# Mongo

Gregor von Laszewski (laszewski@gmail.com)

# 1 - MongoDB in Python

Gregor von Laszewski (laszewski@gmail.com)

Learning Objectives

• Introduction to basic MongoDB knowledge
• Use of MongoDB via PyMongo
• Use of MongoEngine MongoEngine and Object-Document mapper,

In today’s era, NoSQL databases have developed an enormous potential to process the unstructured data efficiently. Modern information is complex, extensive, and may not have pre-existing relationships. With the advent of the advanced search engines, machine learning, and Artificial Intelligence, technology expectations to process, store, and analyze such data have grown tremendously [@www-upwork]. The NoSQL database engines such as MongoDB, Redis, and Cassandra have successfully overcome the traditional relational database challenges such as scalability, performance, unstructured data growth, agile sprint cycles, and growing needs of processing data in real-time with minimal hardware processing power [@www-guru99]. The NoSQL databases are a new generation of engines that do not necessarily require SQL language and are sometimes also called Not Only SQL databases. However, most of them support various third-party open connectivity drivers that can map NoSQL queries to SQL’s. It would be safe to say that although NoSQL databases are still far from replacing the relational databases, they are adding an immense value when used in hybrid IT environments in conjunction with relational databases, based on the application specific needs [@www-guru99]. We will be covering the MongoDB technology, its driver PyMongo, its object-document mapper MongoEngine, and the Flask-PyMongo micro-web framework that make MongoDB more attractive and user-friendly.

## Cloudmesh MongoDB Usage Quickstart

Before you read on we like you to read this quickstart. The easiest way for many of the activities we do to interact with MongoDB is to use our cloudmesh functionality. This prelude section is not intended to describe all the details, but get you started quickly while leveraging cloudmesh

This is done via the cloudmesh cmd5 and the cloudmesh_community/cm code:

To install mongo on for example macOS you can use

$cms admin mongo install  To start, stop and see the status of mongo you can use $ cms admin mongo start
$cms admin mongo stop$ cms admin mongo status


To add an object to Mongo, you simply have to define a dict with predefined values for kind and cloud. In future such attributes can be passed to the function to determine the MongoDB collection.

from cloudmesh.mongo.DataBaseDecorator import DatabaseUpdate

@DatabaseUpdate
def test():
data ={
"kind": "test",
"cloud": "testcloud",
"value": "hello"
}
return data

result = test()


When you invoke the function it will automatically store the information into MongoDB. Naturally this requires that the ~/.cloudmesh/cloudmesh.yaml file is properly configured.

## MongoDB

Today MongoDB is one of leading NoSQL database which is fully capable of handling dynamic changes, processing large volumes of complex and unstructured data, easily using object-oriented programming features; as well as distributed system challenges [@www-mongodb]. At its core, MongoDB is an open source, cross-platform, document database mainly written in C++ language.

### Installation

MongoDB can be installed on various Unix Platforms, including Linux, Ubuntu, Amazon Linux, etc [@www-digitaloceaninst]. This section focuses on installing MongoDB on Ubuntu 18.04 Bionic Beaver used as a standard OS for a virtual machine used as a part of Big Data Application Class during the 2018 Fall semester.

#### Installation procedure

Before installing, it is recommended to configure the non-root user and provide the administrative privileges to it, in order to be able to perform general MongoDB admin tasks. This can be accomplished by login as the root user in the following manner [@www-digitaloceanprep].

$adduser mongoadmin$ usermod -aG sudo sammy


When logged in as a regular user, one can perform actions with superuser privileges by typing sudo before each command [@www-digitaloceanprep].

Once the user set up is completed, one can login as a regular user (mongoadmin) and use the following instructions to install MongoDB.

To update the Ubuntu packages to the most recent versions, use the next command:

$sudo apt update  To install the MongoDB package: $ sudo apt install -y mongodb


To check the service and database status:

$sudo systemctl status mongodb  Verifying the status of a successful MongoDB installation can be confirmed with an output similar to this: $ mongodb.service - An object/document-oriented database
Active: **active** (running) since Sat 2018-11-15 07:48:04 UTC; 2min 17s ago
Docs: man:mongod(1)
Main PID: 2312 (mongod)
CGroup: /system.slice/mongodb.service
└─2312 /usr/bin/mongod --unixSocketPrefix=/run/mongodb --config /etc/mongodb.conf


To verify the configuration, more specifically the installed version, server, and port, use the following command:

$mongo --eval 'db.runCommand({ connectionStatus: 1 })'  Similarly, to restart MongoDB, use the following: $ sudo systemctl restart mongodb


To allow access to MongoDB from an outside hosted server one can use the following command which opens the fire-wall connections [@www-digitaloceaninst].

$sudo ufw allow from your_other_server_ip/32 to any port 27017  Status can be verified by using: $ sudo ufw status


Other MongoDB configurations can be edited through the /etc/mongodb.conf files such as port and hostnames, file paths.

$sudo nano /etc/mongodb.conf  Also, to complete this step, a server’s IP address must be added to the bindIP value [@www-digitaloceaninst]. $ logappend=true

bind_ip = 127.0.0.1,your_server_ip
*port = 27017*


MongoDB is now listening for a remote connection that can be accessed by anyone with appropriate credentials [@www-digitaloceaninst].

### Collections and Documents

Each database within Mongo environment contains collections which in turn contain documents. Collections and documents are analogous to tables and rows respectively to the relational databases. The document structure is in a key-value form which allows storing of complex data types composed out of field and value pairs. Documents are objects which correspond to native data types in many programming languages, hence a well defined, embedded document can help reduce expensive joins and improve query performance. The _id field helps to identify each document uniquely [@www-guru99].

MongoDB offers flexibility to write records that are not restricted by column types. The data storage approach is flexible as it allows one to store data as it grows and to fulfill varying needs of applications and/or users. It supports JSON like binary points known as BSON where data can be stored without specifying the type of data. Moreover, it can be distributed to multiple machines at high speed. It includes a sharding feature that partitions and spreads the data out across various servers. This makes MongoDB an excellent choice for cloud data processing. Its utilities can load high volumes of data at high speed which ultimately provides greater flexibility and availability in a cloud-based environment [@www-upwork].

The dynamic schema structure within MongoDB allows easy testing of the small sprints in the Agile project management life cycles and research projects that require frequent changes to the data structure with minimal downtime. Contrary to this flexible process, modifying the data structure of relational databases can be a very tedious process [@www-upwork].

#### Collection example

The following collection example for a person named Albert includes additional information such as age, status, and group [@www-mongocollection].

{
name: "Albert"
age: "21"
status: "Open"
group: ["AI" , "Machine Learning"]
}


#### Document structure

{
field1: value1,
field2: value2,
field3: value3,
...
fieldN: valueN
}


#### Collection Operations

If collection does not exists, MongoDB database will create a collection by default.

> db.myNewCollection1.insertOne( { x: 1 } )
> db.myNewCollection2.createIndex( { y: 1 } )


### MongoDB Querying

The data retrieval patterns, the frequency of data manipulation statements such as insert, updates, and deletes may demand for the use of indexes or incorporating the sharding feature to improve query performance and efficiency of MongoDB environment [@www-guru99]. One of the significant difference between relational databases and NoSQL databases are joins. In the relational database, one can combine results from two or more tables using a common column, often called as key. The native table contains the primary key column while the referenced table contains a foreign key. This mechanism allows one to make changes in a single row instead of changing all rows in the referenced table. This action is referred to as normalization. MongoDB is a document database and mainly contains denormalized data which means the data is repeated instead of indexed over a specific key. If the same data is required in more than one table, it needs to be repeated. This constraint has been eliminated in MongoDB’s new version 3.2. The new release introduced a $lookup feature which more likely works as a left-outer-join. Lookups are restricted to aggregated functions which means that data usually need some type of filtering and grouping operations to be conducted beforehand. For this reason, joins in MongoDB require more complicated querying compared to the traditional relational database joins. Although at this time, lookups are still very far from replacing joins, this is a prominent feature that can resolve some of the relational data challenges for MongoDB [@www-sitepoint]. MongoDB queries support regular expressions as well as range asks for specific fields that eliminate the need of returning entire documents [@www-guru99]. MongoDB collections do not enforce document structure like SQL databases which is a compelling feature. However, it is essential to keep in mind the needs of the applications[@www-upwork]. #### Mongo Queries examples The queries can be executed from Mongo shell as well as through scripts. To query the data from a MongoDB collection, one would use MongoDB’s find() method. > db.COLLECTION_NAME.find()  The output can be formatted by using the pretty() command. > db.mycol.find().pretty()  The MongoDB insert statements can be performed in the following manner: > db.COLLECTION_NAME.insert(document)  “The$lookup command performs a left-outer-join to an unsharded collection in the same database to filter in documents from the joined collection for processing” [@www-mongodblookup].

${$lookup:
{
from: <collection to join>,
localField: <field from the input documents>,
foreignField: <field from the documents of the "from" collection>,
as: <output array field>
}
}


This operation is equivalent to the following SQL operation:

 $SELECT *, <output array field> FROM collection WHERE <output array field> IN (SELECT * FROM <collection to join> WHERE <foreignField> = <collection.localField>);  To perform a Like Match (Regex), one would use the following command: > db.products.find( { sku: {$regex: /789$/ } } )  ### MongoDB Basic Functions When it comes to the technical elements of MongoDB, it posses a rich interface for importing and storage of external data in various formats. By using the Mongo Import/Export tool, one can easily transfer contents from JSON, CSV, or TSV files into a database. MongoDB supports CRUD (create, read, update, delete) operations efficiently and has detailed documentation available on the product website. It can also query the geospatial data, and it is capable of storing geospatial data in GeoJSON objects. The aggregation operation of the MongoDB process data records and returns computed results. MongoDB aggregation framework is modeled on the concept of data pipelines [@www-mongoexportimport]. #### Import/Export functions examples To import JSON documents, one would use the following command: $ mongoimport --db users --collection contacts --file contacts.json


The CSV import uses the input file name to import a collection, hence, the collection name is optional [@www-mongoexportimport].

$mongoimport --db users --type csv --headerline --file /opt/backups/contacts.csv  Mongoexport is a utility that produces a JSON or CSV export of data stored in a MongoDB instance” [@www-mongoexportimport]. $ mongoexport --db test --collection traffic --out traffic.json


### Security Features

Data security is a crucial aspect of the enterprise infrastructure management and is the reason why MongoDB provides various security features such as ole based access control, numerous authentication options, and encryption. It supports mechanisms such as SCRAM, LDAP, and Kerberos authentication. The administrator can create role/collection-based access control; also roles can be predefined or custom. MongoDB can audit activities such as DDL, CRUD statements, authentication and authorization operations [@www-mongosecurity].

#### Collection based access control example

A user defined role can contain the following privileges [@www-mongosecurity].

$privileges: [ { resource: { db: "products", collection: "inventory" }, actions: [ "find", "update"] }, { resource: { db: "products", collection: "orders" }, actions: [ "find" ] } ]  ### MongoDB Cloud Service In regards to the cloud technologies, MongoDB also offers fully automated cloud service called Atlas with competitive pricing options. Mongo Atlas Cloud interface offers interactive GUI for managing cloud resources and deploying applications quickly. The service is equipped with geographically distributed instances to ensure no single point failure. Also, a well-rounded performance monitoring interface allows users to promptly detect anomalies and generate index suggestions to optimize the performance and reliability of the database. Global technology leaders such as Google, Facebook, eBay, and Nokia are leveraging MongoDB and Atlas cloud services making MongoDB one of the most popular choices among the NoSQL databases [@www-mongoatlas]. ## PyMongo PyMongo is the official Python driver or distribution that allows work with a NoSQL type database called MongoDB [@api-mongodb-com-api]. The first version of the driver was developed in 2009 [@www-pymongo-blog], only two years after the development of MongoDB was started. This driver allows developers to combine both Python’s versatility and MongoDB’s flexible schema nature into successful applications. Currently, this driver supports MongoDB versions 2.6, 3.0, 3.2, 3.4, 3.6, and 4.0 [@www-github]. MongoDB and Python represent a compatible fit considering that BSON (binary JSON) used in this NoSQL database is very similar to Python dictionaries, which makes the collaboration between the two even more appealing [@www-mongodb-slideshare]. For this reason, dictionaries are the recommended tools to be used in PyMongo when representing documents [@www-gearheart]. ### Installation Prior to being able to exploit the benefits of Python and MongoDB simultaneously, the PyMongo distribution must be installed using pip. To install it on all platforms, the following command should be used [@www-api-mongodb-installation]: $ python -m pip install pymongo

Specific versions of PyMongo can be installed with command lines such as in our example where the 3.5.1 version is installed [@www-api-mongodb-installation].

$python -m pip install pymongo==3.5.1  A single line of code can be used to upgrade the driver as well [@www-api-mongodb-installation]. $ python -m pip install --upgrade pymongo


Furthermore, the installation process can be completed with the help of the easy_install tool, which requires users to use the following command [@www-api-mongodb-installation].

$python -m easy_install pymongo  To do an upgrade of the driver using this tool, the following command is recommended [@www-api-mongodb-installation]: $ python -m easy_install -U pymongo


There are many other ways of installing PyMongo directly from the source, however, they require for C extension dependencies to be installed prior to the driver installation step, as they are the ones that skim through the sources on GitHub and use the most up-to-date links to install the driver [@www-api-mongodb-installation].

To check if the installation was completed accurately, the following command is used in the Python console [@www-realpython].

import pymongo


If the command returns zero exceptions within the Python shell, one can consider for the PyMongo installation to have been completed successfully.

### Dependencies

The PyMongo driver has a few dependencies that should be taken into consideration prior to its usage. Currently, it supports CPython 2.7, 3.4+, PyPy, and PyPy 3.5+ interpreters [@www-github]. An optional dependency that requires some additional components to be installed is the GSSAPI authentication [@www-github]. For the Unix based machines, it requires pykerberos, while for the Windows machines WinKerberos is needed to fullfill this requirement [@www-github]. The automatic installation of this dependency can be done simultaneously with the driver installation, in the following manner:

$python -m pip install pymongo[gssapi]  Other third-party dependencies such as ipaddress, certifi, or wincerstore are necessary for connections with help of TLS/SSL and can also be simultaneously installed along with the driver installation [@www-github]. ### Running PyMongo with Mongo Deamon Once PyMongo is installed, the Mongo deamon can be run with a very simple command in a new terminal window [@www-realpython]. $ mongod


### Connecting to a database using MongoClient

In order to be able to establish a connection with a database, a MongoClient class needs to be imported, which sub-sequentially allows the MongoClient object to communicate with the database [@www-realpython].

from pymongo import MongoClient
client = MongoClient()


This command allows a connection with a default, local host through port 27017, however, depending on the programming requirements, one can also specify those by listing them in the client instance or use the same information via the Mongo URI format [@www-realpython].

### Accessing Databases

Since MongoClient plays a server role, it can be used to access any desired databases in an easy way. To do that, one can use two different approaches. The first approach would be doing this via the attribute method where the name of the desired database is listed as an attribute, and the second approach, which would include a dictionary-style access [@www-realpython]. For example, to access a database called cloudmesh_community, one would use the following commands for the attribute and for the dictionary method, respectively.

db = client.cloudmesh_community
db = client['cloudmesh_community']


### Creating a Database

Creating a database is a straight forward process. First, one must create a MongoClient object and specify the connection (IP address) as well as the name of the database they are trying to create [@www-w3schools]. The example of this command is presented in the followng section:

import pymongo
client = pymongo.MongoClient('mongodb://localhost:27017/')
db = client['cloudmesh']


### Inserting and Retrieving Documents (Querying)

Creating documents and storing data using PyMongo is equally easy as accessing and creating databases. In order to add new data, a collection must be specified first. In this example, a decision is made to use the cloudmesh group of documents.

cloudmesh = db.cloudmesh


Once this step is completed, data may be inserted using the insert_one() method, which means that only one document is being created. Of course, insertion of multiple documents at the same time is possible as well with use of the insert_many() method [@www-realpython]. An example of this method is as follows:

course_info = {
'course': 'Big Data Applications and Analytics',
'instructor': ' Gregor von Laszewski',
'chapter': 'technologies'
}
result = cloudmesh.insert_one(course_info)


Another example of this method would be to create a collection. If we wanted to create a collection of students in the cloudmesh_community, we would do it in the following manner:

student = [ {'name': 'John', 'st_id': 52642},
{'name': 'Mercedes', 'st_id': 5717},
{'name': 'Anna', 'st_id': 5654},
{'name': 'Greg', 'st_id': 5423},
{'name': 'Amaya', 'st_id': 3540},
{'name': 'Cameron', 'st_id': 2343},
{'name': 'Bozer', 'st_id': 4143},
{'name': 'Cody', 'price': 2165} ]

client = MongoClient('mongodb://localhost:27017/')

with client:
db = client.cloudmesh
db.students.insert_many(student)


Retrieving documents is equally simple as creating them. The find_one() method can be used to retrieve one document [@www-realpython]. An implementation of this method is given in the following example.

gregors_course = cloudmesh.find_one({'instructor':'Gregor von Laszewski'})


Similarly, to retieve multiple documents, one would use the find() method instead of the find_one(). For example, to find all courses thought by professor von Laszewski, one would use the following command:

gregors_course = cloudmesh.find({'instructor':'Gregor von Laszewski'})


One thing that users should be cognizant of when using the find() method is that it does not return results in an array format but as a cursor object, which is a combination of methods that work together to help with data querying [@www-realpython]. In order to return individual documents, iteration over the result must be completed [@www-realpython].

### Limiting Results

When it comes to working with large databases it is always useful to limit the number of query results. PyMongo supports this option with its limit() method [@www-w3schools]. This method takes in one parameter which specifies the number of documents to be returned [@www-w3schools]. For example, if we had a collection with a large number of cloud technologies as individual documents, one could modify the query results to return only the top 10 technologies. To do this, the following example could be utilized:

client = pymongo.MongoClient('mongodb://localhost:27017/')
db = client['cloudmesh']
col = db['technologies']
topten = col.find().limit(10)


### Updating Collection

Updating documents is very similar to inserting and retrieving the same. Depending on the number of documents to be updated, one would use the update_one() or update_many() method [@www-w3schools]. Two parameters need to be passed in the update_one() method for it to successfully execute. The first argument is the query object that specifies the document to be changed, and the second argument is the object that specifies the new value in the document. An example of the update_one() method in action is the following:

myquery = { 'course': 'Big Data Applications and Analytics' }
newvalues = { '$set': { 'course': 'Cloud Computing' } }  Updating all documents that fall under the same criteria can be done with the update_many method [@www-w3schools]. For example, to update all documents in which course title starts with letter B with a different instructor information, we would do the following: client = pymongo.MongoClient('mongodb://localhost:27017/') db = client['cloudmesh'] col = db['courses'] query = { 'course': { '$regex': '^B' } }
newvalues = { '$set': { 'instructor': 'Gregor von Laszewski' } } edited = col.update_many(query, newvalues)  ### Counting Documents Counting documents can be done with one simple operation called count_documents() instead of using a full query [@www-pymongo-tutorial]. For example, we can count the documents in the cloudmesh_commpunity by using the following command: cloudmesh = count_documents({})  To create a more specific count, one would use a command similar to this: cloudmesh = count_documents({'author': 'von Laszewski'})  This technology supports some more advanced querying options as well. Those advanced queries allow one to add certain contraints and narrow down the results even more. For example, to get the courses thought by professor von Laszewski after a certain date, one would use the following command: d = datetime.datetime(2017, 11, 12, 12) for course in cloudmesh.find({'date': {'$lt': d}}).sort('author'):
pprint.pprint(course)


### Indexing

Indexing is a very important part of querying. It can greately improve query performance but also add functionality and aide in storing documents [@www-pymongo-tutorial].

“To create a unique index on a key that rejects documents whose value for that key already exists in the index” [@www-pymongo-tutorial].

We need to firstly create the index in the following manner:

result = db.profiles.create_index([('user_id', pymongo.ASCENDING)],
unique=True)
sorted(list(db.profiles.index_information()))


This command acutally creates two different indexes. The first one is the *_id* , created by MongoDB automatically, and the second one is the user_id, created by the user.

The purpose of those indexes is to cleverly prevent future additions of invalid user_ids into a collection.

### Sorting

Sorting on the server-side is also avaialable via MongoDB. The PyMongo sort() method is equivalent to the SQL order by statement and it can be performed as pymongo.ascending and pymongo.descending [@book-ohiggins]. This method is much more efficient as it is being completed on the server-side, compared to the sorting completed on the client side. For example, to return all users with first name Gregor sorted in descending order by birthdate we would use a command such as this:

users = cloudmesh.users.find({'firstname':'Gregor'}).sort(('dateofbirth', pymongo.DESCENDING))
for user in users:
print user.get('email')


### Aggregation

Aggregation operations are used to process given data and produce summarized results. Aggregation operations collect data from a number of documents and provide collective results by grouping data. PyMongo in its documentation offers a separate framework that supports data aggregation. This aggregation framework can be used to

“provide projection capabilities to reshape the returned data” [@www-mongo-aggregation].

In the aggregation pipeline, documents pass through multiple pipeline stages which convert documents into result data. The basic pipeline stages include filters. Those filters act like document transformation by helping change the document output form. Other pipelines help group or sort documents with specific fields. By using native operations from MongoDB, the pipeline operators are efficient in aggregating results.

The addFields stage is used to add new fields into documents. It reshapes each document in stream, similarly to the project stage. The output document will contain existing fields from input documents and the newly added fields @www-docs-mongodb]. The following example shows how to add student details into a document.

  db.cloudmesh_community.aggregate([
{
$addFields: { "document.StudentDetails": {$concat:['$document.student.FirstName', '$document.student.LastName']
}
}
} ])


The bucket stage is used to categorize incoming documents into groups based on specified expressions. Those groups are called buckets [@www-docs-mongodb]. The following example shows the bucket stage in action.

db.user.aggregate([
{ "$group": { "_id": { "city": "$city",
"age": {
"$let": { "vars": { "age": { "$subtract" :[{ "$year": new Date() },{ "$year": "$birthDay" }] }}, "in": { "$switch": {
"branches": [
{ "case": { "$lt": [ "$$age", 20 ] }, "then": 0 }, { "case": { "lt": [ "$$age", 30 ] }, "then": 20 }, { "case": { "$lt": [ "$$age", 40 ] }, "then": 30 }, { "case": { "lt": [ "$$age", 50 ] }, "then": 40 },
{ "case": { "$lt": [ "$$age", 200 ] }, "then": 50 } ] } } } } }, "count": { "sum": 1 }}})  In the bucketAuto stage, the boundaries are automatically determined in an attempt to evenly distribute documents into a specified number of buckets. In the following operation, input documents are grouped into four buckets according to the values in the price field [@www-docs-mongodb]. db.artwork.aggregate( [ { bucketAuto: { groupBy: "price", buckets: 4 } } ] )  The collStats stage returns statistics regarding a collection or view [@www-docs-mongodb]. db.matrices.aggregate( [ { collStats: { latencyStats: { histograms: true } } } ] )  The count stage passes a document to the next stage that contains the number documents that were input to the stage [@www-docs-mongodb]. db.scores.aggregate( [ { match: { score: { gt: 80 } } }, { count: "passing_scores" } ])  The facet stage helps process multiple aggregation pipelines in a single stage [@www-docs-mongodb]. db.artwork.aggregate( [ { facet: { "categorizedByTags": [ { unwind: "tags" }, { sortByCount: "tags" } ], "categorizedByPrice": [ // Filter out documents without a price e.g., _id: 7 { match: { price: { exists: 1 } } }, { bucket: { groupBy: "price", boundaries: [ 0, 150, 200, 300, 400 ], default: "Other", output: { "count": { sum: 1 }, "titles": { push: "title" } } } }], "categorizedByYears(Auto)": [ { bucketAuto: { groupBy: "year",buckets: 4 } } ]}}])  The geoNear stage returns an ordered stream of documents based on the proximity to a geospatial point. The output documents include an additional distance field and can include a location identifier field [@www-docs-mongodb]. db.places.aggregate([ { geoNear: { near: { type: "Point", coordinates: [ -73.99279 , 40.719296 ] }, distanceField: "dist.calculated", maxDistance: 2, query: { type: "public" }, includeLocs: "dist.location", num: 5, spherical: true } }])  The graphLookup stage performs a recursive search on a collection. To each output document, it adds a new array field that contains the traversal results of the recursive search for that document [@www-docs-mongodb]. db.travelers.aggregate( [ { graphLookup: { from: "airports", startWith: "nearestAirport", connectFromField: "connects", connectToField: "airport", maxDepth: 2, depthField: "numConnections", as: "destinations" } } ] )  The group stage consumes the document data per each distinct group. It has a RAM limit of 100 MB. If the stage exceeds this limit, the group produces an error [@www-docs-mongodb]. db.sales.aggregate( [ { group : { _id : { month: { month: "date" }, day: { dayOfMonth: "date" }, year: { year: "date" } }, totalPrice: { sum: { multiply: [ "price", "quantity" ] } }, averageQuantity: { avg: "quantity" }, count: { sum: 1 } } } ] )  The indexStats stage returns statistics regarding the use of each index for a collection [@www-docs-mongodb]. db.orders.aggregate( [ { indexStats: { } } ] )  The limit stage is used for controlling the number of documents passed to the next stage in the pipeline [@www-docs-mongodb]. db.article.aggregate( { limit : 5 } )  The listLocalSessions stage gives the session information currently connected to mongos or mongod instance [@www-docs-mongodb]. db.aggregate( [ { listLocalSessions: { allUsers: true } } ] )  The listSessions stage lists out all session that have been active long enough to propagate to the system.sessions collection [@www-docs-mongodb].  use config db.system.sessions.aggregate( [ { listSessions: { allUsers: true } } ] )  The lookup stage is useful for performing outer joins to other collections in the same database [@www-docs-mongodb]. { lookup: { from: <collection to join>, localField: <field from the input documents>, foreignField: <field from the documents of the "from" collection>, as: <output array field> } }  The match stage is used to filter the document stream. Only matching documents pass to next stage [@www-docs-mongodb]. db.articles.aggregate( [ { match : { author : "dave" } } ] )  The project stage is used to reshape the documents by adding or deleting the fields. db.books.aggregate( [ { project : { title : 1 , author : 1 } } ] )  The redact stage reshapes stream documents by restricting information using information stored in documents themselves [@www-docs-mongodb].  db.accounts.aggregate( [ { match: { status: "A" } }, { redact: { cond: { if: { eq: [ "level", 5 ] }, then: "$$PRUNE", else: "$$DESCEND" } } } ]);  The replaceRoot stage is used to replace a document with a specified embedded document [@www-docs-mongodb].  db.produce.aggregate( [ {$replaceRoot: { newRoot: "$in_stock" } } ] )  The sample stage is used to sample out data by randomly selecting number of documents form input [@www-docs-mongodb].  db.users.aggregate( [ {$sample: { size: 3 } } ]
)


The skip stage skips specified initial number of documents and passes remaining documents to the pipeline [@www-docs-mongodb].

db.article.aggregate(
{ $skip : 5 } );  The sort stage is useful while reordering document stream by a specified sort key [@www-docs-mongodb].  db.users.aggregate( [ {$sort : { age : -1, posts: 1 } }
]
)


The sortByCounts stage groups the incoming documents based on a specified expression value and counts documents in each distinct group [@www-docs-mongodb].

db.exhibits.aggregate(
[ { $unwind: "$tags" },  { $sortByCount: "$tags" } ] )


The unwind stage deconstructs an array field from the input documents to output a document for each element [@www-docs-mongodb].

db.inventory.aggregate( [ { $unwind: "$sizes" } ] )
db.inventory.aggregate( [ { $unwind: { path: "$sizes" } } ] )


The out stage is used to write aggregation pipeline results into a collection. This stage should be the last stage of a pipeline [@www-docs-mongodb].

db.books.aggregate( [
{ $group : { _id : "$author", books: { $push: "$title" } } },
{ $out : "authors" } ] )  Another option from the aggregation operations is the Map/Reduce framework, which essentially includes two different functions, map and reduce. The first one provides the key value pair for each tag in the array, while the latter one “sums over all of the emitted values for a given key” [@www-mongo-aggregation]. The last step in the Map/Reduce process it to call the map_reduce() function and iterate over the results [@www-mongo-aggregation]. The Map/Reduce operation provides result data in a collection or returns results in-line. One can perform subsequent operations with the same input collection if the output of the same is written to a collection [@www-docs-map-reduce]. An operation that produces results in a in-line form must provide results with in the BSON document size limit. The current limit for a BSON document is 16 MB. These types of operations are not supported by views [@www-docs-map-reduce]. The PyMongo’s API supports all features of the MongoDB’s Map/Reduce engine [@www-api-map-reduce]. Moreover, Map/Reduce has the ability to get more detailed results by passing full_response=True argument to the map_reduce() function [@www-api-map-reduce]. ### Deleting Documents from a Collection The deletion of documents with PyMongo is fairly straight forward. To do so, one would use the remove() method of the PyMongo Collection object [@book-ohiggins]. Similarly to the reads and updates, specification of documents to be removed is a must. For example, removal of the entire document collection with a score of 1, would required one to use the following command: cloudmesh.users.remove({"score":1, safe=True})  The safe parameter set to True ensures the operation was completed [@book-ohiggins]. ### Copying a Database Copying databases within the same mongod instance or between different mongod servers is made possible with the command() method after connecting to the desired mongod instance [@www-pymongo-documentation-copydb]. For example, to copy the cloudmesh database and name the new database cloudmesh_copy, one would use the command() method in the following manner: client.admin.command('copydb', fromdb='cloudmesh', todb='cloudmesh_copy')  There are two ways to copy a database between servers. If a server is not password-prodected, one would not need to pass in the credentials nor to authenticate to the admin database [@www-pymongo-documentation-copydb]. In that case, to copy a database one would use the following command: client.admin.command('copydb', fromdb='cloudmesh', todb='cloudmesh_copy', fromhost='source.example.com')  On the other hand, if the server where we are copying the database to is protected, one would use this command instead: client = MongoClient('target.example.com', username='administrator', password='pwd') client.admin.command('copydb', fromdb='cloudmesh', todb='cloudmesh_copy', fromhost='source.example.com')  ### PyMongo Strengths One of PyMongo strengths is that allows document creation and querying natively “through the use of existing language features such as nested dictionaries and lists” [@book-ohiggins]. For moderately experienced Python developers, it is very easy to learn it and quickly feel comfortable with it. “For these reasons, MongoDB and Python make a powerful combination for rapid, iterative development of horizontally scalable backend applications” [@book-ohiggins]. According to [@book-ohiggins], MongoDB is very applicable to modern applications, which makes PyMongo equally valuable [@book-ohiggins]. ## MongoEngine “MongoEngine is an Object-Document Mapper, written in Python for working with MongoDB” [@www-docs-mongoengine]. It is actually a library that allows a more advanced communication with MongoDB compared to PyMongo. As MongoEngine is technically considered to be an object-document mapper(ODM), it can also be considered to be “equivalent to a SQL-based object relational mapper(ORM)” [@www-realpython]. The primary technique why one would use an ODM includes data conversion between computer systems that are not compatible with each other [@www-wikiodm]. For the purpose of converting data to the appropriate form, a virtual object database must be created within the utilized programming language [@www-wikiodm]. This library is also used to define schemata for documents within MongoDB, which ultimately helps with minimizing coding errors as well defining methods on existing fields [@www-mongoengine-schema]. It is also very beneficial to the overall workflow as it tracks changes made to the documents and aids in the document saving process [@www-mongoengine-instances]. ### Installation The installation process for this technology is fairly simple as it is considered to be a library. To install it, one would use the following command [@www-installing]: $ pip install mongoengine


A bleeding-edge version of MongoEngine can be installed directly from GitHub by first cloning the repository on the local machine, virtual machine, or cloud.

### Connecting to a database using MongoEngine

Once installed, MongoEngine needs to be connected to an instance of the mongod, similarly to PyMongo [@www-connecting]. The connect() function must be used to successfully complete this step and the argument that must be used in this function is the name of the desired database [@www-connecting]. Prior to using this function, the function name needs to be imported from the MongoEngine library.

from mongoengine import connect
connect('cloudmesh_community')


Similarly to the MongoClient, MongoEngine uses the local host and port 27017 by default, however, the connect() function also allows specifying other hosts and port arguments as well [@www-connecting].

connect('cloudmesh_community', host='196.185.1.62', port=16758)


Other types of connections are also supported (i.e. URI) and they can be completed by providing the URI in the connect() function [@www-connecting].

### Querying using MongoEngine

To query MongoDB using MongoEngine an objects attribute is used, which is, technically, a part of the document class [@www-querying]. This attribute is called the QuerySetManager which in return

“creates a new QuerySet object on access” [@www-querying].

To be able to access individual documents from a database, this object needs to be iterated over. For example, to return/print all students in the cloudmesh_community object (database), the following command would be used.

for user in cloudmesh_community.objects:
print cloudmesh_community.student


MongoEngine also has a capability of query filtering which means that a keyword can be used within the called QuerySet object to retrieve specific information [@www-querying]. Let us say one would like to iterate over cloudmesh_community students that are natives of Indiana. To achieve this, one would use the following command:

indy_students = cloudmesh_community.objects(state='IN')


This library also allows the use of all operators except for the equality operator in its queries, and moreover, has the capability of handling string queries, geo queries, list querying, and querying of the raw PyMongo queries [@www-querying].

The string queries are useful in performing text operations in the conditional queries. A query to find a document exactly matching and with state ACTIVE can be performed in the following manner:

db.cloudmesh_community.find( State.exact("ACTIVE") )


The query to retrieve document data for names that start with a case sensitive AL can be written as:

db.cloudmesh_community.find( Name.startswith("AL") )


To perform an exact same query for the non-key-sensitive AL one would use the following command:

db.cloudmesh_community.find( Name.istartswith("AL") )


The MongoEngine allows data extraction of geographical locations by using Geo queries. The geo_within operator checks if a geometry is within a polygon.

  cloudmesh_community.objects(
point__geo_within=[[[40, 5], [40, 6], [41, 6], [40, 5]]])
cloudmesh_community.objects(
point__geo_within={"type": "Polygon",
"coordinates": [[[40, 5], [40, 6], [41, 6], [40, 5]]]})


The list query looks up the documents where the specified fields matches exactly to the given value. To match all pages that have the word coding as an item in the tags list one would use the following query:

  class Page(Document):
tags = ListField(StringField())

Page.objects(tags='coding')


Overall, it would be safe to say that MongoEngine has good compatibility with Python. It provides different functions to utilize Python easily with MongoDBand which makes this pair even more attractive to application developers.

### Installation

Flask-PyMongo can be installed with an easy command such as this:

$pip install Flask-PyMongo  PyMongo can be added in the following manner:  from flask import Flask from flask_pymongo import PyMongo app = Flask(__name__) app.config["MONGO_URI"] = "mongodb://localhost:27017/cloudmesh_community" mongo = PyMongo(app)  ### Configuration There are two ways to configure Flask-PyMongo. The first way would be to pass a MongoDB URI to the PyMongo constructor, while the second way would be to “assign it to the MONGO_URI Flask confiuration variable” [@www-flask-pymongo]. ### Connection to multiple databases/servers Multiple PyMongo instances can be used to connect to multiple databases or database servers. To achieve this, once would use a command similar to the following:  app = Flask(__name__) mongo1 = PyMongo(app, uri="mongodb://localhost:27017/cloudmesh_community_one") mongo2 = PyMongo(app, uri="mongodb://localhost:27017/cloudmesh_community_two") mongo3 = PyMongo(app, uri= "mongodb://another.host:27017/cloudmesh_community_Three")  ### Flask-PyMongo Methods Flask-PyMongo provides helpers for some common tasks. One of them is the Collection.find_one_or_404 method shown in the following example:  @app.route("/user/<username>") def user_profile(username): user = mongo.db.cloudmesh_community.find_one_or_404({"_id": username}) return render_template("user.html", user=user)  This method is very similar to the MongoDB’s find_one() method, however, instead of returning None it causes a 404 Not Found HTTP status [@www-flask-pymongo]. Similarly, the PyMongo.send_file and PyMongo.save_file methods work on the file-like objects and save them to GridFS using the given file name [@www-flask-pymongo]. ### Additional Libraries Flask-MongoAlchemy and Flask-MongoEngine are the additional libraries that can be used to connect to a MongoDB database while using enhanced features with the Flask app. The Flask-MongoAlchemy is used as a proxy between Python and MongoDB to connect. It provides an option such as server or database based authentication to connect to MongoDB. While the default is set server based, to use a database-based authentication, the config value MONGOALCHEMY_SERVER_AUTH parameter must be set to False [@www-pythonhosted-MongoAlchemy]. Flask-MongoEngine is the Flask extension that provides integration with the MongoEngine. It handles connection management for the apps. It can be installed through pip and set up very easily as well. The default configuration is set to the local host and port 27017. For the custom port and in cases where MongoDB is running on another server, the host and port must be explicitly specified in connect strings within the MONGODB_SETTINGS dictionary with app.config, along with the database username and password, in cases where a database authentication is enabled. The URI style connections are also supported and supply the URI as the host in the MONGODB_SETTINGS dictionary with app.config. There are various custom query sets that are available within Flask-Mongoengine that are attached to Mongoengine’s default queryset [@www-flask-mongoengine]. ### Classes and Wrappers Attributes such as cx and db in the PyMongo objects are the ones that help provide access to the MongoDB server [@www-flask-pymongo]. To achieve this, one must pass the Flask app to the constructor or call init_app() [@www-flask-pymongo]. “Flask-PyMongo wraps PyMongo’s MongoClient, Database, and Collection classes, and overrides their attribute and item accessors” [@www-flask-pymongo]. This type of wrapping allows Flask-PyMongo to add methods to Collection while at the same time allowing a MongoDB-style dotted expressions in the code [@www-flask-pymongo]. type(mongo.cx) type(mongo.db) type(mongo.db.cloudmesh_community)  Flask-PyMongo creates connectivity between Python and Flask using a MongoDB database and supports “extensions that can add application features as if they were implemented in Flask itself” [@www-wiki-flask], hence, it can be used as an additional Flask functionality in Python code. The extensions are there for the purpose of supporting form validations, authentication technologies, object-relational mappers and framework related tools which ultimately adds a lot of strength to this micro-web framework [@www-wiki-flask]. One of the main reasons and benefits why it is frequently used with MongoDB is its capability of adding more control over databases and history [@www-wiki-flask]. # 2 - Mongoengine Gregor von Laszewski (laszewski@gmail.com) ## Introduction MongoEngine is a document mapper for working with mongoldb with python. To be able to use mongo engine MongodD should be already installed and running. ## Install and connect Mongoengine can be installed by running: $ pip install mongo engine


This will install six, pymongo and mongoengine.

To connect to mongoldb use connect () function by specifying mongoldb instance name. You don’t need to go to mongo shell but this can be done from unix shell or cmd line. In this case we are connecting to a database named student_db.

from mongo engine import * connect (‘student_db’)


If mongodb is running on a port different from default port , port number and host need to be specified. If mongoldb needs authentication username and password need to be specified.

## Basics

Mongodb does not enforce schemas. Comparing to RDBMS, Row in mongoldb is called a “document” and table can be compared to Collection. Defining a schema is helpful as it minimizes coding error’s. To define a schema we create a class that inherits from document.

from mongoengine import *

class Student(Document):
first_name = StringField(max_length=50)
last_name = StringField(max_length=50)


:o2: TODO: Can you fix the code sections and look at the examples we provided.

Fields are not mandatory but if needed, set the required keyword argument to True. There are multiple values available for field types. Each field can be customized by by keyword argument. If each student is sending text messages to Universities central database , these can be stored using Mongodb. Each text can have different data types, some might have images or some might have url’s. So we can create a class text and link it to student by using Reference field (similar to foreign key in RDBMS).

class Text(Document):
title = StringField(max_length=120, required=True)
author = ReferenceField(Student)
meta = {'allow_inheritance': True}

class OnlyText(Text):
content = StringField()

class ImagePost(Text):
image_path = StringField()



MongoDb supports adding tags to individual texts rather then storing them separately and then having them referenced.Similarly Comments can also be stored directly in a Text.

class Text(Document):
title = StringField(max_length=120, required=True)
author = ReferenceField(User)
tags = ListField(StringField(max_length=30))

for text in OnlyText.objects:

for text in Text.objects(tags='mongodb'):