Merge pull request #174 from LinuxForHealth/Issue#173-Version-and-Alt…

…ernate-coding-support Issue #173 CWE Version & Alternate Coding support
LinuxForHealth · Aug 23, 2021 · 93a6594 · 93a6594
2 parents 9facbb2 + 9955088
commit 93a6594
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Showing 7 changed files with 166 additions and 32 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:
@@ -52,6 +49,8 @@ coding_5:
    condition: $coding NOT_NULL
    generateList: true
 
+# If hideText is not passed by parent, the value is NULL, making it backward compatible with all other uses of CodeableConcept
+# Any value in hideText will cause the text to be hidden.  Used by Identifier_SystemID.   
 text:
    condition: $hideText NULL  && $displayText NOT_NULL
    type: STRING
@@ -62,5 +61,3 @@ text:
 # ----------------
 # Orphan comments:
 # ----------------
-# Was at begin of line:56 :# If hideText is not passed by parent, the value is NULL, making it backward compatible with all other uses of CodeableConcept
-# Was at begin of line:57 :# Any value in hideText will cause the text to be hidden.  Used by Identifier_SystemID.
diff --git a/src/main/resources/hl7/resource/Patient.yml b/src/main/resources/hl7/resource/Patient.yml
@@ -177,9 +177,7 @@ extension:
          valueCodeableConcept:
             valueOf: datatype/CodeableConcept
             expressionType: resource
-            condition: $coding NOT_NULL
-            vars:
-               coding: CODING_SYSTEM_V2, CWE   
+            specs: CWE
 
 communication:
    condition: $language NOT_NULL