Python

This package provides a wrapper over psycopg2 connection which provides CRUD operations for resources in Fhirbase.

Installation

You can install the package using PyPI:

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 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

To run example, just do:

git clone https://github.com/fhirbase/fhirbase.py.git
cd fhirbase.py
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