ResourceType added for ResearchSubject, TNM Cat, and Staging templates

julianxcarter · julianxcarter · commit a52c716ac070 · 2021-01-22T13:45:18.000-05:00
diff --git a/src/templates/ResearchSubjectTemplate.js b/src/templates/ResearchSubjectTemplate.js
@@ -14,7 +14,7 @@ function studyTemplate(trialResearchID) {
 function individualTemplate(patientId) {
   return {
     individual: {
-      ...reference({ id: patientId }),
+      ...reference({ id: patientId, resourceType: 'Patient' }),
     },
   };
 }
diff --git a/src/templates/StagingTemplate.js b/src/templates/StagingTemplate.js
@@ -25,7 +25,7 @@ function hasMemberTemplate(categoryIds) {
   if (!categoryIds || categoryIds.length === 0) return {};
 
   return {
-    hasMember: categoryIds.map((id) => reference({ id })),
+    hasMember: categoryIds.map((id) => reference({ id, resourceType: 'Observation' })),
   };
 }
 
@@ -75,10 +75,10 @@ function stagingTemplate({
       ],
     },
     ...stagingMethodTemplate({ code: stagingSystem, system: stagingCodeSystem }),
-    subject: reference({ id: subjectId }),
+    subject: reference({ id: subjectId, resourceType: 'Patient' }),
     effectiveDateTime,
     ...valueX({ code: stageGroup, system: 'http://cancerstaging.org' }, 'valueCodeableConcept'),
-    focus: [reference({ id: conditionId })],
+    focus: [reference({ id: conditionId, resourceType: 'Condition' })],
     ...hasMemberTemplate(categoryIds),
   };
 }
diff --git a/src/templates/TNMCategoryTemplate.js b/src/templates/TNMCategoryTemplate.js
@@ -98,11 +98,11 @@ function tnmCategoryTemplate({
         }),
       ],
     },
-    subject: reference({ id: subjectId }),
+    subject: reference({ id: subjectId, resourceType: 'Patient' }),
     ...stagingMethodTemplate({ code: stagingSystem, system: stagingCodeSystem }),
     effectiveDateTime,
     ...valueX({ code: valueCode, system: 'http://cancerstaging.org' }, 'valueCodeableConcept'),
-    focus: [reference({ id: conditionId })],
+    focus: [reference({ id: conditionId, resourceType: 'Condition' })],
   };
 }
 
diff --git a/test/extractors/fixtures/csv-clinical-trial-information-bundle.json b/test/extractors/fixtures/csv-clinical-trial-information-bundle.json
@@ -21,7 +21,7 @@
             "value": "example-researchId"
           }
         },
-        "individual": { "reference": "urn:uuid:EXAMPLE-MRN" }
+        "individual": { "reference": "urn:uuid:EXAMPLE-MRN", "type": "Patient" }
       }
     },
     {
diff --git a/test/extractors/fixtures/csv-staging-bundle.json b/test/extractors/fixtures/csv-staging-bundle.json
@@ -32,7 +32,8 @@
           ]
         },
         "subject": {
-          "reference": "urn:uuid:pat-mrn-1"
+          "reference": "urn:uuid:pat-mrn-1",
+          "type": "Patient"
         },
         "method": {
           "coding": [
@@ -53,7 +54,8 @@
         },
         "focus": [
           {
-            "reference": "urn:uuid:cond-1"
+            "reference": "urn:uuid:cond-1",
+            "type": "Condition"
           }
         ]
       }
@@ -88,7 +90,8 @@
           ]
         },
         "subject": {
-          "reference": "urn:uuid:pat-mrn-1"
+          "reference": "urn:uuid:pat-mrn-1",
+          "type": "Patient"
         },
         "method": {
           "coding": [
@@ -109,7 +112,8 @@
         },
         "focus": [
           {
-            "reference": "urn:uuid:cond-1"
+            "reference": "urn:uuid:cond-1",
+            "type": "Condition"
           }
         ]
       }
@@ -144,7 +148,8 @@
           ]
         },
         "subject": {
-          "reference": "urn:uuid:pat-mrn-1"
+          "reference": "urn:uuid:pat-mrn-1",
+          "type": "Patient"
         },
         "method": {
           "coding": [
@@ -165,7 +170,8 @@
         },
         "focus": [
           {
-            "reference": "urn:uuid:cond-1"
+            "reference": "urn:uuid:cond-1",
+            "type": "Condition"
           }
         ]
       }
@@ -208,7 +214,8 @@
           ]
         },
         "subject": {
-          "reference": "urn:uuid:pat-mrn-1"
+          "reference": "urn:uuid:pat-mrn-1",
+          "type": "Patient"
         },
         "effectiveDateTime": "2020-01-01",
         "valueCodeableConcept": {
@@ -221,18 +228,22 @@
         },
         "focus": [
           {
-            "reference": "urn:uuid:cond-1"
+            "reference": "urn:uuid:cond-1",
+            "type": "Condition"
           }
         ],
         "hasMember": [
           {
-            "reference": "urn:uuid:ed5faf7f2a1cef061d7584afd463e60eb7202104700647e92fbb7c9419eb7897"
+            "reference": "urn:uuid:ed5faf7f2a1cef061d7584afd463e60eb7202104700647e92fbb7c9419eb7897",
+            "type": "Observation"
           },
           {
-            "reference": "urn:uuid:88992af10e3a822f2a946628de91012d5afae49a25d1641db09e9d6ed4ca24c3"
+            "reference": "urn:uuid:88992af10e3a822f2a946628de91012d5afae49a25d1641db09e9d6ed4ca24c3",
+            "type": "Observation"
           },
           {
-            "reference": "urn:uuid:1373d3fb234cad0b03912cfbba16bdc4eabbd6217d83b838f6d9c1343bc9b394"
+            "reference": "urn:uuid:1373d3fb234cad0b03912cfbba16bdc4eabbd6217d83b838f6d9c1343bc9b394",
+            "type": "Observation"
           }
         ]
       }
diff --git a/test/templates/fixtures/maximal-staging-resource.json b/test/templates/fixtures/maximal-staging-resource.json
@@ -34,7 +34,8 @@
     ]
   },
   "subject": {
-    "reference": "urn:uuid:example-mrn"
+    "reference": "urn:uuid:example-mrn",
+    "type": "Patient"
   },
   "effectiveDateTime": "2020-01-01",
   "valueCodeableConcept": {
@@ -47,18 +48,22 @@
   },
   "focus": [
     {
-      "reference": "urn:uuid:example-condition-id"
+      "reference": "urn:uuid:example-condition-id",
+      "type": "Condition"
     }
   ],
   "hasMember": [
     {
-      "reference": "urn:uuid:t-category-id"
+      "reference": "urn:uuid:t-category-id",
+      "type": "Observation"
     },
     {
-      "reference": "urn:uuid:n-category-id"
+      "reference": "urn:uuid:n-category-id",
+      "type": "Observation"
     },
     {
-      "reference": "urn:uuid:m-category-id"
+      "reference": "urn:uuid:m-category-id",
+      "type": "Observation"
     }
   ]
 }
diff --git a/test/templates/fixtures/metastases-category-clinical-resource.json b/test/templates/fixtures/metastases-category-clinical-resource.json
@@ -26,7 +26,8 @@
     ]
   },
   "subject": {
-    "reference": "urn:uuid:example-mrn"
+    "reference": "urn:uuid:example-mrn",
+    "type": "Patient"
   },
   "effectiveDateTime": "2020-01-01",
   "valueCodeableConcept": {
@@ -39,7 +40,8 @@
   },
   "focus": [
     {
-      "reference": "urn:uuid:example-condition-id"
+      "reference": "urn:uuid:example-condition-id",
+      "type": "Condition"
     }
   ]
 }
diff --git a/test/templates/fixtures/metastases-category-pathologic-resource.json b/test/templates/fixtures/metastases-category-pathologic-resource.json
@@ -26,7 +26,8 @@
     ]
   },
   "subject": {
-    "reference": "urn:uuid:example-mrn"
+    "reference": "urn:uuid:example-mrn",
+    "type": "Patient"
   },
   "effectiveDateTime": "2020-01-01",
   "valueCodeableConcept": {
@@ -39,7 +40,8 @@
   },
   "focus": [
     {
-      "reference": "urn:uuid:example-condition-id"
+      "reference": "urn:uuid:example-condition-id",
+      "type": "Condition"
     }
   ]
 }
diff --git a/test/templates/fixtures/minimal-staging-clinical-resource.json b/test/templates/fixtures/minimal-staging-clinical-resource.json
@@ -26,7 +26,8 @@
     ]
   },
   "subject": {
-    "reference": "urn:uuid:example-mrn"
+    "reference": "urn:uuid:example-mrn",
+    "type": "Patient"
   },
   "effectiveDateTime": "2020-01-01",
   "valueCodeableConcept": {
@@ -39,7 +40,8 @@
   },
   "focus": [
     {
-      "reference": "urn:uuid:example-condition-id"
+      "reference": "urn:uuid:example-condition-id",
+      "type": "Condition"
     }
   ]
 }
diff --git a/test/templates/fixtures/minimal-staging-pathologic-resource.json b/test/templates/fixtures/minimal-staging-pathologic-resource.json
@@ -26,7 +26,8 @@
     ]
   },
   "subject": {
-    "reference": "urn:uuid:example-mrn"
+    "reference": "urn:uuid:example-mrn",
+    "type": "Patient"
   },
   "effectiveDateTime": "2020-01-01",
   "valueCodeableConcept": {
@@ -39,7 +40,8 @@
   },
   "focus": [
     {
-      "reference": "urn:uuid:example-condition-id"
+      "reference": "urn:uuid:example-condition-id",
+      "type": "Condition"
     }
   ]
 }
diff --git a/test/templates/fixtures/nodes-category-clinical-resource.json b/test/templates/fixtures/nodes-category-clinical-resource.json
@@ -26,7 +26,8 @@
     ]
   },
   "subject": {
-    "reference": "urn:uuid:example-mrn"
+    "reference": "urn:uuid:example-mrn",
+    "type": "Patient"
   },
   "effectiveDateTime": "2020-01-01",
   "valueCodeableConcept": {
@@ -39,7 +40,8 @@
   },
   "focus": [
     {
-      "reference": "urn:uuid:example-condition-id"
+      "reference": "urn:uuid:example-condition-id",
+      "type": "Condition"
     }
   ]
 }
diff --git a/test/templates/fixtures/nodes-category-pathologic-resource.json b/test/templates/fixtures/nodes-category-pathologic-resource.json
@@ -26,7 +26,8 @@
     ]
   },
   "subject": {
-    "reference": "urn:uuid:example-mrn"
+    "reference": "urn:uuid:example-mrn",
+    "type": "Patient"
   },
   "effectiveDateTime": "2020-01-01",
   "valueCodeableConcept": {
@@ -39,7 +40,8 @@
   },
   "focus": [
     {
-      "reference": "urn:uuid:example-condition-id"
+      "reference": "urn:uuid:example-condition-id",
+      "type": "Condition"
     }
   ]
 }
diff --git a/test/templates/fixtures/tumor-category-clinical-resource.json b/test/templates/fixtures/tumor-category-clinical-resource.json
@@ -26,7 +26,8 @@
     ]
   },
   "subject": {
-    "reference": "urn:uuid:example-mrn"
+    "reference": "urn:uuid:example-mrn",
+    "type": "Patient"
   },
   "effectiveDateTime": "2020-01-01",
   "valueCodeableConcept": {
@@ -39,7 +40,8 @@
   },
   "focus": [
     {
-      "reference": "urn:uuid:example-condition-id"
+      "reference": "urn:uuid:example-condition-id",
+      "type": "Condition"
     }
   ]
 }
diff --git a/test/templates/fixtures/tumor-category-pathologic-resource.json b/test/templates/fixtures/tumor-category-pathologic-resource.json
@@ -26,7 +26,8 @@
     ]
   },
   "subject": {
-    "reference": "urn:uuid:example-mrn"
+    "reference": "urn:uuid:example-mrn",
+    "type": "Patient"
   },
   "effectiveDateTime": "2020-01-01",
   "valueCodeableConcept": {
@@ -39,7 +40,8 @@
   },
   "focus": [
     {
-      "reference": "urn:uuid:example-condition-id"
+      "reference": "urn:uuid:example-condition-id",
+      "type": "Condition"
     }
   ]
 }

Original file line number	Diff line number	Diff line change
`@@ -14,7 +14,7 @@ function studyTemplate(trialResearchID) {`
`14`	`14`	`function individualTemplate(patientId) {`
`15`	`15`	`return {`
`16`	`16`	`individual: {`
`17`		`- ...reference({ id: patientId }),`
	`17`	`+ ...reference({ id: patientId, resourceType: 'Patient' }),`
`18`	`18`	`},`
`19`	`19`	`};`
`20`	`20`	`}`
Original file line number	Diff line number	Diff line change
`@@ -21,7 +21,7 @@`
`21`	`21`	`"value": "example-researchId"`
`22`	`22`	`}`
`23`	`23`	`},`
`24`		`- "individual": { "reference": "urn:uuid:EXAMPLE-MRN" }`
	`24`	`+ "individual": { "reference": "urn:uuid:EXAMPLE-MRN", "type": "Patient" }`
`25`	`25`	`}`
`26`	`26`	`},`
`27`	`27`	`{`
Original file line number	Diff line number	Diff line change
`@@ -32,7 +32,8 @@`
`32`	`32`	`]`
`33`	`33`	`},`
`34`	`34`	`"subject": {`
`35`		`- "reference": "urn:uuid:pat-mrn-1"`
	`35`	`+ "reference": "urn:uuid:pat-mrn-1",`
	`36`	`+ "type": "Patient"`
`36`	`37`	`},`
`37`	`38`	`"method": {`
`38`	`39`	`"coding": [`
`@@ -53,7 +54,8 @@`
`53`	`54`	`},`
`54`	`55`	`"focus": [`
`55`	`56`	`{`
`56`		`- "reference": "urn:uuid:cond-1"`
	`57`	`+ "reference": "urn:uuid:cond-1",`
	`58`	`+ "type": "Condition"`
`57`	`59`	`}`
`58`	`60`	`]`
`59`	`61`	`}`
`@@ -88,7 +90,8 @@`
`88`	`90`	`]`
`89`	`91`	`},`
`90`	`92`	`"subject": {`
`91`		`- "reference": "urn:uuid:pat-mrn-1"`
	`93`	`+ "reference": "urn:uuid:pat-mrn-1",`
	`94`	`+ "type": "Patient"`
`92`	`95`	`},`
`93`	`96`	`"method": {`
`94`	`97`	`"coding": [`
`@@ -109,7 +112,8 @@`
`109`	`112`	`},`
`110`	`113`	`"focus": [`
`111`	`114`	`{`
`112`		`- "reference": "urn:uuid:cond-1"`
	`115`	`+ "reference": "urn:uuid:cond-1",`
	`116`	`+ "type": "Condition"`
`113`	`117`	`}`
`114`	`118`	`]`
`115`	`119`	`}`
`@@ -144,7 +148,8 @@`
`144`	`148`	`]`
`145`	`149`	`},`
`146`	`150`	`"subject": {`
`147`		`- "reference": "urn:uuid:pat-mrn-1"`
	`151`	`+ "reference": "urn:uuid:pat-mrn-1",`
	`152`	`+ "type": "Patient"`
`148`	`153`	`},`
`149`	`154`	`"method": {`
`150`	`155`	`"coding": [`
`@@ -165,7 +170,8 @@`
`165`	`170`	`},`
`166`	`171`	`"focus": [`
`167`	`172`	`{`
`168`		`- "reference": "urn:uuid:cond-1"`
	`173`	`+ "reference": "urn:uuid:cond-1",`
	`174`	`+ "type": "Condition"`
`169`	`175`	`}`
`170`	`176`	`]`
`171`	`177`	`}`
`@@ -208,7 +214,8 @@`
`208`	`214`	`]`
`209`	`215`	`},`
`210`	`216`	`"subject": {`
`211`		`- "reference": "urn:uuid:pat-mrn-1"`
	`217`	`+ "reference": "urn:uuid:pat-mrn-1",`
	`218`	`+ "type": "Patient"`
`212`	`219`	`},`
`213`	`220`	`"effectiveDateTime": "2020-01-01",`
`214`	`221`	`"valueCodeableConcept": {`
`@@ -221,18 +228,22 @@`
`221`	`228`	`},`
`222`	`229`	`"focus": [`
`223`	`230`	`{`
`224`		`- "reference": "urn:uuid:cond-1"`
	`231`	`+ "reference": "urn:uuid:cond-1",`
	`232`	`+ "type": "Condition"`
`225`	`233`	`}`
`226`	`234`	`],`
`227`	`235`	`"hasMember": [`
`228`	`236`	`{`
`229`		`- "reference": "urn:uuid:ed5faf7f2a1cef061d7584afd463e60eb7202104700647e92fbb7c9419eb7897"`
	`237`	`+ "reference": "urn:uuid:ed5faf7f2a1cef061d7584afd463e60eb7202104700647e92fbb7c9419eb7897",`
	`238`	`+ "type": "Observation"`
`230`	`239`	`},`
`231`	`240`	`{`
`232`		`- "reference": "urn:uuid:88992af10e3a822f2a946628de91012d5afae49a25d1641db09e9d6ed4ca24c3"`
	`241`	`+ "reference": "urn:uuid:88992af10e3a822f2a946628de91012d5afae49a25d1641db09e9d6ed4ca24c3",`
	`242`	`+ "type": "Observation"`
`233`	`243`	`},`
`234`	`244`	`{`
`235`		`- "reference": "urn:uuid:1373d3fb234cad0b03912cfbba16bdc4eabbd6217d83b838f6d9c1343bc9b394"`
	`245`	`+ "reference": "urn:uuid:1373d3fb234cad0b03912cfbba16bdc4eabbd6217d83b838f6d9c1343bc9b394",`
	`246`	`+ "type": "Observation"`
`236`	`247`	`}`
`237`	`248`	`]`
`238`	`249`	`}`
Original file line number	Diff line number	Diff line change
`@@ -34,7 +34,8 @@`
`34`	`34`	`]`
`35`	`35`	`},`
`36`	`36`	`"subject": {`
`37`		`- "reference": "urn:uuid:example-mrn"`
	`37`	`+ "reference": "urn:uuid:example-mrn",`
	`38`	`+ "type": "Patient"`
`38`	`39`	`},`
`39`	`40`	`"effectiveDateTime": "2020-01-01",`
`40`	`41`	`"valueCodeableConcept": {`
`@@ -47,18 +48,22 @@`
`47`	`48`	`},`
`48`	`49`	`"focus": [`
`49`	`50`	`{`
`50`		`- "reference": "urn:uuid:example-condition-id"`
	`51`	`+ "reference": "urn:uuid:example-condition-id",`
	`52`	`+ "type": "Condition"`
`51`	`53`	`}`
`52`	`54`	`],`
`53`	`55`	`"hasMember": [`
`54`	`56`	`{`
`55`		`- "reference": "urn:uuid:t-category-id"`
	`57`	`+ "reference": "urn:uuid:t-category-id",`
	`58`	`+ "type": "Observation"`
`56`	`59`	`},`
`57`	`60`	`{`
`58`		`- "reference": "urn:uuid:n-category-id"`
	`61`	`+ "reference": "urn:uuid:n-category-id",`
	`62`	`+ "type": "Observation"`
`59`	`63`	`},`
`60`	`64`	`{`
`61`		`- "reference": "urn:uuid:m-category-id"`
	`65`	`+ "reference": "urn:uuid:m-category-id",`
	`66`	`+ "type": "Observation"`
`62`	`67`	`}`
`63`	`68`	`]`
`64`	`69`	`}`
Original file line number	Diff line number	Diff line change
`@@ -26,7 +26,8 @@`
`26`	`26`	`]`
`27`	`27`	`},`
`28`	`28`	`"subject": {`
`29`		`- "reference": "urn:uuid:example-mrn"`
	`29`	`+ "reference": "urn:uuid:example-mrn",`
	`30`	`+ "type": "Patient"`
`30`	`31`	`},`
`31`	`32`	`"effectiveDateTime": "2020-01-01",`
`32`	`33`	`"valueCodeableConcept": {`
`@@ -39,7 +40,8 @@`
`39`	`40`	`},`
`40`	`41`	`"focus": [`
`41`	`42`	`{`
`42`		`- "reference": "urn:uuid:example-condition-id"`
	`43`	`+ "reference": "urn:uuid:example-condition-id",`
	`44`	`+ "type": "Condition"`
`43`	`45`	`}`
`44`	`46`	`]`
`45`	`47`	`}`