@jbrowse/plugin-data-management 1.7.11 → 2.1.0

package/esm/ucsc-trackhub/ucscTrackHub.js

@@ -0,0 +1,348 @@
+import { objectHash } from '@jbrowse/core/util';
+import { openLocation } from '@jbrowse/core/util/io';
+import { generateUnsupportedTrackConf, generateUnknownTrackConf, } from '@jbrowse/core/util/tracks';
+import ucscAssemblies from './ucscAssemblies';
+export { ucscAssemblies };
+export async function fetchHubFile(hubFileLocation) {
+    try {
+        const hubFileText = await openLocation(hubFileLocation).readFile('utf8');
+        const { HubFile } = await import('@gmod/ucsc-hub');
+        return new HubFile(hubFileText);
+    }
+    catch (error) {
+        throw new Error(`Not a valid hub.txt file, got error: '${error}'`);
+    }
+}
+export async function fetchGenomesFile(genomesFileLocation) {
+    const genomesFileText = await openLocation(genomesFileLocation).readFile('utf8');
+    const { GenomesFile } = await import('@gmod/ucsc-hub');
+    return new GenomesFile(genomesFileText);
+}
+export async function fetchTrackDbFile(trackDbFileLocation) {
+    const text = await openLocation(trackDbFileLocation).readFile('utf8');
+    const { TrackDbFile } = await import('@gmod/ucsc-hub');
+    return new TrackDbFile(text);
+}
+export function generateTracks(trackDb, trackDbFileLocation, assemblyName, sequenceAdapter) {
+    const tracks = [];
+    trackDb.forEach((track, trackName) => {
+        const trackKeys = Array.from(track.keys());
+        const parentTrackKeys = [
+            'superTrack',
+            'compositeTrack',
+            'container',
+            'view',
+        ];
+        if (trackKeys.some(key => parentTrackKeys.includes(key))) {
+            return;
+        }
+        const parentTracks = [];
+        let currentTrackName = trackName;
+        do {
+            currentTrackName = trackDb.get(currentTrackName).get('parent');
+            if (currentTrackName) {
+                ;
+                [currentTrackName] = currentTrackName.split(' ');
+                parentTracks.push(trackDb.get(currentTrackName));
+            }
+        } while (currentTrackName);
+        parentTracks.reverse();
+        const categories = parentTracks.map(parentTrack => parentTrack.get('shortLabel'));
+        const res = makeTrackConfig(track, categories, trackDbFileLocation, trackDb, sequenceAdapter);
+        res.trackId = `ucsc-trackhub-${objectHash(res)}`;
+        res.assemblyNames = [assemblyName];
+        tracks.push(res);
+    });
+    return tracks;
+}
+function makeTrackConfig(track, categories, trackDbFileLocation, trackDb, sequenceAdapter) {
+    let trackType = track.get('type');
+    if (!trackType) {
+        trackType = trackDb.get(track.get('parent')).get('type');
+    }
+    let baseTrackType = trackType.split(' ')[0];
+    if (baseTrackType === 'bam' &&
+        track.get('bigDataUrl').toLowerCase().endsWith('cram')) {
+        baseTrackType = 'cram';
+    }
+    let bigDataLocation;
+    if (trackDbFileLocation.uri) {
+        bigDataLocation = {
+            uri: new URL(track.get('bigDataUrl'), trackDbFileLocation.uri).href,
+            locationType: 'UriLocation',
+        };
+    }
+    else {
+        bigDataLocation = {
+            localPath: track.get('bigDataUrl'),
+            locationType: 'LocalPathLocation',
+        };
+    }
+    let bigDataIndexLocation;
+    switch (baseTrackType) {
+        case 'bam':
+            if (trackDbFileLocation.uri) {
+                bigDataIndexLocation = track.get('bigDataIndex')
+                    ? {
+                        uri: new URL(track.get('bigDataIndex'), trackDbFileLocation.uri)
+                            .href,
+                        locationType: 'UriLocation',
+                    }
+                    : {
+                        uri: new URL(`${track.get('bigDataUrl')}.bai`, trackDbFileLocation.uri).href,
+                        locationType: 'UriLocation',
+                    };
+            }
+            else {
+                bigDataIndexLocation = track.get('bigDataIndex')
+                    ? {
+                        localPath: track.get('bigDataIndex'),
+                        locationType: 'LocalPathLocation',
+                    }
+                    : {
+                        localPath: `${track.get('bigDataUrl')}.bai`,
+                        locationType: 'LocalPathLocation',
+                    };
+            }
+            return {
+                type: 'AlignmentsTrack',
+                name: track.get('shortLabel'),
+                description: track.get('longLabel'),
+                category: categories,
+                adapter: {
+                    type: 'BamAdapter',
+                    bamLocation: bigDataLocation,
+                    index: {
+                        location: bigDataIndexLocation,
+                    },
+                },
+            };
+        case 'bed':
+            return generateUnsupportedTrackConf(track.get('shortLabel'), baseTrackType, categories);
+        case 'bed5FloatScore':
+            return generateUnsupportedTrackConf(track.get('shortLabel'), baseTrackType, categories);
+        case 'bedGraph':
+            return generateUnsupportedTrackConf(track.get('shortLabel'), baseTrackType, categories);
+        case 'bedRnaElements':
+            return generateUnsupportedTrackConf(track.get('shortLabel'), baseTrackType, categories);
+        case 'bigBarChart':
+            return {
+                type: 'FeatureTrack',
+                name: track.get('shortLabel'),
+                description: track.get('longLabel'),
+                category: categories,
+                adapter: {
+                    type: 'BigBedAdapter',
+                    bigBedLocation: bigDataLocation,
+                },
+                renderer: {
+                    type: 'SvgFeatureRenderer',
+                },
+            };
+        case 'bigBed':
+            return {
+                type: 'FeatureTrack',
+                name: track.get('shortLabel'),
+                description: track.get('longLabel'),
+                category: categories,
+                adapter: {
+                    type: 'BigBedAdapter',
+                    bigBedLocation: bigDataLocation,
+                },
+            };
+        case 'bigGenePred':
+            return {
+                type: 'FeatureTrack',
+                name: track.get('shortLabel'),
+                description: track.get('longLabel'),
+                category: categories,
+                adapter: {
+                    type: 'BigBedAdapter',
+                    bigBedLocation: bigDataLocation,
+                },
+            };
+        case 'bigChain':
+            return {
+                type: 'FeatureTrack',
+                name: track.get('shortLabel'),
+                description: track.get('longLabel'),
+                category: categories,
+                adapter: {
+                    type: 'BigBedAdapter',
+                    bigBedLocation: bigDataLocation,
+                },
+                renderer: {
+                    type: 'SvgFeatureRenderer',
+                },
+            };
+        case 'bigInteract':
+            return {
+                type: 'FeatureTrack',
+                name: track.get('shortLabel'),
+                description: track.get('longLabel'),
+                category: categories,
+                adapter: {
+                    type: 'BigBedAdapter',
+                    bigBedLocation: bigDataLocation,
+                },
+                renderer: {
+                    type: 'SvgFeatureRenderer',
+                },
+            };
+        case 'bigMaf':
+            return {
+                type: 'FeatureTrack',
+                name: track.get('shortLabel'),
+                description: track.get('longLabel'),
+                category: categories,
+                adapter: {
+                    type: 'BigBedAdapter',
+                    bigBedLocation: bigDataLocation,
+                },
+                renderer: {
+                    type: 'SvgFeatureRenderer',
+                },
+            };
+        case 'bigPsl':
+            return {
+                type: 'FeatureTrack',
+                name: track.get('shortLabel'),
+                description: track.get('longLabel'),
+                category: categories,
+                adapter: {
+                    type: 'BigBedAdapter',
+                    bigBedLocation: bigDataLocation,
+                },
+                renderer: {
+                    type: 'SvgFeatureRenderer',
+                },
+            };
+        case 'bigWig':
+            return {
+                type: 'QuantitativeTrack',
+                name: track.get('shortLabel'),
+                description: track.get('longLabel'),
+                category: categories,
+                adapter: {
+                    type: 'BigWigAdapter',
+                    bigWigLocation: bigDataLocation,
+                },
+            };
+        case 'broadPeak':
+            return generateUnsupportedTrackConf(track.get('shortLabel'), baseTrackType, categories);
+        case 'coloredExon':
+            return generateUnsupportedTrackConf(track.get('shortLabel'), baseTrackType, categories);
+        case 'cram':
+            if (trackDbFileLocation.uri) {
+                bigDataIndexLocation = track.get('bigDataIndex')
+                    ? {
+                        uri: new URL(track.get('bigDataIndex'), trackDbFileLocation.uri)
+                            .href,
+                        locationType: 'UriLocation',
+                    }
+                    : {
+                        uri: new URL(`${track.get('bigDataUrl')}.crai`, trackDbFileLocation.uri).href,
+                        locationType: 'UriLocation',
+                    };
+            }
+            else {
+                bigDataIndexLocation = track.get('bigDataIndex')
+                    ? {
+                        localPath: track.get('bigDataIndex'),
+                        locationType: 'LocalPathLocation',
+                    }
+                    : {
+                        localPath: `${track.get('bigDataUrl')}.crai`,
+                        locationType: 'LocalPathLocation',
+                    };
+            }
+            return {
+                type: 'AlignmentsTrack',
+                name: track.get('shortLabel'),
+                description: track.get('longLabel'),
+                category: categories,
+                adapter: {
+                    type: 'CramAdapter',
+                    cramLocation: bigDataLocation,
+                    craiLocation: bigDataIndexLocation,
+                    sequenceAdapter,
+                },
+            };
+        case 'gvf':
+            return generateUnsupportedTrackConf(track.get('shortLabel'), baseTrackType, categories);
+        case 'ld2':
+            return generateUnsupportedTrackConf(track.get('shortLabel'), baseTrackType, categories);
+        case 'narrowPeak':
+            return generateUnsupportedTrackConf(track.get('shortLabel'), baseTrackType, categories);
+        case 'bigNarrowPeak':
+            return {
+                type: 'FeatureTrack',
+                name: track.get('shortLabel'),
+                description: track.get('longLabel'),
+                category: categories,
+                adapter: {
+                    type: 'BigBedAdapter',
+                    bigBedLocation: bigDataLocation,
+                },
+            };
+        case 'peptideMapping':
+            return generateUnsupportedTrackConf(track.get('shortLabel'), baseTrackType, categories);
+        case 'vcfTabix':
+            if (trackDbFileLocation.uri) {
+                bigDataIndexLocation = track.get('bigDataIndex')
+                    ? {
+                        uri: new URL(track.get('bigDataIndex'), trackDbFileLocation.uri)
+                            .href,
+                        locationType: 'UriLocation',
+                    }
+                    : {
+                        uri: new URL(`${track.get('bigDataUrl')}.tbi`, trackDbFileLocation.uri).href,
+                        locationType: 'UriLocation',
+                    };
+            }
+            else {
+                bigDataIndexLocation = track.get('bigDataIndex')
+                    ? {
+                        localPath: track.get('bigDataIndex'),
+                        locationType: 'LocalPathLocation',
+                    }
+                    : {
+                        localPath: `${track.get('bigDataUrl')}.tbi`,
+                        locationType: 'LocalPathLocation',
+                    };
+            }
+            return {
+                type: 'VariantTrack',
+                name: track.get('shortLabel'),
+                description: track.get('longLabel'),
+                category: categories,
+                adapter: {
+                    type: 'VcfTabixAdapter',
+                    vcfGzLocation: bigDataLocation,
+                    index: {
+                        location: bigDataIndexLocation,
+                    },
+                },
+            };
+        case 'wig':
+            return generateUnsupportedTrackConf(track.get('shortLabel'), baseTrackType, categories);
+        case 'wigMaf':
+            return generateUnsupportedTrackConf(track.get('shortLabel'), baseTrackType, categories);
+        case 'hic':
+            return {
+                type: 'HicTrack',
+                name: track.get('shortLabel'),
+                description: track.get('longLabel'),
+                category: categories,
+                adapter: {
+                    type: 'HicAdapter',
+                    hicLocation: bigDataLocation,
+                },
+            };
+        case 'halSnake':
+            return generateUnsupportedTrackConf(track.get('shortLabel'), baseTrackType, categories);
+        default:
+            return generateUnknownTrackConf(track.get('shortLabel'), baseTrackType, categories);
+    }
+}
+//# sourceMappingURL=ucscTrackHub.js.map

package/esm/ucsc-trackhub/ucscTrackHub.js.map

@@ -0,0 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-data-management",
-  "version": "1.7.11",
+  "version": "2.1.0",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
     "jbrowse",
@@ -20,39 +20,47 @@
   "main": "dist/index.js",
   "files": [
     "dist",
-    "src"
+    "src",
+    "esm"
   ],
   "scripts": {
-    "build": "babel src --root-mode upward --out-dir dist --extensions .ts,.js,.tsx,.jsx",
+    "build": "npm-run-all build:*",
     "test": "cd ../..; jest plugins/data-management",
     "prepublishOnly": "yarn test",
     "prepack": "yarn build; yarn useDist",
     "postpack": "yarn useSrc",
     "useDist": "node ../../scripts/useDist.js",
     "useSrc": "node ../../scripts/useSrc.js",
-    "postbuild": "tsc --build tsconfig.build.json"
+    "prebuild": "npm run clean",
+    "build:esm": "tsc --build tsconfig.build.esm.json",
+    "build:es5": "tsc --build tsconfig.build.es5.json",
+    "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
     "@babel/runtime": "^7.17.9",
     "@gmod/ucsc-hub": "^0.1.3",
-    "@material-ui/icons": "^4.9.1",
+    "@mui/icons-material": "^5.0.1",
     "clsx": "^1.1.0",
     "react-virtualized-auto-sizer": "^1.0.2",
     "react-vtree": "^3.0.0-beta.1",
     "react-window": "^1.8.6"
   },
   "peerDependencies": {
-    "@jbrowse/core": "^1.0.0",
-    "@jbrowse/plugin-config": "^1.0.0",
-    "@material-ui/core": "^4.12.2",
-    "@material-ui/lab": "^4.0.0-alpha.45",
-    "mobx-react": "^6.0.0",
-    "mobx-state-tree": "3.14.1",
+    "@jbrowse/core": "^2.0.0",
+    "@jbrowse/plugin-config": "^2.0.0",
+    "@mui/material": "^5.0.0",
+    "mobx": "^6.0.0",
+    "mobx-react": "^7.0.0",
+    "mobx-state-tree": "^5.0.0",
     "prop-types": "^15.0.0",
-    "react": ">=16.8.0"
+    "react": ">=16.8.0",
+    "tss-react": "^3.0.0"
   },
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "5c21beb48a21f08b0091d293f09ac99174c48f77"
+  "distModule": "esm/index.js",
+  "srcModule": "src/index.ts",
+  "module": "esm/index.js",
+  "gitHead": "0db0462fa1f9f15ab4869da085bcab032b9483c3"
 }

package/src/AddConnectionWidget/components/AddConnectionWidget.js

@@ -1,18 +1,22 @@
+import React, { useState } from 'react'
 import { getSession } from '@jbrowse/core/util'
-import Button from '@material-ui/core/Button'
-import Step from '@material-ui/core/Step'
-import StepContent from '@material-ui/core/StepContent'
-import StepLabel from '@material-ui/core/StepLabel'
-import Stepper from '@material-ui/core/Stepper'
-import { makeStyles } from '@material-ui/core/styles'
-import Typography from '@material-ui/core/Typography'
+import {
+  Button,
+  Step,
+  StepContent,
+  StepLabel,
+  Stepper,
+  Typography,
+} from '@mui/material'
+import { makeStyles } from 'tss-react/mui'
 import { observer, PropTypes as MobxPropTypes } from 'mobx-react'
 import { getEnv } from 'mobx-state-tree'
-import React, { useState } from 'react'
+
+// locals
 import ConfigureConnection from './ConfigureConnection'
 import ConnectionTypeSelect from './ConnectionTypeSelect'
 
-const useStyles = makeStyles(theme => ({
+const useStyles = makeStyles()(theme => ({
   root: {
     marginTop: theme.spacing(1),
   },
@@ -35,7 +39,7 @@ function AddConnectionWidget({ model }) {
   const [configModel, setConfigModel] = useState({})
   const [configModelReady, setConfigModelReady] = useState(true)
   const [activeStep, setActiveStep] = useState(0)
-  const classes = useStyles()
+  const { classes } = useStyles()
 
   const session = getSession(model)
 

package/src/AddConnectionWidget/components/ConnectionTypeSelect.tsx

@@ -1,8 +1,6 @@
-import IconButton from '@material-ui/core/IconButton'
-import MenuItem from '@material-ui/core/MenuItem'
-import TextField from '@material-ui/core/TextField'
 import React, { useEffect } from 'react'
-import OpenInNewIcon from '@material-ui/icons/OpenInNew'
+import { IconButton, MenuItem, TextField } from '@mui/material'
+import OpenInNewIcon from '@mui/icons-material/OpenInNew'
 
 import ConnectionType from '@jbrowse/core/pluggableElementTypes/ConnectionType'