Merge pull request #28 from ncpi-fhir/fix-kids-first-refs

🐛 Fix Kids First References
NIH-NCPI · Aug 7, 2020 · c9a9443 · c9a9443
2 parents 3220939 + befa801
commit c9a9443
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Showing 16 changed files with 46 additions and 41 deletions.
diff --git a/docs/naming_conventions.md b/docs/naming_conventions.md
@@ -37,7 +37,7 @@ Based on observations, the FHIR spec seems to use PascalCase for
 resource types (e.g. `Patient`, `SearchParameter`) and camelCase
 (e.g. `gender`, `birthDate`) for resource attributes.
 
-The Kids First resource `id` values will be lowercased with hyphens between
+The NCPI resource `id` values will be lowercased with hyphens between
 words (e.g. `age-at-event`, `sequencing-experiment`).  
 
 ## Resource File Name
@@ -122,8 +122,8 @@ Patient-pt-001.json
 ## Specific Rules for StructureDefinitions
 
 The following rules apply to non-Extension type `StructureDefinitions` and
-are intended to help Kids First separate the constraints for
-Protected Health Information (PHI) from the constraints in base Kids First
+are intended to help NCPI separate the constraints for
+Protected Health Information (PHI) from the constraints in base NCPI
 profiles.
 
 All `StructureDefinition.id` values will be split into two tokens. The first

diff --git a/ncpi_fhir_utility/app.py b/ncpi_fhir_utility/app.py
@@ -373,7 +373,7 @@ def _update_ig_config(
             continue
 
         # Create the config entry
-        entry = _create_resource_config(rd)
+        entry = _create_resource_config(rd, ig_resource.get("publisher"))
 
         # Add/remove configuration entries
         if add:
@@ -395,13 +395,15 @@ def _update_ig_config(
     )
 
 
-def _create_resource_config(resource_dict):
+def _create_resource_config(resource_dict, publisher=""):
     """
     Create the expected IG configuration entry for a resource
 
     :param resource_dict: The resource payload from which a config entry will
     be created. See ncpi_fhir_utility.loader.load_resources.
     :type resource_dict: dict
+    :param publisher: The value of ImplementationGuide.publisher
+    :type publisher: str
     :returns: IG config entry for the resource
     """
     rid = resource_dict["content"].get("id")
@@ -427,10 +429,13 @@ def _create_resource_config(resource_dict):
         if profiles:
             suffix = f", Profiles: {profiles}"
 
+    if publisher:
+        publisher = publisher + " "
+
     return {
         "reference": {"reference": f"{rtype}/{rid}"},
-        "name": f"Kids First {rtype}/{rid}",
-        "description": f"Kids First {rtype} {rid}{suffix}",
+        "name": f"{publisher}{rtype}/{rid}",
+        "description": f"{publisher}{rtype} {rid}{suffix}",
         "exampleBoolean": is_example,
     }
 

diff --git a/ncpi_fhir_utility/cli.py b/ncpi_fhir_utility/cli.py
@@ -1,5 +1,5 @@
 """
-Entry point for the Kids First FHIR Model CLI which lets users:
+Entry point for the NCPI FHIR Model CLI which lets users:
 
 - Validate FHIR model files (conformance resources, example resources)
 - Convert FHIR model files between xml/json

diff --git a/ncpi_fhir_utility/config.py b/ncpi_fhir_utility/config.py
@@ -73,4 +73,4 @@ def fhir_version_name(fhir_version):
     "stu3": ("torinox-latest", "fhir"),
 }
 
-OUR_URLS = "http://fhir.kids-first.io,https://fhir.kids-first.io"
+OUR_URLS = "http://fhir.ncpi.io,https://fhir.ncpi.io"
diff --git a/tests/data/examples/invalid/Patient-pt-001.json b/tests/data/examples/invalid/Patient-pt-001.json
@@ -2,7 +2,7 @@
     "resourceType":"Patient",
     "id": "participant-example",
     "meta": {
-        "profile": "http://fhir.kids-first.io/StructureDefinition/DoesNotExist"
+        "profile": "http://fhir.ncpi.io/StructureDefinition/DoesNotExist"
     },
     "gender": "female",
     "name": [

diff --git a/tests/data/examples/valid/Patient-pt-001.json b/tests/data/examples/valid/Patient-pt-001.json
@@ -3,7 +3,7 @@
     "id": "pt-001",
     "meta": {
         "profile": [
-            "http://fhir.kids-first.io/StructureDefinition/participant"
+            "http://fhir.ncpi.io/StructureDefinition/participant"
         ]
     },
     "gender": "female",

diff --git a/tests/data/examples/valid/ResearchStudy-rs-001.json b/tests/data/examples/valid/ResearchStudy-rs-001.json
@@ -2,7 +2,7 @@
     "resourceType":"ResearchStudy",
     "id": "rs-001",
     "meta": {
-        "profile": ["http://fhir.kids-first.io/StructureDefinition/study"]
+        "profile": ["http://fhir.ncpi.io/StructureDefinition/study"]
     },
     "status": "completed",
     "title": "Study of Ewing's Sarcoma"

diff --git a/tests/data/extensions/valid/StructureDefinition-proband-status.json b/tests/data/extensions/valid/StructureDefinition-proband-status.json
@@ -1,11 +1,11 @@
 {
     "resourceType":"StructureDefinition",
     "id": "proband-status",
-    "url": "http://fhir.kids-first.io/StructureDefinition/proband-status",
+    "url": "http://fhir.ncpi.io/StructureDefinition/proband-status",
     "name": "Proband status",
     "title": "Participant Proband Status",
     "date": "2019-07-16",
-    "publisher": "Kids First DRC",
+    "publisher": "NCPI DRC",
     "description": "Whether or not the participant is a proband or subject of study in the research study",
     "status":"draft",
     "fhirVersion":"4.0.0",
@@ -31,7 +31,7 @@
             {
                 "id":"Extension.url",
                 "path":"Extension.url",
-                "fixedUri":"http://fhir.kids-first.io/StructureDefinition/proband-status"
+                "fixedUri":"http://fhir.ncpi.io/StructureDefinition/proband-status"
             },
             {
                 "id":"Extension.value[x]:valueBoolean",

diff --git a/tests/data/profiles/invalid/StructureDefinition-Participant.json b/tests/data/profiles/invalid/StructureDefinition-Participant.json
@@ -1,6 +1,6 @@
 {
   "resourceType": "StructureDefinition",
-  "url": "http://fhir.kids-first.io/StructureDefinition/Participant",
+  "url": "http://fhir.ncpi.io/StructureDefinition/Participant",
   "name": "Participant",
   "status": "draft",
   "fhirVersion": "4.0.0",

diff --git a/tests/data/profiles/valid/StructureDefinition-participant.json b/tests/data/profiles/valid/StructureDefinition-participant.json
@@ -1,7 +1,7 @@
 {
   "resourceType": "StructureDefinition",
   "id": "participant",
-  "url": "http://fhir.kids-first.io/StructureDefinition/participant",
+  "url": "http://fhir.ncpi.io/StructureDefinition/participant",
   "name": "Participant",
   "status": "draft",
   "fhirVersion": "4.0.0",

diff --git a/tests/data/profiles/valid/StructureDefinition-study.json b/tests/data/profiles/valid/StructureDefinition-study.json
@@ -1,13 +1,13 @@
 {
     "resourceType": "StructureDefinition",
     "id": "study",
-    "url": "http://fhir.kids-first.io/StructureDefinition/study",
+    "url": "http://fhir.ncpi.io/StructureDefinition/study",
     "version": "0.1.0",
     "name": "ResearchStudy",
     "title": "Research Study",
     "status": "draft",
-    "publisher": "Kids First",
-    "description": "A research study within the Kids First ecosystem",
+    "publisher": "NCPI",
+    "description": "A research study within the NCPI ecosystem",
     "fhirVersion": "4.0.0",
     "kind": "resource",
     "abstract": false,

diff --git a/tests/data/site_root/ig.ini b/tests/data/site_root/ig.ini
@@ -1,5 +1,5 @@
 [IG]
-ig = input/ImplementationGuide-KidsFirst.json
+ig = input/ImplementationGuide-NCPI.json
 template = fhir.base.template
 usage-stats-opt-out = false
 copyrightyear = 2020+

diff --git a/.../input/ImplementationGuide-KidsFirst.json → ..._root/input/ImplementationGuide-NCPI.json b/.../input/ImplementationGuide-KidsFirst.json → ..._root/input/ImplementationGuide-NCPI.json
@@ -1,11 +1,11 @@
 {
     "contact": [
         {
-            "name": "Kids First DRC",
+            "name": "NCPI",
             "telecom": [
                 {
                     "system": "email",
-                    "value": "mailto:support@kidsfirstdrc.org"
+                    "value": "mailto:support@ncpi.org"
                 }
             ]
         }
@@ -18,7 +18,7 @@
                 {
                     "generation": "markdown",
                     "nameUrl": "index.html",
-                    "title": "Kids First Implementation Guide"
+                    "title": "NCPI Implementation Guide"
                 }
             ],
             "title": "Table of Contents"
@@ -55,18 +55,18 @@
         ],
         "resource": []
     },
-    "description": "Documentation for the Kids First FHIR data model",
+    "description": "Documentation for the NCPI FHIR data model",
     "fhirVersion": [
         "4.0.1"
     ],
-    "id": "KidsFirst",
+    "id": "NCPI",
     "license": "CC0-1.0",
-    "name": "KidsFirstImplementationGuide",
-    "packageId": "kidsfirst",
-    "publisher": "Kids First DRC",
+    "name": "NCPIImplementationGuide",
+    "packageId": "ncpi",
+    "publisher": "NCPI",
     "resourceType": "ImplementationGuide",
     "status": "active",
-    "title": "Kids First Implementation Guide",
-    "url": "http://fhir.kids-first.io/ImplementationGuide/KidsFirst",
+    "title": "NCPI Implementation Guide",
+    "url": "http://fhir.ncpi.io/ImplementationGuide/NCPI",
     "version": "0.1.0"
 }
diff --git a/tests/data/site_root/input/pages/index.md b/tests/data/site_root/input/pages/index.md
@@ -1,6 +1,6 @@
 ### Description
 
-The Kids First FHIR Implementation Guide
+The NCPI FHIR Implementation Guide
 
 ### Authors
 

diff --git a/tests/data/site_root/package-list.json b/tests/data/site_root/package-list.json
@@ -1,13 +1,13 @@
 {
   "package-id": "kidsfirst",
-  "title": "KidsFirst Implementation Guide",
-  "canonical": "http://fhir.kids-first.io",
+  "title": "NCPI Implementation Guide",
+  "canonical": "http://fhir.ncpi.io",
   "introduction": "An example of how FSH can be used to create an IG about kidsfirst",
   "list": [
     {
       "version": "current",
       "desc": "Draft",
-      "path": "http://fhir.kids-first.io",
+      "path": "http://fhir.ncpi.io",
       "status": "ci-build",
       "current": true
     }

diff --git a/tests/data/site_root/package.json b/tests/data/site_root/package.json
@@ -1,15 +1,15 @@
 {
   "name": "kidsfirst",
   "version": "0.1.0",
-  "canonical": "http://fhir.kids-first.io",
-  "url": "http://fhir.kids-first.io",
-  "title": "Kids First Implementation Guide",
-  "description": "Documentation for the Kids First FHIR data model",
+  "canonical": "http://fhir.ncpi.io",
+  "url": "http://fhir.ncpi.io",
+  "title": "NCPI Implementation Guide",
+  "description": "Documentation for the NCPI FHIR data model",
   "dependencies": {
     "hl7.fhir.r4.core": "4.0.1"
   },
   "keywords": [
-    "Kids First",
+    "NCPI",
     "NIH",
     "Pediatric"
   ],
@@ -22,4 +22,4 @@
     }
   ],
   "license": "CC0-1.0"
-}
+}