Welcome to collective.fhirpath’s documentation!¶

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__ == "Organization"

>>> 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

Use `FHIRModelServiceMixin`¶

For better performance optimization, you should use FHIRModelServiceMixin to response FHIRModel, FhirFieldValue object efficiently.

Example 1:

>>> from plone.restapi.services import Service
>>> from collective.fhirpath.utils import FHIRModelServiceMixin
>>> class MyFHIRGetService(FHIRModelServiceMixin, Service):
....     """ """
....     def reply(self):
....        # do return bellow's types of data
....        # could be ``dict`` type data
....        # could be instance of ``FHIRAbstractModel`` derrived class.
....        # could be instance of ``plone.app.fhirfield.FhirResourceValue`` derrived class.
....        # or self.reply_no_content()

configuration¶

This product provides three plone registry based records fhirpath.es.index.mapping.nested_fields.limit, fhirpath.es.index.mapping.depth.limit, fhirpath.es.index.mapping.total_fields.limit. Those are related to ElasticSearch index mapping setup, if you aware about it, then you have option to modify from plone control panel (Registry).

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<email2nazrul@gmail.com>

License¶

The project is licensed under the GPLv2.

RESTfull API Service¶

Server Side codex examples¶

Search aka GET Service¶

# -*- coding: utf-8 -*-
from collective.elasticsearch.es import ElasticSearchCatalog
from collective.fhirpath.utils import FHIRModelServiceMixin
from fhirpath.enums import FHIR_VERSION
from fhirpath.interfaces import IElasticsearchEngineFactory
from fhirpath.interfaces import IFhirSearch
from fhirpath.interfaces import ISearchContextFactory
from plone import api
from plone.restapi.services import Service
from zope.component import queryMultiAdapter
from zope.interface import implementer
from zope.publisher.interfaces import IPublishTraverse


@implementer(IPublishTraverse)
class FHIRSearchService(FHIRModelServiceMixin, Service):
    """ """

    def __init__(self, context, request):
        """ """
        super(FHIRSearchService, self).__init__(context, request)
        self.params = []

    def get_es_catalog(self):
        """ """
        return ElasticSearchCatalog(api.portal.get_tool("portal_catalog"))

    def get_factory(self, resource_type, unrestricted=False):
        """ """
        factory = queryMultiAdapter(
            (self.get_es_catalog(),), IElasticsearchEngineFactory
        )
        engine = factory(fhir_release=FHIR_VERSION.STU3)
        context = queryMultiAdapter((engine,), ISearchContextFactory)(
            resource_type, unrestricted=unrestricted
        )

        factory = queryMultiAdapter((context,), IFhirSearch)
        return factory

    def reply(self):
        """ """
        bundle = self.build_result()

        if self.resource_id:
            if bundle.total == 0:
                return self.reply_no_content(404)
            return bundle.entry[0].resource

        return bundle

    def publishTraverse(self, request, name):  # noqa: N802
        # Consume any path segments after /@fhir as parameters
        self.params.append(name)
        return self

    @property
    def resource_id(self):
        """ """
        if 1 < len(self.params):
            return self.params[1]
        return None

    @property
    def resource_type(self):
        """ """

        if 0 < len(self.params):
            _rt = self.params[0]
            return _rt
        return None

    def _get_fhir_fieldname(self, resource_type=None):
        """We assume FHIR Field name is ``{resource type}_resource``"""
        resource_type = resource_type or self.resource_type

        return "{0}_resource".format(resource_type.lower())

    def get_query_string(self):
        """ """
        if self.resource_id:
            return "_id={0}".format(self.resource_id)

        return self.request["QUERY_STRING"]

    def build_result(self):
        """ """
        factory = self.get_factory(self.resource_type)

        return factory(query_string=self.get_query_string())

FHIR Resource Add aka POST Service¶

# -*- coding: utf-8 -*-
from Acquisition import aq_base
from Acquisition.interfaces import IAcquirer
from collective.fhirpath.utils import FHIRModelServiceMixin
from plone.restapi.deserializer import json_body
from plone.restapi.exceptions import DeserializationError
from plone.restapi.interfaces import IDeserializeFromJson
from plone.restapi.services import Service
from plone.restapi.services.content.utils import add as add_obj
from plone.restapi.services.content.utils import create as create_obj
from Products.CMFPlone.utils import safe_hasattr
from zope.component import queryMultiAdapter
from zope.event import notify
from zope.interface import alsoProvides
from zope.interface import implementer
from zope.lifecycleevent import ObjectCreatedEvent
from zope.publisher.interfaces import IPublishTraverse

import json
import plone.protect.interfaces


__author__ = "Md Nazrul Islam <nazrul@zitelab.dk>"


@implementer(IPublishTraverse)
class FHIRResourceAdd(FHIRModelServiceMixin, Service):
    """Creates a new FHIR Resource object.
    """

    def __init__(self, context, request):
        """ """
        super(FHIRResourceAdd, self).__init__(context, request)
        self.params = []

    def publishTraverse(self, request, name):  # noqa: N802
        # Consume any path segments after /@fhir as parameters
        self.params.append(name)
        return self

    @property
    def resource_type(self):
        """ """

        if 0 < len(self.params):
            _rt = self.params[0]
            return _rt
        return None

    def reply(self):
        """ """
        data = json_body(self.request)
        # Disable CSRF protection
        if "IDisableCSRFProtection" in dir(plone.protect.interfaces):
            alsoProvides(self.request, plone.protect.interfaces.IDisableCSRFProtection)

        response = self._create_object(data)

        if isinstance(response, dict) and "error" in response:
            self.request.response.setStatus(400)

        return response

    def _create_object(self, fhir):
        """ """
        form_data = {
            "@type": fhir["resourceType"],
            "id": fhir["id"],
            "title": "{0}-{1}".format(self.resource_type, fhir["id"]),
        }
        fhir_field_name = "{0}_resource".format(fhir["resourceType"].lower())
        form_data[fhir_field_name] = fhir

        self.request["BODY"] = json.dumps(form_data)

        context = self.context
        obj = create_obj(
            context, form_data["@type"], id_=form_data["id"], title=form_data["title"]
        )

        if isinstance(obj, dict) and "error" in obj:
            self.request.response.setStatus(400)
            return obj

        # Acquisition wrap temporarily to satisfy things like vocabularies
        # depending on tools
        temporarily_wrapped = False
        if IAcquirer.providedBy(obj) and not safe_hasattr(obj, "aq_base"):
            obj = obj.__of__(context)
            temporarily_wrapped = True

        # Update fields
        deserializer = queryMultiAdapter((obj, self.request), IDeserializeFromJson)
        if deserializer is None:
            self.request.response.setStatus(501)
            return dict(
                error=dict(
                    message="Cannot deserialize type {0}".format(obj.portal_type)
                )
            )

        try:
            deserializer(validate_all=True, create=True)
        except DeserializationError as e:
            self.request.response.setStatus(400)
            return dict(error=dict(type="DeserializationError", message=str(e)))

        if temporarily_wrapped:
            obj = aq_base(obj)

        # Notify Dexterity Created
        if not getattr(deserializer, "notifies_create", False):
            notify(ObjectCreatedEvent(obj))

        # Adding to Container
        add_obj(context, obj, rename=False)

        self.request.response.setStatus(201)
        response = getattr(obj, fhir_field_name)

        self.request.response.setHeader(
            "Location",
            "/".join(
                [
                    self.context.portal_url(),
                    "@fhir",
                    response.resource_type,
                    response.id,
                ]
            ),
        )

        return response

FHIR Resource Update aka PATCH Service¶

# -*- coding: utf-8 -*-
from collective.elasticsearch.es import ElasticSearchCatalog
from collective.fhirpath.interfaces import IZCatalogFhirSearch
from collective.fhirpath.utils import FHIRModelServiceMixin
from fhirpath.enums import FHIR_VERSION
from fhirpath.interfaces import IElasticsearchEngineFactory
from fhirpath.interfaces import ISearchContextFactory
from plone import api
from plone.restapi.deserializer import json_body
from plone.restapi.services import Service
from plone.restapi.services.locking.locking import is_locked
from zope.component import queryMultiAdapter
from zope.interface import alsoProvides
from zope.interface import implementer
from zope.publisher.interfaces import IPublishTraverse

import plone.protect.interfaces


@implementer(IPublishTraverse)
class FHIRResourcePatch(FHIRModelServiceMixin, Service):
    """Patch a FHIR Resource object.
    """

    def __init__(self, context, request):
        """ """
        super(FHIRResourcePatch, self).__init__(context, request)
        self.params = []

    def publishTraverse(self, request, name):  # noqa: N802
        # Consume any path segments after /@fhir as parameters
        self.params.append(name)
        return self

    def get_es_catalog(self):
        """ """
        return ElasticSearchCatalog(api.portal.get_tool("portal_catalog"))

    def get_factory(self, resource_type, unrestricted=False):
        """ """
        factory = queryMultiAdapter(
            (self.get_es_catalog(),), IElasticsearchEngineFactory
        )
        engine = factory(fhir_release=FHIR_VERSION.STU3)
        context = queryMultiAdapter((engine,), ISearchContextFactory)(
            resource_type, unrestricted=unrestricted
        )

        factory = queryMultiAdapter((context,), IZCatalogFhirSearch)
        return factory

    @property
    def resource_id(self):
        """ """
        if 1 < len(self.params):
            return self.params[1]
        return None

    @property
    def resource_type(self):
        """ """

        if 0 < len(self.params):
            _rt = self.params[0]
            return _rt
        return None

    def reply(self):
        """ """
        query_string = "_id={0}".format(self.resource_id)

        factory = self.get_factory(self.resource_type)
        brains = factory(query_string=query_string)

        if len(brains) == 0:
            self.reply_no_content(404)

        obj = brains[0].getObject()

        if is_locked(obj, self.request):
            self.request.response.setStatus(403)
            return dict(error=dict(type="Forbidden", message="Resource is locked."))

        data = json_body(self.request)

        # Disable CSRF protection
        if "IDisableCSRFProtection" in dir(plone.protect.interfaces):
            alsoProvides(self.request, plone.protect.interfaces.IDisableCSRFProtection)

        fhir_value = getattr(obj, "{0}_resource".format(self.resource_type.lower()))
        fhir_value.patch(data["patch"])

        self.request.response.setStatus(204)
        # Return None
        self.reply_no_content(204)

REST Service registration (configuration.zcml)¶

<configure xmlns="http://namespaces.zope.org/zope"
  xmlns:plone="http://namespaces.plone.org/plone"
  xmlns:zcml="http://namespaces.zope.org/zcml">


  <include package="plone.rest" file="configure.zcml" />
  <plone:service method="GET"
                 name="@fhir"
                 for="Products.CMFCore.interfaces.ISiteRoot"
                 factory=".get.FHIRSearchService"
                 permission="zope2.View"
  />

  <plone:service method="POST" name="@fhir" for="Products.CMFCore.interfaces.ISiteRoot" factory=".post.FHIRResourceAdd" permission="cmf.ManagePortal" />

  <plone:service method="PATCH" name="@fhir" for="Products.CMFCore.interfaces.ISiteRoot" factory=".patch.FHIRResourcePatch" permission="cmf.ManagePortal" />

</configure>

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

>>> response.json()['resourceType'] == 'Patient'
True

>>> response = admin_session.get('/@fhir/Patient/19c5245f-fake-id')
>>> response.status_code
404

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

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

Changelog¶

0.6.1 (2020-09-09)¶

plone.app.fhirfield:default``has been added in dependency, so no need separete install of ``plone.app.fhirfield.

0.6.0 (2020-09-09)¶

Improvements

FHIRModelServiceMixin class has been available under utils module, which can be used with your plone.restapi services to response type as FhirModel aka pydantic’s BaseModel or plone.app.fhirfield.FhirFieldValue object with the best possible effecient way.

0.5.0 (2020-08-18)¶

Improvements

Supports the revolutionary version of fhir.resources via fhirpath we may expect some refactor on your existing codebase because of some breaking changes, please see changes at fhir.resources, plone.app.fhirfield and fhirpath.
Brings back support for Python version 3.6
Three configurations (fhirpath.es.index.mapping.nested_fields.limit, fhirpath.es.index.mapping.depth.limit, fhirpath.es.index.mapping.total_fields.limit) based on plone registry has now been available.

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]

Welcome to collective.fhirpath’s documentation!¶

Background (collective.fhirpath)¶

Installation¶

How It Works¶

Usages¶

Use `FHIRModelServiceMixin`¶

configuration¶

Documentation¶

Contribute¶

Support¶

License¶

RESTfull API Service¶

Server Side codex examples¶

REST Client Examples¶

Changelog¶

0.6.1 (2020-09-09)¶

0.6.0 (2020-09-09)¶

0.5.0 (2020-08-18)¶

0.4.0 (2020-05-15)¶

0.3.0 (2019-11-10)¶

0.2.0 (2019-09-16)¶

0.1.0 (2019-09-06)¶

collective.fhirpath

Navigation

Related Topics

Welcome to collective.fhirpath’s documentation!¶

Background (collective.fhirpath)¶

Installation¶

How It Works¶

Usages¶

Use FHIRModelServiceMixin¶

configuration¶

Documentation¶

Contribute¶

Support¶

License¶

RESTfull API Service¶

Server Side codex examples¶

REST Client Examples¶

Changelog¶

0.6.1 (2020-09-09)¶

0.6.0 (2020-09-09)¶

0.5.0 (2020-08-18)¶

0.4.0 (2020-05-15)¶

0.3.0 (2019-11-10)¶

0.2.0 (2019-09-16)¶

0.1.0 (2019-09-06)¶

Use `FHIRModelServiceMixin`¶