@sjcrh/proteinpaint-client 2.81.2-3 → 2.81.5

package/dist/{AppHeader-6IGQURSX.js → AppHeader-PBT75IXA.js}

@@ -4,18 +4,18 @@ import {
 } from "./chunk-FIY7FBE5.js";
 import {
   InputSearch
-} from "./chunk-PU7EMWOK.js";
+} from "./chunk-HR3FNUVU.js";
 import "./chunk-7KFEDC2T.js";
 import "./chunk-FCPSU6WB.js";
 import "./chunk-WX2C2ZIZ.js";
 import "./chunk-CVWXP35F.js";
 import "./chunk-OTWQWP6Z.js";
 import "./chunk-6BHKLDWV.js";
-import "./chunk-TU4H4R2T.js";
+import "./chunk-LGC254YE.js";
 import {
   get_tklst
-} from "./chunk-QU5I6QUG.js";
-import "./chunk-22KNFYBP.js";
+} from "./chunk-MB56W3DF.js";
+import "./chunk-24U25WMU.js";
 import "./chunk-JOCEI72L.js";
 import "./chunk-6MSAGRRE.js";
 import "./chunk-MKAF2BHB.js";
@@ -31,7 +31,7 @@ import "./chunk-ALPXXDQD.js";
 import "./chunk-CTQFEFIV.js";
 import {
   block_init_default
-} from "./chunk-L5YZZHMR.js";
+} from "./chunk-WHNSPT6X.js";
 import {
   throwMsgWithFilePathAndFnName
 } from "./chunk-RKJGIOIF.js";
@@ -227,7 +227,7 @@ async function findgene2paint(str, app, genomename, jwt) {
       debugmode: app.debugmode
     };
     first_genetrack_tolist(g, par2.tklst);
-    import("./block-YM7DNWQJ.js").then((b) => new b.Block(par2)).catch((err) => {
+    import("./block-5CVR6BZF.js").then((b) => new b.Block(par2)).catch((err) => {
       app.error0(err);
     });
     return;
@@ -715,7 +715,7 @@ var AppHeader = class _AppHeader {
     {
       const row2 = headinfo.append("div").style("padding-left", "15px");
       const link = `https://github.com/stjude/proteinpaint/pkgs/container/ppfull`;
-      const version = this.data.pkgver ? `Version: <a href="${link}" target="${this.data.pkgver}">${this.data.pkgver}</a>` : `Code date: ${this.data.codedate}`;
+      const version = this.data.pkgver ? `Release version: <a href="${link}" target="${this.data.pkgver}">${this.data.pkgver}</a>` : `Code date: ${this.data.codedate}`;
       row2.attr("id", "sjpp-serverstat").append("span").html(`${version}, server launched: ${this.data.launchdate || "??"}.`);
       if (this.data.hasblat) {
         row2.append("a").style("margin-left", "10px").text("Running BLAT").on("click", async (event) => {
@@ -833,7 +833,7 @@ var AppHeader = class _AppHeader {
         debugmode: app.debugmode
       };
       first_genetrack_tolist(g, par.tklst);
-      import("./block-YM7DNWQJ.js").then((b) => new b.Block(par));
+      import("./block-5CVR6BZF.js").then((b) => new b.Block(par));
       app.drawer.dispatch({ type: "is_apps_btn_active", value: false });
     });
     return g_browser_btn;
@@ -846,4 +846,4 @@ var AppHeader = class _AppHeader {
 export {
   AppHeader
 };
-//# sourceMappingURL=AppHeader-6IGQURSX.js.map
+//# sourceMappingURL=AppHeader-PBT75IXA.js.map

package/dist/{AppHeader-6IGQURSX.js.map → AppHeader-PBT75IXA.js.map}

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../src/header/omniSearch.js", "../appdrawer/card.js", "../appdrawer/dsButton.js", "../appdrawer/layout.js", "../appdrawer/mainBtn.js", "../appdrawer/store.js", "../appdrawer/app.js", "../src/header/AppHeader.ts"],
-  "sourcesContent": ["import { dofetch3 } from '#common/dofetch'\nimport { openSandbox } from '../../appdrawer/adSandbox'\nimport { throwMsgWithFilePathAndFnName } from '../../dom/sayerror.ts'\nimport { string2pos } from '../coord'\nimport { newSandboxDiv } from '../../dom/sandbox.ts'\nimport * as parseurl from '../app.parseurl'\nimport urlmap from '#common/urlmap'\nimport { first_genetrack_tolist } from '#common/1stGenetk'\nimport blockinit from '../block.init'\nimport { select as d3select } from 'd3-selection'\n\n/*\n----EXPORTED----\nsearchItems()\nfindgenelst()\nfindgene2paint()\n\n----Internal----\nfindAppDrawerElements()\ngetExampleNames()\ngetFilteredElements()\n*/\n\nexport async function searchItems(app, tip, help, publications, jwt) {\n\tconst userInput = d3select('input').property('value').trim()\n\tconst data = [\n\t\t{\n\t\t\ttitle: 'Genes',\n\t\t\tdefault: true,\n\t\t\titems: await findgenelst(userInput, app.selectgenome.property('value'), jwt),\n\t\t\tcolor: '#F2F2F2',\n\t\t\tcallback: d => {\n\t\t\t\tapp.drawer.dispatch({ type: 'is_apps_btn_active', value: false })\n\t\t\t\ttip.hide()\n\t\t\t\tfindgene2paint(d, app, app.selectgenome.property('value'), jwt)\n\t\t\t}\n\t\t}\n\t]\n\tawait findAppDrawerElements(app, userInput, data, tip)\n\t//Keep 'Help' section second last\n\tdata.push({\n\t\ttitle: 'Help',\n\t\tdefault: false,\n\t\titems: help.filter(d => d.label.toLowerCase().includes(userInput.toLowerCase())),\n\t\tcolor: '#faebd9',\n\t\tcallback: d => {\n\t\t\twindow.open(d.link, d.label)\n\t\t}\n\t})\n\tdata.push({\n\t\ttitle: 'Publications',\n\t\tdefault: false,\n\t\titems: publications.filter(\n\t\t\td =>\n\t\t\t\td.title.toLowerCase().includes(userInput.toLowerCase()) ||\n\t\t\t\td.appHeaderTitle.toLowerCase().includes(userInput.toLowerCase())\n\t\t),\n\t\tcolor: '#E6E6FA',\n\t\tcallback: d => {\n\t\t\twindow.open(d.doi, d.title)\n\t\t}\n\t})\n\treturn data\n}\n\nasync function findAppDrawerElements(app, input, data, tip) {\n\tconst re = await dofetch3(app.cardsPath + '/index.json')\n\tif (re.error) throwMsgWithFilePathAndFnName(`Problem retrieving ../cards/index.json`)\n\tconst userInput = input.toLowerCase().trim()\n\tconst elements = [...re.elements]\n\tlet filteredElements\n\tif (userInput.length > 2) {\n\t\t/** Adding the examples to the search terms is expensive\n\t\t * Limit when all card files are loaded based on user input\n\t\t * Maybe timeout instead? or combination of the two?\n\t\t */\n\t\tawait getExampleNames(elements, app)\n\t\tfilteredElements = getFilteredElements(elements, userInput)\n\t} else {\n\t\tfilteredElements = getFilteredElements(elements, userInput)\n\t}\n\n\tconst opts = {\n\t\tapp: app.drawer.opts,\n\t\tsandboxDiv: app.drawer.opts.sandboxDiv,\n\t\tgenomes: app.genomes,\n\t\tfromApp: true\n\t}\n\n\tdata.push(\n\t\t{\n\t\t\ttitle: 'Tracks and Apps',\n\t\t\titems: filteredElements.filter(c => c.type == 'card'),\n\t\t\tcolor: '#e1edf7',\n\t\t\tcallback: element => {\n\t\t\t\tapp.drawer.dispatch({ type: 'is_apps_btn_active', value: false })\n\t\t\t\ttip.hide()\n\t\t\t\topenSandbox(element, opts)\n\t\t\t}\n\t\t},\n\t\t{\n\t\t\ttitle: 'Datasets',\n\t\t\titems: filteredElements.filter(c => c.type == 'dsButton'),\n\t\t\tcolor: '#e5f5e4',\n\t\t\tcallback: element => {\n\t\t\t\tapp.drawer.dispatch({ type: 'is_apps_btn_active', value: false })\n\t\t\t\ttip.hide()\n\t\t\t\topenSandbox(element, opts)\n\t\t\t}\n\t\t}\n\t)\n\treturn data\n}\n\nasync function getExampleNames(elements, app) {\n\tconst promises = elements.map(async elem => {\n\t\tif (elem.hidden || elem.type != 'card' || !elem.sandboxJson) return elem\n\t\tconst exs = await dofetch3(app.cardsPath + `/${elem.sandboxJson}.json`)\n\t\tif (exs?.ppcalls.length > 0) {\n\t\t\tfor (const c of exs.ppcalls) {\n\t\t\t\tif (c.isUI) return\n\t\t\t\tif (c?.label) elem.searchterms.push(c.label)\n\t\t\t}\n\t\t}\n\t})\n\n\tawait Promise.all(promises)\n}\n\nfunction getFilteredElements(elements, userInput) {\n\treturn elements\n\t\t.filter(elem => {\n\t\t\tif (elem.hidden) return false\n\t\t\tlet searchTermFound = (elem.searchterms || []).reduce((searchTermFound, searchTerm) => {\n\t\t\t\tif (searchTermFound) return true\n\t\t\t\treturn searchTerm.toLowerCase().includes(userInput)\n\t\t\t}, false)\n\t\t\treturn searchTermFound || elem.name.toLowerCase().includes(userInput)\n\t\t})\n\t\t.sort((a, b) => a.name.localeCompare(b.name))\n}\n\nexport async function findgenelst(str, genome, jwt) {\n\t//TODO - including something here about if user input includes a special character to return rather than comment out catch\n\tif (str.length == 0) return\n\ttry {\n\t\tconst data = await dofetch3('/genelookup', {\n\t\t\tbody: {\n\t\t\t\tinput: str,\n\t\t\t\tgenome,\n\t\t\t\tjwt\n\t\t\t}\n\t\t})\n\n\t\tif (data.error) throw data.error\n\t\tif (!data.hits) throw '.hits[] missing'\n\t\treturn data.hits\n\t} catch (err) {\n\t\t// err is likely \"invalid character in gene name\". ignore and continue\n\t\t// if (err.stack) console.log(err.stack)\n\t\t// throw err\n\t}\n}\n\nexport async function findgene2paint(str, app, genomename, jwt) {\n\tconst g = app.genomes[genomename]\n\tif (!g) {\n\t\tconsole.error('unknown genome ' + genomename)\n\t\treturn\n\t}\n\tconst sandbox_div = newSandboxDiv(app.drawer.opts.sandboxDiv)\n\tsandbox_div.header.html(\n\t\t'<div style=\"display:inline-block;\">' +\n\t\t\tstr +\n\t\t\t'</div><div class=\"sjpp-output-sandbox-title\">' +\n\t\t\tgenomename +\n\t\t\t'</div>'\n\t)\n\t// may yield tklst from url parameters\n\tconst urlp = urlmap()\n\tconst tklst = await parseurl.get_tklst(urlp, g)\n\n\tconst pos = string2pos(str, g)\n\tif (pos) {\n\t\t// input is coordinate, launch block\n\t\tconst par = {\n\t\t\thostURL: app.hostURL,\n\t\t\tjwt,\n\t\t\tholder: sandbox_div.body,\n\t\t\tgenome: g,\n\t\t\tnobox: true,\n\t\t\tchr: pos.chr,\n\t\t\tstart: pos.start,\n\t\t\tstop: pos.stop,\n\t\t\tdogtag: genomename,\n\t\t\ttklst,\n\t\t\tdebugmode: app.debugmode\n\t\t}\n\t\tfirst_genetrack_tolist(g, par.tklst)\n\n\t\timport('../block.js')\n\t\t\t.then(b => new b.Block(par))\n\t\t\t.catch(err => {\n\t\t\t\tapp.error0(err)\n\t\t\t})\n\t\treturn\n\t}\n\n\t// input string is not coordinate, find gene match\n\tconst par = {\n\t\thostURL: app.hostURL,\n\t\tjwt,\n\t\tquery: str,\n\t\tgenome: g,\n\t\tholder: sandbox_div.body,\n\t\tvariantPageCall_snv: app.variantPageCall_snv,\n\t\tsamplecart: app.samplecart,\n\t\ttklst,\n\t\tdebugmode: app.debugmode\n\t}\n\n\t// add svcnv tk from url param\n\tconst tmp = sessionStorage.getItem('urlp_mds')\n\tif (tmp) {\n\t\tconst l = tmp.split(',')\n\t\tif (l.length == 2) {\n\t\t\tpar.datasetqueries = [{ dataset: l[0], querykey: l[1] }]\n\t\t}\n\t}\n\n\tawait blockinit(par)\n}\n", "import { getCompInit } from '#rx'\nimport { rgb } from 'd3-color'\nimport { openSandbox } from './adSandbox'\nimport { slideDrawer } from './mainBtn'\n\n/*\n.opts{\n\t.app{\n\t\t.holder\n\t\t.element{}\n\t\t.sandboxDiv\n\t}\n}\n\nTODOs: \n\n- responsiveness of image on window resize \n\t- expand image size on resize\n\t- non square, take better use of space\n- Need fn in utils to decide black or white text based on background color contrast\n- Unify card and nestedCard layout. Only call one layout function for both\n\t- optional non image card layout\n\t- Make ribbons appear on nested cards\n- element.section only required if columnsLayout provided\n\n*/\n\nclass AppDrawerCard {\n\t// handles types 'card' and 'nestedCard'\n\tconstructor(opts) {\n\t\tthis.type = 'card'\n\t\tthis.opts = this.validateOpts(opts)\n\t\tthis.holder = opts.holder\n\t\tthis.dom = opts.dom\n\t\tthis.sandboxDiv = opts.sandboxDiv\n\t\tsetRenderers(this)\n\t}\n\n\tvalidateOpts(opts) {\n\t\tif (!opts.element.name) throw `Card .name is missing`\n\t\tif (opts.element.type == 'card') {\n\t\t\tif (!opts.element.sandboxJson && !opts.element.sandboxHtml)\n\t\t\t\tthrow `Either .sandboxJson or .sandboxHtml is missing for card=${opts.element.name}`\n\t\t}\n\t\tif (opts.element.type == 'nestedCard') {\n\t\t\tif (!opts.element.children || opts.element.children.length == 0)\n\t\t\t\tthrow `Missing .children for nested card = ${opts.element.name}`\n\t\t}\n\t\tif (opts.element.ribbon) {\n\t\t\tif (!opts.element.ribbon.text) throw `Missing ribbon .text for ${opts.element.type} = ${opts.element.name}`\n\n\t\t\t//ProteinPaint app drawer specific validation\n\t\t\tif (\n\t\t\t\t(opts.element.ribbon.text.toUpperCase() == 'NEW' || opts.element.ribbon.text.toUpperCase() == 'UPDATED') &&\n\t\t\t\t!opts.element.ribbon.expireDate\n\t\t\t)\n\t\t\t\tthrow `${opts.element.type} = ${\n\t\t\t\t\topts.element.name\n\t\t\t\t} ribbon is ${opts.element.ribbon.text.toUpperCase()} but .expireDate is missing. Please provide`\n\n\t\t\tif (opts.element.ribbon.expireDate) {\n\t\t\t\tif (opts.element.ribbon.expireDate >= 0) {\n\t\t\t\t\tthrow `Flag for ${opts.element.type} = ${opts.element.name} is not a valid date`\n\t\t\t\t} //TODO add validation for format?\n\t\t\t}\n\t\t}\n\t\treturn opts\n\t}\n\n\tmain() {}\n}\n\nexport const cardInit = getCompInit(AppDrawerCard)\n\nfunction setRenderers(self) {\n\tconst card = self.holder.append('li')\n\tif (self.opts.element.type == 'card') {\n\t\tcard.classed('sjpp-track', true).html(\n\t\t\t`<div class=\"sjpp-track-h\"><span style=\"font-size:14.5px;font-weight:500;\">${self.opts.element.name}</span></div>\n\t\t\t\t${\n\t\t\t\t\tself.opts.element.description\n\t\t\t\t\t\t? `<span class=\"sjpp-track-blurb\" style=\"cursor:default\">${self.opts.element.description}</span></div>`\n\t\t\t\t\t\t: ' '\n\t\t\t\t}\n\t\t\t\t<span class=\"sjpp-track-image\"><img src=\"${self.opts.element.image}\" alt=\"${\n\t\t\t\tself.opts.element.description\n\t\t\t}\"></img></span>\n\t\t\t\t</div>`\n\t\t)\n\t} else if (self.opts.element.type == 'nestedCard') {\n\t\tcard.classed('sjpp-app-drawer-card', true).html(\n\t\t\t`<p style=\"margin-left: 12px; font-size:14.5px;font-weight:500; display: block;\">${self.opts.element.name}</p>\n\t\t\t<p style=\"display: block; font-size: 13px; font-weight: 300; margin-left: 20px; justify-content: center; font-style:oblique; color: #403f3f;\">${self.opts.element.description}</p>`\n\t\t)\n\t}\n\n\tself.makeRibbon = function(ribbon) {\n\t\t//only relevant for 'card', not 'nestedCard'\n\t\tconst ribbonDiv = card\n\t\t\t.append('div')\n\t\t\t.classed('sjpp-app-drawer-card-ribbon', true)\n\t\t\t.style('align-items', 'center')\n\t\t\t.style('justify-content', 'center')\n\n\t\t//*********TODO: move from diagonal to straight on right side */\n\t\tconst text = ribbon.text.toUpperCase()\n\t\t//Enforce color palette for proteinpaint homepage ribbons\n\t\tconst color =\n\t\t\ttext == 'BETA'\n\t\t\t\t? '#418cb5'\n\t\t\t\t: text == 'NEW'\n\t\t\t\t? '#1ba176'\n\t\t\t\t: text == 'UPDATED'\n\t\t\t\t? 'orange'\n\t\t\t\t: ribbon.color\n\t\t\t\t? ribbon.color\n\t\t\t\t: 'red'\n\n\t\tribbonDiv\n\t\t\t.append('span')\n\t\t\t.text(text)\n\t\t\t.style('color', 'white')\n\t\t\t.style('background-color', rgb(color).darker())\n\t\t\t.style('height', 'auto')\n\t\t\t.style('width', '100%')\n\t\t\t.style('top', '15%')\n\t\t\t.style('left', '-30%')\n\t\t\t.style('font-size', '11.5px')\n\t\t\t.style('text-transform', 'uppercase')\n\t\t\t.style('text-align', 'center')\n\t}\n\n\tif (self.opts.element.ribbon) {\n\t\tconst today = new Date()\n\t\tconst ribbonExpireDate = new Date(self.opts.element.ribbon.expireDate)\n\t\t//Allows ribbons to expire or appear indefinitely\n\t\tif (ribbonExpireDate > today || ribbonExpireDate == 'Invalid Date') self.makeRibbon(self.opts.element.ribbon)\n\t}\n\n\tcard.on('click', async event => {\n\t\tevent.stopPropagation()\n\t\tawait self.app.dispatch({\n\t\t\ttype: 'is_apps_btn_active',\n\t\t\tvalue: false\n\t\t})\n\t\tslideDrawer(self)\n\t\tawait openSandbox(self.opts.element, self.opts)\n\t})\n}\n", "import { getInitFxn } from '#rx'\nimport * as utils from './utils'\nimport { openSandbox } from './adSandbox'\nimport { slideDrawer } from './mainBtn'\n\n/*\n.opts{\n\t.app\n\t.holder\n\t.element{}\n\t.dom{}\n\t.state{}\n\t.sandboxDiv\n}\n*/\n\nclass AppDrawerButton {\n\tconstructor(opts) {\n\t\tthis.type = 'button' // works for 'dsButton'. May expand to other button types\n\t\tthis.opts = this.validateOpts(opts)\n\t\tthis.holder = opts.holder\n\t\tthis.dom = opts.dom\n\t\tthis.sandboxDiv = opts.sandboxDiv\n\t\tsetRenderers(this)\n\t}\n\n\tvalidateOpts(opts) {\n\t\tif (!opts.element.name) throw `Button name is missing`\n\t\tif (!opts.element.sandboxJson && !opts.element.sandboxHtml)\n\t\t\tthrow `Either .sandboxJson or .sandboxHtml is missing for button=${opts.element.name}`\n\t\treturn opts\n\t}\n\n\tmain() {}\n}\n\nexport const buttonInit = getInitFxn(AppDrawerButton)\n\nfunction setRenderers(self) {\n\tconst btn = utils.makeButton({ div: self.holder, text: self.opts.element.name, margin: '20px 20px 0px' })\n\tbtn.attr('class', 'sjpp-appdrawer-dataset-btn').on('click', async event => {\n\t\tevent.stopPropagation()\n\t\tawait self.app.dispatch({\n\t\t\ttype: 'is_apps_btn_active',\n\t\t\tvalue: false\n\t\t})\n\t\tslideDrawer(self)\n\t\tawait openSandbox(self.opts.element, self.opts)\n\t})\n}\n", "import { getCompInit } from '#rx'\nimport { rgb } from 'd3-color'\nimport { defaultcolor } from '#shared/common.js'\nimport { cardInit } from './card'\nimport { buttonInit } from './dsButton'\nimport { select } from 'd3-selection'\nimport { dofetch3, sayerror } from '#src/client'\n\n/*\n.opts{}\n    .app{}\n\t.dom{}\n\t.state{}\n\nQuestions: \n\t- Organize in window based on section size to make best use of space?\n    - For the column layout: \n        1. Cap number of columns?\n        2. Allow y overflow for >2 columns (like Trello)?\n*/\n\nclass AppDrawerLayoutComp {\n\tconstructor(opts) {\n\t\tthis.type = 'layout'\n\t\tthis.dom = {\n\t\t\tholder: opts.dom.drawerDiv,\n\t\t\twrapper: opts.dom.wrapper,\n\t\t\tsandboxDiv: opts.dom.sandboxDiv\n\t\t}\n\t\tthis.state = opts.state\n\t\tthis.hasStatePreMain = true\n\t}\n\n\tasync validateIndexJson() {\n\t\tconst index = await this.getIndexJson()\n\t\tif (!index.elements) throw `Missing elements array`\n\t\tif (!index.elements.length) throw `No element objects provided`\n\t\tif (index.columnsLayout) {\n\t\t\tif (index.columnsLayout.length == 0) throw `Missing column objects`\n\t\t\tconst allGridAreaValues = index.columnsLayout.map(s => s.gridarea)\n\t\t\tif (allGridAreaValues.length != new Set(allGridAreaValues).size) throw `Duplicate values for .gridarea found`\n\t\t\tconst allSectionIdValues = []\n\t\t\tfor (const col of index.columnsLayout) {\n\t\t\t\tif (!col.gridarea) throw `Missing column .gridarea for column = ${col.name}`\n\t\t\t\tif (!col.sections || col.sections.length == 0) throw `Missing section objects for column = ${col.name}`\n\t\t\t\tfor (const section of col.sections) {\n\t\t\t\t\tif (!section.id)\n\t\t\t\t\t\tthrow `Missing section .id in ${section.name ? `section = ${section.name}` : `column = ${col.name} array`}`\n\t\t\t\t\tallSectionIdValues.push(section.id)\n\t\t\t\t}\n\t\t\t\tif (col.sections.length != new Set(col.sections).size) {\n\t\t\t\t\tthrow `Non-unique levels in line ${lineNum}: ${JSON.stringify(levelNames)}`\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (allSectionIdValues.length != new Set(allSectionIdValues).size) throw `Duplicate values for section.id found`\n\n\t\t\t// Required element attributes when columnsLayout specified\n\t\t\tfor (const element of index.elements) {\n\t\t\t\tif (!element.section) throw `.section is missing for ${element.type} = ${element.name}`\n\t\t\t\tif (!allSectionIdValues.some(d => d == element.section))\n\t\t\t\t\tthrow `section = ${element.section} for ${element.type} = ${element.name} is not a column section`\n\t\t\t}\n\t\t}\n\t\treturn index\n\t}\n\n\tasync getIndexJson() {\n\t\t// Proteinpaint specific index.\n\t\t// TODO: Later modifiy to accept user index.\n\t\tconst re = await dofetch3(this.app.cardsPath + '/index.json')\n\t\tif (re.error) {\n\t\t\tsayerror(this.dom.holder.append('div'), re.error)\n\t\t\treturn\n\t\t}\n\t\treturn re\n\t}\n\n\tvalidateElements() {\n\t\tconst features = JSON.parse(sessionStorage.getItem('optionalFeatures')) || {}\n\t\tthis.elements = this.index.elements.filter(e => !e.hidden && (!e.configFeature || features[e.configFeature]))\n\t}\n\n\tasync init() {\n\t\tthis.index = await this.validateIndexJson()\n\t\tthis.elementsRendered = false\n\t\tsetRenderers(this)\n\t\tthis.validateElements()\n\t\tthis.layout = this.index.columnsLayout ? this.index.columnsLayout : null\n\t\tthis.components = {\n\t\t\telements: []\n\t\t}\n\t}\n\n\tasync main() {\n\t\t// prevent elements from reloading each time\n\t\tif (this.elementsRendered == true) return\n\t\tthis.elementsRendered = true\n\t\tfor (const element of this.elements) {\n\t\t\tconst holder = select(this.layout ? `#${element.section} > .sjpp-element-list` : `.sjpp-element-list`)\n\t\t\tif (element.type == 'card' || element.type == 'nestedCard') {\n\t\t\t\tthis.components.elements.push(\n\t\t\t\t\tawait cardInit({\n\t\t\t\t\t\tapp: this.app,\n\t\t\t\t\t\tholder: holder\n\t\t\t\t\t\t\t.style('display', 'grid')\n\t\t\t\t\t\t\t.style('grid-template-columns', 'repeat(auto-fit, minmax(320px, 1fr))')\n\t\t\t\t\t\t\t.style('gap', '10px')\n\t\t\t\t\t\t\t.style('list-style', 'none')\n\t\t\t\t\t\t\t.style('margin', '15px 0px'),\n\t\t\t\t\t\telement,\n\t\t\t\t\t\tdom: this.opts.dom,\n\t\t\t\t\t\tstate: this.state,\n\t\t\t\t\t\tsandboxDiv: this.dom.sandboxDiv\n\t\t\t\t\t})\n\t\t\t\t)\n\t\t\t} else if (element.type == 'dsButton') {\n\t\t\t\tthis.components.elements.push(\n\t\t\t\t\tawait buttonInit({\n\t\t\t\t\t\tapp: this.app,\n\t\t\t\t\t\tholder,\n\t\t\t\t\t\telement,\n\t\t\t\t\t\tdom: this.opts.dom,\n\t\t\t\t\t\tstate: this.state,\n\t\t\t\t\t\tsandboxDiv: this.dom.sandboxDiv\n\t\t\t\t\t})\n\t\t\t\t)\n\t\t\t}\n\t\t}\n\t}\n}\n\nexport const layoutInit = getCompInit(AppDrawerLayoutComp)\n\nfunction setRenderers(self) {\n\tif (!self.index.columnsLayout) noDefinedLayout(self)\n\tif (self.index.columnsLayout) columnsLayout(self)\n}\n\nfunction noDefinedLayout(self) {\n\tconst flexLayout = self.dom.wrapper\n\t\t.append('div')\n\t\t.style('display', 'flex')\n\t\t.style('padding', '10px')\n\t\t.classed('sjpp-element-list', true)\n\treturn flexLayout\n}\n\nfunction columnsLayout(self) {\n\t// Allow user to create multiple columns in parent grid\n\tconst parentGrid = self.dom.wrapper\n\t\t.append('div')\n\t\t.style('display', 'grid')\n\t\t.style('grid-template-columns', 'repeat(auto-fit, minmax(425px, 1fr))')\n\t\t.style('gap', '10px')\n\t\t.style('padding', '10px')\n\t\t.style('text-align', 'left')\n\n\t//Allow user to create multiple parent columns in columnsLayout\n\tconst gridareas = []\n\tfor (const column of self.index.columnsLayout) gridareas.push(column.gridarea)\n\tparentGrid.style('grid-template-areas', `\"${gridareas.toString().replace(',', ' ')}\"`)\n\tfor (const col of self.index.columnsLayout) {\n\t\tconst newCol = parentGrid.append('div').style('grid-area', col.gridarea).classed('.sjpp-track-cols', true)\n\t\tfor (const section of col.sections) addSection(section, newCol)\n\t}\n\n\tfunction addSection(section, newCol) {\n\t\tconst newSection = newCol.append('div').attr('id', section.id)\n\t\tif (section.name)\n\t\t\tnewSection\n\t\t\t\t.append('h5')\n\t\t\t\t.classed('sjpp-appdrawer-cols', true)\n\t\t\t\t.style('color', rgb(defaultcolor).darker())\n\t\t\t\t.text(section.name)\n\t\tnewSection.append('div').classed('sjpp-element-list', true).style('padding', '10px')\n\n\t\treturn newSection\n\t}\n}\n", "import { getCompInit } from '#rx'\nimport { layoutInit } from './layout'\n\n/*\n.opts{}\n    .app{}\n\t.dom{}\n\t.state{}\n\nTODOs: \n- Replace drawerFullHeight with a different approach\n\t- Causes the drawer to only partially appear when the window zooms in\n*/\n\nclass MainHeadboxBtn {\n\tconstructor(opts) {\n\t\tthis.type = 'mainBtn'\n\t\tthis.opts = this.validateOpts(opts)\n\t\tthis.dom = opts.dom\n\t\tthis.state = opts.state\n\t\tthis.hasStatePreMain = true\n\t\tsetRenderers(this)\n\t}\n\n\tvalidateOpts(opts) {\n\t\treturn opts.app.opts\n\t}\n\n\tgetState(appState) {\n\t\treturn {\n\t\t\tappBtnActive: appState.appBtnActive\n\t\t}\n\t}\n\n\tasync init() {\n\t\tthis.btnRendered = false\n\t\tthis.drawerFullHeight = ''\n\t\ttry {\n\t\t\t//detect whether to show examples right away, which is when the url is barebone without any route paths or search parameters\n\t\t\tif (window.location.pathname == '/' && !window.location.search.length)\n\t\t\t\tawait this.app.dispatch({ type: 'is_apps_btn_active', value: true })\n\t\t\tthis.components = {\n\t\t\t\tlayout: []\n\t\t\t}\n\t\t} catch (e) {\n\t\t\tthrow e\n\t\t}\n\t}\n\n\tasync main(appState) {\n\t\tif (this.app.getState(appState).appBtnActive == true && this.btnRendered == false) {\n\t\t\tthis.dom.drawerDiv.style('background-color', '#f5f5f5') //Quick fix for drawerDiv initially appearing before layout init\n\t\t\t//Init layout only once when 'Apps' button is active for the first time\n\t\t\tthis.components.layout.push(\n\t\t\t\tawait layoutInit({\n\t\t\t\t\tapp: this.app,\n\t\t\t\t\tdom: this.dom,\n\t\t\t\t\tstate: this.state\n\t\t\t\t})\n\t\t\t)\n\t\t\t//Give the drawerDiv time to render before calculating height\n\t\t\tsetTimeout(() => {\n\t\t\t\tthis.drawerFullHeight = this.dom.drawerDiv.node().getBoundingClientRect().height + 5\n\t\t\t}, this.state.duration + 5)\n\t\t\tslideDrawer(this)\n\t\t\tthis.btnRendered = true\n\t\t}\n\t\tif (this.state.appBtnActive == false && this.btnRendered == true) slideDrawer(this)\n\t}\n}\n\nexport const mainBtnInit = getCompInit(MainHeadboxBtn)\n\nfunction setRenderers(self) {\n\tself.dom.btnWrapper\n\t\t.style('background-color', self.state.appBtnActive ? '#b2b2b2' : '#f2f2f2')\n\t\t.style('color', self.state.appBtnActive ? '#fff' : '#000')\n\t\t.on('click', async event => {\n\t\t\tevent.stopPropagation()\n\t\t\tawait self.app.dispatch({ type: 'is_apps_btn_active' })\n\t\t\tslideDrawer(self)\n\t\t\tif (self.state.appBtnActive) {\n\t\t\t\tsetTimeout(() => {\n\t\t\t\t\tself.drawerFullHeight = self.dom.drawerDiv.node().getBoundingClientRect().height + 5\n\t\t\t\t}, self.state.duration + 5)\n\t\t\t}\n\t\t})\n\n\tself.dom.btn\n\t\t.attr('class', 'sja_menuoption')\n\t\t.style('display', 'inline-block')\n\t\t.style('background-color', 'transparent')\n\t\t.style('color', self.state.appBtnActive ? '#fff' : '#000')\n\t\t.style('padding', self.opts.padw_sm)\n\t\t.style('margin', '0px 5px')\n\t\t.style('cursor', 'pointer')\n\t\t.text('Apps')\n\n\t// an empty spacer div, needed since the arrows are absolutely positioned\n\tself.dom.drawerHint\n\t\t.style('position', 'relative')\n\t\t.style('display', 'inline-block')\n\t\t.style('height', self.state.arrowSize.closed + 'px')\n\t\t.style('width', self.state.appBtnActive ? self.state.hintWidth.open : self.state.hintWidth.closed)\n\t\t.style('background-color', 'transparent')\n\t\t.style('text-align', 'center')\n\t\t.style('cursor', 'pointer')\n\n\tself.dom.drawerArrow\n\t\t.style('position', 'absolute')\n\t\t.style('font-size', self.state.arrowSize.closed + 'px')\n\t\t.style('right', self.state.hintPos.closed.rt + 'px')\n\t\t.style('bottom', self.state.hintPos.closed.btm + 'px')\n\t\t.style('background-color', 'transparent')\n\t\t.style('color', self.state.arrowColor.closed)\n\t\t.style('opacity', self.state.appBtnActive ? 0 : 1)\n\t\t.style('cursor', 'pointer')\n\t\t.html('&#9660;')\n\n\tself.dom.drawerArrowOpen\n\t\t.style('position', 'absolute')\n\t\t.style('font-size', self.state.arrowSize.open + 'px')\n\t\t.style('left', self.state.hintPos.open.left + 'px')\n\t\t.style('bottom', self.state.hintPos.open.btm + 'px')\n\t\t.style('transform', 'rotate(180deg)')\n\t\t.style('background-color', 'transparent')\n\t\t.style('color', self.state.arrowColor.open)\n\t\t.style('opacity', self.state.appBtnActive ? 1 : 0)\n\t\t.style('cursor', 'pointer')\n\t\t.style('pointer-events', self.state.appBtnActive ? 'auto' : 'none')\n\t\t.html('&#9660;')\n\n\tself.drawerFullHeight = self.dom.drawerRow.node().getBoundingClientRect().height + 5\n}\n\nexport async function slideDrawer(self) {\n\tself.dom.btnWrapper\n\t\t.transition()\n\t\t.duration(self.opts.state.duration)\n\t\t.style('background-color', self.state.appBtnActive ? '#b2b2b2' : '#f2f2f2')\n\t\t.style('color', self.state.appBtnActive ? '#fff' : '#000')\n\n\tself.dom.btn\n\t\t.transition()\n\t\t.duration(self.opts.state.duration)\n\t\t.style('color', self.state.appBtnActive ? '#fff' : '#000')\n\n\tself.dom.drawerDiv\n\t\t.style('display', 'inline-block')\n\t\t.transition()\n\t\t.duration(self.opts.state.duration)\n\t\t.style('top', self.state.appBtnActive ? '0px' : '-' + self.drawerFullHeight + 'px')\n\n\tself.dom.drawerRow\n\t\t.transition()\n\t\t.duration(self.opts.state.duration)\n\t\t.style('height', self.state.appBtnActive ? self.drawerFullHeight + 'px' : '0px')\n\n\tself.dom.drawerHint\n\t\t.transition()\n\t\t.duration(self.opts.state.duration)\n\t\t.style('width', self.state.appBtnActive ? self.opts.state.hintWidth.open : self.opts.state.hintWidth.closed)\n\n\tself.dom.drawerArrow\n\t\t.transition()\n\t\t.duration(self.opts.state.duration)\n\t\t.style('opacity', self.state.appBtnActive ? 0 : 1)\n\n\tself.dom.drawerArrowOpen\n\t\t.style('pointer-events', self.state.appBtnActive ? 'auto' : 'none')\n\t\t.transition()\n\t\t.duration(self.opts.state.duration)\n\t\t.style('opacity', self.state.appBtnActive ? 1 : 0)\n}\n", "import { getStoreInit } from '#rx'\n\n/*\n.opts{}\n\n*/\n\nclass AppDrawerStore {\n\tconstructor(opts) {\n\t\tthis.type = 'store'\n\t\tthis.defaultState = {\n\t\t\t// for apps drawer animation\n\t\t\tduration: 500,\n\t\t\thintPos: {\n\t\t\t\topen: { btm: -42, left: 13 },\n\t\t\t\tclosed: { btm: 3, rt: 5 }\n\t\t\t},\n\t\t\thintWidth: { open: '0px', closed: '18px' },\n\t\t\tarrowSize: { open: 42, closed: 20 },\n\t\t\tarrowColor: { open: 'rgb(242,242,242)', closed: 'rgb(85,85,85)' },\n\t\t\tappBtnActive: false\n\t\t}\n\t}\n\n\tasync init() {}\n}\n\nexport const appDrawerStoreInit = getStoreInit(AppDrawerStore)\n\nAppDrawerStore.prototype.actions = {\n\tis_apps_btn_active(action) {\n\t\tthis.state.appBtnActive = 'value' in action ? action.value : !this.state.appBtnActive\n\t}\n}\n", "import { getAppInit } from '#rx'\nimport { mainBtnInit } from './mainBtn'\nimport { appDrawerStoreInit } from './store'\n\n/*\n.opts{}\n    .holder\n    .genomes{}\n        - client-side genome object\n\t.drawerRow\n\t.sandboxDiv\n\t.genome_browser_btn\n\t.debugmode\n\t.headbox\n\t.padw_sm\n\nTODOs: \n\nQuestions: \n*/\n\nclass AppDrawerApp {\n\tconstructor(opts) {\n\t\tthis.type = 'app'\n\n\t\tconst drawerDiv = opts.drawerRow\n\t\t\t.append('div')\n\t\t\t.style('position', 'relative')\n\t\t\t.style('margin', '0 20px')\n\t\t\t.style('padding', `0 ${opts.padw_sm}`)\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('overflow', 'hidden')\n\t\t\t.style('border-radius', '0px 0px 5px 5px')\n\t\t\t.style('width', '93vw')\n\t\t\t.classed('sjpp-drawer-div', true)\n\n\t\tconst btnWrapper = opts.headbox\n\t\t\t.append('div')\n\t\t\t.style('position', 'relative')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('margin-left', '5px')\n\t\t\t.style('margin-right', '5px')\n\t\t\t.style('border-radius', '5px')\n\t\t\t.classed('sjpp-apps-btn-wrapper', true)\n\n\t\tthis.dom = {\n\t\t\tdrawerRow: opts.drawerRow,\n\t\t\tdrawerDiv,\n\t\t\tsandboxDiv: opts.sandboxDiv,\n\t\t\tbtnWrapper,\n\t\t\tbtn: btnWrapper.append('div'),\n\t\t\tdrawerHint: btnWrapper.append('div'),\n\t\t\tdrawerArrow: btnWrapper.append('div'),\n\t\t\tdrawerArrowOpen: btnWrapper.append('div'),\n\t\t\twrapper: drawerDiv.append('div')\n\t\t}\n\t}\n\n\tpreApiFreeze(api) {\n\t\tapi.cardsPath = this.opts.cardsPath\n\t}\n\n\tasync init() {\n\t\ttry {\n\t\t\tthis.store = await appDrawerStoreInit({ app: this.api, state: this.opts.state })\n\t\t\tthis.state = await this.store.copyState()\n\t\t\tthis.components = {\n\t\t\t\tmainBtn: await mainBtnInit({\n\t\t\t\t\tapp: this.api,\n\t\t\t\t\tdom: this.dom,\n\t\t\t\t\tstate: this.state,\n\t\t\t\t\tindexJson: this.indexJson\n\t\t\t\t})\n\t\t\t}\n\t\t\tawait this.api.dispatch()\n\t\t} catch (e) {\n\t\t\tthrow e\n\t\t}\n\t}\n\n\tmain() {}\n}\n\nexport const appDrawerInit = getAppInit(AppDrawerApp)\n", "import { first_genetrack_tolist } from '#common/1stGenetk'\nimport { InputSearch, Menu, newSandboxDiv } from '#dom'\nimport { searchItems } from './omniSearch.js'\nimport { appDrawerInit } from '../../appdrawer/app.js'\nimport { rgb as d3rgb } from 'd3-color'\nimport { defaultcolor } from '#shared/common.js'\nimport { dofetch3 } from '#common/dofetch'\nimport { ClientCopyGenome } from 'types/global.ts'\n\ntype Citation = {\n\tid: number\n\ttitle: string\n\tappHeaderTitle: string\n\tyear: number\n\tjournal: string\n\tpmid: number\n\tpmidURL: string\n\tdoi: string\n}\n\ntype AppHeaderOpts = {\n\t/** menu created in app.js */\n\theadtip: Menu\n\t/** runpp app */\n\tapp: any\n\t/** server returned data */\n\tdata: any\n\t/** token */\n\tjwt: any\n}\n\nexport class AppHeader {\n\theadtip: Menu\n\tapp: any\n\tdata: any\n\tjwt: any\n\t/** List of publications defined in the app drawer\n\t * Appears in button in the header and in search results\n\t */\n\tpublications: Citation[]\n\t/** Used in both the Help button and omni search\n\t * .onlySearch is used to filter out items that should not appear in the Help button\n\t */\n\tstatic help = [\n\t\t{\n\t\t\tlabel: 'Embed in your website',\n\t\t\tlink: 'https://github.com/stjude/proteinpaint/wiki/Embedding'\n\t\t},\n\t\t{\n\t\t\tlabel: 'URL parameters',\n\t\t\tlink: 'https://github.com/stjude/proteinpaint/wiki/URL-parameters'\n\t\t},\n\t\t{\n\t\t\tlabel: 'All tutorials',\n\t\t\tlink: 'https://github.com/stjude/proteinpaint/wiki/'\n\t\t},\n\t\t{\n\t\t\tlabel: 'User community',\n\t\t\tlink: 'https://groups.google.com/g/proteinpaint'\n\t\t},\n\t\t{\n\t\t\tlabel: 'License ProteinPaint',\n\t\t\tlink: 'https://www.stjude.org/research/why-st-jude/shared-resources/technology-licensing/technologies/proteinpaint-web-application-for-visualizing-genomic-data-sj-15-0021.html',\n\t\t\tonlySearch: true\n\t\t},\n\t\t{\n\t\t\tlabel: 'Our Team',\n\t\t\tlink: 'https://proteinpaint.stjude.org/team/',\n\t\t\tonlySearch: true\n\t\t}\n\t]\n\n\tconstructor(opts: AppHeaderOpts) {\n\t\tthis.headtip = opts.headtip\n\t\tthis.app = opts.app\n\t\tthis.data = opts.data\n\t\tthis.jwt = opts.jwt\n\t\tthis.publications = []\n\t}\n\n\tasync createPublicationsList() {\n\t\tconst re = await dofetch3(this.app.cardsPath + '/citations.json')\n\t\tif (re.error) console.error(`Problem retrieving ../cards/citations.json`)\n\t\t//Sort in reverse chronological order for the publications button\n\t\tthis.publications = re?.publications?.length\n\t\t\t? re.publications.filter((d: Citation) => d.appHeaderTitle).sort((a: Citation, b: Citation) => b.year - a.year)\n\t\t\t: []\n\t}\n\n\tasync makeheader() {\n\t\tawait this.createPublicationsList()\n\n\t\tconst color = d3rgb(defaultcolor)\n\t\tconst padw_lg = '13px'\n\t\tconst padw_input = '5px 10px'\n\t\tconst padw_sm = '7px 10px'\n\t\tconst doc_width = document.documentElement.clientWidth\n\t\t// head\n\t\tconst row = this.app.holder\n\t\t\t.append('div')\n\t\t\t.style('white-space', 'nowrap')\n\t\t\t.style(\n\t\t\t\t'border-bottom',\n\t\t\t\tdoc_width > 1600 ? 'solid 1px rgba(' + color.r + ',' + color.g + ',' + color.b + ',.3)' : ''\n\t\t\t)\n\n\t\tconst headbox = row\n\t\t\t.append('div')\n\t\t\t.style('margin', '10px')\n\t\t\t.style('padding', '8px')\n\t\t\t.style('padding-bottom', '12px')\n\t\t\t.style('display', doc_width < 1600 ? 'block' : 'inline-block')\n\t\t\t.style(\n\t\t\t\t'border-bottom',\n\t\t\t\tdoc_width < 1600 ? 'solid 1px rgba(' + color.r + ',' + color.g + ',' + color.b + ',.3)' : ''\n\t\t\t)\n\n\t\t// .style('border-radius', '5px')\n\t\t// .style('background-color', 'rgba(' + color.r + ',' + color.g + ',' + color.b + ',.1)')\n\t\tconst headinfo = row\n\t\t\t.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('padding', padw_sm)\n\t\t\t.style('padding-left', '25px')\n\t\t\t.style('font-size', '.8em')\n\t\t\t.style('color', d3rgb(defaultcolor).darker())\n\n\t\t{\n\t\t\t// a row for server stats\n\t\t\tconst row = headinfo.append('div').style('padding-left', '15px')\n\t\t\t// link to the published ppfull container version, instead of github release tarball which we do not advertise;\n\t\t\t// github's pkgs/container link has a timestamp before the tag, which cannot be computed here (but may be able to query later?)\n\t\t\tconst link = `https://github.com/stjude/proteinpaint/pkgs/container/ppfull` // url to list of published container versions\n\t\t\tconst version = this.data.pkgver\n\t\t\t\t? `Version: <a href=\"${link}\" target=\"${this.data.pkgver}\">${this.data.pkgver}</a>`\n\t\t\t\t: `Code date: ${this.data.codedate}` // default to using code date as before if pkgver is not available\n\t\t\trow\n\t\t\t\t.attr('id', 'sjpp-serverstat')\n\t\t\t\t.append('span')\n\t\t\t\t.html(`${version}, server launched: ${this.data.launchdate || '??'}.`)\n\t\t\tif (this.data.hasblat) {\n\t\t\t\trow\n\t\t\t\t\t.append('a')\n\t\t\t\t\t.style('margin-left', '10px')\n\t\t\t\t\t.text('Running BLAT')\n\t\t\t\t\t.on('click', async event => {\n\t\t\t\t\t\tthis.headtip.clear().showunder(event.target)\n\t\t\t\t\t\tconst div = this.headtip.d.append('div').style('margin', '10px')\n\t\t\t\t\t\tconst wait = div.append('div').text('Loading...')\n\t\t\t\t\t\ttry {\n\t\t\t\t\t\t\tconst data = await dofetch3('blat?serverstat=1')\n\t\t\t\t\t\t\tif (data.error) throw data.error\n\t\t\t\t\t\t\tif (!data.lst) throw 'invalid response'\n\t\t\t\t\t\t\twait.remove()\n\t\t\t\t\t\t\tfor (const i of data.lst) {\n\t\t\t\t\t\t\t\tdiv.append('div').text(i)\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t} catch (e: any) {\n\t\t\t\t\t\t\twait.text(e.message || e)\n\t\t\t\t\t\t\tif (e.stack) console.error(e.stack)\n\t\t\t\t\t\t}\n\t\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\tif (this.data.headermessage) {\n\t\t\theadinfo.append('div').html(this.data.headermessage)\n\t\t}\n\n\t\t// 1\n\t\theadbox\n\t\t\t.append('div')\n\t\t\t.text('ProteinPaint')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('padding', padw_lg)\n\t\t\t.style('color', defaultcolor)\n\t\t\t.style('font-size', '1.3em')\n\t\t\t.style('font-weight', 'bold')\n\n\t\t// 2, search box\n\t\tconst omniSearch = new InputSearch({\n\t\t\tholder: headbox,\n\t\t\ttip: this.headtip,\n\t\t\tstyle: {\n\t\t\t\tpadding: padw_sm,\n\t\t\t\tborder: `'solid 1px ${defaultcolor}`\n\t\t\t},\n\t\t\tsize: 32,\n\t\t\tplaceholder: 'Gene, position, SNP, app, or dataset',\n\t\t\ttitle: 'Search by gene, SNP, position, app, or dataset',\n\t\t\tsearchItems: async () => {\n\t\t\t\treturn await searchItems(this.app, this.headtip, AppHeader.help, this.publications, this.jwt)\n\t\t\t}\n\t\t})\n\n\t\tomniSearch.initUI()\n\n\t\tconst genome_select_div = headbox.append('div').attr('class', 'sjpp-genome-select-div').style('padding', padw_sm)\n\n\t\tconst get_placeholder = () => {\n\t\t\tconst currG = this.app.genomes[this.app.selectgenome.property('value')]\n\t\t\t/** Defaults */\n\t\t\tconst opts2Show = ['Gene', 'position', 'app']\n\t\t\t/** Show all the genomic options together */\n\t\t\tif (currG.hasSNP) opts2Show.splice(2, 0, 'SNP')\n\t\t\tif (Object.keys(currG.datasets).length) opts2Show.push('dataset')\n\t\t\tconst str = opts2Show.join(', ').replace(/,(?=[^,]*$)/, ', or')\n\t\t\treturn str\n\t\t}\n\n\t\tthis.app.selectgenome = genome_select_div\n\t\t\t.append('select')\n\t\t\t.attr('aria-label', 'Select a genome')\n\t\t\t.attr('class', 'sjpp-genome-select')\n\t\t\t.style('padding', padw_input)\n\t\t\t.style('border', 'solid 1px ' + defaultcolor)\n\t\t\t.on('change', () => {\n\t\t\t\tthis.update_genome_browser_btn(this.app)\n\t\t\t\tomniSearch.updatePlaceholder(get_placeholder())\n\t\t\t})\n\n\t\tconst filterGenomes = Object.values(this.app.genomes).filter((g: any) => !g.hideOnClient) as ClientCopyGenome[]\n\t\tfor (const n of filterGenomes) {\n\t\t\tthis.app.selectgenome.append('option').attr('n', n.name).text(`${n.species} ${n.name}`).property('value', n.name)\n\t\t}\n\t\tthis.app.genome_browser_btn = this.make_genome_browser_btn(this.app, headbox, this.jwt)\n\n\t\tthis.app.drawer = await appDrawerInit({\n\t\t\tholder: this.app.holder,\n\t\t\tgenomes: this.app.genomes,\n\t\t\tdrawerRow: this.app.holder\n\t\t\t\t.append('div')\n\t\t\t\t.style('position', 'relative')\n\t\t\t\t.style('overflow-x', 'visible')\n\t\t\t\t.style('overflow-y', 'hidden')\n\t\t\t\t.classed('sjpp-drawer-row', true),\n\t\t\tsandboxDiv: this.app.holder.append('div').style('margin-top', '15px').classed('sjpp-drawer-sandbox', true),\n\t\t\tgenome_browser_btn: this.app.genome_browser_btn,\n\t\t\tdebugmode: this.app.debugmode,\n\t\t\theadbox,\n\t\t\tpadw_sm,\n\t\t\tcardsPath: this.app.cardsPath\n\t\t})\n\n\t\t//Help button\n\t\theadbox\n\t\t\t.append('span')\n\t\t\t.classed('sja_menuoption', true)\n\t\t\t.attr('id', 'sjpp-header-help-btn')\n\t\t\t.style('padding', padw_sm)\n\t\t\t.text('Help')\n\t\t\t.on('click', async event => {\n\t\t\t\tconst p = event.target.getBoundingClientRect()\n\t\t\t\tconst div = this.headtip.clear().show(p.left - 0, p.top + p.height + 5)\n\n\t\t\t\tawait div.d\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.style('padding', '5px 20px')\n\t\t\t\t\t.selectAll('p')\n\t\t\t\t\t.data(AppHeader.help.filter(d => !d.onlySearch))\n\t\t\t\t\t.enter()\n\t\t\t\t\t.append('p')\n\t\t\t\t\t.html(d => `<a href=${d.link} target=_blank>${d.label}</a>`)\n\t\t\t})\n\n\t\t//Publications button\n\t\t//Citations not available on CI server\n\t\tif (this.publications.length > 0) {\n\t\t\theadbox\n\t\t\t\t.append('span')\n\t\t\t\t.classed('sja_menuoption', true)\n\t\t\t\t.attr('id', 'sjpp-header-publications-btn')\n\t\t\t\t.style('padding', padw_sm)\n\t\t\t\t.style('margin', '0px 5px')\n\t\t\t\t.text('Publications')\n\t\t\t\t.on('click', async event => {\n\t\t\t\t\tconst p = event.target.getBoundingClientRect()\n\t\t\t\t\tconst div = this.headtip.clear().show(p.left - 150, p.top + p.height + 5)\n\n\t\t\t\t\tawait div.d\n\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t.style('padding', '5px 20px')\n\t\t\t\t\t\t.selectAll('p')\n\t\t\t\t\t\t.data(this.publications)\n\t\t\t\t\t\t.enter()\n\t\t\t\t\t\t.append('p')\n\t\t\t\t\t\t.html((d: any) => `<a href=${d.doi} target=_blank>${d.appHeaderTitle}, ${d.journal}, ${d.year}</a>`)\n\t\t\t\t})\n\t\t}\n\t}\n\n\tmake_genome_browser_btn(app, headbox, jwt) {\n\t\tif (app.selectgenome.node().options.length === 0) {\n\t\t\tconsole.error(`No selected selectgenome options.`)\n\t\t\treturn\n\t\t}\n\n\t\tconst padw = '8px'\n\t\tconst genome_btn_div = headbox.append('span')\n\t\tconst genomename = app.selectgenome.node().options[app.selectgenome.property('selectedIndex')].value\n\n\t\tconst g_browser_btn = genome_btn_div\n\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t.attr('id', 'genome_btn')\n\t\t\t.style('padding', padw)\n\t\t\t.datum(genomename)\n\t\t\t.text(genomename + ' genome browser')\n\t\t\t.on('click', () => {\n\t\t\t\t//Grab the current genome selected\n\t\t\t\tconst genomeSelected = app.selectgenome.node().value\n\t\t\t\tconst g = app.genomes[genomeSelected]\n\t\t\t\tif (!g) {\n\t\t\t\t\talert('Invalid genome name: ' + genomeSelected)\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tconst sandbox_div = newSandboxDiv(app.drawer.opts.sandboxDiv)\n\t\t\t\tsandbox_div.header.text(genomeSelected + ' genome browser')\n\n\t\t\t\tconst par = {\n\t\t\t\t\thostURL: app.hostURL,\n\t\t\t\t\tjwt,\n\t\t\t\t\tholder: sandbox_div.body,\n\t\t\t\t\tgenome: g,\n\t\t\t\t\tchr: g.defaultcoord.chr,\n\t\t\t\t\tstart: g.defaultcoord.start,\n\t\t\t\t\tstop: g.defaultcoord.stop,\n\t\t\t\t\tnobox: true,\n\t\t\t\t\ttklst: [],\n\t\t\t\t\tdebugmode: app.debugmode\n\t\t\t\t}\n\t\t\t\tfirst_genetrack_tolist(g, par.tklst)\n\n\t\t\t\timport('../block.js').then(b => new b.Block(par))\n\t\t\t\tapp.drawer.dispatch({ type: 'is_apps_btn_active', value: false })\n\t\t\t})\n\t\treturn g_browser_btn\n\t}\n\n\tupdate_genome_browser_btn(app) {\n\t\tapp.genome_browser_btn.text(app.selectgenome.node().value + ' genome browser')\n\t\tapp.genome_browser_btn.datum(app.selectgenome.node().value)\n\t}\n}\n"],
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+  "sourcesContent": ["import { dofetch3 } from '#common/dofetch'\nimport { openSandbox } from '../../appdrawer/adSandbox'\nimport { throwMsgWithFilePathAndFnName } from '../../dom/sayerror.ts'\nimport { string2pos } from '../coord'\nimport { newSandboxDiv } from '../../dom/sandbox.ts'\nimport * as parseurl from '../app.parseurl'\nimport urlmap from '#common/urlmap'\nimport { first_genetrack_tolist } from '#common/1stGenetk'\nimport blockinit from '../block.init'\nimport { select as d3select } from 'd3-selection'\n\n/*\n----EXPORTED----\nsearchItems()\nfindgenelst()\nfindgene2paint()\n\n----Internal----\nfindAppDrawerElements()\ngetExampleNames()\ngetFilteredElements()\n*/\n\nexport async function searchItems(app, tip, help, publications, jwt) {\n\tconst userInput = d3select('input').property('value').trim()\n\tconst data = [\n\t\t{\n\t\t\ttitle: 'Genes',\n\t\t\tdefault: true,\n\t\t\titems: await findgenelst(userInput, app.selectgenome.property('value'), jwt),\n\t\t\tcolor: '#F2F2F2',\n\t\t\tcallback: d => {\n\t\t\t\tapp.drawer.dispatch({ type: 'is_apps_btn_active', value: false })\n\t\t\t\ttip.hide()\n\t\t\t\tfindgene2paint(d, app, app.selectgenome.property('value'), jwt)\n\t\t\t}\n\t\t}\n\t]\n\tawait findAppDrawerElements(app, userInput, data, tip)\n\t//Keep 'Help' section second last\n\tdata.push({\n\t\ttitle: 'Help',\n\t\tdefault: false,\n\t\titems: help.filter(d => d.label.toLowerCase().includes(userInput.toLowerCase())),\n\t\tcolor: '#faebd9',\n\t\tcallback: d => {\n\t\t\twindow.open(d.link, d.label)\n\t\t}\n\t})\n\tdata.push({\n\t\ttitle: 'Publications',\n\t\tdefault: false,\n\t\titems: publications.filter(\n\t\t\td =>\n\t\t\t\td.title.toLowerCase().includes(userInput.toLowerCase()) ||\n\t\t\t\td.appHeaderTitle.toLowerCase().includes(userInput.toLowerCase())\n\t\t),\n\t\tcolor: '#E6E6FA',\n\t\tcallback: d => {\n\t\t\twindow.open(d.doi, d.title)\n\t\t}\n\t})\n\treturn data\n}\n\nasync function findAppDrawerElements(app, input, data, tip) {\n\tconst re = await dofetch3(app.cardsPath + '/index.json')\n\tif (re.error) throwMsgWithFilePathAndFnName(`Problem retrieving ../cards/index.json`)\n\tconst userInput = input.toLowerCase().trim()\n\tconst elements = [...re.elements]\n\tlet filteredElements\n\tif (userInput.length > 2) {\n\t\t/** Adding the examples to the search terms is expensive\n\t\t * Limit when all card files are loaded based on user input\n\t\t * Maybe timeout instead? or combination of the two?\n\t\t */\n\t\tawait getExampleNames(elements, app)\n\t\tfilteredElements = getFilteredElements(elements, userInput)\n\t} else {\n\t\tfilteredElements = getFilteredElements(elements, userInput)\n\t}\n\n\tconst opts = {\n\t\tapp: app.drawer.opts,\n\t\tsandboxDiv: app.drawer.opts.sandboxDiv,\n\t\tgenomes: app.genomes,\n\t\tfromApp: true\n\t}\n\n\tdata.push(\n\t\t{\n\t\t\ttitle: 'Tracks and Apps',\n\t\t\titems: filteredElements.filter(c => c.type == 'card'),\n\t\t\tcolor: '#e1edf7',\n\t\t\tcallback: element => {\n\t\t\t\tapp.drawer.dispatch({ type: 'is_apps_btn_active', value: false })\n\t\t\t\ttip.hide()\n\t\t\t\topenSandbox(element, opts)\n\t\t\t}\n\t\t},\n\t\t{\n\t\t\ttitle: 'Datasets',\n\t\t\titems: filteredElements.filter(c => c.type == 'dsButton'),\n\t\t\tcolor: '#e5f5e4',\n\t\t\tcallback: element => {\n\t\t\t\tapp.drawer.dispatch({ type: 'is_apps_btn_active', value: false })\n\t\t\t\ttip.hide()\n\t\t\t\topenSandbox(element, opts)\n\t\t\t}\n\t\t}\n\t)\n\treturn data\n}\n\nasync function getExampleNames(elements, app) {\n\tconst promises = elements.map(async elem => {\n\t\tif (elem.hidden || elem.type != 'card' || !elem.sandboxJson) return elem\n\t\tconst exs = await dofetch3(app.cardsPath + `/${elem.sandboxJson}.json`)\n\t\tif (exs?.ppcalls.length > 0) {\n\t\t\tfor (const c of exs.ppcalls) {\n\t\t\t\tif (c.isUI) return\n\t\t\t\tif (c?.label) elem.searchterms.push(c.label)\n\t\t\t}\n\t\t}\n\t})\n\n\tawait Promise.all(promises)\n}\n\nfunction getFilteredElements(elements, userInput) {\n\treturn elements\n\t\t.filter(elem => {\n\t\t\tif (elem.hidden) return false\n\t\t\tlet searchTermFound = (elem.searchterms || []).reduce((searchTermFound, searchTerm) => {\n\t\t\t\tif (searchTermFound) return true\n\t\t\t\treturn searchTerm.toLowerCase().includes(userInput)\n\t\t\t}, false)\n\t\t\treturn searchTermFound || elem.name.toLowerCase().includes(userInput)\n\t\t})\n\t\t.sort((a, b) => a.name.localeCompare(b.name))\n}\n\nexport async function findgenelst(str, genome, jwt) {\n\t//TODO - including something here about if user input includes a special character to return rather than comment out catch\n\tif (str.length == 0) return\n\ttry {\n\t\tconst data = await dofetch3('/genelookup', {\n\t\t\tbody: {\n\t\t\t\tinput: str,\n\t\t\t\tgenome,\n\t\t\t\tjwt\n\t\t\t}\n\t\t})\n\n\t\tif (data.error) throw data.error\n\t\tif (!data.hits) throw '.hits[] missing'\n\t\treturn data.hits\n\t} catch (err) {\n\t\t// err is likely \"invalid character in gene name\". ignore and continue\n\t\t// if (err.stack) console.log(err.stack)\n\t\t// throw err\n\t}\n}\n\nexport async function findgene2paint(str, app, genomename, jwt) {\n\tconst g = app.genomes[genomename]\n\tif (!g) {\n\t\tconsole.error('unknown genome ' + genomename)\n\t\treturn\n\t}\n\tconst sandbox_div = newSandboxDiv(app.drawer.opts.sandboxDiv)\n\tsandbox_div.header.html(\n\t\t'<div style=\"display:inline-block;\">' +\n\t\t\tstr +\n\t\t\t'</div><div class=\"sjpp-output-sandbox-title\">' +\n\t\t\tgenomename +\n\t\t\t'</div>'\n\t)\n\t// may yield tklst from url parameters\n\tconst urlp = urlmap()\n\tconst tklst = await parseurl.get_tklst(urlp, g)\n\n\tconst pos = string2pos(str, g)\n\tif (pos) {\n\t\t// input is coordinate, launch block\n\t\tconst par = {\n\t\t\thostURL: app.hostURL,\n\t\t\tjwt,\n\t\t\tholder: sandbox_div.body,\n\t\t\tgenome: g,\n\t\t\tnobox: true,\n\t\t\tchr: pos.chr,\n\t\t\tstart: pos.start,\n\t\t\tstop: pos.stop,\n\t\t\tdogtag: genomename,\n\t\t\ttklst,\n\t\t\tdebugmode: app.debugmode\n\t\t}\n\t\tfirst_genetrack_tolist(g, par.tklst)\n\n\t\timport('../block.js')\n\t\t\t.then(b => new b.Block(par))\n\t\t\t.catch(err => {\n\t\t\t\tapp.error0(err)\n\t\t\t})\n\t\treturn\n\t}\n\n\t// input string is not coordinate, find gene match\n\tconst par = {\n\t\thostURL: app.hostURL,\n\t\tjwt,\n\t\tquery: str,\n\t\tgenome: g,\n\t\tholder: sandbox_div.body,\n\t\tvariantPageCall_snv: app.variantPageCall_snv,\n\t\tsamplecart: app.samplecart,\n\t\ttklst,\n\t\tdebugmode: app.debugmode\n\t}\n\n\t// add svcnv tk from url param\n\tconst tmp = sessionStorage.getItem('urlp_mds')\n\tif (tmp) {\n\t\tconst l = tmp.split(',')\n\t\tif (l.length == 2) {\n\t\t\tpar.datasetqueries = [{ dataset: l[0], querykey: l[1] }]\n\t\t}\n\t}\n\n\tawait blockinit(par)\n}\n", "import { getCompInit } from '#rx'\nimport { rgb } from 'd3-color'\nimport { openSandbox } from './adSandbox'\nimport { slideDrawer } from './mainBtn'\n\n/*\n.opts{\n\t.app{\n\t\t.holder\n\t\t.element{}\n\t\t.sandboxDiv\n\t}\n}\n\nTODOs: \n\n- responsiveness of image on window resize \n\t- expand image size on resize\n\t- non square, take better use of space\n- Need fn in utils to decide black or white text based on background color contrast\n- Unify card and nestedCard layout. Only call one layout function for both\n\t- optional non image card layout\n\t- Make ribbons appear on nested cards\n- element.section only required if columnsLayout provided\n\n*/\n\nclass AppDrawerCard {\n\t// handles types 'card' and 'nestedCard'\n\tconstructor(opts) {\n\t\tthis.type = 'card'\n\t\tthis.opts = this.validateOpts(opts)\n\t\tthis.holder = opts.holder\n\t\tthis.dom = opts.dom\n\t\tthis.sandboxDiv = opts.sandboxDiv\n\t\tsetRenderers(this)\n\t}\n\n\tvalidateOpts(opts) {\n\t\tif (!opts.element.name) throw `Card .name is missing`\n\t\tif (opts.element.type == 'card') {\n\t\t\tif (!opts.element.sandboxJson && !opts.element.sandboxHtml)\n\t\t\t\tthrow `Either .sandboxJson or .sandboxHtml is missing for card=${opts.element.name}`\n\t\t}\n\t\tif (opts.element.type == 'nestedCard') {\n\t\t\tif (!opts.element.children || opts.element.children.length == 0)\n\t\t\t\tthrow `Missing .children for nested card = ${opts.element.name}`\n\t\t}\n\t\tif (opts.element.ribbon) {\n\t\t\tif (!opts.element.ribbon.text) throw `Missing ribbon .text for ${opts.element.type} = ${opts.element.name}`\n\n\t\t\t//ProteinPaint app drawer specific validation\n\t\t\tif (\n\t\t\t\t(opts.element.ribbon.text.toUpperCase() == 'NEW' || opts.element.ribbon.text.toUpperCase() == 'UPDATED') &&\n\t\t\t\t!opts.element.ribbon.expireDate\n\t\t\t)\n\t\t\t\tthrow `${opts.element.type} = ${\n\t\t\t\t\topts.element.name\n\t\t\t\t} ribbon is ${opts.element.ribbon.text.toUpperCase()} but .expireDate is missing. Please provide`\n\n\t\t\tif (opts.element.ribbon.expireDate) {\n\t\t\t\tif (opts.element.ribbon.expireDate >= 0) {\n\t\t\t\t\tthrow `Flag for ${opts.element.type} = ${opts.element.name} is not a valid date`\n\t\t\t\t} //TODO add validation for format?\n\t\t\t}\n\t\t}\n\t\treturn opts\n\t}\n\n\tmain() {}\n}\n\nexport const cardInit = getCompInit(AppDrawerCard)\n\nfunction setRenderers(self) {\n\tconst card = self.holder.append('li')\n\tif (self.opts.element.type == 'card') {\n\t\tcard.classed('sjpp-track', true).html(\n\t\t\t`<div class=\"sjpp-track-h\"><span style=\"font-size:14.5px;font-weight:500;\">${self.opts.element.name}</span></div>\n\t\t\t\t${\n\t\t\t\t\tself.opts.element.description\n\t\t\t\t\t\t? `<span class=\"sjpp-track-blurb\" style=\"cursor:default\">${self.opts.element.description}</span></div>`\n\t\t\t\t\t\t: ' '\n\t\t\t\t}\n\t\t\t\t<span class=\"sjpp-track-image\"><img src=\"${self.opts.element.image}\" alt=\"${\n\t\t\t\tself.opts.element.description\n\t\t\t}\"></img></span>\n\t\t\t\t</div>`\n\t\t)\n\t} else if (self.opts.element.type == 'nestedCard') {\n\t\tcard.classed('sjpp-app-drawer-card', true).html(\n\t\t\t`<p style=\"margin-left: 12px; font-size:14.5px;font-weight:500; display: block;\">${self.opts.element.name}</p>\n\t\t\t<p style=\"display: block; font-size: 13px; font-weight: 300; margin-left: 20px; justify-content: center; font-style:oblique; color: #403f3f;\">${self.opts.element.description}</p>`\n\t\t)\n\t}\n\n\tself.makeRibbon = function(ribbon) {\n\t\t//only relevant for 'card', not 'nestedCard'\n\t\tconst ribbonDiv = card\n\t\t\t.append('div')\n\t\t\t.classed('sjpp-app-drawer-card-ribbon', true)\n\t\t\t.style('align-items', 'center')\n\t\t\t.style('justify-content', 'center')\n\n\t\t//*********TODO: move from diagonal to straight on right side */\n\t\tconst text = ribbon.text.toUpperCase()\n\t\t//Enforce color palette for proteinpaint homepage ribbons\n\t\tconst color =\n\t\t\ttext == 'BETA'\n\t\t\t\t? '#418cb5'\n\t\t\t\t: text == 'NEW'\n\t\t\t\t? '#1ba176'\n\t\t\t\t: text == 'UPDATED'\n\t\t\t\t? 'orange'\n\t\t\t\t: ribbon.color\n\t\t\t\t? ribbon.color\n\t\t\t\t: 'red'\n\n\t\tribbonDiv\n\t\t\t.append('span')\n\t\t\t.text(text)\n\t\t\t.style('color', 'white')\n\t\t\t.style('background-color', rgb(color).darker())\n\t\t\t.style('height', 'auto')\n\t\t\t.style('width', '100%')\n\t\t\t.style('top', '15%')\n\t\t\t.style('left', '-30%')\n\t\t\t.style('font-size', '11.5px')\n\t\t\t.style('text-transform', 'uppercase')\n\t\t\t.style('text-align', 'center')\n\t}\n\n\tif (self.opts.element.ribbon) {\n\t\tconst today = new Date()\n\t\tconst ribbonExpireDate = new Date(self.opts.element.ribbon.expireDate)\n\t\t//Allows ribbons to expire or appear indefinitely\n\t\tif (ribbonExpireDate > today || ribbonExpireDate == 'Invalid Date') self.makeRibbon(self.opts.element.ribbon)\n\t}\n\n\tcard.on('click', async event => {\n\t\tevent.stopPropagation()\n\t\tawait self.app.dispatch({\n\t\t\ttype: 'is_apps_btn_active',\n\t\t\tvalue: false\n\t\t})\n\t\tslideDrawer(self)\n\t\tawait openSandbox(self.opts.element, self.opts)\n\t})\n}\n", "import { getInitFxn } from '#rx'\nimport * as utils from './utils'\nimport { openSandbox } from './adSandbox'\nimport { slideDrawer } from './mainBtn'\n\n/*\n.opts{\n\t.app\n\t.holder\n\t.element{}\n\t.dom{}\n\t.state{}\n\t.sandboxDiv\n}\n*/\n\nclass AppDrawerButton {\n\tconstructor(opts) {\n\t\tthis.type = 'button' // works for 'dsButton'. May expand to other button types\n\t\tthis.opts = this.validateOpts(opts)\n\t\tthis.holder = opts.holder\n\t\tthis.dom = opts.dom\n\t\tthis.sandboxDiv = opts.sandboxDiv\n\t\tsetRenderers(this)\n\t}\n\n\tvalidateOpts(opts) {\n\t\tif (!opts.element.name) throw `Button name is missing`\n\t\tif (!opts.element.sandboxJson && !opts.element.sandboxHtml)\n\t\t\tthrow `Either .sandboxJson or .sandboxHtml is missing for button=${opts.element.name}`\n\t\treturn opts\n\t}\n\n\tmain() {}\n}\n\nexport const buttonInit = getInitFxn(AppDrawerButton)\n\nfunction setRenderers(self) {\n\tconst btn = utils.makeButton({ div: self.holder, text: self.opts.element.name, margin: '20px 20px 0px' })\n\tbtn.attr('class', 'sjpp-appdrawer-dataset-btn').on('click', async event => {\n\t\tevent.stopPropagation()\n\t\tawait self.app.dispatch({\n\t\t\ttype: 'is_apps_btn_active',\n\t\t\tvalue: false\n\t\t})\n\t\tslideDrawer(self)\n\t\tawait openSandbox(self.opts.element, self.opts)\n\t})\n}\n", "import { getCompInit } from '#rx'\nimport { rgb } from 'd3-color'\nimport { defaultcolor } from '#shared/common.js'\nimport { cardInit } from './card'\nimport { buttonInit } from './dsButton'\nimport { select } from 'd3-selection'\nimport { dofetch3, sayerror } from '#src/client'\n\n/*\n.opts{}\n    .app{}\n\t.dom{}\n\t.state{}\n\nQuestions: \n\t- Organize in window based on section size to make best use of space?\n    - For the column layout: \n        1. Cap number of columns?\n        2. Allow y overflow for >2 columns (like Trello)?\n*/\n\nclass AppDrawerLayoutComp {\n\tconstructor(opts) {\n\t\tthis.type = 'layout'\n\t\tthis.dom = {\n\t\t\tholder: opts.dom.drawerDiv,\n\t\t\twrapper: opts.dom.wrapper,\n\t\t\tsandboxDiv: opts.dom.sandboxDiv\n\t\t}\n\t\tthis.state = opts.state\n\t\tthis.hasStatePreMain = true\n\t}\n\n\tasync validateIndexJson() {\n\t\tconst index = await this.getIndexJson()\n\t\tif (!index.elements) throw `Missing elements array`\n\t\tif (!index.elements.length) throw `No element objects provided`\n\t\tif (index.columnsLayout) {\n\t\t\tif (index.columnsLayout.length == 0) throw `Missing column objects`\n\t\t\tconst allGridAreaValues = index.columnsLayout.map(s => s.gridarea)\n\t\t\tif (allGridAreaValues.length != new Set(allGridAreaValues).size) throw `Duplicate values for .gridarea found`\n\t\t\tconst allSectionIdValues = []\n\t\t\tfor (const col of index.columnsLayout) {\n\t\t\t\tif (!col.gridarea) throw `Missing column .gridarea for column = ${col.name}`\n\t\t\t\tif (!col.sections || col.sections.length == 0) throw `Missing section objects for column = ${col.name}`\n\t\t\t\tfor (const section of col.sections) {\n\t\t\t\t\tif (!section.id)\n\t\t\t\t\t\tthrow `Missing section .id in ${section.name ? `section = ${section.name}` : `column = ${col.name} array`}`\n\t\t\t\t\tallSectionIdValues.push(section.id)\n\t\t\t\t}\n\t\t\t\tif (col.sections.length != new Set(col.sections).size) {\n\t\t\t\t\tthrow `Non-unique levels in line ${lineNum}: ${JSON.stringify(levelNames)}`\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (allSectionIdValues.length != new Set(allSectionIdValues).size) throw `Duplicate values for section.id found`\n\n\t\t\t// Required element attributes when columnsLayout specified\n\t\t\tfor (const element of index.elements) {\n\t\t\t\tif (!element.section) throw `.section is missing for ${element.type} = ${element.name}`\n\t\t\t\tif (!allSectionIdValues.some(d => d == element.section))\n\t\t\t\t\tthrow `section = ${element.section} for ${element.type} = ${element.name} is not a column section`\n\t\t\t}\n\t\t}\n\t\treturn index\n\t}\n\n\tasync getIndexJson() {\n\t\t// Proteinpaint specific index.\n\t\t// TODO: Later modifiy to accept user index.\n\t\tconst re = await dofetch3(this.app.cardsPath + '/index.json')\n\t\tif (re.error) {\n\t\t\tsayerror(this.dom.holder.append('div'), re.error)\n\t\t\treturn\n\t\t}\n\t\treturn re\n\t}\n\n\tvalidateElements() {\n\t\tconst features = JSON.parse(sessionStorage.getItem('optionalFeatures')) || {}\n\t\tthis.elements = this.index.elements.filter(e => !e.hidden && (!e.configFeature || features[e.configFeature]))\n\t}\n\n\tasync init() {\n\t\tthis.index = await this.validateIndexJson()\n\t\tthis.elementsRendered = false\n\t\tsetRenderers(this)\n\t\tthis.validateElements()\n\t\tthis.layout = this.index.columnsLayout ? this.index.columnsLayout : null\n\t\tthis.components = {\n\t\t\telements: []\n\t\t}\n\t}\n\n\tasync main() {\n\t\t// prevent elements from reloading each time\n\t\tif (this.elementsRendered == true) return\n\t\tthis.elementsRendered = true\n\t\tfor (const element of this.elements) {\n\t\t\tconst holder = select(this.layout ? `#${element.section} > .sjpp-element-list` : `.sjpp-element-list`)\n\t\t\tif (element.type == 'card' || element.type == 'nestedCard') {\n\t\t\t\tthis.components.elements.push(\n\t\t\t\t\tawait cardInit({\n\t\t\t\t\t\tapp: this.app,\n\t\t\t\t\t\tholder: holder\n\t\t\t\t\t\t\t.style('display', 'grid')\n\t\t\t\t\t\t\t.style('grid-template-columns', 'repeat(auto-fit, minmax(320px, 1fr))')\n\t\t\t\t\t\t\t.style('gap', '10px')\n\t\t\t\t\t\t\t.style('list-style', 'none')\n\t\t\t\t\t\t\t.style('margin', '15px 0px'),\n\t\t\t\t\t\telement,\n\t\t\t\t\t\tdom: this.opts.dom,\n\t\t\t\t\t\tstate: this.state,\n\t\t\t\t\t\tsandboxDiv: this.dom.sandboxDiv\n\t\t\t\t\t})\n\t\t\t\t)\n\t\t\t} else if (element.type == 'dsButton') {\n\t\t\t\tthis.components.elements.push(\n\t\t\t\t\tawait buttonInit({\n\t\t\t\t\t\tapp: this.app,\n\t\t\t\t\t\tholder,\n\t\t\t\t\t\telement,\n\t\t\t\t\t\tdom: this.opts.dom,\n\t\t\t\t\t\tstate: this.state,\n\t\t\t\t\t\tsandboxDiv: this.dom.sandboxDiv\n\t\t\t\t\t})\n\t\t\t\t)\n\t\t\t}\n\t\t}\n\t}\n}\n\nexport const layoutInit = getCompInit(AppDrawerLayoutComp)\n\nfunction setRenderers(self) {\n\tif (!self.index.columnsLayout) noDefinedLayout(self)\n\tif (self.index.columnsLayout) columnsLayout(self)\n}\n\nfunction noDefinedLayout(self) {\n\tconst flexLayout = self.dom.wrapper\n\t\t.append('div')\n\t\t.style('display', 'flex')\n\t\t.style('padding', '10px')\n\t\t.classed('sjpp-element-list', true)\n\treturn flexLayout\n}\n\nfunction columnsLayout(self) {\n\t// Allow user to create multiple columns in parent grid\n\tconst parentGrid = self.dom.wrapper\n\t\t.append('div')\n\t\t.style('display', 'grid')\n\t\t.style('grid-template-columns', 'repeat(auto-fit, minmax(425px, 1fr))')\n\t\t.style('gap', '10px')\n\t\t.style('padding', '10px')\n\t\t.style('text-align', 'left')\n\n\t//Allow user to create multiple parent columns in columnsLayout\n\tconst gridareas = []\n\tfor (const column of self.index.columnsLayout) gridareas.push(column.gridarea)\n\tparentGrid.style('grid-template-areas', `\"${gridareas.toString().replace(',', ' ')}\"`)\n\tfor (const col of self.index.columnsLayout) {\n\t\tconst newCol = parentGrid.append('div').style('grid-area', col.gridarea).classed('.sjpp-track-cols', true)\n\t\tfor (const section of col.sections) addSection(section, newCol)\n\t}\n\n\tfunction addSection(section, newCol) {\n\t\tconst newSection = newCol.append('div').attr('id', section.id)\n\t\tif (section.name)\n\t\t\tnewSection\n\t\t\t\t.append('h5')\n\t\t\t\t.classed('sjpp-appdrawer-cols', true)\n\t\t\t\t.style('color', rgb(defaultcolor).darker())\n\t\t\t\t.text(section.name)\n\t\tnewSection.append('div').classed('sjpp-element-list', true).style('padding', '10px')\n\n\t\treturn newSection\n\t}\n}\n", "import { getCompInit } from '#rx'\nimport { layoutInit } from './layout'\n\n/*\n.opts{}\n    .app{}\n\t.dom{}\n\t.state{}\n\nTODOs: \n- Replace drawerFullHeight with a different approach\n\t- Causes the drawer to only partially appear when the window zooms in\n*/\n\nclass MainHeadboxBtn {\n\tconstructor(opts) {\n\t\tthis.type = 'mainBtn'\n\t\tthis.opts = this.validateOpts(opts)\n\t\tthis.dom = opts.dom\n\t\tthis.state = opts.state\n\t\tthis.hasStatePreMain = true\n\t\tsetRenderers(this)\n\t}\n\n\tvalidateOpts(opts) {\n\t\treturn opts.app.opts\n\t}\n\n\tgetState(appState) {\n\t\treturn {\n\t\t\tappBtnActive: appState.appBtnActive\n\t\t}\n\t}\n\n\tasync init() {\n\t\tthis.btnRendered = false\n\t\tthis.drawerFullHeight = ''\n\t\ttry {\n\t\t\t//detect whether to show examples right away, which is when the url is barebone without any route paths or search parameters\n\t\t\tif (window.location.pathname == '/' && !window.location.search.length)\n\t\t\t\tawait this.app.dispatch({ type: 'is_apps_btn_active', value: true })\n\t\t\tthis.components = {\n\t\t\t\tlayout: []\n\t\t\t}\n\t\t} catch (e) {\n\t\t\tthrow e\n\t\t}\n\t}\n\n\tasync main(appState) {\n\t\tif (this.app.getState(appState).appBtnActive == true && this.btnRendered == false) {\n\t\t\tthis.dom.drawerDiv.style('background-color', '#f5f5f5') //Quick fix for drawerDiv initially appearing before layout init\n\t\t\t//Init layout only once when 'Apps' button is active for the first time\n\t\t\tthis.components.layout.push(\n\t\t\t\tawait layoutInit({\n\t\t\t\t\tapp: this.app,\n\t\t\t\t\tdom: this.dom,\n\t\t\t\t\tstate: this.state\n\t\t\t\t})\n\t\t\t)\n\t\t\t//Give the drawerDiv time to render before calculating height\n\t\t\tsetTimeout(() => {\n\t\t\t\tthis.drawerFullHeight = this.dom.drawerDiv.node().getBoundingClientRect().height + 5\n\t\t\t}, this.state.duration + 5)\n\t\t\tslideDrawer(this)\n\t\t\tthis.btnRendered = true\n\t\t}\n\t\tif (this.state.appBtnActive == false && this.btnRendered == true) slideDrawer(this)\n\t}\n}\n\nexport const mainBtnInit = getCompInit(MainHeadboxBtn)\n\nfunction setRenderers(self) {\n\tself.dom.btnWrapper\n\t\t.style('background-color', self.state.appBtnActive ? '#b2b2b2' : '#f2f2f2')\n\t\t.style('color', self.state.appBtnActive ? '#fff' : '#000')\n\t\t.on('click', async event => {\n\t\t\tevent.stopPropagation()\n\t\t\tawait self.app.dispatch({ type: 'is_apps_btn_active' })\n\t\t\tslideDrawer(self)\n\t\t\tif (self.state.appBtnActive) {\n\t\t\t\tsetTimeout(() => {\n\t\t\t\t\tself.drawerFullHeight = self.dom.drawerDiv.node().getBoundingClientRect().height + 5\n\t\t\t\t}, self.state.duration + 5)\n\t\t\t}\n\t\t})\n\n\tself.dom.btn\n\t\t.attr('class', 'sja_menuoption')\n\t\t.style('display', 'inline-block')\n\t\t.style('background-color', 'transparent')\n\t\t.style('color', self.state.appBtnActive ? '#fff' : '#000')\n\t\t.style('padding', self.opts.padw_sm)\n\t\t.style('margin', '0px 5px')\n\t\t.style('cursor', 'pointer')\n\t\t.text('Apps')\n\n\t// an empty spacer div, needed since the arrows are absolutely positioned\n\tself.dom.drawerHint\n\t\t.style('position', 'relative')\n\t\t.style('display', 'inline-block')\n\t\t.style('height', self.state.arrowSize.closed + 'px')\n\t\t.style('width', self.state.appBtnActive ? self.state.hintWidth.open : self.state.hintWidth.closed)\n\t\t.style('background-color', 'transparent')\n\t\t.style('text-align', 'center')\n\t\t.style('cursor', 'pointer')\n\n\tself.dom.drawerArrow\n\t\t.style('position', 'absolute')\n\t\t.style('font-size', self.state.arrowSize.closed + 'px')\n\t\t.style('right', self.state.hintPos.closed.rt + 'px')\n\t\t.style('bottom', self.state.hintPos.closed.btm + 'px')\n\t\t.style('background-color', 'transparent')\n\t\t.style('color', self.state.arrowColor.closed)\n\t\t.style('opacity', self.state.appBtnActive ? 0 : 1)\n\t\t.style('cursor', 'pointer')\n\t\t.html('&#9660;')\n\n\tself.dom.drawerArrowOpen\n\t\t.style('position', 'absolute')\n\t\t.style('font-size', self.state.arrowSize.open + 'px')\n\t\t.style('left', self.state.hintPos.open.left + 'px')\n\t\t.style('bottom', self.state.hintPos.open.btm + 'px')\n\t\t.style('transform', 'rotate(180deg)')\n\t\t.style('background-color', 'transparent')\n\t\t.style('color', self.state.arrowColor.open)\n\t\t.style('opacity', self.state.appBtnActive ? 1 : 0)\n\t\t.style('cursor', 'pointer')\n\t\t.style('pointer-events', self.state.appBtnActive ? 'auto' : 'none')\n\t\t.html('&#9660;')\n\n\tself.drawerFullHeight = self.dom.drawerRow.node().getBoundingClientRect().height + 5\n}\n\nexport async function slideDrawer(self) {\n\tself.dom.btnWrapper\n\t\t.transition()\n\t\t.duration(self.opts.state.duration)\n\t\t.style('background-color', self.state.appBtnActive ? '#b2b2b2' : '#f2f2f2')\n\t\t.style('color', self.state.appBtnActive ? '#fff' : '#000')\n\n\tself.dom.btn\n\t\t.transition()\n\t\t.duration(self.opts.state.duration)\n\t\t.style('color', self.state.appBtnActive ? '#fff' : '#000')\n\n\tself.dom.drawerDiv\n\t\t.style('display', 'inline-block')\n\t\t.transition()\n\t\t.duration(self.opts.state.duration)\n\t\t.style('top', self.state.appBtnActive ? '0px' : '-' + self.drawerFullHeight + 'px')\n\n\tself.dom.drawerRow\n\t\t.transition()\n\t\t.duration(self.opts.state.duration)\n\t\t.style('height', self.state.appBtnActive ? self.drawerFullHeight + 'px' : '0px')\n\n\tself.dom.drawerHint\n\t\t.transition()\n\t\t.duration(self.opts.state.duration)\n\t\t.style('width', self.state.appBtnActive ? self.opts.state.hintWidth.open : self.opts.state.hintWidth.closed)\n\n\tself.dom.drawerArrow\n\t\t.transition()\n\t\t.duration(self.opts.state.duration)\n\t\t.style('opacity', self.state.appBtnActive ? 0 : 1)\n\n\tself.dom.drawerArrowOpen\n\t\t.style('pointer-events', self.state.appBtnActive ? 'auto' : 'none')\n\t\t.transition()\n\t\t.duration(self.opts.state.duration)\n\t\t.style('opacity', self.state.appBtnActive ? 1 : 0)\n}\n", "import { getStoreInit } from '#rx'\n\n/*\n.opts{}\n\n*/\n\nclass AppDrawerStore {\n\tconstructor(opts) {\n\t\tthis.type = 'store'\n\t\tthis.defaultState = {\n\t\t\t// for apps drawer animation\n\t\t\tduration: 500,\n\t\t\thintPos: {\n\t\t\t\topen: { btm: -42, left: 13 },\n\t\t\t\tclosed: { btm: 3, rt: 5 }\n\t\t\t},\n\t\t\thintWidth: { open: '0px', closed: '18px' },\n\t\t\tarrowSize: { open: 42, closed: 20 },\n\t\t\tarrowColor: { open: 'rgb(242,242,242)', closed: 'rgb(85,85,85)' },\n\t\t\tappBtnActive: false\n\t\t}\n\t}\n\n\tasync init() {}\n}\n\nexport const appDrawerStoreInit = getStoreInit(AppDrawerStore)\n\nAppDrawerStore.prototype.actions = {\n\tis_apps_btn_active(action) {\n\t\tthis.state.appBtnActive = 'value' in action ? action.value : !this.state.appBtnActive\n\t}\n}\n", "import { getAppInit } from '#rx'\nimport { mainBtnInit } from './mainBtn'\nimport { appDrawerStoreInit } from './store'\n\n/*\n.opts{}\n    .holder\n    .genomes{}\n        - client-side genome object\n\t.drawerRow\n\t.sandboxDiv\n\t.genome_browser_btn\n\t.debugmode\n\t.headbox\n\t.padw_sm\n\nTODOs: \n\nQuestions: \n*/\n\nclass AppDrawerApp {\n\tconstructor(opts) {\n\t\tthis.type = 'app'\n\n\t\tconst drawerDiv = opts.drawerRow\n\t\t\t.append('div')\n\t\t\t.style('position', 'relative')\n\t\t\t.style('margin', '0 20px')\n\t\t\t.style('padding', `0 ${opts.padw_sm}`)\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('overflow', 'hidden')\n\t\t\t.style('border-radius', '0px 0px 5px 5px')\n\t\t\t.style('width', '93vw')\n\t\t\t.classed('sjpp-drawer-div', true)\n\n\t\tconst btnWrapper = opts.headbox\n\t\t\t.append('div')\n\t\t\t.style('position', 'relative')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('margin-left', '5px')\n\t\t\t.style('margin-right', '5px')\n\t\t\t.style('border-radius', '5px')\n\t\t\t.classed('sjpp-apps-btn-wrapper', true)\n\n\t\tthis.dom = {\n\t\t\tdrawerRow: opts.drawerRow,\n\t\t\tdrawerDiv,\n\t\t\tsandboxDiv: opts.sandboxDiv,\n\t\t\tbtnWrapper,\n\t\t\tbtn: btnWrapper.append('div'),\n\t\t\tdrawerHint: btnWrapper.append('div'),\n\t\t\tdrawerArrow: btnWrapper.append('div'),\n\t\t\tdrawerArrowOpen: btnWrapper.append('div'),\n\t\t\twrapper: drawerDiv.append('div')\n\t\t}\n\t}\n\n\tpreApiFreeze(api) {\n\t\tapi.cardsPath = this.opts.cardsPath\n\t}\n\n\tasync init() {\n\t\ttry {\n\t\t\tthis.store = await appDrawerStoreInit({ app: this.api, state: this.opts.state })\n\t\t\tthis.state = await this.store.copyState()\n\t\t\tthis.components = {\n\t\t\t\tmainBtn: await mainBtnInit({\n\t\t\t\t\tapp: this.api,\n\t\t\t\t\tdom: this.dom,\n\t\t\t\t\tstate: this.state,\n\t\t\t\t\tindexJson: this.indexJson\n\t\t\t\t})\n\t\t\t}\n\t\t\tawait this.api.dispatch()\n\t\t} catch (e) {\n\t\t\tthrow e\n\t\t}\n\t}\n\n\tmain() {}\n}\n\nexport const appDrawerInit = getAppInit(AppDrawerApp)\n", "import { first_genetrack_tolist } from '#common/1stGenetk'\nimport { InputSearch, Menu, newSandboxDiv } from '#dom'\nimport { searchItems } from './omniSearch.js'\nimport { appDrawerInit } from '../../appdrawer/app.js'\nimport { rgb as d3rgb } from 'd3-color'\nimport { defaultcolor } from '#shared/common.js'\nimport { dofetch3 } from '#common/dofetch'\nimport { ClientCopyGenome } from 'types/global.ts'\n\ntype Citation = {\n\tid: number\n\ttitle: string\n\tappHeaderTitle: string\n\tyear: number\n\tjournal: string\n\tpmid: number\n\tpmidURL: string\n\tdoi: string\n}\n\ntype AppHeaderOpts = {\n\t/** menu created in app.js */\n\theadtip: Menu\n\t/** runpp app */\n\tapp: any\n\t/** server returned data */\n\tdata: any\n\t/** token */\n\tjwt: any\n}\n\nexport class AppHeader {\n\theadtip: Menu\n\tapp: any\n\tdata: any\n\tjwt: any\n\t/** List of publications defined in the app drawer\n\t * Appears in button in the header and in search results\n\t */\n\tpublications: Citation[]\n\t/** Used in both the Help button and omni search\n\t * .onlySearch is used to filter out items that should not appear in the Help button\n\t */\n\tstatic help = [\n\t\t{\n\t\t\tlabel: 'Embed in your website',\n\t\t\tlink: 'https://github.com/stjude/proteinpaint/wiki/Embedding'\n\t\t},\n\t\t{\n\t\t\tlabel: 'URL parameters',\n\t\t\tlink: 'https://github.com/stjude/proteinpaint/wiki/URL-parameters'\n\t\t},\n\t\t{\n\t\t\tlabel: 'All tutorials',\n\t\t\tlink: 'https://github.com/stjude/proteinpaint/wiki/'\n\t\t},\n\t\t{\n\t\t\tlabel: 'User community',\n\t\t\tlink: 'https://groups.google.com/g/proteinpaint'\n\t\t},\n\t\t{\n\t\t\tlabel: 'License ProteinPaint',\n\t\t\tlink: 'https://www.stjude.org/research/why-st-jude/shared-resources/technology-licensing/technologies/proteinpaint-web-application-for-visualizing-genomic-data-sj-15-0021.html',\n\t\t\tonlySearch: true\n\t\t},\n\t\t{\n\t\t\tlabel: 'Our Team',\n\t\t\tlink: 'https://proteinpaint.stjude.org/team/',\n\t\t\tonlySearch: true\n\t\t}\n\t]\n\n\tconstructor(opts: AppHeaderOpts) {\n\t\tthis.headtip = opts.headtip\n\t\tthis.app = opts.app\n\t\tthis.data = opts.data\n\t\tthis.jwt = opts.jwt\n\t\tthis.publications = []\n\t}\n\n\tasync createPublicationsList() {\n\t\tconst re = await dofetch3(this.app.cardsPath + '/citations.json')\n\t\tif (re.error) console.error(`Problem retrieving ../cards/citations.json`)\n\t\t//Sort in reverse chronological order for the publications button\n\t\tthis.publications = re?.publications?.length\n\t\t\t? re.publications.filter((d: Citation) => d.appHeaderTitle).sort((a: Citation, b: Citation) => b.year - a.year)\n\t\t\t: []\n\t}\n\n\tasync makeheader() {\n\t\tawait this.createPublicationsList()\n\n\t\tconst color = d3rgb(defaultcolor)\n\t\tconst padw_lg = '13px'\n\t\tconst padw_input = '5px 10px'\n\t\tconst padw_sm = '7px 10px'\n\t\tconst doc_width = document.documentElement.clientWidth\n\t\t// head\n\t\tconst row = this.app.holder\n\t\t\t.append('div')\n\t\t\t.style('white-space', 'nowrap')\n\t\t\t.style(\n\t\t\t\t'border-bottom',\n\t\t\t\tdoc_width > 1600 ? 'solid 1px rgba(' + color.r + ',' + color.g + ',' + color.b + ',.3)' : ''\n\t\t\t)\n\n\t\tconst headbox = row\n\t\t\t.append('div')\n\t\t\t.style('margin', '10px')\n\t\t\t.style('padding', '8px')\n\t\t\t.style('padding-bottom', '12px')\n\t\t\t.style('display', doc_width < 1600 ? 'block' : 'inline-block')\n\t\t\t.style(\n\t\t\t\t'border-bottom',\n\t\t\t\tdoc_width < 1600 ? 'solid 1px rgba(' + color.r + ',' + color.g + ',' + color.b + ',.3)' : ''\n\t\t\t)\n\n\t\t// .style('border-radius', '5px')\n\t\t// .style('background-color', 'rgba(' + color.r + ',' + color.g + ',' + color.b + ',.1)')\n\t\tconst headinfo = row\n\t\t\t.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('padding', padw_sm)\n\t\t\t.style('padding-left', '25px')\n\t\t\t.style('font-size', '.8em')\n\t\t\t.style('color', d3rgb(defaultcolor).darker())\n\n\t\t{\n\t\t\t// a row for server stats\n\t\t\tconst row = headinfo.append('div').style('padding-left', '15px')\n\t\t\t// link to the published ppfull container version, instead of github release tarball which we do not advertise;\n\t\t\t// github's pkgs/container link has a timestamp before the tag, which cannot be computed here (but may be able to query later?)\n\t\t\tconst link = `https://github.com/stjude/proteinpaint/pkgs/container/ppfull` // url to list of published container versions\n\t\t\tconst version = this.data.pkgver\n\t\t\t\t? `Release version: <a href=\"${link}\" target=\"${this.data.pkgver}\">${this.data.pkgver}</a>`\n\t\t\t\t: `Code date: ${this.data.codedate}` // default to using code date as before if pkgver is not available\n\t\t\trow\n\t\t\t\t.attr('id', 'sjpp-serverstat')\n\t\t\t\t.append('span')\n\t\t\t\t.html(`${version}, server launched: ${this.data.launchdate || '??'}.`)\n\t\t\tif (this.data.hasblat) {\n\t\t\t\trow\n\t\t\t\t\t.append('a')\n\t\t\t\t\t.style('margin-left', '10px')\n\t\t\t\t\t.text('Running BLAT')\n\t\t\t\t\t.on('click', async event => {\n\t\t\t\t\t\tthis.headtip.clear().showunder(event.target)\n\t\t\t\t\t\tconst div = this.headtip.d.append('div').style('margin', '10px')\n\t\t\t\t\t\tconst wait = div.append('div').text('Loading...')\n\t\t\t\t\t\ttry {\n\t\t\t\t\t\t\tconst data = await dofetch3('blat?serverstat=1')\n\t\t\t\t\t\t\tif (data.error) throw data.error\n\t\t\t\t\t\t\tif (!data.lst) throw 'invalid response'\n\t\t\t\t\t\t\twait.remove()\n\t\t\t\t\t\t\tfor (const i of data.lst) {\n\t\t\t\t\t\t\t\tdiv.append('div').text(i)\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t} catch (e: any) {\n\t\t\t\t\t\t\twait.text(e.message || e)\n\t\t\t\t\t\t\tif (e.stack) console.error(e.stack)\n\t\t\t\t\t\t}\n\t\t\t\t\t})\n\t\t\t}\n\t\t}\n\t\tif (this.data.headermessage) {\n\t\t\theadinfo.append('div').html(this.data.headermessage)\n\t\t}\n\n\t\t// 1\n\t\theadbox\n\t\t\t.append('div')\n\t\t\t.text('ProteinPaint')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('padding', padw_lg)\n\t\t\t.style('color', defaultcolor)\n\t\t\t.style('font-size', '1.3em')\n\t\t\t.style('font-weight', 'bold')\n\n\t\t// 2, search box\n\t\tconst omniSearch = new InputSearch({\n\t\t\tholder: headbox,\n\t\t\ttip: this.headtip,\n\t\t\tstyle: {\n\t\t\t\tpadding: padw_sm,\n\t\t\t\tborder: `'solid 1px ${defaultcolor}`\n\t\t\t},\n\t\t\tsize: 32,\n\t\t\tplaceholder: 'Gene, position, SNP, app, or dataset',\n\t\t\ttitle: 'Search by gene, SNP, position, app, or dataset',\n\t\t\tsearchItems: async () => {\n\t\t\t\treturn await searchItems(this.app, this.headtip, AppHeader.help, this.publications, this.jwt)\n\t\t\t}\n\t\t})\n\n\t\tomniSearch.initUI()\n\n\t\tconst genome_select_div = headbox.append('div').attr('class', 'sjpp-genome-select-div').style('padding', padw_sm)\n\n\t\tconst get_placeholder = () => {\n\t\t\tconst currG = this.app.genomes[this.app.selectgenome.property('value')]\n\t\t\t/** Defaults */\n\t\t\tconst opts2Show = ['Gene', 'position', 'app']\n\t\t\t/** Show all the genomic options together */\n\t\t\tif (currG.hasSNP) opts2Show.splice(2, 0, 'SNP')\n\t\t\tif (Object.keys(currG.datasets).length) opts2Show.push('dataset')\n\t\t\tconst str = opts2Show.join(', ').replace(/,(?=[^,]*$)/, ', or')\n\t\t\treturn str\n\t\t}\n\n\t\tthis.app.selectgenome = genome_select_div\n\t\t\t.append('select')\n\t\t\t.attr('aria-label', 'Select a genome')\n\t\t\t.attr('class', 'sjpp-genome-select')\n\t\t\t.style('padding', padw_input)\n\t\t\t.style('border', 'solid 1px ' + defaultcolor)\n\t\t\t.on('change', () => {\n\t\t\t\tthis.update_genome_browser_btn(this.app)\n\t\t\t\tomniSearch.updatePlaceholder(get_placeholder())\n\t\t\t})\n\n\t\tconst filterGenomes = Object.values(this.app.genomes).filter((g: any) => !g.hideOnClient) as ClientCopyGenome[]\n\t\tfor (const n of filterGenomes) {\n\t\t\tthis.app.selectgenome.append('option').attr('n', n.name).text(`${n.species} ${n.name}`).property('value', n.name)\n\t\t}\n\t\tthis.app.genome_browser_btn = this.make_genome_browser_btn(this.app, headbox, this.jwt)\n\n\t\tthis.app.drawer = await appDrawerInit({\n\t\t\tholder: this.app.holder,\n\t\t\tgenomes: this.app.genomes,\n\t\t\tdrawerRow: this.app.holder\n\t\t\t\t.append('div')\n\t\t\t\t.style('position', 'relative')\n\t\t\t\t.style('overflow-x', 'visible')\n\t\t\t\t.style('overflow-y', 'hidden')\n\t\t\t\t.classed('sjpp-drawer-row', true),\n\t\t\tsandboxDiv: this.app.holder.append('div').style('margin-top', '15px').classed('sjpp-drawer-sandbox', true),\n\t\t\tgenome_browser_btn: this.app.genome_browser_btn,\n\t\t\tdebugmode: this.app.debugmode,\n\t\t\theadbox,\n\t\t\tpadw_sm,\n\t\t\tcardsPath: this.app.cardsPath\n\t\t})\n\n\t\t//Help button\n\t\theadbox\n\t\t\t.append('span')\n\t\t\t.classed('sja_menuoption', true)\n\t\t\t.attr('id', 'sjpp-header-help-btn')\n\t\t\t.style('padding', padw_sm)\n\t\t\t.text('Help')\n\t\t\t.on('click', async event => {\n\t\t\t\tconst p = event.target.getBoundingClientRect()\n\t\t\t\tconst div = this.headtip.clear().show(p.left - 0, p.top + p.height + 5)\n\n\t\t\t\tawait div.d\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.style('padding', '5px 20px')\n\t\t\t\t\t.selectAll('p')\n\t\t\t\t\t.data(AppHeader.help.filter(d => !d.onlySearch))\n\t\t\t\t\t.enter()\n\t\t\t\t\t.append('p')\n\t\t\t\t\t.html(d => `<a href=${d.link} target=_blank>${d.label}</a>`)\n\t\t\t})\n\n\t\t//Publications button\n\t\t//Citations not available on CI server\n\t\tif (this.publications.length > 0) {\n\t\t\theadbox\n\t\t\t\t.append('span')\n\t\t\t\t.classed('sja_menuoption', true)\n\t\t\t\t.attr('id', 'sjpp-header-publications-btn')\n\t\t\t\t.style('padding', padw_sm)\n\t\t\t\t.style('margin', '0px 5px')\n\t\t\t\t.text('Publications')\n\t\t\t\t.on('click', async event => {\n\t\t\t\t\tconst p = event.target.getBoundingClientRect()\n\t\t\t\t\tconst div = this.headtip.clear().show(p.left - 150, p.top + p.height + 5)\n\n\t\t\t\t\tawait div.d\n\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t.style('padding', '5px 20px')\n\t\t\t\t\t\t.selectAll('p')\n\t\t\t\t\t\t.data(this.publications)\n\t\t\t\t\t\t.enter()\n\t\t\t\t\t\t.append('p')\n\t\t\t\t\t\t.html((d: any) => `<a href=${d.doi} target=_blank>${d.appHeaderTitle}, ${d.journal}, ${d.year}</a>`)\n\t\t\t\t})\n\t\t}\n\t}\n\n\tmake_genome_browser_btn(app, headbox, jwt) {\n\t\tif (app.selectgenome.node().options.length === 0) {\n\t\t\tconsole.error(`No selected selectgenome options.`)\n\t\t\treturn\n\t\t}\n\n\t\tconst padw = '8px'\n\t\tconst genome_btn_div = headbox.append('span')\n\t\tconst genomename = app.selectgenome.node().options[app.selectgenome.property('selectedIndex')].value\n\n\t\tconst g_browser_btn = genome_btn_div\n\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t.attr('id', 'genome_btn')\n\t\t\t.style('padding', padw)\n\t\t\t.datum(genomename)\n\t\t\t.text(genomename + ' genome browser')\n\t\t\t.on('click', () => {\n\t\t\t\t//Grab the current genome selected\n\t\t\t\tconst genomeSelected = app.selectgenome.node().value\n\t\t\t\tconst g = app.genomes[genomeSelected]\n\t\t\t\tif (!g) {\n\t\t\t\t\talert('Invalid genome name: ' + genomeSelected)\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tconst sandbox_div = newSandboxDiv(app.drawer.opts.sandboxDiv)\n\t\t\t\tsandbox_div.header.text(genomeSelected + ' genome browser')\n\n\t\t\t\tconst par = {\n\t\t\t\t\thostURL: app.hostURL,\n\t\t\t\t\tjwt,\n\t\t\t\t\tholder: sandbox_div.body,\n\t\t\t\t\tgenome: g,\n\t\t\t\t\tchr: g.defaultcoord.chr,\n\t\t\t\t\tstart: g.defaultcoord.start,\n\t\t\t\t\tstop: g.defaultcoord.stop,\n\t\t\t\t\tnobox: true,\n\t\t\t\t\ttklst: [],\n\t\t\t\t\tdebugmode: app.debugmode\n\t\t\t\t}\n\t\t\t\tfirst_genetrack_tolist(g, par.tklst)\n\n\t\t\t\timport('../block.js').then(b => new b.Block(par))\n\t\t\t\tapp.drawer.dispatch({ type: 'is_apps_btn_active', value: false })\n\t\t\t})\n\t\treturn g_browser_btn\n\t}\n\n\tupdate_genome_browser_btn(app) {\n\t\tapp.genome_browser_btn.text(app.selectgenome.node().value + ' genome browser')\n\t\tapp.genome_browser_btn.datum(app.selectgenome.node().value)\n\t}\n}\n"],
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   "names": ["searchTermFound", "par", "setRenderers", "setRenderers", "setRenderers", "row"]
 }

package/dist/{DEanalysis-G4CCMC7Q.js → DEanalysis-N4XXOEXM.js}

@@ -1,14 +1,14 @@
 import "./chunk-Q7EFDAC2.js";
 import {
   controlsInit
-} from "./chunk-LOV6H3RZ.js";
-import "./chunk-X5ZQI22O.js";
+} from "./chunk-KYGN5FG7.js";
+import "./chunk-Z3TD3CHR.js";
 import "./chunk-U6ZCLI5S.js";
-import "./chunk-WA6VYIW4.js";
+import "./chunk-47W2ODRY.js";
 import "./chunk-CLHA5AEH.js";
 import {
   axisstyle
-} from "./chunk-PU7EMWOK.js";
+} from "./chunk-HR3FNUVU.js";
 import "./chunk-7KFEDC2T.js";
 import "./chunk-FCPSU6WB.js";
 import "./chunk-WX2C2ZIZ.js";
@@ -21,7 +21,7 @@ import {
 import {
   downloadTable,
   renderTable
-} from "./chunk-TU4H4R2T.js";
+} from "./chunk-LGC254YE.js";
 import "./chunk-ZYRXVRSD.js";
 import "./chunk-SJ4KZVLF.js";
 import "./chunk-ALPXXDQD.js";
@@ -229,7 +229,9 @@ var DEanalysis = class {
     output.mid_sample_size_cutoff = 8;
     output.high_sample_size_cutoff = 30;
     await this.setControls(output);
-    this.dom.header.style("opacity", 0.6).style("padding-left", "10px").style("font-size", "0.75em").text("DIFFERENTIAL GENE EXPRESSION");
+    this.dom.header.html(
+      this.config.state.groups[0].name + " vs " + this.config.state.groups[1].name + ' <span style="font-size:.8em;opacity:.7">DIFFERENTIAL GENE EXPRESSION</span>'
+    );
     render_volcano(this, output);
   }
 };
@@ -404,11 +406,11 @@ async function render_volcano(self, output) {
         value: num_significant_genes + num_non_significant_genes
       },
       {
-        label: "Group1 sample size",
+        label: self.config.state.groups[0].name + " sample size",
         value: sample_size1
       },
       {
-        label: "Group2 sample size",
+        label: self.config.state.groups[1].name + " sample size",
         value: sample_size2
       }
     ];
@@ -605,4 +607,4 @@ export {
   makeChartBtnMenu,
   openHiercluster
 };
-//# sourceMappingURL=DEanalysis-G4CCMC7Q.js.map
+//# sourceMappingURL=DEanalysis-N4XXOEXM.js.map

package/dist/DEanalysis-N4XXOEXM.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/DEanalysis.js"],
+  "sourcesContent": ["import { axisstyle } from '#dom/axisstyle'\nimport { table2col } from '#dom/table2col'\nimport { Menu } from '../dom/menu'\nimport { renderTable } from '../dom/table'\nimport * as d3axis from 'd3-axis'\nimport { controlsInit } from './controls'\nimport { select as d3select } from 'd3-selection'\nimport { getCompInit, copyMerge } from '#rx'\nimport { dofetch3 } from '#common/dofetch'\nimport { scaleLog, scaleLinear } from 'd3-scale'\nimport { d3lasso } from '../common/lasso'\nimport { downloadTable } from '../dom/table'\nimport { roundValueAuto } from '#shared/roundValue.js'\n\n/*\n\nopts{}\n\tsamplelst{}\n\t\tgroups[]\n\nthis{}\n\tapp{}\n\t\tvocabApi\n*/\n\nconst hlcolor = '#ffa200'\nconst tip = new Menu()\nclass DEanalysis {\n\tconstructor() {\n\t\tthis.type = 'DEanalysis'\n\t}\n\tasync init(opts) {\n\t\tconst config = opts.plots.find(p => p.id === this.id)\n\t\tconst controlsDiv = this.opts.holder.append('div').style('display', 'inline-block')\n\t\tconst mainDiv = this.opts.holder.append('div').style('display', 'inline-block').style('margin-left', '50px')\n\t\tconst holder = mainDiv.append('div').style('display', 'inline-block')\n\t\tconst detailsDiv = mainDiv\n\t\t\t.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('vertical-align', 'top')\n\t\t\t.style('margin-top', '50px')\n\n\t\tconst tableDiv = this.opts.holder.append('div').style('margin-left', '50px')\n\n\t\tthis.dom = {\n\t\t\tholder,\n\t\t\theader: this.opts.header,\n\t\t\tcontrolsDiv,\n\t\t\tdetailsDiv,\n\t\t\ttableDiv\n\t\t}\n\t}\n\n\tasync setControls(output) {\n\t\tthis.dom.controlsDiv.selectAll('*').remove()\n\t\tconst inputs = [\n\t\t\t{\n\t\t\t\tlabel: 'Minimum read count',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'DEanalysis',\n\t\t\t\tsettingsKey: 'min_count',\n\t\t\t\ttitle: 'Relative cpm cutoff for filtering a gene compared to all samples and genes in dataset',\n\t\t\t\tmin: 0,\n\t\t\t\tmax: 10000\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Minimum total read count',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'DEanalysis',\n\t\t\t\tsettingsKey: 'min_total_count',\n\t\t\t\ttitle: 'Minimum total read count required for each sample',\n\t\t\t\tmin: 0,\n\t\t\t\tmax: 10000\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'P-value significance (linear scale)',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'DEanalysis',\n\t\t\t\tsettingsKey: 'pvalue',\n\t\t\t\ttitle: 'P-value significance',\n\t\t\t\tmin: 0,\n\t\t\t\tmax: 1\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Fold change (log scale)',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'DEanalysis',\n\t\t\t\tsettingsKey: 'foldchange',\n\t\t\t\ttitle: 'Fold change',\n\t\t\t\tmin: -10,\n\t\t\t\tmax: 10\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'P-value table',\n\t\t\t\ttype: 'checkbox',\n\t\t\t\tchartType: 'DEanalysis',\n\t\t\t\tsettingsKey: 'pvaluetable',\n\t\t\t\ttitle: 'Display table showing original and adjusted pvalues for all significant genes',\n\t\t\t\tboxLabel: ''\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'P-value',\n\t\t\t\ttype: 'radio',\n\t\t\t\tchartType: 'DEanalysis',\n\t\t\t\tsettingsKey: 'adjusted_original_pvalue',\n\t\t\t\ttitle: 'Toggle between original and adjusted pvalues for volcano plot',\n\t\t\t\toptions: [\n\t\t\t\t\t{ label: 'adjusted', value: 'adjusted' },\n\t\t\t\t\t{ label: 'original', value: 'original' }\n\t\t\t\t]\n\t\t\t}\n\t\t]\n\n\t\tif (\n\t\t\t(output.mid_sample_size_cutoff >= output.sample_size1 &&\n\t\t\t\toutput.mid_sample_size_cutoff < output.sample_size2 &&\n\t\t\t\toutput.sample_size2 < output.high_sample_size_cutoff) ||\n\t\t\t(output.mid_sample_size_cutoff >= output.sample_size2 &&\n\t\t\t\toutput.mid_sample_size_cutoff < output.sample_size1 &&\n\t\t\t\toutput.sample_size1 < output.high_sample_size_cutoff)\n\t\t) {\n\t\t\t// Invoked only when one sample size is low than the mid_sample_size_cutoff and the other one is higher but the higher sample size is lower than the high cutoff so that the DE computation does not take a lot of time on the server\n\t\t\tinputs.push({\n\t\t\t\tlabel: 'Method',\n\t\t\t\ttype: 'radio',\n\t\t\t\tchartType: 'DEanalysis',\n\t\t\t\tsettingsKey: 'method',\n\t\t\t\ttitle: 'Toggle between edgeR and wilcoxon test',\n\t\t\t\toptions: [\n\t\t\t\t\t{ label: 'edgeR', value: 'edgeR' },\n\t\t\t\t\t{ label: 'wilcoxon', value: 'wilcoxon' }\n\t\t\t\t]\n\t\t\t})\n\t\t\tthis.settings.method = output.method\n\t\t\tthis.state.config = output.method\n\t\t}\n\n\t\tif (this.app.opts.genome.termdbs) {\n\t\t\t// Check if genome build contains termdbs, only then enable gene ora\n\t\t\tinputs.push({\n\t\t\t\tlabel: 'Gene set overrepresentation analysis',\n\t\t\t\ttype: 'radio',\n\t\t\t\tchartType: 'DEanalysis',\n\t\t\t\tsettingsKey: 'gene_ora',\n\t\t\t\ttitle: 'Toggle between analyzing upregulated, downregulated or both genes',\n\t\t\t\toptions: [\n\t\t\t\t\t{ label: 'upregulated', value: 'upregulated' },\n\t\t\t\t\t{ label: 'downregulated', value: 'downregulated' },\n\t\t\t\t\t{ label: 'both', value: 'both' }\n\t\t\t\t]\n\t\t\t})\n\t\t}\n\n\t\tif (this.app.opts.genome.termdbs && !this.settings.gsea) {\n\t\t\t// Check if genome build contains termdbs, only then enable gene ora\n\t\t\tinputs.push({\n\t\t\t\tlabel: 'Gene set enrichment analysis',\n\t\t\t\ttype: 'radio',\n\t\t\t\tchartType: 'DEanalysis',\n\t\t\t\tsettingsKey: 'gsea',\n\t\t\t\ttitle: 'Gene set enrichment analysis',\n\t\t\t\toptions: [{ label: 'Submit', value: 'Submit' }]\n\t\t\t})\n\t\t}\n\n\t\tif (this.settings.pvaluetable == true) {\n\t\t\t// This currently does not work as hierarchial clustering code needs to be changed\n\t\t\tinputs.push({\n\t\t\t\tlabel: 'Hierarchial Clustering',\n\t\t\t\ttype: 'radio',\n\t\t\t\tchartType: 'DEanalysis',\n\t\t\t\tsettingsKey: 'hierCluster',\n\t\t\t\ttitle: 'Toggle between various methods for selecting genes for hierarchial clustering',\n\t\t\t\toptions: [\n\t\t\t\t\t{ label: 'Top 100 genes', value: 'top100' },\n\t\t\t\t\t{ label: 'Top 100 upregulated', value: 'top100up' },\n\t\t\t\t\t{ label: 'Top 100 downregulated', value: 'top100down' }\n\t\t\t\t]\n\t\t\t})\n\t\t\tthis.settings.hierCluster = 'top100'\n\t\t}\n\n\t\tthis.components = {\n\t\t\tcontrols: await controlsInit({\n\t\t\t\tapp: this.app,\n\t\t\t\tid: this.id,\n\t\t\t\tholder: this.dom.controlsDiv,\n\t\t\t\tinputs: inputs\n\t\t\t})\n\t\t}\n\t\tthis.components.controls.on('downloadClick.DEanalysis', () => {\n\t\t\tdownloadTable(this.table_rows, this.table_cols)\n\t\t})\n\t}\n\tgetState(appState) {\n\t\tconst config = appState.plots.find(p => p.id === this.id)\n\t\tif (!config) throw `No plot with id='${this.id}' found`\n\t\treturn {\n\t\t\tconfig\n\t\t}\n\t}\n\n\tasync main() {\n\t\tthis.config = JSON.parse(JSON.stringify(this.state.config))\n\t\tthis.settings = this.config.settings.DEanalysis\n\t\tif (this.dom.detailsDiv) {\n\t\t\tthis.dom.detailsDiv.selectAll('*').remove()\n\t\t}\n\t\tif (this.dom.holder) {\n\t\t\tthis.dom.holder.selectAll('*').remove()\n\t\t}\n\t\tconst wait = this.dom.detailsDiv.append('div').text('Loading...')\n\t\tconst output = await runDEanalysis(this) // \"this.config\" was changed from \"this.state.config\". Hope this does not create any problems.\n\t\twait.remove()\n\t\toutput.mid_sample_size_cutoff = 8 // mid sample size cutoff for method toggle to appear\n\t\toutput.high_sample_size_cutoff = 30 // high sample size cutoff for method toggle to not appear, so that very high sample-size groups are not analyzed by edgeR. The exact cutoff value will need to be determined with more examples.\n\t\tawait this.setControls(output)\n\t\tthis.dom.header.html(\n\t\t\tthis.config.state.groups[0].name +\n\t\t\t\t' vs ' +\n\t\t\t\tthis.config.state.groups[1].name +\n\t\t\t\t' <span style=\"font-size:.8em;opacity:.7\">DIFFERENTIAL GENE EXPRESSION</span>'\n\t\t)\n\t\trender_volcano(this, output)\n\t}\n}\n\nasync function render_volcano(self, output) {\n\t/*\nm {}\n- gene\n- logfoldchange\n- averagevalue\n- pvalue\n\nadd:\n- vo_circle\n\t*/\n\n\t// Delete previous holder, if present\n\tconst sample_size1 = output.sample_size1\n\tconst sample_size2 = output.sample_size2\n\tconst mavb = output.data\n\tconst holder = self.dom.holder\n\tholder.selectAll('*').remove()\n\tself.dom.detailsDiv.selectAll('*').remove()\n\tself.dom.tableDiv.selectAll('*').remove()\n\tlet minlogfc = 0,\n\t\tmaxlogfc = 0,\n\t\tminlogpv = 0,\n\t\tmaxlogpv = 0\n\tfor (const d of mavb) {\n\t\tminlogfc = Math.min(minlogfc, d.fold_change)\n\t\tmaxlogfc = Math.max(maxlogfc, d.fold_change)\n\t\tif (d.adjusted_p_value == 0) {\n\t\t\tcontinue\n\t\t} else {\n\t\t\tminlogpv = Math.min(minlogpv, d.adjusted_p_value)\n\t\t\tmaxlogpv = Math.max(maxlogpv, d.adjusted_p_value)\n\t\t}\n\t}\n\n\tlet yaxisw,\n\t\txaxish,\n\t\twidth,\n\t\theight,\n\t\txpad,\n\t\typad,\n\t\ttoppad = 50,\n\t\trightpad = 50,\n\t\tradius\n\n\tconst svg = holder.append('svg')\n\tconst yaxisg = svg.append('g')\n\tconst xaxisg = svg.append('g')\n\tconst xlab = svg.append('text').text('log2(fold change)').attr('fill', 'black').attr('text-anchor', 'middle')\n\tconst ylab = svg.append('text').text('-log10(adjusted P value)').attr('fill', 'black').attr('text-anchor', 'middle')\n\n\tmavb.vo_dotarea = svg.append('g')\n\n\tconst box = mavb.vo_dotarea\n\t\t.append('rect')\n\t\t.attr('stroke', '#ededed')\n\t\t.attr('fill', 'none')\n\t\t.attr('shape-rendering', 'crispEdges')\n\tconst xscale = scaleLinear().domain([minlogfc, maxlogfc])\n\tconst yscale = scaleLinear().domain([minlogpv, maxlogpv])\n\tlet radiusscale\n\tconst dotg = mavb.vo_dotarea\n\t\t.selectAll()\n\t\t.data(mavb)\n\t\t.enter()\n\t\t.append('g')\n\t\t.each(function (d) {\n\t\t\td.vo_g = this\n\t\t})\n\tconst fold_change_cutoff = self.settings.foldchange\n\t//console.log(\"self.settings:\",self.settings)\n\t//self.config.settings.DEanalysis.min_count = self.settings.min_count\n\t//self.config.settings.DEanalysis.min_total_count = self.settings.min_total_count\n\tif (self.settings.pvalue == 0) throw 'p-value significance cannot be zero'\n\tconst p_value_cutoff = -Math.log10(self.settings.pvalue)\n\tconst p_value_adjusted_original = self.settings.adjusted_original_pvalue\n\tlet num_significant_genes = 0\n\tlet num_non_significant_genes = 0\n\tself.table_rows = []\n\tconst circle = dotg\n\t\t.append('circle')\n\t\t.attr('stroke', d => {\n\t\t\tlet color\n\t\t\tconst value3 = roundValueAuto(d.fold_change)\n\t\t\tconst value4 = roundValueAuto(Math.pow(10, -d.original_p_value))\n\t\t\tconst value5 = roundValueAuto(Math.pow(10, -d.adjusted_p_value))\n\t\t\tif (\n\t\t\t\tp_value_adjusted_original == 'adjusted' &&\n\t\t\t\td.adjusted_p_value > p_value_cutoff &&\n\t\t\t\tMath.abs(d.fold_change) > fold_change_cutoff\n\t\t\t) {\n\t\t\t\tcolor = 'red'\n\t\t\t\tnum_significant_genes += 1\n\n\t\t\t\tself.table_rows.push([\n\t\t\t\t\t{ value: d.gene_name },\n\t\t\t\t\t{ value: d.gene_symbol },\n\t\t\t\t\t{ value: value3 },\n\t\t\t\t\t{ value: value4 },\n\t\t\t\t\t{ value: value5 }\n\t\t\t\t])\n\t\t\t} else if (\n\t\t\t\tp_value_adjusted_original == 'original' &&\n\t\t\t\td.original_p_value > p_value_cutoff &&\n\t\t\t\tMath.abs(d.fold_change) > fold_change_cutoff\n\t\t\t) {\n\t\t\t\tcolor = 'red'\n\t\t\t\tnum_significant_genes += 1\n\t\t\t\tself.table_rows.push([\n\t\t\t\t\t{ value: d.gene_name },\n\t\t\t\t\t{ value: d.gene_symbol },\n\t\t\t\t\t{ value: value3 },\n\t\t\t\t\t{ value: value4 },\n\t\t\t\t\t{ value: value5 }\n\t\t\t\t])\n\t\t\t} else {\n\t\t\t\tcolor = 'black'\n\t\t\t\tnum_non_significant_genes += 1\n\t\t\t}\n\t\t\treturn color\n\t\t})\n\t\t.attr('stroke-opacity', 0.2)\n\t\t.attr('stroke-width', 1)\n\t\t.attr('fill', hlcolor)\n\t\t.attr('fill-opacity', 0)\n\t\t.each(function (d) {\n\t\t\td.vo_circle = this\n\t\t})\n\t\t.on('mouseover', circlemouseover)\n\t\t.on('mouseout', circlemouseout)\n\t//.on('click', (event, d) => {\n\t//\tcircleclick(d, mavb, event.clientX, event.clientY)\n\t//})\n\tself.table_rows.sort((a, b) => a[2].value - b[2].value).reverse() // Sorting genes in descending order of fold change\n\t//console.log(\n\t//\t'Percentage of significant genes:',\n\t//\t(num_significant_genes * 100) / (num_significant_genes + num_non_significant_genes)\n\t//)\n\n\tconst logfc0line = mavb.vo_dotarea.append('line').attr('stroke', '#ccc').attr('shape-rendering', 'crispEdges')\n\n\tfunction resize(w, h) {\n\t\twidth = w\n\t\theight = h\n\t\tyaxisw = Math.max(50, width / 8)\n\t\txaxish = Math.max(50, height / 8)\n\n\t\tradius = Math.max(width, height) / 80\n\t\tconst maxradius = radius * 3\n\t\tif (radiusscale) radiusscale.range([radius, maxradius])\n\t\tcircle.each(d => {\n\t\t\td.vo_radius = radiusscale ? radiusscale(Math.abs(d.tvalue)) : radius\n\t\t})\n\n\t\txpad = Math.max(maxradius, width / 50)\n\t\typad = Math.max(maxradius, height / 50)\n\t\tyaxisg.attr('transform', 'translate(' + yaxisw + ',' + toppad + ')')\n\t\txaxisg.attr('transform', 'translate(' + (yaxisw + xpad) + ',' + (toppad + height + ypad) + ')')\n\t\txlab.attr('x', yaxisw + xpad + width / 2).attr('y', toppad + height + ypad + xaxish - 5)\n\t\tylab.attr('transform', 'translate(15,' + (toppad + height / 2) + ') rotate(-90)')\n\t\tmavb.vo_dotarea.attr('transform', 'translate(' + (yaxisw + xpad) + ',' + toppad + ')')\n\t\tbox.attr('width', width).attr('height', height)\n\t\txscale.range([0, width])\n\t\tyscale.range([height, 0])\n\t\tdotg.attr('transform', d => {\n\t\t\treturn 'translate(' + xscale(d.fold_change) + ',' + yscale(d.adjusted_p_value) + ')'\n\t\t})\n\t\tcircle.attr('r', d => {\n\t\t\treturn d.vo_radius\n\t\t})\n\t\tlogfc0line.attr('x1', xscale(0)).attr('x2', xscale(0)).attr('y2', height)\n\n\t\tsvg.attr('width', yaxisw + xpad + width + rightpad).attr('height', toppad + height + ypad + xaxish)\n\t\taxisstyle({\n\t\t\taxis: yaxisg.call(d3axis.axisLeft().scale(yscale)),\n\t\t\tcolor: 'black',\n\t\t\tshowline: true\n\t\t})\n\t\taxisstyle({\n\t\t\taxis: xaxisg.call(d3axis.axisBottom().scale(xscale)),\n\t\t\tcolor: 'black',\n\t\t\tshowline: true\n\t\t})\n\t}\n\tresize(400, 400)\n\n\tif (mavb[0].adjusted_p_value != undefined) {\n\t\t// enable pvalue switching between adjusted and unadjusted\n\t\tconst row = holder.append('div').style('margin', '20px')\n\t\tminlogpv = 0\n\t\tmaxlogpv = 0\n\t\tlet text_string\n\t\tfor (const d of mavb) {\n\t\t\tlet pv\n\t\t\tif (p_value_adjusted_original == 'adjusted') {\n\t\t\t\tpv = d.adjusted_p_value\n\t\t\t} else {\n\t\t\t\tpv = d.original_p_value\n\t\t\t}\n\t\t\tif (pv == 0) continue\n\t\t\tminlogpv = Math.min(minlogpv, pv)\n\t\t\tmaxlogpv = Math.max(maxlogpv, pv)\n\t\t}\n\t\tyscale.domain([minlogpv, maxlogpv])\n\t\taxisstyle({\n\t\t\taxis: yaxisg.call(d3axis.axisLeft().scale(yscale)),\n\t\t\tcolor: 'black',\n\t\t\tshowline: true\n\t\t})\n\t\tdotg.attr('transform', d => {\n\t\t\tlet pv\n\t\t\tif (p_value_adjusted_original == 'adjusted') {\n\t\t\t\tpv = d.adjusted_p_value\n\t\t\t} else {\n\t\t\t\tpv = d.original_p_value\n\t\t\t}\n\t\t\treturn 'translate(' + xscale(d.fold_change) + ',' + yscale(pv) + ')'\n\t\t})\n\t\tif (p_value_adjusted_original == 'adjusted') {\n\t\t\ttext_string = '-log10(adjusted P value)'\n\t\t} else {\n\t\t\ttext_string = '-log10(original P value)'\n\t\t}\n\t\tylab.text(text_string)\n\t\tconst table_stats = table2col({ holder: self.dom.detailsDiv })\n\t\tconst addStats = [\n\t\t\t{\n\t\t\t\tlabel: 'Percentage of significant genes',\n\t\t\t\tvalue: roundValueAuto((num_significant_genes * 100) / (num_significant_genes + num_non_significant_genes))\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Number of significant genes',\n\t\t\t\tvalue: num_significant_genes\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Number of total genes',\n\t\t\t\tvalue: num_significant_genes + num_non_significant_genes\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: self.config.state.groups[0].name + ' sample size',\n\t\t\t\tvalue: sample_size1\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: self.config.state.groups[1].name + ' sample size',\n\t\t\t\tvalue: sample_size2\n\t\t\t}\n\t\t]\n\n\t\tfor (const dataRow of addStats) {\n\t\t\tconst [td1, td2] = table_stats.addRow()\n\t\t\ttd1.text(dataRow.label)\n\t\t\ttd2.style('text-align', 'end').text(dataRow.value)\n\t\t}\n\n\t\tself.table_cols = [\n\t\t\t{ label: 'Gene Name' },\n\t\t\t{ label: 'Gene Symbol' },\n\t\t\t{ label: 'log2 Fold change' },\n\t\t\t{ label: 'Original p-value (linear scale)' },\n\t\t\t{ label: 'Adjusted p-value (linear scale)' }\n\t\t]\n\t\tif (self.settings.pvaluetable == true) {\n\t\t\tconst d = self.dom.tableDiv.append('div').html(`<br>DE analysis results`)\n\t\t\trenderTable({\n\t\t\t\tcolumns: self.table_cols,\n\t\t\t\trows: self.table_rows,\n\t\t\t\tdiv: d,\n\t\t\t\tshowLines: true,\n\t\t\t\tmaxHeight: '150vh',\n\t\t\t\tresize: true\n\t\t\t})\n\t\t} else {\n\t\t\tself.dom.tableDiv.selectAll('*').remove()\n\t\t}\n\n\t\tif (self.settings.gene_ora && self.app.opts.genome.termdbs) {\n\t\t\t// Currently backend only uses msigdb, but in future may use other databases in genome.termdbs{}. In ui will need to generate a <select> to choose one key of termdbs{}.\n\t\t\t//console.log('Run gene ora:', self.settings.gene_ora)\n\t\t\t//console.log('output.data:', output.data)\n\t\t\tconst sample_genes = []\n\t\t\tconst background_genes = []\n\t\t\t//console.log('self:', self)\n\t\t\t//console.log('fold_change_cutoff:', fold_change_cutoff)\n\n\t\t\t// Need to handle those genes which do not have a name\n\t\t\tif (self.settings.gene_ora == 'upregulated') {\n\t\t\t\tfor (const gene of output.data) {\n\t\t\t\t\tif (gene.gene_symbol.length > 0) {\n\t\t\t\t\t\t// Do not include blank rows\n\t\t\t\t\t\tif (fold_change_cutoff < Math.abs(gene.fold_change) && gene.fold_change > 0) {\n\t\t\t\t\t\t\tsample_genes.push(gene.gene_symbol)\n\t\t\t\t\t\t}\n\t\t\t\t\t\tbackground_genes.push(gene.gene_symbol)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t} else if (self.settings.gene_ora == 'downregulated') {\n\t\t\t\tfor (const gene of output.data) {\n\t\t\t\t\tif (gene.gene_symbol.length > 0) {\n\t\t\t\t\t\t// Do not include blank rows\n\t\t\t\t\t\tif (fold_change_cutoff < Math.abs(gene.fold_change) && gene.fold_change < 0) {\n\t\t\t\t\t\t\tsample_genes.push(gene.gene_symbol)\n\t\t\t\t\t\t}\n\t\t\t\t\t\tbackground_genes.push(gene.gene_symbol)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t} else if (self.settings.gene_ora == 'both') {\n\t\t\t\tfor (const gene of output.data) {\n\t\t\t\t\tif (gene.gene_symbol.length > 0) {\n\t\t\t\t\t\t// Do not include blank rows\n\t\t\t\t\t\tif (fold_change_cutoff < Math.abs(gene.fold_change)) {\n\t\t\t\t\t\t\tsample_genes.push(gene.gene_symbol)\n\t\t\t\t\t\t}\n\t\t\t\t\t\tbackground_genes.push(gene.gene_symbol)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\tconsole.log('Unrecognized option')\n\t\t\t}\n\n\t\t\tconst geneORAparams = {\n\t\t\t\tsample_genes: sample_genes.toString(),\n\t\t\t\tbackground_genes: background_genes.toString(),\n\t\t\t\tgenome: self.app.vocabApi.opts.state.vocab.genome\n\t\t\t}\n\t\t\tconst config = {\n\t\t\t\tchartType: 'geneORA',\n\t\t\t\tgeneORAparams: geneORAparams\n\t\t\t}\n\t\t\tself.app.dispatch({\n\t\t\t\ttype: 'plot_create',\n\t\t\t\tconfig\n\t\t\t})\n\t\t}\n\n\t\tif (self.settings.gsea && self.app.opts.genome.termdbs) {\n\t\t\t// Currently backend only uses msigdb, but in future may use other databases in genome.termdbs{}. 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+  "names": []
+}

package/dist/{Disco-ZLOF2OSY.js → Disco-HFIKRNBB.js}

@@ -1,15 +1,15 @@
 import {
   svgLegend
-} from "./chunk-FPQKVUJW.js";
+} from "./chunk-NWHIPXEK.js";
 import {
   configUiInit
-} from "./chunk-X5ZQI22O.js";
+} from "./chunk-Z3TD3CHR.js";
 import {
   topBarInit
 } from "./chunk-U6ZCLI5S.js";
-import "./chunk-WA6VYIW4.js";
+import "./chunk-47W2ODRY.js";
 import "./chunk-CLHA5AEH.js";
-import "./chunk-PU7EMWOK.js";
+import "./chunk-HR3FNUVU.js";
 import "./chunk-7KFEDC2T.js";
 import "./chunk-FCPSU6WB.js";
 import "./chunk-WX2C2ZIZ.js";
@@ -17,7 +17,7 @@ import "./chunk-CVWXP35F.js";
 import "./chunk-OTWQWP6Z.js";
 import "./chunk-6BHKLDWV.js";
 import "./chunk-EG3MKQQH.js";
-import "./chunk-TU4H4R2T.js";
+import "./chunk-LGC254YE.js";
 import "./chunk-ZYRXVRSD.js";
 import "./chunk-SJ4KZVLF.js";
 import "./chunk-ALPXXDQD.js";
@@ -222,7 +222,7 @@ var DiscoInteractions = class {
           }
         ]
       };
-      const _ = await import("./block.init-MFZ6BKQR.js");
+      const _ = await import("./block.init-7PZ4PJTK.js");
       await _.default(arg);
     };
   }
@@ -2459,4 +2459,4 @@ export {
   discoInit,
   getPlotConfig
 };
-//# sourceMappingURL=Disco-ZLOF2OSY.js.map
+//# sourceMappingURL=Disco-HFIKRNBB.js.map