From 6adc1e2696ec997c2e6b74043e06cfd87c6486c1 Mon Sep 17 00:00:00 2001
From: Terry Truong <terry06890@gmail.com>
Date: Mon, 4 Jul 2022 20:46:36 +1000
Subject: Add help-info content

---
 src/components/HelpModal.vue     | 412 ++++++++++++++++++++++++++++++++++++---
 src/components/SettingsModal.vue |  11 +-
 src/components/TileInfoModal.vue |  20 +-
 3 files changed, 397 insertions(+), 46 deletions(-)

(limited to 'src/components')

diff --git a/src/components/HelpModal.vue b/src/components/HelpModal.vue
index f410d42..57ae90e 100644
--- a/src/components/HelpModal.vue
+++ b/src/components/HelpModal.vue
@@ -1,44 +1,367 @@
 <template>
 <div class="fixed left-0 top-0 w-full h-full bg-black/40" @click="onClose">
 	<div class="absolute left-1/2 -translate-x-1/2 top-1/2 -translate-y-1/2
-		w-4/5 max-w-[20cm] max-h-[80%] overflow-auto" :style="styles">
+		w-4/5 max-w-[16cm] max-h-[80%] overflow-auto" :style="styles">
 		<close-icon @click.stop="onClose" ref="closeIcon"
 			class="block absolute top-1 right-1 md:top-2 md:right-2 w-8 h-8 hover:cursor-pointer"/>
-		<h1 class="text-center text-xl font-bold py-2 border-b border-stone-400">Help</h1>
-		<div class="p-2 border-b border-stone-400">
-			<s-collapsible class="border border-stone-400 rounded">
-				<template v-slot:summary="slotProps">
-					<div class="p-1 text-center"
-						:style="{backgroundColor: !slotProps.collapsed ? 'gray' : 'transparent'}">
-						<down-icon class="inline-block w-5 h-5 transition-transform duration-300"
-							:class="{'-rotate-90': slotProps.collapsed}"/>
-						Summary text
+		<h1 class="text-center text-xl font-bold pt-2 pb-1">Help</h1>
+		<div class="flex flex-col gap-2 p-2">
+			<s-collapsible :class="scClasses">
+				<template #summary="slotProps">
+					<div :class="scSummaryClasses">
+						<down-icon :class="slotProps.collapsed ? downIconClasses : downIconExpandedClasses"/>
+						What is the Tree of Life?
 					</div>
 				</template>
-				<template v-slot:content>
-					<div class="p-1">
-						Lorem ipsum dolor sit amet, consectetur adipiscing
-						elit, sed do eiusmod tempor incididunt ut labore
-						et dolore magna aliqua. Ut enim ad minim veniam,
-						quis nostrud exercitation ullamco laboris nisi ut
-						aliquip ex ea commodo consequat. 
+				<template #content>
+					<div :class="contentClasses">
+						<p>
+							In theory, the Tree of Life represents all living organisms, along with their parents,
+							grandparents, and so on, all the way up to a single common ancestor.
+						</p>
+						<div class="my-2 w-4/5 mx-auto flex flex-col items-center gap-1 md:flex-row md:gap-2 md:w-fit">
+							<img src="data:," width="240" height="180" alt="Simple Tree of Life"
+								class="border border-black block mx-auto md:mx-0 md:shrink-0"/>
+							<p class="text-sm md:max-w-[4cm]">
+								Each dot is a <strong>node</strong>, and represents a <strong>taxon</strong>,
+								which might be a species, genus, or otherwise. The top node is the
+								<strong>root</strong>, and those without children are <strong>leaves</strong>.
+							</p>
+						</div>
+						<p>
+							The metaphor doesn't always fit. For example, many bacteria can transfer
+							DNA to each other without creating children. But the concept is still helpful for
+							visualisation.
+						</p>
+						<br/>
+						<p>
+							Determining the structure of the tree is an ongoing area
+							of work, but much of it has been traced out using genetic information,
+							statistical analysis, and human inference.
+						</p>
+					</div>
+				</template>
+			</s-collapsible>
+			<s-collapsible :class="scClasses">
+				<template #summary="slotProps">
+					<div :class="scSummaryClasses">
+						<down-icon :class="slotProps.collapsed ? downIconClasses : downIconExpandedClasses"/>
+						Visualising the Tree
+					</div>
+				</template>
+				<template #content>
+					<div :class="contentClasses">
+						<p>
+							Tilo attempts to display the Tree of Life by representing nodes with tiles,
+							and placing tiles within other tiles to show tree structure.
+						</p>
+						<img src="data:," width="400" height="200" alt="Tree with Tile layout"
+							class="border border-black block mx-auto mt-2"/>
+						<br/>
+						<p>
+							Within a tile's header:
+							<ul class="list-disc pl-4">
+								<li>
+									The color denotes the number of children.
+									White means zero,
+									<span style="color: limegreen">green</span> means 1+,
+									<span style="color: darkorange">orange</span> means 10+,
+									and <span style="color: crimson">red</span> means 100+.
+								</li>
+								<li>
+									An asterisk indicates that the node's placement lack evidence, or is disputed.
+									<span class="text-xs md:text-sm text-stone-500">
+										(In the Open Tree of Life, each node has zero or more associated hypothetical
+										trees that either support or conflict with it. The asterisk is added if
+										there are no supporting trees, or if there is a single conflicting tree.)
+									</span>
+								</li>
+							</ul>
+						</p>
+						<br/>
+						<p>
+							There are many other methods of visualisation, which can enable viewing
+							many more nodes as text, or for exploring a more natural tree-like diagram.
+							Examples include
+							<a href="https://itol.embl.de/">iTOL</a>
+								<external-link-icon :class="linkIconClasses"/>
+							and <a href="https://www.onezoom.org/">OneZoom</a>
+								<external-link-icon :class="linkIconClasses"/>.
+							<div class="flex gap-2 justify-evenly mt-1 md:mt-2">
+								<img src="data:," width="200" height="200" alt="iTOL"
+									class="border border-black block"/>
+								<img src="data:," width="200" height="200" alt="OneZoom"
+									class="border border-black block"/>
+							</div>
+						</p>
+					</div>
+				</template>
+			</s-collapsible>
+			<s-collapsible :class="scClasses">
+				<template #summary="slotProps">
+					<div :class="scSummaryClasses">
+						<down-icon :class="slotProps.collapsed ? downIconClasses : downIconExpandedClasses"/>
+						Using Tilo
+					</div>
+				</template>
+				<template #content>
+					<div :class="contentClasses">
+						<p>
+							This section provides some details not included in the tutorial.
+						</p>
+						<br/>
+						<h1 class="text-lg font-bold">Settings</h1>
+						<ul class="list-disc pl-4">
+							<li>
+								<h2 class="font-bold">Sweep leaves left</h2>
+								<p>
+									If disabled, an expanded tile's children are simply laid out in order.
+									This can leave a lot of empty space when large children are next to small ones.
+									Moving the unexpanded children (the 'leaves') to the left helps avoid this.
+									<img src="data:," width="400" height="200" alt="Sweep leaves setting effect"
+										class="border border-black block mx-auto my-1"/>
+								</p>
+							</li>
+							<li>
+								<h2 class="font-bold">Sweep into parent</h2>
+								<p>
+									If enabled, leaves being swept left can be moved beyond the tile's
+									rectangle, into leftover space in the parent.
+									<img src="data:," width="400" height="200" alt="Sweep into parent setting effect"
+										class="border border-black block mx-auto my-1"/>
+								</p>
+							</li>
+							<li>
+								<h2 class="font-bold">Trees to use</h2>
+								<p>
+									Three choices are available, and all are simplified versions of
+									the tree from the Open Tree of Life.
+									<span class="text-xs md:text-sm text-stone-500">
+										(Without this, some nodes would have over 10,000 children, and
+										significantly slow the browser down during rendering)
+									</span>
+								</p>
+								<ul class="list-[circle] pl-4">
+									<li>
+										<span class="font-bold">Complex:</span>
+										The least simplified choice. In short, it only includes
+										nodes that have an image or description, with a soft limit of 600 children.
+										<span class="text-xs md:text-sm text-stone-500">
+											(Has about 450,000 nodes)
+										</span>
+									</li>
+									<li>
+										<span class="font-bold">Visual:</span>
+										Only keeps nodes with images, with a soft limit of 300 children.
+										<span class="text-xs md:text-sm text-stone-500">
+											(Has about 140,000 nodes)
+										</span>
+									</li>
+									<li>
+										<span class="font-bold">Minimal:</span>
+										Created using a rough list of 'well known'
+										taxons, and adding a few more at random.
+										<span class="text-xs md:text-sm text-stone-500">
+											(Has about 3,300 nodes)
+										</span>
+									</li>
+								</ul>
+							</li>
+							<li>
+								<h2 class="font-bold">Slider Resets</h2>
+								<p>
+									You can {{touchDevice ? 'tap' : 'click'}} on
+									a slider's label to reset it to the default value.
+								</p>
+							</li>
+						</ul>
+						<br/>
+						<h1 class="text-lg font-bold">Keyboard Shortcuts</h1>
+						<ul class="list-disc pl-4">
+							<li>Ctrl-F opens the search bar</li>
+							<li>Ctrl-Shift-F toggles the search animation</li>
+							<li>Esc closes an open pane, and cancels an active search or auto mode</li>
+						</ul>
+						<br/>
+						<h1 class="text-lg font-bold">Unusual Node Names</h1>
+						<ul class="list-disc pl-4">
+							<li>
+								<h2 class="font-bold">Disambiguation Nodes</h2>
+								<p>
+									These have names like 'Iris [2]'. When multiple nodes have the same
+									name, all but one gets an '[N]' appended, where N is 2 or above.
+								</p>
+							</li>
+							<li>
+								<h2 class="font-bold">Compound Nodes</h2>
+								<p>
+									These are only present in the Complex tree, and have names like
+									'[Homo Sapiens + Homo Heidelbergensis]'. They provide structure for other nodes,
+									and are named after two prominent descendants.
+								</p>
+							</li>
+						</ul>
+						<br/>
+						<h1 class="text-lg font-bold">Overflowing Tiles</h1>
+						<p>
+							Some tiles have too many children to fit on-screen at once, and are displayed
+							with a scroll bar. For layout reasons, this is only done if they are the
+							outermost tile, so you may need to {{touchDevice ? 'double tap' : 'click and hold'}}
+							the tile to expand it.
+						</p>
+					</div>
+				</template>
+			</s-collapsible>
+			<s-collapsible :class="scClasses">
+				<template #summary="slotProps">
+					<div :class="scSummaryClasses">
+						<down-icon :class="slotProps.collapsed ? downIconClasses : downIconExpandedClasses"/>
+						Data Sources
+					</div>
+				</template>
+				<template #content>
+					<div :class="contentClasses">
+						<h1 class="text-lg font-bold">Sources</h1>
+						<ul class="list-disc pl-4">
+							<li>
+								The tree structure was obtained from the Open Tree of Life
+								<a href="https://tree.opentreeoflife.org/about/synthesis-release"
+									:style="anchorStyles">synthesis release</a>
+									<external-link-icon :class="linkIconClasses"/>
+								 version 13.4, accessed 23/04/2022.
+							</li>
+							<li>
+								The images and alternative-names data was partly obtained from the
+								Encyclopedia of Life. Name data was obtained from
+								<a href="https://opendata.eol.org/dataset/vernacular-names" :style="anchorStyles"
+									>here</a><external-link-icon :class="linkIconClasses"/>,
+								and image metadata from
+								<a href="https://opendata.eol.org/dataset/images-list" :style="anchorStyles"
+									>here</a><external-link-icon :class="linkIconClasses"/>,
+								accessed 24/04/2022.
+							</li>
+							<li>
+								The short descriptions, along with the remaining images and name data,
+								were obtained from Wikipedia. Descriptions were extracted from the
+								<a href="https://dumps.wikimedia.org/enwiki/" :style="anchorStyles">Wikipedia dump</a>
+									<external-link-icon :class="linkIconClasses"/> for 01/05/22,
+								and also obtained from the
+								<a href="https://databus.dbpedia.org/dbpedia/collections/latest-core"
+									:style="anchorStyles">DBpedia knowledge base</a>
+									<external-link-icon :class="linkIconClasses"/>
+								for 01/03/22. Images were downloaded from Wikipedia during Jun 2022.
+							</li>
+						</ul>
+						<br/>
+						<h1 class="text-lg font-bold">Data Inconsistencies</h1>
+						<p>
+							When handling datasets this large, these are almost unavoidable. Significant effort
+							was expended to minimise them, but, inevitably, there are always more. The most prominent
+							types are listed below. If you find a major error, feel free to let me know at
+							<a href="mailto:terry06890@gmail.com" :style="anchorStyles">terry06890@gmail.com</a>.
+						</p>
+						<ul class="list-disc pl-4">
+							<li>
+								<h2 class="font-bold">Errors in Node Linkage</h2>
+								<p>
+									The datasets don't share the same set of node identifiers. So, in order to
+									link nodes from one dataset with another, their plain names were used.
+									This doesn't work when names are ambiguous. For example, 'Proboscidea'
+									might denote a taxon for elephants, but also plants. Most of these were
+									manually corrected, but there are almost certainly more.
+								</p>
+							</li>
+							<li>
+								<h2 class="font-bold">Errors Within the Datasets</h2>
+								<p>
+									Some issues are internal to the datasets themselves. For example, an image from
+									EOL might display a plant that is in the wrong taxon. As most of the datasets are
+									large projects distributed over many people over a long period of time, these
+									errors are difficult to avoid, and may require specialised knowledge to resolve.
+								</p>
+							</li>
+							<li>
+								<h2 class="font-bold">Errors in Descriptions</h2>
+								<p>
+									The short descriptions were extracted using imprecise heuristics.
+									There are many cases of leftover wikitext markup, or cut-off sentences.
+								</p>
+							</li>
+						</ul>
+						<br/>
+						<h1 class="text-lg font-bold">Some Possible Points of Confusion</h1>
+						<ul class="list-disc pl-4">
+							<li>
+								<h2 class="font-bold">Unexpected Images</h2>
+								<p>
+									Not all the images are well-suited for display. For example, many
+									birds have their heads cropped out. And some fish are shown in a
+									preserved form that is hard to recognise. And some moths are shown
+									alongside a more prominent plant, and are hard to see.
+								</p>
+							</li>
+							<li>
+								<h2 class="font-bold">Unexpected Search Results</h2>
+								<ul class="list-[circle] pl-4">
+									<li>
+										In the Complex tree, searching for 'orange', then pressing enter, brings up
+										a kind of butterfly, instead of a citrus plant. This is because suggestions
+										are not yet ordered by how well known the taxon is.
+									</li>
+									<li>
+										In some cases, a search might unexpectedly have no results. For example,
+										searching for 'golden retriever' brings up nothing. This is because
+										breeds of domestic dog are not considered separate species, but as
+										variant descendants of Canis familiaris.
+									</li>
+								</ul>
+							</li>
+						</ul>
+					</div>
+				</template>
+			</s-collapsible>
+			<s-collapsible :class="scClasses">
+				<template #summary="slotProps">
+					<div :class="scSummaryClasses">
+						<down-icon :class="slotProps.collapsed ? downIconClasses : downIconExpandedClasses"/>
+						Other Credits
+					</div>
+				</template>
+				<template #content>
+					<div :class="contentClasses">
+						<ul class="list-disc pl-4">
+							<li>
+								The UI was built using the
+								<a href="https://vuejs.org/" :style="anchorStyles">Vue framework</a>
+									<external-link-icon :class="linkIconClasses"/>
+							</li>
+							<li>
+								Styling was enhanced using
+								<a href="https://tailwindcss.com/" :style="anchorStyles">Tailwind</a>
+									<external-link-icon :class="linkIconClasses"/>
+							</li>
+							<li>
+								The font is called
+								<a href="https://design.ubuntu.com/font/" :style="anchorStyles">Ubuntu Font</a>
+									<external-link-icon :class="linkIconClasses"/>
+							</li>
+							<li>Icons were obtained from
+								<a href="https://feathericons.com/" :style="anchorStyles">Feathericons</a>
+									<external-link-icon :class="linkIconClasses"/>
+								and <a href="https://ionic.io/ionicons" :style="anchorStyles">Ionicons</a>
+									<external-link-icon :class="linkIconClasses"/>
+							</li>
+							<li>
+								Images were cropped using
+								<a href="https://github.com/jwagner/smartcrop.js" :style="anchorStyles">Smartcrop</a>
+									<external-link-icon :class="linkIconClasses"/>
+							</li>
+						</ul>
 					</div>
 				</template>
 			</s-collapsible>
-			<ul class="list-disc ml-3">
-				<li>What is the Tree of Life? ('tips', )</li>
-				<li>Visualising the Tree (OneZoom, iTol) (tile layout, )</li>
-				<li>Using Tilo
-					(tutorial)
-					(leaf header colors, asterisk, compound nodes/names/images, overflown-root, )
-					(settings: layout methods, reduced trees, click-label-to-reset)
-					(keyboard shortcuts)
-				</li>
-				<li>Data sources (OTOL, EOL, Wikipedia) (imprecision: tree, names, images, descs, )</li>
-				<li>Project page, error contact, other credits (feathericons, ionicons), </li>
-			</ul>
 		</div>
-		<s-button :disabled="tutOpen" class="mx-auto my-2"
+		<s-button v-if="!tutOpen" class="mx-auto mb-2"
 			:style="{color: uiOpts.textColor, backgroundColor: uiOpts.bgColor}" @click.stop="onStartTutorial">
 			Start Tutorial
 		</s-button>
@@ -52,6 +375,7 @@ import SButton from './SButton.vue';
 import SCollapsible from './SCollapsible.vue';
 import CloseIcon from './icon/CloseIcon.vue';
 import DownIcon from './icon/DownIcon.vue';
+import ExternalLinkIcon from './icon/ExternalLinkIcon.vue';
 import {UiOptions} from '../lib';
 
 export default defineComponent({
@@ -67,6 +391,32 @@ export default defineComponent({
 				boxShadow: this.uiOpts.shadowNormal,
 			};
 		},
+		scClasses(): string {
+			return 'border border-stone-400 rounded';
+		},
+		scSummaryClasses(): string {
+			return "relative text-center p-1 bg-stone-300 hover:brightness-90 hover:bg-lime-200 md:p-2";
+		},
+		downIconClasses(): string {
+			return 'block absolute w-6 h-6 my-auto mx-1 transition-transform duration-300';
+		},
+		downIconExpandedClasses(): string {
+			return this.downIconClasses + ' -rotate-90';
+		},
+		contentClasses(): string {
+			return 'p-2 text-sm md:text-base';
+		},
+		anchorStyles(): Record<string,string> {
+			return {
+				color: this.uiOpts.altColorDark,
+			};
+		},
+		linkIconClasses(): string {
+			return 'inline-block w-3 h-3 ml-1';
+		},
+		touchDevice(): boolean {
+			return this.uiOpts.touchDevice;
+		},
 	},
 	methods: {
 		onClose(evt: Event){
@@ -79,7 +429,7 @@ export default defineComponent({
 			this.$emit('close');
 		},
 	},
-	components: {SButton, SCollapsible, CloseIcon, DownIcon, },
+	components: {SButton, SCollapsible, CloseIcon, DownIcon, ExternalLinkIcon, },
 	emits: ['close', 'start-tutorial', ],
 });
 </script>
diff --git a/src/components/SettingsModal.vue b/src/components/SettingsModal.vue
index 73b204d..c946095 100644
--- a/src/components/SettingsModal.vue
+++ b/src/components/SettingsModal.vue
@@ -4,8 +4,8 @@
 		min-w-[8cm] max-w-[80%] max-h-[80%] overflow-auto" :style="styles">
 		<close-icon @click.stop="onClose" ref="closeIcon"
 			class="block absolute top-1 right-1 md:top-2 md:right-2 w-8 h-8 hover:cursor-pointer" />
-		<h1 class="text-xl md:text-2xl font-bold text-center py-2 border-b border-stone-400">Settings</h1>
-		<div class="border-b border-stone-400 pb-2">
+		<h1 class="text-xl md:text-2xl font-bold text-center py-2" :class="borderBClasses">Settings</h1>
+		<div class="pb-2" :class="borderBClasses">
 			<h2 class="font-bold md:text-xl text-center pt-1 md:pt-2 md:pb-1">Timing</h2>
 			<div class="grid grid-cols-[130px_minmax(0,1fr)_65px] gap-1 px-2 md:px-3">
 				<!-- Row 1 -->
@@ -24,7 +24,7 @@
 				<div class="my-auto text-right">{{uiOpts.autoActionDelay}} ms</div>
 			</div>
 		</div>
-		<div class="border-b border-stone-400 pb-2">
+		<div class="pb-2" :class="borderBClasses">
 			<h2 class="font-bold md:text-xl text-center pt-1 md:pt-2 md:pb-1">Layout</h2>
 			<div class="flex gap-2 justify-around px-2 pb-1">
 				<div>
@@ -76,7 +76,7 @@
 				<div class="my-auto text-right">{{pxToDisplayStr(lytOpts.tileSpacing)}}</div>
 			</div>
 		</div>
-		<div class="border-b border-stone-400 pb-2 px-2 md:px-3">
+		<div class="pb-2 px-2 md:px-3" :class="borderBClasses">
 			<h2 class="font-bold md:text-xl text-center pt-1 md:pt-2 -mb-2 ">Other</h2>
 			<div>
 				Tree to use
@@ -139,6 +139,9 @@ export default defineComponent({
 				boxShadow: this.uiOpts.shadowNormal,
 			};
 		},
+		borderBClasses(): string {
+			return 'border-b border-stone-400';
+		},
 		rLabelClasses(): string { // For reset-upon-click labels
 			return "w-fit hover:cursor-pointer hover:text-lime-600";
 		},
diff --git a/src/components/TileInfoModal.vue b/src/components/TileInfoModal.vue
index e1b31db..29901ee 100644
--- a/src/components/TileInfoModal.vue
+++ b/src/components/TileInfoModal.vue
@@ -4,13 +4,11 @@
 		max-w-[80%] min-w-[8cm] md:min-w-[14cm] max-h-[80%]"
 		:style="styles">
 		<div class="pb-1 md:pb-2">
-			<div class="flex">
-				<h1 class="text-center text-xl font-bold grow pt-2 pb-1 md:text-2xl md:pt-3 md:pb-1">
-					{{getDisplayName(nodeName, tolNode)}}
-				</h1>
-				<close-icon @click.stop="onClose" ref="closeIcon"
-					class="block m-1 md:m-2 w-8 h-8 hover:cursor-pointer"/>
-			</div>
+			<close-icon @click.stop="onClose" ref="closeIcon"
+				class="block absolute top-1 right-1 md:m-2 w-8 h-8 hover:cursor-pointer"/>
+			<h1 class="text-center text-xl font-bold pt-2 pb-1 mx-10 md:text-2xl md:pt-3 md:pb-1">
+				{{getDisplayName(nodeName, tolNode)}}
+			</h1>
 			<div class="flex justify-evenly text-sm md:text-base">
 				<div> Children: {{tolNode.children.length}} </div>
 				<div> Tips: {{tolNode.tips}} </div>
@@ -85,10 +83,10 @@
 					<div>{{descInfos[idx]!.text}}</div>
 					<div class="text-sm text-right">
 						From
-						<a :href="'https://en.wikipedia.org/?curid=' + descInfos[idx]!.wikiId" target="_blank">
-							Wikipedia
-						</a>
-						<external-link-icon class="inline-block w-3 h-3"/>
+						<a :href="'https://en.wikipedia.org/?curid=' + descInfos[idx]!.wikiId"
+							target="_blank">Wikipedia</a>
+						<external-link-icon class="inline-block w-3 h-3 ml-1"/>
+						{{descInfos[idx]!.fromDbp ? '(via DBpedia)' : ''}}
 					</div>
 				</div>
 				<div v-else class="text-center">
-- 
cgit v1.2.3