Introduce ".well-known/smart-configuration", change liberty config layout, and update user's guide

.github/workflows/build.yml

@@ -234,6 +234,7 @@ jobs:
     - name: Build parent without tests
       run: |
         mvn -B install --file fhir-parent -DskipTests -P integration --no-transfer-progress
+        mvn -B dockerfile:build -f fhir-install --no-transfer-progress
     - name: Server Integration Tests
       run: |
         export WORKSPACE=${GITHUB_WORKSPACE}
@@ -290,6 +291,7 @@ jobs:
     - name: Build parent without tests
       run: |
         mvn -B install --file fhir-parent -DskipTests -P integration --no-transfer-progress
+        mvn -B dockerfile:build -f fhir-install --no-transfer-progress
     - name: Server Integration Tests
       run: |
         export WORKSPACE=${GITHUB_WORKSPACE}

build/README-DB2.md

@@ -6,7 +6,7 @@ Running fhir server integration tests using docker db2.
 ## Prerequisites
 
 - [Docker](https://www.docker.com)
-- `ibmcom/ibm-fhir-server:latest` (built with the fhir-install module)
+- `ibmcom/ibm-fhir-server:latest` (built from the fhir-install module)
 
 
 ## Run

fhir-client/src/main/java/com/ibm/fhir/client/impl/FHIRClientImpl.java

@@ -1,5 +1,5 @@
 /*
- * (C) Copyright IBM Corp. 2016,2019
+ * (C) Copyright IBM Corp. 2016, 2020
  *
  * SPDX-License-Identifier: Apache-2.0
  */
@@ -58,7 +58,7 @@
  */
 public class FHIRClientImpl implements FHIRClient {
 
-    private static final String KEYSTORE_TYPE_JKS = "JKS";
+    private static final String KEYSTORE_TYPE = "pkcs12";
 
     private Client client = null;
     private Properties clientProperties = null;
@@ -866,7 +866,7 @@ private void initProperties(Properties props) throws Exception {
                 if (trustStoreLoc != null && trustStoreEncodedPwd != null) {
                     setTrustStoreLocation(trustStoreLoc);
                     setTrustStorePassword(FHIRUtilities.decode(trustStoreEncodedPwd));
-                    setTrustStore(loadKeyStoreFile(getTrustStoreLocation(), getTrustStorePassword(), KEYSTORE_TYPE_JKS));
+                    setTrustStore(loadKeyStoreFile(getTrustStoreLocation(), getTrustStorePassword(), KEYSTORE_TYPE));
                 }
             }
 
@@ -875,7 +875,7 @@ private void initProperties(Properties props) throws Exception {
                 setKeyStoreLocation(getRequiredProperty(PROPNAME_KEYSTORE_LOCATION));
                 setKeyStorePassword(FHIRUtilities.decode(getRequiredProperty(PROPNAME_KEYSTORE_PASSWORD)));
                 setKeyStoreKeyPassword(FHIRUtilities.decode(getRequiredProperty(PROPNAME_KEYSTORE_KEY_PASSWORD)));
-                setKeyStore(loadKeyStoreFile(getKeyStoreLocation(), getKeyStorePassword(), KEYSTORE_TYPE_JKS));
+                setKeyStore(loadKeyStoreFile(getKeyStoreLocation(), getKeyStorePassword(), KEYSTORE_TYPE));
             }
 
             setLoggingEnabled(Boolean.parseBoolean(getProperty(PROPNAME_LOGGING_ENABLED, "false")));

fhir-client/src/test/java/com/ibm/fhir/client/sample/FHIRClientSample.java

@@ -1,5 +1,5 @@
 /*
- * (C) Copyright IBM Corp. 2016,2019
+ * (C) Copyright IBM Corp. 2016, 2020
  *
  * SPDX-License-Identifier: Apache-2.0
  */
@@ -27,28 +27,28 @@
 public class FHIRClientSample {
     public final static int OK = 200;
     public final static int CREATED = 201;
-    
+
     public static void main(String[] args) throws Exception {
-        
+
         // Create properties to be used to configure the client.
         Properties clientProperties = new Properties();
-        clientProperties.setProperty(FHIRClient.PROPNAME_BASE_URL, "http://localhost:9080/fhir-server/api/v4");
-        
+        clientProperties.setProperty(FHIRClient.PROPNAME_BASE_URL, "https://localhost:9443/fhir-server/api/v4");
+
         // Retrieve an instance of the FHIRClient interface.
         FHIRClient client = FHIRClientFactory.getClient(clientProperties);
-                
+
         // Create and initialize patient.
-        Patient patient = Patient.builder().build();
+        Patient patient = Patient.builder().id("test").build();
         // patient.set...
-        
+
         // 1) Persist the patient and then display its location URI (e.g. "Patient/123/_history/1").
         FHIRResponse response = client.create(patient);
         if (response.getStatus() == CREATED) {
             System.out.println("Patient resource was persisted, location = " + response.getLocation());
         } else {
             System.out.println("Error persisting patient, status code = " + response.getStatus());
         }
-        
+
         // 2) Retrieve an Observation.
         response = client.read("Observation", "123");
         if (response.getStatus() == OK) {
@@ -60,28 +60,28 @@ public static void main(String[] args) throws Exception {
             OperationOutcome operationOutcome = response.getResource(OperationOutcome.class);
             // display operationOutcome message, etc.
         }
-        
+
         // 3) Retrieve a specific version of a MedicationAdministration.
         response = client.vread("MedicationAdministration", "12345", "2");
         // Check status code, retrieve resource, etc.
-        
+
         // 4) Retrieve the most recent 5 versions of a Patient.
         FHIRParameters parameters = new FHIRParameters().count(5);
         response = client.history("Patient", "123", parameters);
         // Check status code, retrieve response bundle, etc.
-        
+
         // 5) Search for patients born on 1/1/1970.
         parameters = new FHIRParameters().searchParam("birthdate", ValuePrefix.EQ, "1970-01-01");
         response = client.search("Patient", parameters);
-        
+
         // 6) Validate a Patient resource.
         response = client.validate(patient);
         // Check status code, retrieve OperationOutcome response resource, etc.
-        
+
         // 7) Invoke a batch request.
         Bundle bundle = Bundle.builder().type(BundleType.BATCH).build();
         // Initialize bundle by adding individual operations (read, vread, create, update, etc.)
-        
+
         response = client.batch(bundle);
         // Check status code, retrieve Bundle response resource, etc.
     }

fhir-client/src/test/java/com/ibm/fhir/client/test/mains/FHIRClientSample.java

@@ -1,5 +1,5 @@
 /*
- * (C) Copyright IBM Corp. 2016,2019
+ * (C) Copyright IBM Corp. 2016, 2020
  *
  * SPDX-License-Identifier: Apache-2.0
  */
@@ -124,7 +124,7 @@ public void run() throws Exception {
      */
     private Properties readProperties() throws Exception {
         Properties props = new Properties();
-        try (InputStream is = resolveFileLocation("fhir-client.properties")) {
+        try (InputStream is = resolveFileLocation("test.properties")) {
             props.load(is);
             return props;
         }
@@ -173,7 +173,7 @@ private void displayOperationOutcome(FHIRResponse response) {
 
     /**
      * Create a new Patient resource with the specified name and mobile
-     * 
+     *
      * @param firstName
      * @param lastName
      * @param mobilePhoneNum

fhir-client/src/test/resources/test.properties

@@ -8,10 +8,10 @@ fhirclient.basicauth.username = fhiruser
 fhirclient.basicauth.password = change-password
 
 fhirclient.clientauth.enabled = true
-fhirclient.keystore.location = fhirClientKeystore.jks
+fhirclient.keystore.location = fhirClientKeyStore.p12
 fhirclient.keystore.password = change-password
 fhirclient.keystore.key.password = change-password
-fhirclient.truststore.location = fhirClientTruststore.jks
+fhirclient.truststore.location = fhirClientTrustStore.p12
 fhirclient.truststore.password = change-password
 
 fhirclient.oAuth2.enabled = false

fhir-database-utils/src/main/java/com/ibm/fhir/database/utils/api/IDatabaseAdapter.java

@@ -396,12 +396,9 @@ public void grantSequencePrivileges(String schemaName, String objectName, Collec
 
 
     /**
-     * Create FHIR data and admin schemas
+     * Create a database schema
      *
      * @param schemaName
-     * @param adminSchemaName
      */
-    public void createFhirSchemas(String schemaName, String adminSchemaName);
-
-
+    public void createSchema(String schemaName);
 }

fhir-database-utils/src/main/java/com/ibm/fhir/database/utils/common/CommonDatabaseAdapter.java

@@ -16,6 +16,7 @@
 import java.util.logging.Logger;
 import java.util.stream.Collectors;
 
+import com.ibm.fhir.database.utils.api.DuplicateNameException;
 import com.ibm.fhir.database.utils.api.IConnectionProvider;
 import com.ibm.fhir.database.utils.api.IDatabaseAdapter;
 import com.ibm.fhir.database.utils.api.IDatabaseStatement;
@@ -508,4 +509,14 @@ public void grantSequencePrivileges(String schemaName, String variableName, Coll
         logger.info("Applying: " + grant); // Grants are very useful to see logged
         runStatement(grant);
     }
+
+    @Override
+    public void createSchema(String schemaName) {
+        try {
+            String ddl = "CREATE SCHEMA " + schemaName;
+            runStatement(ddl);
+        } catch (DuplicateNameException e) {
+            logger.log(Level.WARNING, "The schema '" + schemaName + "' already exists; proceed with caution.");
+        }
+    }
 }

fhir-database-utils/src/main/java/com/ibm/fhir/database/utils/db2/Db2Adapter.java

@@ -20,7 +20,6 @@
 import java.util.logging.Logger;
 
 import com.ibm.fhir.database.utils.api.DataAccessException;
-import com.ibm.fhir.database.utils.api.DuplicateNameException;
 import com.ibm.fhir.database.utils.api.IConnectionProvider;
 import com.ibm.fhir.database.utils.api.IDatabaseStatement;
 import com.ibm.fhir.database.utils.api.IDatabaseTarget;
@@ -435,22 +434,6 @@ public boolean checkCompatibility(String adminSchema) {
         return true;
     }
 
-    @Override
-    public void createFhirSchemas(String schemaName, String adminSchemaName) {
-        try {
-            String ddl = "CREATE SCHEMA " + schemaName;
-            runStatement(ddl);
-        } catch (DuplicateNameException e) {
-            logger.log(Level.WARNING, "The schema '" + schemaName + "' already exists; proceed with caution.");
-        }
-        try {
-            String ddl = "CREATE SCHEMA " + adminSchemaName;
-            runStatement(ddl);
-        } catch (DuplicateNameException e) {
-            logger.log(Level.WARNING, "The schema '" + adminSchemaName + "' already exists; proceed with caution.");
-        }
-    }
-
     @Override
     public void runStatement(IDatabaseStatement stmt) {
         super.runStatement(stmt);

fhir-database-utils/src/main/java/com/ibm/fhir/database/utils/derby/DerbyAdapter.java

@@ -240,14 +240,6 @@ protected List<String> prefixTenantColumn(String tenantColumnName, List<String>
         return columns;
     }
 
-    @Override
-    public void createFhirSchemas(String schemaName, String adminSchemaName) {
-        String ddl = "CREATE SCHEMA " + schemaName;
-        runStatement(ddl);
-        ddl = "CREATE SCHEMA " + adminSchemaName;
-        runStatement(ddl);
-    }
-
     @Override
     public void runStatement(IDatabaseStatement stmt) {
         if (stmt instanceof AddForeignKeyConstraint) {

fhir-database-utils/src/main/java/com/ibm/fhir/database/utils/derby/DerbyTranslator.java

@@ -13,6 +13,7 @@
 import com.ibm.fhir.database.utils.api.ConnectionDetails;
 import com.ibm.fhir.database.utils.api.ConnectionException;
 import com.ibm.fhir.database.utils.api.DataAccessException;
+import com.ibm.fhir.database.utils.api.DuplicateNameException;
 import com.ibm.fhir.database.utils.api.IDatabaseTranslator;
 import com.ibm.fhir.database.utils.api.LockException;
 import com.ibm.fhir.database.utils.api.UndefinedNameException;
@@ -52,7 +53,8 @@ public boolean isDuplicate(SQLException x) {
 
     @Override
     public boolean isAlreadyExists(SQLException x) {
-        return "42710".equals(x.getSQLState());
+        // X0Y68 is for a schema, X0Y32 is for an object (e.g. a table)
+        return "X0Y68".equals(x.getSQLState()) || "X0Y32".equals(x.getSQLState());
     }
 
     @Override
@@ -86,6 +88,9 @@ else if (isConnectionError(x)) {
         else if (isDuplicate(x)) {
             return new UniqueConstraintViolationException(x);
         }
+        else if (isAlreadyExists(x)) {
+            return new DuplicateNameException(x);
+        }
         else if (isUndefinedName(x)) {
             return new UndefinedNameException(x);
         }

fhir-database-utils/src/main/java/com/ibm/fhir/database/utils/model/BlobColumn.java

@@ -9,12 +9,12 @@
 import com.ibm.fhir.database.utils.api.IDatabaseTypeAdapter;
 
 /**
- * Blob Column
+ * Binary Large OBject (BLOB) Column
  */
 public class BlobColumn extends ColumnBase {
-    
+
     private final long size;
-    
+
     private final int inlineSize;
 
     /**

fhir-database-utils/src/main/java/com/ibm/fhir/database/utils/model/ClobColumn.java

@@ -0,0 +1,27 @@
+/*
+ * (C) Copyright IBM Corp. 2020
+ *
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+package com.ibm.fhir.database.utils.model;
+
+import com.ibm.fhir.database.utils.api.IDatabaseTypeAdapter;
+
+/**
+ * Character Large OBject (CLOB) Column
+ */
+public class ClobColumn extends ColumnBase {
+    public ClobColumn(String name, boolean nullable) {
+        super(name, nullable);
+    }
+
+    public ClobColumn(String name, boolean nullable, String defaultVal) {
+        super(name, nullable, defaultVal);
+    }
+
+    @Override
+    public String getTypeInfo(IDatabaseTypeAdapter adapter) {
+        return "CLOB";
+    }
+}

fhir-database-utils/src/main/java/com/ibm/fhir/database/utils/model/ColumnBase.java

@@ -1,5 +1,5 @@
 /*
- * (C) Copyright IBM Corp. 2019
+ * (C) Copyright IBM Corp. 2019, 2020
  *
  * SPDX-License-Identifier: Apache-2.0
  */
@@ -12,13 +12,16 @@
  * An immutable definition of a column in a table
  */
 public abstract class ColumnBase {
-    
+
     // Name of the column
     private final String name;
-    
+
     // Does the column allow null values
     private final boolean nullable;
 
+    // The default value for the column (usually null)
+    private final String defaultVal;
+
     /**
      * Protected constructor - for use by subclasses
      * @param name
@@ -27,6 +30,19 @@ public abstract class ColumnBase {
     protected ColumnBase(String name, boolean nullable) {
         this.name = name;
         this.nullable = nullable;
+        this.defaultVal = null;
+    }
+
+    /**
+     * Protected constructor - for use by subclasses
+     * @param name
+     * @param nullable
+     * @param defaultVal
+     */
+    protected ColumnBase(String name, boolean nullable, String defaultVal) {
+        this.name = name;
+        this.nullable = nullable;
+        this.defaultVal = defaultVal;
     }
 
     /**
@@ -45,6 +61,14 @@ public boolean isNullable() {
         return nullable;
     }
 
+    /**
+     * Getter for the default value of this column
+     * @return possibly null
+     */
+    public String getDefaultVal() {
+        return defaultVal;
+    }
+
     /**
      * Get the type info string
      * @param adapter