Metadata-Version: 2.1
Name: fhirpath
Version: 0.4.1
Summary: FHIRPath implementation in Python.
Home-page: https://nazrul.me/fhirpath/
Author: Md Nazrul Islam
Author-email: email2nazrul@gmail.com
License: GNU General Public License v3
Project-URL: CI: Travis, https://travis-ci.com/nazrulworld/fhirpath
Project-URL: Coverage: codecov, https://codecov.io/github/nazrulworld/fhirpath
Project-URL: Docs: RTD, https://fhirpath.readthedocs.io/
Project-URL: GitHub: issues, https://github.com/nazrulworld/fhirpath/issues
Project-URL: GitHub: repo, https://github.com/nazrulworld/fhirpath
Keywords: fhirpath
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Healthcare Industry
Classifier: Intended Audience :: Information Technology
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Requires-Python: >=3.5
Requires-Dist: Click (>=6.0)
Requires-Dist: zope.interface (>=4.6.0)
Requires-Dist: zope.component (>=4.5)
Requires-Dist: multidict
Requires-Dist: decorator
Requires-Dist: fhir.resources (>=5.0.1)
Requires-Dist: jsonpatch
Requires-Dist: yarl
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: pytest ; extra == 'test'
Requires-Dist: pytest-cov ; extra == 'test'
Requires-Dist: pytest-mock ; extra == 'test'
Requires-Dist: pytest-docker-fixtures ; extra == 'test'
Requires-Dist: pytest-runner ; extra == 'test'

============
Introduction
============

.. image:: https://img.shields.io/travis/nazrulworld/fhirpath.svg
        :target: https://travis-ci.org/nazrulworld/fhirpath

.. image:: https://readthedocs.org/projects/fhirpath/badge/?version=latest
        :target: https://fhirpath.readthedocs.io/en/latest/?badge=latest
        :alt: Documentation Status

.. image:: https://codecov.io/gh/nazrulworld/fhirpath/branch/master/graph/badge.svg
   :target: https://codecov.io/gh/nazrulworld/fhirpath/branch/master
   :alt: Test Coverage

.. image:: https://img.shields.io/pypi/pyversions/fhirpath.svg
   :target: https://pypi.python.org/pypi/fhirpath/
   :alt: Python Versions

.. image:: https://img.shields.io/lgtm/grade/python/g/nazrulworld/fhirpath.svg?logo=lgtm&logoWidth=18
    :target: https://lgtm.com/projects/g/nazrulworld/fhirpath/context:python
    :alt: Language grade: Python

.. image:: https://img.shields.io/pypi/v/fhirpath.svg
   :target: https://pypi.python.org/pypi/fhirpath

.. image:: https://img.shields.io/pypi/l/fhirpath.svg
   :target: https://pypi.python.org/pypi/fhirpath/
   :alt: License

.. image:: https://fire.ly/wp-content/themes/fhir/images/fhir.svg
        :target: https://www.hl7.org/fhir/fhirpath.html
        :alt: HL7® FHIR®

FHIRPath_ (STU1) implementation in Python. This library is built in ORM_ like approach. Our goal is to make 100% (as much as possible)
FHIRPath_ (STU1) specification compliance product.

* Supports FHIR® ``STU3`` and ``R4``.
* Supports multiple provider´s engine. Now Plone_ & guillotina_ framework powered providers `fhirpath-guillotina`_ and `collective.fhirpath`_ respectively are supported and more coming soon.
* Supports multiple dialects, for example elasticsearch_, GraphQL_, PostgreSQL_. Although now elasticsearch_ has been supported.
* Provide full support of `FHIR Search <https://www.hl7.org/fhir/search.html>`_ with easy to use API.


Usages
------

This library is kind of abstract type, where all specifications from FHIRPath_ (STU1) are implemented rather than completed solution (ready to go).
The main reason behind this design pattern, to support multiple database systems as well as well as any framework, there is no dependency.

``fhirpath`` never taking care of creating indexes, mappings (elasticsearch) and storing data, if you want to use this library, you have to go
through any of existing providers (see list bellow) or make your own provider (should not too hard work).


Simple example
~~~~~~~~~~~~~~

Assumption:

1. Elasticsearch server 7.x.x Installed.

2. Mappings and indexes are handled manually.

3. Data (document) also are stored manually.


Create Connection and Engine::

    >>> from fhirpath.connectors import create_connection
    >>> from fhirpath.engine.es import ElasticsearchEngine
    >>> from fhirpath.engine import dialect_factory
    >>> from fhirpath.enums import FHIR_VERSION

    >>> host, port = "127.0.0.1", 9200
    >>> conn_str = "es://@{0}:{1}/".format(host, port)
    >>> connection = create_connection(conn_str, "elasticsearch.Elasticsearch")
    >>> connection.raw_connection.ping()
    True
    >>> engine = ElasticsearchEngine(FHIR_VERSION.R4, lambda x: connection, dialect_factory)


Basic Search::

    >>> from fhirpath.search import Search
    >>> from fhirpath.search import SearchContext

    >>> search_context = SearchContext(engine, "Organization")
    >>> params = (
    ....    ("active", "true"),
    ....    ("_lastUpdated", "2010-05-28T05:35:56+00:00"),
    ....    ("_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"),
    .... )
    >>> fhir_search = Search(search_context, params=params)
    >>> bundle = fhir_search()
    >>> len(bundle.entry) == 0
    True

Basic Query::

    >>> from fhirpath.enums import SortOrderType
    >>> from fhirpath.query import Q_
    >>> from fhirpath.fql import T_
    >>> from fhirpath.fql import V_
    >>> from fhirpath.fql import exists_
    >>> query_builder = Q_(resource="Organization", engine=engine)
    >>>  query_builder = (
    ....    query_builder.where(T_("Organization.active") == V_("true"))
    ....    .where(T_("Organization.meta.lastUpdated", "2010-05-28T05:35:56+00:00"))
    ....    .sort(sort_("Organization.meta.lastUpdated", SortOrderType.DESC))
    .... )
    >>> query_result = query_builder(async_result=False)
    >>> for resource in query_result:
    ....    assert resource.__class__.__name__ == "OrganizationModel"
    >>> # test fetch all
    >>> result = query_result.fetchall()
    >>> result.__class__.__name__ == "EngineResult"
    True

    >>> query_builder = Q_(resource="ChargeItem", engine=engine)
    >>> query_builder = query_builder.where(exists_("ChargeItem.enteredDate"))
    >>> result = query_builder(async_result=False).single()
    >>> result is not None
    True
    >>> isinstance(result, builder._from[0][1])
    True

    >>> query_builder = Q_(resource="ChargeItem", engine=engine)
    >>> query_builder = query_builder.where(exists_("ChargeItem.enteredDate"))
    >>> result = query_builder(async_result=False).first()
    >>> result is not None
    True
    >>> isinstance(result, builder._from[0][1])
    True


Available Provider (known)
--------------------------

Currently very few numbers of providers available, however more will coming soon.

`fhirpath-guillotina`_
~~~~~~~~~~~~~~~~~~~~~~

A `guillotina`_ framework powered provider, battery included, ready to go! `Please follow associated documentation. <https://fhirpath-guillotina.readthedocs.io/en/latest/>`_

1. **Engine**: Elasticsearch

2. **PyPi**: https://pypi.org/project/fhirpath-guillotina/

3. **Source**: https://github.com/nazrulworld/fhirpath_guillotina


`collective.fhirpath`_
~~~~~~~~~~~~~~~~~~~~~~

A `Plone`_ powered provider, like `fhirpath-guillotina`_ every thing is included. ready to go, although has a dependency
on `plone.app.fhirfield`_.

1. **Engine**: Elasticsearch

2. **PyPi**: https://pypi.org/project/collective.fhirpath/

3. **Source**: https://github.com/nazrulworld/collective.fhirpath


unlisted
~~~~~~~~
Why are you waiting for? You are welcome to list your provider here!
Developing provider should not be so hard, as ``fhirpath`` is giving you convenient APIs.

ToDo
----

1. `fhirbase`_ engine aka provider implementation.

2. https://stackoverflow.com/questions/27920911/elasticsearch-query-on-array-index



Credits
-------

This package skeleton was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.

.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
.. _`FHIRPath`: http://hl7.org/fhirpath/
.. _`FHIR`: http://hl7.org/fhir/
.. _`ORM`: https://en.wikipedia.org/wiki/Object-relational_mapping
.. _`Plone`: https://plone.org
.. _`guillotina`: https://guillotina.readthedocs.io/en/latest/
.. _`elasticsearch`: https://www.elastic.co/products/elasticsearch
.. _`GraphQL`: https://graphql.org/
.. _`PostgreSQL`: https://www.postgresql.org/
.. _`fhirpath-guillotina`: https://pypi.org/project/fhirpath-guillotina/
.. _`collective.fhirpath`: https://pypi.org/project/collective.fhirpath/
.. _`plone.app.fhirfield`: https://pypi.org/project/plone.app.fhirfield/
.. _`fhirbase`: https://github.com/fhirbase/fhirbase


© Copyright HL7® logo, FHIR® logo and the flaming fire are registered trademarks
owned by `Health Level Seven International <https://www.hl7.org/legal/trademarks.cfm?ref=https://pypi.org/project/fhir-resources/>`_

**"FHIR® is the registered trademark of HL7 and is used with the permission of HL7.
Use of the FHIR trademark does not constitute endorsement of this product by HL7"**


=======
History
=======

0.4.1 (2019-11-05)
------------------

Bugfixes

- ``fhirpath.search.Search.parse_query_string`` now returning ``MuliDict``(what is expected) instead of ``MultiDictProxy``.


0.4.0 (2019-10-24)
------------------

Improvements

- Now full ``select`` features are accepted, meaning that you can provide multiple path in ``select`` section. for example ``select(Patient.name, Patient.gender)``.

- FHIRPath ``count()`` and ``empty()`` functions are supported.

- Supports path navigation with index and functions inside ``select``. Example ``[index]``, ``last()``, ``first()``, ``Skip()``, ``Take()``, ``count()``.

Breakings

- ``QueryResult.first`` and ``QueryResult.single`` are no longer return FHIR Model instance instead returning ``fhirpath.engine.EngineResultRow``.

- ``QueryResult.fetchall`` returning list of ``fhirpath.engine.EngineResultRow`` instead of FHIR JSON.

- ``QueryResult`` iteration returning list of FHIR Model instance on condition (if select is `*`), other than returning list of ``fhirpath.engine.EngineResultRow``.


0.3.1 (2019-10-08)
------------------

Improvements

- Add support for search parameter expression that contains with space+as (``MedicationRequest.medication as CodeableConcept``)

Bugfixes

- ``not`` modifier is now working for ``Coding`` and ``CodeableConcept``.

- "ignore_unmapped" now always True in case of nested query.

- "unmapped_type" now set explicitly long value. See related issue https://stackoverflow.com/questions/17051709/no-mapping-found-for-field-in-order-to-sort-on-in-elasticsearch


0.3.0 (2019-09-30)
------------------

Improvements

- Supports multiple AND values for same search parameter!.

- Add support FHIR version ``STU3`` compability for Money type search.[nazrulworld]

- IN Query support added.[nazrulworld]

- Support PathElement that contains string path with .as(), thus suports for Search also.

- Supports ``Duration`` type in Search.

- Add support ``composite`` type search param.


Bugfixes

- Multiple search values (IN search)

- Missing ``text`` for HumanName and Address search.



0.2.0 (2019-09-15)
------------------

Breakings:

- Built-in providers ( ``guillotina_app`` and ``plone_app`` ) have been wiped as both becoming separate pypi project.

- ``queries`` module has been moved from ``fql`` sub-package to fhirpath package and also renamed as ``query``.


Improvements:

- There are so many improvements made for almost all most modules.

- FhirSearch coverages are increased.

- Sort, Limit facilities added in Query as well in FhirSearch.


Bugfixes:

- numbers of bugs fixed.



0.1.1 (2019-08-15)
------------------

- First working version has been released. Of-course not full featured.


0.1.0 (2018-12-15)
------------------

* First release on PyPI.(Just register purpose, not usable at all, next release coming soon)


