@jbrowse/cli 3.7.0 → 4.0.1

package/dist/commands/sort-gff-utils/process-utils.js

@@ -1,23 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.waitForProcessClose = waitForProcessClose;
-exports.handleProcessError = handleProcessError;
-async function waitForProcessClose(child) {
-    return new Promise((resolve, reject) => {
-        child.on('close', code => {
-            resolve(code);
-        });
-        child.on('error', err => {
-            reject(err);
-        });
-    });
-}
-function handleProcessError(error) {
-    if (error instanceof Error) {
-        console.error(`Process error: ${error.message}`);
-    }
-    else {
-        console.error('Unknown process error:', error);
-    }
-    process.exit(1);
-}

package/dist/commands/sort-gff-utils/sort-utils.js

@@ -1,55 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.getMinimalEnvironment = getMinimalEnvironment;
-exports.createSortCommandForStdin = createSortCommandForStdin;
-exports.createSortCommandForFile = createSortCommandForFile;
-exports.spawnSortProcessFromFile = spawnSortProcessFromFile;
-exports.spawnSortProcessFromStdin = spawnSortProcessFromStdin;
-exports.spawnSortProcess = spawnSortProcess;
-const child_process_1 = require("child_process");
-const tmp_1 = __importDefault(require("tmp"));
-function getMinimalEnvironment() {
-    return {
-        ...process.env,
-        LC_ALL: 'C',
-    };
-}
-function createSortCommandForStdin() {
-    // Create a temporary file to store stdin content, then process it
-    // This allows us to read the data twice - once for headers, once for sorting
-    const tmpFile = tmp_1.default.fileSync({
-        prefix: 'jbrowse-sort-gff',
-    }).name;
-    const sortCmd = `sort -t"\`printf '\\t'\`" -k1,1 -k4,4n`;
-    // Save stdin to temp file, extract headers, sort non-headers, then cleanup
-    return `cat > ${tmpFile} && (grep "^#" ${tmpFile}; grep -v "^#" ${tmpFile} | ${sortCmd}) && rm -f ${tmpFile}`;
-}
-function createSortCommandForFile(file) {
-    // When reading from a file, we can read it multiple times directly
-    // Need to wrap in parentheses to ensure both grep outputs are combined
-    return `(grep "^#" "${file}"; grep -v "^#" "${file}" | sort -t"\`printf '\\t'\`" -k1,1 -k4,4n)`;
-}
-function spawnSortProcessFromFile(file) {
-    const command = createSortCommandForFile(file);
-    const env = getMinimalEnvironment();
-    return (0, child_process_1.spawn)('sh', ['-c', command], {
-        env,
-        stdio: 'inherit',
-    });
-}
-function spawnSortProcessFromStdin() {
-    const command = createSortCommandForStdin();
-    const env = getMinimalEnvironment();
-    return (0, child_process_1.spawn)('sh', ['-c', command], {
-        env,
-        stdio: 'inherit',
-    });
-}
-function spawnSortProcess(options) {
-    return options.file
-        ? spawnSortProcessFromFile(options.file)
-        : spawnSortProcessFromStdin();
-}

package/dist/commands/sort-gff-utils/validators.js

@@ -1,21 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.validateFileArgument = validateFileArgument;
-exports.validateRequiredCommands = validateRequiredCommands;
-const command_exists_1 = require("command-exists");
-function validateFileArgument(file) {
-    // Allow no file argument for stdin input
-    if (!file && process.stdin.isTTY) {
-        console.error('Error: Missing required argument: file');
-        console.error('Usage: jbrowse sort-gff <file>');
-        console.error('       OR pipe data via stdin: cat file.gff | jbrowse sort-gff');
-        process.exit(1);
-    }
-}
-function validateRequiredCommands() {
-    const requiredCommands = ['sh', 'sort', 'grep'];
-    const missingCommands = requiredCommands.filter(cmd => !(0, command_exists_1.sync)(cmd));
-    if (missingCommands.length > 0) {
-        throw new Error('Error: Unable to sort, requires unix type environment with sort, grep');
-    }
-}

package/dist/commands/text-index-utils/adapter-utils.js

@@ -1,63 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.getLoc = getLoc;
-exports.createTrixAdapter = createTrixAdapter;
-exports.createPerTrackTrixAdapter = createPerTrackTrixAdapter;
-exports.getAdapterLocation = getAdapterLocation;
-function getLoc(elt) {
-    return elt.locationType === 'LocalPathLocation' ? elt.localPath : elt.uri;
-}
-function createTrixAdapter(id, asm, assemblyNames) {
-    return {
-        type: 'TrixTextSearchAdapter',
-        textSearchAdapterId: id,
-        ixFilePath: {
-            uri: `trix/${asm}.ix`,
-            locationType: 'UriLocation',
-        },
-        ixxFilePath: {
-            uri: `trix/${asm}.ixx`,
-            locationType: 'UriLocation',
-        },
-        metaFilePath: {
-            uri: `trix/${asm}_meta.json`,
-            locationType: 'UriLocation',
-        },
-        assemblyNames: assemblyNames || [asm],
-    };
-}
-function createPerTrackTrixAdapter(trackId, assemblyNames) {
-    return {
-        type: 'TrixTextSearchAdapter',
-        textSearchAdapterId: `${trackId}-index`,
-        ixFilePath: {
-            uri: `trix/${trackId}.ix`,
-            locationType: 'UriLocation',
-        },
-        ixxFilePath: {
-            uri: `trix/${trackId}.ixx`,
-            locationType: 'UriLocation',
-        },
-        metaFilePath: {
-            uri: `trix/${trackId}_meta.json`,
-            locationType: 'UriLocation',
-        },
-        assemblyNames: assemblyNames,
-    };
-}
-function getAdapterLocation(adapter) {
-    const { type } = adapter || {};
-    if (type === 'Gff3TabixAdapter') {
-        return adapter.gffGzLocation || adapter;
-    }
-    else if (type === 'Gff3Adapter') {
-        return adapter.gffLocation || adapter;
-    }
-    else if (type === 'VcfAdapter') {
-        return adapter.vcfLocation || adapter;
-    }
-    else if (type === 'VcfTabixAdapter') {
-        return adapter.vcfGzLocation || adapter;
-    }
-    return undefined;
-}

package/dist/commands/text-index-utils/aggregate.js

@@ -1,87 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.aggregateIndex = aggregateIndex;
-const fs_1 = __importDefault(require("fs"));
-const path_1 = __importDefault(require("path"));
-const config_utils_1 = require("./config-utils");
-const indexing_utils_1 = require("./indexing-utils");
-async function aggregateIndex(flags) {
-    const { out, target, tracks, assemblies, attributes, quiet, force, exclude, dryrun, prefixSize, } = flags;
-    const outFlag = target || out || '.';
-    const isDir = fs_1.default.lstatSync(outFlag).isDirectory();
-    const confPath = isDir ? path_1.default.join(outFlag, 'config.json') : outFlag;
-    const outLocation = path_1.default.dirname(confPath);
-    const config = (0, config_utils_1.readConf)(confPath);
-    const trixDir = path_1.default.join(outLocation, 'trix');
-    if (!fs_1.default.existsSync(trixDir)) {
-        fs_1.default.mkdirSync(trixDir);
-    }
-    const aggregateTextSearchAdapters = config.aggregateTextSearchAdapters || [];
-    const asms = assemblies?.split(',') ||
-        config.assemblies?.map(a => a.name) ||
-        (config.assembly ? [config.assembly.name] : []);
-    if (!asms.length) {
-        throw new Error('No assemblies found');
-    }
-    for (const asm of asms) {
-        const trackConfigs = (0, config_utils_1.getTrackConfigs)(confPath, tracks?.split(','), asm);
-        if (!trackConfigs.length) {
-            console.log(`Indexing assembly ${asm}...(no tracks found)...`);
-            continue;
-        }
-        console.log(`Indexing assembly ${asm}...`);
-        if (dryrun) {
-            console.log(trackConfigs.map(e => `${e.trackId}	${e.adapter?.type}`).join('\n'));
-        }
-        else {
-            const id = `${asm}-index`;
-            const idx = aggregateTextSearchAdapters.findIndex(x => x.textSearchAdapterId === id);
-            if (idx !== -1 && !force) {
-                console.log(`Note: ${asm} has already been indexed with this configuration, use --force to overwrite this assembly. Skipping for now`);
-                continue;
-            }
-            await (0, indexing_utils_1.indexDriver)({
-                trackConfigs,
-                outLocation,
-                quiet,
-                name: asm,
-                attributes: attributes.split(','),
-                typesToExclude: exclude.split(','),
-                assemblyNames: [asm],
-                prefixSize,
-            });
-            const trixConf = {
-                type: 'TrixTextSearchAdapter',
-                textSearchAdapterId: id,
-                ixFilePath: {
-                    uri: `trix/${asm}.ix`,
-                    locationType: 'UriLocation',
-                },
-                ixxFilePath: {
-                    uri: `trix/${asm}.ixx`,
-                    locationType: 'UriLocation',
-                },
-                metaFilePath: {
-                    uri: `trix/${asm}_meta.json`,
-                    locationType: 'UriLocation',
-                },
-                assemblyNames: [asm],
-            };
-            if (idx === -1) {
-                aggregateTextSearchAdapters.push(trixConf);
-            }
-            else {
-                aggregateTextSearchAdapters[idx] = trixConf;
-            }
-        }
-    }
-    if (!dryrun) {
-        (0, config_utils_1.writeConf)({
-            ...config,
-            aggregateTextSearchAdapters,
-        }, confPath);
-    }
-}

package/dist/commands/text-index-utils/config-utils.js

@@ -1,59 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.readConf = readConf;
-exports.writeConf = writeConf;
-exports.getConfigPath = getConfigPath;
-exports.ensureTrixDir = ensureTrixDir;
-exports.getAssemblyNames = getAssemblyNames;
-exports.getTrackConfigs = getTrackConfigs;
-const fs_1 = __importDefault(require("fs"));
-const path_1 = __importDefault(require("path"));
-const common_1 = require("../../types/common");
-function readConf(configPath) {
-    return JSON.parse(fs_1.default.readFileSync(configPath, 'utf8'));
-}
-function writeConf(obj, configPath) {
-    fs_1.default.writeFileSync(configPath, JSON.stringify(obj, null, 2));
-}
-function getConfigPath(outFlag) {
-    const isDir = fs_1.default.lstatSync(outFlag).isDirectory();
-    const configPath = isDir ? path_1.default.join(outFlag, 'config.json') : outFlag;
-    const outLocation = path_1.default.dirname(configPath);
-    return { configPath, outLocation };
-}
-function ensureTrixDir(outLocation) {
-    const trixDir = path_1.default.join(outLocation, 'trix');
-    if (!fs_1.default.existsSync(trixDir)) {
-        fs_1.default.mkdirSync(trixDir);
-    }
-    return trixDir;
-}
-function getAssemblyNames(config, assemblies) {
-    const asms = assemblies?.split(',') ||
-        config.assemblies?.map(a => a.name) ||
-        (config.assembly ? [config.assembly.name] : []);
-    if (!asms.length) {
-        throw new Error('No assemblies found');
-    }
-    return asms;
-}
-function getTrackConfigs(configPath, trackIds, assemblyName) {
-    const { tracks } = readConf(configPath);
-    if (!tracks) {
-        return [];
-    }
-    const trackIdsToIndex = trackIds || tracks.map(track => track.trackId);
-    return trackIdsToIndex
-        .map(trackId => {
-        const currentTrack = tracks.find(t => trackId === t.trackId);
-        if (!currentTrack) {
-            throw new Error(`Track not found in config.json for trackId ${trackId}, please add track configuration before indexing.`);
-        }
-        return currentTrack;
-    })
-        .filter(track => (0, common_1.supported)(track.adapter?.type))
-        .filter(track => assemblyName ? track.assemblyNames.includes(assemblyName) : true);
-}

package/dist/commands/text-index-utils/index.js

@@ -1,9 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.indexFileList = exports.perTrackIndex = exports.aggregateIndex = void 0;
-var aggregate_1 = require("./aggregate");
-Object.defineProperty(exports, "aggregateIndex", { enumerable: true, get: function () { return aggregate_1.aggregateIndex; } });
-var per_track_1 = require("./per-track");
-Object.defineProperty(exports, "perTrackIndex", { enumerable: true, get: function () { return per_track_1.perTrackIndex; } });
-var file_list_1 = require("./file-list");
-Object.defineProperty(exports, "indexFileList", { enumerable: true, get: function () { return file_list_1.indexFileList; } });

package/dist/commands/text-index-utils/per-track.js

@@ -1,65 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.perTrackIndex = perTrackIndex;
-const fs_1 = __importDefault(require("fs"));
-const path_1 = __importDefault(require("path"));
-const adapter_utils_1 = require("./adapter-utils");
-const config_utils_1 = require("./config-utils");
-const indexing_utils_1 = require("./indexing-utils");
-const validators_1 = require("./validators");
-async function perTrackIndex(flags) {
-    const { out, target, tracks, assemblies, attributes, quiet, force, exclude, prefixSize, } = flags;
-    const outFlag = target || out || '.';
-    const isDir = fs_1.default.lstatSync(outFlag).isDirectory();
-    const confFilePath = isDir ? path_1.default.join(outFlag, 'config.json') : outFlag;
-    const outLocation = path_1.default.dirname(confFilePath);
-    const config = (0, config_utils_1.readConf)(confFilePath);
-    const configTracks = config.tracks || [];
-    const trixDir = path_1.default.join(outLocation, 'trix');
-    if (!fs_1.default.existsSync(trixDir)) {
-        fs_1.default.mkdirSync(trixDir);
-    }
-    (0, validators_1.validateAssembliesForPerTrack)(assemblies);
-    const confs = (0, config_utils_1.getTrackConfigs)(confFilePath, tracks?.split(','));
-    if (!confs.length) {
-        throw new Error('Tracks not found in config.json, please add track configurations before indexing.');
-    }
-    for (const trackConfig of confs) {
-        const { textSearching, trackId, assemblyNames } = trackConfig;
-        if (textSearching?.textSearchAdapter && !force) {
-            console.log(`Note: ${trackId} has already been indexed with this configuration, use --force to overwrite this track. Skipping for now`);
-            continue;
-        }
-        console.log(`Indexing track ${trackId}...`);
-        await (0, indexing_utils_1.indexDriver)({
-            trackConfigs: [trackConfig],
-            attributes: attributes.split(','),
-            outLocation,
-            quiet,
-            name: trackId,
-            typesToExclude: exclude.split(','),
-            assemblyNames,
-            prefixSize,
-        });
-        if (!textSearching?.textSearchAdapter) {
-            // modifies track with new text search adapter
-            const index = configTracks.findIndex(track => trackId === track.trackId);
-            if (index !== -1) {
-                configTracks[index] = {
-                    ...trackConfig,
-                    textSearching: {
-                        ...textSearching,
-                        textSearchAdapter: (0, adapter_utils_1.createPerTrackTrixAdapter)(trackId, assemblyNames),
-                    },
-                };
-            }
-            else {
-                console.log("Error: can't find trackId");
-            }
-        }
-        (0, config_utils_1.writeConf)({ ...config, tracks: configTracks }, confFilePath);
-    }
-}