Merge pull request #3685 from IBM/issue-3242-export

issue #3242 - use the fhirVersion from the import/export request
LinuxForHealth · Jun 10, 2022 · e796463 · e796463
2 parents 00bb3b3 + 1410fb0
commit e796463
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Showing 8 changed files with 46 additions and 34 deletions.
diff --git a/...hir-operation-bulkdata/src/main/java/com/ibm/fhir/operation/bulkdata/ExportOperation.java b/...hir-operation-bulkdata/src/main/java/com/ibm/fhir/operation/bulkdata/ExportOperation.java
@@ -12,6 +12,7 @@
 import javax.ws.rs.core.MediaType;
 
 import com.ibm.fhir.core.FHIRMediaType;
+import com.ibm.fhir.core.FHIRVersionParam;
 import com.ibm.fhir.exception.FHIROperationException;
 import com.ibm.fhir.model.resource.OperationDefinition;
 import com.ibm.fhir.model.resource.Parameters;
@@ -66,7 +67,8 @@ protected Parameters doInvoke(FHIROperationContext operationContext, Class<? ext
         Parameters response = null;
         OperationConstants.ExportType exportType = export.checkExportType(operationContext.getType(), resourceType);
 
-        Set<String> types = export.checkAndValidateTypes(exportType, getParameters(parameters, OperationConstants.PARAM_TYPE));
+        FHIRVersionParam fhirVersion = (FHIRVersionParam) operationContext.getProperty(FHIROperationContext.PROPNAME_FHIR_VERSION);
+        Set<String> types = export.checkAndValidateTypes(exportType, fhirVersion, getParameters(parameters, OperationConstants.PARAM_TYPE));
 
         if (!ExportType.INVALID.equals(exportType)) {
 

diff --git a/...hir-operation-bulkdata/src/main/java/com/ibm/fhir/operation/bulkdata/ImportOperation.java b/...hir-operation-bulkdata/src/main/java/com/ibm/fhir/operation/bulkdata/ImportOperation.java
@@ -9,6 +9,7 @@
 import java.io.InputStream;
 import java.util.List;
 
+import com.ibm.fhir.core.FHIRVersionParam;
 import com.ibm.fhir.exception.FHIROperationException;
 import com.ibm.fhir.model.format.Format;
 import com.ibm.fhir.model.parser.FHIRParser;
@@ -70,7 +71,8 @@ protected Parameters doInvoke(FHIROperationContext operationContext, Class<? ext
         String inputSource = util.retrieveInputSource();
 
         // Parameter: input
-        List<Input> inputs = util.retrieveInputs();
+        FHIRVersionParam fhirVersion = (FHIRVersionParam) operationContext.getProperty(FHIROperationContext.PROPNAME_FHIR_VERSION);
+        List<Input> inputs = util.retrieveInputs(fhirVersion);
 
         // Parameter: storageDetail
         StorageDetail storageDetail = util.retrieveStorageDetails();
@@ -86,7 +88,7 @@ private void checkImportType(FHIROperationContext.Type type) throws FHIROperatio
         // Check Import Type is System.  We only support system right now.
 
         if (!FHIROperationContext.Type.SYSTEM.equals(type)) {
-            throw buildExceptionWithIssue("Invalid call $import operation call only system is allowed",
+            throw buildExceptionWithIssue("Invalid call; $import can only be invoked at the system level",
                     IssueType.INVALID);
         }
     }

diff --git a/...a/src/main/java/com/ibm/fhir/operation/bulkdata/config/preflight/impl/AzurePreflight.java b/...a/src/main/java/com/ibm/fhir/operation/bulkdata/config/preflight/impl/AzurePreflight.java
@@ -1,5 +1,5 @@
 /*
- * (C) Copyright IBM Corp. 2021
+ * (C) Copyright IBM Corp. 2021, 2022
  *
  * SPDX-License-Identifier: Apache-2.0
  */
@@ -41,13 +41,13 @@ public void preflight() throws FHIROperationException {
     /**
      * validates the azure provider is properly configured.
      *
-     * @param source
+     * @param storageProvider
      * @throws FHIROperationException
      */
-    public void validate(String source) throws FHIROperationException {
+    public void validate(String storageProvider) throws FHIROperationException {
         ConfigurationAdapter adapter = ConfigurationFactory.getInstance();
-        if (adapter.isStorageProviderAuthTypeConnectionString(source)) {
-            String conn = adapter.getStorageProviderAuthTypeConnectionString(source);
+        if (adapter.isStorageProviderAuthTypeConnectionString(storageProvider)) {
+            String conn = adapter.getStorageProviderAuthTypeConnectionString(storageProvider);
             if (conn == null || conn.isEmpty()) {
                 throw export.buildOperationException("bad configuration for the Azure Blob Container's connection configuration", IssueType.EXCEPTION);
             }
@@ -56,7 +56,7 @@ public void validate(String source) throws FHIROperationException {
         }
 
         // Used to get the Azure Container
-        if (adapter.getStorageProviderBucketName(source) == null || adapter.getStorageProviderBucketName(source).isEmpty()) {
+        if (adapter.getStorageProviderBucketName(storageProvider) == null || adapter.getStorageProviderBucketName(storageProvider).isEmpty()) {
             throw export.buildOperationException("bad configuration for the basic configuration with bucketname", IssueType.EXCEPTION);
         }
     }

diff --git a/...ation-bulkdata/src/main/java/com/ibm/fhir/operation/bulkdata/util/BulkDataExportUtil.java b/...ation-bulkdata/src/main/java/com/ibm/fhir/operation/bulkdata/util/BulkDataExportUtil.java
@@ -22,6 +22,7 @@
 
 import com.ibm.fhir.config.FHIRConfigHelper;
 import com.ibm.fhir.core.FHIRMediaType;
+import com.ibm.fhir.core.FHIRVersionParam;
 import com.ibm.fhir.exception.FHIROperationException;
 import com.ibm.fhir.model.resource.OperationOutcome.Issue;
 import com.ibm.fhir.model.resource.Parameters;
@@ -161,11 +162,13 @@ public Instant checkAndExtractSince(Parameters parameters) {
      * processes both the Parameters object and the query parameters
      *
      * @param exportType
+     * @param fhirVersion
      * @param parameters
      * @return
      * @throws FHIROperationException
      */
-    public Set<String> checkAndValidateTypes(OperationConstants.ExportType exportType, List<Parameter> parameters) throws FHIROperationException {
+    public Set<String> checkAndValidateTypes(OperationConstants.ExportType exportType, FHIRVersionParam fhirVersion, List<Parameter> parameters)
+            throws FHIROperationException {
         /*
          * Only resources of the specified resource types(s) SHALL be included in the response. If this parameter is
          * omitted, the server SHALL return all supported resources within the scope of the client authorization. For
@@ -179,7 +182,7 @@ public Set<String> checkAndValidateTypes(OperationConstants.ExportType exportTyp
          * within the file set. For example _type=Practitioner could be used to bulk data extract all Practitioner
          * resources from a FHIR endpoint.
          */
-        Set<String> supportedResourceTypes = FHIRConfigHelper.getSupportedResourceTypes();
+        Set<String> supportedResourceTypes = FHIRConfigHelper.getSupportedResourceTypes(fhirVersion);
         Set<String> result = new HashSet<>();
         if (parameters != null) {
             for (Parameters.Parameter parameter : parameters) {
@@ -203,7 +206,7 @@ public Set<String> checkAndValidateTypes(OperationConstants.ExportType exportTyp
             }
         }
 
-        // The case where no resourceTypes are specified, inlining only the supported ResourceTypes
+        // The case where no resourceTypes are specified on a system export, inlining only the supported ResourceTypes
         if (result.isEmpty() && ExportType.SYSTEM.equals(exportType)) {
             result = new HashSet<>(supportedResourceTypes);
         } else if (ExportType.PATIENT.equals(exportType) || ExportType.GROUP.equals(exportType)) {
@@ -234,7 +237,7 @@ private Set<String> filterTypesToPatientResourceTypes(Set<String> resourceTypes)
                 result.add(resourceType);
             } else {
                 LOG.info("Requested type '" + Encode.forHtml(resourceType) + "' cannot be in the Patient compartment;"
-                        + "this is not supported for Patient/Group export and so this type will be skipped");
+                        + " this is not supported for Patient/Group export and so this type will be skipped");
             }
         }
 

diff --git a/...ation-bulkdata/src/main/java/com/ibm/fhir/operation/bulkdata/util/BulkDataImportUtil.java b/...ation-bulkdata/src/main/java/com/ibm/fhir/operation/bulkdata/util/BulkDataImportUtil.java
@@ -6,6 +6,7 @@
 
 package com.ibm.fhir.operation.bulkdata.util;
 
+import static com.ibm.fhir.model.util.ModelSupport.FHIR_STRING;
 import static com.ibm.fhir.operation.bulkdata.util.CommonUtil.buildExceptionWithIssue;
 
 import java.util.ArrayList;
@@ -16,8 +17,10 @@
 import java.util.Set;
 
 import com.ibm.fhir.config.FHIRConfigHelper;
+import com.ibm.fhir.core.FHIRVersionParam;
 import com.ibm.fhir.exception.FHIROperationException;
 import com.ibm.fhir.model.resource.Parameters;
+import com.ibm.fhir.model.type.Uri;
 import com.ibm.fhir.model.type.code.IssueType;
 import com.ibm.fhir.model.util.ModelSupport;
 import com.ibm.fhir.operation.bulkdata.OperationConstants;
@@ -95,7 +98,7 @@ public String retrieveInputSource() throws FHIROperationException {
             Iterator<FHIRPathNode> iter = result.iterator();
             while (iter.hasNext()) {
                 FHIRPathElementNode node = (FHIRPathElementNode) iter.next();
-                return node.asElementNode().element().as(com.ibm.fhir.model.type.Uri.class).getValue();
+                return node.asElementNode().element().as(Uri.class).getValue();
             }
         } catch (NoSuchElementException | ClassCastException | FHIRPathException e) {
             throw buildExceptionWithIssue("invalid $import parameter value in 'inputSource'", e, IssueType.INVALID);
@@ -105,17 +108,18 @@ public String retrieveInputSource() throws FHIROperationException {
     }
 
     /**
-     * processes the retrieve inputs from the Parameters object and evaluationContext.
+     * Validate and retrieve the inputs from the Parameters object.
      *
+     * @param fhirVersion
      * @return
      * @throws FHIROperationException
      */
-    public List<Input> retrieveInputs() throws FHIROperationException {
+    public List<Input> retrieveInputs(FHIRVersionParam fhirVersion) throws FHIROperationException {
         // Parameter: input (required)
         List<Input> inputs = new ArrayList<>();
 
         try {
-            Set<String> supportedResourceTypes = FHIRConfigHelper.getSupportedResourceTypes();
+            Set<String> supportedResourceTypes = FHIRConfigHelper.getSupportedResourceTypes(fhirVersion);
             Collection<FHIRPathNode> result = evaluator.evaluate(evaluationContext, "parameter.where(name = 'input')");
 
             Iterator<FHIRPathNode> iter = result.iterator();
@@ -230,7 +234,7 @@ public StorageDetail retrieveStorageDetails() throws FHIROperationException {
                 EvaluationContext evaluationContextPartType = new EvaluationContext(node.element());
                 Collection<FHIRPathNode> resultPartType = evaluator.evaluate(evaluationContextPartType, "value");
                 String type =
-                        ((FHIRPathElementNode) resultPartType.iterator().next()).element().as(com.ibm.fhir.model.type.String.class).getValue();
+                        ((FHIRPathElementNode) resultPartType.iterator().next()).element().as(FHIR_STRING).getValue();
 
                 // Checks if not valid, and throws exception
                 if (!OperationConstants.STORAGE_TYPES.contains(type)) {

diff --git a/...n-bulkdata/src/test/java/com/ibm/fhir/operation/bulkdata/util/BulkDataExportUtilTest.java b/...n-bulkdata/src/test/java/com/ibm/fhir/operation/bulkdata/util/BulkDataExportUtilTest.java
@@ -33,6 +33,7 @@
 
 import com.ibm.fhir.config.FHIRConfiguration;
 import com.ibm.fhir.config.FHIRRequestContext;
+import com.ibm.fhir.core.FHIRVersionParam;
 import com.ibm.fhir.exception.FHIRException;
 import com.ibm.fhir.exception.FHIROperationException;
 import com.ibm.fhir.model.resource.Group;
@@ -281,58 +282,58 @@ public void testCheckAndExtractSinceWithInvalidType() {
     @Test(expectedExceptions = { com.ibm.fhir.exception.FHIROperationException.class })
     public void testCheckAndValidateTypesEmpty() throws FHIROperationException {
         List<Parameter> parameters = List.of(Parameter.builder().name(string("_type")).value(string("1")).build());
-        util.checkAndValidateTypes(ExportType.SYSTEM, parameters);
+        util.checkAndValidateTypes(ExportType.SYSTEM, FHIRVersionParam.VERSION_43, parameters);
         fail();
     }
 
     @Test(expectedExceptions = { com.ibm.fhir.exception.FHIROperationException.class })
     public void testCheckAndValidateTypesNull() throws FHIROperationException {
         List<Parameter> parameters = List.of(Parameter.builder().name(string("_type")).value((Element)null).build());
-        util.checkAndValidateTypes(ExportType.SYSTEM, parameters);
+        util.checkAndValidateTypes(ExportType.SYSTEM, FHIRVersionParam.VERSION_43, parameters);
         fail();
     }
 
     @Test(expectedExceptions = { com.ibm.fhir.exception.FHIROperationException.class })
     public void testCheckAndValidateTypesNullQPS() throws FHIROperationException {
         List<Parameter> parameters = List.of(Parameter.builder().name(string("_type")).value((Element) null).build());
-        util.checkAndValidateTypes(ExportType.SYSTEM, parameters);
+        util.checkAndValidateTypes(ExportType.SYSTEM, FHIRVersionParam.VERSION_43, parameters);
         fail();
     }
 
     @Test
     public void testCheckAndValidateTypesPatientWithoutComma() throws FHIROperationException {
         List<Parameter> parameters = List.of(Parameter.builder().name(string("_type")).value(string("Patient")).build());
-        Set<String> types = util.checkAndValidateTypes(ExportType.SYSTEM, parameters);
+        Set<String> types = util.checkAndValidateTypes(ExportType.SYSTEM, FHIRVersionParam.VERSION_43, parameters);
         assertNotNull(types);
     }
 
     @Test
     public void testCheckAndValidateTypesPatientWithComma() throws FHIROperationException {
         List<Parameter> parameters = List.of(Parameter.builder().name(string("_type")).value(string("Patient,")).build());
-        Set<String> types = util.checkAndValidateTypes(ExportType.SYSTEM, parameters);
+        Set<String> types = util.checkAndValidateTypes(ExportType.SYSTEM, FHIRVersionParam.VERSION_43, parameters);
         assertNotNull(types);
     }
 
     @Test
     public void testCheckAndValidateTypesPatientMedicationWithComma() throws FHIROperationException {
         List<Parameter> parameters = List.of(Parameter.builder().name(string("_type")).value(string("Patient,Medication")).build());
-        Set<String> types = util.checkAndValidateTypes(ExportType.SYSTEM, parameters);
+        Set<String> types = util.checkAndValidateTypes(ExportType.SYSTEM, FHIRVersionParam.VERSION_43, parameters);
         assertNotNull(types);
     }
 
     @Test(expectedExceptions = { com.ibm.fhir.exception.FHIROperationException.class })
     public void testCheckAndValidateTypesPatientMedicationWithExtraComma() throws FHIROperationException {
         // parameters
         List<Parameter> parameters = List.of(Parameter.builder().name(string("_type")).value(string("Patient,,Medication")).build());
-        util.checkAndValidateTypes(ExportType.SYSTEM, parameters);
+        util.checkAndValidateTypes(ExportType.SYSTEM, FHIRVersionParam.VERSION_43, parameters);
         fail();
     }
 
     @Test
     public void testCheckAndValidateTypesWithExtraComma() throws FHIROperationException {
         // parameters
         List<Parameter> parameters = List.of(Parameter.builder().name(string("_type")).value(string(",,")).build());
-        Set<String> result = util.checkAndValidateTypes(ExportType.SYSTEM, parameters);
+        Set<String> result = util.checkAndValidateTypes(ExportType.SYSTEM, FHIRVersionParam.VERSION_43, parameters);
         assertNotNull(result);
         assertFalse(result.isEmpty());
     }
@@ -341,14 +342,14 @@ public void testCheckAndValidateTypesWithExtraComma() throws FHIROperationExcept
     public void testCheckAndValidateTypesNoParameters() throws FHIROperationException {
         // parameters
         List<Parameter> parameters = List.of(Parameter.builder().name(string("french")).value(string("Patient,,Medication")).build());
-        Set<String> result = util.checkAndValidateTypes(ExportType.SYSTEM, parameters);
+        Set<String> result = util.checkAndValidateTypes(ExportType.SYSTEM, FHIRVersionParam.VERSION_43, parameters);
         assertNotNull(result);
         assertFalse(result.isEmpty());
     }
 
     @Test
     public void testCheckAndValidateTypesEmptyParameters() throws FHIROperationException {
-        Set<String> result = util.checkAndValidateTypes(ExportType.SYSTEM, null);
+        Set<String> result = util.checkAndValidateTypes(ExportType.SYSTEM, FHIRVersionParam.VERSION_43, null);
         assertNotNull(result);
         assertFalse(result.isEmpty());
     }

diff --git a/...n-bulkdata/src/test/java/com/ibm/fhir/operation/bulkdata/util/BulkDataImportUtilTest.java b/...n-bulkdata/src/test/java/com/ibm/fhir/operation/bulkdata/util/BulkDataImportUtilTest.java
@@ -32,6 +32,7 @@
 
 import com.ibm.fhir.config.FHIRConfiguration;
 import com.ibm.fhir.config.FHIRRequestContext;
+import com.ibm.fhir.core.FHIRVersionParam;
 import com.ibm.fhir.exception.FHIRException;
 import com.ibm.fhir.exception.FHIROperationException;
 import com.ibm.fhir.model.format.Format;
@@ -66,8 +67,8 @@ public void testBulkImportUtilInputs() throws IOException, FHIRException {
         FHIRRequestContext.set(context);
         context.setTenantId("not-config");
         BulkDataImportUtil util = new BulkDataImportUtil(getContext(), loadTestFile("/testdata/import/import-demo.json"));
-        assertFalse(util.retrieveInputs().isEmpty());
-        assertEquals(util.retrieveInputs().size(), 2);
+        assertFalse(util.retrieveInputs(FHIRVersionParam.VERSION_43).isEmpty());
+        assertEquals(util.retrieveInputs(FHIRVersionParam.VERSION_43).size(), 2);
     }
 
     @Test
@@ -160,7 +161,7 @@ public void testCheckAllowedResourceTypesForInputs() throws IOException, FHIRExc
         FHIRRequestContext.set(context);
         context.setTenantId("config");
         BulkDataImportUtil util = new BulkDataImportUtil(getContext(), loadTestFile("/testdata/import/import-demo-config.json"));
-        util.retrieveInputs();
+        util.retrieveInputs(FHIRVersionParam.VERSION_43);
     }
 
     @Test(expectedExceptions = { FHIROperationException.class })
@@ -169,7 +170,7 @@ public void testCheckAllowedResourceTypesForInputsBad() throws IOException, FHIR
         FHIRRequestContext.set(context);
         context.setTenantId("not-config");
         BulkDataImportUtil util = new BulkDataImportUtil(getContext(), loadTestFile("/testdata/import/import-demo-not-config.json"));
-        util.retrieveInputs();
+        util.retrieveInputs(FHIRVersionParam.VERSION_43);
     }
 
     public Parameters loadTestFile(String file) throws FHIRParserException, IOException {

diff --git a/...ation-everything/src/main/java/com/ibm/fhir/operation/everything/EverythingOperation.java b/...ation-everything/src/main/java/com/ibm/fhir/operation/everything/EverythingOperation.java
@@ -46,7 +46,6 @@
 import com.ibm.fhir.model.type.code.BundleType;
 import com.ibm.fhir.model.type.code.HTTPVerb;
 import com.ibm.fhir.model.type.code.IssueType;
-import com.ibm.fhir.model.type.code.SearchEntryMode;
 import com.ibm.fhir.model.util.ModelSupport;
 import com.ibm.fhir.model.util.ReferenceFinder;
 import com.ibm.fhir.registry.FHIRRegistry;
@@ -205,7 +204,7 @@ protected Parameters doInvoke(FHIROperationContext operationContext, Class<? ext
         MultivaluedMap<String, String> queryParametersWithoutDates = new MultivaluedHashMap<String,String>(queryParameters);
         boolean startOrEndProvided = queryParametersWithoutDates.remove(DATE_QUERY_PARAMETER) != null;
 
-        List<String> defaultResourceTypes = new ArrayList<String>(0);
+        List<String> defaultResourceTypes;
         try {
             FHIRVersionParam fhirVersion = (FHIRVersionParam) operationContext.getProperty(FHIROperationContext.PROPNAME_FHIR_VERSION);
             defaultResourceTypes = getDefaultIncludedResourceTypes(resourceHelper, fhirVersion);