nazrulworld/collective.fhirpath

Plone powered provider for fhirptah

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.