col-browser 2.2.0 → 2.2.2

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Files changed (31) hide show
  1. package/README.md +1 -1
  2. package/es/chunks/DatasetlogoWithFallback-B9WXvNCA.js +24 -0
  3. package/es/chunks/DatasetlogoWithFallback-B9WXvNCA.js.map +1 -0
  4. package/es/chunks/{Distributions-CXIEJ6e6.js → Distributions-Cwl_75VG.js} +349 -348
  5. package/es/chunks/{Distributions-CXIEJ6e6.js.map → Distributions-Cwl_75VG.js.map} +1 -1
  6. package/es/chunks/{MetricsPresentation-U_CO8JoH.js → MetricsPresentation-DKCJQOtf.js} +2 -2
  7. package/es/chunks/{MetricsPresentation-U_CO8JoH.js.map → MetricsPresentation-DKCJQOtf.js.map} +1 -1
  8. package/es/chunks/{DatasetlogoWithFallback-CbP7vRs_.js → PresentationItem-C4yZ555-.js} +243 -262
  9. package/es/chunks/PresentationItem-C4yZ555-.js.map +1 -0
  10. package/es/chunks/index-BmhRLlZh.js +100 -0
  11. package/es/chunks/index-BmhRLlZh.js.map +1 -0
  12. package/es/index.js +1 -1
  13. package/es/routing.js +1 -1
  14. package/es/sourceDataset.js +57 -56
  15. package/es/sourceDataset.js.map +1 -1
  16. package/es/sourceDatasetList.js +5 -4
  17. package/es/sourceDatasetList.js.map +1 -1
  18. package/es/taxon.js +18 -12
  19. package/es/taxon.js.map +1 -1
  20. package/es/taxonDistribution.js +1 -1
  21. package/es/tree.js +60 -57
  22. package/es/tree.js.map +1 -1
  23. package/package.json +1 -1
  24. package/types/index.d.ts +13 -0
  25. package/umd/col-browser.js +150 -134
  26. package/umd/col-browser.js.map +1 -1
  27. package/umd/col-browser.min.js +5 -5
  28. package/umd/col-browser.min.js.map +1 -1
  29. package/es/chunks/DatasetlogoWithFallback-CbP7vRs_.js.map +0 -1
  30. package/es/chunks/index-CNK3JADR.js +0 -95
  31. package/es/chunks/index-CNK3JADR.js.map +0 -1
package/es/tree.js.map CHANGED
@@ -1 +1 @@
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- {"version":3,"file":"tree.js","sources":["../src/ColTree/treeCache.js","../src/ColTree/TaxonSources.js","../src/ColTree/ColTreeContext.js","../src/ColTree/ColTreeNode.js","../src/ColTree/ColTree.js","../src/ColTree/index.js","../src/entries/tree.js"],"sourcesContent":["import { createContext } from \"react\";\nimport DataLoader from \"dataloader\";\nimport { getDatasetsBatch, getPublishersBatch } from \"../api/dataset\";\n\n// Shared DataLoaders for the Tree subtree. Created once per (datasetKey,\n// mounted Tree) and provided via TreeCacheContext so every TaxonSources,\n// every sector-dataset decoration in ColTree, and any other in-tree\n// consumer hits the same in-memory cache. Without this, each TaxonSources\n// instance creates its own loader and the same source/publisher dataset\n// is fetched once per node it appears under.\n//\n// DataLoader batches calls inside a microtask and caches resolved values\n// indefinitely for the lifetime of the loader.\n\nexport const TreeCacheContext = createContext({\n datasetLoader: null,\n publisherLoader: null,\n});\n\nexport const createTreeCache = (datasetKey) => ({\n datasetLoader: new DataLoader((ids) => getDatasetsBatch(ids, datasetKey)),\n publisherLoader: new DataLoader((ids) =>\n getPublishersBatch(ids, datasetKey)\n ),\n});\n","import React from \"react\";\nimport { Popover, Spin, Divider } from \"antd\";\nimport DataLoader from \"dataloader\";\nimport { sortBy } from \"lodash-es\";\nimport { LinkTo } from \"../router\";\nimport { TreeCacheContext } from \"./treeCache\";\nimport { getDatasetsBatch, getPublishersBatch } from \"../api/dataset\";\nimport config from \"../config\";\n\nclass TaxonSources extends React.Component {\n static contextType = TreeCacheContext;\n\n constructor(props) {\n super(props);\n this.state = {\n data: [],\n showInNode: false,\n loading: false,\n };\n }\n\n // Returns the shared cache from TreeCacheContext if available, or a\n // throwaway local DataLoader so the popover still works even if context\n // doesn't reach this instance (which used to leave the spinner stuck\n // because getData early-returned with no loading state set).\n getDatasetLoader = () => {\n const { datasetKey } = this.props;\n if (this.context?.datasetLoader) return this.context.datasetLoader;\n if (!this._localDatasetLoader) {\n this._localDatasetLoader = new DataLoader((ids) =>\n getDatasetsBatch(ids, datasetKey)\n );\n }\n return this._localDatasetLoader;\n };\n\n getPublisherLoader = () => {\n const { datasetKey } = this.props;\n if (this.context?.publisherLoader) return this.context.publisherLoader;\n if (!this._localPublisherLoader) {\n this._localPublisherLoader = new DataLoader((ids) =>\n getPublishersBatch(ids, datasetKey)\n );\n }\n return this._localPublisherLoader;\n };\n\n componentDidMount = () => {\n const { sourceDatasetKeys } = this.props;\n if (sourceDatasetKeys && sourceDatasetKeys.length < 4) {\n this.setState({ showInNode: true }, this.getData);\n }\n };\n\n getData = () => {\n const { sourceDatasetKeys } = this.props;\n if (!sourceDatasetKeys?.length) return;\n this.setState({ loading: true });\n const loader = this.getDatasetLoader();\n Promise.all(\n sourceDatasetKeys.map((s) => loader.load(s).catch(() => null))\n )\n .then((data) => {\n this.setState({ data: sortBy(data, [\"alias\"]), loading: false });\n })\n .catch(() => {\n this.setState({ data: [], loading: false });\n });\n };\n\n getPublisherData = () => {\n const { publisherDatasetKeys } = this.props;\n if (!publisherDatasetKeys) return;\n const loader = this.getPublisherLoader();\n Promise.all(\n Object.keys(publisherDatasetKeys).map((s) =>\n loader\n .load(s)\n .then((publisher) => ({\n ...publisher,\n datasets: publisherDatasetKeys[s],\n }))\n .catch(() => null)\n )\n )\n .then((data) => {\n this.setState({ publishers: sortBy(data.filter(Boolean), [\"alias\"]) });\n })\n .catch(() => {\n this.setState({ publishers: [] });\n });\n };\n\n render = () => {\n const { data, showInNode, popOverVisible, loading } = this.state;\n const { taxon, datasetKey } = this.props;\n const linkStyle = { color: \"orange\", fontSize: \"11px\" };\n const publisherUrl = (uuid) =>\n `${config.clbPortal}/dataset/${datasetKey}/publisher/${uuid}`;\n\n if (showInNode) {\n return data\n .filter((d) => !!d)\n .map((d, index) => (\n <LinkTo\n to=\"source\"\n args={d.key}\n key={d.key}\n className=\"col-tree-data-source\"\n style={linkStyle}\n >\n {(index ? \", \" : \"\") + (d.alias || d.key)}\n </LinkTo>\n ));\n }\n\n return (\n <div style={{ display: \"inline\" }} id={`taxon_sources_${taxon.id}`}>\n <Popover\n getPopupContainer={() =>\n document.getElementById(`taxon_sources_${taxon.id}`)\n }\n content={\n loading || data.length === 0 ? (\n <div\n style={{ minWidth: \"200px\", textAlign: \"center\", padding: \"8px 0\" }}\n >\n <Spin size=\"small\" />\n </div>\n ) : (\n <div style={{ maxWidth: \"500px\" }}>\n {data.length > 0 && (\n <div>\n {data\n .filter((d) => !!d)\n .map((d, index) => (\n <LinkTo\n to=\"source\"\n args={d.key}\n key={d.key}\n className=\"col-tree-data-source\"\n style={linkStyle}\n >\n {(index ? \", \" : \"\") + (d.alias || d.key)}\n </LinkTo>\n ))}\n </div>\n )}\n {this.state.publishers && this.state.publishers.length > 0 && (\n <div style={{ marginTop: \"12px\" }}>\n <strong>Publishers</strong>\n <div>\n {this.state.publishers\n .filter((d) => !!d)\n .map((d, index) => (\n <a\n key={d.id}\n href={publisherUrl(d.id)}\n target=\"_blank\"\n rel=\"noopener noreferrer\"\n style={linkStyle}\n >\n {(index ? \", \" : \"\") + (d.alias || d.id)}\n {d.datasets?.length\n ? ` (${d.datasets.length.toLocaleString(\"en-GB\")})`\n : \"\"}\n </a>\n ))}\n </div>\n </div>\n )}\n </div>\n )\n }\n title={\n <div style={{ padding: \"4px 0\" }}>\n <span style={{ fontWeight: 500 }}>Sources for </span>\n <em>{taxon?.name}</em>\n <Divider style={{ margin: \"8px 0 0\" }} />\n </div>\n }\n open={popOverVisible}\n onOpenChange={(visible) =>\n this.setState({ popOverVisible: visible }, () => {\n if (visible && this.state.data.length === 0) this.getData();\n if (\n visible &&\n this.props.publisherDatasetKeys &&\n !this.state.publishers\n ) {\n this.getPublisherData();\n }\n })\n }\n trigger=\"click\"\n placement=\"rightTop\"\n >\n <a\n className=\"col-tree-data-source\"\n role=\"button\"\n tabIndex={0}\n style={{ cursor: \"pointer\", color: \"orange\", fontSize: \"11px\" }}\n onClick={(e) => e.preventDefault()}\n >\n Multiple sources\n </a>\n </Popover>\n </div>\n );\n };\n}\n\nexport default TaxonSources;\n","import React from \"react\";\n\nexport const ColTreeContext = React.createContext();\n","import React from \"react\";\nimport { Tag } from \"antd\";\nimport { get, isUndefined } from \"lodash-es\";\nimport TaxonSources from \"./TaxonSources\";\nimport MergedDataBadge from \"../components/MergedDataBadge\";\nimport {ColTreeContext} from \"./ColTreeContext\"\nimport { LinkTo } from \"../router\";\n\nclass ColTreeNode extends React.Component {\n constructor(props) {\n super(props);\n this.state = {\n style: {},\n provisional: this.props.taxon.status === \"provisionally accepted\",\n loading: false,\n };\n }\n\n rankIsAboveSpecies = (rank) => {\n return this.props.rank.indexOf(rank) < this.props.rank.indexOf(\"species\");\n };\n\n render = () => {\n const {\n taxon,\n taxon: { sector, sourceDatasetKeys, publisherDatasetKeys },\n datasetKey,\n } = this.props;\n\n const sectorSourceDataset = get(sector, \"dataset\");\n/* const hasDatasetSectors = datasetSectors && ( sector && sector.subjectDatasetKey ? Object.keys(omit(datasetSectors, [sector.subjectDatasetKey])).length > 0 : true)\n */ \nconst hasDatasetSectors =\n(sourceDatasetKeys || []).filter((d) => sector?.subjectDatasetKey !== d)\n .length > 0;\n const estimate = taxon.estimate && taxon.estimates ? taxon.estimates.find(e => e.estimate === taxon.estimate) : null;\n // Virtual \"Not assigned\" placeholders inserted by the API\n // (insertPlaceholder=true) aren't real taxa, so they can't be linked\n // to a taxon page.\n const isPlaceholder =\n typeof taxon.id === \"string\" && taxon.id.indexOf(\"incertae-sedis\") > -1;\n\n return (\n <ColTreeContext.Consumer>\n {({ showInfo }) => (\n <div id={taxon.id}>\n <span>\n <span className=\"tree-node-rank\">{taxon.rank}: </span>\n {isPlaceholder ? (\n <span dangerouslySetInnerHTML={{ __html: taxon.labelHtml }} />\n ) : (\n <LinkTo to=\"taxon\" args={taxon.id}>\n <span dangerouslySetInnerHTML={{ __html: taxon.labelHtml }} />\n </LinkTo>\n )}\n {taxon?.merged && (\n <MergedDataBadge style={{ marginLeft: \"4px\" }} datasetKey={taxon?.datasetKey} verbatimSourceKey={taxon?.verbatimSourceKey}/>\n )}\n </span>\n {/* estimate && (\n <span>\n {\" \"}\n • <TaxonEstimate estimate={estimate} taxon={taxon} />\n </span>\n ) */}\n {showInfo && taxon.status === \"provisionally accepted\" && (\n <React.Fragment> • <Tag color=\"warning\" style={{marginRight: 0}}>\n prov.\n </Tag>\n </React.Fragment>\n )}\n\n {!isUndefined(taxon.count) &&\n this.rankIsAboveSpecies(taxon?.rank) && (\n <span>\n {\" \"}\n • {Number(taxon.count).toLocaleString()}{\" \"}\n {showInfo && !isUndefined(taxon.speciesEstimate) && (\n <span>\n {\" \"}\n of{\" \"}\n {Number(\n taxon.speciesEstimate\n ).toLocaleString()}{\" \"}\n est.{\" \"}\n </span>\n )}\n spp.\n </span>\n )} \n \n \n {showInfo && sector && (\n <span>\n <span> • </span>\n <LinkTo\n to=\"source\"\n args={sector.subjectDatasetKey}\n style={hasDatasetSectors ? {fontWeight: 'bold'} : null}\n className=\"col-tree-data-source\"\n >\n {get(sectorSourceDataset, \"alias\") || sector.subjectDatasetKey}{hasDatasetSectors && \", \"}\n </LinkTo>\n </span>\n )}\n {showInfo && hasDatasetSectors && (\n <React.Fragment> <TaxonSources\n sourceDatasetKeys={sourceDatasetKeys}\n publisherDatasetKeys={publisherDatasetKeys}\n taxon={taxon}\n datasetKey={datasetKey}\n />\n </React.Fragment>\n )}\n \n </div>\n )}\n </ColTreeContext.Consumer>\n\n );\n };\n}\n\nexport default ColTreeNode;\n","import React from \"react\";\nimport { Tree, Alert, Spin, Button, Skeleton } from \"antd\";\nimport { flatten, get, isArray } from \"lodash-es\";\nimport client from \"../api/client\";\nimport config from \"../config\";\nimport ColTreeNode from \"./ColTreeNode\";\nimport ErrorMsg from \"../components/ErrorMsg\";\nimport { getSectorsBatch } from \"../api/sector\";\nimport DataLoader from \"dataloader\";\nimport { TreeCacheContext } from \"./treeCache\";\n\nconst CHILD_PAGE_SIZE = 1000; // How many children will we load at a time\n\nclass LoadMoreChildrenTreeNode extends React.Component {\n constructor(props) {\n super(props);\n this.state = { loading: false };\n }\n\n onClick = () => {\n this.setState({ loading: true }, () =>\n this.props.onClick().then(() => this.setState({ loading: false }))\n );\n };\n render = () => {\n const { loading } = this.state;\n return (\n <React.Fragment>\n {loading && <Spin />}\n {!loading && (\n <a onClick={this.onClick}>\n <strong>Load more...</strong>\n </a>\n )}\n </React.Fragment>\n );\n };\n}\n\nclass ColTree extends React.Component {\n static contextType = TreeCacheContext;\n\n constructor(props) {\n super(props);\n\n this.state = {\n rootLoading: true,\n treeData: [],\n loadedKeys: [],\n expandedKeys: [],\n rootTotal: 0,\n error: null,\n nodeNotFoundErr: null,\n rank: []\n };\n this.treeRef = React.createRef();\n }\n\n // datasetLoader comes from the shared TreeCacheContext so multiple tree\n // nodes (and TaxonSources instances) share one in-memory cache instead\n // of each re-fetching the same source datasets.\n get datasetLoader() {\n return this.context.datasetLoader;\n }\n\n componentDidMount = () => {\n const { datasetKey } = this.props;\n this.loadRoot();\n this.sectorLoader = new DataLoader((ids) =>\n getSectorsBatch(ids, datasetKey)\n );\n this.getRank()\n const { treeRef } = this.props;\n treeRef(this);\n };\n\n componentDidUpdate = (prevProps) => {\n if (\n prevProps.defaultExpandKey !== this.props.defaultExpandKey ||\n prevProps.hideExtinct !== this.props.hideExtinct ||\n prevProps.insertPlaceholder !== this.props.insertPlaceholder\n ) {\n this.reloadRoot();\n }\n };\n\n getRank = () => {\n client(`${config.dataApi}vocab/rank`).then((res) =>\n this.setState({ rank: res.data.map((r) => r.name) })\n );\n };\n\n reloadRoot = () =>\n this.setState(\n {\n rootLoading: true,\n treeData: [],\n loadedKeys: [],\n rootTotal: 0,\n error: null,\n nodeNotFoundErr: null,\n },\n this.loadRoot\n );\n\n \n\n loadRoot = async () => {\n const {\n showSourceTaxon,\n datasetKey,\n hideExtinct,\n insertPlaceholder,\n type,\n expandedTaxonKey,\n } = this.props;\n\n const defaultExpandKey = expandedTaxonKey;\n const { defaultTaxonKey } = this.props;\n\n this.setState({ rootLoading: true, treeData: [] });\n return client(\n `${\n config.dataApi\n }dataset/${datasetKey}/tree?projectKey=${datasetKey}${type ? \"&type=\"+type :\"\"}&limit=${CHILD_PAGE_SIZE}&offset=${\n this.state.treeData.length\n }${hideExtinct ? `&extinct=false&extinct=` : \"\"}${insertPlaceholder ? \"&insertPlaceholder=true\" : \"\"}`\n )\n .then(this.decorateWithSectorsAndDataset)\n .then((res) => {\n const mainTreeData = res.data.result || [];\n const rootTotal = res.data.total;\n const treeData = mainTreeData.map((tx) => {\n let dataRef = {\n taxon: tx,\n key: tx.id,\n datasetKey,\n childCount: tx.childCount,\n isLeaf: tx.childCount === 0,\n childOffset: 0,\n };\n dataRef.title = (\n <ColTreeNode\n taxon={tx}\n \n \n datasetKey={datasetKey}\n showSourceTaxon={showSourceTaxon}\n reloadChildren={() => this.fetchChildPage(dataRef, true)}\n rank={this.state.rank}\n />\n );\n dataRef.ref = dataRef;\n return dataRef;\n });\n\n this.setState({\n rootTotal: rootTotal,\n rootLoading: false,\n treeData: [...this.state.treeData, ...treeData],\n expandedKeys:\n treeData.length < 10 ? treeData.map((n) => n.taxon.id).filter(n => n ===\"CS5HF\") : [],\n error: null,\n },\n () => {\n if (defaultExpandKey) {\n return this.expandToTaxon(defaultExpandKey);\n } else if (defaultTaxonKey) {\n return this.expandToTaxon(defaultTaxonKey);\n }\n });\n if (treeData.length === 1) {\n this.fetchChildPage(treeData[treeData.length - 1]);\n }\n })\n .catch((err) => {\n this.setState({\n treeData: [],\n rootLoading: false,\n expandedKeys: [],\n error: err,\n });\n });\n };\n\n expandToTaxon = async (defaultExpandKey) => {\n const {\n showSourceTaxon,\n datasetKey,\n hideExtinct,\n type\n } = this.props;\n\n this.setState({ rootLoading: true/* , treeData: [] */ });\n const { data } = await client(\n `${\n config.dataApi\n }dataset/${datasetKey}/tree/${defaultExpandKey}?projectKey=${datasetKey}&insertPlaceholder=true${type ? \"&type=\"+type :\"\"}${\n hideExtinct ? `&extinct=false` : \"\"\n }`\n ).then((res) =>\n this.decorateWithSectorsAndDataset({\n data: { result: res.data },\n }).then(() => res)\n );\n\n if (data.length === 0) {\n return this.setState(\n {\n error: {\n message: `No classification found for Taxon ID: ${defaultExpandKey}`,\n },\n },\n this.loadRoot\n );\n }\n const tx = data[data.length - 1];\n let root = {\n taxon: tx,\n key: tx.id,\n datasetKey,\n childCount: tx.childCount,\n isLeaf: tx.childCount === 0,\n childOffset: 0,\n };\n root.title = (\n <ColTreeNode\n taxon={tx}\n \n \n datasetKey={datasetKey}\n showSourceTaxon={showSourceTaxon}\n rank={this.state.rank}\n reloadChildren={() => this.fetchChildPage(root, true)}\n />\n );\n\n root.ref = root;\n const root_ = root;\n for (let i = data.length - 2; i >= 0; i--) {\n const tx = data[i];\n const node = {\n taxon: tx,\n key: tx.id,\n datasetKey,\n childCount: tx.childCount,\n isLeaf: tx.childCount === 0,\n childOffset: 0,\n };\n node.ref = node;\n node.title = (\n <ColTreeNode\n taxon={tx}\n \n \n datasetKey={datasetKey}\n showSourceTaxon={showSourceTaxon}\n rank={this.state.rank}\n reloadChildren={() => this.fetchChildPage(node, true)}\n />\n );\n\n root.children = [node];\n root = node;\n }\n\n /* const treeData = [root_]; */\nconst { treeData } = this.state;\n var rootIndex = treeData.findIndex((x) => x.key == root_.key);\n treeData[rootIndex] = root_;\n const loadedKeys = [...data.map((t) => t.id).reverse()];\n\n this.setState({ treeData }, () =>\n this.reloadLoadedKeys(loadedKeys, defaultExpandKey)\n );\n };\n\n fetchChildPage = async (dataRef, reloadAll, dontUpdateState) => {\n const {\n showSourceTaxon,\n datasetKey,\n hideExtinct,\n insertPlaceholder,\n type\n } = this.props;\n const { treeData } = this.state;\n const childcount = get(dataRef, \"childCount\");\n const limit = CHILD_PAGE_SIZE;\n const offset = get(dataRef, \"childOffset\");\n const res = await client(\n `${config.dataApi}dataset/${datasetKey}/tree/${\n dataRef.taxon.id //taxonKey\n }/children?limit=${limit}&offset=${offset}&projectKey=${datasetKey}${type ? \"&type=\"+type :\"\"}${\n hideExtinct ? `&extinct=false` : \"\"\n }${insertPlaceholder ? \"&insertPlaceholder=true\" : \"\"}`\n );\n await this.decorateWithSectorsAndDataset(res);\n\n const data = res.data.result\n ? res.data.result.map((tx) => {\n let childDataRef = {\n taxon: tx,\n key: tx.id,\n datasetKey,\n childCount: tx.childCount,\n isLeaf: tx.childCount === 0,\n childOffset: 0,\n parent: dataRef,\n name: tx.name,\n };\n\n childDataRef.title = (\n <ColTreeNode\n taxon={tx}\n \n \n datasetKey={datasetKey}\n showSourceTaxon={showSourceTaxon}\n rank={this.state.rank}\n reloadChildren={() => this.fetchChildPage(childDataRef, true)}\n />\n );\n childDataRef.ref = childDataRef;\n\n return childDataRef;\n })\n : [];\n\n // reloadAll is used to force reload all children from offset 0 - used when new children have been posted\n dataRef.children =\n dataRef.children && offset !== 0 && !reloadAll\n ? [...dataRef.children, ...data]\n : data;\n // If extinct are filtered out, you cannot rely on childCount\n if (res.data.last && dataRef.childCount > dataRef.children.length) {\n dataRef.childCount = dataRef.children.length;\n }\n if (!res.data.last) {\n const loadMoreFn = () => {\n dataRef.childOffset += CHILD_PAGE_SIZE;\n if (\n dataRef.children[dataRef.children.length - 1].key ===\n \"__loadMoreBTN__\"\n ) {\n dataRef.children = dataRef.children.slice(0, -1);\n }\n return this.fetchChildPage(dataRef, false);\n };\n dataRef.children = [\n ...dataRef.children,\n {\n title: (\n <LoadMoreChildrenTreeNode\n onClick={loadMoreFn}\n key=\"__loadMoreBTN__\"\n />\n ),\n key: \"__loadMoreBTN__\",\n childCount: 0,\n isLeaf: true,\n },\n ];\n }\n if (!dontUpdateState) {\n this.setState({\n treeData: [...treeData],\n loadedKeys: [...new Set([...this.state.loadedKeys, dataRef.key])],\n });\n }\n };\n\n decorateWithSectorsAndDataset = (res) => {\n if (!res.data.result) return res;\n return Promise.all(\n res.data.result\n .filter((tx) => !!tx.sectorDatasetKey)\n .map((tx) =>\n this.datasetLoader\n .load(tx.sectorDatasetKey)\n .then(\n (dataset) =>\n (tx.sector = {\n id: tx.sectorKey,\n subjectDatasetKey: tx.sectorDatasetKey,\n dataset: dataset,\n })\n )\n )\n ).then(() => res);\n };\n\n onLoadData = (treeNode, reloadAll = false) => {\n if (reloadAll) {\n treeNode.childOffset = 0;\n }\n return this.fetchChildPage(treeNode.ref, reloadAll);\n };\n\n findNode = (id, nodeArray) => {\n let node = null;\n\n node = nodeArray.find((n) => get(n, \"taxon.id\") === id);\n\n if (node) {\n return node;\n } else {\n const children = nodeArray.map((n) => get(n, \"children\") || []);\n const flattenedChildren = flatten(children); //.flat();\n if (flattenedChildren.length === 0) {\n return null;\n } else {\n return this.findNode(id, flattenedChildren);\n }\n }\n };\n\n pageThroughChildrenUntilTaxonFound = async (parentNode, taxonId) => {\n let node;\n while (!node && parentNode.children.length < parentNode.childCount) {\n parentNode.childOffset += CHILD_PAGE_SIZE;\n if (\n parentNode.children[parentNode.children.length - 1].key ===\n \"__loadMoreBTN__\"\n ) {\n parentNode.children = parentNode.children.slice(0, -1);\n }\n await this.fetchChildPage(parentNode, false, true);\n node = this.findNode(taxonId, parentNode.children);\n }\n if (!node) {\n node = parentNode.children.find((c) =>\n get(c, \"taxon.id\") ? c.taxon.id.indexOf(\"incertae-sedis\") > -1 : false\n );\n }\n return node;\n };\n\n reloadLoadedKeys = async (keys, expandKey, expandAll = true) => {\n this.setState({ rootLoading: true });\n const { loadedKeys: storedKeys } = this.state;\n // const defaultExpandKey = get(qs.parse(get(location, \"search\")), 'taxonKey');\n\n let { treeData } = this.state;\n const targetTaxon = expandKey ? this.findNode(expandKey, treeData) : null;\n const loadedKeys = keys ? [...keys] : [...storedKeys];\n for (let index = 0; index < loadedKeys.length; index++) {\n let node = this.findNode(loadedKeys[index], treeData);\n if (!node && targetTaxon && loadedKeys[index - 1]) {\n // If the node is not found look for insertae sedis nodes in the children of the parent and insert the 'Not assigned' between the parent and the node\n const parentNode = this.findNode(loadedKeys[index - 1], treeData);\n if (\n parentNode &&\n isArray(get(parentNode, \"children\")) &&\n parentNode.children.length > 0\n ) {\n node = await this.pageThroughChildrenUntilTaxonFound(\n parentNode,\n loadedKeys[index]\n );\n if (node) {\n loadedKeys.splice(index, 0, node.taxon.id);\n } else {\n // It has gone missing from the tree\n this.setState(\n {\n nodeNotFoundErr: (\n <span>Cannot find taxon {expandKey} in tree &#128549;</span>\n ),\n rootLoading: false,\n }/* ,\n () => {\n if (\n this.props.treeType === \"CATALOGUE\" &&\n typeof this.props.addMissingTargetKey === \"function\"\n ) {\n this.props.addMissingTargetKey(expandKey);\n }\n } */\n );\n }\n }\n }\n if (node) {\n await this.fetchChildPage(node, true, true);\n let targetNode = node.children.find(\n (c) => get(c, \"taxon.id\") === get(targetTaxon, \"taxon.id\")\n );\n if (\n targetTaxon &&\n index === loadedKeys.length - 2 &&\n get(node, \"taxon.id\") !== get(targetTaxon, \"taxon.id\") &&\n isArray(node.children) &&\n !targetNode\n ) {\n if (node.children.length < node.childCount) {\n // its the parent of the taxon we are after - if its not in the first page, insert it\n targetNode = await this.pageThroughChildrenUntilTaxonFound(\n node,\n get(targetTaxon, \"taxon.id\")\n );\n // node.children = [targetTaxon, ...node.children];\n if (targetNode) {\n this.setState({ treeData: [...this.state.treeData] }, () => {\n setTimeout(() => {\n const elmnt = document.getElementById(expandKey);\n elmnt.scrollIntoView({ behavior: \"smooth\", block: \"center\" });\n /* if (get(this, \"treeRef.current\")) {\n this.treeRef.current.scrollTo({ key: expandKey });\n } */\n }, 100);\n });\n } else {\n // It has gone missing from the tree\n this.setState(\n {\n nodeNotFoundErr: (\n <span>Cannot find taxon {expandKey} in tree &#128549;</span>\n ),\n rootLoading: false,\n },\n () => {\n if (\n this.props.treeType === \"CATALOGUE\" &&\n typeof this.props.addMissingTargetKey === \"function\"\n ) {\n this.props.addMissingTargetKey(expandKey);\n }\n }\n );\n }\n }\n }\n }\n }\n const newState = { loadedKeys, rootLoading: false };\n if (expandAll) {\n newState.expandedKeys = loadedKeys;\n }\n this.setState(newState, () => {\n if (expandKey) {\n setTimeout(() => {\n const elmnt = document.getElementById(expandKey);\n elmnt.scrollIntoView({ behavior: \"smooth\", block: \"center\" });\n /* if (get(this, \"treeRef.current\")) {\n this.treeRef.current.scrollTo({ key: expandKey });\n } */\n }, 100);\n }\n });\n };\n\n render() {\n const {\n error,\n rootTotal,\n rootLoading,\n treeData,\n defaultExpandAll,\n nodeNotFoundErr,\n loadedKeys,\n expandedKeys,\n } = this.state;\n const { treeType, dataset, height, expandedTaxonKey } = this.props;\n void height;\n const defaultExpandKey = expandedTaxonKey;\n\n return (\n <div>\n {error && (\n <React.Fragment>\n {get(error, \"response.data.code\") !== 404 ? (\n <Alert\n closable\n onClose={() => this.setState({ error: null })}\n style={{ marginTop: \"8px\" }}\n message={<ErrorMsg error={error} />}\n type=\"error\"\n />\n ) : (\n <Alert\n closable\n onClose={() => this.setState({ error: null })}\n style={{ marginTop: \"8px\" }}\n message={\n <Custom404\n error={error}\n treeType={treeType}\n dataset={dataset}\n loadRoot={this.loadRoot}\n />\n }\n type=\"warning\"\n />\n )}\n </React.Fragment>\n )}\n {nodeNotFoundErr && (\n <Alert\n closable\n onClose={() => this.setState({ nodeNotFoundErr: null })}\n style={{ marginTop: \"8px\" }}\n message={nodeNotFoundErr}\n type=\"warning\"\n />\n )}\n {rootLoading && <Skeleton paragraph={{ rows: 10 }} active />}\n {!rootLoading && treeData.length > 0 && (\n <Tree\n ref={this.treeRef}\n defaultExpandAll={defaultExpandAll}\n // height={height || 600}\n // defaultExpandedKeys={defaultExpandedKeys}\n loadData={this.onLoadData}\n onLoad={(loadedKeys) => this.setState({ loadedKeys })}\n loadedKeys={loadedKeys}\n expandedKeys={expandedKeys}\n treeData={treeData}\n filterTreeNode={(node) => node.key === defaultExpandKey}\n onExpand={(expandedKeys, obj) => {\n this.setState({ expandedKeys });\n if (this.props.onExpandedTaxonKeyChange) {\n this.props.onExpandedTaxonKeyChange(\n obj.expanded ? obj.node.key : null\n );\n }\n }}\n ></Tree>\n )}\n\n {!error && treeData.length < rootTotal && (\n <Button loading={rootLoading} onClick={this.loadRoot}>\n Load more{\" \"}\n </Button>\n )}\n </div>\n );\n }\n}\n\nexport default ColTree;\n","import React from \"react\";\nimport ColTree from \"./ColTree\";\nimport { get } from \"lodash-es\";\nimport NameAutocomplete from \"./NameAutocomplete\";\nimport client, { setAuth } from \"../api/client\";\nimport { Row, Col, Checkbox } from \"antd\";\nimport { ColTreeContext } from \"./ColTreeContext\";\nimport { TreeCacheContext, createTreeCache } from \"./treeCache\";\nimport { getDataset } from \"../api/dataset\";\nimport Citation from \"../components/DatasetCitation\";\nimport { RouterContext, buildRouter } from \"../router\";\nimport { readSetting, writeSetting } from \"../storage\";\n\nconst INFRASPECIFIC_RANKS = [\n \"infraspecific name\",\n \"species\",\n \"variety\",\n \"form\",\n];\n\nclass ColTreeWrapper extends React.Component {\n static contextType = RouterContext;\n\n constructor(props) {\n super(props);\n setAuth(this.props.auth);\n this.state = {\n hideExtinct: readSetting(\"tree-extant-only\", false),\n showInfo: readSetting(\"tree-show-source\", false),\n dataset: null,\n };\n // Per-Tree DataLoader cache. Rebuilt only if datasetKey changes (rare).\n this.cache = createTreeCache(this.props.datasetKey);\n }\n\n componentDidUpdate(prevProps) {\n if (prevProps.datasetKey !== this.props.datasetKey) {\n this.cache = createTreeCache(this.props.datasetKey);\n }\n }\n\n componentDidMount = async () => {\n const { datasetKey, citation } = this.props;\n if (citation) {\n try {\n const { data: dataset } = await getDataset(datasetKey);\n this.setState({ dataset });\n } catch (err) {\n // ignore\n }\n }\n };\n\n render = () => {\n const {\n datasetKey,\n defaultTaxonKey,\n expandedTaxonKey,\n onExpandedTaxonKeyChange,\n showTreeOptions,\n linkToSpeciesPage,\n citation,\n type,\n insertPlaceholder = true,\n } = this.props;\n const { hideExtinct, dataset } = this.state;\n\n const handleSelectName = (name) => {\n const key = get(name, \"key\");\n if (!key) return;\n const rank = get(name, \"rank\");\n if (linkToSpeciesPage && INFRASPECIFIC_RANKS.includes(rank)) {\n // Leaf-like selection: jump to the 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+ {"version":3,"file":"tree.js","sources":["../src/ColTree/treeCache.js","../src/ColTree/TaxonSources.js","../src/ColTree/ColTreeContext.js","../src/ColTree/ColTreeNode.js","../src/ColTree/ColTree.js","../src/ColTree/index.js","../src/entries/tree.js"],"sourcesContent":["import { createContext } from \"react\";\nimport DataLoader from \"dataloader\";\nimport { getDatasetsBatch, getPublishersBatch } from \"../api/dataset\";\n\n// Shared DataLoaders for the Tree subtree. Created once per (datasetKey,\n// mounted Tree) and provided via TreeCacheContext so every TaxonSources,\n// every sector-dataset decoration in ColTree, and any other in-tree\n// consumer hits the same in-memory cache. Without this, each TaxonSources\n// instance creates its own loader and the same source/publisher dataset\n// is fetched once per node it appears under.\n//\n// DataLoader batches calls inside a microtask and caches resolved values\n// indefinitely for the lifetime of the loader.\n\nexport const TreeCacheContext = createContext({\n datasetLoader: null,\n publisherLoader: null,\n});\n\nexport const createTreeCache = (datasetKey) => ({\n datasetLoader: new DataLoader((ids) => getDatasetsBatch(ids, datasetKey)),\n publisherLoader: new DataLoader((ids) =>\n getPublishersBatch(ids, datasetKey)\n ),\n});\n","import React from \"react\";\nimport { Popover, Spin, Divider } from \"antd\";\nimport DataLoader from \"dataloader\";\nimport { sortBy } from \"lodash-es\";\nimport { LinkTo } from \"../router\";\nimport { TreeCacheContext } from \"./treeCache\";\nimport { getDatasetsBatch, getPublishersBatch } from \"../api/dataset\";\nimport config from \"../config\";\n\nclass TaxonSources extends React.Component {\n static contextType = TreeCacheContext;\n\n constructor(props) {\n super(props);\n this.state = {\n data: [],\n showInNode: false,\n loading: false,\n };\n }\n\n // Returns the shared cache from TreeCacheContext if available, or a\n // throwaway local DataLoader so the popover still works even if context\n // doesn't reach this instance (which used to leave the spinner stuck\n // because getData early-returned with no loading state set).\n getDatasetLoader = () => {\n const { datasetKey } = this.props;\n if (this.context?.datasetLoader) return this.context.datasetLoader;\n if (!this._localDatasetLoader) {\n this._localDatasetLoader = new DataLoader((ids) =>\n getDatasetsBatch(ids, datasetKey)\n );\n }\n return this._localDatasetLoader;\n };\n\n getPublisherLoader = () => {\n const { datasetKey } = this.props;\n if (this.context?.publisherLoader) return this.context.publisherLoader;\n if (!this._localPublisherLoader) {\n this._localPublisherLoader = new DataLoader((ids) =>\n getPublishersBatch(ids, datasetKey)\n );\n }\n return this._localPublisherLoader;\n };\n\n componentDidMount = () => {\n const { sourceDatasetKeys } = this.props;\n if (sourceDatasetKeys && sourceDatasetKeys.length < 4) {\n this.setState({ showInNode: true }, this.getData);\n }\n };\n\n getData = () => {\n const { sourceDatasetKeys } = this.props;\n if (!sourceDatasetKeys?.length) return;\n this.setState({ loading: true });\n const loader = this.getDatasetLoader();\n Promise.all(\n sourceDatasetKeys.map((s) => loader.load(s).catch(() => null))\n )\n .then((data) => {\n this.setState({ data: sortBy(data, [\"alias\"]), loading: false });\n })\n .catch(() => {\n this.setState({ data: [], loading: false });\n });\n };\n\n getPublisherData = () => {\n const { publisherDatasetKeys } = this.props;\n if (!publisherDatasetKeys) return;\n const loader = this.getPublisherLoader();\n Promise.all(\n Object.keys(publisherDatasetKeys).map((s) =>\n loader\n .load(s)\n .then((publisher) => ({\n ...publisher,\n datasets: publisherDatasetKeys[s],\n }))\n .catch(() => null)\n )\n )\n .then((data) => {\n this.setState({ publishers: sortBy(data.filter(Boolean), [\"alias\"]) });\n })\n .catch(() => {\n this.setState({ publishers: [] });\n });\n };\n\n render = () => {\n const { data, showInNode, popOverVisible, loading } = this.state;\n const { taxon, datasetKey } = this.props;\n const linkStyle = { color: \"orange\", fontSize: \"11px\" };\n const publisherUrl = (uuid) =>\n `${config.clbPortal}/dataset/${datasetKey}/publisher/${uuid}`;\n\n if (showInNode) {\n return data\n .filter((d) => !!d)\n .map((d, index) => (\n <LinkTo\n to=\"source\"\n args={d.key}\n key={d.key}\n className=\"col-tree-data-source\"\n style={linkStyle}\n >\n {(index ? \", \" : \"\") + (d.alias || d.key)}\n </LinkTo>\n ));\n }\n\n return (\n <div style={{ display: \"inline\" }} id={`taxon_sources_${taxon.id}`}>\n <Popover\n getPopupContainer={() =>\n document.getElementById(`taxon_sources_${taxon.id}`)\n }\n content={\n loading || data.length === 0 ? (\n <div\n style={{ minWidth: \"200px\", textAlign: \"center\", padding: \"8px 0\" }}\n >\n <Spin size=\"small\" />\n </div>\n ) : (\n <div style={{ maxWidth: \"500px\" }}>\n {data.length > 0 && (\n <div>\n {data\n .filter((d) => !!d)\n .map((d, index) => (\n <LinkTo\n to=\"source\"\n args={d.key}\n key={d.key}\n className=\"col-tree-data-source\"\n style={linkStyle}\n >\n {(index ? \", \" : \"\") + (d.alias || d.key)}\n </LinkTo>\n ))}\n </div>\n )}\n {this.state.publishers && this.state.publishers.length > 0 && (\n <div style={{ marginTop: \"12px\" }}>\n <strong>Publishers</strong>\n <div>\n {this.state.publishers\n .filter((d) => !!d)\n .map((d, index) => (\n <a\n key={d.id}\n href={publisherUrl(d.id)}\n target=\"_blank\"\n rel=\"noopener noreferrer\"\n style={linkStyle}\n >\n {(index ? \", \" : \"\") + (d.alias || d.id)}\n {d.datasets?.length\n ? ` (${d.datasets.length.toLocaleString(\"en-GB\")})`\n : \"\"}\n </a>\n ))}\n </div>\n </div>\n )}\n </div>\n )\n }\n title={\n <div style={{ padding: \"4px 0\" }}>\n <span style={{ fontWeight: 500 }}>Sources for </span>\n <em>{taxon?.name}</em>\n <Divider style={{ margin: \"8px 0 0\" }} />\n </div>\n }\n open={popOverVisible}\n onOpenChange={(visible) =>\n this.setState({ popOverVisible: visible }, () => {\n if (visible && this.state.data.length === 0) this.getData();\n if (\n visible &&\n this.props.publisherDatasetKeys &&\n !this.state.publishers\n ) {\n this.getPublisherData();\n }\n })\n }\n trigger=\"click\"\n placement=\"rightTop\"\n >\n <a\n className=\"col-tree-data-source\"\n role=\"button\"\n tabIndex={0}\n style={{ cursor: \"pointer\", color: \"orange\", fontSize: \"11px\" }}\n onClick={(e) => e.preventDefault()}\n >\n Multiple sources\n </a>\n </Popover>\n </div>\n );\n };\n}\n\nexport default TaxonSources;\n","import React from \"react\";\n\nexport const ColTreeContext = React.createContext();\n","import React from \"react\";\nimport { Tag } from \"antd\";\nimport { get, isUndefined } from \"lodash-es\";\nimport TaxonSources from \"./TaxonSources\";\nimport MergedDataBadge from \"../components/MergedDataBadge\";\nimport {ColTreeContext} from \"./ColTreeContext\"\nimport { LinkTo } from \"../router\";\n\nclass ColTreeNode extends React.Component {\n constructor(props) {\n super(props);\n this.state = {\n style: {},\n provisional: this.props.taxon.status === \"provisionally accepted\",\n loading: false,\n };\n }\n\n rankIsAboveSpecies = (rank) => {\n return this.props.rank.indexOf(rank) < this.props.rank.indexOf(\"species\");\n };\n\n render = () => {\n const {\n taxon,\n taxon: { sector, sourceDatasetKeys, publisherDatasetKeys },\n datasetKey,\n } = this.props;\n\n const sectorSourceDataset = get(sector, \"dataset\");\n/* const hasDatasetSectors = datasetSectors && ( sector && sector.subjectDatasetKey ? Object.keys(omit(datasetSectors, [sector.subjectDatasetKey])).length > 0 : true)\n */ \nconst hasDatasetSectors =\n(sourceDatasetKeys || []).filter((d) => sector?.subjectDatasetKey !== d)\n .length > 0;\n const estimate = taxon.estimate && taxon.estimates ? taxon.estimates.find(e => e.estimate === taxon.estimate) : null;\n // Virtual \"Not assigned\" placeholders inserted by the API\n // (insertPlaceholder=true) aren't real taxa, so they can't be linked\n // to a taxon page.\n const isPlaceholder =\n typeof taxon.id === \"string\" && taxon.id.indexOf(\"incertae-sedis\") > -1;\n\n return (\n <ColTreeContext.Consumer>\n {({ showInfo }) => (\n <div id={taxon.id}>\n <span>\n <span className=\"tree-node-rank\">{taxon.rank}: </span>\n {isPlaceholder ? (\n <span dangerouslySetInnerHTML={{ __html: taxon.labelHtml }} />\n ) : (\n <LinkTo to=\"taxon\" args={taxon.id}>\n <span dangerouslySetInnerHTML={{ __html: taxon.labelHtml }} />\n </LinkTo>\n )}\n {taxon?.merged && (\n <MergedDataBadge style={{ marginLeft: \"4px\" }} datasetKey={taxon?.datasetKey} verbatimSourceKey={taxon?.verbatimSourceKey}/>\n )}\n </span>\n {/* estimate && (\n <span>\n {\" \"}\n • <TaxonEstimate estimate={estimate} taxon={taxon} />\n </span>\n ) */}\n {showInfo && taxon.status === \"provisionally accepted\" && (\n <React.Fragment> • <Tag color=\"warning\" style={{marginRight: 0}}>\n prov.\n </Tag>\n </React.Fragment>\n )}\n\n {!isUndefined(taxon.count) &&\n this.rankIsAboveSpecies(taxon?.rank) && (\n <span>\n {\" \"}\n • {Number(taxon.count).toLocaleString()}{\" \"}\n {showInfo && !isUndefined(taxon.speciesEstimate) && (\n <span>\n {\" \"}\n of{\" \"}\n {Number(\n taxon.speciesEstimate\n ).toLocaleString()}{\" \"}\n est.{\" \"}\n </span>\n )}\n spp.\n </span>\n )} \n \n \n {showInfo && sector && (\n <span>\n <span> • </span>\n <LinkTo\n to=\"source\"\n args={sector.subjectDatasetKey}\n style={hasDatasetSectors ? {fontWeight: 'bold'} : null}\n className=\"col-tree-data-source\"\n >\n {get(sectorSourceDataset, \"alias\") || sector.subjectDatasetKey}{hasDatasetSectors && \", \"}\n </LinkTo>\n </span>\n )}\n {showInfo && hasDatasetSectors && (\n <React.Fragment> <TaxonSources\n sourceDatasetKeys={sourceDatasetKeys}\n publisherDatasetKeys={publisherDatasetKeys}\n taxon={taxon}\n datasetKey={datasetKey}\n />\n </React.Fragment>\n )}\n \n </div>\n )}\n </ColTreeContext.Consumer>\n\n );\n };\n}\n\nexport default ColTreeNode;\n","import React from \"react\";\nimport { Tree, Alert, Spin, Button, Skeleton } from \"antd\";\nimport { flatten, get, isArray } from \"lodash-es\";\nimport client from \"../api/client\";\nimport config from \"../config\";\nimport ColTreeNode from \"./ColTreeNode\";\nimport ErrorMsg from \"../components/ErrorMsg\";\nimport { getSectorsBatch } from \"../api/sector\";\nimport DataLoader from \"dataloader\";\nimport { TreeCacheContext } from \"./treeCache\";\n\nconst CHILD_PAGE_SIZE = 1000; // How many children will we load at a time\n\nclass LoadMoreChildrenTreeNode extends React.Component {\n constructor(props) {\n super(props);\n this.state = { loading: false };\n }\n\n onClick = () => {\n this.setState({ loading: true }, () =>\n this.props.onClick().then(() => this.setState({ loading: false }))\n );\n };\n render = () => {\n const { loading } = this.state;\n return (\n <React.Fragment>\n {loading && <Spin />}\n {!loading && (\n <a onClick={this.onClick}>\n <strong>Load more...</strong>\n </a>\n )}\n </React.Fragment>\n );\n };\n}\n\nclass ColTree extends React.Component {\n static contextType = TreeCacheContext;\n\n constructor(props) {\n super(props);\n\n this.state = {\n rootLoading: true,\n treeData: [],\n loadedKeys: [],\n expandedKeys: [],\n rootTotal: 0,\n error: null,\n nodeNotFoundErr: null,\n rank: []\n };\n this.treeRef = React.createRef();\n }\n\n // datasetLoader comes from the shared TreeCacheContext so multiple tree\n // nodes (and TaxonSources instances) share one in-memory cache instead\n // of each re-fetching the same source datasets.\n get datasetLoader() {\n return this.context.datasetLoader;\n }\n\n componentDidMount = () => {\n const { datasetKey } = this.props;\n this.loadRoot();\n this.sectorLoader = new DataLoader((ids) =>\n getSectorsBatch(ids, datasetKey)\n );\n this.getRank()\n const { treeRef } = this.props;\n treeRef(this);\n };\n\n componentDidUpdate = (prevProps) => {\n if (\n prevProps.defaultExpandKey !== this.props.defaultExpandKey ||\n prevProps.hideExtinct !== this.props.hideExtinct ||\n prevProps.insertPlaceholder !== this.props.insertPlaceholder\n ) {\n this.reloadRoot();\n }\n };\n\n getRank = () => {\n client(`${config.dataApi}vocab/rank`).then((res) =>\n this.setState({ rank: res.data.map((r) => r.name) })\n );\n };\n\n reloadRoot = () =>\n this.setState(\n {\n rootLoading: true,\n treeData: [],\n loadedKeys: [],\n rootTotal: 0,\n error: null,\n nodeNotFoundErr: null,\n },\n this.loadRoot\n );\n\n \n\n loadRoot = async () => {\n const {\n showSourceTaxon,\n datasetKey,\n hideExtinct,\n insertPlaceholder,\n type,\n expandedTaxonKey,\n } = this.props;\n\n const defaultExpandKey = expandedTaxonKey;\n const { defaultTaxonKey } = this.props;\n\n this.setState({ rootLoading: true, treeData: [] });\n return client(\n `${\n config.dataApi\n }dataset/${datasetKey}/tree?projectKey=${datasetKey}${type ? \"&type=\"+type :\"\"}&limit=${CHILD_PAGE_SIZE}&offset=${\n this.state.treeData.length\n }${hideExtinct ? `&extinct=false&extinct=` : \"\"}${insertPlaceholder ? \"&insertPlaceholder=true\" : \"\"}`\n )\n .then(this.decorateWithSectorsAndDataset)\n .then((res) => {\n const mainTreeData = res.data.result || [];\n const rootTotal = res.data.total;\n const treeData = mainTreeData.map((tx) => {\n let dataRef = {\n taxon: tx,\n key: tx.id,\n datasetKey,\n childCount: tx.childCount,\n isLeaf: tx.childCount === 0,\n childOffset: 0,\n };\n dataRef.title = (\n <ColTreeNode\n taxon={tx}\n \n \n datasetKey={datasetKey}\n showSourceTaxon={showSourceTaxon}\n reloadChildren={() => this.fetchChildPage(dataRef, true)}\n rank={this.state.rank}\n />\n );\n dataRef.ref = dataRef;\n return dataRef;\n });\n\n this.setState({\n rootTotal: rootTotal,\n rootLoading: false,\n treeData: [...this.state.treeData, ...treeData],\n // Nothing is auto-expanded by default. Consumers open a specific root\n // (or deep taxon) by passing `defaultTaxonKey`/`expandedTaxonKey` —\n // e.g. defaultTaxonKey=\"CS5HF\" opens Eukaryota in current COL releases.\n expandedKeys: [],\n error: null,\n },\n () => {\n if (defaultExpandKey) {\n return this.expandToTaxon(defaultExpandKey);\n } else if (defaultTaxonKey) {\n return this.expandToTaxon(defaultTaxonKey);\n }\n });\n if (treeData.length === 1) {\n this.fetchChildPage(treeData[treeData.length - 1]);\n }\n })\n .catch((err) => {\n this.setState({\n treeData: [],\n rootLoading: false,\n expandedKeys: [],\n error: err,\n });\n });\n };\n\n expandToTaxon = async (defaultExpandKey) => {\n const {\n showSourceTaxon,\n datasetKey,\n hideExtinct,\n type\n } = this.props;\n\n this.setState({ rootLoading: true/* , treeData: [] */ });\n const { data } = await client(\n `${\n config.dataApi\n }dataset/${datasetKey}/tree/${defaultExpandKey}?projectKey=${datasetKey}&insertPlaceholder=true${type ? \"&type=\"+type :\"\"}${\n hideExtinct ? `&extinct=false` : \"\"\n }`\n ).then((res) =>\n this.decorateWithSectorsAndDataset({\n data: { result: res.data },\n }).then(() => res)\n );\n\n if (data.length === 0) {\n return this.setState(\n {\n error: {\n message: `No classification found for Taxon ID: ${defaultExpandKey}`,\n },\n },\n this.loadRoot\n );\n }\n const tx = data[data.length - 1];\n let root = {\n taxon: tx,\n key: tx.id,\n datasetKey,\n childCount: tx.childCount,\n isLeaf: tx.childCount === 0,\n childOffset: 0,\n };\n root.title = (\n <ColTreeNode\n taxon={tx}\n \n \n datasetKey={datasetKey}\n showSourceTaxon={showSourceTaxon}\n rank={this.state.rank}\n reloadChildren={() => this.fetchChildPage(root, true)}\n />\n );\n\n root.ref = root;\n const root_ = root;\n for (let i = data.length - 2; i >= 0; i--) {\n const tx = data[i];\n const node = {\n taxon: tx,\n key: tx.id,\n datasetKey,\n childCount: tx.childCount,\n isLeaf: tx.childCount === 0,\n childOffset: 0,\n };\n node.ref = node;\n node.title = (\n <ColTreeNode\n taxon={tx}\n \n \n datasetKey={datasetKey}\n showSourceTaxon={showSourceTaxon}\n rank={this.state.rank}\n reloadChildren={() => this.fetchChildPage(node, true)}\n />\n );\n\n root.children = [node];\n root = node;\n }\n\n /* const treeData = [root_]; */\nconst { treeData } = this.state;\n var rootIndex = treeData.findIndex((x) => x.key == root_.key);\n treeData[rootIndex] = root_;\n const loadedKeys = [...data.map((t) => t.id).reverse()];\n\n this.setState({ treeData }, () =>\n this.reloadLoadedKeys(loadedKeys, defaultExpandKey)\n );\n };\n\n fetchChildPage = async (dataRef, reloadAll, dontUpdateState) => {\n const {\n showSourceTaxon,\n datasetKey,\n hideExtinct,\n insertPlaceholder,\n type\n } = this.props;\n const { treeData } = this.state;\n const childcount = get(dataRef, \"childCount\");\n const limit = CHILD_PAGE_SIZE;\n const offset = get(dataRef, \"childOffset\");\n const res = await client(\n `${config.dataApi}dataset/${datasetKey}/tree/${\n dataRef.taxon.id //taxonKey\n }/children?limit=${limit}&offset=${offset}&projectKey=${datasetKey}${type ? \"&type=\"+type :\"\"}${\n hideExtinct ? `&extinct=false` : \"\"\n }${insertPlaceholder ? \"&insertPlaceholder=true\" : \"\"}`\n );\n await this.decorateWithSectorsAndDataset(res);\n\n const data = res.data.result\n ? res.data.result.map((tx) => {\n let childDataRef = {\n taxon: tx,\n key: tx.id,\n datasetKey,\n childCount: tx.childCount,\n isLeaf: tx.childCount === 0,\n childOffset: 0,\n parent: dataRef,\n name: tx.name,\n };\n\n childDataRef.title = (\n <ColTreeNode\n taxon={tx}\n \n \n datasetKey={datasetKey}\n showSourceTaxon={showSourceTaxon}\n rank={this.state.rank}\n reloadChildren={() => this.fetchChildPage(childDataRef, true)}\n />\n );\n childDataRef.ref = childDataRef;\n\n return childDataRef;\n })\n : [];\n\n // reloadAll is used to force reload all children from offset 0 - used when new children have been posted\n dataRef.children =\n dataRef.children && offset !== 0 && !reloadAll\n ? [...dataRef.children, ...data]\n : data;\n // If extinct are filtered out, you cannot rely on childCount\n if (res.data.last && dataRef.childCount > dataRef.children.length) {\n dataRef.childCount = dataRef.children.length;\n }\n if (!res.data.last) {\n const loadMoreFn = () => {\n dataRef.childOffset += CHILD_PAGE_SIZE;\n if (\n dataRef.children[dataRef.children.length - 1].key ===\n \"__loadMoreBTN__\"\n ) {\n dataRef.children = dataRef.children.slice(0, -1);\n }\n return this.fetchChildPage(dataRef, false);\n };\n dataRef.children = [\n ...dataRef.children,\n {\n title: (\n <LoadMoreChildrenTreeNode\n onClick={loadMoreFn}\n key=\"__loadMoreBTN__\"\n />\n ),\n key: \"__loadMoreBTN__\",\n childCount: 0,\n isLeaf: true,\n },\n ];\n }\n if (!dontUpdateState) {\n this.setState({\n treeData: [...treeData],\n loadedKeys: [...new Set([...this.state.loadedKeys, dataRef.key])],\n });\n }\n };\n\n decorateWithSectorsAndDataset = (res) => {\n if (!res.data.result) return res;\n return Promise.all(\n res.data.result\n .filter((tx) => !!tx.sectorDatasetKey)\n .map((tx) =>\n this.datasetLoader\n .load(tx.sectorDatasetKey)\n .then(\n (dataset) =>\n (tx.sector = {\n id: tx.sectorKey,\n subjectDatasetKey: tx.sectorDatasetKey,\n dataset: dataset,\n })\n )\n )\n ).then(() => res);\n };\n\n onLoadData = (treeNode, reloadAll = false) => {\n if (reloadAll) {\n treeNode.childOffset = 0;\n }\n return this.fetchChildPage(treeNode.ref, reloadAll);\n };\n\n findNode = (id, nodeArray) => {\n let node = null;\n\n node = nodeArray.find((n) => get(n, \"taxon.id\") === id);\n\n if (node) {\n return node;\n } else {\n const children = nodeArray.map((n) => get(n, \"children\") || []);\n const flattenedChildren = flatten(children); //.flat();\n if (flattenedChildren.length === 0) {\n return null;\n } else {\n return this.findNode(id, flattenedChildren);\n }\n }\n };\n\n pageThroughChildrenUntilTaxonFound = async (parentNode, taxonId) => {\n let node;\n while (!node && parentNode.children.length < parentNode.childCount) {\n parentNode.childOffset += CHILD_PAGE_SIZE;\n if (\n parentNode.children[parentNode.children.length - 1].key ===\n \"__loadMoreBTN__\"\n ) {\n parentNode.children = parentNode.children.slice(0, -1);\n }\n await this.fetchChildPage(parentNode, false, true);\n node = this.findNode(taxonId, parentNode.children);\n }\n if (!node) {\n node = parentNode.children.find((c) =>\n get(c, \"taxon.id\") ? c.taxon.id.indexOf(\"incertae-sedis\") > -1 : false\n );\n }\n return node;\n };\n\n reloadLoadedKeys = async (keys, expandKey, expandAll = true) => {\n this.setState({ rootLoading: true });\n const { loadedKeys: storedKeys } = this.state;\n // const defaultExpandKey = get(qs.parse(get(location, \"search\")), 'taxonKey');\n\n let { treeData } = this.state;\n const targetTaxon = expandKey ? this.findNode(expandKey, treeData) : null;\n const loadedKeys = keys ? [...keys] : [...storedKeys];\n for (let index = 0; index < loadedKeys.length; index++) {\n let node = this.findNode(loadedKeys[index], treeData);\n if (!node && targetTaxon && loadedKeys[index - 1]) {\n // If the node is not found look for insertae sedis nodes in the children of the parent and insert the 'Not assigned' between the parent and the node\n const parentNode = this.findNode(loadedKeys[index - 1], treeData);\n if (\n parentNode &&\n isArray(get(parentNode, \"children\")) &&\n parentNode.children.length > 0\n ) {\n node = await this.pageThroughChildrenUntilTaxonFound(\n parentNode,\n loadedKeys[index]\n );\n if (node) {\n loadedKeys.splice(index, 0, node.taxon.id);\n } else {\n // It has gone missing from the tree\n this.setState(\n {\n nodeNotFoundErr: (\n <span>Cannot find taxon {expandKey} in tree &#128549;</span>\n ),\n rootLoading: false,\n }/* ,\n () => {\n if (\n this.props.treeType === \"CATALOGUE\" &&\n typeof this.props.addMissingTargetKey === \"function\"\n ) {\n this.props.addMissingTargetKey(expandKey);\n }\n } */\n );\n }\n }\n }\n if (node) {\n await this.fetchChildPage(node, true, true);\n let targetNode = node.children.find(\n (c) => get(c, \"taxon.id\") === get(targetTaxon, \"taxon.id\")\n );\n if (\n targetTaxon &&\n index === loadedKeys.length - 2 &&\n get(node, \"taxon.id\") !== get(targetTaxon, \"taxon.id\") &&\n isArray(node.children) &&\n !targetNode\n ) {\n if (node.children.length < node.childCount) {\n // its the parent of the taxon we are after - if its not in the first page, insert it\n targetNode = await this.pageThroughChildrenUntilTaxonFound(\n node,\n get(targetTaxon, \"taxon.id\")\n );\n // node.children = [targetTaxon, ...node.children];\n if (targetNode) {\n this.setState({ treeData: [...this.state.treeData] }, () => {\n setTimeout(() => {\n const elmnt = document.getElementById(expandKey);\n elmnt.scrollIntoView({ behavior: \"smooth\", block: \"center\" });\n /* if (get(this, \"treeRef.current\")) {\n this.treeRef.current.scrollTo({ key: expandKey });\n } */\n }, 100);\n });\n } else {\n // It has gone missing from the tree\n this.setState(\n {\n nodeNotFoundErr: (\n <span>Cannot find taxon {expandKey} in tree &#128549;</span>\n ),\n rootLoading: false,\n },\n () => {\n if (\n this.props.treeType === \"CATALOGUE\" &&\n typeof this.props.addMissingTargetKey === \"function\"\n ) {\n this.props.addMissingTargetKey(expandKey);\n }\n }\n );\n }\n }\n }\n }\n }\n const newState = { loadedKeys, rootLoading: false };\n if (expandAll) {\n newState.expandedKeys = loadedKeys;\n }\n this.setState(newState, () => {\n if (expandKey) {\n setTimeout(() => {\n const elmnt = document.getElementById(expandKey);\n elmnt.scrollIntoView({ behavior: \"smooth\", block: \"center\" });\n /* if (get(this, \"treeRef.current\")) {\n this.treeRef.current.scrollTo({ key: expandKey });\n } */\n }, 100);\n }\n });\n };\n\n render() {\n const {\n error,\n rootTotal,\n rootLoading,\n treeData,\n defaultExpandAll,\n nodeNotFoundErr,\n loadedKeys,\n expandedKeys,\n } = this.state;\n const { treeType, dataset, height, expandedTaxonKey } = this.props;\n void height;\n const defaultExpandKey = expandedTaxonKey;\n\n return (\n <div>\n {error && (\n <React.Fragment>\n {get(error, \"response.data.code\") !== 404 ? (\n <Alert\n closable\n onClose={() => this.setState({ error: null })}\n style={{ marginTop: \"8px\" }}\n message={<ErrorMsg error={error} />}\n type=\"error\"\n />\n ) : (\n <Alert\n closable\n onClose={() => this.setState({ error: null })}\n style={{ marginTop: \"8px\" }}\n message={\n <Custom404\n error={error}\n treeType={treeType}\n dataset={dataset}\n loadRoot={this.loadRoot}\n />\n }\n type=\"warning\"\n />\n )}\n </React.Fragment>\n )}\n {nodeNotFoundErr && (\n <Alert\n closable\n onClose={() => this.setState({ nodeNotFoundErr: null })}\n style={{ marginTop: \"8px\" }}\n message={nodeNotFoundErr}\n type=\"warning\"\n />\n )}\n {rootLoading && <Skeleton paragraph={{ rows: 10 }} active />}\n {!rootLoading && treeData.length > 0 && (\n <Tree\n ref={this.treeRef}\n defaultExpandAll={defaultExpandAll}\n // height={height || 600}\n // defaultExpandedKeys={defaultExpandedKeys}\n loadData={this.onLoadData}\n onLoad={(loadedKeys) => this.setState({ loadedKeys })}\n loadedKeys={loadedKeys}\n expandedKeys={expandedKeys}\n treeData={treeData}\n filterTreeNode={(node) => node.key === defaultExpandKey}\n onExpand={(expandedKeys, obj) => {\n this.setState({ expandedKeys });\n if (this.props.onExpandedTaxonKeyChange) {\n this.props.onExpandedTaxonKeyChange(\n obj.expanded ? obj.node.key : null\n );\n }\n }}\n ></Tree>\n )}\n\n {!error && treeData.length < rootTotal && (\n <Button loading={rootLoading} onClick={this.loadRoot}>\n Load more{\" \"}\n </Button>\n )}\n </div>\n );\n }\n}\n\nexport default ColTree;\n","import React from \"react\";\nimport ColTree from \"./ColTree\";\nimport { get } from \"lodash-es\";\nimport NameAutocomplete from \"./NameAutocomplete\";\nimport client, { setAuth } from \"../api/client\";\nimport { Row, Col, Checkbox } from \"antd\";\nimport { ColTreeContext } from \"./ColTreeContext\";\nimport { TreeCacheContext, createTreeCache } from \"./treeCache\";\nimport { getDataset } from \"../api/dataset\";\nimport Citation from \"../components/DatasetCitation\";\nimport { RouterContext, buildRouter } from \"../router\";\nimport { readSetting, writeSetting } from \"../storage\";\n\nconst INFRASPECIFIC_RANKS = [\n \"infraspecific name\",\n \"species\",\n \"variety\",\n \"form\",\n];\n\nclass ColTreeWrapper extends React.Component {\n static contextType = RouterContext;\n\n constructor(props) {\n super(props);\n setAuth(this.props.auth);\n this.state = {\n hideExtinct: readSetting(\"tree-extant-only\", false),\n showInfo: readSetting(\"tree-show-source\", false),\n dataset: null,\n };\n // Per-Tree DataLoader cache. 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package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "col-browser",
3
- "version": "2.2.0",
3
+ "version": "2.2.2",
4
4
  "description": "Catalogue of Life browse and search React components",
5
5
  "main": "umd/col-browser.js",
6
6
  "module": "es/index.js",
package/types/index.d.ts CHANGED
@@ -41,6 +41,12 @@ export interface TreeProps
41
41
  extends DatasetKeyProps,
42
42
  ThemeProps,
43
43
  NavigationProps {
44
+ /**
45
+ * Uncontrolled fallback: the taxon to expand to on load when
46
+ * `expandedTaxonKey` is not set. Nothing is expanded unless one of these is
47
+ * provided — pass a root id to open it, e.g. `"CS5HF"` opens Eukaryota in
48
+ * current Catalogue of Life releases.
49
+ */
44
50
  defaultTaxonKey?: string;
45
51
  expandedTaxonKey?: string;
46
52
  onExpandedTaxonKeyChange?: (taxonKey: string | null) => void;
@@ -150,6 +156,13 @@ export interface WithRoutingOptions {
150
156
  navigation?: "spa" | "reload";
151
157
  /** Per-kind URL prefixes used to read/write the controlled identifier. */
152
158
  paths?: Partial<Record<WithRoutingOptions["kind"], string>>;
159
+ /**
160
+ * Reserved query string (e.g. "?v=br") appended to every generated link and
161
+ * preserved across the component's own state writes, but excluded from its
162
+ * parsed state — so a release/variant marker never leaks into Search filters
163
+ * or Tree state.
164
+ */
165
+ query?: string;
153
166
  }
154
167
 
155
168
  /**