@sjcrh/proteinpaint-client 2.195.0 → 2.196.0

package/dist/chunk-MTHEEXT2.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../mass/sessionBtn.js", "../mass/about.ts", "../mass/chat.ts", "../mass/nav.js"],
+  "sourcesContent": ["import { getCompInit } from '#rx'\nimport { Menu } from '#dom/menu'\nimport { to_textfile } from '#dom/downloadTextfile'\nimport { dofetch3 } from '#common/dofetch'\nimport { parentCorsMessage } from '#common/embedder-helpers'\nimport { select } from 'd3-selection'\nimport { importPlot } from '#plots/importPlot.js'\n\nclass MassSessionBtn {\n\tstatic type = 'sessionBtn'\n\n\tconstructor() {\n\t\tthis.type = MassSessionBtn.type\n\t\tthis.route = 'termdb'\n\t\tthis.embedderOrigin = window.location.origin\n\t\tthis.hostURL = sessionStorage.getItem('hostURL') || this.embedderOrigin\n\t}\n\n\tasync init(appState) {\n\t\tconst tip = new Menu({ padding: '0px' })\n\t\tconst copytip = new Menu({ padding: '5px' })\n\t\tthis.dom = {\n\t\t\tbutton: this.opts.button,\n\t\t\ttip,\n\t\t\tcopytip\n\t\t}\n\n\t\tthis.dom.button.on('click', event => {\n\t\t\tevent.stopPropagation()\n\t\t\tthis.dom.tip.clear()\n\t\t\tthis.showMenu()\n\t\t})\n\n\t\tthis.dslabel = appState.vocab.dslabel\n\t\tthis.savedSessions = JSON.parse(localStorage.getItem('savedMassSessions') || `{}`)\n\t\tthis.requiredAuth = appState.termdbConfig?.requiredAuth?.find(a => a.route == this.route && a.type == 'jwt')\n\t}\n\n\tasync showMenu() {\n\t\tthis.dom.tip.clear().d.style('padding', 0)\n\t\tthis.dom.tip.d.attr('id', 'sjpp-session-menu')\n\t\tconst gt = `<span style='margin-left: 24px; float: right'>&gt;</span>`\n\t\tconst options = [\n\t\t\t{ label: `Open`, title: 'Recover a saved session', callback: this.open },\n\t\t\t{ label: `Save`, title: 'Save the current view', callback: this.save },\n\t\t\t{ label: `Share`, title: 'Share the current view', callback: this.getSessionUrl }\n\t\t]\n\n\t\tif (!this.serverCachedSessions) await this.setServerCachedSessions()\n\t\tif (Object.keys(this.savedSessions).length || Object.keys(this.serverCachedSessions).length) {\n\t\t\toptions.push({ label: `Delete`, title: 'Delete a saved session', callback: this.delete })\n\t\t}\n\n\t\tthis.dom.tip\n\t\t\t.clear()\n\t\t\t.d.selectAll('.sja_menuoption sja_sharp_border')\n\t\t\t.data(options)\n\t\t\t.enter()\n\t\t\t.append('div')\n\t\t\t.attr('class', 'sja_menuoption sja_sharp_border')\n\t\t\t.attr('data-testid', d => `sjpp-session-btn-${d.label.toLowerCase().replace(/\\s/g, '-')}`)\n\t\t\t.attr('aria-label', d => d.title)\n\t\t\t.html(d => d.label)\n\t\t\t.on('click', (event, d) => {\n\t\t\t\tthis.dom.tip.clear().d.style('padding', '10px')\n\t\t\t\tevent.stopPropagation()\n\t\t\t\tthis.showBackBtn()\n\t\t\t\td.callback.call(this)\n\t\t\t})\n\n\t\tthis.dom.tip.showunder(this.dom.button.node())\n\t}\n\n\tasync open() {\n\t\tconst radioName = `sjpp-session-open-radio-` + Math.random().toString().slice(-6)\n\t\t// always open in the current tab for now, to avoid the tricky part of the code\n\t\t// that involves parent-child window messaging\n\t\t// TODO: re-enable when the new tab option works reliably\n\t\tthis.dom.tip.d.append('div').style('display', 'none').style('padding', '3px 9px').html(`\n\t\t\t<b>Open in</b>\n\t\t\t<label>\n\t\t\t\t<input type='radio' name='${radioName}' value='new' style='margin-right: 0; vertical-align: bottom'/>\n\t\t\t\t<span>a new tab</span>\n\t\t\t</label>\n\t\t\t<label style='margin-left: 5px'>\n\t\t\t\t<input type='radio' name='${radioName}' value='current' checked=checked style='margin-right: 0; vertical-align: bottom'/>\n\t\t\t\t<span>current tab</span>\n\t\t\t</label>\n\t\t`)\n\n\t\tconst t = await this.listSessions({\n\t\t\ttrClickHandler: async (event, d) => {\n\t\t\t\tconst { loc, id } = d\n\t\t\t\tif (!id) return\n\t\t\t\tif (loc.includes('browser')) {\n\t\t\t\t\tthis.sessionName = id\n\t\t\t\t\tconst state = structuredClone(this.savedSessions[id])\n\t\t\t\t\tawait preprocessState(state, this.app)\n\t\t\t\t\tconst targetWindow = this.dom.tip.d.node().querySelector(`[name=\"${radioName}\"]:checked`).value\n\t\t\t\t\tif (targetWindow == 'current') {\n\t\t\t\t\t\tthis.app.dispatch({ type: 'app_refresh', state })\n\t\t\t\t\t} else if (window.location.origin == this.hostURL) {\n\t\t\t\t\t\twindow.open(`/?mass-session-id=${id}&src=browser`)\n\t\t\t\t\t} else {\n\t\t\t\t\t\tif (state.embedder) parentCorsMessage({ state })\n\t\t\t\t\t\telse {\n\t\t\t\t\t\t\tconst { protocol, host, search, origin, href } = window.location\n\t\t\t\t\t\t\tconst embedder = { protocol, host, search, origin, href }\n\t\t\t\t\t\t\tparentCorsMessage({ state: Object.assign({ embedder }, state) })\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\tthis.dom.tip.hide()\n\t\t\t\t} else if (loc == 'server') {\n\t\t\t\t\tconst headers = await this.app.vocabApi.mayGetAuthHeaders(this.route)\n\t\t\t\t\tconst body = { id, route: this.route, dslabel: this.dslabel, embedder: window.location.hostname }\n\t\t\t\t\tconst res = await dofetch3(`/massSession?`, { headers, body })\n\t\t\t\t\tif (!res.state) throw res.error || 'unable to get the cached session from the server'\n\t\t\t\t\tawait preprocessState(res.state, this.app)\n\t\t\t\t\tthis.savedSessions[id] = res.state\n\n\t\t\t\t\tconst targetWindow = this.dom.tip.d.node().querySelector(`[name=\"${radioName}\"]:checked`).value\n\t\t\t\t\tif (targetWindow == 'current') {\n\t\t\t\t\t\tthis.app.dispatch({ type: 'app_refresh', state: res.state })\n\t\t\t\t\t} else if (window.location.origin == this.hostURL) {\n\t\t\t\t\t\twindow.open(`/?mass-session-id=${id}&src=cred&dslabel=${this.dslabel}&route=${this.route}`)\n\t\t\t\t\t} else {\n\t\t\t\t\t\t// server-cached sessions should have an state.embedder object, no need to check\n\t\t\t\t\t\tparentCorsMessage(res)\n\t\t\t\t\t}\n\t\t\t\t\tthis.dom.tip.hide()\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\n\t\tt.headtr.select('th').html('Open from')\n\n\t\t// open session from a local file\n\t\tconst tr1 = t.tbody.insert('tr', 'tr')\n\t\ttr1.append('td').style('text-align', 'center').style('padding', '3px 9px').html('Local file')\n\t\tconst label = tr1.append('td').style('text-align', 'left').append('label')\n\t\tlabel\n\t\t\t.append('span')\n\t\t\t.style('padding', '3px 9px')\n\t\t\t.style('text-decoration', 'underline')\n\t\t\t.style('cursor', 'pointer')\n\t\t\t.html('Choose File')\n\t\tlabel\n\t\t\t.append('input')\n\t\t\t.attr('type', 'file')\n\t\t\t.attr('placeholder', 'file name')\n\t\t\t.style('opacity', 0)\n\t\t\t.style('width', '0.1px')\n\t\t\t.style('height', '0.1px')\n\t\t\t.style('position', 'absolute')\n\t\t\t.on('change', async () => {\n\t\t\t\tconst file = event.target.files.item(0)\n\t\t\t\tconst json = await file.text()\n\t\t\t\tlet sessionName = file.name\n\t\t\t\tif (this.savedSessions[sessionName]) {\n\t\t\t\t\tsessionName = prompt(\n\t\t\t\t\t\t`Leave as-is to overwrite a session with the same name, or enter a different session name.`,\n\t\t\t\t\t\tsessionName\n\t\t\t\t\t)\n\t\t\t\t}\n\t\t\t\tthis.sessionName = sessionName\n\t\t\t\tconst state = JSON.parse(json)\n\t\t\t\tawait preprocessState(state, this.app)\n\t\t\t\tthis.savedSessions[sessionName] = state\n\t\t\t\tlocalStorage.setItem('savedMassSessions', JSON.stringify(this.savedSessions))\n\t\t\t\tconst targetWindow = this.dom.tip.d.node().querySelector(`[name=\"${radioName}\"]:checked`).value\n\t\t\t\tif (targetWindow == 'current') {\n\t\t\t\t\tthis.app.dispatch({ type: 'app_refresh', state })\n\t\t\t\t} else if (window.location.origin == this.hostURL) {\n\t\t\t\t\twindow.open(`/?mass-session-id=${sessionName}&src=browser`)\n\t\t\t\t} else {\n\t\t\t\t\tif (state.embedder) parentCorsMessage({ state })\n\t\t\t\t\telse {\n\t\t\t\t\t\tconst { protocol, host, search, origin, href } = window.location\n\t\t\t\t\t\tconst embedder = { protocol, host, search, origin, href }\n\t\t\t\t\t\tparentCorsMessage({ state: Object.assign({ embedder }, state) })\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tthis.dom.tip.hide()\n\t\t\t})\n\t}\n\n\tasync listSessions(opts = {}) {\n\t\tconst table = this.dom.tip.d.append('table').attr('class', 'sjpp-controls-table')\n\n\t\tconst headtr = table.append('thead').append('tr')\n\t\theadtr\n\t\t\t.selectAll('th')\n\t\t\t.data(['Cache Location', 'Session ID'])\n\t\t\t.enter()\n\t\t\t.append('th')\n\t\t\t.style('text-align', (d, i) => (i === 0 ? 'center' : 'left'))\n\t\t\t.style('padding', '3px 9px')\n\t\t\t.html(d => d)\n\n\t\tconst sessionIds = Object.keys(this.savedSessions).map(id => ({ loc: 'browser', id }))\n\t\tif (!this.serverCachedSessions) await this.setServerCachedSessions()\n\t\tsessionIds.push(...this.serverCachedSessions.map(id => ({ loc: 'server', id })))\n\n\t\tconst tbody = table.append('tbody')\n\t\tconst trs = tbody\n\t\t\t.selectAll('tr')\n\t\t\t.data(sessionIds)\n\t\t\t.enter()\n\t\t\t.append('tr')\n\t\t\t.on('click', opts.trClickHandler || null)\n\n\t\ttrs\n\t\t\t.selectAll('td')\n\t\t\t.data(d => [d, d])\n\t\t\t.enter()\n\t\t\t.append('td')\n\t\t\t.style('text-align', (d, i) => (i === 0 ? 'center' : 'left'))\n\t\t\t.style('padding', '3px 9px')\n\t\t\t.style('cursor', 'pointer')\n\t\t\t.html((d, i) => (i === 0 ? d.loc : d.id))\n\n\t\tif (!this.serverCachedSessions.length && this.requiredAuth && !this.app.vocabApi.hasVerifiedToken()) {\n\t\t\tconst tbody2 = table\n\t\t\t\t.append('tbody')\n\t\t\t\t.append('tr')\n\t\t\t\t.selectAll('td')\n\t\t\t\t.data(['server', 'requires sign-in'])\n\t\t\t\t.enter()\n\t\t\t\t.append('td')\n\t\t\t\t.style('text-align', (d, i) => (i === 0 ? 'center' : 'left'))\n\t\t\t\t.style('padding', '3px 9px')\n\t\t\t\t.html(d => d)\n\t\t}\n\t\treturn { table, headtr, tbody, trs }\n\t}\n\n\tasync setServerCachedSessions() {\n\t\tconst state = this.app.getState()\n\t\tthis.requiredAuth = state.termdbConfig?.requiredAuth?.find(a => a.route == this.route && a.type == 'jwt')\n\t\tif (!this.requiredAuth) {\n\t\t\tthis.serverCachedSessions = []\n\t\t\treturn\n\t\t}\n\t\tconst headers = this.app.vocabApi.mayGetAuthHeaders(this.route)\n\t\tconst body = { route: this.route, dslabel: this.dslabel, embedder: window.location.hostname }\n\t\tconst res = await dofetch3('/sessionIds', { headers, body })\n\t\tthis.serverCachedSessions = res.sessionIds || []\n\t}\n\n\tasync save(d) {\n\t\tconst div = this.dom.tip.d\n\t\tconst inputDiv = div.append('div')\n\t\tinputDiv.append('span').html('Save as')\n\t\tconst sessionNames = Object.keys(this.savedSessions)\n\t\tif (!this.serverCachedSessions) await this.setServerCachedSessions()\n\t\tsessionNames.push(...this.serverCachedSessions.filter(d => !sessionNames.includes(d)))\n\t\tconst placeholder = this.sessionName || 'unnamed-session'\n\t\tconst input = inputDiv\n\t\t\t.append('input')\n\t\t\t.attr('type', 'text')\n\t\t\t.attr('placeholder', placeholder)\n\t\t\t.style('width', '220px')\n\t\t\t.on('input', () => {\n\t\t\t\tsearchResultDiv.selectAll('*').remove()\n\t\t\t\tconst value = input.property('value')\n\t\t\t\tconst exactMatch = sessionNames.filter(s => s === value)\n\t\t\t\tconst startsWith = sessionNames.filter(s => s.startsWith(value))\n\t\t\t\tconst includes = sessionNames.filter(s => s.includes(value) && s !== value && !startsWith.includes(s))\n\t\t\t\tsearchResultDiv\n\t\t\t\t\t.selectAll('div')\n\t\t\t\t\t.data([...exactMatch, ...startsWith, ...includes])\n\t\t\t\t\t.enter()\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t\t.attr('data-testid', `sjpp-save-session-option`)\n\t\t\t\t\t.html(d => d)\n\t\t\t\t\t.on('click', (event, d) => {\n\t\t\t\t\t\tinput.property('value', d)\n\t\t\t\t\t\tsearchResultDiv.selectAll('*').remove()\n\t\t\t\t\t})\n\t\t\t})\n\n\t\tconst searchResultDiv = div.append('div')\n\t\tconst submitDiv = div.append('div')\n\t\tsubmitDiv.append('span').html('Save to&nbsp;')\n\t\tsubmitDiv\n\t\t\t.append('button')\n\t\t\t.style('min-width', '80px')\n\t\t\t.html('Browser')\n\t\t\t.attr(\n\t\t\t\t'title',\n\t\t\t\t`Save the session in your current browser's cache. The session can be easily recovered, but not shared among your other devices`\n\t\t\t)\n\t\t\t.on('click', () => {\n\t\t\t\tthis.sessionName = input.property('value') || placeholder\n\t\t\t\tthis.savedSessions[this.sessionName] = this.app.getState()\n\t\t\t\tlocalStorage.setItem('savedMassSessions', JSON.stringify(this.savedSessions))\n\t\t\t\tthis.confirmAction(`Cached '<b>${this.sessionName}</b>' in browser`)\n\t\t\t})\n\n\t\tsubmitDiv\n\t\t\t.append('button')\n\t\t\t.style('min-width', '80px')\n\t\t\t.html('File')\n\t\t\t.attr(\n\t\t\t\t'title',\n\t\t\t\t`Save the session into a local file. The session can be easily recoved using the 'Open from local file' option.`\n\t\t\t)\n\t\t\t.on('click', () => {\n\t\t\t\tconst name = input.property('value') || placeholder\n\t\t\t\tthis.savedSessions[name] = this.app.getState()\n\t\t\t\tthis.download(name)\n\t\t\t\tthis.confirmAction(`Downloaded '<b>${name}</b>'`)\n\t\t\t})\n\n\t\t// assume that a jwt-type credential will include the user email in the jwt payload,\n\t\t// which could be trusted for saving sessions under cachedir/termdbSessions/[embedderHostName]/[email]\n\t\tif (this.requiredAuth) {\n\t\t\tconst requiresSignIn = this.app.vocabApi.hasVerifiedToken() ? '' : 'Requires sign-in. '\n\t\t\tsubmitDiv\n\t\t\t\t.append('button')\n\t\t\t\t.style('min-width', '80px')\n\t\t\t\t.html('Server')\n\t\t\t\t.attr(\n\t\t\t\t\t'title',\n\t\t\t\t\t`${requiresSignIn}Save the session into a remote server. The session can be easily shared across your different devices and recovered using the 'Open from server' option.`\n\t\t\t\t)\n\t\t\t\t.property('disabled', !this.app.vocabApi.hasVerifiedToken())\n\t\t\t\t.on('click', async () => {\n\t\t\t\t\tif (!this.app.vocabApi.hasVerifiedToken()) {\n\t\t\t\t\t\talert('Requires sign-in')\n\t\t\t\t\t\treturn\n\t\t\t\t\t}\n\t\t\t\t\tconst name = input.property('value') || placeholder\n\t\t\t\t\tthis.savedSessions[name] = this.app.getState()\n\t\t\t\t\tconst res = await this.getSessionUrl(name)\n\t\t\t\t\tif (res.id != name) throw `error saving ${name}`\n\t\t\t\t\t// this.download(name)\n\t\t\t\t\tthis.confirmAction(`Saved '<b>${name}</b>' on the server`)\n\t\t\t\t})\n\t\t}\n\t}\n\n\tdownload(name = '') {\n\t\tconst sessionName = name || this.sessionName\n\t\tconst ext = sessionName?.endsWith('.txt') ? '' : '.txt'\n\t\tconst filename = `${sessionName}${ext}`\n\t\tto_textfile(filename, JSON.stringify(this.savedSessions[sessionName]))\n\t}\n\n\tasync getSessionUrl(filename = '') {\n\t\tconst headers = await this.app.vocabApi.mayGetAuthHeaders('termdb')\n\t\tconst state = structuredClone(this.app.getState())\n\t\tconst { protocol, host, search, origin, href } = window.location\n\t\tstate.embedder = { protocol, host, search, origin, href }\n\t\tif (filename) {\n\t\t\t// a non-empty filename value implies saving by email and having auth session,\n\t\t\t// since it's easy for different users to use the same non-random filename\n\t\t\tstate.__sessionFor__ = {\n\t\t\t\troute: this.route,\n\t\t\t\tfilename,\n\t\t\t\tdslabel: this.dslabel,\n\t\t\t\tembedder: window.location.hostname\n\t\t\t}\n\t\t}\n\t\tconst res = await dofetch3('/massSession', {\n\t\t\theaders,\n\t\t\tmethod: 'POST',\n\t\t\tbody: JSON.stringify(state)\n\t\t})\n\n\t\tif (filename) {\n\t\t\treturn res\n\t\t} else {\n\t\t\tconst url = `${this.hostURL}/?mass-session-id=${res.id}&noheader=1`\n\t\t\tthis.dom.tip.showunder(this.dom.button.node())\n\t\t\tconst linkDiv = this.dom.tip.d.append('div').style('margin', '10px')\n\t\t\tlinkDiv\n\t\t\t\t.append('div')\n\t\t\t\t.style('display', 'flex')\n\t\t\t\t.style('margin-bottom', '12px')\n\t\t\t\t.html(`Open or copy the session link.`)\n\n\t\t\tconst a = linkDiv.append('a').style('display', 'none').attr('href', url).attr('target', '_blank').html(res.id)\n\n\t\t\t// open button\n\t\t\tlinkDiv\n\t\t\t\t.append('button')\n\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t.text('Open link')\n\t\t\t\t.on('click', () => {\n\t\t\t\t\ta.node().click()\n\t\t\t\t})\n\n\t\t\t// copy button\n\t\t\tlinkDiv\n\t\t\t\t.append('button')\n\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t.style('margin-left', '10px')\n\t\t\t\t.text('Copy link')\n\t\t\t\t.on('click', async event => {\n\t\t\t\t\tawait navigator.clipboard.writeText(url)\n\t\t\t\t\tthis.dom.copytip.clear().showunder(event.target)\n\t\t\t\t\tthis.dom.copytip.d.append('div').html('&#10003;')\n\t\t\t\t\tsetTimeout(() => {\n\t\t\t\t\t\tthis.dom.copytip.hide()\n\t\t\t\t\t}, 1000)\n\t\t\t\t})\n\n\t\t\tif (this.hostURL != window.location.origin) {\n\t\t\t\t// Avoid the multi-window/tab sequence to recover the session:\n\t\t\t\t// intercept the click on the URL link, so that the embedder URL is opened\n\t\t\t\t// instead of the hostURL with mass session id, and this window will post\n\t\t\t\t// a message to the child window with the link data instead\n\t\t\t\t//\n\t\t\t\t// NOTE: the multi-window/tab sequence is only necessary when the URL link\n\t\t\t\t// was not opened by the embedder window\n\t\t\t\t//\n\t\t\t\ta.on('click', event => {\n\t\t\t\t\tevent.preventDefault()\n\t\t\t\t\tparentCorsMessage({ state }, 'noredirect')\n\t\t\t\t\treturn false\n\t\t\t\t})\n\t\t\t}\n\n\t\t\tlinkDiv.append('div').html(`\n\t\t\t\t\t<br>\n\t\t\t\t\t<div style=\"max-width: 400px; font-size: 1em; opacity:.6\">\n\t\t\t\t\t<span>NOTES</span>\n\t\t\t\t\t<ul>\n\t\t\t\t\t<li>A recovered session may hide data or views to users that are not authorized to access the saved datasets or features.</li>\n\t\t\t\t\t<li>This session will be saved for ${this.opts.massSessionDuration} days.</li>\n\t\t\t\t\t</ul>\n\t\t\t\t\t</div>`)\n\t\t\tsetTimeout(() => {\n\t\t\t\tthis.dom.button.property('disabled', false)\n\t\t\t}, 1000)\n\t\t}\n\t}\n\n\tasync delete() {\n\t\tconst t = await this.listSessions({\n\t\t\ttrClickHandler: function (event) {\n\t\t\t\tconst input = this.lastChild.querySelector('input')\n\t\t\t\tconst checked = event.target == input ? input.checked : !input.checked\n\t\t\t\tselect(this).style('text-decoration', checked ? 'line-through' : '')\n\t\t\t\tif (event.target != input) input.checked = checked\n\t\t\t\tconst checkedRows = t.table.node().querySelectorAll('input:checked')\n\t\t\t\tsubmitBtn.property('disabled', checkedRows.length ? false : true)\n\t\t\t}\n\t\t})\n\n\t\t// add a 3rd column for the checkboxes\n\t\tt.headtr.append('th').html('Delete')\n\t\tt.trs.each(function (d) {\n\t\t\tselect(this)\n\t\t\t\t.append('td')\n\t\t\t\t.style('text-align', 'center')\n\t\t\t\t.append('input')\n\t\t\t\t.attr('type', 'checkbox')\n\t\t\t\t.attr('value', d.id)\n\t\t})\n\n\t\tconst submitBtn = this.dom.tip.d\n\t\t\t.append('div')\n\t\t\t.style('text-align', 'center')\n\t\t\t.append('button')\n\t\t\t.html('Delete selected sessions')\n\t\t\t.property('disabled', true)\n\t\t\t.on('click', async () => {\n\t\t\t\tconst inputs = t.table.node().querySelectorAll('input')\n\t\t\t\tconst sessionIdsDeletedFromServer = []\n\t\t\t\tfor (const input of inputs) {\n\t\t\t\t\tif (select(input).property('checked')) {\n\t\t\t\t\t\tconst d = input.parentNode.parentNode.__data__\n\t\t\t\t\t\tif (d.loc == 'browser') {\n\t\t\t\t\t\t\tdelete this.savedSessions[input.value] //checkedIds.push(input.value)\n\t\t\t\t\t\t} else if (d.loc == 'server') {\n\t\t\t\t\t\t\tdelete this.serverCachedSessions[input.value]\n\t\t\t\t\t\t\tsessionIdsDeletedFromServer.push(input.value)\n\t\t\t\t\t\t} else throw `unknown cache location=${d.loc}`\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tlocalStorage.setItem('savedMassSessions', JSON.stringify(this.savedSessions))\n\t\t\t\ttry {\n\t\t\t\t\tconst headers = await this.app.vocabApi.mayGetAuthHeaders('termdb')\n\t\t\t\t\tconst body = {\n\t\t\t\t\t\tids: sessionIdsDeletedFromServer,\n\t\t\t\t\t\troute: this.route,\n\t\t\t\t\t\tdslabel: this.dslabel,\n\t\t\t\t\t\tembedder: window.location.hostname\n\t\t\t\t\t}\n\t\t\t\t\tconst res = dofetch3(`/massSession?`, { method: 'DELETE', headers, body })\n\t\t\t\t} catch (e) {\n\t\t\t\t\tthrow e\n\t\t\t\t}\n\t\t\t\tthis.dom.tip.hide()\n\t\t\t})\n\t}\n\n\tshowBackBtn() {\n\t\tthis.dom.tip.d\n\t\t\t.append('div')\n\t\t\t.attr('class', 'sja_clbtext2')\n\t\t\t.style('margin-bottom', '10px')\n\t\t\t.style('cursor', 'pointer')\n\t\t\t.html(`&lt; Session Menu`)\n\t\t\t.on('click', () => this.showMenu())\n\t}\n\n\tconfirmAction(html) {\n\t\tthis.dom.tip.clear().d.append('div').html(html).transition().delay(3000).duration(1000).style('opacity', 0)\n\n\t\tsetTimeout(() => {\n\t\t\tthis.dom.tip.hide()\n\t\t}, 3500)\n\t}\n}\n\n// may need to edit state based on updated expectations,\n// such as new or deprecated plot settings keys/values\nasync function preprocessState(state, app) {\n\tdelete state.termdbConfig\n\tif (state.plots) {\n\t\tconst promises = []\n\t\tfor (const plot of state.plots) {\n\t\t\tpromises.push(\n\t\t\t\t(async () => {\n\t\t\t\t\tconst _ = await importPlot(plot.chartType)\n\t\t\t\t\treturn await _.getPlotConfig(plot, app)\n\t\t\t\t})()\n\t\t\t)\n\t\t}\n\t\ttry {\n\t\t\tawait Promise.all(promises)\n\t\t} catch (e) {\n\t\t\tconsole.log(e)\n\t\t\tapp.printError(e)\n\t\t}\n\t}\n}\n\nexport const sessionBtnInit = getCompInit(MassSessionBtn)\n", "import { getId } from './nav'\nimport { type AppApi, getCompInit } from '#rx'\nimport type { Elem, Div, H2 } from '../types/d3'\nimport type { SelectCohortEntry } from '#types'\nimport { renderTable, type TableRow } from '#dom'\nimport { select } from 'd3-selection'\n\n/* \n\"about\" tab will display following contents inside this.subheader:\n- if ds uses subcohorts:\n\t- <h2> for selectCohort.title\n\t- description\n\t- radio button options\n- custom html via massNav.about.html (todo images and cartoon)\n- active items to launch demo plots\n- server info\n*/\n\nconst cohortTableActiveColor = 'yellow'\n\n// this type is fully defined in MassNav def in dataset.ts but not in a form that can extract \"about\" config to share. thus need to repeat here to avoid tsc err\ntype AboutObj = {\n\thtml: string\n\tactiveItems?: { items: any }\n\tdisclaimer?: any\n}\n\ntype MassAboutOpts = {\n\t/** Optional. Set in the dataset file under .massNav.tabs.about. Otherwise null. */\n\taboutOverrides: AboutObj | null\n\t/** Required. Provided from nav component */\n\tapp: AppApi\n\t/** Required. Provided from nav component */\n\tinstanceNum: number\n\t/** Optional. Set in the dataset file under .termdb.selectCohort. Otherwise null. */\n\tselectCohort: SelectCohortEntry | null\n\t/** Required. .dom.subheader.about in nav component, assigned to this.subheader */\n\tsubheader: Elem\n}\n\ntype MassAboutDom = {\n\t/** Fine print dom shown between the cohort specific content and the server info */\n\tcohortAsterisk?: Div\n\t/** Displays description */\n\tcohortDescription: Div\n\t/** Div for cohort radio buttons */\n\tcohortOpts?: Div\n\t/** Text above radio cohort options */\n\tcohortPrompt?: Div\n\t/**  */\n\tcohortTable?: Div\n\t/** Title above the cohort introduction/content */\n\tcohortTitle?: H2\n}\n//TODO: Make a validate opts fn\nexport class MassAbout {\n\tstatic type = 'about'\n\n\taboutOverrides: AboutObj | null\n\tapp: AppApi\n\tdom: MassAboutDom\n\tinstanceNum: number\n\tselectCohort: SelectCohortEntry | null\n\tsubheader: Elem // where all contents are rendered\n\ttype: string\n\topts: MassAboutOpts\n\tstate: any\n\n\tconstructor(opts: MassAboutOpts) {\n\t\tthis.opts = opts\n\t\tthis.type = MassAbout.type\n\t\tthis.app = opts.app\n\t\tthis.subheader = opts.subheader\n\t\tthis.instanceNum = opts.instanceNum\n\t\tthis.aboutOverrides = opts.aboutOverrides\n\t\tthis.selectCohort = opts.selectCohort\n\t\tthis.dom = {\n\t\t\tcohortDescription: this.subheader\n\t\t\t\t.append('div')\n\t\t\t\t.attr('data-testid', 'sjpp-about-cohort-desc')\n\t\t\t\t.style('margin-left', '10px')\n\t\t}\n\n\t\tif (opts?.selectCohort?.title) {\n\t\t\tthis.dom.cohortTitle = opts.subheader\n\t\t\t\t.append('h2')\n\t\t\t\t.attr('data-testid', 'sjpp-about-cohort-title')\n\t\t\t\t.style('margin-left', '10px')\n\t\t\t\t.text(opts.selectCohort.title)\n\t\t}\n\n\t\tif (opts.selectCohort?.prompt) {\n\t\t\tthis.dom.cohortPrompt = this.subheader\n\t\t\t\t.append('div')\n\t\t\t\t.attr('data-testid', 'sjpp-about-cohort-prompt')\n\t\t\t\t.style('margin-left', '10px')\n\t\t\t\t.style('padding-top', '30px')\n\t\t\t\t.style('padding-bottom', '10px')\n\t\t\t\t.style('font-weight', 'bold')\n\t\t\t\t.style('font-size', '1.2em')\n\t\t\t\t.text(opts.selectCohort.prompt)\n\t\t}\n\n\t\tif (opts.selectCohort) {\n\t\t\tthis.dom.cohortOpts = this.subheader.append('div').style('margin-bottom', '30px').style('margin-left', '10px')\n\t\t}\n\t}\n\n\t/* render all contents into this.subheader\n\tdo it through init() means that contents are rendered just once on launching mass ui and won't be rerendered or updated\n\tsince there's no reason to update about tab contents while user is interacting with mass ui\n\t*/\n\tinit(appState) {\n\t\t/** If selectCohort available, options in the about html will not show */\n\t\tthis.initCohort(appState)\n\t\tthis.initCustomHtml()\n\t\tthis.initActiveItems()\n\t\tthis.initDisclaimer()\n\t\t//Always show the release version and server launch date at the bottom\n\t\tthis.showServerInfo()\n\t}\n\n\tasync main() {\n\t\t// do not render unless the cohort tab is active\n\t\tif (this.state.nav.activeTab !== 0) return\n\t\tawait this.renderCohortsTable()\n\t\tif (this.opts.selectCohort) {\n\t\t\tif (this.opts.selectCohort.description) {\n\t\t\t\tthis.dom.cohortDescription.html(this.opts.selectCohort.description)\n\t\t\t} else if (this.opts.selectCohort.descriptionByCohort) {\n\t\t\t\tthis.dom.cohortDescription.html(\n\t\t\t\t\tthis.opts.selectCohort.descriptionByCohort[\n\t\t\t\t\t\tthis.state.termdbConfig.selectCohort.values[this.state.activeCohort].keys.join(',')\n\t\t\t\t\t]\n\t\t\t\t)\n\t\t\t}\n\t\t}\n\t}\n\n\tinitCohort = appState => {\n\t\tif (this.selectCohort == null) return\n\t\t//Move to validate opts fn\n\t\tif (!this.selectCohort.values) return\n\n\t\tconst instanceNum = this.instanceNum\n\t\tconst activeCohort = appState.activeCohort\n\t\tconst app = this.app\n\n\t\t//TODO: replace with make_radios\n\t\tthis.dom\n\t\t\t.cohortOpts!.append('table')\n\t\t\t.attr('data-testid', 'sjpp-about-cohort-options-table')\n\t\t\t.selectAll('tr')\n\t\t\t.data(this.selectCohort.values)\n\t\t\t.enter()\n\t\t\t.append('tr')\n\t\t\t.each(function (d, i, nodes) {\n\t\t\t\tconst tr = select(nodes[i])\n\t\t\t\tconst td0 = tr.append('td')\n\t\t\t\tconst radioName = 'sja-termdb-cohort-' + instanceNum\n\t\t\t\tconst radioId = radioName + '-' + i\n\t\t\t\ttd0\n\t\t\t\t\t.append('input')\n\t\t\t\t\t.style('scale', '1.2')\n\t\t\t\t\t.attr('type', 'radio')\n\t\t\t\t\t.attr('name', radioName)\n\t\t\t\t\t.attr('id', radioId)\n\t\t\t\t\t.attr('value', i)\n\t\t\t\t\t.property('checked', i === activeCohort)\n\t\t\t\t\t.style('margin-right', '5px')\n\t\t\t\t\t.style('margin-left', '0px')\n\t\t\t\t\t.on('click', async event => {\n\t\t\t\t\t\tconst state = app.getState()\n\t\t\t\t\t\tconst clearOnChange = state.termdbConfig.selectCohort.clearOnChange\n\t\t\t\t\t\tif (clearOnChange) {\n\t\t\t\t\t\t\tconst subactions: any[] = []\n\t\t\t\t\t\t\tconst toBeCleared: string[] = []\n\t\t\t\t\t\t\tconst plots = state.plots\n\t\t\t\t\t\t\tconst filter = state.termfilter.filter.lst.find(f => f.tag == 'filterUiRoot')?.lst\n\t\t\t\t\t\t\tconst groups = state.groups\n\n\t\t\t\t\t\t\tif (clearOnChange.plots && plots?.length) toBeCleared.push('plots')\n\t\t\t\t\t\t\tfor (const plot of plots) {\n\t\t\t\t\t\t\t\tsubactions.push({\n\t\t\t\t\t\t\t\t\ttype: 'plot_delete',\n\t\t\t\t\t\t\t\t\tid: plot.id\n\t\t\t\t\t\t\t\t})\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\tif (clearOnChange.filter && filter?.length) toBeCleared.push('filters')\n\t\t\t\t\t\t\tsubactions.push({\n\t\t\t\t\t\t\t\ttype: 'filter_replace',\n\t\t\t\t\t\t\t\tfilter: {\n\t\t\t\t\t\t\t\t\ttype: 'tvslst',\n\t\t\t\t\t\t\t\t\tin: true,\n\t\t\t\t\t\t\t\t\tjoin: '',\n\t\t\t\t\t\t\t\t\ttag: 'filterUiRoot',\n\t\t\t\t\t\t\t\t\tlst: []\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t})\n\t\t\t\t\t\t\tif (clearOnChange.groups && groups?.length) {\n\t\t\t\t\t\t\t\ttoBeCleared.push('groups')\n\t\t\t\t\t\t\t\tfor (const group of groups) {\n\t\t\t\t\t\t\t\t\tsubactions.push({\n\t\t\t\t\t\t\t\t\t\ttype: 'delete_group',\n\t\t\t\t\t\t\t\t\t\tname: group.name\n\t\t\t\t\t\t\t\t\t})\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\tfor (const term of state.customTerms) {\n\t\t\t\t\t\t\t\t\tsubactions.push({\n\t\t\t\t\t\t\t\t\t\ttype: 'delete_customTerm',\n\t\t\t\t\t\t\t\t\t\tname: term.name\n\t\t\t\t\t\t\t\t\t})\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\tsubactions.push({ type: 'cohort_set', activeCohort: i })\n\t\t\t\t\t\t\tif (toBeCleared.length) {\n\t\t\t\t\t\t\t\tconst confirm = window.confirm(\n\t\t\t\t\t\t\t\t\t`Changing the cohort will clear all ${joinByComma(\n\t\t\t\t\t\t\t\t\t\ttoBeCleared\n\t\t\t\t\t\t\t\t\t)}. To proceed, click \"OK\". To save the session, click \"Cancel\" and then click the \"Session\" button at the top of the page.`\n\t\t\t\t\t\t\t\t)\n\t\t\t\t\t\t\t\tif (!confirm) {\n\t\t\t\t\t\t\t\t\tevent.preventDefault()\n\t\t\t\t\t\t\t\t\treturn\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\tapp.dispatch({\n\t\t\t\t\t\t\t\ttype: 'app_refresh',\n\t\t\t\t\t\t\t\tsubactions\n\t\t\t\t\t\t\t})\n\t\t\t\t\t\t} else app.dispatch({ type: 'cohort_set', activeCohort: i })\n\t\t\t\t\t})\n\n\t\t\t\ttd0\n\t\t\t\t\t.append('label')\n\t\t\t\t\t.style('font-size', '1.4em')\n\t\t\t\t\t.attr('for', radioId)\n\t\t\t\t\t.attr('colspan', 2)\n\t\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t\t.html((d: any) => d.label)\n\n\t\t\t\ttr.selectAll('td')\n\t\t\t\t\t.style('max-width', '600px')\n\t\t\t\t\t.style('padding-bottom', '10px')\n\t\t\t\t\t.style('padding-right', '20px')\n\t\t\t\t\t.style('vertical-align', 'top')\n\t\t\t})\n\n\t\tthis.dom.cohortTable = this.subheader\n\t\t\t.append('div')\n\t\t\t.attr('data-testid', 'sjpp-about-cohort-table')\n\t\t\t.style('margin-left', '12px')\n\n\t\tif (this.selectCohort.asterisk) {\n\t\t\tthis.dom.cohortAsterisk = this.subheader\n\t\t\t\t.append('div')\n\t\t\t\t.attr('data-testid', 'sjpp-about-cohort-asterisk')\n\t\t\t\t.style('margin', '10px')\n\t\t\t\t.style('font-size', '.8em')\n\t\t\t\t.text(this.selectCohort.asterisk)\n\t\t}\n\t}\n\n\trenderCohortsTable = async () => {\n\t\tif (!this.dom.cohortTable) return\n\t\tthis.dom.cohortTable.selectAll('*').remove()\n\t\tconst columns = [{ label: 'Feature' }]\n\t\tconst rows: TableRow[] = []\n\t\tconst result = await this.app.vocabApi.getCohortsData()\n\t\tif ('error' in result) throw result.error\n\t\tif (this.selectCohort?.values) {\n\t\t\t// selectCohort.values[] contains ordered set of cohorts\n\t\t\t// ensure cohorts in cohorts table follow this order\n\t\t\tconst values = this.selectCohort.values\n\t\t\tresult.cohorts.sort((a, b) => {\n\t\t\t\tconst aIndex = values.findIndex(v => v.keys.toString() == a.cohort)\n\t\t\t\tconst bIndex = values.findIndex(v => v.keys.toString() == b.cohort)\n\t\t\t\tif (aIndex < bIndex) return -1\n\t\t\t\tif (aIndex > bIndex) return 1\n\t\t\t\treturn 0\n\t\t\t})\n\t\t}\n\t\tif (!result.cfeatures.length) return\n\t\tfor (const feature of result.features) rows.push([{ value: feature.name }])\n\t\tfor (const cohort of result.cohorts) {\n\t\t\tif (cohort.subcohorts?.length) continue\n\t\t\tcolumns.push({ label: cohort.name })\n\t\t\tfor (const [i, feature] of result.features.entries()) {\n\t\t\t\tconst cf = result.cfeatures.find(cf => cf.idfeature === feature.idfeature && cf.cohort === cohort.cohort)\n\t\t\t\tif (cf) rows[i].push({ value: cf.value })\n\t\t\t}\n\t\t}\n\n\t\trenderTable({\n\t\t\trows,\n\t\t\tcolumns,\n\t\t\tdiv: this.dom.cohortTable,\n\t\t\tshowLines: false,\n\t\t\tmaxHeight: '60vh',\n\t\t\theader: { style: { 'font-size': '1.2em', 'font-weight': 'bold' } }\n\t\t})\n\n\t\tthis.dom.cohortTable.select('table').style('border-collapse', 'collapse')\n\t\tthis.dom.cohortTable.selectAll(`tbody > tr > td`).style('background-color', 'transparent').style('padding', '6px')\n\t\tconst state = this.app.getState()\n\t\tconst selectCohort = state.termdbConfig.selectCohort\n\t\tconst activeCohort = state.activeCohort\n\t\tconst keys = selectCohort.values[activeCohort].keys\n\t\tlet selector = `tbody > tr > td:nth-child(${activeCohort + 2})`\n\t\tconst combined = keys.length > 1\n\t\tif (combined) {\n\t\t\tselector = ''\n\t\t\tfor (const key of keys) {\n\t\t\t\tconst i = result.cohorts.map(c => c.cohort).indexOf(key)\n\t\t\t\tif (selector !== '') selector += ','\n\t\t\t\tselector += `tbody > tr > td:nth-child(${i + 2})`\n\t\t\t}\n\t\t}\n\t\tconst activeColumns = this.dom.cohortTable.selectAll(selector)\n\t\tconst color = state.termdbConfig.massNav?.activeColor || cohortTableActiveColor\n\t\tactiveColumns.style('background-color', color)\n\t}\n\n\tinitCustomHtml = () => {\n\t\tif (this.selectCohort != null) return\n\t\tif (!this.aboutOverrides?.html) return\n\t\tthis.subheader\n\t\t\t.append('div')\n\t\t\t.attr('data-testid', 'sjpp-custom-about-content')\n\t\t\t.style('padding', '10px')\n\t\t\t.html(this.aboutOverrides.html)\n\t}\n\n\tinitActiveItems = () => {\n\t\tif (!this.aboutOverrides?.activeItems) return\n\n\t\t// todo: customize general holder by activeItems.holderStyle{}\n\t\tconst div = this.subheader\n\t\t\t.append('div')\n\t\t\t.attr('data-testid', 'sjpp-custom-about-activeItems')\n\t\t\t.style('padding', '0px 0px 10px 20px')\n\n\t\tfor (const item of this.aboutOverrides.activeItems.items) {\n\t\t\t// todo: by item.type, item.divStyle{}\n\t\t\tdiv\n\t\t\t\t.append('div')\n\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t.style('margin', '5px')\n\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t.attr('data-testid', 'sjpp-custom-active-item-btn')\n\t\t\t\t.html(item.title)\n\t\t\t\t.on('click', async () => {\n\t\t\t\t\t/* First, set the active tab to toggle to the plots tab and wait for the tab to be set,\n\t\t\t\t\totherwise the plotDiv is hidden when rendering and\n\t\t\t\t\tmay cause issues. A known issue is that getMaxLabelWidth getBBox on a hidden div returns width=0\n\t\t\t\t\tthis affects the legend rendering in plots like the scatter resulting in overlapping texts\n\t\t\t\t\t*/\n\t\t\t\t\tawait this.app.dispatch({\n\t\t\t\t\t\ttype: 'tab_set',\n\t\t\t\t\t\tactiveTab: 1\n\t\t\t\t\t})\n\t\t\t\t\t// after switching tab so plot div is shown, dispatch to create the plot\n\t\t\t\t\tthis.app.dispatch({\n\t\t\t\t\t\ttype: 'plot_create',\n\t\t\t\t\t\tid: getId(),\n\t\t\t\t\t\tconfig: structuredClone(item.plot)\n\t\t\t\t\t})\n\t\t\t\t})\n\t\t}\n\t}\n\n\tinitDisclaimer = () => {\n\t\tconst d = this.aboutOverrides?.disclaimer\n\t\tif (!d) return\n\t\t// customize styling from d{}\n\t\tconst div = this.subheader\n\t\t\t.append('div')\n\t\t\t.attr('data-testid', 'sjpp-custom-about-disclaimer')\n\t\t\t.style('margin', '10px 0 20px 10px')\n\t\t\t.style('opacity', 0.7)\n\t\t\t.style('padding', '10px')\n\t\t\t.style('background-color', '#f8f9fa')\n\t\t\t.style('border-left', '4px solid #6c757d')\n\t\t\t.style('font-size', '0.8em')\n\t\tdiv.append('div').style('margin-bottom', '8px').style('font-weight', 'bold').text('DISCLAIMER')\n\t\tdiv.append('div').text(d.text)\n\t}\n\n\tshowServerInfo = () => {\n\t\tconst state = this.app.getState()\n\t\tconst about = state.termdbConfig.massNav?.tabs?.about\n\t\tif (!about && !this.app.opts.pkgver && !this.app.opts.launchDate) return\n\t\tconst dataRelease = about?.dataRelease\n\t\tconst additionalInfo = about?.additionalInfo\n\t\tconst div = this.subheader\n\t\t\t.append('div')\n\t\t\t.attr('data-testid', 'sjpp-about-server-info')\n\t\t\t.style('margin', '10px')\n\t\t\t.style('font-size', '.8em')\n\n\t\tconst htmlArr: string[] = []\n\t\tif (dataRelease) {\n\t\t\thtmlArr.push(`Data Release: <a href=${dataRelease.link} target=_blank>${dataRelease.version}</a>`)\n\t\t}\n\t\tif (this.app.opts.pkgver) {\n\t\t\thtmlArr.push(\n\t\t\t\t`Software Release: <a href=https://github.com/stjude/proteinpaint/pkgs/container/ppfull target=_blank>${this.app.opts.pkgver}</a>`\n\t\t\t)\n\t\t}\n\t\tif (this.app.opts.launchDate) {\n\t\t\thtmlArr.push(`Server Launched: ${this.app.opts.launchDate}`)\n\t\t}\n\t\tif (additionalInfo) {\n\t\t\thtmlArr.push(additionalInfo)\n\t\t}\n\t\tdiv.append('div').html(htmlArr.join('; '))\n\t}\n}\n\nexport const aboutInit = getCompInit(MassAbout)\n\nfunction joinByComma(arr) {\n\tif (!arr.length) return ''\n\telse if (arr.length == 1) return arr[0]\n\telse if (arr.length == 2) return arr.join(' and ')\n\telse return `${arr.slice(0, -1).join(', ')}, and ${arr.slice(-1)}`\n}\n", "import { getCompInit, type RxComponent } from '#rx'\nimport type { MassAppApi } from './types/mass'\nimport { Menu } from '#dom'\nimport { keyupEnter } from '#src/client'\nimport { dofetch3 } from '#common/dofetch'\nimport type { ChatRequest, ChatResponse, OmnisearchResult } from '#types'\nimport { sayerror } from '../dom/sayerror.ts'\nimport { select } from 'd3-selection'\nimport { fillTermWrapper } from '#termsetting'\nimport { dtsnvindel, dtcnv, dtsv, dtfusionrna } from '#shared/common.js'\nimport { DNA_METHYLATION } from '#shared/terms.js'\nimport { getDNAMethUnit } from '#tw/dnaMethylation'\nimport { first_genetrack_tolist } from '#common/1stGenetk'\n\nconst MIN_PROMPT_LENGTH_FOR_OMNISEARCH = 3 // Set a minimum prompt length for omnisearch to trigger\nconst MAX_PROMPT_LENGTH_FOR_OMNISEARCH = 15 // Set a maximum prompt length for omnisearch to trigger\nconst MIN_PROMPT_LENGTH_FOR_CHAT = 5 // Set a minimum prompt length for chat submission\n\n/** Build a region-based dnaMethylation term for the given coordinates. */\nfunction makeMethylationRegionTerm(opts: { chr: string; start: number; stop: number }, vocabApi: any) {\n\tconst { chr, start, stop } = opts\n\tif (!chr || !Number.isInteger(start) || !Number.isInteger(stop)) throw new Error('invalid coordinate')\n\treturn {\n\t\tchr,\n\t\tstart,\n\t\tstop,\n\t\ttype: DNA_METHYLATION,\n\t\tunit: getDNAMethUnit('region', vocabApi),\n\t\tgenomicFeatureType: 'region'\n\t}\n}\n\n/**\n * Embed a genome browser of a gene/region into `holder` with a \"Submit Region\" button. On submit,\n * builds a region-based dnaMethylation term from the region the user navigated to and passes it to\n * `callback`. Returns the Block instance. Used by the mass omnisearch to open a methylation region\n * picker for a gene. (The dnaMethylation search handler keeps its own equivalent inline logic.)\n */\nasync function embedMethylationRegionPicker(opts: {\n\tholder: any\n\tgenomeObj: any\n\tvocabApi: any\n\tchr: string\n\tstart: number\n\tstop: number\n\tcallback: (term: any) => void | Promise<void>\n\tdebug?: boolean\n}) {\n\tconst { holder, genomeObj, vocabApi, chr, start, stop, callback } = opts\n\tif (!chr || !Number.isInteger(start) || !Number.isInteger(stop)) throw new Error('unable to retrieve gene coordinate')\n\n\tholder.selectAll('*').remove()\n\tholder.style('display', 'block')\n\tholder.append('div').style('opacity', 0.6).text('Navigate genome browser to desired region')\n\n\tconst arg: any = {\n\t\tholder,\n\t\tgenome: genomeObj, // genome obj\n\t\tchr,\n\t\tstart,\n\t\tstop,\n\t\ttklst: [],\n\t\tnobox: true,\n\t\twidth: 500,\n\t\thidegenelegend: true,\n\t\tdebugmode: opts.debug\n\t}\n\tfirst_genetrack_tolist(genomeObj, arg.tklst)\n\tconst _ = await import('#src/block')\n\tconst blockInstance = new _.Block(arg)\n\n\tholder\n\t\t.append('div')\n\t\t.attr('data-testid', 'sjpp-dnaMethylation-submitDiv')\n\t\t.style('margin', '10px 0px')\n\t\t.append('button')\n\t\t.style('border', 'none')\n\t\t.style('border-radius', '20px')\n\t\t.style('padding', '10px 15px')\n\t\t.text('Submit Region')\n\t\t.on('click', async () => {\n\t\t\tconst { chr, start, stop } = blockInstance.rglst[0]\n\t\t\tawait callback(makeMethylationRegionTerm({ chr, start, stop }, vocabApi))\n\t\t})\n\n\treturn blockInstance\n}\n\nclass MassAiChatBot implements RxComponent {\n\tstatic type = 'chat'\n\ttype: string\n\topts: any\n\tapp: MassAppApi\n\tdom!: any\n\tstate: any\n\tid!: string\n\tclear: any\n\tshowTerms: any\n\tnoResult: any\n\tisChat: any\n\n\tconstructor(opts: any) {\n\t\tthis.type = MassAiChatBot.type\n\t\tthis.opts = opts\n\t\tthis.app = opts.app\n\t\tthis.opts.usecase = this.opts.usecase || { target: 'dictionary', detail: 'term' }\n\t\tthis.opts.targetType = this.opts.targetType ? this.opts.targetType : 'Dictionary Variables'\n\t\tthis.isChat = this.app.getState().termdbConfig?.queries?.chat // Storing if chat is supported by the dataset for easy access in other methods\n\t\tsetRenderers(this) // needed so that this.showTerms, noResult, clear work\n\t}\n\n\tgetState(appState: any) {\n\t\treturn {\n\t\t\tcohortStr:\n\t\t\t\tappState.activeCohort == -1 || !appState.termdbConfig.selectCohort\n\t\t\t\t\t? ''\n\t\t\t\t\t: appState.termdbConfig.selectCohort.values[appState.activeCohort].keys.slice().sort().join(','),\n\t\t\tsearch: appState.search,\n\t\t\tnav: appState.nav\n\t\t}\n\t}\n\n\tasync init() {\n\t\t// Note: no server-side request here \u2014 the omnisearch resolves dictionary terms, genes, and the\n\t\t// dataset's gene data types together in a single request per search (see doSearch), so nothing is\n\t\t// fetched eagerly at component init.\n\t\tthis.initDom()\n\t}\n\n\t// Search method, adapted from MassSearch.doSearch\n\tasync doSearch(prompt: string) {\n\t\tif (!prompt) {\n\t\t\tthis.clear({ hide: true })\n\t\t\treturn\n\t\t}\n\t\tconst cohortStr = this.getState(this.app.getState()).cohortStr\n\t\t// Single server request that searches dictionary variables and genes together, and reports the\n\t\t// dataset's gene data types. The server (termdb/chat, runOmnisearch) does the gene lookup for the\n\t\t// search results, so the client does not need an extra genelookup request during omnisearch.\n\t\tconst data: OmnisearchResult = await dofetch3('termdb/chat', {\n\t\t\tbody: {\n\t\t\t\tgenome: this.app.vocabApi.vocab.genome,\n\t\t\t\tdslabel: this.app.vocabApi.vocab.dslabel,\n\t\t\t\tomnisearch: true,\n\t\t\t\tprompt,\n\t\t\t\tcohortStr,\n\t\t\t\tusecase: this.opts.usecase,\n\t\t\t\ttreeFilter: this.app.vocabApi.state?.treeFilter\n\t\t\t}\n\t\t})\n\t\tif (data.error) throw data.error\n\t\tconst lst: any[] = Array.isArray(data.dictionaryTerms) ? data.dictionaryTerms : []\n\t\t// Each gene match carries its own available data types (a gene may have e.g. SNV/indel while\n\t\t// another does not), so action buttons are decided per gene rather than dataset-wide.\n\t\tconst genes: { gene: string; dataTypes: any; coord?: any }[] = Array.isArray(data.genes) ? data.genes : []\n\n\t\t// Build one entry per gene, skipping any whose name already appears among the dictionary results.\n\t\t// Each gene renders as a single row whose buttons are the actions available for that gene, and\n\t\t// its own per-variant-type options (SNV/indel, CNV, SV/fusion) are attached for showTerm to use.\n\t\tconst dictNames = new Set(lst.map((t: any) => t.name?.toUpperCase()))\n\t\tconst geneMap = new Map<string, any>()\n\t\tfor (const g of genes) {\n\t\t\tconst gene = g?.gene\n\t\t\tif (!gene || dictNames.has(gene.toUpperCase())) continue\n\t\t\tconst dt = g.dataTypes || {}\n\t\t\t// per-gene variant sub-type buttons; svfusion maps to two dts (SV and fusion), tried in order\n\t\t\tconst geneVariantTypes: any[] = []\n\t\t\tif (dt.snvindel) geneVariantTypes.push({ label: 'SNV/indel', testid: 'snvindel', dtCandidates: [dtsnvindel] })\n\t\t\tif (dt.cnv) geneVariantTypes.push({ label: 'CNV', testid: 'cnv', dtCandidates: [dtcnv] })\n\t\t\tif (dt.svfusion)\n\t\t\t\tgeneVariantTypes.push({ label: 'SV/fusion', testid: 'svfusion', dtCandidates: [dtsv, dtfusionrna] })\n\t\t\tconst entry: any = { name: gene, gene, isGene: true }\n\t\t\tif (dt.geneExpression) entry.isGeneExpression = true\n\t\t\tif (geneVariantTypes.length) {\n\t\t\t\tentry.isGeneVariant = true\n\t\t\t\tentry.geneVariantTypes = geneVariantTypes\n\t\t\t}\n\t\t\tif (dt.dnaMethylation) {\n\t\t\t\tentry.isMethylation = true\n\t\t\t\t// server-resolved default coordinate, used to seed the genome browser region picker\n\t\t\t\tentry.coord = g.coord\n\t\t\t}\n\t\t\t// only list a gene if it has at least one available data type / action\n\t\t\tif (entry.isGeneExpression || entry.isGeneVariant || entry.isMethylation) {\n\t\t\t\tgeneMap.set(gene.toUpperCase(), entry)\n\t\t\t}\n\t\t}\n\t\tfor (const entry of geneMap.values()) lst.push(entry)\n\t\tif (!lst.length) {\n\t\t\t// Show the \"No match...\" message one time at the first miss\n\t\t\tif (!this.dom.noMatchShown) {\n\t\t\t\tthis.dom.noMatchShown = true\n\t\t\t\tthis.noResult()\n\t\t\t}\n\t\t} else {\n\t\t\tthis.dom.noMatchShown = false\n\t\t\tthis.showTerms({ lst })\n\t\t}\n\t}\n\n\tinitDom() {\n\t\t//const cohortStr = this.getState(appState).cohortStr\n\t\tlet text = 'Search an item'\n\t\tlet height = '1px' // No white space needed for search only\n\t\tif (this.isChat) {\n\t\t\ttext = 'Ask a question'\n\t\t\theight = '200px'\n\t\t}\n\t\tthis.dom = {\n\t\t\ttip: new Menu({ padding: '5px' }),\n\t\t\tdiv: this.opts.subheader,\n\t\t\terror: this.opts.subheader.append('div').attr('id', 'sjpp-corrVolcano-error').style('opacity', 0.75),\n\t\t\tbubbleDiv: this.opts.subheader\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'sjpp_show_scrollbar')\n\t\t\t\t.style('margin', '5px 20px 0px 20px')\n\t\t\t\t.style('height', height)\n\t\t\t\t.style('overflow', 'auto')\n\t\t\t\t.style('scroll-behavior', 'smooth')\n\t\t}\n\n\t\tconst inputSel = this.dom.div\n\t\t\t.append('input')\n\t\t\t.attr('type', 'search')\n\t\t\t.style('margin', '15px')\n\t\t\t.style('padding', '17px')\n\t\t\t.style('border-radius', '34px')\n\t\t\t.attr('size', 70)\n\t\t\t.attr('placeholder', text)\n\n\t\t// Store the input node so the search result tip can position under it\n\t\tthis.dom.inputNode = inputSel.node()\n\n\t\t// Result panel inside the tip, mirroring MassSearch.initUI\n\t\tthis.dom.resultDiv = this.dom.tip.d\n\t\t\t.style('border-left', 'solid 1px rgb(133,182,225)')\n\t\t\t.style('padding-left', '5px')\n\t\t\t.attr('tabindex', -1)\n\n\t\tinputSel\n\t\t\t.on('keyup.search', async (event: KeyboardEvent) => {\n\t\t\t\tif (keyupEnter(event)) return\n\t\t\t\tconst prompt = (event.target as HTMLInputElement).value.trim()\n\t\t\t\tif (!prompt) {\n\t\t\t\t\tthis.dom.noMatchShown = false\n\t\t\t\t\tthis.clear({ hide: true })\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tif (MIN_PROMPT_LENGTH_FOR_OMNISEARCH <= prompt.length && prompt.length <= MAX_PROMPT_LENGTH_FOR_OMNISEARCH) {\n\t\t\t\t\t//console.log(\n\t\t\t\t\t//\t`User prompt: \"${prompt}\", cohortStr: \"${cohortStr}\", usecase: \"${this.opts.usecase}\", targetType: \"${this.opts.targetType}\"`\n\t\t\t\t\t//)\n\t\t\t\t\ttry {\n\t\t\t\t\t\tawait this.doSearch(prompt) // Search as user types\n\t\t\t\t\t} catch (e: any) {\n\t\t\t\t\t\tif (e.stack) console.log(e.stack)\n\t\t\t\t\t\tsayerror(this.dom.resultDiv, 'Error: ' + (e.message || e))\n\t\t\t\t\t}\n\t\t\t\t} else {\n\t\t\t\t\tthis.dom.noMatchShown = false\n\t\t\t\t\tthis.clear({ hide: true })\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t})\n\t\t\t.on('keyup.submit', async (event: any) => {\n\t\t\t\tif (!keyupEnter(event)) return\n\t\t\t\tif (!this.isChat) {\n\t\t\t\t\t// Prevents unnecessary server side call when chat not supported by ds\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tconst prompt = event.target.value.trim()\n\t\t\t\tif (!prompt) return\n\t\t\t\tthis.addBubble({ msg: escapeHtml(prompt), me: 1 })\n\t\t\t\tevent.target.value = ''\n\t\t\t\tconst serverBubble = this.addBubble({ msg: '...' }) // Keep server bubble always below prompt bubble so that responses are below the prompt always\n\t\t\t\tif (prompt.length <= MIN_PROMPT_LENGTH_FOR_CHAT) {\n\t\t\t\t\tserverBubble.text('Your prompt is too short. Enter a longer prompt.')\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tconst body: ChatRequest = {\n\t\t\t\t\tgenome: this.app.vocabApi.vocab.genome,\n\t\t\t\t\tdslabel: this.app.vocabApi.vocab.dslabel,\n\t\t\t\t\tfilter: this.app.vocabApi.state.termfilter?.filter,\n\t\t\t\t\tprompt\n\t\t\t\t}\n\t\t\t\ttry {\n\t\t\t\t\tconst data = await dofetch3('termdb/chat', { body })\n\t\t\t\t\tif (data.error) throw data.error\n\n\t\t\t\t\tconst result: ChatResponse = data\n\t\t\t\t\tif (result.type === 'text') {\n\t\t\t\t\t\tserverBubble.text(result.text)\n\t\t\t\t\t} else if (result.type === 'html') {\n\t\t\t\t\t\tserverBubble.html(result.html)\n\t\t\t\t\t} else if (result.type === 'plot') {\n\t\t\t\t\t\t// Determine if plot state is complete or not. A field whose value carries a\n\t\t\t\t\t\t// `possible_options` array means the server could not resolve that term and\n\t\t\t\t\t\t// is offering the user a choice. If found, show click boxes; otherwise the\n\t\t\t\t\t\t// plot state is complete and can be dispatched directly.\n\t\t\t\t\t\tconst optionField = findPossibleOptionsField(result.plot)\n\t\t\t\t\t\tif (optionField) {\n\t\t\t\t\t\t\tthis.showPossibleOptions(serverBubble, result.plot, optionField, result.msg)\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\tthis.app.dispatch({\n\t\t\t\t\t\t\t\ttype: 'plot_create',\n\t\t\t\t\t\t\t\tconfig: result.plot\n\t\t\t\t\t\t\t})\n\t\t\t\t\t\t\tserverBubble.text(`${result.msg ? result.msg + '. ' : ''}Please refer to the plot generated below.`)\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t} catch (e: any) {\n\t\t\t\t\tif (e.stack) console.log(e.stack)\n\t\t\t\t\tserverBubble.html(`Error: ${e.message || e}`)\n\t\t\t\t}\n\t\t\t})\n\t\t\t.node()\n\t\t\t.focus()\n\t}\n\n\taddBubble(arg: { msg: string; me?: number }) {\n\t\t/** {\nmsg: add a chat bubble for this msg; msg is html as it might contain hyperlinks\nme: if 1, is me; otherwise is ai\n}\nreturn the created bubble and allow to be modified\n*/\n\t\tconst bubble = this.dom.bubbleDiv\n\t\t\t.append('div')\n\t\t\t.style('padding', '10px')\n\t\t\t.html(`${arg.me ? '<span style=\"font-size:.7em\">[ME]</span> ' : ''}${arg.msg}`)\n\t\tif (arg.me) bubble.style('background', '#f1f1f1')\n\t\t// set this to scroll to bottom\n\t\tconst n = this.dom.bubbleDiv.node()\n\t\tn.scrollTop = n.scrollHeight\n\t\treturn bubble\n\t}\n\n\t// Render click boxes for an incomplete plot state. `fieldKey` is the field of `plot` whose\n\t// value holds `possible_options`. Clicking a box completes the plot state by replacing that\n\t// field with the chosen option's id and dispatches plot_create.\n\tshowPossibleOptions(bubble: any, plot: any, fieldKey: string, msg?: string) {\n\t\tconst options = plot[fieldKey].possible_options || []\n\t\tbubble.text(`${msg ? msg + '. ' : ''}Multiple options are available. Please select one:`)\n\t\tconst boxDiv = bubble.append('div').style('margin-top', '5px')\n\t\tfor (const opt of options) {\n\t\t\tboxDiv\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t.attr('data-testid', `sjpp-mass-chat-option-${opt.id}`)\n\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t.style('margin', '3px')\n\t\t\t\t.style('padding', '5px 10px')\n\t\t\t\t.style('border-radius', '5px')\n\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t.text(opt.name)\n\t\t\t\t.on('click', () => {\n\t\t\t\t\t// Complete the plot state with the chosen option's id and dispatch the plot.\n\t\t\t\t\tconst config = JSON.parse(JSON.stringify(plot))\n\t\t\t\t\tconfig[fieldKey] = { id: opt.id }\n\t\t\t\t\tthis.app.dispatch({\n\t\t\t\t\t\ttype: 'plot_create',\n\t\t\t\t\t\tconfig\n\t\t\t\t\t})\n\t\t\t\t\tbubble.selectAll('*').remove()\n\t\t\t\t\tbubble.text(`Selected \"${opt.name}\". Please refer to the plot generated below.`)\n\t\t\t\t})\n\t\t}\n\t}\n\n\tmain() {\n\t\t// If the subheader is hidden, it means the chat component is not visible, so we skip focusing the input to avoid accidental typing into the search/chat bar. The user can click on the chat again to focus when they want to use it.\n\t\tif (this.opts.subheader.style('display') == 'none') {\n\t\t\tthis.dom.inputNode.blur()\n\t\t\treturn\n\t\t}\n\t\tif (this.opts?.focus != 'off') this.dom.inputNode.focus()\n\t}\n}\n\nexport const chatInit = getCompInit(MassAiChatBot)\n\n// Prevents HTML/script injection in the chat UI (XSS) by entering markup in the prompt (Proposed fix by copilot)\nfunction escapeHtml(s: string): string {\n\treturn s\n\t\t.replace(/&/g, '&amp;')\n\t\t.replace(/</g, '&lt;')\n\t\t.replace(/>/g, '&gt;')\n\t\t.replace(/\"/g, '&quot;')\n\t\t.replace(/'/g, '&#39;')\n}\n\n// Scan a plot state for a field whose value carries a `possible_options` array, indicating the\n// server could not resolve that term and is offering the user a list of choices. Returns the field\n// name (e.g. 'term') or null if the plot state is complete.\nfunction findPossibleOptionsField(plot: any): string | null {\n\tif (!plot || typeof plot !== 'object') return null\n\tfor (const key of Object.keys(plot)) {\n\t\tconst val = plot[key]\n\t\tif (val && typeof val === 'object' && Array.isArray(val.possible_options)) return key\n\t}\n\treturn null\n}\n\n// Minimal renderers ported from MassSearch\nfunction setRenderers(self: any) {\n\tlet text = 'No match'\n\tif (self.isChat) {\n\t\ttext = 'No match. Using the chatbot...'\n\t}\n\tself.noResult = () => {\n\t\tself.clear()\n\t\tself.dom.resultDiv.append('div').text(text).style('padding', '3px 3px 3px 0px').style('opacity', 0.5)\n\n\t\t// Hide the popup after 2 seconds\n\t\tsetTimeout(() => {\n\t\t\tself.clear({ hide: true })\n\t\t}, 1500)\n\t}\n\n\tself.showTerms = (data: any) => {\n\t\tif (self.opts.disable_terms)\n\t\t\tdata.lst.forEach((t: any) => {\n\t\t\t\tif (t.disabled) self.opts.disable_terms.push(t)\n\t\t\t})\n\t\tself.clear({ hide: !data.lst.length })\n\t\tif (data.lst.length) {\n\t\t\tself.dom.resultDiv.append('table').selectAll().data(data.lst).enter().append('tr').each(self.showTerm)\n\t\t}\n\t}\n\n\t// dispatch a plot and reset the search box/popup\n\tself.launchPlot = async (config: any) => {\n\t\tif (self.state?.nav?.activeTab == 0) {\n\t\t\tawait self.app.dispatch({ type: 'tab_set', activeTab: 1 })\n\t\t}\n\t\tself.app.dispatch({ type: 'plot_create', config })\n\t\tself.dom.inputNode.value = '' // clear the search box\n\t\tself.clear({ hide: true })\n\t}\n\n\t// open a mutated-vs-wildtype barchart for one gene, restricted to a variant data type.\n\t// dtCandidates are tried in order (svfusion has two dts) until a matching predefined groupset\n\t// is found, since fillTermWrapper throws when the dataset lacks a groupset for a given dt.\n\tself.launchGeneVariantPlot = async (gene: string, dtCandidates: number[]) => {\n\t\tlet tw: any\n\t\tlet lastErr: any\n\t\tfor (const dt of dtCandidates) {\n\t\t\tconst candidate: any = {\n\t\t\t\tterm: {\n\t\t\t\t\tid: gene,\n\t\t\t\t\tname: gene,\n\t\t\t\t\tgenes: [{ kind: 'gene', id: gene, gene, name: gene, type: 'geneVariant' }],\n\t\t\t\t\ttype: 'geneVariant'\n\t\t\t\t},\n\t\t\t\tq: { type: 'predefined-groupset', dtLst: [dt] }\n\t\t\t}\n\t\t\ttry {\n\t\t\t\tawait fillTermWrapper(candidate, self.app.vocabApi)\n\t\t\t\ttw = candidate\n\t\t\t\tbreak\n\t\t\t} catch (e) {\n\t\t\t\tlastErr = e\n\t\t\t}\n\t\t}\n\t\tif (!tw) throw lastErr\n\t\tawait self.launchPlot({ chartType: 'summary', term: tw })\n\t}\n\n\t// DNA methylation: open a genome browser at the gene's default coordinates inline in the result\n\t// area with a \"Submit Region\" button (see embedMethylationRegionPicker above); on submit, open a\n\t// violin plot of the region-based dnaMethylation term's per-sample beta values.\n\tself.launchMethylationPlot = async (gene: string, coord: { chr: string; start: number; stop: number }) => {\n\t\t// coord is the gene's default genomic coordinate, resolved server-side by the omnisearch\n\t\t// (GeneMatch.coord) and used to seed the genome browser track \u2014 no genelookup request here.\n\t\tif (!coord) throw `Could not resolve coordinates for gene \"${gene}\"`\n\n\t\t// render the region picker inline in the chat result area, replacing the result list\n\t\tself.dom.tip.clear()\n\t\tself.dom.tip.showunder(self.dom.inputNode)\n\t\tconst holder = self.dom.resultDiv.append('div').style('margin', '10px')\n\t\tholder.append('div').style('margin-bottom', '5px').text(gene)\n\n\t\tawait embedMethylationRegionPicker({\n\t\t\tholder: holder.append('div'),\n\t\t\tgenomeObj: self.app.opts.genome,\n\t\t\tvocabApi: self.app.vocabApi,\n\t\t\tchr: coord.chr,\n\t\t\tstart: coord.start,\n\t\t\tstop: coord.stop,\n\t\t\tcallback: async (term: any) => {\n\t\t\t\tawait self.launchPlot({ chartType: 'summary', term: { term } })\n\t\t\t}\n\t\t})\n\t}\n\n\tself.showTerm = function (term: any) {\n\t\tconst tr = select(this)\n\n\t\tif (term.isGene) {\n\t\t\t// Gene row: gene name as a plain label, with an action button per available data type\n\t\t\t// ('Gene expression', variant types, 'DNA methylation') \u2014 all shown together in the same row.\n\t\t\ttr.append('td').text(term.name).style('padding', '5px 10px')\n\t\t\tconst btnTd = tr.append('td')\n\t\t\tconst addBtn = (label: string, testid: string, onClick: () => Promise<void>) => {\n\t\t\t\tbtnTd\n\t\t\t\t\t.append('span')\n\t\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t\t.attr('data-testid', testid)\n\t\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t\t.style('margin', '0px 3px')\n\t\t\t\t\t.style('padding', '5px 10px')\n\t\t\t\t\t.style('border-radius', '5px')\n\t\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t\t.text(label)\n\t\t\t\t\t.on('click', () => void onClick().catch(e => sayerror(self.dom.resultDiv, 'Error: ' + (e?.message || e))))\n\t\t\t}\n\t\t\tif (term.isGeneExpression) {\n\t\t\t\t// open a summary plot of the gene's expression\n\t\t\t\taddBtn('Gene expression', `sjpp-mass-chat-gene-exp-${term.gene}`, async () => {\n\t\t\t\t\tawait self.launchPlot({\n\t\t\t\t\t\tchartType: 'summary',\n\t\t\t\t\t\tterm: { term: { gene: term.gene, name: term.name, type: 'geneExpression' } }\n\t\t\t\t\t})\n\t\t\t\t})\n\t\t\t}\n\t\t\tif (term.isGeneVariant) {\n\t\t\t\t// one button per variant data type available for THIS gene (snvindel/cnv/svfusion);\n\t\t\t\t// each opens a mutated-vs-wildtype barchart restricted to that data type.\n\t\t\t\tfor (const vt of term.geneVariantTypes || []) {\n\t\t\t\t\taddBtn(vt.label, `sjpp-mass-chat-gene-${vt.testid}-${term.gene}`, async () => {\n\t\t\t\t\t\tawait self.launchGeneVariantPlot(term.gene, vt.dtCandidates)\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (term.isMethylation) {\n\t\t\t\t// open a violin plot of the gene's per-sample DNA methylation beta values\n\t\t\t\taddBtn('DNA methylation', `sjpp-mass-chat-gene-methylation-${term.gene}`, async () => {\n\t\t\t\t\tawait self.launchMethylationPlot(term.gene, term.coord)\n\t\t\t\t})\n\t\t\t}\n\t\t\treturn\n\t\t}\n\n\t\t// Dictionary term row\n\t\tconst button = tr.append('td').text(term.name)\n\t\tif (term.type) {\n\t\t\tbutton\n\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t.attr('class', 'sja_menuoption')\n\t\t\t\t.attr('data-testid', `sjpp-mass-chat-term-${term.id}`)\n\t\t\t\t.on('click', async () => {\n\t\t\t\t\tawait self.launchPlot({\n\t\t\t\t\t\tchartType: term.type == 'survival' ? 'survival' : 'summary',\n\t\t\t\t\t\tterm: { term }\n\t\t\t\t\t})\n\t\t\t\t})\n\t\t} else {\n\t\t\tbutton.style('padding', '5px 10px').style('opacity', 0.5)\n\t\t}\n\n\t\ttr.append('td')\n\t\t\t.text((term.__ancestorNames || []).join(' > '))\n\t\t\t.style('opacity', 0.5)\n\t\t\t.style('font-size', '.7em')\n\t}\n\n\tself.clear = (opts: any = {}) => {\n\t\tself.dom.tip.clear()\n\t\tif (opts.hide) self.dom.tip.hide()\n\t\telse self.dom.tip.showunder(self.dom.inputNode)\n\t}\n}\n", "import { getCompInit, multiInit } from '#rx'\nimport { recoverInit } from '../rx/src/recover'\nimport { chartsInit } from './charts'\nimport { groupsInit } from './groups'\nimport { sessionBtnInit } from './sessionBtn'\nimport { aboutInit } from './about.ts'\nimport { chatInit } from './chat.ts'\nimport { dofetch3 } from '#common/dofetch'\nimport { Menu, icons as icon_functions } from '#dom'\nimport { getFilterItemByTag, filterRxCompInit } from '#filter/filter'\n\n/*\ntodo: steps to add a new tab\n*/\n\nconst activeTabBgColor = '#ececec', // default bg color of active tab; inactive tab is transparent\n\tactiveTabBgColorHover = '#e0e0e0',\n\tactiveTabTextColor = 'black',\n\tinactiveTabBgColorHover = '#fcfced',\n\tinactiveTabTextColor = 'gray'\n\n// to be used for assigning unique\n// radio button names by object instance\n// otherwise termdp app popups\nlet instanceNum = 0\n\n// to distinguish from IDs assigned by other code or users\nconst idPrefix = '_MASS_AUTOID_' + Math.random().toString().slice(-6)\nlet id = (+new Date()).toString().slice(-8)\n\nconst headtip = new Menu({ padding: '0px', offsetX: 0, offsetY: 0 })\nheadtip.d.style('z-index', 5555)\n// headtip must get a crazy high z-index so it can stay on top of all, no matter if server config has base_zindex or not\n\n// data elements for navigation header tabs\nconst aboutTab = { top: 'ABOUT', mid: '', btm: '', subheader: 'about' }\nconst chartTab = { top: 'CHARTS', mid: 'NONE', btm: '', subheader: 'charts' }\nconst groupsTab = { top: 'GROUPS', mid: 'NONE', btm: '', subheader: 'groups' }\nconst filterTab = { top: 'FILTER', mid: 'NONE', btm: '', subheader: 'filter' }\nconst cartTab = { top: 'CART', mid: 'NONE', btm: '', subheader: 'cart' }\n\nexport function getId() {\n\treturn idPrefix + '_' + id++\n}\n\nclass TdbNav {\n\tstatic type = 'nav'\n\n\tconstructor(opts) {\n\t\tthis.type = TdbNav.type\n\t\tthis.instanceNum = instanceNum++\n\t\tthis.tabs = [] // array of tab objects corresponding to what's shown on header, based on ds customization. hidden tabs are not in this array. filled in initUI()\n\t\tthis.activeTab = 0 // array index for .tabs[]; -1 for no active tabs and all closed\n\t\tthis.activeCohort = 0 // -1 = unselected, 0,1,2... = selected\n\t\tthis.samplecounts = {} // tracks sample count by .activeCohort value and stringified filter json\n\t\tthis.searching = false\n\t\tthis.massSessionDuration = opts.massSessionDuration\n\t\tthis.sessionDaysLeft = opts.app.opts.sessionDaysLeft || null\n\t\tthis.sessionId = opts.app.opts.sessionId || null\n\t\tthis.pkgver = opts.pkgver || null //Release version\n\t\tsetInteractivity(this)\n\t\tsetRenderers(this)\n\t}\n\n\tasync init(appState) {\n\t\ttry {\n\t\t\tthis.cohortFilter = getFilterItemByTag(appState.termfilter.filter, 'cohortFilter')\n\t\t\tthis.initUI(appState)\n\t\t\tif (appState?.termdbConfig?.selectCohort) {\n\t\t\t\tthis.dom.tds.filter(d => d.colNum === 0).style('display', '')\n\t\t\t\tthis.cohortNames = appState.termdbConfig.selectCohort.values.map(d => d.keys.slice().sort().join(','))\n\t\t\t}\n\n\t\t\tthis.components = await multiInit({\n\t\t\t\tfilter: filterRxCompInit({\n\t\t\t\t\tapp: this.app,\n\t\t\t\t\tvocabApi: this.app.vocabApi,\n\t\t\t\t\tholder: this.dom.subheader.filter.append('div').style('margin', '5px'),\n\t\t\t\t\thideLabel: this.opts.header_mode === 'with_tabs',\n\t\t\t\t\temptyLabel: '+Add new filter',\n\t\t\t\t\tcallback: filter => {\n\t\t\t\t\t\tthis.app.dispatch({\n\t\t\t\t\t\t\ttype: 'filter_replace',\n\t\t\t\t\t\t\tfilter\n\t\t\t\t\t\t})\n\t\t\t\t\t}\n\t\t\t\t}),\n\t\t\t\tcharts: chartsInit({\n\t\t\t\t\tapp: this.app,\n\t\t\t\t\tholder: this.dom.subheader.charts,\n\t\t\t\t\tvocab: this.opts.vocab\n\t\t\t\t}),\n\t\t\t\tgroups: groupsInit({\n\t\t\t\t\tapp: this.app,\n\t\t\t\t\tholder: this.dom.subheader.groups,\n\t\t\t\t\tvocab: this.opts.vocab\n\t\t\t\t}),\n\t\t\t\trecover: recoverInit({\n\t\t\t\t\tapp: this.app,\n\t\t\t\t\tholder: this.dom.recoverDiv,\n\t\t\t\t\t// TODO: ???? may limit the tracked state to only the filter, activeCohort ???\n\t\t\t\t\tgetState: appState => appState,\n\t\t\t\t\treactsTo: action => action.type != 'plot_edit',\n\t\t\t\t\tmaxHistoryLen: 5\n\t\t\t\t}),\n\t\t\t\tsessionBtn: sessionBtnInit({\n\t\t\t\t\tapp: this.app,\n\t\t\t\t\tbutton: this.dom.saveBtn,\n\t\t\t\t\tmassSessionDuration: this.opts.massSessionDuration,\n\t\t\t\t\tsessionDaysLeft: this.app.opts.sessionDaysLeft || null\n\t\t\t\t}),\n\t\t\t\tabout: aboutInit({\n\t\t\t\t\tapp: this.app,\n\t\t\t\t\tsubheader: this.dom.subheader.about,\n\t\t\t\t\tinstanceNum: this.instanceNum,\n\t\t\t\t\taboutOverrides: appState?.termdbConfig?.massNav?.tabs?.about || null,\n\t\t\t\t\tselectCohort: appState?.termdbConfig?.selectCohort || null\n\t\t\t\t}),\n\t\t\t\tchat: chatInit({\n\t\t\t\t\tapp: this.app,\n\t\t\t\t\tsubheader: this.dom.subheader.chat\n\t\t\t\t})\n\t\t\t})\n\t\t\tthis.mayShowMessage_sessionDaysLeft()\n\t\t} catch (e) {\n\t\t\tthrow e\n\t\t}\n\t}\n\n\treactsTo(action) {\n\t\tif (action.type.includes('cache_termq')) return true\n\t\tif (action.type.startsWith('filter')) return true\n\t\tif (action.type.startsWith('cohort')) return true\n\t\tif (action.type.startsWith('tab')) return true\n\n\t\t// do not use startsWith('plot_') to exclude 'plot_edit' as no need for nav to react to that\n\t\tif (action.type == 'plot_prep') return true\n\t\tif (action.type == 'plot_create') return true\n\t\tif (action.type == 'plot_delete') return true\n\n\t\tif (action.type == 'app_refresh') return true\n\t\tif (action.type.endsWith('_customTerm')) return true\n\t\tif (action.type.endsWith('_group')) return true\n\t}\n\n\tgetState(appState) {\n\t\treturn {\n\t\t\tsearching: this.searching, // for detection of internal state change\n\t\t\tnav: appState.nav,\n\t\t\tactiveCohort: appState.activeCohort,\n\t\t\ttermdbConfig: appState.termdbConfig,\n\t\t\tfilter: appState.termfilter.filter,\n\t\t\tplots: appState.plots,\n\t\t\tgroups: appState.groups\n\t\t}\n\t}\n\n\tasync main() {\n\t\tthis.dom.tabDiv.style('display', this.state.nav.header_mode === 'with_tabs' ? 'inline-block' : 'none')\n\t\tthis.dom.tip.hide()\n\t\tthis.activeTab = this.state.nav.activeTab\n\t\tthis.prevCohort = this.activeCohort\n\t\tthis.activeCohort = +this.state.activeCohort\n\t\tthis.filterUiRoot = getFilterItemByTag(this.state.filter, 'filterUiRoot')\n\t\tthis.cohortFilter = getFilterItemByTag(this.state.filter, 'cohortFilter')\n\t\tif (this.cohortNames) {\n\t\t\tthis.activeCohortName = this.cohortNames[this.activeCohort]\n\t\t\tif (this.activeCohort !== -1)\n\t\t\t\tthis.activeCohortLabel = this.state.termdbConfig.selectCohort.values[this.activeCohort].shortLabel\n\t\t}\n\t\tthis.filterJSON = JSON.stringify(this.state.filter)\n\n\t\tthis.cohortsData = await this.app.vocabApi.getCohortsData()\n\n\t\tif (this.state.nav.header_mode === 'with_tabs') {\n\t\t\tif (!(this.activeCohort in this.samplecounts)) {\n\t\t\t\tthis.samplecounts[this.activeCohort] = await this.app.vocabApi.getCohortSampleCount(this.activeCohortName)\n\t\t\t}\n\t\t\tif (!(this.filterJSON in this.samplecounts)) {\n\t\t\t\tif (!this.filterUiRoot || !this.filterUiRoot.lst.length) {\n\t\t\t\t\tthis.samplecounts[this.filterJSON] = this.samplecounts[this.activeCohort]\n\t\t\t\t} else {\n\t\t\t\t\tconst n = await this.app.vocabApi.getFilteredSampleCount(this.filterJSON)\n\t\t\t\t\tthis.samplecounts[this.filterJSON] = n\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tthis.updateUI()\n\t}\n}\n\nexport const navInit = getCompInit(TdbNav)\n\nfunction setRenderers(self) {\n\tself.initUI = appState => {\n\t\tconst verifiedToken = self.app.vocabApi.verifiedToken\n\t\tconst invalidTokenErrorHandling = appState.termdbConfig.invalidTokenErrorHandling\n\t\t//Show error message if login failed and all charts require login. If the dataset does not require login verifiedToken is true\n\t\t//Currently only the profile and carereg always require a token.\n\t\t// Note that if the user did not login the public token was used. So only if the user did login and the token passed was invalid this error is shown\n\t\tif (!verifiedToken && invalidTokenErrorHandling?.affectedCharts?.includes('*'))\n\t\t\tthrow new Error(appState.termdbConfig.invalidTokenErrorHandling.errorMessage)\n\t\tconst header = self.opts.holder.append('div').style('white-space', 'nowrap')\n\t\tconst massNav = appState.termdbConfig?.massNav || {}\n\t\tlet titleDiv = header\n\t\t\t.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('float', 'right')\n\t\t\t.style('font-size', '1.1em')\n\t\t\t.style('margin', '50px 10px 0 0')\n\t\t\t.text(massNav?.title?.text) //this line will be executed in update UI to reflect cohort changes\n\n\t\tconst tabDiv = header.append('div').style('display', 'none').style('vertical-align', 'bottom')\n\t\tconst controlsDiv = header\n\t\t\t//Fix for adding message underneath the search bar and buttons\n\t\t\t.append('div')\n\t\t\t.style('vertical-align', 'top')\n\t\t\t.style('margin', '10px')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('float', 'right')\n\n\t\tif (self.opts.header_mode === 'only_buttons') {\n\t\t\t// if header_mode is only_buttons, show only buttons\n\t\t\ttabDiv.style('display', 'none')\n\t\t\ttitleDiv.style('display', 'none')\n\t\t\tcontrolsDiv.style('display', 'none')\n\t\t}\n\t\tself.opts.holder.attr('class', 'sjpp-nav')\n\t\tself.dom = {\n\t\t\tholder: self.opts.holder,\n\t\t\theader,\n\t\t\ttabDiv,\n\t\t\tcontrolsDiv,\n\t\t\tsearchDiv: controlsDiv.append('div').style('margin', '10px'),\n\t\t\tsessionDiv: controlsDiv.append('div').style('display', 'inline-block'),\n\t\t\trecoverDiv: controlsDiv.append('div').style('display', 'inline-block'),\n\t\t\tpdfDiv: controlsDiv\n\t\t\t\t.append('div')\n\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t.style('padding', '4px')\n\t\t\t\t.style('vertical-align', 'middle'),\n\t\t\tdeleteAllDiv: controlsDiv\n\t\t\t\t.append('div')\n\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t.style('padding', '4px')\n\t\t\t\t.style('vertical-align', 'middle'),\n\n\t\t\thelpDiv: controlsDiv.append('div').style('display', 'none'),\n\t\t\tsessionElapsedMessageDiv: controlsDiv.append('div').style('display', 'none'),\n\t\t\tsubheaderDiv: self.opts.holder.append('div').style('display', 'block').style('border-bottom', '1px solid #000'),\n\t\t\tmessageDiv: self.opts.holder.append('div').style('margin', '30px').style('display', 'none'),\n\t\t\ttitleDiv,\n\t\t\ttip: new Menu({ padding: '5px' })\n\t\t}\n\t\ticon_functions['trash'](self.dom.deleteAllDiv, {\n\t\t\thandler: self.deletePlots,\n\t\t\ttitle: 'Delete all plots. To revert, click Undo button'\n\t\t})\n\n\t\ticon_functions['pdf'](self.dom.pdfDiv, {\n\t\t\thandler: self.opts.downloadPlots,\n\t\t\ttitle: 'Generate a PDF of all the plots opened'\n\t\t})\n\n\t\tif (self.opts.header_mode === 'with_cohortHtmlSelect') {\n\t\t\t// not part of filter div\n\t\t\tself.dom.cohortStandaloneDiv = header\n\t\t\t\t.append('div')\n\t\t\t\t.style('display', 'inline-block')\n\t\t\t\t.style('margin', '10px')\n\t\t\t\t.style('vertical-align', 'top')\n\n\t\t\tself.dom.cohortStandaloneDiv.append('label').html('Cohort: ')\n\t\t\tself.dom.cohortSelect = self.dom.cohortStandaloneDiv.append('select').on('change', async function () {\n\t\t\t\tself.app.dispatch({ type: 'cohort_set', activeCohort: +this.value })\n\t\t\t})\n\n\t\t\tself.dom.cohortSelect\n\t\t\t\t.selectAll('option')\n\t\t\t\t.data(appState.termdbConfig.selectCohort.values)\n\t\t\t\t.enter()\n\t\t\t\t.append('option')\n\t\t\t\t.attr('value', (d, i) => i)\n\t\t\t\t.property('selected', (d, i) => i === appState.activeCohort)\n\t\t\t\t.html(d => d.shortLabel)\n\t\t}\n\n\t\tself.dom.subheader = Object.freeze({\n\t\t\t// For either the COHORT or ABOUT tab\n\t\t\tabout: self.dom.subheaderDiv\n\t\t\t\t.append('div')\n\t\t\t\t.attr('data-testid', 'sjpp-mass-nav-subheader-about')\n\t\t\t\t.style('display', 'none'),\n\t\t\tsearch: self.dom.subheaderDiv\n\t\t\t\t.append('div')\n\t\t\t\t.attr('data-testid', 'sjpp-mass-nav-subheader-search')\n\t\t\t\t.style('display', 'none'),\n\t\t\tgroups: self.dom.subheaderDiv\n\t\t\t\t.append('div')\n\t\t\t\t.attr('data-testid', 'sjpp-mass-nav-subheader-groups')\n\t\t\t\t.style('display', 'none'),\n\t\t\tcharts: self.dom.subheaderDiv\n\t\t\t\t.append('div')\n\t\t\t\t.attr('data-testid', 'sjpp-mass-nav-subheader-charts')\n\t\t\t\t.style('display', 'none'),\n\t\t\tfilter: self.dom.subheaderDiv\n\t\t\t\t.append('div')\n\t\t\t\t.attr('data-testid', 'sjpp-mass-nav-subheader-filter')\n\t\t\t\t.style('display', 'none'),\n\t\t\tchat: self.dom.subheaderDiv\n\t\t\t\t.append('div')\n\t\t\t\t.attr('data-testid', 'sjpp-mass-nav-subheader-chat')\n\t\t\t\t.style('display', 'none')\n\t\t\t// cart: self.dom.subheaderDiv.append('div').style('display', 'none').html('<br/>Cart feature under construction - work in progress<br/>&nbsp;<br/>'),\n\t\t})\n\n\t\tif (!massNav.tabs?.about?.hide) {\n\t\t\t// about tab is not hidden\n\t\t\tself.tabs.push(aboutTab)\n\t\t\t// about tab contents are conditionally determined by 1) override 2) ds using or not using cohort.\n\t\t\t// furbish an override object with default properties based on conditions if those properties are missing\n\t\t\tconst override = Object.assign({}, massNav.tabs?.about)\n\t\t\tif (appState.termdbConfig?.selectCohort) {\n\t\t\t\t// ds has cohort selection and no customization to about tab\n\t\t\t\tif (!override.top) override.top = 'COHORT'\n\t\t\t\t// do not assign \"mid\" here as it will be dynamically assigned with active cohort name\n\t\t\t} else {\n\t\t\t\t// ds doesn't use cohort selection. if mid is missing, use dslabel\n\t\t\t\tif (!override.mid) override.mid = self.pickDatasetLabel(appState)\n\t\t\t}\n\t\t\tObject.assign(aboutTab, override) // apply ds customizations\n\t\t}\n\t\tif (!massNav.tabs?.charts?.hide) {\n\t\t\t// charts tab is not hidden\n\t\t\tself.tabs.push(chartTab)\n\t\t\tObject.assign(chartTab, massNav.tabs?.charts)\n\t\t}\n\t\tif (!massNav.tabs?.groups?.hide) {\n\t\t\t// group tab is not hidden\n\t\t\tself.tabs.push(groupsTab)\n\t\t\tObject.assign(groupsTab, massNav.tabs?.groups)\n\t\t}\n\t\tif (!massNav.tabs?.filter?.hide) {\n\t\t\t// filter tab is not hidden\n\t\t\tself.tabs.push(filterTab)\n\t\t\tObject.assign(filterTab, massNav.tabs?.filter)\n\t\t}\n\t\t/** When chat is enabled for a ds, show name as \"CHAT\". When not enabled, it should show \"SEARCH\" with ONLY omnisearch functionality\n\t\t **/\n\t\tif (!massNav.tabs?.chat?.hide) {\n\t\t\tif (appState.termdbConfig?.queries?.chat) {\n\t\t\t\tconst chatTab = { top: 'CHAT', mid: '', btm: '', subheader: 'chat' }\n\t\t\t\tObject.assign(chatTab, massNav.tabs?.chat)\n\t\t\t\tchatTab.top = 'CHAT' // Copilot mentioned that Object.assign may overwrite {chat/search}.top. Therefore this line has been added.\n\t\t\t\tself.tabs.push(chatTab)\n\t\t\t} else {\n\t\t\t\tconst searchTab = { top: 'SEARCH', mid: '', btm: '', subheader: 'chat' }\n\t\t\t\tObject.assign(searchTab, massNav.tabs?.chat)\n\t\t\t\tsearchTab.top = 'SEARCH' // Copilot mentioned that Object.assign may overwrite {chat/search}.top. Therefore this line has been added.\n\t\t\t\tself.tabs.push(searchTab)\n\t\t\t}\n\t\t}\n\n\t\tconst table = self.dom.tabDiv\n\t\t\t.append('table')\n\t\t\t.attr('data-testid', 'sjpp-nav-tabs-table')\n\t\t\t.style('border-collapse', 'collapse')\n\n\t\t// using a table layout for tabs, iterate through each tab\n\t\t// once for each of [top, mid, btm] row\n\t\ttable\n\t\t\t.selectAll('tr')\n\t\t\t.data(['top', 'mid', 'btm'])\n\t\t\t.enter()\n\t\t\t.append('tr')\n\t\t\t.attr('class', (d, i) => `sjpp-nav-tabs-row-${i}`)\n\t\t\t.style('font-size', (d, i) => (i == 1 ? '20px' : '12px'))\n\t\t\t.selectAll('td')\n\t\t\t.data((key, i) =>\n\t\t\t\tself.tabs.map((row, colNum) => {\n\t\t\t\t\treturn {\n\t\t\t\t\t\trowNum: i,\n\t\t\t\t\t\tkey,\n\t\t\t\t\t\tcolNum,\n\t\t\t\t\t\tlabel: row[key],\n\t\t\t\t\t\tsubheader: row.subheader,\n\t\t\t\t\t\tdisabled: row.disabled,\n\t\t\t\t\t\tdisabledMessage: row.disabledMessage\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t)\n\t\t\t.enter()\n\t\t\t.append('td')\n\t\t\t.attr('class', d => `sjpp-nav-tab-col-${d.colNum}`)\n\t\t\t// hide the about (e.g. cohort tab) until there is termdbConfig.selectCohort or termdbCongfig.massNav.tabs.about\n\t\t\t.style('display', 'none') // d => (d.colNum === 0 || self.activeCohort !== -1 ? '' : 'none'))\n\t\t\t.style('width', '100px')\n\t\t\t.style('padding', d => (d.rowNum === 0 ? '12px 12px 3px 12px' : '3px 12px'))\n\t\t\t.style('text-align', 'center')\n\t\t\t.style('border-left', '1px solid #ccc')\n\t\t\t.style('border-right', '1px solid #ccc')\n\t\t\t.style('color', '#aaa')\n\t\t\t.style('opacity', d => (d.disabled ? 0.5 : 1))\n\t\t\t.style('cursor', d => (d.disabled ? 'not-allowed' : 'pointer'))\n\t\t\t.attr('title', d => d.disabledMessage || '')\n\t\t\t.html(d => d.label)\n\t\t\t.on('click', (event, d) => {\n\t\t\t\tself.setTab(event, d)\n\t\t\t})\n\t\t\t.on('mouseover', (event, d) => {\n\t\t\t\tself.mouseover(event, d)\n\t\t\t})\n\t\t\t.on('mouseout', () => {\n\t\t\t\tself.mouseout()\n\t\t\t})\n\n\t\tself.dom.trs = table.selectAll('tr')\n\t\tself.dom.tds = table.selectAll('td')\n\t\tself.subheaderKeys = self.tabs.map(d => d.subheader)\n\n\t\tself.dom.saveBtn = self.dom.sessionDiv\n\t\t\t.append('button')\n\t\t\t.attr('data-testid', 'sjpp-nav-session-btn')\n\t\t\t.style('margin', '10px')\n\t\t\t.text('Session \u25BC')\n\n\t\t//.on('click', self.getSessionUrl)\n\n\t\tif (self.sessionDaysLeft != null) {\n\t\t\t//Only show if called from `mass-session-id` URL\n\t\t\tself.dom.fileBtn = self.dom.sessionDiv\n\t\t\t\t.append('button')\n\t\t\t\t.attr('data-testid', 'sjpp-nav-file-btn')\n\t\t\t\t.style('margin', '10px')\n\t\t\t\t.text('Export Session')\n\t\t\t\t.on('click', event => {\n\t\t\t\t\tself.getSessionFile(event)\n\t\t\t\t})\n\t\t}\n\t}\n\n\tself.deletePlots = () => {\n\t\tconst state = self.app.getState()\n\t\tconst subactions = []\n\t\tfor (const plot of state.plots) subactions.push({ type: 'plot_delete', id: plot.id })\n\n\t\tself.app.dispatch({ type: 'app_refresh', subactions })\n\t}\n\n\tself.mayShowMessage_sessionDaysLeft = () => {\n\t\tif (!Number.isFinite(self.sessionDaysLeft)) {\n\t\t\t// info not available, do not show msg\n\t\t\treturn\n\t\t}\n\t\tself.dom.sessionElapsedMessageDiv.style('display', 'block')\n\t\tself.dom.remainingDaysMessage = self.dom.sessionElapsedMessageDiv\n\t\t\t.append('div')\n\t\t\t.style('display', 'block')\n\t\t\t.style('opacity', '0.65')\n\t\t\t.html(\n\t\t\t\t`<u>${self.sessionDaysLeft} days</u> left until this session is removed. Click the \"Session \u25BC\" button and select \"Save\" option to create a new one.`\n\t\t\t)\n\t}\n\n\tself.updateUI = async () => {\n\t\tif (!self.dom.subheaderDiv) return\n\t\tif (self.activeTab && self.state.termdbConfig.selectCohort && self.activeCohort == -1) {\n\t\t\t// showing charts or filter tab; cohort selection is enabled but no cohort is selected\n\t\t\tself.dom.subheaderDiv.style('display', 'none')\n\t\t\tself.dom.messageDiv.selectAll('text').remove()\n\t\t\tself.dom.messageDiv.style('display', '').text('No cohort selected. Please select a cohort in the \"COHORT\" tab.')\n\t\t} else {\n\t\t\tif (self.dom.subheaderDiv) self.dom.subheaderDiv.style('display', self.activeTab != -1 ? 'block' : 'none')\n\t\t\tif (self.dom.messageDiv) self.dom.messageDiv.style('display', 'none')\n\t\t}\n\t\tconst selectCohort = self.state.termdbConfig.selectCohort\n\t\tconst massNav = self.state.termdbConfig.massNav\n\t\tself.dom.searchDiv.style('display', selectCohort && self.activeCohort == -1 ? 'none' : 'inline-block')\n\t\t//self.dom.holder.style('margin-bottom', self.state.nav.header_mode === 'with_tabs' ? '20px' : '')//To be checked why it was needed\n\t\tself.dom.header.style('border-bottom', self.state.nav.header_mode === 'with_tabs' ? '1px solid #000' : '')\n\t\tself.dom.tds\n\t\t\t.style('display', '')\n\t\t\t//Only show black text when the tab is active and the subheader is displayed\n\t\t\t.style('color', d => (d.colNum == self.activeTab ? activeTabTextColor : inactiveTabTextColor))\n\t\t\t.style('background-color', d =>\n\t\t\t\td.colNum == self.activeTab && self.dom.subheaderDiv.style('display') != 'none'\n\t\t\t\t\t? self.state.termdbConfig.massNav?.activeColor || activeTabBgColor\n\t\t\t\t\t: 'transparent'\n\t\t\t)\n\t\t\t.html(function (d, i) {\n\t\t\t\tif (d.key == 'top') return this.innerHTML\n\n\t\t\t\tif (d.subheader == 'groups') {\n\t\t\t\t\tif (d.key == 'mid') return self.state.groups.length || 'NONE'\n\t\t\t\t\treturn ''\n\t\t\t\t}\n\n\t\t\t\tif (d.subheader === 'charts') {\n\t\t\t\t\t// only a plot in it's own sandbox will be counted; do not separately count child plots in the same sandbox\n\t\t\t\t\tconst n = self.state.plots.filter(p => !p.parentId).length\n\t\t\t\t\tif (d.key == 'mid') return !n ? 'NONE' : n\n\t\t\t\t\telse return ''\n\t\t\t\t} else if (d.subheader === 'about') {\n\t\t\t\t\tif (self.activeCohort != -1 && self.activeCohort in self.samplecounts) {\n\t\t\t\t\t\tconst aboutMap = {\n\t\t\t\t\t\t\ttop: this.innerHTML,\n\t\t\t\t\t\t\tmid: self.activeCohortLabel,\n\t\t\t\t\t\t\tbtm: self.samplecounts[self.activeCohort]\n\t\t\t\t\t\t}\n\t\t\t\t\t\treturn aboutMap[d.key] || ''\n\t\t\t\t\t} else if (!selectCohort) {\n\t\t\t\t\t\tconst aboutMap = {\n\t\t\t\t\t\t\ttop: massNav?.tabs?.about?.top || 'ABOUT',\n\t\t\t\t\t\t\tmid: massNav?.tabs?.about?.mid || this.innerHTML,\n\t\t\t\t\t\t\tbtm: massNav?.tabs?.about?.btm || self.samplecounts[self.activeCohort]\n\t\t\t\t\t\t}\n\t\t\t\t\t\treturn aboutMap[d.key] || ''\n\t\t\t\t\t} else {\n\t\t\t\t\t\treturn d.key === 'mid' ? 'NONE' : this.innerHTML\n\t\t\t\t\t}\n\t\t\t\t} else if (d.subheader === 'filter') {\n\t\t\t\t\tconst filter = self.filterUiRoot ? self.filterUiRoot : { lst: [] }\n\t\t\t\t\tif (filter.lst.length === 0) {\n\t\t\t\t\t\t// Do not show number of samples at bottom of FILTER tab when no filter applied\n\t\t\t\t\t\treturn d.key === 'mid' ? 'NONE' : ''\n\t\t\t\t\t} else {\n\t\t\t\t\t\tconst n = self.samplecounts[self.filterJSON] != undefined ? '' + self.samplecounts[self.filterJSON] : ''\n\t\t\t\t\t\treturn d.key === 'mid' ? filter.lst.length : n\n\t\t\t\t\t}\n\t\t\t\t} else {\n\t\t\t\t\treturn d.key === 'mid' ? this.innerHTML : '&nbsp;'\n\t\t\t\t}\n\t\t\t})\n\n\t\t// const visibleSubheaders = []\n\t\tfor (const key in self.dom.subheader) {\n\t\t\tself.dom.subheader[key].style(\n\t\t\t\t'display',\n\t\t\t\tself.activeTab == -1 ? 'none' : self.tabs[self.activeTab].subheader === key ? 'block' : 'none'\n\t\t\t)\n\t\t}\n\n\t\tif (self.opts.header_mode === 'with_cohortHtmlSelect') {\n\t\t\tself.dom.cohortSelect.selectAll('option').property('value', self.activeCohort)\n\t\t}\n\t}\n}\n\nfunction setInteractivity(self) {\n\tself.setTab = async (event, d) => {\n\t\t// a disabled tab is shown to advertise the capability but cannot be activated\n\t\tif (d.disabled) return\n\t\tif (d.colNum === self.activeTab && !self.searching) {\n\t\t\t// The about tab should not be hidden on double click with or without plots\n\t\t\tif (self.activeTab == 0) return\n\t\t\tself.prevCohort = self.activeCohort\n\t\t\tawait self.updateUI()\n\n\t\t\t// if the user double-clicks on the same tab, hide the subheader\n\t\t\tself.app.dispatch({ type: 'tab_set', activeTab: -1 })\n\t\t\treturn\n\t\t}\n\t\tself.activeTab = d.colNum\n\t\tself.searching = false\n\t\tself.app.dispatch({ type: 'tab_set', activeTab: self.activeTab })\n\t\tconst chartsIdx = self.subheaderKeys.indexOf('charts')\n\t\tif (self.activeTab == chartsIdx && self.activeCohort != -1 && !self.state.plots.length) {\n\t\t\t// show dictionary or default plot in charts tab if no other\n\t\t\t// plots have been created\n\t\t\tconst defaultChartType = self.state.termdbConfig.defaultChartType || 'dictionary'\n\t\t\tself.app.dispatch({\n\t\t\t\ttype: 'plot_create',\n\t\t\t\tid: getId(),\n\t\t\t\tconfig: { chartType: defaultChartType }\n\t\t\t})\n\t\t}\n\t}\n\n\tself.mouseover = (event, d) => {\n\t\tconst defaultActiveColor = self.state.termdbConfig.massNav?.activeColor || activeTabBgColor\n\t\tself.dom.tds.style('background-color', t => {\n\t\t\t//light yellow for inactive tabs and grey-yellow for this active tab\n\t\t\tif (t.colNum === d.colNum)\n\t\t\t\treturn self.activeTab == t.colNum\n\t\t\t\t\t? self.state.termdbConfig.massNav?.activeColorHover || activeTabBgColorHover\n\t\t\t\t\t: inactiveTabBgColorHover\n\t\t\treturn self.activeTab == t.colNum ? defaultActiveColor : 'transparent'\n\t\t})\n\t}\n\n\tself.mouseout = () => {\n\t\tconst defaultActiveColor = self.state.termdbConfig.massNav?.activeColor || activeTabBgColor\n\t\tself.dom.tds.style('background-color', t => (self.activeTab == t.colNum ? defaultActiveColor : 'transparent'))\n\t}\n\n\tself.getSessionFile = async event => {\n\t\t//Download mass-session-id file\n\t\tconst res = await dofetch3(`/massSession?id=${self.sessionId}`)\n\t\tconst a = document.createElement('a')\n\t\tconst dataStr = 'data:application/json;charset=utf-8,' + encodeURIComponent(JSON.stringify(res.state))\n\t\ta.setAttribute('href', dataStr)\n\t\ta.download = `${self.sessionId}.json`\n\t\ta.click()\n\t\ta.remove()\n\t}\n\n\tself.pickDatasetLabel = appState => {\n\t\tconst dslabel = appState.vocab.dslabel.toUpperCase()\n\t\treturn dslabel.length > 10 ? `${dslabel.slice(0, 10)}...` : dslabel\n\t}\n}\n"],
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+  "names": ["event", "id", "d", "instanceNum", "event", "d", "cf", "chr", "start", "stop", "prompt", "event", "setRenderers", "appState", "event"]
+}

package/dist/chunk-MTZSN3H4.js

@@ -0,0 +1,302 @@
+import {
+  appear2 as appear,
+  axisstyle,
+  bwSetting,
+  disappear2 as disappear,
+  makeNumericAxisConfig,
+  rgb2hex
+} from "./chunk-WY2PGUVX.js";
+import {
+  dofetch3
+} from "./chunk-LYVLF6HO.js";
+import {
+  axisLeft
+} from "./chunk-LOZEKOES.js";
+import {
+  format,
+  linear
+} from "./chunk-SOTB4FRE.js";
+
+// src/block.tk.bigwig.js
+function bigwigfromtemplate(tk, template) {
+  tk.scale = {};
+  if (template.scale) {
+    for (const k in template.scale) {
+      tk.scale[k] = template.scale[k];
+    }
+  } else {
+    tk.scale.auto = 1;
+  }
+  if (tk.normalize) {
+  } else {
+    tk.normalize = {
+      dividefactor: 1,
+      disable: 1
+    };
+  }
+  tk.barheight = template.height || 50;
+  tk.height_main = tk.toppad + tk.barheight + tk.bottompad;
+  if (!tk.ncolor) tk.ncolor = "#BD005E";
+  if (!tk.ncolor2) tk.ncolor2 = "#5E00BD";
+  if (!tk.pcolor) tk.pcolor = "#005EBD";
+  if (!tk.pcolor2) tk.pcolor2 = "#FA7D00";
+}
+function bigwigmaketk(tk, block) {
+  tk.img = tk.glider.append("image");
+  tk.tklabel.attr("y", tk.barheight / 2);
+  tk.leftaxis = tk.gleft.append("g");
+  tk.config_handle = block.maketkconfighandle(tk).on("click", () => {
+    tk.tkconfigtip.clear().showunder(tk.config_handle.node());
+    bigwigconfigpanel(tk, block, tk.tkconfigtip.d, () => bigwigload(tk, block));
+  });
+}
+async function bigwigload(tk, block) {
+  block.tkcloakon(tk);
+  const par = block.tkarg_q(tk);
+  if (tk.dotplotfactor) par.dotplotfactor = tk.dotplotfactor;
+  if (tk.bgcolor) par.bgcolor = tk.bgcolor;
+  tk.height_main = tk.toppad + tk.barheight + tk.bottompad;
+  tk.img.attr("width", block.width).attr("height", tk.barheight);
+  let errtext;
+  try {
+    let data;
+    if (tk.imgData) {
+      data = tk.imgData;
+    } else {
+      data = await dofetch3("tkbigwig", { method: "POST", body: JSON.stringify(par) });
+    }
+    if (data.error) throw data.error;
+    if (!data.src) throw "data.src missing";
+    tk.tklabel.transition().attr("y", tk.barheight / 2);
+    tk.img.attr("xlink:href", data.src);
+    if (data.minv != void 0) {
+      tk.scale.min = data.minv;
+    }
+    if (data.maxv != void 0) {
+      tk.scale.max = data.maxv;
+    }
+    tk.leftaxis.selectAll("*").remove();
+    if (data.nodata) {
+      throw "No data in view range";
+    }
+    const scale = linear().domain([tk.scale.min, tk.scale.max]).range([tk.barheight, 0]);
+    const axis = axisLeft().scale(scale).tickValues([tk.scale.min, tk.scale.max]);
+    if (tk.integer4axis) {
+      axis.tickFormat(format("d"));
+    }
+    axisstyle({
+      axis: tk.leftaxis.call(axis),
+      color: "black",
+      showline: true
+    });
+  } catch (err) {
+    tk.img.attr("width", 0).attr("height", 0);
+    if (err.stack) {
+      console.log(err.stack);
+    }
+    errtext = typeof err == "string" ? err : err.message;
+  } finally {
+    block.tkcloakoff(tk, { error: errtext });
+    block.block_setheight();
+    for (const panel of tk.subpanels) {
+      bigwigloadsubpanel(tk, block, panel);
+    }
+  }
+}
+async function bigwigloadsubpanel(tk, block, panel) {
+  block.tkcloakon_subpanel(panel);
+  const par = block.tkarg_q(tk);
+  if (tk.dotplotfactor) {
+    par.dotplotfactor = tk.dotplotfactor;
+  }
+  par.width = panel.width;
+  par.rglst = [
+    {
+      chr: panel.chr,
+      start: panel.start,
+      stop: panel.stop,
+      width: panel.width
+    }
+  ];
+  delete par.percentile;
+  delete par.autoscale;
+  panel.img.attr("width", panel.width).attr("height", tk.barheight);
+  let errtext;
+  try {
+    if (tk.imgData) throw "subpanel not supported by imgData yet";
+    const data = await dofetch3("tkbigwig", { method: "POST", body: JSON.stringify(par) });
+    if (data.error) throw data.error;
+    panel.img.attr("xlink:href", data.src);
+  } catch (err) {
+    panel.img.attr("width", 0).attr("height", 0);
+    if (err.stack) {
+      console.log(err.stack);
+    }
+    errtext = typeof err == "string" ? err : err.message;
+  } finally {
+    block.tkcloakoff_subpanel(panel, { error: errtext });
+  }
+}
+function bigwigconfigpanel(tk, block, holder, loader) {
+  const config = {
+    pcolor: {},
+    ncolor: {},
+    pcolor2: {},
+    ncolor2: {},
+    // .row
+    // .lab
+    dotplot: {},
+    // .row
+    dividefactor: {}
+  };
+  {
+    const row = holder.append("div").style("margin-bottom", "15px");
+    row.append("span").html("Height  ");
+    row.append("input").attr("size", 5).property("value", tk.barheight).on("keyup", (event) => {
+      if (event.code != "Enter") return;
+      const s = event.target.value;
+      if (s == "") return;
+      const v = Number.parseInt(s);
+      if (Number.isNaN(v) || v <= 1) {
+        alert("track height must be positive integer");
+        return;
+      }
+      tk.barheight = v;
+      loader(bwSetting.height);
+    });
+  }
+  config.pcolor.row = holder.append("div").style("margin-bottom", "15px");
+  config.pcolor.lab = config.pcolor.row.append("span").text("Positive value color").style("padding-right", "10px");
+  config.pcolor.row.append("input").attr("type", "color").property("value", rgb2hex(tk.pcolor)).on("change", (event) => {
+    tk.pcolor = event.target.value;
+    loader(bwSetting.pcolor);
+  });
+  config.ncolor.row = holder.append("div").style("margin-bottom", "15px");
+  config.ncolor.lab = config.ncolor.row.append("span").text("Negative value color").style("padding-right", "10px");
+  config.ncolor.row.append("input").attr("type", "color").property("value", rgb2hex(tk.ncolor)).on("change", (event) => {
+    tk.ncolor = event.target.value;
+    loader(bwSetting.ncolor);
+  });
+  if (!tk.scale.auto) {
+    config.pcolor2.row = holder.append("div").style("margin-bottom", "15px");
+    config.pcolor2.lab = config.pcolor2.row.append("span").html("&ge;Max color").style("padding-right", "10px");
+    config.pcolor2.row.append("input").attr("type", "color").property("value", rgb2hex(tk.pcolor2)).on("change", (event) => {
+      tk.pcolor2 = event.target.value;
+      loader(bwSetting.pcolor2);
+    });
+    config.ncolor2.row = holder.append("div").style("margin-bottom", "15px");
+    config.ncolor2.lab = config.ncolor2.row.append("span").html("&le;Min color").style("padding-right", "10px");
+    config.ncolor2.row.append("input").attr("type", "color").property("value", rgb2hex(tk.ncolor2)).on("change", (event) => {
+      tk.ncolor2 = event.target.value;
+      loader(bwSetting.ncolor2);
+    });
+  }
+  {
+    const setting = {};
+    if (tk.scale.auto) {
+      setting.auto = 1;
+    } else if (tk.scale.percentile) {
+      setting.percentile = tk.scale.percentile;
+    } else {
+      setting.fixed = { min: tk.scale.min, max: tk.scale.max };
+    }
+    makeNumericAxisConfig({
+      holder: holder.append("div").style("margin-bottom", "15px"),
+      setting,
+      callback: (s) => {
+        if (s.auto) {
+          tk.scale.auto = 1;
+          loader(bwSetting.autoscale);
+          return;
+        }
+        if (s.fixed) {
+          delete tk.scale.auto;
+          delete tk.scale.percentile;
+          tk.scale.max = s.fixed.max;
+          tk.scale.min = s.fixed.min;
+          loader(bwSetting.fixedscale);
+          return;
+        }
+        delete tk.scale.auto;
+        tk.scale.percentile = s.percentile;
+        loader(bwSetting.percentilescale);
+      }
+    });
+  }
+  {
+    config.dotplot.row = holder.append("div").style("margin-bottom", "15px");
+    config.dotplot.row.append("span").html("Dot plot&nbsp;&nbsp;");
+    const s = config.dotplot.row.append("select").on("change", (event) => {
+      const i = event.target.selectedIndex;
+      if (i == 0) {
+        delete tk.dotplotfactor;
+      } else {
+        tk.dotplotfactor = Number.parseInt(event.target.options[i].innerHTML);
+      }
+      loader(i == 0 ? bwSetting.nodotplot : bwSetting.usedotplot);
+    });
+    let o = s.append("option").text("no");
+    if (!tk.dotplotfactor) {
+      o.property("selected", 1);
+    }
+    o = s.append("option").text("5");
+    if (tk.dotplotfactor == 5) {
+      o.property("selected", 1);
+    }
+    o = s.append("option").text("10");
+    if (tk.dotplotfactor == 10) {
+      o.property("selected", 1);
+    }
+    o = s.append("option").text("15");
+    if (tk.dotplotfactor == 15) {
+      o.property("selected", 1);
+    }
+    o = s.append("option").text("20");
+    if (tk.dotplotfactor == 20) {
+      o.property("selected", 1);
+    }
+  }
+  config.dividefactor.row = holder.append("div");
+  {
+    const id = Math.random().toString();
+    const input = config.dividefactor.row.append("input").attr("type", "checkbox").attr("id", id);
+    if (!tk.normalize.disable) {
+      input.property("checked", 1);
+    }
+    config.dividefactor.row.append("label").html("&nbsp;Apply normalization").attr("for", id);
+    const folder = config.dividefactor.row.append("div").style("margin", "5px 10px 0px 20px").style("display", tk.normalize.disable ? "none" : "block");
+    folder.append("span").html("Divide raw value by&nbsp;");
+    const factorinput = folder.append("input").attr("type", "number").style("width", "60px").property("value", tk.normalize.dividefactor).on("keyup", (event) => {
+      if (event.code != "Enter" && event.code != "NumpadEnter") return;
+      const v = event.target.value;
+      if (v <= 0) {
+        return;
+      }
+      tk.normalize.dividefactor = v;
+      loader(bwSetting.usedividefactor);
+    });
+    folder.append("div").text("Enter a value above zero").style("font-size", ".7em").style("color", "#858585");
+    input.on("change", (event) => {
+      if (event.target.checked) {
+        appear(folder);
+        delete tk.normalize.disable;
+        factorinput.property("value", tk.normalize.dividefactor);
+        loader(bwSetting.usedividefactor);
+        return;
+      }
+      disappear(folder);
+      tk.normalize.disable = 1;
+      loader(bwSetting.nodividefactor);
+    });
+  }
+  return config;
+}
+
+export {
+  bigwigfromtemplate,
+  bigwigmaketk,
+  bigwigload,
+  bigwigloadsubpanel,
+  bigwigconfigpanel
+};
+//# sourceMappingURL=chunk-MTZSN3H4.js.map