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issue #2143 - load compartment definitions from the registry #2381

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May 19, 2021
Merged

issue #2143 - load compartment definitions from the registry #2381

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19 changes: 9 additions & 10 deletions fhir-search/src/main/java/com/ibm/fhir/search/compartment/CompartmentCache.java
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
/*
* (C) Copyright IBM Corp. 2019
* (C) Copyright IBM Corp. 2019, 2021
*
* SPDX-License-Identifier: Apache-2.0
*/
Expand All @@ -16,8 +16,6 @@
/**
* Compartment Cache is a localized class to cache the compartment information and provide helper methods to add to the
* cache.
*
* @author pbastide
*/
public class CompartmentCache {

Expand All @@ -32,21 +30,22 @@ public CompartmentCache() {

/**
* add the code and parameters to the given compartment cache.
*
* @param inclusionCode
* @param params
*
* @param inclusionResourceCode the name of the resource type that can be within the target compartment type
* @param params the inclusion criteria used to determine whether a resource of type {@code inclusionResourceCode}
* is in a target compartment
*/
public void add(java.lang.String inclusionCode, List<com.ibm.fhir.model.type.String> params) {
public void add(java.lang.String inclusionResourceCode, List<com.ibm.fhir.model.type.String> params) {
if (params != null) {
// Fast Conversion to java.lang.String
List<String> paramsAsStrings = params.stream().map(param -> param.getValue()).collect(Collectors.toList());
codeAndParams.put(inclusionCode, paramsAsStrings);
codeAndParams.put(inclusionResourceCode, paramsAsStrings);
}
}

/**
* gets the resource types (codes) in the compartment
*
*
* @return
*/
public List<String> getResourceTypesInCompartment() {
Expand All @@ -55,7 +54,7 @@ public List<String> getResourceTypesInCompartment() {

/**
* get parameters by resource type in the compartment cache.
*
*
* @param resourceType
* @return
*/
Expand Down
194 changes: 42 additions & 152 deletions fhir-search/src/main/java/com/ibm/fhir/search/compartment/CompartmentUtil.java
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Original file line number Diff line number Diff line change
@@ -1,95 +1,52 @@
/*
* (C) Copyright IBM Corp. 2019, 2020
* (C) Copyright IBM Corp. 2019, 2021
*
* SPDX-License-Identifier: Apache-2.0
*/

package com.ibm.fhir.search.compartment;

import java.io.IOException;
import java.io.InputStreamReader;
import java.io.PrintStream;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.Set;
import java.util.logging.Logger;

import com.ibm.fhir.exception.FHIRException;
import com.ibm.fhir.model.format.Format;
import com.ibm.fhir.model.generator.FHIRGenerator;
import com.ibm.fhir.model.generator.exception.FHIRGeneratorException;
import com.ibm.fhir.model.parser.FHIRParser;
import com.ibm.fhir.model.resource.Bundle;
import com.ibm.fhir.model.resource.CompartmentDefinition;
import com.ibm.fhir.model.resource.CompartmentDefinition.Resource;
import com.ibm.fhir.model.type.code.BundleType;
import com.ibm.fhir.path.FHIRPathNode;
import com.ibm.fhir.path.FHIRPathResourceNode;
import com.ibm.fhir.path.evaluator.FHIRPathEvaluator;
import com.ibm.fhir.path.evaluator.FHIRPathEvaluator.EvaluationContext;
import com.ibm.fhir.registry.FHIRRegistry;
import com.ibm.fhir.search.exception.FHIRSearchException;
import com.ibm.fhir.search.exception.SearchExceptionUtil;

/**
* This class supplements SearchUtil with compartment-specific utilities. <br>
* The compartments are defined using FHIR R4 CompartmentDefinitions. <br>
* The R4 CompartmentDefintions and boundaries are defined at https://www.hl7.org/fhir/compartmentdefinition.html <br>
* The R4 CompartmentDefintions and boundaries are defined at https://hl7.org/fhir/R4/compartmentdefinition.html <br>
* <br>
* CompartmentDefintion:
* <ul>
* <li>Patient - https://www.hl7.org/fhir/compartmentdefinition-patient.json</li>
* <li>Encounter - https://www.hl7.org/fhir/compartmentdefinition-encounter.json</li>
* <li>RelatedPerson - https://www.hl7.org/fhir/compartmentdefinition-relatedperson.json</li>
* <li>Practitioner - https://www.hl7.org/fhir/compartmentdefinition-practitioner.json</li>
* <li>Device - https://www.hl7.org/fhir/compartmentdefinition-device.json</li>
* <li>Patient - https://hl7.org/fhir/R4/compartmentdefinition-patient.json</li>
* <li>Encounter - https://hl7.org/fhir/R4/compartmentdefinition-encounter.json</li>
* <li>RelatedPerson - https://hl7.org/fhir/R4/compartmentdefinition-relatedperson.json</li>
* <li>Practitioner - https://hl7.org/fhir/R4/compartmentdefinition-practitioner.json</li>
* <li>Device - https://hl7.org/fhir/R4/compartmentdefinition-device.json</li>
* </ul>
*
* This class extracts the Compartment Logic from SearchUtil, converts the Custom Compartment logic and format into the
* ComponentDefintion, adds support for the the default definition.
*
* <br>
* Load the class in the classloader to initialize static members. Call this before using the class in order to avoid a
* slight performance hit on first use.
* Call {@link #init()} to initialize static members and avoid a slight performance hit on first use.
*/
public class CompartmentUtil {

private static final String CLASSNAME = CompartmentUtil.class.getName();
private static final Logger log = Logger.getLogger(CLASSNAME);

// FHIR:
public static final String FHIR_PATH_BUNDLE_ENTRY = "entry.children()";
public static final String RESOURCE = "/compartments.json";

// List of compartmentDefinitions.
private static final Set<String> compartmentDefinitions = new HashSet<String>() {

private static final long serialVersionUID = 7152515293380769882L;

{
add("/compartments/compartmentdefinition-device.json");
add("/compartments/compartmentdefinition-encounter.json");
add("/compartments/compartmentdefinition-patient.json");
add("/compartments/compartmentdefinition-practitioner.json");
add("/compartments/compartmentdefinition-relatedperson.json");
}
};

// Map of Compartment name to CompartmentCache
private static final Map<String, CompartmentCache> compartmentMap = new HashMap<>();

// Map of Resource type to ResourceCompartmentCache
// Map of Inclusion resource type to ResourceCompartmentCache
private static final Map<String, ResourceCompartmentCache> resourceCompartmentMap = new HashMap<>();

static {
// make one pass over the configuration to build both maps
// make one pass over the CompartmentDefinitions to build both maps
buildMaps(compartmentMap, resourceCompartmentMap);
}


/**
* Loads the class in the classloader to initialize static members. Call this before using the class in order to
* avoid a slight performance hit on first use.
Expand All @@ -99,11 +56,8 @@ public static void init() {
}

// Exceptions:
public static final String PARSE_EXCEPTION = "Unable to parse the entry that is read from compartments.json %s";
public static final String IO_EXCEPTION = "Unable to read the entry that is read from compartments.json %s";
public static final String INVALID_COMPARTMENT = "Invalid compartment: %s";
public static final String INVALID_COMPARTMENT_AND_RESOURCE = "Invalid resource type: %s for compartment: %s";
public static final String FROM_STREAM = "from_stream";

private CompartmentUtil() {
// No Operation
Expand All @@ -115,76 +69,39 @@ private CompartmentUtil() {
* @implNote the maps being built are passed in as arguments to aid unit testing
* @param compMap map of compartment name to CompartmentCache
* @param resourceCompMap map of resource type name to ResourceCompartmentCache
* @throws IOException
*/
public static final void buildMaps(Map<String, CompartmentCache> compMap, Map<String, ResourceCompartmentCache> resourceCompMap) {
buildMaps(RESOURCE, compMap, resourceCompMap);
}

/**
* Builds an in-memory model of the Compartment map defined in compartments.json, for supporting compartment based
* FHIR searches.
* @implNote the maps being built are passed in as arguments to aid unit testing
* @param the source resource to be read using getResourceAsStream
* @param compMap map of compartment name to CompartmentCache
* @param resourceCompMap map of resource type name to ResourceCompartmentCache
* @throws IOException
*/
public static final void buildMaps(String source, Map<String, CompartmentCache> compMap, Map<String, ResourceCompartmentCache> resourceCompMap) {
if (compMap == null) {
throw new IllegalArgumentException("compMap must not be null");
}

if (resourceCompMap == null) {
throw new IllegalArgumentException("resourceCompMap must not be null");
}

try (InputStreamReader reader = new InputStreamReader(CompartmentUtil.class.getResourceAsStream(source))) {
Bundle bundle = FHIRParser.parser(Format.JSON).parse(reader);

FHIRPathEvaluator evaluator = FHIRPathEvaluator.evaluator();
EvaluationContext evaluationContext = new EvaluationContext(bundle);

Collection<FHIRPathNode> result = evaluator.evaluate(evaluationContext, FHIR_PATH_BUNDLE_ENTRY);

Iterator<FHIRPathNode> iter = result.iterator();
while (iter.hasNext()) {
FHIRPathResourceNode node = iter.next().asResourceNode();

// Convert to Resource and lookup.
CompartmentDefinition compartmentDefinition = node.resource().as(CompartmentDefinition.class);
String compartmentName = compartmentDefinition.getCode().getValue();

// The cached object (a smaller/lighter lookup resource) used for point lookups
CompartmentCache compartmentDefinitionCache = new CompartmentCache();

// Iterates over the resources embedded in the CompartmentDefinition.
for (Resource resource : compartmentDefinition.getResource()) {
String inclusionCode = resource.getCode().getValue();
List<com.ibm.fhir.model.type.String> params = resource.getParam();
// Make sure to only add the valid resource types (at least with one inclusion) instead of all types.
if (!params.isEmpty()) {
compartmentDefinitionCache.add(inclusionCode, params);

// Look up the ResourceCompartmentCache and create a new one if needed
ResourceCompartmentCache rcc = resourceCompMap.get(inclusionCode);
if (rcc == null) {
rcc = new ResourceCompartmentCache();
resourceCompMap.put(inclusionCode, rcc);
}

// Add the mapping for this parameter to the target compartment name
rcc.add(params, compartmentName);
Objects.requireNonNull(compMap, "compMap");
Objects.requireNonNull(compMap, "resourceCompMap");

Collection<CompartmentDefinition> definitions = FHIRRegistry.getInstance().getResources(CompartmentDefinition.class);
for (CompartmentDefinition compartmentDefinition : definitions) {
String compartmentName = compartmentDefinition.getCode().getValue();

// The cached object (a smaller/lighter lookup resource) used for point lookups
CompartmentCache compartmentDefinitionCache = new CompartmentCache();

// Iterates over the resources embedded in the CompartmentDefinition.
for (Resource resource : compartmentDefinition.getResource()) {
String inclusionResourceCode = resource.getCode().getValue();
List<com.ibm.fhir.model.type.String> params = resource.getParam();
// Make sure to only add the valid resource types (at least with one inclusion) instead of all types.
if (!params.isEmpty()) {
compartmentDefinitionCache.add(inclusionResourceCode, resource.getParam());

// Look up the ResourceCompartmentCache and create a new one if needed
ResourceCompartmentCache rcc = resourceCompMap.get(inclusionResourceCode);
if (rcc == null) {
rcc = new ResourceCompartmentCache();
resourceCompMap.put(inclusionResourceCode, rcc);
}
}

compMap.put(compartmentName, compartmentDefinitionCache);
// Add the mapping for this parameter to the target compartment name
rcc.add(params, compartmentName);
}
}

} catch (FHIRException e) {
log.warning(String.format(PARSE_EXCEPTION, FROM_STREAM));
} catch (IOException e1) {
log.warning(String.format(IO_EXCEPTION, FROM_STREAM));
compMap.put(compartmentName, compartmentDefinitionCache);
}
}

Expand Down Expand Up @@ -241,42 +158,15 @@ public static void checkValidCompartmentAndResource(final String compartment, fi
}
}

/**
* builds the bundle and the resources for the compartments.json and puts out to the output stream.
*
* @throws FHIRGeneratorException
*/
public static void buildCompositeBundle(PrintStream out) throws FHIRGeneratorException {

Bundle.Builder build = Bundle.builder().type(BundleType.COLLECTION);
for (String compartmentDefintion : compartmentDefinitions) {

try (InputStreamReader reader = new InputStreamReader(CompartmentUtil.class.getResourceAsStream(compartmentDefintion))) {
CompartmentDefinition compartmentDefinitionResource = FHIRParser.parser(Format.JSON).parse(reader);

build.entry(Bundle.Entry.builder().resource(compartmentDefinitionResource).build());

} catch (FHIRException e) {
log.warning(String.format(PARSE_EXCEPTION, compartmentDefintion));
} catch (IOException e1) {
log.warning(String.format(IO_EXCEPTION, compartmentDefintion));
}
}

Bundle bundle = build.build();
FHIRGenerator.generator(Format.JSON, true).generate(bundle, out);
out.println(bundle.toString());

}

/**
* Get the map of parameter names used as compartment references for the
* given resource type. For example for CareTeam:
* <pre>
* participant -> {RelatedPerson, Patient}
* patient -> {Patient}
* encounter -> {Encounter}
* ...
* etc.
* </pre>
* @param resourceType the resource type name
* @return a map of parameter name to set of compartment names
*/
Expand Down
3 changes: 2 additions & 1 deletion fhir-search/src/main/java/com/ibm/fhir/search/compartment/ResourceCompartmentCache.java
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
/*
* (C) Copyright IBM Corp. 2020
* (C) Copyright IBM Corp. 2020, 2021
*
* SPDX-License-Identifier: Apache-2.0
*/
Expand Down Expand Up @@ -37,6 +37,7 @@ public ResourceCompartmentCache() {
* In the schema, we therefore have to store (unique) values for this parameter
* as both patient_compartment and relatedperson_compartment token references.
* @param params a list of model parameter names
* @param compartmentName the compartment associated with these parameters
*/
public void add(List<com.ibm.fhir.model.type.String> params, java.lang.String compartmentName) {
if (params != null) {
Expand Down
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