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issue #3242 - update $everything to use ResourcesConfigAdapter
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1. add the FHIRVersionParam to the OperationContext
2. use that with a ResourcesConfigAdapter to get the list of applicable
resource types in EverythingOperation.getDefaultIncludedResourceTypes

Signed-off-by: Lee Surprenant <lmsurpre@us.ibm.com>
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@lmsurpre
lmsurpre committed Feb 5, 2022
1 parent 502eebe commit 1196c93
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Showing 3 changed files with 49 additions and 46 deletions.
7 changes: 6 additions & 1 deletion fhir-server-spi/src/main/java/com/ibm/fhir/server/spi/operation/FHIROperationContext.java
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
/*
* (C) Copyright IBM Corp. 2017, 2021
* (C) Copyright IBM Corp. 2017, 2022
*
* SPDX-License-Identifier: Apache-2.0
*/
Expand Down Expand Up @@ -84,6 +84,11 @@ public enum Type { SYSTEM, RESOURCE_TYPE, INSTANCE }
*/
public static final String PROPNAME_RESPONSE_PARAMETERS = "RESPONSE_PARAMETERS";

/**
* The FHIRVersionParam for this invocation
*/
public static final String PROPNAME_FHIR_VERSION = "FHIR_VERSION";

private final Type type;
private final String code;
private Map<String, Object> properties = null;
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2 changes: 2 additions & 0 deletions fhir-server/src/main/java/com/ibm/fhir/server/util/FHIRRestHelper.java
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Original file line number Diff line number Diff line change
Expand Up @@ -2589,6 +2589,7 @@ private void setOperationContextProperties(FHIROperationContext operationContext
operationContext.setProperty(FHIROperationContext.PROPNAME_REQUEST_BASE_URI, getRequestBaseUri(resourceTypeName));
operationContext.setProperty(FHIROperationContext.PROPNAME_REQUEST_PARAMETERS, requestParameters);
operationContext.setProperty(FHIROperationContext.PROPNAME_PERSISTENCE_IMPL, persistence);
operationContext.setProperty(FHIROperationContext.PROPNAME_FHIR_VERSION, fhirVersion);
}

@Override
Expand Down Expand Up @@ -2957,6 +2958,7 @@ public void validateInteraction(Interaction interaction, String resourceType) th
List<String> interactions = null;
boolean resourceValid = true;

// TODO: replace with ResourcesConfigAdapter
// Retrieve the interaction configuration
try {
StringBuilder defaultInteractionsConfigPath = new StringBuilder(FHIRConfiguration.PROPERTY_RESOURCES).append("/Resource/")
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86 changes: 41 additions & 45 deletions ...ation-everything/src/main/java/com/ibm/fhir/operation/everything/EverythingOperation.java
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Original file line number Diff line number Diff line change
Expand Up @@ -22,8 +22,13 @@
import javax.ws.rs.core.MultivaluedMap;

import com.ibm.fhir.config.FHIRConfigHelper;
import com.ibm.fhir.config.FHIRConfiguration;
import com.ibm.fhir.config.FHIRRequestContext;
import com.ibm.fhir.config.Interaction;
import com.ibm.fhir.config.PropertyGroup;
import com.ibm.fhir.config.ResourcesConfigAdapter;
import com.ibm.fhir.core.FHIRConstants;
import com.ibm.fhir.core.FHIRVersionParam;
import com.ibm.fhir.core.HTTPHandlingPreference;
import com.ibm.fhir.exception.FHIROperationException;
import com.ibm.fhir.model.resource.Bundle;
Expand Down Expand Up @@ -186,11 +191,12 @@ protected Parameters doInvoke(FHIROperationContext operationContext, Class<? ext

List<String> defaultResourceTypes = new ArrayList<String>(0);
try {
defaultResourceTypes = getDefaultIncludedResourceTypes(resourceHelper);
FHIRVersionParam fhirVersion = (FHIRVersionParam) operationContext.getProperty(FHIROperationContext.PROPNAME_FHIR_VERSION);
defaultResourceTypes = getDefaultIncludedResourceTypes(resourceHelper, fhirVersion);
} catch (FHIRSearchException e) {
throw new Error("There has been an error retrieving the list of included resources of the $everything operation.", e);
}

List<String> resourceTypesOverride = getOverridenIncludedResourceTypes(parameters, defaultResourceTypes);
List<String> resourceTypes = resourceTypesOverride.isEmpty() ? defaultResourceTypes : resourceTypesOverride;

Expand All @@ -203,9 +209,9 @@ protected Parameters doInvoke(FHIROperationContext operationContext, Class<? ext
}

// Need to construct a new version of the map each time through the loop to edit
MultivaluedMap<String, String> tempSearchParameters =
MultivaluedMap<String, String> tempSearchParameters =
new MultivaluedHashMap<String, String>(searchParameters);

Bundle results = null;
int currentResourceCount = 0;
try {
Expand Down Expand Up @@ -339,22 +345,14 @@ protected List<String> getOverridenIncludedResourceTypes(Parameters parameters,
* @return the list of patient subresources that will be included in the $everything operation
* @throws FHIRSearchException
*/
private List<String> getDefaultIncludedResourceTypes(FHIRResourceHelpers resourceHelper) throws FHIRSearchException {
private List<String> getDefaultIncludedResourceTypes(FHIRResourceHelpers resourceHelper, FHIRVersionParam fhirVersion) throws FHIRSearchException {
List<String> resourceTypes = new ArrayList<>(CompartmentUtil.getCompartmentResourceTypes(PATIENT));

try {
List<String> supportedResourceTypes = FHIRConfigHelper.getSupportedResourceTypes();
// Examine the resource types to see if they support SEARCH
for (String resourceType: supportedResourceTypes) {
try {
resourceHelper.validateInteraction(FHIRResourceHelpers.Interaction.SEARCH, resourceType);
} catch (FHIROperationException e) {
if (LOG.isLoggable(Level.FINE)) {
LOG.fine("Removing resourceType " + resourceType + " because it does not support SEARCH");
}
supportedResourceTypes.remove(resourceType);
}
}
PropertyGroup resourcesGroup = FHIRConfigHelper.getPropertyGroup(FHIRConfiguration.PROPERTY_RESOURCES);
ResourcesConfigAdapter configAdapter = new ResourcesConfigAdapter(resourcesGroup, fhirVersion);
Set<String> supportedResourceTypes = configAdapter.getSupportedResourceTypes(Interaction.SEARCH);

if (LOG.isLoggable(Level.FINE)) {
StringBuilder resourceTypeBuilder = new StringBuilder(supportedResourceTypes.size());
resourceTypeBuilder.append("supportedResourceTypes are: ");
Expand All @@ -364,17 +362,15 @@ private List<String> getDefaultIncludedResourceTypes(FHIRResourceHelpers resourc
}
LOG.fine(resourceTypeBuilder.toString());
}

// Need to have this if check to support server config files that do not specify resources
if (!supportedResourceTypes.isEmpty()) {
resourceTypes.retainAll(supportedResourceTypes);
}

resourceTypes.retainAll(supportedResourceTypes);
} catch (Exception e) {
FHIRSearchException exceptionWithIssue = new FHIRSearchException("There has been an error retrieving the list of supported resource types of the $everything operation.", e);
FHIRSearchException exceptionWithIssue = new FHIRSearchException("There has been an error retrieving the list "
+ "of supported resource types for the $everything operation.", e);
LOG.throwing(this.getClass().getName(), "doInvoke", exceptionWithIssue);
throw exceptionWithIssue;
}

if (LOG.isLoggable(Level.FINE)) {
StringBuilder resourceTypeBuilder = new StringBuilder(resourceTypes.size());
resourceTypeBuilder.append("resourceTypes are: ");
Expand Down Expand Up @@ -420,23 +416,23 @@ private static Uri uri(FHIROperationContext operationContext, String uriPath) {
.value(requestBaseURI + "/" + uriPath)
.build();
}

private void addIncludesSearchParameters(String compartmentMemberType, MultivaluedMap<String, String> searchParameters)
throws Exception {
// Add in Location, Medication, Organization, and Practitioner resources which are pointed to
// from search parameters only if the request does not have a _type parameter or it does have a
// from search parameters only if the request does not have a _type parameter or it does have a
// _type parameter that includes these

List<String> allowedIncludes = new ArrayList<String>(10);

try {
allowedIncludes = FHIRConfigHelper.getSearchPropertyRestrictions(compartmentMemberType, FHIRConfigHelper.SEARCH_PROPERTY_TYPE_INCLUDE);
} catch (Exception e) {
FHIRSearchException exceptionWithIssue = new FHIRSearchException("There has been an error retrieving the list of supported search parameters for the $everything operation.", e);
LOG.throwing(this.getClass().getName(), "doInvoke", exceptionWithIssue);
throw exceptionWithIssue;
throw exceptionWithIssue;
}

// Add in _includes for all search parameters that are Location, Medication, Organization, or Practitioner
if (compartmentMemberType.equals(ResourceType.Value.ADVERSE_EVENT.value())) {
addSearchParameterIfNotExcluded(compartmentMemberType, "location", ResourceType.Value.LOCATION, searchParameters, allowedIncludes);
Expand Down Expand Up @@ -469,7 +465,7 @@ private void addIncludesSearchParameters(String compartmentMemberType, Multivalu
addSearchParameterIfNotExcluded(compartmentMemberType, "author", ResourceType.Value.PRACTITIONER, searchParameters, allowedIncludes);
} else if (compartmentMemberType.equals(ResourceType.Value.CARE_PLAN.value())) {
addSearchParameterIfNotExcluded(compartmentMemberType, "performer", ResourceType.Value.ORGANIZATION, searchParameters, allowedIncludes);
addSearchParameterIfNotExcluded(compartmentMemberType, "performer", ResourceType.Value.PRACTITIONER, searchParameters, allowedIncludes);
addSearchParameterIfNotExcluded(compartmentMemberType, "performer", ResourceType.Value.PRACTITIONER, searchParameters, allowedIncludes);
} else if (compartmentMemberType.equals(ResourceType.Value.CARE_TEAM.value())) {
addSearchParameterIfNotExcluded(compartmentMemberType, "participant", ResourceType.Value.ORGANIZATION,searchParameters, allowedIncludes);
addSearchParameterIfNotExcluded(compartmentMemberType, "participant", ResourceType.Value.PRACTITIONER, searchParameters, allowedIncludes);
Expand Down Expand Up @@ -516,7 +512,7 @@ private void addIncludesSearchParameters(String compartmentMemberType, Multivalu
addSearchParameterIfNotExcluded(compartmentMemberType, "organization", ResourceType.Value.ORGANIZATION, searchParameters, allowedIncludes);
} else if (compartmentMemberType.equals(ResourceType.Value.COVERAGE.value())) {
addSearchParameterIfNotExcluded(compartmentMemberType, "payor", ResourceType.Value.ORGANIZATION, searchParameters, allowedIncludes);
addSearchParameterIfNotExcluded(compartmentMemberType, "policy-holder", ResourceType.Value.ORGANIZATION, searchParameters, allowedIncludes);
addSearchParameterIfNotExcluded(compartmentMemberType, "policy-holder", ResourceType.Value.ORGANIZATION, searchParameters, allowedIncludes);
} else if (compartmentMemberType.equals(ResourceType.Value.COVERAGE_ELIGIBILITY_REQUEST.value())) {
addSearchParameterIfNotExcluded(compartmentMemberType, "enterer", ResourceType.Value.PRACTITIONER, searchParameters, allowedIncludes);
addSearchParameterIfNotExcluded(compartmentMemberType, "facility", ResourceType.Value.LOCATION, searchParameters, allowedIncludes);
Expand Down Expand Up @@ -552,7 +548,7 @@ private void addIncludesSearchParameters(String compartmentMemberType, Multivalu
addSearchParameterIfNotExcluded(compartmentMemberType, "participant", ResourceType.Value.PRACTITIONER, searchParameters, allowedIncludes);
} else if (compartmentMemberType.equals(ResourceType.Value.EPISODE_OF_CARE.value())) {
addSearchParameterIfNotExcluded(compartmentMemberType, "care-manager", ResourceType.Value.PRACTITIONER, searchParameters, allowedIncludes);
addSearchParameterIfNotExcluded(compartmentMemberType, "organization", ResourceType.Value.ORGANIZATION, searchParameters, allowedIncludes);
addSearchParameterIfNotExcluded(compartmentMemberType, "organization", ResourceType.Value.ORGANIZATION, searchParameters, allowedIncludes);
} else if (compartmentMemberType.equals(ResourceType.Value.EXPLANATION_OF_BENEFIT.value())) {
addSearchParameterIfNotExcluded(compartmentMemberType, "care-team", ResourceType.Value.ORGANIZATION, searchParameters, allowedIncludes);
addSearchParameterIfNotExcluded(compartmentMemberType, "care-team", ResourceType.Value.PRACTITIONER, searchParameters, allowedIncludes);
Expand All @@ -570,7 +566,7 @@ private void addIncludesSearchParameters(String compartmentMemberType, Multivalu
addSearchParameterIfNotExcluded(compartmentMemberType, "subject", ResourceType.Value.ORGANIZATION, searchParameters, allowedIncludes);
addSearchParameterIfNotExcluded(compartmentMemberType, "subject", ResourceType.Value.PRACTITIONER, searchParameters, allowedIncludes);
} else if (compartmentMemberType.equals(ResourceType.Value.GOAL.value())) {
addSearchParameterIfNotExcluded(compartmentMemberType, "subject", ResourceType.Value.ORGANIZATION, searchParameters, allowedIncludes);
addSearchParameterIfNotExcluded(compartmentMemberType, "subject", ResourceType.Value.ORGANIZATION, searchParameters, allowedIncludes);
} else if (compartmentMemberType.equals(ResourceType.Value.GROUP.value())) {
addSearchParameterIfNotExcluded(compartmentMemberType, "member", ResourceType.Value.MEDICATION, searchParameters, allowedIncludes);
addSearchParameterIfNotExcluded(compartmentMemberType, "member", ResourceType.Value.PRACTITIONER, searchParameters, allowedIncludes);
Expand Down Expand Up @@ -669,7 +665,7 @@ private void addIncludesSearchParameters(String compartmentMemberType, Multivalu
addSearchParameterIfNotExcluded(compartmentMemberType, "performer", ResourceType.Value.PRACTITIONER, searchParameters, allowedIncludes);
addSearchParameterIfNotExcluded(compartmentMemberType, "requester", ResourceType.Value.ORGANIZATION, searchParameters, allowedIncludes);
addSearchParameterIfNotExcluded(compartmentMemberType, "requester", ResourceType.Value.PRACTITIONER, searchParameters, allowedIncludes);
addSearchParameterIfNotExcluded(compartmentMemberType, "subject", ResourceType.Value.LOCATION, searchParameters, allowedIncludes);
addSearchParameterIfNotExcluded(compartmentMemberType, "subject", ResourceType.Value.LOCATION, searchParameters, allowedIncludes);
} else if (compartmentMemberType.equals(ResourceType.Value.SPECIMEN.value())) {
addSearchParameterIfNotExcluded(compartmentMemberType, "collector", ResourceType.Value.PRACTITIONER, searchParameters, allowedIncludes);
addSearchParameterIfNotExcluded(compartmentMemberType, "subject", ResourceType.Value.LOCATION, searchParameters, allowedIncludes);
Expand All @@ -685,19 +681,19 @@ private void addIncludesSearchParameters(String compartmentMemberType, Multivalu
addSearchParameterIfNotExcluded(compartmentMemberType, "supplier", ResourceType.Value.ORGANIZATION, searchParameters, allowedIncludes);
} else if (compartmentMemberType.equals(ResourceType.Value.VISION_PRESCRIPTION.value())) {
addSearchParameterIfNotExcluded(compartmentMemberType, "prescriber", ResourceType.Value.PRACTITIONER, searchParameters, allowedIncludes);
}
}

// BodyStructure, ResearchSubject, and RelatedPerson have no references to:
// Location, Medication, Organization, and Practitioner
// DeviceUseStatement, EnrollmentRequest, FamilyMemberHistory, ChargeItem,
// ImmunizationEvaluation, ImmunizationRecommendation, MolecularSequence,
// and NutritionOrder have no search parameters that reference:

// DeviceUseStatement, EnrollmentRequest, FamilyMemberHistory, ChargeItem,
// ImmunizationEvaluation, ImmunizationRecommendation, MolecularSequence,
// and NutritionOrder have no search parameters that reference:
// Location, Medication, Organization, and Practitioner
}
private void addSearchParameterIfNotExcluded(String compartmentMemberType, String code,
ResourceType.Value subResourceType, MultivaluedMap<String, String> searchParameters,

private void addSearchParameterIfNotExcluded(String compartmentMemberType, String code,
ResourceType.Value subResourceType, MultivaluedMap<String, String> searchParameters,
List<String> allowedIncludes) {
// Need to make sure the search parameter has not been excluded
String parameterName = compartmentMemberType + ":" + code + ":" + subResourceType.value();
Expand Down

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