Using MongoDB and Python

Using MongoDB and Python Michael Bright Python User Group, Grenoble 23 Fevrier 2016

Databases Relational Databases (RDBMS) “Les SGBDRs” (OLTP – Online Transaction Processing) • Based on relational database model invented by E.F. Codd (IBM) in 1970 • SQL (SEQUEL): expressive query language • Achieves performance increase through “vertical scaling” (higher performance node) NoSQL (No SQL, or “Not just SQL”?) existed before RDBMS, resurged out of a need for more Scalability for Web2.0 - Columnar, e.g. Cassandra, Hbase, Vertica - Document Oriented, e.g. CouchDB, MongoDB, RethinkDB - Graph, e.g. Neo4J - Key-value, e.g. CouchDB, Dynamo, Riak, Redis, Oracle NoSQL, MUMPS - Multi-model, e.g. Alchemy, ArangoDB • Achieves performance increase through “horizontal scaling” (by adding nodes) OLAP – Online Analytic Processing

Databases for scalability The need for scalability requires distribution of processing making it more difficult to satisfy all criteria, according to the CAP Theorem (2000) - Consistency (Atomicity) - Availability (A request will always receive a response) - Partition Tolerance (if nodes become disconnected, the system continues to function) It is impossible to satisfy all three constraints (proved by MIT, 2002). RDBMS - favour Consistency and Availability but cannot scale horizontally NoSQL - favour Consistency and Partitioning or Availability and Partitioning

Relational vs. NoSQL Relational databases provide - Rich query language (SQL) - Strong consistency - Secondary indices NoSQL provides - Flexibility - “dynamic schema” allows missing or extra fields, embedded structures - Scalability - Adding nodes allows to scale data size - Performance - Adding nodes allows to scale performance MongoDB combines both sets of advantages

MongoDB – a Document-Oriented DB Open source DB on github with commercial support from MongoDB Inc (was 10gen). • Dynamic schema (schema-less) aids agile development • A document is an associative array (possibly more than 1-level deep), e.g. JSON Object • Uses BSON (binary JSON format) for serialization (easy to parse) • Binaries downloadable for Linux(es), Windows, OSX, Solaris • Drivers available in many languages • Provides an aggregation framework • Is the “M” in MEAN

MongoDB – Performance • Written in C++ • It achieves high performance, especially on dynamic queries • Allows primary & secondary indices (main tuning element) • Is horizontally scalable across many nodes • Extensive use of memory-mapped files i.e. read-through write-through memory caching. • Provides high availability with Master/slave replication • Provides Sharding (horizontal partitioning of data across nodes) • Horizontal partitioning : complete documents (or rows) are stored on a node • Vertical partitioning: documents (or rows) are split across nodes

MongoDB – Terminology RDBMS MongoDB Table, View ➜ Collection Row ➜ Document Index ➜ Index Join ➜ Embedded Document Foreign Key ➜ Reference Partition ➜ Shard

MongoDB – Enterprise Products There are supported products for the enterprise • MongoDB Enterprise: for production workloads • MongoDB Compass: Data and Schema visualization tool • MongoDB Connector for BI: Allows users to visualize their MongoDB Enterprise data using existing relational business intelligence tools such as Tableau. Foreign data wrapper with PostgreSQL to provide a relational SQL view on MongoDB data

MongoDB v3.2: new features • The default storage engine is now WiredTiger • Following acquisition of WiredTiger, Inc. • Introduced as an optional engine in MongoDB 3.0 • Has more granular concurrency control and native compression (lowering storage costs, increasing h/w utilization, throughput and providing more predictable performance) • Replication election enhancements • Config servers as replica sets • readConcern, and document validations. • OpsManager 2.0

MongoDB v3.2: new aggregation features • $sample, $lookup • $indexStats • $filter,$slice,$arrayElemAt, $isArray, $concatArrays • Partial Indexes • Document Validation • 4 bit testing operators • 2 new Accumulators for $group • 10 new Arithmetic expression operators

MongoDB components Components mongod - The database daemon process. mongos - Sharding controller. mongo - The database shell (uses interactive javascript). Utilities mongodump - MongoDB dump tool - for backups, snapshots, etc. mongorestore - MongoDB restore a dump mongoexport - Export a single collection to test (JSON, CSV) mongoimport - Import from JSON or CSV mongofiles - Utility for putting and getting files from MongoDB GridFS mongostat - Show performance statistics

MongoDB University (http://university.mongodb.com/)

MongoDB drivers exist for many languages 12 official drivers, plus many community languages

MongoDB docs: (https://docs.mongodb.org/manual/)

MongoDB shell > mongo MongoDB shell version: 3.2.3 connecting to: test > show dbs Money_UK 0.000GB aggregation_example 0.000GB local 0.000GB test 0.000GB > use Money_UK switched to db Money_UK > show collections CARD SAVING

MongoDB shell > use test switched to db test > db.newcoll.insert({ 'field1': 'an example' }) WriteResult({ "nInserted" : 1 }) > db.newcoll.find().count() 1 > db.newcoll.find() { "_id" : ObjectId("56cc7446bb127b86163cf226"), "field1" : "an example" } > db.newcoll.findOne() { "_id" : ObjectId("56cc7446bb127b86163cf226"), "field1" : "an example" } > db.newcoll.find({'_id':ObjectId("56cc7446bb127b86163cf226")}) { "_id" : ObjectId("56cc7446bb127b86163cf226"), "field1" : "an example" }

MongoDB shell > var doc2={'field1': 'example', 'field2': 'example2'} > db.newcoll.insert(doc2) WriteResult({ "nInserted" : 1 }) > db.newcoll.find().count() 2 > db.newcoll.find().pretty() { "_id" : ObjectId("56cc7446bb127b86163cf226"), "field1" : "an example" } { "_id" : ObjectId("56cc7711bb127b86163cf227"), "field1" : "example", "field2" : "example2" }

MongoDB indexing Indexing is the single biggest tunable performance factor. Can index on a single field, e.g. on ascending or descending values: db.newcoll.ensureIndex( { ‘field1’: 1 } ) // or -1: descending Or subfields: db.newcoll.ensureIndex( { ‘arr.subfield’: 1 } ) Or multiple fields: db.newcoll.ensureIndex( { ‘arr.subfield’: 1, ‘field2’: -1 } )

MongoDB indexing - 2 It is also possible to provide hints to the indexer, on uniqueness, sparseness or to request index creation as a background task, e.g. db.newcoll.ensureIndex( { ‘field1’: 1 }, { ‘unique’: true} ) db.newcoll.ensureIndex( { ‘field1’: 1 , ‘field2’: 1}, { ‘sparse’: true} ) db.newcoll.ensureIndex( { ‘field1’: 1 }, { ‘background’: true} )

MongoDB searching We can search based on a single field db.newcoll.find( { ‘field1’: ‘any match’ } ) Or subfields: db.newcoll.find( { ‘arr.subfield’: ‘sub field match’ } ) Or multiple fields: db.newcoll.find( { ‘arr.subfield’: ‘sub field match’, ‘field2’: ‘match2’ } ) Available indices will be used if possible

MongoDB sorting We can sort the results in ascending or descending order db.newcoll.find().sort( { ‘field1’: 1 } ) // or -1: descending or db.newcoll.find().sort( { ‘field1’: 1, ‘field2’: -1 } ) Available indices will be used if possible

MongoDB projections We can reduce the number of returned fields (the projection). This may enable data access directly from the index. In this example we limit the returned fields to ‘field1’ (and the ‘_id’ index). db.newcoll.find({ ‘field1’: ‘example’ }, { ‘field1’: 1} ) In this example we limit the returned fields to ‘field1’ (without the ‘_id’ index). db.newcoll.find({ ‘field1’: ‘example’ }, { ‘_id’: 0, ‘field1’: 1} ) We can also override the default index db.newcoll.find({ ‘field1’: ‘example’ }, { ‘_id’: ‘field1’ } )

MongoDB explain plan We can request explanation of how a query will be handled (showing possible index use) > db.newcoll.find().explain() { "queryPlanner" : { "plannerVersion" : 1, "namespace" : "test.newcoll", "indexFilterSet" : false, "parsedQuery" : { "$and" : [ ] }, "winningPlan" : { "stage" : "COLLSCAN", "filter" : { "$and" : [ ] }, "direction" : "forward" }, "rejectedPlans" : [ ] }, "serverInfo" : { "host" : "MJBRIGHT7", "port" : 27017, "version" : "3.2.3", "gitVersion" : "b326ba837cf6f49d65c2f85e1b70f6f31ece7937" }, "ok" : 1 }

MongoDB special index types • Geospatial Indexes (2d Sphere) • Text Indexes • TTL Collections (expireAfterSeconds) • Hashed Indexes for sharding

MongoDB aggregation framework Aggregation uses a pipeline of operations amongst • $match • $project • $unwind • $group • $sort

MongoDB aggregation example pipeline = [ { "$project": { // Select fields of interest 'year': { "$dateToString": { 'format': "%Y", 'date': "$date" } }, 'tags': 1, 'value': 1, }, }, { "$match": { 'year': str(year) }}, { "$group": {"_id": "$tags", "total": {"$sum": {"$abs": "$value"}}} }, { "$sort": SON([("total", -1), ("_id", -1)]) } ] cursor = db.collection.aggregate(pipeline)

MongoDB aggregation example pipeline = [ { "$project": { 'year': { "$dateToString": { 'format': "%Y", 'date': "$date" } }, 'tags': 1, 'value': 1, }, }, { "$match": { 'year': str(year) }}, // match on fields { "$group": {"_id": "$tags", "total": {"$sum": {"$abs": "$value"}}} }, { "$sort": SON([("total", -1), ("_id", -1)]) } ] cursor = db.collection.aggregate(pipeline)

MongoDB aggregation example pipeline = [ { "$project": { 'year': { "$dateToString": { 'format': "%Y", 'date': "$date" } }, 'tags': 1, 'value': 1, }, }, { "$match": { 'year': str(year) }}, { "$group": {"_id": "$tags", "total": {"$sum": {"$abs": "$value"}}} }, // ‘reduce’ { "$sort": SON([("total", -1), ("_id", -1)]) } ] cursor = db.collection.aggregate(pipeline)

MongoDB aggregation example pipeline = [ { "$project": { 'year': { "$dateToString": { 'format': "%Y", 'date': "$date" } }, 'tags': 1, 'value': 1, }, }, { "$match": { 'year': str(year) }}, { "$group": {"_id": "$tags", "total": {"$sum": {"$abs": "$value"}}} }, { "$sort": SON([("total", -1), ("_id", -1)]) } // sort the results ] cursor = db.collection.aggregate(pipeline)

PyMongo – ca y est, on arrive ! But first …

PyMongo – ca y est, on arrive ! … there are alternatives to the official PyMongo driver. • Motor is a full-featured, non-blocking MongoDB driver for Python Tornado applications. • TxMongo is an asynchronous Twisted Python driver for MongoDB.

PyMongo – ca y est, on arrive ! … and other Python/MongoDB tools ORM-like Layers New users are recommended to begin with PyMongo. Nevertheless other implementations are available providing higher abstraction. Humongolus, MongoKit, Ming, MongoAlchemy, MongoEngine, Minimongo, Manga, MotorEngine Framework Tools This section lists tools and adapters that have been designed to work with various Python frameworks and libraries. Django MongoDB Engine, Mango, Django MongoEngine, mongodb_beaker, Log4Mongo, MongoLog, C5t, rod.recipe.mongodb, repoze-what-plugins-mongodb, Mongobox, Flask- MongoAlchemy, Flask-MongoKit, Flask-PyMongo.

Using MongoDB and Python

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