issue #3855 - remove "ibm" from prefix for internal search params

1. ibm-internal-X-Compartment -> internal-X-Compartment
2. ibm_composite_X -> internal-composite-X

And various other updates to avoid "ibm-" references in the code.

Signed-off-by: Lee Surprenant <lmsurpre@merative.com>

docs/package.json

@@ -1,5 +1,5 @@
 {
-  "name": "ibm-fhir-server-site",
+  "name": "fhir-server-site",
   "version": "1.0.1",
   "license": "Apache-2.0",
   "scripts": {

fhir-audit/src/main/java/org/linuxforhealth/fhir/audit/beans/AuditLogEntry.java

@@ -128,26 +128,32 @@ public void setConfigData(ConfigData configData) {
         this.configData = configData;
     }
 
+    @Deprecated
     public String getClientCertCn() {
         return clientCertCn;
     }
 
+    @Deprecated
     public void setClientCertCn(String clientCertCn) {
         this.clientCertCn = clientCertCn;
     }
 
+    @Deprecated
     public String getClientCertIssuerOu() {
         return clientCertIssuerOu;
     }
 
+    @Deprecated
     public void setClientCertIssuerOu(String clientCertIssuerOu) {
         this.clientCertIssuerOu = clientCertIssuerOu;
     }
 
+    @Deprecated
     public String getCorrelationId() {
         return correlationId;
     }
 
+    @Deprecated
     public void setCorrelationId(String correlationId) {
         this.correlationId = correlationId;
     }

fhir-examples/src/main/java/org/linuxforhealth/fhir/examples/Index.java

@@ -48,7 +48,7 @@ public enum Index {
     /**
      * Both R4 spec and IBM generated examples
      */
-    ALL_XML("/spec-xml.txt", "/ibm-xml.txt"),
+    ALL_XML("/spec-xml.txt", "/generated-xml.txt"),
 
     /**
      * Small mix of spec and IBM examples used for unit tests to keep build times short

fhir-persistence-jdbc/src/main/java/org/linuxforhealth/fhir/persistence/jdbc/impl/FHIRPersistenceJDBCImpl.java

@@ -2138,7 +2138,7 @@ private boolean isWholeSystem(SearchParameter sp) {
     }
 
     /**
-     * Augment the given allParameters list with ibm-internal parameters that represent the relationship
+     * Augment the given allParameters list with internal parameters that represent the relationship
      * between the fhirResource and its compartments. These parameter values are subsequently used
      * to improve the performance of compartment-based FHIR search queries. See
      * {@link CompartmentHelper#makeCompartmentParamName(String)} for details on how the
@@ -2206,7 +2206,7 @@ protected void addCompartmentParams(List<ExtractedParameterValue> allParameters,
     }
 
     /**
-     * Augment the given allParameters list with ibm-internal parameters that represent the relationship
+     * Augment the given allParameters list with internal parameters that represent the relationship
      * between the url and version parameters. These parameter values are subsequently used in
      * canonical reference searches. See {@link CompartmentHelper#makeCompartmentParamName(String)} for
      * details on how the parameter name is composed.

fhir-persistence-jdbc/src/main/java/org/linuxforhealth/fhir/persistence/jdbc/util/JDBCParameterBuildingVisitor.java

@@ -231,7 +231,7 @@ public boolean visit(java.lang.String elementName, int elementIndex, org.linuxfo
             // See SearchUtil#parseQueryParameterValuesString.
             if (system == null) {
                 // Can't find an explicit system, so see if there's an implicit one
-                // attached to the code as an (IBM-defined) extension.
+                // attached to the code as an (LinuxForHealth-defined) extension.
                 system = SearchHelper.findImplicitSystem(code.getExtension());
             }
 

fhir-persistence-schema/src/main/resources/parameter_names.properties

@@ -279,99 +279,99 @@ has-member
 has-member:identifier
 holder
 holder:identifier
-ibm-internal-Device-Compartment
-ibm-internal-Encounter-Compartment
-ibm-internal-Patient-Compartment
-ibm-internal-Practitioner-Compartment
-ibm-internal-RelatedPerson-Compartment
-ibm_composite_accession:of-type_type
-ibm_composite_accession:of-type_value
-ibm_composite_base_canonical_uri
-ibm_composite_base_canonical_version
-ibm_composite_characteristic-value_characteristic
-ibm_composite_characteristic-value_characteristic:text
-ibm_composite_characteristic-value_value
-ibm_composite_characteristic-value_value:text
-ibm_composite_code-value-concept_code
-ibm_composite_code-value-concept_value-concept
-ibm_composite_code-value-date_code
-ibm_composite_code-value-date_value-date
-ibm_composite_code-value-quantity_code
-ibm_composite_code-value-quantity_value-quantity
-ibm_composite_code-value-string_code
-ibm_composite_code-value-string_value-string
-ibm_composite_combo-code-value-concept_combo-code
-ibm_composite_combo-code-value-concept_combo-value-concept
-ibm_composite_combo-code-value-quantity_combo-code
-ibm_composite_combo-code-value-quantity_combo-code:text
-ibm_composite_combo-code-value-quantity_combo-value-quantity
-ibm_composite_component-code-value-concept_component-code
-ibm_composite_component-code-value-concept_component-value-concept
-ibm_composite_component-code-value-quantity_component-code
-ibm_composite_component-code-value-quantity_component-code:text
-ibm_composite_component-code-value-quantity_component-value-quantity
-ibm_composite_composed-of_canonical_uri
-ibm_composite_composed-of_canonical_version
-ibm_composite_container-id:of-type_type
-ibm_composite_container-id:of-type_value
-ibm_composite_container-identifier:of-type_type
-ibm_composite_container-identifier:of-type_value
-ibm_composite_context-type-quantity_context-quantity
-ibm_composite_context-type-quantity_context-type
-ibm_composite_context-type-value_context
-ibm_composite_context-type-value_context-type
-ibm_composite_context-type-value_context:text
-ibm_composite_definition_canonical_uri
-ibm_composite_definition_canonical_version
-ibm_composite_depends-on_canonical_uri
-ibm_composite_depends-on_canonical_version
-ibm_composite_derived-from_canonical_uri
-ibm_composite_derived-from_canonical_version
-ibm_composite_global_canonical_uri
-ibm_composite_global_canonical_version
-ibm_composite_group-identifier:of-type_type
-ibm_composite_group-identifier:of-type_value
-ibm_composite_guide_canonical_uri
-ibm_composite_guide_canonical_version
-ibm_composite_identifier:of-type_type
-ibm_composite_identifier:of-type_value
-ibm_composite_instantiates-canonical_canonical_uri
-ibm_composite_instantiates-canonical_canonical_version
-ibm_composite_measure_canonical_uri
-ibm_composite_measure_canonical_version
-ibm_composite_other_canonical_uri
-ibm_composite_other_canonical_version
-ibm_composite_parent_canonical_uri
-ibm_composite_parent_canonical_version
-ibm_composite_predecessor_canonical_uri
-ibm_composite_predecessor_canonical_version
-ibm_composite_questionnaire_canonical_uri
-ibm_composite_questionnaire_canonical_version
-ibm_composite_referenceseqid-window-coordinate_referenceseqid
-ibm_composite_referenceseqid-window-coordinate_window-end
-ibm_composite_referenceseqid-window-coordinate_window-start
-ibm_composite_related-id:of-type_type
-ibm_composite_related-id:of-type_value
-ibm_composite_request:of-type_type
-ibm_composite_request:of-type_value
-ibm_composite_requisition:of-type_type
-ibm_composite_requisition:of-type_value
-ibm_composite_resource-profile_canonical_uri
-ibm_composite_resource-profile_canonical_version
-ibm_composite_source_canonical_uri
-ibm_composite_source_canonical_version
-ibm_composite_successor_canonical_uri
-ibm_composite_successor_canonical_version
-ibm_composite_supplements_canonical_uri
-ibm_composite_supplements_canonical_version
-ibm_composite_supported-profile_canonical_uri
-ibm_composite_supported-profile_canonical_version
-ibm_composite_target_canonical_uri
-ibm_composite_target_canonical_version
-ibm_composite_url_canonical_uri
-ibm_composite_url_canonical_version
-ibm_composite_valueset_canonical_uri
-ibm_composite_valueset_canonical_version
+internal-Device-Compartment
+internal-Encounter-Compartment
+internal-Patient-Compartment
+internal-Practitioner-Compartment
+internal-RelatedPerson-Compartment
+internal-composite_accession:of-type_type
+internal-composite_accession:of-type_value
+internal-composite_base_canonical_uri
+internal-composite_base_canonical_version
+internal-composite_characteristic-value_characteristic
+internal-composite_characteristic-value_characteristic:text
+internal-composite_characteristic-value_value
+internal-composite_characteristic-value_value:text
+internal-composite_code-value-concept_code
+internal-composite_code-value-concept_value-concept
+internal-composite_code-value-date_code
+internal-composite_code-value-date_value-date
+internal-composite_code-value-quantity_code
+internal-composite_code-value-quantity_value-quantity
+internal-composite_code-value-string_code
+internal-composite_code-value-string_value-string
+internal-composite_combo-code-value-concept_combo-code
+internal-composite_combo-code-value-concept_combo-value-concept
+internal-composite_combo-code-value-quantity_combo-code
+internal-composite_combo-code-value-quantity_combo-code:text
+internal-composite_combo-code-value-quantity_combo-value-quantity
+internal-composite_component-code-value-concept_component-code
+internal-composite_component-code-value-concept_component-value-concept
+internal-composite_component-code-value-quantity_component-code
+internal-composite_component-code-value-quantity_component-code:text
+internal-composite_component-code-value-quantity_component-value-quantity
+internal-composite_composed-of_canonical_uri
+internal-composite_composed-of_canonical_version
+internal-composite_container-id:of-type_type
+internal-composite_container-id:of-type_value
+internal-composite_container-identifier:of-type_type
+internal-composite_container-identifier:of-type_value
+internal-composite_context-type-quantity_context-quantity
+internal-composite_context-type-quantity_context-type
+internal-composite_context-type-value_context
+internal-composite_context-type-value_context-type
+internal-composite_context-type-value_context:text
+internal-composite_definition_canonical_uri
+internal-composite_definition_canonical_version
+internal-composite_depends-on_canonical_uri
+internal-composite_depends-on_canonical_version
+internal-composite_derived-from_canonical_uri
+internal-composite_derived-from_canonical_version
+internal-composite_global_canonical_uri
+internal-composite_global_canonical_version
+internal-composite_group-identifier:of-type_type
+internal-composite_group-identifier:of-type_value
+internal-composite_guide_canonical_uri
+internal-composite_guide_canonical_version
+internal-composite_identifier:of-type_type
+internal-composite_identifier:of-type_value
+internal-composite_instantiates-canonical_canonical_uri
+internal-composite_instantiates-canonical_canonical_version
+internal-composite_measure_canonical_uri
+internal-composite_measure_canonical_version
+internal-composite_other_canonical_uri
+internal-composite_other_canonical_version
+internal-composite_parent_canonical_uri
+internal-composite_parent_canonical_version
+internal-composite_predecessor_canonical_uri
+internal-composite_predecessor_canonical_version
+internal-composite_questionnaire_canonical_uri
+internal-composite_questionnaire_canonical_version
+internal-composite_referenceseqid-window-coordinate_referenceseqid
+internal-composite_referenceseqid-window-coordinate_window-end
+internal-composite_referenceseqid-window-coordinate_window-start
+internal-composite_related-id:of-type_type
+internal-composite_related-id:of-type_value
+internal-composite_request:of-type_type
+internal-composite_request:of-type_value
+internal-composite_requisition:of-type_type
+internal-composite_requisition:of-type_value
+internal-composite_resource-profile_canonical_uri
+internal-composite_resource-profile_canonical_version
+internal-composite_source_canonical_uri
+internal-composite_source_canonical_version
+internal-composite_successor_canonical_uri
+internal-composite_successor_canonical_version
+internal-composite_supplements_canonical_uri
+internal-composite_supplements_canonical_version
+internal-composite_supported-profile_canonical_uri
+internal-composite_supported-profile_canonical_version
+internal-composite_target_canonical_uri
+internal-composite_target_canonical_version
+internal-composite_url_canonical_uri
+internal-composite_url_canonical_version
+internal-composite_valueset_canonical_uri
+internal-composite_valueset_canonical_version
 id-type
 identified
 identifier
@@ -829,4 +829,4 @@ substance-code
 substance-code:text
 substance-definition
 trigger-description
-# End of 4.1.0
+# End of 4.3.0

fhir-search/src/main/java/org/linuxforhealth/fhir/search/compartment/CompartmentHelper.java

@@ -34,11 +34,11 @@
  * <br>
  * Default CompartmentDefintion:
  * <ul>
- * <li>Patient - https://hl7.org/fhir/R4/compartmentdefinition-patient.json</li>
- * <li>Encounter - https://hl7.org/fhir/R4/compartmentdefinition-encounter.json</li>
- * <li>RelatedPerson - https://hl7.org/fhir/R4/compartmentdefinition-relatedperson.json</li>
- * <li>Practitioner - https://hl7.org/fhir/R4/compartmentdefinition-practitioner.json</li>
- * <li>Device - https://hl7.org/fhir/R4/compartmentdefinition-device.json</li>
+ * <li>Patient - https://hl7.org/fhir/R4B/compartmentdefinition-patient.json</li>
+ * <li>Encounter - https://hl7.org/fhir/R4B/compartmentdefinition-encounter.json</li>
+ * <li>RelatedPerson - https://hl7.org/fhir/R4B/compartmentdefinition-relatedperson.json</li>
+ * <li>Practitioner - https://hl7.org/fhir/R4B/compartmentdefinition-practitioner.json</li>
+ * <li>Device - https://hl7.org/fhir/R4B/compartmentdefinition-device.json</li>
  * </ul>
  */
 public class CompartmentHelper {
@@ -220,7 +220,7 @@ public Map<String, Set<java.lang.String>> getCompartmentParamsForResourceType(ja
      */
     public static String makeCompartmentParamName(String compartmentName) {
         final StringBuilder result = new StringBuilder();
-        result.append("ibm-internal-")
+        result.append("internal-")
             .append(compartmentName)
             .append("-Compartment");
         return result.toString();

fhir-search/src/main/java/org/linuxforhealth/fhir/search/util/SearchHelper.java

@@ -132,7 +132,7 @@ public class SearchHelper {
     // compartment parameter reference which can be ignore
     private static final String COMPARTMENT_PARM_DEF = "{def}";
 
-    private static final String IBM_COMPOSITE_PREFIX = "ibm_composite_";
+    private static final String COMPOSITE_PREFIX = "internal-composite_";
 
     // The functionality is split into a new class.
     private static final Sort sort = new Sort();
@@ -2252,7 +2252,7 @@ private static void checkQueryParameterValuesForLogicalIdOnly(String parameterCo
      */
     public static String makeCompositeSubCode(String compositeCode, String subParameterCode) {
         final StringBuilder result = new StringBuilder();
-        result.append(IBM_COMPOSITE_PREFIX);
+        result.append(COMPOSITE_PREFIX);
         result.append(compositeCode);
         result.append("_");
         result.append(subParameterCode);

fhir-search/src/test/java/org/linuxforhealth/fhir/search/test/CompartmentParseQueryParmsTest.java

@@ -39,8 +39,8 @@
  * Test the parsing of compartment related search data from SearchHelper.
  */
 public class CompartmentParseQueryParmsTest extends BaseSearchTest {
-    private static final String INTERNAL_PATIENT_COMPARTMENT_PARAM = "ibm-internal-Patient-Compartment";
-    private static final String INTERNAL_RELATEDPERSON_COMPARTMENT_PARAM = "ibm-internal-RelatedPerson-Compartment";
+    private static final String INTERNAL_PATIENT_COMPARTMENT_PARAM = "internal-Patient-Compartment";
+    private static final String INTERNAL_RELATEDPERSON_COMPARTMENT_PARAM = "internal-RelatedPerson-Compartment";
 
     /**
      * This method tests parsing compartment related query parms, passing an invalid compartment.

fhir-server-webapp/src/main/liberty/config/configDropins/defaults/bulkdata.xml

@@ -39,8 +39,9 @@
     <databaseStore dataSourceRef="fhirbatchDS" id="BatchDatabaseStore" schema="${BATCH_DB_SCHEMA}" tablePrefix="" createTables="false"/>
 
     <!--
-         The defaultHostName is set in the deployment.yaml https://github.com/Alvearie/alvearie-helm/blob/main/charts/ibm-fhir-server/templates/deployment.yaml#L159
-         and is subsequently used by the bulkdata configurations
+         The defaultHostName is subsequently used in the bulkdata configuration and must be set to avoid liberty batch issues.
+         For example, in the helm chart:
+         https://github.com/Alvearie/alvearie-helm/blob/main/charts/ibm-fhir-server/templates/deployment.yaml#L179
     -->
     <variable name="defaultHostName" value="${env.MY_POD_NAME}"/>
 </server>

fhir-server-webapp/src/main/liberty/config/configDropins/defaults/datasource.xml

@@ -1,7 +1,7 @@
 <server>
     <!-- ============================================================== -->
     <!-- This datasource aligns with the Apache Derby database that is  -->
-    <!-- created by the ibmcom/ibm-fhir-server BOOTSTRAP_DB process.    -->
+    <!-- created by the linuxforhealth/fhir-server BOOTSTRAP_DB process.-->
     <!-- ============================================================== -->
 
     <!-- ============================================================== -->