@sjcrh/proteinpaint-client 2.182.0 → 2.183.0

package/dist/chunk-2SRMRC6L.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../src/app.observer.js", "../common/globals.js", "../dom/menu.js"],
-  "sourcesContent": ["import { select as d3select } from 'd3-selection'\n\nexport const clickableSjClasses = [\n\t'sja_menuoption',\n\t'sja_clb',\n\t'sja_clbtext',\n\t'sja_clbtext2',\n\t'sjpp-dslabel',\n\t'sjpp-active-tiny-button',\n\t'sja_inset_a',\n\t'sjpp-matrix-label',\n\t'sjpp-matrix-divide-by-label',\n\t'sjpp-matrix-legend-g'\n]\n\n// buttons, inputs, a (link) and other elements have native support\n// for tab and Enter-to-click keyboard navigation; the tagNames below\n// are for elements that do not natively support keyboard navigation,\n// and will be detected as requiring support if they have one of the\n// clickableSjClasses\n// TODO: find a way to group svg text when tabbing, before re-enabling\nconst svgClickable = new Set([\n\t/*'text' /*, 'rect'*/\n])\nconst targetTagNames = new Set(['DIV', 'SPAN', 'TEXT', 'LABEL', 'g', ...[...svgClickable]])\n\nexport const renderWait = 500\nconst observedElems = new WeakSet()\n\n/*\n  observeElem() will monitor for added DOM elements, so that the\n  MutationObserver callback can detect elements that should have\n  certain attributes and/or event handlers to satisfy portal \n  requirements such as Section 508 or style guides.\n\n  elem: \n    should just be the .sja_root_holder element,\n    no need to monitor child elements, call once in src/app.js\n    in runproteinpaint() function\n\n  NOTE: When called on .sja_root_holder, the menu divs will not\n  be observed since those are attached directly on the document.body.\n  The 'client/menu.js' code has `setTabNavigation()` for this reason.\n*/\nexport function observeElem(elem) {\n\tif (window.location.pathname === '/puppet.html') return\n\tif (observedElems.has(elem)) return\n\tobservedElems.add(elem)\n\tobserver.observe(elem, { childList: true, subtree: true })\n}\n\nconst observer = new MutationObserver(function (mutationsList, observer) {\n\tconst relevantElems = new Set()\n\tfor (const mutation of mutationsList) {\n\t\tfor (const elem of mutation.addedNodes) {\n\t\t\t// Check if the elem is an Element (not a text node, etc.)\n\t\t\tif (elem.nodeType === Node.ELEMENT_NODE) {\n\t\t\t\tif (!targetTagNames.has(elem.tagName) || elem.tabIndex !== -1) continue\n\t\t\t\trelevantElems.add(elem)\n\t\t\t}\n\t\t}\n\t\t// TODO: may automate other behavior to satisfy Section 508 or other requirements\n\t}\n\n\tif (!relevantElems.size) return\n\t// give time for the added elements to have their attributes set\n\tsetTimeout(() => {\n\t\tfor (const elem of relevantElems) {\n\t\t\tif (elem.getAttribute('tabindex') !== null) continue\n\t\t\tconst selem = d3select(elem)\n\t\t\tif (\n\t\t\t\t!selem.on('click') &&\n\t\t\t\t!svgClickable.has(elem.tagName) &&\n\t\t\t\t!clickableSjClasses.find(cls => elem.classList?.contains(cls))\n\t\t\t)\n\t\t\t\tcontinue\n\t\t\t//console.log(36, elem.tabIndex, elem.getAttribute('tabindex'))\n\t\t\tselem\n\t\t\t\t// svg elems will be grouped\n\t\t\t\t.attr('tabindex', 0) //svgClickable.has(elem.tagName) ? -1 : 0)\n\t\t\t\t.on('keyup.root_observer', event => {\n\t\t\t\t\tif (event.key == 'Enter') {\n\t\t\t\t\t\tconst box = event.target.getBoundingClientRect()\n\t\t\t\t\t\tconst clientX = box.x + 0.5 * box.width\n\t\t\t\t\t\tconst clientY = box.y + box.height\n\t\t\t\t\t\t//event.target.dispatchEvent(new MouseEvent('mousemove', { bubbles: true, clientX, clientY }))\n\t\t\t\t\t\tevent.target.dispatchEvent(new MouseEvent('mousedown', { bubbles: true, clientX, clientY }))\n\t\t\t\t\t\tevent.target.dispatchEvent(new MouseEvent('mouseup', { bubbles: true, clientX, clientY }))\n\t\t\t\t\t\tevent.target.dispatchEvent(new MouseEvent('click', { bubbles: true, clientX, clientY }))\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t}\n\t\trelevantElems.clear()\n\t}, renderWait)\n})\n", "// the exported variables, accessors here may be shared and mutated at-will by other code\n// best to avoid if possible\n\n// base_zindex was moved out of src/client.js to avoid a circular import in dom/menu.js,\n// which breaks the pretest:unit bundling\nlet base_zindex = 100\n\nexport function get_base_zindex() {\n\treturn base_zindex\n}\n\nexport function set_base_zindex(i) {\n\tbase_zindex = i\n}\n", "import { select as d3select } from 'd3-selection'\nimport { get_base_zindex } from '#common/globals'\nimport { clickableSjClasses, renderWait } from '#src/app.observer'\nimport { sleep } from '#rx'\n\n/*\narg{}\n---All are optional---\n\tparent_menu\n\t\t- define if menu is launched within another menu\n\tpadding: STR\n\t\t- css value for menu.d.style.padding\n\tborder: STR\n\t\t- css value for menu.d.style.border\n\toffsetX: INT \n\t\t- default = 20\n\t\t- offset for left position (x = x + offsetX)\n\toffsetY: INT\n\t\t- default = 20\n\t\t- offset for top position (y = y + offsetY)\n\thideXmute, hideYmute: INT\n\t\t- default = 0\n\t\t- cancel tip hiding if the cursor's X,Y movement is less than the corresponding \n\t\thide*mute value. See notes in constructor\n\tclearSelector: STR\n\t\t-clear only specific elems within menu.d, not all of menu.d\n\tonHide()\n\t\t- override default hide() with callback\n*/\n\nexport const focusableSelector =\n\t`a[href], button, input, textarea, select, details, [tabindex]:not([tabindex=\"-1\"]), ` +\n\tclickableSjClasses.map(c => `.${c}`).join(',')\n\nconst showMenuTriggers = new Set([/*'mousemove',*/ 'mousedown', 'mouseup', 'click'])\nconst urlpath = window.location.pathname\nconst isTestPage = urlpath.includes('testrun.html') || urlpath.includes('puppet.html')\n\nlet stickyDiv\n\nexport class Menu {\n\tconstructor(arg = {}) {\n\t\tthis.typename = Math.random().toString()\n\n\t\tconst body = d3select(document.body)\n\t\tthis.d = body\n\t\t\t.append('div')\n\t\t\t.attr('class', 'sja_menu_div')\n\t\t\t.attr('data-testid', 'sjpp-menu-div')\n\t\t\t.style('display', 'none')\n\t\t\t.style('position', 'absolute')\n\t\t\t.style('background-color', 'white')\n\t\t\t.on('mousedown.menu' + this.typename, event => {\n\t\t\t\t/* \n\t\t\t\t\tWhen clicking on non-interactive elements within a menu, \n\t\t\t\t\tit should trigger other menus to be hidden. For example,\n\t\t\t\t\tclicking on an empty spot in a parent menu should close \n\t\t\t\t\tany submenu that are open, which is done by allowing the \n\t\t\t\t\tmousedown event to propagate to the body (default behavior).\n\t\t\t\t*/\n\t\t\t\tconst t = d3select(event.target)\n\t\t\t\tif (\n\t\t\t\t\t/*** \n\t\t\t\t\t\tNOTE on interactive menu elements: \n\t\t\t\t\t\tAny menu element (input, button, etc) that has event listeners\n\t\t\t\t\t  is expected to handle that event, including possibly closing any\n\t\t\t\t\t  associated menus, and thus no need to propagate the mousedown event \n\t\t\t\t\t\tto the document body\n\t\t\t\t\t***/\n\t\t\t\t\tt.on('mousedown') ||\n\t\t\t\t\tt.on('click') ||\n\t\t\t\t\t// also assume that the following elements have event listeners by default,\n\t\t\t\t\t// so same logic of not wanting to propagate the event to the body\n\t\t\t\t\t['INPUT', 'SELECT', 'TEXTAREA'].includes(event.target.tagName.toUpperCase())\n\t\t\t\t) {\n\t\t\t\t\tevent.stopPropagation()\n\t\t\t\t} /* else {\n\t\t\t\t\t // allow the bubbling of the mouse event to the document body\n\t\t\t\t}*/\n\t\t\t})\n\t\t\t.on('keyup', event => {\n\t\t\t\tif (event.key == 'Escape') this.hide()\n\t\t\t})\n\n\t\tthis.dnode = this.d.node()\n\n\t\tthis.setRelatedMenus(arg)\n\n\t\tbody.on('mousedown.menu' + this.typename, event => {\n\t\t\t// when pressing the mouse cursor on the menu itself or any of its submenu, it should stay open\n\t\t\tif (this.dnode.contains(event.target)) return\n\t\t\t// this assumes that the mousedown occured on the menu holder itself (not any of its child elements)\n\t\t\tif (event.target.parent_menu === this.dnode) return\n\t\t\t// detect if mousedown occurred on any descendent menu\n\t\t\tif (this.dnode.ancestor_menus?.includes(this.dnode)) return\n\t\t\t// detect in case the mousedown occurred on a menu's child element,\n\t\t\t// in which case the menu's parent should still be not hidden\n\t\t\tconst menu = event.target.closest('.sja_menu_div')\n\t\t\tif (menu && (menu.parent_menu === this.dnode || menu.ancestor_menus?.includes(this.dnode))) return // the menu div that was clicked, does it have parent or ancestor menus, and is my DOM div one of them? if yes, I shouldn't hide myself\n\t\t\t// close a menu for all other mousedown events outside of its own div or submenu\n\t\t\tthis.hide()\n\t\t})\n\n\t\tconst base_zindex = get_base_zindex()\n\t\tif (base_zindex) {\n\t\t\tthis.d.style('z-index', base_zindex + 1)\n\t\t}\n\n\t\tthis.d.style('padding', 'padding' in arg ? arg.padding : '10px')\n\t\tif (arg.border) {\n\t\t\tthis.d.style('border', arg.border)\n\t\t} else {\n\t\t\tthis.d.style('box-shadow', '0px 2px 4px 1px #999')\n\t\t}\n\t\tthis.offsetX = Number.isInteger(arg.offsetX) ? arg.offsetX : 20\n\t\tthis.offsetY = Number.isInteger(arg.offsetY) ? arg.offsetY : 20\n\t\t// The hideXmute and hideYmute options would cancel tip hiding if the\n\t\t// cursor's X,Y movement is less than the corresponding hide*mute value.\n\t\t// This helps avoid flickering when the tooltip div blocks a stationary cursor,\n\t\t// which trigers an unwanted mouseout of the element that triggered a mouseover.\n\t\t// Also useful for decreasing the sensitivity of the mouseout behavior in general.\n\t\tthis.hideXmute = Number.isInteger(arg.hideXmute) ? arg.hideXmute : 0\n\t\tthis.hideYmute = Number.isInteger(arg.hideYmute) ? arg.hideYmute : 0\n\t\tthis.prevX = -1\n\t\tthis.prevY = -1\n\t\t// string selector option to limit clear()/removal of elements\n\t\t// so that other elements may persist within tip.d\n\t\tthis.clearSelector = arg.clearSelector\n\n\t\tif (arg.onHide) this.onHide = arg.onHide\n\t}\n\n\tsetRelatedMenus(arg) {\n\t\t// detect if this menu is launched from within another menu\n\t\t// (aka, the 'parent_menu'); this value may be empty (undefined, null)\n\t\t// check if this.d isn't empty before assigning parent_menu\n\t\tif (Object.values(this.d._groups[0]).length) this.dnode.parent_menu = arg.parent_menu //; console.log(74, this.dnode.parent_menu)\n\n\t\t// collect all ancestor menus so that they can be detected\n\t\t// in the mousedown.menu event listener\n\t\tthis.dnode.ancestor_menus = arg.ancestor_menus || [] // attach property to DOM node, since other code does not know about any menu instance directly, but can detect properties of other menus by DOM node\n\t\tif (this.dnode.parent_menu && !this.dnode.ancestor_menus.includes(this.dnode.parent_menu)) {\n\t\t\tthis.dnode.ancestor_menus.push(this.dnode.parent_menu)\n\t\t}\n\t\tconst ancestor_menus = this.dnode.ancestor_menus.slice(0)\n\t\twhile (ancestor_menus.length) {\n\t\t\tconst m = ancestor_menus.pop()\n\t\t\tif (!m) continue // m may be a null element, needs to be skipped\n\t\t\tif (m.parent_menu && !this.dnode.ancestor_menus.includes(m.parent_menu)) {\n\t\t\t\tthis.dnode.ancestor_menus.push(m.parent_menu)\n\t\t\t}\n\t\t\tif (m.ancestor_menus) {\n\t\t\t\tfor (const mm of m.ancestor_menus) {\n\t\t\t\t\tif (!this.dnode.ancestor_menus.includes(mm)) this.dnode.ancestor_menus.push(mm)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\n\tclear() {\n\t\t// always use d3-selection.remove() in case it handles cancelling event listeners or other\n\t\t// housekeeping tasks, but this does not remove html text that are not nested inside tags like <span>\n\t\t// TODO: research if d3-selection.remove() has no advantage over native replaceChildren()\n\t\tif (this.clearSelector) {\n\t\t\tconst elem = this.d.select(this.clearSelector)\n\t\t\telem.selectAll('*').remove()\n\t\t\t// this will remove all text that are not nested inside html tags\n\t\t\telem.node().replaceChildren()\n\t\t} else {\n\t\t\tthis.d.selectAll('*').remove()\n\t\t\t// this will remove all text that are not nested inside html tags\n\t\t\tthis.dnode.replaceChildren()\n\t\t}\n\t\treturn this\n\t}\n\t/*\n\t To note: if shift and scroll are true, shift sets x & y.\n\t Set shift to false to use scroll\n   \n   _elem: the element for which the menu was launched, optional\n\t*/\n\tshow(_x, _y, shift = true, down = true, scroll = true, elem = null) {\n\t\tlet x = _x\n\t\tlet y = _y\n\t\tthis.prevX = _x\n\t\tthis.prevY = _y\n\n\t\t// show around a given point\n\t\tdocument.body.appendChild(this.dnode)\n\t\tthis.d.style('display', 'block')\n\t\tif (scroll) {\n\t\t\tx = x + window.scrollX\n\t\t\ty = y + window.scrollY\n\t\t}\n\t\tif (shift) {\n\t\t\tx = x + this.offsetX\n\t\t\ty = y + this.offsetY\n\t\t}\n\t\tconst width = window.innerWidth\n\t\tconst height = window.innerHeight\n\t\tconst middlex = width / 2\n\t\tconst middley = height / 2\n\t\tconst p = this.dnode.getBoundingClientRect()\n\n\t\t//does not fit to the left\n\t\tif (width - x < middlex && x + p.width > width) this.d.style('left', null).style('right', width - x + 'px')\n\t\telse this.d.style('left', x + 'px').style('right', null)\n\n\t\t// NOTE: always set the top position, not bottom which is not reliable when\n\t\t// the body {position: 'relative'}, in case PP is embedded in an external portal\n\t\t// with different css styles for <body> where sja_menu_divs are appended\n\t\tif (!down && height - y < middley && y - window.scrollY > p.height) {\n\t\t\t// does not fit to the bottom\n\t\t\tthis.d.style('top', `${y - p.height}px`).style('bottom', null)\n\t\t} else this.d.style('top', y + 'px').style('bottom', null)\n\t\tthis.d.transition().style('opacity', 1)\n\n\t\tif (elem) this.setTabNavigation(elem)\n\t\t// assume the global event.target corresponds to a clicked/\"moused\" element that launched the menu\n\t\telse if (showMenuTriggers.has(window.event?.type)) this.setTabNavigation(window.event.target)\n\n\t\tif (elem) this.stickyPosition(elem)\n\t\treturn this\n\t}\n\n\t// simplified alternative to show(), with less arguments\n\t// _x, _y: desired position in the client window\n\t// opts{}:\n\t//   elem: the element for which the menu was launched, will get focus when tabbing back from the menu\n\tshow2(_x, _y, opts = {}) {\n\t\tlet x = _x\n\t\tlet y = _y\n\t\tthis.prevX = _x\n\t\tthis.prevY = _y\n\n\t\t// show around a given point\n\t\tdocument.body.appendChild(this.dnode)\n\t\tthis.d.style('display', 'block')\n\n\t\t// the event.clientX and event.clientY are already veiwport positions.\n\t\t// when position == absolute, (what we have now) the scroll position has to be considered.\n\t\t// when position == fixed, relative to the viewport, the scroll could be ignored, but the menu doesn't follow the scroll\n\t\tx = x + window.scrollX + this.offsetX // by adding the scroll, the postion of menu becomes relative to document.body\n\t\ty = y + window.scrollY + this.offsetY\n\n\t\tconst width = window.innerWidth\n\t\tconst height = window.innerHeight\n\t\tconst middlex = width / 2\n\t\tconst middley = height / 2\n\t\tconst p = this.dnode.getBoundingClientRect()\n\n\t\t//does not fit to the right\n\t\t// \"right\" is relative to the right side of menu and window\n\t\tif (x + p.width > width) this.d.style('left', '').style('right', '5px')\n\t\telse this.d.style('left', x + 'px').style('right', '')\n\n\t\t// for now, the users have to scroll down to see the entire menu if there is not enough height for the menu\n\t\t// TODO: reposition the menu to make it at least partially visible.\n\t\tthis.d.style('top', y + 'px').style('bottom', '')\n\t\tthis.d.transition().style('opacity', 1)\n\n\t\tif (opts.elem) this.setTabNavigation(opts.elem)\n\t\treturn this\n\t}\n\n\t// opts{}: can supply offsetX and offsetY\n\t// necessary because .showunder() uses .show(shift=false), which\n\t// ignores offsetY in the constructor option\n\tshowunder(elem, _opts = {}) {\n\t\t// route to .show()\n\t\tconst opts = Object.assign({ offsetX: 0, offsetY: 0 }, _opts)\n\t\tconst p = elem.getBoundingClientRect()\n\t\tconst x = p.left + window.scrollX + opts.offsetX\n\t\tconst y = p.top + p.height + window.scrollY + 5 + opts.offsetY\n\n\t\treturn this.show(x, y, false, true, false, elem)\n\n\t\t/*\n\t\tthis.d\n\t\t\t.style('display','block')\n\t\t\t.style('right',null)\n\t\t\t.style('bottom',null)\n\t\t\t.style('left', (p.left+window.scrollX)+'px')\n\t\t\t.style('top',  (p.top + p.height + window.scrollY + (yspace || 5) )+'px' )\n\t\t\t.transition().style('opacity',1)\n\t\treturn this\n\t\t*/\n\t}\n\n\tasync setTabNavigation(elem, numTries = 0) {\n\t\t// For Section 508 compliance: assume that the elem triggered showing the menu\n\t\t// and support back-navigation to it from the menu using shift-tab\n\n\t\tconst clickableElems = [...this.d.node().querySelectorAll(focusableSelector)].filter(elem => elem.checkVisibility())\n\t\tif (!clickableElems.length) {\n\t\t\t// give time for menu focusable elements to be rendered, up to a number of a certain of tries\n\t\t\tif (numTries < 30) setTimeout(() => this.setTabNavigation(elem, numTries++), 100)\n\t\t\treturn\n\t\t}\n\n\t\tconst firstFocusableChildElem = d3select(clickableElems[0])\n\n\t\tfor (const elem of clickableElems) {\n\t\t\tconst s = d3select(elem)\n\t\t\tif (!elem.getAttribute('tabindex')) s.attr('tabindex', 0)\n\t\t\tif (!s.on('keyup'))\n\t\t\t\tsetTimeout(() => {\n\t\t\t\t\ts.on('keyup.menu_tab_nav', event => {\n\t\t\t\t\t\tif (event.key == 'Enter') elem.click()\n\t\t\t\t\t})\n\t\t\t\t}, renderWait) // wait for rendered elements to include enforced tabindex, before any triggered click()\n\t\t}\n\n\t\tlet lastTabbedTime = Date.now()\n\t\tfunction setLastTabbedTime(event) {\n\t\t\t// navigating away from the first clickable element, if this triggers\n\t\t\t// the blur of the first element then the 'onblur' timing should be very quick\n\t\t\tif (event.key == 'Tab' && event.shiftKey) lastTabbedTime = Date.now()\n\t\t}\n\t\tfunction focusOnLauncherElem(tip, launcherElem) {\n\t\t\t// detect if the blur is caused by something other than a tabbed navigation away from the first element\n\t\t\tif (Date.now() - lastTabbedTime > tabWait) return\n\t\t\t// do not trigger focusing back to firstFocusableChildElem or closing the tooltip\n\t\t\t// if there is no activeElement or if it's inside the tooltip\n\t\t\tif (\n\t\t\t\tdocument.activeElement === document.body ||\n\t\t\t\ttip.dnode.contains(document.activeElement) ||\n\t\t\t\tevent.target?.closest('.sja_menu_div')?.ancestor_menus?.includes(this.dnode)\n\t\t\t)\n\t\t\t\treturn\n\t\t\ttip.hide()\n\t\t\tlauncherElem.focus() // switch focus back to the clicked elem that launched the menu, when shift-tabbing from the first focusable child element\n\t\t}\n\n\t\tconst tabWait = 100\n\t\tfirstFocusableChildElem\n\t\t\t.on('keydown.menu_tab_nav', setLastTabbedTime)\n\t\t\t.on('blur.menu_tab_nav', () => focusOnLauncherElem(this, elem))\n\n\t\tconst searchElem = elem.type === 'search' ? elem : elem.querySelector(`input[type='search']`)\n\t\tif (!searchElem) {\n\t\t\tsetTimeout(() => (clickableElems.find(priorityFocusElem) || clickableElems[0]).focus(), renderWait)\n\t\t} else if (searchElem) {\n\t\t\t// do not autofocus on menu, since the user may still be typing the text to search\n\t\t\tconst search = d3select(searchElem)\n\t\t\tif (!search.on('keyup')) {\n\t\t\t\tsearch.on('keyup', event => {\n\t\t\t\t\tif (!event.key.startsWith('Arrow')) return\n\t\t\t\t\tconst clickableElems = [...this.d.node().querySelectorAll(focusableSelector)].filter(elem =>\n\t\t\t\t\t\telem.checkVisibility()\n\t\t\t\t\t)\n\t\t\t\t\tif (!clickableElems.length) return\n\t\t\t\t\tif (event.key == 'ArrowDown') {\n\t\t\t\t\t\tclickableElems[0].focus()\n\t\t\t\t\t\td3select(clickableElems[0])\n\t\t\t\t\t\t\t.on('keydown.menu_tab_nav', setLastTabbedTime)\n\t\t\t\t\t\t\t.on('blur.menu_tab_nav', () => focusOnLauncherElem(this, searchElem))\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t}\n\t\t}\n\t}\n\n\tshowunderoffset(dom) {\n\t\tconst p = dom.getBoundingClientRect()\n\t\tconst y = p.top + p.height + window.scrollY + 5\n\t\treturn this.show(p.left, y, true, true, false)\n\n\t\t/*\n\t\tthis.d\n\t\t\t.style('display','block')\n\t\t\t.style('right',null)\n\t\t\t.style('bottom',null)\n\t\t\t.style('left', (p.left+window.scrollX)+'px')\n\t\t\t.style('top',  (p.top + p.height + window.scrollY + (yspace || 5) )+'px' )\n\t\t\t.transition().style('opacity',1)\n\t\treturn this\n\t\t*/\n\t}\n\n\t// stickyPosition() prevents the menu from being scrolled away (above or below) the clicked element,\n\t// an issue seen when the clicked element is nested inside a sticky-positioned div such as\n\t// the MASS nav header, whereas the menu div that's attached to the body will scroll freely past the\n\t// 'stuck' clicked element\n\tstickyPosition(elem, _opts = {}) {\n\t\t// only setup an observer on click event, not other transient mouse events such as mousemove,\n\t\t// to limit the performance penalty to known static button/label interactions\n\t\tif (!window.event || window.event.type != 'click' || !elem.__data__?.stickyAncestor) return\n\n\t\tconst top = 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-  "names": ["observer", "event", "event", "base_zindex", "elem", "clickableElems"]
-}

package/dist/chunk-5OHXYXLD.js

@@ -1,46 +0,0 @@
-// ../shared/utils/src/roundValue.js
-function roundValue(value, digits) {
-  const v = Number(value);
-  if (Number.isInteger(v)) return v;
-  if (Math.abs(v) < 1) return Number(v.toPrecision(digits));
-  return Number(v.toFixed(digits));
-}
-function roundValueAuto(value, format = false, defaultDigits = 2) {
-  if (!value && value != 0) return value;
-  const dp = decimalPlacesUntilFirstNonZero(value);
-  const digits = Math.abs(value) > 1 ? defaultDigits : dp > 0 ? dp + 1 : defaultDigits;
-  if (format) return formatValue(value, digits);
-  return roundValue(value, digits);
-}
-function decimalPlacesUntilFirstNonZero(number) {
-  const numberStr = number.toString();
-  const decimalIndex = numberStr.indexOf(".");
-  if (decimalIndex === -1 || decimalIndex === numberStr.length - 1) {
-    return 0;
-  }
-  let decimalPlaces = 0;
-  for (let i = decimalIndex + 1; i < numberStr.length; i++) {
-    if (numberStr[i] === "0") {
-      decimalPlaces++;
-    } else if (numberStr[i] >= "1" && numberStr[i] <= "9") {
-      break;
-    }
-  }
-  return decimalPlaces;
-}
-function formatValue(value, digits) {
-  const v = Number(value);
-  if (Number.isInteger(v)) return v;
-  const abs = Math.abs(v);
-  if (abs < 1 || abs > 9999) {
-    return abs > 9999 ? v.toPrecision(digits) : Number(v.toPrecision(digits));
-  }
-  return Number(v.toFixed(digits));
-}
-
-export {
-  roundValue,
-  roundValueAuto,
-  decimalPlacesUntilFirstNonZero
-};
-//# sourceMappingURL=chunk-5OHXYXLD.js.map

package/dist/chunk-5OHXYXLD.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../../shared/utils/src/roundValue.js"],
-  "sourcesContent": ["/*\nround a value to specified digits\n    - if value is integer, value is returned\n    - if value is a fractional float, round to precision\n    - if value is not a fractional float, round to decimal point\n    - TODO: handle scientific notation\nvalue: given value\ndigits: number of digits to round to\n*/\n\nexport function roundValue(value, digits) {\n\tconst v = Number(value)\n\tif (Number.isInteger(v)) return v\n\tif (Math.abs(v) < 1) return Number(v.toPrecision(digits))\n\treturn Number(v.toFixed(digits))\n}\n\n/** Rounds numbers to the appropriate decimal point\n * if format is true, returns either a number or string in\n * scientific notation.\n *\n * TODO: Review digit logic.\n */\n\nexport function roundValueAuto(value, format = false, defaultDigits = 2) {\n\tif (!value && value != 0) return value\n\tconst dp = decimalPlacesUntilFirstNonZero(value)\n\tconst digits = Math.abs(value) > 1 ? defaultDigits : dp > 0 ? dp + 1 : defaultDigits\n\tif (format) return formatValue(value, digits)\n\treturn roundValue(value, digits)\n}\n\nexport function decimalPlacesUntilFirstNonZero(number) {\n\t// Convert number to string\n\tconst numberStr = number.toString()\n\n\t// Find the position of the decimal point\n\tconst decimalIndex = numberStr.indexOf('.')\n\n\t// If decimal point is not found or number is an integer, return 0\n\tif (decimalIndex === -1 || decimalIndex === numberStr.length - 1) {\n\t\treturn 0\n\t}\n\n\t// Iterate through characters after the decimal point\n\tlet decimalPlaces = 0\n\tfor (let i = decimalIndex + 1; i < numberStr.length; i++) {\n\t\t// Increment the count of decimal places until a non-zero digit is found\n\t\tif (numberStr[i] === '0') {\n\t\t\tdecimalPlaces++\n\t\t} else if (numberStr[i] >= '1' && numberStr[i] <= '9') {\n\t\t\tbreak\n\t\t}\n\t}\n\n\treturn decimalPlaces\n}\n\n/* \nsimple logic to return a number close to original while rounding up decimals.\nsupplements roundValueAuto which rounds 12345 to 1.2e4 which is only suitable for human quick glance but not subsequent computing\n\nTODO:\n10000 and 10001 to 1e4\n0.00001 to 1e-5\n1.00001 to 1\n*/\nexport function roundValue2(value) {\n\tif (!Number.isFinite(value)) return value // not a number\n\tif (Number.isInteger(value)) return value // is integer, do not convert\n\tconst abs = Math.abs(value)\n\tif (abs > 100) return Math.round(value) // 12345.1234 to 12345 (compared to 1.2e4 from roundValueAuto)\n\tif (abs > 10) return Number(value.toFixed(1)) // 99.1234 to 99.1\n\tif (abs > 1) return Number(value.toFixed(2)) // 9.1234 to 9.12\n\tif (abs > 0.1) return Number(value.toFixed(3)) // 0.12345 to 0.123\n\tif (abs > 0.01) return Number(value.toFixed(4)) // 0.012345 to 0.0123\n\treturn value // as is\n}\n\n/** Use to return displayed values in scientific notation\n * Do not use for values intended for calculation later.\n */\nexport function formatValue(value, digits) {\n\tconst v = Number(value)\n\tif (Number.isInteger(v)) return v\n\tconst abs = Math.abs(v)\n\tif (abs < 1 || abs > 9999) {\n\t\t//Number() reverts positive values less than 10^21 to a whole number\n\t\t//To return the value in scientific notation, use toPrecision without Number()\n\t\treturn abs > 9999 ? v.toPrecision(digits) : Number(v.toPrecision(digits))\n\t}\n\treturn Number(v.toFixed(digits))\n}\n"],
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-  "names": []
-}

package/dist/chunk-6MSCYO7K.js

@@ -1,119 +0,0 @@
-import {
-  GENE_EXPRESSION,
-  METABOLITE_INTENSITY,
-  PROTEOME_ABUNDANCE,
-  SINGLECELL_GENE_EXPRESSION
-} from "./chunk-MDL2HG3N.js";
-
-// common/termutils.js
-function sample_match_termvaluesetting(row, filter, geneVariant$ids) {
-  const lst = !filter ? [] : filter.type == "tvslst" ? filter.lst : [filter];
-  let numberofmatchedterms = 0;
-  for (const item of lst) {
-    if (item.type == "tvslst") {
-      if (sample_match_termvaluesetting(row, item)) {
-        numberofmatchedterms++;
-      }
-    } else {
-      const t = item.tvs;
-      let samplevalue;
-      if (t.term.type == "geneVariant") {
-        samplevalue = geneVariant$ids.map((g) => row[g]).filter((s) => s);
-      } else if (t.term.type == "integer" || t.term.type == "float" || t.term.type == GENE_EXPRESSION || t.term.type == METABOLITE_INTENSITY || t.term.type == PROTEOME_ABUNDANCE) {
-        samplevalue = row[t.term.id] || row[t.term.$id]?.key;
-      } else if (t.term.type == "survival") {
-        samplevalue = row[t.term.$id]?.key;
-      } else {
-        samplevalue = row[t.term.id] || row[t.term.$id]?.value;
-      }
-      let thistermmatch;
-      if (t.term.type == "categorical") {
-        if (samplevalue === void 0) {
-          if (t.isnot) thistermmatch = !thistermmatch;
-          if (thistermmatch) numberofmatchedterms++;
-          continue;
-        }
-        const valueset = t.valueset ? t.valueset : new Set(t.values.map((i) => i.key));
-        thistermmatch = valueset.has(samplevalue);
-      } else if (t.term.type == "integer" || t.term.type == "float" || t.term.type == GENE_EXPRESSION || t.term.type == METABOLITE_INTENSITY || t.term.type == PROTEOME_ABUNDANCE) {
-        if (samplevalue === void 0) {
-          if (t.isnot) thistermmatch = !thistermmatch;
-          if (thistermmatch) numberofmatchedterms++;
-          continue;
-        }
-        for (const range of t.ranges) {
-          if ("value" in range) {
-            thistermmatch = samplevalue === range.value;
-            if (thistermmatch) break;
-          } else if (samplevalue == range.name) {
-            thistermmatch = true;
-            break;
-          } else {
-            if (t.term.values) {
-              const v = t.term.values[samplevalue.toString()];
-              if (v && v.uncomputable) {
-                continue;
-              }
-            }
-            let left, right;
-            if (range.startunbounded) {
-              left = true;
-            } else if ("start" in range) {
-              if (range.startinclusive) {
-                left = samplevalue >= range.start;
-              } else {
-                left = samplevalue > range.start;
-              }
-            }
-            if (range.stopunbounded) {
-              right = true;
-            } else if ("stop" in range) {
-              if (range.stopinclusive) {
-                right = samplevalue <= range.stop;
-              } else {
-                right = samplevalue < range.stop;
-              }
-            }
-            thistermmatch = left && right;
-          }
-          if (thistermmatch) break;
-        }
-      } else if (t.term.type == "condition") {
-        const key = getPrecomputedKey(t);
-        const anno = samplevalue && samplevalue[key];
-        if (anno) {
-          thistermmatch = Array.isArray(anno) ? t.values.find((d) => anno.includes(d.key)) : t.values.find((d) => d.key == anno);
-        }
-      } else if (t.term.type == "survival") {
-        if (samplevalue === void 0) {
-          if (t.isnot) thistermmatch = !thistermmatch;
-          if (thistermmatch) numberofmatchedterms++;
-          continue;
-        }
-        const valueset = t.valueset ? t.valueset : new Set(t.values.map((i) => i.key));
-        thistermmatch = valueset.has(samplevalue);
-      } else if (t.term.type == "geneVariant" && t.legendFilterType == "geneVariant_hard") {
-        const f = t.values[0];
-        thistermmatch = samplevalue.find((s) => {
-          for (const v of s.values) {
-            if (v.dt == f.dt && (!v.origin || v.origin == f.origin) && f.mclasslst.includes(v.class)) return true;
-          }
-        }) && true;
-      } else if (t.term.type == SINGLECELL_GENE_EXPRESSION) {
-      } else {
-        throw "unknown term type";
-      }
-      if (t.isnot) {
-        thistermmatch = !thistermmatch;
-      }
-      if (thistermmatch) numberofmatchedterms++;
-    }
-    if (filter.join == "or" && numberofmatchedterms) return true;
-  }
-  if (numberofmatchedterms == lst.length) return true;
-}
-
-export {
-  sample_match_termvaluesetting
-};
-//# sourceMappingURL=chunk-6MSCYO7K.js.map

package/dist/chunk-75EBDB7G.js

@@ -1,21 +0,0 @@
-// ../shared/types/src/routes/termdb.violinBox.ts
-function isErrorResponse(response) {
-  return "error" in response && "status" in response;
-}
-function isBoxPlotResponse(response) {
-  return !isErrorResponse(response) && "charts" in response && "descrStats" in response;
-}
-
-// ../shared/types/src/routes/samplewsimages.ts
-var WSImage = class {
-  constructor(filename) {
-    this.filename = filename;
-  }
-};
-
-export {
-  WSImage,
-  isErrorResponse,
-  isBoxPlotResponse
-};
-//# sourceMappingURL=chunk-75EBDB7G.js.map

package/dist/chunk-75EBDB7G.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../../shared/types/src/routes/termdb.violinBox.ts", "../../shared/types/src/routes/samplewsimages.ts"],
-  "sourcesContent": ["import type { RoutePayload } from './routeApi.js'\nimport type { TermWrapper } from '../terms/tw.ts'\nimport type { Filter } from '../filter.ts'\nimport type { ErrorResponse } from './errorResponse.ts'\nimport type { DescrStats } from './termdb.descrstats.ts'\n\n/** Common properties shared by both violin and box plots */\ntype CommonProps = {\n\t/** numeric tw to fetch numeric data. tw.q.mode must be continuous */\n\ttw: TermWrapper\n\tdslabel: string\n\tgenome: string\n\t/** overlay tw for multiple violins/boxplots */\n\toverlayTw?: TermWrapper\n\t/** tw to divide to multiple charts */\n\tdivideTw?: TermWrapper\n\t/** mass filter */\n\tfilter?: Filter\n\t/** read-only invisible filter */\n\tfilter0?: any\n\t/** TODO: Needs description FIXME delete */\n\tcurrentGeneNames?: string[]\n\t/** if true, use log scale; if false or undefined, use linear scale */\n\tisLogScale?: boolean\n}\n\n/** Request type for violin plots with required violin-specific parameters */\nexport type ViolinRequest = CommonProps & {\n\t/** Indicates the type of chart to render */\n\tplotType: 'violin'\n\t/** A number representing the dimension perpendicular to the violin spread */\n\taxisHeight?: number\n\t/** A string representing the type of symbol used on the plot */\n\tdatasymbol?: string\n\t/** A number representing the device's pixel ratio */\n\tdevicePixelRatio: number\n\t/** If true, uses KDE method to build plot */\n\tisKDE?: boolean\n\t/** A string with two possible values: 'horizontal' or 'vertical' */\n\torientation: string\n\t/** A number representing the radius of the data symbols */\n\tradius: number\n\t/** A number representing the right margin */\n\trightMargin?: number\n\t/** Term may be scaled from regression analysis */\n\tscale?: any\n\t/** A number representing the width of the stroke */\n\tstrokeWidth?: number\n\t/** A number representing the width of the SVG box */\n\tsvgw: number\n\t/** Number of bins to build the plot. Default is 20. */\n\tticks?: number\n}\n\n/** Request type for box plots with required box-specific parameters */\nexport type BoxRequest = CommonProps & {\n\t/** Indicates the type of chart to render */\n\tplotType: 'box'\n\t/** sort plots by median value */\n\torderByMedian?: boolean\n\t/** Remove outliers from the plot */\n\tremoveOutliers?: boolean\n\t/** If true, show association tests table */\n\tshowAssocTests?: boolean\n}\n\n/**Unified request type for violin and boxplot - union of ViolinRequest and BoxRequest */\nexport type ViolinBoxRequest = ViolinRequest | BoxRequest\n\nexport type ViolinBoxResponse = ViolinResponse | BoxPlotResponse | ErrorResponse\n\n/** Type guard to check if response is an ErrorResponse */\nexport function isErrorResponse(response: ViolinBoxResponse): response is ErrorResponse {\n\treturn 'error' in response && 'status' in response\n}\n\n/** Type guard to check if response is a BoxPlotResponse */\nexport function isBoxPlotResponse(response: ViolinBoxResponse): response is BoxPlotResponse {\n\treturn !isErrorResponse(response) && 'charts' in response && 'descrStats' in response\n}\n\n/** Type guard to check if response is a ViolinResponse */\nexport function isViolinResponse(response: ViolinBoxResponse): response is ViolinResponse {\n\treturn !isErrorResponse(response) && 'min' in response && 'max' in response\n}\n\n/** Violin response types */\ninterface BinsEntries {\n\tx0: number\n\tx1: number\n\tdensity: number\n}\n\ninterface ValuesEntries {\n\tid: string\n\tlabel: string\n\tvalue: number\n}\n\ninterface PValueEntries {\n\tvalue?: string\n\thtml?: string\n}\n\ntype ViolinDensity = {\n\tbins: BinsEntries[]\n\tdensityMax: number\n\tdensityMin: number\n}\n\nexport type ViolinPlotEntry = {\n\tcolor: string\n\tchartId: string\n\tdensity: ViolinDensity\n\tlabel: string\n\tplotValueCount: number\n\tseriesId: string\n\tsrc: string\n\tsummaryStats: ValuesEntries[]\n}\n\nexport type ViolinResponse = {\n\tbins: { [index: string]: any }\n\tcharts: {\n\t\t[index: string]: {\n\t\t\tchartId: string\n\t\t\tplots: ViolinPlotEntry[]\n\t\t\tpvalues?: PValueEntries[][]\n\t\t}\n\t}\n\tmin: number\n\tmax: number\n\tuncomputableValues: { [index: string]: number }[] | null\n\tdescrStats?: DescrStats\n}\n\n/** Boxplot response types */\nexport type BoxPlotData = {\n\tw1: number | undefined\n\tw2: number | undefined\n\tp05: number\n\tp25: number\n\tp50: number\n\tp75: number\n\tp95: number\n\tiqr: number\n\tout: { value: number }[]\n}\n\nexport type BoxPlotEntry = {\n\tboxplot: BoxPlotData & { label: string }\n\tcolor?: string\n\tdescrStats: DescrStats\n\tisHidden?: boolean\n\tkey: string\n\tseriesId?: string\n}\n\nexport type BoxPlotChartEntry = {\n\tchartId: string\n\tplots: BoxPlotEntry[]\n\tsampleCount: number\n\twilcoxon?: [{ value: string }, { value: string }, { html: string }][]\n}\n\nexport type BoxPlotResponse = {\n\tabsMin?: number\n\tabsMax?: number\n\tbins?: {\n\t\t[index: string]: any\n\t}\n\tcharts: {\n\t\t[chartId: string]: BoxPlotChartEntry\n\t}\n\tdescrStats: DescrStats\n\tuncomputableValues: { label: string; value: number }[] | null\n}\n\nexport const violinBoxPayload: RoutePayload = {\n\trequest: {\n\t\ttypeId: 'ViolinBoxRequest'\n\t},\n\tresponse: {\n\t\ttypeId: 'ViolinBoxResponse'\n\t},\n\texamples: [\n\t\t{\n\t\t\trequest: {\n\t\t\t\tbody: {\n\t\t\t\t\tplotType: 'violin',\n\t\t\t\t\tgenome: 'hg38-test',\n\t\t\t\t\tdslabel: 'TermdbTest',\n\t\t\t\t\ttw: {\n\t\t\t\t\t\tterm: { id: 'aaclassic_5', type: 'float' },\n\t\t\t\t\t\tq: { mode: 'continuous' }\n\t\t\t\t\t},\n\t\t\t\t\tdevicePixelRatio: 2,\n\t\t\t\t\tsvgw: 200,\n\t\t\t\t\torientation: 'horizontal',\n\t\t\t\t\tdatasymbol: 'rug',\n\t\t\t\t\tradius: 5,\n\t\t\t\t\tisLogScale: false\n\t\t\t\t}\n\t\t\t},\n\t\t\tresponse: {\n\t\t\t\theader: { status: 200 }\n\t\t\t}\n\t\t},\n\t\t{\n\t\t\trequest: {\n\t\t\t\tbody: {\n\t\t\t\t\tplotType: 'box',\n\t\t\t\t\tgenome: 'hg38-test',\n\t\t\t\t\tdslabel: 'TermdbTest',\n\t\t\t\t\ttw: {\n\t\t\t\t\t\tterm: { id: 'agedx', type: 'float' },\n\t\t\t\t\t\tq: { mode: 'continuous' }\n\t\t\t\t\t},\n\t\t\t\t\toverlayTw: {\n\t\t\t\t\t\tterm: { id: 'sex', type: 'categorical' }\n\t\t\t\t\t},\n\t\t\t\t\torderByMedian: true\n\t\t\t\t}\n\t\t\t},\n\t\t\tresponse: {\n\t\t\t\theader: { status: 200 }\n\t\t\t}\n\t\t}\n\t]\n}\n", "import type { RoutePayload } from './routeApi.ts'\nimport type { WSIClass } from '../dataset.ts'\nimport type { Annotation, Prediction } from './aiProjectSelectedWSImages.ts'\n\nexport type SampleWSImagesRequest = {\n\tgenome: string\n\tdslabel: string\n\tsample_id: string\n\twsimage: string\n}\n\nexport type SampleWSImagesResponse = {\n\tsampleWSImages: WSImage[]\n}\n\nexport class WSImage {\n\tid?: number\n\tfilename: string\n\tmetadata?: string\n\tpredictionLayers?: Array<string>\n\tannotations?: Array<Annotation>\n\tpredictions?: Array<Prediction>\n\tclasses?: Array<WSIClass>\n\t/** ds defined uncertainity labels and colors */\n\tuncertainty?: any\n\t/** Color to highlight active patches */\n\tactivePatchColor?: string\n\t/** Tile size in pixels needed for AI scripts */\n\ttileSize?: number\n\n\tconstructor(filename: string) {\n\t\tthis.filename = filename\n\t}\n}\n\nexport const sampleWSImagesPayload: RoutePayload = {\n\trequest: {\n\t\ttypeId: 'SampleWSImagesRequest'\n\t},\n\tresponse: {\n\t\ttypeId: 'SampleWSImagesResponse'\n\t}\n\t// examples: []\n}\n"],
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-}