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

pip install fhirbase

Importfhirbase andpsycopg2 libraries:

import fhirbaseimport psycopg2

Create a connection usingpsycopg2.connect:

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

Create an instance ofFHIRBase:

fb = fhirbase.FHIRBase(connection)

Now you can use the following methods ofFHIRBase instance:

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

CRUD methods work withFHIR resources.A resource represented as a dict with a specifiedresourceType 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)

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())

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)', ['{}'])

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',}

Creates a resource.Iftxid 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'},}

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

Keyid is required inresource 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'},}

Deletes a resource.If txid is not specified, a new unique logical transaction id will be generated.Keysid andresourceType are required inresource 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')

Reads a resource.Keysid andresourceType are required inresource 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')

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'))

To run example, just do:

docker-compose builddocker-compose up -d

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

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