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https://github.com/nazrulworld/collective.fhirpath

Plone powered provider for fhirptah
https://github.com/nazrulworld/collective.fhirpath

fhir fhirpath healthcare healthtech hl7 plone

Last synced: about 1 month ago
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Plone powered provider for fhirptah

Host: GitHub
URL: https://github.com/nazrulworld/collective.fhirpath
Owner: nazrulworld
License: gpl-2.0
Created: 2019-08-26T10:48:27.000Z (over 5 years ago)
Default Branch: master
Last Pushed: 2022-06-13T12:55:41.000Z (over 2 years ago)
Last Synced: 2024-10-29T00:29:00.081Z (about 2 months ago)
Topics: fhir, fhirpath, healthcare, healthtech, hl7, plone
Language: Python
Size: 395 KB
Stars: 0
Watchers: 2
Forks: 0
Open Issues: 0
Metadata Files:
- Readme: README.rst
- Changelog: CHANGES.rst
- License: LICENSE.GPL

Awesome Lists containing this project

README

        .. image:: https://img.shields.io/pypi/status/collective.fhirpath.svg

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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::

    

    

        

            

        

    

**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

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/