Merge pull request #305 from standardhealth/dev6

Moving master to CIMPL 6 with Objective FHIR namespace
standardhealth · Jun 11, 2019 · c4fa225 · c4fa225
2 parents 2bdaa34 + 530e50f
commit c4fa225
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diff --git a/.travis.yml b/.travis.yml
@@ -12,7 +12,7 @@ before_install:
   - cd shr-cli/
   - yarn
 script:
-  - node . -s es6 ../spec/ > run.log
+  - node . ../spec/ > run.log
   - cat run.log
   - errors=$(grep "errors" run.log | sed $'s,\x1b\\[[0-9;]*[a-zA-Z],,g')
   - if [[ "$errors" != "0 errors" ]]; then ( echo There were errors in running shr-cli. ; exit 1 ); fi
diff --git a/spec/Examples_mCODE/mCODECancerStageGroupExample01.json b/spec/Examples_mCODE/mCODECancerStageGroupExample01.json
@@ -3,7 +3,7 @@
   "id": "mCODECancerStageGroupExample01",
   "meta": {
     "profile": [
-      "http://hl7.org/fhir/us/shr/StructureDefinition/onco-core-CancerStageGroup"
+      "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-CancerStageGroup"
     ]
   },
   "text": {
@@ -49,7 +49,7 @@
   },
   "extension": [
     {
-        "url": "http://hl7.org/fhir/us/shr/StructureDefinition/onco-core-PrimaryCancerCondition-extension",
+        "url": "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-PrimaryCancerCondition-extension",
         "reference": "Condition/mCODEPrimaryCancerConditionExample01"
     }
   ]

diff --git a/spec/Examples_mCODE/mCODEGeneticMutationTestResultExample01.json b/spec/Examples_mCODE/mCODEGeneticMutationTestResultExample01.json
@@ -3,7 +3,7 @@
   "id": "mCODEGeneticMutationTestResultExample01",
   "meta": {
     "profile": [
-      "http://hl7.org/fhir/us/shr/StructureDefinition/onco-core-GeneticMutationTestResult"
+      "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-GeneticMutationTestResult"
     ]
   },
   "text": {
@@ -55,10 +55,10 @@
   },
   "extension": [
     {
-        "url": "http://hl7.org/fhir/us/shr/StructureDefinition/onco-core-MutationTested-extension",
+        "url": "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-MutationTested-extension",
         "extension": [
           {
-            "url": "http://hl7.org/fhir/us/shr/StructureDefinition/onco-core-GeneStudied-extension",
+            "url": "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-GeneStudied-extension",
             "valueCodeableConcept": {
                 "coding": [
                   {
@@ -70,7 +70,7 @@
             }
           },
           { 
-            "url": "http://hl7.org/fhir/us/shr/StructureDefinition/onco-core-VariantIdentifier-extension",
+            "url": "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-VariantIdentifier-extension",
             "valueCodeableConcept": {
               "coding": [
                 {
@@ -82,7 +82,7 @@
             }
           },
           { 
-            "url": "http://hl7.org/fhir/us/shr/StructureDefinition/onco-core-VariantDescription-extension",
+            "url": "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-VariantDescription-extension",
             "valueString": "NM_000455.4:c.921-1G>C"
           }
         ] 

diff --git a/spec/Examples_mCODE/mCODEGeneticVariantFoundExample01.json b/spec/Examples_mCODE/mCODEGeneticVariantFoundExample01.json
@@ -3,7 +3,7 @@
   "id": "mCODEGeneticVariantFoundExample01",
   "meta": {
     "profile": [
-      "http://hl7.org/fhir/us/shr/StructureDefinition/onco-core-GeneticVariantFound"
+      "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-GeneticVariantFound"
     ]
   },
   "text": {

diff --git a/spec/Examples_mCODE/mCODEGeneticVariantTestedExample01.json b/spec/Examples_mCODE/mCODEGeneticVariantTestedExample01.json
@@ -3,7 +3,7 @@
   "id": "mCODEGeneticVariantTestedExample01",
   "meta": {
     "profile": [
-      "http://hl7.org/fhir/us/shr/StructureDefinition/onco-core-GeneticVariantTested"
+      "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-GeneticVariantTested"
     ]
   },
   "text": {
@@ -55,10 +55,10 @@
   },
   "extension": [
     {
-        "url": "http://hl7.org/fhir/us/shr/StructureDefinition/onco-core-VariantTested-extension",
+        "url": "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-VariantTested-extension",
         "extension": [
           {
-            "url": "http://hl7.org/fhir/us/shr/StructureDefinition/onco-core-GeneStudied-extension",
+            "url": "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-GeneStudied-extension",
             "valueCodeableConcept": {
                 "coding": [
                   {
@@ -70,7 +70,7 @@
             }
           },
           { 
-            "url": "http://hl7.org/fhir/us/shr/StructureDefinition/onco-core-VariantIdentifier-extension",
+            "url": "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-VariantIdentifier-extension",
             "valueCodeableConcept": {
               "coding": [
                 {
@@ -82,7 +82,7 @@
             }
           },
           { 
-            "url": "http://hl7.org/fhir/us/shr/StructureDefinition/onco-core-VariantDescription-extension",
+            "url": "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-VariantDescription-extension",
             "valueString": "NM_000455.4:c.921-1G>C"
           }
         ] 

diff --git a/spec/Examples_mCODE/mCODEGenomicsReportExample01.json b/spec/Examples_mCODE/mCODEGenomicsReportExample01.json
@@ -5,7 +5,7 @@
     "versionId": "0.1",
     "lastUpdated": "2019-04-01T15:35:58.045+00:00",
     "profile": [
-      "http://hl7.org/fhir/us/shr/StructureDefinition/onco-core-GenomicsReport"
+      "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-GenomicsReport"
     ]
   },
   "text": {

diff --git a/spec/Examples_mCODE/mCODEOrganizationExampleFM1.json b/spec/Examples_mCODE/mCODEOrganizationExampleFM1.json
@@ -3,7 +3,7 @@
   "id": "mCODEOrganizationExampleFM1",
   "meta": {
     "profile": [
-      "http://hl7.org/fhir/us/shr/StructureDefinition/shr-core-Organization"
+      "http://hl7.org/fhir/us/mcode/StructureDefinition/obf-Organization"
     ]
   },
   "text": {
@@ -18,7 +18,7 @@
   ],
   "extension": [
     {
-      "url": "http://hl7.org/fhir/us/shr/StructureDefinition/shr-core-Status-extension",
+      "url": "http://hl7.org/fhir/us/mcode/StructureDefinition/obf-Status-extension",
       "valueCodeableConcept": 
       {
         "coding": [

diff --git a/spec/Examples_mCODE/mCODEPatientExample01.json b/spec/Examples_mCODE/mCODEPatientExample01.json
@@ -3,7 +3,7 @@
   "id": "mCODEPatientExample01",
   "meta": {
     "profile": [
-      "http://hl7.org/fhir/us/shr/StructureDefinition/shr-core-Patient"
+      "http://hl7.org/fhir/us/mcode/StructureDefinition/obf-Patient"
     ]
   },
   "text": {

diff --git a/spec/Examples_mCODE/mCODEPractitionerExample01.json b/spec/Examples_mCODE/mCODEPractitionerExample01.json
@@ -3,7 +3,7 @@
   "id": "mCODEPractitionerExample01",
   "meta": {
     "profile": [
-      "http://hl7.org/fhir/us/shr/StructureDefinition/shr-core-Practitioner"
+      "http://hl7.org/fhir/us/mcode/StructureDefinition/obf-Practitioner"
     ]
   },
   "text": {

diff --git a/spec/Examples_mCODE/mCODEPrimaryCancerConditionExample01.json b/spec/Examples_mCODE/mCODEPrimaryCancerConditionExample01.json
@@ -3,7 +3,7 @@
   "id": "mCODEPrimaryCancerConditionExample01",
   "meta": {
     "profile": [
-      "http://hl7.org/fhir/us/shr/StructureDefinition/onco-core-PrimaryCancerCondition"
+      "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-PrimaryCancerCondition"
     ]
   },
   "text": {
@@ -42,11 +42,11 @@
   "onsetDateTime": "2019-04-01",
   "extension": [
     {
-      "url": "http://hl7.org/fhir/us/shr/StructureDefinition/shr-core-DateOfDiagnosis-extension",
+      "url": "http://hl7.org/fhir/us/mcode/StructureDefinition/obf-DateOfDiagnosis-extension",
       "valueDate": "2019-04-01"
     },
     {
-      "url": "http://hl7.org/fhir/us/shr/StructureDefinition/onco-core-HistologyMorphologyBehavior-extension",
+      "url": "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-HistologyMorphologyBehavior-extension",
       "valueCodeableConcept": {
         "coding": [
           {
@@ -84,7 +84,7 @@
       ],
       "extension": [
         {
-            "url": "http://hl7.org/fhir/us/shr/StructureDefinition/shr-core-Laterality-extension",
+            "url": "http://hl7.org/fhir/us/mcode/StructureDefinition/obf-Laterality-extension",
             "valueCodeableConcept": {
             "coding": [ 
               {

diff --git a/spec/Examples_mCODE/mCODETNMClinicalDistantMetastasesCategoryExample01.json b/spec/Examples_mCODE/mCODETNMClinicalDistantMetastasesCategoryExample01.json
@@ -3,7 +3,7 @@
   "id": "mCODETNMClinicalDistantMetastasesCategoryExample01",
   "meta": {
     "profile": [
-      "http://hl7.org/fhir/us/shr/StructureDefinition/onco-core-TNMClinicalDistantMetastasesCategory"
+      "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-TNMClinicalDistantMetastasesCategory"
     ]
   },
   "text": {
@@ -49,7 +49,7 @@
   },
   "extension": [
     {
-        "url": "http://hl7.org/fhir/us/shr/StructureDefinition/onco-core-PrimaryCancerCondition-extension",
+        "url": "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-PrimaryCancerCondition-extension",
         "valueReference": "Condition/mCODEPrimaryCancerConditionExample01"
     }
   ]

diff --git a/spec/Examples_mCODE/mCODETNMClinicalPrimaryTumorCategoryExample01.json b/spec/Examples_mCODE/mCODETNMClinicalPrimaryTumorCategoryExample01.json
@@ -3,7 +3,7 @@
   "id": "mCODETNMClinicalPrimaryTumorCategoryExample01",
   "meta": {
     "profile": [
-      "http://hl7.org/fhir/us/shr/StructureDefinition/onco-core-TNMClinicalPrimaryTumorCategory"
+      "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-TNMClinicalPrimaryTumorCategory"
     ]
   },
   "text": {
@@ -49,7 +49,7 @@
   },
   "extension": [
     {
-        "url": "http://hl7.org/fhir/us/shr/StructureDefinition/onco-core-PrimaryCancerCondition-extension",
+        "url": "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-PrimaryCancerCondition-extension",
         "valueReference": "Condition/mCODEPrimaryCancerConditionExample01"
     }
   ]

diff --git a/spec/Examples_mCODE/mCODETNMClinicalRegionalNodesCategoryExample01.json b/spec/Examples_mCODE/mCODETNMClinicalRegionalNodesCategoryExample01.json
@@ -3,7 +3,7 @@
   "id": "mCODETNMClinicalRegionalNodesCategoryExample01",
   "meta": {
     "profile": [
-      "http://hl7.org/fhir/us/shr/StructureDefinition/onco-core-TNMClinicalRegionalNodesCategory"
+      "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-TNMClinicalRegionalNodesCategory"
     ]
   },
   "text": {
@@ -50,7 +50,7 @@
   },
   "extension": [
     {
-        "url": "http://hl7.org/fhir/us/shr/StructureDefinition/onco-core-PrimaryCancerCondition-extension",
+        "url": "http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-PrimaryCancerCondition-extension",
         "valueReference": "Condition/mCODEPrimaryCancerConditionExample01"
     }
   ]

diff --git a/spec/IndexFolder_Oncocore/implementation.html b/spec/IndexFolder_Oncocore/implementation.html
@@ -1,4 +1,4 @@
-<h1><a name="#Implementation"></a>Appendix A: Technical  Implementation Notes</h1>
+<h1><a name="#Implementation"></a>Appendix A: Technical Implementation Notes</h1>
 
 <p>This section contains content specific for FHIR implementers.  This allows for introductory and overview content to be shared among the broader community which includes clinicians, project leaders, and executive decision makers.</p>
 
@@ -61,7 +61,7 @@ <h2><a name="#TerminologyOverview"></a>FHIR Terminology Overview</h2>
 
 <p>This implementation guide supplies terminology bindings drawn primarily from LOINC for "observables", and SNOMED-CT for values, results and findings. When appropriate codes are not available in the preferred vocabulary, alternative vocabularies are used, in the following order of preference: SNOMED-CT (if the element is an observable), NCI Thesaurus and Metathesaurus, and local codes.</P>
 
-<p>Value sets from the FHIR specification are reused to the extent possible. In addition to the FHIR shr.base specification (DSTU2, DSTU3 and R4), Argonaut Data Query Implementation Guide, and the US Core Implementation Guide were also considered.</p>
+<p>Value sets from the FHIR specification are reused to the extent possible. In addition, Argonaut Data Query Implementation Guide, and the US Core Implementation Guide were also used when necessary.</p>
 
 <p>There may be differences across these specifications in the value sets used, as well as binding strength. This guide addresses these discrepancies by using the lowest common denominator amongst the specifications. This approach is not without challenges, as there cases where different value sets are required by different specifications, which leaves no choice but to opt for one value set over another.</p>
 

diff --git a/spec/LandingPageBreastCancer.html b/spec/LandingPageBreastCancer.html
@@ -47,7 +47,7 @@ <h2><a name="Contents"></a>Implementation Guide Contents</h2>
 </ul>
 </li>
 <li><a href="profiles.html">FHIR Profiles</a>. With logical models in place, they can be mapped to FHIR resources. This step requires more knowledge of FHIR than the logical model step. The result is a set of FHIR profiles, which are FHIR Resources that have been shaped (constrained and extended) to match the intent of the logical models. Similar to the Logical Models, the profiles have been separated into "Primary profiles" and "Supporting profiles".</li>
-<li><a href="extensions.html">Extensions</a>. Extensions are new properties/attributes that do not appear in the shr.base FHIR resources, which are needed to create a FHIR profile. An attempt has been made to minimize the number of extensions appearing in this IG by using Observation.component to represent dependent parts of observations, such as MitoticCountScore and TubuleFormationScore in HistologicGrade.</li>
+<li><a href="extensions.html">Extensions</a>. Extensions are new properties/attributes that do not appear in FHIR resources, which are needed to create a FHIR profile. An attempt has been made to minimize the number of extensions appearing in this IG by using Observation.component to represent dependent parts of observations, such as MitoticCountScore and TubuleFormationScore in HistologicGrade.</li>
 <li><a href="valuesets.html">Value Sets</a>. Value sets are the enumeration of values for coded attribues. Due to copyright restrictions on AJCC-derived content, certain critical value sets have been redacted, diminishing the usefulness of this specification.</li>
 <li><a href="codesystems.html">Code Systems</a>. All value sets require a code system. Value sets that are not drawn from standard terminology, such as locally-defined value sets, do not have a natural code system. FHIR overcomes this by generating a custom code system for each locally-defined value set.</li>
 <li><a href="downloads.html">Downloads</a>. Formal class definitions, in StructureDefinition form, can be downloaded here.</li>

diff --git a/spec/LandingPageObf.html b/spec/LandingPageObf.html
@@ -0,0 +1,36 @@
+<p>
+  This is a preliminary version of the Objective FHIR Core Module Implementation Guide, based on Health Level 7 (HL7) Fast Healthcare Interoperability Resources (FHIR).<br/>
+</p>
+<h2>Background</h2>
+<p>
+The goal of the Standard Health Record (SHR) Collaborative is to provide a high quality, computable source of patient information by establishing FHIR implementation guides (IG) in a number of high-impact clinical areas. SHR has an explicit goal of promoting semantic interoperability by creating horizontally consistent IGs that share common data structures and profiles. This goal is realized though unique distributed modeling environment and tooling that allows multiple projects to share the same basic logical model framework, which is then automatically converted into FHIR.</p>
+<p>SHR standards are intended to encourage and facilitate reliable and repeatable collection and aggregation of a wide range of patient-focused data. Through the SHR, we realize greater transparency, empowerment, and clinical interoperability that supports patients, caregivers, clinicians, researchers, scientists, and public health organizations.</p> 
+<p>
+For more information see the <a href="http://standardhealthrecord.org">Standard Health Record Collaborative <img style="text-align: baseline" src="external.png" /></a>.
+</p>
+
+<h2>The Objective FHIR Module</h2>
+<p>
+Objective FHIR ("obf") is the basis for all SHR-based profiles and implementation guides. It contains class definitions that are used across all clinically-focused modules. These definitions are closely aligned to FHIR, but exist in an object-oriented class hierarchy. Using the CIMPL language, the user can extend that hierarchy using class-based inheritance, specialization, extension, and constraints -- paralleling the capabilities of FHIR profiling. Objective FHIR provides far greater consistency, abstraction, inheritance, and re-use than any other FHIR-based environment.
+</p>
+<p>
+OBF can be described as an <b>object-oriented version of FHIR</b>. The classes closely correspond to FHIR R4, but they differ in carefully considered ways that increase consistency and reusability. Attribute names in OBF may differ from FHIR (usually in obvious ways). OBF names are chosen so they are meaningful outside of the context of a single class. Hypothetically, an attribute named 'date' in a FHIR resource lacks context (date of what?); so to be reusable, we might rename it OccurrenceDate, if it represence the date of occurrence of some event.
+</p>
+
+<p><b>
+    <a href="modeldoc.html">BROWSE THE OBJECTIVE FHIR CORE CLASS HIERARCHY</a> or <a href="logical.html">SEE THE EQUIVALENT FHIR LOGICAL MODEL</a>.
+    </b></p>
+
+<p>
+In addition, FHIR attribute names sometimes change from one FHIR version to the next. Objective FHIR protects you from these changes. By using Objective FHIR, naming is independent of the FHIR version. You model in one environment, and CIMPL tooling automatically translates to all the major releases of FHIR (DSTU2, STU3, and R4). The DSTU2 version is fully compatible with Argonaut Data Query Implementation Guide Version 1.0.0; the STU3 version is fully compatible with US Core Implementation Guide STU 2 (which is based on FHIR STU3).
+</p>
+<p><b>
+<a href="profiles.html">SEE THE OBJECTIVE FHIR CORE PROFILES</a>
+</b></p>
+
+<p>
+The other intentional divergence from FHIR is designed to achieve greater consistency and clinical accuracy. For example, in FHIR R4, of 148 resources, 30 resources lack an identifier attribute, only 101 have a status attribute, and only 23 have an author. In OBF, through the use of class inheritance, we assure that the right attributes appear consistently on the right classes.
+</p>
+<p>
+This IG defines FHIR profiles, extensions, value sets, and code systems necessary to implement other IGs based on Objective FHIR. The profiles in this IG are based on FHIR R4, but equivalent profiles consistent with DSTU 2 and STU 3 are easy to produce.
+</p>