@nextage/omics-lib 1.0.6 → 1.0.8
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/build/omics/types/genotype.d.ts +4 -4
- package/build/omics/types/genotype.d.ts.map +1 -1
- package/build/omics/types/sample.d.ts +1 -1
- package/build/omics/types/sample.d.ts.map +1 -1
- package/build/utils/functs.d.ts +27 -0
- package/build/utils/functs.d.ts.map +1 -1
- package/build/utils/functs.js +53 -3
- package/build/utils/functs.js.map +1 -1
- package/package.json +5 -1
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@@ -2,10 +2,10 @@ import { BaseDBItem } from '../../types';
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export interface IGenotype extends BaseDBItem {
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variantId: string;
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sampleId: string;
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-
sequencingSampleId
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GT
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VAF
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8
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DP
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5
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sequencingSampleId?: string;
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GT?: string;
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VAF?: number;
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DP?: number;
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alleles: string[];
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}
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//# sourceMappingURL=genotype.d.ts.map
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"genotype.d.ts","sourceRoot":"","sources":["../../../src/omics/types/genotype.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,aAAa,CAAA;AAExC,MAAM,WAAW,SAAU,SAAQ,UAAU;IAC3C,SAAS,
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{"version":3,"file":"genotype.d.ts","sourceRoot":"","sources":["../../../src/omics/types/genotype.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,aAAa,CAAA;AAExC,MAAM,WAAW,SAAU,SAAQ,UAAU;IAC3C,SAAS,EAAY,MAAM,CAAC;IAC5B,QAAQ,EAAa,MAAM,CAAC;IAC5B,kBAAkB,CAAC,EAAE,MAAM,CAAC;IAC5B,EAAE,CAAC,EAAkB,MAAM,CAAC;IAC5B,GAAG,CAAC,EAAiB,MAAM,CAAC;IAC5B,EAAE,CAAC,EAAkB,MAAM,CAAC;IAC5B,OAAO,EAAc,MAAM,EAAE,CAAC;CAC/B"}
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"sample.d.ts","sourceRoot":"","sources":["../../../src/omics/types/sample.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,aAAa,CAAA;AAExC,MAAM,WAAW,OAAQ,SAAQ,UAAU;IACzC,eAAe,
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{"version":3,"file":"sample.d.ts","sourceRoot":"","sources":["../../../src/omics/types/sample.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,aAAa,CAAA;AAExC,MAAM,WAAW,OAAQ,SAAQ,UAAU;IACzC,eAAe,EAAM,MAAM,CAAC;IAC5B,kBAAkB,CAAC,EAAE,MAAM,CAAC;IAC5B,QAAQ,EAAa,kBAAkB,CAAC;CACzC;AAED,MAAM,WAAW,kBAAkB;IACjC,SAAS,EAAE,MAAM,CAAC;IAClB,OAAO,EAAI,MAAM,CAAC;IAClB,OAAO,EAAI,MAAM,CAAC;IAClB,SAAS,EAAE,MAAM,CAAC;CACnB"}
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package/build/utils/functs.d.ts
CHANGED
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@@ -1,3 +1,4 @@
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import schedule from 'node-schedule';
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import { AppObject, BaseUser } from '../interfaces';
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import { AppData, AppMongoDB } from '../types';
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/**
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@@ -57,4 +58,30 @@ export declare function getTenant(user?: BaseUser): string | undefined;
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* @returns
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*/
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export declare function validateUrl(input: string): string;
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/**
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*
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* @param {*} rule
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* @param {*} options
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* @param {*} method
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*/
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export declare function scheduleJob(rule: any, { recurrence, startTime, endTime }: {
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recurrence?: boolean;
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startTime?: string;
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endTime?: string;
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}, method?: () => void): schedule.Job | null;
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/**
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* Schedule multiple jobs.
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* Input rules have following format:
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* { rule (string/obj), recurrence (bool), method (function) }
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*
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* Example:
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* let jobs = scheduleJobs([
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* { rule: { minute: 56 }, options: { recurrence: true }, method: () => { console.log('JOB AT MIN 56!') } },
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* { rule: '* * * * *', options: { recurrence: true }, method: () => { console.log('JOB EVERY MINUTE!') } },
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* { rule: '* * * * *', options: { recurrence: true, startTime: '10:55' }, method: () => { console.log('JOB EVERY MINUTE after 10:53!') } }
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* ]);
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*
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* @param {*} rules array of rules objects
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*/
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export declare function scheduleJobs(rules?: any[]): schedule.Job[];
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//# sourceMappingURL=functs.d.ts.map
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@@ -1 +1 @@
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{"version":3,"file":"functs.d.ts","sourceRoot":"","sources":["../../src/utils/functs.ts"],"names":[],"mappings":"
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{"version":3,"file":"functs.d.ts","sourceRoot":"","sources":["../../src/utils/functs.ts"],"names":[],"mappings":"AAGA,OAAO,QAAQ,MAA4B,eAAe,CAAC;AAI3D,OAAO,EAAE,SAAS,EAAE,QAAQ,EAAE,MAAa,eAAe,CAAC;AAC3D,OAAO,EAAE,OAAO,EAAE,UAAU,EAAE,MAAa,UAAU,CAAC;AAEtD;;GAEG;AACH,wBAAsB,UAAU,CAAC,GAAG,EAAE,MAAM,EAAE,OAAO,EAAE,OAAO,GAAG,OAAO,CAAC,OAAO,CAAC,CAyBhF;AAED;;GAEG;AACH,wBAAsB,kBAAkB,IAAI,OAAO,CAAC,UAAU,CAAC,CAgB9D;AAED;;;GAGG;AACH,wBAAgB,OAAO,CAAC,GAAG,EAAE,MAAM,QAuBlC;AAkBD;;;;GAIG;AACH,wBAAsB,UAAU,CAAC,IAAI,GAAE,MAAW,GAAG,OAAO,CAAC,OAAO,CAAC,CAYpE;AAED;;;;GAIG;AACH,wBAAgB,OAAO,CAAC,MAAM,EAAE,GAAG,EAAE,IAAI,EAAE,MAAM,GAAG,GAAG,CAGtD;AAED;;;;;GAKG;AACH,wBAAgB,OAAO,CAAC,MAAM,EAAE,GAAG,EAAE,IAAI,EAAE,MAAM,EAAE,KAAK,EAAE,GAAG,GAAG,GAAG,CAGlE;AAED;;;GAGG;AACH,wBAAgB,kBAAkB,CAAC,GAAG,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,GAAG,MAAM,EAAE,CAgBvE;AAED;;;;;;GAMG;AACH,wBAAgB,SAAS,CAAC,IAAI,EAAE,SAAS,EAAE,IAAI,CAAC,EAAE,QAAQ,EAAE,oBAAoB,UAAQ,GAAG,IAAI,CAc9F;AAED;;;;GAIG;AACH,wBAAgB,SAAS,CAAC,IAAI,CAAC,EAAE,QAAQ,GAAG,MAAM,GAAG,SAAS,CAO7D;AAED;;;;GAIG;AACH,wBAAgB,WAAW,CAAC,KAAK,EAAE,MAAM,GAAG,MAAM,CAmBjD;AAED;;;;;GAKG;AACH,wBAAgB,WAAW,CAAC,IAAI,EAAE,GAAG,EAAE,EAAE,UAAU,EAAE,SAAS,EAAE,OAAO,EAAE,EAAE;IAAE,UAAU,CAAC,EAAE,OAAO,CAAC;IAAC,SAAS,CAAC,EAAE,MAAM,CAAC;IAAC,OAAO,CAAC,EAAE,MAAM,CAAC;CAAE,EAAE,MAAM,GAAE,MAAM,IAAqD,GAAG,QAAQ,CAAC,GAAG,GAAG,IAAI,CAwBpO;AAED;;;;;;;;;;;;;GAaG;AACH,wBAAgB,YAAY,CAAC,KAAK,GAAE,GAAG,EAAO,GAAG,QAAQ,CAAC,GAAG,EAAE,CAW9D"}
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package/build/utils/functs.js
CHANGED
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@@ -13,11 +13,15 @@ exports.findFilesRecursive = findFilesRecursive;
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exports.setTenant = setTenant;
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exports.getTenant = getTenant;
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exports.validateUrl = validateUrl;
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exports.scheduleJob = scheduleJob;
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exports.scheduleJobs = scheduleJobs;
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const moment_1 = __importDefault(require("moment"));
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const node_fs_1 = __importDefault(require("node:fs"));
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const node_path_1 = __importDefault(require("node:path"));
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const node_schedule_1 = __importDefault(require("node-schedule"));
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const validator_1 = __importDefault(require("validator"));
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const dotenv_1 = require("dotenv");
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const lodash_1 = require("lodash");
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/**
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* Init main application configuration stored in NxFrame APP Singleton
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*/
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@@ -116,7 +120,7 @@ async function pathExists(path = '') {
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* @param path
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*/
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function getAttr(object, path) {
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return lodash_1.
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return (0, lodash_1.get)(object, path);
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}
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/**
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*
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* @param value
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*/
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function setAttr(object, path, value) {
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return lodash_1.
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return (0, lodash_1.set)(object, path, value);
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}
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/**
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* Scan recoursively a directory to find files ending with fname
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@@ -193,4 +197,50 @@ function validateUrl(input) {
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throw new Error('Forbidden URL');
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return parsed.toString();
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}
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/**
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*
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* @param {*} options
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* @param {*} method
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*/
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function scheduleJob(rule, { recurrence, startTime, endTime }, method = () => console.log('Scheduled job', new Date())) {
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if (!rule)
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return null;
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if (recurrence && (0, lodash_1.isObject)(rule) && !(0, lodash_1.isDate)(rule)) {
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console.log('recurrence job');
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rule = Object.assign(new node_schedule_1.default.RecurrenceRule(), rule);
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}
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// set up job start/end time
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if (startTime || endTime) {
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rule = { rule };
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if (startTime)
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rule.start = (0, moment_1.default)(startTime, 'HH:mm').toDate();
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if (endTime)
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rule.end = (0, moment_1.default)(endTime, 'HH:mm').toDate();
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}
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return node_schedule_1.default.scheduleJob(rule, method);
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}
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/**
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* Schedule multiple jobs.
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* Input rules have following format:
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* { rule (string/obj), recurrence (bool), method (function) }
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*
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* Example:
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* let jobs = scheduleJobs([
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* { rule: { minute: 56 }, options: { recurrence: true }, method: () => { console.log('JOB AT MIN 56!') } },
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* { rule: '* * * * *', options: { recurrence: true }, method: () => { console.log('JOB EVERY MINUTE!') } },
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* { rule: '* * * * *', options: { recurrence: true, startTime: '10:55' }, method: () => { console.log('JOB EVERY MINUTE after 10:53!') } }
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* ]);
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*
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* @param {*} rules array of rules objects
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*/
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function scheduleJobs(rules = []) {
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let jobs = [];
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rules.forEach(({ rule, options, method }) => {
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const job = scheduleJob(rule, options, method);
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if (job)
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jobs.push(job);
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});
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return jobs;
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}
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//# sourceMappingURL=functs.js.map
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{"version":3,"file":"functs.js","sourceRoot":"","sources":["../../src/utils/functs.ts"],"names":[],"mappings":";;;;;
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+
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|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@nextage/omics-lib",
|
|
3
|
-
"version": "1.0.
|
|
3
|
+
"version": "1.0.8",
|
|
4
4
|
"main": "./build/index.js",
|
|
5
5
|
"types": "./build/index.d.ts",
|
|
6
6
|
"files": [
|
|
@@ -26,7 +26,9 @@
|
|
|
26
26
|
"@types/helmet": "^4.0.0",
|
|
27
27
|
"@types/i18n": "^0.13.12",
|
|
28
28
|
"@types/lodash": "^4.17.24",
|
|
29
|
+
"@types/moment": "^2.11.29",
|
|
29
30
|
"@types/morgan": "^1.9.9",
|
|
31
|
+
"@types/node-schedule": "^2.1.8",
|
|
30
32
|
"@types/passport": "^1.0.16",
|
|
31
33
|
"@types/passport-local": "^1.0.38",
|
|
32
34
|
"@types/validator": "^13.15.10",
|
|
@@ -44,10 +46,12 @@
|
|
|
44
46
|
"helmet": "^7.1.0",
|
|
45
47
|
"i18n": "^0.15.1",
|
|
46
48
|
"lodash": "^4.17.23",
|
|
49
|
+
"moment": "^2.30.1",
|
|
47
50
|
"mongoose": "^9.3.0",
|
|
48
51
|
"mongoose-update-if-current": "^1.4.0",
|
|
49
52
|
"morgan": "^1.10.0",
|
|
50
53
|
"nats": "^2.29.3",
|
|
54
|
+
"node-schedule": "^2.1.1",
|
|
51
55
|
"openid-client": "^5.7.1",
|
|
52
56
|
"passport": "^0.7.0",
|
|
53
57
|
"passport-local": "^1.0.0",
|