Work-around for issue #4.

Adds a secondary filter to `rdf_compare`, a filter to skip decimal precision
differences to `base_test_case.py` and invokes the skip in test_all_fhir_elements.

The basic problem is now focused exclusively in test_issue4.

fhirtordf/rdfsupport/rdfcompare.py

@@ -25,7 +25,7 @@
 # LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
 # OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
 # OF THE POSSIBILITY OF SUCH DAMAGE.
-from typing import Optional, List, Set
+from typing import Optional, List, Set, Callable
 
 from rdflib import URIRef, Graph, OWL, RDF, BNode
 from rdflib.compare import graph_diff
@@ -114,13 +114,15 @@ def dump_nt_sorted(g: Graph) -> List[str]:
     return [l.decode('ascii') for l in sorted(g.serialize(format='nt').splitlines()) if l]
 
 
-def rdf_compare(g1: Graph, g2: Graph, ignore_owl_version: bool=False, ignore_type_arcs: bool = False) -> str:
+def rdf_compare(g1: Graph, g2: Graph, ignore_owl_version: bool=False, ignore_type_arcs: bool = False,
+                compare_filter: Optional[Callable[[Graph, Graph, Graph], None]]=None) -> str:
     """
     Compare graph g1 and g2
     :param g1: first graph
     :param g2: second graph
     :param ignore_owl_version:
     :param ignore_type_arcs:
+    :param compare_filter: Final adjustment for graph difference. Used, for example, to deal with FHIR decimal problems.
     :return: List of differences as printable lines or blank if everything matches
     """
     def graph_for_subject(g: Graph, subj: Node) -> Graph:
@@ -155,6 +157,8 @@ def primary_subjects(g: Graph) -> Set[Node]:
         s_in_g1 = graph_for_subject(g1, s)
         s_in_g2 = graph_for_subject(g2, s)
         in_both, in_first, in_second = graph_diff(skolemize(s_in_g1), skolemize(s_in_g2))
+        if compare_filter:
+            compare_filter(in_both, in_first, in_second)
         if len(list(in_first)) or len(list(in_second)):
             rval += "\n\nSubject {} DIFFERENCE: ".format(s) + '=' * 30
             if len(in_first):

tests/fhir_tests/test_all_fhir_elements.py

@@ -33,7 +33,7 @@
 from fhirtordf.fhir.fhirmetavoc import FHIRMetaVocEntry
 from fhirtordf.loaders.fhirresourceloader import FHIRResource
 from fhirtordf.rdfsupport.rdfcompare import rdf_compare
-from tests.utils.base_test_case import make_and_clear_directory
+from tests.utils.base_test_case import make_and_clear_directory, fhir_decimal_issue_filter
 from tests.utils.build_test_harness import ValidationTestCase
 
 
@@ -61,7 +61,7 @@ def setUpClass(cls):
                                                   and '.schema.' not in fn and '.diff.' not in fn
 FHIRInstanceTestCase.base_dir = 'http://hl7.org/fhir'
 FHIRInstanceTestCase.max_size = 20                 # maximum file size in kb
-# FHIRInstanceTestCase.start_at = "valueset-example-intensional"
+# FHIRInstanceTestCase.start_at = "imagingstudy-example"
 
 
 # Comparing to FHIR, so make certain we're doing FHIR dates
@@ -76,7 +76,11 @@ def json_to_ttl(self: FHIRInstanceTestCase, dirpath: str, fname: str) -> bool:
     if os.path.exists(test_ttl_fname):
         target = Graph()
         target.load(test_ttl_fname, format="turtle")
-        diffs = rdf_compare(target, source.graph, ignore_owl_version=True, ignore_type_arcs=True)
+        diffs_nc = rdf_compare(target, source.graph, ignore_owl_version=True, ignore_type_arcs=True)
+        diffs = rdf_compare(target, source.graph, ignore_owl_version=True, ignore_type_arcs=True,
+                            compare_filter=fhir_decimal_issue_filter)
+        if diffs_nc and not diffs:
+            print("---> {} has decimal precision issues".format(fname))
         if diffs:
             with open(os.path.join(self.output_directory, turtle_fname), 'w') as f:
                 f.write(diffs)

tests/issue_tests/test_issue2.py

@@ -0,0 +1,160 @@
+# Copyright (c) 2017, Mayo Clinic
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without modification,
+# are permitted provided that the following conditions are met:
+#
+# Redistributions of source code must retain the above copyright notice, this
+#     list of conditions and the following disclaimer.
+#
+#     Redistributions in binary form must reproduce the above copyright notice,
+#     this list of conditions and the following disclaimer in the documentation
+#     and/or other materials provided with the distribution.
+#
+#     Neither the name of the Mayo Clinic nor the names of its contributors
+#     may be used to endorse or promote products derived from this software
+#     without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
+# IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
+# INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
+# BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, 
+# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+# OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
+# OF THE POSSIBILITY OF SUCH DAMAGE.
+
+import unittest
+
+import os
+from jsonasobj import loads
+from rdflib import Graph
+
+from fhirtordf.rdfsupport.rdfcompare import rdf_compare
+from tests.utils.base_test_case import FHIRGraph
+
+data = """{
+  "resourceType": "Bundle",
+  "id": "b248b1b2-1686-4b94-9936-37d7a5f94b51",
+  "meta": {
+    "lastUpdated": "2012-05-29T23:45:32Z"
+  },
+  "type": "collection",
+  "entry": [
+    {
+      "fullUrl": "http://hl7.org/fhir/Patient/1",
+      "resource": {
+        "resourceType": "Patient",
+        "id": "1",
+        "meta": {
+          "lastUpdated": "2012-05-29T23:45:32Z"
+        },
+        "text": {
+          "status": "generated",
+          "div": ""
+        },
+        "identifier": [
+          {
+            "type": {
+              "coding": [
+                {
+                  "system": "http://hl7.org/fhir/v2/0203",
+                  "code": "SS"
+                }
+              ]
+            },
+            "system": "http://hl7.org/fhir/sid/us-ssn",
+            "value": "444222222"
+          }
+        ]
+      }
+    }
+  ]
+}"""
+
+expected = """@prefix fhir: <http://hl7.org/fhir/> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix v2-0203: <http://hl7.org/fhir/v2/0203> .
+@prefix w5: <http://hl7.org/fhir/w5#> .
+@prefix xml: <http://www.w3.org/XML/1998/namespace> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+
+<http://hl7.org/fhir/Bundle/b248b1b2-1686-4b94-9936-37d7a5f94b51> a fhir:Bundle ;
+    fhir:nodeRole fhir:treeRoot ;
+    fhir:Bundle.entry [
+        fhir:Bundle.entry.fullUrl [
+            fhir:value "http://hl7.org/fhir/Patient/1"
+        ] ;
+        fhir:Bundle.entry.resource <http://hl7.org/fhir/Patient/1> ;
+        fhir:index "0"^^xsd:integer
+    ] ;
+    fhir:Bundle.type [
+        fhir:value "collection"
+    ] ;
+    fhir:Resource.id [
+        fhir:value "b248b1b2-1686-4b94-9936-37d7a5f94b51"
+    ] ;
+    fhir:Resource.meta [
+        fhir:Meta.lastUpdated [
+            fhir:value "2012-05-29T23:45:32+00:00"^^xsd:dateTime
+        ]
+    ] .
+
+<http://hl7.org/fhir/Bundle/b248b1b2-1686-4b94-9936-37d7a5f94b51.ttl> a owl:Ontology ;
+    owl:imports fhir:fhir.ttl .
+
+<http://hl7.org/fhir/Patient/1> a fhir:Patient ;
+    fhir:DomainResource.text [
+        fhir:Narrative.div "" ;
+        fhir:Narrative.status [
+            fhir:value "generated"
+        ]
+    ] ;
+    fhir:Patient.identifier [
+        fhir:index "0"^^xsd:integer ;
+        fhir:Identifier.system [
+            fhir:value "http://hl7.org/fhir/sid/us-ssn"
+        ] ;
+        fhir:Identifier.type [
+            fhir:CodeableConcept.coding [
+                a <http://hl7.org/fhir/v2/0203/SS> ;
+                fhir:index "0"^^xsd:integer ;
+                fhir:Coding.code [
+                    fhir:value "SS"
+                ] ;
+                fhir:Coding.system [
+                    fhir:value "http://hl7.org/fhir/v2/0203"
+                ]
+            ]
+        ] ;
+        fhir:Identifier.value [
+            fhir:value "444222222"
+        ]
+    ] ;
+    fhir:Resource.id [
+        fhir:value "1"
+    ] ;
+    fhir:Resource.meta [
+        fhir:Meta.lastUpdated [
+            fhir:value "2012-05-29T23:45:32+00:00"^^xsd:dateTime
+        ]
+    ] .
+"""
+
+
+class Issue2TestCase(unittest.TestCase):
+    def test_reference(self):
+        test_json = loads(data)
+        from fhirtordf.loaders.fhirresourceloader import FHIRResource
+        test_rdf = FHIRResource(FHIRGraph(), None, "http://hl7.org/fhir", test_json)
+        g = test_rdf.graph
+        expected_graph = Graph()
+        diffs = rdf_compare(expected_graph, test_rdf.graph, ignore_owl_version=True, ignore_type_arcs=True)
+        self.assertEqual("", diffs)
+
+if __name__ == '__main__':
+    unittest.main()

tests/issue_tests/test_issue4.py

@@ -0,0 +1,85 @@
+# Copyright (c) 2017, Mayo Clinic
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without modification,
+# are permitted provided that the following conditions are met:
+#
+# Redistributions of source code must retain the above copyright notice, this
+#     list of conditions and the following disclaimer.
+#
+#     Redistributions in binary form must reproduce the above copyright notice,
+#     this list of conditions and the following disclaimer in the documentation
+#     and/or other materials provided with the distribution.
+#
+#     Neither the name of the Mayo Clinic nor the names of its contributors
+#     may be used to endorse or promote products derived from this software
+#     without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
+# IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
+# INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
+# BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, 
+# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+# OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
+# OF THE POSSIBILITY OF SUCH DAMAGE.
+
+import unittest
+
+from jsonasobj import loads
+from rdflib import URIRef, Literal, XSD
+
+from fhirtordf.rdfsupport.namespaces import FHIR
+from tests.utils.base_test_case import FHIRGraph
+
+json_data = """{
+  "resourceType": "VisionPrescription",
+  "id": "33123",
+  "text": {
+    "status": "generated",
+    "div": "(cut)"
+  },
+   "dispense": [
+    {
+      "product": {
+        "coding": [
+          {
+            "system": "http://hl7.org/fhir/ex-visionprescriptionproduct",
+            "code": "lens"
+          }
+        ]
+      },
+      "eye": "right",
+      "sphere": -2.00,
+      "prism": 0.5,
+      "base": "down",
+      "add": 2.00
+    }
+  ]
+}
+  """
+
+
+class Issue4TestCase(unittest.TestCase):
+    def test_decimal(self):
+        test_json = loads(json_data)
+        from fhirtordf.loaders.fhirresourceloader import FHIRResource
+        test_rdf = FHIRResource(FHIRGraph(), None, "http://hl7.org/fhir", test_json)
+        g = test_rdf.graph
+        # rdflib supports decimal precision if you create the data as a string.
+        self.assertNotEqual(Literal("2.00", datatype=XSD.decimal), Literal("2.0", datatype=XSD.decimal))
+        self.assertEqual(Literal(2.00), Literal(2.0))
+
+        # FHIR requires that *all* decimals use the first form.  While the diopter example above
+        # would work, issues arise in situations where numbers really ARE decimal...
+        self.assertEqual(Literal("2.00", datatype=XSD.decimal),
+                         g.value(
+                             g.value(
+                                 g.value(URIRef("http://hl7.org/fhir/VisionPrescription/33123"),
+                                         FHIR.VisionPrescription.dispense),
+                                 FHIR.VisionPrescription.dispense.add), FHIR.value))
+
+if __name__ == '__main__':
+    unittest.main()

tests/utils/base_test_case.py

@@ -31,7 +31,7 @@
 from typing import Union
 
 from dateutil.parser import parse
-from rdflib import Graph
+from rdflib import Graph, Literal, XSD
 
 test_directory = os.path.join(os.path.split(os.path.abspath(__file__))[0], '..')
 test_data_directory = os.path.join(test_directory, 'data')
@@ -86,3 +86,18 @@ def make_and_clear_directory(directory: str):
     os.makedirs(directory)
     with open(safety_file, "w") as f:
         f.write("Generated for safety.  Must be present for test to clear this directory.")
+
+
+def fhir_decimal_issue_filter(in_both: Graph, in_first: Graph, in_second: Graph) -> None:
+    """ FHIR currently requires a non-standard JSON parser that can differentiate between '"x": 1.0' and '"x": 1.00'
+        The filter below treats RDF representation of both as the same, and is used to make decimal values
+        pass unit tests
+    """
+    for s, p, o in list(in_first):
+        o_2 = in_second.value(s, p)
+        if o_2 and isinstance(o_2, Literal) and o_2.datatype == XSD.decimal and \
+                   isinstance(o, Literal) and o.datatype == XSD.decimal:
+            if o.value == o_2.value:
+                in_both.add((s, p, o))
+                in_first.remove((s, p, o))
+                in_second.remove((s, p, o_2))