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
Integrations
.NET
Last modified 4yr ago