collective.fhirpath 0.4.0

Plone powered provider for fhirpath

Background (collective.fhirpath)

fhirpath implementation in Plone, essential battery included, ready to use.

Installation

Install collective.fhirpath by adding it to your buildout:

[buildout]
...
eggs +=
    collective.fhirpath

and then running bin/buildout

From Plone controlpanel in the addon settings, install collective.fhirpath.

How It Works

``FhirResource`` the fhirfield

Make sure this specialized field is used properly according to plone.app.fhirfield documentation.

Make field indexable

A specilized Catalog PluginIndexes is named FhirFieldIndex is available, you will use it as like other catalog indexes.

Example:

<?xml version="1.0"?>
<object name="portal_catalog" meta_type="Plone Catalog Tool">
    <index name="organization_resource" meta_type="FhirFieldIndex">
        <indexed_attr value="organization_resource"/>
    </index>
</object>

Elasticsearch settings

Make sure elasticsearch has been configured accourding to collective.elasticsearch docs.

Usages

FHIR Search::

>>> from fhirpath.interfaces import IElasticsearchEngineFactory
>>> from fhirpath.interfaces import IFhirSearch
>>> from fhirpath.interfaces import ISearchContextFactory
>>> from plone import api
>>> from collective.elasticsearch.es import ElasticSearchCatalog
>>> from zope.component import queryMultiAdapter

>>> es_catalog = ElasticSearchCatalog(api.portal.get_tool("portal_catalog"))
>>> factory = queryMultiAdapter(
....        (es_catalog,), IElasticsearchEngineFactory
.... )
>>> engine = factory(fhir_release="STU3")
>>> search_context = queryMultiAdapter((engine,), ISearchContextFactory)(
.... resource_type, unrestricted=False)
>>> search_factory = queryMultiAdapter((search_context,), IFhirSearch)

>>> params = (
....        ("_profile", "http://hl7.org/fhir/Organization"),
....        ("identifier", "urn:oid:2.16.528.1|91654"),
....        ("type", "http://hl7.org/fhir/organization-type|prov"),
....        ("address-postalcode", "9100 AA"),
....        ("address", "Den Burg"),
....    )
>>> bundle = search_factory(params)
>>> len(bundle.entry)
2
>>> # with query string.
>>> # query_string = self.request["QUERY_STRING]
>>> query_string = "_profile=http://hl7.org/fhir/Organization&identifier=urn:oid:2.16.528.1|91654&type=http://hl7.org/fhir/organization-type|prov&address-postalcode=9100+AA"
>>> bundle = search_factory(query_string=query_string)
>>> len(bundle.entry)
2

ZCatlog FHIR Search::

>>> from collective.fhirpath.interfaces import IZCatalogFhirSearch
>>> zcatalog_factory = queryMultiAdapter((search_context,), IZCatalogFhirSearch)

>>> # with query string.
>>> # query_string = self.request["QUERY_STRING]
>>> query_string = "_profile=http://hl7.org/fhir/Organization&identifier=urn:oid:2.16.528.1|91654&type=http://hl7.org/fhir/organization-type|prov&address-postalcode=9100+AA"
>>> brains = zcatalog_factory(query_string=query_string)
>>> len(brains)
2

FHIR Query::

>>> from fhirpath.interfaces import IElasticsearchEngineFactory
>>> from fhirpath.interfaces import IFhirSearch
>>> from fhirpath.interfaces import ISearchContextFactory
>>> from plone import api
>>> from collective.elasticsearch.es import ElasticSearchCatalog
>>> from zope.component import queryMultiAdapter
>>> from fhirpath.query import Q_
>>> from fhirpath.fql import T_
>>> from fhirpath.fql import sort_
>>> from fhirpath.enums import SortOrderType

>>> es_catalog = ElasticSearchCatalog(api.portal.get_tool("portal_catalog"))
>>> factory = queryMultiAdapter(
....        (es_catalog,), IElasticsearchEngineFactory
.... )
>>> engine = factory(fhir_release="STU3")
>>> query_builder = Q_(resource="Organization", engine=engine)
....    query_builder = query_builder.where(
....        T_("Organization.meta.profile", "http://hl7.org/fhir/Organization")
....    ).sort(sort_("Organization.meta.lastUpdated", SortOrderType.DESC))

>>> result = query_builder(async_result=False, unrestricted=True).fetchall()
>>> result.header.total
2
>>> query_result = query_builder(async_result=False, unrestricted=True)
>>> for resource in query_result:
....        count += 1
....        assert resource.__class__.__name__ == "OrganizationModel"

>>> query_builder = Q_(resource="Organization", engine=engine)
>>> query_builder = query_builder.where(T_("Organization.id", "f001"))
>>> result_query = query_builder(async_result=False, unrestricted=True)
>>> resource = result_query.single()
>>> resource is not None
True

>>> query_builder = Q_(resource="Organization", engine=engine)
>>> query_builder = query_builder.where(
....        T_("Organization.meta.profile", "http://hl7.org/fhir/Organization")
....    )
>>> result_query = builder(async_result=False, unrestricted=True)
>>> result = result_query.first()
>>> isinstance(result, result_query._query.get_from()[0][1])
True

Documentation

Full documentation for end users can be found in the “docs” folder, and is also available online at https://collective-fhirpath.readthedocs.io/

Contribute

• Issue Tracker: https://github.com/nazrulworld/collective.fhirpath/issues

• Source Code: https://github.com/nazrulworld/collective.fhirpath

• Documentation: https://collective-fhirpath.readthedocs.io/

Support

If you are having issues, please let us know at: Md Nazrul Islam<[e-mail]>

License

The project is licensed under the GPLv2.

REST Client Examples

Getting single resource, here we are getting Patient resource by ID.

Example(1):

>>> response = admin_session.get('/@fhir/Patient/19c5245f-89a8-49f8-b244-666b32adb92e')
>>> response.status_code
200
<BLANKLINE>
>>> response.json()['resourceType'] == 'Patient'
True
<BLANKLINE>
>>> response = admin_session.get('/@fhir/Patient/19c5245f-fake-id')
>>> response.status_code
404
<BLANKLINE>

Search Observation by Patient reference with status condition. Any observation until December 2017 and earlier than January 2017.

Example(2):

>>> response = admin_session.get('/@fhir/Observation?patient=Patient/19c5245f-89a8-49f8-b244-666b32adb92e&status=final&_lastUpdated=lt2017-12-31T00%3A00%3A00%2B00%3A00&_lastUpdated=gt2017-01-01T00%3A00%3A00%2B00%3A00')
>>> response.status_code
200
>>> response.json()["total"]
1
<BLANKLINE>

Add FHIR Resource through REST API

Example(3):

>>> import os
>>> import json
>>> import uuid
>>> import DateTime
>>> import time

>>> with open(os.path.join(FIXTURE_PATH, 'Patient.json'), 'r') as f:
...     fhir_json = json.load(f)

>>> fhir_json['id'] = str(uuid.uuid4())
>>> fhir_json['name'][0]['text'] = 'Another Patient'
>>> response = admin_session.post('/@fhir/Patient', json=fhir_json)
>>> response.status_code
201
>>> time.sleep(1)
>>> response = admin_session.get('/@fhir/Patient?active=true')
>>> response.json()["total"]
2

Update (PATCH) FHIR Resource the Patient is currently activated, we will deactive.

Example(4):

>>> patch = [{'op': 'replace', 'path': '/active', 'value': False}]
>>> response = admin_session.patch('/@fhir/Patient/19c5245f-89a8-49f8-b244-666b32adb92e', json={'patch': patch})
>>> response.status_code
204
<BLANKLINE>

Contributors

• Md Nazrul Islam, [e-mail] (author)

Changelog

0.4.0 (2020-05-15)

Breakings

• As a part of supporting latest fhirpath version (from 0.6.1), drop python version later than 3.7.0.

• ElasticsearchEngineFactory.__call__’s argument name fhir_version changed to fhir_release.

0.3.0 (2019-11-10)

Improvements

• ZCatalog featured fhir search added, from which you will get ZCatalog´s brain feature.

• FhirFieldIndex named PluginIndex is now available.

• FHIR STU3``and ``R4 search mapping is now available.

• Others improvements that make able to use in production project (of course without guarantee.)

0.2.0 (2019-09-16)

• first working versions, with lots of improvements.

0.1.0 (2019-09-06)

• Initial release. [nazrulworld]