = sampleIDList.concat(sampleOptions[sample]);
}
}
// Call plantefp.cgi webservice to retrieve information about the target tissue expression data
if (!this.eFPObjects[svgName] || !this.eFPObjects[svgName].locusCalled.includes(locus)) {
await this.#callPlantEFP(sampleDB, locus, sampleIDList, svgName, sampleOptions);
} else if (this.eFPObjects[svgName]) {
await this.#addSVGtoDOM(svgName, locus, this.includeDropdownAll);
}
}
async #processLocalStorageEFPObjectData() {
if (Object.keys(this.localStorageSample).length === 0) {
// Grab localStorage's sample data:
let localStorageSampleValues = localStorage.getItem("bar_eplant-efp-data");
if (localStorageSampleValues) {
localStorageSampleValues = JSON.parse(localStorageSampleValues);
this.localStorageSample = localStorageSampleValues;
await this.#checkLocalStorageEFPObjectSize();
// Check if week passed expiration
if (
!localStorageSampleValues.expiry ||
!(new Date().getTime() - localStorageSampleValues.expiry <= 7 * 24 * 60 * 60 * 1000)
) {
// If this.eFPObjects is empty, give it the localStorageSampleValues data
if (Object.keys(this.eFPObjects).length === 0) {
this.eFPObjects = localStorageSampleValues;
} else {
// Go through this.eFPObjects and localStorageSampleValues and add in any missing data
// Data is in format of this.eFPObjects[compendium] and in [compendium], see if there is a [locus].
// See which loci are missing and add them in (if any), and if so, go through the [sample] and add in any missing data
for (const [compendium, compendiumData] of Object.entries(localStorageSampleValues)) {
if (compendium !== "expiry") {
if (this.eFPObjects[compendium]) {
// Check if locus is missing
const missingLoci = [];
// Go through the [locusCalled] array and see if any are missing
for (const locus of compendiumData.locusCalled) {
if (!this.eFPObjects[compendium].locusCalled.includes(locus)) {
missingLoci.push(locus);
}
}
// If there are missing loci, add them in
if (missingLoci.length > 0) {
// Go through the sample data and add in any missing data
for (const [sample, sampleData] of Object.entries(compendiumData.sample)) {
if (this.eFPObjects[compendium].sample[sample]) {
// Go through the [locus] and see if any are missing
for (const locus of missingLoci) {
if (!this.eFPObjects[compendium].sample[sample][locus]) {
this.eFPObjects[compendium].sample[sample][locus] =
sampleData[locus];
}
}
} else {
this.eFPObjects[compendium].sample[sample] = sampleData;
}
}
}
} else {
this.eFPObjects[compendium] = compendiumData;
}
}
}
}
}
}
}
}
async #checkLocalStorageEFPObjectSize(svgKeep = undefined) {
// Ensure that the localStorage is not too large (no more than 1MB)
// If it is, then remove the the first SVG in the eFPObjects object if not the one that is currently being kept (svgKeep) or 'expiry'
// Check size of this.localStorageSample
// Convert to string
const localStorageSampleString = JSON.stringify(this.localStorageSample);
// Get size of string
const localStorageSampleSize = localStorageSampleString.length * 2;
// If the localStorageSampleSize is too large, remove the first SVG in the eFPObjects object if not the one that is currently being kept (svgKeep) or 'expiry'
if (localStorageSampleSize > 1000000) {
// Go through the eFPObjects object and remove the first SVG if not the one that is currently being kept (svgKeep) or 'expiry'
for (const [svgName, _svgData] of Object.entries(this.eFPObjects)) {
if (svgName !== svgKeep && svgName !== "expiry") {
delete this.eFPObjects[svgName];
break;
}
}
}
}
/**
* Calls the plantefp.cgi webservice to retrieve expression data from the BAR
* @param {String} datasource Which database the information is contained in
* @param {String} locus The AGI ID (example: AT3G24650)
* @param {Array} samples List of sample ID's which the exact expression data is related to
* @param {String} svg Which SVG is being called
* @param {Array} sampleSubunits List of the SVG's subunits
*/
async #callPlantEFP(datasource, locus, samples, svg, sampleSubunits) {
// Create URL
let url = "https://bar.utoronto.ca/~asullivan/webservices/plantefp.cgi?";
url += `datasource=${datasource}&`;
url += `id=${locus}&`;
url += "samples=[";
for (let i = 0; i < samples.length; i += 1) {
let sampleName = samples[i].trim();
sampleName = sampleName.replace(/\+/g, "%2B");
sampleName = sampleName.replace(/ /g, "%20");
url += `"${sampleName}"`;
if (i !== samples.length - 1) {
url += ",";
}
}
url += "]";
const methods = { mode: "cors" };
let alreadyRetrievedData = false;
if (this.eFPObjects?.[svg]?.[locus]?.includes("locus")) {
alreadyRetrievedData = true;
}
if (sampleSubunits && !alreadyRetrievedData) {