Python
This package provides a wrapper over
psycopg2
connection which provides CRUD operations for resources in Fhirbase.You can install the package using PyPI:
pip install fhirbase
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)
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 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. 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'},
}
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'},
}
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')
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')
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:
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
Last modified 4yr ago