Metadata-Version: 2.1
Name: collective.fhirpath
Version: 0.8.0
Summary: Plone powered provider for fhirpath
Home-page: https://github.com/nazrulworld/collective.fhirpath
Author: Md Nazrul Islam
Author-email: email2nazru@gmail.com
License: GPL version 2
Project-URL: PyPI, https://pypi.python.org/pypi/collective.fhirpath
Project-URL: Source, https://github.com/nazrulworld/collective.fhirpath
Project-URL: Tracker, https://github.com/nazrulworld/collective.fhirpath/issues
Project-URL: Documentation, https://collective-fhirpath.readthedocs.io/en/latest/
Keywords: Python Plone FHIR Healthcare HL7
Platform: UNKNOWN
Classifier: Environment :: Web Environment
Classifier: Development Status :: 4 - Beta
Classifier: Framework :: Plone
Classifier: Framework :: Plone :: Addon
Classifier: Framework :: Plone :: 5.2
Classifier: Framework :: Plone :: 5.3
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Operating System :: OS Independent
Classifier: License :: OSI Approved :: GNU General Public License v2 (GPLv2)
Requires-Python: >=3.6
Requires-Dist: setuptools
Requires-Dist: z3c.jbot
Requires-Dist: plone.restapi
Requires-Dist: plone.app.dexterity
Requires-Dist: collective.elasticsearch (<4.0.0,>=3.0.5)
Requires-Dist: plone.app.fhirfield (<5.0.0,>=4.2.0)
Requires-Dist: fhirpath (>=0.10.5)
Requires-Dist: fhir.resources[orjson] (>=6.1.0)
Provides-Extra: docs
Requires-Dist: sphinx ; extra == 'docs'
Requires-Dist: sphinx-rtd-theme ; extra == 'docs'
Requires-Dist: sphinxcontrib-httpdomain ; extra == 'docs'
Requires-Dist: sphinxcontrib-httpexample ; extra == 'docs'
Provides-Extra: test
Requires-Dist: plone.app.testing ; extra == 'test'
Requires-Dist: plone.app.contenttypes ; extra == 'test'
Requires-Dist: plone.app.robotframework[debug] ; extra == 'test'
Requires-Dist: collective.MockMailHost ; extra == 'test'
Requires-Dist: sphinx ; extra == 'test'
Requires-Dist: sphinx-rtd-theme ; extra == 'test'
Requires-Dist: sphinxcontrib-httpdomain ; extra == 'test'
Requires-Dist: sphinxcontrib-httpexample ; extra == 'test'

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    :alt: Latest Version

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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.

.. _`elasticsearch`: https://www.elastic.co/products/elasticsearch
.. _`fhirpath`: https://pypi.org/project/fhirpath/
.. _`PostgreSQL`: https://www.postgresql.org/
.. _`plone.app.fhirfield`: https://pypi.org/project/plone.app.fhirfield/
.. _`collective.elasticsearch`: https://pypi.org/project/collective.elasticsearch/


.. _restapi_examples_doctest:

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, email2nazrul@gmail.com (author)


Changelog
=========


0.8.0 (2022-06-13)
------------------

New features

- A patch has been added in response to `issue#91 <https://github.com/collective/collective.elasticsearch/issues/91>`_ on ``collective.elasticsearch``.


0.7.6 (2021-05-04)
------------------

- minimum ``fhir.resources`` version is now ``6.1.0`` and minimum ``collective.elasticsearch`` version is now ``3.0.5``


0.7.5 (2020-12-17)
------------------

- minimum ``fhir.resources`` version is now ``6.0.0``, see it's associated changes at https://pypi.org/project/fhir.resources/6.0.0/.

- minimum ``fhirpath``version is now ``0.10.5``, see it's associated improvements and bug fixes at https://pypi.org/project/fhirpath/0.10.4/

- minimum ``plone.app.fhirfield``version is now ``4.2.0``, see it's associated improvements and bug fixes at https://pypi.org/project/plone.app.fhirfield/4.2.0/

0.7.4 (2020-11-19)
------------------

- Minimum required ``fhirpath`` version is now ``0.10.4`` (see it's changes log) and added compabilities.


0.7.3 (2020-10-24)
------------------

- new helper function ``json_body`` has been created, which is using ``orjson`` deserializer.

- ``FHIRModelServiceMixin`` is now more performance optimized.


0.7.2 (2020-10-06)
------------------

- Bundle resposne as ``dict`` option enable in ZCatalog based search.


0.7.1 (2020-10-05)
------------------

- ``fhirpath``minimum version has been updated, which includes minimum ``fhir.resources`` version ``6.0.0b5``.

- Improvements for ``FHIRModelServiceMixin`` as orjson serializer used.


0.7.0 (2020-09-25)
------------------

Improvements

- Issue #2 `ZCatalog based search should have option to return bundle type alongside as LazyBrain <https://github.com/nazrulworld/collective.fhirpath/issues/2>`_

- Supports all features from ``fhirpath`` 0.8.0.

- Elasticsearch Mappings JSON files are updated.

Fixes

- ``utils.FHIRModelServiceMixin`` can now handle ``list`` type data in response.


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 <https://pypi.org/project/fhir.resources/>`_ via `fhirpath <https://pypi.org/project/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]


