Merge branch '3-accession-overview' into 'master'

Resolve "Accession overview"

Closes #3

See merge request !6

entrypoints/index.html

@@ -19,6 +19,9 @@
     <li class="nav-item">
       <a class="nav-link active" href="#/">Home</a>
     </li>
+    <li class="nav-item">
+      <a class="nav-link" href="#/overview">Overview</a>
+    </li>
     <li class="nav-item">
       <a class="nav-link" href="#/api-info">API Info</a>
     </li>

package.json

@@ -36,6 +36,7 @@
     "history": "^4.0.0",
     "i18next": "^19.0.0",
     "react": "^16.0.0",
+    "d3": "^6.2.0",
     "react-dom": "^16.0.0",
     "react-i18next": "^11.0.0",
     "react-router-dom": "^5.0.0"

src/d3js/TreeMap.tsx

+import * as React from 'react';
+
+import { d3, DOM } from 'd3js';
+
+interface IProps {
+  nullLabel?: string;
+  style: object;
+  data: any;
+}
+
+/**
+ * TreeMap based on https://observablehq.com/@d3/zoomable-treemap
+ */
+export const TreeMap = ({ nullLabel = 'NULL', style, data }: IProps) => {
+  const chartRef = React.useRef(null);
+
+  if (typeof window !== 'undefined' && d3) {
+    const format = d3.format(',d');
+
+    const name = (d) => d.data.term || d.data.name;
+    const nameWithPath = (d) => d.ancestors().reverse().map(name).join(' / ');
+
+    // useEffect
+    React.useEffect(() => {
+      // console.log('React effect!', chartRef, data);
+
+      if (! data || ! chartRef.current) {
+        return;
+      }
+
+      const headerHeight = 60;
+
+      const width = chartRef.current.parentNode.getBoundingClientRect().width;
+      let height = chartRef.current.parentNode.getBoundingClientRect().height;
+
+      const svg = d3.select(chartRef.current)
+        .attr('height', height)
+        .attr('width', width)
+
+      height -= headerHeight;
+      const color = d3.scaleOrdinal(d3.quantize(d3.interpolateSpectral, data.children.length + 1));
+
+      const tile = (node, x0, y0, x1, y1) => {
+        d3.treemapBinary(node, 0, 0, width, height);
+        for (const child of node.children) {
+          child.x0 = x0 + child.x0 / width * (x1 - x0);
+          child.x1 = x0 + child.x1 / width * (x1 - x0);
+          child.y0 = y0 + child.y0 / height * (y1 - y0);
+          child.y1 = y0 + child.y1 / height * (y1 - y0);
+        }
+      }
+
+      const treemap = (data) => d3.treemap().tile(tile)(d3.hierarchy(data).sum((d) => d.count).sort((a, b) => b.count - a.count));
+
+      const x = d3.scaleLinear().rangeRound([0, width]);
+      const y = d3.scaleLinear().rangeRound([0, height]);
+
+      svg
+        .attr('viewBox', [0, -headerHeight - 0, width, height + headerHeight])
+        .style('font', '14px sans-serif');
+
+      const old = svg.selectAll('g');
+      // console.log('SVG', svg, old);
+      if (old) {
+        // console.log('Removing', old);
+        old.remove();
+      }
+
+      let group = svg.append('g')
+        .call(render, treemap(data));
+
+      group.exit().remove();
+
+      function render(group, root) {
+        const node = group
+          .selectAll('g')
+          .data(root.children.concat(root))
+          .join('g');
+
+        node.filter((d) => d === root ? d.parent : d.children)
+          .attr('cursor', 'pointer')
+          .on('click', (d) => d === root ? zoomout(root) : zoomin(d));
+
+        node.append('title')
+          .text((d) => `${nameWithPath(d)}\n${format(d.value)}`);
+
+        node.append('rect')
+          .attr('id', (d) => (d.leafUid = DOM.uid('leaf')).id)
+          .attr('fill', (d) => d === root ? '#fff' : d.children ? '#ccc' : color(d.data.term))
+          .attr('stroke', '#fff');
+
+        node.append('clipPath')
+          .attr('id', (d) => (d.clipUid = DOM.uid('clip')).id)
+          .append('use')
+          .attr('xlink:href', (d) => d.leafUid.href);
+
+        node.append('text')
+          .attr('clip-path', (d) => d.clipUid)
+          .attr('font-weight', (d) => d === root ? 'bold' : null)
+          .selectAll('tspan')
+          .data((d) => [ (d === root ? nameWithPath(d) : name(d)) ].concat(format(d.value)))
+          .join('tspan')
+          .attr('x', 3)
+          .attr('y', (d, i, nodes) => `${(i === nodes.length - 1 ? 1 : 0) * 0.3 + 1.1 + i * 0.9}em`)
+          .attr('fill-opacity', (d, i, nodes) => i === nodes.length - 1 ? 0.7 : null)
+          .attr('font-weight', (d, i, nodes) => i === nodes.length - 1 ? 'normal' : null)
+          .text((d) => d);
+
+        group.call(position, root);
+      }
+
+      function position(group, root) {
+        group.selectAll('g')
+          .attr('transform', (d) => d === root ? 'translate(0,-60)' : `translate(${x(d.x0)},${y(d.y0)})`)
+          .select('rect')
+          .attr('width', (d) => d === root ? width : x(d.x1) - x(d.x0))
+          .attr('height', (d) => d === root ? 60 : y(d.y1) - y(d.y0));
+      }
+
+      // When zooming in, draw the new nodes on top, and fade them in.
+      function zoomin(d) {
+        const group0 = group.attr('pointer-events', 'none');
+        const group1 = group = svg.append('g').call(render, d);
+
+        x.domain([d.x0, d.x1]);
+        y.domain([d.y0, d.y1]);
+
+        svg.transition()
+          .duration(750)
+          .call((t) => group0.transition(t).remove()
+            .call(position, d.parent))
+          .call((t) => group1.transition(t)
+            .attrTween('opacity', () => d3.interpolate(0, 1))
+            .call(position, d));
+      }
+
+      // When zooming out, draw the old nodes on top, and fade them out.
+      function zoomout(d) {
+        const group0 = group.attr('pointer-events', 'none');
+        const group1 = group = svg.insert('g', '*').call(render, d.parent);
+
+        x.domain([d.parent.x0, d.parent.x1]);
+        y.domain([d.parent.y0, d.parent.y1]);
+
+        svg.transition()
+          .duration(750)
+          .call((t) => group0.transition(t).remove()
+            .attrTween('opacity', () => d3.interpolate(1, 0))
+            .call(position, d))
+          .call((t) => group1.transition(t)
+            .call(position, d.parent));
+      }
+
+    }, [ data ]);
+  }
+
+  console.log('Rendering TreeMap', style, chartRef);
+
+  return (
+    <svg style={ style } ref={ chartRef }></svg>
+  );
+};

src/d3js/index.ts

+import { TreeMap } from './TreeMap';
+
+let d3 = null;
+if (typeof window !== 'undefined') {
+  d3 = require('d3');
+}
+
+let defLoc = '';
+if (typeof document !== 'undefined' && document.location) {
+  defLoc = document.location.hash
+    ? document.location.href.substring(0, document.location.href.length - document.location.hash.length)
+    : document.location.href;
+}
+
+/**
+ * Reimplementation of DOM.uid used by Observable.
+ */
+class UID {
+  private static location = defLoc;
+  public id: string;
+  public href: URL;
+
+  public constructor(id: string) {
+    this.id = id;
+    this.href = new URL(`#${id}`, UID.location);
+  }
+
+  public toString() {
+    return 'url(' + this.href + ')';
+  }
+};
+
+/**
+ * Implementation of DOM class used by Observable.
+ */
+class DOM {
+  private static prefix = `${new Date().getTime()}`;
+  private static counter = {};
+  public static uid = (scope: string) => {
+    const id = DOM.counter.hasOwnProperty(scope) ? DOM.counter[scope] = DOM.counter[scope] + 1 : DOM.counter[scope] = 1;
+    return new UID(`O-${DOM.prefix}-${scope}-${id}`);
+  }
+};
+
+export { d3, DOM, TreeMap };

src/genesys.tsx

@@ -33,13 +33,13 @@ function checkAccessTokens(apiUrl: string, clientId: string, clientSecret: strin
       throw error;
     });
 
-    // if (cookieToken) {
-    //   return Promise.resolve(true);
-    // } else {
-    //   cookies.remove(AUTH_COOKIE);
-    //   return appLogin;
-    // }
-    return appLogin;
+  // if (cookieToken) {
+  //   return Promise.resolve(true);
+  // } else {
+  //   cookies.remove(AUTH_COOKIE);
+  //   return appLogin;
+  // }
+  return appLogin;
 };
 
 export function showGenesysUI(holdingNode: HTMLElement, config: Config = DefaultConfig, language: string = "en") {

src/locales/en/translations.json

@@ -27,6 +27,33 @@
     "storageType": "Type of germplasm storage",
     "datasets": "Datasets",
     "subsets": "Subsets",
+    "overview": {
+      "title": "Accession overview",
+      "subTitle": "Summary information about selected accessions",
+      "about": "About",
+      "total": "Total",
+      "Other": "Other",
+      "Not specified": "Not specified",
+      "NULL": "Data not recorded",
+      "institute code": "Holding Institute",
+      "institute country code3": "Country of holding institute",
+      "crop shortName": "Crop",
+      "cropName": "Crop name",
+      "sampStat": "Biological status of accession",
+      "taxonomy genus": "Genus name provided to Genesys",
+      "taxonomy genusSpecies": "Species name provided to Genesys",
+      "taxonomy grinTaxonomySpecies": "Matched GRIN taxon",
+      "taxonomy currentTaxonomySpecies": "Current GRIN taxon",
+      "countryOfOrigin code3": "Provenance of material",
+      "donorCode": "FAO WIEWS code of donor institute",
+      "mlsStatus": "ITGPRFA Multi-lateral system",
+      "available": "Available for distribution",
+      "duplSite": "Site of safety duplication",
+      "breederCode": "Breeder code",
+      "sgsv": "Safety duplicated in Svalbard",
+      "storage": "Type of Germplasm storage",
+      "aegis": "AEGIS"
+    },
     "coll": {
       "collCode": "Collecting institute code",
       "collNumb": "Collecting number",
@@ -101,6 +128,32 @@
       "61": "Roadside",
       "62": "Field margin",
       "99": "Other"
+    },
+    "mlsStatus": {
+      "true": "Accession is part of the Multi-lateral system of ITPGRFA",
+      "false": "Not declared in the Multi-lateral system of ITPGRFA",
+      "1": "Accession is part of the Multi-lateral system of ITPGRFA",
+      "0": "Not declared in the Multi-lateral system of ITPGRFA",
+      "null": "Status not provided"
+    },
+    "available": {
+      "0": "Not available for distribution",
+      "1": "Available for distribution",
+      "true": "Available for distribution",
+      "false": "Not available for distribution",
+      "null": "Availability not provided"
+    },
+    "sgsv": {
+      "true": "Backed up in SGSV",
+      "false": "Not in SGSV",
+      "1": "Backed up in SGSV",
+      "0": "Not in SGSV"
+    },
+    "aegisStatus": {
+      "true": "Accession is part of the European Collection",
+      "false": "Accession is not part of the European Collection",
+      "1": "Accession is part of the European Collection",
+      "0": "Accession is not part of the European Collection"
     }
   },
   "cart": {

src/ui/AccessionOverviewSection.tsx

+import * as React from 'react';
+import {withTranslation, WithTranslation} from 'react-i18next';
+// model
+import AccessionOverview from '@genesys/client/model/accession/AccessionOverview';
+import PropertiesCard from "ui/PropertiesCard";
+import {VocabularyService} from "@genesys/client/service";
+
+interface IAccessionOverviewPageState {
+  countryCodes: object;
+}
+
+interface IAccessionOverviewPageProps extends React.ClassAttributes<any> {
+  overview: AccessionOverview;
+}
+
+class AccessionOverviewSection extends React.Component<IAccessionOverviewPageProps & WithTranslation, IAccessionOverviewPageState> {
+  public constructor(props) {
+    super(props);
+
+    this.state = {
+      countryCodes: null,
+    }
+  }
+
+  private overviewKeys = ['institute.code', 'institute.country.code3', 'cropName', 'crop.shortName', 'sampStat', 'taxonomy.genus', 'taxonomy.genusSpecies',
+    'taxonomy.grinTaxonomySpecies.name', 'taxonomy.currentTaxonomySpecies.name',
+    'countryOfOrigin.code3', 'donorCode', 'mlsStatus', 'available', 'duplSite', 'sgsv', 'storage', 'breederCode', 'aegis'];
+
+  public async componentDidMount() {
+    const codes = await VocabularyService.decode3166Alpha3Terms(this.props.i18n.language);
+    this.setState({countryCodes: codes})
+  }
+
+  public render() {
+    const {overview, t} = this.props;
+
+    const {countryCodes} = this.state;
+
+
+    if (!overview) {
+      return null;
+    }
+
+    const overviewsTerms = new Map();
+
+    this.overviewKeys.forEach((key) => {
+      const overviewEl = overview[key];
+      const terms = overviewEl && overviewEl.terms ? [].concat(overviewEl.terms) : [];
+      if (overviewEl && overviewEl.other && overviewEl.other > 0) {
+        terms.push({term: 'accession.overview.Other', count: overviewEl.other});
+      }
+      if (overviewEl && overviewEl.missing && overviewEl.missing > 0) {
+        terms.push({term: 'accession.overview.Not specified', count: overviewEl.missing});
+      }
+      overviewsTerms.set(key, terms);
+    });
+
+    return (
+      <div className="row pl-5">
+        {overviewsTerms && overviewsTerms.get('institute.code') &&
+          <PropertiesCard
+            propertiesList={overviewsTerms.get('institute.code')}
+            title={t(`accession.overview.institute code`)}
+            propertyItemProps={{numeric: true}}
+          />
+        }
+        {overviewsTerms && overviewsTerms.get('institute.country.code3') &&
+          <PropertiesCard
+            propertiesList={overviewsTerms.get('institute.country.code3')}
+            countyCodes={countryCodes}
+            title={t(`accession.overview.institute country code3`)}
+            propertyItemProps={{numeric: true}}
+          />
+        }
+        {overviewsTerms && overviewsTerms.get('crop.shortName') &&
+          <PropertiesCard
+            propertiesList={overviewsTerms.get('crop.shortName')}
+            title={t(`accession.overview.crop shortName`)}
+            propertyItemProps={{numeric: true}}
+          />
+        }
+        {overviewsTerms && overviewsTerms.get('cropName') &&
+          <PropertiesCard
+            propertiesList={overviewsTerms.get('cropName')}
+            title={t(`accession.overview.cropName`)}
+            propertyItemProps={{numeric: true}}
+          />
+        }
+        {overviewsTerms && overviewsTerms.get('taxonomy.genus') &&
+          <PropertiesCard
+            propertiesList={overviewsTerms.get('taxonomy.genus')}
+            title={t(`accession.overview.taxonomy genus`)}
+            propertyItemProps={{numeric: true, titleStyle: {fontStyle: 'italic'}}}
+          />
+        }
+        {overviewsTerms && overviewsTerms.get('taxonomy.genusSpecies') &&
+          <PropertiesCard
+            propertiesList={overviewsTerms.get('taxonomy.genusSpecies')}
+            title={t(`accession.overview.taxonomy genusSpecies`)}
+            propertyItemProps={{numeric: true, titleStyle: {fontStyle: 'italic'}}}
+          />
+        }
+
+        {overviewsTerms && overviewsTerms.get('taxonomy.grinTaxonomySpecies.name') &&
+          <PropertiesCard
+            propertiesList={overviewsTerms.get('taxonomy.grinTaxonomySpecies.name')}
+            title={t(`accession.overview.taxonomy grinTaxonomySpecies`)}
+            propertyItemProps={{numeric: true, titleStyle: {fontStyle: 'italic'}}}
+          />
+        }
+        {overviewsTerms && overviewsTerms.get('taxonomy.currentTaxonomySpecies.name') &&
+          <PropertiesCard
+            propertiesList={overviewsTerms.get('taxonomy.currentTaxonomySpecies.name')}
+            title={t(`accession.overview.taxonomy currentTaxonomySpecies`)}
+            propertyItemProps={{numeric: true, titleStyle: {fontStyle: 'italic'}}}
+          />
+        }
+
+        {overviewsTerms && overviewsTerms.get('sampStat') &&
+          <PropertiesCard
+            propertiesList={overviewsTerms.get('sampStat')}
+            translationGroup="sampleStatus"
+            title={t(`accession.overview.sampStat`)}
+            propertyItemProps={{numeric: true}}
+          />
+        }
+        {overviewsTerms && overviewsTerms.get('storage') &&
+          <PropertiesCard
+            propertiesList={overviewsTerms.get('storage')}
+            translationGroup="storage"
+            title={t(`accession.overview.storage`)}
+            propertyItemProps={{numeric: true}}
+          />
+        }
+        {overviewsTerms && overviewsTerms.get('countryOfOrigin.code3') &&
+          <PropertiesCard
+            propertiesList={overviewsTerms.get('countryOfOrigin.code3')}
+            countyCodes={countryCodes}
+            title={t(`accession.overview.countryOfOrigin code3`)}
+            propertyItemProps={{numeric: true}}
+          />
+        }
+        {overviewsTerms && overviewsTerms.get('donorCode') &&
+          <PropertiesCard
+            propertiesList={overviewsTerms.get('donorCode')}
+            title={t(`accession.overview.donorCode`)}
+            propertyItemProps={{numeric: true}}
+          />
+        }
+        {overviewsTerms && overviewsTerms.get('duplSite') &&
+          <PropertiesCard
+            propertiesList={overviewsTerms.get('duplSite')}
+            title={t(`accession.overview.duplSite`)}
+            propertyItemProps={{numeric: true}}
+          />
+        }
+        {overviewsTerms && overviewsTerms.get('breederCode') &&
+          <PropertiesCard
+            propertiesList={overviewsTerms.get('breederCode')}
+            title={t(`accession.overview.breederCode`)}
+            propertyItemProps={{numeric: true}}
+          />
+        }
+        {overviewsTerms && overviewsTerms.get('mlsStatus') &&
+          <PropertiesCard
+            propertiesList={overviewsTerms.get('mlsStatus')}
+            translationGroup="mlsStatus"
+            title={t(`accession.overview.mlsStatus`)}
+            propertyItemProps={{numeric: true}}
+          />
+        }
+        {overviewsTerms && overviewsTerms.get('aegis') &&
+          <PropertiesCard
+            propertiesList={overviewsTerms.get('aegis')}
+            translationGroup="aegisStatus"
+            title={t(`accession.overview.aegis`)}
+            propertyItemProps={{numeric: true}}
+          />
+        }
+        {overviewsTerms && overviewsTerms.get('available') &&
+          <PropertiesCard
+            propertiesList={overviewsTerms.get('available')}
+            translationGroup="available"
+            title={t(`accession.overview.available`)}
+            propertyItemProps={{numeric: true}}
+          />
+        }
+        {overviewsTerms && overviewsTerms.get('historic') &&
+          <PropertiesCard
+            propertiesList={overviewsTerms.get('historic')}
+            translationGroup="historic"
+            title={t(`accession.overview.historic`)}
+            propertyItemProps={{numeric: true}}
+          />
+        }
+        {overviewsTerms && overviewsTerms.get('sgsv') &&
+          <PropertiesCard
+            propertiesList={overviewsTerms.get('sgsv')}
+            translationGroup="sgsv"
+            title={t(`accession.overview.sgsv`)}
+            propertyItemProps={{numeric: true}}
+          />
+        }
+      </div>
+    );
+  }
+}
+
+export default withTranslation()(AccessionOverviewSection);

src/ui/App.tsx

@@ -6,6 +6,7 @@ import AccessionList from './AccessionListPage';
 import AccessionDetails from './AccessionDetailsPage';
 import { createHashHistory } from 'history';
 import CartPage from './CartPage';
+import OverviewPage from "ui/OverviewPage";
 
 const hashHistory = createHashHistory({});
 
@@ -27,6 +28,7 @@ export default class App extends React.Component<IAppProps, any> {
               <Route path="/" exact render={ (props) => <AccessionList { ...props } filter={ this.props.filter }/> }/>
               <Route path="/api-info" exact component={ ApiInfoPage }/>
               <Route path="/cart/" exact component={ CartPage }/>
+              <Route path="/overview" exact component={ OverviewPage }/>
               <Route component={ NotFound }/>
             </Switch>
 

src/ui/Navigation.tsx

@@ -14,6 +14,7 @@ class Navigation extends React.Component<INavigation, any> {
         <nav>
           <ul style={ { display: 'flex', listStyle: 'none' } }>
             <li style={ { marginRight: '20px' } }><Link to="/">{t("nav.home")}</Link></li>
+            <li style={ { marginRight: '20px' } }><Link to="/overview">{t('nav.overview')}</Link></li>
             <li style={ { marginRight: '20px' } }><Link to="/api-info">{t("nav.apiInfo")}</Link></li>
             <li style={ { marginRight: '20px' } }><Link to="/cart/">{t('nav.cart')}</Link></li>
           </ul>

src/ui/Number.tsx

+import * as React from 'react';
+import {WithTranslation, withTranslation} from "react-i18next";
+
+interface INumber extends React.ClassAttributes<any>, WithTranslation {
+  value: number;
+  config?: Intl.NumberFormatOptions;
+}
+
+
+// Print a number
+// TBD maybe use l10n instead?
+class Number extends React.Component<INumber, any> {
+  public constructor(props) {
+    super(props);
+  }
+
+  public render() {
+    const {value, config = {}, i18n} = this.props
+
+    if (typeof value === 'number') {
+      return <span>{ value.toLocaleString(i18n.language, { maximumFractionDigits: 6, ...config }) }</span>;
+    } else {
+      return <span>&mdash;</span>;
+    }
+  }
+}
+
+export default React.memo(withTranslation()(Number));

src/ui/OverviewPage.tsx

+import * as React from 'react';
+import { WithTranslation, withTranslation } from 'react-i18next';