Issue #173 CWE Version & Alternate Coding support

LinuxForHealth · Aug 21, 2021 · 946b2c1 · 946b2c1
1 parent a66a0ee
commit 946b2c1
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Showing 6 changed files with 89 additions and 21 deletions.
diff --git a/src/main/java/io/github/linuxforhealth/core/terminology/SimpleCode.java b/src/main/java/io/github/linuxforhealth/core/terminology/SimpleCode.java
@@ -13,19 +13,29 @@ public class SimpleCode {
   private String system;
   private String code;
   private String display;
+  private String version;
 
   /**
    * Returns simple representation of Code.
    * 
    * @param code
    * @param system
    * @param display
+   * @param version
    */
 
   public SimpleCode(String code, String system, String display) {
     this.code = code;
     this.system = system;
     this.display = display;
+    this.version = null;
+  }
+
+  public SimpleCode(String code, String system, String display, String version) {
+    this.code = code;
+    this.system = system;
+    this.display = display;
+    this.version = version;
   }
 
   public String getSystem() {
@@ -36,12 +46,18 @@ public String getCode() {
     return code;
   }
 
-
-
   public String getDisplay() {
     return display;
   }
 
+  public String getVersion() {
+    return version;
+  }
+
+  public void setVersion(String version) {
+    this.version = version;
+  }
+
   public String toString() {
     return ReflectionToStringBuilder.toString(this);
   }

diff --git a/src/main/java/io/github/linuxforhealth/hl7/data/Hl7DataHandlerUtil.java b/src/main/java/io/github/linuxforhealth/hl7/data/Hl7DataHandlerUtil.java
@@ -95,6 +95,22 @@ public static String getOriginalDisplayText(Object obj) {
         return null;
     }
 
+    public static String getVersion(Object obj) {
+        if (obj instanceof CWE) {
+            CWE id = (CWE) obj;
+            ST st = id.getCodingSystemVersionID();
+            if (st != null) {
+                String str = st.getValue();
+                if (str != null) {
+                    return str.trim();
+                }
+                return null;
+            }
+            return null;
+        }
+        return null;
+    }
+
     private static String getAssociatedtable(CWE id) {
         ID val = id.getCwe3_NameOfCodingSystem();
         if (val != null && StringUtils.startsWith(val.getValue(), "HL7")) {

diff --git a/src/main/java/io/github/linuxforhealth/hl7/data/SimpleDataTypeMapper.java b/src/main/java/io/github/linuxforhealth/hl7/data/SimpleDataTypeMapper.java
@@ -33,6 +33,7 @@ public enum SimpleDataTypeMapper {
   NAMED_UUID(SimpleDataValueResolver.NAMED_UUID),
   OBJECT(SimpleDataValueResolver.OBJECT),
   CODING_SYSTEM_V2(SimpleDataValueResolver.CODING_SYSTEM_V2),
+  CODING_SYSTEM_V2_ALTERNATE(SimpleDataValueResolver.CODING_SYSTEM_V2_ALTERNATE),
   SYSTEM_URL(SimpleDataValueResolver.SYSTEM_URL),
   SYSTEM_ID(SimpleDataValueResolver.SYSTEM_ID),
 

diff --git a/src/main/java/io/github/linuxforhealth/hl7/data/SimpleDataValueResolver.java b/src/main/java/io/github/linuxforhealth/hl7/data/SimpleDataValueResolver.java
@@ -251,10 +251,28 @@ public class SimpleDataValueResolver {
         return value;
     };
 
+    public static final ValueExtractor<Object, SimpleCode> CODING_SYSTEM_V2_ALTERNATE = (Object value) -> {
+        // ensure we have a CWE
+        if (value instanceof CWE) {
+            CWE cwe = (CWE) value;
+            String table = Hl7DataHandlerUtil.getStringValue(cwe.getCwe6_NameOfAlternateCodingSystem());
+            String code = Hl7DataHandlerUtil.getStringValue(cwe.getCwe4_AlternateIdentifier()); 
+            String text = Hl7DataHandlerUtil.getStringValue(cwe.getCwe5_AlternateText());
+            String version = Hl7DataHandlerUtil.getStringValue(cwe.getCwe8_AlternateCodingSystemVersionID());
+            return commonCodingSystemV2(table, code, text, version);
+        } 
+        return null;
+    };
+
     public static final ValueExtractor<Object, SimpleCode> CODING_SYSTEM_V2 = (Object value) -> {
         String table = Hl7DataHandlerUtil.getTableNumber(value);
         String code = Hl7DataHandlerUtil.getStringValue(value);
         String text = Hl7DataHandlerUtil.getOriginalDisplayText(value);
+        String version = Hl7DataHandlerUtil.getVersion(value);
+        return commonCodingSystemV2(table, code, text, version);
+    };
+
+    private static final SimpleCode commonCodingSystemV2 (String table, String code, String text, String version) {
         if (table != null && code != null) {
             // Found table and a code. Try looking it up.
             SimpleCode coding = TerminologyLookup.lookup(table, code);
@@ -265,8 +283,9 @@ public class SimpleDataValueResolver {
 
                     if (display.isEmpty()) {
                         // We have a table, code, but unknown display, so we can't tell if it's good, use the original display text
-                        coding = new SimpleCode(coding.getCode(), coding.getSystem(), text);
+                        coding = new SimpleCode(coding.getCode(), coding.getSystem(), text, version);
                     }
+                    coding.setVersion(version);
                     // We have a table, code, and display, so code was valid
                     return coding;
                 } else {
@@ -276,15 +295,15 @@ public class SimpleDataValueResolver {
                 }
             } else { 
                 // No success looking up the code, build our own fall-back system using table name
-                return new SimpleCode(code, "urn:id:"+table, text) ;
+                return new SimpleCode(code, "urn:id:"+table, text, version) ;
             }
         } else if (code != null) {
             // A code but no system: build a simple systemless code
             return new SimpleCode(code, null, null);
         } else {
             return null;
         }
-    };
+    }
 
     public static final ValueExtractor<Object, String> BUILD_IDENTIFIER_FROM_CWE = (Object value) -> {
         CWE newValue = ((CWE) value);

diff --git a/src/main/resources/hl7/datatype/CodeableConcept.yml b/src/main/resources/hl7/datatype/CodeableConcept.yml
@@ -26,17 +26,14 @@ coding_2:
    vars:
       code: ID |IS |TX
 
+# Generalized CWE for alternate codes handles mismatched systems and codes       
 coding_3:
-   valueOf: datatype/Coding
+   valueOf: $coding
    generateList: true
-   expressionType: resource
-   condition: $code NOT_NULL &&  $coding NULL
+   condition: $coding NOT_NULL
    specs: CWE
    vars:
-      code: CWE.4
-      system: CWE.6
-      display: CWE.5
-      version: CWE.8
+      coding: CODING_SYSTEM_V2_ALTERNATE, CWE          
 
 # Generalized CWE through CODING_SYSTEM_V2 handles mismatched systems and codes      
 coding_4:

diff --git a/src/test/java/io/github/linuxforhealth/hl7/segments/CodeableConceptTest.java b/src/test/java/io/github/linuxforhealth/hl7/segments/CodeableConceptTest.java
@@ -303,37 +303,56 @@ void testCodeableConceptForNDC() {
     }
 
     @Test
-    public void testCodeableConceptForI9() {
+    public void testCodeableConceptForLoincAltenativeI9WithVersions() {
 
-        // With a valid (to us) but unregistered (to FHIR) system, we should produce:
+        // With a valid (to us) but unregistered (to FHIR) system, and with a version, we should produce:
         // "code": {
         //     "coding": [ {
-        //       "system": <known-to-us-system-via-our-lookup>,
+        //       "system": <known-to-us-system-via-our-lookup>,  << FIRST CODING
+        //       "display": <original-display-value>
+        //       "code": <code-from-input>
+        //       "version": <version>        
+        //     },
+        //     {    
+        //       "system": <known-to-us-system-via-our-lookup>,  << SECOND (ALTERNATE CODING)
         //       "display": <original-display-value>
         //       "code": <code-from-input>
+        //       "version": <version>        
         //     } ],
         //     "text": <original-display-value>
         //   },
 
-        String conditionWithCodeableConcept = "MSH|^~\\&|||||20040629164652|1|PPR^PC1|331|P|2.3.1||\n"
+        String conditionWithVersionedAlternateCodeableConcept = "MSH|^~\\&|||||20040629164652|1|PPR^PC1|331|P|2.3.1||\n"
                 + "PID|||1234^^^^MR||DOE^JANE^|||F||||||||||||||||||||||\n"
-                + "PRB|AD|2004062916460000|596.5^BLADDER DYSFUNCTION^I9||||20040629||||||ACTIVE|||20040629";
+                + "PRB|AD|2004062916460000|2148-5^CREATININE^LN^F-11380^CREATININE^I9^474747^22222||||20040629||||||ACTIVE|||20040629";
 
-        Condition condition = ResourceUtils.getCondition(conditionWithCodeableConcept);
+        Condition condition = ResourceUtils.getCondition(conditionWithVersionedAlternateCodeableConcept);
 
         assertThat(condition.hasCode()).isTrue();
         CodeableConcept condCC = condition.getCode();
         assertThat(condCC.hasText()).isTrue();
-        assertThat(condCC.getText()).isEqualTo("BLADDER DYSFUNCTION");
+        assertThat(condCC.getText()).isEqualTo("CREATININE");
         assertThat(condCC.hasCoding()).isTrue();
 
         Coding condCoding = condCC.getCoding().get(0);
         assertThat(condCoding.hasSystem()).isTrue();
+        assertThat(condCoding.getSystem()).isEqualTo("http://loinc.org");
+        assertThat(condCoding.hasCode()).isTrue();
+        assertThat(condCoding.getCode()).isEqualTo("2148-5");
+        assertThat(condCoding.hasDisplay()).isTrue();
+        assertThat(condCoding.getDisplay()).isEqualTo("CREATININE");
+        assertThat(condCoding.hasVersion()).isTrue();
+        assertThat(condCoding.getVersion()).isEqualTo("474747");
+
+        condCoding = condCC.getCoding().get(1);
+        assertThat(condCoding.hasSystem()).isTrue();
         assertThat(condCoding.getSystem()).isEqualTo("http://terminology.hl7.org/CodeSystem/icd9");
         assertThat(condCoding.hasCode()).isTrue();
-        assertThat(condCoding.getCode()).isEqualTo("596.5");
+        assertThat(condCoding.getCode()).isEqualTo("F-11380");
         assertThat(condCoding.hasDisplay()).isTrue();
-        assertThat(condCoding.getDisplay()).isEqualTo("BLADDER DYSFUNCTION");
+        assertThat(condCoding.getDisplay()).isEqualTo("CREATININE");
+        assertThat(condCoding.hasVersion()).isTrue();
+        assertThat(condCoding.getVersion()).isEqualTo("22222");
     }
 
 }