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@@ -0,0 +1,128 @@
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+"use strict";
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+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
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+ if (k2 === undefined) k2 = k;
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+ var desc = Object.getOwnPropertyDescriptor(m, k);
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+ if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
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+ desc = { enumerable: true, get: function() { return m[k]; } };
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+ }
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+ Object.defineProperty(o, k2, desc);
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+}) : (function(o, m, k, k2) {
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+ if (k2 === undefined) k2 = k;
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+ o[k2] = m[k];
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+}));
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+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
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+ Object.defineProperty(o, "default", { enumerable: true, value: v });
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+}) : function(o, v) {
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+ o["default"] = v;
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+});
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+var __importStar = (this && this.__importStar) || function (mod) {
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+ if (mod && mod.__esModule) return mod;
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+ var result = {};
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+ if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
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+ __setModuleDefault(result, mod);
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+ return result;
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+};
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+var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
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+ function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
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+ return new (P || (P = Promise))(function (resolve, reject) {
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+ function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
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+ function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
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+ function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
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+ step((generator = generator.apply(thisArg, _arguments || [])).next());
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+ });
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+};
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+var __asyncValues = (this && this.__asyncValues) || function (o) {
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+ if (!Symbol.asyncIterator) throw new TypeError("Symbol.asyncIterator is not defined.");
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+ var m = o[Symbol.asyncIterator], i;
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+ return m ? m.call(o) : (o = typeof __values === "function" ? __values(o) : o[Symbol.iterator](), i = {}, verb("next"), verb("throw"), verb("return"), i[Symbol.asyncIterator] = function () { return this; }, i);
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+ function verb(n) { i[n] = o[n] && function (v) { return new Promise(function (resolve, reject) { v = o[n](v), settle(resolve, reject, v.done, v.value); }); }; }
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+ function settle(resolve, reject, d, v) { Promise.resolve(v).then(function(v) { resolve({ value: v, done: d }); }, reject); }
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+};
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+var __importDefault = (this && this.__importDefault) || function (mod) {
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+ return (mod && mod.__esModule) ? mod : { "default": mod };
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+};
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+Object.defineProperty(exports, "__esModule", { value: true });
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+const fs_1 = __importDefault(require("fs"));
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+const readline_1 = __importDefault(require("readline"));
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+const neo4j = __importStar(require("neo4j-driver"));
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+const line$ = (path) => readline_1.default.createInterface({
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+ input: fs_1.default.createReadStream(path),
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+ crlfDelay: Infinity
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+});
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+const templateGTnode = (args) => {
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+ let tmp = 'CREATE (gt:GoTerm {';
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+ Object.keys(args).forEach((dd, ii) => {
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+ const delim = ii === 0 ? '' : ', ';
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+ tmp += `${delim}${dd}: "${args[dd].replace(/"/g, '')}"`;
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+ });
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+ tmp += '})';
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+ return tmp;
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+};
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+const templateEdge = (from, to) => {
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+ return `MATCH (from:GoTerm {id: '${from}'})
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+ MATCH (to:GoTerm {id: '${to}'})
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+ CREATE (from)-[rel:is_a]->(to)`;
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+};
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+const insert = (oboPath) => __awaiter(void 0, void 0, void 0, function* () {
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+ var e_1, _a;
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+ let delim = false;
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+ const results = [];
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+ const vertexes = [];
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+ const edges = [];
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+ let result = {};
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+ try {
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+ for (var _b = __asyncValues(line$(oboPath)), _c; _c = yield _b.next(), !_c.done;) {
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+ const line = _c.value;
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+ if (line === '[Term]') {
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+ delim = true;
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+ }
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+ else if (line === '' && delim) {
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+ delim = false;
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+ vertexes.push(templateGTnode(result));
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+ if (result === null || result === void 0 ? void 0 : result.is_a) {
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+ if (/^GO:[0-9]*/.test(result.is_a)) {
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+ edges.push(templateEdge(result.id, result.is_a.match(/^GO:[0-9]*/)[0]));
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+ }
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+ }
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+ result = {};
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+ results.push(result);
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+ }
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+ else if (delim)
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+ result[line.split(': ')[0]] = line.split(': ')[1].replace("\"", "");
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+ }
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+ }
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+ catch (e_1_1) { e_1 = { error: e_1_1 }; }
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+ finally {
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+ try {
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+ if (_c && !_c.done && (_a = _b.return)) yield _a.call(_b);
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+ }
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+ finally { if (e_1) throw e_1.error; }
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+ }
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+ return { vertexes, edges };
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+});
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+const runNeo = (session, sql) => {
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+ return new Promise((resolve, reject) => {
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+ try {
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+ session.run(sql).then((result) => resolve(result)).catch((err) => reject(err));
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+ }
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+ catch (error) {
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+ reject(error);
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+ }
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+ });
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+};
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+(() => __awaiter(void 0, void 0, void 0, function* () {
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+ const oboPath = '/home/thomas/NGS/ref/GO/go-basic.obo';
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+ var driver = neo4j.driver('neo4j://localhost', neo4j.auth.basic('neo4j', '123456'));
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+ var session = driver.session();
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+ console.log(session);
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+ const rr = yield insert(oboPath);
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+ // const rr = await getGOterms('GO:0008150', oboPath)
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+ console.log(rr.edges[0]);
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+ for (const v of rr.vertexes) {
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+ yield runNeo(session, v);
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+ }
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+ for (const e of rr.edges) {
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+ yield runNeo(session, e);
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+ }
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+ yield driver.close();
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+}))();
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