Regenerate models based off of R4 (4.0.1)

Also:
- Fixed the pytest config so that tests can pass again.
- Bumped the fhirclient version to 4.2.0.
- Fixed up some docs.

.bumpversion.cfg

@@ -1,3 +1,3 @@
 [bumpversion]
-current_version = 4.1.0
+current_version = 4.2.0
 files = fhirclient/client.py

.gitignore

@@ -11,5 +11,5 @@ session_data
 
 # IDE files
 *.sublime-*
-
+/.idea/
 .DS_Store

CONTRIBUTING.md

@@ -33,5 +33,5 @@ If you have any question or concerns, feel free to reach out to us at
 [pep257]: http://www.python.org/dev/peps/pep-0257/
 [good commit messages]: http://tbaggery.com/2008/04/19/a-note-about-git-commit-messages.html
 [squash]: http://gitready.com/advanced/2009/02/10/squashing-commits-with-rebase.html
-[AUTHORS.md]: https://github.com/smart-on-fhir/client-py/blob/master/AUTHORS.md
+[AUTHORS.md]: https://github.com/smart-on-fhir/client-py/blob/main/AUTHORS.md
 [procedures]: http://twistedmatrix.com/trac/wiki/CompatibilityPolicy

README.md

@@ -2,14 +2,14 @@ SMART FHIR Client
 =================
 
 This is _fhirclient_, a flexible Python client for [FHIR][] servers supporting the [SMART on FHIR][smart] protocol.
-The client is compatible with Python 2.7.10 and Python 3.
 
 Client versioning is not identical to FHIR versioning.
-The `master` branch is usually on the latest version of the client as shown below, possibly on bugfix releases thereof.
+The `main` branch is usually on the latest version of the client as shown below, possibly on bugfix releases thereof.
 The `develop` branch should be on recent freezes, and the `feature/latest-ci` branch is periodically updated to the latest FHIR continuous integration builds.
 
-   Version |          FHIR |  
------------|---------------|---------
+   Version | FHIR         |  
+-----------|--------------|---------
+ **4.2.0** |       `4.0.1` | (R4)
  **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)
@@ -224,6 +224,6 @@ Using setuptools (*Note*: Alternatively, you can use twine https://pypi.python.o
 [smart]: http://docs.smarthealthit.org
 [fhir-parser]: https://github.com/smart-on-fhir/fhir-parser
 [docs]: https://smart-on-fhir.github.io/client-py
-[flask_app]: https://github.com/smart-on-fhir/client-py/blob/master/flask_app.py
+[flask_app]: https://github.com/smart-on-fhir/client-py/blob/main/flask_app.py
 [doxygen]: http://www.stack.nl/~dimitri/doxygen
 [doxypypy]: https://github.com/Feneric/doxypypy

fhir-parser-resources/fhirsearch_tests.py

@@ -1,10 +1,10 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-from models.fhirsearch import FHIRSearch
+from fhirclient.models.fhirsearch import FHIRSearch
 
 if '__main__' == __name__:
-    from models.patient import Patient
+    from fhirclient.models.patient import Patient
     print('1 '+FHIRSearch(Patient, {'name': 'Willis'}).construct())
     print('1 '+Patient.where({'name': 'Willis'}).construct())
     # print('1 '+Patient.where().name('Willis').construct())

fhir-parser-resources/settings.py

@@ -22,6 +22,7 @@
 # unit tests
 write_unittests = True
 tpl_unittest_target = '../fhirclient/models'    # target directory to write the generated unit test files to
+tpl_unittest_target_ptrn = '{}_tests.py'        # TODO: remove in future when we re-organize tests
 
 
 # all these files should be copied to dirname(`tpl_resource_target_ptrn`): tuples of (path/to/file, module, array-of-class-names)

fhir-parser-resources/template-elementfactory.py

@@ -17,10 +17,21 @@ def instantiate(cls, resource_type, jsondict):
         :param dict jsondict: The JSON dictionary to use for data
         :returns: A resource of the respective type or `Element`
         """
-        {%- for klass in classes %}{% if klass.resource_type %}
+        {%- for klass in classes %}
+        {%- if klass.resource_type %}
         if "{{ klass.resource_type }}" == resource_type:
             from . import {{ klass.module }}
             return {{ klass.module }}.{{ klass.name }}(jsondict)
+        {%- elif klass.name %}
+        {#- backwards compatibility:
+         # fhir-parser stopped providing resource_type for non-resources.
+         # But we already shipped code that allowed creating non-resources.
+         # So to avoid an API break, we keep generating this for all classes.
+         # Can reconsider whether we want this once we jump to R5. (R4-QUIRK)
+         #}
+        if "{{ klass.name }}" == resource_type:
+            from . import {{ klass.module }}
+            return {{ klass.module }}.{{ klass.name }}(jsondict)
         {%- endif %}{% endfor %}
         from . import element
         return element.Element(jsondict)

fhir-parser-resources/template-resource.py

@@ -24,6 +24,15 @@ class {{ klass.name }}({% if klass.superclass in imports %}{{ klass.superclass.m
 {%- if klass.resource_type %}
 
     resource_type = "{{ klass.resource_type }}"
+{%- elif klass.name %}
+{#- backwards compatibility:
+# fhir-parser stopped providing resource_type for non-resources.
+# But we already shipped code that had this property for all classes.
+# So to avoid an API break, we keep generating this for all classes.
+# Can remove once we jump to R5. (R4-QUIRK)
+#}
+
+    resource_type = "{{ klass.name }}"
 {%- endif %}
 
     def __init__(self, jsondict=None, strict=True):
@@ -33,7 +42,8 @@ def __init__(self, jsondict=None, strict=True):
         :param dict jsondict: A JSON dictionary to use for initialization
         :param bool strict: If True (the default), invalid variables will raise a TypeError
         """
-    {%- for prop in klass.properties %}
+    {#- sorted just to avoid churn during another update - can remove as its own PR at some point #}
+    {%- for prop in klass.properties|sort(attribute="name", case_sensitive=True) %}
 
         self.{{ prop.name }} = None
         """ {{ prop.short|wordwrap(67, wrapstring="\n        ") }}.
@@ -55,7 +65,8 @@ def elementProperties(self):
         {%- endif %}{% endfor %}
         {%- endif %}
         js.extend([
-        {%- for prop in klass.properties %}
+        {#- sorted just to avoid churn during another update - can remove as its own PR at some point #}
+        {%- for prop in klass.properties|sort(attribute="name", case_sensitive=True) %}
             ("{{ prop.name }}", "{{ prop.orig_name }}",
             {%- if prop.module_name %} {{ prop.module_name }}.{% else %} {% endif %}{{ prop.class_name }}, {# #}
             {{- prop.is_array }},

fhirclient/client.py

@@ -4,7 +4,7 @@
 
 from server import FHIRServer, FHIRUnauthorizedException, FHIRNotFoundException
 
-__version__ = '4.1.0'
+__version__ = '4.2.0'
 __author__ = 'SMART Platforms Team'
 __license__ = 'APACHE2'
 __copyright__ = "Copyright 2017 Boston Children's Hospital"

fhirclient/fhirreference_tests.py

@@ -20,7 +20,7 @@
 class TestResourceReference(unittest.TestCase):
 
     def testContainedResourceDetection(self):
-        with io.open('test_contained_resource.json', 'r', encoding='utf-8') as h:
+        with io.open('fhirclient/test_contained_resource.json', 'r', encoding='utf-8') as h:
             data = json.load(h)
         q = questionnaire.Questionnaire(data)
         self.assertIsNotNone(q, "Must instantiate Questionnaire")
@@ -52,7 +52,7 @@ def testContainedResourceDetection(self):
         self.assertEqual('ValueSet', contained.resource_type)
 
     def testRelativeReference(self):
-        with io.open('test_relative_reference.json', 'r', encoding='utf-8') as h:
+        with io.open('fhirclient/test_relative_reference.json', 'r', encoding='utf-8') as h:
             data = json.load(h)
         q = questionnaire.Questionnaire(data)
         self.assertIsNotNone(q, "Must instantiate Questionnaire")
@@ -81,7 +81,7 @@ def testRelativeReference(self):
         self.assertIsNotNone(relative, "Must resolve relative ValueSet even if requesting `Resource`")
 
     def testBundleReferences(self):
-        with io.open('test_bundle.json', 'r', encoding='utf-8') as h:
+        with io.open('fhirclient/test_bundle.json', 'r', encoding='utf-8') as h:
             data = json.load(h)
         b = bundle.Bundle(data)
         self.assertIsNotNone(b, "Must instantiate Bundle")
@@ -128,7 +128,7 @@ def __init__(self):
     def request_json(self, path, nosign=False):
         assert path
         parts = os.path.split(path)
-        filename = '_'.join(parts) + '.json'
+        filename = 'fhirclient/' + '_'.join(parts) + '.json'
         with io.open(filename, 'r', encoding='utf-8') as handle:
             return json.load(handle)
         return None

fhirclient/models/account.py

@@ -1,8 +1,8 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#  Generated from FHIR 4.0.0-a53ec6ee1b (http://hl7.org/fhir/StructureDefinition/Account) on 2019-05-07.
-#  2019, SMART Health IT.
+#  Generated from FHIR 4.0.1-9346c8cc45 (http://hl7.org/fhir/StructureDefinition/Account) on 2024-07-15.
+#  2024, SMART Health IT.
 
 
 from . import domainresource

fhirclient/models/account_tests.py

@@ -1,8 +1,8 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#  Generated from FHIR 4.0.0-a53ec6ee1b on 2019-05-07.
-#  2019, SMART Health IT.
+#  Generated from FHIR 4.0.1-9346c8cc45 on 2024-07-15.
+#  2024, 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.json")
+        inst = self.instantiate_from("account-example-with-guarantor.json")
         self.assertIsNotNone(inst, "Must have instantiated a Account instance")
         self.implAccount1(inst)
 
@@ -33,28 +33,32 @@ def testAccount1(self):
 
     def implAccount1(self, inst):
         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.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.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://terminology.hl7.org/CodeSystem/v3-ActCode")
         self.assertEqual(inst.type.text, "patient")
 
     def testAccount2(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.implAccount2(inst)
 
@@ -65,24 +69,20 @@ def testAccount2(self):
 
     def implAccount2(self, inst):
         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.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.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")

fhirclient/models/activitydefinition.py

@@ -1,8 +1,8 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#  Generated from FHIR 4.0.0-a53ec6ee1b (http://hl7.org/fhir/StructureDefinition/ActivityDefinition) on 2019-05-07.
-#  2019, SMART Health IT.
+#  Generated from FHIR 4.0.1-9346c8cc45 (http://hl7.org/fhir/StructureDefinition/ActivityDefinition) on 2024-07-15.
+#  2024, SMART Health IT.
 
 
 from . import domainresource
@@ -91,7 +91,8 @@ def __init__(self, jsondict=None, strict=True):
         List of `Identifier` items (represented as `dict` in JSON). """
 
         self.intent = None
-        """ proposal | plan | order.
+        """ proposal | plan | directive | order | original-order | reflex-order
+        | filler-order | instance-order | option.
         Type `str`. """
 
         self.jurisdiction = None