@apollo-annotation/jbrowse-plugin-apollo 0.3.6 → 0.3.7

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@apollo-annotation/jbrowse-plugin-apollo",
-  "version": "0.3.6",
+  "version": "0.3.7",
   "description": "Apollo plugin for JBrowse 2",
   "keywords": [
     "jbrowse",
@@ -48,9 +48,9 @@
     }
   },
   "dependencies": {
-    "@apollo-annotation/common": "^0.3.6",
-    "@apollo-annotation/mst": "^0.3.6",
-    "@apollo-annotation/shared": "^0.3.6",
+    "@apollo-annotation/common": "^0.3.7",
+    "@apollo-annotation/mst": "^0.3.7",
+    "@apollo-annotation/shared": "^0.3.7",
     "@emotion/react": "^11.10.6",
     "@emotion/styled": "^11.10.6",
     "@gmod/gff": "1.2.0",

package/src/ApolloInternetAccount/addMenuItems.ts

@@ -10,6 +10,7 @@ import {
   ImportFeatures,
   ManageUsers,
 } from '../components'
+import { AddAssemblyAliases } from '../components/AddAssemblyAliases'
 import { type ApolloSessionModel } from '../session'
 
 export function addMenuItems(rootModel: AbstractMenuManager) {
@@ -81,6 +82,23 @@ export function addMenuItems(rootModel: AbstractMenuManager) {
       )
     },
   })
+  rootModel.appendToMenu('Apollo', {
+    label: 'Add Assembly aliases',
+    onClick: (session: ApolloSessionModel) => {
+      ;(session as unknown as AbstractSessionModel).queueDialog(
+        (doneCallback) => [
+          AddAssemblyAliases,
+          {
+            session,
+            handleClose: () => {
+              doneCallback()
+            },
+            changeManager: session.apolloDataStore.changeManager,
+          },
+        ],
+      )
+    },
+  })
   rootModel.appendToMenu('Apollo', {
     label: 'Manage Users',
     onClick: (session: ApolloSessionModel) => {

package/src/ChangeManager.ts

@@ -76,7 +76,10 @@ export class ChangeManager {
         jobsManager.abortJob(job.name, String(error))
       }
       console.error(error)
-      session.notify(String(error), 'error')
+      session.notify(
+        `Error encountered in client: ${String(error)}. Data may be out of sync, please refresh the page`,
+        'error',
+      )
       return
     }
 
@@ -123,10 +126,10 @@ export class ChangeManager {
       if (change.notification) {
         session.notify(change.notification, 'success')
       }
-    }
-    if (addToRecents) {
-      // Push the change into array
-      this.recentChanges.push(change)
+      if (addToRecents) {
+        // Push the change into array
+        this.recentChanges.push(change)
+      }
     }
 
     if (updateJobsManager) {
@@ -136,7 +139,8 @@ export class ChangeManager {
 
   async revert(change: Change, submitToBackend = true) {
     const inverseChange = change.getInverse()
-    return this.submit(inverseChange, { submitToBackend, addToRecents: false })
+    const opts = { submitToBackend, addToRecents: false }
+    return this.submit(inverseChange, opts)
   }
 
   /**

package/src/FeatureDetailsWidget/Attributes.tsx

@@ -105,13 +105,15 @@ export const Attributes = observer(function Attributes({
       typeName: 'FeatureAttributeChange',
       assembly,
       featureId: _id,
-      attributes: remainingAttributes,
+      oldAttributes: attributesSerialized,
+      newAttributes: remainingAttributes,
     })
     void changeManager.submit(change)
   }
 
   function modifyFeatureAttribute(key: string, attribute: string[]) {
     const serializedAttributes = { ...getSnapshot(attributes) }
+    const oldAttributes = structuredClone(serializedAttributes)
     if (!(key in serializedAttributes)) {
       notify(`"${key}" not found in feature attributes`, 'error')
       return
@@ -127,13 +129,15 @@ export const Attributes = observer(function Attributes({
       typeName: 'FeatureAttributeChange',
       assembly,
       featureId: feature._id,
-      attributes: serializedAttributes,
+      oldAttributes,
+      newAttributes: serializedAttributes,
     })
     void changeManager.submit(change)
   }
 
   function addFeatureAttribute(key: string, attribute: string[]) {
     const serializedAttributes = { ...getSnapshot(attributes) }
+    const oldAttributes = structuredClone(serializedAttributes)
     if (key in serializedAttributes) {
       notify(`Feature already has attribute "${key}"`, 'error')
       return
@@ -145,7 +149,8 @@ export const Attributes = observer(function Attributes({
       typeName: 'FeatureAttributeChange',
       assembly,
       featureId: feature._id,
-      attributes: serializedAttributes,
+      oldAttributes,
+      newAttributes: serializedAttributes,
     })
     void changeManager.submit(change)
   }

package/src/FeatureDetailsWidget/TranscriptSequence.tsx

@@ -13,6 +13,7 @@ import { observer } from 'mobx-react'
 import React, { useEffect, useRef, useState } from 'react'
 
 import { type ApolloSessionModel } from '../session'
+import { copyToClipboard } from '../util/copyToClipboard'
 
 const SEQUENCE_WRAP_LENGTH = 60
 
@@ -112,13 +113,12 @@ function getSequenceSegments(
       const [firstLocation] = cdsLocations
       const locs: { min: number; max: number }[] = []
       for (const loc of firstLocation) {
-        let sequence = getSequence(loc.min, loc.max)
-        if (strand === -1) {
-          sequence = revcom(sequence)
-        }
-        wholeSequence += sequence
+        wholeSequence += getSequence(loc.min, loc.max)
         locs.push({ min: loc.min, max: loc.max })
       }
+      if (strand === -1) {
+        wholeSequence = revcom(wholeSequence)
+      }
       const sequenceLines = splitStringIntoChunks(
         wholeSequence,
         SEQUENCE_WRAP_LENGTH,
@@ -131,13 +131,12 @@ function getSequenceSegments(
       const [firstLocation] = cdsLocations
       const locs: { min: number; max: number }[] = []
       for (const loc of firstLocation) {
-        let sequence = getSequence(loc.min, loc.max)
-        if (strand === -1) {
-          sequence = revcom(sequence)
-        }
-        wholeSequence += sequence
+        wholeSequence += getSequence(loc.min, loc.max)
         locs.push({ min: loc.min, max: loc.max })
       }
+      if (strand === -1) {
+        wholeSequence = revcom(wholeSequence)
+      }
       let protein = ''
       for (let i = 0; i < wholeSequence.length; i += 3) {
         const codonSeq: string = wholeSequence.slice(i, i + 3).toUpperCase()
@@ -275,19 +274,12 @@ export const TranscriptSequence = observer(function TranscriptSequence({
     setLocationIntervals(locIntervals)
   }
 
-  // Function to copy text to clipboard
-  const copyToClipboard = () => {
+  const onCopyClick = () => {
     const seqDiv = seqRef.current
     if (!seqDiv) {
       return
     }
-    const textBlob = new Blob([seqDiv.outerText], { type: 'text/plain' })
-    const htmlBlob = new Blob([seqDiv.outerHTML], { type: 'text/html' })
-    const clipboardItem = new ClipboardItem({
-      [textBlob.type]: textBlob,
-      [htmlBlob.type]: htmlBlob,
-    })
-    void navigator.clipboard.write([clipboardItem])
+    void copyToClipboard(seqDiv)
   }
 
   return (
@@ -306,7 +298,7 @@ export const TranscriptSequence = observer(function TranscriptSequence({
       </Select>
       <Button
         variant="contained"
-        onClick={copyToClipboard}
+        onClick={onCopyClick}
         style={{ marginLeft: 10 }}
         size="medium"
       >