make text indexing paths configurable, index definitions by default

GMOD · Aug 1, 2023 · 03e59ea · 03e59ea
1 parent 64f7d2f
commit 03e59ea
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Showing 5 changed files with 33 additions and 9 deletions.
diff --git a/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/fulltext.ts b/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/fulltext.ts
@@ -8,7 +8,11 @@ import { OntologyTerm } from '..'
 function getStringAt(obj: Record<string, unknown>, path: string[]) {
   let thing = obj
   for (const key of path) {
-    thing = thing[key] as Record<string, unknown>
+    if (key in thing) {
+      thing = thing[key] as Record<string, unknown>
+    } else {
+      return
+    }
   }
   return String(thing)
 }
@@ -29,9 +33,11 @@ export function getWords(node: OntologyDBNode, paths: string[][]) {
   const wordSet = new Set<string>()
   for (const path of paths) {
     const text = getStringAt(node, path)
-    stringToWords(text).forEach((word) => {
-      wordSet.add(word)
-    })
+    if (text) {
+      stringToWords(text).forEach((word) => {
+        wordSet.add(word)
+      })
+    }
   }
   return wordSet
 }

diff --git a/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/indexeddb-storage.ts b/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/indexeddb-storage.ts
@@ -96,7 +96,7 @@ export async function loadOboGraphJson(this: OntologyStore, db: Database) {
     const nodeStore = tx.objectStore('nodes')
     const fullTextIndexPaths = this.options.textIndexing?.indexPaths
       ? this.options.textIndexing?.indexPaths.map((p) => p.split('/'))
-      : [['lbl']]
+      : [['lbl'], ['meta', 'definition', 'val']]
     for (const node of graph.nodes ?? []) {
       if (isOntologyDBNode(node)) {
         await nodeStore.add({

diff --git a/packages/jbrowse-plugin-apollo/src/OntologyManager/index.ts b/packages/jbrowse-plugin-apollo/src/OntologyManager/index.ts
@@ -7,7 +7,7 @@ import {
 import { autorun } from 'mobx'
 import { Instance, addDisposer, getSnapshot, types } from 'mobx-state-tree'
 
-import OntologyStore from './OntologyStore'
+import OntologyStore, { OntologyStoreOptions } from './OntologyStore'
 import { OntologyDBNode } from './OntologyStore/indexeddb-schema'
 
 export { isDeprecated } from './OntologyStore/indexeddb-schema'
@@ -17,6 +17,7 @@ export const OntologyRecordType = types
     name: types.string,
     version: 'unversioned',
     source: types.union(LocalPathLocation, UriLocation, BlobLocation),
+    options: types.frozen<OntologyStoreOptions>(),
   })
   .volatile((_self) => ({
     dataStore: undefined as undefined | OntologyStore,
@@ -31,6 +32,7 @@ export const OntologyRecordType = types
         self.name,
         self.version,
         getSnapshot(self.source),
+        self.options,
       )
     },
     afterCreate() {
@@ -104,8 +106,14 @@ export const OntologyManagerType = types
       name: string,
       version: string,
       source: Instance<typeof LocalPathLocation> | Instance<typeof UriLocation>,
+      options?: OntologyStoreOptions,
     ) {
-      const newlen = self.ontologies.push({ name, version, source })
+      const newlen = self.ontologies.push({
+        name,
+        version,
+        source,
+        options: options ?? {},
+      })
       // access it immediately to fire its lifecycle hooks
       // (see https://github.com/mobxjs/mobx-state-tree/issues/1665)
       self.ontologies[newlen - 1].ping()
@@ -140,6 +148,12 @@ export const OntologyRecordConfiguration = ConfigurationSchema(
         uri: 'http://example.com/myontology.json',
       },
     },
+    textIndexingPaths: {
+      type: 'frozen',
+      description:
+        'JSON paths for text fields that will be indexed for text searching',
+      defaultValue: ['lbl', 'meta/definition/val'],
+    },
   },
 )
 

diff --git a/packages/jbrowse-plugin-apollo/src/components/OntologyTermMultiSelect.tsx b/packages/jbrowse-plugin-apollo/src/components/OntologyTermMultiSelect.tsx
@@ -208,6 +208,7 @@ export function OntologyTermMultiSelect({
         const label = option.lbl ?? '(no label)'
         const matches = highlightMatch(label, inputValue, {
           insideWords: true,
+          findAllOccurrences: true,
         })
         parts = highlightParse(label, matches)
         return (

diff --git a/packages/jbrowse-plugin-apollo/src/session.ts b/packages/jbrowse-plugin-apollo/src/session.ts
@@ -219,15 +219,18 @@ function clientDataStoreFactory(
         >[]
 
         for (const ont of configuredOntologies || []) {
-          const [name, version, source] = [
+          const [name, version, source, indexPaths] = [
             readConfObject(ont, 'name') as string,
             readConfObject(ont, 'version') as string,
             readConfObject(ont, 'source') as
               | Instance<typeof LocalPathLocation>
               | Instance<typeof UriLocation>,
+            readConfObject(ont, 'textIndexingPaths') as string[],
           ]
           if (!ontologyManager.findOntology(name)) {
-            ontologyManager.addOntology(name, version, source)
+            ontologyManager.addOntology(name, version, source, {
+              textIndexing: { indexPaths },
+            })
           }
         }