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

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

@@ -279,11 +279,11 @@ 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
+internal-Device-Compartment
+internal-Encounter-Compartment
+internal-Patient-Compartment
+internal-Practitioner-Compartment
+internal-RelatedPerson-Compartment
 ibm_composite_accession:of-type_type
 ibm_composite_accession:of-type_value
 ibm_composite_base_canonical_uri
@@ -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

@@ -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/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.-->
     <!-- ============================================================== -->
 
     <!-- ============================================================== -->

fhir-server/src/main/java/org/linuxforhealth/fhir/server/util/RestAuditLogger.java

@@ -7,12 +7,10 @@
 package org.linuxforhealth.fhir.server.util;
 
 import java.security.Principal;
-import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Date;
 import java.util.HashSet;
 import java.util.Iterator;
-import java.util.List;
 import java.util.Set;
 import java.util.logging.Level;
 import java.util.logging.Logger;
@@ -56,11 +54,6 @@ public class RestAuditLogger {
     private static final String CLASSNAME = RestAuditLogger.class.getName();
     private static final Logger log = java.util.logging.Logger.getLogger(CLASSNAME);
 
-    private static final String HEADER_IBM_APP_USER = "IBM-App-User";
-    private static final String HEADER_CLIENT_CERT_CN = "IBM-App-cli-CN";
-    private static final String HEADER_CLIENT_CERT_ISSUER_OU = "IBM-App-iss-OU";
-    private static final String HEADER_CORRELATION_ID = "IBM-DP-correlationid";
-
     private static final String COMPONENT_ID = "fhir-server";
 
     private static final IPHandler componentIpHandler = new IPHandler();
@@ -370,16 +363,16 @@ public static void logBundle(HttpServletRequest request, Bundle requestBundle, B
                 // Transaction
                 logBundleTransaction(auditLogSvc, request, requestBundle, responseBundle, startTime, endTime, responseStatus);
             }
-            
+
         }
         log.exiting(CLASSNAME, METHODNAME);
     }
 
     /**
      * Logs the Bundle as a batch in multiple messages
-     * 
-     * @implNote batch fail or succeed as a individual processing unit. 
-     * 
+     *
+     * @implNote batch fail or succeed as a individual processing unit.
+     *
      * @param auditLogSvc
      * @param request
      * @param requestBundle
@@ -401,7 +394,7 @@ private static void logBundleBatch(AuditLogService auditLogSvc, HttpServletReque
 
                 AuditLogEntry entry = initLogEntry(AuditLogEventType.FHIR_BUNDLE);
 
-                populateAuditLogEntry(entry, request, responseEntry.getResource(), startTime, endTime, responseStatus); 
+                populateAuditLogEntry(entry, request, responseEntry.getResource(), startTime, endTime, responseStatus);
                 if (requestEntry.getRequest() != null && requestEntry.getRequest().getMethod() != null) {
                     boolean operation =  requestEntry.getRequest().getUrl().getValue().contains("$")
                                             || requestEntry.getRequest().getUrl().getValue().contains("/%24");
@@ -489,9 +482,9 @@ private static void logBundleBatch(AuditLogService auditLogSvc, HttpServletReque
 
     /**
      * Logs the Bundle as a Transaction in a single request
-     * 
-     * @implNote transactions fail or succeed as a single processing unit. 
-     * 
+     *
+     * @implNote transactions fail or succeed as a single processing unit.
+     *
      * @param auditLogSvc
      * @param request
      * @param requestBundle
@@ -788,21 +781,11 @@ protected static AuditLogEntry populateAuditLogEntry(AuditLogEntry entry, HttpSe
         log.entering(CLASSNAME, METHODNAME);
 
         String patientIdExtUrl;
-        List<String> userList = new ArrayList<>();
-
-        // Build a list of possible user names. Pick the first non-null user name to include in the audit log entry.
-        userList.add(request.getHeader(HEADER_IBM_APP_USER));
-        userList.add(request.getHeader(HEADER_CLIENT_CERT_CN));
 
+        // Note: we used to support overriding the user name from a specific header; that was removed for 5.0
         Principal userPrincipal = request.getUserPrincipal();
         if (userPrincipal != null) {
-            userList.add(userPrincipal.getName());
-        }
-        for (String userName : userList) {
-            if (userName != null && !userName.isEmpty()) {
-                entry.setUserName(userName);
-                break;
-            }
+            entry.setUserName(userPrincipal.getName());
         }
 
         entry.setLocation(new StringBuilder().append(request.getRemoteAddr()).append("/").append(request.getRemoteHost()).toString());
@@ -827,10 +810,6 @@ protected static AuditLogEntry populateAuditLogEntry(AuditLogEntry entry, HttpSe
             }
         }
 
-        entry.setClientCertCn(request.getHeader(HEADER_CLIENT_CERT_CN));
-        entry.setClientCertIssuerOu(request.getHeader(HEADER_CLIENT_CERT_ISSUER_OU));
-        entry.setCorrelationId(request.getHeader(HEADER_CORRELATION_ID));
-
         patientIdExtUrl = FHIRConfigHelper.getStringProperty(FHIRConfiguration.PROPERTY_AUDIT_PATIENT_ID_EXTURL, null);
         entry.setPatientId(FHIRUtil.getExtensionStringValue(resource, patientIdExtUrl));
         entry.getContext().setRequestUniqueId(FHIRRequestContext.get().getRequestUniqueId());

fhir-smart/src/test/java/org/linuxforhealth/fhir/smart/test/AuthzPolicyEnforcementTest.java

@@ -610,7 +610,7 @@ public void testBeforeSearch(String scopeString, List<String> contextIds, Set<Re
                 assertEquals(searchContext.getSearchParameters().size(), 2);
                 List<QueryParameter> searchParms = searchContext.getSearchParameters();
                 QueryParameter compartmentSearchParm = searchParms.get(0);
-                assertTrue("ibm-internal-Patient-Compartment".equals(compartmentSearchParm.getCode()));
+                assertTrue("internal-Patient-Compartment".equals(compartmentSearchParm.getCode()));
                 assertEquals(compartmentSearchParm.getType(), Type.REFERENCE);
                 assertTrue(compartmentSearchParm.isInclusionCriteria());
                 assertFalse(compartmentSearchParm.isChained());