From 06007a093e60fec850cee72873566e790df50935 Mon Sep 17 00:00:00 2001
From: Yash Kumar Verma <yk.verma2000@gmail.com>
Date: Fri, 26 Mar 2021 12:00:08 +0530
Subject: [PATCH 01/23] feat(mongoDB): create service for db operations

- util.js for commonly used utility functions that are consumed by database service
- jsDOC for each method added, with references to mongoDB documentation for respective functions
- all database operations encapsulated into one parent class
- single point connector that provides connection instances to entire project
- kills application process if connection fails
- provision to support multiple database connections
---
 service/database/connector.js |  61 ++++++++++++
 service/database/index.js     | 169 ++++++++++++++++++++++++++++++++++
 service/database/util.js      |  21 +++++
 3 files changed, 251 insertions(+)
 create mode 100644 service/database/connector.js
 create mode 100644 service/database/index.js
 create mode 100644 service/database/util.js

diff --git a/service/database/connector.js b/service/database/connector.js
new file mode 100644
index 0000000..024ed9f
--- /dev/null
+++ b/service/database/connector.js
@@ -0,0 +1,61 @@
+const { MongoClient } = require("mongodb");
+
+/**
+ * @class MongoDBConnector
+ * @description This class is the single point configuration place for all
+ * operations that relate to the connection of the application with the
+ * database server.
+ *
+ * This class provides the connection objects that are used by database
+ * operations throughout the project.
+ */
+class MongoDBConnector {
+  /**
+   * @constructor to initialize connection to database server
+   */
+  constructor() {
+    /** connection specifics */
+    const connectionString = process.env.MONGO_URI || "127.0.0.1:27017";
+    const databaseName = process.env.MONGO_DB || "camic";
+    const url = `mongodb://${connectionString}/${databaseName}`;
+
+    /** connection configurations */
+    const configs = {
+      useUnifiedTopology: true,
+      useNewUrlParser: true,
+    };
+
+    this.name = databaseName;
+    this.client = new MongoClient(url, configs);
+  }
+
+  /**
+   * @async method to initialize the connection and store in application state
+   */
+  async init() {
+    await this.client.connect();
+    console.log(`[database:${this.name}] connected`);
+    this.db = {};
+    this.db[this.name] = this.client.db(this.name);
+  }
+}
+
+/** initialize an instance of mongoDB connection and kill process if connection fails */
+const connector = new MongoDBConnector();
+connector.init().catch((e) => {
+  console.error("error connecting to database");
+  process.exit(1);
+});
+
+/**
+ * to load connection instances in database operations
+ * @param {string} [databaseName=camic] Returns a connection to the said database
+ */
+const getConnection = (databaseName = "camic") => {
+  return connector.db[databaseName];
+};
+
+/** export the connector to be used by utility functions */
+module.exports = {
+  getConnection,
+};
diff --git a/service/database/index.js b/service/database/index.js
new file mode 100644
index 0000000..46b8ca0
--- /dev/null
+++ b/service/database/index.js
@@ -0,0 +1,169 @@
+const { getConnection } = require("./connector");
+const { transformIdToObjectId } = require("./util");
+
+/**
+ * @class Mongo
+ * @description Handles database operations, called via handler. This is like a generic that
+ * is used through the project to perform basic operations on the database.
+ */
+class Mongo {
+  /**
+   * Runs the MongoDB find() method to fetch documents.
+   *
+   * @async
+   * @param {string} database Name of the database
+   * @param {string} collectionName Name of the collection to run operation on
+   * @param {document} query Specifies selection filter using query operators.
+   * To return all documents in a collection, omit this parameter or pass an empty document ({}).
+   * @param {boolean} [transform=false] check to transform the IDs to ObjectID in response
+   *
+   * {@link https://docs.mongodb.com/manual/reference/method/db.collection.find/ Read MongoDB Reference}
+   */
+  static async find(database, collectionName, query, transform = true) {
+    try {
+      query = transformIdToObjectId(query);
+
+      const collection = getConnection(database).collection(collectionName);
+      const data = await collection.find(query).toArray();
+
+      /** allow caller method to toggle response transformation */
+      if (transform) {
+        data.forEach((x) => {
+          x["_id"] = {
+            $oid: x["_id"],
+          };
+        });
+      }
+
+      return data;
+    } catch (e) {
+      return e;
+    }
+  }
+
+  /**
+   * Runs a distinct find operation based on given query
+   *
+   * @async
+   * @param {string} database Name of the database
+   * @param {string} collectionName Name of the collection to run operations on
+   * @param {string} upon Field for which to return distinct values.
+   * @param {Document} query A query that specifies the documents from
+   * which to retrieve the distinct values.
+   *
+   * {@link https://docs.mongodb.com/manual/reference/method/db.collection.distinct Read MongoDB Reference}
+   */
+  static async distinct(database, collectionName, upon, query) {
+    try {
+      const collection = getConnection(database).collection(collectionName);
+      const data = await collection.distinct(upon, query);
+      return data;
+    } catch (e) {
+      return [];
+    }
+  }
+
+  /**
+   * Runs insertion operation to create an array of new documents
+   *
+   * @async
+   * @param {string} database Name of the database
+   * @param {string} collectionName Name of collection to run operation on
+   * @param {Array<document>} data Array of documents to insert into collection
+   *
+   * {@link https://docs.mongodb.com/manual/reference/method/db.collection.insertMany/  Read MongoDB Reference}
+   */
+  static async add(database, collectionName, data) {
+    /** if not an array, transform into array */
+    if (!Array.isArray(data)) {
+      data = [data];
+    }
+
+    try {
+      const collection = getConnection(database).collection(collectionName);
+      const data = await collection.insertMany(data);
+      return data;
+    } catch (e) {
+      return [];
+    }
+  }
+
+  /**
+   * Runs the delete operation on the first document that satisfies the filter conditions
+   *
+   * @async
+   * @param {string} database Name of the database
+   * @param {string} collectionName Name of collection to run operation on
+   * @param {document} query Specifies deletion criteria using query operators
+   *
+   * {@link https://docs.mongodb.com/manual/reference/method/db.collection.deleteOne/ Read MongoDB Reference}
+   */
+  static async delete(database, collectionName, filter) {
+    try {
+      filter = transformIdToObjectId(filter);
+
+      const collection = getConnection(database).collection(collectionName);
+      const result = await collection.deleteOne(filter);
+      delete result.connection;
+
+      return result;
+    } catch (error) {
+      return [];
+    }
+  }
+
+  /**
+   * Runs aggregate operation on given pipeline
+   *
+   * @async
+   * @param {string} database Name of the database
+   * @param {string} collectionName Name of collection to run operation on
+   * @param {Array} pipeline Array containing all the aggregation framework commands for the execution.
+   *
+   * {@link https://docs.mongodb.com/manual/reference/method/db.collection.aggregate/ Read MongoDB Reference}
+   */
+  static async aggregate(database, collectionName, pipeline) {
+    try {
+      const collection = getConnection(database).collection(collectionName);
+      const result = await collection.aggregate(pipeline).toArray();
+      return result;
+    } catch (error) {
+      return [];
+    }
+  }
+
+  /**
+   * Runs updateOne operation on documents that satisfy the filter condition.
+   *
+   * @async
+   * @param {string} database Name of the database
+   * @param {string} collectionName name of collection to run operation on
+   * @param {document} filter selection criteria for the update
+   * @param {document|pipeline} updates modifications to apply to filtered documents,
+   * can be a document or a aggregation pipeline
+   *
+   * {@link https://docs.mongodb.com/manual/reference/method/db.collection.updateOne/ Read MongoDB Reference}
+   */
+  static async update(database, collectionName, filter, updates) {
+    try {
+      filter = transformIdToObjectId(filter);
+
+      const collection = await getConnection(database).collection(collectionName);
+      const result = await collection.updateOne(filter, updates);
+      delete result.connection;
+      return result;
+    } catch (e) {
+      return e;
+    }
+  }
+}
+
+/** export to be import using the destructuring syntax */
+module.exports = {
+  add: Mongo.add,
+  find: Mongo.find,
+  update: Mongo.update,
+  delete: Mongo.delete,
+  aggregate: Mongo.aggregate,
+  distinct: Mongo.distinct,
+};
diff --git a/service/database/util.js b/service/database/util.js
new file mode 100644
index 0000000..d9edc27
--- /dev/null
+++ b/service/database/util.js
@@ -0,0 +1,21 @@
+const { ObjectID } = require("mongodb");
+
+/**
+ * Utility function to transform id from String format to ObjectID format
+ * See attached link for full reference:
+ *
+ * @description if the query contains a _id property, transforms it to an
+ * ObjectID format.
+ * @param {Object} query Incoming Query for database operation
+ *
+ * @link https://docs.mongodb.com/manual/reference/method/ObjectId/
+ */
+const transformIdToObjectId = (query) => {
+  if (query["_id"]) {
+    query["_id"] = new ObjectID(query["_id"]);
+  }
+
+  return query;
+};
+
+module.exports = { transformIdToObjectId };

From 43da6cb4d4db623f30c5cb22454c0471ac388ce4 Mon Sep 17 00:00:00 2001
From: Yash Kumar Verma <yk.verma2000@gmail.com>
Date: Fri, 26 Mar 2021 12:22:06 +0530
Subject: [PATCH 02/23] refactor(handler): integrate db service,
 callback->async-await

- transform callbacks to async-await syntax
- replace direct database calls with db-service calls
- refactor monitor to eliminate redundant code
---
 handlers/dataHandlers.js              | 208 +++-----------------------
 handlers/dataTransformationHandler.js | 118 +++++----------
 handlers/monitorHandlers.js           |  44 +++---
 3 files changed, 74 insertions(+), 296 deletions(-)

diff --git a/handlers/dataHandlers.js b/handlers/dataHandlers.js
index 7852339..dfd9fd7 100644
--- a/handlers/dataHandlers.js
+++ b/handlers/dataHandlers.js
@@ -1,185 +1,11 @@
-var mongo = require('mongodb');
-
-var MONGO_URI = process.env.MONGO_URI || 'mongodb://localhost';
-var DISABLE_SEC = (process.env.DISABLE_SEC === 'true') || false;
-
-
-function mongoFind(database, collection, query) {
-  return new Promise(function(res, rej) {
-    try {
-      mongo.MongoClient.connect(MONGO_URI, function(err, db) {
-        if (err) {
-          rej(err);
-        } else {
-          if (query['_id']) {
-            query['_id'] = new mongo.ObjectID(query['_id']);
-          }
-          var dbo = db.db(database);
-          dbo.collection(collection).find(query).toArray(function(err, result) {
-            if (err) {
-              rej(err);
-            }
-            // compatible wiht bindaas odd format
-            result.forEach((x) => {
-              x['_id'] = {
-                '$oid': x['_id'],
-              };
-            });
-            res(result);
-            db.close();
-          });
-        }
-      });
-    } catch (error) {
-      rej(error);
-    }
-  });
-}
-
-function mongoDistinct(database, collection, upon, query) {
-  return new Promise(function(res, rej) {
-    try {
-      mongo.MongoClient.connect(MONGO_URI, function(err, db) {
-        if (err) {
-          rej(err);
-        } else {
-          var dbo = db.db(database);
-          dbo.collection(collection).distinct(upon, query, function(err, result) {
-            if (err) {
-              rej(err);
-            }
-            res(result);
-            db.close();
-          });
-        }
-      });
-    } catch (error) {
-      console.error(error);
-      rej(error);
-    }
-  });
-}
-
-function mongoAdd(database, collection, data) {
-  return new Promise(function(res, rej) {
-    // if data not array, make it one
-    if (!Array.isArray(data)) {
-      data = [data];
-    }
-    try {
-      mongo.MongoClient.connect(MONGO_URI, function(err, db) {
-        if (err) {
-          rej(err);
-        } else {
-          var dbo = db.db(database);
-          dbo.collection(collection).insertMany(data, function(err, result) {
-            if (err) {
-              rej(err);
-            }
-            res(result);
-            db.close();
-          });
-        }
-      });
-    } catch (error) {
-      console.error(error);
-      rej(error);
-    }
-  });
-}
-
-function mongoDelete(database, collection, query) {
-  return new Promise(function(res, rej) {
-    mongo.MongoClient.connect(MONGO_URI, function(err, db) {
-      try {
-        if (err) {
-          rej(err);
-        } else {
-          var dbo = db.db(database);
-          if (query['_id']) {
-            query['_id'] = new mongo.ObjectID(query['_id']);
-          }
-          dbo.collection(collection).deleteOne(query, function(err, result) {
-            if (err) {
-              rej(err);
-            }
-            delete result.connection;
-            res(result);
-            db.close();
-          });
-        }
-      } catch (error) {
-        console.error(error);
-        rej(error);
-      }
-    });
-  });
-}
-
-function mongoAggregate(database, collection, pipeline) {
-  return new Promise(function(res, rej) {
-    mongo.MongoClient.connect(MONGO_URI, function(err, db) {
-      try {
-        if (err) {
-          rej(err);
-        } else {
-          var dbo = db.db(database);
-          dbo.collection(collection).aggregate(pipeline).toArray(function(err, result) {
-            if (err) {
-              rej(err);
-            }
-            // compatible wiht bindaas odd format
-            // result.forEach((x) => {
-            //   x['_id'] = {
-            //     '$oid': x['_id'],
-            //   };
-            // });
-            res(result);
-            db.close();
-          });
-        }
-      } catch (error) {
-        console.error(error);
-        rej(error);
-      }
-    });
-  });
-}
-
-function mongoUpdate(database, collection, query, newVals) {
-  return new Promise(function(res, rej) {
-    try {
-      mongo.MongoClient.connect(MONGO_URI, function(err, db) {
-        if (err) {
-          rej(err);
-        } else {
-          var dbo = db.db(database);
-          if (query['_id']) {
-            query['_id'] = new mongo.ObjectID(query['_id']);
-          }
-          dbo.collection(collection).updateOne(query, newVals, function(err, result) {
-            if (err) {
-              console.log(err);
-              rej(err);
-            }
-            delete result.connection;
-            res(result);
-            db.close();
-          });
-        }
-      });
-    } catch (error) {
-      rej(error);
-    }
-  });
-}
+const DISABLE_SEC = (process.env.DISABLE_SEC === 'true') || false;
+const mongoDB = require("../service/database");
 
 var General = {};
 General.find = function(db, collection) {
   return function(req, res, next) {
     var query = req.query;
-    delete query.token;
-    mongoFind(db, collection, query).then((x) => {
+    mongoDB.add(db, collection, query).then((x) => {
       req.data = x;
       next();
     }).catch((e) => next(e));
@@ -190,7 +16,7 @@ General.get = function(db, collection) {
   return function(req, res, next) {
     var query = req.query;
     delete query.token;
-    mongoFind(db, collection, {_id: req.query.id}).then((x) => {
+    mongoDB.find(db, collection, {_id: req.query.id}).then((x) => {
       req.data = x;
       next();
     }).catch((e) => next(e));
@@ -201,7 +27,7 @@ General.distinct = function(db, collection, upon) {
   return function(req, res, next) {
     var query = req.query;
     delete query.token;
-    mongoDistinct(db, collection, upon, query).then((x) => {
+    mongoDB.distinct(db, collection, upon, query).then((x) => {
       req.data = x;
       next();
     }).catch((e) => next(e));
@@ -211,7 +37,7 @@ General.distinct = function(db, collection, upon) {
 General.add = function(db, collection) {
   return function(req, res, next) {
     var data = JSON.parse(req.body);
-    mongoAdd(db, collection, data).then((x) => {
+    mongoDB.add(db, collection, data).then((x) => {
       req.data = x;
       next();
     }).catch((e) => next(e));
@@ -225,7 +51,7 @@ General.update = function(db, collection) {
     var newVals = {
       $set: JSON.parse(req.body),
     };
-    mongoUpdate(db, collection, query, newVals).then((x) => {
+    mongoDB.update(db, collection, query, newVals).then((x) => {
       req.data = x;
       next();
     }).catch((e) => next(e));
@@ -236,7 +62,7 @@ General.delete = function(db, collection) {
   return function(req, res, next) {
     var query = req.query;
     delete query.token;
-    mongoDelete(db, collection, query).then((x) => {
+    mongoDB.delete(db, collection, query).then((x) => {
       req.data = x;
       next();
     }).catch((e) => next(e));
@@ -249,7 +75,7 @@ Presetlabels.add = function(req, res, next) {
   var query = req.query;
   delete query.token;
   var labels = JSON.parse(req.body);
-  mongoUpdate('camic', 'configuration', {'config_name': 'preset_label'}, {$push: {configuration: labels}}).then((x) => {
+  mongoDB.update('camic', 'configuration', {'config_name': 'preset_label'}, {$push: {configuration: labels}}).then((x) => {
     req.data = x;
     next();
   }).catch((e) => next(e));
@@ -287,7 +113,7 @@ Presetlabels.update = function(req, res, next) {
     newVals['$unset']['configuration.$.key'] = 1;
   }
 
-  mongoUpdate('camic', 'configuration',
+  mongoDB.update('camic', 'configuration',
       {
         'config_name': 'preset_label',
         'configuration.id': query.id,
@@ -301,7 +127,7 @@ Presetlabels.update = function(req, res, next) {
 Presetlabels.remove = function(req, res, next) {
   var query = req.query;
   delete query.token;
-  mongoUpdate('camic', 'configuration',
+  mongoDB.update('camic', 'configuration',
       {
         'config_name': 'preset_label',
       }, {$pull: {configuration: {id: query.id}}}).then((x) => {
@@ -337,7 +163,7 @@ Mark.spatial = function(req, res, next) {
       '$gt': parseFloat(query.footprint),
     };
   }
-  mongoFind('camic', 'mark', query).then((x) => {
+  mongoDB.find('camic', 'mark', query).then((x) => {
     req.data = x;
     next();
   }).catch((e) => next(e));
@@ -383,7 +209,7 @@ Mark.multi = function(req, res, next) {
     };
   }
 
-  mongoFind('camic', 'mark', query).then((x) => {
+  mongoDB.find('camic', 'mark', query).then((x) => {
     req.data = x;
     next();
   }).catch((e) => next(e));
@@ -415,12 +241,12 @@ Mark.findMarkTypes = function(req, res, next) {
         },
       },
     ];
-    mongoAggregate('camic', 'mark', pipeline).then((x) => {
+    mongoDB.aggregate('camic', 'mark', pipeline).then((x) => {
       req.data = x;
       next();
     }).catch((e) => next(e));
   } else {
-    mongoDistinct('camic', 'mark', 'provenance.analysis', query).then((x) => {
+    mongoDB.distinct('camic', 'mark', 'provenance.analysis', query).then((x) => {
       req.data = x;
       next();
     }).catch((e) => next(e));
@@ -431,7 +257,7 @@ var Heatmap = {};
 Heatmap.types = function(req, res, next) {
   var query = req.query;
   delete query.token;
-  mongoFind('camic', 'heatmap', query, {
+  mongoDB.find('camic', 'heatmap', query, {
     'data': 0,
   }).then((x) => {
     x.forEach((x)=>delete x.data);
@@ -443,7 +269,7 @@ Heatmap.types = function(req, res, next) {
 var User = {};
 
 User.forLogin = function(email) {
-  return mongoFind('camic', 'user', {'email': email});
+  return mongoDB.find('camic', 'user', {'email': email});
 };
 
 User.wcido = function(req, res, next) {
diff --git a/handlers/dataTransformationHandler.js b/handlers/dataTransformationHandler.js
index 3458777..7f09a07 100644
--- a/handlers/dataTransformationHandler.js
+++ b/handlers/dataTransformationHandler.js
@@ -1,5 +1,5 @@
-const client = require("mongodb").MongoClient;
 const fs = require("fs");
+const mongoDB = require("../service/database");
 
 class DataTransformationHandler {
   constructor(url, path) {
@@ -37,7 +37,7 @@ class DataTransformationHandler {
     return config;
   }
 
-  connect() {
+  async connect() {
     if (this.isProcessing) {
       return;
     }
@@ -45,88 +45,48 @@ class DataTransformationHandler {
       this.cleanHandler();
       return;
     }
+
     this.isProcessing = true;
     const query = {config_name: "preset_label"};
-    client
-        .connect(this.url, {useNewUrlParser: true})
-        .then((dbc) => {
-          const collection = dbc.db("camic").collection("configuration");
-          collection.find(query).toArray((err, rs) => {
-            if (err) {
-              this.isProcessing = false;
-              console.log(`||-- The 'Preset Labels' Document Upgrade Is Failed --||`);
-              console.log(err);
-              dbc.close();
-              this.cleanHandler();
-              return;
-            }
-            // add default data
-            if (rs.length < 1) {
-              // read default data from json
-              const defaultData = this.loadDefaultData();
-              // insert default data
-              collection.insertOne(defaultData, (err, result) => {
-                if (err) {
-                  this.isProcessing = false;
-                  console.log(`||-- The 'Preset Labels' Document Upgrade Is Failed --||`);
-                  console.log(err);
-                  dbc.close();
-                  this.cleanHandler();
-                  return;
-                }
-                dbc.close();
-                // clear handler
-                this.cleanHandler();
-              });
-              return;
-            }
+    try {
+      /** fetch saved configurations */
+      const rs = await mongoDB.find("camic", "configuration", query, false);
+
+      /** read default data and write to database */
+      if (rs.length < 1) {
+        const defaultData = this.loadDefaultData();
+        await mongoDB.add("camic", "configuration", defaultData);
+      }
 
-            if (rs.length > 0 && rs[0].version != "1.0.0") {
-              const config = rs[0];
-              const list = [];
-              if (config.configuration && Array.isArray(config.configuration)) {
-                config.configuration.forEach((node) => {
-                  this.extractNode(node, list);
-                });
-              }
-              config.configuration = list;
-              config.version = '1.0.0';
-              if (!(list && list.length)) return;
-              collection.deleteOne(query, (err, result) => {
-                if (err) {
-                  this.isProcessing = false;
-                  console.log(`||-- The 'Preset Labels' Document Upgrade Is Failed --||`);
-                  console.log(err);
-                  dbc.close();
-                  this.cleanHandler();
-                  return;
-                }
-                collection.insertOne(config, (err, result) => {
-                  if (err) {
-                    this.isProcessing = false;
-                    console.log(`||-- The 'Preset Labels' Document Upgrade Is Failed --||`);
-                    console.log(err);
-                    dbc.close();
-                    this.cleanHandler();
-                    return;
-                  }
-                  this.isProcessing = false;
-                  console.log(`||-- The Document At The 'configuration' Collection Has Been Upgraded To Version 1.0.0 --||`);
-                  dbc.close();
-                  this.cleanHandler();
-                });
-              });
-            }
+      /** if not default configuration */
+      if (rs.length > 0 && rs[0].version != "1.0.0") {
+        const config = rs[0];
+        const list = [];
+        if (config.configuration && Array.isArray(config.configuration)) {
+          config.configuration.forEach((node) => {
+            this.extractNode(node, list);
           });
-        }).catch((err) => {
-          console.log(`||-- The 'Preset Labels' Document Upgrade Is Failed --||`);
-          console.log(err.message);
-          this.isProcessing = false;
-          if (this.max == this.counter) {
-            this.cleanHandler();
-          }
-        });
+        }
+
+        config.configuration = list;
+        config.version = "1.0.0";
+        if (!(list && list.length)) {
+          return;
+        }
+
+        /** delete old stored object and insert new one */
+        await mongoDB.delete("camic", "configuration", query);
+        await mongoDB.add("camic", "configuration", config);
+        this.isProcessing = false;
+        this.cleanHandler();
+      }
+    } catch (err) {
+      console.log(`||-- The 'Preset Labels' Document Upgrade Is Failed --||`);
+      console.log(err);
+      this.cleanHandler();
+    }
   }
+
   extractNode(node, list) {
     if (node.children && Array.isArray(node.children)) {
       node.children.forEach((n) => {
diff --git a/handlers/monitorHandlers.js b/handlers/monitorHandlers.js
index 05bf5ca..642b04a 100644
--- a/handlers/monitorHandlers.js
+++ b/handlers/monitorHandlers.js
@@ -1,29 +1,21 @@
-var mongo = require('mongodb');
+const {getConnection} = require("../service/database/connector");
 
-var MONGO_URI = process.env.MONGO_URI || 'mongodb://localhost';
-// handle monitoring checks
-
-let monitor = {};
-
-monitor.check = function(type) {
-  if (type == "basic") {
-    return new Promise(function(res, rej) {
-      let checkMsg = {"status": "up", "checkType": "basic"};
-      res(checkMsg);
-    });
-  }
-  if (type == "mongo") {
-    return new Promise(function(res, rej) {
-      mongo.MongoClient.connect(MONGO_URI, function(err, db) {
-        if (err) {
-          rej(err);
-        } else {
-          res({"status": "up", "checkType": "mongo"});
-        }
-      });
-    });
-  }
+/**
+ * @param {string} type Monitor to check status of database connection
+ * @returns {Promise<{status:string, checkType:string}>} status of service
+ */
+const check = function(type) {
+  return new Promise((resolve, reject) => {
+    if (type === "basic") {
+      resolve({status: "up", checkType: "basic"});
+    } else if (type === "mongo") {
+      if (getConnection() === undefined) {
+        const error = new Error("Error connecting to database");
+        reject(error);
+      }
+      resolve({status: "up", checkType: "mongo"});
+    }
+  });
 };
 
-
-module.exports = monitor;
+module.exports = {check};

From 18fcc0d3d9f21590f728fd39142b2b03dc3d03c3 Mon Sep 17 00:00:00 2001
From: Yash Kumar Verma <yk.verma2000@gmail.com>
Date: Sat, 27 Mar 2021 08:58:54 +0530
Subject: [PATCH 03/23] fix(mongodb): duplicate mongodb:// in connection str

---
 service/database/connector.js | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/service/database/connector.js b/service/database/connector.js
index 024ed9f..6b28ab7 100644
--- a/service/database/connector.js
+++ b/service/database/connector.js
@@ -15,9 +15,9 @@ class MongoDBConnector {
    */
   constructor() {
     /** connection specifics */
-    const connectionString = process.env.MONGO_URI || "127.0.0.1:27017";
+    const connectionString = process.env.MONGO_URI || "mongodb://127.0.0.1:27017";
     const databaseName = process.env.MONGO_DB || "camic";
-    const url = `mongodb://${connectionString}/${databaseName}`;
+    const url = `${connectionString}/${databaseName}`;
 
     /** connection configurations */
     const configs = {

From 7a50ef5dbf750645eb32412e770001db61feb348 Mon Sep 17 00:00:00 2001
From: Yash Kumar Verma <yk.verma2000@gmail.com>
Date: Thu, 1 Apr 2021 20:52:12 +0530
Subject: [PATCH 04/23] fix(db/util): do not change original args

---
 service/database/util.js | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/service/database/util.js b/service/database/util.js
index d9edc27..3dea949 100644
--- a/service/database/util.js
+++ b/service/database/util.js
@@ -11,11 +11,15 @@ const { ObjectID } = require("mongodb");
  * @link https://docs.mongodb.com/manual/reference/method/ObjectId/
  */
 const transformIdToObjectId = (query) => {
-  if (query["_id"]) {
-    query["_id"] = new ObjectID(query["_id"]);
+  const payload = { ...query };
+  try {
+    if (payload["_id"]) {
+      payload["_id"] = new ObjectID(payload["_id"]);
+    }
+    return payload;
+  } catch (e) {
+    return query;
   }
-
-  return query;
 };
 
 module.exports = { transformIdToObjectId };

From 41e742bfc83f8f1740af2497e2ca18a91d04b436 Mon Sep 17 00:00:00 2001
From: Yash Kumar Verma <yk.verma2000@gmail.com>
Date: Thu, 1 Apr 2021 20:52:35 +0530
Subject: [PATCH 05/23] test(db): add unit tests for db service

- unit tests for connector
- unit tests for util
- log functions for db service methods
- handle cases with invalid ObjectID
---
 service/database/index.js |  14 ++-
 test/unit/database.js     | 216 ++++++++++++++++++++++++++++++++++++++
 2 files changed, 226 insertions(+), 4 deletions(-)
 create mode 100644 test/unit/database.js

diff --git a/service/database/index.js b/service/database/index.js
index 46b8ca0..fe781b6 100644
--- a/service/database/index.js
+++ b/service/database/index.js
@@ -37,6 +37,7 @@ class Mongo {
 
       return data;
     } catch (e) {
+      console.error(e);
       return e;
     }
   }
@@ -59,6 +60,7 @@ class Mongo {
       const data = await collection.distinct(upon, query);
       return data;
     } catch (e) {
+      console.error(e);
       return [];
     }
   }
@@ -81,9 +83,10 @@ class Mongo {
 
     try {
       const collection = getConnection(database).collection(collectionName);
-      const data = await collection.insertMany(data);
-      return data;
+      const res = await collection.insertMany(data);
+      return res;
     } catch (e) {
+      console.error(e);
       return [];
     }
   }
@@ -107,7 +110,8 @@ class Mongo {
       delete result.connection;
 
       return result;
-    } catch (error) {
+    } catch (e) {
+      console.error(e);
       return [];
     }
   }
@@ -127,7 +131,8 @@ class Mongo {
       const collection = getConnection(database).collection(collectionName);
       const result = await collection.aggregate(pipeline).toArray();
       return result;
-    } catch (error) {
+    } catch (e) {
+      console.error(e);
       return [];
     }
   }
@@ -153,6 +158,7 @@ class Mongo {
       delete result.connection;
       return result;
     } catch (e) {
+      console.error(e);
       return e;
     }
   }
diff --git a/test/unit/database.js b/test/unit/database.js
new file mode 100644
index 0000000..ec327d3
--- /dev/null
+++ b/test/unit/database.js
@@ -0,0 +1,216 @@
+const chai = require("chai");
+const { ObjectID } = require("mongodb");
+var should = chai.should();
+
+const { getConnection } = require("./../../service/database/connector");
+const MongoDB = require("./../../service/database/index");
+const Util = require("./../../service/database/util");
+
+/**
+ * The services are designed to operate as independent units and therefore by
+ * design, must not depend / interfere with the main codebase. This allows
+ * development and debugging without touching the application codebase.
+ */
+const DB = {
+  NAME: "camic",
+  COLLECTION: "users",
+};
+
+/**
+ * all tests for service/database
+ */
+describe("service/database", () => {
+  /** wait for connection before initiating tests */
+  before(async () => {
+    const connection = () =>
+      new Promise((resolve) => {
+        setTimeout(resolve(true), 1000 * 2);
+      });
+    await connection();
+  });
+
+  /** test suite for connector */
+  describe("connector", () => {
+    it("should be defined and callable", () => {
+      getConnection.should.not.be.undefined;
+      (typeof getConnection).should.equal("function");
+    });
+
+    it("should return a valid connection when no argument provided", () => {
+      const connection = getConnection();
+      connection.should.not.be.undefined;
+    });
+
+    it("should return a valid connection when database name provided", () => {
+      const connection = getConnection("camic");
+      connection.should.not.be.undefined;
+      connection.serverConfig.should.not.be.undefined;
+    });
+
+    it("should inject configuration objects", () => {
+      const connection = getConnection("camic");
+      connection.serverConfig.s.options.useUnifiedTopology.should.be.true;
+    });
+  });
+
+  /** test suite for utility functions */
+  describe("util", () => {
+    it("should be defined and callable", () => {
+      Util.should.not.be.undefined;
+      Util.transformIdToObjectId.should.not.be.undefined;
+      (typeof Util.transformIdToObjectId).should.equal("function");
+    });
+
+    it("should not alter argument if property _id not exist", () => {
+      const original = {
+        something: "awesome",
+        repo: "caracal",
+        valid: true,
+        version: 1,
+        string: "F",
+      };
+
+      const processed = Util.transformIdToObjectId(original);
+      processed.should.eql(processed);
+    });
+
+    it("should not alter original object passed into function", () => {
+      const original = {
+        foo: "bar",
+        number: 1,
+        _id: "507f1f77bcf86cd799439011",
+      };
+
+      const processed = Util.transformIdToObjectId(original);
+      (typeof original._id).should.be.equal("string");
+      (typeof processed._id).should.be.equal("object");
+    });
+
+    it("should alter datatype of property with valid _id", () => {
+      const original = {
+        foo: "bar",
+        number: 1,
+        _id: "507f1f77bcf86cd799439011",
+      };
+
+      (typeof original._id).should.be.equal("string");
+      const processed = Util.transformIdToObjectId(original);
+      (typeof processed._id).should.be.equal("object");
+    });
+
+    it("should not break if datatype of id not a valid ObjectID", () => {
+      const original = {
+        foo: "bar",
+        number: 1,
+        _id: "507f1_invalid_6cd799439011",
+      };
+
+      (typeof original._id).should.be.equal("string");
+      const processed = Util.transformIdToObjectId(original);
+      (typeof processed._id).should.be.equal("string");
+    });
+  });
+
+  /** test suite for core functionality */
+  describe("service", () => {
+    /** dummy payload for unit tests */
+    const USERS = [
+      {
+        _id: new ObjectID(),
+        name: "user 1",
+        age: 20,
+        config: {
+          foo: "bar",
+        },
+      },
+      {
+        _id: new ObjectID(),
+        name: "user 2",
+        age: 20,
+        config: {
+          foo: "bar",
+        },
+      },
+    ];
+
+    /** seed values before execution of each unit */
+    beforeEach(async () => {
+      await getConnection().collection(DB.COLLECTION).insertMany(USERS);
+    });
+
+    /** clear database after each unit */
+    afterEach(async () => {
+      await getConnection().collection(DB.COLLECTION).deleteMany({ age: 20 });
+    });
+
+    /** ensures that service always provides all database functionality */
+    it("should be defined and callable", () => {
+      MongoDB.should.not.be.undefined;
+      (typeof MongoDB).should.be.equal("object");
+      (typeof MongoDB.add).should.be.equal("function");
+      (typeof MongoDB.aggregate).should.be.equal("function");
+      (typeof MongoDB.delete).should.be.equal("function");
+      (typeof MongoDB.distinct).should.be.equal("function");
+      (typeof MongoDB.find).should.be.equal("function");
+      (typeof MongoDB.update).should.be.equal("function");
+    });
+
+    describe(".add", () => {
+      /** if it's callable, it means it's defined. */
+      it("should be callable", () => {
+        (typeof MongoDB.add).should.be.equal("function");
+      });
+
+      /** normal insert operations for single document */
+      it("should insert single document into collection", async () => {
+        const user = {
+          _id: new ObjectID(),
+          name: "testUser1",
+          age: 20,
+          config: {
+            foo: "bar",
+          },
+        };
+
+        const res = await MongoDB.add(DB.NAME, DB.COLLECTION, user);
+        res.insertedCount.should.be.equal(1);
+        res.result.n.should.be.equal(1);
+      });
+
+      /** should  */
+      it("should insert multiple document into collection", async () => {
+        const users = [
+          {
+            _id: new ObjectID(),
+            name: "testUser1",
+            age: 20,
+            config: {
+              foo: "bar",
+            },
+          },
+          {
+            _id: new ObjectID(),
+            name: "testUser2",
+            age: 20,
+            config: {
+              foo: "bar",
+            },
+          },
+        ];
+
+        const res = await MongoDB.add(DB.NAME, DB.COLLECTION, users);
+        res.insertedCount.should.be.equal(2);
+        res.result.n.should.be.equal(2);
+      });
+    });
+
+    /**
+     * @todo: unit tests for following methods
+     * .aggregate()
+     * .delete()
+     * .find()
+     * .update()
+     * .distinct()
+     */
+  });
+});

From 383ac1f8af608a0114756e9cae1de13bc0eef8bd Mon Sep 17 00:00:00 2001
From: Yash Kumar Verma <yk.verma2000@gmail.com>
Date: Tue, 13 Apr 2021 01:18:41 +0530
Subject: [PATCH 06/23] chore(lint): typo fix, linting issue

---
 handlers/dataHandlers.js | 2 +-
 test/unit/database.js    | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/handlers/dataHandlers.js b/handlers/dataHandlers.js
index dfd9fd7..b89b5af 100644
--- a/handlers/dataHandlers.js
+++ b/handlers/dataHandlers.js
@@ -5,7 +5,7 @@ var General = {};
 General.find = function(db, collection) {
   return function(req, res, next) {
     var query = req.query;
-    mongoDB.add(db, collection, query).then((x) => {
+    mongoDB.find(db, collection, query).then((x) => {
       req.data = x;
       next();
     }).catch((e) => next(e));
diff --git a/test/unit/database.js b/test/unit/database.js
index ec327d3..d3e1080 100644
--- a/test/unit/database.js
+++ b/test/unit/database.js
@@ -1,8 +1,8 @@
 const chai = require("chai");
-const { ObjectID } = require("mongodb");
+const {ObjectID} = require("mongodb");
 var should = chai.should();
 
-const { getConnection } = require("./../../service/database/connector");
+const {getConnection} = require("./../../service/database/connector");
 const MongoDB = require("./../../service/database/index");
 const Util = require("./../../service/database/util");
 
@@ -140,7 +140,7 @@ describe("service/database", () => {
 
     /** clear database after each unit */
     afterEach(async () => {
-      await getConnection().collection(DB.COLLECTION).deleteMany({ age: 20 });
+      await getConnection().collection(DB.COLLECTION).deleteMany({age: 20});
     });
 
     /** ensures that service always provides all database functionality */

From 9793afa32af656e03c8fb1ae253dc9dde6c75214 Mon Sep 17 00:00:00 2001
From: Yash Kumar Verma <yk.verma2000@gmail.com>
Date: Mon, 12 Apr 2021 14:06:09 +0530
Subject: [PATCH 07/23] chore(setup): add setup script to initialize project

- generates keys by calling keys/make_key.sh if not exists
- install node modules if not exists
- generates a routes.json file from routes.json.example if not exists
- generates .env file from .env.example if not exists
- downloads latest seeding script from distro repo and runs against user database
- allows custom database name and host during run
---
 README.md       |   7 +++
 setup_script.sh | 141 ++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 148 insertions(+)
 create mode 100755 setup_script.sh

diff --git a/README.md b/README.md
index a89dc0e..3fac21e 100644
--- a/README.md
+++ b/README.md
@@ -54,3 +54,10 @@ userFilter -- list of values which must be present in given field in filtered da
 \*\* -- immune to filters (can see everything)
 Public -- users with no userFilter are assigned this filter
 An item with no filter value is returned in all cases, and is thus also public.
+
+## Local Development Environment
+In order to quickly setup a development environment, make use of the `setup_script.sh` script. This will setup the project, initialize and seed the database configurations, import routes and initialize environment config files and generate the keys required.
+
+Run the script with  `./setup_script` or `bash ./setup_script.sh`
+
+The script is configured to load a database named "`camic`" from server at "`127.0.0.1`". In order to specify different name and host, simply pass the two while calling the script, like `./setup_script custom_host custom_database_name`
diff --git a/setup_script.sh b/setup_script.sh
new file mode 100755
index 0000000..7b1b049
--- /dev/null
+++ b/setup_script.sh
@@ -0,0 +1,141 @@
+#!/bin/bash
+
+###
+## ensure that required params are passed into script
+###
+if [ -n "$1" ]; then
+    HOST=$1
+else
+    echo "[ database ] : name not passed, set to default value (127.0.0.1)"
+    HOST="127.0.0.1"
+fi
+
+###
+## specify which database to operate on, if not specified, set default to camic
+###
+if [ -n "$2" ]; then
+    DB_NAME=$2
+    echo "[ database ] : name set as ${DB_NAME}"
+else
+    echo "[ database ] : name not passed, set to default value (camic)"
+    DB_NAME="camic"
+fi
+
+###
+## check if the system has required services installed
+###
+if ! command -v "mongo" &>/dev/null; then
+    echo "mongo could not be found on path. Please ensure that mongo is installed and is on PATH"
+    exit
+fi
+
+if ! command -v "node" &>/dev/null; then
+    echo "node could not be found on path. Please ensure that node is installed and is on PATH"
+    exit
+fi
+
+###
+## try connecting to mongodb instance
+###
+until mongo --host "${HOST}" --eval "print(\"Connected!\")" >/dev/null; do
+    sleep 2
+done
+echo "[ database ] : connection established"
+
+###
+## check if database exists
+###
+QUERY="db.getMongo().getDBNames().indexOf(\"${DB_NAME}\")"
+COMMAND="mongo ${HOST} --eval '${QUERY}' --quiet"
+if [ $(mongo ${HOST} --eval ${QUERY} --quiet) -lt 0 ]; then
+    echo "[ database ] : does not exist"
+    exit 1
+else
+    echo "[ database ] : database named ${DB_NAME} found"
+fi
+
+###
+## ask developer if they wish to seed the database
+###
+read -p "[ resource ] : Do you wish to initialize the database with indexes and configs? (y/n) : " yn
+case $yn in
+[Yy]*)
+    ###
+    ## Download the files from github and save to local directory
+    ###
+    echo "[ resource ] : downloading seeding files"
+
+    # resource targets
+    RESOURCE_IDX="https://raw.githubusercontent.com/camicroscope/Distro/master/config/mongo_idx.js"
+    RESOURCE_COLLECTION="https://raw.githubusercontent.com/camicroscope/Distro/master/config/mongo_collections.js"
+    RESOURCE_DEFAULT_DATA="https://raw.githubusercontent.com/camicroscope/Distro/master/config/default_data.js"
+
+    # get data from resource targets
+    wget -q RESOURCE_IDX -O .seeder.idx.js
+    wget -q RESOURCE_DEFAULT_DATA -O .seeder.default.js
+    wget -q RESOURCE_COLLECTION -O .seeder.collection.js
+
+    echo "[ resource ] : clearing old configurations"
+    echo "[ resource ] : seeding collections"
+    mongo --quiet --host $HOST $DB_NAME .seeder.collection.js
+    echo "[ resource ] : seeding indexes"
+    mongo --quiet --host $HOST $DB_NAME .seeder.idx.js
+    echo "[ resource ] : seeding configurations"
+    mongo --quiet --host $HOST $DB_NAME .seeder.default.js
+
+    ###
+    ## ask the user if they want to remove the seeding files
+    ###
+    read -p "[ resource ] : Do you wish to keep the seeding files generated ? (y/n) :" yn
+    case $yn in
+    [Yy]*) echo "[ resource ] : The seeder files are present in current directory with name : .seeder.*.js" ;;
+    [Nn]*) rm .seeder.* ;;
+    *) echo "[ resource ] : Please answer y/n." ;;
+    esac
+    ;;
+    ### seeder file cleanup ends here
+
+[Nn]*) echo "[ resource ] : database initialization skipped" ;;
+*) echo "[ resource ] : skipped" ;;
+esac
+### seeder prompt ends here
+
+###
+## load the default routes.json file if it does not exist in the file system
+###
+if [ -f "routes.json" ]; then
+    echo "[ routes   ] : routes.json file already exists"
+else
+    cp routes.json.example routes.json
+    echo "[ routes   ] : routes.json file generated from routes.json.example"
+fi
+
+if [ -f "keys/key" ] && [ -f "keys/key.pub" ]; then
+    echo "[ keys     ] : public and private keys already exist"
+else
+    bash ./keys/make_key.sh
+    echo "[ routes   ] : routes.json file generated from routes.json.example"
+fi
+
+###
+## install the packages if not done already
+###
+if [ ! -d "node_modules" ]; then
+    echo "[ modules  ] : packages not installed, running : npm install"
+    npm install
+else
+    echo "[ modules  ] : packages directory already exist, to reinstall, delete the node_modules folder and run npm install"
+fi
+
+###
+## initialize the environment variable configs
+###
+if [ ! -f ".env" ]; then
+    echo "[ env      ] : .env file not found"
+    cp .env.example .env
+else
+    echo "[ env      ] : .env file already exists"
+fi
+
+echo ""
+echo "If you face issues due to permissions and login handlers, setting the DISABLE_SEC to false in .env file might help."

From f91a9a6323f591058655d653550f2cd6e79a8361 Mon Sep 17 00:00:00 2001
From: Yash Kumar Verma <yk.verma2000@gmail.com>
Date: Thu, 15 Apr 2021 17:36:43 +0530
Subject: [PATCH 08/23] chore(db): return -> throw to catch errors

---
 service/database/index.js | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/service/database/index.js b/service/database/index.js
index fe781b6..58cb7c8 100644
--- a/service/database/index.js
+++ b/service/database/index.js
@@ -38,7 +38,7 @@ class Mongo {
       return data;
     } catch (e) {
       console.error(e);
-      return e;
+      throw e;
     }
   }
 
@@ -61,7 +61,7 @@ class Mongo {
       return data;
     } catch (e) {
       console.error(e);
-      return [];
+      throw e;
     }
   }
 
@@ -87,7 +87,7 @@ class Mongo {
       return res;
     } catch (e) {
       console.error(e);
-      return [];
+      throw e;
     }
   }
 
@@ -112,7 +112,7 @@ class Mongo {
       return result;
     } catch (e) {
       console.error(e);
-      return [];
+      throw e;
     }
   }
 
@@ -133,7 +133,7 @@ class Mongo {
       return result;
     } catch (e) {
       console.error(e);
-      return [];
+      throw e;
     }
   }
 
@@ -153,13 +153,15 @@ class Mongo {
     try {
       filter = transformIdToObjectId(filter);
 
-      const collection = await getConnection(database).collection(collectionName);
+      const collection = await getConnection(database).collection(
+        collectionName
+      );
       const result = await collection.updateOne(filter, updates);
       delete result.connection;
       return result;
     } catch (e) {
       console.error(e);
-      return e;
+      throw e;
     }
   }
 }

From 6d9786fecdaaaced76fd2fd823a07f0ad3cbdfa3 Mon Sep 17 00:00:00 2001
From: Ryan Birmingham <birm@rbirm.us>
Date: Mon, 26 Apr 2021 12:50:04 -0400
Subject: [PATCH 09/23] ignore node_modules in docker

---
 .dockerignore | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 .dockerignore

diff --git a/.dockerignore b/.dockerignore
new file mode 100644
index 0000000..3c3629e
--- /dev/null
+++ b/.dockerignore
@@ -0,0 +1 @@
+node_modules

From 8221a6f75c577b43617a7c2c0a0ac57c2ccecf87 Mon Sep 17 00:00:00 2001
From: Ryan Birmingham <birm@rbirm.us>
Date: Wed, 28 Apr 2021 10:36:21 -0400
Subject: [PATCH 10/23] fix typo in pubkey check

---
 handlers/authHandlers.js | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/handlers/authHandlers.js b/handlers/authHandlers.js
index 0db87ae..c5c470f 100644
--- a/handlers/authHandlers.js
+++ b/handlers/authHandlers.js
@@ -45,13 +45,13 @@ try {
 }
 
 try {
-  const prikeyPath = './keys/key.pub';
-  if (fs.existsSync(prikeyPath)) {
-    var PUBKEY = fs.readFileSync(prikeyPath, 'utf8');
+  const pubkeyPath = './keys/key.pub';
+  if (fs.existsSync(pubkeyPath)) {
+    var PUBKEY = fs.readFileSync(pubkeyPath, 'utf8');
   } else {
     if (DISABLE_SEC || ENABLE_SECURITY_AT && Date.parse(ENABLE_SECURITY_AT) > Date.now()) {
       PUBKEY = '';
-      console.warn('pubkey null since DISABLE_SEC and no prikey provided');
+      console.warn('pubkey null since DISABLE_SEC and no pubkey provided');
     } else {
       console.error('pubkey does not exist');
     }

From ff4fc5854863b3c1c520f6f7bb9d126aefa17bc3 Mon Sep 17 00:00:00 2001
From: Ryan Birmingham <birm@rbirm.us>
Date: Wed, 7 Apr 2021 15:41:55 -0400
Subject: [PATCH 11/23] hotfix ci build

---
 .github/workflows/buildah.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/buildah.yml b/.github/workflows/buildah.yml
index 370fe85..22bc34f 100644
--- a/.github/workflows/buildah.yml
+++ b/.github/workflows/buildah.yml
@@ -18,3 +18,4 @@ jobs:
           ./Dockerfile
         build-args: |
           viewer=develop
+          fork=camicroscope

From 51a2ef22c95a5e7e4837e076dcc7d936c8a11518 Mon Sep 17 00:00:00 2001
From: Ryan Birmingham <birm@rbirm.us>
Date: Mon, 26 Apr 2021 12:50:04 -0400
Subject: [PATCH 12/23] ignore node_modules in docker

---
 .dockerignore | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 .dockerignore

diff --git a/.dockerignore b/.dockerignore
new file mode 100644
index 0000000..3c3629e
--- /dev/null
+++ b/.dockerignore
@@ -0,0 +1 @@
+node_modules

From 8ab1baa550718262dd41159513c3121a038369b4 Mon Sep 17 00:00:00 2001
From: Ryan Birmingham <birm@rbirm.us>
Date: Wed, 28 Apr 2021 10:36:21 -0400
Subject: [PATCH 13/23] fix typo in pubkey check

---
 handlers/authHandlers.js | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/handlers/authHandlers.js b/handlers/authHandlers.js
index 0db87ae..c5c470f 100644
--- a/handlers/authHandlers.js
+++ b/handlers/authHandlers.js
@@ -45,13 +45,13 @@ try {
 }
 
 try {
-  const prikeyPath = './keys/key.pub';
-  if (fs.existsSync(prikeyPath)) {
-    var PUBKEY = fs.readFileSync(prikeyPath, 'utf8');
+  const pubkeyPath = './keys/key.pub';
+  if (fs.existsSync(pubkeyPath)) {
+    var PUBKEY = fs.readFileSync(pubkeyPath, 'utf8');
   } else {
     if (DISABLE_SEC || ENABLE_SECURITY_AT && Date.parse(ENABLE_SECURITY_AT) > Date.now()) {
       PUBKEY = '';
-      console.warn('pubkey null since DISABLE_SEC and no prikey provided');
+      console.warn('pubkey null since DISABLE_SEC and no pubkey provided');
     } else {
       console.error('pubkey does not exist');
     }

From 2261887edc978b8cd6e125f0449972e3b4c878a7 Mon Sep 17 00:00:00 2001
From: siddhanth339 <sidrk339@gmail.com>
Date: Tue, 4 May 2021 01:21:45 +0530
Subject: [PATCH 14/23] Update setup_script to fetch landing page

---
 caracal.js                    |  12 +-
 service/database/connector.js |  12 +-
 setup_script.sh               |  72 +++++++++++
 static/additional_links.json  |   8 ++
 static/login.html             | 218 +++++++++++++++++++++++-----------
 5 files changed, 247 insertions(+), 75 deletions(-)
 create mode 100644 static/additional_links.json

diff --git a/caracal.js b/caracal.js
index 5d829c8..95fc882 100644
--- a/caracal.js
+++ b/caracal.js
@@ -24,6 +24,8 @@ const Model = require('./handlers/modelTrainer.js');
 const DataTransformationHandler = require('./handlers/dataTransformationHandler.js');
 // TODO validation of data
 
+const {connector} = require("./service/database/connector")
+
 var WORKERS = process.env.NUM_THREADS || 4;
 
 var PORT = process.env.PORT || 4010;
@@ -196,7 +198,13 @@ var startApp = function(app) {
 
 throng(WORKERS, startApp(app));
 
-const handler = new DataTransformationHandler(MONGO_URI, './json/configuration.json');
-handler.startHandler();
+/** initialize DataTransformationHandler only after database is ready */
+connector.init().then(() => {
+  const handler = new DataTransformationHandler(MONGO_URI, './json/configuration.json');
+  handler.startHandler();
+}).catch((e) => {
+  console.error("error connecting to database");
+  process.exit(1);
+});
 
 module.exports = app; // for tests
diff --git a/service/database/connector.js b/service/database/connector.js
index 6b28ab7..9364abb 100644
--- a/service/database/connector.js
+++ b/service/database/connector.js
@@ -15,7 +15,8 @@ class MongoDBConnector {
    */
   constructor() {
     /** connection specifics */
-    const connectionString = process.env.MONGO_URI || "mongodb://127.0.0.1:27017";
+    const connectionString =
+      process.env.MONGO_URI || "mongodb://127.0.0.1:27017";
     const databaseName = process.env.MONGO_DB || "camic";
     const url = `${connectionString}/${databaseName}`;
 
@@ -42,10 +43,10 @@ class MongoDBConnector {
 
 /** initialize an instance of mongoDB connection and kill process if connection fails */
 const connector = new MongoDBConnector();
-connector.init().catch((e) => {
-  console.error("error connecting to database");
-  process.exit(1);
-});
+// connector.init().catch((e) => {
+//   console.error("error connecting to database");
+//   process.exit(1);
+// });
 
 /**
  * to load connection instances in database operations
@@ -58,4 +59,5 @@ const getConnection = (databaseName = "camic") => {
 /** export the connector to be used by utility functions */
 module.exports = {
   getConnection,
+  connector,
 };
diff --git a/setup_script.sh b/setup_script.sh
index 7b1b049..5b84294 100755
--- a/setup_script.sh
+++ b/setup_script.sh
@@ -34,6 +34,78 @@ if ! command -v "node" &>/dev/null; then
     exit
 fi
 
+###
+# check for the existence of required files in the Distro and camicroscope repository
+###
+echo "Checking for required files"
+
+if [[ ! -d ../Distro/db ]]
+then echo "../Distro/db does not exist"
+     exit
+fi
+
+if [[ ! -d ../Distro/config ]]
+then echo "../Distro/config does not exist"
+     exit
+fi
+
+if [[ ! -d ../Distro/jwt_keys ]]
+then echo "../Distro/jwt_keys does not exist"
+     exit
+fi
+
+if [[ ! -d ../caMicroscope ]]
+then echo "../caMicroscope does not exist"
+     exit
+fi
+
+echo "Required files exist."
+
+echo "Copying files..." 
+
+if [[ ! -d ../data ]]
+then 
+    mkdir ../data
+    cp -r ../Distro/db ../data/
+fi
+
+if [[ ! -d ../config ]]
+then 
+    mkdir ../config
+    cp -r ../Distro/config ../config/
+fi
+
+if [[ ! -d ./static ]]
+then
+    mkdir ./static
+    cp ../Distro/config/login.html ./static/login.html
+fi
+
+if [[ ! -d ./keys/jwt_keys ]]
+then
+    cp -r ../Distro/jwt_keys ./keys/
+fi
+
+if [[ ! -f ./contentSecurityPolicy.json ]]
+then
+    cp ../Distro/config/contentSecurityPolicy.json ./contentSecurityPolicy.json
+fi
+
+if [[ ! -f ./static/additional_links.json ]]
+then
+    cp ../Distro/config/additional_links.json ./static/additional_links.json
+fi
+
+if [[ ! -d ./camicroscope ]]
+then 
+    cp -r ../caMicroscope ./camicroscope
+fi
+
+echo "Copying files complete!"
+
+
+
+
 ###
 ## try connecting to mongodb instance
 ###
diff --git a/static/additional_links.json b/static/additional_links.json
new file mode 100644
index 0000000..00f1ad5
--- /dev/null
+++ b/static/additional_links.json
@@ -0,0 +1,8 @@
+[
+    {
+        "displayName":"Bug Report",
+        "url":"https://goo.gl/forms/mgyhx4ADH0UuEQJ53",
+        "icon": "bug_report",
+        "openInNewTab": true
+    }
+]
diff --git a/static/login.html b/static/login.html
index 05602aa..ff760a1 100644
--- a/static/login.html
+++ b/static/login.html
@@ -1,77 +1,159 @@
+<!DOCTYPE html>
 <html>
-<meta name="google-signin-client_id" content="XXX.apps.googleusercontent.com">
-<script src="https://apis.google.com/js/platform.js" async defer></script>
-<div class="g-signin2" data-onsuccess="onSignIn"></div>
-<a href="#" onclick="signOut();">Sign out</a>
-<script>
-  function signOut() {
-    var auth2 = gapi.auth2.getAuthInstance();
-    auth2.signOut().then(function () {
-      console.log('User signed out.');
-    });
-  }
-</script>
-<script>
-// google's jwk is here: https://www.googleapis.com/oauth2/v3/certs
-function randomString(length) {
-    var bytes = new Uint8Array(length);
-    var random = window.crypto.getRandomValues(bytes);
-    var result = [];
-    var charset = '0123456789ABCDEFGHIJKLMNOPQRSTUVXYZabcdefghijklmnopqrstuvwxyz-._~'
-    random.forEach(function (c) {
-        result.push(charset[c % charset.length]);
-    });
-    return result.join('');
-}
+<head>
+  <title>CaMicroscope</title>
+  <meta charset="utf-8" />
+  <meta name="google-signin-client_id" content="539699277901-buh78f048405grejogqbrskj233rt0d0.apps.googleusercontent.com">
+  <meta name="viewport" content="width=device-width, initial-scale=1" />
+  <link rel="stylesheet" href="./apps/landing/main.css" />
+  <script type="text/javascript" src="./common/util.js"></script>
+</head>
+<body>
+  <header id="header">
+    <label style="color:white;padding:0 15px;font-size:20px;position:relative;">CaMicroscope<a target="_blank" style="position:absolute;right:2vw;" href="https://docs.google.com/forms/d/e/1FAIpQLScL91LxrpAZjU88GBZP9gmcdgdf8__uNUwhws2lzU6Lr4qNwA/viewform">Feedback</a></label>
+    <nav id="nav">
+        <ul>
+            <!-- <li><a target="_blank" href="https://docs.google.com/forms/d/e/1FAIpQLScL91LxrpAZjU88GBZP9gmcdgdf8__uNUwhws2lzU6Lr4qNwA/viewform">Feedback</a></li> -->
+            <!-- <li><a href="./login.html?logout=true">Sign Out</a></li> -->
+        </ul>
+    </nav>
+  </header>
+  <section id="main" class="wrapper" style="padding:3em;">
+    <div class="inner">
+      <header class="major">
+        <h2 style="margin:0;">caMicroscope</h2>
+      </header>
+      <!-- Content -->
 
-function getUrlParam(name, url) {
-    if (!url) url = window.location.href;
-    name = name.replace(/[\[\]]/g, '\\$&');
-    var regex = new RegExp('[?&#]' + name + '(=([^&#]*)|&|#|$)'),
-        results = regex.exec(url);
-    if (!results) return null;
-    if (!results[2]) return '';
-    return decodeURIComponent(results[2].replace(/\+/g, ' '));
-}
+      <div class="content">
+        <p><strong>caMicroscope</strong> is a tool to view, label, and annotate biomedical images.</p>
+        <a href="#" class="image fit"><img src="./apps/landing/banner1.jpg" alt="" /></a>
 
-function onSignIn(googleUser) {
-  var id_token = googleUser.getAuthResponse().id_token;
-  console.info(id_token)
-  // trade for camic token
-  var cookie_name = "token" // "token" is expected by elevate router
-  var base_deployment_url = window.location.toString().split("/").slice(0,-1).join("/")
-  var redirect_uri = base_deployment_url + "/login.html"
-  var default_redirect = base_deployment_url + "/apps/table.html"
-  var state
-  if (getUrlParam("state"))
-  {
-    state = decodeURIComponent(getUrlParam("state"))
-  }
-  if (!state){
-    state = default_redirect
-  }
+      </div>
 
-  if (id_token){
-    document.cookie = cookie_name + "=" + id_token;
-    fetch("./auth/Token/check",
-    {headers: {
-        'Authorization': "Bearer " + id_token
-     }}
-    ).then(x=>x.json()).then(x=>{
-      console.log("{id provider", id_token)
-      console.log("{auth service}", x)
-      if (x.hasOwnProperty('token')){
-        document.cookie = cookie_name + "=" + x.token;
-        window.location = state
+      <div class="posts" style="justify-content: center;">
+        <!-- Organizer -->
+        <section class="post">
+          <a href="#" class="image"><img src="./apps/landing/camic.jpg" alt=""/></a>
+            <div class="content">
+                <h3>Please Sign In With Your Google Account</h3>
+                <div id="google-signin2"></div>
+            </div>
+        </section>
+      </div>
+  </section>
+
+  <script>
+    function onSuccess(googleUser) {
+      // don't if we're logging out
+      if (getUrlParam("logout")) {
+        removeUserConsentAcceptance(getUserId());
+        signOut();
+        deleteCookies();
+        console.log("logging out");
+        window.location.href = "./login.html";
       } else {
-        window.alert("User not added")
-        window.location = "./apps/signup/signup"
+        var id_token = googleUser.getAuthResponse().id_token;
+        // console.info(id_token);
+        // trade for camic token
+        var cookie_name = "token"; // "token" is expected by elevate router
+        var base_deployment_url = window.location
+          .toString()
+          .split("/")
+          .slice(0, -1)
+          .join("/");
+        var redirect_uri = base_deployment_url + "/login.html";
+        var default_redirect = base_deployment_url + "/apps/table.html";
+        var state;
+        if (getUrlParam("state")) {
+          state = decodeURIComponent(getUrlParam("state"));
+        }
+        if (!state) {
+          state = default_redirect;
+        }
+        if (id_token) {
+          document.cookie = cookie_name + "=" + id_token;
+          fetch("./auth/Token/check", {
+            headers: {
+              Authorization: "Bearer " + id_token
+            }
+          })
+            .then(x => x.json())
+            .then(x => {
+              if (x.hasOwnProperty("token")) {
+                document.cookie = cookie_name + "=" + x.token;
+                let token_data = parseJwt(x.token);
+                window.location = "./apps/landing/landing.html";
+              } else {
+                window.alert("User not added");
+                window.location = "./apps/signup/signup.html";
+              }
+            });
+        }
       }
+    }
 
-    })
-  }
-}
+    function onFailure(error) {
+      console.error(error);
+    }
 
+    function renderButton() {
+      gapi.signin2.render('google-signin2', {
+        'scope': 'profile email',
+        'width': 240,
+        'height': 50,
+        'longtitle': true,
+        'theme': 'dark',
+        'onsuccess': onSuccess,
+        'onfailure': onFailure
+      });
+    }
 
-</script>
-<html>
+    function signOut() {
+      var auth2 = gapi.auth2.getAuthInstance();
+      auth2.signOut().then(function() {
+        console.log("User signed out.");
+      });
+    }
+
+    function deleteCookies() {
+      var allcookies = document.cookie.split(";");
+      for (var i = 0; i < allcookies.length; i++) {
+        var cookie = allcookies[i];
+        var eqPos = cookie.indexOf("=");
+        var name = eqPos > -1 ? cookie.substr(0, eqPos) : cookie;
+        document.cookie = name + "=;expires=Thu, 01 Jan 1970 00:00:00 GMT;";
+      }
+    }
+
+    // google's jwk is here: https://www.googleapis.com/oauth2/v3/certs
+    function randomString(length) {
+      var bytes = new Uint8Array(length);
+      var random = window.crypto.getRandomValues(bytes);
+      var result = [];
+      var charset =
+        "0123456789ABCDEFGHIJKLMNOPQRSTUVXYZabcdefghijklmnopqrstuvwxyz-._~";
+      random.forEach(function(c) {
+        result.push(charset[c % charset.length]);
+      });
+      return result.join("");
+    }
+
+    function getUrlParam(name, url) {
+      if (!url) url = window.location.href;
+      name = name.replace(/[\[\]]/g, "\\$&");
+      var regex = new RegExp("[?&#]" + name + "(=([^&#]*)|&|#|$)"),
+        results = regex.exec(url);
+      if (!results) return null;
+      if (!results[2]) return "";
+      return decodeURIComponent(results[2].replace(/\+/g, " "));
+    }
+  </script>
+
+  <script src="https://apis.google.com/js/platform.js?onload=renderButton" async defer></script>
+
+  <script>
+
+  </script>
+</body>
+</html>

From 05bd6cc58b3ee5b9f2c6fda97eb1897ebbc6a79f Mon Sep 17 00:00:00 2001
From: siddhanth339 <sidrk339@gmail.com>
Date: Tue, 4 May 2021 09:51:56 +0530
Subject: [PATCH 15/23] update setup_script

---
 setup_script.sh | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/setup_script.sh b/setup_script.sh
index 5b84294..7a800bb 100755
--- a/setup_script.sh
+++ b/setup_script.sh
@@ -39,10 +39,10 @@ fi
 ###
 echo "Checking for required files"
 
-if [[ ! -d ../Distro/db ]]
-then echo "../Distro/db does not exist"
-     exit
-fi
+#if [[ ! -d ../Distro/db ]]
+#then echo "../Distro/db does not exist"
+#     exit
+#fi
 
 if [[ ! -d ../Distro/config ]]
 then echo "../Distro/config does not exist"

From 39348d83b550b1623dfbdb41d1f173d83bb0dbe9 Mon Sep 17 00:00:00 2001
From: siddhanth339 <40331239+siddhanth339@users.noreply.github.com>
Date: Wed, 5 May 2021 21:49:08 +0530
Subject: [PATCH 16/23] Update README.md

---
 README.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/README.md b/README.md
index 3fac21e..cf84b4e 100644
--- a/README.md
+++ b/README.md
@@ -58,6 +58,10 @@ An item with no filter value is returned in all cases, and is thus also public.
 ## Local Development Environment
 In order to quickly setup a development environment, make use of the `setup_script.sh` script. This will setup the project, initialize and seed the database configurations, import routes and initialize environment config files and generate the keys required.
 
+First clone the <a href = "https://github.com/camicroscope/Caracal/tree/backup-dev">Caracal (backup-dev branch)</a>, <a href = "https://github.com/camicroscope/caMicroscope">caMicroscope</a> and the <a href = "https://github.com/camicroscope/Distro">Distro</a> repositories and make sure that all of them are in the same parent directory.
+
 Run the script with  `./setup_script` or `bash ./setup_script.sh`
 
 The script is configured to load a database named "`camic`" from server at "`127.0.0.1`". In order to specify different name and host, simply pass the two while calling the script, like `./setup_script custom_host custom_database_name`
+
+Run `npm start` to start the application and see it running at `localhost:4010`

From b3d441a25514f8b25e65c7fd349d9b0b31e1f1c6 Mon Sep 17 00:00:00 2001
From: siddhanth339 <sidrk339@gmail.com>
Date: Wed, 5 May 2021 21:57:07 +0530
Subject: [PATCH 17/23] removed redundant lines from setup_script

---
 setup_script.sh | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/setup_script.sh b/setup_script.sh
index 7a800bb..c90afff 100755
--- a/setup_script.sh
+++ b/setup_script.sh
@@ -63,11 +63,11 @@ echo "Required files exist."
 
 echo "Copying files..." 
 
-if [[ ! -d ../data ]]
-then 
-    mkdir ../data
-    cp -r ../Distro/db ../data/
-fi
+#if [[ ! -d ../data ]]
+#then 
+#    mkdir ../data
+#    cp -r ../Distro/db ../data/
+#fi
 
 if [[ ! -d ../config ]]
 then 

From a986e1b215d33e3bed5fb4b4982af077f21276ea Mon Sep 17 00:00:00 2001
From: Yash Kumar Verma <yk.verma2000@gmail.com>
Date: Sat, 1 May 2021 09:54:17 +0000
Subject: [PATCH 18/23] fix(db): await before dataTransformationHandler call

- wait for database to initialize before calling dataTransformationHandler
---
 caracal.js                    | 13 +++++++++++--
 service/database/connector.js |  9 ++++-----
 2 files changed, 15 insertions(+), 7 deletions(-)

diff --git a/caracal.js b/caracal.js
index 5d829c8..8516348 100644
--- a/caracal.js
+++ b/caracal.js
@@ -24,6 +24,8 @@ const Model = require('./handlers/modelTrainer.js');
 const DataTransformationHandler = require('./handlers/dataTransformationHandler.js');
 // TODO validation of data
 
+const {connector} = require("./service/database/connector");
+
 var WORKERS = process.env.NUM_THREADS || 4;
 
 var PORT = process.env.PORT || 4010;
@@ -196,7 +198,14 @@ var startApp = function(app) {
 
 throng(WORKERS, startApp(app));
 
-const handler = new DataTransformationHandler(MONGO_URI, './json/configuration.json');
-handler.startHandler();
+/** initialize DataTransformationHandler only after database is ready */
+connector.init().then(() => {
+  const handler = new DataTransformationHandler(MONGO_URI, './json/configuration.json');
+  handler.startHandler();
+}).catch((e) => {
+  console.error("error connecting to database");
+  process.exit(1);
+});
 
 module.exports = app; // for tests
+
diff --git a/service/database/connector.js b/service/database/connector.js
index 6b28ab7..b24d580 100644
--- a/service/database/connector.js
+++ b/service/database/connector.js
@@ -15,7 +15,8 @@ class MongoDBConnector {
    */
   constructor() {
     /** connection specifics */
-    const connectionString = process.env.MONGO_URI || "mongodb://127.0.0.1:27017";
+    const connectionString =
+      process.env.MONGO_URI || "mongodb://127.0.0.1:27017";
     const databaseName = process.env.MONGO_DB || "camic";
     const url = `${connectionString}/${databaseName}`;
 
@@ -42,10 +43,6 @@ class MongoDBConnector {
 
 /** initialize an instance of mongoDB connection and kill process if connection fails */
 const connector = new MongoDBConnector();
-connector.init().catch((e) => {
-  console.error("error connecting to database");
-  process.exit(1);
-});
 
 /**
  * to load connection instances in database operations
@@ -58,4 +55,6 @@ const getConnection = (databaseName = "camic") => {
 /** export the connector to be used by utility functions */
 module.exports = {
   getConnection,
+  connector,
 };
+

From faa16df98a86ff29aeff4f3044689457a6915f77 Mon Sep 17 00:00:00 2001
From: Ryan Birmingham <birm@rbirm.us>
Date: Fri, 7 May 2021 11:31:53 -0400
Subject: [PATCH 19/23] update dependencies

---
 package-lock.json | 345 +++++++++++++++++++++-------------------------
 package.json      |  14 +-
 2 files changed, 164 insertions(+), 195 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index 53f5e04..d4cdab5 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -31,16 +31,16 @@
       }
     },
     "@tensorflow/tfjs": {
-      "version": "2.7.0",
-      "resolved": "https://registry.npmjs.org/@tensorflow/tfjs/-/tfjs-2.7.0.tgz",
-      "integrity": "sha512-LTYK6+emFweYa3zn/o511JUR6s14/yGZpoXvFSUtdwolYHI+J50r/CyYeFpvtoTD7uwcNFQhbBAtp4L4e3Hsaw==",
-      "requires": {
-        "@tensorflow/tfjs-backend-cpu": "2.7.0",
-        "@tensorflow/tfjs-backend-webgl": "2.7.0",
-        "@tensorflow/tfjs-converter": "2.7.0",
-        "@tensorflow/tfjs-core": "2.7.0",
-        "@tensorflow/tfjs-data": "2.7.0",
-        "@tensorflow/tfjs-layers": "2.7.0",
+      "version": "2.8.6",
+      "resolved": "https://registry.npmjs.org/@tensorflow/tfjs/-/tfjs-2.8.6.tgz",
+      "integrity": "sha512-/Hk3YCAreNicuQJsAIG32UGHaQj8UwX8y8ZrKVb/CrXOhrRyZmxGSZt9KMVe8MDoydenuGhZCqJUIaWdIKIA5g==",
+      "requires": {
+        "@tensorflow/tfjs-backend-cpu": "2.8.6",
+        "@tensorflow/tfjs-backend-webgl": "2.8.6",
+        "@tensorflow/tfjs-converter": "2.8.6",
+        "@tensorflow/tfjs-core": "2.8.6",
+        "@tensorflow/tfjs-data": "2.8.6",
+        "@tensorflow/tfjs-layers": "2.8.6",
         "argparse": "^1.0.10",
         "chalk": "^4.1.0",
         "core-js": "3",
@@ -57,9 +57,9 @@
           }
         },
         "chalk": {
-          "version": "4.1.0",
-          "resolved": "https://registry.npmjs.org/chalk/-/chalk-4.1.0.tgz",
-          "integrity": "sha512-qwx12AxXe2Q5xQ43Ac//I6v5aXTipYrSESdOgzrN+9XjgEpyjpKuvSGaN4qE93f7TQTlerQQ8S+EQ0EyDoVL1A==",
+          "version": "4.1.1",
+          "resolved": "https://registry.npmjs.org/chalk/-/chalk-4.1.1.tgz",
+          "integrity": "sha512-diHzdDKxcU+bAsUboHLPEDQiw0qEe0qd7SYUn3HgcFlWgbDcfLGswOHYeGrHKzG9z6UYf01d9VFMfZxPM1xZSg==",
           "requires": {
             "ansi-styles": "^4.1.0",
             "supports-color": "^7.1.0"
@@ -94,20 +94,20 @@
       }
     },
     "@tensorflow/tfjs-backend-cpu": {
-      "version": "2.7.0",
-      "resolved": "https://registry.npmjs.org/@tensorflow/tfjs-backend-cpu/-/tfjs-backend-cpu-2.7.0.tgz",
-      "integrity": "sha512-R6ORcWq3ub81ABvBZEZ8Ok5OOT59B4AsRe66ds7B/NK0nN+k6y37bR3ZDVjgkEKNWNvzB7ydODikge3GNmgQIQ==",
+      "version": "2.8.6",
+      "resolved": "https://registry.npmjs.org/@tensorflow/tfjs-backend-cpu/-/tfjs-backend-cpu-2.8.6.tgz",
+      "integrity": "sha512-x9WTTE9p3Pon2D0d6HH1UCIJsU1w3v9sF3vxJcp+YStrjDefWoW5pwxHCckEKTRra7GWg3CwMKK3Si2dat4H1A==",
       "requires": {
         "@types/seedrandom": "2.4.27",
         "seedrandom": "2.4.3"
       }
     },
     "@tensorflow/tfjs-backend-webgl": {
-      "version": "2.7.0",
-      "resolved": "https://registry.npmjs.org/@tensorflow/tfjs-backend-webgl/-/tfjs-backend-webgl-2.7.0.tgz",
-      "integrity": "sha512-K7Rk5YTSWOZ969EZvh3w786daPn2ub4mA2JsX7mXKhBPUaOP9dKbBdLj9buCuMcu4zVq2pAp0QwpHSa4PHm3xg==",
+      "version": "2.8.6",
+      "resolved": "https://registry.npmjs.org/@tensorflow/tfjs-backend-webgl/-/tfjs-backend-webgl-2.8.6.tgz",
+      "integrity": "sha512-kPgm3Dim0Li5MleybYKSZVUCu91ipDjZtTA5RrJx/Dli115qwWdiRGOHYwsIEY61hZoE0m3amjWLUBxtwMW1Nw==",
       "requires": {
-        "@tensorflow/tfjs-backend-cpu": "2.7.0",
+        "@tensorflow/tfjs-backend-cpu": "2.8.6",
         "@types/offscreencanvas": "~2019.3.0",
         "@types/seedrandom": "2.4.27",
         "@types/webgl-ext": "0.0.30",
@@ -116,14 +116,14 @@
       }
     },
     "@tensorflow/tfjs-converter": {
-      "version": "2.7.0",
-      "resolved": "https://registry.npmjs.org/@tensorflow/tfjs-converter/-/tfjs-converter-2.7.0.tgz",
-      "integrity": "sha512-SBpKYn/MkN8US7DeTcnvqHpvp/WKcwzpdgkQF+eHMHEbS1lXSlt4BHhOFgRdLPzy1gEC9+6P0VdTE8NQ737t/Q=="
+      "version": "2.8.6",
+      "resolved": "https://registry.npmjs.org/@tensorflow/tfjs-converter/-/tfjs-converter-2.8.6.tgz",
+      "integrity": "sha512-Uv4YC66qjVC9UwBxz0IeLZ8KS2CReh63WlGRtHcSwDEYiwsa7cvp9H6lFSSPT7kiJmrK6JtHeJGIVcTuNnSt9w=="
     },
     "@tensorflow/tfjs-core": {
-      "version": "2.7.0",
-      "resolved": "https://registry.npmjs.org/@tensorflow/tfjs-core/-/tfjs-core-2.7.0.tgz",
-      "integrity": "sha512-4w5zjK6C5nkLatHpzARVQNd5QKtIocJRwjZIwWcScT9z2z1dX4rVmDoUpYg1cdD4H+yRRdI0awRaI3SL34yy8Q==",
+      "version": "2.8.6",
+      "resolved": "https://registry.npmjs.org/@tensorflow/tfjs-core/-/tfjs-core-2.8.6.tgz",
+      "integrity": "sha512-jS28M1POUOjnWgx3jp1v5D45DUQE8USsAHHkL/01z75KnYCAAmgqJSH4YKLiYACg3eBLWXH/KTcSc6dHAX7Kfg==",
       "requires": {
         "@types/offscreencanvas": "~2019.3.0",
         "@types/seedrandom": "2.4.27",
@@ -133,26 +133,26 @@
       }
     },
     "@tensorflow/tfjs-data": {
-      "version": "2.7.0",
-      "resolved": "https://registry.npmjs.org/@tensorflow/tfjs-data/-/tfjs-data-2.7.0.tgz",
-      "integrity": "sha512-gsVklCwqqlxhykI7U2Uy5c2hjommQCAi+3y2/LER4TNtzQTzWaGKyIXvuLuL0tE896yuzXILIMZhkUjDmUiGxA==",
+      "version": "2.8.6",
+      "resolved": "https://registry.npmjs.org/@tensorflow/tfjs-data/-/tfjs-data-2.8.6.tgz",
+      "integrity": "sha512-zoDUfd5TfkYdviqu2bObwyJGXJiOvBckOTP9j36PUs6s+4DbTIDttyxdfeEaiiLX9ZUFU58CoW+3LI/dlFVyoQ==",
       "requires": {
         "@types/node-fetch": "^2.1.2",
         "node-fetch": "~2.6.1"
       }
     },
     "@tensorflow/tfjs-layers": {
-      "version": "2.7.0",
-      "resolved": "https://registry.npmjs.org/@tensorflow/tfjs-layers/-/tfjs-layers-2.7.0.tgz",
-      "integrity": "sha512-78zsD2LLrHQuDYv0EeV83LiF0M69lKsBfuTB3FIBgS85gapZPyHh4wooKda2Y4H9EtLogU+C6bArZuDo8PaX+g=="
+      "version": "2.8.6",
+      "resolved": "https://registry.npmjs.org/@tensorflow/tfjs-layers/-/tfjs-layers-2.8.6.tgz",
+      "integrity": "sha512-fdZ0i/R2dIKmy8OB5tBAsm5IbAHfJpI6AlbjxpgoU3aWj1HCdDo+pMji928MkDJhP01ISgFTgw/7PseGNaUflw=="
     },
     "@tensorflow/tfjs-node": {
-      "version": "2.7.0",
-      "resolved": "https://registry.npmjs.org/@tensorflow/tfjs-node/-/tfjs-node-2.7.0.tgz",
-      "integrity": "sha512-0cWplm7AE40gi2llqoAp+lD/0X3dVJ8kb7Arrqb5lMhShRWUFZpULH+F0fJI6Yax4LBTzBi2SZKGL/O8krZsxg==",
+      "version": "2.8.6",
+      "resolved": "https://registry.npmjs.org/@tensorflow/tfjs-node/-/tfjs-node-2.8.6.tgz",
+      "integrity": "sha512-lq7fielTU42K8hyzvbmLTKzp4WqIAdgpWdbUPoHpXDCqTgWGb1UfMaDt/oxBkA7i9DFvyN3cem/tdeQRC95pLA==",
       "requires": {
-        "@tensorflow/tfjs": "2.7.0",
-        "@tensorflow/tfjs-core": "2.7.0",
+        "@tensorflow/tfjs": "2.8.6",
+        "@tensorflow/tfjs-core": "2.8.6",
         "adm-zip": "^0.4.11",
         "google-protobuf": "^3.9.2",
         "https-proxy-agent": "^2.2.1",
@@ -203,12 +203,12 @@
       "dev": true
     },
     "@types/express": {
-      "version": "4.17.9",
-      "resolved": "https://registry.npmjs.org/@types/express/-/express-4.17.9.tgz",
-      "integrity": "sha512-SDzEIZInC4sivGIFY4Sz1GG6J9UObPwCInYJjko2jzOf/Imx/dlpume6Xxwj1ORL82tBbmN4cPDIDkLbWHk9hw==",
+      "version": "4.17.11",
+      "resolved": "https://registry.npmjs.org/@types/express/-/express-4.17.11.tgz",
+      "integrity": "sha512-no+R6rW60JEc59977wIxreQVsIEOAYwgCqldrA/vkpCnbD7MqTefO97lmoBe4WE0F156bC4uLSP1XHDOySnChg==",
       "requires": {
         "@types/body-parser": "*",
-        "@types/express-serve-static-core": "*",
+        "@types/express-serve-static-core": "^4.17.18",
         "@types/qs": "*",
         "@types/serve-static": "*"
       }
@@ -223,9 +223,9 @@
       }
     },
     "@types/express-serve-static-core": {
-      "version": "4.17.17",
-      "resolved": "https://registry.npmjs.org/@types/express-serve-static-core/-/express-serve-static-core-4.17.17.tgz",
-      "integrity": "sha512-YYlVaCni5dnHc+bLZfY908IG1+x5xuibKZMGv8srKkvtul3wUuanYvpIj9GXXoWkQbaAdR+kgX46IETKUALWNQ==",
+      "version": "4.17.19",
+      "resolved": "https://registry.npmjs.org/@types/express-serve-static-core/-/express-serve-static-core-4.17.19.tgz",
+      "integrity": "sha512-DJOSHzX7pCiSElWaGR8kCprwibCB/3yW6vcT8VG3P0SJjnv19gnWG/AZMfM60Xj/YJIp/YCaDHyvzsFVeniARA==",
       "requires": {
         "@types/node": "*",
         "@types/qs": "*",
@@ -241,9 +241,9 @@
       }
     },
     "@types/mime": {
-      "version": "2.0.3",
-      "resolved": "https://registry.npmjs.org/@types/mime/-/mime-2.0.3.tgz",
-      "integrity": "sha512-Jus9s4CDbqwocc5pOAnh8ShfrnMcPHuJYzVcSUU7lrh8Ni5HuIqX3oilL86p3dlTrk0LzHRCgA/GQ7uNCw6l2Q=="
+      "version": "1.3.2",
+      "resolved": "https://registry.npmjs.org/@types/mime/-/mime-1.3.2.tgz",
+      "integrity": "sha512-YATxVxgRqNH6nHEIsvg6k2Boc1JHI9ZbH5iWFFv/MTkchz3b1ieGDa5T0a9RznNdI0KhVbdbWSN+KWWrQZRxTw=="
     },
     "@types/node": {
       "version": "12.12.14",
@@ -251,18 +251,18 @@
       "integrity": "sha512-u/SJDyXwuihpwjXy7hOOghagLEV1KdAST6syfnOk6QZAMzZuWZqXy5aYYZbh8Jdpd4escVFP0MvftHNDb9pruA=="
     },
     "@types/node-fetch": {
-      "version": "2.5.7",
-      "resolved": "https://registry.npmjs.org/@types/node-fetch/-/node-fetch-2.5.7.tgz",
-      "integrity": "sha512-o2WVNf5UhWRkxlf6eq+jMZDu7kjgpgJfl4xVNlvryc95O/6F2ld8ztKX+qu+Rjyet93WAWm5LjeX9H5FGkODvw==",
+      "version": "2.5.10",
+      "resolved": "https://registry.npmjs.org/@types/node-fetch/-/node-fetch-2.5.10.tgz",
+      "integrity": "sha512-IpkX0AasN44hgEad0gEF/V6EgR5n69VEqPEgnmoM8GsIGro3PowbWs4tR6IhxUTyPLpOn+fiGG6nrQhcmoCuIQ==",
       "requires": {
         "@types/node": "*",
         "form-data": "^3.0.0"
       },
       "dependencies": {
         "form-data": {
-          "version": "3.0.0",
-          "resolved": "https://registry.npmjs.org/form-data/-/form-data-3.0.0.tgz",
-          "integrity": "sha512-CKMFDglpbMi6PyN+brwB9Q/GOw0eAnsrEZDgcsH5Krhz5Od/haKHAX0NmQfha2zPPz0JpWzA7GJHGSnvCRLWsg==",
+          "version": "3.0.1",
+          "resolved": "https://registry.npmjs.org/form-data/-/form-data-3.0.1.tgz",
+          "integrity": "sha512-RHkBKtLWUVwd7SqRIvCZMEvAMoGUp0XU+seQiZejj0COz3RI3hWP4sCv3gZWWLjJTd7rGwcsF5eKZGii0r/hbg==",
           "requires": {
             "asynckit": "^0.4.0",
             "combined-stream": "^1.0.8",
@@ -277,9 +277,9 @@
       "integrity": "sha512-esIJx9bQg+QYF0ra8GnvfianIY8qWB0GBx54PK5Eps6m+xTj86KLavHv6qDhzKcu5UUOgNfJ2pWaIIV7TRUd9Q=="
     },
     "@types/qs": {
-      "version": "6.9.5",
-      "resolved": "https://registry.npmjs.org/@types/qs/-/qs-6.9.5.tgz",
-      "integrity": "sha512-/JHkVHtx/REVG0VVToGRGH2+23hsYLHdyG+GrvoUGlGAd0ErauXDyvHtRI/7H7mzLm+tBCKA7pfcpkQ1lf58iQ=="
+      "version": "6.9.6",
+      "resolved": "https://registry.npmjs.org/@types/qs/-/qs-6.9.6.tgz",
+      "integrity": "sha512-0/HnwIfW4ki2D8L8c9GVcG5I72s9jP5GSLVF0VIXDW00kmIpA6O33G7a8n59Tmh7Nz0WUC3rSb7PTY/sdW2JzA=="
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     "@types/range-parser": {
       "version": "1.2.3",
@@ -292,11 +292,11 @@
       "integrity": "sha1-nbVjk33YaRX2kJK8QyWdL0hXjkE="
     },
     "@types/serve-static": {
-      "version": "1.13.8",
-      "resolved": "https://registry.npmjs.org/@types/serve-static/-/serve-static-1.13.8.tgz",
-      "integrity": "sha512-MoJhSQreaVoL+/hurAZzIm8wafFR6ajiTM1m4A0kv6AGeVBl4r4pOV8bGFrjjq1sGxDTnCoF8i22o0/aE5XCyA==",
+      "version": "1.13.9",
+      "resolved": "https://registry.npmjs.org/@types/serve-static/-/serve-static-1.13.9.tgz",
+      "integrity": "sha512-ZFqF6qa48XsPdjXV5Gsz0Zqmux2PerNd3a/ktL45mHpa19cuMi/cL8tcxdAx497yRh+QtYPuofjT9oWw9P7nkA==",
       "requires": {
-        "@types/mime": "*",
+        "@types/mime": "^1",
         "@types/node": "*"
       }
     },
@@ -415,9 +415,9 @@
       }
     },
     "anymatch": {
-      "version": "3.1.1",
-      "resolved": "https://registry.npmjs.org/anymatch/-/anymatch-3.1.1.tgz",
-      "integrity": "sha512-mM8522psRCqzV+6LhomX5wgp25YVibjh8Wj23I5RPkPppSVSjyKD2A2mBJmWGa+KN7f2D6LNh9jkBCeyLktzjg==",
+      "version": "3.1.2",
+      "resolved": "https://registry.npmjs.org/anymatch/-/anymatch-3.1.2.tgz",
+      "integrity": "sha512-P43ePfOAIupkguHUycrc4qJ9kz8ZiuOUijaETwX7THt0Y/GNK7v0aa8rY816xWjZ7rJdA5XdMcpVFTKMq+RvWg==",
       "dev": true,
       "requires": {
         "normalize-path": "^3.0.0",
@@ -542,9 +542,9 @@
       "dev": true
     },
     "bson": {
-      "version": "1.1.5",
-      "resolved": "https://registry.npmjs.org/bson/-/bson-1.1.5.tgz",
-      "integrity": "sha512-kDuEzldR21lHciPQAIulLs1LZlCXdLziXI6Mb/TDkwXhb//UORJNPXgcRs2CuO4H0DcMkpfT3/ySsP3unoZjBg=="
+      "version": "1.1.6",
+      "resolved": "https://registry.npmjs.org/bson/-/bson-1.1.6.tgz",
+      "integrity": "sha512-EvVNVeGo4tHxwi8L6bPj3y3itEvStdwvvlojVxxbyYfoaxJ6keLgrTuKdyfEAszFK+H3olzBuafE0yoh0D1gdg=="
     },
     "buffer-equal-constant-time": {
       "version": "1.0.1",
@@ -569,16 +569,16 @@
       "dev": true
     },
     "chai": {
-      "version": "4.2.0",
-      "resolved": "https://registry.npmjs.org/chai/-/chai-4.2.0.tgz",
-      "integrity": "sha512-XQU3bhBukrOsQCuwZndwGcCVQHyZi53fQ6Ys1Fym7E4olpIqqZZhhoFJoaKVvV17lWQoXYwgWN2nF5crA8J2jw==",
+      "version": "4.3.4",
+      "resolved": "https://registry.npmjs.org/chai/-/chai-4.3.4.tgz",
+      "integrity": "sha512-yS5H68VYOCtN1cjfwumDSuzn/9c+yza4f3reKXlE5rUg7SFcCEy90gJvydNgOYtblyf4Zi6jIWRnXOgErta0KA==",
       "dev": true,
       "requires": {
         "assertion-error": "^1.1.0",
         "check-error": "^1.0.2",
         "deep-eql": "^3.0.1",
         "get-func-name": "^2.0.0",
-        "pathval": "^1.1.0",
+        "pathval": "^1.1.1",
         "type-detect": "^4.0.5"
       }
     },
@@ -657,9 +657,9 @@
       "dev": true
     },
     "cliui": {
-      "version": "7.0.3",
-      "resolved": "https://registry.npmjs.org/cliui/-/cliui-7.0.3.tgz",
-      "integrity": "sha512-Gj3QHTkVMPKqwP3f7B4KPkBZRMR9r4rfi5bXFpg1a+Svvj8l7q5CnkBkVQzfxT5DFSsGk2+PascOgL0JYkL2kw==",
+      "version": "7.0.4",
+      "resolved": "https://registry.npmjs.org/cliui/-/cliui-7.0.4.tgz",
+      "integrity": "sha512-OcRE68cOsVMXp1Yvonl/fzkQOyjLSu/8bhPDfQt0e0/Eb283TKP20Fs2MqoPsr9SwA595rRCA+QMzYc9nBP+JQ==",
       "requires": {
         "string-width": "^4.2.0",
         "strip-ansi": "^6.0.0",
@@ -760,9 +760,9 @@
       "dev": true
     },
     "core-js": {
-      "version": "3.6.5",
-      "resolved": "https://registry.npmjs.org/core-js/-/core-js-3.6.5.tgz",
-      "integrity": "sha512-vZVEEwZoIsI+vPEuoF9Iqf5H7/M3eeQqWlQnYa8FSKKePuYTf5MWnxb5SDAzCa60b3JBRS5g9b+Dq7b1y/RCrA=="
+      "version": "3.12.0",
+      "resolved": "https://registry.npmjs.org/core-js/-/core-js-3.12.0.tgz",
+      "integrity": "sha512-SaMnchL//WwU2Ot1hhkPflE8gzo7uq1FGvUJ8GKmi3TOU7rGTHIU+eir1WGf6qOtTyxdfdcp10yPdGZ59sQ3hw=="
     },
     "core-util-is": {
       "version": "1.0.2",
@@ -827,9 +827,9 @@
       "integrity": "sha1-hMbhWbgZBP3KWaDvRM2HDTElD5o="
     },
     "denque": {
-      "version": "1.4.1",
-      "resolved": "https://registry.npmjs.org/denque/-/denque-1.4.1.tgz",
-      "integrity": "sha512-OfzPuSZKGcgr96rf1oODnfjqBFmr1DVoc/TrItj3Ohe0Ah1C5WX5Baquw/9U9KovnQ88EqmJbD66rKYUQYN1tQ=="
+      "version": "1.5.0",
+      "resolved": "https://registry.npmjs.org/denque/-/denque-1.5.0.tgz",
+      "integrity": "sha512-CYiCSgIF1p6EUByQPlGkKnP1M9g0ZV3qMIrqMqZqdwazygIA/YP2vrbcyl1h/WppKJTdl1F85cXIle+394iDAQ=="
     },
     "depd": {
       "version": "1.1.2",
@@ -862,9 +862,9 @@
       }
     },
     "dotenv": {
-      "version": "8.2.0",
-      "resolved": "https://registry.npmjs.org/dotenv/-/dotenv-8.2.0.tgz",
-      "integrity": "sha512-8sJ78ElpbDJBHNeBzUbUVLsqKdccaa/BXF1uPTw3GrvQTBgrQrtObr2mUrE38vzYd8cEv+m/JBfDLioYcfXoaw=="
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diff --git a/package.json b/package.json
index 016a5e4..7c6d741 100644
--- a/package.json
+++ b/package.json
@@ -20,26 +20,26 @@
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-    "helmet": "^4.1.0",
+    "helmet": "^4.6.0",
     "http-proxy-middleware": "^0.20.0",
     "inkjet": "^2.1.2",
     "jsonwebtoken": "^8.5.1",
-    "jwks-rsa": "^1.12.1",
-    "mongodb": "^3.3.5",
+    "jwks-rsa": "^1.12.3",
+    "mongodb": "^3.6.6",
     "throng": "^4.0.0"
   },
   "devDependencies": {
-    "chai": "^4.2.0",
+    "chai": "^4.3.4",
     "chai-http": "^4.3.0",
     "cookie-parser": "^1.4.4",
     "eslint": "^6.8.0",
     "eslint-config-google": "^0.14.0",
     "eslint-plugin-security": "^1.4.0",
-    "mocha": "^8.3.2"
+    "mocha": "^8.4.0"
   }
 }

From 557ecdc1b8ce0a310cb0a8b33a19f396590e855c Mon Sep 17 00:00:00 2001
From: Yash Kumar Verma <yk.verma2000@gmail.com>
Date: Sun, 9 May 2021 20:03:43 +0530
Subject: [PATCH 20/23] test(database): unit tests for remaining functions

- initialize connection inside test file (#104)
- tests for @todo items
- .aggregate()
- .delete()
- .find()
- .update()
- .distinct()
---
 test/unit/database.js | 184 ++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 177 insertions(+), 7 deletions(-)

diff --git a/test/unit/database.js b/test/unit/database.js
index d3e1080..88157ea 100644
--- a/test/unit/database.js
+++ b/test/unit/database.js
@@ -2,7 +2,10 @@ const chai = require("chai");
 const {ObjectID} = require("mongodb");
 var should = chai.should();
 
-const {getConnection} = require("./../../service/database/connector");
+const {
+  getConnection,
+  connector,
+} = require("./../../service/database/connector");
 const MongoDB = require("./../../service/database/index");
 const Util = require("./../../service/database/util");
 
@@ -24,7 +27,14 @@ describe("service/database", () => {
   before(async () => {
     const connection = () =>
       new Promise((resolve) => {
-        setTimeout(resolve(true), 1000 * 2);
+        connector
+            .init()
+            .then(() => {
+              resolve(true);
+            })
+            .catch(() => {
+              console.error("Error connecting to database");
+            });
       });
     await connection();
   });
@@ -141,6 +151,9 @@ describe("service/database", () => {
     /** clear database after each unit */
     afterEach(async () => {
       await getConnection().collection(DB.COLLECTION).deleteMany({age: 20});
+      await getConnection()
+          .collection(DB.COLLECTION)
+          .deleteMany({for: "aggregate"});
     });
 
     /** ensures that service always provides all database functionality */
@@ -157,7 +170,7 @@ describe("service/database", () => {
 
     describe(".add", () => {
       /** if it's callable, it means it's defined. */
-      it("should be callable", () => {
+      it("should be defined and callable", () => {
         (typeof MongoDB.add).should.be.equal("function");
       });
 
@@ -207,10 +220,167 @@ describe("service/database", () => {
     /**
      * @todo: unit tests for following methods
      * .aggregate()
-     * .delete()
-     * .find()
-     * .update()
-     * .distinct()
      */
+    describe(".delete", () => {
+      /** if its callable, means its defined */
+      it("should be defined and callable", () => {
+        (typeof MongoDB.delete).should.be.equal("function");
+      });
+
+      it("should delete a single document by id", async () => {
+        const res = await MongoDB.delete(DB.NAME, DB.COLLECTION, {
+          _id: USERS[0]._id,
+        });
+        res.result.ok.should.be.equal(1);
+        res.deletedCount.should.be.equal(1);
+      });
+
+      it("should only delete one document even if filter matches many", async () => {
+        const res = await MongoDB.delete(DB.NAME, DB.COLLECTION, {
+          age: 20,
+        });
+        res.result.ok.should.be.equal(1);
+        res.deletedCount.should.be.equal(1);
+      });
+
+      it("should not throw error if filter returns empty data", async () => {
+        const res = await MongoDB.delete(DB.NAME, DB.COLLECTION, {
+          age: 50,
+        });
+        res.result.ok.should.be.equal(1);
+        res.deletedCount.should.be.equal(0);
+      });
+    });
+
+    describe(".find", () => {
+      /** if its callable, means its defined */
+      it("should be defined and callable", () => {
+        (typeof MongoDB.find).should.be.equal("function");
+      });
+
+      it("should list all data when empty filter provided", async () => {
+        const result = await MongoDB.find(DB.NAME, DB.COLLECTION, {});
+        result.length.should.be.equal(2);
+      });
+
+      it("should list all data matching given filter", async () => {
+        const result = await MongoDB.find(DB.NAME, DB.COLLECTION, {age: 20});
+        result.length.should.be.equal(2);
+      });
+
+      it("should list specific document when filtered via unique id", async () => {
+        const result = await MongoDB.find(DB.NAME, DB.COLLECTION, {
+          _id: USERS[0]._id,
+        });
+        result.length.should.be.equal(1);
+        result[0].name.should.equal(USERS[0].name);
+      });
+
+      it("should return empty array if no data matches given filter", async () => {
+        const result = await MongoDB.find(DB.NAME, DB.COLLECTION, {age: 21});
+        result.length.should.be.equal(0);
+      });
+    });
+
+    describe(".update", () => {
+      it("should be defined and callable", () => {
+        (typeof MongoDB.update).should.be.equal("function");
+      });
+
+      it("should update a single document even when filter matches multiple items", async () => {
+        const res = await MongoDB.update(
+            DB.NAME,
+            DB.COLLECTION,
+            {age: 20},
+            {
+              $set: {name: "new name"},
+            },
+        );
+        res.modifiedCount.should.equal(1);
+        res.matchedCount.should.equal(1);
+      });
+
+      it("should not update any document when filters do not match any document", async () => {
+        const res = await MongoDB.update(
+            DB.NAME,
+            DB.COLLECTION,
+            {age: 50},
+            {
+              $set: {name: "new name"},
+            },
+        );
+        res.modifiedCount.should.equal(0);
+        res.matchedCount.should.equal(0);
+      });
+    });
+
+    describe(".distinct", () => {
+      it("should be defined and callable", () => {
+        (typeof MongoDB.distinct).should.be.equal("function");
+      });
+
+      it("should return array of distinct values of passed filter", async () => {
+        const res = await MongoDB.distinct(DB.NAME, DB.COLLECTION, "age", {});
+        res.length.should.be.equal(1);
+        res[0].should.be.equal(20);
+      });
+
+      it("should return all elements if none repeated in passed filter", async () => {
+        const res = await MongoDB.distinct(DB.NAME, DB.COLLECTION, "name", {});
+        res.length.should.be.equal(2);
+      });
+    });
+
+    describe(".aggregate", () => {
+      it("should be defined and callable", () => {
+        (typeof MongoDB.aggregate).should.be.equal("function");
+      });
+
+      it("should run a function pipeline on data", async () => {
+        await MongoDB.add(DB.NAME, DB.COLLECTION, [
+          {
+            _id: new ObjectID(),
+            name: "user 1",
+            type: "a",
+            by: "bot",
+            price: 10,
+            for: "aggregate",
+          },
+          {
+            _id: new ObjectID(),
+            name: "user 2",
+            type: "a",
+            by: "bot",
+            price: 20,
+            for: "aggregate",
+          },
+          {
+            _id: new ObjectID(),
+            name: "user 3",
+            type: "b",
+            by: "human",
+            price: 30,
+            for: "aggregate",
+          },
+          {
+            _id: new ObjectID(),
+            name: "user 4",
+            type: "b",
+            by: "human",
+            price: 40,
+            for: "aggregate",
+          },
+        ]);
+
+        const res = await MongoDB.aggregate(DB.NAME, DB.COLLECTION, [
+          {$match: {type: "a"}},
+          {$group: {_id: "$by", total: {$sum: "$price"}}},
+          {$sort: {total: -1}},
+        ]);
+
+        res.length.should.be.equal(1);
+        res[0]._id.should.be.equal("bot");
+      });
+    });
   });
 });

From 7fa20254365202d77b0dc8c1d46cfd9a4a0749d0 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 10 May 2021 20:52:59 +0000
Subject: [PATCH 21/23] Bump lodash from 4.17.19 to 4.17.21

Bumps [lodash](https://github.com/lodash/lodash) from 4.17.19 to 4.17.21.
- [Release notes](https://github.com/lodash/lodash/releases)
- [Commits](https://github.com/lodash/lodash/compare/4.17.19...4.17.21)

Signed-off-by: dependabot[bot] <support@github.com>
---
 package-lock.json | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index 53f5e04..af1c51c 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -1913,9 +1913,9 @@
       }
     },
     "lodash": {
-      "version": "4.17.19",
-      "resolved": "https://registry.npmjs.org/lodash/-/lodash-4.17.19.tgz",
-      "integrity": "sha512-JNvd8XER9GQX0v2qJgsaN/mzFCNA5BRe/j8JN9d+tWyGLSodKQHKFicdwNYzWwI3wjRnaKPsGj1XkBjx/F96DQ=="
+      "version": "4.17.21",
+      "resolved": "https://registry.npmjs.org/lodash/-/lodash-4.17.21.tgz",
+      "integrity": "sha512-v2kDEe57lecTulaDIuNTPy3Ry4gLGJ6Z1O3vE1krgXZNrsQ+LFTGHVxVjcXPs17LhbZVGedAJv8XZ1tvj5FvSg=="
     },
     "lodash.clonedeep": {
       "version": "4.5.0",

From 16787ae543a09ce3b7ba09a842407c92705ca872 Mon Sep 17 00:00:00 2001
From: Ryan Birmingham <birm@rbirm.us>
Date: Sun, 6 Jun 2021 22:02:52 -0400
Subject: [PATCH 22/23] try node 16

---
 Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index 8070c85..f49610a 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,4 @@
-FROM node:14-stretch-slim
+FROM node:16-stretch-slim
 RUN apt-get update  &&  apt-get upgrade -y  &&  apt-get install -y git build-essential python3
 RUN mkdir /src
 COPY . /src

From bbec015682d30bbcb17787e17b791403c184873b Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 11 Jun 2021 08:46:49 +0000
Subject: [PATCH 23/23] Bump glob-parent from 5.1.1 to 5.1.2

Bumps [glob-parent](https://github.com/gulpjs/glob-parent) from 5.1.1 to 5.1.2.
- [Release notes](https://github.com/gulpjs/glob-parent/releases)
- [Changelog](https://github.com/gulpjs/glob-parent/blob/main/CHANGELOG.md)
- [Commits](https://github.com/gulpjs/glob-parent/compare/v5.1.1...v5.1.2)

---
updated-dependencies:
- dependency-name: glob-parent
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 package-lock.json | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index 53f5e04..3ba4de3 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -1385,9 +1385,9 @@
       }
     },
     "glob-parent": {
-      "version": "5.1.1",
-      "resolved": "https://registry.npmjs.org/glob-parent/-/glob-parent-5.1.1.tgz",
-      "integrity": "sha512-FnI+VGOpnlGHWZxthPGR+QhR78fuiK0sNLkHQv+bL9fQi57lNNdquIbna/WrfROrolq8GK5Ek6BiMwqL/voRYQ==",
+      "version": "5.1.2",
+      "resolved": "https://registry.npmjs.org/glob-parent/-/glob-parent-5.1.2.tgz",
+      "integrity": "sha512-AOIgSQCepiJYwP3ARnGx+5VnTu2HBYdzbGP45eLw1vr3zB3vZLeyed1sC9hnbcOc9/SrMyM5RPQrkGz4aS9Zow==",
       "dev": true,
       "requires": {
         "is-glob": "^4.0.1"