jbrowse-plugin-msaview 2.3.8 → 2.4.0

package/src/utils/taxonomyNames.ts

@@ -21,9 +21,16 @@ async function getDB() {
   })
 }
 
-async function getCachedCommonName(taxid: number) {
+async function getCachedTaxonomies(taxids: number[]) {
   const db = await getDB()
-  return db.get(STORE_NAME, taxid) as Promise<CachedTaxonomy | undefined>
+  const tx = db.transaction(STORE_NAME, 'readonly')
+  const results = await Promise.all(
+    taxids.map(
+      taxid => tx.store.get(taxid) as Promise<CachedTaxonomy | undefined>,
+    ),
+  )
+  await tx.done
+  return results
 }
 
 async function saveTaxonomyCache(entries: CachedTaxonomy[]) {
@@ -45,9 +52,11 @@ export async function fetchTaxonomyInfo(
 ): Promise<Map<number, TaxonomyInfo>> {
   const result = new Map<number, TaxonomyInfo>()
   const uncachedTaxids: number[] = []
+  const cachedResults = await getCachedTaxonomies(taxids)
 
-  for (const taxid of taxids) {
-    const cached = await getCachedCommonName(taxid)
+  for (let i = 0; i < taxids.length; i++) {
+    const taxid = taxids[i]!
+    const cached = cachedResults[i]
     if (cached) {
       result.set(taxid, {
         sciname: cached.sciname,

package/src/version.ts

@@ -1 +1 @@
-export const version = '2.3.8'
+export const version = '2.4.0'

package/dist/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.d.ts

@@ -1,8 +0,0 @@
-import React from 'react';
-import type { AbstractTrackModel, Feature } from '@jbrowse/core/util';
-declare const EnsemblGeneTree: ({ model, feature, handleClose, }: {
-    model: AbstractTrackModel;
-    feature: Feature;
-    handleClose: () => void;
-}) => React.JSX.Element;
-export default EnsemblGeneTree;

package/dist/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.js

@@ -1,70 +0,0 @@
-import React, { useState } from 'react';
-import { ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui';
-import { getContainingView, getSession } from '@jbrowse/core/util';
-import { Button, DialogActions, DialogContent, Link } from '@mui/material';
-import { observer } from 'mobx-react';
-import { makeStyles } from 'tss-react/mui';
-import { ensemblGeneTreeLaunchView } from './ensemblGeneTreeLaunchView';
-import { useGeneTree } from './useGeneTree';
-import { getGeneDisplayName } from '../../util';
-import TranscriptSelector from '../TranscriptSelector';
-import { useTranscriptSelection } from '../useTranscriptSelection';
-const useStyles = makeStyles()({
-    dialogContent: {
-        width: '80em',
-        display: 'flex',
-        flexDirection: 'column',
-        gap: 16,
-    },
-});
-const EnsemblGeneTree = observer(function ({ model, feature, handleClose, }) {
-    const session = getSession(model);
-    const view = getContainingView(model);
-    const { classes } = useStyles();
-    const [launchViewError, setLaunchViewError] = useState();
-    const { options, selectedId, setSelectedId, selectedTranscript, proteinSequence, error: featureSequenceError, } = useTranscriptSelection({ feature, view });
-    const { treeData, isTreeLoading, treeError } = useGeneTree(selectedId);
-    const loadingMessage = isTreeLoading
-        ? 'Loading tree data from Ensembl GeneTree'
-        : undefined;
-    const e = treeError ?? launchViewError ?? featureSequenceError;
-    return (React.createElement(React.Fragment, null,
-        React.createElement(DialogContent, { className: classes.dialogContent },
-            e ? React.createElement(ErrorMessage, { error: e }) : null,
-            loadingMessage ? React.createElement(LoadingEllipses, { message: loadingMessage }) : null,
-            treeData ? (React.createElement("div", null,
-                React.createElement("div", null,
-                    "Found Ensembl Compara GeneTree: ",
-                    treeData.geneTreeId),
-                React.createElement(Link, { target: "_blank", href: `https://useast.ensembl.org/Multi/GeneTree/Image?gt=${treeData.geneTreeId}` },
-                    "See ",
-                    treeData.geneTreeId,
-                    " at Ensembl"))) : null,
-            React.createElement(TranscriptSelector, { feature: feature, options: options, selectedId: selectedId, selectedTranscript: selectedTranscript, onTranscriptChange: setSelectedId, proteinSequence: proteinSequence })),
-        React.createElement(DialogActions, null,
-            React.createElement(Button, { color: "primary", variant: "contained", onClick: () => {
-                    try {
-                        if (!treeData) {
-                            return;
-                        }
-                        setLaunchViewError(undefined);
-                        ensemblGeneTreeLaunchView({
-                            feature,
-                            view,
-                            session,
-                            newViewTitle: getGeneDisplayName(feature),
-                            data: treeData,
-                        });
-                        handleClose();
-                    }
-                    catch (e) {
-                        console.error(e);
-                        setLaunchViewError(e);
-                    }
-                } }, "Submit"),
-            React.createElement(Button, { color: "secondary", variant: "contained", onClick: () => {
-                    handleClose();
-                } }, "Cancel"))));
-});
-export default EnsemblGeneTree;
-//# sourceMappingURL=EnsemblGeneTree.js.map

package/dist/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.js.map

@@ -1 +0,0 @@
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package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeLaunchView.d.ts

@@ -1,13 +0,0 @@
-import type { AbstractSessionModel, Feature } from '@jbrowse/core/util';
-import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-export declare function ensemblGeneTreeLaunchView({ session, newViewTitle, view, feature, data, }: {
-    session: AbstractSessionModel;
-    newViewTitle: string;
-    view: LinearGenomeViewModel;
-    feature: Feature;
-    data: {
-        tree: string;
-        msa: string;
-        treeMetadata: string;
-    };
-}): void;

package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeLaunchView.js

@@ -1,12 +0,0 @@
-export function ensemblGeneTreeLaunchView({ session, newViewTitle, view, feature, data, }) {
-    session.addView('MsaView', {
-        type: 'MsaView',
-        displayName: newViewTitle,
-        colWidth: 10,
-        rowHeight: 12,
-        data,
-        connectedViewId: view.id,
-        connectedFeature: feature.toJSON(),
-    });
-}
-//# sourceMappingURL=ensemblGeneTreeLaunchView.js.map

package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeLaunchView.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"ensemblGeneTreeLaunchView.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeLaunchView.ts"],"names":[],"mappings":"AAGA,MAAM,UAAU,yBAAyB,CAAC,EACxC,OAAO,EACP,YAAY,EACZ,IAAI,EACJ,OAAO,EACP,IAAI,GAWL;IACC,OAAO,CAAC,OAAO,CAAC,SAAS,EAAE;QACzB,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,YAAY;QACzB,QAAQ,EAAE,EAAE;QACZ,SAAS,EAAE,EAAE;QACb,IAAI;QACJ,eAAe,EAAE,IAAI,CAAC,EAAE;QACxB,gBAAgB,EAAE,OAAO,CAAC,MAAM,EAAE;KACnC,CAAC,CAAA;AACJ,CAAC"}

package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeUtils.d.ts

@@ -1,6 +0,0 @@
-export declare function geneTreeFetcher(id2: string): Promise<{
-    geneTreeId: string;
-    tree: string;
-    msa: string;
-    treeMetadata: string;
-}>;

package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeUtils.js

@@ -1,25 +0,0 @@
-import { gatherSequencesFromTree } from './gatherSequencesFromTree';
-import { fetchWithLocalStorageCache, jsonfetch, textfetch } from './util';
-const base = 'https://rest.ensembl.org';
-export async function geneTreeFetcher(id2) {
-    const id = id2.replace(/\..*/, '');
-    const { species } = await fetchWithLocalStorageCache(`${id}-ensembl`, () => jsonfetch(`${base}/lookup/id/${id}?content-type=application/json`));
-    const treeBase = `${base}/genetree/member/id/${species}/${id}`;
-    const geneTreeResult = await fetchWithLocalStorageCache(`${id}-msa`, () => jsonfetch(`${treeBase}?content-type=application/json;aligned=1;sequence=pep`));
-    // we query again to get newick format tree. could probably extract from json
-    // as alternative
-    const tree = await fetchWithLocalStorageCache(`${id}-tree`, () => textfetch(`${treeBase}?nh_format=simple;content-type=text/x-nh`));
-    const res = gatherSequencesFromTree(geneTreeResult.tree);
-    return {
-        geneTreeId: geneTreeResult.id,
-        tree,
-        msa: res.map(r => `>${r.id}\n${r.seq}`).join('\n'),
-        treeMetadata: JSON.stringify(Object.fromEntries(res.map(r => [
-            r.id,
-            {
-                genome: r.species,
-            },
-        ]))),
-    };
-}
-//# sourceMappingURL=ensemblGeneTreeUtils.js.map

package/dist/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeUtils.js.map

@@ -1 +0,0 @@
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package/dist/LaunchMsaView/components/EnsemblGeneTree/gatherSequencesFromTree.d.ts

@@ -1,2 +0,0 @@
-import type { TreeNode, TreeRow } from './types';
-export declare function gatherSequencesFromTree(tree: TreeNode, arr?: TreeRow[]): TreeRow[];

package/dist/LaunchMsaView/components/EnsemblGeneTree/gatherSequencesFromTree.js

@@ -1,20 +0,0 @@
-export function gatherSequencesFromTree(tree, arr = []) {
-    if (tree.children) {
-        for (const child of tree.children) {
-            if (child.sequence) {
-                const id = child.sequence.id[0]?.accession;
-                if (id) {
-                    arr.push({
-                        id,
-                        seq: child.sequence.mol_seq.seq,
-                        species: child.taxonomy.common_name || child.taxonomy.scientific_name,
-                        genomicLocString: child.sequence.mol_seq.location,
-                    });
-                }
-            }
-            gatherSequencesFromTree(child, arr);
-        }
-    }
-    return arr;
-}
-//# sourceMappingURL=gatherSequencesFromTree.js.map

package/dist/LaunchMsaView/components/EnsemblGeneTree/gatherSequencesFromTree.js.map

@@ -1 +0,0 @@
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package/dist/LaunchMsaView/components/EnsemblGeneTree/types.d.ts

@@ -1,24 +0,0 @@
-export interface TreeNodeSequence {
-    mol_seq: {
-        seq: string;
-        location?: string;
-    };
-    id: {
-        accession: string;
-    }[];
-}
-export interface TreeNodeTaxonomy {
-    common_name: string;
-    scientific_name: string;
-}
-export interface TreeNode {
-    children?: TreeNode[];
-    sequence?: TreeNodeSequence;
-    taxonomy: TreeNodeTaxonomy;
-}
-export interface TreeRow {
-    id: string;
-    seq: string;
-    species: string;
-    genomicLocString?: string;
-}

package/dist/LaunchMsaView/components/EnsemblGeneTree/types.js

@@ -1,2 +0,0 @@
-export {};
-//# sourceMappingURL=types.js.map

package/dist/LaunchMsaView/components/EnsemblGeneTree/types.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"types.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/EnsemblGeneTree/types.ts"],"names":[],"mappings":""}

package/dist/LaunchMsaView/components/EnsemblGeneTree/useGeneTree.d.ts

@@ -1,10 +0,0 @@
-export declare function useGeneTree(geneId: string): {
-    treeData: {
-        geneTreeId: string;
-        tree: string;
-        msa: string;
-        treeMetadata: string;
-    } | undefined;
-    isTreeLoading: boolean;
-    treeError: any;
-};

package/dist/LaunchMsaView/components/EnsemblGeneTree/useGeneTree.js

@@ -1,11 +0,0 @@
-import useSWR from 'swr';
-import { geneTreeFetcher } from './ensemblGeneTreeUtils';
-export function useGeneTree(geneId) {
-    const { data, error, isLoading } = useSWR(() => (geneId ? ['geneTree', geneId] : null), ([, geneId]) => geneTreeFetcher(geneId), {
-        revalidateOnFocus: false,
-        revalidateOnReconnect: false,
-        revalidateIfStale: false,
-    });
-    return { treeData: data, isTreeLoading: isLoading, treeError: error };
-}
-//# sourceMappingURL=useGeneTree.js.map

package/dist/LaunchMsaView/components/EnsemblGeneTree/useGeneTree.js.map

@@ -1 +0,0 @@
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package/dist/LaunchMsaView/components/EnsemblGeneTree/util.d.ts

@@ -1 +0,0 @@
-export { fetchWithLocalStorageCache, jsonfetch, textfetch, unzipfetch, } from '../../../utils/fetch';

package/dist/LaunchMsaView/components/EnsemblGeneTree/util.js

@@ -1,2 +0,0 @@
-export { fetchWithLocalStorageCache, jsonfetch, textfetch, unzipfetch, } from '../../../utils/fetch';
-//# sourceMappingURL=util.js.map

package/dist/LaunchMsaView/components/EnsemblGeneTree/util.js.map

@@ -1 +0,0 @@
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package/src/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.tsx

@@ -1,123 +0,0 @@
-import React, { useState } from 'react'
-
-import { ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui'
-import { getContainingView, getSession } from '@jbrowse/core/util'
-import { Button, DialogActions, DialogContent, Link } from '@mui/material'
-import { observer } from 'mobx-react'
-import { makeStyles } from 'tss-react/mui'
-
-import { ensemblGeneTreeLaunchView } from './ensemblGeneTreeLaunchView'
-import { useGeneTree } from './useGeneTree'
-import { getGeneDisplayName } from '../../util'
-import TranscriptSelector from '../TranscriptSelector'
-import { useTranscriptSelection } from '../useTranscriptSelection'
-
-import type { AbstractTrackModel, Feature } from '@jbrowse/core/util'
-import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
-
-const useStyles = makeStyles()({
-  dialogContent: {
-    width: '80em',
-    display: 'flex',
-    flexDirection: 'column',
-    gap: 16,
-  },
-})
-
-const EnsemblGeneTree = observer(function ({
-  model,
-  feature,
-  handleClose,
-}: {
-  model: AbstractTrackModel
-  feature: Feature
-  handleClose: () => void
-}) {
-  const session = getSession(model)
-  const view = getContainingView(model) as LinearGenomeViewModel
-  const { classes } = useStyles()
-  const [launchViewError, setLaunchViewError] = useState<unknown>()
-  const {
-    options,
-    selectedId,
-    setSelectedId,
-    selectedTranscript,
-    proteinSequence,
-    error: featureSequenceError,
-  } = useTranscriptSelection({ feature, view })
-  const { treeData, isTreeLoading, treeError } = useGeneTree(selectedId)
-
-  const loadingMessage = isTreeLoading
-    ? 'Loading tree data from Ensembl GeneTree'
-    : undefined
-  const e = treeError ?? launchViewError ?? featureSequenceError
-
-  return (
-    <>
-      <DialogContent className={classes.dialogContent}>
-        {e ? <ErrorMessage error={e} /> : null}
-        {loadingMessage ? <LoadingEllipses message={loadingMessage} /> : null}
-        {treeData ? (
-          <div>
-            <div>Found Ensembl Compara GeneTree: {treeData.geneTreeId}</div>
-            <Link
-              target="_blank"
-              href={`https://useast.ensembl.org/Multi/GeneTree/Image?gt=${treeData.geneTreeId}`}
-            >
-              See {treeData.geneTreeId} at Ensembl
-            </Link>
-          </div>
-        ) : null}
-
-        <TranscriptSelector
-          feature={feature}
-          options={options}
-          selectedId={selectedId}
-          selectedTranscript={selectedTranscript}
-          onTranscriptChange={setSelectedId}
-          proteinSequence={proteinSequence}
-        />
-      </DialogContent>
-
-      <DialogActions>
-        <Button
-          color="primary"
-          variant="contained"
-          onClick={() => {
-            try {
-              if (!treeData) {
-                return
-              }
-              setLaunchViewError(undefined)
-
-              ensemblGeneTreeLaunchView({
-                feature,
-                view,
-                session,
-                newViewTitle: getGeneDisplayName(feature),
-                data: treeData,
-              })
-              handleClose()
-            } catch (e) {
-              console.error(e)
-              setLaunchViewError(e)
-            }
-          }}
-        >
-          Submit
-        </Button>
-        <Button
-          color="secondary"
-          variant="contained"
-          onClick={() => {
-            handleClose()
-          }}
-        >
-          Cancel
-        </Button>
-      </DialogActions>
-    </>
-  )
-})
-
-export default EnsemblGeneTree

package/src/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeLaunchView.ts

@@ -1,30 +0,0 @@
-import type { AbstractSessionModel, Feature } from '@jbrowse/core/util'
-import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
-
-export function ensemblGeneTreeLaunchView({
-  session,
-  newViewTitle,
-  view,
-  feature,
-  data,
-}: {
-  session: AbstractSessionModel
-  newViewTitle: string
-  view: LinearGenomeViewModel
-  feature: Feature
-  data: {
-    tree: string
-    msa: string
-    treeMetadata: string
-  }
-}) {
-  session.addView('MsaView', {
-    type: 'MsaView',
-    displayName: newViewTitle,
-    colWidth: 10,
-    rowHeight: 12,
-    data,
-    connectedViewId: view.id,
-    connectedFeature: feature.toJSON(),
-  })
-}

package/src/LaunchMsaView/components/EnsemblGeneTree/ensemblGeneTreeUtils.ts

@@ -1,47 +0,0 @@
-import { gatherSequencesFromTree } from './gatherSequencesFromTree'
-import { fetchWithLocalStorageCache, jsonfetch, textfetch } from './util'
-
-import type { TreeNode } from './types'
-
-const base = 'https://rest.ensembl.org'
-
-export async function geneTreeFetcher(id2: string) {
-  const id = id2.replace(/\..*/, '')
-  const { species } = await fetchWithLocalStorageCache(`${id}-ensembl`, () =>
-    jsonfetch<{ species: string }>(
-      `${base}/lookup/id/${id}?content-type=application/json`,
-    ),
-  )
-  const treeBase = `${base}/genetree/member/id/${species}/${id}`
-  const geneTreeResult = await fetchWithLocalStorageCache(`${id}-msa`, () =>
-    jsonfetch<{ tree: TreeNode; id: string }>(
-      `${treeBase}?content-type=application/json;aligned=1;sequence=pep`,
-    ),
-  )
-
-  // we query again to get newick format tree. could probably extract from json
-  // as alternative
-  const tree = await fetchWithLocalStorageCache<string>(`${id}-tree`, () =>
-    textfetch(`${treeBase}?nh_format=simple;content-type=text/x-nh`),
-  )
-
-  const res = gatherSequencesFromTree(geneTreeResult.tree)
-  return {
-    geneTreeId: geneTreeResult.id,
-    tree,
-    msa: res.map(r => `>${r.id}\n${r.seq}`).join('\n'),
-    treeMetadata: JSON.stringify(
-      Object.fromEntries(
-        res.map(
-          r =>
-            [
-              r.id,
-              {
-                genome: r.species,
-              },
-            ] as const,
-        ),
-      ),
-    ),
-  }
-}

package/src/LaunchMsaView/components/EnsemblGeneTree/gatherSequencesFromTree.ts

@@ -1,22 +0,0 @@
-import type { TreeNode, TreeRow } from './types'
-
-export function gatherSequencesFromTree(tree: TreeNode, arr: TreeRow[] = []) {
-  if (tree.children) {
-    for (const child of tree.children) {
-      if (child.sequence) {
-        const id = child.sequence.id[0]?.accession
-        if (id) {
-          arr.push({
-            id,
-            seq: child.sequence.mol_seq.seq,
-            species:
-              child.taxonomy.common_name || child.taxonomy.scientific_name,
-            genomicLocString: child.sequence.mol_seq.location,
-          })
-        }
-      }
-      gatherSequencesFromTree(child, arr)
-    }
-  }
-  return arr
-}

package/src/LaunchMsaView/components/EnsemblGeneTree/types.ts

@@ -1,28 +0,0 @@
-export interface TreeNodeSequence {
-  mol_seq: {
-    seq: string
-    location?: string
-  }
-  id: {
-    accession: string
-  }[]
-}
-
-export interface TreeNodeTaxonomy {
-  common_name: string
-  scientific_name: string
-}
-
-// This is a self-referential tree data structure
-export interface TreeNode {
-  children?: TreeNode[]
-  sequence?: TreeNodeSequence
-  taxonomy: TreeNodeTaxonomy
-}
-
-export interface TreeRow {
-  id: string
-  seq: string
-  species: string
-  genomicLocString?: string
-}

package/src/LaunchMsaView/components/EnsemblGeneTree/useGeneTree.ts

@@ -1,17 +0,0 @@
-import useSWR from 'swr'
-
-import { geneTreeFetcher } from './ensemblGeneTreeUtils'
-
-export function useGeneTree(geneId: string) {
-  const { data, error, isLoading } = useSWR(
-    () => (geneId ? ['geneTree', geneId] : null),
-    ([, geneId]) => geneTreeFetcher(geneId),
-    {
-      revalidateOnFocus: false,
-      revalidateOnReconnect: false,
-      revalidateIfStale: false,
-    },
-  )
-
-  return { treeData: data, isTreeLoading: isLoading, treeError: error }
-}

package/src/LaunchMsaView/components/EnsemblGeneTree/util.ts

@@ -1,6 +0,0 @@
-export {
-  fetchWithLocalStorageCache,
-  jsonfetch,
-  textfetch,
-  unzipfetch,
-} from '../../../utils/fetch'