Merge pull request #49 from mcode/convert-tnm-to-staging

Add API to convert TNM values to a cancer stage number

TNM Staging.md

@@ -0,0 +1,23 @@
+# Converting TNM to a Staging Value
+
+The current algorithm for determining the numeric staging algorithm is based on
+the [TNM classification](https://www.ncbi.nlm.nih.gov/books/NBK553187/) and
+works as follows:
+
+1. If M is 1, staging is 4. Skip remaining steps.
+2. If N is greater than 0, staging is 3. Skip remaining steps.
+3. If T is greater than 2, staging is 2. Skip remaining steps.
+4. If T is 1, staging is 1. Skip remaining steps.
+5. If T is "is" (in situ), staging is 0. Skip remaining steps.
+6. Otherwise, the value is T0 N0 M0 which is effectively "no cancer." This has no corresponding staging, so staging is `null`.
+
+This breaks down as follows:
+
+| T      | N          | M  | Staging |
+|--------|------------|----|---------|
+| T0     | N0         | M0 | `null`  |
+| Tis    | N0         | M0 | 0       |
+| T1, T2 | N0         | M0 | 1       |
+| T3, T4 | N0         | M0 | 2       |
+| (any)  | N1, N2, N3 | M0 | 3       |
+| (any)  | (any)      | M1 | 4       |

spec/fhir-util.spec.ts

@@ -1,5 +1,11 @@
 import { FhirResource } from 'fhir/r4';
-import { FHIRDate, FHIRDateAccuracy, resourceContainsProfile } from '../src/fhir-util';
+import {
+  FHIRDate,
+  FHIRDateAccuracy,
+  codeableConceptContains,
+  codeableConceptContainsCode,
+  resourceContainsProfile
+} from '../src/fhir-util';
 
 describe('#resourceContainsProfile', () => {
   it('handles resources with no meta', () => {
@@ -117,3 +123,145 @@ describe('FHIRDate', () => {
     });
   });
 });
+
+describe('codeableConceptContains', () => {
+  // Simple test set
+  const CODE_SET = { '1_2': ['1', '2'], '3_4': ['3', '4'] };
+  it('handles a codeable concept with no codes', () => {
+    expect(codeableConceptContains({}, CODE_SET)).toBeFalse();
+  });
+  it('returns false for codes in the other system', () => {
+    expect(
+      codeableConceptContains(
+        {
+          coding: [
+            {
+              system: '1_2',
+              code: '3'
+            },
+            {
+              system: '3_4',
+              code: '1'
+            }
+          ]
+        },
+        CODE_SET
+      )
+    ).toBeFalse();
+  });
+  it('handles partial codes', () => {
+    expect(
+      codeableConceptContains(
+        {
+          coding: [
+            {
+              code: '1'
+            },
+            {
+              system: '3_4'
+            }
+          ]
+        },
+        CODE_SET
+      )
+    ).toBeFalse();
+  });
+  it('returns true for codes that exist', () => {
+    expect(
+      codeableConceptContains(
+        {
+          coding: [
+            {
+              system: 'ignore me',
+              code: 'code'
+            },
+            {
+              system: '3_4',
+              code: '4'
+            }
+          ]
+        },
+        CODE_SET
+      )
+    ).toBeTrue();
+  });
+});
+
+describe('codeableConceptContainsCode', () => {
+  // Simple test set
+  const SYSTEM = '1_2';
+  const CODE_SET = ['1', '2'];
+  it('handles a codeable concept with no codes', () => {
+    expect(codeableConceptContainsCode({}, SYSTEM, CODE_SET)).toBeFalse();
+  });
+  it("returns false for codes that don't exist", () => {
+    expect(
+      codeableConceptContainsCode(
+        {
+          coding: [
+            {
+              system: '1_2',
+              code: '3'
+            }
+          ]
+        },
+        SYSTEM,
+        CODE_SET
+      )
+    ).toBeFalse();
+  });
+  it('returns false for codes in another system', () => {
+    expect(
+      codeableConceptContainsCode(
+        {
+          coding: [
+            {
+              system: '3_4',
+              code: '1'
+            }
+          ]
+        },
+        SYSTEM,
+        CODE_SET
+      )
+    ).toBeFalse();
+  });
+  it('handles partial codes', () => {
+    expect(
+      codeableConceptContainsCode(
+        {
+          coding: [
+            {
+              code: '1'
+            },
+            {
+              system: '3_4'
+            }
+          ]
+        },
+        SYSTEM,
+        CODE_SET
+      )
+    ).toBeFalse();
+  });
+  it('returns true for codes that exist', () => {
+    expect(
+      codeableConceptContainsCode(
+        {
+          coding: [
+            {
+              system: 'ignore me',
+              code: 'code'
+            },
+            {
+              system: '1_2',
+              code: '2'
+            }
+          ]
+        },
+        SYSTEM,
+        CODE_SET
+      )
+    ).toBeTrue();
+  });
+});