{ "info": { "author": "Md Nazrul Islam", "author_email": "email2nazrul@gmail.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 4 - Beta", "Intended Audience :: Developers", "Intended Audience :: Healthcare Industry", "Intended Audience :: Information Technology", "License :: OSI Approved :: GNU General Public License v3 (GPLv3)", "Natural Language :: English", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3 :: Only", "Programming Language :: Python :: 3.6", "Programming Language :: Python :: 3.7", "Programming Language :: Python :: 3.8", "Programming Language :: Python :: 3.9", "Typing :: Typed" ], "description": "============\nIntroduction\n============\n\n.. image:: https://img.shields.io/travis/nazrulworld/fhirpath.svg\n :target: https://travis-ci.org/nazrulworld/fhirpath\n\n.. image:: https://readthedocs.org/projects/fhirpath/badge/?version=latest\n :target: https://fhirpath.readthedocs.io/en/latest/?badge=latest\n :alt: Documentation Status\n\n.. image:: https://codecov.io/gh/nazrulworld/fhirpath/branch/master/graph/badge.svg\n :target: https://codecov.io/gh/nazrulworld/fhirpath/branch/master\n :alt: Test Coverage\n\n.. image:: https://img.shields.io/pypi/pyversions/fhirpath.svg\n :target: https://pypi.python.org/pypi/fhirpath/\n :alt: Python Versions\n\n.. image:: https://img.shields.io/lgtm/grade/python/g/nazrulworld/fhirpath.svg?logo=lgtm&logoWidth=18\n :target: https://lgtm.com/projects/g/nazrulworld/fhirpath/context:python\n :alt: Language grade: Python\n\n.. image:: https://img.shields.io/pypi/v/fhirpath.svg\n :target: https://pypi.python.org/pypi/fhirpath\n\n.. image:: https://img.shields.io/pypi/l/fhirpath.svg\n :target: https://pypi.python.org/pypi/fhirpath/\n :alt: License\n\n.. image:: https://static.pepy.tech/personalized-badge/fhirpath?period=total&units=international_system&left_color=black&right_color=green&left_text=Downloads\n :target: https://pepy.tech/project/fhirpath\n :alt: Downloads\n\n.. image:: https://www.hl7.org/fhir/assets/images/fhir-logo-www.png\n :target: https://www.hl7.org/fhir/fhirpath.html\n :alt: HL7\u00ae FHIR\u00ae\n\nFHIRPath_ Normative Release (v2.0.0) implementation in Python, along side it\nprovides support for `FHIR Search `_ API and\nQuery (we called it ``fql(FHIR Query Language)``)\nAPI to fetch FHIR resources from any data-source(database).\nThis library is built in ORM_ like approach. Our goal is to make 100% (as much as possible)\nFHIRPath_ Normative Release (v2.0.0) specification compliance product.\n\n* Supports FHIR\u00ae ``STU3`` and ``R4``.\n* Supports multiple provider\u00b4s engine. Now Plone_ & guillotina_ framework powered providers `fhirpath-guillotina`_ and `collective.fhirpath`_ respectively are supported and more coming soon.\n* Supports multiple dialects, for example elasticsearch_, GraphQL_, PostgreSQL_. Although now elasticsearch_ has been supported.\n* Provide full support of `FHIR Search `_ with easy to use API.\n\n\nUsages\n------\n\nThis library is kind of abstract type, where all specifications from FHIRPath_ Normative Release (v2.0.0) are implemented rather than completed solution (ready to go).\nThe main reason behind this design pattern, to support multiple database systems as well as well as any framework, there is no dependency.\n\n``fhirpath`` never taking care of creating indexes, mappings (elasticsearch) and storing data, if you want to use this library, you have to go\nthrough any of existing providers (see list bellow) or make your own provider (should not too hard work).\n\n\nSimple example\n~~~~~~~~~~~~~~\n\nAssumption:\n\n1. Elasticsearch server 7.x.x Installed.\n\n2. Mappings and indexes are handled manually.\n\n3. Data (document) also are stored manually.\n\n\nCreate Connection and Engine::\n\n >>> from fhirpath.connectors import create_connection\n >>> from fhirpath.engine.es import ElasticsearchEngine\n >>> from fhirpath.engine import dialect_factory\n >>> from fhirpath.enums import FHIR_VERSION\n\n >>> host, port = \"127.0.0.1\", 9200\n >>> conn_str = \"es://@{0}:{1}/\".format(host, port)\n >>> connection = create_connection(conn_str, \"elasticsearch.Elasticsearch\")\n >>> connection.raw_connection.ping()\n True\n >>> engine = ElasticsearchEngine(FHIR_VERSION.R4, lambda x: connection, dialect_factory)\n\n\nBasic Search::\n\n >>> from fhirpath.search import Search\n >>> from fhirpath.search import SearchContext\n\n >>> search_context = SearchContext(engine, \"Organization\")\n >>> params = (\n .... (\"active\", \"true\"),\n .... (\"_lastUpdated\", \"2010-05-28T05:35:56+00:00\"),\n .... (\"_profile\", \"http://hl7.org/fhir/Organization\"),\n .... (\"identifier\", \"urn:oid:2.16.528.1|91654\"),\n .... (\"type\", \"http://hl7.org/fhir/organization-type|prov\"),\n .... (\"address-postalcode\", \"9100 AA\"),\n .... (\"address\", \"Den Burg\"),\n .... )\n >>> fhir_search = Search(search_context, params=params)\n >>> bundle = fhir_search()\n >>> len(bundle.entry) == 0\n True\n\nBasic Query::\n\n >>> from fhirpath.enums import SortOrderType\n >>> from fhirpath.query import Q_\n >>> from fhirpath.fql import T_\n >>> from fhirpath.fql import V_\n >>> from fhirpath.fql import exists_\n >>> query_builder = Q_(resource=\"Organization\", engine=engine)\n >>> query_builder = (\n .... query_builder.where(T_(\"Organization.active\") == V_(\"true\"))\n .... .where(T_(\"Organization.meta.lastUpdated\", \"2010-05-28T05:35:56+00:00\"))\n .... .sort(sort_(\"Organization.meta.lastUpdated\", SortOrderType.DESC))\n .... )\n >>> query_result = query_builder(async_result=False)\n >>> for resource in query_result:\n .... assert resource.__class__.__name__ == \"OrganizationModel\"\n >>> # test fetch all\n >>> result = query_result.fetchall()\n >>> result.__class__.__name__ == \"EngineResult\"\n True\n\n >>> query_builder = Q_(resource=\"ChargeItem\", engine=engine)\n >>> query_builder = query_builder.where(exists_(\"ChargeItem.enteredDate\"))\n >>> result = query_builder(async_result=False).single()\n >>> result is not None\n True\n >>> isinstance(result, builder._from[0][1])\n True\n\n >>> query_builder = Q_(resource=\"ChargeItem\", engine=engine)\n >>> query_builder = query_builder.where(exists_(\"ChargeItem.enteredDate\"))\n >>> result = query_builder(async_result=False).first()\n >>> result is not None\n True\n >>> isinstance(result, builder._from[0][1])\n True\n\n\nAvailable Provider (known)\n--------------------------\n\nCurrently very few numbers of providers available, however more will coming soon.\n\n`fhirpath-guillotina`_\n~~~~~~~~~~~~~~~~~~~~~~\n\nA `guillotina`_ framework powered provider, battery included, ready to go! `Please follow associated documentation. `_\n\n1. **Engine**: Elasticsearch\n\n2. **PyPi**: https://pypi.org/project/fhirpath-guillotina/\n\n3. **Source**: https://github.com/nazrulworld/fhirpath_guillotina\n\n\n`collective.fhirpath`_\n~~~~~~~~~~~~~~~~~~~~~~\n\nA `Plone`_ powered provider, like `fhirpath-guillotina`_ every thing is included. ready to go, although has a dependency\non `plone.app.fhirfield`_.\n\n1. **Engine**: Elasticsearch\n\n2. **PyPi**: https://pypi.org/project/collective.fhirpath/\n\n3. **Source**: https://github.com/nazrulworld/collective.fhirpath\n\n\nunlisted\n~~~~~~~~\nWhy are you waiting for? You are welcome to list your provider here!\nDeveloping provider should not be so hard, as ``fhirpath`` is giving you convenient APIs.\n\n\nElasticsearch Custom Analyzer\n-----------------------------\nTo get some special search features for reference type field, you will need to setup custom analyzer for your elasticsearch index.\n\nExample Custom Analyzer::\n\n settings = {\n \"analysis\": {\n \"normalizer\": {\n \"fhir_token_normalizer\": {\"filter\": [\"lowercase\", \"asciifolding\"]}\n },\n \"analyzer\": {\n \"fhir_reference_analyzer\": {\n \"tokenizer\": \"keyword\",\n \"filter\": [\"fhir_reference_filter\"],\n },\n },\n \"filter\": {\n \"fhir_reference_filter\": {\n \"type\": \"pattern_capture\",\n \"preserve_original\": True,\n \"patterns\": [r\"(?:\\w+\\/)?(https?\\:\\/\\/.*|[a-zA-Z0-9_-]+)\"],\n },\n },\n \"char_filter\": {},\n \"tokenizer\": {},\n }\n\n\nExample Mapping (Reference Field)::\n\n \"properties\": {\n \"reference\": {\n \"type\": \"text\",\n \"index\": true,\n \"store\": false,\n \"analyzer\": \"fhir_reference_analyzer\"\n }\n\n\nToDo\n----\n\n1. `fhirbase`_ engine aka provider implementation.\n\n2. All methods/functions are defined in `FHIRPath`_ specification, would be completed.\n\n3. Implement https://github.com/ijl/orjson\n4. https://developers.redhat.com/blog/2017/11/16/speed-python-using-rust/\n\nCredits\n-------\n\nThis package skeleton was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.\n\n.. _Cookiecutter: https://github.com/audreyr/cookiecutter\n.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage\n.. _`FHIRPath`: http://hl7.org/fhirpath/N1/\n.. _`FHIR`: http://hl7.org/fhir/\n.. _`ORM`: https://en.wikipedia.org/wiki/Object-relational_mapping\n.. _`Plone`: https://plone.org\n.. _`guillotina`: https://guillotina.readthedocs.io/en/latest/\n.. _`elasticsearch`: https://www.elastic.co/products/elasticsearch\n.. _`GraphQL`: https://graphql.org/\n.. _`PostgreSQL`: https://www.postgresql.org/\n.. _`fhirpath-guillotina`: https://pypi.org/project/fhirpath-guillotina/\n.. _`collective.fhirpath`: https://pypi.org/project/collective.fhirpath/\n.. _`plone.app.fhirfield`: https://pypi.org/project/plone.app.fhirfield/\n.. _`fhirbase`: https://github.com/fhirbase/fhirbase\n\n\n\u00a9 Copyright HL7\u00ae logo, FHIR\u00ae logo and the flaming fire are registered trademarks\nowned by `Health Level Seven International `_\n\n**\"FHIR\u00ae is the registered trademark of HL7 and is used with the permission of HL7.\nUse of the FHIR trademark does not constitute endorsement of this product by HL7\"**\n\n\n=======\nHistory\n=======\n\n0.10.5 (2020-12-17)\n-------------------\n\nImprovement\n\n- ``BundleWrapper`` is providing two optional methods, ``calculate_fhir_base_url`` and ``resolve_absolute_uri`` and is now also taking optional parameter ``base_url``.\n\n\nFixes\n- fixes ``ElasticSearchDialect.create_term`` [Kartik Sayani]\n\n- fixes ``EngineResult.extract_references``. [Jason Paumier]\n\n- fixes how composite search params are parsed. [Jason Paumier]\n\n- Issue#28 `Nested GroupTerm search returns no matches `_\n\n- fixes ``SearchContext.normalize_param`` for composite search params [nazrulworld]\n\n0.10.4 (2020-11-19)\n-------------------\n\n- fixes ``FHIRAbstractModel`` comparing at ``utils`` module for BundleWrapper.\n\n- ``fallback_callable`` helper function is available at ``utils`` module.\n\n\n0.10.3 (2020-11-17)\n-------------------\n\nImprovements\n\n- More helper functions (``get_local_timezone``, ``timestamp_utc``, ``timestamp_utc``) are created.\n\n- ``initial_bundle_data`` method is now available in Base Elasticsearch engine class,\n meaning that it is possible construct Bundle initial data into the derived class, so more flexibility.\n\nBugfixes\n\n- Default bundle initial data was constructed ``meta.lastUpdated`` value with utc now time but without timezone offset, so\n during json serialization, timezone info was missed as a result reverse construct of Bundle complains validation error.\n\n0.10.2 (2020-11-06)\n-------------------\n\nImprovements\n\n- ``orjson`` is no longer required. ``json_dumps`` and ``json_loads`` now dynamically supports\n orjson and simplejson.\n\n\n0.10.1 (2020-11-04)\n-------------------\n\nBugfixes\n\n- ``Connection.raw_connection`` was wrongly wrapped by ``AsyncElasticsearchConnection/ElasticsearchConnection.from_url()`` with self, instead of ``elasticsearch.AsyncElasticsearch/elasticsearch.Elasticsearch``'s instance.\n\n\n0.10.0 (2020-11-04)\n-------------------\n\nImprovements\n\n\n- Introducing `AsyncElasticsearchConnection`` and ``AsyncElasticsearchEngine`` the asyncio based connection and engine for Elasticsearch. See `Using Asyncio with Elasticsearch `_\n\n- Added ``orjson`` based json serializer for Elasticsearch by default (when connection is made from connection factory).\n\n- Added support for `_summary=text|data|count|true|false`. [arkhn]\n\n- Added support for `_elements` search parameter. [arkhn]\n\n\nBreaking\n\n- ``async_result`` parameter is no longer needed for SearchContext, Search and Query (included async version) as from now all\n engine contains that information (``engine_class.is_async()``).\n\n0.9.1 (2020-10-24)\n------------------\n\n- Added supports for ``_format`` and ``_pretty`` params, now there should no complain for those, instead of simply ignored. [nazrulworld]\n\n\n0.9.0 (2020-10-24)\n------------------\n\n- Handle ``:identifier`` modifier for reference search parameters [simonvadee]\n\n- fixes `BundleWrapper`` as_json mode, now includes with ``resourceType`` value. [nazrulworld]\n\n- ``Dict`` response option has bee added in ``fhirpath.search.fhir_search`` [nazrulworld]\n\n- Ignore empty search params #21 [simonvadee]\n\n- Just for performance optimization issue minimum required ``zope.interface`` version is ``5.1.2``.\n\n0.8.1 (2020-10-05)\n------------------\n\n- Disable pydantic validation for Bundle in fhirpath.utils.BundleWrapper [simonvadee]\n\n- Two helper functions ``json_dumps`` and ``json_loads`` are now available under utils module [nazrulworld]\n\n- Only apply search prefix on affected types #17 [simonvadee]\n\n0.8.0 (2020-09-25)\n------------------\n\nImprovements\n\n- add supports for some important FHIR search parameters (``_has``, ``_include`` and ``_revinclude``) [simonvadee]\n\n- enable search on several resource types (_type search param) [Jasopaum]\n\n- Issue #8 `Add search support for without any params or query string if context has resource type `_ [nazrulworld]\n\n- Issue #9 `multiple negative not working `_ [nazrulworld]\n\nBreaking\n\n- ``fhirpath.search.SearchContext.resource_name`` has been changed ``fhirpath.search.SearchContext.resource_type`` and\n now datatype is List instead of string. Please check your API. [Jasopaum]\n\n- For case of ``Elasticsearch`` based engine, you should use custom analyzer (``fhir_reference_analyzer``) for FHIR Reference type. For details see readme.\n\n\n0.7.1 (2020-08-07)\n------------------\n\n- added missing ``isodate`` package dependency.\n\n\n0.7.0 (2020-08-07)\n------------------\n\nImprovements\n\n- Issue#5: Now ``ElasticsearchEngine::get_index_name`` takes one optional parameter ``resource_type``.\n\n- Add supports for python version 3.6.\n\nBreaking\n\n- Make full capability with `fhir.resources `_ version ``6.x.x``,\n please have a look of revolutionary changes of ``fhir.resources``.\n\n0.6.2 (2020-06-30)\n------------------\n\n- ``fhirspec`` and ``fhir.resources`` versions are pinned.\n\n\n0.6.1 (2020-05-09)\n------------------\nA must update release (from ``0.6.0``)!\n\nBugfixes\n\n- fix: issues, those arieses due to fix bellow issue.\n- fix: ``fhirpath.storage.FHIR_RESOURCE_CLASS_STORAGE``, ``fhirpath.storage.PATH_INFO_STORAGE``, ``fhirpath.storage.SEARCH_PARAMETERS_STORAGE`` and ``fhirpath.storage.FHIR_RESOURCE_SPEC_STORAGE`` took wrong FHIR release as keys.\n\n\n0.6.0 (2020-05-08)\n------------------\n\nBreaking\n\n- Hard dependency on `fhirspec `_.\n- Minimum python version 3.7 is required.\n- Minimum required ``fhir.resources`` version is now ``5.1.0`` meaning FHIR R4 4.0.1 and STU3 3.0.2.\n Please follow changes log https://pypi.org/project/fhir.resources/5.1.0/.\n\n\n\n0.5.1 (2020-03-18)\n------------------\n\nNew features\n\n- ``__main__`` module has been created, now possible to see version and/or initiated required FHIR versions.\n For example ``python -m \"fhirpath\" --version``, ``python -m \"fhirpath\" --init-setup`` [nazrulworld]\n\nImprovements\n\n- Updated fix version of elasticsearch mappings.\n\n\n0.5.0 (2020-03-11)\n------------------\n\nNew Features\n\n- ``FHIRPath`` (Normative Release) support available. A dedicated class is now available ```fhirpath.FHIRPath``,\n although it is working in progress (meaning that many methods/functions are yet to do complete.)\n\nImprovements\n\n- Add support for important FHIR search modifier ``:contains``. See https://github.com/nazrulworld/fhirpath/issues/1\n\n- Add support for ``:above``FHIR search modifier and `\u00e8b`` prefix. See https://github.com/nazrulworld/fhirpath/issues/2\n\n- Add support for ``:bellow`` FHIR search modifier and ``sa`` prefix. See https://github.com/nazrulworld/fhirpath/issues/2\n\n\nBugfixes\n\n- Upgrade to this version is recommended as it includes couples of major bug fixes.\n\n\nBreaking\n\n- The ``fhirpath.navigator`` module has been removed and introduced new module ``fhirpath.model``.\n ``fhirpath.utils.Model`` has been moved to `fhirpath.model``.\n\n\n0.4.1 (2019-11-05)\n------------------\n\nBugfixes\n\n- ``fhirpath.search.Search.parse_query_string`` now returning ``MuliDict``(what is expected) instead of ``MultiDictProxy``.\n\n\n0.4.0 (2019-10-24)\n------------------\n\nImprovements\n\n- Now full ``select`` features are accepted, meaning that you can provide multiple path in ``select`` section. for example ``select(Patient.name, Patient.gender)``.\n\n- FHIRPath ``count()`` and ``empty()`` functions are supported.\n\n- Supports path navigation with index and functions inside ``select``. Example ``[index]``, ``last()``, ``first()``, ``Skip()``, ``Take()``, ``count()``.\n\nBreakings\n\n- ``QueryResult.first`` and ``QueryResult.single`` are no longer return FHIR Model instance instead returning ``fhirpath.engine.EngineResultRow``.\n\n- ``QueryResult.fetchall`` returning list of ``fhirpath.engine.EngineResultRow`` instead of FHIR JSON.\n\n- ``QueryResult`` iteration returning list of FHIR Model instance on condition (if select is `*`), other than returning list of ``fhirpath.engine.EngineResultRow``.\n\n\n0.3.1 (2019-10-08)\n------------------\n\nImprovements\n\n- Add support for search parameter expression that contains with space+as (``MedicationRequest.medication as CodeableConcept``)\n\nBugfixes\n\n- ``not`` modifier is now working for ``Coding`` and ``CodeableConcept``.\n\n- \"ignore_unmapped\" now always True in case of nested query.\n\n- \"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\n\n\n0.3.0 (2019-09-30)\n------------------\n\nImprovements\n\n- Supports multiple AND values for same search parameter!.\n\n- Add support FHIR version ``STU3`` compability for Money type search.[nazrulworld]\n\n- IN Query support added.[nazrulworld]\n\n- Support PathElement that contains string path with .as(), thus suports for Search also.\n\n- Supports ``Duration`` type in Search.\n\n- Add support ``composite`` type search param.\n\n\nBugfixes\n\n- Multiple search values (IN search)\n\n- Missing ``text`` for HumanName and Address search.\n\n\n\n0.2.0 (2019-09-15)\n------------------\n\nBreakings:\n\n- Built-in providers ( ``guillotina_app`` and ``plone_app`` ) have been wiped as both becoming separate pypi project.\n\n- ``queries`` module has been moved from ``fql`` sub-package to fhirpath package and also renamed as ``query``.\n\n\nImprovements:\n\n- There are so many improvements made for almost all most modules.\n\n- FhirSearch coverages are increased.\n\n- Sort, Limit facilities added in Query as well in FhirSearch.\n\n\nBugfixes:\n\n- numbers of bugs fixed.\n\n\n\n0.1.1 (2019-08-15)\n------------------\n\n- First working version has been released. Of-course not full featured.\n\n\n0.1.0 (2018-12-15)\n------------------\n\n* First release on PyPI.(Just register purpose, not usable at all, next release coming soon)\n\n\n", "description_content_type": "", "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://nazrul.me/fhirpath/", "keywords": "fhirpath,HL7,FHIR,healthcare", "license": "GNU General Public License v3", "maintainer": "", "maintainer_email": "", "name": "fhirpath", "package_url": "https://pypi.org/project/fhirpath/", "platform": "", "project_url": "https://pypi.org/project/fhirpath/", "project_urls": { "CI: Travis": "https://travis-ci.org/nazrulworld/fhirpath", "Coverage: codecov": "https://codecov.io/github/nazrulworld/fhirpath", "Docs: RTD": "https://fhirpath.readthedocs.io/", "GitHub: issues": "https://github.com/nazrulworld/fhirpath/issues", "GitHub: repo": "https://github.com/nazrulworld/fhirpath", "Homepage": "https://nazrul.me/fhirpath/" }, 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