first commit

bio-parsers.d.ts

@@ -0,0 +1 @@
+declare module 'bio-parsers';

index.js

@@ -0,0 +1,68 @@
+'use strict';
+var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
+    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
+    return new (P || (P = Promise))(function (resolve, reject) {
+        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
+        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
+        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
+        step((generator = generator.apply(thisArg, _arguments || [])).next());
+    });
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const path_1 = __importDefault(require("path"));
+const piscina_1 = __importDefault(require("piscina"));
+(() => __awaiter(void 0, void 0, void 0, function* () {
+    const getEsearch = new piscina_1.default({
+        filename: path_1.default.resolve(__dirname, './workers/esearch.js')
+    });
+    // const orders = 
+    // [
+    //     {
+    //         params: {
+    //             db: 'nuccore',
+    //             term: 'NM_001143971.2'
+    //         },
+    //         xpath: 'string((//Id)[1])'
+    //     },
+    //     {
+    //         params: {
+    //             db: 'gene',
+    //             term: 'NM_001143971.2'
+    //         },
+    //         xpath: 'string((//Id)[1])'
+    //     },
+    // ]
+    // const results = await Promise.all(orders.map(e => getEsearch.run(e)))
+    // console.log(results);
+    const orders = [
+        // {
+        //     params: {
+        //         db: 'nuccore',
+        //         id: '1674999401',
+        //         rettype: 'gb',
+        //         retmode: 'text'
+        //     },
+        //     xpath: '/',
+        //     endpoint: 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi'
+        // },
+        // {
+        //     db: 'nuccore',
+        //     id: '1674999401',
+        //     rettype: 'native',
+        //     retmode: 'xml',
+        //     endpoint: 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi'
+        // },
+        {
+            db: 'pubmed',
+            id: '19393038',
+            retmode: 'xml',
+            endpoint: 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi',
+            query: `**.AbstractText`
+        },
+    ];
+    const results = yield Promise.all(orders.map(e => getEsearch.run(e)));
+    console.log(results);
+}))();

index.ts

@@ -0,0 +1,61 @@
+'use strict'
+
+import path from "path"
+import Piscina from "piscina"
+
+
+(async()=>{
+    const getEsearch = new Piscina({
+        filename: path.resolve(__dirname, './workers/esearch.js')
+    })
+
+    // const orders = 
+    // [
+    //     {
+    //         params: {
+    //             db: 'nuccore',
+    //             term: 'NM_001143971.2'
+    //         },
+    //         xpath: 'string((//Id)[1])'
+    //     },
+    //     {
+    //         params: {
+    //             db: 'gene',
+    //             term: 'NM_001143971.2'
+    //         },
+    //         xpath: 'string((//Id)[1])'
+    //     },
+    // ]
+    // const results = await Promise.all(orders.map(e => getEsearch.run(e)))
+    // console.log(results);
+
+    const orders =
+    [
+        // {
+        //     params: {
+        //         db: 'nuccore',
+        //         id: '1674999401',
+        //         rettype: 'gb',
+        //         retmode: 'text'
+        //     },
+        //     xpath: '/',
+        //     endpoint: 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi'
+        // },
+        // {
+        //     db: 'nuccore',
+        //     id: '1674999401',
+        //     rettype: 'native',
+        //     retmode: 'xml',
+        //     endpoint: 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi'
+        // },
+        {
+            db: 'pubmed',
+            id: '19393038',
+            retmode: 'xml',
+            endpoint: 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi',
+            query: `**.AbstractText`
+        },
+    ]
+    const results = await Promise.all(orders.map(e => getEsearch.run(e)))
+    console.log(results);
+})()

package-lock.json

@@ -0,0 +1,585 @@
+{
+  "name": "ncbiparse",
+  "version": "1.0.0",
+  "lockfileVersion": 2,
+  "requires": true,
+  "packages": {
+    "": {
+      "name": "ncbiparse",
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+        "xml2json": "^0.12.0",
+        "xmldom": "^0.6.0",
+        "xpath": "^0.0.32"
+      },
+      "devDependencies": {
+        "@types/node": "^17.0.19",
+        "@types/xml2js": "^0.4.9",
+        "@types/xml2json": "^0.11.4",
+        "@types/xmldom": "^0.1.31",
+        "typescript": "^4.5.5"
+      }
+    },
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+      "license": "Apache-2.0"
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+    },
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+      "resolved": "https://registry.npmjs.org/xmldom/-/xmldom-0.6.0.tgz",
+      "integrity": "sha512-iAcin401y58LckRZ0TkI4k0VSM1Qg0KGSc3i8rU+xrxe19A/BN1zHyVSJY7uoutVlaTSzYyk/v5AmkewAP7jtg=="
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+      "resolved": "https://registry.npmjs.org/xpath/-/xpath-0.0.32.tgz",
+      "integrity": "sha512-rxMJhSIoiO8vXcWvSifKqhvV96GjiD5wYb8/QHdoRyQvraTpp4IEv944nhGausZZ3u7dhQXteZuZbaqfpB7uYw=="
+    }
+  }
+}

package.json

@@ -0,0 +1,30 @@
+{
+  "name": "ncbiparse",
+  "version": "1.0.0",
+  "description": "",
+  "main": "index.js",
+  "scripts": {
+    "build": "tsc",
+    "test": "echo \"Error: no test specified\" && exit 1"
+  },
+  "keywords": [],
+  "author": "",
+  "license": "ISC",
+  "devDependencies": {
+    "@types/node": "^17.0.19",
+    "@types/xml2js": "^0.4.9",
+    "@types/xml2json": "^0.11.4",
+    "@types/xmldom": "^0.1.31",
+    "typescript": "^4.5.5"
+  },
+  "dependencies": {
+    "axios": "^0.26.0",
+    "fast-xml-parser": "^4.0.3",
+    "genbank-parser": "^1.2.4",
+    "jsonata": "^1.8.6",
+    "piscina": "^3.2.0",
+    "xml2json": "^0.12.0",
+    "xmldom": "^0.6.0",
+    "xpath": "^0.0.32"
+  }
+}

tsconfig.json

@@ -0,0 +1,101 @@
+{
+  "compilerOptions": {
+    /* Visit https://aka.ms/tsconfig.json to read more about this file */
+
+    /* Projects */
+    // "incremental": true,                              /* Enable incremental compilation */
+    // "composite": true,                                /* Enable constraints that allow a TypeScript project to be used with project references. */
+    // "tsBuildInfoFile": "./",                          /* Specify the folder for .tsbuildinfo incremental compilation files. */
+    // "disableSourceOfProjectReferenceRedirect": true,  /* Disable preferring source files instead of declaration files when referencing composite projects */
+    // "disableSolutionSearching": true,                 /* Opt a project out of multi-project reference checking when editing. */
+    // "disableReferencedProjectLoad": true,             /* Reduce the number of projects loaded automatically by TypeScript. */
+
+    /* Language and Environment */
+    "target": "es2016",                                  /* Set the JavaScript language version for emitted JavaScript and include compatible library declarations. */
+    // "lib": [],                                        /* Specify a set of bundled library declaration files that describe the target runtime environment. */
+    // "jsx": "preserve",                                /* Specify what JSX code is generated. */
+    // "experimentalDecorators": true,                   /* Enable experimental support for TC39 stage 2 draft decorators. */
+    // "emitDecoratorMetadata": true,                    /* Emit design-type metadata for decorated declarations in source files. */
+    // "jsxFactory": "",                                 /* Specify the JSX factory function used when targeting React JSX emit, e.g. 'React.createElement' or 'h' */
+    // "jsxFragmentFactory": "",                         /* Specify the JSX Fragment reference used for fragments when targeting React JSX emit e.g. 'React.Fragment' or 'Fragment'. */
+    // "jsxImportSource": "",                            /* Specify module specifier used to import the JSX factory functions when using `jsx: react-jsx*`.` */
+    // "reactNamespace": "",                             /* Specify the object invoked for `createElement`. This only applies when targeting `react` JSX emit. */
+    // "noLib": true,                                    /* Disable including any library files, including the default lib.d.ts. */
+    // "useDefineForClassFields": true,                  /* Emit ECMAScript-standard-compliant class fields. */
+
+    /* Modules */
+    "module": "commonjs",                                /* Specify what module code is generated. */
+    // "rootDir": "./",                                  /* Specify the root folder within your source files. */
+    // "moduleResolution": "node",                       /* Specify how TypeScript looks up a file from a given module specifier. */
+    // "baseUrl": "./",                                  /* Specify the base directory to resolve non-relative module names. */
+    // "paths": {},                                      /* Specify a set of entries that re-map imports to additional lookup locations. */
+    // "rootDirs": [],                                   /* Allow multiple folders to be treated as one when resolving modules. */
+    // "typeRoots": [],                                  /* Specify multiple folders that act like `./node_modules/@types`. */
+    // "types": [],                                      /* Specify type package names to be included without being referenced in a source file. */
+    // "allowUmdGlobalAccess": true,                     /* Allow accessing UMD globals from modules. */
+    // "resolveJsonModule": true,                        /* Enable importing .json files */
+    // "noResolve": true,                                /* Disallow `import`s, `require`s or `<reference>`s from expanding the number of files TypeScript should add to a project. */
+
+    /* JavaScript Support */
+    // "allowJs": true,                                  /* Allow JavaScript files to be a part of your program. Use the `checkJS` option to get errors from these files. */
+    // "checkJs": true,                                  /* Enable error reporting in type-checked JavaScript files. */
+    // "maxNodeModuleJsDepth": 1,                        /* Specify the maximum folder depth used for checking JavaScript files from `node_modules`. Only applicable with `allowJs`. */
+
+    /* Emit */
+    // "declaration": true,                              /* Generate .d.ts files from TypeScript and JavaScript files in your project. */
+    // "declarationMap": true,                           /* Create sourcemaps for d.ts files. */
+    // "emitDeclarationOnly": true,                      /* Only output d.ts files and not JavaScript files. */
+    // "sourceMap": true,                                /* Create source map files for emitted JavaScript files. */
+    // "outFile": "./",                                  /* Specify a file that bundles all outputs into one JavaScript file. If `declaration` is true, also designates a file that bundles all .d.ts output. */
+    // "outDir": "./",                                   /* Specify an output folder for all emitted files. */
+    // "removeComments": true,                           /* Disable emitting comments. */
+    // "noEmit": true,                                   /* Disable emitting files from a compilation. */
+    // "importHelpers": true,                            /* Allow importing helper functions from tslib once per project, instead of including them per-file. */
+    // "importsNotUsedAsValues": "remove",               /* Specify emit/checking behavior for imports that are only used for types */
+    // "downlevelIteration": true,                       /* Emit more compliant, but verbose and less performant JavaScript for iteration. */
+    // "sourceRoot": "",                                 /* Specify the root path for debuggers to find the reference source code. */
+    // "mapRoot": "",                                    /* Specify the location where debugger should locate map files instead of generated locations. */
+    // "inlineSourceMap": true,                          /* Include sourcemap files inside the emitted JavaScript. */
+    // "inlineSources": true,                            /* Include source code in the sourcemaps inside the emitted JavaScript. */
+    // "emitBOM": true,                                  /* Emit a UTF-8 Byte Order Mark (BOM) in the beginning of output files. */
+    // "newLine": "crlf",                                /* Set the newline character for emitting files. */
+    // "stripInternal": true,                            /* Disable emitting declarations that have `@internal` in their JSDoc comments. */
+    // "noEmitHelpers": true,                            /* Disable generating custom helper functions like `__extends` in compiled output. */
+    // "noEmitOnError": true,                            /* Disable emitting files if any type checking errors are reported. */
+    // "preserveConstEnums": true,                       /* Disable erasing `const enum` declarations in generated code. */
+    // "declarationDir": "./",                           /* Specify the output directory for generated declaration files. */
+    // "preserveValueImports": true,                     /* Preserve unused imported values in the JavaScript output that would otherwise be removed. */
+
+    /* Interop Constraints */
+    // "isolatedModules": true,                          /* Ensure that each file can be safely transpiled without relying on other imports. */
+    // "allowSyntheticDefaultImports": true,             /* Allow 'import x from y' when a module doesn't have a default export. */
+    "esModuleInterop": true,                             /* Emit additional JavaScript to ease support for importing CommonJS modules. This enables `allowSyntheticDefaultImports` for type compatibility. */
+    // "preserveSymlinks": true,                         /* Disable resolving symlinks to their realpath. This correlates to the same flag in node. */
+    "forceConsistentCasingInFileNames": true,            /* Ensure that casing is correct in imports. */
+
+    /* Type Checking */
+    "strict": true,                                      /* Enable all strict type-checking options. */
+    // "noImplicitAny": true,                            /* Enable error reporting for expressions and declarations with an implied `any` type.. */
+    // "strictNullChecks": true,                         /* When type checking, take into account `null` and `undefined`. */
+    // "strictFunctionTypes": true,                      /* When assigning functions, check to ensure parameters and the return values are subtype-compatible. */
+    // "strictBindCallApply": true,                      /* Check that the arguments for `bind`, `call`, and `apply` methods match the original function. */
+    // "strictPropertyInitialization": true,             /* Check for class properties that are declared but not set in the constructor. */
+    // "noImplicitThis": true,                           /* Enable error reporting when `this` is given the type `any`. */
+    // "useUnknownInCatchVariables": true,               /* Type catch clause variables as 'unknown' instead of 'any'. */
+    // "alwaysStrict": true,                             /* Ensure 'use strict' is always emitted. */
+    // "noUnusedLocals": true,                           /* Enable error reporting when a local variables aren't read. */
+    // "noUnusedParameters": true,                       /* Raise an error when a function parameter isn't read */
+    // "exactOptionalPropertyTypes": true,               /* Interpret optional property types as written, rather than adding 'undefined'. */
+    // "noImplicitReturns": true,                        /* Enable error reporting for codepaths that do not explicitly return in a function. */
+    // "noFallthroughCasesInSwitch": true,               /* Enable error reporting for fallthrough cases in switch statements. */
+    // "noUncheckedIndexedAccess": true,                 /* Include 'undefined' in index signature results */
+    // "noImplicitOverride": true,                       /* Ensure overriding members in derived classes are marked with an override modifier. */
+    // "noPropertyAccessFromIndexSignature": true,       /* Enforces using indexed accessors for keys declared using an indexed type */
+    // "allowUnusedLabels": true,                        /* Disable error reporting for unused labels. */
+    // "allowUnreachableCode": true,                     /* Disable error reporting for unreachable code. */
+
+    /* Completeness */
+    // "skipDefaultLibCheck": true,                      /* Skip type checking .d.ts files that are included with TypeScript. */
+    "skipLibCheck": true                                 /* Skip type checking all .d.ts files. */
+  }
+}

workers/esearch.js

@@ -0,0 +1,43 @@
+"use strict";
+var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
+    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
+    return new (P || (P = Promise))(function (resolve, reject) {
+        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
+        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
+        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
+        step((generator = generator.apply(thisArg, _arguments || [])).next());
+    });
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const axios_1 = __importDefault(require("axios"));
+const genbank_parser_1 = __importDefault(require("genbank-parser"));
+const fast_xml_parser_1 = require("fast-xml-parser");
+const jsonata_1 = __importDefault(require("jsonata"));
+const getEsearch = (params) => __awaiter(void 0, void 0, void 0, function* () {
+    const endpoint = (params === null || params === void 0 ? void 0 : params.endpoint) ? params.endpoint : 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi';
+    const query = (params === null || params === void 0 ? void 0 : params.query) || '';
+    const allowedParams = ['id', 'db', 'retmode', 'rettype'];
+    // console.log('query :', `${endpoint}?${Object.keys(params).flatMap(k => allowedParams.includes(k) ? k + '=' + params[k] : []).join('&')}`);
+    const response = yield axios_1.default.get(`${endpoint}?${Object.keys(params).flatMap(k => allowedParams.includes(k) ? k + '=' + params[k] : []).join('&')}`);
+    let results = Array.isArray(response.data) ? response.data.join('') : response.data;
+    if (params === null || params === void 0 ? void 0 : params.retmode) {
+        switch (params.retmode) {
+            case 'xml':
+                const parser = new fast_xml_parser_1.XMLParser({ ignoreAttributes: false, alwaysCreateTextNode: false, attributeNamePrefix: "attr-" });
+                results = parser.parse(results);
+                break;
+            case 'gb':
+                results = (0, genbank_parser_1.default)(results);
+                break;
+            default:
+                break;
+        }
+    }
+    if (query !== '')
+        results = (0, jsonata_1.default)(query).evaluate(results);
+    return results;
+});
+module.exports = (params) => __awaiter(void 0, void 0, void 0, function* () { return yield getEsearch(params); });

workers/esearch.ts

@@ -0,0 +1,38 @@
+import axios from 'axios'
+import genbankParser from 'genbank-parser'
+import { XMLParser } from 'fast-xml-parser'
+import jsonata from "jsonata"
+
+const getEsearch = async (
+    params: any
+) => {
+    const endpoint = params?.endpoint ? params.endpoint : 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi'
+    const query = params?.query || ''
+    const allowedParams = ['id', 'db', 'retmode', 'rettype']
+    
+    // console.log('query :', `${endpoint}?${Object.keys(params).flatMap(k => allowedParams.includes(k) ? k + '=' + params[k] : []).join('&')}`);
+    const response = await axios.get(`${endpoint}?${Object.keys(params).flatMap(k => allowedParams.includes(k) ? k + '=' + params[k] : []).join('&')}`)
+    
+    let results = Array.isArray(response.data) ? response.data.join('') : response.data
+    if (params?.retmode) {
+        switch (params.retmode) {
+            case 'xml':
+                const parser = new XMLParser({
+                    ignoreAttributes : false, alwaysCreateTextNode: false, attributeNamePrefix : "attr-", allowBooleanAttributes: true
+            })
+                results = parser.parse(results)
+                break;
+            case 'gb':
+                results = genbankParser(results)
+                break;
+            default:
+                break;
+        }
+    }
+
+    if (query !== '') results = jsonata(query).evaluate(results)
+
+    return results
+}
+
+module.exports = async (params:any) => await getEsearch(params)

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