Move Liberty OAuth tables to the FHIR_OAUTH schema and gen by default

Previously, a user needed to create these tables themselves if they
wanted to use liberty as an OAuth 2.0 provider with a databaseStore
(e.g. to dynamically manage OAuth 2.0 clients).

Now these tables will be created/updated as part of the
fhir-persistence-schema create-schema/update-schema actions, or as part
of derby bootstrapping.

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

docs/src/pages/guides/FHIRServerUsersGuide.md

@@ -220,9 +220,9 @@ To configure the FHIR server to use the JDBC persistence layer, complete the fol
 1.  First, modify the `fhirServer/persistence/factoryClassname` property in `fhir-server-config.json` to specify the JDBC persistence factory, like this:
     ```
     {
-        “fhirServer”: {
+        "fhirServer": {
             …
-            “persistence”: {
+            "persistence": {
                 "factoryClassname": "com.ibm.fhir.persistence.jdbc.FHIRPersistenceJDBCFactory",
                 …
             }
@@ -232,13 +232,13 @@ To configure the FHIR server to use the JDBC persistence layer, complete the fol
 2.  Next, modify the `fhirServer/persistence/jdbc/dataSourceJndiName` property in `fhir-server-config.json` to specify the proxy datasource's JNDI name, like this:
     ```
     {
-        “fhirServer”: {
+        "fhirServer": {
             …
-            “persistence”: {
+            "persistence": {
                 …
                 "jdbc": {
                     …
-                    “dataSourceJndiName”: “jdbc/fhirProxyDataSource”
+                    "dataSourceJndiName": "jdbc/fhirProxyDataSource"
                 }
                 …
             }
@@ -557,7 +557,7 @@ By default, notification messages are published for all _create_ and _update_ pe
             "common":{
                 "includeResourceTypes":[
                      "Observation",
-                     “Patient”
+                     "Patient"
                 ]
             },
         …
@@ -851,7 +851,7 @@ Response resource:
 ```
 
 ## 4.8 Using local references within request bundles
-Inter-dependencies between resources are typically defined by one resource containing a field of type `Reference` which contains an _external reference_<sup id="a5">[5](#f5)</sup> to another resource. For example, an `Observation` resource could reference a `Patient` resource via the Observation's `subject` field. The value that is stored in the `Reference-type` field (for example, `subject` in the case of the `Observation` resource) could be an absolute URL, such as `https://fhirserver1:9443/fhir-server/api/v4/Patient/12345`, or a relative URL (for example, `“Patient/12345”`).
+Inter-dependencies between resources are typically defined by one resource containing a field of type `Reference` which contains an _external reference_<sup id="a5">[5](#f5)</sup> to another resource. For example, an `Observation` resource could reference a `Patient` resource via the Observation's `subject` field. The value that is stored in the `Reference-type` field (for example, `subject` in the case of the `Observation` resource) could be an absolute URL, such as `https://fhirserver1:9443/fhir-server/api/v4/Patient/12345`, or a relative URL (for example, `Patient/12345`).
 
 In order to establish a reference to a resource, you must first know its resource identifier. However, if you are using a request bundle to create both the referenced resource (`Patient` in this example) and the resource which references it (`Observation`), then it is impossible to know the `Patient`resource identifier before the request bundle has been process (that is, before the new `Patient` resource is created).
 

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;
@@ -499,4 +500,14 @@ 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;
@@ -431,22 +430,6 @@ 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

@@ -236,14 +236,6 @@ 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

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

@@ -1,5 +1,5 @@
 /*
- * (C) Copyright IBM Corp. 2019
+ * (C) Copyright IBM Corp. 2019, 2020
  *
  * SPDX-License-Identifier: Apache-2.0
  */
@@ -16,19 +16,20 @@ public class ColumnDef implements Comparable<ColumnDef> {
     private long size;
     private Integer precision;
     private int inlineSize;
-
+    private String defaultVal;
+
     /**
      * Public constructor
      * @param name
      */
     public ColumnDef(String name) {
         this.name = name;
     }
-    
+
     public String getName() {
         return name;
     }
-    
+
     public boolean isNullable() {
         return nullable;
     }
@@ -53,13 +54,22 @@ public Integer getPrecision() {
     public void setPrecision(int precision) {
         this.precision = precision;
     }
+    public String getDefaultVal() {
+        return defaultVal;
+    }
+    /**
+     * @implNote Currently only works for CLOB columns
+     */
+    public void setDefaultVal(String defaultVal) {
+        this.defaultVal = defaultVal;
+    }
 
     @Override
     public int compareTo(ColumnDef that) {
         return this.name.compareTo(that.name);
     }
-    
-    @Override 
+
+    @Override
     public boolean equals(Object other) {
         if (other instanceof ColumnDef) {
             ColumnDef that = (ColumnDef)other;
@@ -69,8 +79,8 @@ public boolean equals(Object other) {
             return false;
         }
     }
-    
-    @Override 
+
+    @Override
     public int hashCode() {
         return this.name.hashCode();
     }
@@ -82,5 +92,4 @@ public int getInlineSize() {
     public void setInlineSize(int inlineSize) {
         this.inlineSize = inlineSize;
     }
-
 }

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

@@ -173,6 +173,9 @@ public List<ColumnBase> buildColumns() {
             case BLOB:
                 column = new BlobColumn(cd.getName(), cd.getSize(), cd.getInlineSize(), cd.isNullable());
                 break;
+            case CLOB:
+                column = new ClobColumn(cd.getName(), cd.isNullable(), cd.getDefaultVal());
+                break;
             default:
                 throw new IllegalStateException("Unsupported column type: " + cd.getColumnType().name());
             }

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

@@ -1,5 +1,5 @@
 /*
- * (C) Copyright IBM Corp. 2019
+ * (C) Copyright IBM Corp. 2019, 2020
  *
  * SPDX-License-Identifier: Apache-2.0
  */
@@ -18,5 +18,6 @@ public enum ColumnType {
     DECIMAL,
     DOUBLE,
     TIMESTAMP,
-    BLOB
+    BLOB,
+    CLOB
 }

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

@@ -1,5 +1,5 @@
 /*
- * (C) Copyright IBM Corp. 2019
+ * (C) Copyright IBM Corp. 2019, 2020
  *
  * SPDX-License-Identifier: Apache-2.0
  */
@@ -10,7 +10,7 @@
  * Basic set of privileges that can be granted to a database object
  */
 public enum Privilege {
-
+    ALL,
     SELECT,
     INSERT,
     UPDATE,