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issue #1708 add custom compartment reference params for faster compar…
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…tment searches

Signed-off-by: Robin Arnold <robin.arnold23@ibm.com>
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@punktilious
punktilious committed Nov 18, 2020
1 parent a98a3db commit d862936
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Showing 13 changed files with 1,137 additions and 263 deletions.
143 changes: 25 additions & 118 deletions ...e-jdbc/src/main/java/com/ibm/fhir/persistence/jdbc/dao/impl/ParameterVisitorBatchDAO.java
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Expand Up @@ -9,8 +9,6 @@
import static com.ibm.fhir.persistence.jdbc.JDBCConstants.UTC;

import java.math.BigDecimal;
import java.net.MalformedURLException;
import java.net.URL;
import java.sql.Connection;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
Expand All @@ -24,7 +22,6 @@
import java.util.logging.Logger;
import java.util.stream.Collectors;

import com.ibm.fhir.config.FHIRRequestContext;
import com.ibm.fhir.persistence.exception.FHIRPersistenceException;
import com.ibm.fhir.persistence.jdbc.dao.api.IResourceReferenceDAO;
import com.ibm.fhir.persistence.jdbc.dao.api.JDBCIdentityCache;
Expand All @@ -41,6 +38,8 @@
import com.ibm.fhir.persistence.jdbc.exception.FHIRPersistenceDataAccessException;
import com.ibm.fhir.persistence.jdbc.impl.ParameterTransactionDataImpl;
import com.ibm.fhir.schema.control.FhirSchemaConstants;
import com.ibm.fhir.search.util.ReferenceValue;
import com.ibm.fhir.search.util.ReferenceValue.ReferenceType;

/**
* Batch insert into the parameter values tables. Avoids having to create one stored procedure
Expand All @@ -51,11 +50,6 @@
public class ParameterVisitorBatchDAO implements ExtractedParameterValueVisitor, AutoCloseable {
private static final Logger logger = Logger.getLogger(ParameterVisitorBatchDAO.class.getName());

private static final String HISTORY = "_history";
private static final String HTTP = "http:";
private static final String HTTPS = "https:";
private static final String URN = "urn:";

// the connection to use for the inserts
private final Connection connection;

Expand Down Expand Up @@ -118,9 +112,6 @@ public class ParameterVisitorBatchDAO implements ExtractedParameterValueVisitor,
// The common cache for all our identity lookup needs
private final JDBCIdentityCache identityCache;

// The server base "https://example.com:9443/" extracted the first time we need it
private String serverBase;

// If not null, we stash certain parameter data here for insertion later
private final ParameterTransactionDataImpl transactionData;

Expand Down Expand Up @@ -746,58 +737,9 @@ private boolean isBase(ExtractedParameterValue param) {
return "Resource".equals(param.getBase());
}

/**
* Get the leading part of the url e.g. https://example.com
* @return
*/
private String getServerUrl() throws FHIRPersistenceException {

if (this.serverBase != null) {
return this.serverBase;
}

String uri = FHIRRequestContext.get().getOriginalRequestUri();

// request URI is not set for all unit-tests, so we need to take that into account
if (uri == null) {
return null;
}

try {
StringBuilder result = new StringBuilder();
URL url = new URL(uri);

result.append(url.getProtocol());
result.append("://");
result.append(url.getHost());

if (url.getPort() != -1) {
result.append(":");
result.append(url.getPort());
}

// https://example.com:9443/
result.append("/");

final String endpoint = "fhir-server/api/v4/";
if (uri.contains(endpoint)) {
result.append(endpoint);
}

// Cache the result so we don't have to compute it over and over
this.serverBase = result.toString();
return this.serverBase;
} catch (MalformedURLException x) {
// not very likely at this point
logger.severe("Malformed server URL: " + uri);
throw new FHIRPersistenceException("Server URL is malformed!");
}
}

@Override
public void visit(ReferenceParmVal rpv) throws FHIRPersistenceException {
String valueString = rpv.getValueString();
if (valueString == null || valueString.isEmpty()) {
if (rpv.getRefValue() == null) {
return;
}

Expand All @@ -809,66 +751,31 @@ public void visit(ReferenceParmVal rpv) throws FHIRPersistenceException {
throw new FHIRPersistenceException("Resource type not found in cache: '" + resourceType + "'");
}

final String base = getServerUrl();
ResourceTokenValueRec rec;
if (base != null && valueString.startsWith(base)) {
// - relative reference https://example.com/Patient/123
// Because this reference is to a local FHIR resource (inside this server), we need use the correct
// resource type name (assigned as the code system)
// - https://localhost:9443/fhir-server/api/v4/Patient/1234
// - https://example.com/Patient/1234
// - https://example.com/Patient/1234/_history/2
valueString = valueString.substring(base.length());

// Patient/1234
// Patient/1234/_history/2
String[] tokens = valueString.split("/");
if (tokens.length > 1) {
String refResourceType = tokens[0];
String refLogicalId = tokens[1];
Integer refVersion = null;
if (tokens.length == 4 && HISTORY.equals(tokens[2])) {
// versioned reference
refVersion = Integer.parseInt(tokens[3]);
}

// Store a token value configured as a reference to another resource
rec = new ResourceTokenValueRec(parameterNameId, resourceType, resourceTypeId, logicalResourceId, refResourceType, refLogicalId, refVersion);
} else {
// stored as a token with the default system
rec = new ResourceTokenValueRec(parameterNameId, resourceType, resourceTypeId, logicalResourceId, TokenParmVal.DEFAULT_TOKEN_SYSTEM, valueString);
}
} else if (valueString.startsWith(HTTP) || valueString.startsWith(HTTPS) || valueString.startsWith(URN)) {
// - absolute URL ==> http://some.system/a/fhir/resource/path
// - absolute URI ==> urn:uuid:53fefa32-1111-2222-3333-55ee120877b7
// stored as a token with the default system
rec = new ResourceTokenValueRec(parameterNameId, resourceType, resourceTypeId, logicalResourceId, TokenParmVal.DEFAULT_TOKEN_SYSTEM, valueString);
} else if (valueString.startsWith("#")) {
// - Internal ==> #fragmentid1
// stored as a token value with the default system
rec = new ResourceTokenValueRec(parameterNameId, resourceType, resourceTypeId, logicalResourceId, TokenParmVal.DEFAULT_TOKEN_SYSTEM, valueString);
} else {
// - Relative ==> Patient/1234
// - Relative ==> Patient/1234/_history/2
String[] tokens = valueString.split("/");
if (tokens.length > 1) {
String refResourceType = tokens[0];
String refLogicalId = tokens[1];
Integer refVersion = null;
if (tokens.length == 4 && HISTORY.equals(tokens[2])) {
// versioned reference
refVersion = Integer.parseInt(tokens[3]);
}
// The ReferenceValue has already been processed to convert the reference to
// the required standard form, ready for insertion as a token value.
ReferenceValue refValue = rpv.getRefValue();

// Store a token value configured as a reference to another resource
rec = new ResourceTokenValueRec(parameterNameId, resourceType, resourceTypeId, logicalResourceId, refResourceType, refLogicalId, refVersion);
// Ignore references containing only a "display" element (apparently supported by the spec,
// but contains nothing useful to store because there's no searchable value).
String refResourceType = refValue.getTargetResourceType();
String refLogicalId = refValue.getValue();
Integer refVersion = refValue.getVersion();
ResourceTokenValueRec rec;

} else {
// SearchReferenceTest system integration tests require support for arbitrary reference strings
// - Relative ==> 1234
final String codeSystem = TokenParmVal.DEFAULT_TOKEN_SYSTEM;
rec = new ResourceTokenValueRec(parameterNameId, resourceType, resourceTypeId, logicalResourceId, codeSystem, valueString);
}
if (refValue.getType() == ReferenceType.DISPLAY_ONLY || refValue.getType() == ReferenceType.INVALID) {
// protect against code regression. Invalid/improper references should be
// filtered out already.
logger.warning("Invalid reference parameter type: " + resourceType + "." + rpv.getName() + " type=" + refValue.getType().name());
throw new IllegalArgumentException("Invalid reference parameter value. See server log for details.");
}

if (refResourceType != null) {
// Store a token value configured as a reference to another resource
rec = new ResourceTokenValueRec(parameterNameId, resourceType, resourceTypeId, logicalResourceId, refResourceType, refLogicalId, refVersion);
} else {
// stored as a token with the default system
rec = new ResourceTokenValueRec(parameterNameId, resourceType, resourceTypeId, logicalResourceId, TokenParmVal.DEFAULT_TOKEN_SYSTEM, refLogicalId);
}

if (this.transactionData != null) {
Expand Down
37 changes: 31 additions & 6 deletions fhir-persistence-jdbc/src/main/java/com/ibm/fhir/persistence/jdbc/dto/ReferenceParmVal.java
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Expand Up @@ -8,6 +8,7 @@

import com.ibm.fhir.persistence.exception.FHIRPersistenceException;
import com.ibm.fhir.search.SearchConstants.Type;
import com.ibm.fhir.search.util.ReferenceValue;

/**
* DTO representing external and local reference parameters
Expand All @@ -21,11 +22,14 @@ public class ReferenceParmVal implements ExtractedParameterValue {
private String name;

// The reference value
private String valueString;
//private String valueString;

// The SearchParameter base type. If "Resource", then this is a Resource-level attribute
private String base;

// The value of the reference after it has been processed to determine target resource type, version etc.
private ReferenceValue refValue;

/**
* Public constructor
*/
Expand All @@ -41,19 +45,40 @@ public String getName() {
return name;
}

public String getValueString() {
return valueString;
}
// public String getValueString() {
// return valueString;
// }

// public void setValueString(String valueString) {
// this.valueString = valueString;
// }

public void setValueString(String valueString) {
this.valueString = valueString;
/**
* Get the refValue
* @return
*/
public ReferenceValue getRefValue() {
return this.refValue;
}

/**
* Set the refValue
* @param refValue
*/
public void setRefValue(ReferenceValue refValue) {
this.refValue = refValue;
}

/**
* Get the reference type of the parameter (the origin, not the target of the reference)
*/
public String getResourceType() {
return resourceType;
}

/**
* Set the reference type of the parameter (the origin, not the target of the reference)
*/
public void setResourceType(String resourceType) {
this.resourceType = resourceType;
}
Expand Down
57 changes: 57 additions & 0 deletions ...stence-jdbc/src/main/java/com/ibm/fhir/persistence/jdbc/impl/FHIRPersistenceJDBCImpl.java
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Expand Up @@ -120,6 +120,7 @@
import com.ibm.fhir.persistence.jdbc.dto.ExtractedParameterValue;
import com.ibm.fhir.persistence.jdbc.dto.NumberParmVal;
import com.ibm.fhir.persistence.jdbc.dto.QuantityParmVal;
import com.ibm.fhir.persistence.jdbc.dto.ReferenceParmVal;
import com.ibm.fhir.persistence.jdbc.dto.StringParmVal;
import com.ibm.fhir.persistence.jdbc.dto.TokenParmVal;
import com.ibm.fhir.persistence.jdbc.exception.FHIRPersistenceDBConnectException;
Expand All @@ -138,9 +139,14 @@
import com.ibm.fhir.search.SearchConstants;
import com.ibm.fhir.search.SearchConstants.Modifier;
import com.ibm.fhir.search.SummaryValueSet;
import com.ibm.fhir.search.compartment.CompartmentUtil;
import com.ibm.fhir.search.context.FHIRSearchContext;
import com.ibm.fhir.search.date.DateTimeHandler;
import com.ibm.fhir.search.exception.FHIRSearchException;
import com.ibm.fhir.search.parameters.QueryParameter;
import com.ibm.fhir.search.reference.value.CompartmentReference;
import com.ibm.fhir.search.util.ReferenceValue;
import com.ibm.fhir.search.util.ReferenceValue.ReferenceType;
import com.ibm.fhir.search.util.SearchUtil;

/**
Expand Down Expand Up @@ -1227,6 +1233,21 @@ private TransactionSynchronizationRegistry getTrxSynchRegistry() throws FHIRPers
}
}

private List<ExtractedParameterValue> extractCompartmentValues(Resource fhirResource, com.ibm.fhir.persistence.jdbc.dto.Resource resourceDTO) throws Exception {

List<ExtractedParameterValue> result = null;

Map<String, Set<java.lang.String>> compartmentRefParams = CompartmentUtil.getCompartmentParamsForResourceType(fhirResource.getClass().getSimpleName());

if (!compartmentRefParams.isEmpty()) {
//result = SearchUtil.extractCompartmentParameterValues(fhirResource, compartmentRefParams);
} else {
result = Collections.emptyList();
}

return result;
}

/**
* Extracts search parameters for the passed FHIR Resource.
* @param fhirResource - Some FHIR Resource
Expand Down Expand Up @@ -1442,12 +1463,48 @@ private List<ExtractedParameterValue> extractSearchParameters(Resource fhirResou
}
}
}

// Augment the extracted parameter list with special values we use to represent compartment relationships.
// These references are stored as tokens and are used by the search query builder
// for compartment-based searches
addCompartmentParams(allParameters, fhirResource);
} finally {
log.exiting(CLASSNAME, METHODNAME);
}
return allParameters;
}

/**
* Augment the given list with additional reference values
* @param allParameters
*/
protected void addCompartmentParams(List<ExtractedParameterValue> allParameters, Resource fhirResource) throws FHIRSearchException {
final String resourceType = fhirResource.getClass().getSimpleName();
Map<String,Set<String>> compartmentRefParams = CompartmentUtil.getCompartmentParamsForResourceType(resourceType);
Map<String, Set<CompartmentReference>> compartmentMap = SearchUtil.extractCompartmentParameterValues(fhirResource, compartmentRefParams);

for (Map.Entry<String, Set<CompartmentReference>> entry: compartmentMap.entrySet()) {
final String compartmentName = entry.getKey();
final String parameterName = CompartmentUtil.makeCompartmentParamName(compartmentName);

// Create a reference parameter value for each CompartmentReference extracted from the resource
for (CompartmentReference compartmentRef: entry.getValue()) {
ReferenceParmVal pv = new ReferenceParmVal();
pv.setName(parameterName);
pv.setResourceType(resourceType);

// ReferenceType doesn't really matter here, but LITERAL_RELATIVE is appropriate
ReferenceValue rv = new ReferenceValue(compartmentName, compartmentRef.getReferenceResourceValue(), ReferenceType.LITERAL_RELATIVE, null);
pv.setRefValue(rv);

if (log.isLoggable(Level.FINE)) {
log.fine("Adding compartment reference parameter: [" + resourceType + "] "+ parameterName + " = " + rv.getTargetResourceType() + "/" + rv.getValue());
}
allParameters.add(pv);
}
}
}

/**
* Create a Parameter DTO from the primitive value.
* Note: this method only sets the value;
Expand Down
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