fhirbase / master-class

JSONB master class

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Requirements

1. Docker and Docker-Compose

2. Pull PostgreSQL 11 image for master class with JsQuery extensions

docker pull aidbox/db:11.1.0-3-g7a1dab6

3. Install psql or any sql terminal\editor

• sudo apt-get install -y postgresql-client - depend on your OS
• pgAdmin
• DBeaver

Agenda

• What's JSONB?
• Why JSONB?
  • ORM Impedance
  • DDD Aggregates & Document databases
  • Nested Data Structures
  • Recursive Data Structures
  • Denormalization on steroids
• What are tread-offs?
  • how fast access to jsonb fields
  • how big is jsonb in database
• How to store? Schema?
• How to update? * How to search in jsonb?
• How to index jsonb?

Intro

• Why do we need JSONb
• Relational-document database
• Document database pro and contra
• Open World Assumption

Key points:

• Flexible open schema (you do not need to add new columns) - variability (validation????)
• Nested hierarchiecal document - Aggregate from DDD (compare with relational) - denormalization on steroid

Getting Started

• Install PostgreSQL11
• Load initial dataset
• JSONB basic operators
• Get data from Github
• Work with jsonb data

See: ./getting-started.md

Trade-offs

Disadvantages

• Access attributes - 10-30%
• Volume
• Lake of data types (only few)

Advantages

• Recursive datatypes
• Open schema
• Nested data structure

Attribute access speed

• 20-30% slower then column
• About twice faster then jsonb
• (unexpected) faster then composite types

See: ./tradeoffs/access.sql

Volume

Patient from https://www.hl7.org/fhir/patient-example.json

Size is 3.6 K (fit page) keys ~ 30 % in bytes

The smaller json and more numbers - the worse

See: ./tradeoffs/volume.sql

JSONB CRUD

• jsonb_extract_path and jsonb_extract_path_text
• Constructors jsonb_build_object jsonb_build_array
• jsonb_strip_nulls
• row_to_json
• || and -
• jsonb_set / jsonb_insert

See: ./crud.md

Search

json-knife

fhirpath

Indexing

Functional idx

create index if not exists valueset_resource_url   on valueset ((resource#>>'{url}')) ;

JSONB idx

create index if not exists concept_resource__gin_tgrm  
on concept using gin ((resource::text) gin_trgm_ops) ;

jsquery idx

Modify JSONB

update codesystem set resource = resource || jsonb_build_object('deprecated', true) 
where resource->>'module' = 'fhir-3.3.0';

• Constraints

Advanced Queries

• JSONB aggregate
• JSON as compositional

Programm with data

You do not need ORM!

Links

Practical hints

• http://erthalion.info/2017/12/21/advanced-json-benchmarks/
• https://blog.2ndquadrant.com/inserting-jsonb-data-in-postgresql-9-6/
• http://johnatten.com/2015/04/22/use-postgres-json-type-and-aggregate-functions-to-map-relational-data-to-json/

Theory

• https://martinfowler.com/books/nosql.html
• https://martinfowler.com/bliki/DDD_Aggregate.html
• https://en.wikipedia.org/wiki/Object-relational_impedance_mismatch