frogpot/dist/index.cjs.map

A library to work with directed graphs that can be projected into trees.

{"version":3,"sources":["../src/index.ts","../src/components/Hierarchy.tsx","../src/path.ts","../src/util.ts","../src/search.ts","../src/graph.ts","../src/hierarchy.ts","../src/loaders/obograph/schema.ts","../src/loaders/index.ts","../src/loaders/obograph/index.ts"],"sourcesContent":["// React\nexport { default as HierarchyTree } from \"./components/Hierarchy\";\nexport { useNodeSearch } from \"./search\";\n\n// Data model\nexport { default as Graph } from \"./graph\";\nexport { default as Hierarchy } from \"./hierarchy\";\nexport { default as Path } from \"./path\";\n\n// Loaders\nexport { default as OBOGraphLoader } from \"./loaders/obograph\";\n\n// Types\nexport type { GraphNode } from \"./types\";\nexport type { OBOGraphNode } from \"./loaders/obograph\";\n","import React, { useState, useEffect, useRef, useImperativeHandle } from \"react\";\nimport Hierarchy, { HierarchyRow } from \"../hierarchy\";\nimport Path from \"../path\";\nimport { GraphNode } from \"../types\";\nimport { takeWhile } from \"../util\";\n\ntype HierarchyTreeProps<T extends GraphNode = GraphNode> = {\n  hierarchy: Hierarchy<T>;\n  rootURI: string;\n  itemURI?: string;\n  preferredPaths?: Array<string>;\n  width?: number;\n  onSelectNode?: (node: T) => void;\n};\n\nexport type HierarchyTreeHandle = {\n  openAndFocusNode: (uri: string) => void;\n};\n\ntype HierarchyTreeState = {\n  expandPaths: Set<string>;\n  showPaths: Set<string>;\n  selectedPath: Path;\n};\n\nconst d = {\n  // width: 1000,\n  tree: {\n    itemHeight: 24,\n    depthIndent: 16,\n  },\n};\n\n// const SELECTION_MARKER = \">\";\n\nfunction drawHierarchyPath(\n  tree: Array<HierarchyRow<GraphNode>>,\n  el: HTMLCanvasElement,\n) {\n  const ctx = el.getContext(\"2d\");\n  if (!ctx) return;\n\n  const dpr = window.devicePixelRatio || 1;\n\n  const cssHeight = tree.length * d.tree.itemHeight;\n\n  el.style.width = \"100%\";\n  el.style.height = `${cssHeight}px`;\n\n  const cssWidth = el.clientWidth;\n\n  el.width = cssWidth * dpr;\n  el.height = cssHeight * dpr;\n\n  ctx.scale(dpr, dpr);\n\n  ctx.clearRect(0, 0, cssWidth, cssHeight);\n  ctx.strokeStyle = \"#666\";\n  ctx.lineWidth = 1;\n  ctx.setLineDash([1, 1]);\n  ctx.beginPath();\n\n  tree.forEach((originItem, i) => {\n    const childItems = takeWhile(\n      tree.slice(i + 1),\n      item => item.depth > originItem.depth,\n    );\n\n    if (childItems.length === 0) return;\n\n    const x0 = originItem.depth * d.tree.depthIndent + 5;\n    const y0 = i * d.tree.itemHeight + d.tree.itemHeight / 2;\n\n    const lastDirectChildIdx =\n      childItems.findLastIndex(item => item.depth === originItem.depth + 1) + 1;\n    // Draw a line down to the last direct child\n    ctx.moveTo(x0, y0);\n    ctx.lineTo(x0, y0 + lastDirectChildIdx * d.tree.itemHeight);\n\n    childItems.forEach((childItem, i) => {\n      if (childItem.depth === originItem.depth + 1) {\n        // Draw a tick\n        const tickWidth = d.tree.depthIndent;\n        const y = y0 + (i + 1) * d.tree.itemHeight;\n        ctx.moveTo(x0, y);\n        ctx.lineTo(x0 + tickWidth, y);\n      }\n    });\n  });\n  ctx.stroke();\n}\n\n/*\nfunction drawPathFor(\n  items: ReturnType<typeof Hierarchy.prototype.buildFlatTree>,\n  curItemIdx: number,\n) {\n  const originItem = items[curItemIdx]!;\n\n  let pathStr = \"M5 0 \";\n  let vIdx = 0;\n\n  const horizontalTicksAt: Array<number> = [];\n\n  for (const treeItem of items.slice(curItemIdx + 1)) {\n    vIdx += 1;\n\n    // This is an item one deeper in the hierarchy\n    if (treeItem.depth === originItem.depth + 1) {\n      horizontalTicksAt.push(vIdx);\n\n      // Draw a line down to the current vertical position\n      pathStr += `L 5 ${vIdx * d.tree.itemHeight - 10}`;\n\n      // Draw a line horizontally and then back\n      pathStr += `l ${d.tree.depthIndent - 12} 0`;\n      pathStr += `m -${d.tree.depthIndent - 12} 0`;\n    } else if (treeItem.depth <= originItem.depth) {\n      break;\n    }\n  }\n\n  return pathStr;\n}\n*/\n\nfunction HierarchyTree<T extends GraphNode = GraphNode>(\n  props: HierarchyTreeProps<T>,\n  ref: React.Ref<HierarchyTreeHandle>,\n) {\n  const { hierarchy, itemURI } = props;\n  const canvasRef = useRef<HTMLCanvasElement>(null);\n\n  const [treeState, setTreeState] = useState<HierarchyTreeState>({\n    expandPaths: new Set(),\n    showPaths: new Set(),\n    selectedPath: hierarchy.getPathsForNode(props.rootURI)[0]!,\n  });\n\n  /*\n  const [showRelations, setShowRelations] = useState(false);\n   */\n\n  useEffect(() => {\n    const expandPaths: Set<string> = new Set();\n\n    let showPaths: Set<string> | null = null;\n\n    if (itemURI) {\n      const node = hierarchy.getNode(itemURI);\n      const paths = hierarchy.getPathsForNode(node);\n      showPaths = new Set(paths.map(path => path.key));\n    }\n\n    setTreeState(prev => ({\n      ...prev,\n      expandPaths,\n      showPaths: showPaths ? showPaths : prev.showPaths,\n    }));\n  }, [itemURI]);\n\n  const tree = hierarchy.projectFlatView({\n    showPaths: [...treeState.showPaths].map(key => Path.fromKey(key)),\n    expandPaths: [...treeState.expandPaths].map(key => Path.fromKey(key)),\n  });\n\n  /*\n  const tree = hierarchy.buildFlatTree(item, {\n    preferredPaths: usePreferredPaths ? preferredPaths : undefined,\n    expandPaths: expandPaths.size > 0 ? [...expandPaths] : undefined,\n  });\n   */\n\n  useImperativeHandle(\n    ref,\n    () => ({\n      openAndFocusNode(uri: string) {\n        const node = hierarchy.getNode(uri);\n        const paths = hierarchy.getPathsForNode(node);\n        const parents = paths.map(p => p.parent()).filter(p => p !== null);\n\n        setTreeState(prev => {\n          const expandPaths = new Set([\n            ...prev.expandPaths,\n            ...parents.map(p => p.key),\n          ]);\n          const showPaths = new Set([...paths.map(path => path.key)]);\n          const selectedPath = paths[0]!;\n\n          return {\n            expandPaths,\n            showPaths,\n            selectedPath,\n          };\n        });\n      },\n    }),\n    [],\n  );\n\n  useEffect(() => {\n    const canvasEl = canvasRef.current;\n    if (!canvasEl) return;\n    drawHierarchyPath(tree, canvasEl);\n  }, [tree]);\n\n  useEffect(() => {\n    const uri = treeState.selectedPath.leaf();\n    if (props.onSelectNode) {\n      props.onSelectNode(hierarchy.getNode(uri));\n    }\n  }, [treeState.selectedPath]);\n\n  const expandPath = (pathKey: string) => {\n    setTreeState(prev => ({\n      ...prev,\n      expandPaths: new Set([...prev.expandPaths, pathKey]),\n    }));\n  };\n\n  const unexpandPath = (pathKey: string) => {\n    const path = Path.fromKey(pathKey);\n\n    setTreeState(prev => {\n      const nextExpandPaths = [...prev.expandPaths].filter(_path => {\n        return !Path.fromKey(_path).startsWith(path);\n      });\n\n      const nextShowPaths = [...prev.showPaths].filter(_path => {\n        return !Path.fromKey(_path).startsWith(path);\n      });\n\n      let nextSelectedPath = treeState.selectedPath;\n\n      if (\n        treeState.selectedPath.startsWith(path) &&\n        !treeState.selectedPath.equals(path)\n      ) {\n        nextSelectedPath = path;\n      }\n\n      return {\n        selectedPath: nextSelectedPath,\n        showPaths: new Set(nextShowPaths),\n        expandPaths: new Set(nextExpandPaths),\n      };\n    });\n  };\n\n  const togglePathExpansion = (path: string) => {\n    if (treeState.expandPaths.has(path)) {\n      unexpandPath(path);\n    } else {\n      expandPath(path);\n    }\n  };\n\n  return (\n    <div\n      tabIndex={0}\n      onKeyDown={e => {\n        const curIdx = tree.findIndex(({ path }) =>\n          path.equals(treeState.selectedPath),\n        );\n        const curItem = tree[curIdx];\n\n        if (e.key === \"ArrowDown\") {\n          e.preventDefault();\n          if (curIdx !== -1) {\n            const nextIdx = curIdx + 1;\n            const nextItem = tree[nextIdx];\n            if (nextItem) {\n              setTreeState(prev => ({\n                ...prev,\n                selectedPath: nextItem.path,\n              }));\n            }\n          }\n        } else if (e.key === \"ArrowUp\") {\n          e.preventDefault();\n          if (curIdx > 0) {\n            const nextIdx = curIdx - 1;\n            const nextItem = tree[nextIdx];\n            if (nextItem) {\n              setTreeState(prev => ({\n                ...prev,\n                selectedPath: nextItem.path,\n              }));\n            }\n          }\n        } else if (e.key === \"ArrowRight\") {\n          e.preventDefault();\n          if (curItem) {\n            expandPath(curItem.path.key);\n          }\n        } else if (e.key === \"ArrowLeft\") {\n          e.preventDefault();\n          if (curItem) {\n            if (treeState.expandPaths.has(curItem.path.key)) {\n              unexpandPath(curItem.path.key);\n            } else {\n              // Select previous level in hierarchy\n              for (let i = curIdx; i >= 0; i--) {\n                if (tree[i]?.depth === curItem.depth - 1) {\n                  setTreeState(prev => ({\n                    ...prev,\n                    selectedPath: tree[i]!.path,\n                  }));\n                  break;\n                }\n              }\n            }\n          }\n        }\n      }}\n    >\n      <div\n        style={{\n          position: \"relative\",\n          border: \"1px solid #ccc\",\n          width: props.width,\n        }}\n      >\n        <canvas\n          ref={canvasRef}\n          style={{\n            pointerEvents: \"none\",\n            position: \"absolute\",\n            top: 0,\n            left: 0,\n          }}\n        />\n        <div style={{ position: \"relative\" }}>\n          {tree.map(({ item, depth, path }) => (\n            <div\n              key={path.key}\n              data-path={path.key}\n              style={{\n                display: \"flex\",\n                alignItems: \"center\",\n\n                lineHeight: `${d.tree.itemHeight}px`,\n                height: `${d.tree.itemHeight}px`,\n\n                paddingLeft: `${depth * d.tree.depthIndent}px`,\n\n                userSelect: \"none\",\n                cursor: \"pointer\",\n              }}\n            >\n              <span\n                onClick={() => togglePathExpansion(path.key)}\n                style={{\n                  display: \"inline-block\",\n                  width: \"18px\",\n                }}\n              >\n                {hierarchy.graph.childrenByURI[item.uri]!.length ===\n                0 ? null : (\n                  <span\n                    style={{\n                      display: \"inline-flex\",\n                      width: 10,\n                      height: 10,\n                      border: \"2px solid #666\",\n                      background: treeState.expandPaths.has(path.key)\n                        ? \"#ccc\"\n                        : \"#fff\",\n                      alignItems: \"center\",\n                      justifyContent: \"center\",\n                    }}\n                  >\n                    {treeState.expandPaths.has(path.key) ? \"\" : \"\"}\n                  </span>\n                )}\n              </span>\n              <span\n                style={{\n                  flex: 1,\n\n                  overflow: \"hidden\",\n                  whiteSpace: \"nowrap\",\n                  textOverflow: \"ellipsis\",\n\n                  backgroundColor: treeState.selectedPath.equals(path)\n                    ? \"#f0f0f0\"\n                    : \"transparent\",\n                }}\n                title={itemURI}\n                onMouseDown={e => {\n                  if (e.detail === 1) {\n                    // Single click: Select node\n                    setTreeState(prev => ({\n                      ...prev,\n                      selectedPath: path,\n                    }));\n                  } else if (e.detail === 2) {\n                    // Double click: Expand hierarchy\n                    togglePathExpansion(path.key);\n                  }\n                }}\n              >\n                {/* showRelations ? relToParent + \" \" : \"\" */}\n                {item.label}\n              </span>\n            </div>\n          ))}\n        </div>\n      </div>\n    </div>\n  );\n}\n\nexport default React.forwardRef(HierarchyTree);\n","export default class Path {\n  steps: Array<string>;\n\n  constructor(steps: Array<string>) {\n    this.steps = steps;\n\n    if (this.steps.length === 0) {\n      throw new Error(\"Cannot create an empty path.\");\n    }\n  }\n\n  get key() {\n    return JSON.stringify(this.steps);\n  }\n\n  static fromKey(k: string) {\n    return new Path(JSON.parse(k));\n  }\n\n  depth() {\n    return this.steps.length;\n  }\n\n  startsWith(other: Path) {\n    return other.isAncestorOf(this) || other.equals(this);\n  }\n\n  isAncestorOf(other: Path) {\n    if (this.steps.length >= other.steps.length) return false;\n    return this.steps.every((val, i) => val === other.steps[i]);\n  }\n\n  equals(other: Path) {\n    if (other.steps.length !== this.steps.length) return false;\n    return this.steps.every((v, i) => v === other.steps[i]);\n  }\n\n  parent(): Path | null {\n    if (this.steps.length <= 1) return null;\n    return new Path(this.steps.slice(0, -1));\n  }\n\n  child(uri: string): Path {\n    return new Path([...this.steps, uri]);\n  }\n\n  leaf() {\n    return this.steps.at(-1)!;\n  }\n}\n","import { GraphNode } from \"./types\";\n\nexport function takeWhile<T>(\n  arr: Array<T>,\n  testFn: (item: T, i: number) => boolean,\n) {\n  const ret: Array<T> = [];\n\n  let i = 0;\n\n  for (const item of arr) {\n    i += 1;\n\n    if (!testFn(item, i)) {\n      break;\n    }\n\n    ret.push(item);\n  }\n\n  return ret;\n}\n\nexport function sortByLabel(a: GraphNode, b: GraphNode) {\n  const aLabel = a.label;\n  const bLabel = b.label;\n\n  if (aLabel === bLabel) return 0;\n  if (!aLabel) return -1;\n  if (!bLabel) return 1;\n\n  return aLabel.localeCompare(bLabel);\n}\n","import { useEffect, useRef, useState, createElement } from \"react\";\nimport MiniSearch, { SearchOptions, SearchResult } from \"minisearch\";\nimport { GraphNode } from \"./types\";\nimport Highlighter, { HighlighterProps } from \"react-highlight-words\";\n\nexport type SearchResultWithNode<T extends GraphNode> = SearchResult & {\n  node: T;\n};\n\nexport class SearchEngine<T extends GraphNode> {\n  items: Array<T>;\n  itemsByURI: Map<string, T>;\n  miniSearch: MiniSearch;\n\n  constructor(items: Array<T>) {\n    this.items = items;\n\n    this.itemsByURI = new Map(items.map(item => [item.uri, item]));\n\n    this.miniSearch = new MiniSearch({\n      idField: \"uri\",\n      fields: [\"label\", \"synonyms\", \"definitions\"],\n      extractField: (doc, fieldName) => {\n        if (fieldName === \"synonyms\" || fieldName === \"definitions\") {\n          // @ts-expect-error Don't worry about cajoling this into types.\n          return doc[fieldName].map(x => x.value).join(\" \");\n        }\n\n        return doc[fieldName];\n      },\n    });\n  }\n\n  search(\n    text: string,\n    options?: SearchOptions,\n  ): Array<SearchResultWithNode<T>> {\n    const results = this.miniSearch.search(text, options);\n\n    return results.map(res => ({\n      ...res,\n      node: this.itemsByURI.get(res.id)!,\n    }));\n  }\n\n  buildIndex() {\n    this.miniSearch.addAll(this.items);\n  }\n}\n\nexport function useSearchEngine<T extends GraphNode>(items: Array<T>) {\n  const engineRef = useRef<SearchEngine<T>>(null);\n\n  const rebuild = (items: Array<T>) => {\n    const engine = new SearchEngine(items);\n    engine.buildIndex();\n    engineRef.current = engine;\n  };\n\n  if (engineRef.current === null) {\n    rebuild(items);\n  }\n\n  useEffect(() => {\n    rebuild(items);\n  }, [items]);\n\n  return { engine: engineRef.current! };\n}\n\nexport function useNodeSearch<T extends GraphNode>(nodes: Array<T>) {\n  const { engine } = useSearchEngine(nodes);\n  const [query, setQuery] = useState(\"\");\n  const [results, setResults] = useState<Array<SearchResultWithNode<T>> | null>(\n    null,\n  );\n\n  useEffect(() => {\n    if (query.trim() === \"\") {\n      setResults(null);\n      return;\n    }\n\n    const results = engine.search(query, {\n      prefix: true,\n      boost: { label: 2 },\n      combineWith: \"and\",\n    });\n\n    setResults(results);\n  }, [query]);\n\n  const searchWords = query.split(\" \").map(word => new RegExp(\"\\\\b\" + word));\n\n  const highlightText = (\n    text: string,\n    props?: Omit<HighlighterProps, \"searchWords\" | \"textToHighlight\">,\n  ) =>\n    createElement(Highlighter, {\n      textToHighlight: text,\n      searchWords,\n      ...props,\n    });\n\n  return { engine, results, query, setQuery, highlightText };\n}\n","import treeverse from \"treeverse\";\nimport { GraphNode } from \"./types\";\nimport Hierarchy from \"./hierarchy\";\nimport { sortByLabel } from \"./util\";\n\ntype Relation = {\n  to: string;\n  predicate: string;\n  inverse: boolean;\n};\n\nexport default class Graph<T extends GraphNode> {\n  roots: Array<T>;\n  nodes: Array<T>;\n  nodesByURI: Record<string, T>;\n\n  childrenByURI: Record<string, Relation[]>;\n  parentsByURI: Record<string, Relation[]>;\n\n  constructor(nodes: Array<T>) {\n    const nodesByURI: Record<string, T> = {};\n    const parentsByURI: Record<string, Relation[]> = {};\n    const childrenByURI: Record<string, Relation[]> = {};\n\n    for (const node of nodes) {\n      nodesByURI[node.uri] = node;\n\n      for (const [relURI, termURIs] of Object.entries(node.children)) {\n        termURIs.forEach(childURI => {\n          if (!Object.hasOwn(childrenByURI, node.uri)) {\n            childrenByURI[node.uri] = [];\n          }\n\n          if (!Object.hasOwn(parentsByURI, childURI)) {\n            parentsByURI[childURI] = [];\n          }\n\n          childrenByURI[node.uri]!.push({\n            to: childURI,\n            predicate: relURI,\n            inverse: false,\n          });\n\n          parentsByURI[childURI]!.push({\n            to: node.uri,\n            predicate: relURI,\n            inverse: true,\n          });\n        });\n      }\n\n      for (const [relURI, termURIs] of Object.entries(node.parents)) {\n        termURIs.forEach(parentURI => {\n          if (!Object.hasOwn(parentsByURI, node.uri)) {\n            parentsByURI[node.uri] = [];\n          }\n\n          if (!Object.hasOwn(childrenByURI, parentURI)) {\n            childrenByURI[parentURI] = [];\n          }\n\n          parentsByURI[node.uri]!.push({\n            to: parentURI,\n            predicate: relURI,\n            inverse: false,\n          });\n\n          childrenByURI[parentURI]!.push({\n            to: node.uri,\n            predicate: relURI,\n            inverse: true,\n          });\n        });\n      }\n\n      if (!Object.hasOwn(childrenByURI, node.uri)) {\n        childrenByURI[node.uri] = [];\n      }\n      if (!Object.hasOwn(parentsByURI, node.uri)) {\n        parentsByURI[node.uri] = [];\n      }\n    }\n\n    const roots = nodes.filter(\n      item =>\n        parentsByURI[item.uri]!.length === 0 &&\n        childrenByURI[item.uri]!.length > 0,\n    );\n\n    this.roots = roots;\n    this.nodes = nodes;\n    this.nodesByURI = nodesByURI;\n    this.parentsByURI = parentsByURI;\n    this.childrenByURI = childrenByURI;\n  }\n\n  items() {\n    return this.nodes;\n  }\n\n  getHierarchy(rootURI: string) {\n    const item = this.getItem(rootURI);\n    return new Hierarchy(item, this);\n  }\n\n  getRootHierarchies() {\n    const ret: Map<string, Hierarchy<T>> = new Map();\n\n    this.roots.forEach(root => {\n      ret.set(root.uri, this.getHierarchy(root.uri));\n    });\n\n    return ret;\n  }\n\n  getItem(uri: string) {\n    const item = this.nodesByURI[uri];\n\n    if (item === undefined) {\n      throw new Error(`No item in graph with URI ${uri}`);\n    }\n    return item;\n  }\n\n  findAllParents(item: T) {\n    const parents: Array<T> = [];\n\n    treeverse.breadth({\n      tree: item,\n      visit(item) {\n        parents.push(item);\n      },\n      getChildren: node =>\n        this.parentsByURI[node.uri]!.map(rel => this.getItem(rel.to)).sort(\n          sortByLabel,\n        ),\n    });\n\n    parents.shift();\n\n    return parents;\n  }\n\n  findAllChildren(item: T) {\n    const children: Array<T> = [];\n\n    treeverse.breadth({\n      tree: item,\n      visit(item) {\n        children.push(item);\n      },\n      getChildren: node =>\n        this.childrenByURI[node.uri]!.map(rel => this.getItem(rel.to)).sort(\n          sortByLabel,\n        ),\n    });\n\n    children.shift();\n\n    return children;\n  }\n}\n","import treeverse from \"treeverse\";\n\nimport { GraphNode } from \"./types\";\nimport Path from \"./path\";\nimport Graph from \"./graph\";\nimport { sortByLabel } from \"./util\";\n\ntype FlatViewOptions = {\n  showPaths?: Array<Path>;\n  expandPaths?: Array<Path>;\n};\n\nexport type HierarchyRow<T extends GraphNode> = {\n  item: T;\n  relToParent: string | null;\n  depth: number;\n  path: Path;\n};\n\nexport default class Hierarchy<T extends GraphNode> {\n  root: T;\n  graph: Graph<T>;\n\n  nodesByURI: Map<string, T>;\n  nodesByPathKey: Map<string, T>;\n  pathsByURI: Map<string, Path[]>;\n\n  constructor(root: T, graph: Graph<T>) {\n    this.root = root;\n    this.graph = graph;\n    this.nodesByURI = new Map();\n    this.nodesByPathKey = new Map();\n    this.pathsByURI = new Map();\n\n    // Precompute all indexes ahead of time. This consists of:\n    //   1. A map indexing nodes by URI\n    //   2. A map indexing nodes by path key\n    //   3. A map indexing paths by URI\n    treeverse.depth({\n      tree: {\n        item: this.root,\n        path: new Path([this.root.uri]),\n      },\n\n      visit: node => {\n        const { item, path } = node;\n\n        if (!this.pathsByURI.has(item.uri)) {\n          this.pathsByURI.set(item.uri, []);\n        }\n\n        this.nodesByURI.set(item.uri, item);\n        this.pathsByURI.get(item.uri)!.push(path);\n        this.nodesByPathKey.set(path.key, item);\n      },\n\n      getChildren: node => {\n        const { item, path } = node;\n        const childRels = this.graph.childrenByURI[item.uri] ?? [];\n\n        return childRels.map(rel => {\n          const child = this.graph.getItem(rel.to);\n\n          return {\n            item: child,\n            path: path.child(child.uri),\n          };\n        });\n      },\n    });\n  }\n\n  getNode(node: string | T | Path) {\n    if (typeof node === \"string\") {\n      const ret = this.nodesByURI.get(node);\n\n      if (!ret) {\n        throw new Error(`No item in hierarchy with URI ${node}`);\n      }\n\n      return ret;\n    } else if (node instanceof Path) {\n      const ret = this.nodesByPathKey.get(node.key);\n\n      if (!ret) {\n        throw new Error(`No item in hierarchy at path ${node.key}`);\n      }\n\n      return ret;\n    } else {\n      return node;\n    }\n  }\n\n  items() {\n    return [...this.nodesByURI.values()].sort(sortByLabel);\n  }\n\n  getPathsForNode(node: string | T) {\n    const _node = this.getNode(node);\n    return this.pathsByURI.get(_node.uri) ?? [];\n  }\n\n  // Produce a projection of this hierarchy, with only certain nodes shown or\n  // expanded. Meant for producing a portion of the hierarchy suitable for\n  // rendering in a UI.\n  //\n  // Returns a one-dimensional array of HierarchyRow objects annotated by their\n  // depth.\n  projectFlatView(opts: FlatViewOptions = {}) {\n    const showPaths = opts.showPaths ?? [];\n    const expandPaths = opts.expandPaths ?? [];\n\n    const showKeys = new Set(showPaths.map(p => p.key));\n    const expandKeys = new Set(expandPaths.map(p => p.key));\n\n    const rows: Array<HierarchyRow<T>> = [];\n\n    const shouldIterateChildren = (path: Path) => {\n      // This is an expanded node-- iterate its children.\n      if (expandKeys.has(path.key)) return true;\n\n      // This is an ancestor of a shown path-- iterate its children.\n      if (showPaths.some(showPath => path.isAncestorOf(showPath))) return true;\n\n      // This node is an ancestor of an expanded path-- iterate its children.\n      if (expandPaths.some(expandPath => path.isAncestorOf(expandPath)))\n        return true;\n\n      return false;\n    };\n\n    const shouldShowPath = (path: Path) => {\n      const pathKey = path.key;\n\n      // Always show the root\n      if (path.depth() === 1) return true;\n\n      // This is an expanded node\n      if (expandKeys.has(pathKey)) return true;\n\n      // This is a shown node\n      if (showKeys.has(pathKey)) return true;\n\n      for (const showPath of showPaths) {\n        // This is an ancestor of an shown node\n        if (path.isAncestorOf(showPath)) return true;\n      }\n\n      for (const expandPath of expandPaths) {\n        // This is an ancestor of an expanded node\n        if (path.isAncestorOf(expandPath)) return true;\n\n        // This is the direct child of an expanded node\n        if (path.parent()?.equals(expandPath)) return true;\n      }\n\n      return false;\n    };\n\n    treeverse.depth({\n      tree: {\n        item: this.root,\n        path: new Path([this.root.uri]),\n        depth: 0,\n        relToParent: null,\n      } as HierarchyRow<T>,\n\n      visit(node) {\n        const { item, path, depth, relToParent } = node;\n\n        if (shouldShowPath(path)) {\n          rows.push({ item, path, depth, relToParent });\n        }\n      },\n\n      getChildren: node => {\n        const { item, path, depth } = node;\n\n        if (!shouldIterateChildren(path)) {\n          return [];\n        }\n\n        const childRels = this.graph.childrenByURI[item.uri] ?? [];\n\n        const children = childRels.map(rel => {\n          const item = this.graph.getItem(rel.to);\n          const relPredicate = !rel.inverse\n            ? `^${rel.predicate}`\n            : rel.predicate;\n\n          return {\n            item,\n            path: path.child(item.uri),\n            depth: depth + 1,\n            relToParent: relPredicate,\n          } as HierarchyRow<T>;\n        });\n\n        // Sort in reverse alphabetical order-- the last node is visited first.\n        children.sort((a, b) => sortByLabel(b.item, a.item));\n\n        return children;\n      },\n    });\n\n    return rows;\n  }\n}\n","import * as z from \"zod\";\n\nexport const OBOMeta = z.object({\n  definition: z.optional(\n    z.object({\n      val: z.string(),\n      pred: z.optional(z.string()),\n      xrefs: z.optional(z.array(z.string())),\n      get meta(): z.ZodOptional<typeof OBOMeta> {\n        return z.optional(OBOMeta);\n      },\n    }),\n  ),\n  comments: z.optional(z.array(z.string())),\n  subsets: z.optional(z.array(z.string())),\n  synonyms: z.optional(\n    z.array(\n      z.object({\n        synonymType: z.optional(z.string()),\n        pred: z.optional(z.string()),\n        val: z.string(),\n        xrefs: z.optional(z.array(z.string())),\n        get meta(): z.ZodOptional<typeof OBOMeta> {\n          return z.optional(OBOMeta);\n        },\n      }),\n    ),\n  ),\n  xrefs: z.optional(\n    z.array(\n      z.object({\n        lbl: z.optional(z.string()),\n        pred: z.optional(z.string()),\n        val: z.string(),\n        xrefs: z.optional(z.array(z.string())),\n        get meta(): z.ZodOptional<typeof OBOMeta> {\n          return z.optional(OBOMeta);\n        },\n      }),\n    ),\n  ),\n  basicPropertyValues: z.optional(\n    z.array(\n      z.object({\n        pred: z.string(),\n        val: z.string(),\n        xrefs: z.optional(z.array(z.string())),\n        get meta(): z.ZodOptional<typeof OBOMeta> {\n          return z.optional(OBOMeta);\n        },\n      }),\n    ),\n  ),\n  version: z.optional(z.string()),\n  deprecatd: z.optional(z.boolean()),\n});\n\nexport const OBOGraph = z.object({\n  id: z.string(),\n  lbl: z.optional(z.string()),\n  meta: z.optional(OBOMeta),\n  nodes: z.array(\n    z.object({\n      id: z.string(),\n      lbl: z.optional(z.string()),\n      type: z.literal([\"CLASS\", \"INDIVIDUAL\", \"PROPERTY\"]),\n      propertyType: z.optional(z.literal([\"ANNOTATION\", \"OBJECT\", \"DATA\"])),\n      meta: z.optional(OBOMeta),\n    }),\n  ),\n  edges: z.array(\n    z.object({\n      sub: z.string(),\n      pred: z.string(),\n      obj: z.string(),\n      meta: z.optional(OBOMeta),\n    }),\n  ),\n  // logicalDefinitionAxioms,\n  // domainRangeAxioms,\n  // propertyChainAxioms,\n});\n\nexport const OBOGraphsSchema = z.object({\n  meta: z.optional(OBOMeta),\n  graphs: z.array(OBOGraph),\n});\n\nexport type OBOGraphs = z.infer<typeof OBOGraphsSchema>;\n\nexport type OBOGraph = z.infer<typeof OBOGraph>;\n","import Graph from \"../graph\";\nimport { GraphNode } from \"../types\";\n\nexport default abstract class GraphLoader<T, U extends GraphNode> {\n  abstract parseGraph(graph: T): Graph<U>;\n  abstract loadGraphFromString(str: string): T;\n\n  fromString(str: string) {\n    const graph = this.loadGraphFromString(str);\n    return this.parseGraph(graph);\n  }\n\n  async fromURI(uri: string, options?: RequestInit) {\n    const resp = await fetch(uri, options);\n\n    if (!resp.ok) {\n      throw Error(`Error requesting ${uri}: ${resp.status} ${resp.statusText}`);\n    }\n\n    const str = await resp.text();\n    const graph = await this.loadGraphFromString(str);\n\n    return this.parseGraph(graph);\n  }\n}\n","import { OBOGraph, OBOGraphsSchema } from \"./schema\";\nimport Graph from \"../../graph\";\nimport { GraphNode } from \"../../types\";\nimport GraphLoader from \"../\";\n\nconst parentProperties: Record<string, string> = {\n  is_a: \"rdfs:subClassOf\",\n  \"http://purl.obolibrary.org/obo/BFO_0000050\": \"BFO:0000050\",\n};\n\nexport type OBOGraphNode = GraphNode & {\n  meta?: OBOGraph[\"meta\"];\n  edges: OBOGraph[\"edges\"];\n};\n\nexport default class OBOGraphLoader extends GraphLoader<\n  OBOGraph,\n  OBOGraphNode\n> {\n  parseGraph(graph: OBOGraph) {\n    const terms: Map<string, OBOGraphNode> = new Map();\n\n    for (const node of graph.nodes) {\n      if (node.type !== \"CLASS\") continue;\n\n      const bpvs = node.meta?.basicPropertyValues || [];\n      const replaced = !!bpvs.some(\n        ({ pred }) => pred === \"http://purl.obolibrary.org/obo/IAO_0100001\",\n      );\n\n      if (replaced) continue;\n\n      const synonyms = node.meta?.synonyms || [];\n      const definition = node.meta?.definition;\n\n      terms.set(node.id, {\n        uri: node.id,\n        label: node.lbl || node.id,\n        definitions: definition ? 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