@jbrowse/plugin-legacy-jbrowse 1.7.11 → 2.0.0

package/esm/JBrowse1Connection/jb1ConfigParse.js.map

@@ -0,0 +1 @@
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package/esm/JBrowse1Connection/jb1ToJb2.d.ts

@@ -0,0 +1,49 @@
+import { Track, RefSeqs } from './types';
+interface Jb2Track {
+    trackId: string;
+    name: string;
+    description?: string;
+    category?: string[];
+    adapter?: Jb2Adapter;
+    type?: string;
+    defaultRendering?: string;
+}
+interface Jb2Adapter {
+    type: string;
+    features?: Jb2Feature[];
+    bamLocation?: Jb2Location;
+    cramLocation?: Jb2Location;
+    craiLocation?: Jb2Location;
+    fastaLocation?: Jb2Location;
+    faiLocation?: Jb2Location;
+    gziLocation?: Jb2Location;
+    twoBitLocation?: Jb2Location;
+    bigWigLocation?: Jb2Location;
+    bigBedLocation?: Jb2Location;
+    vcfGzLocation?: Jb2Location;
+    gffLocation?: Jb2Location;
+    gffGzLocation?: Jb2Location;
+    gtfLocation?: Jb2Location;
+    bedGzLocation?: Jb2Location;
+    index?: {
+        location: Jb2Location;
+        indexType?: string;
+    };
+    rootUrlTemplate?: Jb2Location;
+    sequenceAdapter?: Jb2Adapter;
+}
+interface Jb2Feature {
+    refName: string;
+    uniqueId: string;
+    start: number;
+    end: number;
+}
+interface Jb2Location {
+    uri?: string;
+    localPath?: string;
+    blobId?: string;
+    locationType?: string;
+}
+export declare function convertTrackConfig(jb1TrackConfig: Track, dataRoot: string, sequenceAdapter: Jb2Adapter): Jb2Track;
+export declare function createRefSeqsAdapter(refSeqs: string | RefSeqs): Promise<Jb2Adapter>;
+export {};

package/esm/JBrowse1Connection/jb1ToJb2.js

@@ -0,0 +1,424 @@
+import { openLocation } from '@jbrowse/core/util/io';
+import { objectHash } from '@jbrowse/core/util';
+import { generateUnknownTrackConf, generateUnsupportedTrackConf, guessAdapter, guessTrackType, UNKNOWN, UNSUPPORTED, } from '@jbrowse/core/util/tracks';
+export function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
+    const jb2TrackConfig = {
+        trackId: objectHash(jb1TrackConfig),
+        name: jb1TrackConfig.key || jb1TrackConfig.label,
+    };
+    const description = jb1TrackConfig.metadata &&
+        (jb1TrackConfig.metadata.description || jb1TrackConfig.metadata.Description);
+    if (description) {
+        jb2TrackConfig.description = description;
+    }
+    const category = jb1TrackConfig.category ||
+        (jb1TrackConfig.metadata && jb1TrackConfig.metadata.category);
+    jb2TrackConfig.category = category ? category.split(/\s*\/\s*/) : [];
+    const { storeClass } = jb1TrackConfig;
+    if (!jb1TrackConfig.urlTemplate) {
+        if (!(storeClass && storeClass.endsWith('FromConfig'))) {
+            const trackIdentifier = jb1TrackConfig.key || jb1TrackConfig.label;
+            console.warn(`Could not import JBrowse1 track "${trackIdentifier}" because it does not have a "urlTemplate" or is not a "FromConfig" track`);
+            return generateUnsupportedTrackConf(jb2TrackConfig.name, trackIdentifier, jb2TrackConfig.category);
+        }
+        return generateFromConfigTrackConfig(jb1TrackConfig, jb2TrackConfig);
+    }
+    const resolveUrlTemplate = (urlTemplate) => {
+        return new URL(urlTemplate, `${dataRoot}/`).href
+            .replace(/%7B/gi, '{')
+            .replace(/%7D/gi, '}');
+    };
+    const urlTemplate = resolveUrlTemplate(jb1TrackConfig.urlTemplate);
+    if (storeClass) {
+        if (storeClass === 'JBrowse/Store/SeqFeature/BAM') {
+            const adapter = {
+                type: 'BamAdapter',
+                bamLocation: { uri: urlTemplate, locationType: 'UriLocation' },
+            };
+            if (jb1TrackConfig.baiUrlTemplate) {
+                adapter.index = {
+                    location: {
+                        uri: resolveUrlTemplate(jb1TrackConfig.baiUrlTemplate),
+                        locationType: 'UriLocation',
+                    },
+                };
+            }
+            else if (jb1TrackConfig.csiUrlTemplate) {
+                adapter.index = {
+                    location: {
+                        uri: resolveUrlTemplate(jb1TrackConfig.csiUrlTemplate),
+                        locationType: 'UriLocation',
+                    },
+                    indexType: 'CSI',
+                };
+            }
+            else {
+                adapter.index = {
+                    location: { uri: `${urlTemplate}.bai`, locationType: 'UriLocation' },
+                };
+            }
+            return {
+                ...jb2TrackConfig,
+                type: 'AlignmentsTrack',
+                adapter,
+            };
+        }
+        if (storeClass === 'JBrowse/Store/SeqFeature/CRAM') {
+            const adapter = {
+                type: 'CramAdapter',
+                cramLocation: { uri: urlTemplate, locationType: 'UriLocation' },
+                sequenceAdapter,
+            };
+            if (jb1TrackConfig.craiUrlTemplate) {
+                adapter.craiLocation = {
+                    uri: resolveUrlTemplate(jb1TrackConfig.craiUrlTemplate),
+                    locationType: 'UriLocation',
+                };
+            }
+            else {
+                adapter.craiLocation = {
+                    uri: `${urlTemplate}.crai`,
+                    locationType: 'UriLocation',
+                };
+            }
+            return {
+                ...jb2TrackConfig,
+                type: 'AlignmentsTrack',
+                adapter,
+            };
+        }
+        if (storeClass === 'JBrowse/Store/SeqFeature/NCList') {
+            return {
+                ...jb2TrackConfig,
+                type: 'FeatureTrack',
+                adapter: {
+                    type: 'NCListAdapter',
+                    rootUrlTemplate: { uri: urlTemplate, locationType: 'UriLocation' },
+                },
+            };
+        }
+        if (storeClass === 'JBrowse/Store/SeqFeature/BigWig' ||
+            storeClass === 'JBrowse/Store/BigWig') {
+            if (jb1TrackConfig.type && jb1TrackConfig.type.endsWith('XYPlot')) {
+                jb2TrackConfig.defaultRendering = 'xyplot';
+            }
+            else if (jb1TrackConfig.type &&
+                jb1TrackConfig.type.endsWith('Density')) {
+                jb2TrackConfig.defaultRendering = 'density';
+            }
+            return {
+                ...jb2TrackConfig,
+                type: 'QuantitativeTrack',
+                adapter: {
+                    type: 'BigWigAdapter',
+                    bigWigLocation: { uri: urlTemplate, locationType: 'UriLocation' },
+                },
+            };
+        }
+        if (storeClass === 'JBrowse/Store/SeqFeature/VCFTabix') {
+            const adapter = {
+                type: 'VcfTabixAdapter',
+                vcfGzLocation: { uri: urlTemplate, locationType: 'UriLocation' },
+            };
+            if (jb1TrackConfig.tbiUrlTemplate) {
+                adapter.index = {
+                    location: {
+                        uri: resolveUrlTemplate(jb1TrackConfig.tbiUrlTemplate),
+                        locationType: 'UriLocation',
+                    },
+                };
+            }
+            else if (jb1TrackConfig.csiUrlTemplate) {
+                adapter.index = {
+                    location: {
+                        uri: resolveUrlTemplate(jb1TrackConfig.csiUrlTemplate),
+                        locationType: 'UriLocation',
+                    },
+                    indexType: 'CSI',
+                };
+            }
+            else {
+                adapter.index = {
+                    location: { uri: `${urlTemplate}.tbi`, locationType: 'UriLocation' },
+                };
+            }
+            return {
+                ...jb2TrackConfig,
+                type: 'VariantTrack',
+                adapter,
+            };
+        }
+        if (storeClass === 'JBrowse/Store/SeqFeature/VCFTribble') {
+            return generateUnsupportedTrackConf(jb2TrackConfig.name, `VCFTribble (${urlTemplate})`, jb2TrackConfig.category);
+        }
+        if (storeClass === 'JBrowse/Store/SeqFeature/GFF3') {
+            return {
+                ...jb2TrackConfig,
+                type: 'FeatureTrack',
+                adapter: {
+                    type: 'Gff3Adapter',
+                    gffLocation: { uri: urlTemplate, locationType: 'UriLocation' },
+                },
+            };
+        }
+        if (storeClass === 'JBrowse/Store/SeqFeature/BigBed') {
+            return {
+                ...jb2TrackConfig,
+                type: 'FeatureTrack',
+                adapter: {
+                    type: 'BigBedAdapter',
+                    bigBedLocation: { uri: urlTemplate, locationType: 'UriLocation' },
+                },
+            };
+        }
+        if (storeClass === 'JBrowse/Store/SeqFeature/GFF3Tabix') {
+            const adapter = {
+                type: 'Gff3TabixAdapter',
+                gffGzLocation: { uri: urlTemplate, locationType: 'UriLocation' },
+            };
+            if (jb1TrackConfig.tbiUrlTemplate) {
+                adapter.index = {
+                    location: {
+                        uri: resolveUrlTemplate(jb1TrackConfig.tbiUrlTemplate),
+                        locationType: 'UriLocation',
+                    },
+                };
+            }
+            else if (jb1TrackConfig.csiUrlTemplate) {
+                adapter.index = {
+                    location: {
+                        uri: resolveUrlTemplate(jb1TrackConfig.csiUrlTemplate),
+                        locationType: 'UriLocation',
+                    },
+                    indexType: 'CSI',
+                };
+            }
+            else {
+                adapter.index = {
+                    location: { uri: `${urlTemplate}.tbi`, locationType: 'UriLocation' },
+                };
+            }
+            return {
+                ...jb2TrackConfig,
+                type: 'FeatureTrack',
+                adapter,
+            };
+        }
+        if (storeClass === 'JBrowse/Store/SeqFeature/BED') {
+            return generateUnsupportedTrackConf(jb2TrackConfig.name, `BED (${urlTemplate})`, jb2TrackConfig.category);
+        }
+        if (storeClass === 'JBrowse/Store/SeqFeature/BEDTabix') {
+            const adapter = {
+                type: 'BedTabixAdapter',
+                bedGzLocation: { uri: urlTemplate, locationType: 'UriLocation' },
+            };
+            if (jb1TrackConfig.tbiUrlTemplate) {
+                adapter.index = {
+                    location: {
+                        uri: resolveUrlTemplate(jb1TrackConfig.tbiUrlTemplate),
+                        locationType: 'UriLocation',
+                    },
+                };
+            }
+            else if (jb1TrackConfig.csiUrlTemplate) {
+                adapter.index = {
+                    location: {
+                        uri: resolveUrlTemplate(jb1TrackConfig.csiUrlTemplate),
+                        locationType: 'UriLocation',
+                    },
+                    indexType: 'CSI',
+                };
+            }
+            else {
+                adapter.index = {
+                    location: { uri: `${urlTemplate}.tbi`, locationType: 'UriLocation' },
+                };
+            }
+            return {
+                ...jb2TrackConfig,
+                type: 'FeatureTrack',
+                adapter,
+            };
+        }
+        if (storeClass === 'JBrowse/Store/SeqFeature/GTF') {
+            return {
+                ...jb2TrackConfig,
+                type: 'FeatureTrack',
+                adapter: {
+                    type: 'GtfAdapter',
+                    gtfLocation: { uri: urlTemplate, locationType: 'UriLocation' },
+                },
+            };
+        }
+        if (storeClass === 'JBrowse/Store/SeqFeature/StaticChunked' ||
+            storeClass === 'JBrowse/Store/Sequence/StaticChunked') {
+            return generateUnsupportedTrackConf(jb2TrackConfig.name, `StaticChunked (${urlTemplate})`, jb2TrackConfig.category);
+        }
+        if (storeClass === 'JBrowse/Store/SeqFeature/UnindexedFasta') {
+            return generateUnsupportedTrackConf(jb2TrackConfig.name, `UnindexedFasta (${urlTemplate})`, jb2TrackConfig.category);
+        }
+        if (storeClass === 'JBrowse/Store/SeqFeature/IndexedFasta') {
+            const adapter = {
+                type: 'IndexedFastaAdapter',
+                fastaLocation: { uri: urlTemplate, locationType: 'UriLocation' },
+            };
+            if (jb1TrackConfig.faiUrlTemplate) {
+                adapter.faiLocation = {
+                    uri: resolveUrlTemplate(jb1TrackConfig.faiUrlTemplate),
+                    locationType: 'UriLocation',
+                };
+            }
+            else {
+                adapter.faiLocation = {
+                    uri: `${urlTemplate}.fai`,
+                    locationType: 'UriLocation',
+                };
+            }
+            return {
+                ...jb2TrackConfig,
+                type: 'SequenceTrack',
+                adapter,
+            };
+        }
+        if (storeClass === 'JBrowse/Store/SeqFeature/BgzipIndexedFasta') {
+            const adapter = {
+                type: 'BgzipFastaAdapter',
+                fastaLocation: { uri: urlTemplate, locationType: 'UriLocation' },
+            };
+            if (jb1TrackConfig.faiUrlTemplate) {
+                adapter.faiLocation = {
+                    uri: resolveUrlTemplate(jb1TrackConfig.faiUrlTemplate),
+                    locationType: 'UriLocation',
+                };
+            }
+            else {
+                adapter.faiLocation = {
+                    uri: `${urlTemplate}.fai`,
+                    locationType: 'UriLocation',
+                };
+            }
+            if (jb1TrackConfig.gziUrlTemplate) {
+                adapter.gziLocation = {
+                    uri: resolveUrlTemplate(jb1TrackConfig.gziUrlTemplate),
+                    locationType: 'UriLocation',
+                };
+            }
+            else {
+                adapter.gziLocation = {
+                    uri: `${urlTemplate}.gzi`,
+                    locationType: 'UriLocation',
+                };
+            }
+            return {
+                ...jb2TrackConfig,
+                type: 'ReferenceSequenceTrack',
+                adapter,
+            };
+        }
+        if (storeClass === 'JBrowse/Store/SeqFeature/TwoBit') {
+            return {
+                ...jb2TrackConfig,
+                type: 'ReferenceSequenceTrack',
+                adapter: {
+                    type: 'TwoBitAdapter',
+                    twoBitLocation: { uri: urlTemplate, locationType: 'UriLocation' },
+                },
+            };
+        }
+    }
+    // If we don't recogize the store class, make a best effort to guess by file type
+    jb2TrackConfig.adapter = guessAdapter({ uri: urlTemplate, locationType: 'UriLocation' }, undefined, urlTemplate);
+    if (!jb2TrackConfig.adapter) {
+        throw new Error('Could not determine adapter');
+    }
+    if (jb2TrackConfig.adapter.type === UNSUPPORTED) {
+        return generateUnsupportedTrackConf(jb2TrackConfig.name, urlTemplate, jb2TrackConfig.category);
+    }
+    if (jb2TrackConfig.adapter.type === UNKNOWN) {
+        return generateUnknownTrackConf(jb2TrackConfig.name, urlTemplate, jb2TrackConfig.category);
+    }
+    jb2TrackConfig.type = guessTrackType(jb2TrackConfig.adapter.type);
+    if (jb2TrackConfig.type === 'QuantitativeTrack') {
+        if (jb1TrackConfig.type && jb1TrackConfig.type.endsWith('XYPlot')) {
+            jb2TrackConfig.defaultRendering = 'xyplot';
+        }
+        else if (jb1TrackConfig.type && jb1TrackConfig.type.endsWith('Density')) {
+            jb2TrackConfig.defaultRendering = 'density';
+        }
+    }
+    return jb2TrackConfig;
+}
+function generateFromConfigTrackConfig(jb1TrackConfig, jb2TrackConfig) {
+    const jb1Features = jb1TrackConfig.features || [];
+    const jb2Features = jb1Features.map((feature) => {
+        const jb2Feature = JSON.parse(JSON.stringify(feature));
+        jb2Feature.refName = feature.seq_id;
+        jb2Feature.uniqueId = `${feature.seq_id}:${feature.start}-${feature.end}:${feature.name || ''}`;
+        return jb2Feature;
+    });
+    jb2TrackConfig.adapter = {
+        type: 'FromConfigAdapter',
+        features: jb2Features,
+    };
+    jb2TrackConfig.type = 'FeatureTrack';
+    return jb2TrackConfig;
+}
+export async function createRefSeqsAdapter(refSeqs) {
+    if (typeof refSeqs === 'string') {
+        // assume refSeqs is a url if it is string
+        refSeqs = {
+            url: refSeqs,
+        };
+    }
+    // check refseq urls
+    if (refSeqs.url) {
+        if (refSeqs.url.match(/.fai$/)) {
+            return {
+                type: 'IndexedFastaAdapter',
+                fastaLocation: {
+                    uri: refSeqs.url.slice(0, -4),
+                    locationType: 'UriLocation',
+                },
+                faiLocation: {
+                    uri: refSeqs.url,
+                    locationType: 'UriLocation',
+                },
+            };
+        }
+        if (refSeqs.url.match(/.2bit$/)) {
+            return {
+                type: 'TwoBitAdapter',
+                twoBitLocation: { uri: refSeqs.url, locationType: 'UriLocation' },
+            };
+        }
+        if (refSeqs.url.match(/.fa$/)) {
+            throw new Error('Unindexed FASTA adapter not available');
+        }
+        if (refSeqs.url.match(/.sizes/)) {
+            throw new Error('chromosome SIZES adapter not available');
+        }
+        const refSeqsJson = await openLocation({
+            uri: refSeqs.url,
+            locationType: 'UriLocation',
+        }).readFile('utf8');
+        const refSeqsData = JSON.parse(refSeqsJson);
+        return refSeqAdapterFromConfig(refSeqsData);
+    }
+    if ('data' in refSeqs) {
+        return refSeqAdapterFromConfig(refSeqs.data || []);
+    }
+    throw new Error(`Could not determine adapter for JBrowse1 refSeqs: ${refSeqs.url || JSON.stringify(refSeqs)}`);
+}
+function refSeqAdapterFromConfig(refSeqsData) {
+    const features = refSeqsData.map((refSeq) => ({
+        refName: refSeq.name,
+        uniqueId: refSeq.name,
+        start: refSeq.start,
+        end: refSeq.end,
+    }));
+    return {
+        type: 'FromConfigAdapter',
+        features,
+    };
+}
+//# sourceMappingURL=jb1ToJb2.js.map

package/esm/JBrowse1Connection/jb1ToJb2.js.map

@@ -0,0 +1 @@
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package/esm/JBrowse1Connection/model.d.ts

@@ -0,0 +1,15 @@
+export default function _default(pluginManager: any): import("mobx-state-tree").IModelType<{
+    name: import("mobx-state-tree").ISimpleType<string>;
+    tracks: import("mobx-state-tree").IArrayType<any>;
+} & {
+    configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
+    type: import("mobx-state-tree").ISimpleType<"JBrowse1Connection">;
+}, {
+    afterAttach(): void;
+    addTrackConf(trackConf: any): any;
+    addTrackConfs(trackConfs: any): any[];
+    setTrackConfs(trackConfs: any): import("mobx-state-tree").IMSTArray<any> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<any>>;
+    clear(): void;
+} & {
+    connect(): void;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/esm/JBrowse1Connection/model.js

@@ -0,0 +1,44 @@
+import { ConfigurationReference, readConfObject, } from '@jbrowse/core/configuration';
+import { getSession } from '@jbrowse/core/util';
+import { BaseConnectionModelFactory } from '@jbrowse/core/pluggableElementTypes/models';
+import { types } from 'mobx-state-tree';
+import configSchema from './configSchema';
+import { fetchJb1 } from './jb1ConfigLoad';
+import { convertTrackConfig } from './jb1ToJb2';
+export default function (pluginManager) {
+    return types.compose('JBrowse1Connection', BaseConnectionModelFactory(pluginManager), types
+        .model({
+        configuration: ConfigurationReference(configSchema),
+        type: types.literal('JBrowse1Connection'),
+    })
+        .actions(self => ({
+        connect() {
+            const dataDirLocation = readConfObject(self.configuration, 'dataDirLocation');
+            const session = getSession(self);
+            fetchJb1(dataDirLocation)
+                .then(config => {
+                const assemblyName = readConfObject(self.configuration, 'assemblyNames')[0];
+                if (!assemblyName) {
+                    throw new Error('assembly name required for JBrowse 1 connection');
+                }
+                const assemblyConf = session.assemblies.find(assembly => readConfObject(assembly, 'name') === assemblyName);
+                const sequenceAdapter = readConfObject(assemblyConf, [
+                    'sequence',
+                    'adapter',
+                ]);
+                const jb2Tracks = config.tracks.map(jb1Track => {
+                    const jb2Track = convertTrackConfig(jb1Track, config.dataRoot, sequenceAdapter);
+                    jb2Track.assemblyNames = [assemblyName];
+                    return jb2Track;
+                });
+                self.setTrackConfs(jb2Tracks);
+            })
+                .catch(error => {
+                console.error(error);
+                session.notify(`There was a problem connecting to the JBrowse 1 data directory "${self.name}". Please make sure you have entered a valid location. The error that was thrown is: "${error}"`, 'error');
+                session.breakConnection(self.configuration);
+            });
+        },
+    })));
+}
+//# sourceMappingURL=model.js.map

package/esm/JBrowse1Connection/model.js.map

@@ -0,0 +1 @@
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