fhirbase.py

FHIRBase connector for python. This package provides wrapper over psycopg2 connection which provides CRUD 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 = fhribase.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. Resource represented as a dict with specified resourceType key as required key. The following methods works with 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 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 row raw from DB to 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 resource representation:

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

.create

Creates resource. If txid is not specified, 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 resource. If txid is not specified, 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 resource. If txid is not specified, new unique logical transaction id will be generated. Keys id and resourceType are required in resource argument in first variant of 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 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 iterator of resources. Note: sql query must return all fields of 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