@apollo-annotation/jbrowse-plugin-apollo 0.3.12 → 1.0.0

package/src/OntologyManager/OntologyStore/fulltext.ts

@@ -5,11 +5,10 @@
 import { checkAbortSignal } from '@jbrowse/core/util/aborting'
 import jsonpath from 'jsonpath'
 
-import type { TextIndexFieldDefinition } from '..'
-
 import { stopwords } from './fulltext-stopwords'
 import type { OntologyDBNode } from './indexeddb-schema'
 import { applyPrefixes } from './prefixes'
+import type { TextIndexFieldDefinition } from './types'
 
 // eslint-disable-next-line import/no-duplicates
 import type OntologyStore from '.'

package/src/OntologyManager/OntologyStore/index.test.ts

@@ -5,7 +5,7 @@ import { fileURLToPath } from 'node:url'
 
 import { beforeAll, describe, expect, it, jest } from '@jest/globals'
 
-import { type OntologyClass, isOntologyClass } from '..'
+import { type OntologyClass, isOntologyClass } from './types'
 
 import OntologyStore from '.'
 
@@ -40,7 +40,10 @@ jest.mock('jsonpath', () => {
 let so: OntologyStore
 
 beforeAll(async () => {
-  const localPath = path.resolve(__dirname, '../../../test_data/so-v3.1.json')
+  const localPath = path.resolve(
+    __dirname,
+    '../../../test_data/so-2024-11-18.json',
+  )
   so = new OntologyStore(
     'Sequence Ontology',
     'automated testing',

package/src/OntologyManager/OntologyStore/index.ts

@@ -15,14 +15,6 @@ import {
   deleteDB,
 } from 'idb/with-async-ittr'
 
-import {
-  type OntologyClass,
-  type OntologyProperty,
-  type OntologyTerm,
-  isOntologyClass,
-  isOntologyProperty,
-} from '..'
-
 import { textSearch } from './fulltext'
 import {
   type OntologyDB,
@@ -35,6 +27,13 @@ import {
   loadOboGraphJson,
   openDatabase,
 } from './indexeddb-storage'
+import {
+  type OntologyClass,
+  type OntologyProperty,
+  type OntologyTerm,
+  isOntologyClass,
+  isOntologyProperty,
+} from './types'
 
 export type SourceLocation = UriLocation | LocalPathLocation | BlobLocation
 

package/src/OntologyManager/OntologyStore/indexeddb-storage.ts

@@ -8,8 +8,6 @@ import {
   openDB,
 } from 'idb/with-async-ittr'
 
-import { defaultTextIndexFields } from '..'
-
 import { PREFIXED_ID_PATH, getWords } from './fulltext'
 import {
   type OntologyDB,
@@ -17,6 +15,7 @@ import {
   isOntologyDBNode,
 } from './indexeddb-schema'
 import type { GraphDocument } from './obo-graph-json-schema'
+import { defaultTextIndexFields } from './types'
 
 import type OntologyStore from '.'
 
@@ -172,6 +171,7 @@ export async function loadOboGraphJson(this: OntologyStore, db: Database) {
     const tx2 = db.transaction('meta', 'readwrite')
     // eslint-disable-next-line @typescript-eslint/unbound-method
     const { update, ...otherOptions } = this.options
+    await tx2.objectStore('meta').delete('meta')
     await tx2.objectStore('meta').add(
       {
         ontologyRecord: {

package/src/OntologyManager/OntologyStore/types.ts

@@ -0,0 +1,27 @@
+import type { OntologyDBNode } from './indexeddb-schema'
+
+export type OntologyTerm = OntologyDBNode
+
+export type OntologyClass = OntologyTerm & { type: 'CLASS' }
+export function isOntologyClass(term: OntologyTerm): term is OntologyClass {
+  return term.type === 'CLASS'
+}
+
+export type OntologyProperty = OntologyTerm & { type: 'PROPERTY' }
+export function isOntologyProperty(
+  term: OntologyTerm,
+): term is OntologyProperty {
+  return term.type === 'PROPERTY'
+}
+
+export interface TextIndexFieldDefinition {
+  /** name to display in the UI for text taken from this field or fields */
+  displayName: string
+  /** JSONPath of the field(s) */
+  jsonPath: string
+}
+export const defaultTextIndexFields: TextIndexFieldDefinition[] = [
+  { displayName: 'Label', jsonPath: '$.lbl' },
+  { displayName: 'Synonym', jsonPath: '$.meta.synonyms[*].val' },
+  { displayName: 'Definition', jsonPath: '$.meta.definition.val' },
+]

package/src/OntologyManager/index.ts

@@ -23,8 +23,11 @@ import type ApolloPluginConfigurationSchema from '../config'
 import type { ApolloRootModel } from '../types'
 
 import OntologyStore, { type OntologyStoreOptions } from './OntologyStore'
-import type { OntologyDBNode } from './OntologyStore/indexeddb-schema'
 import { applyPrefixes, expandPrefixes } from './OntologyStore/prefixes'
+import {
+  type OntologyTerm,
+  defaultTextIndexFields,
+} from './OntologyStore/types'
 
 export { isDeprecated } from './OntologyStore/indexeddb-schema'
 
@@ -200,17 +203,17 @@ export const OntologyManagerType = types
 
 export default OntologyManagerType
 
-export interface TextIndexFieldDefinition {
-  /** name to display in the UI for text taken from this field or fields */
-  displayName: string
-  /** JSONPath of the field(s) */
-  jsonPath: string
-}
-export const defaultTextIndexFields: TextIndexFieldDefinition[] = [
-  { displayName: 'Label', jsonPath: '$.lbl' },
-  { displayName: 'Synonym', jsonPath: '$.meta.synonyms[*].val' },
-  { displayName: 'Definition', jsonPath: '$.meta.definition.val' },
-]
+export type {
+  OntologyClass,
+  OntologyProperty,
+  OntologyTerm,
+  TextIndexFieldDefinition,
+} from './OntologyStore/types'
+export {
+  defaultTextIndexFields,
+  isOntologyClass,
+  isOntologyProperty,
+} from './OntologyStore/types'
 
 export const OntologyRecordConfiguration = ConfigurationSchema(
   'OntologyRecord',
@@ -248,17 +251,3 @@ export const OntologyRecordConfiguration = ConfigurationSchema(
 export interface OntologyManager extends Instance<typeof OntologyManagerType> {}
 // eslint-disable-next-line @typescript-eslint/no-empty-object-type
 export interface OntologyRecord extends Instance<typeof OntologyRecordType> {}
-
-export type OntologyTerm = OntologyDBNode
-
-export type OntologyClass = OntologyTerm & { type: 'CLASS' }
-export function isOntologyClass(term: OntologyTerm): term is OntologyClass {
-  return term.type === 'CLASS'
-}
-
-export type OntologyProperty = OntologyTerm & { type: 'PROPERTY' }
-export function isOntologyProperty(
-  term: OntologyTerm,
-): term is OntologyProperty {
-  return term.type === 'PROPERTY'
-}

package/src/TabularEditor/HybridGrid/featureContextMenuItems.ts

@@ -32,7 +32,6 @@ export function featureContextMenuItems(
 ) {
   const internetAccount = getApolloInternetAccount(session)
   const role = internetAccount ? internetAccount.role : 'admin'
-  const admin = role === 'admin'
   const readOnly = !(role && ['admin', 'user'].includes(role))
   const menuItems: MenuItem[] = []
   if (feature) {
@@ -102,7 +101,7 @@ export function featureContextMenuItems(
       },
       {
         label: 'Delete feature',
-        disabled: !admin,
+        disabled: readOnly,
         onClick: () => {
           ;(session as unknown as AbstractSessionModel).queueDialog(
             (doneCallback) => [
@@ -124,7 +123,7 @@ export function featureContextMenuItems(
       },
       {
         label: 'Merge transcripts',
-        disabled: !admin,
+        disabled: readOnly,
         onClick: () => {
           ;(session as unknown as AbstractSessionModel).queueDialog(
             (doneCallback) => [
@@ -146,7 +145,7 @@ export function featureContextMenuItems(
       },
       {
         label: 'Merge exons',
-        disabled: !admin,
+        disabled: readOnly,
         onClick: () => {
           ;(session as unknown as AbstractSessionModel).queueDialog(
             (doneCallback) => [
@@ -168,7 +167,7 @@ export function featureContextMenuItems(
       },
       {
         label: 'Split exon',
-        disabled: !admin,
+        disabled: readOnly,
         onClick: () => {
           ;(session as unknown as AbstractSessionModel).queueDialog(
             (doneCallback) => [

package/src/components/AddChildFeature.tsx

@@ -1,6 +1,9 @@
 /* eslint-disable @typescript-eslint/unbound-method */
 
-import type { AnnotationFeature } from '@apollo-annotation/mst'
+import type {
+  AnnotationFeature,
+  AnnotationFeatureSnapshot,
+} from '@apollo-annotation/mst'
 import { AddFeatureChange } from '@apollo-annotation/shared'
 import {
   Button,
@@ -65,17 +68,21 @@ export function AddChildFeature({
     event.preventDefault()
     setErrorMessage('')
     const _id = new ObjectID().toHexString()
+    const addedFeature: AnnotationFeatureSnapshot = {
+      _id,
+      refSeq: sourceFeature.refSeq,
+      min: Number(start) - 1,
+      max: Number(end),
+      type,
+    }
+    if (sourceFeature.strand) {
+      addedFeature.strand = sourceFeature.strand
+    }
     const change = new AddFeatureChange({
       changedIds: [sourceFeature._id],
       typeName: 'AddFeatureChange',
       assembly: sourceAssemblyId,
-      addedFeature: {
-        _id,
-        refSeq: sourceFeature.refSeq,
-        min: Number(start) - 1,
-        max: Number(end),
-        type,
-      },
+      addedFeature,
       parentFeatureId: sourceFeature._id,
     })
     void changeManager.submit(change).then(() => {

package/src/components/ColorFeature.tsx

@@ -0,0 +1,167 @@
+/* eslint-disable @typescript-eslint/unbound-method */
+
+import type { AnnotationFeature } from '@apollo-annotation/mst'
+import { FeatureAttributeChange } from '@apollo-annotation/shared'
+import { getSnapshot } from '@jbrowse/mobx-state-tree'
+import {
+  Button,
+  DialogActions,
+  DialogContent,
+  DialogContentText,
+} from '@mui/material'
+import React, { useState } from 'react'
+
+import type { ChangeManager } from '../ChangeManager'
+import type { ApolloSessionModel } from '../session'
+
+import { Dialog } from './Dialog'
+
+const PRESET_COLORS = [
+  '#cc79a7',
+  '#d65e00',
+  '#e69f00',
+  '#f0e442',
+  '#56b3e9',
+  '#0072b2',
+  '#009e73',
+] as const
+
+interface ColorFeatureProps {
+  session: ApolloSessionModel
+  handleClose(): void
+  sourceFeature: AnnotationFeature
+  sourceAssemblyId: string
+  changeManager: ChangeManager
+}
+
+export function ColorFeature({
+  changeManager,
+  handleClose,
+  sourceAssemblyId,
+  sourceFeature,
+}: ColorFeatureProps) {
+  const existingColor = sourceFeature.attributes.get('apollo_color')?.[0]
+  const [color, setColor] = useState<string>(existingColor ?? PRESET_COLORS[0])
+
+  async function onSubmit(event: React.FormEvent<HTMLFormElement>) {
+    event.preventDefault()
+    const currentColor = sourceFeature.attributes.get('apollo_color')?.[0]
+    if (currentColor === color) {
+      handleClose()
+      return
+    }
+    const oldAttributes = getSnapshot(sourceFeature.attributes)
+    const newAttributes = { ...oldAttributes, apollo_color: [color] }
+    const change = new FeatureAttributeChange({
+      changedIds: [sourceFeature._id],
+      typeName: 'FeatureAttributeChange',
+      assembly: sourceAssemblyId,
+      featureId: sourceFeature._id,
+      oldAttributes,
+      newAttributes,
+    })
+    await changeManager.submit(change)
+    handleClose()
+  }
+
+  async function onRemove() {
+    const oldAttributes = getSnapshot(sourceFeature.attributes)
+    const { apollo_color: _removed, ...newAttributes } = oldAttributes
+    const change = new FeatureAttributeChange({
+      changedIds: [sourceFeature._id],
+      typeName: 'FeatureAttributeChange',
+      assembly: sourceAssemblyId,
+      featureId: sourceFeature._id,
+      oldAttributes,
+      newAttributes,
+    })
+    await changeManager.submit(change)
+    handleClose()
+  }
+
+  return (
+    <Dialog
+      open
+      title="Color feature"
+      handleClose={handleClose}
+      maxWidth={false}
+      data-testid="color-feature"
+    >
+      <form
+        onSubmit={(event) => {
+          void onSubmit(event)
+        }}
+      >
+        <DialogContent style={{ display: 'flex', flexDirection: 'column' }}>
+          <DialogContentText>
+            Choose a color for this feature.
+          </DialogContentText>
+          <div style={{ display: 'flex', gap: 8, marginTop: 8 }}>
+            {PRESET_COLORS.map((preset) => {
+              const selected = color.toLowerCase() === preset
+              return (
+                <button
+                  key={preset}
+                  type="button"
+                  aria-label={preset}
+                  aria-pressed={selected}
+                  onClick={() => {
+                    setColor(preset)
+                  }}
+                  style={{
+                    width: 32,
+                    height: 32,
+                    padding: 0,
+                    borderRadius: 4,
+                    border: '1px solid rgba(0, 0, 0, 0.3)',
+                    outline: selected ? '2px solid currentColor' : 'none',
+                    outlineOffset: 2,
+                    backgroundColor: preset,
+                    cursor: 'pointer',
+                  }}
+                />
+              )
+            })}
+          </div>
+          <div
+            style={{
+              display: 'flex',
+              alignItems: 'center',
+              gap: 8,
+              marginTop: 16,
+            }}
+          >
+            <label htmlFor="color-feature-custom">Custom:</label>
+            <input
+              id="color-feature-custom"
+              type="color"
+              value={color}
+              onChange={(event) => {
+                setColor(event.target.value)
+              }}
+            />
+          </div>
+        </DialogContent>
+        <DialogActions>
+          <Button variant="contained" type="submit">
+            Submit
+          </Button>
+          <Button
+            variant="outlined"
+            color="error"
+            type="button"
+            disabled={existingColor === undefined}
+            onClick={() => {
+              void onRemove()
+            }}
+          >
+            Remove color
+          </Button>
+          <Button variant="outlined" type="button" onClick={handleClose}>
+            Cancel
+          </Button>
+        </DialogActions>
+      </form>
+    </Dialog>
+  )
+}

package/src/components/CreateApolloAnnotation.tsx

@@ -9,6 +9,7 @@ import {
   LocationStartChange,
 } from '@apollo-annotation/shared'
 import type { Assembly } from '@jbrowse/core/assemblyManager/assembly'
+import { readConfObject } from '@jbrowse/core/configuration'
 import type { AbstractSessionModel } from '@jbrowse/core/util'
 import { getSnapshot } from '@jbrowse/mobx-state-tree'
 import {
@@ -30,6 +31,7 @@ import ObjectID from 'bson-objectid'
 import React, { useEffect, useMemo, useState } from 'react'
 
 import type { ApolloSessionModel } from '../session'
+import { removeSkippedAttributes } from '../util'
 
 import { Dialog } from './Dialog'
 
@@ -162,6 +164,11 @@ export function CreateApolloAnnotation({
   region,
 }: CreateApolloAnnotationProps) {
   const apolloSessionModel = session as unknown as ApolloSessionModel
+  const configuredSkippedAttributes = readConfObject(
+    apolloSessionModel.getPluginConfiguration(),
+    'skippedAttributesOnCopy',
+  ) as string[] | undefined
+  const skippedAttributesOnCopy = new Set(configuredSkippedAttributes ?? [])
   const { featureTypeOntology } =
     apolloSessionModel.apolloDataStore.ontologyManager
   const childIds = useMemo(
@@ -340,23 +347,28 @@ export function CreateApolloAnnotation({
 
   // Copies gene feature along with its selected children
   const copyGeneFeature = async () => {
+    const copiedAnnotationFeature = {
+      ...annotationFeature,
+    } as AnnotationFeatureSnapshot
+    removeSkippedAttributes(copiedAnnotationFeature, skippedAttributesOnCopy)
+
     let change
     if (
-      annotationFeature.children &&
+      copiedAnnotationFeature.children &&
       checkedChildrens.length !==
-        Object.values(annotationFeature.children).length
+        Object.values(copiedAnnotationFeature.children).length
     ) {
       // IF SOME CHILDREN ARE CHECKED
       const childrens: Record<string, AnnotationFeatureSnapshot> = {}
       for (const childId of checkedChildrens) {
-        childrens[childId] = annotationFeature.children[childId]
+        childrens[childId] = copiedAnnotationFeature.children[childId]
       }
       change = new AddFeatureChange({
         changedIds: [annotationFeature._id],
         typeName: 'AddFeatureChange',
         assembly: assembly.name,
         addedFeature: {
-          ...annotationFeature,
+          ...copiedAnnotationFeature,
           children: childrens,
         },
       })
@@ -366,7 +378,7 @@ export function CreateApolloAnnotation({
         changedIds: [annotationFeature._id],
         typeName: 'AddFeatureChange',
         assembly: assembly.name,
-        addedFeature: annotationFeature,
+        addedFeature: copiedAnnotationFeature,
       })
     }
 
@@ -380,7 +392,10 @@ export function CreateApolloAnnotation({
       return
     }
     for (const transcriptId of Object.keys(transcripts)) {
-      const transcript = transcripts[transcriptId]
+      const transcript = {
+        ...transcripts[transcriptId],
+      } as AnnotationFeatureSnapshot
+      removeSkippedAttributes(transcript, skippedAttributesOnCopy)
       transcript.strand = selectedDestinationFeature.strand
 
       // update strand of transcript children if they exist
@@ -405,9 +420,20 @@ export function CreateApolloAnnotation({
   const createNewGeneFeatureWithTranscripts = async (
     childrens: Record<string, AnnotationFeatureSnapshot>,
   ) => {
+    const copiedChildrens: Record<string, AnnotationFeatureSnapshot> = {}
+    for (const [childId, child] of Object.entries(childrens)) {
+      const copiedChild = { ...child } as AnnotationFeatureSnapshot
+      removeSkippedAttributes(copiedChild, skippedAttributesOnCopy)
+      copiedChildrens[childId] = copiedChild
+    }
+
     const newGeneId = new ObjectID().toHexString()
-    const min = Math.min(...Object.values(childrens).map((child) => child.min))
-    const max = Math.max(...Object.values(childrens).map((child) => child.max))
+    const min = Math.min(
+      ...Object.values(copiedChildrens).map((child) => child.min),
+    )
+    const max = Math.max(
+      ...Object.values(copiedChildrens).map((child) => child.max),
+    )
     const change = new AddFeatureChange({
       changedIds: [newGeneId],
       typeName: 'AddFeatureChange',
@@ -419,7 +445,7 @@ export function CreateApolloAnnotation({
         max,
         strand: annotationFeature.strand,
         type: 'gene',
-        children: childrens,
+        children: copiedChildrens,
         attributes: {
           name: [getGeneNameOrId(annotationFeature)],
           gene_name: [getGeneNameOrId(annotationFeature)],