PHC7065 CRITICAL SKILLS IN DATA MANIPULATION FOR POPULATION SCIENCE

NoSQL Databases

Hui Hu Ph.D.

Department of Epidemiology

College of Public Health and Health Professions & College of Medicine

April 1, 2019

NoSQL Databases and Semi-structured Data Models

Introduction to MongoDB

Lab: MongoDB

NoSQL Databases and Semi-structured Data Model

NoSQL

NoSQL: "non SQL", "non relational" or "not only SQL"
It provides a mechanism for storage and retrieval of data which is modeled in means other than the tabular relations used in relational databases
NoSQL systems are also sometimes called "Not only SQL" to emphasize that they may support SQL-like query languages.

Types of NoSQL Databases

Column: Accumulo, Cassandra, Druid, HBase, Vertica, SAP HANA
Document: Apache CouchDB, ArangoDB, Clusterpoint, Couchbase, DocumentDB, HyperDex, IBM Domino, MarkLogic, MongoDB, OrientDB, Qizx, RethinkDB
Key-value: Aerospike, ArangoDB, Couchbase, Dynamo, FairCom c-treeACE, FoundationDB, HyperDex, MemcacheDB, MUMPS, Oracle NoSQL Database, OrientDB, Redis, Riak, Berkeley DB
Graph: AllegroGraph, ArangoDB, InfiniteGraph, Apache Giraph, MarkLogic, Neo4J, OrientDB, Virtuoso, Stardog
Multi-model: Alchemy Database, ArangoDB, CortexDB, Couchbase, FoundationDB, MarkLogic, OrientDB

Semi-structured Data

A form of structured data that does not conform with the formal structure of data models associated with relational databases or other forms of data tables
It contains tags or other markers to separate semantic elements and enforce hierarchies of records and fields within the data
Also known as self-describing structure
The data model behind the web

html

Semi-structured data are usually tree-structured

body

Tree Data Structure

Paper
- getParent -> document
- getChildren -> title, author, source
- getSibling -> report
"June 12, 2000"
- root-to-node path: document/report/date/"June 12, 2000"
Queries need tree navigation
- e.g. author of "XML query data model"

xml

The entities belonging to the same class may have different attributes even though they are grouped together, and the attributes' order is not important

Extensive Markup Language

Allows the querying of both schema and data
- What is the name of the element which contains a sub-element whose value is "CellType"?

JSON

JavaScript Object Notation

Key-value pairs
Tuple
Arrays (indicated by square brackets)

[
    {
     _id: 1,
     name: "john",
     age: 21,
     type: 1,
     status: "A",
     favorites: {artist:"Picasso",food:"pizza"},
     finished: [17,3],
     badges: ["blue","black"],
     points: [
         {points: 85, bonus: 10},
         {points: 70, bonus: 5}
     ]
    },
    {
     _id: 2,
     name: "mike",
     age: 20
    }
]

One structure can be embedded in another structure

Introduction to MongoDB

MongoDB

MongoDB (from "humongous") is a cross-platform document-oriented database.
Classified as a NoSQL database, MongoDB eschews the traditional table-based relational database structure in favor of JSON-like documents with dynamic schemas (BSON), making the integration of data in certain types of applications easier and faster
SQL to MongoDB Mapping Chart

Connect to MongoDB using "mongolite" package in R

MongoDB is a collection of documents

con <- mongo(collection="collectionName", db="dbName", url="url")

Similar to Table in relational databases

con <- mongo(collection="Students", db="phc7065", url="mongodb://localhost:27017")

Example:

find()

SELECT

con$find()

Query 1:
- SQL: SELECT * FROM Student
- MongoDB: con$find()
Query 2:
- SQL: SELECT a, b FROM Student
- MongoDB:
con$find(
{},
fields='{"a":1,"b":1,"_id":0}'
)
Query 3:
- SQL: SELECT a FROM Student WHERE b="c"
- MongoDB:
con$find( '{"b":"c"}', fields='{"a":1,"_id":0}' )

Examples (continued)

Query 4:
- SQL: SELECT DISTINCT a FROM Student WHERE c>10
- MongoDB:
unique(con$find( '{"c":{"$gt":10}}',fields: '{"a":1,"_id":0}' ))
Some Operators of MongoDB:
$eq, $gt, $gte, $lt, $lte, $ne
$in, $nin
$or, $and, $not, $nor

Array Operations

Find students who are taking courses "a" and "b"
- con$find( '{"courses": {"$in":["a","b"]} }' )
Find students who are not taking courses "a" and "c"
- con$find( '{"courses": {"$nin":["a","c"]} }' )
Find the second and third elements of courses
- con$find( '{}', fields='{"courses": {"$slice": [1,2]} }' )
- con$find( '{}', fields='{"courses": {"$slice": -2} }' )
Find a student whose second element in courses is "b"
- con$find('{"courses.1":"b"}')

{_id:1,
name:"John",
age:20,
courses: ["a","b","c"]}

Compound Statements

Find students with age 20 or 21 and who are taking course "a" or "b" as their first course
SELECT * FROM Students
WHERE (age=20 OR age=21) AND (course0="a" OR course0="b")
con$find('{
"$and":[
{"$or": [{"age":20},{"age":21}] },
   {"$or": [{"courses.0":"a"},{"courses.0":"b"}] }
   ]
   }')

{_id:1,
name:"John",
age:20,
courses: ["a","b","c"]}

Queries over Nested Elements

_id:1,
    points: [
        {points: 90, bonus:10}
        {points: 60, bonus:20}
    ]

_id:2,
    points: [
        {points: 53, bonus:20}
        {points: 64, bonus:11}
    ]

_id:1,
    points: [
        {points: 99, bonus:17}
        {points: 10, bonus:24}
    ]

con$find( '{"points.0.points": {"$lte": 80} }' )
con$find( '{"points.points": {"$lte": 80} }' )
con$find( '{ "points.points":{"$lte":80}, "points.bonus": {"$lte": 20} }' )

Counting and Distinct

con$count('{"age":{"$exists":true}}')

SELECT COUNT(age) FROM Students

SELECT COUNT(DISTINCT age) FROM Students

length(con$distinct('age'))

Aggregation

con$aggregate('[
    {"$group":{"_id":"$department","meanAge":{"$avg":"$age"}}}
]')

SELECT MEAN(age) FROM Students GROUP BY department;

SELECT MEAN(age) FROM Students 
WHERE course0='a' OR course1='a' OR course2='a' 
GROUP BY department;

con$aggregate('[
    {"$match":{"courses":{"$in":["a"]}}}
    {"$group":{"_id":"$department","meanAge":{"$avg":"$age"}}}
]')

Multi-attribute Aggregation

con$aggregate('[
    {
     "$group":{
        "_id":{"department":"$department","college":"$college"},
        "meanAge":{"$avg":"$age"}
        }
    }
]')

SELECT MEAN(age) FROM Students GROUP BY department, college;

Aggregation with Text Search

con$aggregate('[
    {"$match":{"$text":{"$search":"Miami Florida"}}},
    {"$sort":{"score":{"$meta":"textScore"}}},
    {"$project":{"hometown":1,"name":1}}
]')

Join

Colleges

Students

con$aggregate('[
    {
     "$lookup":{
        "from":"Students",
        "localField":"name",
        "foreignField":"college",
        "as":"students"
      }
    }
]'')

con$aggregate('[
    {
     "$lookup":{
        "from":"Colleges",
        "localField":"college",
        "foreignField":"name",
        "as":"colleges"
      }
    }
]')

MongoDB

git pull

https://docs.mongodb.com/manual/tutorial/install-mongodb-on-ubuntu/

PHC7065-Spring2019-Lecture8

By Hui Hu

PHC7065-Spring2019-Lecture8

Slides for Lecture 8, Spring 2019, PHC7065 Critical Skills in Data Manipulation for Population Science

1,183

PHC7065 CRITICAL SKILLS IN DATA MANIPULATION FOR POPULATION SCIENCE

NoSQL Databases

Lab: MongoDB

NoSQL Databases and Semi-structured Data Model

NoSQL

Types of NoSQL Databases

Semi-structured Data

html

Tree Data Structure

xml

JSON

Introduction to MongoDB

MongoDB

Connect to MongoDB using "mongolite" package in R

find()

Examples (continued)

Array Operations

Compound Statements

Queries over Nested Elements

Counting and Distinct

Aggregation

Aggregation

Multi-attribute Aggregation

Aggregation with Text Search

Join

Join

MongoDB

git pull

PHC7065-Spring2019-Lecture8

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