30:Tdee,rendering = { let width = 1190.551, height = 841.89, originalFontSize = 6, fontSize = originalFontSize; const svg = d3 .create("svg") .attr("viewBox", [0, 0, width, height]); svg.append("rect") .attr("fill", "#A7CAD3") .attr("width", width) .attr("height", height) // Legend margin svg.append("line") .attr("stroke", "#bbb") .attr("x1", 200) .attr("y1", 0) .attr("x2", 200) .attr("y2", height); const Legend = svg.append("image").attr("href", await FileAttachment("Legenda.png").url()) const g1 = svg.append("g"); const g = g1.append("g").attr("transform", `translate(${width / 2}, ${height / 2})`); const nodes = g.append("g").classed("nodes", true); const links = g.append("g").classed("links", true); const node = nodes .selectAll(".node-group") .data(spatialization.nodes) //.join("g") .enter() .append("g") .classed("node-group", true) .attr("transform", (d) => `translate(${d.attributes.x}, ${d.attributes.y})`) .style("cursor","pointer") .each(function (d) { drawNodes(this, fontSize, d) }) .call(drag()); const link = links.selectAll(".link-group") .data(spatialization.edges) .enter() .append("g") .classed("link-group", true) .each(function (d) {drawEdges(this, d)}); function drag() { function dragged(event) { d3.select(this).attr( "transform", (d) => `translate(${event.x}, ${event.y})` ).each((d)=>{ d.attributes.x = event.x; d.attributes.y = event.y; }); g.selectAll("line") .filter((d) => d.source === event.subject.key) .attr("x1", event.x) .attr("y1", event.y); g.selectAll("line") .filter((d) => d.target === event.subject.key) .attr("x2", event.x) .attr("y2", event.y); g.selectAll(".edges-head") .filter((d) => d.target === event.subject.key) .attr("cx", event.x) .attr("cy", event.y) } return d3.drag().on("drag", dragged) } const title = svg .append("text") .attr("x", 5) .attr("y", height-10) .attr("font-size", 16) .attr("font-family", "sans-serif") .attr("fill", "#FFF") .text(networkName); const spatializationValues = svg .append("text") .attr("x", width/2) .attr("y", height-10) .attr("font-size", 16) .attr("font-family", "sans-serif") .attr("fill", "#FFF") .attr("text-anchor", "middle") .text(`Rotation: ${alpha} – Gravity: ${gravity} – Scale: ${scalingRatio} – Edge Weight Influ: ${edgeWeightInfluence} – Weight GD: ${weightGD}`); const transformations = svg .append("text") .attr("x", width-5) .attr("y", height-10) .attr("font-size", 16) .attr("font-family", "sans-serif") .attr("fill", "#FFF") .attr("text-anchor", "end") .text(`K: 1 – X: 0 – Y: 0`); svg.call( d3.zoom().on("zoom", ({ transform }) => { const display = JSON.parse(JSON.stringify(transform)); display.x = Math.round(display.x * 100) / 100 display.y = Math.round(display.y * 100) / 100 display.k = Math.round(display.k * 100) / 100 transformations.text(`K: ${display.k} – X: ${display.x} – Y: ${display.y}`) g1.attr("transform", transform); //fontSize = originalFontSize / transform.k; nodes .selectAll(".label") .attr("font-size", fontSize) .selectAll(".labelRow") .attr("dy", fontSize); }) ); return svg.node(); }31:T537,spatialization = { // we define original positions so that force-atlas2 returns always the same spatiualization graphologyLayout.circular.assign(graph, {scale: 1000}); const customSettings = { adjustSizes: false, // should the node's sizes be taken into account? barnesHutOptimize: false, // whether to use the Barnes-Hut approximation to compute repulsion barnesHutTheta: 0.1, // Barnes-Hut approximation theta parameter edgeWeightInfluence: edgeWeightInfluence, // influence of the edge's weights on the layout gravity: gravity, // strength of the layout's gravity. linLogMode: false, // whether to use Noack's LinLog model. outboundAttractionDistribution: false, // ??? scalingRatio: scalingRatio, slowDown: 10, strongGravityMode: false } forceAtlas2.assign(graph, { iterations: 5000, settings: customSettings }); //noverlap.assign(graph, {settings:{margin:5}}); // Rotate the graph graph.forEachNode((node, attributes) => { const x = attributes.x, y = attributes.y, c = {a:0, b:0}; const x1 = (x - c.a)*Math.cos(alpha) - (y - c.b)*Math.sin(alpha) + c.a; const y1 = (x-c.a)*Math.sin(alpha) + (y - c.b)*Math.cos(alpha) + c.b; attributes.x = x1; attributes.y = y1; }); return graph.export(); }32:Tdd6,function drawNodes(element, fontSize, data) { switch (data.attributes.type) { case "Avant-text": element.appendChild(d3.select(avantText).clone(true).node()); break; case "Diary Entry": element.appendChild(d3.select(diaryEntry).clone(true).node()); break; case "Book": element.appendChild(d3.select(book).clone(true).node()); break; case "PeriodicalArticle": element.appendChild(d3.select(article).clone(true).node()); break; case "Periodical": element.appendChild(d3.select(periodical).clone(true).node()); break; case "Missing node type": element.appendChild(d3.select(missingType).clone(true).node()); break; case "Missing node in dataset": element.appendChild(d3.select(missingNode).clone(true).node()); break; default: element.appendChild(d3.select(partOf).clone(true).node()); } if (data.attributes.geneticStage==="MAI") { let side = 17; let gs_width = 1; let gs_rx = 4; switch (data.attributes.geneticStage) { case "Clean copy": break; case "Final manuscript": side = 18; gs_width= 2; gs_rx = 5; break; case "Corrected proofs": side = 20; gs_width= 3; gs_rx = 6; break; } d3.select(element).append("rect") .attr("fill","none") .attr("stroke","#6BA3AA") .attr("stroke-width", gs_width) .attr("stroke-location","outside") .attr("x",-side/2) .attr("y",-side/2) .attr("width",side) .attr("height", side) .attr("rx", gs_rx) } if (data.attributes.geneticStage) { let side = 17; let gs_width = 1; let gs_rx = 4; switch (data.attributes.geneticStage) { case "Clean copy": break; case "Final manuscript": side = 18; gs_width= 2; gs_rx = 5; break; case "Corrected proofs": side = 20; gs_width= 3; gs_rx = 6; break; } d3.select(element).select("*") .attr("stroke","#6BA3AA") .attr("stroke-alignment","outer") .attr("stroke-width", gs_width) .attr("stroke-location","outside") } if(redNodes.indexOf(data.key)!==-1){ d3.select(element).select("g path").attr("fill","#ED6056").style("fill","#ED6056"); } if (data.attributes.visuals) { element.appendChild(d3.select(hasVisuals).clone(true).node()); } const label = d3 .select(element) .append("text") .classed("label", true) .attr("pointer-events","none") .attr("opacity", 0.8) .attr("text-anchor", "middle") .attr("font-size", fontSize) .attr("font-family", "'Helmet', sans-serif") .attr("y", 8) .attr("fill", "#fff"); label.append("tspan").attr("font-weight", "bold").text(data.attributes.title); if (data.attributes.date) { label .append("tspan") .classed("labelRow", true) .attr("x", 0) .attr("dy", fontSize) .attr("font-family", "'DM Mono', monospace") .text(data.attributes.date); } if (data.attributes.shelfmark) { label .append("tspan") .classed("labelRow", true) .attr("x", 0) .attr("dy", fontSize) .attr("font-family", "monospace") .text(data.attributes.shelfmark); } }33:T7b2,function drawEdges(element, data){ const group = d3.select(element) group.append("line") .attr( "x1", (data) => spatialization.nodes.find((dd) => dd.key === data.source).attributes.x ) .attr( "y1", (data) => spatialization.nodes.find((dd) => dd.key === data.source).attributes.y ) .attr( "x2", (data) => spatialization.nodes.find((dd) => dd.key === data.target).attributes.x ) .attr( "y2", (data) => spatialization.nodes.find((dd) => dd.key === data.target).attributes.y ) .attr("stroke", function (data) { switch (data.attributes.category) { case "geneticDossier": return "#ED6056"; break; case "msPartIsPartOf": return "#FFF"; break; case "pubPartIsPartOf": return "#FFF"; break; default: return "#333"; } }) .attr("stroke-width", 0.75) .attr("stroke-dasharray", (data) => { if (data.attributes.category.includes("IsRewritten")) { return 2; } else { return 0; } }); group.append("circle") .classed("edges-head", true) .attr( "cx", (data) => spatialization.nodes.find((dd) => dd.key === data.target).attributes.x ) .attr( "cy", (data) => spatialization.nodes.find((dd) => dd.key === data.target).attributes.y ) .attr("r", 1) .attr("fill", function (data) { switch (data.attributes.category) { case "geneticDossier": return "#ED6056"; break; case "msPartIsPartOf": return "#FFF"; break; case "pubPartIsPartOf": return "#FFF"; break; default: return "#333"; } }) }34:T58a,nodes = { const nodes = []; let obj; edges.forEach((edge) => { if (nodes.map((d) => d.id).indexOf(edge.source) === -1) { const sourceNode = json.find((d) => d["@id"] === edge.source); obj = { id: sourceNode["@id"], title: getTitle(sourceNode), type: edge.sourceType, shelfmark: getShelfmark(sourceNode), date: getDate(sourceNode), visuals: getVisuals(sourceNode), geneticStage: getGeneticStage(sourceNode) } obj = sanitizeStringsForXML(obj) nodes.push(obj); } if (nodes.map((d) => d.id).indexOf(edge.target) === -1) { const targetNode = json.find((d) => d["@id"] === edge.target); obj = { id: edge.target, title: "Missing node in dataset", type: edge.targetType, shelfmark: "Missing node in dataset", date: "Missing node in dataset", visuals: "Missing node in dataset", geneticStage: "Missing node in dataset" }; if (targetNode) { obj = { id: edge.target, title: getTitle(targetNode), type: edge.targetType, shelfmark: getShelfmark(targetNode), date: getDate(targetNode), visuals: getVisuals(targetNode), geneticStage: getGeneticStage(targetNode) }; } obj = sanitizeStringsForXML(obj) nodes.push(obj); } }); return nodes; }35:T5d7,function removeXMLInvalidChars(str, removeDiscouragedChars) { // By John Doherty https://gist.github.com/john-doherty/b9195065884cdbfd2017a4756e6409cc // remove everything forbidden by XML 1.0 specifications, plus the unicode replacement character U+FFFD var regex = /((?:[\0-\x08\x0B\f\x0E-\x1F\uFFFD\uFFFE\uFFFF]|[\uD800-\uDBFF](?![\uDC00-\uDFFF])|(?:[^\uD800-\uDBFF]|^)[\uDC00-\uDFFF]))/g; // ensure we have a string str = String(str || '').replace(regex, ''); if (removeDiscouragedChars) { // remove everything discouraged by XML 1.0 specifications regex = new RegExp( '([\\x7F-\\x84]|[\\x86-\\x9F]|[\\uFDD0-\\uFDEF]|(?:\\uD83F[\\uDFFE\\uDFFF])|(?:\\uD87F[\\uDF' + 'FE\\uDFFF])|(?:\\uD8BF[\\uDFFE\\uDFFF])|(?:\\uD8FF[\\uDFFE\\uDFFF])|(?:\\uD93F[\\uDFFE\\uD' + 'FFF])|(?:\\uD97F[\\uDFFE\\uDFFF])|(?:\\uD9BF[\\uDFFE\\uDFFF])|(?:\\uD9FF[\\uDFFE\\uDFFF])' + '|(?:\\uDA3F[\\uDFFE\\uDFFF])|(?:\\uDA7F[\\uDFFE\\uDFFF])|(?:\\uDABF[\\uDFFE\\uDFFF])|(?:\\' + 'uDAFF[\\uDFFE\\uDFFF])|(?:\\uDB3F[\\uDFFE\\uDFFF])|(?:\\uDB7F[\\uDFFE\\uDFFF])|(?:\\uDBBF' + '[\\uDFFE\\uDFFF])|(?:\\uDBFF[\\uDFFE\\uDFFF])(?:[\\0-\\t\\x0B\\f\\x0E-\\u2027\\u202A-\\uD7FF\\' + 'uE000-\\uFFFF]|[\\uD800-\\uDBFF][\\uDC00-\\uDFFF]|[\\uD800-\\uDBFF](?![\\uDC00-\\uDFFF])|' + '(?:[^\\uD800-\\uDBFF]|^)[\\uDC00-\\uDFFF]))', 'g'); str = str.replace(regex, ''); } return str; }36:T6ab,function swatches({ color, columns = null, format = x => x, swatchSize = 15, swatchWidth = swatchSize, swatchHeight = swatchSize, marginLeft = 0 }) { const id = DOM.uid().id; if (columns !== null) return html`

${color.domain().map(value => { const label = format(value); return html`

${document.createTextNode(label)}

`; })}

`; return html`

${color.domain().map(value => html`${document.createTextNode(format(value))}`)}

`; }37:[{"id":"723774af9e78649f1d841f6b21a6029b083fa9d341f53a191e8809117f6b252480b0a6fd82a1f58b19a06d178a1cfe3ec109a3c4fcdee60ebe692216cb64063e","href":"https://static.observableusercontent.com/files/723774af9e78649f1d841f6b21a6029b083fa9d341f53a191e8809117f6b252480b0a6fd82a1f58b19a06d178a1cfe3ec109a3c4fcdee60ebe692216cb64063e","name":"Legenda.png","type":"image/png","lastModified":1637710224753.03,"size":39205},{"id":"641b9e66369b702eba35a165718a18f35bf9ab900cdfd7324dc8a6b2230d93ba1bcb29f037c2da1726f78eeafd5a5a547104d2d84297378585492aab9c3366c6","href":"https://static.observableusercontent.com/files/641b9e66369b702eba35a165718a18f35bf9ab900cdfd7324dc8a6b2230d93ba1bcb29f037c2da1726f78eeafd5a5a547104d2d84297378585492aab9c3366c6","name":"AvantText.svg","type":"image/svg+xml","lastModified":1637710224753.03,"size":236},{"id":"1b8330d0ed17808c695d6d2bfc35805599e3d67ed55bb6217ee7fd547f171a4d1ca658e297971e2bbc453ffec910381b53b5face3eab20aefe49d297e2d8fb5f","href":"https://static.observableusercontent.com/files/1b8330d0ed17808c695d6d2bfc35805599e3d67ed55bb6217ee7fd547f171a4d1ca658e297971e2bbc453ffec910381b53b5face3eab20aefe49d297e2d8fb5f","name":"Part.svg","type":"image/svg+xml","lastModified":1637710224753.03,"size":200},{"id":"65699b4a605048d6507af82c7e5c234bb3975fc1dc53c17a1e3b6aa19243f5c2f492e1ed547122858dd0534ae7691a78333ce6c08b827ace9e8b4e99ac17c4c2","href":"https://static.observableusercontent.com/files/65699b4a605048d6507af82c7e5c234bb3975fc1dc53c17a1e3b6aa19243f5c2f492e1ed547122858dd0534ae7691a78333ce6c08b827ace9e8b4e99ac17c4c2","name":"Missing-Node.svg","type":"image/svg+xml","lastModified":1637710224753.03,"size":958},{"id":"4efe17303c65b8d8b9c4a56c9f4fe9121f166a21862ff917c1eaaff6ac05c8b2116ad8ed3ac8b0c3ddb784a91264047c8cb1fc069377c699a72abc8ced55b999","href":"https://static.observableusercontent.com/files/4efe17303c65b8d8b9c4a56c9f4fe9121f166a21862ff917c1eaaff6ac05c8b2116ad8ed3ac8b0c3ddb784a91264047c8cb1fc069377c699a72abc8ced55b999","name":"Book.svg","type":"image/svg+xml","lastModified":1637710224753.03,"size":643},{"id":"636f8d6688af7a44faa2973ca1d768a13ca63438fdfef2b9757583519ba727305ef496998f612b3ffa4de7862660b53de539e6e4fcdc5e4a786b0128232964a5","href":"https://static.observableusercontent.com/files/636f8d6688af7a44faa2973ca1d768a13ca63438fdfef2b9757583519ba727305ef496998f612b3ffa4de7862660b53de539e6e4fcdc5e4a786b0128232964a5","name":"Diary.svg","type":"image/svg+xml","lastModified":1637710224753.03,"size":444},{"id":"e1e1ecf33b8624d027ebc2f21ca667e882bc750a1f665336f960892bd0b8effb8cd3f2c196c450efba3d85d5d8905f769228b9952b1ecc6ae863de86df7b6c53","href":"https://static.observableusercontent.com/files/e1e1ecf33b8624d027ebc2f21ca667e882bc750a1f665336f960892bd0b8effb8cd3f2c196c450efba3d85d5d8905f769228b9952b1ecc6ae863de86df7b6c53","name":"hasVisuals.svg","type":"image/svg+xml","lastModified":1637710224753.03,"size":860},{"id":"0e8055d5a9bb2f59b8bc3767ed0ac217a7328c503e5dc6a7f2b4e217eea2fabdca839622be242fcca8ade6eeb62c3ff0333c00d889fdbd78fb53cbd8d441f026","href":"https://static.observableusercontent.com/files/0e8055d5a9bb2f59b8bc3767ed0ac217a7328c503e5dc6a7f2b4e217eea2fabdca839622be242fcca8ade6eeb62c3ff0333c00d889fdbd78fb53cbd8d441f026","name":"Article.svg","type":"image/svg+xml","lastModified":1637710224753.03,"size":1047},{"id":"77d66ae5c9422ca804a9ea7110736c88b6b31c2e827b860a0e46b6e502b9f7865947d8b341133620985b73249bb3b798319058156f579eba68543b2fcb6f88fb","href":"https://static.observableusercontent.com/files/77d66ae5c9422ca804a9ea7110736c88b6b31c2e827b860a0e46b6e502b9f7865947d8b341133620985b73249bb3b798319058156f579eba68543b2fcb6f88fb","name":"Periodical@1.svg","type":"image/svg+xml","lastModified":1637710224753.03,"size":705},{"id":"f1ed1a76c80bdd90063e0d39ecdb1a4c717e12392a187f8504e60bed1db0b71d21242ede89ac53cef9f424ff07e93b9df63b0052ff20d6809e26ab4523834dc0","href":"https://static.observableusercontent.com/files/f1ed1a76c80bdd90063e0d39ecdb1a4c717e12392a187f8504e60bed1db0b71d21242ede89ac53cef9f424ff07e93b9df63b0052ff20d6809e26ab4523834dc0","name":"Screenshot 2021-11-22 at 12.11.07.png","type":"image/png","lastModified":1637710224753.03,"size":144666},{"id":"15c6650f98299c060e37d3727e9062412c748ac65bce8f951f2bbc76c0b247b9d7f1cf3a3844b4316f7045e5a4851c7ff790ee1cc7d0a065cb706fd40458eec3","href":"https://static.observableusercontent.com/files/15c6650f98299c060e37d3727e9062412c748ac65bce8f951f2bbc76c0b247b9d7f1cf3a3844b4316f7045e5a4851c7ff790ee1cc7d0a065cb706fd40458eec3","name":"bypass genetic dossier small.jpg","type":"image/jpeg","lastModified":1637710224753.03,"size":36675},{"id":"fa61c4f6529636c8c8ccb1bd633c2f6663a43110239661b24e27c555e3f0b5f31d1ffcb0c64971b9d870fe7b483b43c8d598b090875114880ce7f14035c27f8a","href":"https://static.observableusercontent.com/files/fa61c4f6529636c8c8ccb1bd633c2f6663a43110239661b24e27c555e3f0b5f31d1ffcb0c64971b9d870fe7b483b43c8d598b090875114880ce7f14035c27f8a","name":"Missing-Type.svg","type":"image/svg+xml","lastModified":1637710224753.03,"size":1502}] 2e:{"title":"Snodaroud","cells":[{"id":0,"value":"# Snodaroud\n*[@iosonosempreio](https://observablehq.com/@iosonosempreio), [@andreabenedetti](https://observablehq.com/@andreabenedetti), [@vpallacci](https://observablehq.com/@vpallacci)*\n\nThis notebook creates visual network graphs about the genetic process of the literary works of Gustave Roud. It reworks the original data structure, identifies nodes and edges, and bypasses nodes corresponding to *genetic dossiers* and *genetic dossier parts*. The project is part of [«Gustave Roud, Œuvres complètes»](https://github.com/gustaveroudproject/geneticNetworksDataViz).\n\nTo start, select a genetic network. Files are hosted on Github and are in `jsonld` format:","pinned":false,"hidden":false,"mode":"md"},{"id":7,"value":"viewof dataUrl = {\n let data = await d3.json(\"https://raw.githubusercontent.com/gustaveroudproject/geneticNetworksDataViz/master/data/dataForObservable.json\");\n return Inputs.select(data)\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":12,"value":"networkName = dataUrl.split(\"/\").at(-1).split(\".\").at(0)","pinned":false,"hidden":false,"mode":"ojs"},{"id":89,"value":"## Visualization","pinned":false,"hidden":false,"mode":"md"},{"id":218,"value":"$30","pinned":false,"hidden":false,"mode":"ojs"},{"id":21,"value":"swatches({\n color: d3.scaleOrdinal(\n [\"Genetic dossier\", \"Is Part Of\", \"Other\"],\n [\"#ED6056\", \"#FFF\", \"#333\"]\n )\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":526,"value":"viewof alpha = Inputs.range([0,Math.PI*2],{step: 0.01, value: 0, label:\"Rotation angle\"})","pinned":false,"hidden":false,"mode":"ojs"},{"id":15,"value":"viewof gravity = Inputs.range([0.1, 5], {step: 0.1, value: 1, label: \"Gravity\"})","pinned":false,"hidden":false,"mode":"ojs"},{"id":17,"value":"viewof scalingRatio = Inputs.range([1, 150], {step: 1, value: 35, label: \"Scale\"})","pinned":false,"hidden":false,"mode":"ojs"},{"id":18,"value":"viewof edgeWeightInfluence = Inputs.range([0, 5], {step: 0.1, value: 1, label: \"Edge weight influence\"})","pinned":false,"hidden":false,"mode":"ojs"},{"id":384,"value":"viewof weightGD = Inputs.range([0.1,5],{step: 0.1, value: 1.6, label:\"Weight edges genetic dossier\"})","pinned":false,"hidden":false,"mode":"ojs"},{"id":278,"value":"DOM.download(() => serialize(rendering), networkName, `Save as ${networkName}.svg`)","pinned":false,"hidden":false,"mode":"ojs"},{"id":368,"value":"DOM.download(() => rasterize(rendering), networkName, `Save as ${networkName}.png`)","pinned":false,"hidden":false,"mode":"ojs"},{"id":202,"value":"#### 🆓 Functions for network visualization","pinned":false,"hidden":false,"mode":"md"},{"id":206,"value":"$31","pinned":false,"hidden":false,"mode":"ojs"},{"id":209,"value":"redNodes = spatialization.edges.filter(edge=>edge.attributes.category===\"geneticDossier\").map(edge=>edge.target)","pinned":false,"hidden":false,"mode":"ojs"},{"id":212,"value":"$32","pinned":false,"hidden":false,"mode":"ojs"},{"id":215,"value":"$33","pinned":false,"hidden":false,"mode":"ojs"},{"id":94,"value":"## Data manipulation","pinned":false,"hidden":false,"mode":"md"},{"id":98,"value":"1️⃣ Load the data and do some cleaning","pinned":false,"hidden":false,"mode":"md"},{"id":101,"value":"json = {\n const jsondl = await d3.text(dataUrl);\n const string = jsondl\n .replaceAll(\"http://rdfh.ch/0112/\",\"\")\n .replaceAll(\"http://rdfh.ch/0112/\",\"\")\n .replaceAll(\"http://www.knora.org/ontology/0112/roud-oeuvres#\",\"\")\n return JSON.parse(string)\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":106,"value":"2️⃣ Create array of edges against a list of connection types that is manually compiled","pinned":false,"hidden":false,"mode":"md"},{"id":116,"value":"connectionsNames = [\n \"msIsAvantTextInGeneticDossier\",\n \"msIsAvantTextInGeneticDossierPart\",\n \"msIsReusedInDossier\",\n \"msIsReusedInDossierPart\",\n \"msIsRewrittenInMs\",\n \"msIsRewrittenInMsPart\",\n \n \"msPartIsPartOf\",\n \"msPartIsReusedInDossier\",\n \"msPartIsReusedInDossierPart\",\n \"msPartIsRewrittenInMs\",\n \"msPartIsRewrittenInMsPart\",\n \n \"geneticDossierResultsInPublication\",\n \"geneticDossierPartResultsInPubPart\",\n \n \"pubPartIsPartOf\",\n \"pubPartIsReusedInDossier\",\n \"pubPartIsReusedInDossierPart\",\n \n \"publicationIsRepublishedDossier\",\n \"publicationIsReusedInDossier\",\n \"publicationIsReusedInDossierPart\",\n\n \"isPublishedInPeriodical\"\n]","pinned":false,"hidden":false,"mode":"ojs"},{"id":119,"value":"edges = {\n const edges = [];\n json.forEach((d) => {\n connectionsNames.forEach((edge) => {\n //console.log(edge, d.manuscriptHasDateComputable);\n if (d.hasOwnProperty(edge)) {\n const source = d[\"@id\"];\n const source_type = recognizeAvantText(\n Array.isArray(d[\"@type\"]) ? d[\"@type\"][0] : \"Missing Type\",\n d\n );\n const type = edge;\n const weight = 1;\n\n d[edge].forEach((target) => {\n const target_id = target[\"@id\"] ? target[\"@id\"] : \"miss\" + ObjectId();\n const target_type = recognizeAvantText(\n getNodeType(json.find((dd) => dd[\"@id\"] === target_id)),\n d\n );\n\n const obj = {\n source: source,\n sourceType: source_type,\n target: target_id,\n targetType: target_type,\n type: type,\n weight: weight\n };\n\n edges.push(obj);\n });\n }\n });\n });\n return edges;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":122,"value":"3️⃣ Create array of nodes","pinned":false,"hidden":false,"mode":"md"},{"id":126,"value":"$34","pinned":false,"hidden":false,"mode":"ojs"},{"id":129,"value":"4️⃣ Bypass the genetic dossiers![bypass genetic dossier.jpg](${await FileAttachment(\"bypass genetic dossier small.jpg\").url()})","pinned":false,"hidden":false,"mode":"md"},{"id":136,"value":"cleanNodes = nodes.filter(node=>node.type!==\"GeneticDossierPart\"&&node.type!==\"GeneticDossier\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":291,"value":"Inputs.table(cleanNodes)","pinned":false,"hidden":false,"mode":"ojs"},{"id":133,"value":"cleanEdges = {\n const cleanEdges = [];\n edges.forEach(edge => {\n if (edge.targetType !== \"GeneticDossierPart\" && edge.targetType !== \"GeneticDossier\") {\n if (edge.sourceType !== \"GeneticDossierPart\" && edge.sourceType !== \"GeneticDossier\") {\n cleanEdges.push(edge)\n }\n } else {\n if (edge.targetType === \"GeneticDossierPart\" || edge.targetType === \"GeneticDossier\") {\n const resultingEdge = edges.find(d=>d.source===edge.target)\n const newEdge = {\n ...edge,\n target: resultingEdge.target,\n targetType: resultingEdge.targetType,\n type: \"geneticDossier\",\n weight: weightGD\n };\n cleanEdges.push(newEdge)\n }\n }\n });\n return cleanEdges\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":295,"value":"Inputs.table(cleanEdges)","pinned":false,"hidden":false,"mode":"ojs"},{"id":139,"value":"#### 🆓 Functions for data manipulation","pinned":false,"hidden":false,"mode":"md"},{"id":145,"value":"function getNodeType(node){\n let type = \"Missing node in dataset\"\n if (node){\n type = Array.isArray(node[\"@type\"])?node[\"@type\"][0]:\"Missing node type\"\n }\n return type\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":147,"value":"function getShelfmark(node) {\n let value = null;\n \n let keys = Object.keys(node).filter(d => d.toLowerCase().includes(\"shelfmark\"));\n\n if (keys.length > 0) {\n const shelfmarkKey = keys[0]\n value = node[shelfmarkKey][0][\"@value\"]\n }\n \n return value;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":149,"value":"function getTitle(node) {\n let value = null;\n let keys = Object.keys(node).filter(d => d.toLowerCase().includes(\"title\"));\n\n if (keys.length > 0) {\n const titleKey = keys[0]\n value = node[titleKey][0][\"@value\"]\n }\n \n return value;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":154,"value":"getDate = function (node) {\n let _date = null;\n let tempKey = Object.keys(node).find((d) => d.includes(\"DateComputable\"));\n if (tempKey) {\n _date = node[tempKey];\n }\n if (!tempKey) {\n tempKey = Object.keys(node).find((d) => d.includes(\"HasDate\"));\n if (tempKey) {\n _date = node[tempKey];\n }\n }\n _date = Array.isArray(_date) ? _date[0][\"@value\"] : _date;\n return _date;\n // keep here for reference\n const dateNames = [\n \"manuscriptHasEstablishedDateComputable\",\n \"publicationHasDate\"\n ];\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":158,"value":"getVisuals = function(node) {\n // check if node has photos or illustrations\n let hasVisuals = null;\n hasVisuals = Object.keys(node).filter(d=>d.includes(\"HasIllustration\")||d.includes(\"HasPhoto\")).length > 0\n return hasVisuals;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":161,"value":"function getGeneticStage(node) {\n let geneticStage = null;\n if (\"hasGeneticStage\" in node) {\n geneticStage = node[\"hasGeneticStage\"][0][\"@value\"]\n }\n return geneticStage;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":143,"value":"recognizeAvantText = function(type, datum) {\n if (type === \"Manuscript\") {\n const keys = Object.keys(datum);\n const temp = keys.filter(d=>d.includes(\"IsAvantText\"))\n if (temp.length === 0) {\n type = \"Diary Entry\"\n } else {\n type = \"Avant-text\"\n }\n }\n return type;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":167,"value":"## Network structure","pinned":false,"hidden":false,"mode":"md"},{"id":313,"value":"viewof nodesSize = Inputs.range([0,25],{step: 1, value: 10, label:\"Nodes size\"})","pinned":false,"hidden":false,"mode":"ojs"},{"id":175,"value":"graph = {\n // init Graph object\n const graph = new Graph();\n\n // load and add nodes\n cleanNodes.forEach((n,i)=>{\n const attributes = {...n, size: nodesSize}\n // const x = Math.random(), y=Math.random();\n // attributes.x = x;\n // attributes.y = y;\n graph.addNode(n.id, attributes)\n });\n\n cleanEdges.forEach(e=>{\n const attributes = {\n category: e.type,\n weight: e.weight\n }\n graph.addEdge(e.source, e.target, attributes)\n });\n\n return graph;\n}","pinned":true,"hidden":false,"mode":"ojs"},{"id":181,"value":"#### Generate the .gexf","pinned":false,"hidden":false,"mode":"md"},{"id":187,"value":"gexfString = gexf.write(graph, {\n formatNode: function(key, attributes) { \n return {\n label: attributes.title,\n attributes: {\n type: attributes.type,\n shelfmark: attributes.shelfmark,\n date: attributes.date,\n geneticStage: attributes.geneticStage,\n hasVisuals: attributes.visuals,\n originalId: attributes.originalId\n }\n };\n },\n formatEdge: function(key, attributes) {\n return {\n label: attributes.type,\n weight: attributes.weight,\n attributes: {\n category: attributes.category\n }\n };\n }\n});","pinned":false,"hidden":false,"mode":"ojs"},{"id":194,"value":"button(gexfString, `${networkName}.gexf`)","pinned":false,"hidden":false,"mode":"ojs"},{"id":23,"value":"# Appendix","pinned":false,"hidden":false,"mode":"md"},{"id":73,"value":"import {button} from \"@densitydesign/download-data-button\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":76,"value":"import {ObjectId} from \"@densitydesign/mongodb-objectid-generator\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":275,"value":"import {serialize, rasterize} from \"@mbostock/saving-svg\"","pinned":true,"hidden":false,"mode":"ojs"},{"id":80,"value":"$35","pinned":false,"hidden":false,"mode":"ojs"},{"id":83,"value":"function sanitizeStringsForXML(object){\n for (let key in object) {\n object[key] = removeXMLInvalidChars(object[key], true)\n }\n return object;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":29,"value":"function entity(character) {\n return `&#${character.charCodeAt(0).toString()};`;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":27,"value":"$36","pinned":false,"hidden":false,"mode":"ojs"},{"id":34,"value":"linkColor = d3.scaleOrdinal().range([\"#ED6056\", \"#ED6056\", \"#333\", \"#FFF\", \"#333\", \"#FFF\", \"#ED6056\"]).domain(d3.map(cleanEdges, e => e.type).sort(d3.ascending))","pinned":false,"hidden":false,"mode":"ojs"},{"id":234,"value":"***Network graph***","pinned":false,"hidden":false,"mode":"md"},{"id":241,"value":"We use [Graphology](https://graphology.github.io/)","pinned":false,"hidden":false,"mode":"md"},{"id":171,"value":"Graph = require(\"graphology\")","pinned":true,"hidden":false,"mode":"ojs"},{"id":173,"value":"forceAtlas2 = require(\"https://bundle.run/graphology-layout-forceatlas2@0.6.1\")","pinned":true,"hidden":false,"mode":"ojs"},{"id":393,"value":"graphologyLayout = require(\"https://bundle.run/graphology-layout@0.4.0\")","pinned":true,"hidden":false,"mode":"ojs"},{"id":302,"value":"noverlap = require(\"https://bundle.run/graphology-layout-noverlap@0.4.1\")","pinned":true,"hidden":false,"mode":"ojs"},{"id":189,"value":"gexf = require(\"https://bundle.run/graphology-gexf@0.8.1\");","pinned":true,"hidden":false,"mode":"ojs"},{"id":38,"value":"***Graphical elements***","pinned":false,"hidden":false,"mode":"md"},{"id":47,"value":"FileAttachment(\"Screenshot 2021-11-22 at 12.11.07.png\").image()","pinned":false,"hidden":false,"mode":"ojs"},{"id":43,"value":"function extractVectors(text) {\n const document = (new DOMParser).parseFromString(text, \"image/svg+xml\");\n // extrapolate the svg node from its original context\n const svg = d3.select(document.documentElement).remove();\n const gliph = svg.select(\"*\")\n return gliph.node()\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":50,"value":"article = {\n const text = await FileAttachment(\"Article.svg\").text();\n return extractVectors(text);\n}","pinned":true,"hidden":false,"mode":"ojs"},{"id":53,"value":"avantText = {\n const text = await FileAttachment(\"AvantText.svg\").text();\n return extractVectors(text);\n}","pinned":true,"hidden":false,"mode":"ojs"},{"id":55,"value":"book = {\n const text = await FileAttachment(\"Book.svg\").text();\n return extractVectors(text);\n}","pinned":true,"hidden":false,"mode":"ojs"},{"id":58,"value":"diaryEntry = {\n const text = await FileAttachment(\"Diary.svg\").text();\n return extractVectors(text);\n}","pinned":true,"hidden":false,"mode":"ojs"},{"id":61,"value":"hasVisuals = {\n const text = await FileAttachment(\"hasVisuals.svg\").text();\n return extractVectors(text);\n}","pinned":true,"hidden":false,"mode":"ojs"},{"id":63,"value":"partOf = {\n const text = await FileAttachment(\"Part.svg\").text();\n return extractVectors(text);\n}","pinned":true,"hidden":false,"mode":"ojs"},{"id":65,"value":"periodical = {\n const text = await FileAttachment(\"Periodical@1.svg\").text();\n return extractVectors(text);\n}","pinned":true,"hidden":false,"mode":"ojs"},{"id":68,"value":"missingType = {\n const text = await FileAttachment(\"Missing-Type.svg\").text();\n return extractVectors(text);\n}","pinned":true,"hidden":false,"mode":"ojs"},{"id":70,"value":"missingNode = {\n const text = await FileAttachment(\"Missing-Node.svg\").text();\n return extractVectors(text);\n}","pinned":true,"hidden":false,"mode":"ojs"}],"files":"$W37","stdlib":"1","titling":"auto"}