Update to FHIR 4.0.0 (#67)

Updates Data models to R4 and closes #59.

.bumpversion.cfg

@@ -1,4 +1,4 @@
 [bumpversion]
-current_version = 3.2.0
+current_version = 4.0.0
 files = fhirclient/client.py
 

.gitignore

@@ -12,3 +12,4 @@ session_data
 # IDE files
 *.sublime-*
 
+.DS_Store

AUTHORS.md

@@ -13,6 +13,7 @@ The following wonderful people contributed directly or indirectly to this projec
 - Josh Mandel <https://github.com/jmandel>
 - Nikolai Schwertner <https://github.com/nschwertner>
 - Pascal Pfiffner <https://github.com/p2>
+- Raheel Sayeed <https://github.com/raheelsayeed> 
 - Trinadh Baranika <https://github.com/bktrinadh>
 
 Please add yourself here alphabetically when you submit your first pull request.

Doxyfile

@@ -38,7 +38,7 @@ PROJECT_NAME           = "SMART on FHIR Python Client"
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 3.2.0
+PROJECT_NUMBER         = 4.0.0
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a

README.md

@@ -10,6 +10,7 @@ The `develop` branch should be on recent freezes, and the `feature/latest-ci` br
 
    Version |          FHIR |  
 -----------|---------------|---------
+ **4.0.0** |       `4.0.0` | (R4)
  **3.0.0** |       `3.0.0` | (STU-3)
    **x.x** |       `1.8.0` | (STU-3 Ballot, Jan 2017)
    **x.x** |       `1.6.0` | (STU-3 Ballot, Sep 2016)

fhir-parser-resources/settings.py

@@ -5,7 +5,7 @@
 from Default.settings import *
 
 # Base URL for where to load specification data from
-specification_url = 'http://hl7.org/fhir/STU3'
+specification_url = 'http://hl7.org/fhir/R4'
 
 # In which directory to find the templates. See below for settings that start with `tpl_`: these are the template names.
 tpl_base = '../fhir-parser-resources'

fhir-parser-resources/template-unittest.py

@@ -36,7 +36,7 @@ def test{{ class.name }}{{ loop.index }}(self):
     def impl{{ class.name }}{{ loop.index }}(self, inst):
     {%- for onetest in tcase.tests %}
     {%- if "str" == onetest.klass.name %}
-        self.assertEqual(inst.{{ onetest.path }}, "{{ onetest.value|replace('"', '\\"') }}")
+        self.assertEqual(inst.{{ onetest.path }}, "{{ onetest.value|replace('\\n', '\\\\n')|replace('"', '\\"') }}")
     {%- else %}{% if "int" == onetest.klass.name or "float" == onetest.klass.name or "NSDecimalNumber" == onetest.klass.name %}
         self.assertEqual(inst.{{ onetest.path }}, {{ onetest.value }})
     {%- else %}{% if "bool" == onetest.klass.name %}

fhirclient/client.py

@@ -4,7 +4,7 @@
 
 from server import FHIRServer, FHIRUnauthorizedException, FHIRNotFoundException
 
-__version__ = '3.2.0'
+__version__ = '4.0.0'
 __author__ = 'SMART Platforms Team'
 __license__ = 'APACHE2'
 __copyright__ = "Copyright 2017 Boston Children's Hospital"

fhirclient/fhirreference_tests.py

@@ -30,24 +30,24 @@ def testContainedResourceDetection(self):
         self.assertEqual('Observation.subject', group.linkId)
         question = group.item[0]
         self.assertEqual('Observation.subject._type', question.linkId)
-        self.assertIsNotNone(question.options)
+        self.assertIsNotNone(question.answerOption)
         with self.assertRaises(Exception):
-            question.options.resolved()
-
+            question.answerOption[0].valueReference.resolved()
+        reference = question.answerOption[0].valueReference
         # 1st resolve, extracting from contained resources
-        contained = question.options.resolved(medication.Medication)
+        contained = reference.resolved(medication.Medication)
         self.assertIsNone(contained, "Must not resolve on resource type mismatch")
-        contained = question.options.resolved(valueset.ValueSet)
+        contained = reference.resolved(valueset.ValueSet)
         self.assertIsNotNone(contained, "Must resolve contained ValueSet")
         self.assertEqual('ValueSet', contained.resource_type)
         self.assertEqual('Type options for Observation.subject', contained.name)
 
         # 2nd resolve, should pull from cache
-        contained = question.options.resolved(medication.Medication)
+        contained = reference.resolved(medication.Medication)
         self.assertIsNone(contained, "Must not resolve on resource type mismatch")
-        contained = question.options.resolved(resource.Resource)
+        contained = reference.resolved(resource.Resource)
         self.assertIsNotNone(contained, "Must resolve contained ValueSet even if requesting `Resource`")
-        contained = question.options.resolved(valueset.ValueSet)
+        contained = reference.resolved(valueset.ValueSet)
         self.assertIsNotNone(contained, "Must resolve contained ValueSet")
         self.assertEqual('ValueSet', contained.resource_type)
 
@@ -63,20 +63,21 @@ def testRelativeReference(self):
         self.assertEqual('Observation.subject', group.linkId)
         question = group.item[0]
         self.assertEqual('Observation.subject._type', question.linkId)
-        self.assertIsNotNone(question.options)
+        self.assertIsNotNone(question.answerOption)
         with self.assertRaises(Exception):
-            question.options.resolved()
+            question.answerOption[0].valueReference.resolved()
+        reference = question.answerOption[0].valueReference
 
         # resolve relative resource
-        relative = question.options.resolved(valueset.ValueSet)
+        relative = reference.resolved(valueset.ValueSet)
         self.assertIsNotNone(relative, "Must resolve relative ValueSet")
         self.assertEqual('ValueSet', relative.resource_type)
         self.assertEqual('Type options for Observation.subject', relative.name)
 
         # 2nd resolve, should pull from cache
-        relative = question.options.resolved(medication.Medication)
+        relative = reference.resolved(medication.Medication)
         self.assertIsNone(relative, "Must not resolve on resource type mismatch")
-        relative = question.options.resolved(resource.Resource)
+        relative = reference.resolved(resource.Resource)
         self.assertIsNotNone(relative, "Must resolve relative ValueSet even if requesting `Resource`")
 
     def testBundleReferences(self):

fhirclient/models/account.py

@@ -1,8 +1,8 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#  Generated from FHIR 3.0.0.11832 (http://hl7.org/fhir/StructureDefinition/Account) on 2017-03-22.
-#  2017, SMART Health IT.
+#  Generated from FHIR 4.0.0-a53ec6ee1b (http://hl7.org/fhir/StructureDefinition/Account) on 2019-05-07.
+#  2019, SMART Health IT.
 
 
 from . import domainresource
@@ -25,14 +25,6 @@ def __init__(self, jsondict=None, strict=True):
         :param bool strict: If True (the default), invalid variables will raise a TypeError
         """
 
-        self.active = None
-        """ Time window that transactions may be posted to this account.
-        Type `Period` (represented as `dict` in JSON). """
-
-        self.balance = None
-        """ How much is in account?.
-        Type `Money` (represented as `dict` in JSON). """
-
         self.coverage = None
         """ The party(s) that are responsible for covering the payment of this
         account, and what order should they be applied to the account.
@@ -43,7 +35,7 @@ def __init__(self, jsondict=None, strict=True):
         Type `str`. """
 
         self.guarantor = None
-        """ Responsible for the account.
+        """ The parties ultimately responsible for balancing the Account.
         List of `AccountGuarantor` items (represented as `dict` in JSON). """
 
         self.identifier = None
@@ -55,20 +47,24 @@ def __init__(self, jsondict=None, strict=True):
         Type `str`. """
 
         self.owner = None
-        """ Who is responsible?.
-        Type `FHIRReference` referencing `Organization` (represented as `dict` in JSON). """
+        """ Entity managing the Account.
+        Type `FHIRReference` (represented as `dict` in JSON). """
 
-        self.period = None
+        self.partOf = None
+        """ Reference to a parent Account.
+        Type `FHIRReference` (represented as `dict` in JSON). """
+
+        self.servicePeriod = None
         """ Transaction window.
         Type `Period` (represented as `dict` in JSON). """
 
         self.status = None
-        """ active | inactive | entered-in-error.
+        """ active | inactive | entered-in-error | on-hold | unknown.
         Type `str`. """
 
         self.subject = None
-        """ What is account tied to?.
-        Type `FHIRReference` referencing `Patient, Device, Practitioner, Location, HealthcareService, Organization` (represented as `dict` in JSON). """
+        """ The entity that caused the expenses.
+        List of `FHIRReference` items (represented as `dict` in JSON). """
 
         self.type = None
         """ E.g. patient, expense, depreciation.
@@ -79,17 +75,16 @@ def __init__(self, jsondict=None, strict=True):
     def elementProperties(self):
         js = super(Account, self).elementProperties()
         js.extend([
-            ("active", "active", period.Period, False, None, False),
-            ("balance", "balance", money.Money, False, None, False),
             ("coverage", "coverage", AccountCoverage, True, None, False),
             ("description", "description", str, False, None, False),
             ("guarantor", "guarantor", AccountGuarantor, True, None, False),
             ("identifier", "identifier", identifier.Identifier, True, None, False),
             ("name", "name", str, False, None, False),
             ("owner", "owner", fhirreference.FHIRReference, False, None, False),
-            ("period", "period", period.Period, False, None, False),
-            ("status", "status", str, False, None, False),
-            ("subject", "subject", fhirreference.FHIRReference, False, None, False),
+            ("partOf", "partOf", fhirreference.FHIRReference, False, None, False),
+            ("servicePeriod", "servicePeriod", period.Period, False, None, False),
+            ("status", "status", str, False, None, True),
+            ("subject", "subject", fhirreference.FHIRReference, True, None, False),
             ("type", "type", codeableconcept.CodeableConcept, False, None, False),
         ])
         return js
@@ -113,9 +108,9 @@ def __init__(self, jsondict=None, strict=True):
         """
 
         self.coverage = None
-        """ The party(s) that are responsible for covering the payment of this
-        account.
-        Type `FHIRReference` referencing `Coverage` (represented as `dict` in JSON). """
+        """ The party(s), such as insurances, that may contribute to the
+        payment of this account.
+        Type `FHIRReference` (represented as `dict` in JSON). """
 
         self.priority = None
         """ The priority of the coverage in the context of this account.
@@ -133,9 +128,10 @@ def elementProperties(self):
 
 
 class AccountGuarantor(backboneelement.BackboneElement):
-    """ Responsible for the account.
+    """ The parties ultimately responsible for balancing the Account.
     
-    Parties financially responsible for the account.
+    The parties responsible for balancing the account if other payment options
+    fall short.
     """
 
     resource_type = "AccountGuarantor"
@@ -154,10 +150,10 @@ def __init__(self, jsondict=None, strict=True):
 
         self.party = None
         """ Responsible entity.
-        Type `FHIRReference` referencing `Patient, RelatedPerson, Organization` (represented as `dict` in JSON). """
+        Type `FHIRReference` (represented as `dict` in JSON). """
 
         self.period = None
-        """ Guarrantee account during.
+        """ Guarantee account during.
         Type `Period` (represented as `dict` in JSON). """
 
         super(AccountGuarantor, self).__init__(jsondict=jsondict, strict=strict)
@@ -185,10 +181,6 @@ def elementProperties(self):
     from . import identifier
 except ImportError:
     identifier = sys.modules[__package__ + '.identifier']
-try:
-    from . import money
-except ImportError:
-    money = sys.modules[__package__ + '.money']
 try:
     from . import period
 except ImportError:

fhirclient/models/account_tests.py

@@ -1,8 +1,8 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#  Generated from FHIR 3.0.0.11832 on 2017-03-22.
-#  2017, SMART Health IT.
+#  Generated from FHIR 4.0.0-a53ec6ee1b on 2019-05-07.
+#  2019, SMART Health IT.
 
 
 import os
@@ -22,7 +22,7 @@ def instantiate_from(self, filename):
         return account.Account(js)
 
     def testAccount1(self):
-        inst = self.instantiate_from("account-example-with-guarantor.json")
+        inst = self.instantiate_from("account-example.json")
         self.assertIsNotNone(inst, "Must have instantiated a Account instance")
         self.implAccount1(inst)
 
@@ -32,38 +32,29 @@ def testAccount1(self):
         self.implAccount1(inst2)
 
     def implAccount1(self, inst):
-        self.assertEqual(inst.active.end.date, FHIRDate("2016-06-30").date)
-        self.assertEqual(inst.active.end.as_json(), "2016-06-30")
-        self.assertEqual(inst.active.start.date, FHIRDate("2016-01-01").date)
-        self.assertEqual(inst.active.start.as_json(), "2016-01-01")
-        self.assertEqual(inst.balance.code, "USD")
-        self.assertEqual(inst.balance.system, "urn:iso:std:iso:4217")
-        self.assertEqual(inst.balance.unit, "USD")
-        self.assertEqual(inst.balance.value, -1200)
         self.assertEqual(inst.coverage[0].priority, 1)
-        self.assertEqual(inst.coverage[1].priority, 2)
         self.assertEqual(inst.description, "Hospital charges")
-        self.assertFalse(inst.guarantor[0].onHold)
-        self.assertEqual(inst.guarantor[0].period.start.date, FHIRDate("2016-01-01").date)
-        self.assertEqual(inst.guarantor[0].period.start.as_json(), "2016-01-01")
-        self.assertEqual(inst.id, "ewg")
+        self.assertEqual(inst.id, "example")
         self.assertEqual(inst.identifier[0].system, "urn:oid:0.1.2.3.4.5.6.7")
         self.assertEqual(inst.identifier[0].value, "654321")
-        self.assertEqual(inst.name, "Inpatient: Peter James Chalmers")
-        self.assertEqual(inst.period.end.date, FHIRDate("2016-06-30").date)
-        self.assertEqual(inst.period.end.as_json(), "2016-06-30")
-        self.assertEqual(inst.period.start.date, FHIRDate("2016-01-01").date)
-        self.assertEqual(inst.period.start.as_json(), "2016-01-01")
+        self.assertEqual(inst.meta.tag[0].code, "HTEST")
+        self.assertEqual(inst.meta.tag[0].display, "test health data")
+        self.assertEqual(inst.meta.tag[0].system, "http://terminology.hl7.org/CodeSystem/v3-ActReason")
+        self.assertEqual(inst.name, "HACC Funded Billing for Peter James Chalmers")
+        self.assertEqual(inst.servicePeriod.end.date, FHIRDate("2016-06-30").date)
+        self.assertEqual(inst.servicePeriod.end.as_json(), "2016-06-30")
+        self.assertEqual(inst.servicePeriod.start.date, FHIRDate("2016-01-01").date)
+        self.assertEqual(inst.servicePeriod.start.as_json(), "2016-01-01")
         self.assertEqual(inst.status, "active")
-        self.assertEqual(inst.text.div, "<div xmlns=\"http://www.w3.org/1999/xhtml\">Inpatient Admission for Peter James Chalmers Account</div>")
+        self.assertEqual(inst.text.div, "<div xmlns=\"http://www.w3.org/1999/xhtml\">HACC Funded Billing for Peter James Chalmers</div>")
         self.assertEqual(inst.text.status, "generated")
         self.assertEqual(inst.type.coding[0].code, "PBILLACCT")
         self.assertEqual(inst.type.coding[0].display, "patient billing account")
-        self.assertEqual(inst.type.coding[0].system, "http://hl7.org/fhir/v3/ActCode")
+        self.assertEqual(inst.type.coding[0].system, "http://terminology.hl7.org/CodeSystem/v3-ActCode")
         self.assertEqual(inst.type.text, "patient")
 
     def testAccount2(self):
-        inst = self.instantiate_from("account-example.json")
+        inst = self.instantiate_from("account-example-with-guarantor.json")
         self.assertIsNotNone(inst, "Must have instantiated a Account instance")
         self.implAccount2(inst)
 
@@ -73,29 +64,28 @@ def testAccount2(self):
         self.implAccount2(inst2)
 
     def implAccount2(self, inst):
-        self.assertEqual(inst.active.end.date, FHIRDate("2016-06-30").date)
-        self.assertEqual(inst.active.end.as_json(), "2016-06-30")
-        self.assertEqual(inst.active.start.date, FHIRDate("2016-01-01").date)
-        self.assertEqual(inst.active.start.as_json(), "2016-01-01")
-        self.assertEqual(inst.balance.code, "USD")
-        self.assertEqual(inst.balance.system, "urn:iso:std:iso:4217")
-        self.assertEqual(inst.balance.unit, "USD")
-        self.assertEqual(inst.balance.value, -1200)
         self.assertEqual(inst.coverage[0].priority, 1)
+        self.assertEqual(inst.coverage[1].priority, 2)
         self.assertEqual(inst.description, "Hospital charges")
-        self.assertEqual(inst.id, "example")
+        self.assertFalse(inst.guarantor[0].onHold)
+        self.assertEqual(inst.guarantor[0].period.start.date, FHIRDate("2016-01-01").date)
+        self.assertEqual(inst.guarantor[0].period.start.as_json(), "2016-01-01")
+        self.assertEqual(inst.id, "ewg")
         self.assertEqual(inst.identifier[0].system, "urn:oid:0.1.2.3.4.5.6.7")
         self.assertEqual(inst.identifier[0].value, "654321")
-        self.assertEqual(inst.name, "HACC Funded Billing for Peter James Chalmers")
-        self.assertEqual(inst.period.end.date, FHIRDate("2016-06-30").date)
-        self.assertEqual(inst.period.end.as_json(), "2016-06-30")
-        self.assertEqual(inst.period.start.date, FHIRDate("2016-01-01").date)
-        self.assertEqual(inst.period.start.as_json(), "2016-01-01")
+        self.assertEqual(inst.meta.tag[0].code, "HTEST")
+        self.assertEqual(inst.meta.tag[0].display, "test health data")
+        self.assertEqual(inst.meta.tag[0].system, "http://terminology.hl7.org/CodeSystem/v3-ActReason")
+        self.assertEqual(inst.name, "Inpatient: Peter James Chalmers")
+        self.assertEqual(inst.servicePeriod.end.date, FHIRDate("2016-06-30").date)
+        self.assertEqual(inst.servicePeriod.end.as_json(), "2016-06-30")
+        self.assertEqual(inst.servicePeriod.start.date, FHIRDate("2016-01-01").date)
+        self.assertEqual(inst.servicePeriod.start.as_json(), "2016-01-01")
         self.assertEqual(inst.status, "active")
-        self.assertEqual(inst.text.div, "<div xmlns=\"http://www.w3.org/1999/xhtml\">HACC Funded Billing for Peter James Chalmers</div>")
+        self.assertEqual(inst.text.div, "<div xmlns=\"http://www.w3.org/1999/xhtml\">Inpatient Admission for Peter James Chalmers Account</div>")
         self.assertEqual(inst.text.status, "generated")
         self.assertEqual(inst.type.coding[0].code, "PBILLACCT")
         self.assertEqual(inst.type.coding[0].display, "patient billing account")
-        self.assertEqual(inst.type.coding[0].system, "http://hl7.org/fhir/v3/ActCode")
+        self.assertEqual(inst.type.coding[0].system, "http://terminology.hl7.org/CodeSystem/v3-ActCode")
         self.assertEqual(inst.type.text, "patient")