From 8f4991e653b12c43c1275bc3c1d88ecaa9ab5c68 Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Thu, 5 May 2022 15:16:18 -0400 Subject: [PATCH 01/68] create graph.js and export Tree class --- frontend/src/utils/graph.js | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 frontend/src/utils/graph.js diff --git a/frontend/src/utils/graph.js b/frontend/src/utils/graph.js new file mode 100644 index 0000000000..fc12364b78 --- /dev/null +++ b/frontend/src/utils/graph.js @@ -0,0 +1,24 @@ +/* + * A class that represents the tree data structure + */ +class Tree { + constructor(data, children = []) { + this.data = data; + this.neighbors = children; + } + + /* + * Performs a right fold with function f. + * The f is a function that takes the data + * of current node and a list of children + * transformed by f + */ + fold(f) { + return f( + this.data, + this.neighbors.map((v) => v.fold(f)) + ) + } +} + +export default Tree; From df4433e816e3ebabc5c806c2732310d66864913f Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Thu, 5 May 2022 15:16:37 -0400 Subject: [PATCH 02/68] add Lineage section with JSON visualization --- .../samples/details/SampleDetailsContent.js | 104 ++++++++++++++++++ 1 file changed, 104 insertions(+) diff --git a/frontend/src/components/samples/details/SampleDetailsContent.js b/frontend/src/components/samples/details/SampleDetailsContent.js index 7324683a2c..eb522b481f 100644 --- a/frontend/src/components/samples/details/SampleDetailsContent.js +++ b/frontend/src/components/samples/details/SampleDetailsContent.js @@ -40,6 +40,7 @@ import { withLibrary, withIndex } from "../../../utils/withItem"; +import Tree from "../../../utils/graph"; import ExperimentRunsListSection from "../../shared/ExperimentRunsListSection"; const { Title, Text } = Typography; @@ -85,6 +86,7 @@ const mapStateToProps = state => ({ indicesByID: state.indices.itemsByID, usersByID: state.users.itemsByID, projectsByID: state.projects.itemsByID, + protocolsByID: state.protocols.itemsByID, }); const actionCreators = {getSample, listVersions}; @@ -100,6 +102,7 @@ const SampleDetailsContent = ({ indicesByID, usersByID, projectsByID, + protocolsByID, getSample, listVersions }) => { @@ -129,6 +132,24 @@ const SampleDetailsContent = ({ const concentration_nm = library && library.concentration_nm ? parseFloat(library.concentration_nm).toFixed(3) : undefined const [sampleMetadata, setSampleMetadata] = useState([]) + const tree = generateLineageData(samplesByID, processMeasurementsByID, protocolsByID, sample) + + // convert Tree class into an object that is compatible + // with bkrem/react-d3-tree + const root = tree.fold((data, children) => { + const [sample, process] = data + return { + name: sample?.name, + attributes: { + id: sample?.id, + ...( + process ? { protocol: protocolsByID[process.protocol]?.name } : {} + ) + }, + children: children + } + }) + // TODO: This spams API requests if (!samplesByID[id]) getSample(id); @@ -299,6 +320,8 @@ const SampleDetailsContent = ({ + Lineage + 
{JSON.stringify(root, null, 2)}
@@ -331,6 +354,87 @@ const SampleDetailsContent = ({ ; }; +function generateLineageData(samplesByID, processMeasurementsByID, protocolsByID, sample) { + let root = new Tree([sample, undefined]) + + // perform Depth-First Search + const stack = [root] + while (stack.length > 0) { + const top = stack.pop() + const [sample, _] = top.data + + // find children for sample on top of stack + top.neighbors = sample + ?.process_measurements + ?.map((id) => { + // get process measurement + + if (!(id in processMeasurementsByID)) + withProcessMeasurement(processMeasurementsByID, id, process => process.id) + + return processMeasurementsByID[id] + }) + .filter((p) => { + // ignore process measurement if + // child_sample field is null (or undefined) + + const id = p?.child_sample + + if (id !== undefined && !samplesByID[id]) { + withSample(samplesByID, id, sample => sample.id) + } + + return id !== undefined && id !== null + }) + .map((p) => { + // create new subtree + + const id = p?.child_sample + const s = id in samplesByID ? samplesByID[id] : undefined + + return new Tree([s, p]) + }) + top.neighbors = top.neighbors ? top.neighbors : [] + + stack.push(...top.neighbors) + } + + // add parents + while (root.data[0]?.child_of?.length > 0) { + const child = root.data[0].id + + const child_of = root.data[0].child_of + const parent_sample = samplesByID[child_of] + const parent_process = parent_sample + ?.process_measurements + ?.map((id) => { + // get process measurement + + if (!(id in processMeasurementsByID)) + withProcessMeasurement(processMeasurementsByID, id, process => process.id) + + return processMeasurementsByID[id] + }) + ?.find((p) => + // find process measurement that created 'child' + + p?.child_sample == child + ) + + // fetch parent + if (!parent_sample) + withSample(samplesByID, child_of, sample => sample.id) + + // update process measurement for 'child' + root.data[1] = parent_process + + // create new supertree + root = new Tree([parent_sample, undefined], [root]) + } + + return root +} + function renderTimelineLabel(version, usersByID) { const user = usersByID[version.revision.user]; const username = user?.username ?? "Loading..."; From 5b8118ce3adccd0a00d5ec3d2e2d1513d3a41c0f Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Fri, 6 May 2022 13:08:57 -0400 Subject: [PATCH 03/68] produce nodes and edge objects for React Flow --- .../samples/details/SampleDetailsContent.js | 56 +++++++++++++------ frontend/src/utils/graph.js | 3 +- 2 files changed, 41 insertions(+), 18 deletions(-) diff --git a/frontend/src/components/samples/details/SampleDetailsContent.js b/frontend/src/components/samples/details/SampleDetailsContent.js index eb522b481f..afd38c4d29 100644 --- a/frontend/src/components/samples/details/SampleDetailsContent.js +++ b/frontend/src/components/samples/details/SampleDetailsContent.js @@ -132,23 +132,44 @@ const SampleDetailsContent = ({ const concentration_nm = library && library.concentration_nm ? parseFloat(library.concentration_nm).toFixed(3) : undefined const [sampleMetadata, setSampleMetadata] = useState([]) - const tree = generateLineageData(samplesByID, processMeasurementsByID, protocolsByID, sample) - - // convert Tree class into an object that is compatible - // with bkrem/react-d3-tree - const root = tree.fold((data, children) => { - const [sample, process] = data - return { - name: sample?.name, - attributes: { - id: sample?.id, - ...( - process ? { protocol: protocolsByID[process.protocol]?.name } : {} + const [nodes, edges] = + generateLineageData(samplesByID, processMeasurementsByID, protocolsByID, sample) + .fold((old_data, new_children, old_chilren) => { + // produce nodes and edges objects + // that React Flow recognizes + + const [parent_sample, _] = old_data + const nodes = new_children.reduce( + (prev, curr) => { + return [...prev, ...curr[0]] + }, + [] ) - }, - children: children - } - }) + const edges = new_children.reduce( + (prev, curr) => { + return [...prev, ...curr[1]] + }, + [] + ) + nodes.push({ + id: parent_sample?.id?.toString() || "", + data: { + label: parent_sample?.name || "" + } + }) + edges.push(...old_chilren.map((c) => { + const [sample_child, process] = c.data + + return { + id: process?.id?.toString(), + source: parent_sample?.id?.toString() || "", + target: sample_child?.id?.toString() || "", + label: process?.protocol in protocolsByID ? protocolsByID[process?.protocol]?.name : "" + } + } + )) + return [nodes, edges] + }) // TODO: This spams API requests if (!samplesByID[id]) @@ -321,7 +342,8 @@ const SampleDetailsContent = ({ Lineage - 
{JSON.stringify(root, null, 2)}
+ 
{JSON.stringify(nodes, null, 2)}
+ 
{JSON.stringify(edges, null, 2)}
 diff --git a/frontend/src/utils/graph.js b/frontend/src/utils/graph.js index fc12364b78..98eab12e71 100644 --- a/frontend/src/utils/graph.js +++ b/frontend/src/utils/graph.js @@ -16,7 +16,8 @@ class Tree { fold(f) { return f( this.data, - this.neighbors.map((v) => v.fold(f)) + this.neighbors.map((v) => v.fold(f)), + this.neighbors, ) } } From 32be41dc8e21191285d9f29d6920fe996680edfc Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Fri, 6 May 2022 15:01:07 -0400 Subject: [PATCH 04/68] implement with react-d3-graph --- frontend/package-lock.json | 12681 +++++++++++++++- frontend/package.json | 1 + .../samples/details/SampleDetailsContent.js | 69 +- 3 files changed, 12592 insertions(+), 159 deletions(-) diff --git a/frontend/package-lock.json b/frontend/package-lock.json index 0a3d321f64..c64c0c141d 100644 --- a/frontend/package-lock.json +++ b/frontend/package-lock.json @@ -1,8 +1,12152 @@ { "name": "fms_web", "version": "0.1.0", - "lockfileVersion": 1, + "lockfileVersion": 2, 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@@ "version": "2.2.0", "resolved": "https://registry.npmjs.org/watchpack/-/watchpack-2.2.0.tgz", "integrity": "sha512-up4YAn/XHgZHIxFBVCdlMiWDj6WaLKpwVeGQk2I5thdYxF/KmF0aaz6TfJZ/hfl1h/XlcDr7k1KH7ThDagpFaA==", - "dev": true, "requires": { "glob-to-regexp": "^0.4.1", "graceful-fs": "^4.1.2" @@ -8923,7 +21325,6 @@ "version": "5.38.1", "resolved": "https://registry.npmjs.org/webpack/-/webpack-5.38.1.tgz", "integrity": "sha512-OqRmYD1OJbHZph6RUMD93GcCZy4Z4wC0ele4FXyYF0J6AxO1vOSuIlU1hkS/lDlR9CDYBz64MZRmdbdnFFoT2g==", - "dev": true, "requires": { "@types/eslint-scope": "^3.7.0", "@types/estree": "^0.0.47", @@ -8953,14 +21354,12 @@ "@types/json-schema": { "version": "7.0.7", "resolved": "https://registry.npmjs.org/@types/json-schema/-/json-schema-7.0.7.tgz", - "integrity": "sha512-cxWFQVseBm6O9Gbw1IWb8r6OS4OhSt3hPZLkFApLjM8TEXROBuQGLAH2i2gZpcXdLBIrpXuTDhH7Vbm1iXmNGA==", - "dev": true + "integrity": "sha512-cxWFQVseBm6O9Gbw1IWb8r6OS4OhSt3hPZLkFApLjM8TEXROBuQGLAH2i2gZpcXdLBIrpXuTDhH7Vbm1iXmNGA==" }, "ajv": { "version": "6.12.6", "resolved": "https://registry.npmjs.org/ajv/-/ajv-6.12.6.tgz", "integrity": "sha512-j3fVLgvTo527anyYyJOGTYJbG+vnnQYvE0m5mmkc1TK+nxAppkCLMIL0aZ4dblVCNoGShhm+kzE4ZUykBoMg4g==", - "dev": true, "requires": { "fast-deep-equal": "^3.1.1", "fast-json-stable-stringify": "^2.0.0", @@ -8972,13 +21371,12 @@ "version": "3.5.2", "resolved": "https://registry.npmjs.org/ajv-keywords/-/ajv-keywords-3.5.2.tgz", "integrity": "sha512-5p6WTN0DdTGVQk6VjcEju19IgaHudalcfabD7yhDGeA6bcQnmL+CpveLJq/3hvfwd1aof6L386Ougkx6RfyMIQ==", - "dev": true + "requires": {} }, "enhanced-resolve": { "version": "5.8.2", "resolved": "https://registry.npmjs.org/enhanced-resolve/-/enhanced-resolve-5.8.2.tgz", "integrity": "sha512-F27oB3WuHDzvR2DOGNTaYy0D5o0cnrv8TeI482VM4kYgQd/FT9lUQwuNsJ0oOHtBUq7eiW5ytqzp7nBFknL+GA==", - "dev": true, "requires": { "graceful-fs": "^4.2.4", "tapable": "^2.2.0" @@ -8988,7 +21386,6 @@ "version": "3.0.0", "resolved": "https://registry.npmjs.org/schema-utils/-/schema-utils-3.0.0.tgz", "integrity": "sha512-6D82/xSzO094ajanoOSbe4YvXWMfn2A//8Y1+MUqFAJul5Bs+yn36xbK9OtNDcRVSBJ9jjeoXftM6CfztsjOAA==", - "dev": true, "requires": { "@types/json-schema": "^7.0.6", "ajv": "^6.12.5", @@ -8998,8 +21395,7 @@ "tapable": { "version": "2.2.0", "resolved": "https://registry.npmjs.org/tapable/-/tapable-2.2.0.tgz", - "integrity": "sha512-FBk4IesMV1rBxX2tfiK8RAmogtWn53puLOQlvO8XuwlgxcYbP4mVPS9Ph4aeamSyyVjOl24aYWAuc8U5kCVwMw==", - "dev": true + "integrity": "sha512-FBk4IesMV1rBxX2tfiK8RAmogtWn53puLOQlvO8XuwlgxcYbP4mVPS9Ph4aeamSyyVjOl24aYWAuc8U5kCVwMw==" } } }, @@ -9266,7 +21662,6 @@ "version": "2.3.0", "resolved": "https://registry.npmjs.org/webpack-sources/-/webpack-sources-2.3.0.tgz", "integrity": "sha512-WyOdtwSvOML1kbgtXbTDnEW0jkJ7hZr/bDByIwszhWd/4XX1A3XMkrbFMsuH4+/MfLlZCUzlAdg4r7jaGKEIgQ==", - "dev": true, "requires": { "source-list-map": "^2.0.1", "source-map": "^0.6.1" @@ -9275,8 +21670,7 @@ "source-map": { "version": "0.6.1", "resolved": "https://registry.npmjs.org/source-map/-/source-map-0.6.1.tgz", - "integrity": "sha512-UjgapumWlbMhkBgzT7Ykc5YXUT46F0iKu8SGXq0bcwP5dz/h0Plj6enJqjz1Zbq2l5WaqYnrVbwWOWMyF3F47g==", - "dev": true + "integrity": "sha512-UjgapumWlbMhkBgzT7Ykc5YXUT46F0iKu8SGXq0bcwP5dz/h0Plj6enJqjz1Zbq2l5WaqYnrVbwWOWMyF3F47g==" } } }, @@ -9409,8 +21803,7 @@ "yocto-queue": { "version": "0.1.0", "resolved": "https://registry.npmjs.org/yocto-queue/-/yocto-queue-0.1.0.tgz", - "integrity": "sha512-rVksvsnNCdJ/ohGc6xgPwyN8eheCxsiLM8mxuE/t/mOVqJewPuO1miLpTHQiRgTKCLexL4MeAFVagts7HmNZ2Q==", - "dev": true + "integrity": "sha512-rVksvsnNCdJ/ohGc6xgPwyN8eheCxsiLM8mxuE/t/mOVqJewPuO1miLpTHQiRgTKCLexL4MeAFVagts7HmNZ2Q==" } } } diff --git a/frontend/package.json b/frontend/package.json index 08c9c58373..de36d51859 100644 --- a/frontend/package.json +++ b/frontend/package.json @@ -41,6 +41,7 @@ "rambda": "^5.9.0", "rc-util": "^5.8.1", "react": "^16.13.1", + "react-d3-graph": "^2.6.0", "react-dom": "^16.13.1", "react-hot-loader": "^4.12.21", "react-redux": "^7.2.0", diff --git a/frontend/src/components/samples/details/SampleDetailsContent.js b/frontend/src/components/samples/details/SampleDetailsContent.js index afd38c4d29..dc9e226720 100644 --- a/frontend/src/components/samples/details/SampleDetailsContent.js +++ b/frontend/src/components/samples/details/SampleDetailsContent.js @@ -17,6 +17,8 @@ import { Typography } from "antd"; +import { Graph } from "react-d3-graph" + import dateToString from "../../../utils/dateToString"; import useTimeline from "../../../utils/useTimeline"; import renderSampleDiff from "../../../utils/renderSampleDiff"; @@ -132,7 +134,7 @@ const SampleDetailsContent = ({ const concentration_nm = library && library.concentration_nm ? parseFloat(library.concentration_nm).toFixed(3) : undefined const [sampleMetadata, setSampleMetadata] = useState([]) - const [nodes, edges] = + const graphData = generateLineageData(samplesByID, processMeasurementsByID, protocolsByID, sample) .fold((old_data, new_children, old_chilren) => { // produce nodes and edges objects @@ -141,35 +143,59 @@ const SampleDetailsContent = ({ const [parent_sample, _] = old_data const nodes = new_children.reduce( (prev, curr) => { - return [...prev, ...curr[0]] + return [...prev, ...curr.nodes] }, [] ) - const edges = new_children.reduce( + const links = new_children.reduce( (prev, curr) => { - return [...prev, ...curr[1]] + return [...prev, ...curr.links] }, [] ) nodes.push({ id: parent_sample?.id?.toString() || "", - data: { - label: parent_sample?.name || "" - } + label: parent_sample?.name || "" }) - edges.push(...old_chilren.map((c) => { + links.push(...old_chilren.map((c) => { const [sample_child, process] = c.data return { - id: process?.id?.toString(), + id: process?.id?.toString() || "", + label: process?.protocol in protocolsByID ? protocolsByID[process?.protocol]?.name : "", source: parent_sample?.id?.toString() || "", target: sample_child?.id?.toString() || "", - label: process?.protocol in protocolsByID ? protocolsByID[process?.protocol]?.name : "" } - } - )) - return [nodes, edges] + })) + return {nodes, links} }) + const graphConfig = { + height: 400, + width: 400, + staticGraph: false, + directed: true, + maxZoom: 12, + minZoom: 0.05, + panAndZoom: true, + d3: { + gravity: -500, + linkLength: 120, + linkStrength: 2, + }, + node: { + color: "#d3d3d3", + fontColor: "black", + renderLabel: true, + labelProperty: node => `${node.label} (#${node.id})` + }, + link: { + color: "lightgray", + fontColor: "black", + strokeWidth: 3, + type: "STRAIGHT", + renderLabel: true, + }, + } // TODO: This spams API requests if (!samplesByID[id]) @@ -342,8 +368,21 @@ const SampleDetailsContent = ({ Lineage - 
{JSON.stringify(nodes, null, 2)}
- 
{JSON.stringify(edges, null, 2)}
+
+ location.href = `/samples/${id}`} + onClickLink={(source, target) => { + const linkId = graphData.links.find( + (link) => { + return (link.source === source && link.target === target) + })?.id + location.href = `/process-measurements/${linkId}` + }} + /> +
From 88e951d59e9311365a4add0663bea04dc7a19791 Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Fri, 6 May 2022 15:42:18 -0400 Subject: [PATCH 05/68] make Lineage a component --- .../samples/details/SampleDetailsContent.js | 165 +++++++++--------- 1 file changed, 84 insertions(+), 81 deletions(-) diff --git a/frontend/src/components/samples/details/SampleDetailsContent.js b/frontend/src/components/samples/details/SampleDetailsContent.js index dc9e226720..9f2c19c0e8 100644 --- a/frontend/src/components/samples/details/SampleDetailsContent.js +++ b/frontend/src/components/samples/details/SampleDetailsContent.js @@ -134,69 +134,6 @@ const SampleDetailsContent = ({ const concentration_nm = library && library.concentration_nm ? parseFloat(library.concentration_nm).toFixed(3) : undefined const [sampleMetadata, setSampleMetadata] = useState([]) - const graphData = - generateLineageData(samplesByID, processMeasurementsByID, protocolsByID, sample) - .fold((old_data, new_children, old_chilren) => { - // produce nodes and edges objects - // that React Flow recognizes - - const [parent_sample, _] = old_data - const nodes = new_children.reduce( - (prev, curr) => { - return [...prev, ...curr.nodes] - }, - [] - ) - const links = new_children.reduce( - (prev, curr) => { - return [...prev, ...curr.links] - }, - [] - ) - nodes.push({ - id: parent_sample?.id?.toString() || "", - label: parent_sample?.name || "" - }) - links.push(...old_chilren.map((c) => { - const [sample_child, process] = c.data - - return { - id: process?.id?.toString() || "", - label: process?.protocol in protocolsByID ? protocolsByID[process?.protocol]?.name : "", - source: parent_sample?.id?.toString() || "", - target: sample_child?.id?.toString() || "", - } - })) - return {nodes, links} - }) - const graphConfig = { - height: 400, - width: 400, - staticGraph: false, - directed: true, - maxZoom: 12, - minZoom: 0.05, - panAndZoom: true, - d3: { - gravity: -500, - linkLength: 120, - linkStrength: 2, - }, - node: { - color: "#d3d3d3", - fontColor: "black", - renderLabel: true, - labelProperty: node => `${node.label} (#${node.id})` - }, - link: { - color: "lightgray", - fontColor: "black", - strokeWidth: 3, - type: "STRAIGHT", - renderLabel: true, - }, - } - // TODO: This spams API requests if (!samplesByID[id]) getSample(id); @@ -368,21 +305,7 @@ const SampleDetailsContent = ({ Lineage -
- location.href = `/samples/${id}`} - onClickLink={(source, target) => { - const linkId = graphData.links.find( - (link) => { - return (link.source === source && link.target === target) - })?.id - location.href = `/process-measurements/${linkId}` - }} - /> -
+ @@ -415,10 +338,11 @@ const SampleDetailsContent = ({ ; }; -function generateLineageData(samplesByID, processMeasurementsByID, protocolsByID, sample) { + +function Lineage({ samplesByID, processMeasurementsByID, protocolsByID, sample }) { let root = new Tree([sample, undefined]) - // perform Depth-First Search + // Depth-First Search const stack = [root] while (stack.length > 0) { const top = stack.pop() @@ -493,7 +417,86 @@ function generateLineageData(samplesByID, processMeasurementsByID, protocolsByID root = new Tree([parent_sample, undefined], [root]) } - return root + const graphData = root.fold((old_data, new_children, old_chilren) => { + // produce nodes and edges objects + // that React Flow recognizes + + const [parent_sample, _] = old_data + const nodes = new_children.reduce( + (prev, curr) => { + return [...prev, ...curr.nodes] + }, + [] + ) + const links = new_children.reduce( + (prev, curr) => { + return [...prev, ...curr.links] + }, + [] + ) + nodes.push({ + id: parent_sample?.id?.toString() || "", + label: parent_sample?.name || "" + }) + links.push(...old_chilren.map((c) => { + const [sample_child, process] = c.data + + return { + id: process?.id?.toString() || "", + label: process?.protocol in protocolsByID ? protocolsByID[process?.protocol]?.name : "", + source: parent_sample?.id?.toString() || "", + target: sample_child?.id?.toString() || "", + } + })) + return { nodes, links } + }) + + const graphConfig = { + height: 400, + width: 400, + staticGraph: false, + directed: true, + maxZoom: 12, + minZoom: 0.05, + panAndZoom: true, + d3: { + gravity: -500, + linkLength: 120, + linkStrength: 2, + }, + node: { + color: "#d3d3d3", + fontColor: "black", + renderLabel: true, + labelProperty: node => `${node.label} (#${node.id})` + }, + link: { + color: "lightgray", + fontColor: "black", + strokeWidth: 3, + type: "STRAIGHT", + renderLabel: true, + labelProperty: link => `${link.label} (#${link.id})` + }, + } + + return ( + <> + location.href = `/samples/${id}`} + onClickLink={(source, target) => { + const linkId = graphData.links.find( + (link) => { + return (link.source === source && link.target === target) + })?.id + location.href = `/process-measurements/${linkId}` + }} + /> + + ) } function renderTimelineLabel(version, usersByID) { From d7c58e575c14c028ed04a19667b1cb9e9b1e185c Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Mon, 9 May 2022 09:53:09 -0400 Subject: [PATCH 06/68] add React.StrictMode --- frontend/src/components/samples/details/SampleDetailsContent.js | 2 ++ 1 file changed, 2 insertions(+) diff --git a/frontend/src/components/samples/details/SampleDetailsContent.js b/frontend/src/components/samples/details/SampleDetailsContent.js index 9f2c19c0e8..21a1d35405 100644 --- a/frontend/src/components/samples/details/SampleDetailsContent.js +++ b/frontend/src/components/samples/details/SampleDetailsContent.js @@ -482,6 +482,7 @@ function Lineage({ samplesByID, processMeasurementsByID, protocolsByID, sample } return ( <> + + ) } From 2e75d057f37ccae5f4450b24abd1f660104e5a7c Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Mon, 9 May 2022 13:23:41 -0400 Subject: [PATCH 07/68] add and use Lineage tab --- .../src/components/samples/details/SampleDetailsContent.js | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/frontend/src/components/samples/details/SampleDetailsContent.js b/frontend/src/components/samples/details/SampleDetailsContent.js index 21a1d35405..6882cc12b6 100644 --- a/frontend/src/components/samples/details/SampleDetailsContent.js +++ b/frontend/src/components/samples/details/SampleDetailsContent.js @@ -304,8 +304,6 @@ const SampleDetailsContent = ({ - Lineage - @@ -332,6 +330,9 @@ const SampleDetailsContent = ({ + + + From b5eba8c64deaa3166d153cecf648c78236f8c7e9 Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Mon, 9 May 2022 13:36:11 -0400 Subject: [PATCH 08/68] use map.flat instead of reduce --- .../samples/details/SampleDetailsContent.js | 16 ++++------------ 1 file changed, 4 insertions(+), 12 deletions(-) diff --git a/frontend/src/components/samples/details/SampleDetailsContent.js b/frontend/src/components/samples/details/SampleDetailsContent.js index 6882cc12b6..879fdd442f 100644 --- a/frontend/src/components/samples/details/SampleDetailsContent.js +++ b/frontend/src/components/samples/details/SampleDetailsContent.js @@ -423,18 +423,10 @@ function Lineage({ samplesByID, processMeasurementsByID, protocolsByID, sample } // that React Flow recognizes const [parent_sample, _] = old_data - const nodes = new_children.reduce( - (prev, curr) => { - return [...prev, ...curr.nodes] - }, - [] - ) - const links = new_children.reduce( - (prev, curr) => { - return [...prev, ...curr.links] - }, - [] - ) + + const nodes = new_children.map((c) => c.nodes).flat() + const links = new_children.map((c) => c.links).flat() + nodes.push({ id: parent_sample?.id?.toString() || "", label: parent_sample?.name || "" From 72df7a6fc8afd040942be81f2b8a015113de4acd Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Mon, 9 May 2022 14:02:22 -0400 Subject: [PATCH 09/68] empty list instead of undefined --- frontend/src/components/samples/details/SampleDetailsContent.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/frontend/src/components/samples/details/SampleDetailsContent.js b/frontend/src/components/samples/details/SampleDetailsContent.js index 879fdd442f..89daeb0617 100644 --- a/frontend/src/components/samples/details/SampleDetailsContent.js +++ b/frontend/src/components/samples/details/SampleDetailsContent.js @@ -341,7 +341,7 @@ const SampleDetailsContent = ({ function Lineage({ samplesByID, processMeasurementsByID, protocolsByID, sample }) { - let root = new Tree([sample, undefined]) + let root = new Tree([sample, []]) // Depth-First Search const stack = [root] From 65629bdb472abec5859a9f7ef7a115ac4e60ab7a Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Mon, 9 May 2022 15:30:18 -0400 Subject: [PATCH 10/68] create and use SampleDetailsLineage.js --- .../samples/details/SampleDetailsContent.js | 163 +--------------- .../samples/details/SampleDetailsLineage.js | 177 ++++++++++++++++++ 2 files changed, 179 insertions(+), 161 deletions(-) create mode 100644 frontend/src/components/samples/details/SampleDetailsLineage.js diff --git a/frontend/src/components/samples/details/SampleDetailsContent.js b/frontend/src/components/samples/details/SampleDetailsContent.js index 89daeb0617..4472bb24f9 100644 --- a/frontend/src/components/samples/details/SampleDetailsContent.js +++ b/frontend/src/components/samples/details/SampleDetailsContent.js @@ -17,8 +17,6 @@ import { Typography } from "antd"; -import { Graph } from "react-d3-graph" - import dateToString from "../../../utils/dateToString"; import useTimeline from "../../../utils/useTimeline"; import renderSampleDiff from "../../../utils/renderSampleDiff"; @@ -30,6 +28,7 @@ import TrackingFieldsContent from "../../TrackingFieldsContent"; import SamplesAssociatedProjects from "../SamplesAssociatedProjects"; import {Depletion} from "../../Depletion"; import SampleDetailsProcessMeasurements from "./SampleDetailsProcessMeasurements"; +import SampleDetailsLineage from "./SampleDetailsLineage"; import {get as getSample, listVersions} from "../../../modules/samples/actions"; import {get as getLibrary} from "../../../modules/libraries/actions"; import api, {withToken} from "../../../utils/api"; @@ -42,7 +41,6 @@ import { withLibrary, withIndex } from "../../../utils/withItem"; -import Tree from "../../../utils/graph"; import ExperimentRunsListSection from "../../shared/ExperimentRunsListSection"; const { Title, Text } = Typography; @@ -88,7 +86,6 @@ const mapStateToProps = state => ({ indicesByID: state.indices.itemsByID, usersByID: state.users.itemsByID, projectsByID: state.projects.itemsByID, - protocolsByID: state.protocols.itemsByID, }); const actionCreators = {getSample, listVersions}; @@ -104,7 +101,6 @@ const SampleDetailsContent = ({ indicesByID, usersByID, projectsByID, - protocolsByID, getSample, listVersions }) => { @@ -331,7 +327,7 @@ const SampleDetailsContent = ({ - + @@ -339,161 +335,6 @@ const SampleDetailsContent = ({ ; }; - -function Lineage({ samplesByID, processMeasurementsByID, protocolsByID, sample }) { - let root = new Tree([sample, []]) - - // Depth-First Search - const stack = [root] - while (stack.length > 0) { - const top = stack.pop() - const [sample, _] = top.data - - // find children for sample on top of stack - top.neighbors = sample - ?.process_measurements - ?.map((id) => { - // get process measurement - - if (!(id in processMeasurementsByID)) - withProcessMeasurement(processMeasurementsByID, id, process => process.id) - - return processMeasurementsByID[id] - }) - .filter((p) => { - // ignore process measurement if - // child_sample field is null (or undefined) - - const id = p?.child_sample - - if (id !== undefined && !samplesByID[id]) { - withSample(samplesByID, id, sample => sample.id) - } - - return id !== undefined && id !== null - }) - .map((p) => { - // create new subtree - - const id = p?.child_sample - const s = id in samplesByID ? samplesByID[id] : undefined - - return new Tree([s, p]) - }) - top.neighbors = top.neighbors ? top.neighbors : [] - - stack.push(...top.neighbors) - } - - // add parents - while (root.data[0]?.child_of?.length > 0) { - const child = root.data[0].id - - const child_of = root.data[0].child_of - const parent_sample = samplesByID[child_of] - const parent_process = parent_sample - ?.process_measurements - ?.map((id) => { - // get process measurement - - if (!(id in processMeasurementsByID)) - withProcessMeasurement(processMeasurementsByID, id, process => process.id) - - return processMeasurementsByID[id] - }) - ?.find((p) => - // find process measurement that created 'child' - - p?.child_sample == child - ) - - // fetch parent - if (!parent_sample) - withSample(samplesByID, child_of, sample => sample.id) - - // update process measurement for 'child' - root.data[1] = parent_process - - // create new supertree - root = new Tree([parent_sample, undefined], [root]) - } - - const graphData = root.fold((old_data, new_children, old_chilren) => { - // produce nodes and edges objects - // that React Flow recognizes - - const [parent_sample, _] = old_data - - const nodes = new_children.map((c) => c.nodes).flat() - const links = new_children.map((c) => c.links).flat() - - nodes.push({ - id: parent_sample?.id?.toString() || "", - label: parent_sample?.name || "" - }) - links.push(...old_chilren.map((c) => { - const [sample_child, process] = c.data - - return { - id: process?.id?.toString() || "", - label: process?.protocol in protocolsByID ? protocolsByID[process?.protocol]?.name : "", - source: parent_sample?.id?.toString() || "", - target: sample_child?.id?.toString() || "", - } - })) - return { nodes, links } - }) - - const graphConfig = { - height: 400, - width: 400, - staticGraph: false, - directed: true, - maxZoom: 12, - minZoom: 0.05, - panAndZoom: true, - d3: { - gravity: -500, - linkLength: 120, - linkStrength: 2, - }, - node: { - color: "#d3d3d3", - fontColor: "black", - renderLabel: true, - labelProperty: node => `${node.label} (#${node.id})` - }, - link: { - color: "lightgray", - fontColor: "black", - strokeWidth: 3, - type: "STRAIGHT", - renderLabel: true, - labelProperty: link => `${link.label} (#${link.id})` - }, - } - - return ( - <> - - location.href = `/samples/${id}`} - onClickLink={(source, target) => { - const linkId = graphData.links.find( - (link) => { - return (link.source === source && link.target === target) - })?.id - location.href = `/process-measurements/${linkId}` - }} - /> - - - ) -} - function renderTimelineLabel(version, usersByID) { const user = usersByID[version.revision.user]; const username = user?.username ?? "Loading..."; diff --git a/frontend/src/components/samples/details/SampleDetailsLineage.js b/frontend/src/components/samples/details/SampleDetailsLineage.js new file mode 100644 index 0000000000..32ec758010 --- /dev/null +++ b/frontend/src/components/samples/details/SampleDetailsLineage.js @@ -0,0 +1,177 @@ +import React from "react"; +import {connect} from "react-redux"; + +import { Graph } from "react-d3-graph" + +import { + withSample, + withProcessMeasurement, +} from "../../../utils/withItem"; +import Tree from "../../../utils/graph"; + +const mapStateToProps = state => ({ + samplesByID: state.samples.itemsByID, + processMeasurementsByID: state.processMeasurements.itemsByID, + protocolsByID: state.protocols.itemsByID, +}); + +const SampleDetailsLineage = ({ + sample, + samplesByID, + processMeasurementsByID, + protocolsByID, +}) => { + let root = new Tree([sample, []]) + + // Depth-First Search + const stack = [root] + while (stack.length > 0) { + const top = stack.pop() + const [sample, _] = top.data + + // find children for sample on top of stack + top.neighbors = sample + ?.process_measurements + ?.map((id) => { + // get process measurement + + if (!(id in processMeasurementsByID)) + withProcessMeasurement(processMeasurementsByID, id, process => process.id) + + return processMeasurementsByID[id] + }) + .filter((p) => { + // ignore process measurement if + // child_sample field is null (or undefined) + + const id = p?.child_sample + + if (id !== undefined && !samplesByID[id]) { + withSample(samplesByID, id, sample => sample.id) + } + + return id !== undefined && id !== null + }) + .map((p) => { + // create new subtree + + const id = p?.child_sample + const s = id in samplesByID ? samplesByID[id] : undefined + + return new Tree([s, p]) + }) + top.neighbors = top.neighbors ? top.neighbors : [] + + stack.push(...top.neighbors) + } + + // add parents + while (root.data[0]?.child_of?.length > 0) { + const child = root.data[0].id + + const child_of = root.data[0].child_of + const parent_sample = samplesByID[child_of] + const parent_process = parent_sample + ?.process_measurements + ?.map((id) => { + // get process measurement + + if (!(id in processMeasurementsByID)) + withProcessMeasurement(processMeasurementsByID, id, process => process.id) + + return processMeasurementsByID[id] + }) + ?.find((p) => + // find process measurement that created 'child' + + p?.child_sample == child + ) + + // fetch parent + if (!parent_sample) + withSample(samplesByID, child_of, sample => sample.id) + + // update process measurement for 'child' + root.data[1] = parent_process + + // create new supertree + root = new Tree([parent_sample, undefined], [root]) + } + + const graphData = root.fold((old_data, new_children, old_chilren) => { + // produce nodes and edges objects + // that React Flow recognizes + + const [parent_sample, _] = old_data + + const nodes = new_children.map((c) => c.nodes).flat() + const links = new_children.map((c) => c.links).flat() + + nodes.push({ + id: parent_sample?.id?.toString() || "", + label: parent_sample?.name || "" + }) + links.push(...old_chilren.map((c) => { + const [sample_child, process] = c.data + + return { + id: process?.id?.toString() || "", + label: process?.protocol in protocolsByID ? protocolsByID[process?.protocol]?.name : "", + source: parent_sample?.id?.toString() || "", + target: sample_child?.id?.toString() || "", + } + })) + return { nodes, links } + }) + + const graphConfig = { + height: 400, + width: 400, + staticGraph: false, + directed: true, + maxZoom: 12, + minZoom: 0.05, + panAndZoom: true, + d3: { + gravity: -500, + linkLength: 120, + linkStrength: 2, + }, + node: { + color: "#d3d3d3", + fontColor: "black", + renderLabel: true, + labelProperty: node => `${node.label} (#${node.id})` + }, + link: { + color: "lightgray", + fontColor: "black", + strokeWidth: 3, + type: "STRAIGHT", + renderLabel: true, + labelProperty: link => `${link.label} (#${link.id})` + }, + } + + return ( + <> + + location.href = `/samples/${id}`} + onClickLink={(source, target) => { + const linkId = graphData.links.find( + (link) => { + return (link.source === source && link.target === target) + })?.id + location.href = `/process-measurements/${linkId}` + }} + /> + + + ) +} + +export default connect(mapStateToProps, undefined)(SampleDetailsLineage); From 64da437a4ba23a9cdb7fbcc408c7beee09882266 Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Mon, 9 May 2022 15:56:30 -0400 Subject: [PATCH 11/68] don't display id --- .../src/components/samples/details/SampleDetailsLineage.js | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/frontend/src/components/samples/details/SampleDetailsLineage.js b/frontend/src/components/samples/details/SampleDetailsLineage.js index 32ec758010..4f4dad4457 100644 --- a/frontend/src/components/samples/details/SampleDetailsLineage.js +++ b/frontend/src/components/samples/details/SampleDetailsLineage.js @@ -141,7 +141,7 @@ const SampleDetailsLineage = ({ color: "#d3d3d3", fontColor: "black", renderLabel: true, - labelProperty: node => `${node.label} (#${node.id})` + labelProperty: node => `${node.label}` }, link: { color: "lightgray", @@ -149,7 +149,7 @@ const SampleDetailsLineage = ({ strokeWidth: 3, type: "STRAIGHT", renderLabel: true, - labelProperty: link => `${link.label} (#${link.id})` + labelProperty: link => `${link.label}` }, } From 0c399ce5c602f334cab50199136686d2ecc9a044 Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Mon, 9 May 2022 15:57:03 -0400 Subject: [PATCH 12/68] make current node red --- .../src/components/samples/details/SampleDetailsLineage.js | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/frontend/src/components/samples/details/SampleDetailsLineage.js b/frontend/src/components/samples/details/SampleDetailsLineage.js index 4f4dad4457..af0221f576 100644 --- a/frontend/src/components/samples/details/SampleDetailsLineage.js +++ b/frontend/src/components/samples/details/SampleDetailsLineage.js @@ -106,10 +106,11 @@ const SampleDetailsLineage = ({ const nodes = new_children.map((c) => c.nodes).flat() const links = new_children.map((c) => c.links).flat() - + nodes.push({ id: parent_sample?.id?.toString() || "", - label: parent_sample?.name || "" + label: parent_sample?.name || "", + color: parent_sample?.id === sample?.id ? "red" : "black" }) links.push(...old_chilren.map((c) => { const [sample_child, process] = c.data From a413f0fab76eb7ce878eec12a9b0e8ba32d62e6d Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Tue, 10 May 2022 09:47:41 -0400 Subject: [PATCH 13/68] Tree to Graph Make data structure more general. --- .../samples/details/SampleDetailsLineage.js | 18 ++++---- frontend/src/utils/graph.js | 43 ++++++++++++------- 2 files changed, 36 insertions(+), 25 deletions(-) diff --git a/frontend/src/components/samples/details/SampleDetailsLineage.js b/frontend/src/components/samples/details/SampleDetailsLineage.js index af0221f576..37abe6fafd 100644 --- a/frontend/src/components/samples/details/SampleDetailsLineage.js +++ b/frontend/src/components/samples/details/SampleDetailsLineage.js @@ -7,7 +7,7 @@ import { withSample, withProcessMeasurement, } from "../../../utils/withItem"; -import Tree from "../../../utils/graph"; +import GraphADT from "../../../utils/graph"; const mapStateToProps = state => ({ samplesByID: state.samples.itemsByID, @@ -21,7 +21,7 @@ const SampleDetailsLineage = ({ processMeasurementsByID, protocolsByID, }) => { - let root = new Tree([sample, []]) + let root = new GraphADT([sample, undefined]) // Depth-First Search const stack = [root] @@ -58,7 +58,7 @@ const SampleDetailsLineage = ({ const id = p?.child_sample const s = id in samplesByID ? samplesByID[id] : undefined - return new Tree([s, p]) + return new GraphADT([s, p]) }) top.neighbors = top.neighbors ? top.neighbors : [] @@ -95,24 +95,24 @@ const SampleDetailsLineage = ({ root.data[1] = parent_process // create new supertree - root = new Tree([parent_sample, undefined], [root]) + root = new GraphADT([parent_sample, undefined], [root]) } - const graphData = root.fold((old_data, new_children, old_chilren) => { + const graphData = root.reduceNeighbors((oldData, oldChildren, newChildren) => { // produce nodes and edges objects // that React Flow recognizes - const [parent_sample, _] = old_data + const [parent_sample, _] = oldData - const nodes = new_children.map((c) => c.nodes).flat() - const links = new_children.map((c) => c.links).flat() + const nodes = newChildren.map((c) => c.nodes).flat() + const links = newChildren.map((c) => c.links).flat() nodes.push({ id: parent_sample?.id?.toString() || "", label: parent_sample?.name || "", color: parent_sample?.id === sample?.id ? "red" : "black" }) - links.push(...old_chilren.map((c) => { + links.push(...oldChildren.map((c) => { const [sample_child, process] = c.data return { diff --git a/frontend/src/utils/graph.js b/frontend/src/utils/graph.js index 98eab12e71..f0002f6805 100644 --- a/frontend/src/utils/graph.js +++ b/frontend/src/utils/graph.js @@ -1,25 +1,36 @@ /* - * A class that represents the tree data structure + * A class that represents a graph */ -class Tree { - constructor(data, children = []) { +class Graph { + constructor(data, neighbors = []) { this.data = data; - this.neighbors = children; + this.neighbors = neighbors; } - /* - * Performs a right fold with function f. - * The f is a function that takes the data - * of current node and a list of children - * transformed by f + /** + * Reduce neighbors into `this` with function `f`. + * @param {(oldData: any, oldNeighbors: any[], newNeighbors: any[], visited: Set) => any} f reducer function + * @param {number} maxDepth maximum depth to search (max 25000?) + * @param {boolean} skipVisited skip visited node in case of cycle in graph + * @param {Set} visited for internal use only */ - fold(f) { - return f( - this.data, - this.neighbors.map((v) => v.fold(f)), - this.neighbors, - ) + reduceNeighbors(f, maxDepth = 25000, skipVisited = false, visited = new Set()) { + if (maxDepth == 0) { + return f(this.data, [], [], visited) + } + + // visit neighbors first + const newNeighbors = this.neighbors + .filter((n) => !skipVisited && !visited.has(n)) + .map((n) => n.reduceNeighbors(f, maxDepth-1, skipVisited, visited)) + this.neighbors.forEach((n) => visited.add(n)) + + // visit this node + const newData = f(this.data, this.neighbors, newNeighbors, visited) + visited.add(this) + + return newData } } -export default Tree; +export default Graph; From 40971479c08b898b5020512e029ea598bcf21c66 Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Tue, 10 May 2022 10:14:50 -0400 Subject: [PATCH 14/68] use symbol for representing current node instead --- .../src/components/samples/details/SampleDetailsLineage.js | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/frontend/src/components/samples/details/SampleDetailsLineage.js b/frontend/src/components/samples/details/SampleDetailsLineage.js index 37abe6fafd..9247a77356 100644 --- a/frontend/src/components/samples/details/SampleDetailsLineage.js +++ b/frontend/src/components/samples/details/SampleDetailsLineage.js @@ -110,7 +110,8 @@ const SampleDetailsLineage = ({ nodes.push({ id: parent_sample?.id?.toString() || "", label: parent_sample?.name || "", - color: parent_sample?.id === sample?.id ? "red" : "black" + symbolType: parent_sample?.id === sample?.id ? "star" : "circle", + color: "black", }) links.push(...oldChildren.map((c) => { const [sample_child, process] = c.data From 3094e7f9e5154fd11b6696d67cc12464439f5499 Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Tue, 10 May 2022 10:38:31 -0400 Subject: [PATCH 15/68] use color to indicate qc flag --- .../samples/details/SampleDetailsLineage.js | 39 +++++++++++-------- 1 file changed, 22 insertions(+), 17 deletions(-) diff --git a/frontend/src/components/samples/details/SampleDetailsLineage.js b/frontend/src/components/samples/details/SampleDetailsLineage.js index 9247a77356..86c71d893f 100644 --- a/frontend/src/components/samples/details/SampleDetailsLineage.js +++ b/frontend/src/components/samples/details/SampleDetailsLineage.js @@ -1,5 +1,5 @@ import React from "react"; -import {connect} from "react-redux"; +import { connect } from "react-redux"; import { Graph } from "react-d3-graph" @@ -103,15 +103,20 @@ const SampleDetailsLineage = ({ // that React Flow recognizes const [parent_sample, _] = oldData - + const nodes = newChildren.map((c) => c.nodes).flat() const links = newChildren.map((c) => c.links).flat() - + + let color = "black" + if (parent_sample?.quality_flag !== null && parent_sample?.quantity_flag !== null) { + color = parent_sample?.quality_flag && parent_sample?.quantity_flag ? "green" : "red" + } + nodes.push({ id: parent_sample?.id?.toString() || "", label: parent_sample?.name || "", symbolType: parent_sample?.id === sample?.id ? "star" : "circle", - color: "black", + color }) links.push(...oldChildren.map((c) => { const [sample_child, process] = c.data @@ -158,19 +163,19 @@ const SampleDetailsLineage = ({ return ( <> - location.href = `/samples/${id}`} - onClickLink={(source, target) => { - const linkId = graphData.links.find( - (link) => { - return (link.source === source && link.target === target) - })?.id - location.href = `/process-measurements/${linkId}` - }} - /> + location.href = `/samples/${id}`} + onClickLink={(source, target) => { + const linkId = graphData.links.find( + (link) => { + return (link.source === source && link.target === target) + })?.id + location.href = `/process-measurements/${linkId}` + }} + /> ) From 0023baef89635bbab313da7f53dad295e8402707 Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Tue, 10 May 2022 11:35:43 -0400 Subject: [PATCH 16/68] document graph constructor --- frontend/src/utils/graph.js | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/frontend/src/utils/graph.js b/frontend/src/utils/graph.js index f0002f6805..bb7c686229 100644 --- a/frontend/src/utils/graph.js +++ b/frontend/src/utils/graph.js @@ -2,6 +2,11 @@ * A class that represents a graph */ class Graph { + /** + * + * @param {any} data data + * @param {Graph[]} neighbors neighbors/children + */ constructor(data, neighbors = []) { this.data = data; this.neighbors = neighbors; From cc8c210eb627ef39577bfeab1895885de84f165a Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Tue, 10 May 2022 12:07:19 -0400 Subject: [PATCH 17/68] use history --- .../components/samples/details/SampleDetailsLineage.js | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/frontend/src/components/samples/details/SampleDetailsLineage.js b/frontend/src/components/samples/details/SampleDetailsLineage.js index 86c71d893f..902b3d12d2 100644 --- a/frontend/src/components/samples/details/SampleDetailsLineage.js +++ b/frontend/src/components/samples/details/SampleDetailsLineage.js @@ -1,5 +1,6 @@ import React from "react"; import { connect } from "react-redux"; +import { useHistory } from "react-router-dom"; import { Graph } from "react-d3-graph" @@ -21,6 +22,8 @@ const SampleDetailsLineage = ({ processMeasurementsByID, protocolsByID, }) => { + const history = useHistory() + let root = new GraphADT([sample, undefined]) // Depth-First Search @@ -167,13 +170,14 @@ const SampleDetailsLineage = ({ id="graph-id" data={graphData} config={graphConfig} - onClickNode={(id, _) => location.href = `/samples/${id}`} + onClickNode={(id, _) => history.push(`/samples/${id}`)} onClickLink={(source, target) => { const linkId = graphData.links.find( (link) => { return (link.source === source && link.target === target) })?.id - location.href = `/process-measurements/${linkId}` + + history.push(`/process-measurements/${linkId ?? sample?.id}`) }} /> From ec8b01f20fa56fd543ae12b2a71fb41963b1b3b8 Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Wed, 11 May 2022 13:38:27 -0400 Subject: [PATCH 18/68] decoupole edge with with subgraph --- .../samples/details/SampleDetailsLineage.js | 33 ++++++++----------- frontend/src/utils/graph.js | 28 ++++++---------- 2 files changed, 24 insertions(+), 37 deletions(-) diff --git a/frontend/src/components/samples/details/SampleDetailsLineage.js b/frontend/src/components/samples/details/SampleDetailsLineage.js index 902b3d12d2..d9571b67d7 100644 --- a/frontend/src/components/samples/details/SampleDetailsLineage.js +++ b/frontend/src/components/samples/details/SampleDetailsLineage.js @@ -24,16 +24,16 @@ const SampleDetailsLineage = ({ }) => { const history = useHistory() - let root = new GraphADT([sample, undefined]) + let root = new GraphADT(sample) // Depth-First Search - const stack = [root] + const stack = [[undefined, root]] while (stack.length > 0) { - const top = stack.pop() - const [sample, _] = top.data + const [_, top] = stack.pop() + const sample = top.data // find children for sample on top of stack - top.neighbors = sample + top.edges = sample ?.process_measurements ?.map((id) => { // get process measurement @@ -61,11 +61,11 @@ const SampleDetailsLineage = ({ const id = p?.child_sample const s = id in samplesByID ? samplesByID[id] : undefined - return new GraphADT([s, p]) + return [p, new GraphADT(s)] }) - top.neighbors = top.neighbors ? top.neighbors : [] + top.edges = top.edges ? top.edges : [] - stack.push(...top.neighbors) + stack.push(...top.edges) } // add parents @@ -94,21 +94,16 @@ const SampleDetailsLineage = ({ if (!parent_sample) withSample(samplesByID, child_of, sample => sample.id) - // update process measurement for 'child' - root.data[1] = parent_process - // create new supertree - root = new GraphADT([parent_sample, undefined], [root]) + root = new GraphADT(parent_sample, [[parent_process, root]]) } - const graphData = root.reduceNeighbors((oldData, oldChildren, newChildren) => { + const graphData = root.reduceNeighbors((parent_sample, children) => { // produce nodes and edges objects // that React Flow recognizes - const [parent_sample, _] = oldData - - const nodes = newChildren.map((c) => c.nodes).flat() - const links = newChildren.map((c) => c.links).flat() + const nodes = children.map(([_0, _1, c]) => c.nodes).flat() + const links = children.map(([_0, _1, c]) => c.links).flat() let color = "black" if (parent_sample?.quality_flag !== null && parent_sample?.quantity_flag !== null) { @@ -121,8 +116,8 @@ const SampleDetailsLineage = ({ symbolType: parent_sample?.id === sample?.id ? "star" : "circle", color }) - links.push(...oldChildren.map((c) => { - const [sample_child, process] = c.data + links.push(...children.map(([process, child_graph, _]) => { + const sample_child = child_graph.data return { id: process?.id?.toString() || "", diff --git a/frontend/src/utils/graph.js b/frontend/src/utils/graph.js index bb7c686229..8de404316d 100644 --- a/frontend/src/utils/graph.js +++ b/frontend/src/utils/graph.js @@ -1,3 +1,5 @@ +let nodeID = 0 + /* * A class that represents a graph */ @@ -5,34 +7,24 @@ class Graph { /** * * @param {any} data data - * @param {Graph[]} neighbors neighbors/children + * @param {any[]} edges array of [edge data, child graph] */ - constructor(data, neighbors = []) { + constructor(data, edges = []) { + this.id = nodeID++; this.data = data; - this.neighbors = neighbors; + this.edges = edges; } /** * Reduce neighbors into `this` with function `f`. - * @param {(oldData: any, oldNeighbors: any[], newNeighbors: any[], visited: Set) => any} f reducer function - * @param {number} maxDepth maximum depth to search (max 25000?) - * @param {boolean} skipVisited skip visited node in case of cycle in graph - * @param {Set} visited for internal use only + * @param {(oldData: any, edges: any[]) => any} f reducer function */ - reduceNeighbors(f, maxDepth = 25000, skipVisited = false, visited = new Set()) { - if (maxDepth == 0) { - return f(this.data, [], [], visited) - } - + reduceNeighbors(f) { // visit neighbors first - const newNeighbors = this.neighbors - .filter((n) => !skipVisited && !visited.has(n)) - .map((n) => n.reduceNeighbors(f, maxDepth-1, skipVisited, visited)) - this.neighbors.forEach((n) => visited.add(n)) + const neighbors = this.edges.map(([e, n]) => [e, n, n.reduceNeighbors(f)]) // visit this node - const newData = f(this.data, this.neighbors, newNeighbors, visited) - visited.add(this) + const newData = f(this.data, neighbors) return newData } From d0a3d7b1fa9eb0fc131aece20dc361815afd5664 Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Wed, 11 May 2022 13:42:17 -0400 Subject: [PATCH 19/68] remove React.StrictNode --- frontend/src/components/samples/details/SampleDetailsLineage.js | 2 -- 1 file changed, 2 deletions(-) diff --git a/frontend/src/components/samples/details/SampleDetailsLineage.js b/frontend/src/components/samples/details/SampleDetailsLineage.js index d9571b67d7..8f02483297 100644 --- a/frontend/src/components/samples/details/SampleDetailsLineage.js +++ b/frontend/src/components/samples/details/SampleDetailsLineage.js @@ -160,7 +160,6 @@ const SampleDetailsLineage = ({ return ( <> - - ) } From e05a8e509fab086abbc0945a7ba9e05cf83dd0e3 Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Wed, 11 May 2022 16:37:09 -0400 Subject: [PATCH 20/68] 100% async tree construction (wip) --- .../samples/details/SampleDetailsLineage.js | 237 ++++++++++-------- frontend/src/utils/graph.js | 3 - 2 files changed, 138 insertions(+), 102 deletions(-) diff --git a/frontend/src/components/samples/details/SampleDetailsLineage.js b/frontend/src/components/samples/details/SampleDetailsLineage.js index 8f02483297..fc2532d811 100644 --- a/frontend/src/components/samples/details/SampleDetailsLineage.js +++ b/frontend/src/components/samples/details/SampleDetailsLineage.js @@ -1,4 +1,4 @@ -import React from "react"; +import React, { useEffect, useState } from "react"; import { connect } from "react-redux"; import { useHistory } from "react-router-dom"; @@ -24,110 +24,145 @@ const SampleDetailsLineage = ({ }) => { const history = useHistory() - let root = new GraphADT(sample) + const [loading, setLoading] = useState(true) + const [nodes, setNodes] = useState([]) + const [links, setLinks] = useState([]) - // Depth-First Search - const stack = [[undefined, root]] - while (stack.length > 0) { - const [_, top] = stack.pop() - const sample = top.data + class MissingData extends Error {} - // find children for sample on top of stack - top.edges = sample - ?.process_measurements - ?.map((id) => { - // get process measurement - - if (!(id in processMeasurementsByID)) - withProcessMeasurement(processMeasurementsByID, id, process => process.id) - - return processMeasurementsByID[id] - }) - .filter((p) => { - // ignore process measurement if - // child_sample field is null (or undefined) + async function fetchProcessMeasurement(id) { + if (id in processMeasurementsByID && processMeasurementsByID[id]) { + return processMeasurementsByID[id] + } else { + withProcessMeasurement(processMeasurementsByID, id, process => process) + throw new MissingData(`Missing Process Measurement #${id}`) + } + } - const id = p?.child_sample + async function fetchSample(id) { + if (id in samplesByID && samplesByID[id]) { + return samplesByID[id] + } else { + withSample(samplesByID, id, s => s) + throw new MissingData(`Missing Sample #${id}`) + } + } - if (id !== undefined && !samplesByID[id]) { - withSample(samplesByID, id, sample => sample.id) - } + async function fetchEdgesOfSample(sample, graphs = new Map()) { + const processMeasurements = (await Promise.all( + sample + .process_measurements + .map(fetchProcessMeasurement) + )).filter((p) => p.child_sample !== null) - return id !== undefined && id !== null + const processMeasurementsAndChildSamples = (await Promise.all( + processMeasurements.map(async (p) => { + return [p, await fetchSample(p.child_sample)] }) - .map((p) => { - // create new subtree + )) - const id = p?.child_sample - const s = id in samplesByID ? samplesByID[id] : undefined + // had to use reduce in order to avoid + // race condition on the `graphs` + const edges = await + processMeasurementsAndChildSamples + .reduce(async (promise, [p, s]) => { + const prev = await promise - return [p, new GraphADT(s)] - }) - top.edges = top.edges ? top.edges : [] + if (!graphs.has(s.id)) { + graphs.set(s.id, new GraphADT(s, await fetchEdgesOfSample(s))) + } - stack.push(...top.edges) + return [...prev, [p, graphs.get(s.id)]] + }, Promise.resolve([])) + + return edges } - // add parents - while (root.data[0]?.child_of?.length > 0) { - const child = root.data[0].id + async function fetchParentRoots(rootOfSubGraph, graphs = new Map()) { + const parentSamples = (await Promise.all( + rootOfSubGraph.data.child_of.map(fetchSample) + )) - const child_of = root.data[0].child_of - const parent_sample = samplesByID[child_of] - const parent_process = parent_sample - ?.process_measurements - ?.map((id) => { - // get process measurement + const parentGraphs = (await + parentSamples.reduce(async (promise, s) => { + const prev = await promise - if (!(id in processMeasurementsByID)) - withProcessMeasurement(processMeasurementsByID, id, process => process.id) + if (!graphs.has(s.id)) { + const p = ( + await Promise.all( + s.process_measurements.map(fetchProcessMeasurement) + ) + ).find((p) => { + // find process that created the child - return processMeasurementsByID[id] - }) - ?.find((p) => - // find process measurement that created 'child' + p.child_sample === rootOfSubGraph.data.id + }) - p?.child_sample == child - ) + graphs.set(s.id, new GraphADT(s, [p, rootOfSubGraph])) + } - // fetch parent - if (!parent_sample) - withSample(samplesByID, child_of, sample => sample.id) + return [...prev, ...await fetchParentRoots(graphs.get(s.id))] + }, Promise.resolve([])) + ).flat() - // create new supertree - root = new GraphADT(parent_sample, [[parent_process, root]]) + return parentGraphs } - const graphData = root.reduceNeighbors((parent_sample, children) => { - // produce nodes and edges objects - // that React Flow recognizes - - const nodes = children.map(([_0, _1, c]) => c.nodes).flat() - const links = children.map(([_0, _1, c]) => c.links).flat() - - let color = "black" - if (parent_sample?.quality_flag !== null && parent_sample?.quantity_flag !== null) { - color = parent_sample?.quality_flag && parent_sample?.quantity_flag ? "green" : "red" - } + useEffect(() => { + const graphs = new Map(); + + (async () => { + // i realized i don't really need to build a graph + // because the `graphs` already contains all the nodes + // and each node contains edges + + const children = await fetchEdgesOfSample(sample, graphs) + const subRoot = new GraphADT(sample, children) + await fetchParentRoots(subRoot, graphs) + + const [nodes, links] = Array.from(graphs.values()).reduce(([nodes, links], g) => { + const parent_sample = g.data + const children = g.edges + + let color = "black" + if (parent_sample.quality_flag !== null && parent_sample.quantity_flag !== null) { + color = parent_sample.quality_flag && parent_sample.quantity_flag ? "green" : "red" + } - nodes.push({ - id: parent_sample?.id?.toString() || "", - label: parent_sample?.name || "", - symbolType: parent_sample?.id === sample?.id ? "star" : "circle", - color - }) - links.push(...children.map(([process, child_graph, _]) => { - const sample_child = child_graph.data - - return { - id: process?.id?.toString() || "", - label: process?.protocol in protocolsByID ? protocolsByID[process?.protocol]?.name : "", - source: parent_sample?.id?.toString() || "", - target: sample_child?.id?.toString() || "", - } - })) - return { nodes, links } - }) + return [ + [ + { + id: parent_sample.id.toString(), + label: parent_sample.name, + symbolType: parent_sample.id === sample.id ? "star" : "circle", + color + }, + ...nodes + ], + [ + ...children.map(([process, child_graph]) => { + const child_sample = child_graph.data + + return { + id: process.id.toString(), + label: process.protocol in protocolsByID ? protocolsByID[process.protocol]?.name : "", + source: parent_sample.id.toString(), + target: child_sample.id.toString(), + } + }), + ...links + ] + ] + }, [[], []]) + + setNodes(nodes) + setLinks(links) + setLoading(false) + })().catch((err) => console.error(err)) + + }, [samplesByID, processMeasurementsByID, protocolsByID]) + + const graphData = { nodes, links } const graphConfig = { height: 400, @@ -160,20 +195,24 @@ const SampleDetailsLineage = ({ return ( <> - history.push(`/samples/${id}`)} - onClickLink={(source, target) => { - const linkId = graphData.links.find( - (link) => { - return (link.source === source && link.target === target) - })?.id - - history.push(`/process-measurements/${linkId ?? sample?.id}`) - }} - /> + { + loading + ? "Loading..." + : history.push(`/samples/${id}`)} + onClickLink={(source, target) => { + const linkId = graphData.links.find( + (link) => { + return (link.source === source && link.target === target) + })?.id + + history.push(`/process-measurements/${linkId ?? sample?.id}`) + }} + /> + } ) } diff --git a/frontend/src/utils/graph.js b/frontend/src/utils/graph.js index 8de404316d..cbabe0e575 100644 --- a/frontend/src/utils/graph.js +++ b/frontend/src/utils/graph.js @@ -1,5 +1,3 @@ -let nodeID = 0 - /* * A class that represents a graph */ @@ -10,7 +8,6 @@ class Graph { * @param {any[]} edges array of [edge data, child graph] */ constructor(data, edges = []) { - this.id = nodeID++; this.data = data; this.edges = edges; } From 210b770d96f990ccfa2d6f18781bc70305ddd3e5 Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Fri, 13 May 2022 10:08:06 -0400 Subject: [PATCH 21/68] give up on async --- .../samples/details/SampleDetailsLineage.js | 202 ++++++++---------- 1 file changed, 89 insertions(+), 113 deletions(-) diff --git a/frontend/src/components/samples/details/SampleDetailsLineage.js b/frontend/src/components/samples/details/SampleDetailsLineage.js index fc2532d811..5a3e607cae 100644 --- a/frontend/src/components/samples/details/SampleDetailsLineage.js +++ b/frontend/src/components/samples/details/SampleDetailsLineage.js @@ -24,149 +24,121 @@ const SampleDetailsLineage = ({ }) => { const history = useHistory() - const [loading, setLoading] = useState(true) - const [nodes, setNodes] = useState([]) - const [links, setLinks] = useState([]) - - class MissingData extends Error {} - - async function fetchProcessMeasurement(id) { - if (id in processMeasurementsByID && processMeasurementsByID[id]) { - return processMeasurementsByID[id] - } else { - withProcessMeasurement(processMeasurementsByID, id, process => process) - throw new MissingData(`Missing Process Measurement #${id}`) - } + const [graphData, setGraphData] = useState({ nodes: [], links: [] }) + + const [width, setWidth] = useState(400) + const [height, setHeight] = useState(400) + + function fetchProcessMeasurement(id) { + return withProcessMeasurement(processMeasurementsByID, id, process => process) } - async function fetchSample(id) { - if (id in samplesByID && samplesByID[id]) { - return samplesByID[id] - } else { - withSample(samplesByID, id, s => s) - throw new MissingData(`Missing Sample #${id}`) - } + function fetchSample(id) { + return withSample(samplesByID, id, s => s) } - async function fetchEdgesOfSample(sample, graphs = new Map()) { - const processMeasurements = (await Promise.all( - sample - .process_measurements + function fetchEdgesOfSample(sample, graphs) { + const processMeasurements = + sample.process_measurements .map(fetchProcessMeasurement) - )).filter((p) => p.child_sample !== null) + .filter((p) => p) + .filter((p) => p.child_sample !== null) - const processMeasurementsAndChildSamples = (await Promise.all( - processMeasurements.map(async (p) => { - return [p, await fetchSample(p.child_sample)] - }) - )) + const processMeasurementsAndChildSamples = + processMeasurements + .map((p) => [p, fetchSample(p.child_sample)]) + .filter(([_, s]) => s) - // had to use reduce in order to avoid - // race condition on the `graphs` - const edges = await + const edges = processMeasurementsAndChildSamples - .reduce(async (promise, [p, s]) => { - const prev = await promise - + .reduce((prev, [p, s]) => { if (!graphs.has(s.id)) { - graphs.set(s.id, new GraphADT(s, await fetchEdgesOfSample(s))) + graphs.set(s.id, new GraphADT(s, fetchEdgesOfSample(s, graphs))) } return [...prev, [p, graphs.get(s.id)]] - }, Promise.resolve([])) + }, []) return edges } - async function fetchParentRoots(rootOfSubGraph, graphs = new Map()) { - const parentSamples = (await Promise.all( - rootOfSubGraph.data.child_of.map(fetchSample) - )) - - const parentGraphs = (await - parentSamples.reduce(async (promise, s) => { - const prev = await promise + function fetchParentRoots(rootOfSubGraph, graphs) { + const parentSamples = + rootOfSubGraph.data.child_of + .map(fetchSample) + .filter((s) => s) - if (!graphs.has(s.id)) { - const p = ( - await Promise.all( - s.process_measurements.map(fetchProcessMeasurement) - ) - ).find((p) => { - // find process that created the child - - p.child_sample === rootOfSubGraph.data.id - }) + const parentGraphs = + parentSamples + .reduce((prev, s) => { + if (!graphs.has(s.id)) { + const ps = + s.process_measurements + .map(fetchProcessMeasurement) + .filter((p) => p) + .filter((p) => p.child_sample === rootOfSubGraph.data.id) - graphs.set(s.id, new GraphADT(s, [p, rootOfSubGraph])) - } + graphs.set(s.id, new GraphADT(s, ps.map((p) => [p, rootOfSubGraph]))) + } - return [...prev, ...await fetchParentRoots(graphs.get(s.id))] - }, Promise.resolve([])) - ).flat() + return [...prev, ...fetchParentRoots(graphs.get(s.id), graphs)] + }, []).flat() - return parentGraphs + return parentGraphs.length > 0 ? parentGraphs : [rootOfSubGraph] } useEffect(() => { const graphs = new Map(); - (async () => { - // i realized i don't really need to build a graph - // because the `graphs` already contains all the nodes - // and each node contains edges - - const children = await fetchEdgesOfSample(sample, graphs) - const subRoot = new GraphADT(sample, children) - await fetchParentRoots(subRoot, graphs) + const children = fetchEdgesOfSample(sample, graphs) + const midRoot = new GraphADT(sample, children) + graphs.set(sample.id, midRoot) + const roots = fetchParentRoots(midRoot, graphs) - const [nodes, links] = Array.from(graphs.values()).reduce(([nodes, links], g) => { - const parent_sample = g.data + setGraphData( + Array.from(graphs.values()).reduce(({ nodes, links }, g) => { + const curr_sample = g.data const children = g.edges - + let color = "black" - if (parent_sample.quality_flag !== null && parent_sample.quantity_flag !== null) { - color = parent_sample.quality_flag && parent_sample.quantity_flag ? "green" : "red" + if (curr_sample.quality_flag !== null && curr_sample.quantity_flag !== null) { + color = curr_sample.quality_flag && curr_sample.quantity_flag ? "green" : "red" } - return [ - [ + return { + nodes: [ + ...nodes, { - id: parent_sample.id.toString(), - label: parent_sample.name, - symbolType: parent_sample.id === sample.id ? "star" : "circle", - color + id: curr_sample.id.toString(), + label: curr_sample.name, + symbolType: curr_sample.id === sample.id ? "star" : "circle", + color, + x: (width / 2).toFixed(), + y: (height / 2).toFixed(), }, - ...nodes ], - [ - ...children.map(([process, child_graph]) => { - const child_sample = child_graph.data - - return { - id: process.id.toString(), - label: process.protocol in protocolsByID ? protocolsByID[process.protocol]?.name : "", - source: parent_sample.id.toString(), - target: child_sample.id.toString(), - } - }), - ...links + links: [ + ...links, + ...children + .map(([process, child_graph]) => { + const child_sample = child_graph.data + + return { + id: process.id.toString(), + label: process.protocol in protocolsByID ? protocolsByID[process.protocol]?.name : "", + source: curr_sample.id.toString(), + target: child_sample.id.toString(), + } + }), ] - ] - }, [[], []]) - - setNodes(nodes) - setLinks(links) - setLoading(false) - })().catch((err) => console.error(err)) - - }, [samplesByID, processMeasurementsByID, protocolsByID]) - - const graphData = { nodes, links } + } + }, { nodes: [], links: [] }) + ) + }, [sample, samplesByID, processMeasurementsByID, protocolsByID]) const graphConfig = { - height: 400, - width: 400, + height, + width, staticGraph: false, directed: true, maxZoom: 12, @@ -180,13 +152,17 @@ const SampleDetailsLineage = ({ node: { color: "#d3d3d3", fontColor: "black", + fontSize: 10, renderLabel: true, - labelProperty: node => `${node.label}` + labelProperty: node => `${node.label}`, + x: (width / 2).toFixed(), + y: (height / 2).toFixed(), }, link: { color: "lightgray", fontColor: "black", - strokeWidth: 3, + fontSize: 10, + strokeWidth: 5, type: "STRAIGHT", renderLabel: true, labelProperty: link => `${link.label}` @@ -196,9 +172,8 @@ const SampleDetailsLineage = ({ return ( <> { - loading - ? "Loading..." - : 0 + ? + : <>Loading... } ) From ab02a2a6c953878959214e3508a7102567bbaac1 Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Fri, 13 May 2022 16:39:22 -0400 Subject: [PATCH 22/68] reject undefined values --- .../samples/details/SampleDetailsLineage.js | 123 ++++++++++-------- 1 file changed, 70 insertions(+), 53 deletions(-) diff --git a/frontend/src/components/samples/details/SampleDetailsLineage.js b/frontend/src/components/samples/details/SampleDetailsLineage.js index 5a3e607cae..c054aaf39a 100644 --- a/frontend/src/components/samples/details/SampleDetailsLineage.js +++ b/frontend/src/components/samples/details/SampleDetailsLineage.js @@ -26,8 +26,18 @@ const SampleDetailsLineage = ({ const [graphData, setGraphData] = useState({ nodes: [], links: [] }) - const [width, setWidth] = useState(400) - const [height, setHeight] = useState(400) + const [width, setWidth] = useState(1280) + const [height, setHeight] = useState(720) + + class MissingData extends Error { } + + function rejectUndefined(x) { + if (x) { + return true + } else { + throw new MissingData() + } + } function fetchProcessMeasurement(id) { return withProcessMeasurement(processMeasurementsByID, id, process => process) @@ -41,13 +51,14 @@ const SampleDetailsLineage = ({ const processMeasurements = sample.process_measurements .map(fetchProcessMeasurement) - .filter((p) => p) + .filter(rejectUndefined) .filter((p) => p.child_sample !== null) const processMeasurementsAndChildSamples = processMeasurements - .map((p) => [p, fetchSample(p.child_sample)]) - .filter(([_, s]) => s) + .map((p) => fetchSample(p.child_sample)) + .filter(rejectUndefined) + .map((s, i) => [processMeasurements[i], s]) const edges = processMeasurementsAndChildSamples @@ -66,7 +77,7 @@ const SampleDetailsLineage = ({ const parentSamples = rootOfSubGraph.data.child_of .map(fetchSample) - .filter((s) => s) + .filter(rejectUndefined) const parentGraphs = parentSamples @@ -75,7 +86,7 @@ const SampleDetailsLineage = ({ const ps = s.process_measurements .map(fetchProcessMeasurement) - .filter((p) => p) + .filter(rejectUndefined) .filter((p) => p.child_sample === rootOfSubGraph.data.id) graphs.set(s.id, new GraphADT(s, ps.map((p) => [p, rootOfSubGraph]))) @@ -88,52 +99,58 @@ const SampleDetailsLineage = ({ } useEffect(() => { - const graphs = new Map(); - - const children = fetchEdgesOfSample(sample, graphs) - const midRoot = new GraphADT(sample, children) - graphs.set(sample.id, midRoot) - const roots = fetchParentRoots(midRoot, graphs) - - setGraphData( - Array.from(graphs.values()).reduce(({ nodes, links }, g) => { - const curr_sample = g.data - const children = g.edges - - let color = "black" - if (curr_sample.quality_flag !== null && curr_sample.quantity_flag !== null) { - color = curr_sample.quality_flag && curr_sample.quantity_flag ? "green" : "red" - } - - return { - nodes: [ - ...nodes, - { - id: curr_sample.id.toString(), - label: curr_sample.name, - symbolType: curr_sample.id === sample.id ? "star" : "circle", - color, - x: (width / 2).toFixed(), - y: (height / 2).toFixed(), - }, - ], - links: [ - ...links, - ...children - .map(([process, child_graph]) => { - const child_sample = child_graph.data - - return { - id: process.id.toString(), - label: process.protocol in protocolsByID ? protocolsByID[process.protocol]?.name : "", - source: curr_sample.id.toString(), - target: child_sample.id.toString(), - } - }), - ] - } - }, { nodes: [], links: [] }) - ) + try { + const graphs = new Map(); + + const children = fetchEdgesOfSample(sample, graphs) + const midRoot = new GraphADT(sample, children) + graphs.set(sample.id, midRoot) + const roots = fetchParentRoots(midRoot, graphs) + + setGraphData( + Array.from(graphs.values()).reduce(({ nodes, links }, g) => { + const curr_sample = g.data + const children = g.edges + + let color = "black" + if (curr_sample.quality_flag !== null && curr_sample.quantity_flag !== null) { + color = curr_sample.quality_flag && curr_sample.quantity_flag ? "green" : "red" + } + + return { + nodes: [ + ...nodes, + { + id: curr_sample.id.toString(), + label: curr_sample.name, + symbolType: curr_sample.id === sample.id ? "star" : "circle", + color, + x: (width / 2).toFixed(), + y: (height / 2).toFixed(), + }, + ], + links: [ + ...links, + ...children + .map(([process, child_graph]) => { + const child_sample = child_graph.data + + return { + id: process.id.toString(), + label: process.protocol in protocolsByID ? protocolsByID[process.protocol]?.name : "", + source: curr_sample.id.toString(), + target: child_sample.id.toString(), + } + }), + ] + } + }, { nodes: [], links: [] }) + ) + } catch (err) { + if (!(err instanceof MissingData)) { + throw err + } + } }, [sample, samplesByID, processMeasurementsByID, protocolsByID]) const graphConfig = { From c87082afcaccfc281a3c53f93611a6ab8cace3f9 Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Mon, 16 May 2022 08:53:28 -0400 Subject: [PATCH 23/68] don't throw exception --- frontend/src/components/samples/details/SampleDetailsLineage.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/frontend/src/components/samples/details/SampleDetailsLineage.js b/frontend/src/components/samples/details/SampleDetailsLineage.js index c054aaf39a..350f299eca 100644 --- a/frontend/src/components/samples/details/SampleDetailsLineage.js +++ b/frontend/src/components/samples/details/SampleDetailsLineage.js @@ -35,7 +35,7 @@ const SampleDetailsLineage = ({ if (x) { return true } else { - throw new MissingData() + return false } } From 4137e4752ab1b578925bc1730f34fcd72b3c979a Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Mon, 16 May 2022 09:59:48 -0400 Subject: [PATCH 24/68] use dagre --- frontend/package-lock.json | 36 ++++++++ frontend/package.json | 1 + .../samples/details/SampleDetailsLineage.js | 92 +++++++++---------- 3 files changed, 83 insertions(+), 46 deletions(-) diff --git a/frontend/package-lock.json b/frontend/package-lock.json index c64c0c141d..e1a4bbb337 100644 --- a/frontend/package-lock.json +++ b/frontend/package-lock.json @@ -15,6 +15,7 @@ "bowser": "^2.11.0", "cheerio": "^1.0.0-rc.9", "cross-fetch": "^3.1.5", + "dagre": "^0.8.5", "date-fns": "^2.15.0", "debounce": "^1.2.0", "dompurify": "^2.2.7", @@ -4329,6 +4330,15 @@ "d3-transition": "1" } }, + "node_modules/dagre": { + "version": "0.8.5", + "resolved": "https://registry.npmjs.org/dagre/-/dagre-0.8.5.tgz", + "integrity": "sha512-/aTqmnRta7x7MCCpExk7HQL2O4owCT2h8NT//9I1OQ9vt29Pa0BzSAkR5lwFUcQ7491yVi/3CXU9jQ5o0Mn2Sw==", + "dependencies": { + "graphlib": "^2.1.8", + "lodash": "^4.17.15" + } + }, "node_modules/dashdash": { "version": "1.14.1", "resolved": "https://registry.npmjs.org/dashdash/-/dashdash-1.14.1.tgz", @@ -5760,6 +5770,14 @@ "resolved": "https://registry.npmjs.org/graceful-fs/-/graceful-fs-4.2.4.tgz", "integrity": "sha512-WjKPNJF79dtJAVniUlGGWHYGz2jWxT6VhN/4m1NdkbZ2nOsEF+cI1Edgql5zCRhs/VsQYRvrXctxktVXZUkixw==" }, + "node_modules/graphlib": { + "version": "2.1.8", + "resolved": "https://registry.npmjs.org/graphlib/-/graphlib-2.1.8.tgz", + "integrity": "sha512-jcLLfkpoVGmH7/InMC/1hIvOPSUh38oJtGhvrOFGzioE1DZ+0YW16RgmOJhHiuWTvGiJQ9Z1Ik43JvkRPRvE+A==", + "dependencies": { + "lodash": "^4.17.15" + } + }, "node_modules/handle-thing": { "version": "2.0.1", "resolved": "https://registry.npmjs.org/handle-thing/-/handle-thing-2.0.1.tgz", @@ -14636,6 +14654,7 @@ "dependencies": { "ansi-regex": { "version": "5.0.0", + "integrity": "sha512-bY6fj56OUQ0hU1KjFNDQuJFezqKdrAyFdIevADiqrWHwSlbmBNMHp5ak2f40Pm8JTFyM2mqxkG6ngkHO11f/lg==", "dev": true }, "emoji-regex": { @@ -15654,6 +15673,15 @@ "d3-transition": "1" } }, + "dagre": { + "version": "0.8.5", + "resolved": "https://registry.npmjs.org/dagre/-/dagre-0.8.5.tgz", + "integrity": "sha512-/aTqmnRta7x7MCCpExk7HQL2O4owCT2h8NT//9I1OQ9vt29Pa0BzSAkR5lwFUcQ7491yVi/3CXU9jQ5o0Mn2Sw==", + "requires": { + "graphlib": "^2.1.8", + "lodash": "^4.17.15" + } + }, "dashdash": { "version": "1.14.1", "resolved": "https://registry.npmjs.org/dashdash/-/dashdash-1.14.1.tgz", @@ -16829,6 +16857,14 @@ "resolved": "https://registry.npmjs.org/graceful-fs/-/graceful-fs-4.2.4.tgz", "integrity": "sha512-WjKPNJF79dtJAVniUlGGWHYGz2jWxT6VhN/4m1NdkbZ2nOsEF+cI1Edgql5zCRhs/VsQYRvrXctxktVXZUkixw==" }, + "graphlib": { + "version": "2.1.8", + "resolved": "https://registry.npmjs.org/graphlib/-/graphlib-2.1.8.tgz", + "integrity": "sha512-jcLLfkpoVGmH7/InMC/1hIvOPSUh38oJtGhvrOFGzioE1DZ+0YW16RgmOJhHiuWTvGiJQ9Z1Ik43JvkRPRvE+A==", + "requires": { + "lodash": "^4.17.15" + } + }, "handle-thing": { "version": "2.0.1", "resolved": "https://registry.npmjs.org/handle-thing/-/handle-thing-2.0.1.tgz", diff --git a/frontend/package.json b/frontend/package.json index de36d51859..4b013f62e0 100644 --- a/frontend/package.json +++ b/frontend/package.json @@ -27,6 +27,7 @@ "bowser": "^2.11.0", "cheerio": "^1.0.0-rc.9", "cross-fetch": "^3.1.5", + "dagre": "^0.8.5", "date-fns": "^2.15.0", "debounce": "^1.2.0", "dompurify": "^2.2.7", diff --git a/frontend/src/components/samples/details/SampleDetailsLineage.js b/frontend/src/components/samples/details/SampleDetailsLineage.js index 350f299eca..6cdbb313a0 100644 --- a/frontend/src/components/samples/details/SampleDetailsLineage.js +++ b/frontend/src/components/samples/details/SampleDetailsLineage.js @@ -10,6 +10,8 @@ import { } from "../../../utils/withItem"; import GraphADT from "../../../utils/graph"; +import dagre from "dagre" + const mapStateToProps = state => ({ samplesByID: state.samples.itemsByID, processMeasurementsByID: state.processMeasurements.itemsByID, @@ -107,45 +109,50 @@ const SampleDetailsLineage = ({ graphs.set(sample.id, midRoot) const roots = fetchParentRoots(midRoot, graphs) - setGraphData( - Array.from(graphs.values()).reduce(({ nodes, links }, g) => { - const curr_sample = g.data - const children = g.edges + const g = new dagre.graphlib.Graph({ directed: true }) + .setGraph({ rankdir: "LR", ranksep: 150, nodesep: 150, marginx: 50, marginy: 50 }) + .setDefaultEdgeLabel(function () { return {}; }); + + for (const [_, graph] of graphs) { + const curr_sample = graph.data + + let color = "black" + if (curr_sample.quality_flag !== null && curr_sample.quantity_flag !== null) { + color = curr_sample.quality_flag && curr_sample.quantity_flag ? "green" : "red" + } + + g.setNode(curr_sample.id.toString(), { + id: curr_sample.id.toString(), + label: curr_sample.name, + width: 10, + height: 10, + color, + symbolType: curr_sample.id === sample.id ? "star" : "circle", + }) + graph.edges.forEach(([_, graph]) => { + g.setEdge(curr_sample.id.toString(), graph.data.id.toString()) + }) + } - let color = "black" - if (curr_sample.quality_flag !== null && curr_sample.quantity_flag !== null) { - color = curr_sample.quality_flag && curr_sample.quantity_flag ? "green" : "red" - } + dagre.layout(g) + setGraphData({ + nodes: g.nodes().map((v) => { return { - nodes: [ - ...nodes, - { - id: curr_sample.id.toString(), - label: curr_sample.name, - symbolType: curr_sample.id === sample.id ? "star" : "circle", - color, - x: (width / 2).toFixed(), - y: (height / 2).toFixed(), - }, - ], - links: [ - ...links, - ...children - .map(([process, child_graph]) => { - const child_sample = child_graph.data - - return { - id: process.id.toString(), - label: process.protocol in protocolsByID ? protocolsByID[process.protocol]?.name : "", - source: curr_sample.id.toString(), - target: child_sample.id.toString(), - } - }), - ] + ...g.node(v), + id: v, } - }, { nodes: [], links: [] }) - ) + }), + links: g.edges().map((e) => { + const [p, _] = graphs.get(parseInt(e.v)).edges.find(([_, s]) => s.data.id.toString() === e.w) + return { + id: p.id.toString(), + source: e.v, + target: e.w, + label: p.protocol in protocolsByID ? protocolsByID[p.protocol]?.name : "", + } + }) + }) } catch (err) { if (!(err instanceof MissingData)) { throw err @@ -156,29 +163,22 @@ const SampleDetailsLineage = ({ const graphConfig = { height, width, - staticGraph: false, - directed: true, + staticGraphWithDragAndDrop: true, maxZoom: 12, minZoom: 0.05, panAndZoom: true, - d3: { - gravity: -500, - linkLength: 120, - linkStrength: 2, - }, node: { color: "#d3d3d3", fontColor: "black", - fontSize: 10, + fontSize: 12, renderLabel: true, labelProperty: node => `${node.label}`, - x: (width / 2).toFixed(), - y: (height / 2).toFixed(), + labelPosition: "top", }, link: { color: "lightgray", fontColor: "black", - fontSize: 10, + fontSize: 12, strokeWidth: 5, type: "STRAIGHT", renderLabel: true, From 494014a83fb2c1b7067646a24072d599b41ed731 Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Tue, 17 May 2022 12:05:28 -0400 Subject: [PATCH 25/68] add sample_lineage service and view --- backend/fms_core/router.py | 2 + backend/fms_core/services/sample_lineage.py | 59 ++++++++++++++++++++- backend/fms_core/viewsets/__init__.py | 2 + backend/fms_core/viewsets/sample_lineage.py | 23 ++++++++ 4 files changed, 84 insertions(+), 2 deletions(-) create mode 100644 backend/fms_core/viewsets/sample_lineage.py diff --git a/backend/fms_core/router.py b/backend/fms_core/router.py index 56dabfc18f..906680437d 100644 --- a/backend/fms_core/router.py +++ b/backend/fms_core/router.py @@ -26,6 +26,7 @@ ProjectViewSet, SequenceViewSet, TaxonViewSet, + SampleLineageViewSet, ) __all__ = ["router"] @@ -56,3 +57,4 @@ router.register(r"revisions", RevisionViewSet) router.register(r"users", UserViewSet) router.register(r"groups", GroupViewSet) +router.register(r"sample-lineage", SampleLineageViewSet, basename="sample-lineage") diff --git a/backend/fms_core/services/sample_lineage.py b/backend/fms_core/services/sample_lineage.py index 43ba9480cc..d7103ecae9 100644 --- a/backend/fms_core/services/sample_lineage.py +++ b/backend/fms_core/services/sample_lineage.py @@ -1,5 +1,6 @@ -from django.core.exceptions import ValidationError -from fms_core.models import SampleLineage +from django.db.models import F +from django.core.exceptions import ValidationError, ObjectDoesNotExist +from fms_core.models import SampleLineage, Sample, ProcessMeasurement def create_sample_lineage(parent_sample, child_sample, process_measurement): @@ -25,3 +26,57 @@ def create_sample_lineage(parent_sample, child_sample, process_measurement): errors.append(str(e)) return (sample_lineage, errors, warnings) + +def create_sample_lineage_graph(parent_sample): + errors = [] + + if not parent_sample: + errors.append(f"Sample is required for sample lineage graph creation") + + nodes = [parent_sample] + edges = [] + + if not errors: + def add_lineage(process_measurements): + queryset = process_measurements.select_related("process").prefetch_related("lineage") + queryset = queryset.annotate(child_sample=F("lineage__child")) + queryset = queryset.annotate(child_sample_name=F("lineage__child__name")) + queryset = queryset.annotate(source_sample_name=F("source_sample__name")) + return queryset + + def query_set_iterator(f, l): + for x in l: + try: + yield f(x) + except ObjectDoesNotExist: + yield None + + # fetch children + stack = [parent_sample] + visited = {parent_sample.id} + while stack: + parent_sample = stack.pop() + new_process_measurements = [ + p + for p in add_lineage(parent_sample.process_measurement.all()) + ] + + sample_lineages = [ + sl + for sl in query_set_iterator(lambda p: p.lineage.get(), new_process_measurements) + ] + + new_child_samples = [ + sl.child + for sl in sample_lineages + if sl and sl.child.id not in visited + ] + + nodes.extend(new_child_samples) + edges.extend(new_process_measurements) + + stack.extend(new_child_samples) + visited.update(s.id for s in new_child_samples) + + + return (nodes, edges, errors) \ No newline at end of file diff --git a/backend/fms_core/viewsets/__init__.py b/backend/fms_core/viewsets/__init__.py index 7a19d9be6e..23a061126e 100644 --- a/backend/fms_core/viewsets/__init__.py +++ b/backend/fms_core/viewsets/__init__.py @@ -23,6 +23,7 @@ from .platform import PlatformViewSet from .library_type import LibraryTypeViewSet from .taxon import TaxonViewSet +from .sample_lineage import SampleLineageViewSet __all__ = [ "ContainerViewSet", @@ -50,4 +51,5 @@ "PlatformViewSet", "LibraryTypeViewSet", "TaxonViewSet", + "SampleLineageViewSet" ] \ No newline at end of file diff --git a/backend/fms_core/viewsets/sample_lineage.py b/backend/fms_core/viewsets/sample_lineage.py new file mode 100644 index 0000000000..291765644d --- /dev/null +++ b/backend/fms_core/viewsets/sample_lineage.py @@ -0,0 +1,23 @@ +from tkinter import W +from fms_core.services.sample_lineage import create_sample_lineage_graph +from rest_framework import viewsets +from rest_framework.decorators import action +from rest_framework.response import Response +from django.core.exceptions import ValidationError + +from fms_core.models import Sample +from fms_core.serializers import SampleSerializer, ProcessMeasurementSerializer + +class SampleLineageViewSet(viewsets.ViewSet): + @action(detail=True, methods=["get"]) + def graph(self, _request, pk): + parent_sample = Sample.objects.get(pk=pk) + nodes, edges, errors = create_sample_lineage_graph(parent_sample) + + if errors: + raise ValidationError(errors) + else: + return Response({ + "nodes": [SampleSerializer(s).data for s in nodes], + "edges": [ProcessMeasurementSerializer(p).data for p in edges] + }) From 01deb57245b5e513375fccf6f5ae5a27ccf0ae4b Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Tue, 17 May 2022 12:10:36 -0400 Subject: [PATCH 26/68] integrate SampleDetailsLineage with sample_lineage api --- .../samples/details/SampleDetailsLineage.js | 183 ++++++------------ frontend/src/utils/api.js | 4 + 2 files changed, 65 insertions(+), 122 deletions(-) diff --git a/frontend/src/components/samples/details/SampleDetailsLineage.js b/frontend/src/components/samples/details/SampleDetailsLineage.js index 6cdbb313a0..28d61a8332 100644 --- a/frontend/src/components/samples/details/SampleDetailsLineage.js +++ b/frontend/src/components/samples/details/SampleDetailsLineage.js @@ -11,14 +11,17 @@ import { import GraphADT from "../../../utils/graph"; import dagre from "dagre" +import api, { withToken } from "../../../utils/api"; const mapStateToProps = state => ({ + token: state.auth.tokens.access, samplesByID: state.samples.itemsByID, processMeasurementsByID: state.processMeasurements.itemsByID, protocolsByID: state.protocols.itemsByID, }); const SampleDetailsLineage = ({ + token, sample, samplesByID, processMeasurementsByID, @@ -31,134 +34,70 @@ const SampleDetailsLineage = ({ const [width, setWidth] = useState(1280) const [height, setHeight] = useState(720) - class MissingData extends Error { } - - function rejectUndefined(x) { - if (x) { - return true - } else { - return false - } - } - - function fetchProcessMeasurement(id) { - return withProcessMeasurement(processMeasurementsByID, id, process => process) - } - - function fetchSample(id) { - return withSample(samplesByID, id, s => s) - } - - function fetchEdgesOfSample(sample, graphs) { - const processMeasurements = - sample.process_measurements - .map(fetchProcessMeasurement) - .filter(rejectUndefined) - .filter((p) => p.child_sample !== null) - - const processMeasurementsAndChildSamples = - processMeasurements - .map((p) => fetchSample(p.child_sample)) - .filter(rejectUndefined) - .map((s, i) => [processMeasurements[i], s]) - - const edges = - processMeasurementsAndChildSamples - .reduce((prev, [p, s]) => { - if (!graphs.has(s.id)) { - graphs.set(s.id, new GraphADT(s, fetchEdgesOfSample(s, graphs))) - } - - return [...prev, [p, graphs.get(s.id)]] - }, []) - - return edges - } - - function fetchParentRoots(rootOfSubGraph, graphs) { - const parentSamples = - rootOfSubGraph.data.child_of - .map(fetchSample) - .filter(rejectUndefined) - - const parentGraphs = - parentSamples - .reduce((prev, s) => { - if (!graphs.has(s.id)) { - const ps = - s.process_measurements - .map(fetchProcessMeasurement) - .filter(rejectUndefined) - .filter((p) => p.child_sample === rootOfSubGraph.data.id) - - graphs.set(s.id, new GraphADT(s, ps.map((p) => [p, rootOfSubGraph]))) + useEffect(() => { + if (sample?.id !== undefined) { + withToken(token, api.sample_lineage.get)(sample.id).then((graph) => { + graph = graph.data + + const g = new dagre.graphlib.Graph({ directed: true }) + .setGraph({ rankdir: "LR", ranksep: 150, nodesep: 150, marginx: 50, marginy: 50 }) + .setDefaultEdgeLabel(function () { return {}; }); + + graph.nodes.forEach((curr_sample) => { + let color = "black" + if (curr_sample.quality_flag !== null && curr_sample.quantity_flag !== null) { + color = curr_sample.quality_flag && curr_sample.quantity_flag ? "green" : "red" } - return [...prev, ...fetchParentRoots(graphs.get(s.id), graphs)] - }, []).flat() - - return parentGraphs.length > 0 ? parentGraphs : [rootOfSubGraph] - } - - useEffect(() => { - try { - const graphs = new Map(); - - const children = fetchEdgesOfSample(sample, graphs) - const midRoot = new GraphADT(sample, children) - graphs.set(sample.id, midRoot) - const roots = fetchParentRoots(midRoot, graphs) - - const g = new dagre.graphlib.Graph({ directed: true }) - .setGraph({ rankdir: "LR", ranksep: 150, nodesep: 150, marginx: 50, marginy: 50 }) - .setDefaultEdgeLabel(function () { return {}; }); - - for (const [_, graph] of graphs) { - const curr_sample = graph.data - - let color = "black" - if (curr_sample.quality_flag !== null && curr_sample.quantity_flag !== null) { - color = curr_sample.quality_flag && curr_sample.quantity_flag ? "green" : "red" - } - - g.setNode(curr_sample.id.toString(), { - id: curr_sample.id.toString(), - label: curr_sample.name, - width: 10, - height: 10, - color, - symbolType: curr_sample.id === sample.id ? "star" : "circle", + g.setNode(curr_sample.id.toString(), { + id: curr_sample.id.toString(), + label: curr_sample.name, + width: 10, + height: 10, + color, + symbolType: curr_sample.id === sample.id ? "star" : "circle", + }) }) - graph.edges.forEach(([_, graph]) => { - g.setEdge(curr_sample.id.toString(), graph.data.id.toString()) - }) - } - - dagre.layout(g) - setGraphData({ - nodes: g.nodes().map((v) => { - return { - ...g.node(v), - id: v, - } - }), - links: g.edges().map((e) => { - const [p, _] = graphs.get(parseInt(e.v)).edges.find(([_, s]) => s.data.id.toString() === e.w) - return { - id: p.id.toString(), - source: e.v, - target: e.w, - label: p.protocol in protocolsByID ? protocolsByID[p.protocol]?.name : "", - } + graph.edges + .filter((process) => process.child_sample !== null) + .forEach((process) => { + g.setEdge(process.source_sample, process.child_sample) + }) + + const pair_to_process = graph.edges + .filter((process) => process.child_sample !== null) + .reduce((prev, p) => { + return { + ...prev, + [`${p.source_sample}:${p.child_sample}`]: p + } + }, {}) + + dagre.layout(g) + + setGraphData({ + nodes: g.nodes() + .map((v) => { + return { + ...g.node(v), + id: v + } + }), + links: g.edges() + .map((e) => { + const p = pair_to_process[`${e.v}:${e.w}`] + return { + id: p.id.toString(), + source: e.v, + target: e.w, + label: p.protocol in protocolsByID ? protocolsByID[p.protocol]?.name : "", + } + }) }) }) - } catch (err) { - if (!(err instanceof MissingData)) { - throw err - } } - }, [sample, samplesByID, processMeasurementsByID, protocolsByID]) + }, [sample]) const graphConfig = { height, @@ -199,7 +138,7 @@ const SampleDetailsLineage = ({ const linkId = graphData.links.find( (link) => { return (link.source === source && link.target === target) - })?.id + }).id history.push(`/process-measurements/${linkId}`) }} diff --git a/frontend/src/utils/api.js b/frontend/src/utils/api.js index 6f6e19db0b..28177787ff 100644 --- a/frontend/src/utils/api.js +++ b/frontend/src/utils/api.js @@ -204,6 +204,10 @@ const api = { query: { search: q => get("/query/search/", { q }, { abort: true }), }, + + sample_lineage: { + get: sampleId => get(`/sample-lineage/${sampleId}/graph`) + } }; From ec20601bc4e892a998568eed9ba156bdb4d80127 Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Tue, 17 May 2022 12:28:59 -0400 Subject: [PATCH 27/68] fetch parents --- backend/fms_core/services/sample_lineage.py | 39 +++++++++++++++++---- 1 file changed, 32 insertions(+), 7 deletions(-) diff --git a/backend/fms_core/services/sample_lineage.py b/backend/fms_core/services/sample_lineage.py index d7103ecae9..b86581a53e 100644 --- a/backend/fms_core/services/sample_lineage.py +++ b/backend/fms_core/services/sample_lineage.py @@ -27,13 +27,13 @@ def create_sample_lineage(parent_sample, child_sample, process_measurement): return (sample_lineage, errors, warnings) -def create_sample_lineage_graph(parent_sample): +def create_sample_lineage_graph(mid_sample): errors = [] - if not parent_sample: + if not mid_sample: errors.append(f"Sample is required for sample lineage graph creation") - nodes = [parent_sample] + nodes = [mid_sample] edges = [] if not errors: @@ -52,13 +52,13 @@ def query_set_iterator(f, l): yield None # fetch children - stack = [parent_sample] - visited = {parent_sample.id} + stack = [mid_sample] + visited = {mid_sample.id} while stack: - parent_sample = stack.pop() + child_sample = stack.pop() new_process_measurements = [ p - for p in add_lineage(parent_sample.process_measurement.all()) + for p in add_lineage(child_sample.process_measurement.all()) ] sample_lineages = [ @@ -77,6 +77,31 @@ def query_set_iterator(f, l): stack.extend(new_child_samples) visited.update(s.id for s in new_child_samples) + + def find_process_measurement(parent_sample, child_sample): + process_measurements = list(add_lineage(parent_sample.process_measurement.all())) + for p in process_measurements: + if p.child_sample == child_sample.id: + return p + + # fetch parents + stack = [mid_sample] + while stack: + child_sample = stack.pop() + + new_parent_samples = [ + s for s in child_sample.child_of.all() if s.id not in visited + ] + + new_process_measurements = [ + find_process_measurement(s, child_sample) for s in new_parent_samples + ] + + nodes.extend(new_parent_samples) + edges.extend(new_process_measurements) + + stack.extend(new_parent_samples) + visited.update(s.id for s in new_parent_samples) return (nodes, edges, errors) \ No newline at end of file From d8f8bbc8334485ed767adb4e3655f5e1f9cb6c4d Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Tue, 17 May 2022 13:20:41 -0400 Subject: [PATCH 28/68] reuse pairToProcess --- .../samples/details/SampleDetailsLineage.js | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/frontend/src/components/samples/details/SampleDetailsLineage.js b/frontend/src/components/samples/details/SampleDetailsLineage.js index 28d61a8332..081716a23d 100644 --- a/frontend/src/components/samples/details/SampleDetailsLineage.js +++ b/frontend/src/components/samples/details/SampleDetailsLineage.js @@ -30,6 +30,7 @@ const SampleDetailsLineage = ({ const history = useHistory() const [graphData, setGraphData] = useState({ nodes: [], links: [] }) + const [pairToProcess, setPairToProcess] = useState({}) const [width, setWidth] = useState(1280) const [height, setHeight] = useState(720) @@ -65,7 +66,7 @@ const SampleDetailsLineage = ({ g.setEdge(process.source_sample, process.child_sample) }) - const pair_to_process = graph.edges + const localPairToProcess = graph.edges .filter((process) => process.child_sample !== null) .reduce((prev, p) => { return { @@ -73,6 +74,8 @@ const SampleDetailsLineage = ({ [`${p.source_sample}:${p.child_sample}`]: p } }, {}) + + setPairToProcess(localPairToProcess) dagre.layout(g) @@ -86,7 +89,7 @@ const SampleDetailsLineage = ({ }), links: g.edges() .map((e) => { - const p = pair_to_process[`${e.v}:${e.w}`] + const p = localPairToProcess[`${e.v}:${e.w}`] return { id: p.id.toString(), source: e.v, @@ -135,11 +138,7 @@ const SampleDetailsLineage = ({ config={graphConfig} onClickNode={(id, _) => history.push(`/samples/${id}`)} onClickLink={(source, target) => { - const linkId = graphData.links.find( - (link) => { - return (link.source === source && link.target === target) - }).id - + const linkId = pairToProcess[`${source}:${target}`].id history.push(`/process-measurements/${linkId}`) }} /> From 23f61cf36ca5f3920095b39857a2510a1c346d2e Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Wed, 18 May 2022 13:57:11 -0400 Subject: [PATCH 29/68] optimize backend --- backend/fms_core/services/sample_lineage.py | 133 ++++++++++++-------- backend/fms_core/viewsets/sample_lineage.py | 4 +- 2 files changed, 80 insertions(+), 57 deletions(-) diff --git a/backend/fms_core/services/sample_lineage.py b/backend/fms_core/services/sample_lineage.py index b86581a53e..c51d642187 100644 --- a/backend/fms_core/services/sample_lineage.py +++ b/backend/fms_core/services/sample_lineage.py @@ -1,4 +1,4 @@ -from django.db.models import F +from django.db.models import F, Q, Count from django.core.exceptions import ValidationError, ObjectDoesNotExist from fms_core.models import SampleLineage, Sample, ProcessMeasurement @@ -33,75 +33,98 @@ def create_sample_lineage_graph(mid_sample): if not mid_sample: errors.append(f"Sample is required for sample lineage graph creation") - nodes = [mid_sample] - edges = [] - if not errors: - def add_lineage(process_measurements): - queryset = process_measurements.select_related("process").prefetch_related("lineage") + def annotate_process_measurements(process_measurements): + queryset = process_measurements.prefetch_related("process").prefetch_related("lineage") queryset = queryset.annotate(child_sample=F("lineage__child")) - queryset = queryset.annotate(child_sample_name=F("lineage__child__name")) - queryset = queryset.annotate(source_sample_name=F("source_sample__name")) return queryset + + def annotate_samples(samples): + queryset = samples.select_related("process_measurement").prefetch_related("process_measurement__lineage") + queryset = queryset.annotate( + child_count=Count( + 'process_measurement', + filter=~Q(process_measurement__lineage__child=None) + ) + ) + return queryset + - def query_set_iterator(f, l): - for x in l: - try: - yield f(x) - except ObjectDoesNotExist: - yield None + total_new_samples = [Sample.objects.filter(pk=mid_sample.id)] + total_new_process_measurements = [] # fetch children - stack = [mid_sample] + stack = [mid_sample.id] visited = {mid_sample.id} while stack: - child_sample = stack.pop() - new_process_measurements = [ - p - for p in add_lineage(child_sample.process_measurement.all()) - ] + parent_sample_id = stack.pop() - sample_lineages = [ - sl - for sl in query_set_iterator(lambda p: p.lineage.get(), new_process_measurements) + new_process_measurements = annotate_process_measurements( + ProcessMeasurement.objects.filter(source_sample=parent_sample_id) + ).filter( + ~Q(child_sample=None) + ) + + new_child_samples_id = [ + p.child_sample for p in new_process_measurements.filter(~Q(child_sample=None)).exclude(id__in=visited) ] + new_child_samples = Sample.objects.filter(id__in=new_child_samples_id) - new_child_samples = [ - sl.child - for sl in sample_lineages - if sl and sl.child.id not in visited - ] + total_new_samples.append(new_child_samples) + total_new_process_measurements.append(new_process_measurements) - nodes.extend(new_child_samples) - edges.extend(new_process_measurements) - - stack.extend(new_child_samples) - visited.update(s.id for s in new_child_samples) - - def find_process_measurement(parent_sample, child_sample): - process_measurements = list(add_lineage(parent_sample.process_measurement.all())) - for p in process_measurements: - if p.child_sample == child_sample.id: - return p + stack.extend(s.id for s in new_child_samples) + visited.update(p.id for p in new_process_measurements) # fetch parents - stack = [mid_sample] + stack = [mid_sample.id] while stack: - child_sample = stack.pop() - - new_parent_samples = [ - s for s in child_sample.child_of.all() if s.id not in visited - ] - - new_process_measurements = [ - find_process_measurement(s, child_sample) for s in new_parent_samples - ] - - nodes.extend(new_parent_samples) - edges.extend(new_process_measurements) - - stack.extend(new_parent_samples) - visited.update(s.id for s in new_parent_samples) + child_sample_id = stack.pop() + child_sample = Sample.objects.filter(id=child_sample_id) + + child_of = child_sample.values('child_of').get()['child_of'] + # child_of is either a None, a single int, or a list of int + try: + list(child_of) + except TypeError: + child_of = [child_of] + + new_parent_samples = Sample.objects.filter(id__in=child_of).exclude(id__in=visited) + new_process_measurements = annotate_process_measurements( + ProcessMeasurement.objects.all() + ).filter( + child_sample=child_sample_id + ) + + total_new_samples.append(new_parent_samples) + total_new_process_measurements.append(new_process_measurements) + + stack.extend(s.id for s in new_parent_samples) + visited.update(p.id for p in new_process_measurements) + + + nodes = [ + s + for queryset in total_new_samples + for s in annotate_samples(queryset).values( + 'id', + 'name', + 'quality_flag', + 'quantity_flag', + 'child_count' + ) + ] + + edges = [ + p + for queryset in total_new_process_measurements + for p in queryset.values( + 'id', + 'source_sample', + 'child_sample', + 'process__protocol__name', + ) + ] return (nodes, edges, errors) \ No newline at end of file diff --git a/backend/fms_core/viewsets/sample_lineage.py b/backend/fms_core/viewsets/sample_lineage.py index 291765644d..5dbf9d6d28 100644 --- a/backend/fms_core/viewsets/sample_lineage.py +++ b/backend/fms_core/viewsets/sample_lineage.py @@ -18,6 +18,6 @@ def graph(self, _request, pk): raise ValidationError(errors) else: return Response({ - "nodes": [SampleSerializer(s).data for s in nodes], - "edges": [ProcessMeasurementSerializer(p).data for p in edges] + "nodes": nodes, + "edges": edges, }) From 027a19721144c63de8cc9105e7c851e2be510967 Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Wed, 18 May 2022 16:04:08 -0400 Subject: [PATCH 30/68] show number of children --- .../samples/details/SampleDetailsLineage.js | 29 +++++++++++++++---- 1 file changed, 24 insertions(+), 5 deletions(-) diff --git a/frontend/src/components/samples/details/SampleDetailsLineage.js b/frontend/src/components/samples/details/SampleDetailsLineage.js index 081716a23d..6b35912e74 100644 --- a/frontend/src/components/samples/details/SampleDetailsLineage.js +++ b/frontend/src/components/samples/details/SampleDetailsLineage.js @@ -53,10 +53,11 @@ const SampleDetailsLineage = ({ g.setNode(curr_sample.id.toString(), { id: curr_sample.id.toString(), label: curr_sample.name, - width: 10, - height: 10, + width: 40, + height: 40, color, symbolType: curr_sample.id === sample.id ? "star" : "circle", + child_count: curr_sample.child_count }) }) @@ -74,7 +75,7 @@ const SampleDetailsLineage = ({ [`${p.source_sample}:${p.child_sample}`]: p } }, {}) - + setPairToProcess(localPairToProcess) dagre.layout(g) @@ -82,9 +83,13 @@ const SampleDetailsLineage = ({ setGraphData({ nodes: g.nodes() .map((v) => { + const child_count = g.node(v).child_count return { ...g.node(v), - id: v + id: v, + viewGenerator: (_) => { + return Node(child_count) + } } }), links: g.edges() @@ -94,7 +99,7 @@ const SampleDetailsLineage = ({ id: p.id.toString(), source: e.v, target: e.w, - label: p.protocol in protocolsByID ? protocolsByID[p.protocol]?.name : "", + label: p.process__protocol__name, } }) }) @@ -148,4 +153,18 @@ const SampleDetailsLineage = ({ ) } +function Node(child_count) { + return ( +
+ {child_count} +
+ ) +} + export default connect(mapStateToProps, undefined)(SampleDetailsLineage); From fdea51a8dace630f751fd5c34956ed90d1902612 Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Thu, 19 May 2022 10:33:38 -0400 Subject: [PATCH 31/68] Revert "show number of children" This reverts commit 027a19721144c63de8cc9105e7c851e2be510967. --- .../samples/details/SampleDetailsLineage.js | 29 ++++--------------- 1 file changed, 5 insertions(+), 24 deletions(-) diff --git a/frontend/src/components/samples/details/SampleDetailsLineage.js b/frontend/src/components/samples/details/SampleDetailsLineage.js index 6b35912e74..081716a23d 100644 --- a/frontend/src/components/samples/details/SampleDetailsLineage.js +++ b/frontend/src/components/samples/details/SampleDetailsLineage.js @@ -53,11 +53,10 @@ const SampleDetailsLineage = ({ g.setNode(curr_sample.id.toString(), { id: curr_sample.id.toString(), label: curr_sample.name, - width: 40, - height: 40, + width: 10, + height: 10, color, symbolType: curr_sample.id === sample.id ? "star" : "circle", - child_count: curr_sample.child_count }) }) @@ -75,7 +74,7 @@ const SampleDetailsLineage = ({ [`${p.source_sample}:${p.child_sample}`]: p } }, {}) - + setPairToProcess(localPairToProcess) dagre.layout(g) @@ -83,13 +82,9 @@ const SampleDetailsLineage = ({ setGraphData({ nodes: g.nodes() .map((v) => { - const child_count = g.node(v).child_count return { ...g.node(v), - id: v, - viewGenerator: (_) => { - return Node(child_count) - } + id: v } }), links: g.edges() @@ -99,7 +94,7 @@ const SampleDetailsLineage = ({ id: p.id.toString(), source: e.v, target: e.w, - label: p.process__protocol__name, + label: p.protocol in protocolsByID ? protocolsByID[p.protocol]?.name : "", } }) }) @@ -153,18 +148,4 @@ const SampleDetailsLineage = ({ ) } -function Node(child_count) { - return ( -
- {child_count} -
- ) -} - export default connect(mapStateToProps, undefined)(SampleDetailsLineage); From 14201251419ce190427ed0a9c6ebfd1c1e62a4d7 Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Thu, 19 May 2022 10:36:19 -0400 Subject: [PATCH 32/68] optimize backend even more --- backend/fms_core/services/sample_lineage.py | 128 +++++------------- .../samples/details/SampleDetailsLineage.js | 2 +- 2 files changed, 36 insertions(+), 94 deletions(-) diff --git a/backend/fms_core/services/sample_lineage.py b/backend/fms_core/services/sample_lineage.py index c51d642187..ac3313f9d1 100644 --- a/backend/fms_core/services/sample_lineage.py +++ b/backend/fms_core/services/sample_lineage.py @@ -1,6 +1,6 @@ from django.db.models import F, Q, Count from django.core.exceptions import ValidationError, ObjectDoesNotExist -from fms_core.models import SampleLineage, Sample, ProcessMeasurement +from fms_core.models import SampleLineage, Sample, DerivedBySample, ProcessMeasurement def create_sample_lineage(parent_sample, child_sample, process_measurement): @@ -34,97 +34,39 @@ def create_sample_lineage_graph(mid_sample): errors.append(f"Sample is required for sample lineage graph creation") if not errors: - def annotate_process_measurements(process_measurements): - queryset = process_measurements.prefetch_related("process").prefetch_related("lineage") - queryset = queryset.annotate(child_sample=F("lineage__child")) - return queryset - - def annotate_samples(samples): - queryset = samples.select_related("process_measurement").prefetch_related("process_measurement__lineage") - queryset = queryset.annotate( - child_count=Count( - 'process_measurement', - filter=~Q(process_measurement__lineage__child=None) - ) - ) - return queryset - - - total_new_samples = [Sample.objects.filter(pk=mid_sample.id)] - total_new_process_measurements = [] - - # fetch children - stack = [mid_sample.id] - visited = {mid_sample.id} - while stack: - parent_sample_id = stack.pop() - - new_process_measurements = annotate_process_measurements( - ProcessMeasurement.objects.filter(source_sample=parent_sample_id) - ).filter( - ~Q(child_sample=None) - ) - - new_child_samples_id = [ - p.child_sample for p in new_process_measurements.filter(~Q(child_sample=None)).exclude(id__in=visited) - ] - new_child_samples = Sample.objects.filter(id__in=new_child_samples_id) - - total_new_samples.append(new_child_samples) - total_new_process_measurements.append(new_process_measurements) - - stack.extend(s.id for s in new_child_samples) - visited.update(p.id for p in new_process_measurements) - - # fetch parents - stack = [mid_sample.id] - while stack: - child_sample_id = stack.pop() - child_sample = Sample.objects.filter(id=child_sample_id) - - child_of = child_sample.values('child_of').get()['child_of'] - # child_of is either a None, a single int, or a list of int - try: - list(child_of) - except TypeError: - child_of = [child_of] - - new_parent_samples = Sample.objects.filter(id__in=child_of).exclude(id__in=visited) - new_process_measurements = annotate_process_measurements( - ProcessMeasurement.objects.all() - ).filter( - child_sample=child_sample_id - ) - - total_new_samples.append(new_parent_samples) - total_new_process_measurements.append(new_process_measurements) - - stack.extend(s.id for s in new_parent_samples) - visited.update(p.id for p in new_process_measurements) - - - nodes = [ - s - for queryset in total_new_samples - for s in annotate_samples(queryset).values( - 'id', - 'name', - 'quality_flag', - 'quantity_flag', - 'child_count' - ) - ] - - edges = [ - p - for queryset in total_new_process_measurements - for p in queryset.values( - 'id', - 'source_sample', - 'child_sample', - 'process__protocol__name', - ) - ] - + nodes = [] + edges = [] + + derivedBySample = ( + DerivedBySample.objects + .filter(sample__id=mid_sample.id) + .select_related("derived_sample__biosample") + .annotate(biosample_id=F("derived_sample__biosample_id")) + .values_list("biosample_id") + ) + + sampleIds = DerivedBySample.objects.filter(derived_sample__biosample__id__in=derivedBySample).values_list("sample__id", flat=True) + samples = Sample.objects.filter(id__in=sampleIds) + process_measurements = ( + ProcessMeasurement + .objects + .filter(source_sample__in=sampleIds) + .select_related("process__lineage") + .annotate(child_sample=F("lineage__child")) + ) + + nodes = list(samples.values( + 'id', + 'name', + 'quality_flag', + 'quantity_flag', + )) + + edges = list(process_measurements.values( + 'id', + 'source_sample', + 'child_sample', + 'process__protocol__name', + )) return (nodes, edges, errors) \ No newline at end of file diff --git a/frontend/src/components/samples/details/SampleDetailsLineage.js b/frontend/src/components/samples/details/SampleDetailsLineage.js index 081716a23d..daf02477ba 100644 --- a/frontend/src/components/samples/details/SampleDetailsLineage.js +++ b/frontend/src/components/samples/details/SampleDetailsLineage.js @@ -94,7 +94,7 @@ const SampleDetailsLineage = ({ id: p.id.toString(), source: e.v, target: e.w, - label: p.protocol in protocolsByID ? protocolsByID[p.protocol]?.name : "", + label: p.process__protocol__name, } }) }) From 48ecdafd1b17b282bf925189ffbda7659ccaf2c7 Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Thu, 19 May 2022 10:39:40 -0400 Subject: [PATCH 33/68] remove tkinter --- backend/fms_core/viewsets/sample_lineage.py | 1 - 1 file changed, 1 deletion(-) diff --git a/backend/fms_core/viewsets/sample_lineage.py b/backend/fms_core/viewsets/sample_lineage.py index 5dbf9d6d28..0e7729b458 100644 --- a/backend/fms_core/viewsets/sample_lineage.py +++ b/backend/fms_core/viewsets/sample_lineage.py @@ -1,4 +1,3 @@ -from tkinter import W from fms_core.services.sample_lineage import create_sample_lineage_graph from rest_framework import viewsets from rest_framework.decorators import action From ffad72225cc3b4df256867d215062be29227735d Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Thu, 19 May 2022 10:40:36 -0400 Subject: [PATCH 34/68] move nodes and edges to top of function --- backend/fms_core/services/sample_lineage.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/backend/fms_core/services/sample_lineage.py b/backend/fms_core/services/sample_lineage.py index ac3313f9d1..2024a83328 100644 --- a/backend/fms_core/services/sample_lineage.py +++ b/backend/fms_core/services/sample_lineage.py @@ -29,14 +29,13 @@ def create_sample_lineage(parent_sample, child_sample, process_measurement): def create_sample_lineage_graph(mid_sample): errors = [] + nodes = [] + edges = [] if not mid_sample: errors.append(f"Sample is required for sample lineage graph creation") if not errors: - nodes = [] - edges = [] - derivedBySample = ( DerivedBySample.objects .filter(sample__id=mid_sample.id) From edfdcc7251e303bb60b54e44b29dcfa305f89fb8 Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Thu, 19 May 2022 10:42:04 -0400 Subject: [PATCH 35/68] flat values_list --- backend/fms_core/services/sample_lineage.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/backend/fms_core/services/sample_lineage.py b/backend/fms_core/services/sample_lineage.py index 2024a83328..eeb13d52f6 100644 --- a/backend/fms_core/services/sample_lineage.py +++ b/backend/fms_core/services/sample_lineage.py @@ -41,7 +41,7 @@ def create_sample_lineage_graph(mid_sample): .filter(sample__id=mid_sample.id) .select_related("derived_sample__biosample") .annotate(biosample_id=F("derived_sample__biosample_id")) - .values_list("biosample_id") + .values_list("biosample_id", flat=True) ) sampleIds = DerivedBySample.objects.filter(derived_sample__biosample__id__in=derivedBySample).values_list("sample__id", flat=True) From 7f1a8bfc2167121b25966868ad35daeaccbd010a Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Thu, 19 May 2022 10:42:50 -0400 Subject: [PATCH 36/68] add space between samples and process_measurements --- backend/fms_core/services/sample_lineage.py | 1 + 1 file changed, 1 insertion(+) diff --git a/backend/fms_core/services/sample_lineage.py b/backend/fms_core/services/sample_lineage.py index eeb13d52f6..2af0f20bed 100644 --- a/backend/fms_core/services/sample_lineage.py +++ b/backend/fms_core/services/sample_lineage.py @@ -46,6 +46,7 @@ def create_sample_lineage_graph(mid_sample): sampleIds = DerivedBySample.objects.filter(derived_sample__biosample__id__in=derivedBySample).values_list("sample__id", flat=True) samples = Sample.objects.filter(id__in=sampleIds) + process_measurements = ( ProcessMeasurement .objects From c8202f5ed4d82e24683b1e53c9a2a020f6a4d8d1 Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Thu, 19 May 2022 10:44:43 -0400 Subject: [PATCH 37/68] process__protocol__name to protocol_name --- backend/fms_core/services/sample_lineage.py | 4 +++- .../src/components/samples/details/SampleDetailsLineage.js | 2 +- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/backend/fms_core/services/sample_lineage.py b/backend/fms_core/services/sample_lineage.py index 2af0f20bed..465f3e335a 100644 --- a/backend/fms_core/services/sample_lineage.py +++ b/backend/fms_core/services/sample_lineage.py @@ -53,6 +53,8 @@ def create_sample_lineage_graph(mid_sample): .filter(source_sample__in=sampleIds) .select_related("process__lineage") .annotate(child_sample=F("lineage__child")) + .select_related("process_protocol") + .annotate(protocol_name=F("process__protocol__name")) ) nodes = list(samples.values( @@ -66,7 +68,7 @@ def create_sample_lineage_graph(mid_sample): 'id', 'source_sample', 'child_sample', - 'process__protocol__name', + 'protocol_name', )) return (nodes, edges, errors) \ No newline at end of file diff --git a/frontend/src/components/samples/details/SampleDetailsLineage.js b/frontend/src/components/samples/details/SampleDetailsLineage.js index daf02477ba..d8e1a939a9 100644 --- a/frontend/src/components/samples/details/SampleDetailsLineage.js +++ b/frontend/src/components/samples/details/SampleDetailsLineage.js @@ -94,7 +94,7 @@ const SampleDetailsLineage = ({ id: p.id.toString(), source: e.v, target: e.w, - label: p.process__protocol__name, + label: p.protocol_name, } }) }) From cfdc4ecb9e61c0eb849a3c8ec8e382b44c4f62e6 Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Thu, 19 May 2022 10:49:31 -0400 Subject: [PATCH 38/68] graph.js no longer needed --- .../samples/details/SampleDetailsLineage.js | 1 - frontend/src/utils/graph.js | 30 ------------------- 2 files changed, 31 deletions(-) delete mode 100644 frontend/src/utils/graph.js diff --git a/frontend/src/components/samples/details/SampleDetailsLineage.js b/frontend/src/components/samples/details/SampleDetailsLineage.js index d8e1a939a9..1a9830350d 100644 --- a/frontend/src/components/samples/details/SampleDetailsLineage.js +++ b/frontend/src/components/samples/details/SampleDetailsLineage.js @@ -8,7 +8,6 @@ import { withSample, withProcessMeasurement, } from "../../../utils/withItem"; -import GraphADT from "../../../utils/graph"; import dagre from "dagre" import api, { withToken } from "../../../utils/api"; diff --git a/frontend/src/utils/graph.js b/frontend/src/utils/graph.js deleted file mode 100644 index cbabe0e575..0000000000 --- a/frontend/src/utils/graph.js +++ /dev/null @@ -1,30 +0,0 @@ -/* - * A class that represents a graph - */ -class Graph { - /** - * - * @param {any} data data - * @param {any[]} edges array of [edge data, child graph] - */ - constructor(data, edges = []) { - this.data = data; - this.edges = edges; - } - - /** - * Reduce neighbors into `this` with function `f`. - * @param {(oldData: any, edges: any[]) => any} f reducer function - */ - reduceNeighbors(f) { - // visit neighbors first - const neighbors = this.edges.map(([e, n]) => [e, n, n.reduceNeighbors(f)]) - - // visit this node - const newData = f(this.data, neighbors) - - return newData - } -} - -export default Graph; From c54a098039b06edf3b89f91be6b592d9c580ce0d Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Thu, 19 May 2022 10:51:39 -0400 Subject: [PATCH 39/68] some refactoring and TODO --- backend/fms_core/services/sample_lineage.py | 4 ++-- .../components/samples/details/SampleDetailsLineage.js | 9 +-------- 2 files changed, 3 insertions(+), 10 deletions(-) diff --git a/backend/fms_core/services/sample_lineage.py b/backend/fms_core/services/sample_lineage.py index 465f3e335a..2cb5fff9fb 100644 --- a/backend/fms_core/services/sample_lineage.py +++ b/backend/fms_core/services/sample_lineage.py @@ -1,5 +1,5 @@ -from django.db.models import F, Q, Count -from django.core.exceptions import ValidationError, ObjectDoesNotExist +from django.db.models import F +from django.core.exceptions import ValidationError from fms_core.models import SampleLineage, Sample, DerivedBySample, ProcessMeasurement diff --git a/frontend/src/components/samples/details/SampleDetailsLineage.js b/frontend/src/components/samples/details/SampleDetailsLineage.js index 1a9830350d..3500ceb66d 100644 --- a/frontend/src/components/samples/details/SampleDetailsLineage.js +++ b/frontend/src/components/samples/details/SampleDetailsLineage.js @@ -4,11 +4,6 @@ import { useHistory } from "react-router-dom"; import { Graph } from "react-d3-graph" -import { - withSample, - withProcessMeasurement, -} from "../../../utils/withItem"; - import dagre from "dagre" import api, { withToken } from "../../../utils/api"; @@ -22,15 +17,13 @@ const mapStateToProps = state => ({ const SampleDetailsLineage = ({ token, sample, - samplesByID, - processMeasurementsByID, - protocolsByID, }) => { const history = useHistory() const [graphData, setGraphData] = useState({ nodes: [], links: [] }) const [pairToProcess, setPairToProcess] = useState({}) + // TODO automatically adjust width and height const [width, setWidth] = useState(1280) const [height, setHeight] = useState(720) From 41a9532d095fb4aae83f2316d7b4d5c063e017a1 Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Thu, 19 May 2022 13:58:04 -0400 Subject: [PATCH 40/68] refactor sample_lineage.py --- backend/fms_core/services/sample_lineage.py | 45 ++++++--------------- backend/fms_core/viewsets/sample_lineage.py | 3 +- 2 files changed, 13 insertions(+), 35 deletions(-) diff --git a/backend/fms_core/services/sample_lineage.py b/backend/fms_core/services/sample_lineage.py index 2cb5fff9fb..6443eb8b6b 100644 --- a/backend/fms_core/services/sample_lineage.py +++ b/backend/fms_core/services/sample_lineage.py @@ -27,48 +27,27 @@ def create_sample_lineage(parent_sample, child_sample, process_measurement): return (sample_lineage, errors, warnings) -def create_sample_lineage_graph(mid_sample): +def create_sample_lineage_graph(sampleId): errors = [] nodes = [] edges = [] - if not mid_sample: - errors.append(f"Sample is required for sample lineage graph creation") + if not Sample.objects.filter(pk=sampleId).exists(): + errors.append(f"Sample with id ${sampleId} does not exist") if not errors: - derivedBySample = ( - DerivedBySample.objects - .filter(sample__id=mid_sample.id) - .select_related("derived_sample__biosample") - .annotate(biosample_id=F("derived_sample__biosample_id")) - .values_list("biosample_id", flat=True) - ) + derivedBySample = DerivedBySample.objects.filter(sample__id=sampleId) \ + .values_list("derived_sample__biosample_id", flat=True) - sampleIds = DerivedBySample.objects.filter(derived_sample__biosample__id__in=derivedBySample).values_list("sample__id", flat=True) + sampleIds = DerivedBySample.objects.filter(derived_sample__biosample__id__in=derivedBySample) \ + .values_list("sample__id", flat=True) samples = Sample.objects.filter(id__in=sampleIds) - process_measurements = ( - ProcessMeasurement - .objects - .filter(source_sample__in=sampleIds) - .select_related("process__lineage") - .annotate(child_sample=F("lineage__child")) - .select_related("process_protocol") - .annotate(protocol_name=F("process__protocol__name")) - ) + process_measurements = ProcessMeasurement.objects.filter(source_sample__in=sampleIds) \ + .select_related("process__lineage").annotate(child_sample=F("lineage__child")) \ + .select_related("process_protocol").annotate(protocol_name=F("process__protocol__name")) - nodes = list(samples.values( - 'id', - 'name', - 'quality_flag', - 'quantity_flag', - )) - - edges = list(process_measurements.values( - 'id', - 'source_sample', - 'child_sample', - 'protocol_name', - )) + nodes = list(samples.values("id", "name", "quality_flag", "quantity_flag")) + edges = list(process_measurements.values("id", "source_sample", "child_sample", "protocol_name")) return (nodes, edges, errors) \ No newline at end of file diff --git a/backend/fms_core/viewsets/sample_lineage.py b/backend/fms_core/viewsets/sample_lineage.py index 0e7729b458..a2bf49b13f 100644 --- a/backend/fms_core/viewsets/sample_lineage.py +++ b/backend/fms_core/viewsets/sample_lineage.py @@ -10,8 +10,7 @@ class SampleLineageViewSet(viewsets.ViewSet): @action(detail=True, methods=["get"]) def graph(self, _request, pk): - parent_sample = Sample.objects.get(pk=pk) - nodes, edges, errors = create_sample_lineage_graph(parent_sample) + nodes, edges, errors = create_sample_lineage_graph(pk) if errors: raise ValidationError(errors) From dc8d64f24d135d27ac3d0b07c8de25d12e0fbcf7 Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Thu, 19 May 2022 14:03:58 -0400 Subject: [PATCH 41/68] reformat/refactor SampleDetailsLineage.js --- .../samples/details/SampleDetailsLineage.js | 121 +++++++++--------- 1 file changed, 59 insertions(+), 62 deletions(-) diff --git a/frontend/src/components/samples/details/SampleDetailsLineage.js b/frontend/src/components/samples/details/SampleDetailsLineage.js index 3500ceb66d..c995692359 100644 --- a/frontend/src/components/samples/details/SampleDetailsLineage.js +++ b/frontend/src/components/samples/details/SampleDetailsLineage.js @@ -23,9 +23,35 @@ const SampleDetailsLineage = ({ const [graphData, setGraphData] = useState({ nodes: [], links: [] }) const [pairToProcess, setPairToProcess] = useState({}) - // TODO automatically adjust width and height - const [width, setWidth] = useState(1280) - const [height, setHeight] = useState(720) + const nodeSize = { width: 10, height: 10 } + + const dagreConfig = { rankdir: "TB", ranksep: 150, nodesep: 150, marginx: 50, marginy: 50 } + + const graphConfig = { + width: 720, + height: 1280, + staticGraphWithDragAndDrop: true, + maxZoom: 12, + minZoom: 0.05, + panAndZoom: true, + node: { + color: "#d3d3d3", + fontColor: "black", + fontSize: 14, + renderLabel: true, + labelProperty: node => `${node.label}`, + labelPosition: "bottom", + }, + link: { + color: "lightgray", + fontColor: "black", + fontSize: 14, + strokeWidth: 5, + type: "STRAIGHT", + renderLabel: true, + labelProperty: link => `${link.label}` + }, + } useEffect(() => { if (sample?.id !== undefined) { @@ -33,8 +59,8 @@ const SampleDetailsLineage = ({ graph = graph.data const g = new dagre.graphlib.Graph({ directed: true }) - .setGraph({ rankdir: "LR", ranksep: 150, nodesep: 150, marginx: 50, marginy: 50 }) - .setDefaultEdgeLabel(function () { return {}; }); + .setGraph(dagreConfig) + .setDefaultEdgeLabel(function () { return {}; }); graph.nodes.forEach((curr_sample) => { let color = "black" @@ -45,27 +71,24 @@ const SampleDetailsLineage = ({ g.setNode(curr_sample.id.toString(), { id: curr_sample.id.toString(), label: curr_sample.name, - width: 10, - height: 10, + ...nodeSize, color, symbolType: curr_sample.id === sample.id ? "star" : "circle", }) }) - graph.edges - .filter((process) => process.child_sample !== null) - .forEach((process) => { - g.setEdge(process.source_sample, process.child_sample) - }) - - const localPairToProcess = graph.edges - .filter((process) => process.child_sample !== null) - .reduce((prev, p) => { - return { - ...prev, - [`${p.source_sample}:${p.child_sample}`]: p - } - }, {}) + graph.edges.filter((process) => process.child_sample !== null) + .forEach((process) => { + g.setEdge(process.source_sample, process.child_sample) + }) + + const localPairToProcess = graph.edges.filter((process) => process.child_sample !== null) + .reduce((prev, p) => { + return { + ...prev, + [`${p.source_sample}:${p.child_sample}`]: p + } + }, {}) setPairToProcess(localPairToProcess) @@ -73,53 +96,27 @@ const SampleDetailsLineage = ({ setGraphData({ nodes: g.nodes() - .map((v) => { - return { - ...g.node(v), - id: v - } - }), + .map((v) => { + return { + ...g.node(v), + id: v + } + }), links: g.edges() - .map((e) => { - const p = localPairToProcess[`${e.v}:${e.w}`] - return { - id: p.id.toString(), - source: e.v, - target: e.w, - label: p.protocol_name, - } - }) + .map((e) => { + const p = localPairToProcess[`${e.v}:${e.w}`] + return { + id: p.id.toString(), + source: e.v, + target: e.w, + label: p.protocol_name, + } + }) }) }) } }, [sample]) - const graphConfig = { - height, - width, - staticGraphWithDragAndDrop: true, - maxZoom: 12, - minZoom: 0.05, - panAndZoom: true, - node: { - color: "#d3d3d3", - fontColor: "black", - fontSize: 12, - renderLabel: true, - labelProperty: node => `${node.label}`, - labelPosition: "top", - }, - link: { - color: "lightgray", - fontColor: "black", - fontSize: 12, - strokeWidth: 5, - type: "STRAIGHT", - renderLabel: true, - labelProperty: link => `${link.label}` - }, - } - return ( <> { From 572e8c5a949112f220ce08cc1b0b9c4eb48ce021 Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Thu, 19 May 2022 15:39:44 -0400 Subject: [PATCH 42/68] iterate over graph.edges instead of g.edges --- .../components/samples/details/SampleDetailsLineage.js | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/frontend/src/components/samples/details/SampleDetailsLineage.js b/frontend/src/components/samples/details/SampleDetailsLineage.js index c995692359..b3bfe184b7 100644 --- a/frontend/src/components/samples/details/SampleDetailsLineage.js +++ b/frontend/src/components/samples/details/SampleDetailsLineage.js @@ -102,13 +102,11 @@ const SampleDetailsLineage = ({ id: v } }), - links: g.edges() - .map((e) => { - const p = localPairToProcess[`${e.v}:${e.w}`] + links: graph.edges.filter((p) => p.child_sample !== null).map((p) => { return { id: p.id.toString(), - source: e.v, - target: e.w, + source: p.source_sample.toString(), + target: p.child_sample.toString(), label: p.protocol_name, } }) From 8ed06b211741be88baeaded42855b29c8fef445c Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Fri, 20 May 2022 10:04:04 -0400 Subject: [PATCH 43/68] provide size and border for div around graph --- .../src/components/samples/details/SampleDetailsLineage.js | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/frontend/src/components/samples/details/SampleDetailsLineage.js b/frontend/src/components/samples/details/SampleDetailsLineage.js index b3bfe184b7..ddf9461a5a 100644 --- a/frontend/src/components/samples/details/SampleDetailsLineage.js +++ b/frontend/src/components/samples/details/SampleDetailsLineage.js @@ -24,12 +24,11 @@ const SampleDetailsLineage = ({ const [pairToProcess, setPairToProcess] = useState({}) const nodeSize = { width: 10, height: 10 } - const dagreConfig = { rankdir: "TB", ranksep: 150, nodesep: 150, marginx: 50, marginy: 50 } + const graphSize = { width: 720, height: 1280 } const graphConfig = { - width: 720, - height: 1280, + ...graphSize, staticGraphWithDragAndDrop: true, maxZoom: 12, minZoom: 0.05, @@ -117,6 +116,7 @@ const SampleDetailsLineage = ({ return ( <> +
{ graphData.nodes.length > 0 ? : <>Loading... } +
) } From b267076ec38a61c0418b26f74dd1f4944ea5b33f Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Fri, 20 May 2022 10:04:40 -0400 Subject: [PATCH 44/68] add legend for lineage --- .../samples/details/SampleDetailsLineage.js | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/frontend/src/components/samples/details/SampleDetailsLineage.js b/frontend/src/components/samples/details/SampleDetailsLineage.js index ddf9461a5a..a45f9bcf6f 100644 --- a/frontend/src/components/samples/details/SampleDetailsLineage.js +++ b/frontend/src/components/samples/details/SampleDetailsLineage.js @@ -116,6 +116,11 @@ const SampleDetailsLineage = ({ return ( <> +
+ +
{ graphData.nodes.length > 0 @@ -136,4 +141,33 @@ const SampleDetailsLineage = ({ ) } +function Legend() { + function Symbol({ shape, color }) { + const output = { + "circle": <>●, + "start": <>★ + } + return + {output[shape]} + + } + + const Entry = ({ symbol, text }) => { + return
+ {text} +
+ } + + const entries = [ + ["start", "black", "You are here"], + ["circle", "black", "Awaiting QC"], + ["circle", "red", "Failed QC"], + ["circle", "green", "Passed QC"], + ].map(([shape, color, text]) => ({ symbol: { shape, color }, text })) + + return <> + {entries.map((entry) => )} + +} + export default connect(mapStateToProps, undefined)(SampleDetailsLineage); From cd4496ba13752983c7f51402e4578a3666ec36a2 Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Fri, 20 May 2022 10:42:28 -0400 Subject: [PATCH 45/68] make border thin --- .../components/samples/details/SampleDetailsLineage.js | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/frontend/src/components/samples/details/SampleDetailsLineage.js b/frontend/src/components/samples/details/SampleDetailsLineage.js index a45f9bcf6f..806c79a444 100644 --- a/frontend/src/components/samples/details/SampleDetailsLineage.js +++ b/frontend/src/components/samples/details/SampleDetailsLineage.js @@ -117,11 +117,15 @@ const SampleDetailsLineage = ({ return ( <>
-
+
{ graphData.nodes.length > 0 ? Date: Fri, 20 May 2022 11:22:34 -0400 Subject: [PATCH 46/68] add instructions --- .../samples/details/SampleDetailsLineage.js | 58 ++++++++++--------- 1 file changed, 31 insertions(+), 27 deletions(-) diff --git a/frontend/src/components/samples/details/SampleDetailsLineage.js b/frontend/src/components/samples/details/SampleDetailsLineage.js index 806c79a444..636d677c78 100644 --- a/frontend/src/components/samples/details/SampleDetailsLineage.js +++ b/frontend/src/components/samples/details/SampleDetailsLineage.js @@ -116,31 +116,35 @@ const SampleDetailsLineage = ({ return ( <> -
- -
-
- { - graphData.nodes.length > 0 - ? history.push(`/samples/${id}`)} - onClickLink={(source, target) => { - const linkId = pairToProcess[`${source}:${target}`].id - history.push(`/process-measurements/${linkId}`) - }} - /> - : <>Loading... - } -
+
+ + +
Click on nodes to visit the sample
+
Click on edges to visit the process
+
Use the mouse to move and zoom the graph
+
+
+ { + graphData.nodes.length > 0 + ? history.push(`/samples/${id}`)} + onClickLink={(source, target) => { + const linkId = pairToProcess[`${source}:${target}`].id + history.push(`/process-measurements/${linkId}`) + }} + /> + : <>Loading... + } +
) } @@ -149,7 +153,7 @@ function Legend() { function Symbol({ shape, color }) { const output = { "circle": <>●, - "start": <>★ + "star": <>★ } return {output[shape]} @@ -163,7 +167,7 @@ function Legend() { } const entries = [ - ["start", "black", "You are here"], + ["star", "black", "You are here"], ["circle", "black", "Awaiting QC"], ["circle", "red", "Failed QC"], ["circle", "green", "Passed QC"], From 176528ee52be85ba674af05c9d5097fd6621bb2a Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Fri, 20 May 2022 13:45:20 -0400 Subject: [PATCH 47/68] use antd components --- .../samples/details/SampleDetailsLineage.js | 59 ++++++++++++------- 1 file changed, 37 insertions(+), 22 deletions(-) diff --git a/frontend/src/components/samples/details/SampleDetailsLineage.js b/frontend/src/components/samples/details/SampleDetailsLineage.js index 636d677c78..e8615b657a 100644 --- a/frontend/src/components/samples/details/SampleDetailsLineage.js +++ b/frontend/src/components/samples/details/SampleDetailsLineage.js @@ -2,6 +2,10 @@ import React, { useEffect, useState } from "react"; import { connect } from "react-redux"; import { useHistory } from "react-router-dom"; +import { Typography, Divider, Card, Space } from 'antd'; + +const { Text } = Typography; + import { Graph } from "react-d3-graph" import dagre from "dagre" @@ -26,7 +30,7 @@ const SampleDetailsLineage = ({ const nodeSize = { width: 10, height: 10 } const dagreConfig = { rankdir: "TB", ranksep: 150, nodesep: 150, marginx: 50, marginy: 50 } - const graphSize = { width: 720, height: 1280 } + const graphSize = { width: 800, height: 600 } const graphConfig = { ...graphSize, staticGraphWithDragAndDrop: true, @@ -116,20 +120,10 @@ const SampleDetailsLineage = ({ return ( <> -
- - -
Click on nodes to visit the sample
-
Click on edges to visit the process
-
Use the mouse to move and zoom the graph
-
-
+ + +
+ { graphData.nodes.length > 0 ? : <>Loading... } -
+ ) } +function Details() { + return <> + + + + + Click on nodes to visit the sample + + + Click on edges to visit the process + + + Use the mouse to move and zoom the graph + + + +} + function Legend() { function Symbol({ shape, color }) { const output = { "circle": <>●, "star": <>★ } - return + return {output[shape]} - + } const Entry = ({ symbol, text }) => { - return
- {text} -
+ return + + {text} + } const entries = [ @@ -174,7 +187,9 @@ function Legend() { ].map(([shape, color, text]) => ({ symbol: { shape, color }, text })) return <> - {entries.map((entry) => )} + + {entries.map((entry) => )} + } From 80e109d13ec022cf12309505cb215f82322bddbc Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Fri, 20 May 2022 13:58:53 -0400 Subject: [PATCH 48/68] graph to { data } --- .../samples/details/SampleDetailsLineage.js | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/frontend/src/components/samples/details/SampleDetailsLineage.js b/frontend/src/components/samples/details/SampleDetailsLineage.js index e8615b657a..5e0e414de1 100644 --- a/frontend/src/components/samples/details/SampleDetailsLineage.js +++ b/frontend/src/components/samples/details/SampleDetailsLineage.js @@ -58,14 +58,13 @@ const SampleDetailsLineage = ({ useEffect(() => { if (sample?.id !== undefined) { - withToken(token, api.sample_lineage.get)(sample.id).then((graph) => { - graph = graph.data + withToken(token, api.sample_lineage.get)(sample.id).then(({data}) => { const g = new dagre.graphlib.Graph({ directed: true }) .setGraph(dagreConfig) .setDefaultEdgeLabel(function () { return {}; }); - graph.nodes.forEach((curr_sample) => { + data.nodes.forEach((curr_sample) => { let color = "black" if (curr_sample.quality_flag !== null && curr_sample.quantity_flag !== null) { color = curr_sample.quality_flag && curr_sample.quantity_flag ? "green" : "red" @@ -80,12 +79,12 @@ const SampleDetailsLineage = ({ }) }) - graph.edges.filter((process) => process.child_sample !== null) + data.edges.filter((process) => process.child_sample !== null) .forEach((process) => { g.setEdge(process.source_sample, process.child_sample) }) - const localPairToProcess = graph.edges.filter((process) => process.child_sample !== null) + const localPairToProcess = data.edges.filter((process) => process.child_sample !== null) .reduce((prev, p) => { return { ...prev, @@ -105,7 +104,7 @@ const SampleDetailsLineage = ({ id: v } }), - links: graph.edges.filter((p) => p.child_sample !== null).map((p) => { + links: data.edges.filter((p) => p.child_sample !== null).map((p) => { return { id: p.id.toString(), source: p.source_sample.toString(), From a43a661aa439e6aef7646e67dbd6884d70704205 Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Tue, 24 May 2022 10:19:48 -0400 Subject: [PATCH 49/68] position current sample to the top left corner --- .../samples/details/SampleDetailsLineage.js | 42 +++++++++++-------- 1 file changed, 25 insertions(+), 17 deletions(-) diff --git a/frontend/src/components/samples/details/SampleDetailsLineage.js b/frontend/src/components/samples/details/SampleDetailsLineage.js index 5e0e414de1..5e3c88fb80 100644 --- a/frontend/src/components/samples/details/SampleDetailsLineage.js +++ b/frontend/src/components/samples/details/SampleDetailsLineage.js @@ -96,23 +96,31 @@ const SampleDetailsLineage = ({ dagre.layout(g) - setGraphData({ - nodes: g.nodes() - .map((v) => { - return { - ...g.node(v), - id: v - } - }), - links: data.edges.filter((p) => p.child_sample !== null).map((p) => { - return { - id: p.id.toString(), - source: p.source_sample.toString(), - target: p.child_sample.toString(), - label: p.protocol_name, - } - }) - }) + const { x: cx, y: cy } = g.node(sample.id.toString()) + const dx = -cx + nodeSize.width * 5 + const dy = -cy + nodeSize.height * 5 + + const nodes = g.nodes() + .map((v) => { + const n = g.node(v) + return { + ...n, + id: v, + x: n.x + dx, + y: n.y + dy, + } + }) + + const links = data.edges.filter((p) => p.child_sample !== null).map((p) => { + return { + id: p.id.toString(), + source: p.source_sample.toString(), + target: p.child_sample.toString(), + label: p.protocol_name, + } + }) + + setGraphData({nodes, links}) }) } }, [sample]) From dc65246a953c13ba06695fa859a666fe37fd090e Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Tue, 24 May 2022 10:45:40 -0400 Subject: [PATCH 50/68] make graph horizontal and extend legend horizontally --- .../samples/details/SampleDetailsLineage.js | 43 ++++++++++--------- 1 file changed, 23 insertions(+), 20 deletions(-) diff --git a/frontend/src/components/samples/details/SampleDetailsLineage.js b/frontend/src/components/samples/details/SampleDetailsLineage.js index 5e3c88fb80..03a24426a3 100644 --- a/frontend/src/components/samples/details/SampleDetailsLineage.js +++ b/frontend/src/components/samples/details/SampleDetailsLineage.js @@ -2,7 +2,7 @@ import React, { useEffect, useState } from "react"; import { connect } from "react-redux"; import { useHistory } from "react-router-dom"; -import { Typography, Divider, Card, Space } from 'antd'; +import { Typography, Divider, Card, Space, Row, Col } from 'antd'; const { Text } = Typography; @@ -28,7 +28,7 @@ const SampleDetailsLineage = ({ const [pairToProcess, setPairToProcess] = useState({}) const nodeSize = { width: 10, height: 10 } - const dagreConfig = { rankdir: "TB", ranksep: 150, nodesep: 150, marginx: 50, marginy: 50 } + const dagreConfig = { rankdir: "LR", ranksep: 150, nodesep: 150, marginx: 50, marginy: 50 } const graphSize = { width: 800, height: 600 } const graphConfig = { @@ -97,8 +97,8 @@ const SampleDetailsLineage = ({ dagre.layout(g) const { x: cx, y: cy } = g.node(sample.id.toString()) - const dx = -cx + nodeSize.width * 5 - const dy = -cy + nodeSize.height * 5 + const dx = graphSize.width/2 - cx + const dy = graphSize.height*3/4 - cy const nodes = g.nodes() .map((v) => { @@ -128,7 +128,7 @@ const SampleDetailsLineage = ({ return ( <> - +
{ @@ -151,21 +151,24 @@ const SampleDetailsLineage = ({ } function Details() { - return <> - - - - - Click on nodes to visit the sample - - - Click on edges to visit the process - - - Use the mouse to move and zoom the graph - - - + return + + + + + + + Click on nodes to visit the sample + + + Click on edges to visit the process + + + Use the mouse to move and zoom the graph + + + + } function Legend() { From 1739eb4d6083671be25b3a6e58f8d981b96a15f5 Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Tue, 24 May 2022 11:33:57 -0400 Subject: [PATCH 51/68] redesign and use popover for legend --- .../samples/details/SampleDetailsLineage.js | 29 ++++++++++--------- 1 file changed, 16 insertions(+), 13 deletions(-) diff --git a/frontend/src/components/samples/details/SampleDetailsLineage.js b/frontend/src/components/samples/details/SampleDetailsLineage.js index 03a24426a3..b7f880c9da 100644 --- a/frontend/src/components/samples/details/SampleDetailsLineage.js +++ b/frontend/src/components/samples/details/SampleDetailsLineage.js @@ -2,7 +2,7 @@ import React, { useEffect, useState } from "react"; import { connect } from "react-redux"; import { useHistory } from "react-router-dom"; -import { Typography, Divider, Card, Space, Row, Col } from 'antd'; +import { Typography, Card, Space, Popover, Button } from 'antd'; const { Text } = Typography; @@ -127,10 +127,13 @@ const SampleDetailsLineage = ({ return ( <> - - -
- + + } + placement={"topRight"} + > + + { graphData.nodes.length > 0 ? - + return
+ - - + + - Click on nodes to visit the sample + Click on node to visit the sample - Click on edges to visit the process + Click on edge to visit the process Use the mouse to move and zoom the graph - - + +
} function Legend() { From 203652481844cb3ca01ddfe47de2b939e64af78e Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Tue, 24 May 2022 11:36:26 -0400 Subject: [PATCH 52/68] center current sample --- .../src/components/samples/details/SampleDetailsLineage.js | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/frontend/src/components/samples/details/SampleDetailsLineage.js b/frontend/src/components/samples/details/SampleDetailsLineage.js index b7f880c9da..5e34ac391b 100644 --- a/frontend/src/components/samples/details/SampleDetailsLineage.js +++ b/frontend/src/components/samples/details/SampleDetailsLineage.js @@ -97,8 +97,8 @@ const SampleDetailsLineage = ({ dagre.layout(g) const { x: cx, y: cy } = g.node(sample.id.toString()) - const dx = graphSize.width/2 - cx - const dy = graphSize.height*3/4 - cy + const dx = graphSize.width/2 - cx + const dy = graphSize.height/2 - cy const nodes = g.nodes() .map((v) => { From 7b4e21cd3b2c531723157b6e06d708c45559a072 Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Tue, 24 May 2022 11:53:09 -0400 Subject: [PATCH 53/68] align dots --- .../samples/details/SampleDetailsLineage.js | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/frontend/src/components/samples/details/SampleDetailsLineage.js b/frontend/src/components/samples/details/SampleDetailsLineage.js index 5e34ac391b..bf8208103e 100644 --- a/frontend/src/components/samples/details/SampleDetailsLineage.js +++ b/frontend/src/components/samples/details/SampleDetailsLineage.js @@ -80,17 +80,17 @@ const SampleDetailsLineage = ({ }) data.edges.filter((process) => process.child_sample !== null) - .forEach((process) => { - g.setEdge(process.source_sample, process.child_sample) - }) + .forEach((process) => { + g.setEdge(process.source_sample, process.child_sample) + }) const localPairToProcess = data.edges.filter((process) => process.child_sample !== null) - .reduce((prev, p) => { - return { - ...prev, - [`${p.source_sample}:${p.child_sample}`]: p - } - }, {}) + .reduce((prev, p) => { + return { + ...prev, + [`${p.source_sample}:${p.child_sample}`]: p + } + }, {}) setPairToProcess(localPairToProcess) From b7247b3e1e7dd6274a5b49ad31b30b4ea483b014 Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Tue, 24 May 2022 15:09:14 -0400 Subject: [PATCH 54/68] reduce apparent whitespace --- .../src/components/samples/details/SampleDetailsLineage.js | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/frontend/src/components/samples/details/SampleDetailsLineage.js b/frontend/src/components/samples/details/SampleDetailsLineage.js index bf8208103e..5ee5e9e7bf 100644 --- a/frontend/src/components/samples/details/SampleDetailsLineage.js +++ b/frontend/src/components/samples/details/SampleDetailsLineage.js @@ -30,7 +30,7 @@ const SampleDetailsLineage = ({ const nodeSize = { width: 10, height: 10 } const dagreConfig = { rankdir: "LR", ranksep: 150, nodesep: 150, marginx: 50, marginy: 50 } - const graphSize = { width: 800, height: 600 } + const graphSize = { width: 800, height: 800 } const graphConfig = { ...graphSize, staticGraphWithDragAndDrop: true, @@ -97,8 +97,8 @@ const SampleDetailsLineage = ({ dagre.layout(g) const { x: cx, y: cy } = g.node(sample.id.toString()) - const dx = graphSize.width/2 - cx - const dy = graphSize.height/2 - cy + const dx = graphSize.width/2.2 - cx + const dy = graphSize.height/2.4 - cy const nodes = g.nodes() .map((v) => { From f7f85c24ba52aff1f8b5acadbbb6d7d755bbd8ab Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Wed, 25 May 2022 13:16:30 -0400 Subject: [PATCH 55/68] _End sentences with a period._ --- .../src/components/samples/details/SampleDetailsLineage.js | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/frontend/src/components/samples/details/SampleDetailsLineage.js b/frontend/src/components/samples/details/SampleDetailsLineage.js index 5ee5e9e7bf..03708b1e78 100644 --- a/frontend/src/components/samples/details/SampleDetailsLineage.js +++ b/frontend/src/components/samples/details/SampleDetailsLineage.js @@ -161,13 +161,13 @@ function Details() { - Click on node to visit the sample + Click on node to visit the sample. - Click on edge to visit the process + Click on edge to visit the process. - Use the mouse to move and zoom the graph + Use the mouse to move and zoom the graph. From 8ba0d20eca1fc74edede0bf090af89e56b6207ae Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Thu, 26 May 2022 09:30:52 -0400 Subject: [PATCH 56/68] add d3@5.5.0 --- frontend/package-lock.json | 153 +++++++++++-------------------------- frontend/package.json | 1 + 2 files changed, 44 insertions(+), 110 deletions(-) diff --git a/frontend/package-lock.json b/frontend/package-lock.json index e1a4bbb337..23fd18eb0e 100644 --- a/frontend/package-lock.json +++ b/frontend/package-lock.json @@ -15,6 +15,7 @@ "bowser": "^2.11.0", "cheerio": "^1.0.0-rc.9", "cross-fetch": "^3.1.5", + "d3": "^5.5.0", "dagre": "^0.8.5", "date-fns": "^2.15.0", "debounce": "^1.2.0", @@ -4018,10 +4019,9 @@ } }, "node_modules/d3": { - "version": "5.16.0", - "resolved": "https://registry.npmjs.org/d3/-/d3-5.16.0.tgz", - "integrity": "sha512-4PL5hHaHwX4m7Zr1UapXW23apo6pexCgdetdJ5kTmADpG/7T9Gkxw0M0tf/pjoB63ezCCm0u5UaFYy2aMt0Mcw==", - "peer": true, + "version": "5.5.0", + "resolved": "https://registry.npmjs.org/d3/-/d3-5.5.0.tgz", + "integrity": "sha512-HRDSYvT3n7kMvJH7Avp7iR0Xsz97bkCFka9aOg04EdyXyiAP8yQzUpLH3712y9R7ffVo1g94t1OYFHBB0yI9vQ==", "dependencies": { "d3-array": "1", "d3-axis": "1", @@ -4059,20 +4059,17 @@ "node_modules/d3-array": { "version": "1.2.4", "resolved": "https://registry.npmjs.org/d3-array/-/d3-array-1.2.4.tgz", - "integrity": "sha512-KHW6M86R+FUPYGb3R5XiYjXPq7VzwxZ22buHhAEVG5ztoEcZZMLov530mmccaqA1GghZArjQV46fuc8kUqhhHw==", - "peer": true + "integrity": "sha512-KHW6M86R+FUPYGb3R5XiYjXPq7VzwxZ22buHhAEVG5ztoEcZZMLov530mmccaqA1GghZArjQV46fuc8kUqhhHw==" }, "node_modules/d3-axis": { "version": "1.0.12", "resolved": "https://registry.npmjs.org/d3-axis/-/d3-axis-1.0.12.tgz", - "integrity": "sha512-ejINPfPSNdGFKEOAtnBtdkpr24c4d4jsei6Lg98mxf424ivoDP2956/5HDpIAtmHo85lqT4pruy+zEgvRUBqaQ==", - "peer": true + "integrity": "sha512-ejINPfPSNdGFKEOAtnBtdkpr24c4d4jsei6Lg98mxf424ivoDP2956/5HDpIAtmHo85lqT4pruy+zEgvRUBqaQ==" }, "node_modules/d3-brush": { "version": "1.1.6", "resolved": "https://registry.npmjs.org/d3-brush/-/d3-brush-1.1.6.tgz", "integrity": "sha512-7RW+w7HfMCPyZLifTz/UnJmI5kdkXtpCbombUSs8xniAyo0vIbrDzDwUJB6eJOgl9u5DQOt2TQlYumxzD1SvYA==", - "peer": true, "dependencies": { "d3-dispatch": "1", "d3-drag": "1", @@ -4085,7 +4082,6 @@ "version": "1.0.6", "resolved": "https://registry.npmjs.org/d3-chord/-/d3-chord-1.0.6.tgz", "integrity": "sha512-JXA2Dro1Fxw9rJe33Uv+Ckr5IrAa74TlfDEhE/jfLOaXegMQFQTAgAw9WnZL8+HxVBRXaRGCkrNU7pJeylRIuA==", - "peer": true, "dependencies": { "d3-array": "1", "d3-path": "1" @@ -4094,20 +4090,17 @@ "node_modules/d3-collection": { "version": "1.0.7", "resolved": "https://registry.npmjs.org/d3-collection/-/d3-collection-1.0.7.tgz", - "integrity": "sha512-ii0/r5f4sjKNTfh84Di+DpztYwqKhEyUlKoPrzUFfeSkWxjW49xU2QzO9qrPrNkpdI0XJkfzvmTu8V2Zylln6A==", - "peer": true + "integrity": "sha512-ii0/r5f4sjKNTfh84Di+DpztYwqKhEyUlKoPrzUFfeSkWxjW49xU2QzO9qrPrNkpdI0XJkfzvmTu8V2Zylln6A==" }, "node_modules/d3-color": { "version": "1.4.1", "resolved": "https://registry.npmjs.org/d3-color/-/d3-color-1.4.1.tgz", - "integrity": "sha512-p2sTHSLCJI2QKunbGb7ocOh7DgTAn8IrLx21QRc/BSnodXM4sv6aLQlnfpvehFMLZEfBc6g9pH9SWQccFYfJ9Q==", - "peer": true + "integrity": "sha512-p2sTHSLCJI2QKunbGb7ocOh7DgTAn8IrLx21QRc/BSnodXM4sv6aLQlnfpvehFMLZEfBc6g9pH9SWQccFYfJ9Q==" }, "node_modules/d3-contour": { "version": "1.3.2", "resolved": "https://registry.npmjs.org/d3-contour/-/d3-contour-1.3.2.tgz", "integrity": "sha512-hoPp4K/rJCu0ladiH6zmJUEz6+u3lgR+GSm/QdM2BBvDraU39Vr7YdDCicJcxP1z8i9B/2dJLgDC1NcvlF8WCg==", - 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"integrity": "sha512-Xh0isrZ5rPYYdqhAVk8VLnMEidhz5aP7htAADH6MfzgmmicPkTo8LhkLxci61/lCB7n7UmE3bN0leRt+qvkLxA==", - "peer": true + "integrity": "sha512-Xh0isrZ5rPYYdqhAVk8VLnMEidhz5aP7htAADH6MfzgmmicPkTo8LhkLxci61/lCB7n7UmE3bN0leRt+qvkLxA==" }, "d3-time-format": { "version": "2.3.0", "resolved": "https://registry.npmjs.org/d3-time-format/-/d3-time-format-2.3.0.tgz", "integrity": "sha512-guv6b2H37s2Uq/GefleCDtbe0XZAuy7Wa49VGkPVPMfLL9qObgBST3lEHJBMUp8S7NdLQAGIvr2KXk8Hc98iKQ==", - "peer": true, "requires": { "d3-time": "1" } @@ -15637,14 +15575,12 @@ "d3-timer": { "version": "1.0.10", "resolved": "https://registry.npmjs.org/d3-timer/-/d3-timer-1.0.10.tgz", - "integrity": "sha512-B1JDm0XDaQC+uvo4DT79H0XmBskgS3l6Ve+1SBCfxgmtIb1AVrPIoqd+nPSv+loMX8szQ0sVUhGngL7D5QPiXw==", - "peer": true + "integrity": "sha512-B1JDm0XDaQC+uvo4DT79H0XmBskgS3l6Ve+1SBCfxgmtIb1AVrPIoqd+nPSv+loMX8szQ0sVUhGngL7D5QPiXw==" }, "d3-transition": { "version": "1.3.2", "resolved": "https://registry.npmjs.org/d3-transition/-/d3-transition-1.3.2.tgz", "integrity": "sha512-sc0gRU4PFqZ47lPVHloMn9tlPcv8jxgOQg+0zjhfZXMQuvppjG6YuwdMBE0TuqCZjeJkLecku/l9R0JPcRhaDA==", - "peer": true, "requires": { "d3-color": "1", "d3-dispatch": "1", @@ -15657,14 +15593,12 @@ "d3-voronoi": { "version": "1.1.4", "resolved": "https://registry.npmjs.org/d3-voronoi/-/d3-voronoi-1.1.4.tgz", - "integrity": "sha512-dArJ32hchFsrQ8uMiTBLq256MpnZjeuBtdHpaDlYuQyjU0CVzCJl/BVW+SkszaAeH95D/8gxqAhgx0ouAWAfRg==", - "peer": true + "integrity": "sha512-dArJ32hchFsrQ8uMiTBLq256MpnZjeuBtdHpaDlYuQyjU0CVzCJl/BVW+SkszaAeH95D/8gxqAhgx0ouAWAfRg==" }, "d3-zoom": { "version": "1.8.3", "resolved": "https://registry.npmjs.org/d3-zoom/-/d3-zoom-1.8.3.tgz", "integrity": "sha512-VoLXTK4wvy1a0JpH2Il+F2CiOhVu7VRXWF5M/LroMIh3/zBAC3WAt7QoIvPibOavVo20hN6/37vwAsdBejLyKQ==", - "peer": true, "requires": { "d3-dispatch": "1", "d3-drag": "1", @@ -20034,8 +19968,7 @@ "rw": { "version": "1.3.3", "resolved": "https://registry.npmjs.org/rw/-/rw-1.3.3.tgz", - "integrity": "sha1-P4Yt+pGrdmsUiF700BEkv9oHT7Q=", - "peer": true + "integrity": "sha1-P4Yt+pGrdmsUiF700BEkv9oHT7Q=" }, "rxjs": { "version": "6.6.7", diff --git a/frontend/package.json b/frontend/package.json index 4b013f62e0..a9fc40bbf1 100644 --- a/frontend/package.json +++ b/frontend/package.json @@ -27,6 +27,7 @@ "bowser": "^2.11.0", "cheerio": "^1.0.0-rc.9", "cross-fetch": "^3.1.5", + "d3": "^5.5.0", "dagre": "^0.8.5", "date-fns": "^2.15.0", "debounce": "^1.2.0", From dc8f4f2017ae1c8da463702c87375163b8fac0bc Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Thu, 26 May 2022 11:39:01 -0400 Subject: [PATCH 57/68] fix indentation --- .../samples/details/SampleDetailsLineage.js | 25 ++++++++++--------- 1 file changed, 13 insertions(+), 12 deletions(-) diff --git a/frontend/src/components/samples/details/SampleDetailsLineage.js b/frontend/src/components/samples/details/SampleDetailsLineage.js index 03708b1e78..eb1785e98b 100644 --- a/frontend/src/components/samples/details/SampleDetailsLineage.js +++ b/frontend/src/components/samples/details/SampleDetailsLineage.js @@ -96,22 +96,23 @@ const SampleDetailsLineage = ({ dagre.layout(g) - const { x: cx, y: cy } = g.node(sample.id.toString()) - const dx = graphSize.width/2.2 - cx - const dy = graphSize.height/2.4 - cy + const { x: cx, y: cy } = g.node(sample.id.toString()) - const nodes = g.nodes() + const dx = graphSize.width/2.2 - cx + const dy = graphSize.height/2.4 - cy + + const nodes = g.nodes() .map((v) => { - const n = g.node(v) + const n = g.node(v) return { ...n, id: v, - x: n.x + dx, - y: n.y + dy, + x: n.x + dx, + y: n.y + dy, } }) - const links = data.edges.filter((p) => p.child_sample !== null).map((p) => { + const links = data.edges.filter((p) => p.child_sample !== null).map((p) => { return { id: p.id.toString(), source: p.source_sample.toString(), @@ -129,10 +130,10 @@ const SampleDetailsLineage = ({ <> } - placement={"topRight"} - > - + content={
} + placement={"topRight"} + > + { graphData.nodes.length > 0 From 2279545469c0fb4dc140f85b5216a93135c1c2b9 Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Thu, 26 May 2022 14:24:07 -0400 Subject: [PATCH 58/68] position current node to the left --- frontend/src/components/samples/details/SampleDetailsLineage.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/frontend/src/components/samples/details/SampleDetailsLineage.js b/frontend/src/components/samples/details/SampleDetailsLineage.js index eb1785e98b..d6882c6c0c 100644 --- a/frontend/src/components/samples/details/SampleDetailsLineage.js +++ b/frontend/src/components/samples/details/SampleDetailsLineage.js @@ -98,7 +98,7 @@ const SampleDetailsLineage = ({ const { x: cx, y: cy } = g.node(sample.id.toString()) - const dx = graphSize.width/2.2 - cx + const dx = nodeSize.width*5 - cx const dy = graphSize.height/2.4 - cy const nodes = g.nodes() From 03bf5ebb2a790a0f7e3cf1c88581fb6f2cc75f88 Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Thu, 26 May 2022 14:24:30 -0400 Subject: [PATCH 59/68] use ref to get width and height for graph --- .../samples/details/SampleDetailsLineage.js | 55 +++++++++++-------- frontend/src/utils/ref.jsx | 34 ++++++++++++ 2 files changed, 65 insertions(+), 24 deletions(-) create mode 100644 frontend/src/utils/ref.jsx diff --git a/frontend/src/components/samples/details/SampleDetailsLineage.js b/frontend/src/components/samples/details/SampleDetailsLineage.js index d6882c6c0c..ff49e57463 100644 --- a/frontend/src/components/samples/details/SampleDetailsLineage.js +++ b/frontend/src/components/samples/details/SampleDetailsLineage.js @@ -10,6 +10,7 @@ import { Graph } from "react-d3-graph" import dagre from "dagre" import api, { withToken } from "../../../utils/api"; +import { useResizeObserver } from "../../../utils/ref" const mapStateToProps = state => ({ token: state.auth.tokens.access, @@ -24,13 +25,17 @@ const SampleDetailsLineage = ({ }) => { const history = useHistory() + const { resizeRef, maxSize } = useResizeObserver(720, 720) + const [graphData, setGraphData] = useState({ nodes: [], links: [] }) const [pairToProcess, setPairToProcess] = useState({}) + // size.height sometimes goes to 1 + const graphSize = { width: maxSize.width, height: Math.max(maxSize.width, maxSize.height) } + const nodeSize = { width: 10, height: 10 } const dagreConfig = { rankdir: "LR", ranksep: 150, nodesep: 150, marginx: 50, marginy: 50 } - const graphSize = { width: 800, height: 800 } const graphConfig = { ...graphSize, staticGraphWithDragAndDrop: true, @@ -99,7 +104,7 @@ const SampleDetailsLineage = ({ const { x: cx, y: cy } = g.node(sample.id.toString()) const dx = nodeSize.width*5 - cx - const dy = graphSize.height/2.4 - cy + const dy = graphSize.height/2 - cy const nodes = g.nodes() .map((v) => { @@ -128,28 +133,30 @@ const SampleDetailsLineage = ({ return ( <> - - } - placement={"topRight"} - > - - - { - graphData.nodes.length > 0 - ? history.push(`/samples/${id}`)} - onClickLink={(source, target) => { - const linkId = pairToProcess[`${source}:${target}`].id - history.push(`/process-measurements/${linkId}`) - }} - /> - : <>Loading... - } - +
+ + } + placement={"topRight"} + > + + + { + graphData.nodes.length > 0 + ? history.push(`/samples/${id}`)} + onClickLink={(source, target) => { + const linkId = pairToProcess[`${source}:${target}`].id + history.push(`/process-measurements/${linkId}`) + }} + /> + : <>Loading... + } + +
) } diff --git a/frontend/src/utils/ref.jsx b/frontend/src/utils/ref.jsx new file mode 100644 index 0000000000..a5d916735f --- /dev/null +++ b/frontend/src/utils/ref.jsx @@ -0,0 +1,34 @@ +import { useRef, useCallback, useEffect, useState } from 'react'; + +/** + * https://gist.github.com/DominicTobias/c8579667e8a8bd7817c1b4d5b274eb4c + * */ +export function useResizeObserver(width, height) { + const ResizeObserver = window.ResizeObserver; + const [size, setSize] = useState({ width, height }); + const resizeObserver = useRef(null); + + const onResize = useCallback(entries => { + const { width, height } = entries[0].contentRect; + setSize({ width, height }); + }, []); + + const ref = useCallback( + node => { + if (node !== null) { + if (resizeObserver.current) { + resizeObserver.current.disconnect(); + } + resizeObserver.current = new ResizeObserver(onResize); + resizeObserver.current.observe(node); + } + }, + [onResize] + ); + + useEffect(() => () => { + resizeObserver.current.disconnect(); + }, []); + + return { ref, size }; +} From b315b8bf497b731979d54485826b5a75d787a1a4 Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Fri, 27 May 2022 11:37:50 -0400 Subject: [PATCH 60/68] improve code quality --- .../samples/details/SampleDetailsLineage.js | 152 ++++++++++-------- 1 file changed, 88 insertions(+), 64 deletions(-) diff --git a/frontend/src/components/samples/details/SampleDetailsLineage.js b/frontend/src/components/samples/details/SampleDetailsLineage.js index ff49e57463..99e6317174 100644 --- a/frontend/src/components/samples/details/SampleDetailsLineage.js +++ b/frontend/src/components/samples/details/SampleDetailsLineage.js @@ -23,19 +23,15 @@ const SampleDetailsLineage = ({ token, sample, }) => { - const history = useHistory() - - const { resizeRef, maxSize } = useResizeObserver(720, 720) + const { ref: resizeRef, size: maxSize } = useResizeObserver(720, 720) const [graphData, setGraphData] = useState({ nodes: [], links: [] }) - const [pairToProcess, setPairToProcess] = useState({}) - - // size.height sometimes goes to 1 - const graphSize = { width: maxSize.width, height: Math.max(maxSize.width, maxSize.height) } + const [nodesToEdges, setNodesToEdges] = useState({}) const nodeSize = { width: 10, height: 10 } - const dagreConfig = { rankdir: "LR", ranksep: 150, nodesep: 150, marginx: 50, marginy: 50 } + // maxSize.height is sometimes outrageously large + const graphSize = { width: maxSize.width, height: maxSize.width } const graphConfig = { ...graphSize, staticGraphWithDragAndDrop: true, @@ -64,58 +60,60 @@ const SampleDetailsLineage = ({ useEffect(() => { if (sample?.id !== undefined) { withToken(token, api.sample_lineage.get)(sample.id).then(({data}) => { - + const samples = data.nodes.reduce((prev, curr) => ({ + ...prev, + [curr.id.toString()]: curr + }), {}) + + // use dagre to position nodes + + const dagreConfig = { + rankdir: "LR", + ranksep: 150, + nodesep: 150, + marginx: 50, + marginy: 50 + } const g = new dagre.graphlib.Graph({ directed: true }) .setGraph(dagreConfig) .setDefaultEdgeLabel(function () { return {}; }); - - data.nodes.forEach((curr_sample) => { - let color = "black" - if (curr_sample.quality_flag !== null && curr_sample.quantity_flag !== null) { - color = curr_sample.quality_flag && curr_sample.quantity_flag ? "green" : "red" - } - - g.setNode(curr_sample.id.toString(), { - id: curr_sample.id.toString(), - label: curr_sample.name, + data.nodes.forEach((sample) => { + g.setNode(sample.id.toString(), { + id: sample.id.toString(), ...nodeSize, - color, - symbolType: curr_sample.id === sample.id ? "star" : "circle", }) }) - data.edges.filter((process) => process.child_sample !== null) .forEach((process) => { g.setEdge(process.source_sample, process.child_sample) - }) - - const localPairToProcess = data.edges.filter((process) => process.child_sample !== null) - .reduce((prev, p) => { - return { - ...prev, - [`${p.source_sample}:${p.child_sample}`]: p - } - }, {}) - - setPairToProcess(localPairToProcess) + }) dagre.layout(g) const { x: cx, y: cy } = g.node(sample.id.toString()) - const dx = nodeSize.width*5 - cx const dy = graphSize.height/2 - cy - const nodes = g.nodes() - .map((v) => { - const n = g.node(v) - return { - ...n, - id: v, - x: n.x + dx, - y: n.y + dy, - } - }) + // create final nodes and links + + const nodes = g.nodes() + .map((v) => { + const n = g.node(v) + const curr_sample = samples[n.id] + let color = "black" + if (curr_sample.quality_flag !== null && curr_sample.quantity_flag !== null) { + color = curr_sample.quality_flag && curr_sample.quantity_flag ? "green" : "red" + } + return { + ...n, + id: v, + x: n.x + dx, + y: n.y + dy, + color, + label: curr_sample.name, + symbolType: curr_sample.id === sample.id ? "star" : "circle", + } + }) const links = data.edges.filter((p) => p.child_sample !== null).map((p) => { return { @@ -127,40 +125,66 @@ const SampleDetailsLineage = ({ }) setGraphData({nodes, links}) + setNodesToEdges( + data.edges.filter((process) => process.child_sample !== null) + .reduce((prev, p) => { + return { + ...prev, + [`${p.source_sample}:${p.child_sample}`]: p + } + }, {}) + ) }) } - }, [sample]) + }, [sample?.id]) return ( <>
- + } - placement={"topRight"} + placement={"topLeft"} > - + - { - graphData.nodes.length > 0 - ? history.push(`/samples/${id}`)} - onClickLink={(source, target) => { - const linkId = pairToProcess[`${source}:${target}`].id - history.push(`/process-measurements/${linkId}`) - }} - /> - : <>Loading... - } - + + { + graphData.nodes.length > 0 + ? + : <>Loading... + } + +
) } +function GraphComponent({ data, config, nodesToEdge }) { + const history = useHistory() + + return history.push(`/samples/${id}`)} + onClickLink={(source, target) => { + const linkId = nodesToEdge[`${source}:${target}`].id + history.push(`/process-measurements/${linkId}`) + }} + /> +} + function Details() { return
@@ -209,7 +233,7 @@ function Legend() { return <> - {entries.map((entry) => )} + {entries.map((entry, index) => )} } From f780115b67a0d98b80e3851c2c968638b18dd2eb Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Fri, 27 May 2022 12:12:07 -0400 Subject: [PATCH 61/68] add reset button --- .../samples/details/SampleDetailsLineage.js | 62 +++++++++++++------ 1 file changed, 43 insertions(+), 19 deletions(-) diff --git a/frontend/src/components/samples/details/SampleDetailsLineage.js b/frontend/src/components/samples/details/SampleDetailsLineage.js index 99e6317174..48d52ee068 100644 --- a/frontend/src/components/samples/details/SampleDetailsLineage.js +++ b/frontend/src/components/samples/details/SampleDetailsLineage.js @@ -1,4 +1,4 @@ -import React, { useEffect, useState } from "react"; +import React, { useCallback, useEffect, useState } from "react"; import { connect } from "react-redux"; import { useHistory } from "react-router-dom"; @@ -27,6 +27,7 @@ const SampleDetailsLineage = ({ const [graphData, setGraphData] = useState({ nodes: [], links: [] }) const [nodesToEdges, setNodesToEdges] = useState({}) + const [reset, setReset] = useState(false) const nodeSize = { width: 10, height: 10 } @@ -138,21 +139,37 @@ const SampleDetailsLineage = ({ } }, [sample?.id]) + useEffect(() => { + if (reset) { + // make the graph visible again + setReset(false) + } + }, [reset]) + return ( <>
- } - placement={"topLeft"} - > + - + } + placement={"topLeft"} + > + + + { graphData.nodes.length > 0 @@ -160,8 +177,9 @@ const SampleDetailsLineage = ({ data={graphData} config={graphConfig} nodesToEdge={nodesToEdges} + reset={reset} /> - : <>Loading... + : Loading... } @@ -170,19 +188,25 @@ const SampleDetailsLineage = ({ ) } -function GraphComponent({ data, config, nodesToEdge }) { +function GraphComponent({ data, config, nodesToEdge, reset }) { const history = useHistory() - return history.push(`/samples/${id}`)} - onClickLink={(source, target) => { - const linkId = nodesToEdge[`${source}:${target}`].id - history.push(`/process-measurements/${linkId}`) - }} - /> + console.log(data) + + // reset will force the graph to rerender + + return reset + ? Loading... + : history.push(`/samples/${id}`)} + onClickLink={(source, target) => { + const linkId = nodesToEdge[`${source}:${target}`].id + history.push(`/process-measurements/${linkId}`) + }} + /> } function Details() { From 15914f472e72a12931e3872037fa9a9ced18ef30 Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Fri, 27 May 2022 12:14:10 -0400 Subject: [PATCH 62/68] refactor --- .../samples/details/SampleDetailsLineage.js | 75 ++++++++----------- 1 file changed, 32 insertions(+), 43 deletions(-) diff --git a/frontend/src/components/samples/details/SampleDetailsLineage.js b/frontend/src/components/samples/details/SampleDetailsLineage.js index 48d52ee068..9883ae7a05 100644 --- a/frontend/src/components/samples/details/SampleDetailsLineage.js +++ b/frontend/src/components/samples/details/SampleDetailsLineage.js @@ -2,7 +2,7 @@ import React, { useCallback, useEffect, useState } from "react"; import { connect } from "react-redux"; import { useHistory } from "react-router-dom"; -import { Typography, Card, Space, Popover, Button } from 'antd'; +import { Typography, Card, Space, Popover, Button, Spin } from 'antd'; const { Text } = Typography; @@ -23,6 +23,7 @@ const SampleDetailsLineage = ({ token, sample, }) => { + const history = useHistory() const { ref: resizeRef, size: maxSize } = useResizeObserver(720, 720) const [graphData, setGraphData] = useState({ nodes: [], links: [] }) @@ -58,6 +59,14 @@ const SampleDetailsLineage = ({ }, } + const dagreConfig = { + rankdir: "LR", + ranksep: 150, + nodesep: 150, + marginx: 50, + marginy: 50 + } + useEffect(() => { if (sample?.id !== undefined) { withToken(token, api.sample_lineage.get)(sample.id).then(({data}) => { @@ -67,14 +76,6 @@ const SampleDetailsLineage = ({ }), {}) // use dagre to position nodes - - const dagreConfig = { - rankdir: "LR", - ranksep: 150, - nodesep: 150, - marginx: 50, - marginy: 50 - } const g = new dagre.graphlib.Graph({ directed: true }) .setGraph(dagreConfig) .setDefaultEdgeLabel(function () { return {}; }); @@ -88,15 +89,14 @@ const SampleDetailsLineage = ({ .forEach((process) => { g.setEdge(process.source_sample, process.child_sample) }) - dagre.layout(g) + // create final nodes and links + const { x: cx, y: cy } = g.node(sample.id.toString()) const dx = nodeSize.width*5 - cx const dy = graphSize.height/2 - cy - // create final nodes and links - const nodes = g.nodes() .map((v) => { const n = g.node(v) @@ -115,7 +115,6 @@ const SampleDetailsLineage = ({ symbolType: curr_sample.id === sample.id ? "star" : "circle", } }) - const links = data.edges.filter((p) => p.child_sample !== null).map((p) => { return { id: p.id.toString(), @@ -124,8 +123,8 @@ const SampleDetailsLineage = ({ label: p.protocol_name, } }) - setGraphData({nodes, links}) + setNodesToEdges( data.edges.filter((process) => process.child_sample !== null) .reduce((prev, p) => { @@ -139,9 +138,12 @@ const SampleDetailsLineage = ({ } }, [sample?.id]) + // Take advantage of the fact that + // useEffect runs after rendering page. + // The graph will be remounted after + // being unmounted. useEffect(() => { if (reset) { - // make the graph visible again setReset(false) } }, [reset]) @@ -172,14 +174,22 @@ const SampleDetailsLineage = ({ { + // graphData must contain at least one node + // after fetching all nodes and edges graphData.nodes.length > 0 - ? - : Loading... + ? reset + ? + : history.push(`/samples/${id}`)} + onClickLink={(source, target) => { + const linkId = nodesToEdges[`${source}:${target}`].id + history.push(`/process-measurements/${linkId}`) + }} + /> + : } @@ -188,27 +198,6 @@ const SampleDetailsLineage = ({ ) } -function GraphComponent({ data, config, nodesToEdge, reset }) { - const history = useHistory() - - console.log(data) - - // reset will force the graph to rerender - - return reset - ? Loading... - : history.push(`/samples/${id}`)} - onClickLink={(source, target) => { - const linkId = nodesToEdge[`${source}:${target}`].id - history.push(`/process-measurements/${linkId}`) - }} - /> -} - function Details() { return
From 37cccc488d8c8e92d831c045cee8ce2e3c8f5654 Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Mon, 30 May 2022 11:30:28 -0400 Subject: [PATCH 63/68] don't fetch samples directly --- backend/fms_core/services/sample_lineage.py | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/backend/fms_core/services/sample_lineage.py b/backend/fms_core/services/sample_lineage.py index 6443eb8b6b..02e6ff1c95 100644 --- a/backend/fms_core/services/sample_lineage.py +++ b/backend/fms_core/services/sample_lineage.py @@ -36,18 +36,20 @@ def create_sample_lineage_graph(sampleId): errors.append(f"Sample with id ${sampleId} does not exist") if not errors: - derivedBySample = DerivedBySample.objects.filter(sample__id=sampleId) \ - .values_list("derived_sample__biosample_id", flat=True) + biosampleIds = DerivedBySample.objects.filter(sample__id=sampleId) \ + .values_list("derived_sample__biosample_id", flat=True) - sampleIds = DerivedBySample.objects.filter(derived_sample__biosample__id__in=derivedBySample) \ - .values_list("sample__id", flat=True) - samples = Sample.objects.filter(id__in=sampleIds) + derivedBySamples = DerivedBySample.objects.filter(derived_sample__biosample__id__in=biosampleIds) \ + .annotate(name=F("sample__name")) \ + .annotate(quality_flag=F("sample__quality_flag")) \ + .annotate(quantity_flag=F("sample__quantity_flag")) \ + sampleIds = derivedBySamples.values_list("sample__id", flat=True) process_measurements = ProcessMeasurement.objects.filter(source_sample__in=sampleIds) \ .select_related("process__lineage").annotate(child_sample=F("lineage__child")) \ .select_related("process_protocol").annotate(protocol_name=F("process__protocol__name")) - nodes = list(samples.values("id", "name", "quality_flag", "quantity_flag")) + nodes = list(derivedBySamples.values("name", "quality_flag", "quantity_flag").annotate(id=F("sample_id"))) edges = list(process_measurements.values("id", "source_sample", "child_sample", "protocol_name")) return (nodes, edges, errors) \ No newline at end of file From 0f95a48460a0c9768b4326c27141a0d75c0fdbea Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Tue, 31 May 2022 09:00:23 -0400 Subject: [PATCH 64/68] remove select_related --- backend/fms_core/services/sample_lineage.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/backend/fms_core/services/sample_lineage.py b/backend/fms_core/services/sample_lineage.py index 02e6ff1c95..55b1bbe10e 100644 --- a/backend/fms_core/services/sample_lineage.py +++ b/backend/fms_core/services/sample_lineage.py @@ -46,8 +46,8 @@ def create_sample_lineage_graph(sampleId): sampleIds = derivedBySamples.values_list("sample__id", flat=True) process_measurements = ProcessMeasurement.objects.filter(source_sample__in=sampleIds) \ - .select_related("process__lineage").annotate(child_sample=F("lineage__child")) \ - .select_related("process_protocol").annotate(protocol_name=F("process__protocol__name")) + .annotate(child_sample=F("lineage__child")) \ + .annotate(protocol_name=F("process__protocol__name")) nodes = list(derivedBySamples.values("name", "quality_flag", "quantity_flag").annotate(id=F("sample_id"))) edges = list(process_measurements.values("id", "source_sample", "child_sample", "protocol_name")) From 52f800f438704ade1fa272fd9a2375c05dfd6402 Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Tue, 31 May 2022 09:17:04 -0400 Subject: [PATCH 65/68] use divs in right places --- .../samples/details/SampleDetailsLineage.js | 46 +++++++++---------- 1 file changed, 23 insertions(+), 23 deletions(-) diff --git a/frontend/src/components/samples/details/SampleDetailsLineage.js b/frontend/src/components/samples/details/SampleDetailsLineage.js index 9883ae7a05..5abd91573d 100644 --- a/frontend/src/components/samples/details/SampleDetailsLineage.js +++ b/frontend/src/components/samples/details/SampleDetailsLineage.js @@ -32,7 +32,7 @@ const SampleDetailsLineage = ({ const nodeSize = { width: 10, height: 10 } - // maxSize.height is sometimes outrageously large + // maxSize.height is sometimes outrageously large or extremely small const graphSize = { width: maxSize.width, height: maxSize.width } const graphConfig = { ...graphSize, @@ -150,29 +150,29 @@ const SampleDetailsLineage = ({ return ( <> -
- - + + + + } + placement={"topLeft"} + > - } - placement={"topLeft"} - > - - - - + + +
+
{ // graphData must contain at least one node // after fetching all nodes and edges @@ -189,11 +189,11 @@ const SampleDetailsLineage = ({ history.push(`/process-measurements/${linkId}`) }} /> - : + : } - - -
+
+
+ ) } From 5bc6aa9f5c28441a599288d65b56a09858dcd44d Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Tue, 31 May 2022 09:48:28 -0400 Subject: [PATCH 66/68] only reposition horizontally if the graph is too wide --- .../src/components/samples/details/SampleDetailsLineage.js | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/frontend/src/components/samples/details/SampleDetailsLineage.js b/frontend/src/components/samples/details/SampleDetailsLineage.js index 5abd91573d..f368e4be1b 100644 --- a/frontend/src/components/samples/details/SampleDetailsLineage.js +++ b/frontend/src/components/samples/details/SampleDetailsLineage.js @@ -93,8 +93,10 @@ const SampleDetailsLineage = ({ // create final nodes and links + const enclosedWidth = Math.max(...g.nodes().map((v) => g.node(v).x)) + const { x: cx, y: cy } = g.node(sample.id.toString()) - const dx = nodeSize.width*5 - cx + const dx = graphSize.width/2 - cx const dy = graphSize.height/2 - cy const nodes = g.nodes() @@ -108,7 +110,7 @@ const SampleDetailsLineage = ({ return { ...n, id: v, - x: n.x + dx, + x: n.x + (enclosedWidth > (graphSize.width - nodeSize.width) ? dx : 0), y: n.y + dy, color, label: curr_sample.name, From f4192662f8a22c174d763c5835fc17af1296c45b Mon Sep 17 00:00:00 2001 From: nafiz1001 Date: Sun, 5 Jun 2022 18:09:16 -0400 Subject: [PATCH 67/68] add docstrings --- backend/fms_core/services/sample_lineage.py | 27 ++++++++++++++++++-- backend/fms_core/viewsets/sample_lineage.py | 28 ++++++++++++++++++++- 2 files changed, 52 insertions(+), 3 deletions(-) diff --git a/backend/fms_core/services/sample_lineage.py b/backend/fms_core/services/sample_lineage.py index 55b1bbe10e..6ba7cbcdee 100644 --- a/backend/fms_core/services/sample_lineage.py +++ b/backend/fms_core/services/sample_lineage.py @@ -1,3 +1,4 @@ +from typing import Dict, List, Tuple from django.db.models import F from django.core.exceptions import ValidationError from fms_core.models import SampleLineage, Sample, DerivedBySample, ProcessMeasurement @@ -27,7 +28,29 @@ def create_sample_lineage(parent_sample, child_sample, process_measurement): return (sample_lineage, errors, warnings) -def create_sample_lineage_graph(sampleId): +def create_sample_lineage_graph(sampleId: int) -> Tuple[List[Dict], List[Dict], List[str]]: + """ + Generates a sample lineage of all samples that share the + same biosample ID of the `sampleId`. Returns a graph that + is acyclical and consists of `nodes` and `edges`. + + Parameters + ---------- + `sampleId` : `int` + ID of an existing sample + + + Returns + ------- + `Tuple[List[Dict], List[Dict], List[str]]` + consisting of `nodes`, `edges` and `errors`. + Each node consists of sample `"name"`, `"quality_flag"` and `"quantity_flag"`. + Each edge consists of process `"id"`, `"source_sample"`, `"child_sample"`, `"protocol_name"` + `errors` contains an error if the ID in `sampleId` does not correspond + to an existing sample. + + """ + errors = [] nodes = [] edges = [] @@ -52,4 +75,4 @@ def create_sample_lineage_graph(sampleId): nodes = list(derivedBySamples.values("name", "quality_flag", "quantity_flag").annotate(id=F("sample_id"))) edges = list(process_measurements.values("id", "source_sample", "child_sample", "protocol_name")) - return (nodes, edges, errors) \ No newline at end of file + return (nodes, edges, errors) diff --git a/backend/fms_core/viewsets/sample_lineage.py b/backend/fms_core/viewsets/sample_lineage.py index a2bf49b13f..d30c42f024 100644 --- a/backend/fms_core/viewsets/sample_lineage.py +++ b/backend/fms_core/viewsets/sample_lineage.py @@ -9,7 +9,33 @@ class SampleLineageViewSet(viewsets.ViewSet): @action(detail=True, methods=["get"]) - def graph(self, _request, pk): + def graph(self, _request, pk) -> Response: + """ + Generates a sample lineage that is + acyclical where each node is a sample + and each edge is a process. For more + information, visit + `fms_core.services.sample_lineage.create_sample_lineage_graph` + + Parameters + ---------- + `_request` : `Any` + ignored + `pk` : `int` + ID of an existing sample + + Returns + ------- + `Response` + `Response` object consisting of `"data"` + and `"edges"` + + Raises + ------ + `ValidationError` + the ID corresponds to a sample that does not exist. + """ + nodes, edges, errors = create_sample_lineage_graph(pk) if errors: From 290fd42fa5f0fc9ccb8acf4fe26105ad474f5e0c Mon Sep 17 00:00:00 2001 From: Nafiz Islam Date: Mon, 6 Jun 2022 15:23:05 -0400 Subject: [PATCH 68/68] tiny tweaks --- .../src/components/samples/details/SampleDetailsLineage.js | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/frontend/src/components/samples/details/SampleDetailsLineage.js b/frontend/src/components/samples/details/SampleDetailsLineage.js index f368e4be1b..2a57b27670 100644 --- a/frontend/src/components/samples/details/SampleDetailsLineage.js +++ b/frontend/src/components/samples/details/SampleDetailsLineage.js @@ -95,6 +95,7 @@ const SampleDetailsLineage = ({ const enclosedWidth = Math.max(...g.nodes().map((v) => g.node(v).x)) + // deltas to center current sample const { x: cx, y: cy } = g.node(sample.id.toString()) const dx = graphSize.width/2 - cx const dy = graphSize.height/2 - cy @@ -110,6 +111,7 @@ const SampleDetailsLineage = ({ return { ...n, id: v, + // if node too far to the right, center it horizontally in the canvas x: n.x + (enclosedWidth > (graphSize.width - nodeSize.width) ? dx : 0), y: n.y + dy, color, @@ -180,7 +182,7 @@ const SampleDetailsLineage = ({ // after fetching all nodes and edges graphData.nodes.length > 0 ? reset - ? + ? : - : + : }