Merge pull request #60 from akb89/develop

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akb89 · Aug 21, 2018 · 6457ecd · 6457ecd
2 parents a93ffec + b8e7be3
commit 6457ecd
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Showing 22 changed files with 188 additions and 157 deletions.
diff --git a/logger/logger.js b/logger/logger.js
@@ -1,35 +1,43 @@
 const winston = require('winston');
 
-const warn = new (winston.Logger)({
+const myFormat = winston.format.combine(winston.format.timestamp(),
+                                        winston.format.colorize(),
+                                        winston.format.printf(logged => `[${logged.timestamp}] ${logged.level}: ${logged.message}`));
+
+const warn = winston.createLogger({
   transports: [
     new (winston.transports.Console)({
+      format: myFormat,
       level: 'warn',
       colorize: true,
     }),
   ],
 });
 
-const info = new (winston.Logger)({
+const info = winston.createLogger({
   transports: [
     new (winston.transports.Console)({
+      format: myFormat,
       level: 'info',
       colorize: true,
     }),
   ],
 });
 
-const verbose = new (winston.Logger)({
+const verbose = winston.createLogger({
   transports: [
     new (winston.transports.Console)({
+      format: myFormat,
       level: 'verbose',
       colorize: true,
     }),
   ],
 });
 
-const debug = new (winston.Logger)({
+const debug = winston.createLogger({
   transports: [
     new (winston.transports.Console)({
+      format: myFormat,
       level: 'debug',
       colorize: true,
     }),

diff --git a/middlewares/core/patterns.js b/middlewares/core/patterns.js
@@ -73,9 +73,9 @@ async function retrievePatternsIDs(context, next) {
   const valenceUnitsIDs = context.valencer.results.tmp.valenceUnitsIDs;
   if (valenceUnitsIDs) {
     const excludedVUids = context.valencer.results.tmp.excludedVUids;
-    const patternsIDs =
-      await getPatternIDsWithPatternModel(context.valencer.models.Pattern)(valenceUnitsIDs,
-                                                                           excludedVUids);
+    const pModel = context.valencer.models.Pattern;
+    const patternsIDs = await getPatternIDsWithPatternModel(pModel)(valenceUnitsIDs,
+                                                                    excludedVUids);
     context.valencer.results.tmp.patternsIDs = patternsIDs || [];
   }
   logger.debug(`context.valencer.results.tmp.patternsIDs.length = ${context.valencer.results.tmp.patternsIDs.length}`);

diff --git a/middlewares/core/valenceUnits.js b/middlewares/core/valenceUnits.js
@@ -20,7 +20,7 @@ const logger = config.logger;
  * single valenceUnit inside a tokenArray pattern (@see formatter)
  *
  */
-function getValenceUnitsIDsWithValenceUnitModel(ValenceUnit) {
+function getVUIDsWithValenceUnitModel(ValenceUnit) {
   return async function getValenceUnitsIDs(valenceUnitAsArrayWithFEids) {
     const valenceUnit = { FE: undefined, PT: undefined, GF: undefined };
     for (const token of valenceUnitAsArrayWithFEids) {
@@ -57,11 +57,10 @@ function getValenceUnitsIDsWithValenceUnitModel(ValenceUnit) {
   };
 }
 
-function getArrayOfArrayOfValenceUnitsIDsWithValenceUnitModel(ValenceUnit) {
+function getArrayOfArrayOfVUidsWithValenceUnitModel(ValenceUnit) {
   return async function getArrayOfArrayOfValenceUnitsIDs(formattedValencePatternArrayWithFEids) {
     return Promise.all(formattedValencePatternArrayWithFEids
-      .map(valenceUnitAsArrayWithFEids =>
-        getValenceUnitsIDsWithValenceUnitModel(ValenceUnit)(valenceUnitAsArrayWithFEids)));
+      .map(vuAsArrayWithFEids => getVUIDsWithValenceUnitModel(ValenceUnit)(vuAsArrayWithFEids)));
   };
 }
 
@@ -73,8 +72,7 @@ async function retrieveValenceUnitsIDs(context, next) {
   const startTime = utils.getStartTime();
   const vuModel = context.valencer.models.ValenceUnit;
   const vpWithFEids = context.valencer.query.vp.withFEids;
-  const valenceUnitsIDs =
-    await getArrayOfArrayOfValenceUnitsIDsWithValenceUnitModel(vuModel)(vpWithFEids);
+  const valenceUnitsIDs = await getArrayOfArrayOfVUidsWithValenceUnitModel(vuModel)(vpWithFEids);
   context.valencer.results.tmp.valenceUnitsIDs = valenceUnitsIDs || [];
   logger.debug(`context.valencer.results.tmp.valenceUnitsIDs.length = ${context.valencer.results.tmp.valenceUnitsIDs.length}`);
   logger.verbose(`context.valencer.results.tmp.valenceUnitsIDs retrieved from database in ${utils.getElapsedTime(startTime)}ms`);
@@ -119,20 +117,20 @@ async function retrieveExcludedVUIDs(context, next) {
   // Do this only if withExtraCoreFEs is set to false
   const startTime = utils.getStartTime();
   if (!context.query.withExtraCoreFEs) {
-    context.valencer.query.feNamesSet =
-      await getFrameElementNamesSet(context.valencer.query.vp.formatted,
-                                    context.valencer.query.vp.withFEids);
+    const feNamesSet = await getFrameElementNamesSet(context.valencer.query.vp.formatted,
+                                                     context.valencer.query.vp.withFEids);
+    context.valencer.query.feNamesSet = feNamesSet;
     logger.verbose(`context.valencer.results.tmp.feNamesSet retrieved from database in ${utils.getElapsedTime(startTime)}ms`);
     const startTime2 = utils.getStartTime();
     const feModel = context.valencer.models.FrameElement;
-    context.valencer.results.tmp.excludedFEids =
-      await getExcludedFEidsWithFEmodel(feModel)(context.valencer.query.feNamesSet);
+    const excludedFEids = await getExcludedFEidsWithFEmodel(feModel)(feNamesSet);
+    context.valencer.results.tmp.excludedFEids = excludedFEids;
     logger.debug(`context.valencer.results.tmp.excludedFEids.length = ${context.valencer.results.tmp.excludedFEids.length}`);
     logger.verbose(`context.valencer.results.tmp.excludedFEids retrieved from database in ${utils.getElapsedTime(startTime2)}ms`);
     const startTime3 = utils.getStartTime();
     const vuModel = context.valencer.models.ValenceUnit;
-    context.valencer.results.tmp.excludedVUids =
-      await getExcludedVUidsWithVUmodel(vuModel)(context.valencer.results.tmp.excludedFEids);
+    const exVUids = await getExcludedVUidsWithVUmodel(vuModel)(excludedFEids);
+    context.valencer.results.tmp.excludedVUids = exVUids;
     logger.verbose(`context.valencer.results.tmp.excludedVUids retrieved from database in ${utils.getElapsedTime(startTime3)}ms`);
   }
   logger.debug(`context.valencer.results.tmp.excludedVUids.length = ${context.valencer.results.tmp.excludedVUids.length}`);

diff --git a/middlewares/database.js b/middlewares/database.js
@@ -1,9 +1,11 @@
 const mongoose = require('mongoose');
-const config = require('./../config');
 const nfc = require('noframenet-core');
+const config = require('./../config');
 
 const logger = config.logger;
 
+mongoose.set('useCreateIndex', true);
+
 function connect() {
   return async function aconnect(context, next) {
     const dbName = context.valencer.dbName;

diff --git a/middlewares/filter.js b/middlewares/filter.js
@@ -28,10 +28,12 @@ async function filterPatternsIDs(context, next) {
   logger.debug(`Filtering patternsIDs with strictVUMatching = ${context.query.strictVUMatching}`);
   const startTime = utils.getStartTime();
   const patternModel = context.valencer.models.Pattern;
-  context.valencer.results.tmp.filteredPatternsIDs =
-    await getFilteredPIDsWithPModel(patternModel)(context.valencer.results.tmp.patternsIDs,
-                                                  context.valencer.results.tmp.valenceUnitsIDs,
-                                                  context.query.strictVUMatching);
+  const pIDs = context.valencer.results.tmp.patternsIDs;
+  const vuIDs = context.valencer.results.tmp.valenceUnitsIDs;
+  const fpIDs = await getFilteredPIDsWithPModel(patternModel)(pIDs,
+                                                              vuIDs,
+                                                              context.query.strictVUMatching);
+  context.valencer.results.tmp.filteredPatternsIDs = fpIDs;
   logger.debug(`context.valencer.results.tmp.filteredPatternsIDs.length = ${context.valencer.results.tmp.filteredPatternsIDs.length}`);
   logger.verbose(`context.valencer.results.tmp.filteredPatternsIDs processed in ${utils.getElapsedTime(startTime)}ms`);
   return next();

diff --git a/middlewares/formatter.js b/middlewares/formatter.js
@@ -19,20 +19,20 @@ const logger = config.logger;
  * to full valid FrameNet PhraseType and GrammaticalFunctions.
  */
 function convertPTandGFtoFNstyle(context, next) {
-  context.valencer.query.vp.formatted = context.valencer.query.vp.formatted.map(vu =>
-    vu.reduce((array, item) => {
-      if (Object.prototype.hasOwnProperty.call(constants.UD_TO_FN_MAPPING, item)) {
-        context.valencer.query.vp.hasUDtags = true;
-        array.push(constants.UD_TO_FN_MAPPING[item].PT);
-        array.push(constants.UD_TO_FN_MAPPING[item].GF);
-      } else if (Object.prototype.hasOwnProperty.call(constants.PENN_CONST_TO_FN_MAPPING, item)) {
-        context.valencer.query.vp.hasPENNtags = true;
-        array.push(constants.PENN_CONST_TO_FN_MAPPING[item]);
-      } else {
-        array.push(item);
-      }
-      return array;
-    }, []));
+  const fVPq = context.valencer.query.vp.formatted.map(vu => vu.reduce((array, item) => {
+    if (Object.prototype.hasOwnProperty.call(constants.UD_TO_FN_MAPPING, item)) {
+      context.valencer.query.vp.hasUDtags = true;
+      array.push(constants.UD_TO_FN_MAPPING[item].PT);
+      array.push(constants.UD_TO_FN_MAPPING[item].GF);
+    } else if (Object.prototype.hasOwnProperty.call(constants.PENN_CONST_TO_FN_MAPPING, item)) {
+      context.valencer.query.vp.hasPENNtags = true;
+      array.push(constants.PENN_CONST_TO_FN_MAPPING[item]);
+    } else {
+      array.push(item);
+    }
+    return array;
+  }, []));
+  context.valencer.query.vp.formatted = fVPq;
   logger.debug(`Formatted query after mapping = ${JSON.stringify(context.valencer.query.vp.formatted)}`);
   return next();
 }
@@ -93,8 +93,9 @@ function getVPasArrayWithFEidsWithFEmodel(FrameElement) {
 
 async function replaceFrameElementNamesByFrameElementIds(context, next) {
   const feModel = context.valencer.models.FrameElement;
-  context.valencer.query.vp.withFEids =
-    await getVPasArrayWithFEidsWithFEmodel(feModel)(context.valencer.query.vp.formatted);
+  const fVPq = context.valencer.query.vp.formatted;
+  const qWithFEids = await getVPasArrayWithFEidsWithFEmodel(feModel)(fVPq);
+  context.valencer.query.vp.withFEids = qWithFEids;
   logger.debug(`context.valencer.query.vp.withFEids = ${JSON.stringify(context.valencer.query.vp.withFEids)}`);
   return next();
 }
@@ -173,8 +174,8 @@ function extractFEnamesSetWithFEmodel(FrameElement) {
 
 async function extractFEnamesSet(context, next) {
   const feModel = context.valencer.models.FrameElement;
-  context.valencer.query.feNamesSet =
-    await extractFEnamesSetWithFEmodel(feModel)(context.valencer.query.vp.formatted);
+  const fVPq = context.valencer.query.vp.formatted;
+  context.valencer.query.feNamesSet = await extractFEnamesSetWithFEmodel(feModel)(fVPq);
   return next();
 }
 

diff --git a/middlewares/processors/annotationSets.js b/middlewares/processors/annotationSets.js
@@ -1,6 +1,6 @@
+const Promise = require('bluebird');
 const config = require('../../config');
 const utils = require('../../utils/utils');
-const Promise = require('bluebird');
 
 const logger = config.logger;
 

diff --git a/middlewares/processors/cluster.js b/middlewares/processors/cluster.js
@@ -52,8 +52,8 @@ async function getFrames(context, next) {
   const startTime = utils.getStartTime();
   logger.info(`Querying for all cluster frames with a valence pattern matching: '${context.query.vp}'`);
   const frModel = context.valencer.models.FrameRelation;
-  context.valencer.results.cluster =
-    await getClusterFramesWithModel(frModel)(context.valencer.results.frames);
+  const cluster = await getClusterFramesWithModel(frModel)(context.valencer.results.frames);
+  context.valencer.results.cluster = cluster;
   logger.verbose(`${context.valencer.results.cluster.length} cluster frames retrieved from database in ${utils.getElapsedTime(startTime)}ms`);
   return next();
 }
@@ -64,9 +64,9 @@ async function getLexUnits(context, next) {
     ${context.valencer.query.frameID} with a valence pattern matching:
     '${context.query.vp}'`);
   const luModel = context.valencer.models.LexUnit;
-  context.valencer.results.cluster =
-    await getClusterLexUnitsWithModel(luModel)(context.valencer.results.lexUnits,
-                                               context.valencer.query.frameID);
+  const cluster = await getClusterLexUnitsWithModel(luModel)(context.valencer.results.lexUnits,
+                                                             context.valencer.query.frameID);
+  context.valencer.results.cluster = cluster;
   logger.verbose(`${context.valencer.results.cluster.length} cluster lexUnits retrieved from database in ${utils.getElapsedTime(startTime)}ms`);
   return next();
 }

diff --git a/middlewares/processors/feHierarchy.js b/middlewares/processors/feHierarchy.js
@@ -18,9 +18,10 @@ async function getByVP(context, next) {
   logger.info(`Querying for FEHierarchy with vp = '${context.query.vp}'`);
   logger.verbose(`Corresponding feNamesSet = '${Array.from(context.valencer.query.feNamesSet)}'`);
   const feHierarchyModel = context.valencer.models.FEHierarchy;
-  const results =
-    await getFEhierarchyWithModel(feHierarchyModel)(context.valencer.query.feNamesSet,
-                                                    context.valencer.query.projections);
+  const feNamesSet = context.valencer.query.feNamesSet;
+  const projections = context.valencer.query.projections;
+  const results = await getFEhierarchyWithModel(feHierarchyModel)(feNamesSet,
+                                                                  projections);
   context.valencer.results.feHierarchy = results;
   logger.verbose(`feHierarchy retrieved from database in ${utils.getElapsedTime(startTime)}ms`);
   return next();

diff --git a/middlewares/processors/frame.js b/middlewares/processors/frame.js
@@ -14,9 +14,9 @@ async function getByID(context, next) {
   const startTime = utils.getStartTime();
   logger.info(`Querying for Frame with _id = ${context.params.id}`);
   const frameModel = context.valencer.models.Frame;
-  context.body =
-    await getFrameWithFrameModel(frameModel)(context.params.id, context.valencer.query.projections,
-                                             context.valencer.query.populations);
+  context.body = await getFrameWithFrameModel(frameModel)(context.params.id,
+                                                          context.valencer.query.projections,
+                                                          context.valencer.query.populations);
   logger.verbose(`Frame with _id = ${context.params.id} retrieved from database in ${utils.getElapsedTime(startTime)}ms`);
   return next();
 }

diff --git a/middlewares/processors/frameHierarchy.js b/middlewares/processors/frameHierarchy.js
@@ -13,9 +13,9 @@ async function getByName(context, next) {
   const startTime = utils.getStartTime();
   logger.info(`Querying for FrameHierarchy for Frame with name = ${context.query.frameName}`);
   const frameHierarchyModel = context.valencer.models.FrameHierarchy;
-  context.body =
-    await getFrameHierarchyWithModel(frameHierarchyModel)(context.query.frameName,
-                                                          context.valencer.query.projections);
+  const projections = context.valencer.query.projections;
+  context.body = await getFrameHierarchyWithModel(frameHierarchyModel)(context.query.frameName,
+                                                                       projections);
   logger.verbose(`FrameHierarchy retrieved from database in ${utils.getElapsedTime(startTime)}ms`);
   return next();
 }

diff --git a/middlewares/processors/frames.js b/middlewares/processors/frames.js
@@ -35,8 +35,8 @@ async function getByVP(context, next) {
   const startTime = utils.getStartTime();
   logger.info(`Querying for Frames with skip = '${context.valencer.query.skip}', limit = '${context.valencer.query.limit}' and vp = '${context.query.vp}'`);
   const annoSetModel = context.valencer.models.AnnotationSet;
-  const frameIDs =
-    await getFrameIDsWithModel(annoSetModel)(context.valencer.results.tmp.filteredPatternsIDs);
+  const fpIDs = context.valencer.results.tmp.filteredPatternsIDs;
+  const frameIDs = await getFrameIDsWithModel(annoSetModel)(fpIDs);
   const [count, results] = await Promise.all([
     getFramesWithModel(context.valencer.models.Frame)(frameIDs, true),
     getFramesWithModel(context.valencer.models.Frame)(frameIDs, false,

diff --git a/middlewares/processors/lexUnits.js b/middlewares/processors/lexUnits.js
@@ -28,8 +28,8 @@ async function getByVP(context, next) {
   const startTime = utils.getStartTime();
   logger.info(`Querying for LexUnits with skip = '${context.valencer.query.skip}', limit = '${context.valencer.query.limit}' and vp = '${context.query.vp}'`);
   const annosetModel = context.valencer.models.AnnotationSet;
-  const lexUnitIDs =
-    await getLexUnitIDsWithModel(annosetModel)(context.valencer.results.tmp.filteredPatternsIDs);
+  const fpIDs = context.valencer.results.tmp.filteredPatternsIDs;
+  const lexUnitIDs = await getLexUnitIDsWithModel(annosetModel)(fpIDs);
   const [count, results] = await Promise.all([
     getLexUnitsWithModel(context.valencer.models.LexUnit)(lexUnitIDs, true),
     getLexUnitsWithModel(context.valencer.models.LexUnit)(lexUnitIDs, false,

diff --git a/package.json b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "Valencer",
-  "version": "5.4.1",
+  "version": "5.4.2",
   "description": "A REST API to query valence patterns in FrameNet",
   "keywords": [
     "FrameNet",
@@ -56,24 +56,24 @@
     "kcors": "^2.2.1",
     "koa": "^2.2.0",
     "koa-compose": "^4.0.0",
-    "koa-compress": "^2.0.0",
+    "koa-compress": "^3.0.0",
     "koa-router": "^7.2.0",
     "mongoose": "^5.0.0",
     "noframenet-core": "^5.4.2",
-    "pm2": "^2.6.1",
-    "winston": "^2.3.1"
+    "pm2": "^3.0.3",
+    "winston": "^3.0.0"
   },
   "devDependencies": {
     "apidoc": "^0.17.6",
     "chai": "^4.1.1",
     "coveralls": "^3.0.0",
-    "eslint": "^4.16.0",
-    "eslint-config-airbnb": "^16.1.0",
+    "eslint": "^5.4.0",
+    "eslint-config-airbnb": "^17.1.0",
     "eslint-plugin-import": "^2.3.0",
     "eslint-plugin-jsx-a11y": "^6.0.3",
     "eslint-plugin-react": "^7.1.0",
     "mocha": "^5.0.0",
-    "nyc": "^11.0.2",
-    "rewire": "^3.0.2"
+    "nyc": "^13.0.1",
+    "rewire": "^4.0.1"
   }
 }
diff --git a/server.js b/server.js
@@ -14,6 +14,8 @@ const zlib = require('zlib');
 const router = require('./routes');
 const config = require('./config');
 
+mongoose.set('useCreateIndex', true);
+
 const logger = config.logger;
 const app = new Koa();
 
@@ -29,7 +31,7 @@ app.use(async (context, next) => {
   try {
     await next();
   } catch (err) {
-    logger.error(err);
+    logger.error(err.message);
     err.expose = true; // expose the error to the context;
     context.status = err.status || 500;
     context.body = err.message;
@@ -52,8 +54,8 @@ function printLogo() {
     printLogo();
     const dbServer = config.databases.server;
     const dbPort = config.databases.port;
-    const dbUri = `mongodb://${dbServer}:${dbPort}`;
-    await mongoose.connect(dbUri);
+    const dbUri = `mongodb://${dbServer}:${dbPort}/''`;
+    await mongoose.connect(dbUri, { useNewUrlParser: true });
     logger.info(`Connected to MongoDB on server: '${dbServer}' and port '${dbPort}'`);
     await app.listen(config.api.port);
     logger.info(`Valencer started on port ${config.api.port}`);