Merge pull request #320 from IBM/issue-2

issue #2 - condense projects and update FHIRServerUsersGuide.md

docs/Conformance.md

@@ -4,11 +4,22 @@ The IBM FHIR Server aims to be a conformant implementation of the HL7 FHIR speci
 ## Capability statement
 The HL7 FHIR specification defines [an interaction](https://www.hl7.org/fhir/R4/http.html#capabilities) for retrieving a machine-readable description of the server's capabilities via the `[base]/metadata` endpoint. The IBM FHIR Server implements this interaction and generates a `CapabilityStatement` resource based on the current server configuration. While the `CapabilityStatement` resource is ideal for certain uses, this markdown document provides a human-readable summary of important details, with a special focus on limitations of the current implementation and deviations from the specification.
 
+The IBM FHIR Server supports only version 4.0.0 of the specification and presently has no support for the MIME-type parameter `fhirVersion`.
+
 ## FHIR HTTP API
-The HL7 FHIR specification is more than just a data format. It defines an [HTTP API](https://www.hl7.org/fhir/R4/http.html) for creating, reading, updating, deleting, and searching over FHIR resources. The IBM FHIR Server implements the full API for every resource defined in the specification, with the following exceptions:
+The HL7 FHIR specification is more than just a data format. It defines an [HTTP API](https://www.hl7.org/fhir/R4/http.html) for creating, reading, updating, deleting, and searching over FHIR resources. The IBM FHIR Server implements almost the full API for every resource defined in the specification, with the following exceptions:
 * history is only supported at the resource instance level (no resource type history and no whole-system history)
 * there are parts of the FHIR search specification which are not fully implemented as documented in the following section
 
+The IBM FHIR Server implements a linear versioning scheme for resources and fully implements the `vread` and `history` interactions, as well as version-aware updates.
+
+### General parameters
+The `_format` parameter is supported and provides a useful mechanism for requesting a specific format (`XML` or `JSON`) in requests made from a browser. In the absence of either an `Accept` header or a `_format` query parameter, the server defaults to `application/fhir+json`.
+
+The `_pretty` parameter is not currently supported, but should be added as part of https://github.com/IBM/FHIR/issues/269.
+
+The `_summary` and `_elements` parameters are supported on the search interaction as documented.
+
 ## Search
 The IBM FHIR Server supports search parameters of type `Number`, `Date/DateTime`, `String`, `Token`, `Reference`, `Quantity`, and `URI`.
 

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

@@ -4,11 +4,10 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-package com.ibm.fhir.client.sample;
+package com.ibm.fhir.client.test.mains;
 
 import static com.ibm.fhir.model.type.String.string;
 
-import java.io.ByteArrayOutputStream;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
@@ -21,6 +20,7 @@
 import com.ibm.fhir.client.FHIRClientFactory;
 import com.ibm.fhir.client.FHIRResponse;
 import com.ibm.fhir.model.format.Format;
+import com.ibm.fhir.model.generator.FHIRGenerator;
 import com.ibm.fhir.model.resource.Observation;
 import com.ibm.fhir.model.resource.OperationOutcome;
 import com.ibm.fhir.model.resource.Patient;
@@ -36,7 +36,6 @@
 import com.ibm.fhir.model.type.code.ContactPointSystem;
 import com.ibm.fhir.model.type.code.ContactPointUse;
 import com.ibm.fhir.model.type.code.ObservationStatus;
-import com.ibm.fhir.model.util.FHIRUtil;
 
 /**
  * This class is sample code that demonstrates the use of the FHIR Server's Client API. This sample is not necessarily
@@ -51,9 +50,6 @@ public static void main(String[] args) throws Exception {
         sample.run();
     }
 
-    public FHIRClientSample() {
-    }
-
     public void run() throws Exception {
         String location;
 
@@ -169,9 +165,7 @@ protected String getLocationLogicalId(String location) {
     private void displayOperationOutcome(FHIRResponse response) {
         try {
             OperationOutcome oo = response.getResource(OperationOutcome.class);
-            ByteArrayOutputStream baos = new ByteArrayOutputStream();
-            FHIRUtil.write(oo, Format.JSON, baos);
-            System.out.println("OperationOutcome: \n" + baos.toString());
+            FHIRGenerator.generator(Format.JSON).generate(oo, System.out);
         } catch (Throwable t) {
             System.out.println("Could not display OperationOutcome from REST API response.");
         }

fhir-connectathon-clients/src/test/java/com/ibm/fhir/connectathon/patient/PatientTrackTest.java → fhir-client/src/test/java/com/ibm/fhir/client/test/mains/PatientTrackTest.java

@@ -4,7 +4,7 @@
  * SPDX-License-Identifier: Apache-2.0
  */
 
-package com.ibm.fhir.connectathon.patient;
+package com.ibm.fhir.client.test.mains;
 
 import static com.ibm.fhir.client.FHIRRequestHeader.header;
 import static com.ibm.fhir.model.type.String.string;
@@ -17,8 +17,6 @@
 import javax.ws.rs.core.Response;
 import javax.ws.rs.core.Response.Status;
 
-import org.testng.annotations.Test;
-
 import com.ibm.fhir.client.FHIRClient;
 import com.ibm.fhir.client.FHIRClientFactory;
 import com.ibm.fhir.client.FHIRParameters;
@@ -62,12 +60,10 @@ private static void log(String msg) {
         System.out.println(msg);
     }
 
-    @Test
     public void printHeader() {
-        log("Starting execution of PatientTrackTest (c) IBM Corporation, 2016.");
+        log("Starting execution of PatientTrackTest (C) IBM Corporation 2016,2019.");
     }
 
-    @Test(dependsOnMethods = { "printHeader" })
     public void connectToServer() throws Exception {
         // Load up our properties file.
         Properties clientProperties = readProperties(CLIENT_PROPERTIES_FILENAME);
@@ -79,7 +75,6 @@ public void connectToServer() throws Exception {
         log("Connecting to FHIR endpoint: " + baseUrl);
     }
 
-    @Test(dependsOnMethods = { "connectToServer" })
     public void inspectConformanceStatement() throws Exception {
         FHIRResponse response = client.metadata();
         if (response.getStatus() != Status.OK.getStatusCode()) {
@@ -118,7 +113,6 @@ public void inspectConformanceStatement() throws Exception {
         log("Server supports search? " + (supportsSearch ? "yes" : "no"));
     }
 
-    @Test(dependsOnMethods = { "inspectConformanceStatement" })
     public void registerPatient() throws Exception {
 
         String location;
@@ -154,7 +148,6 @@ public void registerPatient() throws Exception {
         patient = displayResponsePatient("Retrieved newly-registered patient:", client, response);
     }
 
-    @Test(dependsOnMethods = { "registerPatient" })
     public void updatePatient() throws Exception {
         log("\n2) Update a patient");
         if (!supportsUpdate) {
@@ -195,7 +188,6 @@ public void updatePatient() throws Exception {
         }
     }
 
-    @Test(dependsOnMethods = { "updatePatient" })
     public void retrieveHistory() throws Exception {
         log("\n3) Retrieve patient history");
         if (!supportsHistory) {
@@ -217,7 +209,6 @@ public void retrieveHistory() throws Exception {
 
     }
 
-    @Test(dependsOnMethods = { "retrieveHistory" })
     public void searchByName() throws Exception {
         // 4) Search for a patient by name.
         log("\n4) Search for a patient by name");
@@ -333,4 +324,15 @@ private Patient modifyPatientContents(Patient patient) {
 
         return patient;
     }
+
+    public static void main(String[] args) throws Exception {
+        PatientTrackTest test = new PatientTrackTest();
+        test.printHeader();
+        test.connectToServer();
+        test.inspectConformanceStatement();
+        test.registerPatient();
+        test.updatePatient();
+        test.retrieveHistory();
+        test.searchByName();
+    }
 }

fhir-config/src/main/java/com/ibm/fhir/config/FHIRConfiguration.java

@@ -12,63 +12,67 @@
 import java.util.List;
 import java.util.logging.Logger;
 
+/**
+ * This class serves up a singleton instance of ConfigurationService containing the FHIR Server's configuration.
+ */
 public class FHIRConfiguration {
 
     private static final Logger log = Logger.getLogger(FHIRConfiguration.class.getName());
 
-    /**
-     * This class serves up a singleton instance of ConfigurationService containing the FHIR Server's configuration.
-     */
     public static final String CONFIG_LOCATION = "config";
     public static final String CONFIG_FILE_BASENAME = "fhir-server-config.json";
     public static final String DEFAULT_TENANT_ID = "default";
     public static final String DEFAULT_DATASTORE_ID = "default";
 
-    // Configuration properties used by various FHIR Server components.
+    // Core server properties
+    public static final String PROPERTY_TENANT_ID_HEADER_NAME = "fhirServer/core/tenantIdHeaderName";
+    public static final String PROPERTY_DATASTORE_ID_HEADER_NAME = "fhirServer/core/datastoreIdHeaderName";
+    public static final String PROPERTY_DEFAULT_TENANT_ID = "fhirServer/core/defaultTenantId";
+    public static final String PROPERTY_DEFAULT_PRETTY_PRINT = "fhirServer/core/defaultPrettyPrint";
+
+    public static final String PROPERTY_SEARCH_PARAMETER_FILTER = "fhirServer/searchParameterFilter";
+
+    // Auth and security properties
     public static final String PROPERTY_TRUSTSTORE_LOCATION = "fhirServer/core/truststoreLocation";
     public static final String PROPERTY_TRUSTSTORE_PASSWORD = "fhirServer/core/truststorePassword";
     public static final String PROPERTY_OAUTH_REGURL = "fhirServer/oauth/regUrl";
     public static final String PROPERTY_OAUTH_AUTHURL = "fhirServer/oauth/authUrl";
     public static final String PROPERTY_OAUTH_TOKENURL = "fhirServer/oauth/tokenUrl";
+
+    public static final String PROPERTY_AUTHFILTER_ENABLED = "fhirServer/authFilter/enabled";
+    public static final String PROPERTY_AUTHORIZED_CLIENT_CERT_CLIENT_CN = "fhirServer/authFilter/authorizedClientCertClientCN";
+    public static final String PROPERTY_AUTHORIZED_CLIENT_CERT_ISSUER_OU = "fhirServer/authFilter/authorizedClientCertIssuerOU";
+
+    // Audit config properties
     public static final String PROPERTY_AUDIT_SERVICE_CLASS_NAME = "fhirServer/audit/serviceClassName";
     public static final String PROPERTY_AUDIT_SERVICE_PROPERTIES = "fhirServer/audit/serviceProperties";
     public static final String PROPERTY_AUDIT_PATIENT_ID_EXTURL = "fhirServer/audit/patientIdExtensionUrl";
     public static final String PROPERTY_AUDIT_RESOURCE_NAME_EXTURL = "fhirServer/audit/resourceNameExtensionUrl";
-    public static final String PROPERTY_ENCRYPTION = "fhirServer/encryption";
     public static final String PROPERTY_UPDATE_CREATE_ENABLED = "fhirServer/persistence/common/updateCreateEnabled";
+
+    // Notification config properties
     public static final String PROPERTY_NOTIFICATION_RESOURCE_TYPES = "fhirServer/notifications/common/includeResourceTypes";
     public static final String PROPERTY_WEBSOCKET_ENABLED = "fhirServer/notifications/websocket/enabled";
     public static final String PROPERTY_KAFKA_ENABLED = "fhirServer/notifications/kafka/enabled";
     public static final String PROPERTY_KAFKA_TOPICNAME = "fhirServer/notifications/kafka/topicName";
     public static final String PROPERTY_KAFKA_CONNECTIONPROPS = "fhirServer/notifications/kafka/connectionProperties";
+
+    // Persistence layer properties
     public static final String PROPERTY_PERSISTENCE_FACTORY = "fhirServer/persistence/factoryClassname";
+    public static final String PROPERTY_DATASOURCES = "fhirServer/persistence/datasources";
     public static final String PROPERTY_JDBC_BOOTSTRAP_DB = "fhirServer/persistence/jdbc/bootstrapDb";
     public static final String PROPERTY_JDBC_DATASOURCE_JNDINAME = "fhirServer/persistence/jdbc/dataSourceJndiName";
     public static final String PROPERTY_JDBC_ENABLE_CODE_SYSTEMS_CACHE = "fhirServer/persistence/jdbc/enableCodeSystemsCache";
     public static final String PROPERTY_JDBC_ENABLE_PARAMETER_NAMES_CACHE = "fhirServer/persistence/jdbc/enableParameterNamesCache";
     public static final String PROPERTY_JDBC_ENABLE_RESOURCE_TYPES_CACHE = "fhirServer/persistence/jdbc/enableResourceTypesCache";
-    public static final String PROPERTY_TENANT_ID_HEADER_NAME = "fhirServer/core/tenantIdHeaderName";
-    public static final String PROPERTY_DATASTORE_ID_HEADER_NAME = "fhirServer/core/datastoreIdHeaderName";
-    public static final String PROPERTY_DEFAULT_TENANT_ID = "fhirServer/core/defaultTenantId";
-    public static final String PROPERTY_DEFAULT_PRETTY_PRINT = "fhirServer/core/defaultPrettyPrint";
-    public static final String PROPERTY_JSON_PARSER_LENIENT = "fhirServer/core/jsonParserLenient";
-    public static final String PROPERTY_JSON_PARSER_VALIDATING = "fhirServer/core/jsonParserValidating";
-    public static final String PROPERTY_DATASOURCES = "fhirServer/persistence/datasources";
-    public static final String PROPERTY_SEARCH_PARAMETER_FILTER = "fhirServer/searchParameterFilter";
-    public static final String PROPERTY_AUTHFILTER_ENABLED = "fhirServer/authFilter/enabled";
-    public static final String PROPERTY_AUTHORIZED_CLIENT_CERT_CLIENT_CN = "fhirServer/authFilter/authorizedClientCertClientCN";
-    public static final String PROPERTY_AUTHORIZED_CLIENT_CERT_ISSUER_OU = "fhirServer/authFilter/authorizedClientCertIssuerOU";
 
-    public static final String PROPERTY_RESOURCE_TYPES_REQUIRING_SUBJECT_ID = "fhirServer/whclsfRouter/resourceNamesRequiringPatientId";
-    public static final String PROPERTY_STUDY_SCOPED_RESOURCES = "fhirServer/whclsfRouter/resourceNamesRequiringConsentEnforcement";
-
+    // Custom header names
     public static final String DEFAULT_TENANT_ID_HEADER_NAME = "X-FHIR-TENANT-ID";
     public static final String DEFAULT_DATASTORE_ID_HEADER_NAME = "X-FHIR-DSID";
     public static final String DEFAULT_PRETTY_RESPONSE_HEADER_NAME = "X-FHIR-FORMATTED";
 
     public static final String FHIR_SERVER_DEFAULT_CONFIG = "config/default/fhir-server-config.json";
 
-
     // Optional "home directory" for config files.  Defaults to current directory.
     private static String configHome = "";
 
@@ -86,8 +90,10 @@ public static FHIRConfiguration getInstance() {
     /**
      * This method is used to configure an explicit top-level directory where FHIR Server configuration
      * information is expected to reside.
+     * <p>
      * For example, by calling this method with value "/mydir", then we'd expect
-     * to find config files whose names are of the form: <code> "/mydir/config/&lt;tenant-id&rt;/fhir-server-config.json".</code>
+     * to find config files whose names are of the form: {@code "/mydir/config/<tenant-id>/fhir-server-config.json"}
+     * <p>
      * The default location for config files is the current working directory (i.e. "" - the empty string).
      * @param s the new config home directory name 
      */
@@ -104,7 +110,8 @@ public static void setConfigHome(String s) {
 
     /**
      * Returns the "home" directory for FHIR Server configuration information (this directory will contain
-     * the "config" directory, etc.).   
+     * the "config" directory, etc.).
+     * <p>
      * The default value of this property is "" which is interpretted to mean the current working directory
      * (which for a running FHIR Server will be $WLP_HOME/wlp/usr/servers/fhir-server).
      */

fhir-config/src/test/java/com/ibm/fhir/config/test/FHIRConfigHelperTest.java

@@ -274,19 +274,6 @@ public void testTenant5() throws Exception {
         l = FHIRConfigHelper.getStringListProperty("collection/groupB/stringList1");
         assertNotNull(l);
         assertEquals(expectedList1, l);
-
-        PropertyGroup pg = FHIRConfigHelper.getPropertyGroup("whclsfRouter/config");
-        assertNotNull(pg);
-        assertNotNull(pg.getBooleanProperty("supportsTransaction"));
-        assertNotNull(pg.getArrayProperty("routingRules"));
-
-        b = FHIRConfigHelper.getBooleanProperty("whclsfRouter/consentEnforcementEnabled", null);
-        assertNotNull(b);
-        assertEquals(Boolean.TRUE, b);
-
-        b = FHIRConfigHelper.getBooleanProperty("whclsfRouter/consentManagementEnabled", null);
-        assertNotNull(b);
-        assertEquals(Boolean.FALSE, b);
     }
 
     @Test