Issue 75 - add tests for invoking custom operation framework with query parms

build/pre-integration-test-docker.sh

@@ -15,6 +15,7 @@ fi
 # Set up installers and config files where docker processing can see them
 cd ${WORKSPACE}/fhir-install/docker
 ./copy-dependencies.sh
+./copy-test-operations.sh
 
 # resolve environment variables in the Dockerfile(s).
 cat ./Dockerfile-fhirtest.template | envsubst > ./Dockerfile-fhirtest

build/pre-integration-test.sh

@@ -50,7 +50,10 @@ ${SIT}/fhir-server-dist/install.sh ${SIT}
 
 echo "Copying configuration to install location..."
 rm -fr ${SIT}/wlp/usr/servers/fhir-server/config/*
-cp -pr ${WORKSPACE}/fhir-install/docker/volumes/dist/config/* ${SIT}/wlp/usr/servers/fhir-server/config
+cp -pr ${WORKSPACE}/fhir-install/docker/volumes/dist/config/* ${SIT}/wlp/usr/servers/fhir-server/config/
+
+echo "Copying test artifacts to install location..."
+cp -pr ${WORKSPACE}/fhir-operation/target/fhir-operation-*-tests.jar ${SIT}/wlp/usr/servers/fhir-server/userlib/
 
 # Start up the fhir server
 echo "

fhir-cli/src/main/java/com/ibm/watson/health/fhir/cli/FHIRCLI.java

@@ -76,7 +76,6 @@ public static void main(String[] args) {
     private static final String copyright = "\nFHIR Client Command Line Interface (fhir-cli)    (c) Copyright IBM Corporation, 2018, 2019.\n";
     private static final String header = "\nProvides access to the FHIR Client API via the command line.\n\nOptions:\n";
     private static final String syntax = "fhir-cli [options]";
-    private static final String CONTENT_LENGTH_HEADER = "Content-Length";
     private static final String DEFAULT_MIMETYPE = FHIRMediaType.APPLICATION_FHIR_JSON;
 
     private static PrintStream console = System.err;
@@ -294,22 +293,7 @@ private void processResponse(InvocationContext ic) throws Exception {
                 println("");
             }
 
-            // If the response contains a resource, then display it per user-specified options.
-            // To check for the presence of a resource in the response, we can't fully trust
-            // the Content-Length response header or the JAX-RS Response.hasEntity() method.
-            // The following scenarios are possible:
-            // 1) Response.hasEntity() could return true even if Content-Length = 0
-            // 2) Content-Length might be missing
-            // Result: we'll try to read the resource if Response.hasEntity() returns true,
-            // AND the Content-Length header is not specified as "0".
-            // In other words, if Content-Length is missing or set to something other than 0 and
-            // Response.hasEntity() is true, then we'll try to read the response entity.
-            String contentLengthStr = jaxrsResponse.getHeaderString(CONTENT_LENGTH_HEADER);
-            int contentLength = -1;
-            if (contentLengthStr != null && !contentLengthStr.isEmpty()) {
-                contentLength = Integer.valueOf(contentLengthStr).intValue();
-            }
-            if (jaxrsResponse.hasEntity() && contentLength != 0) {
+            if (!response.isEmpty()) {
                 Resource responseObj = response.getResource(Resource.class);
                 if (responseObj != null) {
                     Writer writer = null;

fhir-client/src/main/java/com/ibm/watson/health/fhir/client/FHIRResponse.java

@@ -105,4 +105,10 @@ public interface FHIRResponse {
      * @throws Exception
      */
     String[] parseLocation(String locationString) throws Exception;
+
+    /**
+     * Returns whether the response contains a FHIR Resource entity.
+     * @return true if the response body is empty, otherwise false 
+     */
+    boolean isEmpty();
 }

fhir-client/src/main/java/com/ibm/watson/health/fhir/client/impl/FHIRResponseImpl.java

@@ -10,11 +10,10 @@
 import java.time.Instant;
 
 import javax.json.JsonObject;
+import javax.ws.rs.core.HttpHeaders;
 import javax.ws.rs.core.Response;
-import javax.xml.datatype.XMLGregorianCalendar;
 
 import com.ibm.watson.health.fhir.client.FHIRResponse;
-import com.ibm.watson.health.fhir.core.FHIRUtilities;
 import com.ibm.watson.health.fhir.model.resource.Resource;
 
 /**
@@ -136,4 +135,24 @@ public String[] parseLocation(String location) throws Exception {
         }
         return result;
     }
+
+    /* (non-Javadoc)
+     * @see com.ibm.watson.health.fhir.client.FHIRResponse#isEmpty()
+     */
+    @Override
+    public boolean isEmpty() {
+        // To check for the presence of a resource in the response, we can't fully trust
+        // the Content-Length response header or the JAX-RS Response.hasEntity() method.
+        // The following scenarios are possible:
+        // 1) Response.hasEntity() could return true even if Content-Length = 0
+        // 2) Content-Length might be missing
+        // Return true if either Response.hasEntity() returns false,
+        // OR the Content-Length header is specified as "0".
+        String contentLengthStr = response.getHeaderString(HttpHeaders.CONTENT_LENGTH);
+        int contentLength = -1;
+        if (contentLengthStr != null && !contentLengthStr.isEmpty()) {
+            contentLength = Integer.valueOf(contentLengthStr).intValue();
+        }
+        return (!response.hasEntity() || contentLength == 0);
+    }
 }

fhir-install/docker/copy-test-operations.sh

@@ -0,0 +1,11 @@
+#!/usr/bin/env bash
+###############################################################################
+# (C) Copyright IBM Corp. 2016, 2019
+#
+# SPDX-License-Identifier: Apache-2.0
+###############################################################################
+
+DIST="volumes/dist"
+
+echo "Copying test artifacts to install location..."
+cp -pr ../../fhir-operation/target/fhir-operation-*-tests.jar $DIST/userlib/

fhir-operation/src/main/java/com/ibm/watson/health/fhir/operation/AbstractOperation.java

@@ -6,7 +6,6 @@
 
 package com.ibm.watson.health.fhir.operation;
 
-import java.lang.reflect.Method;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -41,6 +40,10 @@ public String getName() {
         else return definition.getCode().getValue();
     }
 
+    /**
+     * Validate the input parameters, invoke the operation, validate the output parameters, and return the result.
+     * @throws FHIROperationException if input or output parameters fail validation or an exception occurs
+     */
     @Override
     public final Parameters invoke(FHIROperationContext operationContext, Class<? extends Resource> resourceType, String logicalId, String versionId,
         Parameters parameters, FHIRResourceHelpers resourceHelper) throws FHIROperationException {
@@ -57,6 +60,11 @@ protected int countParameters(Parameters parameters, String name) {
         return getParameters(parameters, name).size();
     }
 
+    /**
+     * This is the method that concrete subclasses must implement to perform the operation logic.
+     * @return The Parameters object to return or null if there is no response Parameters object to return
+     * @throws FHIROperationException
+     */
     protected abstract Parameters doInvoke(FHIROperationContext operationContext, Class<? extends Resource> resourceType, String logicalId, String versionId,
         Parameters parameters, FHIRResourceHelpers resourceHelper) throws FHIROperationException;
 
@@ -82,6 +90,10 @@ protected List<OperationDefinition.Parameter> getParameterDefinitions(OperationP
 
     protected List<Parameters.Parameter> getParameters(Parameters parameters, String name) {
         List<Parameters.Parameter> result = new ArrayList<Parameters.Parameter>();
+        if (parameters == null) {
+             return result;
+        }
+
         for (Parameters.Parameter parameter : parameters.getParameter()) {
             if (parameter.getName() != null && name.equals(parameter.getName().getValue())) {
                 result.add(parameter);
@@ -141,7 +153,7 @@ protected void validateOutputParameters(Parameters result) throws FHIROperationE
         validateParameters(result, OperationParameterUse.OUT);
     }
 
-    protected void validateParameters(Parameters parameters, OperationParameterUse use) throws FHIROperationException {        
+    protected void validateParameters(Parameters parameters, OperationParameterUse use) throws FHIROperationException {
         String direction = OperationParameterUse.IN.equals(use) ? "input" : "output";
 
         // Retrieve the set of parameters from the OperationDefinition matching the specified use (in/out).
@@ -158,7 +170,7 @@ protected void validateParameters(Parameters parameters, OperationParameterUse u
                 throw buildExceptionWithIssue(msg, IssueType.ValueSet.REQUIRED);
             }
             if (!"*".equals(max)) {
-                int maxValue = Integer.parseInt(max);                
+                int maxValue = Integer.parseInt(max);
                 if (count > maxValue) {
                     String msg = "Number of occurrences of " + direction + " parameter: '" + name + "' greater than allowed maximum: " + maxValue;
                     throw buildExceptionWithIssue(msg, IssueType.ValueSet.INVALID);
@@ -199,9 +211,13 @@ protected void validateParameters(Parameters parameters, OperationParameterUse u
             }
         }
 
-        // Next, verify that each parameter contained in the Parameters object is defined
-        // in the OperationDefinition.   This will root out any extaneous parameters included
+
+        // Next, if parameters is not null, verify that each parameter contained in the Parameters object is defined
+        // in the OperationDefinition. This will root out any extaneous parameters included
         // in the Parameters object.
+        if (parameters == null) {
+            return;
+        }
         for (Parameters.Parameter p : parameters.getParameter()) {
             String name = p.getName().getValue();
 

fhir-operation/src/main/java/com/ibm/watson/health/fhir/operation/util/FHIROperationUtil.java

@@ -46,7 +46,6 @@ public static Parameters getInputParameters(OperationDefinition definition,
             Parameters.Builder parametersBuilder = Parameters.builder();
             parametersBuilder.id(Id.of("InputParameters"));
             if (definition != null) {
-
                 for (OperationDefinition.Parameter parameter : definition.getParameter()) {
                     if (OperationParameterUse.IN.getValue().equals(parameter.getUse().getValue())) {
                         String name = parameter.getName().getValue();
@@ -82,6 +81,8 @@ public static Parameters getInputParameters(OperationDefinition definition,
                                 parameterBuilder.value(Code.of(value));
                             } else if ("oid".equals(typeName)) {
                                 parameterBuilder.value(Oid.of(value));
+                            } else if ("id".equals(typeName)) {
+                                parameterBuilder.value(Id.of(value));
                             } else if ("unsignedInt".equals(typeName)) {
                                 parameterBuilder.value(UnsignedInt.of(value));
                             } else if ("positiveInt".equals(typeName)) {
@@ -144,6 +145,9 @@ public static Parameters getOutputParameters(Resource resource) throws Exception
     }
 
     public static boolean hasSingleResourceOutputParameter(Parameters parameters) {
+        if (parameters == null) {
+            return false;
+        }
         return parameters.getParameter().size() == 1 &&
                 "return".equals(parameters.getParameter().get(0).getName().getValue()) &&
                 parameters.getParameter().get(0).getResource() != null;

fhir-operation/src/test/java/com/ibm/watson/health/fhir/operation/test/MyOperation.java

@@ -1,16 +1,21 @@
 /**
- * (C) Copyright IBM Corp. 2016,2017,2018,2019
+ * (C) Copyright IBM Corp. 2016,2019
  *
  * SPDX-License-Identifier: Apache-2.0
  */
 
 package com.ibm.watson.health.fhir.operation.test;
 
+import static com.ibm.watson.health.fhir.model.type.String.string;
+
+import java.util.Arrays;
+import java.util.List;
+
 import com.ibm.watson.health.fhir.exception.FHIROperationException;
 import com.ibm.watson.health.fhir.model.resource.OperationDefinition;
 import com.ibm.watson.health.fhir.model.resource.Parameters;
-import com.ibm.watson.health.fhir.model.resource.Resource;
 import com.ibm.watson.health.fhir.model.resource.Parameters.Parameter;
+import com.ibm.watson.health.fhir.model.resource.Resource;
 import com.ibm.watson.health.fhir.model.type.Boolean;
 import com.ibm.watson.health.fhir.model.type.Code;
 import com.ibm.watson.health.fhir.model.type.FHIRAllTypes;
@@ -27,30 +32,67 @@
 public class MyOperation extends AbstractOperation {
     @Override
     protected OperationDefinition buildOperationDefinition() {
-        OperationDefinition.Builder OperationDefinitionBuilder =  OperationDefinition.builder().name(String.of("My Operation")).status( 
-        		PublicationStatus.of(PublicationStatus.ValueSet.DRAFT)).kind(OperationKind.of(OperationKind.ValueSet.OPERATION)).code(Code.of("hello")).affectsState(Boolean.of(true)).experimental( Boolean.of(true)).instance(Boolean.of(false));
-
-        OperationDefinition.Parameter.Builder inputParameterBuilder = OperationDefinition.Parameter.builder().name(Code.of("input")).use( 
-            OperationParameterUse.OUT).min(Integer.of(1)).id("1");
-
-        OperationDefinitionBuilder.parameter(inputParameterBuilder.type(FHIRAllTypes.STRING).build());
-
-        OperationDefinition.Parameter.Builder outputParameterBuilder = OperationDefinition.Parameter.builder().name(Code.of("output")).use( 
-        		OperationParameterUse.OUT).min(Integer.of(1)).id("1");
-
-        OperationDefinitionBuilder.parameter(outputParameterBuilder.type(FHIRAllTypes.STRING).build());
+        OperationDefinition.Builder operationDefinitionBuilder =  OperationDefinition.builder()
+                .name(String.of("My Operation"))
+                .status(PublicationStatus.of(PublicationStatus.ValueSet.DRAFT))
+                .kind(OperationKind.of(OperationKind.ValueSet.OPERATION))
+                .code(Code.of("hello"))
+                .affectsState(Boolean.of(true))
+                .system(Boolean.of(true))
+                .type(Boolean.of(false))
+                .experimental(Boolean.of(true))
+                .instance(Boolean.of(false));
 
+        // All primitives except "xhtml" and "base64Binary"
+        List<FHIRAllTypes> primitives = Arrays.asList(
+            FHIRAllTypes.BOOLEAN, FHIRAllTypes.CANONICAL, FHIRAllTypes.CODE, FHIRAllTypes.DATE, 
+            FHIRAllTypes.DATE_TIME, FHIRAllTypes.ID, FHIRAllTypes.INSTANT, FHIRAllTypes.INTEGER,
+            FHIRAllTypes.OID, FHIRAllTypes.POSITIVE_INT, FHIRAllTypes.STRING, FHIRAllTypes.TIME,
+            FHIRAllTypes.UNSIGNED_INT, FHIRAllTypes.URI, FHIRAllTypes.URL, FHIRAllTypes.UUID);
 
-        return OperationDefinitionBuilder.build();
+        for (FHIRAllTypes primitive : primitives) {
+            OperationDefinition.Parameter inputParameter = OperationDefinition.Parameter.builder()
+                    .name(Code.of("input-" + primitive.getValue()))
+                    .use(OperationParameterUse.IN)
+                    .min(Integer.of(0))
+                    .max(string("1"))
+                    .type(primitive)
+                    .id("1")
+                    .build();
+            operationDefinitionBuilder.parameter(inputParameter);
+
+            OperationDefinition.Parameter outputParameter = OperationDefinition.Parameter.builder()
+                    .name(Code.of("output-" + primitive.getValue()))
+                    .use(OperationParameterUse.OUT)
+                    .min(Integer.of(0))
+                    .max(string("1"))
+                    .type(primitive)
+                    .id("1")
+                    .build();
+            operationDefinitionBuilder.parameter(outputParameter);
+        }
+
+        return operationDefinitionBuilder.build();
     }
 
     @Override
     protected Parameters doInvoke(FHIROperationContext context, Class<? extends Resource> resourceType, java.lang.String logicalId, java.lang.String versionId, Parameters parameters, FHIRResourceHelpers resourceHelper)
         throws FHIROperationException {
         try {
-            Parameter inputParameter = parameters.getParameter().get(0);
+            if (parameters.getParameter().isEmpty()) {
+                return null;
+            }
+
+            Parameters.Builder returnParametersBuilder = Parameters.builder();
+
+            for (Parameter inputParameter : parameters.getParameter()) {
+                returnParametersBuilder.parameter(Parameter.builder()
+                    .name(string(inputParameter.getName().getValue().replace("input", "output")))
+                    .value(inputParameter.getValue())
+                    .build());
+            }
 
-            return Parameters.builder().parameter(Parameter.builder().name(String.of("output")).value(inputParameter.getValue()).build()).build();
+            return returnParametersBuilder.build();
         } catch (Exception e) {
             throw new FHIROperationException("An error occured invoking operation: " + getName(), e);
         }