30:Tae7,{ if (foundCached) { return html`(Preview Only mode)`; } if (querySoFar === "") { return html``; } else { const container = DOM.element("div", { id: "images", style: "border: 3px solid #CCC; padding: 3px; max-width: 600px;" }); const resultset = html`

Search returned ${ (await list_of_ids(querySoFar)).split("\n").length } items, then filtered to these with scientific names:

`; container.appendChild(resultset); const default_img = "https://commons.wikimedia.org/wiki/Special:FilePath/Coraz%C3%B3n.svg"; details_result.results.bindings .map((item) => { const pic = item.pic || { value: default_img }; return { ...item, img_src: pic.value }; }) .filter((d) => d.taxonname !== undefined) .forEach((item) => { const img_src = item.img_src.replace("http://", "https://"); const item_div = DOM.element("div", { class: "item", width: 200, style: "overflow: auto;" }); const img = DOM.element("img", { src: img_src, width: 50, title: item.itemLabel.value, style: "float: left; padding-right: 0.5em" }); const wiki = item.article ? `Wikipedia |` : ``; const p = DOM.element("p"); p.innerHTML = ` Name: ${ item.itemLabel.value } | ${wiki} Taxon ${item.taxonname?.value} | Common name ${ item.taxoncommon?.value || item.itemLabel.value + "*" } | NCBI: ${item.ncbi_on_wikidata?.value} `; item_div.appendChild(img); item_div.appendChild(p); p.appendChild( html` ${Inputs.button( "Add", { value: null, width: "60px", reduce: () => { nodes.data = [ ...nodes.data, { common_name: item.taxoncommon?.value || item.itemLabel.value, sci_name: item.taxonname?.value, img: item?.img_src?.value, nbci_on_wikidata: item?.ncbi_on_wikidata?.value } ]; viewof nodes.dispatchEvent( new Event("input", { bubbles: true }) ); } } )}` ); container.appendChild(item_div); }); return container; } }31:T6c6,details_sparql = async (querySoFar) => { return ` SELECT ?item (SAMPLE(?itemLabel) AS ?itemLabel) (SAMPLE(?itemDescription) AS ?itemDescription) (SAMPLE(?pic) AS ?pic) (SAMPLE(?taxonname) AS ?taxonname) (SAMPLE(?taxoncommon) AS ?taxoncommon) (SAMPLE(?instance_of) AS ?instance_of) (SAMPLE(?article) AS ?article) (SAMPLE(?ncbi_on_wikidata) as ?ncbi_on_wikidata) (GROUP_CONCAT(DISTINCT ?country; SEPARATOR=", ") AS ?countries) (GROUP_CONCAT(DISTINCT ?countryLabel; SEPARATOR=", ") AS ?countryLabels) WHERE \{ VALUES ?item \{ ${await list_of_ids(querySoFar)} \} OPTIONAL \{ ?item wdt:P18 ?pic. \} OPTIONAL \{ ?item wdt:P225 ?taxonname. \} OPTIONAL \{ ?item wdt:P17 ?country. \} OPTIONAL \{ ?item wdt:P569 ?date_of_birth. \} OPTIONAL \{ ?item wdt:P31 ?instance_of. \} OPTIONAL \{ ?item wdt:P17 ?country. \} OPTIONAL \{ ?item wdt:P569 ?date_of_birth. \} OPTIONAL \{ ?item wdt:P685 ?ncbi_on_wikidata. \} #look for english wikipedia article OPTIONAL \{ ?article schema:about ?item . ?article schema:inLanguage "en" . ?article schema:isPartOf . \} # follow the instancesOf "organisms known by a particular common name" for more taxons OPTIONAL { ?item p:P31 ?statement. ?statement ps:P31 wd:Q55983715. ?statement pq:P642 ?of. ?of wdt:P1843 ?taxoncommon. FILTER((LANG(?taxoncommon)) = "en") ?of wdt:P225 ?taxonname. } OPTIONAL \{ ?item wdt:P1843 ?taxoncommon. FILTER (lang(?taxoncommon) = 'en') \} SERVICE wikibase:label \{ bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". ?item rdfs:label ?itemLabel. ?item rdfs:description ?itemDescription. ?country rdfs:label ?countryLabel. \} \} GROUP BY ?item`; }32:T59e,prepTreePhylotree = { if (nodes.data.length < 1) { return; } const t = new Phylotree.phylotree(nwkOut); t.nodes.each((d) => { d.data.properties = {}; d.data.properties.nbci = "" + d.data.name; const p = d.data.attribute?.match( /(1\[&&NHX)(sci_name)=(.*?)(rank)=(.*?)(dist)=(.*)(name)=(\d+)]/ ); d.data.properties.sci_name = p && p[3]; d.data.properties.rank = p && p[5]; d.data.properties.dist = p && p[7]; d.data.properties.nbci_num = p && Number(p[9]); d.data.name = d.data.properties.sci_name; d.data.branch_length = d.data.properties.dist; d.branch_length = d.data.properties.dist; d.data.original_data = nodes.data.find( // (n) => d.data.properties.sci_name && d.data.properties.sci_name.toLowerCase() === n["Significant Classification"].toLowerCase().trim() (n) => d.data.properties.sci_name && d.data.properties.sci_name.toLowerCase() === n["sci_name"].toLowerCase() ); d.data.name = `${ (d.data.original_data && d.data.original_data["common_name"].slice( 0, displayToggles["truncate-characters-to"] )) || d.data.properties.sci_name }` || d.data.properties.nbci; d.data.title = `${ (d.data.original_data && d.data.original_data["common_name"]) || d.data.properties.sci_name }` || d.data.properties.nbci; }); return t; }33:T1c47,//http://www.eattheweeds.com/edible-cultivated-flowers/ edibleFlowers2 = [ { common_name: "Balloon Flower", sci_name: "Platycodon grandiflorus" }, { common_name: "Baobob", sci_name: "Adansonia digitata" }, { common_name: "Bauhinias", sci_name: "Bauhinia variegata" }, { common_name: "Camel Foot / Orchard Tree", sci_name: "Bauhinia purpurea" }, { common_name: "Bee Balm", sci_name: "Monarda didyma" }, { common_name: "Black Salsify", sci_name: "Scorzonera hispanica" }, { common_name: "Calamint", sci_name: "Calamintha grandifolia" }, { common_name: "Rampion", sci_name: "Campanula rapunculus" }, { common_name: "Clustered Bellflower", sci_name: "Campanula glomerata" }, { common_name: "Campanula punctata", sci_name: "Campanula punctata" }, { common_name: "Rover Bellflower", sci_name: "Campanula rapunculoides" }, { common_name: "Campanula rapunculus", sci_name: "Campanula rapunculus" }, { common_name: "Campanula versicolor", sci_name: "Campanula versicolor" }, { common_name: "Star Fruit", sci_name: "Averrhoa carambola" }, { common_name: "Cucumber tree (bilimbi)", sci_name: "Averrhoa bilimbi" }, { common_name: "Chamaemelum nobile", sci_name: "Chamaemelum nobile" }, { common_name: "German chamomile", sci_name: "Matricaria recutita" }, { common_name: "Carnations", sci_name: "Dianthus caryophyllus" }, { common_name: "Marigold", sci_name: "Calendula officinalis" }, { common_name: "Catnip", sci_name: "Nepeta cataria" }, { common_name: "Chrysanthemum", sci_name: "Chrysanthemum morifolium" }, { common_name: "Dame’s Rocket", sci_name: "Hesperis matronalis" }, { common_name: "Daylily", sci_name: "Hemerocallis" }, { common_name: "Dendrobium phalaenopsis (orchid)", sci_name: "Dendrobium phalaenopsis" }, { common_name: "False Roselle", sci_name: "Hibiscus acetosella" }, { common_name: "Roselle/Jamaican Hibiscus", sci_name: "Hibiscus sabdariffa" }, { common_name: "Fennel", sci_name: "Foeniculum vulgare" }, { common_name: "Forget Me Not", sci_name: "Myosotis sylvatica" }, { common_name: "Fragrant Water Lily", sci_name: "Nymphaea odorata" }, { common_name: "Yellow (American) Water Lily", sci_name: "Nymphaea mexicana" }, { common_name: "Fritilary’s Bell Blossoms", sci_name: "Fritillaria verticillata" }, { common_name: "Fritillaria camtschatcensis (edible bulbs)", sci_name: "Fritillaria camtschatcensis" }, { common_name: "Garden Sorrel", sci_name: "Rumex acetosa" }, { common_name: "Gardenia jasminoides", sci_name: "Gardenia jasminoides" }, { common_name: "Geranium (latter genus)", sci_name: "Pelargonium" }, { common_name: "Ginger", sci_name: "Zingiber officinale" }, { common_name: "Gladiola", sci_name: "Gladiolus" }, { common_name: "Hollyhocks", sci_name: "Alcea rosea" }, { common_name: "Honeysuckle", sci_name: "Lonicera japonica" }, { common_name: "Horseradish", sci_name: "Armoracia rusticana" }, { common_name: "Impatiens", sci_name: "Impatiens wallerana" }, { common_name: "Italian Bugloss", sci_name: "Anchusa azurea" }, { common_name: "Jasmine", sci_name: "Jasminum officinale" }, { common_name: "Carolina Jasmine (false/inedible/toxic)", sci_name: "Gelsemium Sempervirens" }, { common_name: "Johnny-Jump-Ups", sci_name: "Viola tricolor" }, { common_name: "Kapok", sci_name: "Ceiba pentandra" }, { common_name: "Lemon Verbena", sci_name: "Aloysia triphylla" }, { common_name: "Lovage", sci_name: "Levisticum officinale" }, { common_name: "Magnolias", sci_name: "Magnolia grandiflora" }, { common_name: "Sweet Bay Magnolia (bay leaf)", sci_name: "Magnolia virginiana" }, { common_name: "Mangos", sci_name: "Mangifera indica" }, { common_name: "Marigolds (lucida)", sci_name: "Tagetes lucida" }, { common_name: "Marigolds (tenuifolia)", sci_name: "Tagetes tenuifolia" }, { common_name: "Oregano", sci_name: "Origanum vulgare" }, { common_name: "Marjoram", sci_name: "Origanum majorana" }, { common_name: "Edible Peas", sci_name: "Pisum" }, { common_name: "edible Petunia hybrid", sci_name: "Petunia x hybrida" }, { common_name: "Phlox paniculata", sci_name: "Phlox paniculata" }, { common_name: "Pineapple Sage", sci_name: "Salvia elegans" }, { common_name: "Scarlet Sage (inedible, toxic)", sci_name: "Salvia coccinea" }, { common_name: "Dill", sci_name: "Anethum graveolens" }, { common_name: "caryophyllus", sci_name: "caryophyllus" }, { common_name: "Pink Carnation", sci_name: "Dianthus plumarius" }, { common_name: "Sweet William Carnation", sci_name: "Dianthus barbatus" }, { common_name: "Hosta/Plantain Lily", sci_name: "Hosta lancifolia" }, { common_name: "Primrose", sci_name: "Primula vulgaris" }, { common_name: "Rose", sci_name: "Rosa" }, { common_name: "Rose of Sharon", sci_name: "Hibiscus syriacus" }, { common_name: "Safflower (false saffron)", sci_name: "Carthamus tinctorius" }, { common_name: "Saffron", sci_name: "Crocus sativus" }, { common_name: "Original saffron parent (uncommon)", sci_name: "Crocus cartwrightianus" }, { common_name: "Snapdragons", sci_name: "Antirrhinum" }, { common_name: "Stock/Gillyflower", sci_name: "Matthiola incana" }, { common_name: "Strawberry", sci_name: "Fragaria ananassa" }, { common_name: "Szechaun Buttons", sci_name: "Spilanthes acmella" }, { common_name: "Szechaun Buttons", sci_name: "Acmella ocleracea" }, { common_name: "Tea Blossom", sci_name: "Camellia sinensis" }, { common_name: "Forsythia", sci_name: "Forsythia" }, { common_name: "Tea Olive", sci_name: "Osmanthus frangrans" }, { common_name: "American Olive", sci_name: "Osmanthus americana" }, { common_name: "Thyme", sci_name: "Thymus vulgaris" }, { common_name: "Tuberose", sci_name: "Polianthes tuberosa" }, { common_name: "Chinese Wisteria", sci_name: "Wisteria sinsensis" }, { common_name: "Wisteria floribunda", sci_name: "Wisteria floribunda" }, { common_name: "Durian", sci_name: "Durio zibethinus" }, { common_name: "Freesia", sci_name: "Freesia" }, { common_name: "Fuchsia", sci_name: "Fuchsia" }, { common_name: "Genanium (main genus)", sci_name: "Geranium" }, { common_name: "Hyacinth Bean", sci_name: "Lablab purpureus" }, { common_name: "Lavender", sci_name: "Lavandula" }, { common_name: "Common lilac", sci_name: "Syringa vulgaris" }, { common_name: "Mustard", sci_name: "Sinapis alba" }, { common_name: "Nasturtium", sci_name: "Nasturtium" }, { common_name: "Okra", sci_name: "Abelmoschus esculentus" }, { common_name: "Onions", sci_name: "Allium" }, { common_name: "Prickly Pear Cactus (etc)", sci_name: "Opuntias" }, { common_name: "Pansy", sci_name: "Viola × wittrockiana" }, { common_name: "Papaya", sci_name: "Carica papaya" }, { common_name: "Parsley", sci_name: "Petroselinum crispum" }, { common_name: "Peony", sci_name: "Paeonia officinalis" }, { common_name: "Rosemary", sci_name: "Salvia rosmarinus" }, { common_name: "Scarlet Runner Bean", sci_name: "Phaseolus coccineus" }, { common_name: "Society Garlic", sci_name: "Tulbaghia violacea" }, { common_name: "Tansy", sci_name: "Tanacetum vulgare" }, { common_name: "Tulip (petal)", sci_name: "Tulipa" } ]34:Tbe9,seafood = [ { common_name: "Human", sci_name: "Homo sapiens" }, { common_name: "chinook salmon", sci_name: "Oncorhynchus tshawytscha" }, { common_name: "Japanese Eel", sci_name: "Anguilla japonica" }, { common_name: "True Crabs", sci_name: "Brachyura" }, { common_name: "King crab", sci_name: "Lithodidae" }, { common_name: "Ranina ranina", sci_name: "Ranina ranina" }, { common_name: "sea urchin", sci_name: "Echinoidea" }, { common_name: "Scallops", sci_name: "Pectinidae" }, { common_name: "Zebra Mussel", sci_name: "Dreissena polymorpha" }, { common_name: "Bivalvia", sci_name: "Bivalvia" }, { common_name: "Clams", sci_name: "Pteriomorphia" }, { common_name: "Pacific oyster", sci_name: "Crassostrea gigas" }, { common_name: "True Lobsters", sci_name: "Homarus" }, { common_name: "Crayfishes", sci_name: "Astacoidea" }, { common_name: "Perch", sci_name: "Perca fluviatilis" }, { common_name: "Yellowfinned Albacore", sci_name: "Thunnus albacares" }, { common_name: "swordfish", sci_name: "Xiphias gladius" }, { common_name: "Escolar", sci_name: "Lepidocybium flavobrunneum" }, { common_name: "Skipjack Tuna", sci_name: "Katsuwonus pelamis" }, { common_name: "Atlantic Bluefin Tuna", sci_name: "Thunnus thynnus" }, { common_name: "Catfish", sci_name: "Siluriformes" }, { common_name: "Anchovy", sci_name: "Engraulidae" }, { common_name: "Arctic Charr", sci_name: "Salvelinus alpinus" }, { common_name: "Mackerel Scad", sci_name: "Decapterus macarellus" }, { common_name: "Pacific cod", sci_name: "Gadus macrocephalus" }, { common_name: "Croaker", sci_name: "Sciaenidae" }, { common_name: "herring smelt", sci_name: "Argentinidae" }, { common_name: "Mahi mahi", sci_name: "Coryphaena hippurus" }, { common_name: "Common mussel", sci_name: "Mytilus edulis" }, { common_name: "Pacific halibut", sci_name: "Hippoglossus stenolepis" }, { common_name: "pollock", sci_name: "Pollachius virens" }, { common_name: "rainbow trout", sci_name: "Oncorhynchus mykiss" }, { common_name: "Striped Bass", sci_name: "Morone saxatilis" }, { common_name: "True Sardine", sci_name: "Sardina pilchardus" }, { common_name: "common sole", sci_name: "Solea solea" }, { common_name: "Squid", sci_name: "Teuthida" }, { common_name: "Tilapia", sci_name: "Tilapia" }, { common_name: "Black tiger prawn", sci_name: "Penaeus monodon" }, { common_name: "Whitefish", sci_name: "Coregonus lavaretus" }, { common_name: "Common octopus", sci_name: "Octopus vulgaris" }, { common_name: "Barramundi", sci_name: "Lates calcarifer" }, { common_name: "American butterfish", sci_name: "Peprilus triacanthus" }, { common_name: "Nile Tilapia", sci_name: "Oreochromis niloticus" }, { common_name: "African Snook – Nile Perch", sci_name: "Lates niloticus" }, { common_name: "Silver Cyprinid – Dagaa", sci_name: "Rastrineobola argentea" }, { common_name: "Pacific Chub Mackerel", sci_name: "Scomber japonicus" }, { common_name: "Atlantic Chub Mackerel", sci_name: "Scomber colias" } ]35:T810,americanDietSample = [ { common_name: "potato", sci_name: "Solanum tuberosum" }, { common_name: "garden tomato", sci_name: "Solanum lycopersicum" }, { common_name: "garden onion", sci_name: "Allium cepa" }, { common_name: "carrot", sci_name: "Daucus carota subsp. sativus" }, { common_name: "garden lettuce", sci_name: "Lactuca sativa" }, { common_name: "sweet corn", sci_name: "Zea mays Saccharata Group" }, { common_name: "romaine lettuce", sci_name: "Lactuca sativa var. longifolia" }, { common_name: "apple", sci_name: "Malus domestica" }, { common_name: "citrus", sci_name: "Citrus" }, { common_name: "banana", sci_name: "Musa" }, { common_name: "strawberry", sci_name: "Fragaria" }, { common_name: "watermelon", sci_name: "Citrullus lanatus" }, { common_name: "pineapple", sci_name: "Ananas comosus" }, { common_name: "Domestic Cattle (meat, milk)", sci_name: "Bos taurus" }, { common_name: "chicken (eggs, meat)", sci_name: "Gallus gallus" }, { common_name: "Domestic Goat (meat, milk)", sci_name: "Capra aegagrus hircus" }, { common_name: "sugar beet", sci_name: "Beta vulgaris" }, { common_name: "sugarcane", sci_name: "Saccharum officinarum" }, { common_name: "broccoli/kale/cabbage etc.", sci_name: "Brassica oleracea var. italica" }, { common_name: "spinach", sci_name: "Spinacia oleracea" }, { common_name: "common wheat", sci_name: "Triticum aestivum" }, { common_name: "soybean", sci_name: "Glycine max" }, { common_name: "garden pea", sci_name: "Pisum sativum" }, { common_name: "Domestic pig", sci_name: "Sus scrofa domesticus" }, { common_name: "coffee", sci_name: "Coffea" }, { common_name: "peanut", sci_name: "Arachis hypogaea" }, { common_name: "cultivated garlic", sci_name: "Allium sativum" }, { common_name: "white shrimp", sci_name: "Litopenaeus setiferus" }, { common_name: "salmon", sci_name: "Salmo salar" }, { common_name: "Skipjack Tuna", sci_name: "Katsuwonus pelamis" }, { common_name: "Nile Tilapia", sci_name: "Oreochromis niloticus" } ]36:Tda0,presetGrouping = { const OnlyHumanAndMouse = [ { common_name: "Human", sci_name: "Homo sapiens", set: "Only Human & Mouse" }, { common_name: "House Mouse", sci_name: "Mus musculus", set: "Only Human & Mouse" } ]; return d3.group( edibleFlowers2 .map((d) => { d["set"] = "Edible flowers 🌺"; return d; }) .concat( dietlife.map((d) => { d["set"] = "Vegetarian Keto edible lifeforms 🍳"; return d; }) ) .concat( camnats.map((d) => { d["set"] = "Cambridge Naturals bulk foods 🍵"; return d; }) ) .concat( seafood.map((d) => { d["set"] = "Seafood 🦑"; return d; }) ) .concat( americanDietSample.map((d) => { d["set"] = "American Diet Sample"; return d; }) ) .concat(OnlyHumanAndMouse) // .concat( // localStorage.getItem("localPhylogenicTree") // ? JSON.parse(localStorage.getItem("localPhylogenicTree")).map((d) => { // const temp = Object.assign({}, d); // temp["set"] = "Your Last Edit"; // return temp; // }) // : [] // ) .concat( first90000OFFIngredients.map((d) => { d["set"] = "OpenFoodFacts Ingredients (first 90k)"; return d; }) ) .concat( foodb_2020_food.map((d) => { d["set"] = "FooDB.ca Foods list 2020 pre-release"; return d; }) ) .concat( wood_database.map((d) => { d["set"] = "Wood-database.com species"; return d; }) ) .concat( forestopia.map((d) => { d["set"] = "forestopia.org species"; return d; }) ) .concat( phytotheca.map((d) => { d["set"] = "phytotheca.com garden species"; return d; }) ) .concat( rainbowTomatoesGarden.map((d) => { d["set"] = "rainbowtomatogarden.com tinned fish species"; return d; }) ) .concat( [].concat(rainbowTomatoesGarden).map((d) => { const temp = Object.assign({}, d); temp["set"] = "Seafood 🦑"; return temp; }) ) .concat( [] .concat([ ...americanDietSample, ...seafood, ...dietlife, ...camnats, ...edibleFlowers2, ...first90000OFFIngredients, ...foodb_2020_food, ...forestopia, ...phytotheca, ...OnlyHumanAndMouse ]) .map((d) => { const temp = Object.assign({}, d); temp["set"] = "All without wood trees"; return temp; }) ) .concat( [] .concat([ ...americanDietSample, ...seafood, ...dietlife, ...camnats, ...edibleFlowers2, ...first90000OFFIngredients, ...foodb_2020_food, ...forestopia, ...wood_database, ...phytotheca, ...OnlyHumanAndMouse ]) .map((d) => { const temp = Object.assign({}, d); temp["set"] = "All"; return temp; }) ), (d) => d.set ); 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Tree","cells":[{"id":0,"value":"md`# Your Own Phylogenetic Tree\nstarts in \"preview only\" to conserve data and for mobile — made with ETE3`","pinned":false,"hidden":false,"mode":"ojs"},{"id":2270,"value":"html`${\n foundCached\n ? \"Preview Only Mode (view horizontally. To edit, use a computer browser, check Always Download below)\"\n : ascii(nodes.data) !== false\n ? \"Creation Mode : ETE3 fully loaded\"\n : html`\"Creation Mode \": `\n}`","pinned":false,"hidden":false,"mode":"ojs"},{"id":2303,"value":"alwaysDownloadEditingData.length > 0\n ? html`

Creation mode is loading or now ready:

`\n : html``","pinned":false,"hidden":false,"mode":"ojs"},{"id":2353,"value":"viewof alwaysDownloadEditingData = Inputs.checkbox([\n \"Always Download Editing Data (400mb uncompressed)\"\n])","pinned":false,"hidden":false,"mode":"ojs"},{"id":1598,"value":"viewof displayToggles = {\n const widthToggle = view`\n Width ${[\n \"width\",\n html``\n ]}\n

Height ${[\n \"height\",\n html``\n ]}\n

\n ${[\n \"fit-to-size\",\n Inputs.radio(\n [\"Fit to Size: Width\", \"Fit to Size: Height\", \"Fit to Size: Fixed\"],\n { value: \"Fit to Size: Height\" }\n )\n ]}\n ${[\n \"direction-layout\",\n Inputs.radio([\"Radial\", \"Linear\"].concat(true ? \"ASCII text\" : []), {\n value: \"Radial\"\n })\n ]}\n\n ${[\n \"truncate-characters-to\",\n Inputs.range([0, 255], {\n step: 1,\n value: 20,\n label: \"common name length limit (0 for scientific)\"\n })\n ]}\n`;\n return widthToggle;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":34,"value":"viz = displayToggles[\"direction-layout\"] != \"ASCII text\"\n ? prepTreePhylotree\n .render({\n height: displayToggles.height,\n width: displayToggles.width,\n // \"max-radius\": 768,\n \"label-nodes-with-name\": true,\n \"top-bottom-spacing\":\n displayToggles[\"fit-to-size\"] === \"Fit to Size: Height\"\n ? \"fit-to-size\"\n : \"fixed-step\", //\"fixed-step\", //\"fit-to-size\"\n \"left-right-spacing\":\n displayToggles[\"fit-to-size\"] === \"Fit to Size: Width\"\n ? \"fit-to-size\"\n : \"fixed-step\",\n // \"align-tips\": true,\n\n // \"node-styler\": colorNodesByName,\n // \"edge-styler\": colorEdgesByTarget,\n \"is-radial\":\n displayToggles[\"direction-layout\"] === \"Radial\" ? true : false,\n zoom: false,\n collapsible: false,\n selectable: false,\n hide: false,\n \"show-menu\": false\n })\n .show()\n : asciiOut\n ? asciiOut\n : \"ASCII display requires Creation Mode/ETE3\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":1258,"value":"viewof example = Inputs.radio(presetGrouping, {\n label: \"Use a preset list\",\n value: presetGrouping.get(\"Edible flowers 🌺\")\n})\n/* TODO: Your Last Edit needs to update presetGrouping more often\n*/","pinned":false,"hidden":false,"mode":"ojs"},{"id":1959,"value":"example === presetGrouping.get(\"Edible flowers 🌺\")\n ? md`Edible flowers are drawn from [this blog post](http://www.eattheweeds.com/edible-cultivated-flowers/)–consume carefully after reading!`\n : md``","pinned":false,"hidden":false,"mode":"ojs"},{"id":1054,"value":"downloadYourList = nodes.data.reverse()","pinned":false,"hidden":false,"mode":"ojs"},{"id":2883,"value":"lookedUpData = await speciesToTaxidLookup(nodes.data) /*use for GOAT */","pinned":false,"hidden":false,"mode":"ojs"},{"id":2327,"value":"html`${\n foundCached\n ? \"Preview Mode (to edit, use a computer browser, check Always Download above)\"\n : ascii(nodes.data) !== false\n ? \"Creation Mode : ETE3 fully loaded\"\n : html`\"Creation Mode \": `\n}`","pinned":false,"hidden":false,"mode":"ojs"},{"id":1508,"value":"viewof querySoFar = Inputs.text({\n label: \"Search Wiki to incorporate a branch to your tree\",\n placeholder: \"Search species\",\n value: \"box turtle\",\n submit: false\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":1517,"value":"$30","pinned":false,"hidden":false,"mode":"ojs"},{"id":1047,"value":"viewof nodes = dataEditor(example, {\n columns: [\"common_name\", \"sci_name\" /*\"ncbi\", \"img_src\"*/],\n format: {\n common_name: (d) =>\n Inputs.text({\n value: d\n }),\n sci_name: (d) => Inputs.text({ value: d }),\n ncbi: (d) => d,\n img_src: (d) => d\n },\n width: {\n qty: \"100px\",\n common_name: \"100px\",\n sci_name: \"50%\"\n // ncbi: \"8%\",\n // img_src: \"8%\"\n },\n tableclass: \"veg\",\n stylesheet: `\n .veg {\n background-color: #eff;\n }\n .col-manual form {\n width: 300px;\n float: left;\n }\n .col-type form {\n width: 70px;\n float: left;\n }\n .veg input[type=range] {\n display: none;\n }\n `\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":2682,"value":"nodes","pinned":true,"hidden":false,"mode":"ojs"},{"id":1043,"value":"{\n let newItem = view`\n

Manually add branches to be incorporated

\n \n ${[\n \"common_name\",\n Inputs.text({\n label: \"common_name\",\n placeholder: \"enter item name\"\n })\n ]}\n ${[\n \"sci_name\",\n Inputs.text({\n label: \"sci_name\",\n placeholder: \"enter item name\"\n })\n ]}\n ${Inputs.button(\"Add Item\", {\n reduce: () => {\n nodes.data = [\n ...nodes.data,\n {\n common_name: newItem.value.common_name,\n sci_name: newItem.value.sci_name\n }\n ];\n viewof nodes.dispatchEvent(new Event(\"input\", { bubbles: true }));\n }\n })}\n\n `;\n\n return newItem;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":1420,"value":"list_of_ids = async (searchSoFar) => {\n const wikitext = async (ins) => {\n if (ins.length < 1) return \"\";\n const URL = `https://www.wikidata.org/w/api.php?action=wbsearchentities&origin=*&format=json&&language=en&limit=50&search=${ins}`;\n console.log(URL);\n return fetch(URL).then((response) => response.json());\n };\n return Array.from(\n (await wikitext(searchSoFar)).search.map((e) => `wd:${e.id}`)\n ).join(\"\\n\");\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":1826,"value":"md`### Code\n\n[pyodide 0.18](https://pyodide.org/en/stable/) + self-built ETE3.js [and loading NCBI data](http://etetoolkit.org/docs/latest/tutorial/tutorial_ncbitaxonomy.html) + [Wikidata Search](https://observablehq.com/@napsternxg/wikidata-typeahead-api) + Phylotree.js \n\nThe first cell below loads the 100mb zipped taxonomy for ETE3, if it has an error, try to re-run that cell.\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":2061,"value":"{\n localStorage.setItem(\"localPhylogenicTree\", JSON.stringify(nodes.data));\n console.log(\"saved\");\n //https://observablehq.com/@stevenweaver/computing-the-center-of-the-tree-with-phylotree-js?collection=@stevenweaver/phylotree-utilities shows how to place circles with titles and use d3\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":2183,"value":"currentNodeDataHashCode = JSON.stringify(nodes.data).hashCode()","pinned":false,"hidden":false,"mode":"ojs"},{"id":2169,"value":"(String.prototype.hashCode = function () {\n var hash = 0;\n for (var i = 0; i < this.length; i++) {\n var character = this.charCodeAt(i);\n hash = (hash << 5) - hash + character;\n hash = hash & hash; // Convert to 32bit integer\n }\n return hash;\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":416,"value":"import { py, pyodide } from \"@thadk/pyodide-18\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":427,"value":"ete3datapy = !foundCached &&\n py`import micropip, os\n# Github Pages does not succeed, perhaps mime types, only raw github.\nmicropip.install(\"https://raw.githubusercontent.com/thadk/pyodide_packages/main/etetoolkit/dist/ete3_ncbidata-0.0.2-py3-none-any.whl\")\n\n# micropip.install(\"http://localhost:8000/etetoolkit/dist/ete3_ncbidata-0.0.2-py3-none-any.whl\")\n#Mention the pyodide dependency for Observable to run it before this: ${ete3py}\n\n#confirm the files loaded\n# os.listdir(\"/lib/python3.9/site-packages/ete3_ncbidata-0.0.2.data/data/ete3_data/\")\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":2626,"value":"","pinned":true,"hidden":false,"mode":"ojs"},{"id":1481,"value":"$31","pinned":false,"hidden":false,"mode":"ojs"},{"id":1501,"value":"details_result = {\n if (querySoFar !== \"\")\n return fetch(\n \"https://query.wikidata.org/sparql?query=\" +\n encodeURIComponent(await details_sparql(querySoFar)),\n {\n headers: {\n accept: \"application/sparql-results+json\"\n }\n }\n ).then((res) => res.json());\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":2187,"value":"cachedNwk = FileAttachment(\"generateCachedNwk(13).json\").json()","pinned":false,"hidden":false,"mode":"ojs"},{"id":2374,"value":"generateCachedNwk = alwaysDownloadEditingData.length > 0 &&\n Promise.all(\n Array.from(presetGrouping).map(async ([key, value]) => ({\n phylogenicTreeHashCode: JSON.stringify(\n value.map(({ common_name, sci_name }) => ({ common_name, sci_name }))\n ).hashCode(),\n originalName: key,\n nwkString: await writeNwk(ncbiTree(value)),\n ascii: await ascii(value)\n }))\n )\n","pinned":false,"hidden":false,"mode":"ojs"},{"id":2629,"value":"// import { share } from \"@tomlarkworthy/shareview\"","pinned":true,"hidden":false,"mode":"ojs"},{"id":516,"value":"// lookup from cache or generate the newick string\nnwkOut = cachedNwk &&\n nodes.data.length > 0 &&\n (cachedNwk.find((n) => n.phylogenicTreeHashCode === currentNodeDataHashCode)\n ? cachedNwk.find(\n (n) => n.phylogenicTreeHashCode === currentNodeDataHashCode\n ).nwkString\n : writeNwk(ncbiTree(nodes.data)))","pinned":false,"hidden":false,"mode":"ojs"},{"id":2499,"value":"asciiOut = cachedNwk && // lookup from cache or generate the ascii string\n nodes.data.length > 0 &&\n (cachedNwk.find((n) => n.phylogenicTreeHashCode === currentNodeDataHashCode)\n ? cachedNwk.find(\n (n) => n.phylogenicTreeHashCode === currentNodeDataHashCode\n ).ascii\n : ascii(nodes.data))","pinned":false,"hidden":false,"mode":"ojs"},{"id":2158,"value":"// d3.hierarchy(prepTreePhylotree.nodes)","pinned":true,"hidden":false,"mode":"ojs"},{"id":2161,"value":"// prepTreePhylotree.getRootNode()","pinned":true,"hidden":false,"mode":"ojs"},{"id":31,"value":"$32","pinned":false,"hidden":false,"mode":"ojs"},{"id":2200,"value":"foundCached = alwaysDownloadEditingData.length !== 0\n ? false\n : cachedNwk.find((n) => n.phylogenicTreeHashCode === currentNodeDataHashCode)","pinned":false,"hidden":false,"mode":"ojs"},{"id":478,"value":"ncbiDB = !foundCached && pyodide.runPython(\n `#${ete3datapy} ${pyodide}\nfrom ete3 import NCBITaxa\nncbi = NCBITaxa(\"/lib/python3.9/site-packages/ete3_ncbidata-0.0.2.data/data/ete3_data/taxa.sqlite\")\nncbi`\n)","pinned":false,"hidden":false,"mode":"ojs"},{"id":1374,"value":"ncbiTree = async (treeNodesSciCommonNames) =>\n treeNodesSciCommonNames.length > 0 &&\n !foundCached &&\n py`\ntree = ${ncbiDB}.get_topology(${(\n await speciesToTaxidLookup(treeNodesSciCommonNames)\n ).map((d) => d.taxid)}, intermediate_nodes=True)\ntree`","pinned":false,"hidden":false,"mode":"ojs"},{"id":2582,"value":"!foundCached &&\n py`\n${ncbiDB}.annotate_tree(${await ncbiTree(nodes.data)}, taxid_attr=\"name\")\n# load the whole leaf name as species taxid\n# tree = PhyloTree('((9606, 9598), 10090);', sp_naming_function=lambda name: name)\n#tax2names, tax2lineages, tax2rank = tree.annotate_ncbi_taxa(dbfile=\"/lib/python3.9/site-packages/ete3_ncbidata-0.0.2.data/data/ete3_data/taxa.sqlite\")\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":2428,"value":"writeNwk = async (treeProxy) =>\n py`#${ete3datapy}\n${await treeProxy}.write(features=[\"sci_name\",\"rank\",\"dist\",\"name\"], format=0, )`","pinned":false,"hidden":false,"mode":"ojs"},{"id":573,"value":"//load the SQLite database from ETE3 in the notebook.\ntaxnamedb = {\n if (foundCached) {\n return;\n }\n ete3datapy;\n return SQLiteDatabaseClient.open(\n pyodide.FS.root.contents[\"lib\"].contents[\"python3.9\"].contents[\n \"site-packages\"\n ].contents[\"ete3_ncbidata-0.0.2.data\"].contents[\"data\"].contents[\n \"ete3_data\"\n ].contents[\"taxa.sqlite\"].contents\n );\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":1072,"value":"speciesToTaxidLookup = (sci_names) => {\n if (foundCached) {\n return;\n }\n const chunks = sqlOrChunk(sci_names);\n\n //for making the improved index in the sqlite database\n let indexBuilderHelper = (sci_names_chunk) =>\n []\n .concat(sci_names_chunk.map((d) => d.sci_name))\n .map((q) => 'spname=\"' + q + '\" COLLATE NOCASE')\n .join(\" OR \");\n\n /* avoid SQLite maximum depth bug without rebuilding sqlite db or client https://stackoverflow.com/posts/17032196 */\n const chunkedIndexBuilderHelper =\n \"(\" + chunks.map(indexBuilderHelper).join(`) OR (`) + \")\";\n\n return taxnamedb.query(\n `SELECT * from species where ${chunkedIndexBuilderHelper} AND NOT taxid = 214093`\n );\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":2858,"value":"sqlOrChunk = chunkArray(\n 250\n) /* avoid SQLite maximum depth bug https://stackoverflow.com/posts/17032196 */","pinned":false,"hidden":false,"mode":"ojs"},{"id":2855,"value":"chunkArray = (chunkSize) => (array) => {\n return array.reduce((acc, each, index, src) => {\n if (!(index % chunkSize)) {\n return [...acc, src.slice(index, index + chunkSize)];\n }\n return acc;\n }, []);\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":2916,"value":"// FileAttachment(\"diet-life - Sheet1.tsv\").tsv()","pinned":false,"hidden":false,"mode":"ojs"},{"id":580,"value":"dietlife = Array.of(\n ...new Set(\n (await FileAttachment(\"diet-life - Sheet1.tsv\").tsv())\n .map((d) => {\n const out = {};\n d[\"Significant Classification\"]\n .trim()\n .toLowerCase()\n .replace(\" family\", \"\")\n .replace(\" lettuce\", \"\")\n .replace(\" seeds\", \"\");\n out[\"sci_name\"] = d[\"Significant Classification\"];\n out[\"common_name\"] = d[\"Foods\"];\n return out;\n })\n .filter((d) => d.sci_name !== \"Animal\")\n .filter((d) => d.sci_name !== \"eudicot\")\n )\n)","pinned":false,"hidden":false,"mode":"ojs"},{"id":1106,"value":"$33","pinned":false,"hidden":false,"mode":"ojs"},{"id":1984,"value":"$34","pinned":false,"hidden":false,"mode":"ojs"},{"id":2007,"value":"$35","pinned":false,"hidden":false,"mode":"ojs"},{"id":2642,"value":"first90000OFFIngredients = FileAttachment(\"first90000Ingredients.json\").json()","pinned":false,"hidden":false,"mode":"ojs"},{"id":2687,"value":"camnats = (await FileAttachment(\"camnat-scinames@6.tsv\").tsv()).filter(\n (n) => n[\"dup or na\"] !== \"x\"\n)","pinned":false,"hidden":false,"mode":"ojs"},{"id":2749,"value":"// data = fetch(\n// `https://thadk-cors.herokuapp.com/https://foodb.ca/public/system/downloads/foodb_2020_04_07_json.zip`\n// ).then(async (response) => {\n// const unzipped = await FileAttachment.prototype.zip.apply(response);\n// return (await unzipped.file(\"foodb_2020_04_07_json/Food.json\")).text();\n// })","pinned":false,"hidden":false,"mode":"ojs"},{"id":2798,"value":"foodb_2020_food = (await FileAttachment(\"foodb_2020_Food@6.json\").json())\n .filter((n) => n.name_scientific !== null && n.name_scientific !== \"\")\n .map((n) => ({\n common_name: n.name,\n sci_name: n.name_scientific /*...n*/\n }))","pinned":false,"hidden":false,"mode":"ojs"},{"id":2824,"value":"wood_database = (await FileAttachment(\"wood_species@1.json\").json())","pinned":false,"hidden":false,"mode":"ojs"},{"id":2888,"value":"forestopia = FileAttachment(\"forestopia.json\").json()","pinned":false,"hidden":false,"mode":"ojs"},{"id":2898,"value":"/* http://www.phytotheca.com/phytotheca/ by CC-GROW */\nphytotheca = FileAttachment(\"phytotheca-species-checked.json\").json()","pinned":false,"hidden":false,"mode":"ojs"},{"id":2953,"value":"rainbowTomatoesGarden = (\n await d3.csv(\n \"https://docs.google.com/spreadsheets/d/e/2PACX-1vS0Gy9RXOxFDpA233k88HJ6hpewVbFqu0Fu0zA0L_qaX6m2XoGqCGvNIQ6-AG9cRaHPLA_22MVrNWzw/pub?gid=1886166847&single=true&output=csv\"\n )\n).map((n) => ({\n sci_name: n[\"sci_name\"],\n common_name: n[\"common_name\"],\n example_product: n[\"example_product\"],\n url: n[\"url\"]\n}))","pinned":false,"hidden":false,"mode":"ojs"},{"id":1764,"value":"$36","pinned":false,"hidden":false,"mode":"ojs"},{"id":443,"value":"ascii = async (treeNodesSciCommonNames) =>\n !foundCached &&\n py`\n${await ncbiTree(\n treeNodesSciCommonNames\n)}.get_ascii(compact=True,attributes=[\"sci_name\", \"rank\"])\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":5,"value":"md`## Dependencies`","pinned":false,"hidden":false,"mode":"ojs"},{"id":433,"value":"packagesPy = await pyodide.loadPackage([\n \"numpy\",\n \"micropip\",\n \"six\"\n // \"biopython\",\n // \"scipy\"\n // ,\"lxml\"\n // ,\"pandas\"\n])","pinned":false,"hidden":false,"mode":"ojs"},{"id":424,"value":"ete3py = {\n console.log(packagesPy);\n // return await pyodide.loadPackage(\"http://localhost:8000/ete3.js\");\n return await pyodide.loadPackage(\n \"https://thadk.net/pyodide_packages/ete3.js\"\n );\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":207,"value":"d3 = require('d3')","pinned":false,"hidden":false,"mode":"ojs"},{"id":205,"value":"color_scale = d3.scaleOrdinal(d3.schemeCategory10);","pinned":false,"hidden":false,"mode":"ojs"},{"id":222,"value":"selection_set = prepTreePhylotree.get_parsed_tags().length > 0\n ? prepTreePhylotree.get_parsed_tags()\n : [\"Foreground\"]","pinned":false,"hidden":false,"mode":"ojs"},{"id":218,"value":"nodeColorizer = function (element, data) {\ntry{\n var count_class = 0;\n\n selection_set.forEach (function (d,i) { if (data[d]) {count_class ++; element.style (\"fill\", color_scale(i), 'important');}});\n\n if (count_class > 1) {\n\n } else {\n if (count_class == 0) {\n element.style (\"fill\", null);\n }\n }\n}\ncatch (e) {\n\n}\n\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":229,"value":"edgeColorizer = function(element, data) {\n //console.log (data[current_selection_name]);\ntry {\n var count_class = 0;\n\n selection_set.forEach (function (d,i) { if (data[d]) {count_class ++; element.style (\"stroke\", color_scale(i), 'important');}});\n\n if (count_class > 1) {\n element.classed (\"branch-multiple\", true);\n } else\n if (count_class == 0) {\n element.style (\"stroke\", null)\n .classed (\"branch-multiple\", false);\n }\n}\ncatch (e) {\n}\n\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":202,"value":"colorNodesByName = function (element, data) {\n nodeColorizer (element, data);\n var m = (data.data.name).split (\"_\");\n if (m.length > 10) {\n element.style (\"stroke\", color_scale(_.lowerCase(m[9])));\n }\n };","pinned":false,"hidden":false,"mode":"ojs"},{"id":199,"value":"colorEdgesByTarget = function (element, data) {\n edgeColorizer(element, data);\n var m = data.target.data.name.split(\"_\");\n if (m.length > 10) {\n element.style(\"stroke\", color_scale(_.lowerCase(m[9])));\n }\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":10,"value":"Phylotree = require(\"phylotree@1.1.0\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":142,"value":"stylesheet = html``","pinned":false,"hidden":false,"mode":"ojs"},{"id":1057,"value":"import { view } from \"@tomlarkworthy/view\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":1045,"value":"import { dataEditor } from '@tomlarkworthy/dataeditor'","pinned":false,"hidden":false,"mode":"ojs"},{"id":2521,"value":"displayToggles[\"direction-layout\"] === \"Radial\" &&\n html``","pinned":false,"hidden":false,"mode":"ojs"}],"files":"$W37","stdlib":"1","titling":"auto"}