Merge branch 'machine-plus-human-identifiers' into uploadsBugFixing

feup-infolab · Aug 2, 2017 · bc7ca45 · bc7ca45
2 parents dc47961 + 222ff3d
commit bc7ca45
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Showing 11 changed files with 149 additions and 195 deletions.
diff --git a/conf/deployment_configs.json b/conf/deployment_configs.json
@@ -228,11 +228,12 @@
       "reload_ontologies_on_startup": true,
       "reload_descriptors_on_startup": true,
       "reload_research_domains_on_startup": true,
-      "reload_descriptor_validation_data" : false,
+      "reload_descriptor_validation_data" : true,
       "clear_session_store": true,
       "clear_caches" : true,
       "log_bootup_actions" : true,
-      "destroy_all_graphs_on_startup": false
+      "destroy_all_graphs": false,
+      "destroy_all_indexes": false
     },
     "baselines": {
     },
@@ -582,17 +583,18 @@
       }
     },
     "startup": {
-      "load_databases": false,
+      "load_databases": true,
       "reload_administrators_on_startup": true,
-      "reload_demo_users_on_startup": true,
+      "reload_demo_users_on_startup": false,
       "reload_ontologies_on_startup": true,
       "reload_descriptors_on_startup": true,
       "reload_research_domains_on_startup": true,
-      "reload_descriptor_validation_data" : false,
+      "reload_descriptor_validation_data" : true,
       "clear_session_store": true,
       "clear_caches" : true,
-      "log_bootup_actions" : false,
-      "destroy_all_graphs_on_startup": true
+      "log_bootup_actions" : true,
+      "destroy_all_graphs": true,
+      "destroy_all_indexes": true
     },
     "baselines": {
     },
@@ -929,15 +931,16 @@
     "startup": {
       "load_databases": true,
       "reload_administrators_on_startup": true,
-      "reload_demo_users_on_startup": true,
+      "reload_demo_users_on_startup": false,
       "reload_ontologies_on_startup": true,
       "reload_descriptors_on_startup": true,
       "reload_research_domains_on_startup": true,
-      "reload_descriptor_validation_data" : false,
+      "reload_descriptor_validation_data" : true,
       "clear_session_store": true,
       "clear_caches" : true,
-      "log_bootup_actions" : false,
-      "destroy_all_graphs_on_startup": true
+      "log_bootup_actions" : true,
+      "destroy_all_graphs": true,
+      "destroy_all_indexes": true
     },
     "baselines": {
     },

diff --git a/conf/scripts/install.sh b/conf/scripts/install.sh
@@ -1,16 +1,5 @@
 #!/usr/bin/env bash
 
-#install NVM, Node 6.10, Node Automatic Version switcher
-curl -o- https://raw.githubusercontent.com/creationix/nvm/v0.33.1/install.sh | bash &&
-export NVM_DIR="$HOME/.nvm" &&
-[ -s "$NVM_DIR/nvm.sh" ] && \. "$NVM_DIR/nvm.sh"
-
-# Want NVM to be loaded on every terminal you open? Add to ~/.bash_profile this:
-
-#export NVM_DIR="$HOME/.nvm" &&
-#[ -s "$NVM_DIR/nvm.sh" ] && \. "$NVM_DIR/nvm.sh"
-
-
 INITIAL_DIR=`pwd`
 NODE_VERSION=`cat .node-version`
 
@@ -19,10 +8,18 @@ then
     echo "Unable to determine the version of NodeJS to install!"
     exit 1
 else
+    #install NVM, Node, Node Automatic Version switcher
+    curl -o- https://raw.githubusercontent.com/creationix/nvm/v0.33.1/install.sh | bash &&
+    export NVM_DIR="$HOME/.nvm" &&
+    [ -s "$NVM_DIR/nvm.sh" ] && \. "$NVM_DIR/nvm.sh" && # This loads nvm
 
-    nvm install $NODE_VERSION
-    npm install -g avn avn-nvm avn-n
-    avn setup
+    nvm install $NODE_VERSION &&
+    npm install -g avn avn-nvm avn-n &&
+    avn setup &&
+
+    [[ -s "$HOME/.avn/bin/avn.sh" ]] && source "$HOME/.avn/bin/avn.sh" && # load avn
+
+    echo "loaded NVM and AVN."
 
     #update npm
     npm install npm
@@ -41,3 +38,7 @@ else
     grunt
 fi
 
+# Want NVM to be loaded on every terminal you open? Add to ~/.bash_profile this:
+
+#export NVM_DIR="$HOME/.nvm" &&
+#[ -s "$NVM_DIR/nvm.sh" ] && \. "$NVM_DIR/nvm.sh"
diff --git a/package.json b/package.json
@@ -7,13 +7,13 @@
     "reinstall": "rm -rf node_modules && npm cache clean && npm install",
     "preinstall": "npm i -g npm && npm i -g gladstone && npm install -g istanbul && npm i -g nyc && npm i -g coveralls",
     "post-install": "",
-    "test": "cross-env NODE_ENV=test node node_modules/.bin/_mocha ./test/index.Test.js -t 60000 --ui bdd",
+    "test": "cross-env NODE_ENV=test node node_modules/.bin/_mocha ./test/index.Test.js -t 15000 --ui bdd --bail",
     "watch": "npm test -w",
     "calculate-coverage": "nyc --temp-directory=coverage --reporter=lcov npm test",
     "report-coverage": "node ./node_modules/coveralls/bin/coveralls.js < ./coverage/lcov.info && node ./node_modules/codeclimate-test-reporter/bin/codeclimate.js < ./coverage/lcov.info && rm -rf coverage",
     "everything": "rm -rf node_modules && npm cache verify && npm install && npm run test && npm run calculate-coverage && npm run report-coverage",
     "remote_debug": "node app.js --debug=5858",
-    "profile": "cross-env NODE_ENV=test node --prof node_modules/.bin/_mocha ./test/index.Test.js -t 60000 --ui bdd"
+    "profile": "cross-env NODE_ENV=test node --prof node_modules/.bin/_mocha ./test/index.Test.js -t 15000 --ui bdd"
   },
   "dependencies": {
     "archiver": "*",

diff --git a/src/app.js b/src/app.js
@@ -37,12 +37,10 @@ let express = require('express'),
     Q = require('q');
 
 /**
- * Promises for reporting the progress of the bootup operation.
+ * Promise for reporting the bootup operation.
  */
 
-let bootupCompletePromise = Q.defer();
 let serverListeningPromise = Q.defer();
-let connectionsInitializedPromise = Q.defer();
 
 self.app = express();
 
@@ -121,15 +119,10 @@ const prepareEnvironment = function(callback)
         }
     ],function(err, results)
     {
-        if(isNull(err))
-        {
-            connectionsInitializedPromise.resolve();
-        }
-        else
+        if(!isNull(err))
         {
             console.error("There was an error performing preliminary setup operations during Dendro bootup!");
             console.error(err.stack);
-            connectionsInitializedPromise.reject(results);
         }
 
         return callback(err, results);
@@ -205,7 +198,6 @@ const startWebServer = function(callback)
         function(app, server, callback)
         {
             self.server = server;
-            bootupCompletePromise.resolve({server: self.server, app: self.app});
 
             if (process.env.NODE_ENV !== "test")
             {
@@ -260,6 +252,4 @@ async.series([
     }]
 );
 
-exports.bootupComplete = bootupCompletePromise.promise;
-exports.connectionsInitialized = connectionsInitializedPromise.promise;
 exports.serverListening = serverListeningPromise.promise;
diff --git a/src/bootup/init/setup_graceful_close.js b/src/bootup/init/setup_graceful_close.js
@@ -4,13 +4,14 @@ const Config = require(Pathfinder.absPathInSrcFolder("models/meta/config.js")).C
 const nodeCleanup = require('node-cleanup');
 const npid = require('npid');
 const async = require('async');
+let pid;
 
 const setupGracefulClose = function(app, server, callback)
 {
     //setup graceful server close
     if(process.env.NODE_ENV !== 'test')
     {
-        const pid = npid.create(Pathfinder.absPathInApp('running.pid'), true); //second arg = overwrite pid if exists
+        pid = npid.create(Pathfinder.absPathInApp('running.pid'), true); //second arg = overwrite pid if exists
         pid.removeOnExit();
     }
 
@@ -111,7 +112,6 @@ const setupGracefulClose = function(app, server, callback)
             haltHTTPServer,
             removePIDFile
         ], function(err, results){
-            // calling process.exit() won't inform parent process of signal
             callback(err, results);
         });
     };

diff --git a/src/bootup/init/setup_passport.js b/src/bootup/init/setup_passport.js
@@ -4,6 +4,7 @@ const Pathfinder = global.Pathfinder;
 const Config = require(Pathfinder.absPathInSrcFolder("models/meta/config.js")).Config;
 const User = require(Pathfinder.absPathInSrcFolder("models/user.js")).User;
 const Logger = require(Pathfinder.absPathInSrcFolder("utils/logger.js")).Logger;
+const isNull = require(Pathfinder.absPathInSrcFolder("utils/null.js")).isNull;
 
 let slug = require('slug'),
     session_key = "dendro_" + slug(Config.host) + "_sessionKey",
@@ -18,29 +19,35 @@ const setupPassport = function(app, callback)
 
     const MongoStore = require('connect-mongo')(expressSession);
 
-    const sessionMongoStore = new MongoStore(
+    const expressSessionParameters = {
+        secret: Config.crypto.secret,
+        genid: function ()
         {
-            "host": Config.mongoDBHost,
-            "port": Config.mongoDbPort,
-            "db": Config.mongoDBSessionStoreCollection,
-            "url": 'mongodb://' + Config.mongoDBHost + ":" + Config.mongoDbPort + "/" + Config.mongoDBSessionStoreCollection
-        });
+            const uuid = require('uuid');
+            return uuid.v4()
+        },
+        key: session_key,
+        cookie: {maxAge: 1000 * 60 * 60 * 24 * 5}, //5 days max session age
+        resave: false,
+        saveUninitialized: false
+    };
 
-    app.use(expressSession(
-        {
-            secret: Config.crypto.secret,
-            genid: function ()
+
+    let sessionMongoStore;
+    if(process.env.NODE_ENV !== "test")
+    {
+        sessionMongoStore = new MongoStore(
             {
-                const uuid = require('uuid');
-                return uuid.v4()
-            },
-            key: session_key,
-            cookie: {maxAge: 1000 * 60 * 60 * 24 * 5}, //5 days max session age
-            store: sessionMongoStore,
-            resave: false,
-            saveUninitialized: false
-        })
-    );
+                "host": Config.mongoDBHost,
+                "port": Config.mongoDbPort,
+                "db": Config.mongoDBSessionStoreCollection,
+                "url": 'mongodb://' + Config.mongoDBHost + ":" + Config.mongoDbPort + "/" + Config.mongoDBSessionStoreCollection
+            });
+
+        expressSessionParameters.store = sessionMongoStore;
+    }
+
+    app.use(expressSession(expressSessionParameters));
 
     const passport = require('passport');
     //set serialization and deserialization methods
@@ -61,7 +68,7 @@ const setupPassport = function(app, callback)
         next(null, req, res);
     });
 
-    if (Config.startup.clear_session_store)
+    if (Config.startup.clear_session_store && !isNull(sessionMongoStore))
     {
         Logger.log_boot_message("info", "Clearing session store!");
         sessionMongoStore.clear(function (err, result)

diff --git a/src/bootup/load/create_indexes.js b/src/bootup/load/create_indexes.js
@@ -10,7 +10,7 @@ const createIndexes = function(app, index, callback)
 {
     Logger.log_boot_message("info","Now trying to connect to ElasticSearch Cluster to check if the required indexes exist or need to be created...");
 
-    index.create_new_index(1, 1, false, function(error, result)
+    index.create_new_index(1, 1, Config.startup.destroy_indexes, function(error, result)
     {
         if(!isNull(error))
         {

diff --git a/src/bootup/load/destroy_all_graphs.js b/src/bootup/load/destroy_all_graphs.js
@@ -6,45 +6,38 @@ const Config = require(Pathfinder.absPathInSrcFolder("models/meta/config.js")).C
 
 const destroyAllGraphs = function(app, callback)
 {
-    if(Config.startup.load_databases && Config.startup.destroy_all_graphs_on_startup)
+    if(Config.startup.load_databases && Config.startup.destroy_all_graphs)
     {
-        if(Config.debug.database.destroy_all_graphs_on_startup)
-        {
-            const graphs = Object.keys(GLOBAL.db);
-            const conn = GLOBAL.db.default.connection;
+        const graphs = Object.keys(Config.db);
+        const conn = Config.db.default.connection;
 
-            async.map(graphs, function(graph, cb){
+        async.map(graphs, function(graph, cb){
 
-                const graphUri = GLOBAL.db[graph].graphUri;
-                conn.deleteGraph(graphUri, function(err){
-                    if(err)
-                    {
-                        return callback(err);
-                    }
-                    else
-                    {
-                        conn.graphExists(graphUri, function(err, exists){
-                            if(exists)
-                            {
-                                console.error("Tried to delete graph " + graphUri + " but it still exists!");
-                                process.exit(1);
-                            }
-                            else
-                            {
-                                cb(null, exists);
-                            }
-                        });
-                    }
-                });
-            }, function(err, res)
-            {
-                return callback(err);
+            const graphUri = Config.db[graph].graphUri;
+            conn.deleteGraph(graphUri, function(err){
+                if(err)
+                {
+                    return callback(err);
+                }
+                else
+                {
+                    conn.graphExists(graphUri, function(err, exists){
+                        if(exists)
+                        {
+                            console.error("Tried to delete graph " + graphUri + " but it still exists!");
+                            process.exit(1);
+                        }
+                        else
+                        {
+                            cb(null, exists);
+                        }
+                    });
+                }
             });
-        }
-        else
+        }, function(err, res)
         {
-            return callback(null);
-        }
+            return callback(err);
+        });
     }
     else
     {