Merge pull request #213 from LinuxForHealth/Issue#212-provide-text-wh…

…en-unknown-id-codings

Issue#212 provide text when unknown id codings

src/main/java/io/github/linuxforhealth/hl7/data/SimpleDataTypeMapper.java

@@ -1,5 +1,5 @@
 /*
- * (C) Copyright IBM Corp. 2020
+ * (C) Copyright IBM Corp. 2020, 2021
  *
  * SPDX-License-Identifier: Apache-2.0
  */
@@ -34,6 +34,7 @@ public enum SimpleDataTypeMapper {
   OBJECT(SimpleDataValueResolver.OBJECT),
   CODING_SYSTEM_V2(SimpleDataValueResolver.CODING_SYSTEM_V2),
   CODING_SYSTEM_V2_ALTERNATE(SimpleDataValueResolver.CODING_SYSTEM_V2_ALTERNATE),
+  CODING_SYSTEM_V2_IDENTIFIER(SimpleDataValueResolver.CODING_SYSTEM_V2_IDENTIFIER),
   SYSTEM_URL(SimpleDataValueResolver.SYSTEM_URL),
   SYSTEM_ID(SimpleDataValueResolver.SYSTEM_ID),
 

src/main/java/io/github/linuxforhealth/hl7/data/SimpleDataValueResolver.java

@@ -324,6 +324,25 @@ public class SimpleDataValueResolver {
         return value;
     };
 
+    // Special case of a SYSTEM V2.  Identifiers allow unknown codes.
+    // When an unknown code is detected, return a null so that the text is displayed instead.
+    // Only a known code returns a coding.
+    public static final ValueExtractor<Object, SimpleCode> CODING_SYSTEM_V2_IDENTIFIER = (Object value) -> {
+        value = checkForAndUnwrapVariesObject(value);
+        String table = Hl7DataHandlerUtil.getTableNumber(value);
+        String code = Hl7DataHandlerUtil.getStringValue(value);
+        if (table != null && code != null) {
+            // Found table and a code. Try looking it up.
+            SimpleCode coding = TerminologyLookup.lookup(table, code);
+            // A non-null, non-empty value in display means a good code from lookup.
+            if (coding != null && coding.getDisplay()!=null && !coding.getDisplay().isEmpty()) {
+                return coding;
+            }
+        }    
+        // All other situations return null.  
+        return null;
+    };
+
     public static final ValueExtractor<Object, SimpleCode> CODING_SYSTEM_V2_ALTERNATE = (Object value) -> {
         value = checkForAndUnwrapVariesObject(value);
         // ensure we have a CWE

src/main/resources/hl7/datatype/CodeableConcept.yml

@@ -19,7 +19,7 @@ coding_1:
 
 coding_2:
    condition: $code NOT_NULL && $coding NULL
-   type: CODING_SYSTEM_V2
+   type: CODING_SYSTEM_V2_IDENTIFIER
    valueOf: ID |IS |TX
    generateList: true
    expressionType: HL7Spec
@@ -49,10 +49,9 @@ 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. 
+# Require available text, and the absense of an identifierCoding
 text:
-   condition: $hideText NULL && $displayText NOT_NULL
+   condition: $displayText NOT_NULL && identifierCoding NULL
    type: STRING
    valueOf: $displayText
    vars:

src/main/resources/hl7/datatype/Identifier_SystemID.yml

@@ -9,9 +9,10 @@ type:
    valueOf: datatype/CodeableConcept
    expressionType: resource
    specs: CX.5 | $type
-   constants: 
-      # Because calculated system id's don't have text, force the calculated text from code to be hidden
-      hideText: 'HIDE'
+   vars: 
+     # Because calculated system id's don't have text if there is a valid system, 
+     # see if there is a valid code and system as input to creating text in the CodeableConcept
+     identifierCoding: CODING_SYSTEM_V2_IDENTIFIER, CX.5
 
 system: 
      condition: $systemExists NOT_NULL

src/test/java/io/github/linuxforhealth/hl7/segments/Hl7IdentifierFHIRConversionTest.java

@@ -110,14 +110,14 @@ public void patientIdentifiersTest() {
     @Test
     public void patientIdentifiersSpecialCasesTest() {
         String patientIdentifiersSpecialCases = "MSH|^~\\&|MIICEHRApplication|MIIC|MIIC|MIIC|201705130822||VXU^V04^VXU_V04|test1100|P|2.5.1|||AL|AL|||||Z22^CDCPHINVS|^^^^^MIIC^SR^^^MIIC|MIIC\n"
-                // First ID has blanks in the authority.  Second ID has no authority provided.
-                + "PID|1||MRN12345678^^^Regional Health ID^MR~111223333^^^^SS|ALTID|Moose^Mickey^J^III^^^||20060504|M||||||||||||||||||||||\n";
+                // First ID has blanks in the authority.  Second ID has no authority provided.  Third ID has an unknown CODE in the standard v2 table. 
+                + "PID|1||MRN12345678^^^Regional Health ID^MR~111223333^^^^SS~A100071402^^^^AnUnknownCode|ALTID|Moose^Mickey^J^III^^^||20060504|M||||||||||||||||||||||\n";
         Patient patient = PatientUtils.createPatientFromHl7Segment(patientIdentifiersSpecialCases);
 
         // Expect 2 identifiers
         assertThat(patient.hasIdentifier()).isTrue();
         List<Identifier> identifiers = patient.getIdentifier();
-        assertThat(identifiers.size()).isEqualTo(2);
+        assertThat(identifiers.size()).isEqualTo(3);
 
         // First identifier (Medical Record) deep check
         Identifier identifier = identifiers.get(0);
@@ -134,7 +134,7 @@ public void patientIdentifiersSpecialCasesTest() {
         assertThat(coding.getCode()).hasToString("MR");
         assertThat(coding.getDisplay()).hasToString("Medical record number");
 
-        // Deep check for second identifier
+        // Second identifier
         identifier = identifiers.get(1);
         // We expect no system because there was no authority.
         assertThat(identifier.hasSystem()).isFalse();
@@ -147,6 +147,22 @@ public void patientIdentifiersSpecialCasesTest() {
         assertThat(coding.getSystem()).hasToString("http://terminology.hl7.org/CodeSystem/v2-0203");
         assertThat(coding.getCode()).hasToString("SS");
         assertThat(coding.getDisplay()).hasToString("Social Security number");
+
+        // Third identifier - unknown code.  Create the following:
+        // "identifier": [ {
+        //         "type": {
+        //           "text": "AnUnknownCode"
+        //         },
+        //         "value": "A100071402"
+        //       },
+        identifier = identifiers.get(2);
+        assertThat(identifier.hasSystem()).isFalse();
+        assertThat(identifier.getValue()).hasToString("A100071402");
+        assertThat(identifier.hasType()).isTrue();
+        cc = identifier.getType();
+        assertThat(cc.hasText()).isTrue();
+        assertThat(cc.getText()).hasToString("AnUnknownCode");     
+        assertThat(cc.hasCoding()).isFalse();
     }
 
     @Test