fhirbase.py

FHIRBase connector for python. This package provides a wrapper over psycopg2 connection which provides CRUD operations for resources in fhirbase.

Install

pip install fhirbase

Usage

Import fhirbase and psycopg2 libraries:

import fhirbase
import psycopg2

Create a connection using psycopg2.connect:

connection = psycopg2.connect(
    dbname='postgres', user='postgres',
    host='localhost', port='5432')

Create an instance of FHIRBase:

fb = fhirbase.FHIRBase(connection)

Now you can use the following methods of FHIRBase instance:

• .execute(sql, params=None, commit=False)
• .execute_without_result(sql, params=None, commit=False)
• .row_to_resource(row)

CRUD methods work with FHIR resources. A resource represented as a dict with a specified resourceType key as a required key. The following methods works with a resource and returns resources.

• .create(resource, txid=None, commit=True)
• .update(resource, txid=None, commit=True)
• .delete(resource, txid=None, commit=True)/.delete(resource_type, id, txid=None, commit=True)
• .read(resource)/.read(resource_type, id)
• .list(sql, params=None)

Methods

.execute

Executes sql with params.

Syntax: .execute(sql, params=None, commit=False)

Returns: context manager with a cursor as context

Example:

with fb.execute('SELECT * FROM patient WHERE id=%s', ['id']) as cursor:
    print(cursor.fetchall())

.execute_without_result

Executes sql with params.

Syntax: .execute_without_result(sql, params=None, commit=False)

Returns: nothing

Example:

fb.execute_without_result('INSERT INTO transaction (resource) VALUES (%s)', ['{}'])

.row_to_resource

Transforms a raw row from DB to a resource.

Syntax: .row_to_resource(row)

Returns: resource representation (dict)

Example:

fb.row_to_resource({
    'resource': {'name': []},
    'ts': 'ts',
    'txid': 'txid',
    'resource_type': 'Patient',
    'meta': {'tag': 'created'},
    'id': 'id',
}))

will return a resource representation:

{
    'id': 'id',
    'meta': {'lastUpdated': 'ts', 'versionId': 'txid'},
    'name': [],
    'resourceType': 'Patient',
}

.create

Creates a resource. If txid is not specified, a new unique logical transaction id will be generated.

Syntax: .create(resource, txid=None, commit=True)

Returns: resource representation (dict)

Example:

fb.create({
    'resourceType': 'Patient',
    'name': [{'text': 'John'}],
})

returns

{
    'resourceType': 'Patient',
    'id': 'UNIQUE ID',
    'name': [{'text': 'John'}],
    'meta': {'lastUpdated': 'timestamp', 'versionId': 'txid'},
}

.update

Updates a resource. If txid is not specified, a new unique logical transaction id will be generated.

Key id is required in resource argument.

Syntax: .update(resource, txid=None, commit=True)

Returns: resource representation (dict)

Example:

fb.update({
    'resourceType': 'Patient',
    'id': 'id',
    'name': [{'text': 'John'}],
})

returns

{
    'resourceType': 'Patient',
    'id': 'UNIQUE ID',
    'name': [{'text': 'John'}],
    'meta': {'lastUpdated': 'timestamp', 'versionId': 'txid'},
}

.delete

Deletes a resource. If txid is not specified, a new unique logical transaction id will be generated. Keys id and resourceType are required in resource argument in the first variant of an usage.

Syntax: .delete(resource, txid=None, commit=True) or .delete(resource_type, id, txid=None, commit=True)

Returns: nothing

Example:

fb.delete({
    'resourceType': 'Patient',
    'id': 'id',
})

or

fb.delete(resource_type='Patient', id='id')

.read

Reads a resource. Keys id and resourceType are required in resource argument in first variant of usage.

Syntax: .read(resource) or .read(resource_type, id)

Returns: resource representation (dict)

Example:

fb.read({
    'resourceType': 'Patient',
    'id': 'id',
})

or

fb.read(resource_type='Patient', id='id')

.list

Executes SQL and returns an iterator of resources. Note: sql query must return all fields of a resource table.

Syntax: .list(sql, params)

Returns: iterator of resources

Example:

for patient in fb.list('SELECT * FROM patient'):
    print(patient)

or

patients = list(fb.list('SELECT * FROM patient'))

Example application

To run example, just do:

docker-compose build
docker-compose up -d

Wait until db starting process will be completed, and run:

docker-compose run --rm fhirbase fhirbase init 3.0.1
docker-compose run --rm fhirbasepy python examples/example.py