@jbrowse/cli 3.5.1 → 3.6.0

package/lib/commands/add-track-json.js

@@ -1,67 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const fs_1 = require("fs");
-const core_1 = require("@oclif/core");
-const base_1 = __importDefault(require("../base"));
-class AddTrackJson extends base_1.default {
-    async run() {
-        const { args, flags: runFlags } = await this.parse(AddTrackJson);
-        const output = runFlags.target || runFlags.out || '.';
-        const isDir = (await fs_1.promises.lstat(output)).isDirectory();
-        this.target = isDir ? `${output}/config.json` : output;
-        const { track: inputtedTrack } = args;
-        this.debug(`Sequence location is: ${inputtedTrack}`);
-        const { update } = runFlags;
-        const config = await this.readJsonFile(this.target);
-        this.debug(`Found existing config file ${this.target}`);
-        const track = await this.readInlineOrFileJson(inputtedTrack);
-        if (!config.tracks) {
-            config.tracks = [];
-        }
-        const idx = config.tracks.findIndex(({ trackId }) => trackId === track.trackId);
-        if (idx !== -1) {
-            const existing = config.tracks[idx]?.name;
-            this.debug(`Found existing track ${existing} in configuration`);
-            if (update) {
-                this.debug(`Overwriting track ${existing} in configuration`);
-                config.tracks[idx] = track;
-            }
-            else {
-                this.error(`Cannot add track ${track.name}, a track with that trackId already exists: ${existing}`, { exit: 160 });
-            }
-        }
-        else {
-            config.tracks.push(track);
-        }
-        this.debug(`Writing configuration to file ${this.target}`);
-        await this.writeJsonFile(this.target, config);
-        this.log(`${idx !== -1 ? 'Overwrote' : 'Added'} assembly "${track.name}" ${idx !== -1 ? 'in' : 'to'} ${this.target}`);
-    }
-}
-AddTrackJson.description = 'Add a track configuration directly from a JSON hunk to the JBrowse 2 configuration';
-AddTrackJson.examples = [
-    '$ jbrowse add-track-json track.json',
-    '$ jbrowse add-track-json track.json --update',
-];
-AddTrackJson.args = {
-    track: core_1.Args.string({
-        required: true,
-        description: 'track JSON file or command line arg blob',
-    }),
-};
-AddTrackJson.flags = {
-    update: core_1.Flags.boolean({
-        char: 'u',
-        description: 'update the contents of an existing track, matched based on trackId',
-    }),
-    target: core_1.Flags.string({
-        description: 'path to config file in JB2 installation directory to write out to.\nCreates ./config.json if nonexistent',
-    }),
-    out: core_1.Flags.string({
-        description: 'synonym for target',
-    }),
-};
-exports.default = AddTrackJson;

package/lib/commands/add-track.js

@@ -1,564 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const fs_1 = __importDefault(require("fs"));
-const path_1 = __importDefault(require("path"));
-const core_1 = require("@oclif/core");
-const json_parse_better_errors_1 = __importDefault(require("json-parse-better-errors"));
-const base_1 = __importDefault(require("../base"));
-const { copyFile, rename, symlink } = fs_1.default.promises;
-const { COPYFILE_EXCL } = fs_1.default.constants;
-function makeLocationProtocol(protocol) {
-    return (location) => {
-        if (protocol === 'uri') {
-            return {
-                uri: location,
-                locationType: 'UriLocation',
-            };
-        }
-        if (protocol === 'localPath') {
-            return {
-                localPath: location,
-                locationType: 'LocalPathLocation',
-            };
-        }
-        throw new Error(`invalid protocol ${protocol}`);
-    };
-}
-function fileOperation({ srcFilename, destFilename, mode, }) {
-    if (mode === 'copy') {
-        return copyFile(srcFilename, destFilename, COPYFILE_EXCL);
-    }
-    else if (mode === 'move') {
-        return rename(srcFilename, destFilename);
-    }
-    else if (mode === 'symlink') {
-        return symlink(path_1.default.resolve(srcFilename), destFilename);
-    }
-    return undefined;
-}
-// get path of destination, and remove file at that path if it exists and force
-// is set
-function destinationFn({ destinationDir, srcFilename, subDir, force, }) {
-    const dest = path_1.default.resolve(path_1.default.join(destinationDir, subDir, path_1.default.basename(srcFilename)));
-    if (force) {
-        try {
-            fs_1.default.unlinkSync(dest);
-        }
-        catch (e) {
-            /* unconditionally unlinkSync, due to
-             * https://github.com/nodejs/node/issues/14025#issuecomment-754021370
-             * and https://github.com/GMOD/jbrowse-components/issues/2768 */
-        }
-    }
-    return dest;
-}
-const isUrl = (loc) => loc?.match(/^https?:\/\//);
-class AddTrack extends base_1.default {
-    async run() {
-        const { args: runArgs, flags: runFlags } = await this.parse(AddTrack);
-        const { track: argsTrack } = runArgs;
-        const { config, skipCheck, force, overwrite, category, description, load, subDir, target, protocol, out, indexFile: index, bed1, bed2, } = runFlags;
-        const output = target || out || '.';
-        const isDir = fs_1.default.lstatSync(output).isDirectory();
-        this.target = isDir ? `${output}/config.json` : output;
-        let { trackType, trackId, name, assemblyNames } = runFlags;
-        const configDir = path_1.default.dirname(this.target);
-        if (!argsTrack) {
-            this.error('No track provided. Example usage: jbrowse add-track yourfile.bam', { exit: 120 });
-        }
-        if (subDir) {
-            const dir = path_1.default.join(configDir, subDir);
-            if (!fs_1.default.existsSync(dir)) {
-                fs_1.default.mkdirSync(dir);
-            }
-        }
-        const location = argsTrack;
-        const mapLoc = (p) => {
-            return !p || isUrl(p) || load === 'inPlace'
-                ? p
-                : path_1.default.join(subDir, path_1.default.basename(p));
-        };
-        const adapter = this.guessAdapter({
-            protocol,
-            location: mapLoc(location),
-            index: index ? mapLoc(index) : undefined,
-            bed1: bed1 ? mapLoc(bed1) : undefined,
-            bed2: bed2 ? mapLoc(bed2) : undefined,
-        });
-        if ([
-            'PAFAdapter',
-            'PairwiseIndexedPAFAdapter',
-            'DeltaAdapter',
-            'ChainAdapter',
-            'MashMapAdapter',
-            'MCScanAnchorsAdapter',
-            'MCScanSimpleAnchorsAdapter',
-        ].includes(adapter.type)) {
-            // @ts-expect-error
-            // this is for the adapter's assembly names
-            adapter.assemblyNames = assemblyNames.split(',').map(a => a.trim());
-        }
-        if (isUrl(location) && load) {
-            this.error('The --load flag is used for local files only, but a URL was provided', { exit: 100 });
-        }
-        else if (!isUrl(location) && !load) {
-            this.error(`The --load flag should be used if a local file is used, example --load
-        copy to copy the file into the config directory. Options for load are
-        copy/move/symlink/inPlace (inPlace for no file operations)`, { exit: 110 });
-        }
-        if (adapter.type === 'UNKNOWN') {
-            this.error('Track type is not recognized', { exit: 120 });
-        }
-        if (adapter.type === 'UNSUPPORTED') {
-            this.error('Track type is not supported', { exit: 130 });
-        }
-        // only add track if there is an existing config.json
-        const configContents = await this.readJsonFile(this.target);
-        if (!configContents.assemblies?.length) {
-            this.error('No assemblies found. Please add one before adding tracks', {
-                exit: 150,
-            });
-        }
-        if (configContents.assemblies.length > 1 && !assemblyNames) {
-            this.error('Too many assemblies, cannot default to one. Please specify the assembly with the --assemblyNames flag');
-        }
-        // set up the track information
-        trackType = trackType || this.guessTrackType(adapter.type);
-        trackId = trackId || path_1.default.basename(location, path_1.default.extname(location));
-        name = name || trackId;
-        assemblyNames = assemblyNames || configContents.assemblies[0]?.name || '';
-        const configObj = config ? (0, json_parse_better_errors_1.default)(config) : {};
-        const trackConfig = {
-            type: trackType,
-            trackId,
-            name,
-            adapter,
-            category: category?.split(',').map(c => c.trim()),
-            assemblyNames: assemblyNames.split(',').map(a => a.trim()),
-            description,
-            ...configObj,
-        };
-        // any special track modifications go here
-        if (trackType === 'AlignmentsTrack') {
-            const assembly = configContents.assemblies.find(asm => asm.name === assemblyNames);
-            if (assembly) {
-                // @ts-expect-error
-                trackConfig.adapter.sequenceAdapter = assembly.sequence.adapter;
-            }
-            else if (!skipCheck) {
-                this.error(`Failed to find assemblyName ${assemblyNames}`);
-            }
-        }
-        if (!configContents.tracks) {
-            configContents.tracks = [];
-        }
-        const idx = configContents.tracks.findIndex(c => c.trackId === trackId);
-        if (idx !== -1) {
-            this.debug(`Found existing trackId ${trackId} in configuration`);
-            if (force || overwrite) {
-                this.debug(`Overwriting track ${trackId} in configuration`);
-                configContents.tracks[idx] = trackConfig;
-            }
-            else {
-                this.error(`Cannot add track with id ${trackId}, a track with that id already exists (use --force to override)`, { exit: 160 });
-            }
-        }
-        else {
-            configContents.tracks.push(trackConfig);
-        }
-        if (load && load !== 'inPlace') {
-            await Promise.all(Object.values(this.guessFileNames({ location, index, bed1, bed2 }))
-                .filter(f => !!f)
-                .map(srcFilename => fileOperation({
-                mode: load,
-                srcFilename,
-                destFilename: destinationFn({
-                    destinationDir: configDir,
-                    srcFilename,
-                    force,
-                    subDir,
-                }),
-            })));
-        }
-        this.debug(`Writing configuration to file ${this.target}`);
-        await this.writeJsonFile(this.target, configContents);
-        this.log(`${idx !== -1 ? 'Overwrote' : 'Added'} track with name "${name}" and trackId "${trackId}" ${idx !== -1 ? 'in' : 'to'} ${this.target}`);
-    }
-    guessFileNames({ location, index, bed1, bed2, }) {
-        if (/\.anchors(.simple)?$/i.test(location)) {
-            return {
-                file: location,
-                bed1: bed1,
-                bed2: bed2,
-            };
-        }
-        else if (/\.bam$/i.test(location)) {
-            return {
-                file: location,
-                index: index || `${location}.bai`,
-            };
-        }
-        else if (/\.cram$/i.test(location)) {
-            return {
-                file: location,
-                index: index || `${location}.crai`,
-            };
-        }
-        else if (/\.gff3?\.b?gz$/i.test(location) ||
-            /\.vcf\.b?gz$/i.test(location) ||
-            /\.bed\.b?gz$/i.test(location) ||
-            /\.pif\.b?gz$/i.test(location)) {
-            return {
-                file: location,
-                index: index || `${location}.tbi`,
-            };
-        }
-        else if (/\.(fa|fasta|fas|fna|mfa)$/i.test(location)) {
-            return {
-                file: location,
-                index: index || `${location}.fai`,
-            };
-        }
-        else if (/\.(fa|fasta|fas|fna|mfa)\.b?gz$/i.test(location)) {
-            return {
-                file: location,
-                index: `${location}.fai`,
-                index2: `${location}.gzi`,
-            };
-        }
-        else if (/\.2bit$/i.test(location) ||
-            /\.bedpe(\.gz)?$/i.test(location) ||
-            /\/trackData.jsonz?$/i.test(location) ||
-            /\/sparql$/i.test(location) ||
-            /\.out(\.gz)?$/i.test(location) ||
-            /\.paf(\.gz)?$/i.test(location) ||
-            /\.delta(\.gz)?$/i.test(location) ||
-            /\.bed?$/i.test(location) ||
-            /\.(bw|bigwig)$/i.test(location) ||
-            /\.(bb|bigbed)$/i.test(location) ||
-            /\.vcf$/i.test(location) ||
-            /\.gtf?$/i.test(location) ||
-            /\.gff3?$/i.test(location) ||
-            /\.chain(\.gz)?$/i.test(location) ||
-            /\.hic$/i.test(location)) {
-            return {
-                file: location,
-            };
-        }
-        return {};
-    }
-    // find way to import this instead of having to paste it
-    guessAdapter({ location, protocol, index, bed1, bed2, }) {
-        const makeLocation = makeLocationProtocol(protocol);
-        if (/\.bam$/i.test(location)) {
-            return {
-                type: 'BamAdapter',
-                bamLocation: makeLocation(location),
-                index: {
-                    location: makeLocation(index || `${location}.bai`),
-                    indexType: index?.toUpperCase().endsWith('CSI') ? 'CSI' : 'BAI',
-                },
-            };
-        }
-        else if (/\.cram$/i.test(location)) {
-            return {
-                type: 'CramAdapter',
-                cramLocation: makeLocation(location),
-                craiLocation: makeLocation(`${location}.crai`),
-            };
-        }
-        else if (/\.gff3?$/i.test(location)) {
-            return {
-                type: 'Gff3Adapter',
-                gffLocation: makeLocation(location),
-            };
-        }
-        else if (/\.gff3?\.b?gz$/i.test(location)) {
-            return {
-                type: 'Gff3TabixAdapter',
-                gffGzLocation: makeLocation(location),
-                index: {
-                    location: makeLocation(index || `${location}.tbi`),
-                    indexType: index?.toUpperCase().endsWith('CSI') ? 'CSI' : 'TBI',
-                },
-            };
-        }
-        else if (/\.gtf?$/i.test(location)) {
-            return {
-                type: 'GtfAdapter',
-                gtfLocation: makeLocation(location),
-            };
-        }
-        else if (/\.vcf$/i.test(location)) {
-            return {
-                type: 'VcfAdapter',
-                vcfLocation: makeLocation(location),
-            };
-        }
-        else if (/\.vcf\.b?gz$/i.test(location)) {
-            return {
-                type: 'VcfTabixAdapter',
-                vcfGzLocation: makeLocation(location),
-                index: {
-                    location: makeLocation(index || `${location}.tbi`),
-                    indexType: index?.toUpperCase().endsWith('CSI') ? 'CSI' : 'TBI',
-                },
-            };
-        }
-        else if (/\.vcf\.idx$/i.test(location)) {
-            return {
-                type: 'UNSUPPORTED',
-            };
-        }
-        else if (/\.bedpe(.gz)?$/i.test(location)) {
-            return {
-                type: 'BedpeAdapter',
-                bedpeLocation: makeLocation(location),
-            };
-        }
-        else if (/\.bed$/i.test(location)) {
-            return {
-                type: 'BedAdapter',
-                bedLocation: makeLocation(location),
-            };
-        }
-        else if (/\.pif\.b?gz$/i.test(location)) {
-            return {
-                type: 'PairwiseIndexedPAFAdapter',
-                pifGzLocation: makeLocation(location),
-                index: {
-                    location: makeLocation(index || `${location}.tbi`),
-                    indexType: index?.toUpperCase().endsWith('CSI') ? 'CSI' : 'TBI',
-                },
-            };
-        }
-        else if (/\.bed\.b?gz$/i.test(location)) {
-            return {
-                type: 'BedTabixAdapter',
-                bedGzLocation: makeLocation(location),
-                index: {
-                    location: makeLocation(index || `${location}.tbi`),
-                    indexType: index?.toUpperCase().endsWith('CSI') ? 'CSI' : 'TBI',
-                },
-            };
-        }
-        else if (/\.(bb|bigbed)$/i.test(location)) {
-            return {
-                type: 'BigBedAdapter',
-                bigBedLocation: makeLocation(location),
-            };
-        }
-        else if (/\.(bw|bigwig)$/i.test(location)) {
-            return {
-                type: 'BigWigAdapter',
-                bigWigLocation: makeLocation(location),
-            };
-        }
-        else if (/\.(fa|fasta|fna|mfa)$/i.test(location)) {
-            return {
-                type: 'IndexedFastaAdapter',
-                fastaLocation: makeLocation(location),
-                faiLocation: makeLocation(index || `${location}.fai`),
-            };
-        }
-        else if (/\.(fa|fasta|fna|mfa)\.b?gz$/i.test(location)) {
-            return {
-                type: 'BgzipFastaAdapter',
-                fastaLocation: makeLocation(location),
-                faiLocation: makeLocation(`${location}.fai`),
-                gziLocation: makeLocation(`${location}.gzi`),
-            };
-        }
-        else if (/\.2bit$/i.test(location)) {
-            return {
-                type: 'TwoBitAdapter',
-                twoBitLocation: makeLocation(location),
-            };
-        }
-        else if (/\.sizes$/i.test(location)) {
-            return {
-                type: 'UNSUPPORTED',
-            };
-        }
-        else if (/\/trackData.jsonz?$/i.test(location)) {
-            return {
-                type: 'NCListAdapter',
-                rootUrlTemplate: makeLocation(location),
-            };
-        }
-        else if (/\/sparql$/i.test(location)) {
-            return {
-                type: 'SPARQLAdapter',
-                endpoint: location,
-            };
-        }
-        else if (/\.hic$/i.test(location)) {
-            return {
-                type: 'HicAdapter',
-                hicLocation: makeLocation(location),
-            };
-        }
-        else if (/\.paf(.gz)?$/i.test(location)) {
-            return {
-                type: 'PAFAdapter',
-                pafLocation: makeLocation(location),
-            };
-        }
-        else if (/\.out(.gz)?$/i.test(location)) {
-            return {
-                type: 'MashMapAdapter',
-                outLocation: makeLocation(location),
-            };
-        }
-        else if (/\.chain(.gz)?$/i.test(location)) {
-            return {
-                type: 'ChainAdapter',
-                chainLocation: makeLocation(location),
-            };
-        }
-        else if (/\.delta(.gz)?$/i.test(location)) {
-            return {
-                type: 'DeltaAdapter',
-                deltaLocation: makeLocation(location),
-            };
-        }
-        else if (/\.anchors(.gz)?$/i.test(location)) {
-            return {
-                type: 'MCScanAnchorsAdapter',
-                mcscanAnchorsLocation: makeLocation(location),
-                bed1Location: bed1 ? makeLocation(bed1) : undefined,
-                bed2Location: bed2 ? makeLocation(bed2) : undefined,
-            };
-        }
-        else if (/\.anchors.simple(.gz)?$/i.test(location)) {
-            return {
-                type: 'MCScanSimpleAnchorsAdapter',
-                mcscanSimpleAnchorsLocation: makeLocation(location),
-                bed1Location: bed1 ? makeLocation(bed1) : undefined,
-                bed2Location: bed2 ? makeLocation(bed2) : undefined,
-            };
-        }
-        return {
-            type: 'UNKNOWN',
-        };
-    }
-    guessTrackType(adapterType) {
-        return adapterTypesToTrackTypeMap[adapterType] || 'FeatureTrack';
-    }
-}
-AddTrack.description = 'Add a track to a JBrowse 2 configuration';
-AddTrack.examples = [
-    '# copy /path/to/my.bam and /path/to/my.bam.bai to current directory and adds track to config.json',
-    '$ jbrowse add-track /path/to/my.bam --load copy',
-    '',
-    '# copy my.bam and my.bam.bai to /path/to/jb2/bam and adds track entry to /path/to/jb2/bam/config.json',
-    '$ jbrowse add-track my.bam --load copy --out /path/to/jb2 --subDir bam',
-    '',
-    '# same as above, but specify path to bai file. needed for if the bai file does not have the extension .bam.bai',
-    '$ jbrowse add-track my.bam --indexFile my.bai --load copy',
-    '',
-    '# creates symlink for /path/to/my.bam and adds track to config.json',
-    '$ jbrowse add-track /path/to/my.bam --load symlink',
-    '',
-    '# add track from URL to config.json, no --load flag needed',
-    '$ jbrowse add-track https://mywebsite.com/my.bam',
-    '',
-    '# --load inPlace adds a track without doing file operations',
-    '$ jbrowse add-track /url/relative/path.bam --load inPlace',
-];
-AddTrack.args = {
-    track: core_1.Args.string({
-        required: true,
-        description: 'Track file or URL',
-    }),
-};
-AddTrack.flags = {
-    trackType: core_1.Flags.string({
-        char: 't',
-        description: 'Type of track, by default inferred from track file',
-    }),
-    name: core_1.Flags.string({
-        char: 'n',
-        description: 'Name of the track. Will be defaulted to the trackId if none specified',
-    }),
-    indexFile: core_1.Flags.string({
-        description: 'Optional index file for the track',
-    }),
-    description: core_1.Flags.string({
-        char: 'd',
-        description: 'Optional description of the track',
-    }),
-    assemblyNames: core_1.Flags.string({
-        char: 'a',
-        description: 'Assembly name or names for track as comma separated string. If none, will default to the assembly in your config file',
-    }),
-    category: core_1.Flags.string({
-        description: 'Optional Comma separated string of categories to group tracks',
-    }),
-    config: core_1.Flags.string({
-        description: `Any extra config settings to add to a track. i.e '{"defaultRendering": "density"}'`,
-    }),
-    target: core_1.Flags.string({
-        description: 'path to config file in JB2 installation to write out to.',
-    }),
-    out: core_1.Flags.string({
-        description: 'synonym for target',
-    }),
-    subDir: core_1.Flags.string({
-        description: 'when using --load a file, output to a subdirectory of the target dir',
-        default: '',
-    }),
-    help: core_1.Flags.help({ char: 'h' }),
-    trackId: core_1.Flags.string({
-        description: 'trackId for the track, by default inferred from filename, must be unique throughout config',
-    }),
-    load: core_1.Flags.string({
-        char: 'l',
-        description: 'Required flag when using a local file. Choose how to manage the track. Copy, symlink, or move the track to the JBrowse directory. Or inPlace to leave track alone',
-        options: ['copy', 'symlink', 'move', 'inPlace'],
-    }),
-    skipCheck: core_1.Flags.boolean({
-        description: 'Skip check for whether or not the file or URL exists or if you are in a JBrowse directory',
-    }),
-    overwrite: core_1.Flags.boolean({
-        description: 'Overwrites existing track if it shares the same trackId',
-    }),
-    force: core_1.Flags.boolean({
-        char: 'f',
-        description: 'Equivalent to `--skipCheck --overwrite`',
-    }),
-    protocol: core_1.Flags.string({
-        description: 'Force protocol to a specific value',
-        default: 'uri',
-    }),
-    bed1: core_1.Flags.string({
-        description: 'Used only for mcscan anchors/simpleAnchors types',
-    }),
-    bed2: core_1.Flags.string({
-        description: 'Used only for mcscan anchors/simpleAnchors types',
-    }),
-};
-exports.default = AddTrack;
-const adapterTypesToTrackTypeMap = {
-    BamAdapter: 'AlignmentsTrack',
-    CramAdapter: 'AlignmentsTrack',
-    BgzipFastaAdapter: 'ReferenceSequenceTrack',
-    BigWigAdapter: 'QuantitativeTrack',
-    IndexedFastaAdapter: 'ReferenceSequenceTrack',
-    TwoBitAdapter: 'ReferenceSequenceTrack',
-    VcfTabixAdapter: 'VariantTrack',
-    VcfAdapter: 'VariantTrack',
-    BedpeAdapter: 'VariantTrack',
-    BedAdapter: 'FeatureTrack',
-    HicAdapter: 'HicTrack',
-    PAFAdapter: 'SyntenyTrack',
-    DeltaAdapter: 'SyntenyTrack',
-    ChainAdapter: 'SyntenyTrack',
-    MashMapAdapter: 'SyntenyTrack',
-    PairwiseIndexedPAFAdapter: 'SyntenyTrack',
-    MCScanAnchorsAdapter: 'SyntenyTrack',
-    MCScanSimpleAnchorsAdapter: 'SyntenyTrack',
-};