@jbrowse/cli 3.5.1 → 3.6.1

package/lib/commands/add-connection.js

@@ -1,170 +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 fetchWithProxy_1 = __importDefault(require("../fetchWithProxy"));
-class AddConnection extends base_1.default {
-    async run() {
-        const { args: runArgs, flags: runFlags } = await this.parse(AddConnection);
-        const output = runFlags.target || runFlags.out || '.';
-        const isDir = fs_1.default.lstatSync(output).isDirectory();
-        this.target = isDir ? `${output}/config.json` : output;
-        const { connectionUrlOrPath } = runArgs;
-        const { assemblyNames, type, name, config, connectionId } = runFlags;
-        const { skipCheck, force } = runFlags;
-        const url = await this.resolveURL(connectionUrlOrPath, !(skipCheck || force));
-        const configContents = await this.readJsonFile(this.target);
-        this.debug(`Using config file ${this.target}`);
-        if (!configContents.assemblies?.length) {
-            this.error('No assemblies found. Please add one before adding connections', { exit: 120 });
-        }
-        const configType = type || this.determineConnectionType(url);
-        const id = connectionId ||
-            [configType, assemblyNames, +Date.now()].filter(f => !!f).join('-');
-        const connectionConfig = {
-            type: configType,
-            name: name || id,
-            ...(configType === 'UCSCTrackHubConnection'
-                ? {
-                    hubTxtLocation: {
-                        uri: url,
-                        locationType: 'UriLocation',
-                    },
-                }
-                : {}),
-            ...(configType === 'JBrowse1Connection'
-                ? {
-                    dataDirLocation: {
-                        uri: url,
-                        locationType: 'UriLocation',
-                    },
-                }
-                : {}),
-            connectionId: id,
-            assemblyNames: assemblyNames
-                ? assemblyNames.split(',')
-                : type === 'JBrowse1Connection'
-                    ? [configContents.assemblies[0]?.name]
-                    : undefined,
-            ...(config ? (0, json_parse_better_errors_1.default)(config) : {}),
-        };
-        if (!configContents.connections) {
-            configContents.connections = [];
-        }
-        const idx = configContents.connections.findIndex(c => c.connectionId === connectionId);
-        if (idx !== -1) {
-            if (runFlags.force || runFlags.overwrite) {
-                configContents.connections[idx] = connectionConfig;
-            }
-            else {
-                this.error(`Cannot add connection with id ${connectionId}, a connection with that id already exists.\nUse --overwrite if you would like to replace the existing connection`, { exit: 150 });
-            }
-        }
-        else {
-            configContents.connections.push(connectionConfig);
-        }
-        this.debug(`Writing configuration to file ${this.target}`);
-        await this.writeJsonFile(this.target, configContents);
-        this.log(`${idx !== -1 ? 'Overwrote' : 'Added'} connection "${name}" ${idx !== -1 ? 'in' : 'to'} ${this.target}`);
-    }
-    async resolveURL(location, check = true) {
-        let locationUrl;
-        try {
-            locationUrl = new URL(location);
-        }
-        catch (error) {
-            this.error('The location provided is not a valid URL', { exit: 160 });
-        }
-        try {
-            if (check) {
-                const response = await (0, fetchWithProxy_1.default)(`${locationUrl}`, { method: 'HEAD' });
-                if (!response.ok) {
-                    this.error(`Response returned with code ${response.status}`);
-                }
-            }
-            return locationUrl.href;
-        }
-        catch (error) {
-            // ignore
-            this.error(`Unable to fetch from URL, ${error}`, { exit: 170 });
-        }
-    }
-    determineConnectionType(url) {
-        if (path_1.default.basename(url) === 'hub.txt') {
-            return 'UCSCTrackHubConnection';
-        }
-        if (url.includes('jbrowse/data')) {
-            return 'JBrowse1Connection';
-        }
-        return 'custom';
-    }
-    isValidJSON(str) {
-        try {
-            JSON.parse(str);
-            return true;
-        }
-        catch (error) {
-            return false;
-        }
-    }
-}
-AddConnection.description = 'Add a connection to a JBrowse 2 configuration';
-AddConnection.examples = [
-    '$ jbrowse add-connection http://mysite.com/jbrowse/data/ -a hg19',
-    '$ jbrowse add-connection http://mysite.com/jbrowse/custom_data_folder/ --type JBrowse1Connection -a hg38',
-    '$ jbrowse add-connection http://mysite.com/path/to/hub.txt',
-    '$ jbrowse add-connection http://mysite.com/path/to/custom_hub_name.txt --type UCSCTrackHubConnection',
-    `$ jbrowse add-connection http://mysite.com/path/to/custom --type custom --config '{"uri":{"url":"https://mysite.com/path/to/custom"}, "locationType": "UriLocation"}' -a hg19`,
-    '$ jbrowse add-connection https://mysite.com/path/to/hub.txt --connectionId newId --name newName --target /path/to/jb2/installation/config.json',
-];
-AddConnection.args = {
-    connectionUrlOrPath: core_1.Args.string({
-        required: true,
-        description: 'URL of data directory\nFor hub file, usually called hub.txt\nFor JBrowse 1, location of JB1 data directory similar to http://mysite.com/jbrowse/data/ ',
-    }),
-};
-AddConnection.flags = {
-    type: core_1.Flags.string({
-        char: 't',
-        description: 'type of connection, ex. JBrowse1Connection, UCSCTrackHubConnection, custom',
-    }),
-    assemblyNames: core_1.Flags.string({
-        char: 'a',
-        description: 'For UCSC, optional: Comma separated list of assembly name(s) to filter from this connection. For JBrowse: a single assembly name',
-    }),
-    config: core_1.Flags.string({
-        char: 'c',
-        description: `Any extra config settings to add to connection in JSON object format, such as '{"uri":"url":"https://sample.com"}, "locationType": "UriLocation"}'`,
-    }),
-    connectionId: core_1.Flags.string({
-        description: `Id for the connection that must be unique to JBrowse.  Defaults to 'connectionType-assemblyName-currentTime'`,
-    }),
-    name: core_1.Flags.string({
-        char: 'n',
-        description: 'Name of the connection. Defaults to connectionId if not provided',
-    }),
-    target: core_1.Flags.string({
-        description: 'path to config file in JB2 installation directory to write out to.',
-    }),
-    out: core_1.Flags.string({
-        description: 'synonym for target',
-    }),
-    help: core_1.Flags.help({ char: 'h' }),
-    skipCheck: core_1.Flags.boolean({
-        description: "Don't check whether or not the data directory URL exists or if you are in a JBrowse directory",
-    }),
-    overwrite: core_1.Flags.boolean({
-        description: 'Overwrites any existing connections if same connection id',
-    }),
-    force: core_1.Flags.boolean({
-        char: 'f',
-        description: 'Equivalent to `--skipCheck --overwrite`',
-    }),
-};
-exports.default = AddConnection;

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;