Remove node fibers

Ref: node fibers #145

package.json

@@ -69,7 +69,6 @@
     "elasticsearch": "^15.4.1",
     "esm": "^3.2.22",
     "express": "^4.13.4",
-    "fibers": "^5.0.0",
     "ftp": "^0.3.10",
     "lodash": "^4.17.11",
     "morgan": "^1.7.0",

src/server/datasource/aggregate.js

@@ -5,7 +5,6 @@ import _ from 'lodash';
 import ROOT_STRAINS from './strains/root';
 import { getOrganismById } from './organisms';
 import { MAX_SEARCH_WS, MAX_FUZZ_ES } from '../config';
-import Future from 'fibers/future';
 
 const ROOT_STRAIN_ORGS = Object.values(ROOT_STRAINS).map(getOrganismById);
 const isRootStrainOrgId = id => ROOT_STRAIN_ORGS.some(org => org.is(id));
@@ -63,32 +62,33 @@ const search = function(searchString, namespace = ['ncbi', 'chebi', 'fplx'], org
     });
   };
 
-  const doStrainFilter = ents => {
-    let task = Future.wrap(function(args, next){ // code in this block runs in its own thread
-      let res = filterStrains(args.ents);
-      let err = null;
-
-      next( err, res );
+  const doStrainFilter = (ents) => {
+    return new Promise((resolve, reject) => {
+      try {
+        const res = filterStrains(ents);
+        resolve(res);
+      } catch (err) {
+        reject(err);
+      }
     });
-
-    return task({ ents }).promise();
   };
 
   const doSearches = () => {
     const join = ress => _.uniqWith(_.concat(...ress), (ent1, ent2) => {
       return ent1.namespace === ent2.namespace && ent1.id === ent2.id;
     });
 
-    const doJoin = ress => {
-      let task = Future.wrap(function(args, next){ // code in this block runs in its own thread
-        let res = join(args.ress);
-        let err = null;
-
-        next( err, res );
+    const doJoin = (ress) => {
+      return new Promise((resolve, reject) => {
+        try {
+          const res = join(ress);
+          resolve(res);
+        } catch (err) {
+          reject(err);
+        }
       });
-
-      return task({ ress }).promise();
     };
+
 
     if( searchString.length === 1 ){
       return doSearch(0);

src/server/datasource/processing.js

@@ -1,20 +1,19 @@
 /** @module processing */
-import Future from 'fibers/future';
 import _ from 'lodash';
 
 import { db } from '../db';
 import logger from '../logger';
 import { CHUNK_SIZE, MAX_SIMULT_CHUNKS } from '../config';
 
 const processChunk = (chunk, processEntry) => {
-  let task = Future.wrap(function(chunk, next){ // code in this block runs in its own thread
-    let processedEntries = chunk.map(processEntry);
-    let err = null;
-
-    next( err, processedEntries );
+  return new Promise((resolve, reject) => {
+    try {
+      const processedEntries = chunk.map(processEntry);
+      resolve(processedEntries);
+    } catch (err) {
+      reject(err);
+    }
   });
-
-  return task(chunk).promise();
 };
 
 /**

src/server/datasource/rank.js

@@ -2,7 +2,6 @@
 import _ from 'lodash';
 import { getOrganismIndex, getDefaultOrganismIndex } from './organisms';
 import dice from 'dice-coefficient'; // sorensen dice coeff
-import Future from 'fibers/future';
 import { sanitizeNameForCmp as sanitize } from '../util';
 
 const DISTANCE_FIELDS = ['name', 'synonyms']; // TODO should share list with db.js
@@ -120,13 +119,14 @@ export const rank = (ents, searchTerm, organismOrdering) => {
 };
 
 export const rankInThread = (ents, searchTerm, organismOrdering) => {
-  let task = Future.wrap(function(args, next){ // code in this block runs in its own thread
-    let res = rank(args.ents, args.searchTerm, args.organismOrdering);
-    let err = null;
-
-    next( err, res );
+  // TODO put back in separate thread if necessary in future
+  return new Promise((resolve, reject) => {
+    try {
+      const res = rank(ents, searchTerm, organismOrdering);
+      resolve(res);
+    } catch (err) {
+      reject(err);
+    }
   });
-
-  return task({ ents, searchTerm, organismOrdering }).promise();
 };