honeymoose
/
hapi-fhir
mirror of https://github.com/hapifhir/hapi-fhir.git
1
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity

Implement Terminology Delta Operations (#1536) 

* Start refactoring terminology delta operations

* Work on delta operations

* Work on concept saving

* Split term services into smaller services

* Work on term delta operations

* Work on term svcs

* Work on term operations

* More work on delta uploader

* Add a test

* Wrk on term service

* Fix compile error

* Some refactoring

* Test fix

* Test fix

* Test fixes

* Test fix

* Test fixes

* Test fixes

* Work on delta

* Work on tests#

* Test fixes

* Improve resequencing logic

* Build test

* More testing

* More build testing

* More work on tests

* CHange test logging

* Fix term service PID issue

* Update src/changes/changes.xml

Co-Authored-By: Diederik Muylwyk <diederik.muylwyk@gmail.com>

* Address review comment

* Some cleanup

* Test fix

* Fix some tests

* Test fixes
This commit is contained in:
James Agnew 2019-10-14 19:14:41 -04:00 committed by GitHub
parent 92c6b88964
commit 2725797610
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
145 changed files with 5080 additions and 3622 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

49
examples/src/main/java/example/ServerMetadataExamples.java
View File

@ -1,15 +1,13 @@
package example;
import ca.uhn.fhir.model.api.Tag;
import ca.uhn.fhir.rest.annotation.Search;
import org.hl7.fhir.r4.model.InstantType;
import org.hl7.fhir.r4.model.Patient;
import java.util.ArrayList;
import java.util.List;
import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
import ca.uhn.fhir.model.api.Tag;
import ca.uhn.fhir.model.api.TagList;
import ca.uhn.fhir.model.dstu2.resource.Patient;
import ca.uhn.fhir.model.primitive.InstantDt;
import ca.uhn.fhir.rest.annotation.Search;
public class ServerMetadataExamples {
// START SNIPPET: serverMethod
@ -21,33 +19,20 @@ public class ServerMetadataExamples {
Patient patient = new Patient();
retVal.add(patient);
patient.setId("Patient/123");
patient.addName().addFamily("Smith").addGiven("John");
patient.addName().setFamily("Smith").addGiven("John");
// Create a tag list and add it to the resource
TagList tags = new TagList();
tags.addTag(Tag.HL7_ORG_FHIR_TAG, "http://foo/tag1.html", "Some tag");
tags.addTag(Tag.HL7_ORG_FHIR_TAG, "http://foo/tag2.html", "Another tag");
ResourceMetadataKeyEnum.TAG_LIST.put(patient, tags);
// Add tags
patient.getMeta().addTag()
.setSystem(Tag.HL7_ORG_FHIR_TAG)
.setCode("some_tag")
.setDisplay("Some tag");
patient.getMeta().addTag()
.setSystem(Tag.HL7_ORG_FHIR_TAG)
.setCode("another_tag")
.setDisplay("Another tag");
// Set some links (these can be provided as relative links or absolute)
// and the server will convert to absolute as appropriate
String linkAlternate = "Patient/7736";
ResourceMetadataKeyEnum.LINK_ALTERNATE.put(patient, linkAlternate);
String linkSearch = "Patient?name=smith&name=john";
ResourceMetadataKeyEnum.LINK_SEARCH.put(patient, linkSearch);
// Set the published and updated dates
InstantDt pubDate = new InstantDt("2011-02-22");
ResourceMetadataKeyEnum.PUBLISHED.put(patient, pubDate);
InstantDt updatedDate = new InstantDt("2014-07-12T11:22:27Z");
ResourceMetadataKeyEnum.UPDATED.put(patient, updatedDate);
// Set the resource title (note that if you are using HAPI's narrative
// generation capability, the narrative generator will often create
// useful titles automatically, and the server will create a default
// title if none is provided)
String title = "Patient John SMITH";
ResourceMetadataKeyEnum.TITLE.put(patient, title);
// Set the last updated date
patient.getMeta().setLastUpdatedElement(new InstantType("2011-02-22T11:22:00.0122Z"));
return retVal;
}

5
hapi-fhir-base/pom.xml
View File

@ -120,6 +120,11 @@
<optional>true</optional>
</dependency>
<dependency>
<groupId>org.awaitility</groupId>
<artifactId>awaitility</artifactId>
<scope>test</scope>
</dependency>
</dependencies>

6
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/FhirContext.java
View File

@ -20,6 +20,7 @@ import ca.uhn.fhir.util.ReflectionUtil;
import ca.uhn.fhir.util.VersionUtil;
import ca.uhn.fhir.validation.FhirValidator;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.builder.ToStringBuilder;
import org.apache.jena.riot.Lang;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseBundle;
@ -896,6 +897,11 @@ public class FhirContext {
}
}
@Override
public String toString() {
return "FhirContext[" + myVersion.getVersion().name() + "]";
}
/**
* Creates and returns a new FhirContext with version {@link FhirVersionEnum#DSTU2 DSTU2}
*/

220
hapi-fhir-base/src/main/java/ca/uhn/fhir/model/api/ResourceMetadataKeyEnum.java
View File

@ -21,7 +21,6 @@ package ca.uhn.fhir.model.api;
*/
import ca.uhn.fhir.model.base.composite.BaseCodingDt;
import ca.uhn.fhir.model.primitive.DecimalDt;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.model.primitive.InstantDt;
import ca.uhn.fhir.model.valueset.BundleEntrySearchModeEnum;
@ -29,7 +28,6 @@ import ca.uhn.fhir.model.valueset.BundleEntryTransactionMethodEnum;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import java.io.Serializable;
@ -92,29 +90,7 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
theResource.setUserData(DELETED_AT.name(), theObject);
}
};
/**
* Denotes the search score which a given resource should match in a transaction. See the FHIR transaction definition for information about this. Corresponds to the value in
* <code>Bundle.entry.score</code> in a Bundle resource.
* <p>
* Note that search URL is only used in FHIR DSTU2 and later.
* </p>
* <p>
* Values for this key are of type <b>{@link DecimalDt}</b>
* </p>
*/
public static final ResourceMetadataKeyEnum<DecimalDt> ENTRY_SCORE = new ResourceMetadataKeyEnum<DecimalDt>("ENTRY_SCORE") {
private static final long serialVersionUID = 1L;
@Override
public DecimalDt get(IResource theResource) {
return getDecimalFromMetadataOrNullIfNone(theResource.getResourceMetadata(), ENTRY_SCORE);
}
@Override
public void put(IResource theResource, DecimalDt theObject) {
theResource.getResourceMetadata().put(ENTRY_SCORE, theObject);
}
};
/**
* If present and populated with a {@link BundleEntrySearchModeEnum}, contains the "bundle entry search mode", which is the value of the status field in the Bundle entry containing this resource.
* The value for this key corresponds to field <code>Bundle.entry.search.mode</code>. This value can be set to provide a status value of "include" for included resources being returned by a
@ -187,67 +163,7 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
}
};
/**
* If present and populated with a string, provides the "alternate link" (the link element in the bundle entry with <code>rel="alternate"</code>). Server implementations may populate this with a
* complete URL, in which case the URL will be placed as-is in the bundle. They may alternately specify a resource relative URL (e.g. "Patient/1243") in which case the server will convert this to
* an absolute URL at runtime.
* <p>
* Values for this key are of type <b>{@link String}</b>
* </p>
*/
public static final ResourceMetadataKeyEnum<String> LINK_ALTERNATE = new ResourceMetadataKeyEnum<String>("LINK_ALTERNATE") {
private static final long serialVersionUID = 1L;
@Override
public String get(IResource theResource) {
return getStringFromMetadataOrNullIfNone(theResource.getResourceMetadata(), LINK_ALTERNATE);
}
@Override
public void put(IResource theResource, String theObject) {
theResource.getResourceMetadata().put(LINK_ALTERNATE, theObject);
}
};
/**
* If present and populated with a string, provides the "search link" (the link element in the bundle entry with <code>rel="search"</code>). Server implementations may populate this with a
* complete URL, in which case the URL will be placed as-is in the bundle. They may alternately specify a resource relative URL (e.g. "Patient?name=tester") in which case the server will convert
* this to an absolute URL at runtime.
* <p>
* Values for this key are of type <b>{@link String}</b>
* </p>
*/
public static final ResourceMetadataKeyEnum<String> LINK_SEARCH = new ResourceMetadataKeyEnum<String>("LINK_SEARCH") {
private static final long serialVersionUID = 1L;
@Override
public String get(IResource theResource) {
return getStringFromMetadataOrNullIfNone(theResource.getResourceMetadata(), LINK_SEARCH);
}
@Override
public void put(IResource theResource, String theObject) {
theResource.getResourceMetadata().put(LINK_SEARCH, theObject);
}
};
/**
* The value for this key represents a previous ID used to identify this resource. This key is currently only used internally during transaction method processing.
* <p>
* Values for this key are of type <b>{@link IdDt}</b>
* </p>
*/
public static final ResourceMetadataKeyEnum<IdDt> PREVIOUS_ID = new ResourceMetadataKeyEnum<IdDt>("PREVIOUS_ID") {
private static final long serialVersionUID = 1L;
@Override
public IdDt get(IResource theResource) {
return getIdFromMetadataOrNullIfNone(theResource.getResourceMetadata(), PREVIOUS_ID);
}
@Override
public void put(IResource theResource, IdDt theObject) {
theResource.getResourceMetadata().put(PREVIOUS_ID, theObject);
}
};
/**
* The value for this key represents a {@link List} of profile IDs that this resource claims to conform to.
* <p>
@ -301,18 +217,8 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
if (obj == null) {
return null;
}
try {
@SuppressWarnings("unchecked")
List<BaseCodingDt> securityLabels = (List<BaseCodingDt>) obj;
if (securityLabels.isEmpty()) {
return null;
}
return securityLabels;
} catch (ClassCastException e) {
throw new InternalErrorException("Found an object of type '" + obj.getClass().getCanonicalName() + "' in resource metadata for key SECURITY_LABELS - Expected "
+ BaseCodingDt.class.getCanonicalName());
}
//noinspection unchecked
return (List<BaseCodingDt>) obj;
}
@Override
@ -337,14 +243,9 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
Object retValObj = theResource.getResourceMetadata().get(TAG_LIST);
if (retValObj == null) {
return null;
} else if (retValObj instanceof TagList) {
if (((TagList) retValObj).isEmpty()) {
return null;
}
} else {
return (TagList) retValObj;
}
throw new InternalErrorException("Found an object of type '" + retValObj.getClass().getCanonicalName() + "' in resource metadata for key " + TAG_LIST.name() + " - Expected "
+ TagList.class.getCanonicalName());
}
@Override
@ -352,25 +253,6 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
theResource.getResourceMetadata().put(TAG_LIST, theObject);
}
};
/**
* If present and populated with a string (as an instance of {@link String}), this value contains the title for this resource, as supplied in any bundles containing the resource.
* <p>
* Values for this key are of type <b>{@link String}</b>
* </p>
*/
public static final ResourceMetadataKeyEnum<String> TITLE = new ResourceMetadataKeyEnum<String>("TITLE") {
private static final long serialVersionUID = 1L;
@Override
public String get(IResource theResource) {
return getStringFromMetadataOrNullIfNone(theResource.getResourceMetadata(), TITLE);
}
@Override
public void put(IResource theResource, String theObject) {
theResource.getResourceMetadata().put(TITLE, theObject);
}
};
/**
* The value for this key is the bundle entry <b>Updated</b> time. This is defined by FHIR as "Last Updated for resource". This value is also used for populating the "Last-Modified" header in the
* case of methods that return a single resource (read, vread, etc.)
@ -398,7 +280,10 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
* <p>
* Values for this key are of type <b>{@link String}</b>
* </p>
*
* @deprecated The {@link IResource#getId()} resource ID will now be populated with the version ID via the {@link IdDt#getVersionIdPart()} method
*/
@Deprecated
public static final ResourceMetadataKeyEnum<String> VERSION = new ResourceMetadataKeyEnum<String>("VERSION") {
private static final long serialVersionUID = 1L;
@ -426,7 +311,7 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
@Override
public IdDt get(IResource theResource) {
return getIdFromMetadataOrNullIfNone(theResource.getResourceMetadata(), VERSION_ID);
return getIdFromMetadataOrNullIfNone(theResource.getResourceMetadata());
}
@Override
@ -474,32 +359,45 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
public abstract void put(IResource theResource, T theObject);
@Override
public String toString() {
return myValue;
public static abstract class ResourceMetadataKeySupportingAnyResource<T, T2> extends ResourceMetadataKeyEnum<T> {
private static final long serialVersionUID = 1L;
public ResourceMetadataKeySupportingAnyResource(String theValue) {
super(theValue);
}
private static DecimalDt getDecimalFromMetadataOrNullIfNone(Map<ResourceMetadataKeyEnum<?>, Object> theResourceMetadata, ResourceMetadataKeyEnum<DecimalDt> theKey) {
Object retValObj = theResourceMetadata.get(theKey);
public abstract T2 get(IAnyResource theResource);
public abstract void put(IAnyResource theResource, T2 theObject);
}
public static final class ExtensionResourceMetadataKey extends ResourceMetadataKeyEnum<ExtensionDt> {
public ExtensionResourceMetadataKey(String theUrl) {
super(theUrl);
}
@Override
public ExtensionDt get(IResource theResource) {
Object retValObj = theResource.getResourceMetadata().get(this);
if (retValObj == null) {
return null;
} else if (retValObj instanceof DecimalDt) {
if (((DecimalDt) retValObj).isEmpty()) {
return null;
} else if (retValObj instanceof ExtensionDt) {
return (ExtensionDt) retValObj;
}
return (DecimalDt) retValObj;
} else if (retValObj instanceof String) {
if (StringUtils.isBlank((String) retValObj)) {
return null;
throw new InternalErrorException("Found an object of type '" + retValObj.getClass().getCanonicalName()
+ "' in resource metadata for key " + this.name() + " - Expected "
+ ExtensionDt.class.getCanonicalName());
}
return new DecimalDt((String) retValObj);
} else if (retValObj instanceof Double) {
return new DecimalDt((Double) retValObj);
@Override
public void put(IResource theResource, ExtensionDt theObject) {
theResource.getResourceMetadata().put(this, theObject);
}
throw new InternalErrorException("Found an object of type '" + retValObj.getClass().getCanonicalName() + "' in resource metadata for key " + theKey.name() + " - Expected "
+ InstantDt.class.getCanonicalName());
}
@SuppressWarnings("unchecked")
private static <T extends Enum<?>> T getEnumFromMetadataOrNullIfNone(Map<ResourceMetadataKeyEnum<?>, Object> theResourceMetadata, ResourceMetadataKeyEnum<T> theKey, Class<T> theEnumType,
IValueSetEnumBinder<T> theBinder) {
@ -515,8 +413,8 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
+ InstantDt.class.getCanonicalName());
}
private static IdDt getIdFromMetadataOrNullIfNone(Map<ResourceMetadataKeyEnum<?>, Object> theResourceMetadata, ResourceMetadataKeyEnum<?> theKey) {
return toId(theKey, theResourceMetadata.get(theKey));
private static IdDt getIdFromMetadataOrNullIfNone(Map<ResourceMetadataKeyEnum<?>, Object> theResourceMetadata) {
return toId(ResourceMetadataKeyEnum.VERSION_ID, theResourceMetadata.get(ResourceMetadataKeyEnum.VERSION_ID));
}
private static List<IdDt> getIdListFromMetadataOrNullIfNone(Map<ResourceMetadataKeyEnum<?>, Object> theResourceMetadata, ResourceMetadataKeyEnum<?> theKey) {
@ -586,49 +484,11 @@ public abstract class ResourceMetadataKeyEnum<T> implements Serializable {
}
return (IdDt) retValObj;
} else if (retValObj instanceof Number) {
return new IdDt(((Number) retValObj).toString());
return new IdDt(retValObj.toString());
}
throw new InternalErrorException("Found an object of type '" + retValObj.getClass().getCanonicalName() + "' in resource metadata for key " + theKey.name() + " - Expected "
+ IdDt.class.getCanonicalName());
}
public static abstract class ResourceMetadataKeySupportingAnyResource<T, T2> extends ResourceMetadataKeyEnum<T> {
private static final long serialVersionUID = 1L;
public ResourceMetadataKeySupportingAnyResource(String theValue) {
super(theValue);
}
public abstract T2 get(IAnyResource theResource);
public abstract void put(IAnyResource theResource, T2 theObject);
}
public static final class ExtensionResourceMetadataKey extends ResourceMetadataKeyEnum<ExtensionDt> {
public ExtensionResourceMetadataKey(String url) {
super(url);
}
@Override
public ExtensionDt get(IResource theResource) {
Object retValObj = theResource.getResourceMetadata().get(this);
if (retValObj == null) {
return null;
} else if (retValObj instanceof ExtensionDt) {
return (ExtensionDt) retValObj;
}
throw new InternalErrorException("Found an object of type '" + retValObj.getClass().getCanonicalName()
+ "' in resource metadata for key " + this.name() + " - Expected "
+ ExtensionDt.class.getCanonicalName());
}
@Override
public void put(IResource theResource, ExtensionDt theObject) {
theResource.getResourceMetadata().put(this, theObject);
}
}
}

12
hapi-fhir-base/src/main/java/ca/uhn/fhir/model/api/Tag.java
View File

@ -168,18 +168,6 @@ public class Tag extends BaseElement implements IElement, IBaseCoding {
return this;
}
public String toHeaderValue() {
StringBuilder b = new StringBuilder();
b.append(this.getTerm());
if (isNotBlank(this.getLabel())) {
b.append("; label=\"").append(this.getLabel()).append('"');
}
if (isNotBlank(this.getScheme())) {
b.append("; scheme=\"").append(this.getScheme()).append('"');
}
return b.toString();
}
@Override
public String toString() {
ToStringBuilder b = new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE);

6
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/client/api/IHttpResponse.java
View File

@ -33,12 +33,6 @@ import java.util.Map;
*/
public interface IHttpResponse {
/**
* @deprecated This method was deprecated in HAPI FHIR 2.2 because its name has a typo. Use {@link #bufferEntity()} instead.
*/
@Deprecated
void bufferEntitity() throws IOException;
/**
* Buffer the message entity data.
* <p>

28
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/TokenParam.java
View File

@ -248,26 +248,30 @@ public class TokenParam extends BaseParam /*implements IQueryParameterType*/ {
@Override
public boolean equals(Object theO) {
if (this == theO) return true;
if (this == theO) {
return true;
}
if (theO == null || getClass() != theO.getClass()) return false;
if (theO == null || getClass() != theO.getClass()) {
return false;
}
TokenParam that = (TokenParam) theO;
return new EqualsBuilder()
.append(myModifier, that.myModifier)
.append(mySystem, that.mySystem)
.append(myValue, that.myValue)
.isEquals();
EqualsBuilder b = new EqualsBuilder();
b.append(myModifier, that.myModifier);
b.append(mySystem, that.mySystem);
b.append(myValue, that.myValue);
return b.isEquals();
}
@Override
public int hashCode() {
return new HashCodeBuilder(17, 37)
.append(myModifier)
.append(mySystem)
.append(myValue)
.toHashCode();
HashCodeBuilder b = new HashCodeBuilder(17, 37);
b.append(myModifier);
b.append(mySystem);
b.append(myValue);
return b.toHashCode();
}
private static String toSystemValue(UriDt theSystem) {

54
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/AsyncUtil.java Normal file
View File

@ -0,0 +1,54 @@
package ca.uhn.fhir.util;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.util.concurrent.CountDownLatch;
import java.util.concurrent.TimeUnit;
public class AsyncUtil {
private static final Logger ourLog = LoggerFactory.getLogger(AsyncUtil.class);
/**
* Non instantiable
*/
private AsyncUtil() {
}
/**
* Calls Thread.sleep and if an InterruptedException occurs, logs a warning but otherwise continues
*
* @param theMillis The number of millis to sleep
* @return Did we sleep the whole amount
*/
public static boolean sleep(long theMillis) {
try {
Thread.sleep(theMillis);
return true;
} catch (InterruptedException theE) {
Thread.currentThread().interrupt();
ourLog.warn("Sleep for {}ms was interrupted", theMillis);
return false;
}
}
public static boolean awaitLatchAndThrowInternalErrorExceptionOnInterrupt(CountDownLatch theInitialCollectionLatch, long theTime, TimeUnit theTimeUnit) {
try {
return theInitialCollectionLatch.await(theTime, theTimeUnit);
} catch (InterruptedException e) {
Thread.currentThread().interrupt();
throw new InternalErrorException(e);
}
}
public static boolean awaitLatchAndIgnoreInterrupt(CountDownLatch theInitialCollectionLatch, long theTime, TimeUnit theTimeUnit) {
try {
return theInitialCollectionLatch.await(theTime, theTimeUnit);
} catch (InterruptedException e) {
Thread.currentThread().interrupt();
ourLog.warn("Interrupted while waiting for latch");
return false;
}
}
}

25
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/AttachmentUtil.java
View File

@ -20,9 +20,8 @@ package ca.uhn.fhir.util;
* #L%
*/
import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.*;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.ICompositeType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
@ -35,12 +34,10 @@ public class AttachmentUtil {
* Fetches the base64Binary value of Attachment.data, creating it if it does not
* already exist.
*/
@SuppressWarnings("unchecked")
public static IPrimitiveType<byte[]> getOrCreateData(FhirContext theContext, ICompositeType theAttachment) {
return getOrCreateChild(theContext, theAttachment, "data", "base64Binary");
}
@SuppressWarnings("unchecked")
public static IPrimitiveType<String> getOrCreateContentType(FhirContext theContext, ICompositeType theAttachment) {
return getOrCreateChild(theContext, theAttachment, "contentType", "string");
}
@ -64,6 +61,16 @@ public class AttachmentUtil {
});
}
public static void setUrl(FhirContext theContext, ICompositeType theAttachment, String theUrl) {
BaseRuntimeChildDefinition entryChild = getChild(theContext, theAttachment, "url");
assert entryChild != null : "Version " + theContext + " has no child " + "url";
String typeName = "uri";
if (theContext.getVersion().getVersion().isEqualOrNewerThan(FhirVersionEnum.R4)) {
typeName = "url";
}
entryChild.getMutator().setValue(theAttachment, newPrimitive(theContext, typeName, theUrl));
}
public static void setContentType(FhirContext theContext, ICompositeType theAttachment, String theContentType) {
BaseRuntimeChildDefinition entryChild = getChild(theContext, theAttachment, "contentType");
entryChild.getMutator().setValue(theAttachment, newPrimitive(theContext, "code", theContentType));
@ -88,7 +95,9 @@ public class AttachmentUtil {
*/
@SuppressWarnings("unchecked")
static <T> IPrimitiveType<T> newPrimitive(FhirContext theContext, String theType, T theValue) {
IPrimitiveType<T> primitive = (IPrimitiveType<T>) theContext.getElementDefinition(theType).newInstance();
BaseRuntimeElementDefinition<?> elementDefinition = theContext.getElementDefinition(theType);
Validate.notNull(elementDefinition, "Unknown type %s for %s", theType, theContext);
IPrimitiveType<T> primitive = (IPrimitiveType<T>) elementDefinition.newInstance();
primitive.setValue(theValue);
return primitive;
}
@ -100,4 +109,8 @@ public class AttachmentUtil {
BaseRuntimeElementCompositeDefinition<?> def = (BaseRuntimeElementCompositeDefinition<?>) theContext.getElementDefinition(theElement.getClass());
return def.getChildByName(theName);
}
public static ICompositeType newInstance(FhirContext theFhirCtx) {
return (ICompositeType) theFhirCtx.getElementDefinition("Attachment").newInstance();
}
}

3
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/ParametersUtil.java
View File

@ -72,6 +72,8 @@ public class ParametersUtil {
}
private static void addClientParameter(FhirContext theContext, Object theValue, IBaseResource theTargetResource, BaseRuntimeChildDefinition paramChild, BaseRuntimeElementCompositeDefinition<?> paramChildElem, String theName) {
Validate.notNull(theValue, "theValue must not be null");
if (theValue instanceof IBaseResource) {
IBase parameter = createParameterRepetition(theContext, theTargetResource, paramChild, paramChildElem, theName);
paramChildElem.getChildByName("resource").getMutator().addValue(parameter, (IBaseResource) theValue);
@ -162,7 +164,6 @@ public class ParametersUtil {
IPrimitiveType<Boolean> value = (IPrimitiveType<Boolean>) theCtx.getElementDefinition("boolean").newInstance();
value.setValue(theValue);
addParameterToParameters(theCtx, theParameters, theName, value);
}
@SuppressWarnings("unchecked")

40
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/StopWatch.java
View File

@ -1,6 +1,7 @@
package ca.uhn.fhir.util;
import com.google.common.annotations.VisibleForTesting;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.time.DateUtils;
import java.text.DecimalFormat;
@ -9,8 +10,6 @@ import java.util.Date;
import java.util.LinkedList;
import java.util.concurrent.TimeUnit;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
/*
* #%L
* HAPI FHIR - Core Library
@ -48,12 +47,14 @@ public class StopWatch {
private long myStarted = now();
private TaskTiming myCurrentTask;
private LinkedList<TaskTiming> myTasks;
/**
* Constructor
*/
public StopWatch() {
super();
}
/**
* Constructor
*
@ -63,7 +64,13 @@ public class StopWatch {
myStarted = theStart.getTime();
}
public StopWatch(long theL) {
/**
* Constructor
*
* @param theStart The time that the stopwatch was started
*/
public StopWatch(long theStart) {
myStarted = theStart;
}
private void addNewlineIfContentExists(StringBuilder theB) {
@ -120,6 +127,8 @@ public class StopWatch {
b.append(": ");
b.append(formatMillis(delta));
}
} else {
b.append("No tasks");
}
TaskTiming last = null;
@ -257,13 +266,12 @@ public class StopWatch {
*/
public void startTask(String theTaskName) {
endCurrentTask();
if (isNotBlank(theTaskName)) {
Validate.notBlank(theTaskName, "Task name must not be blank");
myCurrentTask = new TaskTiming()
.setTaskName(theTaskName)
.setStart(now());
myTasks.add(myCurrentTask);
}
}
/**
* Formats value in an appropriate format. See {@link #formatMillis(long)}}
@ -331,18 +339,18 @@ public class StopWatch {
/**
* Append a right-aligned and zero-padded numeric value to a `StringBuilder`.
*/
static private void append(StringBuilder tgt, String pfx, int dgt, long val) {
tgt.append(pfx);
if (dgt > 1) {
int pad = (dgt - 1);
for (long xa = val; xa > 9 && pad > 0; xa /= 10) {
static void appendRightAlignedNumber(StringBuilder theStringBuilder, String thePrefix, int theNumberOfDigits, long theValueToAppend) {
theStringBuilder.append(thePrefix);
if (theNumberOfDigits > 1) {
int pad = (theNumberOfDigits - 1);
for (long xa = theValueToAppend; xa > 9 && pad > 0; xa /= 10) {
pad--;
}
for (int xa = 0; xa < pad; xa++) {
tgt.append('0');
theStringBuilder.append('0');
}
}
tgt.append(val);
theStringBuilder.append(theValueToAppend);
}
/**
@ -399,11 +407,11 @@ public class StopWatch {
}
} else {
long millisAsLong = (long) theMillis;
append(buf, "", 2, ((millisAsLong % DateUtils.MILLIS_PER_DAY) / DateUtils.MILLIS_PER_HOUR));
append(buf, ":", 2, ((millisAsLong % DateUtils.MILLIS_PER_HOUR) / DateUtils.MILLIS_PER_MINUTE));
append(buf, ":", 2, ((millisAsLong % DateUtils.MILLIS_PER_MINUTE) / DateUtils.MILLIS_PER_SECOND));
appendRightAlignedNumber(buf, "", 2, ((millisAsLong % DateUtils.MILLIS_PER_DAY) / DateUtils.MILLIS_PER_HOUR));
appendRightAlignedNumber(buf, ":", 2, ((millisAsLong % DateUtils.MILLIS_PER_HOUR) / DateUtils.MILLIS_PER_MINUTE));
appendRightAlignedNumber(buf, ":", 2, ((millisAsLong % DateUtils.MILLIS_PER_MINUTE) / DateUtils.MILLIS_PER_SECOND));
if (theMillis <= DateUtils.MILLIS_PER_MINUTE) {
append(buf, ".", 3, (millisAsLong % DateUtils.MILLIS_PER_SECOND));
appendRightAlignedNumber(buf, ".", 3, (millisAsLong % DateUtils.MILLIS_PER_SECOND));
}
}
return buf.toString();

156
hapi-fhir-base/src/main/java/ca/uhn/fhir/validation/SchemaBaseValidator.java
View File

@ -19,26 +19,32 @@ package ca.uhn.fhir.validation;
* limitations under the License.
* #L%
*/
import java.io.*;
import java.nio.charset.Charset;
import java.util.*;
import javax.xml.XMLConstants;
import javax.xml.transform.Source;
import javax.xml.transform.stream.StreamSource;
import javax.xml.validation.*;
import org.apache.commons.io.IOUtils;
import org.apache.commons.io.input.BOMInputStream;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.w3c.dom.ls.LSInput;
import org.w3c.dom.ls.LSResourceResolver;
import org.xml.sax.*;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import org.apache.commons.io.IOUtils;
import org.apache.commons.io.input.BOMInputStream;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.w3c.dom.ls.LSInput;
import org.w3c.dom.ls.LSResourceResolver;
import org.xml.sax.SAXException;
import org.xml.sax.SAXNotRecognizedException;
import org.xml.sax.SAXParseException;
import javax.xml.XMLConstants;
import javax.xml.transform.Source;
import javax.xml.transform.stream.StreamSource;
import javax.xml.validation.Schema;
import javax.xml.validation.SchemaFactory;
import javax.xml.validation.Validator;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.StringReader;
import java.nio.charset.StandardCharsets;
import java.util.*;
public class SchemaBaseValidator implements IValidatorModule {
public static final String RESOURCES_JAR_NOTE = "Note that as of HAPI FHIR 1.2, DSTU2 validation files are kept in a separate JAR (hapi-fhir-validation-resources-XXX.jar) which must be added to your classpath. See the HAPI FHIR download page for more information.";
@ -47,7 +53,7 @@ public class SchemaBaseValidator implements IValidatorModule {
private static final Set<String> SCHEMA_NAMES;
static {
HashSet<String> sn = new HashSet<String>();
HashSet<String> sn = new HashSet<>();
sn.add("xml.xsd");
sn.add("xhtml1-strict.xsd");
sn.add("fhir-single.xsd");
@ -59,15 +65,15 @@ public class SchemaBaseValidator implements IValidatorModule {
SCHEMA_NAMES = Collections.unmodifiableSet(sn);
}
private Map<String, Schema> myKeyToSchema = new HashMap<String, Schema>();
private final Map<String, Schema> myKeyToSchema = new HashMap<>();
private FhirContext myCtx;
public SchemaBaseValidator(FhirContext theContext) {
myCtx = theContext;
}
private void doValidate(IValidationContext<?> theContext, String schemaName) {
Schema schema = loadSchema("dstu", schemaName);
private void doValidate(IValidationContext<?> theContext) {
Schema schema = loadSchema();
try {
Validator validator = schema.newValidator();
@ -87,8 +93,8 @@ public class SchemaBaseValidator implements IValidatorModule {
*/
validator.setProperty(XMLConstants.ACCESS_EXTERNAL_DTD, "");
validator.setProperty(XMLConstants.ACCESS_EXTERNAL_SCHEMA, "");
}catch (SAXNotRecognizedException ex){
ourLog.warn("Jaxp 1.5 Support not found.",ex);
} catch (SAXNotRecognizedException ex) {
ourLog.warn("Jaxp 1.5 Support not found.", ex);
}
validator.validate(new StreamSource(new StringReader(encodedResource)));
@ -99,17 +105,14 @@ public class SchemaBaseValidator implements IValidatorModule {
message.setMessage(e.getLocalizedMessage());
message.setSeverity(ResultSeverityEnum.FATAL);
theContext.addValidationMessage(message);
} catch (SAXException e) {
// Catch all
throw new ConfigurationException("Could not load/parse schema file", e);
} catch (IOException e) {
} catch (SAXException | IOException e) {
// Catch all
throw new ConfigurationException("Could not load/parse schema file", e);
}
}
private Schema loadSchema(String theVersion, String theSchemaName) {
String key = theVersion + "-" + theSchemaName;
private Schema loadSchema() {
String key = "fhir-single.xsd";
synchronized (myKeyToSchema) {
Schema schema = myKeyToSchema.get(key);
@ -117,7 +120,7 @@ public class SchemaBaseValidator implements IValidatorModule {
return schema;
}
Source baseSource = loadXml(null, theSchemaName);
Source baseSource = loadXml("fhir-single.xsd");
SchemaFactory schemaFactory = SchemaFactory.newInstance(XMLConstants.W3C_XML_SCHEMA_NS_URI);
schemaFactory.setResourceResolver(new MyResourceResolver());
@ -129,69 +132,40 @@ public class SchemaBaseValidator implements IValidatorModule {
* https://www.owasp.org/index.php/XML_External_Entity_(XXE)_Processing
*/
schemaFactory.setProperty(XMLConstants.ACCESS_EXTERNAL_DTD, "");
}catch (SAXNotRecognizedException snex){
ourLog.warn("Jaxp 1.5 Support not found.",snex);
} catch (SAXNotRecognizedException e) {
ourLog.warn("Jaxp 1.5 Support not found.", e);
}
schema = schemaFactory.newSchema(new Source[] { baseSource });
schema = schemaFactory.newSchema(new Source[]{baseSource});
} catch (SAXException e) {
throw new ConfigurationException("Could not load/parse schema file: " + theSchemaName, e);
throw new ConfigurationException("Could not load/parse schema file: " + "fhir-single.xsd", e);
}
myKeyToSchema.put(key, schema);
return schema;
}
}
private Source loadXml(String theSystemId, String theSchemaName) {
Source loadXml(String theSchemaName) {
String pathToBase = myCtx.getVersion().getPathToSchemaDefinitions() + '/' + theSchemaName;
ourLog.debug("Going to load resource: {}", pathToBase);
InputStream baseIs = FhirValidator.class.getResourceAsStream(pathToBase);
try (InputStream baseIs = FhirValidator.class.getResourceAsStream(pathToBase)) {
if (baseIs == null) {
throw new InternalErrorException("Schema not found. " + RESOURCES_JAR_NOTE);
}
baseIs = new BOMInputStream(baseIs, false);
InputStreamReader baseReader = new InputStreamReader(baseIs, Charset.forName("UTF-8"));
Source baseSource = new StreamSource(baseReader, theSystemId);
//FIXME resource leak
return baseSource;
try (BOMInputStream bomInputStream = new BOMInputStream(baseIs, false)) {
try (InputStreamReader baseReader = new InputStreamReader(bomInputStream, StandardCharsets.UTF_8)) {
// Buffer so that we can close the input stream
String contents = IOUtils.toString(baseReader);
return new StreamSource(new StringReader(contents), null);
}
}
} catch (IOException e) {
throw new InternalErrorException(e);
}
}
@Override
public void validateResource(IValidationContext<IBaseResource> theContext) {
doValidate(theContext, "fhir-single.xsd");
}
private static class MyErrorHandler implements org.xml.sax.ErrorHandler {
private IValidationContext<?> myContext;
public MyErrorHandler(IValidationContext<?> theContext) {
myContext = theContext;
}
private void addIssue(SAXParseException theException, ResultSeverityEnum theSeverity) {
SingleValidationMessage message = new SingleValidationMessage();
message.setLocationLine(theException.getLineNumber());
message.setLocationCol(theException.getColumnNumber());
message.setMessage(theException.getLocalizedMessage());
message.setSeverity(theSeverity);
myContext.addValidationMessage(message);
}
@Override
public void error(SAXParseException theException) {
addIssue(theException, ResultSeverityEnum.ERROR);
}
@Override
public void fatalError(SAXParseException theException) {
addIssue(theException, ResultSeverityEnum.FATAL);
}
@Override
public void warning(SAXParseException theException) {
addIssue(theException, ResultSeverityEnum.WARNING);
}
doValidate(theContext);
}
private final class MyResourceResolver implements LSResourceResolver {
@ -225,4 +199,38 @@ public class SchemaBaseValidator implements IValidatorModule {
}
}
private static class MyErrorHandler implements org.xml.sax.ErrorHandler {
private IValidationContext<?> myContext;
MyErrorHandler(IValidationContext<?> theContext) {
myContext = theContext;
}
private void addIssue(SAXParseException theException, ResultSeverityEnum theSeverity) {
SingleValidationMessage message = new SingleValidationMessage();
message.setLocationLine(theException.getLineNumber());
message.setLocationCol(theException.getColumnNumber());
message.setMessage(theException.getLocalizedMessage());
message.setSeverity(theSeverity);
myContext.addValidationMessage(message);
}
@Override
public void error(SAXParseException theException) {
addIssue(theException, ResultSeverityEnum.ERROR);
}
@Override
public void fatalError(SAXParseException theException) {
addIssue(theException, ResultSeverityEnum.FATAL);
}
@Override
public void warning(SAXParseException theException) {
addIssue(theException, ResultSeverityEnum.WARNING);
}
}
}

8
hapi-fhir-base/src/main/resources/ca/uhn/fhir/i18n/hapi-messages.properties
View File

@ -125,9 +125,9 @@ ca.uhn.fhir.jpa.binstore.BinaryAccessProvider.unknownPath=Unable to find content
ca.uhn.fhir.jpa.binstore.BinaryAccessProvider.unknownType=Content in resource of type {0} at path {1} is not appropriate for binary storage: {2}
ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl.cannotCreateDuplicateCodeSystemUrl=Can not create multiple CodeSystem resources with CodeSystem.url "{0}", already have one with resource ID: {1}
ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl.cannotCreateDuplicateConceptMapUrl=Can not create multiple ConceptMap resources with ConceptMap.url "{0}", already have one with resource ID: {1}
ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl.cannotCreateDuplicateValueSetUrl=Can not create multiple ValueSet resources with ValueSet.url "{0}", already have one with resource ID: {1}
ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl.expansionTooLarge=Expansion of ValueSet produced too many codes (maximum {0}) - Operation aborted!
ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.cannotCreateDuplicateCodeSystemUrl=Can not create multiple CodeSystem resources with CodeSystem.url "{0}", already have one with resource ID: {1}
ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.cannotCreateDuplicateConceptMapUrl=Can not create multiple ConceptMap resources with ConceptMap.url "{0}", already have one with resource ID: {1}
ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.cannotCreateDuplicateValueSetUrl=Can not create multiple ValueSet resources with ValueSet.url "{0}", already have one with resource ID: {1}
ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl.expansionTooLarge=Expansion of ValueSet produced too many codes (maximum {0}) - Operation aborted!
ca.uhn.fhir.jpa.util.jsonpatch.JsonPatchUtils.failedToApplyPatch=Failed to apply JSON patch to {0}: {1}

35
hapi-fhir-base/src/test/java/ca/uhn/fhir/model/api/ResourceMetadataKeyEnumTest.java Normal file
View File

@ -0,0 +1,35 @@
package ca.uhn.fhir.model.api;
import org.junit.Test;
import static org.junit.Assert.*;
public class ResourceMetadataKeyEnumTest {
@Test
public void testHashCode() {
assertEquals(-60968467, ResourceMetadataKeyEnum.PUBLISHED.hashCode());
}
@Test
public void testEquals() {
assertNotEquals(ResourceMetadataKeyEnum.PROFILES, null);
assertNotEquals(ResourceMetadataKeyEnum.PROFILES, "");
assertNotEquals(ResourceMetadataKeyEnum.PROFILES, ResourceMetadataKeyEnum.PUBLISHED);
assertEquals(ResourceMetadataKeyEnum.PROFILES, ResourceMetadataKeyEnum.PROFILES);
}
@Test
public void testExtensionResourceEquals() {
assertNotEquals(new ResourceMetadataKeyEnum.ExtensionResourceMetadataKey("http://foo"), new ResourceMetadataKeyEnum.ExtensionResourceMetadataKey("http://bar"));
assertNotEquals(new ResourceMetadataKeyEnum.ExtensionResourceMetadataKey("http://foo"), null);
assertNotEquals(new ResourceMetadataKeyEnum.ExtensionResourceMetadataKey("http://foo"), "");
assertEquals(new ResourceMetadataKeyEnum.ExtensionResourceMetadataKey("http://foo"), new ResourceMetadataKeyEnum.ExtensionResourceMetadataKey("http://foo"));
ResourceMetadataKeyEnum.ExtensionResourceMetadataKey foo = new ResourceMetadataKeyEnum.ExtensionResourceMetadataKey("http://foo");
assertEquals(foo, foo);
}
}

46
hapi-fhir-base/src/test/java/ca/uhn/fhir/model/api/TagTest.java Normal file
View File

@ -0,0 +1,46 @@
package ca.uhn.fhir.model.api;
import org.junit.Test;
import java.net.URI;
import java.net.URISyntaxException;
import static org.junit.Assert.*;
public class TagTest {
@Test
public void testEquals() {
Tag tag1 = new Tag().setScheme("scheme").setTerm("term").setLabel("label");
Tag tag2 = new Tag().setScheme("scheme").setTerm("term").setLabel("label");
Tag tag3 = new Tag().setScheme("scheme2").setTerm("term").setLabel("label");
Tag tag4 = new Tag().setScheme("scheme").setTerm("term2").setLabel("label");
assertEquals(tag1, tag1);
assertEquals(tag1, tag2);
assertNotEquals(tag1, tag3);
assertNotEquals(tag1, tag4);
assertNotEquals(tag1, null);
assertNotEquals(tag1, "");
}
@Test
public void testHashCode() {
Tag tag1 = new Tag().setScheme("scheme").setTerm("term").setLabel("label");
assertEquals(1920714536, tag1.hashCode());
}
@Test
public void testConstructors() throws URISyntaxException {
assertTrue(new Tag().isEmpty());
assertFalse(new Tag("http://foo").isEmpty());
assertFalse(new Tag("http://foo", "http://bar").isEmpty());
assertFalse(new Tag(new URI("http://foo"), new URI("http://bar"), "Label").isEmpty());
assertTrue(new Tag((URI)null, null, "Label").isEmpty());
assertEquals("http://foo", new Tag(new URI("http://foo"), new URI("http://bar"), "Label").getSystem());
assertEquals("http://bar", new Tag(new URI("http://foo"), new URI("http://bar"), "Label").getCode());
assertEquals("Label", new Tag(new URI("http://foo"), new URI("http://bar"), "Label").getDisplay());
}
}

23
hapi-fhir-base/src/test/java/ca/uhn/fhir/rest/param/TokenParamTest.java
View File

@ -2,13 +2,34 @@ package ca.uhn.fhir.rest.param;
import org.junit.Test;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.*;
public class TokenParamTest {
@Test
public void testEquals() {
TokenParam tokenParam1 = new TokenParam("foo", "bar");
TokenParam tokenParam2 = new TokenParam("foo", "bar");
TokenParam tokenParam3 = new TokenParam("foo", "baz");
assertEquals(tokenParam1, tokenParam1);
assertEquals(tokenParam1, tokenParam2);
assertNotEquals(tokenParam1, tokenParam3);
assertNotEquals(tokenParam1, null);
assertNotEquals(tokenParam1, "");
}
@Test
public void testHashCode() {
TokenParam tokenParam1 = new TokenParam("foo", "bar");
assertEquals(4716638, tokenParam1.hashCode());
}
@Test
public void testIsEmpty() {
assertFalse(new TokenParam("foo", "bar").isEmpty());
assertTrue(new TokenParam("", "").isEmpty());
assertTrue(new TokenParam().isEmpty());
assertEquals("", new TokenParam().getValueNotNull());
}
}

62
hapi-fhir-base/src/test/java/ca/uhn/fhir/util/AsyncUtilTest.java Normal file
View File

@ -0,0 +1,62 @@
package ca.uhn.fhir.util;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import org.junit.Test;
import java.util.concurrent.CountDownLatch;
import java.util.concurrent.TimeUnit;
import java.util.concurrent.atomic.AtomicBoolean;
import static org.awaitility.Awaitility.await;
public class AsyncUtilTest {
@Test
public void testSleep() {
AsyncUtil.sleep(10);
}
@Test
public void testSleepWithInterrupt() {
AtomicBoolean outcomeHolder = new AtomicBoolean(true);
Thread thread = new Thread(() -> {
boolean outcome = AsyncUtil.sleep(10000);
outcomeHolder.set(outcome);
});
thread.start();
thread.interrupt();
await().until(()-> outcomeHolder.get() == false);
}
@Test
public void testAwaitLatchAndThrowInternalErrorException() {
AtomicBoolean outcomeHolder = new AtomicBoolean(false);
CountDownLatch latch = new CountDownLatch(1);
Thread thread = new Thread(() -> {
try {
AsyncUtil.awaitLatchAndThrowInternalErrorExceptionOnInterrupt(latch, 10, TimeUnit.SECONDS);
} catch (InternalErrorException e) {
outcomeHolder.set(true);
}
});
thread.start();
thread.interrupt();
await().until(()-> outcomeHolder.get());
}
@Test
public void testAwaitLatchIgnoreInterruption() {
AtomicBoolean outcomeHolder = new AtomicBoolean(true);
CountDownLatch latch = new CountDownLatch(1);
Thread thread = new Thread(() -> {
boolean outcome = AsyncUtil.awaitLatchAndIgnoreInterrupt(latch, 10, TimeUnit.SECONDS);
outcomeHolder.set(outcome);
});
thread.start();
thread.interrupt();
await().until(()-> outcomeHolder.get() == false);
}
}

80
hapi-fhir-base/src/test/java/ca/uhn/fhir/util/StopWatchTest.java
View File

@ -128,6 +128,56 @@ public class StopWatchTest {
assertEquals("TASK1: 500ms\nTASK2: 100ms", taskDurations);
}
@Test
public void testFormatTaskDurationsDelayBetweenTasks() {
StopWatch sw = new StopWatch();
StopWatch.setNowForUnitTestForUnitTest(1000L);
sw.startTask("TASK1");
StopWatch.setNowForUnitTestForUnitTest(1500L);
sw.endCurrentTask();
StopWatch.setNowForUnitTestForUnitTest(2000L);
sw.startTask("TASK2");
StopWatch.setNowForUnitTestForUnitTest(2100L);
sw.endCurrentTask();
StopWatch.setNowForUnitTestForUnitTest(2200L);
String taskDurations = sw.formatTaskDurations();
ourLog.info(taskDurations);
assertEquals("TASK1: 500ms\n" +
"Between: 500ms\n" +
"TASK2: 100ms\n" +
"After last task: 100ms", taskDurations);
}
@Test
public void testFormatTaskDurationsLongDelayBeforeStart() {
StopWatch sw = new StopWatch(0);
StopWatch.setNowForUnitTestForUnitTest(1000L);
sw.startTask("TASK1");
StopWatch.setNowForUnitTestForUnitTest(1500L);
sw.startTask("TASK2");
StopWatch.setNowForUnitTestForUnitTest(1600L);
String taskDurations = sw.formatTaskDurations();
ourLog.info(taskDurations);
assertEquals("Before first task: 1000ms\nTASK1: 500ms\nTASK2: 100ms", taskDurations);
}
@Test
public void testFormatTaskDurationsNoTasks() {
StopWatch sw = new StopWatch(0);
String taskDurations = sw.formatTaskDurations();
ourLog.info(taskDurations);
assertEquals("No tasks", taskDurations);
}
@Test
public void testFormatThroughput60Ops4Min() {
StopWatch sw = new StopWatch(DateUtils.addMinutes(new Date(), -4));
@ -210,4 +260,34 @@ public class StopWatchTest {
assertThat(string, matchesPattern("^[0-9]{3,4}ms$"));
}
@Test
public void testAppendRightAlignedNumber() {
StringBuilder b= new StringBuilder();
b.setLength(0);
StopWatch.appendRightAlignedNumber(b, "PFX", 0, 100);
assertEquals("PFX100", b.toString());
b.setLength(0);
StopWatch.appendRightAlignedNumber(b, "PFX", 1, 100);
assertEquals("PFX100", b.toString());
b.setLength(0);
StopWatch.appendRightAlignedNumber(b, "PFX", 2, 100);
assertEquals("PFX100", b.toString());
b.setLength(0);
StopWatch.appendRightAlignedNumber(b, "PFX", 3, 100);
assertEquals("PFX100", b.toString());
b.setLength(0);
StopWatch.appendRightAlignedNumber(b, "PFX", 4, 100);
assertEquals("PFX0100", b.toString());
b.setLength(0);
StopWatch.appendRightAlignedNumber(b, "PFX", 10, 100);
assertEquals("PFX0000000100", b.toString());
}
}

4
hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/ToggleSearchParametersCommand.java
View File

@ -20,7 +20,7 @@ package ca.uhn.fhir.cli;
* #L%
*/
import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.ParseException;
@ -44,7 +44,7 @@ public class ToggleSearchParametersCommand extends BaseCommand {
Options options = new Options();
addFhirVersionOption(options);
addBaseUrlOption(options);
addRequiredOption(options, "u", "url", true, "The code system URL associated with this upload (e.g. " + IHapiTerminologyLoaderSvc.SCT_URI + ")");
addRequiredOption(options, "u", "url", true, "The code system URL associated with this upload (e.g. " + ITermLoaderSvc.SCT_URI + ")");
addBasicAuthOption(options);
return options;
}

156
hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/UploadTerminologyCommand.java
View File

@ -20,35 +20,32 @@ package ca.uhn.fhir.cli;
* #L%
*/
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
import ca.uhn.fhir.jpa.term.TerminologyLoaderSvcImpl;
import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
import ca.uhn.fhir.util.AttachmentUtil;
import ca.uhn.fhir.util.ParametersUtil;
import com.google.common.base.Charsets;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.ParseException;
import org.apache.commons.io.IOUtils;
import org.hl7.fhir.instance.model.api.IBaseParameters;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.instance.model.api.ICompositeType;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import java.util.stream.Collectors;
import java.util.zip.ZipEntry;
import java.util.zip.ZipOutputStream;
import static org.apache.commons.lang3.StringUtils.isBlank;
public class UploadTerminologyCommand extends BaseCommand {
public static final String UPLOAD_TERMINOLOGY = "upload-terminology";
static final String UPLOAD_TERMINOLOGY = "upload-terminology";
// TODO: Don't use qualified names for loggers in HAPI CLI.
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(UploadTerminologyCommand.class);
@ -68,9 +65,8 @@ public class UploadTerminologyCommand extends BaseCommand {
addFhirVersionOption(options);
addBaseUrlOption(options);
addRequiredOption(options, "u", "url", true, "The code system URL associated with this upload (e.g. " + IHapiTerminologyLoaderSvc.SCT_URI + ")");
addRequiredOption(options, "u", "url", true, "The code system URL associated with this upload (e.g. " + ITermLoaderSvc.SCT_URI + ")");
addOptionalOption(options, "d", "data", true, "Local file to use to upload (can be a raw file or a ZIP containing the raw file)");
addOptionalOption(options, null, "custom", false, "Indicates that this upload uses the HAPI FHIR custom external terminology format");
addOptionalOption(options, "m", "mode", true, "The upload mode: SNAPSHOT (default), ADD, REMOVE");
addBasicAuthOption(options);
addVerboseLoggingOption(options);
@ -109,104 +105,86 @@ public class UploadTerminologyCommand extends BaseCommand {
switch (mode) {
case SNAPSHOT:
uploadSnapshot(inputParameters, termUrl, datafile, theCommandLine, client);
invokeOperation(theCommandLine, termUrl, datafile, client, inputParameters, JpaConstants.OPERATION_UPLOAD_EXTERNAL_CODE_SYSTEM);
break;
case ADD:
uploadDelta(theCommandLine, termUrl, datafile, client, inputParameters, JpaConstants.OPERATION_APPLY_CODESYSTEM_DELTA_ADD, false);
invokeOperation(theCommandLine, termUrl, datafile, client, inputParameters, JpaConstants.OPERATION_APPLY_CODESYSTEM_DELTA_ADD);
break;
case REMOVE:
uploadDelta(theCommandLine, termUrl, datafile, client, inputParameters, JpaConstants.OPERATION_APPLY_CODESYSTEM_DELTA_REMOVE, true);
invokeOperation(theCommandLine, termUrl, datafile, client, inputParameters, JpaConstants.OPERATION_APPLY_CODESYSTEM_DELTA_REMOVE);
break;
}
}
private void uploadDelta(CommandLine theCommandLine, String theTermUrl, String[] theDatafile, IGenericClient theClient, IBaseParameters theInputParameters, String theOperationName, boolean theFlatten) {
ParametersUtil.addParameterToParametersUri(myFhirCtx, theInputParameters, "url", theTermUrl);
private void invokeOperation(CommandLine theCommandLine, String theTermUrl, String[] theDatafile, IGenericClient theClient, IBaseParameters theInputParameters, String theOperationName) throws ParseException {
ParametersUtil.addParameterToParametersUri(myFhirCtx, theInputParameters, TerminologyUploaderProvider.PARAM_SYSTEM, theTermUrl);
List<IHapiTerminologyLoaderSvc.FileDescriptor> fileDescriptors = new ArrayList<>();
ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
ZipOutputStream zipOutputStream = new ZipOutputStream(byteArrayOutputStream, Charsets.UTF_8);
boolean haveCompressedContents = false;
try {
for (String nextDataFile : theDatafile) {
for (String next : theDatafile) {
try (FileInputStream inputStream = new FileInputStream(next)) {
byte[] bytes = IOUtils.toByteArray(inputStream);
fileDescriptors.add(new IHapiTerminologyLoaderSvc.FileDescriptor() {
@Override
public String getFilename() {
return next;
try (FileInputStream fileInputStream = new FileInputStream(nextDataFile)) {
if (!nextDataFile.endsWith(".zip")) {
ourLog.info("Compressing and adding file: {}", nextDataFile);
ZipEntry nextEntry = new ZipEntry(stripPath(nextDataFile));
zipOutputStream.putNextEntry(nextEntry);
IOUtils.copy(fileInputStream, zipOutputStream);
haveCompressedContents = true;
zipOutputStream.flush();
ourLog.info("Finished compressing {} into {}", nextEntry.getSize(), nextEntry.getCompressedSize());
} else {
ourLog.info("Adding file: {}", nextDataFile);
ICompositeType attachment = AttachmentUtil.newInstance(myFhirCtx);
AttachmentUtil.setUrl(myFhirCtx, attachment, "file:" + nextDataFile);
AttachmentUtil.setData(myFhirCtx, attachment, IOUtils.toByteArray(fileInputStream));
ParametersUtil.addParameterToParameters(myFhirCtx, theInputParameters, TerminologyUploaderProvider.PARAM_FILE, attachment);
}
}
@Override
public InputStream getInputStream() {
return new ByteArrayInputStream(bytes);
}
});
zipOutputStream.flush();
zipOutputStream.close();
} catch (IOException e) {
throw new CommandFailureException("Failed to read from file \"" + next + "\": " + e.getMessage());
}
throw new ParseException(e.toString());
}
TermCodeSystemVersion codeSystemVersion = new TermCodeSystemVersion();
TerminologyLoaderSvcImpl.LoadedFileDescriptors descriptors = new TerminologyLoaderSvcImpl.LoadedFileDescriptors(fileDescriptors);
TerminologyLoaderSvcImpl.processCustomTerminologyFiles(descriptors, codeSystemVersion);
CodeSystem codeSystem = new CodeSystem();
codeSystem.setUrl(theTermUrl);
addCodesToCodeSystem(codeSystemVersion.getConcepts(), codeSystem.getConcept(), theFlatten);
ParametersUtil.addParameterToParameters(myFhirCtx, theInputParameters, "value", codeSystem);
if (theCommandLine.hasOption("custom")) {
ParametersUtil.addParameterToParametersCode(myFhirCtx, theInputParameters, "contentMode", "custom");
if (haveCompressedContents) {
ICompositeType attachment = AttachmentUtil.newInstance(myFhirCtx);
AttachmentUtil.setUrl(myFhirCtx, attachment, "file:/files.zip");
AttachmentUtil.setData(myFhirCtx, attachment, byteArrayOutputStream.toByteArray());
ParametersUtil.addParameterToParameters(myFhirCtx, theInputParameters, TerminologyUploaderProvider.PARAM_FILE, attachment);
}
ourLog.info("Beginning upload - This may take a while...");
IBaseParameters response = theClient
if (ourLog.isDebugEnabled() || "true".equals(System.getProperty("test"))) {
ourLog.info("Submitting parameters: {}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(theInputParameters));
}
IBaseParameters response;
try {
response = theClient
.operation()
.onType(myFhirCtx.getResourceDefinition("CodeSystem").getImplementingClass())
.named(theOperationName)
.withParameters(theInputParameters)
.execute();
ourLog.info("Upload complete!");
ourLog.info("Response:\n{}", myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(response));
} catch (BaseServerResponseException e) {
if (e.getOperationOutcome() != null) {
ourLog.error("Received the following response:\n{}", myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome()));
}
throw e;
}
private void addCodesToCodeSystem(Collection<TermConcept> theSourceConcepts, List<CodeSystem.ConceptDefinitionComponent> theTargetConcept, boolean theFlatten) {
for (TermConcept nextSourceConcept : theSourceConcepts) {
CodeSystem.ConceptDefinitionComponent nextTarget = new CodeSystem.ConceptDefinitionComponent();
nextTarget.setCode(nextSourceConcept.getCode());
nextTarget.setDisplay(nextSourceConcept.getDisplay());
theTargetConcept.add(nextTarget);
List<TermConcept> children = nextSourceConcept.getChildren().stream().map(t -> t.getChild()).collect(Collectors.toList());
if (theFlatten) {
addCodesToCodeSystem(children, theTargetConcept, theFlatten);
} else {
addCodesToCodeSystem(children, nextTarget.getConcept(), theFlatten);
}
}
}
private void uploadSnapshot(IBaseParameters theInputparameters, String theTermUrl, String[] theDatafile, CommandLine theCommandLine, IGenericClient theClient) {
ParametersUtil.addParameterToParametersUri(myFhirCtx, theInputparameters, "url", theTermUrl);
for (String next : theDatafile) {
ParametersUtil.addParameterToParametersString(myFhirCtx, theInputparameters, "localfile", next);
}
if (theCommandLine.hasOption("custom")) {
ParametersUtil.addParameterToParametersCode(myFhirCtx, theInputparameters, "contentMode", "custom");
}
ourLog.info("Beginning upload - This may take a while...");
IBaseParameters response = theClient
.operation()
.onType(myFhirCtx.getResourceDefinition("CodeSystem").getImplementingClass())
.named(JpaConstants.OPERATION_UPLOAD_EXTERNAL_CODE_SYSTEM)
.withParameters(theInputparameters)
.execute();
ourLog.info("Upload complete!");
ourLog.info("Response:\n{}", myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(response));
@ -216,4 +194,12 @@ public class UploadTerminologyCommand extends BaseCommand {
SNAPSHOT, ADD, REMOVE
}
public static String stripPath(String thePath) {
String retVal = thePath;
if (retVal.contains("/")) {
retVal = retVal.substring(retVal.lastIndexOf("/"));
}
return retVal;
}
}

2
hapi-fhir-cli/hapi-fhir-cli-api/src/main/resources/logback-cli-on.xml
View File

@ -34,7 +34,7 @@
<!--
It's useful to have this log when uploading big terminologies
-->
<logger name="ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl" additivity="false" level="info">
<logger name="ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl" additivity="false" level="info">
<appender-ref ref="STDOUT" />
</logger>

164
hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/UploadTerminologyCommandTest.java
View File

@ -1,18 +1,20 @@
package ca.uhn.fhir.cli;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.BaseTest;
import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
import ca.uhn.fhir.jpa.term.UploadStatistics;
import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
import ca.uhn.fhir.jpa.term.custom.CustomTerminologySet;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.test.utilities.JettyUtil;
import com.google.common.base.Charsets;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
import org.eclipse.jetty.server.Server;
import org.eclipse.jetty.servlet.ServletHandler;
import org.eclipse.jetty.servlet.ServletHolder;
import org.hamcrest.Matchers;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.IdType;
import org.junit.After;
import org.junit.Before;
@ -25,15 +27,19 @@ import org.mockito.junit.MockitoJUnitRunner;
import java.io.*;
import java.util.List;
import java.util.concurrent.atomic.AtomicInteger;
import java.util.zip.ZipEntry;
import java.util.zip.ZipOutputStream;
import static org.junit.Assert.*;
import static org.hamcrest.Matchers.greaterThan;
import static org.hamcrest.Matchers.matchesPattern;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertThat;
import static org.mockito.ArgumentMatchers.any;
import static org.mockito.ArgumentMatchers.eq;
import static org.mockito.Mockito.*;
@RunWith(MockitoJUnitRunner.class)
public class UploadTerminologyCommandTest {
public class UploadTerminologyCommandTest extends BaseTest {
static {
System.setProperty("test", "true");
@ -42,26 +48,24 @@ public class UploadTerminologyCommandTest {
private Server myServer;
private FhirContext myCtx = FhirContext.forR4();
@Mock
private IHapiTerminologyLoaderSvc myTerminologyLoaderSvc;
@Mock
private IHapiTerminologySvc myTerminologySvc;
private ITermLoaderSvc myTermLoaderSvc;
@Captor
private ArgumentCaptor<List<IHapiTerminologyLoaderSvc.FileDescriptor>> myDescriptorList;
@Captor
private ArgumentCaptor<CodeSystem> myCodeSystemCaptor;
private ArgumentCaptor<List<ITermLoaderSvc.FileDescriptor>> myDescriptorListCaptor;
private int myPort;
private String myConceptsFileName = "target/concepts.csv";
private String myHierarchyFileName = "target/hierarchy.csv";
private File myConceptsFile = new File(myConceptsFileName);
private File myHierarchyFile = new File(myHierarchyFileName);
private File myArchiveFile;
private String myArchiveFileName;
@Test
public void testTerminologyUpload_AddDelta() throws IOException {
public void testAddDelta() throws IOException {
writeConceptAndHierarchyFiles();
when(myTerminologySvc.applyDeltaCodesystemsAdd(eq("http://foo"), any(), any())).thenReturn(new AtomicInteger(100));
when(myTermLoaderSvc.loadDeltaAdd(eq("http://foo"), anyList(), any())).thenReturn(new UploadStatistics(100, new IdType("CodeSystem/101")));
App.main(new String[]{
UploadTerminologyCommand.UPLOAD_TERMINOLOGY,
@ -73,25 +77,69 @@ public class UploadTerminologyCommandTest {
"-d", myHierarchyFileName
});
verify(myTerminologySvc, times(1)).applyDeltaCodesystemsAdd(any(), isNull(), myCodeSystemCaptor.capture());
verify(myTermLoaderSvc, times(1)).loadDeltaAdd(eq("http://foo"), myDescriptorListCaptor.capture(), any());
CodeSystem codeSystem = myCodeSystemCaptor.getValue();
assertEquals(1, codeSystem.getConcept().size());
assertEquals("http://foo", codeSystem.getUrl());
assertEquals("ANIMALS", codeSystem.getConcept().get(0).getCode());
assertEquals("Animals", codeSystem.getConcept().get(0).getDisplay());
assertEquals(2, codeSystem.getConcept().get(0).getConcept().size());
assertEquals("CATS", codeSystem.getConcept().get(0).getConcept().get(0).getCode());
assertEquals("Cats", codeSystem.getConcept().get(0).getConcept().get(0).getDisplay());
assertEquals("DOGS", codeSystem.getConcept().get(0).getConcept().get(1).getCode());
assertEquals("Dogs", codeSystem.getConcept().get(0).getConcept().get(1).getDisplay());
List<ITermLoaderSvc.FileDescriptor> listOfDescriptors = myDescriptorListCaptor.getValue();
assertEquals(1, listOfDescriptors.size());
assertEquals("file:/files.zip", listOfDescriptors.get(0).getFilename());
assertThat(IOUtils.toByteArray(listOfDescriptors.get(0).getInputStream()).length, greaterThan(100));
}
@Test
public void testTerminologyUpload_RemoveDelta() throws IOException {
public void testAddDeltaUsingCompressedFile() throws IOException {
writeConceptAndHierarchyFiles();
writeArchiveFile(myConceptsFile, myHierarchyFile);
when(myTermLoaderSvc.loadDeltaAdd(eq("http://foo"), anyList(), any())).thenReturn(new UploadStatistics(100, new IdType("CodeSystem/101")));
App.main(new String[]{
UploadTerminologyCommand.UPLOAD_TERMINOLOGY,
"-v", "r4",
"-m", "ADD",
"-t", "http://localhost:" + myPort,
"-u", "http://foo",
"-d", myArchiveFileName
});
verify(myTermLoaderSvc, times(1)).loadDeltaAdd(eq("http://foo"), myDescriptorListCaptor.capture(), any());
List<ITermLoaderSvc.FileDescriptor> listOfDescriptors = myDescriptorListCaptor.getValue();
assertEquals(1, listOfDescriptors.size());
assertThat(listOfDescriptors.get(0).getFilename(), matchesPattern("^file:.*temp.*\\.zip$"));
assertThat(IOUtils.toByteArray(listOfDescriptors.get(0).getInputStream()).length, greaterThan(100));
}
private void writeArchiveFile(File... theFiles) throws IOException {
ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
ZipOutputStream zipOutputStream = new ZipOutputStream(byteArrayOutputStream, Charsets.UTF_8);
for (File next : theFiles) {
ZipEntry nextEntry = new ZipEntry(UploadTerminologyCommand.stripPath(next.getAbsolutePath()));
zipOutputStream.putNextEntry(nextEntry);
try (FileInputStream fileInputStream = new FileInputStream(next)) {
IOUtils.copy(fileInputStream, zipOutputStream);
}
}
zipOutputStream.flush();
zipOutputStream.close();
myArchiveFile = File.createTempFile("temp", ".zip");
myArchiveFile.deleteOnExit();
myArchiveFileName = myArchiveFile.getAbsolutePath();
try (FileOutputStream fos = new FileOutputStream(myArchiveFile, false)) {
fos.write(byteArrayOutputStream.toByteArray());
}
}
@Test
public void testRemoveDelta() throws IOException {
writeConceptAndHierarchyFiles();
when(myTerminologySvc.applyDeltaCodesystemsRemove(eq("http://foo"), any())).thenReturn(new AtomicInteger(100));
when(myTermLoaderSvc.loadDeltaRemove(eq("http://foo"), anyList(), any())).thenReturn(new UploadStatistics(100, new IdType("CodeSystem/101")));
App.main(new String[]{
UploadTerminologyCommand.UPLOAD_TERMINOLOGY,
@ -103,46 +151,38 @@ public class UploadTerminologyCommandTest {
"-d", myHierarchyFileName
});
verify(myTerminologySvc, times(1)).applyDeltaCodesystemsRemove(any(), myCodeSystemCaptor.capture());
verify(myTermLoaderSvc, times(1)).loadDeltaRemove(eq("http://foo"), myDescriptorListCaptor.capture(), any());
List<ITermLoaderSvc.FileDescriptor> listOfDescriptors = myDescriptorListCaptor.getValue();
assertEquals(1, listOfDescriptors.size());
assertEquals("file:/files.zip", listOfDescriptors.get(0).getFilename());
assertThat(IOUtils.toByteArray(listOfDescriptors.get(0).getInputStream()).length, greaterThan(100));
CodeSystem codeSystem = myCodeSystemCaptor.getValue();
assertEquals(3, codeSystem.getConcept().size());
assertEquals("http://foo", codeSystem.getUrl());
assertEquals("ANIMALS", codeSystem.getConcept().get(0).getCode());
assertEquals("Animals", codeSystem.getConcept().get(0).getDisplay());
assertEquals("CATS", codeSystem.getConcept().get(1).getCode());
assertEquals("Cats", codeSystem.getConcept().get(1).getDisplay());
assertEquals("DOGS", codeSystem.getConcept().get(2).getCode());
assertEquals("Dogs", codeSystem.getConcept().get(2).getDisplay());
}
@Test
public void testTerminologyUpload_Snapshot() throws IOException {
public void testSnapshot() throws IOException {
writeConceptAndHierarchyFiles();
when(myTerminologyLoaderSvc.loadCustom(eq("http://foo"), any(), any())).thenReturn(new IHapiTerminologyLoaderSvc.UploadStatistics(100, new IdType("CodeSystem/123")));
when(myTermLoaderSvc.loadCustom(any(), anyList(), any())).thenReturn(new UploadStatistics(100, new IdType("CodeSystem/101")));
App.main(new String[]{
UploadTerminologyCommand.UPLOAD_TERMINOLOGY,
"-v", "r4",
"-m", "SNAPSHOT",
"--custom",
"-t", "http://localhost:" + myPort,
"-u", "http://foo",
"-d", myConceptsFileName,
"-d", myHierarchyFileName
});
verify(myTerminologyLoaderSvc, times(1)).loadCustom(any(), myDescriptorList.capture(), any());
verify(myTermLoaderSvc, times(1)).loadCustom(any(), myDescriptorListCaptor.capture(), any());
List<IHapiTerminologyLoaderSvc.FileDescriptor> listOfDescriptors = myDescriptorList.getValue();
assertEquals(2, listOfDescriptors.size());
assertThat(listOfDescriptors.get(0).getFilename(), Matchers.endsWith("concepts.csv"));
assertInputStreamEqualsFile(myConceptsFile, listOfDescriptors.get(0).getInputStream());
assertThat(listOfDescriptors.get(1).getFilename(), Matchers.endsWith("hierarchy.csv"));
assertInputStreamEqualsFile(myHierarchyFile, listOfDescriptors.get(1).getInputStream());
List<ITermLoaderSvc.FileDescriptor> listOfDescriptors = myDescriptorListCaptor.getValue();
assertEquals(1, listOfDescriptors.size());
assertEquals("file:/files.zip", listOfDescriptors.get(0).getFilename());
assertThat(IOUtils.toByteArray(listOfDescriptors.get(0).getInputStream()).length, greaterThan(100));
}
@ -161,27 +201,41 @@ public class UploadTerminologyCommandTest {
}
}
private void assertInputStreamEqualsFile(File theExpectedFile, InputStream theActualInputStream) throws IOException {
try (FileInputStream fis = new FileInputStream(theExpectedFile)) {
byte[] expectedBytes = IOUtils.toByteArray(fis);
byte[] actualBytes = IOUtils.toByteArray(theActualInputStream);
assertArrayEquals(expectedBytes, actualBytes);
@Test
public void testAddInvalidFileName() throws IOException {
writeConceptAndHierarchyFiles();
try {
App.main(new String[]{
UploadTerminologyCommand.UPLOAD_TERMINOLOGY,
"-v", "r4",
"-m", "ADD",
"-t", "http://localhost:" + myPort,
"-u", "http://foo",
"-d", myConceptsFileName + "/foo.csv",
"-d", myHierarchyFileName
});
} catch (Error e) {
assertThat(e.toString(), Matchers.containsString("FileNotFoundException: target/concepts.csv/foo.csv"));
}
}
@After
public void after() throws Exception {
JettyUtil.closeServer(myServer);
FileUtils.deleteQuietly(myConceptsFile);
FileUtils.deleteQuietly(myHierarchyFile);
FileUtils.deleteQuietly(myArchiveFile);
}
@Before
public void start() throws Exception {
public void before() throws Exception {
myServer = new Server(0);
TerminologyUploaderProvider provider = new TerminologyUploaderProvider(myCtx, myTerminologyLoaderSvc, myTerminologySvc);
TerminologyUploaderProvider provider = new TerminologyUploaderProvider(myCtx, myTermLoaderSvc);
ServletHandler proxyHandler = new ServletHandler();
RestfulServer servlet = new RestfulServer(myCtx);

8
hapi-fhir-client-okhttp/src/main/java/ca/uhn/fhir/okhttp/client/OkHttpRestfulResponse.java
View File

@ -51,17 +51,12 @@ public class OkHttpRestfulResponse extends BaseHttpResponse implements IHttpResp
this.myResponse = theResponse;
}
@Override
public void bufferEntitity() throws IOException {
bufferEntity();
}
@Override
public void bufferEntity() throws IOException {
if (myEntityBuffered) {
return;
}
InputStream responseEntity = readEntity();
try (InputStream responseEntity = readEntity()) {
if (responseEntity != null) {
myEntityBuffered = true;
try {
@ -71,6 +66,7 @@ public class OkHttpRestfulResponse extends BaseHttpResponse implements IHttpResp
}
}
}
}
@Override
public void close() {

19
hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/apache/ApacheHttpResponse.java
View File

@ -21,6 +21,7 @@ package ca.uhn.fhir.rest.client.apache;
*/
import java.io.*;
import java.nio.charset.Charset;
import java.nio.charset.StandardCharsets;
import java.util.*;
import ca.uhn.fhir.rest.client.impl.BaseHttpResponse;
@ -53,28 +54,22 @@ public class ApacheHttpResponse extends BaseHttpResponse implements IHttpRespons
this.myResponse = theResponse;
}
@Deprecated // override deprecated method
@Override
public void bufferEntitity() throws IOException {
bufferEntity();
}
@Override
public void bufferEntity() throws IOException {
if (myEntityBuffered) {
return;
}
InputStream respEntity = readEntity();
try (InputStream respEntity = readEntity()) {
if (respEntity != null) {
this.myEntityBuffered = true;
try {
this.myEntityBytes = IOUtils.toByteArray(respEntity);
} catch (IllegalStateException e) {
// FIXME resouce leak
throw new InternalErrorException(e);
}
}
}
}
@Override
public void close() {
@ -103,7 +98,7 @@ public class ApacheHttpResponse extends BaseHttpResponse implements IHttpRespons
if (Constants.STATUS_HTTP_204_NO_CONTENT != myResponse.getStatusLine().getStatusCode()) {
ourLog.debug("Response did not specify a charset, defaulting to utf-8");
}
charset = Charset.forName("UTF-8");
charset = StandardCharsets.UTF_8;
}
return new InputStreamReader(readEntity(), charset);
@ -115,11 +110,7 @@ public class ApacheHttpResponse extends BaseHttpResponse implements IHttpRespons
if (myResponse.getAllHeaders() != null) {
for (Header next : myResponse.getAllHeaders()) {
String name = next.getName().toLowerCase();
List<String> list = headers.get(name);
if (list == null) {
list = new ArrayList<>();
headers.put(name, list);
}
List<String> list = headers.computeIfAbsent(name, k -> new ArrayList<>());
list.add(next.getValue());
}

20
hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/interceptor/LoggingInterceptor.java
View File

@ -22,6 +22,7 @@ package ca.uhn.fhir.rest.client.interceptor;
import java.io.IOException;
import java.io.InputStream;
import java.nio.charset.StandardCharsets;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
@ -94,9 +95,7 @@ public class LoggingInterceptor implements IClientInterceptor {
if (content != null) {
myLog.info("Client request body:\n{}", content);
}
} catch (IllegalStateException e) {
myLog.warn("Failed to replay request contents (during logging attempt, actual FHIR call did not fail)", e);
} catch (IOException e) {
} catch (IllegalStateException | IOException e) {
myLog.warn("Failed to replay request contents (during logging attempt, actual FHIR call did not fail)", e);
}
}
@ -147,11 +146,8 @@ public class LoggingInterceptor implements IClientInterceptor {
}
if (myLogResponseBody) {
//TODO: Use of a deprecated method should be resolved.
theResponse.bufferEntitity();
InputStream respEntity = null;
try {
respEntity = theResponse.readEntity();
theResponse.bufferEntity();
try (InputStream respEntity = theResponse.readEntity()) {
if (respEntity != null) {
final byte[] bytes;
try {
@ -159,12 +155,10 @@ public class LoggingInterceptor implements IClientInterceptor {
} catch (IllegalStateException e) {
throw new InternalErrorException(e);
}
myLog.info("Client response body:\n{}", new String(bytes, "UTF-8"));
myLog.info("Client response body:\n{}", new String(bytes, StandardCharsets.UTF_8));
} else {
myLog.info("Client response body: (none)");
}
} finally {
IOUtils.closeQuietly(respEntity);
}
}
}
@ -178,7 +172,9 @@ public class LoggingInterceptor implements IClientInterceptor {
Iterator<String> values = theHeaders.get(key).iterator();
while(values.hasNext()) {
String value = values.next();
b.append(key + ": " + value);
b.append(key);
b.append(": ");
b.append(value);
if (nameEntries.hasNext() || values.hasNext()) {
b.append('\n');
}

5
hapi-fhir-jaxrsserver-base/src/main/java/ca/uhn/fhir/jaxrs/client/JaxRsHttpResponse.java
View File

@ -51,11 +51,6 @@ public class JaxRsHttpResponse extends BaseHttpResponse implements IHttpResponse
this.myResponse = theResponse;
}
@Override
public void bufferEntitity() throws IOException {
bufferEntity();
}
@Override
public void bufferEntity() throws IOException {
if(!myBufferedEntity && myResponse.hasEntity()) {

1
hapi-fhir-jpaserver-base/pom.xml
View File

@ -46,7 +46,6 @@
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-csv</artifactId>
<version>1.3</version>
</dependency>
<dependency>

19
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/BaseTest.java Normal file
View File

@ -0,0 +1,19 @@
package ca.uhn.fhir.jpa;
import com.google.common.base.Charsets;
import org.apache.commons.io.IOUtils;
import java.io.IOException;
import java.io.InputStream;
public class BaseTest {
protected String loadResource(String theClasspath) throws IOException {
InputStream stream = BaseTest.class.getResourceAsStream(theClasspath);
if (stream==null) {
throw new IllegalArgumentException("Unable to find resource: " + theClasspath);
}
return IOUtils.toString(stream, Charsets.UTF_8);
}
}

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseConfig.java
View File

@ -32,6 +32,13 @@ import ca.uhn.fhir.jpa.subscription.module.cache.LinkedBlockingQueueSubscribable
import ca.uhn.fhir.jpa.subscription.module.channel.ISubscribableChannelFactory;
import ca.uhn.fhir.jpa.subscription.module.matcher.ISubscriptionMatcher;
import ca.uhn.fhir.jpa.subscription.module.matcher.InMemorySubscriptionMatcher;
import ca.uhn.fhir.jpa.term.TermCodeSystemStorageSvcImpl;
import ca.uhn.fhir.jpa.term.TermDeferredStorageSvcImpl;
import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
import ca.uhn.fhir.jpa.term.TermReindexingSvcImpl;
import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
import ca.uhn.fhir.jpa.term.api.ITermReindexingSvc;
import ca.uhn.fhir.rest.server.interceptor.consent.IConsentContextServices;
import org.hibernate.jpa.HibernatePersistenceProvider;
import org.hl7.fhir.utilities.graphql.IGraphQLStorageServices;
@ -256,7 +263,6 @@ public abstract class BaseConfig {
}
public static void configureEntityManagerFactory(LocalContainerEntityManagerFactoryBean theFactory, FhirContext theCtx) {
theFactory.setJpaDialect(hibernateJpaDialect(theCtx.getLocalizer()));
theFactory.setPackagesToScan("ca.uhn.fhir.jpa.model.entity", "ca.uhn.fhir.jpa.entity");

34
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseConfigDstu3Plus.java Normal file
View File

@ -0,0 +1,34 @@
package ca.uhn.fhir.jpa.config;
import ca.uhn.fhir.jpa.term.TermCodeSystemStorageSvcImpl;
import ca.uhn.fhir.jpa.term.TermDeferredStorageSvcImpl;
import ca.uhn.fhir.jpa.term.TermReindexingSvcImpl;
import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
import ca.uhn.fhir.jpa.term.api.ITermReindexingSvc;
import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
@Configuration
public abstract class BaseConfigDstu3Plus extends BaseConfig {
@Bean
public ITermCodeSystemStorageSvc termCodeSystemStorageSvc() {
return new TermCodeSystemStorageSvcImpl();
}
@Bean
public ITermDeferredStorageSvc termDeferredStorageSvc() {
return new TermDeferredStorageSvcImpl();
}
@Bean
public ITermReindexingSvc termReindexingSvc() {
return new TermReindexingSvcImpl();
}
@Bean
public abstract ITermVersionAdapterSvc terminologyVersionAdapterSvc();
}

10
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseDstu2Config.java
View File

@ -7,8 +7,10 @@ import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
import ca.uhn.fhir.jpa.searchparam.extractor.SearchParamExtractorDstu2;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
import ca.uhn.fhir.jpa.searchparam.registry.SearchParamRegistryDstu2;
import ca.uhn.fhir.jpa.term.HapiTerminologySvcDstu2;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
import ca.uhn.fhir.jpa.term.TermReadSvcDstu2;
import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
import ca.uhn.fhir.jpa.term.TermVersionAdapterSvcDstu2;
import ca.uhn.fhir.jpa.util.ResourceCountCache;
import ca.uhn.fhir.model.dstu2.composite.MetaDt;
import ca.uhn.fhir.validation.IValidatorModule;
@ -134,8 +136,8 @@ public class BaseDstu2Config extends BaseConfig {
}
@Bean(autowire = Autowire.BY_TYPE)
public IHapiTerminologySvc terminologyService() {
return new HapiTerminologySvcDstu2();
public ITermReadSvc terminologyService() {
return new TermReadSvcDstu2();
}
}

51
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/dstu3/BaseDstu3Config.java
View File

@ -3,6 +3,7 @@ package ca.uhn.fhir.jpa.config.dstu3;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.ParserOptions;
import ca.uhn.fhir.jpa.config.BaseConfig;
import ca.uhn.fhir.jpa.config.BaseConfigDstu3Plus;
import ca.uhn.fhir.jpa.dao.FulltextSearchSvcImpl;
import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
@ -12,10 +13,12 @@ import ca.uhn.fhir.jpa.provider.GraphQLProvider;
import ca.uhn.fhir.jpa.searchparam.extractor.SearchParamExtractorDstu3;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
import ca.uhn.fhir.jpa.searchparam.registry.SearchParamRegistryDstu3;
import ca.uhn.fhir.jpa.term.HapiTerminologySvcDstu3;
import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvcDstu3;
import ca.uhn.fhir.jpa.term.TerminologyLoaderSvcImpl;
import ca.uhn.fhir.jpa.term.TermReadSvcDstu3;
import ca.uhn.fhir.jpa.term.TermLoaderSvcImpl;
import ca.uhn.fhir.jpa.term.TermVersionAdapterSvcDstu3;
import ca.uhn.fhir.jpa.term.api.ITermReadSvcDstu3;
import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
import ca.uhn.fhir.jpa.util.ResourceCountCache;
import ca.uhn.fhir.jpa.validation.JpaValidationSupportChainDstu3;
import ca.uhn.fhir.validation.IValidatorModule;
@ -26,7 +29,6 @@ import org.hl7.fhir.dstu3.hapi.validation.CachingValidationSupport;
import org.hl7.fhir.dstu3.hapi.validation.FhirInstanceValidator;
import org.hl7.fhir.dstu3.model.Bundle;
import org.hl7.fhir.r5.utils.IResourceValidator;
import org.springframework.beans.factory.annotation.Autowire;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Lazy;
@ -55,13 +57,19 @@ import org.springframework.transaction.annotation.EnableTransactionManagement;
@Configuration
@EnableTransactionManagement
public class BaseDstu3Config extends BaseConfig {
public class BaseDstu3Config extends BaseConfigDstu3Plus {
@Override
public FhirContext fhirContext() {
return fhirContextDstu3();
}
@Bean
@Override
public ITermVersionAdapterSvc terminologyVersionAdapterSvc() {
return new TermVersionAdapterSvcDstu3();
}
@Bean
@Primary
public FhirContext fhirContextDstu3() {
@ -109,10 +117,9 @@ public class BaseDstu3Config extends BaseConfig {
return new JpaValidationSupportChainDstu3();
}
@Bean(name = "myJpaValidationSupportDstu3", autowire = Autowire.BY_NAME)
@Bean(name = "myJpaValidationSupportDstu3")
public ca.uhn.fhir.jpa.dao.dstu3.IJpaValidationSupportDstu3 jpaValidationSupportDstu3() {
ca.uhn.fhir.jpa.dao.dstu3.JpaValidationSupportDstu3 retVal = new ca.uhn.fhir.jpa.dao.dstu3.JpaValidationSupportDstu3();
return retVal;
return new ca.uhn.fhir.jpa.dao.dstu3.JpaValidationSupportDstu3();
}
@Bean(name = "myResourceCountsCache")
@ -122,13 +129,12 @@ public class BaseDstu3Config extends BaseConfig {
return retVal;
}
@Bean(autowire = Autowire.BY_TYPE)
@Bean
public IFulltextSearchSvc searchDaoDstu3() {
FulltextSearchSvcImpl searchDao = new FulltextSearchSvcImpl();
return searchDao;
return new FulltextSearchSvcImpl();
}
@Bean(autowire = Autowire.BY_TYPE)
@Bean
public SearchParamExtractorDstu3 searchParamExtractor() {
return new SearchParamExtractorDstu3();
}
@ -138,10 +144,9 @@ public class BaseDstu3Config extends BaseConfig {
return new SearchParamRegistryDstu3();
}
@Bean(name = "mySystemDaoDstu3", autowire = Autowire.BY_NAME)
@Bean(name = "mySystemDaoDstu3")
public IFhirSystemDao<org.hl7.fhir.dstu3.model.Bundle, org.hl7.fhir.dstu3.model.Meta> systemDaoDstu3() {
ca.uhn.fhir.jpa.dao.dstu3.FhirSystemDaoDstu3 retVal = new ca.uhn.fhir.jpa.dao.dstu3.FhirSystemDaoDstu3();
return retVal;
return new ca.uhn.fhir.jpa.dao.dstu3.FhirSystemDaoDstu3();
}
@Bean(name = "mySystemProviderDstu3")
@ -152,18 +157,18 @@ public class BaseDstu3Config extends BaseConfig {
return retVal;
}
@Bean(autowire = Autowire.BY_TYPE)
public IHapiTerminologyLoaderSvc terminologyLoaderService() {
return new TerminologyLoaderSvcImpl();
@Bean
public ITermLoaderSvc termLoaderService() {
return new TermLoaderSvcImpl();
}
@Bean(autowire = Autowire.BY_TYPE)
public IHapiTerminologySvcDstu3 terminologyService() {
return new HapiTerminologySvcDstu3();
@Bean
public ITermReadSvcDstu3 terminologyService() {
return new TermReadSvcDstu3();
}
@Primary
@Bean(autowire = Autowire.BY_NAME, name = "myJpaValidationSupportChainDstu3")
@Bean(name = "myJpaValidationSupportChainDstu3")
public IValidationSupport validationSupportChainDstu3() {
return new CachingValidationSupport(jpaValidationSupportChain());
}

25
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r4/BaseR4Config.java
View File

@ -3,6 +3,7 @@ package ca.uhn.fhir.jpa.config.r4;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.ParserOptions;
import ca.uhn.fhir.jpa.config.BaseConfig;
import ca.uhn.fhir.jpa.config.BaseConfigDstu3Plus;
import ca.uhn.fhir.jpa.dao.FulltextSearchSvcImpl;
import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
@ -12,10 +13,10 @@ import ca.uhn.fhir.jpa.provider.GraphQLProvider;
import ca.uhn.fhir.jpa.searchparam.extractor.SearchParamExtractorR4;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
import ca.uhn.fhir.jpa.searchparam.registry.SearchParamRegistryR4;
import ca.uhn.fhir.jpa.term.HapiTerminologySvcR4;
import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvcR4;
import ca.uhn.fhir.jpa.term.TerminologyLoaderSvcImpl;
import ca.uhn.fhir.jpa.term.*;
import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
import ca.uhn.fhir.jpa.term.api.ITermReadSvcR4;
import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
import ca.uhn.fhir.jpa.util.ResourceCountCache;
import ca.uhn.fhir.jpa.validation.JpaValidationSupportChainR4;
import ca.uhn.fhir.validation.IValidatorModule;
@ -55,13 +56,19 @@ import org.springframework.transaction.annotation.EnableTransactionManagement;
@Configuration
@EnableTransactionManagement
public class BaseR4Config extends BaseConfig {
public class BaseR4Config extends BaseConfigDstu3Plus {
@Override
public FhirContext fhirContext() {
return fhirContextR4();
}
@Bean
@Override
public ITermVersionAdapterSvc terminologyVersionAdapterSvc() {
return new TermVersionAdapterSvcR4();
}
@Bean
@Primary
public FhirContext fhirContextR4() {
@ -154,13 +161,13 @@ public class BaseR4Config extends BaseConfig {
}
@Bean(autowire = Autowire.BY_TYPE)
public IHapiTerminologyLoaderSvc terminologyLoaderService() {
return new TerminologyLoaderSvcImpl();
public ITermLoaderSvc termLoaderService() {
return new TermLoaderSvcImpl();
}
@Bean(autowire = Autowire.BY_TYPE)
public IHapiTerminologySvcR4 terminologyService() {
return new HapiTerminologySvcR4();
public ITermReadSvcR4 terminologyService() {
return new TermReadSvcR4();
}
@Primary

25
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r5/BaseR5Config.java
View File

@ -3,6 +3,7 @@ package ca.uhn.fhir.jpa.config.r5;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.ParserOptions;
import ca.uhn.fhir.jpa.config.BaseConfig;
import ca.uhn.fhir.jpa.config.BaseConfigDstu3Plus;
import ca.uhn.fhir.jpa.dao.FulltextSearchSvcImpl;
import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
@ -12,10 +13,10 @@ import ca.uhn.fhir.jpa.provider.GraphQLProvider;
import ca.uhn.fhir.jpa.searchparam.extractor.SearchParamExtractorR5;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
import ca.uhn.fhir.jpa.searchparam.registry.SearchParamRegistryR5;
import ca.uhn.fhir.jpa.term.HapiTerminologySvcR5;
import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvcR5;
import ca.uhn.fhir.jpa.term.TerminologyLoaderSvcImpl;
import ca.uhn.fhir.jpa.term.*;
import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
import ca.uhn.fhir.jpa.term.api.ITermReadSvcR5;
import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
import ca.uhn.fhir.jpa.util.ResourceCountCache;
import ca.uhn.fhir.jpa.validation.JpaValidationSupportChainR5;
import ca.uhn.fhir.validation.IValidatorModule;
@ -55,13 +56,19 @@ import org.springframework.transaction.annotation.EnableTransactionManagement;
@Configuration
@EnableTransactionManagement
public class BaseR5Config extends BaseConfig {
public class BaseR5Config extends BaseConfigDstu3Plus {
@Override
public FhirContext fhirContext() {
return fhirContextR5();
}
@Bean
@Override
public ITermVersionAdapterSvc terminologyVersionAdapterSvc() {
return new TermVersionAdapterSvcR5();
}
@Bean
@Primary
public FhirContext fhirContextR5() {
@ -154,13 +161,13 @@ public class BaseR5Config extends BaseConfig {
}
@Bean(autowire = Autowire.BY_TYPE)
public IHapiTerminologyLoaderSvc terminologyLoaderService() {
return new TerminologyLoaderSvcImpl();
public ITermLoaderSvc terminologyLoaderService() {
return new TermLoaderSvcImpl();
}
@Bean(autowire = Autowire.BY_TYPE)
public IHapiTerminologySvcR5 terminologyService() {
return new HapiTerminologySvcR5();
public ITermReadSvcR5 terminologyService() {
return new TermReadSvcR5();
}
@Primary

67
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
View File

@ -20,13 +20,13 @@ import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.search.ISearchCoordinatorSvc;
import ca.uhn.fhir.jpa.search.PersistedJpaBundleProvider;
import ca.uhn.fhir.jpa.search.cache.ISearchCacheSvc;
import ca.uhn.fhir.jpa.search.cache.ISearchResultCacheSvc;
import ca.uhn.fhir.jpa.searchparam.ResourceMetaParams;
import ca.uhn.fhir.jpa.searchparam.extractor.LogicalReferenceHelper;
import ca.uhn.fhir.jpa.searchparam.extractor.ResourceIndexedSearchParams;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
import ca.uhn.fhir.jpa.util.AddRemoveCount;
import ca.uhn.fhir.jpa.util.JpaInterceptorBroadcaster;
import ca.uhn.fhir.model.api.IResource;
@ -53,7 +53,6 @@ import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetai
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.util.CoverageIgnore;
import ca.uhn.fhir.util.MetaUtil;
import ca.uhn.fhir.util.StopWatch;
import ca.uhn.fhir.util.XmlUtil;
import com.google.common.annotations.VisibleForTesting;
import com.google.common.base.Charsets;
@ -62,8 +61,6 @@ import com.google.common.hash.HashFunction;
import com.google.common.hash.Hashing;
import org.apache.commons.lang3.NotImplementedException;
import org.apache.commons.lang3.Validate;
import org.hibernate.Session;
import org.hibernate.internal.SessionImpl;
import org.hl7.fhir.instance.model.api.*;
import org.hl7.fhir.r4.model.Bundle.HTTPVerb;
import org.slf4j.Logger;
@ -81,7 +78,6 @@ import javax.annotation.PostConstruct;
import javax.persistence.*;
import javax.persistence.criteria.CriteriaBuilder;
import javax.persistence.criteria.CriteriaQuery;
import javax.persistence.criteria.Predicate;
import javax.persistence.criteria.Root;
import javax.xml.stream.events.Characters;
import javax.xml.stream.events.XMLEvent;
@ -139,7 +135,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
@Autowired
protected ISearchParamRegistry mySerarchParamRegistry;
@Autowired
protected IHapiTerminologySvc myTerminologySvc;
protected ITermReadSvc myTerminologySvc;
@Autowired
protected IResourceHistoryTableDao myResourceHistoryTableDao;
@Autowired
@ -161,8 +157,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
@Autowired
private ISearchCacheSvc mySearchCacheSvc;
@Autowired
private ISearchResultCacheSvc mySearchResultCacheSvc;
@Autowired
private ISearchParamPresenceSvc mySearchParamPresenceSvc;
@Autowired
private DaoRegistry myDaoRegistry;
@ -192,20 +186,18 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
* none was created, returns null.
*/
protected ForcedId createForcedIdIfNeeded(ResourceTable theEntity, IIdType theId, boolean theCreateForPureNumericIds) {
ForcedId retVal = null;
if (theId.isEmpty() == false && theId.hasIdPart() && theEntity.getForcedId() == null) {
if (!theCreateForPureNumericIds && IdHelperService.isValidPid(theId)) {
return null;
if (theCreateForPureNumericIds || !IdHelperService.isValidPid(theId)) {
retVal = new ForcedId();
retVal.setResourceType(theEntity.getResourceType());
retVal.setForcedId(theId.getIdPart());
retVal.setResource(theEntity);
theEntity.setForcedId(retVal);
}
}
ForcedId fid = new ForcedId();
fid.setResourceType(theEntity.getResourceType());
fid.setForcedId(theId.getIdPart());
fid.setResource(theEntity);
theEntity.setForcedId(fid);
return fid;
}
return null;
return retVal;
}
private void extractTagsHapi(IResource theResource, ResourceTable theEntity, Set<ResourceTag> allDefs) {
@ -285,39 +277,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
}
private void findMatchingTagIds(RequestDetails theRequest, String theResourceName, IIdType theResourceId, Set<Long> tagIds, Class<? extends BaseTag> entityClass) {
{
CriteriaBuilder builder = myEntityManager.getCriteriaBuilder();
CriteriaQuery<Tuple> cq = builder.createTupleQuery();
Root<? extends BaseTag> from = cq.from(entityClass);
cq.multiselect(from.get("myTagId").as(Long.class)).distinct(true);
if (theResourceName != null) {
Predicate typePredicate = builder.equal(from.get("myResourceType"), theResourceName);
if (theResourceId != null) {
cq.where(typePredicate, builder.equal(from.get("myResourceId"), myIdHelperService.translateForcedIdToPid(theResourceName, theResourceId.getIdPart(), theRequest)));
} else {
cq.where(typePredicate);
}
}
TypedQuery<Tuple> query = myEntityManager.createQuery(cq);
for (Tuple next : query.getResultList()) {
tagIds.add(next.get(0, Long.class));
}
}
}
protected void flushJpaSession() {
SessionImpl session = (SessionImpl) myEntityManager.unwrap(Session.class);
int insertionCount = session.getActionQueue().numberOfInsertions();
int updateCount = session.getActionQueue().numberOfUpdates();
StopWatch sw = new StopWatch();
myEntityManager.flush();
ourLog.debug("Session flush took {}ms for {} inserts and {} updates", sw.getMillis(), insertionCount, updateCount);
}
private Set<ResourceTag> getAllTagDefinitions(ResourceTable theEntity) {
HashSet<ResourceTag> retVal = Sets.newHashSet();
if (theEntity.isHasTags()) {
@ -358,7 +317,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
}
}
@SuppressWarnings("unchecked")
public <R extends IBaseResource> IFhirResourceDao<R> getDao(Class<R> theType) {
return myDaoRegistry.getResourceDaoOrNull(theType);
}
@ -446,6 +404,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
newVersion = Long.toString(newVersionLong);
}
assert theResourceId != null;
IIdType newId = theResourceId.withVersion(newVersion);
theResource.getIdElement().setValue(newId.getValue());
theSavedEntity.setVersion(newVersionLong);

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/SearchBuilder.java
View File

@ -39,7 +39,7 @@ import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
import ca.uhn.fhir.jpa.searchparam.ResourceMetaParams;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
import ca.uhn.fhir.jpa.term.VersionIndependentConcept;
import ca.uhn.fhir.jpa.util.*;
import ca.uhn.fhir.model.api.*;
@ -64,7 +64,6 @@ import ca.uhn.fhir.util.UrlUtil;
import com.google.common.collect.Lists;
import com.google.common.collect.Maps;
import com.google.common.collect.Sets;
import org.apache.commons.lang3.ObjectUtils;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.HashCodeBuilder;
@ -135,7 +134,7 @@ public class SearchBuilder implements ISearchBuilder {
@Autowired
private ISearchParamRegistry mySearchParamRegistry;
@Autowired
private IHapiTerminologySvc myTerminologySvc;
private ITermReadSvc myTerminologySvc;
@Autowired
private MatchUrlService myMatchUrlService;
private List<Long> myAlsoIncludePids;

13
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoCodeSystemDstu3.java
View File

@ -26,6 +26,7 @@ import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
import ca.uhn.fhir.jpa.entity.TermCodeSystem;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
import ca.uhn.fhir.jpa.util.LogicUtil;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.param.TokenParam;
@ -41,6 +42,7 @@ import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.springframework.beans.factory.annotation.Autowired;
import javax.annotation.Nonnull;
import java.util.ArrayList;
import java.util.Date;
import java.util.List;
@ -54,21 +56,22 @@ public class FhirResourceDaoCodeSystemDstu3 extends FhirResourceDaoDstu3<CodeSys
@Autowired
private ITermCodeSystemDao myCsDao;
@Autowired
private ValidationSupportChain myValidationSupport;
@Autowired
protected ITermCodeSystemStorageSvc myTerminologyCodeSystemStorageSvc;
@Override
public List<IIdType> findCodeSystemIdsContainingSystemAndCode(String theCode, String theSystem, RequestDetails theRequest) {
List<IIdType> valueSetIds;
Set<Long> ids = searchForIds(new SearchParameterMap(CodeSystem.SP_CODE, new TokenParam(theSystem, theCode)), theRequest );
valueSetIds = new ArrayList<>();
List<IIdType> valueSetIds = new ArrayList<>();
for (Long next : ids) {
valueSetIds.add(new IdType("CodeSystem", next));
}
return valueSetIds;
}
@Nonnull
@Override
public IContextValidationSupport.LookupCodeResult lookupCode(IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, Coding theCoding, RequestDetails theRequestDetails) {
boolean haveCoding = theCoding != null && isNotBlank(theCoding.getSystem()) && isNotBlank(theCoding.getCode());
@ -119,7 +122,7 @@ public class FhirResourceDaoCodeSystemDstu3 extends FhirResourceDaoDstu3<CodeSys
if (isNotBlank(codeSystemUrl)) {
TermCodeSystem persCs = myCsDao.findByCodeSystemUri(codeSystemUrl);
if (persCs != null) {
myTerminologySvc.deleteCodeSystem(persCs);
myTerminologyCodeSystemStorageSvc.deleteCodeSystem(persCs);
}
}
}
@ -134,7 +137,7 @@ public class FhirResourceDaoCodeSystemDstu3 extends FhirResourceDaoDstu3<CodeSys
org.hl7.fhir.r4.model.CodeSystem cs = VersionConvertor_30_40.convertCodeSystem(csDstu3);
addPidToResource(theEntity, cs);
myTerminologySvc.storeNewCodeSystemVersionIfNeeded(cs, theEntity);
myTerminologyCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(cs, theEntity);
return retVal;
}

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoConceptMapDstu3.java
View File

@ -27,7 +27,7 @@ import ca.uhn.fhir.jpa.term.TranslationResult;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElement;
import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElementTarget;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import org.hl7.fhir.convertors.VersionConvertor_30_40;
@ -42,11 +42,9 @@ import java.util.HashSet;
import java.util.List;
import java.util.Set;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class FhirResourceDaoConceptMapDstu3 extends FhirResourceDaoDstu3<ConceptMap> implements IFhirResourceDaoConceptMap<ConceptMap> {
@Autowired
private IHapiTerminologySvc myHapiTerminologySvc;
private ITermReadSvc myHapiTerminologySvc;
@Override
public TranslationResult translate(TranslationRequest theTranslationRequest, RequestDetails theRequestDetails) {

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoValueSetDstu3.java
View File

@ -24,7 +24,7 @@ import ca.uhn.fhir.context.support.IContextValidationSupport;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
import ca.uhn.fhir.jpa.util.LogicUtil;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
@ -62,7 +62,7 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet>
private static final Logger ourLog = LoggerFactory.getLogger(FhirResourceDaoValueSetDstu3.class);
@Autowired
private IHapiTerminologySvc myHapiTerminologySvc;
private ITermReadSvc myHapiTerminologySvc;
@Autowired
private DefaultProfileValidationSupport myDefaultProfileValidationSupport;

7
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCodeSystemR4.java
View File

@ -26,6 +26,7 @@ import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
import ca.uhn.fhir.jpa.entity.TermCodeSystem;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
import ca.uhn.fhir.jpa.util.LogicUtil;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.param.TokenParam;
@ -56,6 +57,8 @@ public class FhirResourceDaoCodeSystemR4 extends FhirResourceDaoR4<CodeSystem> i
private ITermCodeSystemDao myCsDao;
@Autowired
private ValidationSupportChain myValidationSupport;
@Autowired
protected ITermCodeSystemStorageSvc myTerminologyCodeSystemStorageSvc;
@Override
public List<IIdType> findCodeSystemIdsContainingSystemAndCode(String theCode, String theSystem, RequestDetails theRequest) {
@ -122,7 +125,7 @@ public class FhirResourceDaoCodeSystemR4 extends FhirResourceDaoR4<CodeSystem> i
if (isNotBlank(codeSystemUrl)) {
TermCodeSystem persCs = myCsDao.findByCodeSystemUri(codeSystemUrl);
if (persCs != null) {
myTerminologySvc.deleteCodeSystem(persCs);
myTerminologyCodeSystemStorageSvc.deleteCodeSystem(persCs);
}
}
}
@ -135,7 +138,7 @@ public class FhirResourceDaoCodeSystemR4 extends FhirResourceDaoR4<CodeSystem> i
CodeSystem cs = (CodeSystem) theResource;
addPidToResource(theEntity, theResource);
myTerminologySvc.storeNewCodeSystemVersionIfNeeded(cs, theEntity);
myTerminologyCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(cs, theEntity);
return retVal;
}

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoConceptMapR4.java
View File

@ -24,7 +24,7 @@ import ca.uhn.fhir.jpa.dao.IFhirResourceDaoConceptMap;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElement;
import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElementTarget;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
import ca.uhn.fhir.jpa.term.TranslationMatch;
import ca.uhn.fhir.jpa.term.TranslationRequest;
import ca.uhn.fhir.jpa.term.TranslationResult;
@ -38,11 +38,9 @@ import java.util.HashSet;
import java.util.List;
import java.util.Set;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class FhirResourceDaoConceptMapR4 extends FhirResourceDaoR4<ConceptMap> implements IFhirResourceDaoConceptMap<ConceptMap> {
@Autowired
private IHapiTerminologySvc myHapiTerminologySvc;
private ITermReadSvc myHapiTerminologySvc;
@Override
public TranslationResult translate(TranslationRequest theTranslationRequest, RequestDetails theRequestDetails) {

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoValueSetR4.java
View File

@ -24,7 +24,7 @@ import ca.uhn.fhir.context.support.IContextValidationSupport;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
import ca.uhn.fhir.jpa.util.LogicUtil;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
@ -56,7 +56,7 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class FhirResourceDaoValueSetR4 extends FhirResourceDaoR4<ValueSet> implements IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> {
@Autowired
private IHapiTerminologySvc myHapiTerminologySvc;
private ITermReadSvc myHapiTerminologySvc;
@Autowired
private DefaultProfileValidationSupport myDefaultProfileValidationSupport;

7
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoCodeSystemR5.java
View File

@ -26,6 +26,7 @@ import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
import ca.uhn.fhir.jpa.entity.TermCodeSystem;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
import ca.uhn.fhir.jpa.util.LogicUtil;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.param.TokenParam;
@ -56,6 +57,8 @@ public class FhirResourceDaoCodeSystemR5 extends FhirResourceDaoR5<CodeSystem> i
private ITermCodeSystemDao myCsDao;
@Autowired
private ValidationSupportChain myValidationSupport;
@Autowired
protected ITermCodeSystemStorageSvc myTerminologyCodeSystemStorageSvc;
@Override
public List<IIdType> findCodeSystemIdsContainingSystemAndCode(String theCode, String theSystem, RequestDetails theRequest) {
@ -122,7 +125,7 @@ public class FhirResourceDaoCodeSystemR5 extends FhirResourceDaoR5<CodeSystem> i
if (isNotBlank(codeSystemUrl)) {
TermCodeSystem persCs = myCsDao.findByCodeSystemUri(codeSystemUrl);
if (persCs != null) {
myTerminologySvc.deleteCodeSystem(persCs);
myTerminologyCodeSystemStorageSvc.deleteCodeSystem(persCs);
}
}
}
@ -135,7 +138,7 @@ public class FhirResourceDaoCodeSystemR5 extends FhirResourceDaoR5<CodeSystem> i
CodeSystem cs = (CodeSystem) theResource;
addPidToResource(theEntity, theResource);
myTerminologySvc.storeNewCodeSystemVersionIfNeeded(org.hl7.fhir.convertors.conv40_50.CodeSystem.convertCodeSystem(cs), theEntity);
myTerminologyCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(org.hl7.fhir.convertors.conv40_50.CodeSystem.convertCodeSystem(cs), theEntity);
return retVal;
}

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoConceptMapR5.java
View File

@ -24,7 +24,7 @@ import ca.uhn.fhir.jpa.dao.IFhirResourceDaoConceptMap;
import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElement;
import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElementTarget;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
import ca.uhn.fhir.jpa.term.TranslationMatch;
import ca.uhn.fhir.jpa.term.TranslationRequest;
import ca.uhn.fhir.jpa.term.TranslationResult;
@ -41,7 +41,7 @@ import java.util.Set;
public class FhirResourceDaoConceptMapR5 extends FhirResourceDaoR5<ConceptMap> implements IFhirResourceDaoConceptMap<ConceptMap> {
@Autowired
private IHapiTerminologySvc myHapiTerminologySvc;
private ITermReadSvc myHapiTerminologySvc;
@Override
public TranslationResult translate(TranslationRequest theTranslationRequest, RequestDetails theRequestDetails) {

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoValueSetR5.java
View File

@ -24,7 +24,7 @@ import ca.uhn.fhir.context.support.IContextValidationSupport;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
import ca.uhn.fhir.jpa.util.LogicUtil;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
@ -56,7 +56,7 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class FhirResourceDaoValueSetR5 extends FhirResourceDaoR5<ValueSet> implements IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> {
@Autowired
private IHapiTerminologySvc myHapiTerminologySvc;
private ITermReadSvc myHapiTerminologySvc;
@Autowired
private DefaultProfileValidationSupport myDefaultProfileValidationSupport;

65
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermCodeSystem.java
View File

@ -22,6 +22,8 @@ package ca.uhn.fhir.jpa.entity;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.util.ValidateUtil;
import org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.HashCodeBuilder;
import org.apache.commons.lang3.builder.ToStringBuilder;
import org.apache.commons.lang3.builder.ToStringStyle;
@ -39,17 +41,17 @@ import static org.apache.commons.lang3.StringUtils.length;
@Entity()
//@formatter:on
public class TermCodeSystem implements Serializable {
private static final long serialVersionUID = 1L;
private static final int MAX_NAME_LENGTH = 200;
public static final int MAX_URL_LENGTH = 200;
private static final long serialVersionUID = 1L;
private static final int MAX_NAME_LENGTH = 200;
@Column(name = "CODE_SYSTEM_URI", nullable = false, length = MAX_URL_LENGTH)
private String myCodeSystemUri;
@OneToOne()
@JoinColumn(name = "CURRENT_VERSION_PID", referencedColumnName = "PID", nullable = true, foreignKey = @ForeignKey(name = "FK_TRMCODESYSTEM_CURVER"))
private TermCodeSystemVersion myCurrentVersion;
@Column(name = "CURRENT_VERSION_PID", nullable = true, insertable = false, updatable = false)
private Long myCurrentVersionPid;
@Id()
@SequenceGenerator(name = "SEQ_CODESYSTEM_PID", sequenceName = "SEQ_CODESYSTEM_PID")
@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_CODESYSTEM_PID")
@ -70,12 +72,32 @@ public class TermCodeSystem implements Serializable {
super();
}
public String getCodeSystemUri() {
return myCodeSystemUri;
@Override
public boolean equals(Object theO) {
if (this == theO) {
return true;
}
public String getName() {
return myName;
if (theO == null || getClass() != theO.getClass()) {
return false;
}
TermCodeSystem that = (TermCodeSystem) theO;
EqualsBuilder b = new EqualsBuilder();
b.append(myCodeSystemUri, that.myCodeSystemUri);
return b.isEquals();
}
@Override
public int hashCode() {
HashCodeBuilder b = new HashCodeBuilder(17, 37);
b.append(myCodeSystemUri);
return b.toHashCode();
}
public String getCodeSystemUri() {
return myCodeSystemUri;
}
public TermCodeSystem setCodeSystemUri(@Nonnull String theCodeSystemUri) {
@ -86,6 +108,15 @@ public class TermCodeSystem implements Serializable {
return this;
}
public String getName() {
return myName;
}
public TermCodeSystem setName(String theName) {
myName = left(theName, MAX_NAME_LENGTH);
return this;
}
public TermCodeSystemVersion getCurrentVersion() {
return myCurrentVersion;
}
@ -103,11 +134,6 @@ public class TermCodeSystem implements Serializable {
return myResource;
}
public TermCodeSystem setName(String theName) {
myName = left(theName, MAX_NAME_LENGTH);
return this;
}
public TermCodeSystem setResource(ResourceTable theResource) {
myResource = theResource;
return this;
@ -115,12 +141,13 @@ public class TermCodeSystem implements Serializable {
@Override
public String toString() {
return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE)
.append("codeSystemUri", myCodeSystemUri)
.append("currentVersion", myCurrentVersion)
.append("pid", myPid)
.append("resourcePid", myResourcePid)
.append("name", myName)
ToStringBuilder b = new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE);
b.append("pid", myPid);
b.append("codeSystemUri", myCodeSystemUri);
b.append("currentVersionPid", myCurrentVersionPid);
b.append("resourcePid", myResourcePid);
b.append("name", myName);
return b
.toString();
}
}

79
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermCodeSystemVersion.java
View File

@ -21,8 +21,11 @@ package ca.uhn.fhir.jpa.entity;
*/
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.util.CoverageIgnore;
import ca.uhn.fhir.util.ValidateUtil;
import org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.HashCodeBuilder;
import org.apache.commons.lang3.builder.ToStringBuilder;
import org.apache.commons.lang3.builder.ToStringStyle;
import javax.persistence.*;
import java.io.Serializable;
@ -36,10 +39,8 @@ import static org.apache.commons.lang3.StringUtils.length;
)
@Entity()
public class TermCodeSystemVersion implements Serializable {
private static final long serialVersionUID = 1L;
public static final int MAX_VERSION_LENGTH = 200;
private static final long serialVersionUID = 1L;
@OneToMany(fetch = FetchType.LAZY, mappedBy = "myCodeSystem")
private Collection<TermConcept> myConcepts;
@ -84,34 +85,6 @@ public class TermCodeSystemVersion implements Serializable {
super();
}
@CoverageIgnore
@Override
public boolean equals(Object obj) {
if (this == obj) {
return true;
}
if (obj == null) {
return false;
}
if (!(obj instanceof TermCodeSystemVersion)) {
return false;
}
TermCodeSystemVersion other = (TermCodeSystemVersion) obj;
if ((myResource.getId() == null) != (other.myResource.getId() == null)) {
return false;
} else if (!myResource.getId().equals(other.myResource.getId())) {
return false;
}
if (myCodeSystemVersionId == null) {
if (other.myCodeSystemVersionId != null) {
return false;
}
} else if (!myCodeSystemVersionId.equals(other.myCodeSystemVersionId)) {
return false;
}
return true;
}
public TermCodeSystem getCodeSystem() {
return myCodeSystem;
@ -154,13 +127,30 @@ public class TermCodeSystemVersion implements Serializable {
return this;
}
@Override
public boolean equals(Object theO) {
if (this == theO) {
return true;
}
if (theO == null || getClass() != theO.getClass()) {
return false;
}
TermCodeSystemVersion that = (TermCodeSystemVersion) theO;
return new EqualsBuilder()
.append(myCodeSystemVersionId, that.myCodeSystemVersionId)
.append(myCodeSystemPid, that.myCodeSystemPid)
.isEquals();
}
@Override
public int hashCode() {
final int prime = 31;
int result = 1;
result = prime * result + ((myResource.getId() == null) ? 0 : myResource.getId().hashCode());
result = prime * result + ((myCodeSystemVersionId == null) ? 0 : myCodeSystemVersionId.hashCode());
return result;
HashCodeBuilder b = new HashCodeBuilder(17, 37);
b.append(myCodeSystemVersionId);
b.append(myCodeSystemPid);
return b.toHashCode();
}
public String getCodeSystemDisplayName() {
@ -180,4 +170,19 @@ public class TermCodeSystemVersion implements Serializable {
getConcepts().add(concept);
return concept;
}
@Override
public String toString() {
ToStringBuilder b = new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE);
b.append("pid", myId);
b.append("codeSystemResourcePid", myResourcePid);
b.append("codeSystemPid", myCodeSystemPid);
b.append("codeSystemVersionId", myCodeSystemVersionId);
return b.toString();
}
TermCodeSystemVersion setCodeSystemPidForUnitTest(long theCodeSystemPid) {
myCodeSystemPid = theCodeSystemPid;
return this;
}
}

30
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConcept.java
View File

@ -37,6 +37,7 @@ import javax.persistence.Index;
import javax.persistence.*;
import java.io.Serializable;
import java.util.*;
import java.util.stream.Collectors;
import static org.apache.commons.lang3.StringUtils.left;
import static org.apache.commons.lang3.StringUtils.length;
@ -108,6 +109,13 @@ public class TermConcept implements Serializable {
setCode(theCode);
}
public TermConcept addChild(RelationshipTypeEnum theRelationshipType) {
TermConcept child = new TermConcept();
child.setCodeSystemVersion(myCodeSystem);
addChild(child, theRelationshipType);
return child;
}
public TermConceptParentChildLink addChild(TermConcept theChild, RelationshipTypeEnum theRelationshipType) {
Validate.notNull(theRelationshipType, "theRelationshipType must not be null");
TermConceptParentChildLink link = new TermConceptParentChildLink();
@ -200,7 +208,7 @@ public class TermConcept implements Serializable {
public TermConcept setCodeSystemVersion(TermCodeSystemVersion theCodeSystemVersion) {
myCodeSystem = theCodeSystemVersion;
if (theCodeSystemVersion.getPid() != null) {
if (theCodeSystemVersion != null && theCodeSystemVersion.getPid() != null) {
myCodeSystemVersionPid = theCodeSystemVersion.getPid();
}
return this;
@ -365,10 +373,13 @@ public class TermConcept implements Serializable {
@Override
public String toString() {
return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE)
.append("code", myCode)
.append("display", myDisplay)
.build();
ToStringBuilder b = new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE);
b.append("code", myCode);
b.append("display", myDisplay);
if (mySequence != null) {
b.append("sequence", mySequence);
}
return b.build();
}
public List<IContextValidationSupport.BaseConceptProperty> toValidationProperties() {
@ -387,4 +398,13 @@ public class TermConcept implements Serializable {
}
return retVal;
}
/**
* Returns a view of {@link #getChildren()} but containing the actual child codes
*/
public List<TermConcept> getChildCodes() {
return getChildren().stream().map(t -> t.getChild()).collect(Collectors.toList());
}
}

11
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptParentChildLink.java
View File

@ -20,11 +20,16 @@ package ca.uhn.fhir.jpa.entity;
* #L%
*/
import org.hibernate.search.annotations.Field;
import org.hibernate.search.annotations.Fields;
import javax.persistence.*;
import java.io.Serializable;
@Entity
@Table(name = "TRM_CONCEPT_PC_LINK")
@Table(name = "TRM_CONCEPT_PC_LINK", indexes = {
@Index(name = "IDX_TRMCONCPCLNK_CSV", columnList = "CODESYSTEM_PID")
})
public class TermConceptParentChildLink implements Serializable {
private static final long serialVersionUID = 1L;
@ -39,6 +44,10 @@ public class TermConceptParentChildLink implements Serializable {
@JoinColumn(name = "CODESYSTEM_PID", nullable = false, foreignKey = @ForeignKey(name = "FK_TERM_CONCEPTPC_CS"))
private TermCodeSystemVersion myCodeSystem;
@Column(name = "CODESYSTEM_PID", insertable = false, updatable = false, nullable = false)
@Fields({@Field(name = "myCodeSystemVersionPid")})
private long myCodeSystemVersionPid;
@ManyToOne(cascade = {})
@JoinColumn(name = "PARENT_PID", nullable = false, referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_TERM_CONCEPTPC_PARENT"))
private TermConcept myParent;

261
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/TerminologyUploaderProvider.java
View File

@ -22,9 +22,8 @@ package ca.uhn.fhir.jpa.provider;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc.UploadStatistics;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
import ca.uhn.fhir.jpa.term.UploadStatistics;
import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
import ca.uhn.fhir.rest.annotation.Operation;
import ca.uhn.fhir.rest.annotation.OperationParam;
import ca.uhn.fhir.rest.api.server.RequestDetails;
@ -34,140 +33,46 @@ import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.util.AttachmentUtil;
import ca.uhn.fhir.util.ParametersUtil;
import ca.uhn.fhir.util.ValidateUtil;
import org.hl7.fhir.convertors.VersionConvertor_30_40;
import org.hl7.fhir.instance.model.api.IBaseParameters;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.ICompositeType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.hl7.fhir.r4.model.CodeSystem;
import org.springframework.beans.factory.annotation.Autowired;
import javax.annotation.Nonnull;
import javax.servlet.http.HttpServletRequest;
import java.io.*;
import java.util.ArrayList;
import java.util.List;
import java.util.concurrent.atomic.AtomicInteger;
import static org.apache.commons.lang3.StringUtils.*;
public class TerminologyUploaderProvider extends BaseJpaProvider {
public static final String CONCEPT_COUNT = "conceptCount";
public static final String TARGET = "target";
public static final String PARENT_CODE = "parentCode";
public static final String VALUE = "value";
public static final String PARAM_FILE = "file";
public static final String PARAM_SYSTEM = "system";
private static final String RESP_PARAM_CONCEPT_COUNT = "conceptCount";
private static final String RESP_PARAM_TARGET = "target";
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TerminologyUploaderProvider.class);
private static final String PACKAGE = "package";
private static final String RESP_PARAM_SUCCESS = "success";
@Autowired
private FhirContext myCtx;
@Autowired
private IHapiTerminologyLoaderSvc myTerminologyLoaderSvc;
@Autowired
private IHapiTerminologySvc myTerminologySvc;
private ITermLoaderSvc myTerminologyLoaderSvc;
/**
* Constructor
*/
public TerminologyUploaderProvider() {
this(null, null, null);
this(null, null);
}
/**
* Constructor
*/
public TerminologyUploaderProvider(FhirContext theContext, IHapiTerminologyLoaderSvc theTerminologyLoaderSvc, IHapiTerminologySvc theTerminologySvc) {
public TerminologyUploaderProvider(FhirContext theContext, ITermLoaderSvc theTerminologyLoaderSvc) {
myCtx = theContext;
myTerminologyLoaderSvc = theTerminologyLoaderSvc;
myTerminologySvc = theTerminologySvc;
}
/**
* <code>
* $apply-codesystem-delta-add
* </code>
*/
@Operation(typeName = "CodeSystem", name = JpaConstants.OPERATION_APPLY_CODESYSTEM_DELTA_ADD, idempotent = false, returnParameters = {
})
public IBaseParameters applyCodeSystemDeltaAdd(
HttpServletRequest theServletRequest,
@OperationParam(name = PARENT_CODE, min = 0, max = 1) IPrimitiveType<String> theParentCode,
@OperationParam(name = VALUE, min = 0, max = 1) IBaseResource theValue,
RequestDetails theRequestDetails
) {
startRequest(theServletRequest);
try {
CodeSystem value;
if (theValue instanceof CodeSystem) {
value = (CodeSystem) theValue;
} else if (theValue instanceof org.hl7.fhir.dstu3.model.CodeSystem) {
value = VersionConvertor_30_40.convertCodeSystem((org.hl7.fhir.dstu3.model.CodeSystem) theValue);
} else if (theValue instanceof org.hl7.fhir.r5.model.CodeSystem) {
value = org.hl7.fhir.convertors.conv40_50.CodeSystem.convertCodeSystem((org.hl7.fhir.r5.model.CodeSystem) theValue);
} else {
throw new InvalidRequestException("Value must be present and be a CodeSystem");
}
String system = value.getUrl();
String parentCode = theParentCode != null ? theParentCode.getValue() : null;
AtomicInteger counter = myTerminologySvc.applyDeltaCodesystemsAdd(system, parentCode, value);
IBaseParameters retVal = ParametersUtil.newInstance(myCtx);
ParametersUtil.addParameterToParametersBoolean(myCtx, retVal, "success", true);
ParametersUtil.addParameterToParametersInteger(myCtx, retVal, "addedConcepts", counter.get());
return retVal;
} finally {
endRequest(theServletRequest);
}
}
/**
* <code>
* $apply-codesystem-delta-remove
* </code>
*/
@Operation(typeName = "CodeSystem", name = JpaConstants.OPERATION_APPLY_CODESYSTEM_DELTA_REMOVE, idempotent = false, returnParameters = {
})
public IBaseParameters applyCodeSystemDeltaRemove(
HttpServletRequest theServletRequest,
@OperationParam(name = VALUE, min = 1, max = 1) IBaseResource theValue,
RequestDetails theRequestDetails
) {
startRequest(theServletRequest);
try {
CodeSystem value;
if (theValue instanceof CodeSystem) {
value = (CodeSystem) theValue;
} else if (theValue instanceof org.hl7.fhir.dstu3.model.CodeSystem) {
value = VersionConvertor_30_40.convertCodeSystem((org.hl7.fhir.dstu3.model.CodeSystem) theValue);
} else if (theValue instanceof org.hl7.fhir.r5.model.CodeSystem) {
value = org.hl7.fhir.convertors.conv40_50.CodeSystem.convertCodeSystem((org.hl7.fhir.r5.model.CodeSystem) theValue);
} else {
throw new InvalidRequestException("Value must be present and be a CodeSystem");
}
String system = value.getUrl();
AtomicInteger counter = myTerminologySvc.applyDeltaCodesystemsRemove(system, value);
IBaseParameters retVal = ParametersUtil.newInstance(myCtx);
ParametersUtil.addParameterToParametersBoolean(myCtx, retVal, "success", true);
ParametersUtil.addParameterToParametersInteger(myCtx, retVal, "removedConcepts", counter.get());
return retVal;
} finally {
endRequest(theServletRequest);
}
}
/**
@ -178,28 +83,31 @@ public class TerminologyUploaderProvider extends BaseJpaProvider {
@Operation(typeName = "CodeSystem", name = JpaConstants.OPERATION_UPLOAD_EXTERNAL_CODE_SYSTEM, idempotent = false, returnParameters = {
// @OperationParam(name = "conceptCount", type = IntegerType.class, min = 1)
})
public IBaseParameters uploadExternalCodeSystem(
public IBaseParameters uploadSnapshot(
HttpServletRequest theServletRequest,
@OperationParam(name = "url", min = 1, typeName = "uri") IPrimitiveType<String> theCodeSystemUrl,
@OperationParam(name = "contentMode", min = 0, typeName = "code") IPrimitiveType<String> theContentMode,
@OperationParam(name = PARAM_SYSTEM, min = 1, typeName = "uri") IPrimitiveType<String> theCodeSystemUrl,
@OperationParam(name = "localfile", min = 1, max = OperationParam.MAX_UNLIMITED, typeName = "string") List<IPrimitiveType<String>> theLocalFile,
@OperationParam(name = PACKAGE, min = 0, max = OperationParam.MAX_UNLIMITED, typeName = "attachment") List<ICompositeType> thePackage,
@OperationParam(name = PARAM_FILE, min = 0, max = OperationParam.MAX_UNLIMITED, typeName = "attachment") List<ICompositeType> theFiles,
RequestDetails theRequestDetails
) {
startRequest(theServletRequest);
if (theCodeSystemUrl == null || isBlank(theCodeSystemUrl.getValueAsString())) {
throw new InvalidRequestException("Missing mandatory parameter: " + PARAM_SYSTEM);
}
if (theLocalFile == null || theLocalFile.size() == 0) {
if (thePackage == null || thePackage.size() == 0) {
if (theFiles == null || theFiles.size() == 0) {
throw new InvalidRequestException("No 'localfile' or 'package' parameter, or package had no data");
}
for (ICompositeType next : thePackage) {
for (ICompositeType next : theFiles) {
ValidateUtil.isTrueOrThrowInvalidRequest(myCtx.getElementDefinition(next.getClass()).getName().equals("Attachment"), "Package must be of type Attachment");
}
}
try {
List<IHapiTerminologyLoaderSvc.FileDescriptor> localFiles = new ArrayList<>();
List<ITermLoaderSvc.FileDescriptor> localFiles = new ArrayList<>();
if (theLocalFile != null && theLocalFile.size() > 0) {
for (IPrimitiveType<String> nextLocalFile : theLocalFile) {
if (isNotBlank(nextLocalFile.getValue())) {
@ -208,7 +116,7 @@ public class TerminologyUploaderProvider extends BaseJpaProvider {
if (!nextFile.exists() || !nextFile.isFile()) {
throw new InvalidRequestException("Unknown file: " + nextFile.getName());
}
localFiles.add(new IHapiTerminologyLoaderSvc.FileDescriptor() {
localFiles.add(new ITermLoaderSvc.FileDescriptor() {
@Override
public String getFilename() {
return nextFile.getAbsolutePath();
@ -227,15 +135,15 @@ public class TerminologyUploaderProvider extends BaseJpaProvider {
}
}
if (thePackage != null) {
for (ICompositeType nextPackage : thePackage) {
if (theFiles != null) {
for (ICompositeType nextPackage : theFiles) {
final String url = AttachmentUtil.getOrCreateUrl(myCtx, nextPackage).getValueAsString();
if (isBlank(url)) {
throw new UnprocessableEntityException("Package is missing mandatory url element");
}
localFiles.add(new IHapiTerminologyLoaderSvc.FileDescriptor() {
localFiles.add(new ITermLoaderSvc.FileDescriptor() {
@Override
public String getFilename() {
return url;
@ -250,33 +158,29 @@ public class TerminologyUploaderProvider extends BaseJpaProvider {
}
}
String codeSystemUrl = theCodeSystemUrl != null ? theCodeSystemUrl.getValue() : null;
codeSystemUrl = defaultString(codeSystemUrl);
String codeSystemUrl = theCodeSystemUrl.getValue();
codeSystemUrl = trim(codeSystemUrl);
String contentMode = theContentMode != null ? theContentMode.getValue() : null;
UploadStatistics stats;
if ("custom".equals(contentMode)) {
stats = myTerminologyLoaderSvc.loadCustom(codeSystemUrl, localFiles, theRequestDetails);
} else {
switch (codeSystemUrl) {
case IHapiTerminologyLoaderSvc.SCT_URI:
case ITermLoaderSvc.SCT_URI:
stats = myTerminologyLoaderSvc.loadSnomedCt(localFiles, theRequestDetails);
break;
case IHapiTerminologyLoaderSvc.LOINC_URI:
case ITermLoaderSvc.LOINC_URI:
stats = myTerminologyLoaderSvc.loadLoinc(localFiles, theRequestDetails);
break;
case IHapiTerminologyLoaderSvc.IMGTHLA_URI:
case ITermLoaderSvc.IMGTHLA_URI:
stats = myTerminologyLoaderSvc.loadImgthla(localFiles, theRequestDetails);
break;
default:
throw new InvalidRequestException("Unknown URL: " + codeSystemUrl);
}
stats = myTerminologyLoaderSvc.loadCustom(codeSystemUrl, localFiles, theRequestDetails);
break;
}
IBaseParameters retVal = ParametersUtil.newInstance(myCtx);
ParametersUtil.addParameterToParametersBoolean(myCtx, retVal, "success", true);
ParametersUtil.addParameterToParametersInteger(myCtx, retVal, CONCEPT_COUNT, stats.getConceptCount());
ParametersUtil.addParameterToParametersReference(myCtx, retVal, TARGET, stats.getTarget().getValue());
ParametersUtil.addParameterToParametersBoolean(myCtx, retVal, RESP_PARAM_SUCCESS, true);
ParametersUtil.addParameterToParametersInteger(myCtx, retVal, RESP_PARAM_CONCEPT_COUNT, stats.getUpdatedConceptCount());
ParametersUtil.addParameterToParametersReference(myCtx, retVal, RESP_PARAM_TARGET, stats.getTarget().getValue());
return retVal;
} finally {
@ -284,5 +188,100 @@ public class TerminologyUploaderProvider extends BaseJpaProvider {
}
}
/**
* <code>
* $apply-codesystem-delta-add
* </code>
*/
@Operation(typeName = "CodeSystem", name = JpaConstants.OPERATION_APPLY_CODESYSTEM_DELTA_ADD, idempotent = false, returnParameters = {
})
public IBaseParameters uploadDeltaAdd(
HttpServletRequest theServletRequest,
@OperationParam(name = PARAM_SYSTEM, min = 1, max = 1, typeName = "uri") IPrimitiveType<String> theSystem,
@OperationParam(name = PARAM_FILE, min = 0, max = OperationParam.MAX_UNLIMITED, typeName = "attachment") List<ICompositeType> theFiles,
RequestDetails theRequestDetails
) {
startRequest(theServletRequest);
try {
validateHaveSystem(theSystem);
validateHaveFiles(theFiles);
List<ITermLoaderSvc.FileDescriptor> files = convertAttachmentsToFileDescriptors(theFiles);
UploadStatistics outcome = myTerminologyLoaderSvc.loadDeltaAdd(theSystem.getValue(), files, theRequestDetails);
return toDeltaResponse(outcome);
} finally {
endRequest(theServletRequest);
}
}
/**
* <code>
* $apply-codesystem-delta-remove
* </code>
*/
@Operation(typeName = "CodeSystem", name = JpaConstants.OPERATION_APPLY_CODESYSTEM_DELTA_REMOVE, idempotent = false, returnParameters = {
})
public IBaseParameters uploadDeltaRemove(
HttpServletRequest theServletRequest,
@OperationParam(name = PARAM_SYSTEM, min = 1, max = 1, typeName = "uri") IPrimitiveType<String> theSystem,
@OperationParam(name = PARAM_FILE, min = 0, max = OperationParam.MAX_UNLIMITED, typeName = "attachment") List<ICompositeType> theFiles,
RequestDetails theRequestDetails
) {
startRequest(theServletRequest);
try {
validateHaveSystem(theSystem);
validateHaveFiles(theFiles);
List<ITermLoaderSvc.FileDescriptor> files = convertAttachmentsToFileDescriptors(theFiles);
UploadStatistics outcome = myTerminologyLoaderSvc.loadDeltaRemove(theSystem.getValue(), files, theRequestDetails);
return toDeltaResponse(outcome);
} finally {
endRequest(theServletRequest);
}
}
private void validateHaveSystem(IPrimitiveType<String> theSystem) {
if (theSystem == null || isBlank(theSystem.getValueAsString())) {
throw new InvalidRequestException("Missing mandatory parameter: " + PARAM_SYSTEM);
}
}
private void validateHaveFiles(List<ICompositeType> theFiles) {
if (theFiles != null) {
for (ICompositeType nextFile : theFiles) {
if (!nextFile.isEmpty()) {
return;
}
}
}
throw new InvalidRequestException("Missing mandatory parameter: " + PARAM_FILE);
}
@Nonnull
private List<ITermLoaderSvc.FileDescriptor> convertAttachmentsToFileDescriptors(@OperationParam(name = PARAM_FILE, min = 0, max = OperationParam.MAX_UNLIMITED, typeName = "attachment") List<ICompositeType> theFiles) {
List<ITermLoaderSvc.FileDescriptor> files = new ArrayList<>();
for (ICompositeType next : theFiles) {
byte[] nextData = AttachmentUtil.getOrCreateData(myCtx, next).getValue();
String nextUrl = AttachmentUtil.getOrCreateUrl(myCtx, next).getValue();
ValidateUtil.isTrueOrThrowInvalidRequest(nextData != null && nextData.length > 0, "Missing Attachment.data value");
ValidateUtil.isNotBlankOrThrowUnprocessableEntity(nextUrl, "Missing Attachment.url value");
files.add(new ITermLoaderSvc.ByteArrayFileDescriptor(nextUrl, nextData));
}
return files;
}
private IBaseParameters toDeltaResponse(UploadStatistics theOutcome) {
IBaseParameters retVal = ParametersUtil.newInstance(myCtx);
ParametersUtil.addParameterToParametersInteger(myCtx, retVal, RESP_PARAM_CONCEPT_COUNT, theOutcome.getUpdatedConceptCount());
ParametersUtil.addParameterToParametersReference(myCtx, retVal, RESP_PARAM_TARGET, theOutcome.getTarget().getValue());
return retVal;
}
}

43
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImpl.java
View File

@ -53,6 +53,7 @@ import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
import ca.uhn.fhir.rest.server.method.PageMethodBinding;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.rest.server.util.ICachedSearchDetails;
import ca.uhn.fhir.util.AsyncUtil;
import ca.uhn.fhir.util.StopWatch;
import com.google.common.annotations.VisibleForTesting;
import org.apache.commons.lang3.Validate;
@ -76,6 +77,7 @@ import org.springframework.transaction.annotation.Transactional;
import org.springframework.transaction.support.TransactionCallbackWithoutResult;
import org.springframework.transaction.support.TransactionTemplate;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import javax.annotation.PostConstruct;
import javax.persistence.EntityManager;
@ -154,12 +156,14 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
public void cancelAllActiveSearches() {
for (SearchTask next : myIdToSearchTask.values()) {
next.requestImmediateAbort();
try {
next.getCompletionLatch().await(30, TimeUnit.SECONDS);
} catch (InterruptedException e) {
ourLog.warn("Failed to wait for completion", e);
AsyncUtil.awaitLatchAndIgnoreInterrupt(next.getCompletionLatch(), 30, TimeUnit.SECONDS);
}
}
@SuppressWarnings("SameParameterValue")
@VisibleForTesting
void setMaxMillisToWaitForRemoteResultsForUnitTest(long theMaxMillisToWaitForRemoteResults) {
myMaxMillisToWaitForRemoteResults = theMaxMillisToWaitForRemoteResults;
}
/**
@ -189,7 +193,6 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
if (searchTask != null) {
ourLog.trace("Local search found");
List<Long> resourcePids = searchTask.getResourcePids(theFrom, theTo);
if (resourcePids != null) {
ourLog.trace("Local search returned {} pids, wanted {}-{} - Search: {}", resourcePids.size(), theFrom, theTo, searchTask.getSearch());
/*
@ -203,7 +206,6 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
}
}
}
}
search = mySearchCacheSvc
.fetchByUuid(theUuid)
@ -244,11 +246,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
}
}
try {
Thread.sleep(500);
} catch (InterruptedException e) {
// ignore
}
AsyncUtil.sleep(500);
}
ourLog.trace("Finished looping");
@ -627,15 +625,9 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
Integer awaitInitialSync() {
ourLog.trace("Awaiting initial sync");
do {
try {
if (getInitialCollectionLatch().await(250, TimeUnit.MILLISECONDS)) {
if (AsyncUtil.awaitLatchAndThrowInternalErrorExceptionOnInterrupt(getInitialCollectionLatch(), 250L, TimeUnit.MILLISECONDS)) {
break;
}
} catch (InterruptedException e) {
// Shouldn't happen
Thread.currentThread().interrupt();
throw new InternalErrorException(e);
}
} while (getSearch().getStatus() == SearchStatusEnum.LOADING);
ourLog.trace("Initial sync completed");
@ -663,7 +655,8 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
return sb;
}
public List<Long> getResourcePids(int theFromIndex, int theToIndex) {
@Nonnull
List<Long> getResourcePids(int theFromIndex, int theToIndex) {
ourLog.debug("Requesting search PIDs from {}-{}", theFromIndex, theToIndex);
boolean keepWaiting;
@ -698,11 +691,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
if (keepWaiting) {
ourLog.info("Waiting as we only have {} results - Search status: {}", mySyncedPids.size(), mySearch.getStatus());
try {
Thread.sleep(500);
} catch (InterruptedException theE) {
// ignore
}
AsyncUtil.sleep(500L);
}
} while (keepWaiting);
@ -1081,11 +1070,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
}
if (myLoadingThrottleForUnitTests != null) {
try {
Thread.sleep(myLoadingThrottleForUnitTests);
} catch (InterruptedException e) {
// ignore
}
AsyncUtil.sleep(myLoadingThrottleForUnitTests);
}
}

16
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/cache/DatabaseSearchCacheSvcImpl.java vendored
View File

@ -48,17 +48,15 @@ import java.util.List;
import java.util.Optional;
public class DatabaseSearchCacheSvcImpl extends BaseSearchCacheSvcImpl {
private static final Logger ourLog = LoggerFactory.getLogger(DatabaseSearchCacheSvcImpl.class);
/*
* Be careful increasing this number! We use the number of params here in a
* DELETE FROM foo WHERE params IN (aaaa)
* DELETE FROM foo WHERE params IN (term,term,term...)
* type query and this can fail if we have 1000s of params
*/
public static final int DEFAULT_MAX_RESULTS_TO_DELETE_IN_ONE_STMT = 500;
public static final int DEFAULT_MAX_RESULTS_TO_DELETE_IN_ONE_PAS = 20000;
public static final long DEFAULT_CUTOFF_SLACK = 10 * DateUtils.MILLIS_PER_SECOND;
private static final Logger ourLog = LoggerFactory.getLogger(DatabaseSearchCacheSvcImpl.class);
private static int ourMaximumResultsToDeleteInOneStatement = DEFAULT_MAX_RESULTS_TO_DELETE_IN_ONE_STMT;
private static int ourMaximumResultsToDeleteInOnePass = DEFAULT_MAX_RESULTS_TO_DELETE_IN_ONE_PAS;
private static Long ourNowForUnitTests;
@ -108,6 +106,14 @@ public class DatabaseSearchCacheSvcImpl extends BaseSearchCacheSvcImpl {
}
void setSearchDaoForUnitTest(ISearchDao theSearchDao) {
mySearchDao = theSearchDao;
}
void setTxManagerForUnitTest(PlatformTransactionManager theTxManager) {
myTxManager = theTxManager;
}
@Override
@Transactional(Transactional.TxType.NEVER)
public Optional<Search> tryToMarkSearchAsInProgress(Search theSearch) {
@ -185,7 +191,7 @@ public class DatabaseSearchCacheSvcImpl extends BaseSearchCacheSvcImpl {
int count = toDelete.getContent().size();
if (count > 0) {
if (ourLog.isDebugEnabled()) {
if (ourLog.isDebugEnabled() || "true".equalsIgnoreCase(System.getProperty("test"))) {
Long total = tt.execute(t -> mySearchDao.count());
ourLog.debug("Deleted {} searches, {} remaining", count, total);
}

1020
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseHapiTerminologySvcImpl.java → hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java
View File

File diff suppressed because it is too large Load Diff

14
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermVersionAdapterSvcImpl.java Normal file
View File

@ -0,0 +1,14 @@
package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
import ca.uhn.fhir.util.ValidateUtil;
import org.hl7.fhir.r4.model.CodeSystem;
public abstract class BaseTermVersionAdapterSvcImpl implements ITermVersionAdapterSvc {
protected void validateCodeSystemForStorage(CodeSystem theCodeSystemResource) {
ValidateUtil.isNotBlankOrThrowUnprocessableEntity(theCodeSystemResource.getUrl(), "Can not store a CodeSystem without a valid URL");
}
}

123
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/LoadedFileDescriptors.java Normal file
View File

@ -0,0 +1,123 @@
package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
import org.apache.commons.io.input.BOMInputStream;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.*;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import java.util.zip.ZipEntry;
import java.util.zip.ZipInputStream;
public class LoadedFileDescriptors implements Closeable {
private static final Logger ourLog = LoggerFactory.getLogger(LoadedFileDescriptors.class);
private List<File> myTemporaryFiles = new ArrayList<>();
private List<ITermLoaderSvc.FileDescriptor> myUncompressedFileDescriptors = new ArrayList<>();
LoadedFileDescriptors(List<ITermLoaderSvc.FileDescriptor> theFileDescriptors) {
try {
for (ITermLoaderSvc.FileDescriptor next : theFileDescriptors) {
if (next.getFilename().toLowerCase().endsWith(".zip")) {
ourLog.info("Uncompressing {} into temporary files", next.getFilename());
try (InputStream inputStream = next.getInputStream()) {
try (BufferedInputStream bufferedInputStream = new BufferedInputStream(inputStream)) {
try (ZipInputStream zis = new ZipInputStream(bufferedInputStream)) {
for (ZipEntry nextEntry; (nextEntry = zis.getNextEntry()) != null; ) {
BOMInputStream fis = new BOMInputStream(zis);
File nextTemporaryFile = File.createTempFile("hapifhir", ".tmp");
ourLog.info("Creating temporary file: {}", nextTemporaryFile.getAbsolutePath());
nextTemporaryFile.deleteOnExit();
try (FileOutputStream fos = new FileOutputStream(nextTemporaryFile, false)) {
IOUtils.copy(fis, fos);
String nextEntryFileName = nextEntry.getName();
myUncompressedFileDescriptors.add(new ITermLoaderSvc.FileDescriptor() {
@Override
public String getFilename() {
return nextEntryFileName;
}
@Override
public InputStream getInputStream() {
try {
return new FileInputStream(nextTemporaryFile);
} catch (FileNotFoundException e) {
throw new InternalErrorException(e);
}
}
});
myTemporaryFiles.add(nextTemporaryFile);
}
}
}
}
}
} else {
myUncompressedFileDescriptors.add(next);
}
}
} catch (IOException e) {
throw new InternalErrorException(e);
}
}
public boolean hasFile(String theFilename) {
return myUncompressedFileDescriptors
.stream()
.map(t -> t.getFilename().replaceAll(".*[\\\\/]", "")) // Strip the path from the filename
.anyMatch(t -> t.equals(theFilename));
}
@Override
public void close() {
for (File next : myTemporaryFiles) {
ourLog.info("Deleting temporary file: {}", next.getAbsolutePath());
FileUtils.deleteQuietly(next);
}
}
List<ITermLoaderSvc.FileDescriptor> getUncompressedFileDescriptors() {
return myUncompressedFileDescriptors;
}
private List<String> notFound(List<String> theExpectedFilenameFragments) {
Set<String> foundFragments = new HashSet<>();
for (String nextExpected : theExpectedFilenameFragments) {
for (ITermLoaderSvc.FileDescriptor next : myUncompressedFileDescriptors) {
if (next.getFilename().contains(nextExpected)) {
foundFragments.add(nextExpected);
break;
}
}
}
ArrayList<String> notFoundFileNameFragments = new ArrayList<>(theExpectedFilenameFragments);
notFoundFileNameFragments.removeAll(foundFragments);
return notFoundFileNameFragments;
}
void verifyMandatoryFilesExist(List<String> theExpectedFilenameFragments) {
List<String> notFound = notFound(theExpectedFilenameFragments);
if (!notFound.isEmpty()) {
throw new UnprocessableEntityException("Could not find the following mandatory files in input: " + notFound);
}
}
void verifyOptionalFilesExist(List<String> theExpectedFilenameFragments) {
List<String> notFound = notFound(theExpectedFilenameFragments);
if (!notFound.isEmpty()) {
ourLog.warn("Could not find the following optional files: " + notFound);
}
}
}

757
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermCodeSystemStorageSvcImpl.java Normal file
View File

@ -0,0 +1,757 @@
package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.data.*;
import ca.uhn.fhir.jpa.dao.index.IdHelperService;
import ca.uhn.fhir.jpa.entity.*;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
import ca.uhn.fhir.jpa.term.custom.CustomTerminologySet;
import ca.uhn.fhir.jpa.util.ScrollableResultsIterator;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.util.ObjectUtil;
import ca.uhn.fhir.util.StopWatch;
import ca.uhn.fhir.util.ValidateUtil;
import com.google.common.collect.ArrayListMultimap;
import com.google.common.collect.ListMultimap;
import org.apache.commons.lang3.Validate;
import org.hibernate.ScrollMode;
import org.hibernate.ScrollableResults;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.ConceptMap;
import org.hl7.fhir.r4.model.ValueSet;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.data.domain.PageRequest;
import org.springframework.data.domain.Slice;
import org.springframework.data.jpa.repository.JpaRepository;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.TransactionDefinition;
import org.springframework.transaction.annotation.Propagation;
import org.springframework.transaction.annotation.Transactional;
import org.springframework.transaction.support.TransactionTemplate;
import javax.annotation.Nonnull;
import javax.persistence.EntityManager;
import javax.persistence.PersistenceContext;
import javax.persistence.PersistenceContextType;
import javax.persistence.TypedQuery;
import javax.persistence.criteria.CriteriaBuilder;
import javax.persistence.criteria.CriteriaQuery;
import javax.persistence.criteria.Predicate;
import javax.persistence.criteria.Root;
import java.util.*;
import java.util.concurrent.TimeUnit;
import java.util.concurrent.atomic.AtomicInteger;
import java.util.function.Supplier;
import java.util.stream.Collectors;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
private static final Logger ourLog = LoggerFactory.getLogger(TermCodeSystemStorageSvcImpl.class);
private static final Object PLACEHOLDER_OBJECT = new Object();
@PersistenceContext(type = PersistenceContextType.TRANSACTION)
protected EntityManager myEntityManager;
@Autowired
protected ITermCodeSystemDao myCodeSystemDao;
@Autowired
protected ITermCodeSystemVersionDao myCodeSystemVersionDao;
@Autowired
protected ITermConceptDao myConceptDao;
@Autowired
protected ITermConceptPropertyDao myConceptPropertyDao;
@Autowired
protected ITermConceptDesignationDao myConceptDesignationDao;
@Autowired
protected IdHelperService myIdHelperService;
@Autowired
private PlatformTransactionManager myTransactionManager;
@Autowired
private ITermConceptParentChildLinkDao myConceptParentChildLinkDao;
@Autowired
private ITermVersionAdapterSvc myTerminologyVersionAdapterSvc;
@Autowired
private ITermDeferredStorageSvc myDeferredStorageSvc;
@Autowired
private FhirContext myContext;
@Autowired
private ITermReadSvc myTerminologySvc;
@Autowired
private DaoConfig myDaoConfig;
@Autowired
private IResourceTableDao myResourceTableDao;
@Override
public Long getValueSetResourcePid(IIdType theIdType) {
return getValueSetResourcePid(theIdType, null);
}
private Long getValueSetResourcePid(IIdType theIdType, RequestDetails theRequestDetails) {
return myIdHelperService.translateForcedIdToPid(theIdType, theRequestDetails);
}
@Transactional
@Override
public UploadStatistics applyDeltaCodeSystemsAdd(String theSystem, CustomTerminologySet theAdditions) {
ValidateUtil.isNotBlankOrThrowInvalidRequest(theSystem, "No system provided");
validateDstu3OrNewer();
theAdditions.validateNoCycleOrThrowInvalidRequest();
TermCodeSystem cs = myCodeSystemDao.findByCodeSystemUri(theSystem);
if (cs == null) {
CodeSystem codeSystemResource = new CodeSystem();
codeSystemResource.setUrl(theSystem);
codeSystemResource.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
myTerminologyVersionAdapterSvc.createOrUpdateCodeSystem(codeSystemResource);
cs = myCodeSystemDao.findByCodeSystemUri(theSystem);
}
TermCodeSystemVersion csv = cs.getCurrentVersion();
Validate.notNull(csv);
CodeSystem codeSystem = myTerminologySvc.getCodeSystemFromContext(theSystem);
if (codeSystem.getContent() != CodeSystem.CodeSystemContentMode.NOTPRESENT) {
throw new InvalidRequestException("CodeSystem with url[" + theSystem + "] can not apply a delta - wrong content mode: " + codeSystem.getContent());
}
Validate.notNull(cs);
Validate.notNull(cs.getPid());
IIdType codeSystemId = cs.getResource().getIdDt();
// Load all concepts for the code system
Map<String, Long> codeToConceptPid = new HashMap<>();
{
ourLog.info("Loading all concepts in CodeSystem versionPid[{}] and url[{}]", cs.getPid(), theSystem);
StopWatch sw = new StopWatch();
CriteriaBuilder criteriaBuilder = myEntityManager.getCriteriaBuilder();
CriteriaQuery<TermConcept> query = criteriaBuilder.createQuery(TermConcept.class);
Root<TermConcept> root = query.from(TermConcept.class);
Predicate predicate = criteriaBuilder.equal(root.get("myCodeSystemVersionPid").as(Long.class), csv.getPid());
query.where(predicate);
TypedQuery<TermConcept> typedQuery = myEntityManager.createQuery(query.select(root));
org.hibernate.query.Query<TermConcept> hibernateQuery = (org.hibernate.query.Query<TermConcept>) typedQuery;
ScrollableResults scrollableResults = hibernateQuery.scroll(ScrollMode.FORWARD_ONLY);
try (ScrollableResultsIterator<TermConcept> scrollableResultsIterator = new ScrollableResultsIterator<>(scrollableResults)) {
while (scrollableResultsIterator.hasNext()) {
TermConcept next = scrollableResultsIterator.next();
codeToConceptPid.put(next.getCode(), next.getId());
}
}
ourLog.info("Loaded {} concepts in {}", codeToConceptPid.size(), sw.toString());
}
// Load all parent/child links
ListMultimap<String, String> parentCodeToChildCodes = ArrayListMultimap.create();
ListMultimap<String, String> childCodeToParentCodes = ArrayListMultimap.create();
{
ourLog.info("Loading all parent/child relationships in CodeSystem url[" + theSystem + "]");
int count = 0;
StopWatch sw = new StopWatch();
CriteriaBuilder criteriaBuilder = myEntityManager.getCriteriaBuilder();
CriteriaQuery<TermConceptParentChildLink> query = criteriaBuilder.createQuery(TermConceptParentChildLink.class);
Root<TermConceptParentChildLink> root = query.from(TermConceptParentChildLink.class);
Predicate predicate = criteriaBuilder.equal(root.get("myCodeSystemVersionPid").as(Long.class), csv.getPid());
root.fetch("myChild");
root.fetch("myParent");
query.where(predicate);
TypedQuery<TermConceptParentChildLink> typedQuery = myEntityManager.createQuery(query.select(root));
org.hibernate.query.Query<TermConceptParentChildLink> hibernateQuery = (org.hibernate.query.Query<TermConceptParentChildLink>) typedQuery;
ScrollableResults scrollableResults = hibernateQuery.scroll(ScrollMode.FORWARD_ONLY);
try (ScrollableResultsIterator<TermConceptParentChildLink> scrollableResultsIterator = new ScrollableResultsIterator<>(scrollableResults)) {
while (scrollableResultsIterator.hasNext()) {
TermConceptParentChildLink next = scrollableResultsIterator.next();
String parentCode = next.getParent().getCode();
String childCode = next.getChild().getCode();
parentCodeToChildCodes.put(parentCode, childCode);
childCodeToParentCodes.put(childCode, parentCode);
count++;
}
}
ourLog.info("Loaded {} parent/child relationships in {}", count, sw.toString());
}
// Account for root codes in the parent->child map
for (String nextCode : codeToConceptPid.keySet()) {
if (childCodeToParentCodes.get(nextCode).isEmpty()) {
parentCodeToChildCodes.put("", nextCode);
}
}
UploadStatistics retVal = new UploadStatistics(codeSystemId);
// Add root concepts
for (TermConcept nextRootConcept : theAdditions.getRootConcepts()) {
List<String> parentCodes = Collections.emptyList();
addConcept(csv, codeToConceptPid, parentCodes, nextRootConcept, parentCodeToChildCodes, retVal, true);
}
// Add unanchored child concepts
for (TermConcept nextUnanchoredChild : theAdditions.getUnanchoredChildConceptsToParentCodes().keySet()) {
List<String> nextParentCodes = theAdditions.getUnanchoredChildConceptsToParentCodes().get(nextUnanchoredChild);
addConcept(csv, codeToConceptPid, nextParentCodes, nextUnanchoredChild, parentCodeToChildCodes, retVal, true);
}
return retVal;
}
@Transactional
@Override
public UploadStatistics applyDeltaCodeSystemsRemove(String theSystem, CustomTerminologySet theValue) {
ValidateUtil.isNotBlankOrThrowInvalidRequest(theSystem, "No system provided");
validateDstu3OrNewer();
TermCodeSystem cs = myCodeSystemDao.findByCodeSystemUri(theSystem);
if (cs == null) {
throw new InvalidRequestException("Unknown code system: " + theSystem);
}
AtomicInteger removeCounter = new AtomicInteger(0);
for (TermConcept nextSuppliedConcept : theValue.getRootConcepts()) {
Optional<TermConcept> conceptOpt = myTerminologySvc.findCode(theSystem, nextSuppliedConcept.getCode());
if (conceptOpt.isPresent()) {
TermConcept concept = conceptOpt.get();
deleteConceptChildrenAndConcept(concept, removeCounter);
}
}
IIdType target = cs.getResource().getIdDt();
return new UploadStatistics(removeCounter.get(), target);
}
@Override
public void deleteCodeSystem(TermCodeSystem theCodeSystem) {
ourLog.info(" * Deleting code system {}", theCodeSystem.getPid());
myEntityManager.flush();
TermCodeSystem cs = myCodeSystemDao.findById(theCodeSystem.getPid()).orElseThrow(IllegalStateException::new);
cs.setCurrentVersion(null);
myCodeSystemDao.save(cs);
myCodeSystemDao.flush();
List<TermCodeSystemVersion> codeSystemVersions = myCodeSystemVersionDao.findByCodeSystemPid(theCodeSystem.getPid());
for (TermCodeSystemVersion next : codeSystemVersions) {
deleteCodeSystemVersion(next.getPid());
}
myCodeSystemVersionDao.deleteForCodeSystem(theCodeSystem);
myCodeSystemDao.delete(theCodeSystem);
myEntityManager.flush();
}
/**
* Returns the number of saved concepts
*/
@Override
public int saveConcept(TermConcept theConcept) {
int retVal = 0;
/*
* If the concept has an ID, we're reindexing, so there's no need to
* save parent concepts first (it's way too slow to do that)
*/
if (theConcept.getId() == null) {
retVal += ensureParentsSaved(theConcept.getParents());
}
if (theConcept.getId() == null || theConcept.getIndexStatus() == null) {
retVal++;
theConcept.setIndexStatus(BaseHapiFhirDao.INDEX_STATUS_INDEXED);
theConcept.setUpdated(new Date());
myConceptDao.save(theConcept);
for (TermConceptProperty next : theConcept.getProperties()) {
myConceptPropertyDao.save(next);
}
for (TermConceptDesignation next : theConcept.getDesignations()) {
myConceptDesignationDao.save(next);
}
}
ourLog.trace("Saved {} and got PID {}", theConcept.getCode(), theConcept.getId());
return retVal;
}
@Override
@Transactional(propagation = Propagation.MANDATORY)
public void storeNewCodeSystemVersionIfNeeded(CodeSystem theCodeSystem, ResourceTable theResourceEntity) {
if (theCodeSystem != null && isNotBlank(theCodeSystem.getUrl())) {
String codeSystemUrl = theCodeSystem.getUrl();
if (theCodeSystem.getContent() == CodeSystem.CodeSystemContentMode.COMPLETE || theCodeSystem.getContent() == null || theCodeSystem.getContent() == CodeSystem.CodeSystemContentMode.NOTPRESENT) {
ourLog.info("CodeSystem {} has a status of {}, going to store concepts in terminology tables", theResourceEntity.getIdDt().getValue(), theCodeSystem.getContentElement().getValueAsString());
Long codeSystemResourcePid = getCodeSystemResourcePid(theCodeSystem.getIdElement());
/*
* If this is a not-present codesystem, we don't want to store a new version if one
* already exists, since that will wipe out the existing concepts. We do create or update
* the TermCodeSystem table though, since that allows the DB to reject changes
* that would result in duplicate CodeSysten.url values.
*/
if (theCodeSystem.getContent() == CodeSystem.CodeSystemContentMode.NOTPRESENT) {
TermCodeSystem codeSystem = myCodeSystemDao.findByCodeSystemUri(theCodeSystem.getUrl());
if (codeSystem != null) {
getOrCreateTermCodeSystem(codeSystemResourcePid, theCodeSystem.getUrl(), theCodeSystem.getUrl(), theResourceEntity);
return;
}
}
TermCodeSystemVersion persCs = new TermCodeSystemVersion();
populateCodeSystemVersionProperties(persCs, theCodeSystem, theResourceEntity);
persCs.getConcepts().addAll(BaseTermReadSvcImpl.toPersistedConcepts(theCodeSystem.getConcept(), persCs));
ourLog.info("Code system has {} concepts", persCs.getConcepts().size());
storeNewCodeSystemVersion(codeSystemResourcePid, codeSystemUrl, theCodeSystem.getName(), theCodeSystem.getVersion(), persCs, theResourceEntity);
}
}
}
@Override
@Transactional(propagation = Propagation.REQUIRED)
public IIdType storeNewCodeSystemVersion(CodeSystem theCodeSystemResource, TermCodeSystemVersion theCodeSystemVersion, RequestDetails theRequest, List<ValueSet> theValueSets, List<ConceptMap> theConceptMaps) {
Validate.notBlank(theCodeSystemResource.getUrl(), "theCodeSystemResource must have a URL");
IIdType csId = myTerminologyVersionAdapterSvc.createOrUpdateCodeSystem(theCodeSystemResource);
Long codeSystemResourcePid = myIdHelperService.translateForcedIdToPid(csId, theRequest);
ResourceTable resource = myResourceTableDao.getOne(codeSystemResourcePid);
ourLog.info("CodeSystem resource has ID: {}", csId.getValue());
populateCodeSystemVersionProperties(theCodeSystemVersion, theCodeSystemResource, resource);
storeNewCodeSystemVersion(codeSystemResourcePid, theCodeSystemResource.getUrl(), theCodeSystemResource.getName(), theCodeSystemResource.getVersion(), theCodeSystemVersion, resource);
myDeferredStorageSvc.addConceptMapsToStorageQueue(theConceptMaps);
myDeferredStorageSvc.addValueSetsToStorageQueue(theValueSets);
return csId;
}
@Override
@Transactional(propagation = Propagation.REQUIRED)
public void storeNewCodeSystemVersion(Long theCodeSystemResourcePid, String theSystemUri, String theSystemName, String theSystemVersionId, TermCodeSystemVersion theCodeSystemVersion, ResourceTable theCodeSystemResourceTable) {
ourLog.info("Storing code system");
ValidateUtil.isTrueOrThrowInvalidRequest(theCodeSystemVersion.getResource() != null, "No resource supplied");
ValidateUtil.isNotBlankOrThrowInvalidRequest(theSystemUri, "No system URI supplied");
// Grab the existing versions so we can delete them later
List<TermCodeSystemVersion> existing = myCodeSystemVersionDao.findByCodeSystemResourcePid(theCodeSystemResourcePid);
/*
* For now we always delete old versions. At some point it would be nice to allow configuration to keep old versions.
*/
ourLog.info("Deleting old code system versions");
for (TermCodeSystemVersion next : existing) {
Long codeSystemVersionPid = next.getPid();
deleteCodeSystemVersion(codeSystemVersionPid);
}
ourLog.info("Flushing...");
myConceptDao.flush();
ourLog.info("Done flushing");
/*
* Do the upload
*/
TermCodeSystem codeSystem = getOrCreateTermCodeSystem(theCodeSystemResourcePid, theSystemUri, theSystemName, theCodeSystemResourceTable);
theCodeSystemVersion.setCodeSystem(codeSystem);
theCodeSystemVersion.setCodeSystemDisplayName(theSystemName);
theCodeSystemVersion.setCodeSystemVersionId(theSystemVersionId);
ourLog.info("Validating all codes in CodeSystem for storage (this can take some time for large sets)");
// Validate the code system
ArrayList<String> conceptsStack = new ArrayList<>();
IdentityHashMap<TermConcept, Object> allConcepts = new IdentityHashMap<>();
int totalCodeCount = 0;
for (TermConcept next : theCodeSystemVersion.getConcepts()) {
totalCodeCount += validateConceptForStorage(next, theCodeSystemVersion, conceptsStack, allConcepts);
}
ourLog.info("Saving version containing {} concepts", totalCodeCount);
TermCodeSystemVersion codeSystemVersion = myCodeSystemVersionDao.saveAndFlush(theCodeSystemVersion);
ourLog.info("Saving code system");
codeSystem.setCurrentVersion(theCodeSystemVersion);
codeSystem = myCodeSystemDao.saveAndFlush(codeSystem);
ourLog.info("Setting CodeSystemVersion[{}] on {} concepts...", codeSystem.getPid(), totalCodeCount);
for (TermConcept next : theCodeSystemVersion.getConcepts()) {
populateVersion(next, codeSystemVersion);
}
ourLog.info("Saving {} concepts...", totalCodeCount);
IdentityHashMap<TermConcept, Object> conceptsStack2 = new IdentityHashMap<>();
for (TermConcept next : theCodeSystemVersion.getConcepts()) {
persistChildren(next, codeSystemVersion, conceptsStack2, totalCodeCount);
}
ourLog.info("Done saving concepts, flushing to database");
myConceptDao.flush();
myConceptParentChildLinkDao.flush();
ourLog.info("Done deleting old code system versions");
if (myDeferredStorageSvc.isStorageQueueEmpty() == false) {
ourLog.info("Note that some concept saving has been deferred");
}
}
private void deleteCodeSystemVersion(final Long theCodeSystemVersionPid) {
ourLog.info(" * Deleting code system version {}", theCodeSystemVersionPid);
PageRequest page1000 = PageRequest.of(0, 1000);
// Parent/Child links
{
String descriptor = "parent/child links";
Supplier<Slice<TermConceptParentChildLink>> loader = () -> myConceptParentChildLinkDao.findByCodeSystemVersion(page1000, theCodeSystemVersionPid);
Supplier<Integer> counter = () -> myConceptParentChildLinkDao.countByCodeSystemVersion(theCodeSystemVersionPid);
doDelete(descriptor, loader, counter, myConceptParentChildLinkDao);
}
// Properties
{
String descriptor = "concept properties";
Supplier<Slice<TermConceptProperty>> loader = () -> myConceptPropertyDao.findByCodeSystemVersion(page1000, theCodeSystemVersionPid);
Supplier<Integer> counter = () -> myConceptPropertyDao.countByCodeSystemVersion(theCodeSystemVersionPid);
doDelete(descriptor, loader, counter, myConceptPropertyDao);
}
// Designations
{
String descriptor = "concept designations";
Supplier<Slice<TermConceptDesignation>> loader = () -> myConceptDesignationDao.findByCodeSystemVersion(page1000, theCodeSystemVersionPid);
Supplier<Integer> counter = () -> myConceptDesignationDao.countByCodeSystemVersion(theCodeSystemVersionPid);
doDelete(descriptor, loader, counter, myConceptDesignationDao);
}
// Concepts
{
String descriptor = "concepts";
// For some reason, concepts are much slower to delete, so use a smaller batch size
PageRequest page100 = PageRequest.of(0, 100);
Supplier<Slice<TermConcept>> loader = () -> myConceptDao.findByCodeSystemVersion(page100, theCodeSystemVersionPid);
Supplier<Integer> counter = () -> myConceptDao.countByCodeSystemVersion(theCodeSystemVersionPid);
doDelete(descriptor, loader, counter, myConceptDao);
}
Optional<TermCodeSystem> codeSystemOpt = myCodeSystemDao.findWithCodeSystemVersionAsCurrentVersion(theCodeSystemVersionPid);
if (codeSystemOpt.isPresent()) {
TermCodeSystem codeSystem = codeSystemOpt.get();
ourLog.info(" * Removing code system version {} as current version of code system {}", theCodeSystemVersionPid, codeSystem.getPid());
codeSystem.setCurrentVersion(null);
myCodeSystemDao.save(codeSystem);
}
ourLog.info(" * Deleting code system version");
myCodeSystemVersionDao.deleteById(theCodeSystemVersionPid);
}
private void validateDstu3OrNewer() {
Validate.isTrue(myContext.getVersion().getVersion().isEqualOrNewerThan(FhirVersionEnum.DSTU3), "Terminology operations only supported in DSTU3+ mode");
}
private void addConcept(TermCodeSystemVersion theCsv, Map<String, Long> theCodeToConceptPid, Collection<String> theParentCodes, TermConcept theConceptToAdd, ListMultimap<String, String> theParentCodeToChildCodes, UploadStatistics theStatisticsTracker, boolean theForceResequence) {
TermConcept nextConceptToAdd = theConceptToAdd;
String nextCodeToAdd = nextConceptToAdd.getCode();
String parentDescription = "(root concept)";
Set<TermConcept> parentConcepts = new HashSet<>();
if (!theParentCodes.isEmpty()) {
parentDescription = "[" + String.join(", ", theParentCodes) + "]";
for (String nextParentCode : theParentCodes) {
Long nextParentCodePid = theCodeToConceptPid.get(nextParentCode);
if (nextParentCodePid == null) {
throw new InvalidRequestException("Unable to add code \"" + nextCodeToAdd + "\" to unknown parent: " + nextParentCode);
}
parentConcepts.add(myConceptDao.getOne(nextParentCodePid));
}
}
ourLog.info("Saving concept {} with parent {}", theStatisticsTracker.getUpdatedConceptCount(), parentDescription);
if (theCodeToConceptPid.containsKey(nextCodeToAdd)) {
TermConcept existingCode = myConceptDao.getOne(theCodeToConceptPid.get(nextCodeToAdd));
existingCode.setIndexStatus(null);
existingCode.setDisplay(nextConceptToAdd.getDisplay());
nextConceptToAdd = existingCode;
}
if (theConceptToAdd.getSequence() == null || theForceResequence) {
// If this is a new code, give it a sequence number based on how many concepts the
// parent already has (or the highest number, if the code has multiple parents)
int sequence = 0;
for (String nextParentCode : theParentCodes) {
theParentCodeToChildCodes.put(nextParentCode, nextCodeToAdd);
sequence = Math.max(sequence, theParentCodeToChildCodes.get(nextParentCode).size());
}
if (theParentCodes.isEmpty()) {
theParentCodeToChildCodes.put("", nextCodeToAdd);
sequence = Math.max(sequence, theParentCodeToChildCodes.get("").size());
}
nextConceptToAdd.setSequence(sequence);
}
// Drop any old parent-child links if they aren't explicitly specified in the
// hierarchy being added
for (Iterator<TermConceptParentChildLink> iter = nextConceptToAdd.getParents().iterator(); iter.hasNext(); ) {
TermConceptParentChildLink nextLink = iter.next();
String parentCode = nextLink.getParent().getCode();
boolean shouldRemove = !theParentCodes.contains(parentCode);
if (shouldRemove) {
ourLog.info("Dropping existing parent/child link from {} -> {}", parentCode, nextCodeToAdd);
myConceptParentChildLinkDao.delete(nextLink);
iter.remove();
List<TermConceptParentChildLink> parentChildrenList = nextLink.getParent().getChildren();
parentChildrenList.remove(nextLink);
}
}
nextConceptToAdd.setParentPids(null);
nextConceptToAdd.setCodeSystemVersion(theCsv);
nextConceptToAdd = myConceptDao.save(nextConceptToAdd);
Long nextConceptPid = nextConceptToAdd.getId();
Validate.notNull(nextConceptPid);
theCodeToConceptPid.put(nextCodeToAdd, nextConceptPid);
theStatisticsTracker.incrementUpdatedConceptCount();
// Add link to new child to the parent if this link doesn't already exist (this will be the
// case for concepts being added to an existing child concept, but won't be the case when
// we're recursively adding children)
for (TermConcept nextParentConcept : parentConcepts) {
if (nextParentConcept.getChildren().stream().noneMatch(t->t.getChild().getCode().equals(nextCodeToAdd))) {
TermConceptParentChildLink parentLink = new TermConceptParentChildLink();
parentLink.setParent(nextParentConcept);
parentLink.setChild(nextConceptToAdd);
parentLink.setCodeSystem(theCsv);
parentLink.setRelationshipType(TermConceptParentChildLink.RelationshipTypeEnum.ISA);
nextParentConcept.getChildren().add(parentLink);
nextConceptToAdd.getParents().add(parentLink);
myConceptParentChildLinkDao.save(parentLink);
}
}
// Save children recursively
for (TermConceptParentChildLink nextChildConceptLink : nextConceptToAdd.getChildren()) {
TermConcept nextChild = nextChildConceptLink.getChild();
Collection<String> parentCodes = nextChild.getParents().stream().map(t -> t.getParent().getCode()).collect(Collectors.toList());
addConcept(theCsv, theCodeToConceptPid, parentCodes, nextChild, theParentCodeToChildCodes, theStatisticsTracker, false);
if (nextChildConceptLink.getId() == null) {
nextChildConceptLink.setCodeSystem(theCsv);
myConceptParentChildLinkDao.save(nextChildConceptLink);
}
}
}
private Long getCodeSystemResourcePid(IIdType theIdType) {
return getCodeSystemResourcePid(theIdType, null);
}
private Long getCodeSystemResourcePid(IIdType theIdType, RequestDetails theRequestDetails) {
return myIdHelperService.translateForcedIdToPid(theIdType, theRequestDetails);
}
private void persistChildren(TermConcept theConcept, TermCodeSystemVersion theCodeSystem, IdentityHashMap<TermConcept, Object> theConceptsStack, int theTotalConcepts) {
if (theConceptsStack.put(theConcept, PLACEHOLDER_OBJECT) != null) {
return;
}
if (theConceptsStack.size() == 1 || theConceptsStack.size() % 10000 == 0) {
float pct = (float) theConceptsStack.size() / (float) theTotalConcepts;
ourLog.info("Have processed {}/{} concepts ({}%)", theConceptsStack.size(), theTotalConcepts, (int) (pct * 100.0f));
}
theConcept.setCodeSystemVersion(theCodeSystem);
theConcept.setIndexStatus(BaseHapiFhirDao.INDEX_STATUS_INDEXED);
if (theConceptsStack.size() <= myDaoConfig.getDeferIndexingForCodesystemsOfSize()) {
saveConcept(theConcept);
} else {
myDeferredStorageSvc.addConceptToStorageQueue(theConcept);
}
for (TermConceptParentChildLink next : theConcept.getChildren()) {
persistChildren(next.getChild(), theCodeSystem, theConceptsStack, theTotalConcepts);
}
for (TermConceptParentChildLink next : theConcept.getChildren()) {
if (theConceptsStack.size() <= myDaoConfig.getDeferIndexingForCodesystemsOfSize()) {
saveConceptLink(next);
} else {
myDeferredStorageSvc.addConceptLinkToStorageQueue(next);
}
}
}
private void populateVersion(TermConcept theNext, TermCodeSystemVersion theCodeSystemVersion) {
if (theNext.getCodeSystemVersion() != null) {
return;
}
theNext.setCodeSystemVersion(theCodeSystemVersion);
for (TermConceptParentChildLink next : theNext.getChildren()) {
populateVersion(next.getChild(), theCodeSystemVersion);
}
}
private void saveConceptLink(TermConceptParentChildLink next) {
if (next.getId() == null) {
myConceptParentChildLinkDao.save(next);
}
}
private int ensureParentsSaved(Collection<TermConceptParentChildLink> theParents) {
ourLog.trace("Checking {} parents", theParents.size());
int retVal = 0;
for (TermConceptParentChildLink nextLink : theParents) {
if (nextLink.getRelationshipType() == TermConceptParentChildLink.RelationshipTypeEnum.ISA) {
TermConcept nextParent = nextLink.getParent();
retVal += ensureParentsSaved(nextParent.getParents());
if (nextParent.getId() == null) {
nextParent.setUpdated(new Date());
myConceptDao.saveAndFlush(nextParent);
retVal++;
ourLog.debug("Saved parent code {} and got id {}", nextParent.getCode(), nextParent.getId());
}
}
}
return retVal;
}
@Nonnull
private TermCodeSystem getOrCreateTermCodeSystem(Long theCodeSystemResourcePid, String theSystemUri, String theSystemName, ResourceTable theCodeSystemResourceTable) {
TermCodeSystem codeSystem = myCodeSystemDao.findByCodeSystemUri(theSystemUri);
if (codeSystem == null) {
codeSystem = myCodeSystemDao.findByResourcePid(theCodeSystemResourcePid);
if (codeSystem == null) {
codeSystem = new TermCodeSystem();
}
codeSystem.setResource(theCodeSystemResourceTable);
} else {
if (!ObjectUtil.equals(codeSystem.getResource().getId(), theCodeSystemResourceTable.getId())) {
String msg = myContext.getLocalizer().getMessage(BaseTermReadSvcImpl.class, "cannotCreateDuplicateCodeSystemUrl", theSystemUri,
codeSystem.getResource().getIdDt().toUnqualifiedVersionless().getValue());
throw new UnprocessableEntityException(msg);
}
}
codeSystem.setCodeSystemUri(theSystemUri);
codeSystem.setName(theSystemName);
codeSystem = myCodeSystemDao.save(codeSystem);
return codeSystem;
}
private void populateCodeSystemVersionProperties(TermCodeSystemVersion theCodeSystemVersion, CodeSystem theCodeSystemResource, ResourceTable theResourceTable) {
theCodeSystemVersion.setResource(theResourceTable);
theCodeSystemVersion.setCodeSystemDisplayName(theCodeSystemResource.getName());
theCodeSystemVersion.setCodeSystemVersionId(theCodeSystemResource.getVersion());
}
private void deleteConceptChildrenAndConcept(TermConcept theConcept, AtomicInteger theRemoveCounter) {
for (TermConceptParentChildLink nextChildLink : theConcept.getChildren()) {
deleteConceptChildrenAndConcept(nextChildLink.getChild(), theRemoveCounter);
myConceptParentChildLinkDao.delete(nextChildLink);
}
myConceptDesignationDao.deleteAll(theConcept.getDesignations());
myConceptPropertyDao.deleteAll(theConcept.getProperties());
myConceptDao.delete(theConcept);
theRemoveCounter.incrementAndGet();
}
private <T> void doDelete(String theDescriptor, Supplier<Slice<T>> theLoader, Supplier<Integer> theCounter, JpaRepository<T, ?> theDao) {
int count;
ourLog.info(" * Deleting {}", theDescriptor);
int totalCount = theCounter.get();
StopWatch sw = new StopWatch();
count = 0;
while (true) {
Slice<T> link = theLoader.get();
if (!link.hasContent()) {
break;
}
TransactionTemplate txTemplate = new TransactionTemplate(myTransactionManager);
txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRED);
txTemplate.execute(t -> {
theDao.deleteAll(link);
return null;
});
count += link.getNumberOfElements();
ourLog.info(" * {} {} deleted - {}/sec - ETA: {}", count, theDescriptor, sw.formatThroughput(count, TimeUnit.SECONDS), sw.getEstimatedTimeRemaining(count, totalCount));
}
theDao.flush();
}
private int validateConceptForStorage(TermConcept theConcept, TermCodeSystemVersion theCodeSystem, ArrayList<String> theConceptsStack,
IdentityHashMap<TermConcept, Object> theAllConcepts) {
ValidateUtil.isTrueOrThrowInvalidRequest(theConcept.getCodeSystemVersion() != null, "CodeSystemVersion is null");
ValidateUtil.isTrueOrThrowInvalidRequest(theConcept.getCodeSystemVersion() == theCodeSystem, "CodeSystems are not equal");
ValidateUtil.isNotBlankOrThrowInvalidRequest(theConcept.getCode(), "CodeSystem contains a code with no code value");
if (theConceptsStack.contains(theConcept.getCode())) {
throw new InvalidRequestException("CodeSystem contains circular reference around code " + theConcept.getCode());
}
theConceptsStack.add(theConcept.getCode());
int retVal = 0;
if (theAllConcepts.put(theConcept, theAllConcepts) == null) {
if (theAllConcepts.size() % 1000 == 0) {
ourLog.info("Have validated {} concepts", theAllConcepts.size());
}
retVal = 1;
}
for (TermConceptParentChildLink next : theConcept.getChildren()) {
next.setCodeSystem(theCodeSystem);
retVal += validateConceptForStorage(next.getChild(), theCodeSystem, theConceptsStack, theAllConcepts);
}
theConceptsStack.remove(theConceptsStack.size() - 1);
return retVal;
}
}

260
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermDeferredStorageSvcImpl.java Normal file
View File

@ -0,0 +1,260 @@
package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.data.ITermConceptDao;
import ca.uhn.fhir.jpa.dao.data.ITermConceptParentChildLinkDao;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
import ca.uhn.fhir.jpa.model.sched.FireAtIntervalJob;
import ca.uhn.fhir.jpa.model.sched.ISchedulerService;
import ca.uhn.fhir.jpa.model.sched.ScheduledJobDefinition;
import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
import ca.uhn.fhir.util.StopWatch;
import com.google.common.annotations.VisibleForTesting;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.r4.model.ConceptMap;
import org.hl7.fhir.r4.model.ValueSet;
import org.quartz.JobExecutionContext;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.TransactionDefinition;
import org.springframework.transaction.annotation.Propagation;
import org.springframework.transaction.annotation.Transactional;
import org.springframework.transaction.support.TransactionTemplate;
import javax.annotation.PostConstruct;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
private static final int SCHEDULE_INTERVAL_MILLIS = 5000;
private static final Logger ourLog = LoggerFactory.getLogger(TermDeferredStorageSvcImpl.class);
@Autowired
protected ITermConceptDao myConceptDao;
@Autowired
protected PlatformTransactionManager myTransactionMgr;
private boolean myProcessDeferred = true;
private List<TermConcept> myDeferredConcepts = Collections.synchronizedList(new ArrayList<>());
private List<ValueSet> myDeferredValueSets = Collections.synchronizedList(new ArrayList<>());
private List<ConceptMap> myDeferredConceptMaps = Collections.synchronizedList(new ArrayList<>());
private List<TermConceptParentChildLink> myConceptLinksToSaveLater = Collections.synchronizedList(new ArrayList<>());
@Autowired
private DaoConfig myDaoConfig;
@Autowired
private ITermConceptParentChildLinkDao myConceptParentChildLinkDao;
@Autowired
private ISchedulerService mySchedulerService;
@Autowired
private ITermVersionAdapterSvc myTerminologyVersionAdapterSvc;
@Autowired
private ITermCodeSystemStorageSvc myConceptStorageSvc;
@Override
public void addConceptToStorageQueue(TermConcept theConcept) {
Validate.notNull(theConcept);
myDeferredConcepts.add(theConcept);
}
@Override
public void addConceptLinkToStorageQueue(TermConceptParentChildLink theConceptLink) {
Validate.notNull(theConceptLink);
myConceptLinksToSaveLater.add(theConceptLink);
}
@Override
public void addConceptMapsToStorageQueue(List<ConceptMap> theConceptMaps) {
Validate.notNull(theConceptMaps);
myDeferredConceptMaps.addAll(theConceptMaps);
}
@Override
public void addValueSetsToStorageQueue(List<ValueSet> theValueSets) {
Validate.notNull(theValueSets);
myDeferredValueSets.addAll(theValueSets);
}
@Override
public void setProcessDeferred(boolean theProcessDeferred) {
myProcessDeferred = theProcessDeferred;
}
private void processDeferredConceptMaps() {
int count = Math.min(myDeferredConceptMaps.size(), 20);
for (ConceptMap nextConceptMap : new ArrayList<>(myDeferredConceptMaps.subList(0, count))) {
ourLog.info("Creating ConceptMap: {}", nextConceptMap.getId());
myTerminologyVersionAdapterSvc.createOrUpdateConceptMap(nextConceptMap);
myDeferredConceptMaps.remove(nextConceptMap);
}
ourLog.info("Saved {} deferred ConceptMap resources, have {} remaining", count, myDeferredConceptMaps.size());
}
private void processDeferredConcepts() {
int codeCount = 0, relCount = 0;
StopWatch stopwatch = new StopWatch();
int count = Math.min(myDaoConfig.getDeferIndexingForCodesystemsOfSize(), myDeferredConcepts.size());
ourLog.info("Saving {} deferred concepts...", count);
while (codeCount < count && myDeferredConcepts.size() > 0) {
TermConcept next = myDeferredConcepts.remove(0);
codeCount += myConceptStorageSvc.saveConcept(next);
}
if (codeCount > 0) {
ourLog.info("Saved {} deferred concepts ({} codes remain and {} relationships remain) in {}ms ({}ms / code)",
codeCount, myDeferredConcepts.size(), myConceptLinksToSaveLater.size(), stopwatch.getMillis(), stopwatch.getMillisPerOperation(codeCount));
}
if (codeCount == 0) {
count = Math.min(myDaoConfig.getDeferIndexingForCodesystemsOfSize(), myConceptLinksToSaveLater.size());
ourLog.info("Saving {} deferred concept relationships...", count);
while (relCount < count && myConceptLinksToSaveLater.size() > 0) {
TermConceptParentChildLink next = myConceptLinksToSaveLater.remove(0);
if (!myConceptDao.findById(next.getChild().getId()).isPresent() || !myConceptDao.findById(next.getParent().getId()).isPresent()) {
ourLog.warn("Not inserting link from child {} to parent {} because it appears to have been deleted", next.getParent().getCode(), next.getChild().getCode());
continue;
}
saveConceptLink(next);
relCount++;
}
}
if (relCount > 0) {
ourLog.info("Saved {} deferred relationships ({} remain) in {}ms ({}ms / entry)",
relCount, myConceptLinksToSaveLater.size(), stopwatch.getMillis(), stopwatch.getMillisPerOperation(relCount));
}
if ((myDeferredConcepts.size() + myConceptLinksToSaveLater.size()) == 0) {
ourLog.info("All deferred concepts and relationships have now been synchronized to the database");
}
}
private void processDeferredValueSets() {
int count = Math.min(myDeferredValueSets.size(), 20);
for (ValueSet nextValueSet : new ArrayList<>(myDeferredValueSets.subList(0, count))) {
ourLog.info("Creating ValueSet: {}", nextValueSet.getId());
myTerminologyVersionAdapterSvc.createOrUpdateValueSet(nextValueSet);
myDeferredValueSets.remove(nextValueSet);
}
ourLog.info("Saved {} deferred ValueSet resources, have {} remaining", count, myDeferredValueSets.size());
}
/**
* This method is present only for unit tests, do not call from client code
*/
@VisibleForTesting
public synchronized void clearDeferred() {
myDeferredValueSets.clear();
myDeferredConceptMaps.clear();
myDeferredConcepts.clear();
}
@Transactional(propagation = Propagation.NEVER)
@Override
public synchronized void saveDeferred() {
if (isProcessDeferredPaused()) {
return;
}
TransactionTemplate tt = new TransactionTemplate(myTransactionMgr);
tt.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRES_NEW);
if (isDeferredConceptsOrConceptLinksToSaveLater()) {
tt.execute(t -> {
processDeferredConcepts();
return null;
});
}
if (isDeferredValueSets()) {
tt.execute(t -> {
processDeferredValueSets();
return null;
});
}
if (isDeferredConceptMaps()) {
tt.execute(t -> {
processDeferredConceptMaps();
return null;
});
}
}
@Override
public boolean isStorageQueueEmpty() {
boolean retVal = true;
retVal &= !isProcessDeferredPaused();
retVal &= !isDeferredConcepts();
retVal &= !isConceptLinksToSaveLater();
retVal &= !isDeferredValueSets();
retVal &= !isDeferredConceptMaps();
return retVal;
}
private void saveConceptLink(TermConceptParentChildLink next) {
if (next.getId() == null) {
myConceptParentChildLinkDao.save(next);
}
}
private boolean isProcessDeferredPaused() {
return !myProcessDeferred;
}
private boolean isDeferredConceptsOrConceptLinksToSaveLater() {
return isDeferredConcepts() || isConceptLinksToSaveLater();
}
private boolean isDeferredConcepts() {
return !myDeferredConcepts.isEmpty();
}
private boolean isConceptLinksToSaveLater() {
return !myConceptLinksToSaveLater.isEmpty();
}
private boolean isDeferredValueSets() {
return !myDeferredValueSets.isEmpty();
}
private boolean isDeferredConceptMaps() {
return !myDeferredConceptMaps.isEmpty();
}
@PostConstruct
public void registerScheduledJob() {
// Register scheduled job to save deferred concepts
// In the future it would be great to make this a cluster-aware task somehow
ScheduledJobDefinition jobDefinition = new ScheduledJobDefinition();
jobDefinition.setId(BaseTermReadSvcImpl.class.getName() + "_saveDeferred");
jobDefinition.setJobClass(SaveDeferredJob.class);
mySchedulerService.scheduleFixedDelay(SCHEDULE_INTERVAL_MILLIS, false, jobDefinition);
}
public static class SaveDeferredJob extends FireAtIntervalJob {
@Autowired
private ITermDeferredStorageSvc myTerminologySvc;
/**
* Constructor
*/
public SaveDeferredJob() {
super(SCHEDULE_INTERVAL_MILLIS);
}
@Override
protected void doExecute(JobExecutionContext theContext) {
myTerminologySvc.saveDeferred();
}
}
}

332
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcImpl.java → hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermLoaderSvcImpl.java
View File

@ -4,8 +4,10 @@ import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
import ca.uhn.fhir.jpa.term.custom.ConceptHandler;
import ca.uhn.fhir.jpa.term.custom.HierarchyHandler;
import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
import ca.uhn.fhir.jpa.term.custom.CustomTerminologySet;
import ca.uhn.fhir.jpa.term.loinc.*;
import ca.uhn.fhir.jpa.term.snomedct.SctHandlerConcept;
import ca.uhn.fhir.jpa.term.snomedct.SctHandlerDescription;
@ -15,7 +17,6 @@ import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.util.ValidateUtil;
import com.google.common.annotations.VisibleForTesting;
import com.google.common.base.Charsets;
@ -23,9 +24,7 @@ import org.apache.commons.csv.CSVFormat;
import org.apache.commons.csv.CSVParser;
import org.apache.commons.csv.CSVRecord;
import org.apache.commons.csv.QuoteMode;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
import org.apache.commons.io.input.BOMInputStream;
import org.apache.commons.lang3.ObjectUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
@ -41,8 +40,7 @@ import javax.validation.constraints.NotNull;
import java.io.*;
import java.util.*;
import java.util.Map.Entry;
import java.util.zip.ZipEntry;
import java.util.zip.ZipInputStream;
import java.util.stream.Collectors;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.*;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
@ -67,64 +65,29 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
* #L%
*/
public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
public static final String SCT_FILE_CONCEPT = "Terminology/sct2_Concept_Full_";
public static final String SCT_FILE_DESCRIPTION = "Terminology/sct2_Description_Full-en";
public static final String SCT_FILE_RELATIONSHIP = "Terminology/sct2_Relationship_Full";
public static final String IMGTHLA_HLA_NOM_TXT = "hla_nom.txt";
public static final String IMGTHLA_HLA_XML = "hla.xml";
public class TermLoaderSvcImpl implements ITermLoaderSvc {
public static final String CUSTOM_CONCEPTS_FILE = "concepts.csv";
public static final String CUSTOM_HIERARCHY_FILE = "hierarchy.csv";
public static final String CUSTOM_CODESYSTEM_JSON = "codesystem.json";
public static final String CUSTOM_CODESYSTEM_XML = "codesystem.xml";
static final String IMGTHLA_HLA_NOM_TXT = "hla_nom.txt";
static final String IMGTHLA_HLA_XML = "hla.xml";
static final String CUSTOM_CODESYSTEM_JSON = "codesystem.json";
private static final String SCT_FILE_CONCEPT = "Terminology/sct2_Concept_Full_";
private static final String SCT_FILE_DESCRIPTION = "Terminology/sct2_Description_Full-en";
private static final String SCT_FILE_RELATIONSHIP = "Terminology/sct2_Relationship_Full";
private static final String CUSTOM_CODESYSTEM_XML = "codesystem.xml";
private static final int LOG_INCREMENT = 1000;
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TerminologyLoaderSvcImpl.class);
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TermLoaderSvcImpl.class);
// FYI: Hardcoded to R4 because that's what the term svc uses internally
private final FhirContext myCtx = FhirContext.forR4();
@Autowired
private IHapiTerminologySvc myTermSvc;
private void dropCircularRefs(TermConcept theConcept, ArrayList<String> theChain, Map<String, TermConcept> theCode2concept, Counter theCircularCounter) {
theChain.add(theConcept.getCode());
for (Iterator<TermConceptParentChildLink> childIter = theConcept.getChildren().iterator(); childIter.hasNext(); ) {
TermConceptParentChildLink next = childIter.next();
TermConcept nextChild = next.getChild();
if (theChain.contains(nextChild.getCode())) {
StringBuilder b = new StringBuilder();
b.append("Removing circular reference code ");
b.append(nextChild.getCode());
b.append(" from parent ");
b.append(next.getParent().getCode());
b.append(". Chain was: ");
for (String nextInChain : theChain) {
TermConcept nextCode = theCode2concept.get(nextInChain);
b.append(nextCode.getCode());
b.append('[');
b.append(StringUtils.substring(nextCode.getDisplay(), 0, 20).replace("[", "").replace("]", "").trim());
b.append("] ");
}
ourLog.info(b.toString(), theConcept.getCode());
childIter.remove();
nextChild.getParents().remove(next);
} else {
dropCircularRefs(nextChild, theChain, theCode2concept, theCircularCounter);
}
}
theChain.remove(theChain.size() - 1);
}
private ITermDeferredStorageSvc myDeferredStorageSvc;
@Autowired
private ITermCodeSystemStorageSvc myCodeSystemStorageSvc;
@Override
public UploadStatistics loadImgthla(List<FileDescriptor> theFiles, RequestDetails theRequestDetails) {
LoadedFileDescriptors descriptors = null;
try {
descriptors = new LoadedFileDescriptors(theFiles);
try (LoadedFileDescriptors descriptors = new LoadedFileDescriptors(theFiles)) {
List<String> mandatoryFilenameFragments = Arrays.asList(
IMGTHLA_HLA_NOM_TXT,
IMGTHLA_HLA_XML
@ -134,15 +97,13 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
ourLog.info("Beginning IMGTHLA processing");
return processImgthlaFiles(descriptors, theRequestDetails);
} finally {
IOUtils.closeQuietly(descriptors);
}
}
@Override
public UploadStatistics loadLoinc(List<FileDescriptor> theFiles, RequestDetails theRequestDetails) {
try (LoadedFileDescriptors descriptors = new LoadedFileDescriptors(theFiles)) {
List<String> loincUploadPropertiesFragment = Arrays.asList(
List<String> loincUploadPropertiesFragment = Collections.singletonList(
LOINC_UPLOAD_PROPERTIES_FILE.getCode()
);
descriptors.verifyMandatoryFilesExist(loincUploadPropertiesFragment);
@ -180,23 +141,6 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
}
}
@NotNull
private Properties getProperties(LoadedFileDescriptors theDescriptors, String thePropertiesFile) {
Properties retVal = new Properties();
for (FileDescriptor next : theDescriptors.getUncompressedFileDescriptors()) {
if (next.getFilename().endsWith(thePropertiesFile)) {
try {
try (InputStream inputStream = next.getInputStream()) {
retVal.load(inputStream);
}
} catch (IOException e) {
throw new InternalErrorException("Failed to read " + thePropertiesFile, e);
}
}
}
return retVal;
}
@Override
public UploadStatistics loadSnomedCt(List<FileDescriptor> theFiles, RequestDetails theRequestDetails) {
try (LoadedFileDescriptors descriptors = new LoadedFileDescriptors(theFiles)) {
@ -216,8 +160,6 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
@Override
public UploadStatistics loadCustom(String theSystem, List<FileDescriptor> theFiles, RequestDetails theRequestDetails) {
try (LoadedFileDescriptors descriptors = new LoadedFileDescriptors(theFiles)) {
IRecordHandler handler;
Optional<String> codeSystemContent = loadFile(descriptors, CUSTOM_CODESYSTEM_JSON, CUSTOM_CODESYSTEM_XML);
CodeSystem codeSystem;
if (codeSystemContent.isPresent()) {
@ -233,14 +175,83 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
codeSystem.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
}
TermCodeSystemVersion csv = new TermCodeSystemVersion();
final Map<String, TermConcept> code2concept = processCustomTerminologyFiles(descriptors, csv);
CustomTerminologySet terminologySet = CustomTerminologySet.load(descriptors, false);
TermCodeSystemVersion csv = terminologySet.toCodeSystemVersion();
IIdType target = storeCodeSystem(theRequestDetails, csv, codeSystem, null, null);
return new UploadStatistics(code2concept.size(), target);
return new UploadStatistics(terminologySet.getSize(), target);
}
}
@Override
public UploadStatistics loadDeltaAdd(String theSystem, List<FileDescriptor> theFiles, RequestDetails theRequestDetails) {
ourLog.info("Processing terminology delta ADD for system[{}] with files: {}", theSystem, theFiles.stream().map(t -> t.getFilename()).collect(Collectors.toList()));
try (LoadedFileDescriptors descriptors = new LoadedFileDescriptors(theFiles)) {
CustomTerminologySet terminologySet = CustomTerminologySet.load(descriptors, false);
return myCodeSystemStorageSvc.applyDeltaCodeSystemsAdd(theSystem, terminologySet);
}
}
@Override
public UploadStatistics loadDeltaRemove(String theSystem, List<FileDescriptor> theFiles, RequestDetails theRequestDetails) {
ourLog.info("Processing terminology delta REMOVE for system[{}] with files: {}", theSystem, theFiles.stream().map(t -> t.getFilename()).collect(Collectors.toList()));
try (LoadedFileDescriptors descriptors = new LoadedFileDescriptors(theFiles)) {
CustomTerminologySet terminologySet = CustomTerminologySet.load(descriptors, true);
return myCodeSystemStorageSvc.applyDeltaCodeSystemsRemove(theSystem, terminologySet);
}
}
private void dropCircularRefs(TermConcept theConcept, ArrayList<String> theChain, Map<String, TermConcept> theCode2concept) {
theChain.add(theConcept.getCode());
for (Iterator<TermConceptParentChildLink> childIter = theConcept.getChildren().iterator(); childIter.hasNext(); ) {
TermConceptParentChildLink next = childIter.next();
TermConcept nextChild = next.getChild();
if (theChain.contains(nextChild.getCode())) {
StringBuilder b = new StringBuilder();
b.append("Removing circular reference code ");
b.append(nextChild.getCode());
b.append(" from parent ");
b.append(next.getParent().getCode());
b.append(". Chain was: ");
for (String nextInChain : theChain) {
TermConcept nextCode = theCode2concept.get(nextInChain);
b.append(nextCode.getCode());
b.append('[');
b.append(StringUtils.substring(nextCode.getDisplay(), 0, 20).replace("[", "").replace("]", "").trim());
b.append("] ");
}
ourLog.info(b.toString(), theConcept.getCode());
childIter.remove();
nextChild.getParents().remove(next);
} else {
dropCircularRefs(nextChild, theChain, theCode2concept);
}
}
theChain.remove(theChain.size() - 1);
}
@NotNull
private Properties getProperties(LoadedFileDescriptors theDescriptors, String thePropertiesFile) {
Properties retVal = new Properties();
for (FileDescriptor next : theDescriptors.getUncompressedFileDescriptors()) {
if (next.getFilename().endsWith(thePropertiesFile)) {
try {
try (InputStream inputStream = next.getInputStream()) {
retVal.load(inputStream);
}
} catch (IOException e) {
throw new InternalErrorException("Failed to read " + thePropertiesFile, e);
}
}
}
return retVal;
}
private Optional<String> loadFile(LoadedFileDescriptors theDescriptors, String... theFilenames) {
for (FileDescriptor next : theDescriptors.getUncompressedFileDescriptors()) {
for (String nextFilename : theFilenames) {
@ -257,15 +268,14 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
return Optional.empty();
}
UploadStatistics processImgthlaFiles(LoadedFileDescriptors theDescriptors, RequestDetails theRequestDetails) {
private UploadStatistics processImgthlaFiles(LoadedFileDescriptors theDescriptors, RequestDetails theRequestDetails) {
final TermCodeSystemVersion codeSystemVersion = new TermCodeSystemVersion();
final Map<String, TermConcept> code2concept = new HashMap<>();
final List<ValueSet> valueSets = new ArrayList<>();
final List<ConceptMap> conceptMaps = new ArrayList<>();
CodeSystem imgthlaCs;
try {
String imgthlaCsString = IOUtils.toString(BaseHapiTerminologySvcImpl.class.getResourceAsStream("/ca/uhn/fhir/jpa/term/imgthla/imgthla.xml"), Charsets.UTF_8);
String imgthlaCsString = IOUtils.toString(BaseTermReadSvcImpl.class.getResourceAsStream("/ca/uhn/fhir/jpa/term/imgthla/imgthla.xml"), Charsets.UTF_8);
imgthlaCs = FhirContext.forR4().newXmlParser().parseResource(CodeSystem.class, imgthlaCsString);
} catch (IOException e) {
throw new InternalErrorException("Failed to load imgthla.xml", e);
@ -353,7 +363,7 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
int valueSetCount = valueSets.size();
int rootConceptCount = codeSystemVersion.getConcepts().size();
int conceptCount = code2concept.size();
int conceptCount = rootConceptCount;
ourLog.info("Have {} total concepts, {} root concepts, {} ValueSets", conceptCount, rootConceptCount, valueSetCount);
// remove this when fully implemented ...
@ -372,7 +382,7 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
CodeSystem loincCs;
try {
String loincCsString = IOUtils.toString(BaseHapiTerminologySvcImpl.class.getResourceAsStream("/ca/uhn/fhir/jpa/term/loinc/loinc.xml"), Charsets.UTF_8);
String loincCsString = IOUtils.toString(BaseTermReadSvcImpl.class.getResourceAsStream("/ca/uhn/fhir/jpa/term/loinc/loinc.xml"), Charsets.UTF_8);
loincCs = FhirContext.forR4().newXmlParser().parseResource(CodeSystem.class, loincCsString);
} catch (IOException e) {
throw new InternalErrorException("Failed to load loinc.xml", e);
@ -501,7 +511,7 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
retVal.setPublisher("Regenstrief Institute, Inc.");
retVal.setDescription("A value set that includes all LOINC codes");
retVal.setCopyright("This content from LOINC® is copyright © 1995 Regenstrief Institute, Inc. and the LOINC Committee, and available at no cost under the license at https://loinc.org/license/");
retVal.getCompose().addInclude().setSystem(IHapiTerminologyLoaderSvc.LOINC_URI);
retVal.getCompose().addInclude().setSystem(ITermLoaderSvc.LOINC_URI);
return retVal;
}
@ -540,7 +550,7 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
long count = circularCounter.getThenAdd();
float pct = ((float) count / rootConcepts.size()) * 100.0f;
ourLog.info(" * Scanning for circular refs - have scanned {} / {} codes ({}%)", count, rootConcepts.size(), pct);
dropCircularRefs(next, new ArrayList<>(), code2concept, circularCounter);
dropCircularRefs(next, new ArrayList<>(), code2concept);
}
codeSystemVersion.getConcepts().addAll(rootConcepts.values());
@ -555,8 +565,13 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
}
@VisibleForTesting
void setTermSvcForUnitTests(IHapiTerminologySvc theTermSvc) {
myTermSvc = theTermSvc;
void setTermDeferredStorageSvc(ITermDeferredStorageSvc theDeferredStorageSvc) {
myDeferredStorageSvc = theDeferredStorageSvc;
}
@VisibleForTesting
void setTermCodeSystemStorageSvcForUnitTests(ITermCodeSystemStorageSvc theTermCodeSystemStorageSvc) {
myCodeSystemStorageSvc = theTermCodeSystemStorageSvc;
}
private IIdType storeCodeSystem(RequestDetails theRequestDetails, final TermCodeSystemVersion theCodeSystemVersion, CodeSystem theCodeSystem, List<ValueSet> theValueSets, List<ConceptMap> theConceptMaps) {
@ -566,135 +581,14 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
List<ConceptMap> conceptMaps = ObjectUtils.defaultIfNull(theConceptMaps, Collections.emptyList());
IIdType retVal;
myTermSvc.setProcessDeferred(false);
retVal = myTermSvc.storeNewCodeSystemVersion(theCodeSystem, theCodeSystemVersion, theRequestDetails, valueSets, conceptMaps);
myTermSvc.setProcessDeferred(true);
myDeferredStorageSvc.setProcessDeferred(false);
retVal = myCodeSystemStorageSvc.storeNewCodeSystemVersion(theCodeSystem, theCodeSystemVersion, theRequestDetails, valueSets, conceptMaps);
myDeferredStorageSvc.setProcessDeferred(true);
return retVal;
}
public static class LoadedFileDescriptors implements Closeable {
private List<File> myTemporaryFiles = new ArrayList<>();
private List<IHapiTerminologyLoaderSvc.FileDescriptor> myUncompressedFileDescriptors = new ArrayList<>();
public LoadedFileDescriptors(List<IHapiTerminologyLoaderSvc.FileDescriptor> theFileDescriptors) {
try {
for (FileDescriptor next : theFileDescriptors) {
if (next.getFilename().toLowerCase().endsWith(".zip")) {
ourLog.info("Uncompressing {} into temporary files", next.getFilename());
try (InputStream inputStream = next.getInputStream()) {
ZipInputStream zis = new ZipInputStream(new BufferedInputStream(inputStream));
for (ZipEntry nextEntry; (nextEntry = zis.getNextEntry()) != null; ) {
BOMInputStream fis = new BOMInputStream(zis);
File nextTemporaryFile = File.createTempFile("hapifhir", ".tmp");
nextTemporaryFile.deleteOnExit();
FileOutputStream fos = new FileOutputStream(nextTemporaryFile, false);
IOUtils.copy(fis, fos);
String nextEntryFileName = nextEntry.getName();
myUncompressedFileDescriptors.add(new FileDescriptor() {
@Override
public String getFilename() {
return nextEntryFileName;
}
@Override
public InputStream getInputStream() {
try {
return new FileInputStream(nextTemporaryFile);
} catch (FileNotFoundException e) {
throw new InternalErrorException(e);
}
}
});
myTemporaryFiles.add(nextTemporaryFile);
}
}
} else {
myUncompressedFileDescriptors.add(next);
}
}
} catch (Exception e) {
close();
throw new InternalErrorException(e);
}
}
boolean hasFile(String theFilename) {
return myUncompressedFileDescriptors
.stream()
.map(t -> t.getFilename().replaceAll(".*[\\\\/]", "")) // Strip the path from the filename
.anyMatch(t -> t.equals(theFilename));
}
@Override
public void close() {
for (File next : myTemporaryFiles) {
FileUtils.deleteQuietly(next);
}
}
List<IHapiTerminologyLoaderSvc.FileDescriptor> getUncompressedFileDescriptors() {
return myUncompressedFileDescriptors;
}
private List<String> notFound(List<String> theExpectedFilenameFragments) {
Set<String> foundFragments = new HashSet<>();
for (String nextExpected : theExpectedFilenameFragments) {
for (FileDescriptor next : myUncompressedFileDescriptors) {
if (next.getFilename().contains(nextExpected)) {
foundFragments.add(nextExpected);
break;
}
}
}
ArrayList<String> notFoundFileNameFragments = new ArrayList<>(theExpectedFilenameFragments);
notFoundFileNameFragments.removeAll(foundFragments);
return notFoundFileNameFragments;
}
private void verifyMandatoryFilesExist(List<String> theExpectedFilenameFragments) {
List<String> notFound = notFound(theExpectedFilenameFragments);
if (!notFound.isEmpty()) {
throw new UnprocessableEntityException("Could not find the following mandatory files in input: " + notFound);
}
}
private void verifyOptionalFilesExist(List<String> theExpectedFilenameFragments) {
List<String> notFound = notFound(theExpectedFilenameFragments);
if (!notFound.isEmpty()) {
ourLog.warn("Could not find the following optional files: " + notFound);
}
}
}
@Nonnull
public static Map<String, TermConcept> processCustomTerminologyFiles(LoadedFileDescriptors theDescriptors, TermCodeSystemVersion theCsv) {
IRecordHandler handler;// Concept File
final Map<String, TermConcept> code2concept = new HashMap<>();
handler = new ConceptHandler(code2concept, theCsv);
iterateOverZipFile(theDescriptors, CUSTOM_CONCEPTS_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
// Hierarchy
if (theDescriptors.hasFile(CUSTOM_HIERARCHY_FILE)) {
handler = new HierarchyHandler(code2concept);
iterateOverZipFile(theDescriptors, CUSTOM_HIERARCHY_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
}
// Add root concepts to CodeSystemVersion
for (TermConcept nextConcept : code2concept.values()) {
if (nextConcept.getParents().isEmpty()) {
theCsv.getConcepts().add(nextConcept);
}
}
return code2concept;
}
private static void iterateOverZipFile(LoadedFileDescriptors theDescriptors, String theFileNamePart, IRecordHandler theHandler, char theDelimiter, QuoteMode theQuoteMode, boolean theIsPartialFilename) {
public static void iterateOverZipFile(LoadedFileDescriptors theDescriptors, String theFileNamePart, IRecordHandler theHandler, char theDelimiter, QuoteMode theQuoteMode, boolean theIsPartialFilename) {
boolean foundMatch = false;
for (FileDescriptor nextZipBytes : theDescriptors.getUncompressedFileDescriptors()) {
@ -748,9 +642,12 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
}
@Nonnull
public static CSVParser newCsvRecords(char theDelimiter, QuoteMode theQuoteMode, Reader theReader) throws IOException {
private static CSVParser newCsvRecords(char theDelimiter, QuoteMode theQuoteMode, Reader theReader) throws IOException {
CSVParser parsed;
CSVFormat format = CSVFormat.newFormat(theDelimiter).withFirstRecordAsHeader();
CSVFormat format = CSVFormat
.newFormat(theDelimiter)
.withFirstRecordAsHeader()
.withTrim();
if (theQuoteMode != null) {
format = format.withQuote('"').withQuoteMode(theQuoteMode);
}
@ -769,12 +666,11 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
return retVal;
}
public static TermConcept getOrCreateConcept(TermCodeSystemVersion codeSystemVersion, Map<String, TermConcept> id2concept, String id) {
public static TermConcept getOrCreateConcept(Map<String, TermConcept> id2concept, String id) {
TermConcept concept = id2concept.get(id);
if (concept == null) {
concept = new TermConcept();
id2concept.put(id, concept);
concept.setCodeSystemVersion(codeSystemVersion);
}
return concept;
}

21
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcDstu2.java → hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermReadSvcDstu2.java
View File

@ -25,9 +25,7 @@ import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import org.hl7.fhir.instance.hapi.validation.IValidationSupport;
import org.hl7.fhir.instance.model.api.IBaseDatatype;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.ConceptMap;
import org.hl7.fhir.r4.model.ValueSet;
import org.springframework.beans.factory.annotation.Autowired;
@ -36,7 +34,7 @@ import java.util.List;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class HapiTerminologySvcDstu2 extends BaseHapiTerminologySvcImpl {
public class TermReadSvcDstu2 extends BaseTermReadSvcImpl {
@Autowired
private IValidationSupport myValidationSupport;
@ -65,22 +63,7 @@ public class HapiTerminologySvcDstu2 extends BaseHapiTerminologySvcImpl {
}
@Override
protected IIdType createOrUpdateCodeSystem(CodeSystem theCodeSystemResource) {
throw new UnsupportedOperationException();
}
@Override
protected void createOrUpdateConceptMap(ConceptMap theNextConceptMap) {
throw new UnsupportedOperationException();
}
@Override
protected void createOrUpdateValueSet(ValueSet theValueSet) {
throw new UnsupportedOperationException();
}
@Override
protected CodeSystem getCodeSystemFromContext(String theSystem) {
public CodeSystem getCodeSystemFromContext(String theSystem) {
return null;
}

68
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcDstu3.java → hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermReadSvcDstu3.java
View File

@ -2,13 +2,13 @@ package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
import ca.uhn.fhir.jpa.term.api.ITermReadSvcDstu3;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.util.CoverageIgnore;
import ca.uhn.fhir.util.UrlUtil;
import ca.uhn.fhir.util.ValidateUtil;
import org.hl7.fhir.convertors.VersionConvertor_30_40;
import org.hl7.fhir.dstu3.hapi.ctx.IValidationSupport;
@ -19,7 +19,6 @@ import org.hl7.fhir.dstu3.model.ValueSet.ValueSetExpansionComponent;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.instance.model.api.IBaseDatatype;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
@ -32,7 +31,6 @@ import java.util.Collections;
import java.util.List;
import java.util.Optional;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
/*
@ -55,27 +53,22 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
* #L%
*/
public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvcImpl implements IValidationSupport, IHapiTerminologySvcDstu3 {
public class TermReadSvcDstu3 extends BaseTermReadSvcImpl implements IValidationSupport, ITermReadSvcDstu3 {
@Autowired
@Qualifier("myValueSetDaoDstu3")
private IFhirResourceDao<ValueSet> myValueSetResourceDao;
@Autowired
@Qualifier("myConceptMapDaoDstu3")
private IFhirResourceDao<ConceptMap> myConceptMapResourceDao;
@Autowired
private IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> myCodeSystemResourceDao;
@Autowired
private IValidationSupport myValidationSupport;
@Autowired
private IHapiTerminologySvc myTerminologySvc;
private ITermReadSvc myTerminologySvc;
@Autowired
private PlatformTransactionManager myTransactionManager;
/**
* Constructor
*/
public HapiTerminologySvcDstu3() {
public TermReadSvcDstu3() {
super();
}
@ -102,55 +95,6 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvcImpl implemen
return false;
}
@Override
protected IIdType createOrUpdateCodeSystem(org.hl7.fhir.r4.model.CodeSystem theCodeSystemResource) {
CodeSystem resourceToStore;
try {
resourceToStore = VersionConvertor_30_40.convertCodeSystem(theCodeSystemResource);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
validateCodeSystemForStorage(theCodeSystemResource);
if (isBlank(resourceToStore.getIdElement().getIdPart())) {
String matchUrl = "CodeSystem?url=" + UrlUtil.escapeUrlParam(theCodeSystemResource.getUrl());
return myCodeSystemResourceDao.update(resourceToStore, matchUrl).getId();
} else {
return myCodeSystemResourceDao.update(resourceToStore).getId();
}
}
@Override
protected void createOrUpdateConceptMap(org.hl7.fhir.r4.model.ConceptMap theConceptMap) {
ConceptMap resourceToStore;
try {
resourceToStore = VersionConvertor_30_40.convertConceptMap(theConceptMap);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
if (isBlank(resourceToStore.getIdElement().getIdPart())) {
String matchUrl = "ConceptMap?url=" + UrlUtil.escapeUrlParam(theConceptMap.getUrl());
myConceptMapResourceDao.update(resourceToStore, matchUrl);
} else {
myConceptMapResourceDao.update(resourceToStore);
}
}
@Override
protected void createOrUpdateValueSet(org.hl7.fhir.r4.model.ValueSet theValueSet) {
ValueSet valueSetDstu3;
try {
valueSetDstu3 = VersionConvertor_30_40.convertValueSet(theValueSet);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
if (isBlank(valueSetDstu3.getIdElement().getIdPart())) {
String matchUrl = "ValueSet?url=" + UrlUtil.escapeUrlParam(theValueSet.getUrl());
myValueSetResourceDao.update(valueSetDstu3, matchUrl);
} else {
myValueSetResourceDao.update(valueSetDstu3);
}
}
@Override
public ValueSetExpansionComponent expandValueSet(FhirContext theContext, ConceptSetComponent theInclude) {
@ -303,7 +247,7 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvcImpl implemen
}
@Override
protected org.hl7.fhir.r4.model.CodeSystem getCodeSystemFromContext(String theSystem) {
public org.hl7.fhir.r4.model.CodeSystem getCodeSystemFromContext(String theSystem) {
CodeSystem codeSystem = myValidationSupport.fetchCodeSystem(myContext, theSystem);
try {
return VersionConvertor_30_40.convertCodeSystem(codeSystem);

44
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcR4.java → hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermReadSvcR4.java
View File

@ -5,11 +5,10 @@ import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.term.api.ITermReadSvcR4;
import ca.uhn.fhir.util.CoverageIgnore;
import ca.uhn.fhir.util.UrlUtil;
import org.hl7.fhir.instance.model.api.IBaseDatatype;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.hapi.ctx.IValidationSupport;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.CodeSystem.ConceptDefinitionComponent;
@ -27,7 +26,6 @@ import java.util.Collections;
import java.util.List;
import java.util.Optional;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
/*
@ -50,14 +48,8 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
* #L%
*/
public class HapiTerminologySvcR4 extends BaseHapiTerminologySvcImpl implements IHapiTerminologySvcR4 {
public class TermReadSvcR4 extends BaseTermReadSvcImpl implements ITermReadSvcR4 {
@Autowired
@Qualifier("myConceptMapDaoR4")
private IFhirResourceDao<ConceptMap> myConceptMapResourceDao;
@Autowired
@Qualifier("myCodeSystemDaoR4")
private IFhirResourceDao<CodeSystem> myCodeSystemResourceDao;
@Autowired
@Qualifier("myValueSetDaoR4")
private IFhirResourceDao<ValueSet> myValueSetResourceDao;
@ -89,36 +81,6 @@ public class HapiTerminologySvcR4 extends BaseHapiTerminologySvcImpl implements
return false;
}
@Override
protected IIdType createOrUpdateCodeSystem(org.hl7.fhir.r4.model.CodeSystem theCodeSystemResource) {
validateCodeSystemForStorage(theCodeSystemResource);
if (isBlank(theCodeSystemResource.getIdElement().getIdPart())) {
String matchUrl = "CodeSystem?url=" + UrlUtil.escapeUrlParam(theCodeSystemResource.getUrl());
return myCodeSystemResourceDao.update(theCodeSystemResource, matchUrl).getId();
} else {
return myCodeSystemResourceDao.update(theCodeSystemResource).getId();
}
}
@Override
protected void createOrUpdateConceptMap(org.hl7.fhir.r4.model.ConceptMap theConceptMap) {
if (isBlank(theConceptMap.getIdElement().getIdPart())) {
String matchUrl = "ConceptMap?url=" + UrlUtil.escapeUrlParam(theConceptMap.getUrl());
myConceptMapResourceDao.update(theConceptMap, matchUrl);
} else {
myConceptMapResourceDao.update(theConceptMap);
}
}
@Override
protected void createOrUpdateValueSet(org.hl7.fhir.r4.model.ValueSet theValueSet) {
if (isBlank(theValueSet.getIdElement().getIdPart())) {
String matchUrl = "ValueSet?url=" + UrlUtil.escapeUrlParam(theValueSet.getUrl());
myValueSetResourceDao.update(theValueSet, matchUrl);
} else {
myValueSetResourceDao.update(theValueSet);
}
}
@Override
public List<VersionIndependentConcept> expandValueSet(String theValueSet) {
@ -233,7 +195,7 @@ public class HapiTerminologySvcR4 extends BaseHapiTerminologySvcImpl implements
}
@Override
protected CodeSystem getCodeSystemFromContext(String theSystem) {
public CodeSystem getCodeSystemFromContext(String theSystem) {
return myValidationSupport.fetchCodeSystem(myContext, theSystem);
}

52
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcR5.java → hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermReadSvcR5.java
View File

@ -5,12 +5,11 @@ import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.term.api.ITermReadSvcR5;
import ca.uhn.fhir.util.CoverageIgnore;
import ca.uhn.fhir.util.UrlUtil;
import ca.uhn.fhir.util.ValidateUtil;
import org.hl7.fhir.instance.model.api.IBaseDatatype;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r5.hapi.ctx.IValidationSupport;
import org.hl7.fhir.r5.model.*;
import org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionComponent;
@ -28,7 +27,6 @@ import java.util.Collections;
import java.util.List;
import java.util.Optional;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
/*
@ -51,14 +49,8 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
* #L%
*/
public class HapiTerminologySvcR5 extends BaseHapiTerminologySvcImpl implements IValidationSupport, IHapiTerminologySvcR5 {
public class TermReadSvcR5 extends BaseTermReadSvcImpl implements IValidationSupport, ITermReadSvcR5 {
@Autowired
@Qualifier("myConceptMapDaoR5")
private IFhirResourceDao<ConceptMap> myConceptMapResourceDao;
@Autowired
@Qualifier("myCodeSystemDaoR5")
private IFhirResourceDao<CodeSystem> myCodeSystemResourceDao;
@Autowired
@Qualifier("myValueSetDaoR5")
private IFhirResourceDao<ValueSet> myValueSetResourceDao;
@ -90,44 +82,6 @@ public class HapiTerminologySvcR5 extends BaseHapiTerminologySvcImpl implements
return false;
}
@Override
protected IIdType createOrUpdateCodeSystem(org.hl7.fhir.r4.model.CodeSystem theCodeSystemResource) {
validateCodeSystemForStorage(theCodeSystemResource);
CodeSystem codeSystemR4 = org.hl7.fhir.convertors.conv40_50.CodeSystem.convertCodeSystem(theCodeSystemResource);
if (isBlank(theCodeSystemResource.getIdElement().getIdPart())) {
String matchUrl = "CodeSystem?url=" + UrlUtil.escapeUrlParam(theCodeSystemResource.getUrl());
return myCodeSystemResourceDao.update(codeSystemR4, matchUrl).getId();
} else {
return myCodeSystemResourceDao.update(codeSystemR4).getId();
}
}
@Override
protected void createOrUpdateConceptMap(org.hl7.fhir.r4.model.ConceptMap theConceptMap) {
ConceptMap conceptMapR4 = org.hl7.fhir.convertors.conv40_50.ConceptMap.convertConceptMap(theConceptMap);
if (isBlank(theConceptMap.getIdElement().getIdPart())) {
String matchUrl = "ConceptMap?url=" + UrlUtil.escapeUrlParam(theConceptMap.getUrl());
myConceptMapResourceDao.update(conceptMapR4, matchUrl);
} else {
myConceptMapResourceDao.update(conceptMapR4);
}
}
@Override
protected void createOrUpdateValueSet(org.hl7.fhir.r4.model.ValueSet theValueSet) {
ValueSet valueSetR4 = org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(theValueSet);
if (isBlank(theValueSet.getIdElement().getIdPart())) {
String matchUrl = "ValueSet?url=" + UrlUtil.escapeUrlParam(theValueSet.getUrl());
myValueSetResourceDao.update(valueSetR4, matchUrl);
} else {
myValueSetResourceDao.update(valueSetR4);
}
}
@Override
public List<VersionIndependentConcept> expandValueSet(String theValueSet) {
@ -244,7 +198,7 @@ public class HapiTerminologySvcR5 extends BaseHapiTerminologySvcImpl implements
}
@Override
protected org.hl7.fhir.r4.model.CodeSystem getCodeSystemFromContext(String theSystem) {
public org.hl7.fhir.r4.model.CodeSystem getCodeSystemFromContext(String theSystem) {
CodeSystem codeSystemR5 = myValidationSupport.fetchCodeSystem(myContext, theSystem);
return org.hl7.fhir.convertors.conv40_50.CodeSystem.convertCodeSystem(codeSystemR5);
}

169
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermReindexingSvcImpl.java Normal file
View File

@ -0,0 +1,169 @@
package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.jpa.dao.data.ITermConceptDao;
import ca.uhn.fhir.jpa.dao.data.ITermConceptParentChildLinkDao;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.model.sched.FireAtIntervalJob;
import ca.uhn.fhir.jpa.model.sched.ISchedulerService;
import ca.uhn.fhir.jpa.model.sched.ScheduledJobDefinition;
import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
import ca.uhn.fhir.jpa.term.api.ITermReindexingSvc;
import ca.uhn.fhir.util.StopWatch;
import com.google.common.annotations.VisibleForTesting;
import com.google.common.collect.ArrayListMultimap;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.time.DateUtils;
import org.quartz.JobExecutionContext;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.data.domain.Page;
import org.springframework.data.domain.PageRequest;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.TransactionDefinition;
import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.support.TransactionCallbackWithoutResult;
import org.springframework.transaction.support.TransactionTemplate;
import javax.annotation.PostConstruct;
import java.util.Collection;
import java.util.List;
import static org.apache.commons.lang3.StringUtils.isBlank;
public class TermReindexingSvcImpl implements ITermReindexingSvc {
private static final Logger ourLog = LoggerFactory.getLogger(TermReindexingSvcImpl.class);
private static final long SCHEDULE_INTERVAL_MILLIS = DateUtils.MILLIS_PER_MINUTE;
private static boolean ourForceSaveDeferredAlwaysForUnitTest;
@Autowired
protected ITermConceptDao myConceptDao;
private ArrayListMultimap<Long, Long> myChildToParentPidCache;
@Autowired
private PlatformTransactionManager myTransactionMgr;
@Autowired
private ITermConceptParentChildLinkDao myConceptParentChildLinkDao;
@Autowired
private ITermCodeSystemStorageSvc myConceptStorageSvc;
@Autowired
private ITermDeferredStorageSvc myDeferredStorageSvc;
@Autowired
private ISchedulerService mySchedulerService;
@Override
public void processReindexing() {
if (myDeferredStorageSvc.isStorageQueueEmpty() == false && !ourForceSaveDeferredAlwaysForUnitTest) {
return;
}
TransactionTemplate tt = new TransactionTemplate(myTransactionMgr);
tt.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRES_NEW);
tt.execute(new TransactionCallbackWithoutResult() {
private void createParentsString(StringBuilder theParentsBuilder, Long theConceptPid) {
Validate.notNull(theConceptPid, "theConceptPid must not be null");
List<Long> parents = myChildToParentPidCache.get(theConceptPid);
if (parents.contains(-1L)) {
return;
} else if (parents.isEmpty()) {
Collection<Long> parentLinks = myConceptParentChildLinkDao.findAllWithChild(theConceptPid);
if (parentLinks.isEmpty()) {
myChildToParentPidCache.put(theConceptPid, -1L);
ourLog.info("Found {} parent concepts of concept {} (cache has {})", 0, theConceptPid, myChildToParentPidCache.size());
return;
} else {
for (Long next : parentLinks) {
myChildToParentPidCache.put(theConceptPid, next);
}
int parentCount = myChildToParentPidCache.get(theConceptPid).size();
ourLog.info("Found {} parent concepts of concept {} (cache has {})", parentCount, theConceptPid, myChildToParentPidCache.size());
}
}
for (Long nextParent : parents) {
if (theParentsBuilder.length() > 0) {
theParentsBuilder.append(' ');
}
theParentsBuilder.append(nextParent);
createParentsString(theParentsBuilder, nextParent);
}
}
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
int maxResult = 1000;
Page<TermConcept> concepts = myConceptDao.findResourcesRequiringReindexing(PageRequest.of(0, maxResult));
if (!concepts.hasContent()) {
if (myChildToParentPidCache != null) {
ourLog.info("Clearing parent concept cache");
myChildToParentPidCache = null;
}
return;
}
if (myChildToParentPidCache == null) {
myChildToParentPidCache = ArrayListMultimap.create();
}
ourLog.info("Indexing {} / {} concepts", concepts.getContent().size(), concepts.getTotalElements());
int count = 0;
StopWatch stopwatch = new StopWatch();
for (TermConcept nextConcept : concepts) {
if (isBlank(nextConcept.getParentPidsAsString())) {
StringBuilder parentsBuilder = new StringBuilder();
createParentsString(parentsBuilder, nextConcept.getId());
nextConcept.setParentPids(parentsBuilder.toString());
}
myConceptStorageSvc.saveConcept(nextConcept);
count++;
}
ourLog.info("Indexed {} / {} concepts in {}ms - Avg {}ms / resource", count, concepts.getContent().size(), stopwatch.getMillis(), stopwatch.getMillisPerOperation(count));
}
});
}
@PostConstruct
public void registerScheduledJob() {
// Register scheduled job to save deferred concepts
// In the future it would be great to make this a cluster-aware task somehow
ScheduledJobDefinition jobDefinition = new ScheduledJobDefinition();
jobDefinition.setId(TermReindexingSvcImpl.class.getName() + "_reindex");
jobDefinition.setJobClass(SaveDeferredJob.class);
mySchedulerService.scheduleFixedDelay(SCHEDULE_INTERVAL_MILLIS, false, jobDefinition);
}
public static class SaveDeferredJob extends FireAtIntervalJob {
@Autowired
private ITermDeferredStorageSvc myTerminologySvc;
/**
* Constructor
*/
public SaveDeferredJob() {
super(SCHEDULE_INTERVAL_MILLIS);
}
@Override
protected void doExecute(JobExecutionContext theContext) {
myTerminologySvc.saveDeferred();
}
}
/**
* This method is present only for unit tests, do not call from client code
*/
@VisibleForTesting
public static void setForceSaveDeferredAlwaysForUnitTest(boolean theForceSaveDeferredAlwaysForUnitTest) {
ourForceSaveDeferredAlwaysForUnitTest = theForceSaveDeferredAlwaysForUnitTest;
}
}

26
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermVersionAdapterSvcDstu2.java Normal file
View File

@ -0,0 +1,26 @@
package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.ConceptMap;
import org.hl7.fhir.r4.model.ValueSet;
public class TermVersionAdapterSvcDstu2 implements ITermVersionAdapterSvc {
@Override
public IIdType createOrUpdateCodeSystem(CodeSystem theCodeSystemResource) {
throw new UnsupportedOperationException();
}
@Override
public void createOrUpdateConceptMap(ConceptMap theNextConceptMap) {
throw new UnsupportedOperationException();
}
@Override
public void createOrUpdateValueSet(ValueSet theValueSet) {
throw new UnsupportedOperationException();
}
}

101
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermVersionAdapterSvcDstu3.java Normal file
View File

@ -0,0 +1,101 @@
package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.util.UrlUtil;
import org.hl7.fhir.convertors.VersionConvertor_30_40;
import org.hl7.fhir.dstu3.model.CodeSystem;
import org.hl7.fhir.dstu3.model.ConceptMap;
import org.hl7.fhir.dstu3.model.ValueSet;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.instance.model.api.IIdType;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.ApplicationContext;
import org.springframework.context.event.ContextRefreshedEvent;
import org.springframework.context.event.ContextStartedEvent;
import org.springframework.context.event.EventListener;
import static org.apache.commons.lang3.StringUtils.isBlank;
public class TermVersionAdapterSvcDstu3 extends BaseTermVersionAdapterSvcImpl implements ITermVersionAdapterSvc {
private IFhirResourceDao<ConceptMap> myConceptMapResourceDao;
private IFhirResourceDao<CodeSystem> myCodeSystemResourceDao;
private IFhirResourceDao<ValueSet> myValueSetResourceDao;
@Autowired
private ApplicationContext myAppCtx;
public TermVersionAdapterSvcDstu3() {
super();
}
/**
* Initialize the beans that are used by this service.
*
* Note: There is a circular dependency here where the CodeSystem DAO
* needs terminology services, and the term services need the CodeSystem DAO.
* So we look these up in a refresh event instead of just autowiring them
* in order to avoid weird circular reference errors.
*/
@SuppressWarnings({"unchecked", "unused"})
@EventListener
public void start(ContextRefreshedEvent theEvent) {
myCodeSystemResourceDao = (IFhirResourceDao<CodeSystem>) myAppCtx.getBean("myCodeSystemDaoDstu3");
myValueSetResourceDao = (IFhirResourceDao<ValueSet>) myAppCtx.getBean("myValueSetDaoDstu3");
myConceptMapResourceDao = (IFhirResourceDao<ConceptMap>) myAppCtx.getBean("myConceptMapDaoDstu3");
}
@Override
public IIdType createOrUpdateCodeSystem(org.hl7.fhir.r4.model.CodeSystem theCodeSystemResource) {
CodeSystem resourceToStore;
try {
resourceToStore = VersionConvertor_30_40.convertCodeSystem(theCodeSystemResource);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
validateCodeSystemForStorage(theCodeSystemResource);
if (isBlank(resourceToStore.getIdElement().getIdPart())) {
String matchUrl = "CodeSystem?url=" + UrlUtil.escapeUrlParam(theCodeSystemResource.getUrl());
return myCodeSystemResourceDao.update(resourceToStore, matchUrl).getId();
} else {
return myCodeSystemResourceDao.update(resourceToStore).getId();
}
}
@Override
public void createOrUpdateConceptMap(org.hl7.fhir.r4.model.ConceptMap theConceptMap) {
ConceptMap resourceToStore;
try {
resourceToStore = VersionConvertor_30_40.convertConceptMap(theConceptMap);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
if (isBlank(resourceToStore.getIdElement().getIdPart())) {
String matchUrl = "ConceptMap?url=" + UrlUtil.escapeUrlParam(theConceptMap.getUrl());
myConceptMapResourceDao.update(resourceToStore, matchUrl);
} else {
myConceptMapResourceDao.update(resourceToStore);
}
}
@Override
public void createOrUpdateValueSet(org.hl7.fhir.r4.model.ValueSet theValueSet) {
ValueSet valueSetDstu3;
try {
valueSetDstu3 = VersionConvertor_30_40.convertValueSet(theValueSet);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
if (isBlank(valueSetDstu3.getIdElement().getIdPart())) {
String matchUrl = "ValueSet?url=" + UrlUtil.escapeUrlParam(theValueSet.getUrl());
myValueSetResourceDao.update(valueSetDstu3, matchUrl);
} else {
myValueSetResourceDao.update(valueSetDstu3);
}
}
}

75
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermVersionAdapterSvcR4.java Normal file
View File

@ -0,0 +1,75 @@
package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
import ca.uhn.fhir.util.UrlUtil;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.ConceptMap;
import org.hl7.fhir.r4.model.ValueSet;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.context.ApplicationContext;
import org.springframework.context.event.ContextRefreshedEvent;
import org.springframework.context.event.EventListener;
import javax.annotation.PostConstruct;
import static org.apache.commons.lang3.StringUtils.isBlank;
public class TermVersionAdapterSvcR4 extends BaseTermVersionAdapterSvcImpl implements ITermVersionAdapterSvc {
private IFhirResourceDao<ConceptMap> myConceptMapResourceDao;
private IFhirResourceDao<CodeSystem> myCodeSystemResourceDao;
private IFhirResourceDao<ValueSet> myValueSetResourceDao;
@Autowired
private ApplicationContext myAppCtx;
/**
* Initialize the beans that are used by this service.
*
* Note: There is a circular dependency here where the CodeSystem DAO
* needs terminology services, and the term services need the CodeSystem DAO.
* So we look these up in a refresh event instead of just autowiring them
* in order to avoid weird circular reference errors.
*/
@SuppressWarnings({"unchecked", "unused"})
@EventListener
public void start(ContextRefreshedEvent theEvent) {
myCodeSystemResourceDao = (IFhirResourceDao<CodeSystem>) myAppCtx.getBean("myCodeSystemDaoR4");
myValueSetResourceDao = (IFhirResourceDao<ValueSet>) myAppCtx.getBean("myValueSetDaoR4");
myConceptMapResourceDao = (IFhirResourceDao<ConceptMap>) myAppCtx.getBean("myConceptMapDaoR4");
}
@Override
public IIdType createOrUpdateCodeSystem(org.hl7.fhir.r4.model.CodeSystem theCodeSystemResource) {
validateCodeSystemForStorage(theCodeSystemResource);
if (isBlank(theCodeSystemResource.getIdElement().getIdPart())) {
String matchUrl = "CodeSystem?url=" + UrlUtil.escapeUrlParam(theCodeSystemResource.getUrl());
return myCodeSystemResourceDao.update(theCodeSystemResource, matchUrl).getId();
} else {
return myCodeSystemResourceDao.update(theCodeSystemResource).getId();
}
}
@Override
public void createOrUpdateConceptMap(org.hl7.fhir.r4.model.ConceptMap theConceptMap) {
if (isBlank(theConceptMap.getIdElement().getIdPart())) {
String matchUrl = "ConceptMap?url=" + UrlUtil.escapeUrlParam(theConceptMap.getUrl());
myConceptMapResourceDao.update(theConceptMap, matchUrl);
} else {
myConceptMapResourceDao.update(theConceptMap);
}
}
@Override
public void createOrUpdateValueSet(org.hl7.fhir.r4.model.ValueSet theValueSet) {
if (isBlank(theValueSet.getIdElement().getIdPart())) {
String matchUrl = "ValueSet?url=" + UrlUtil.escapeUrlParam(theValueSet.getUrl());
myValueSetResourceDao.update(theValueSet, matchUrl);
} else {
myValueSetResourceDao.update(theValueSet);
}
}
}

80
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermVersionAdapterSvcR5.java Normal file
View File

@ -0,0 +1,80 @@
package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
import ca.uhn.fhir.util.UrlUtil;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r5.model.CodeSystem;
import org.hl7.fhir.r5.model.ConceptMap;
import org.hl7.fhir.r5.model.ValueSet;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.ApplicationContext;
import org.springframework.context.event.ContextRefreshedEvent;
import org.springframework.context.event.EventListener;
import static org.apache.commons.lang3.StringUtils.isBlank;
public class TermVersionAdapterSvcR5 extends BaseTermVersionAdapterSvcImpl implements ITermVersionAdapterSvc {
private IFhirResourceDao<ConceptMap> myConceptMapResourceDao;
private IFhirResourceDao<CodeSystem> myCodeSystemResourceDao;
private IFhirResourceDao<ValueSet> myValueSetResourceDao;
@Autowired
private ApplicationContext myAppCtx;
/**
* Initialize the beans that are used by this service.
*
* Note: There is a circular dependency here where the CodeSystem DAO
* needs terminology services, and the term services need the CodeSystem DAO.
* So we look these up in a refresh event instead of just autowiring them
* in order to avoid weird circular reference errors.
*/
@SuppressWarnings({"unchecked", "unused"})
@EventListener
public void start(ContextRefreshedEvent theEvent) {
myCodeSystemResourceDao = (IFhirResourceDao<CodeSystem>) myAppCtx.getBean("myCodeSystemDaoR5");
myValueSetResourceDao = (IFhirResourceDao<ValueSet>) myAppCtx.getBean("myValueSetDaoR5");
myConceptMapResourceDao = (IFhirResourceDao<ConceptMap>) myAppCtx.getBean("myConceptMapDaoR5");
}
@Override
public IIdType createOrUpdateCodeSystem(org.hl7.fhir.r4.model.CodeSystem theCodeSystemResource) {
validateCodeSystemForStorage(theCodeSystemResource);
CodeSystem codeSystemR4 = org.hl7.fhir.convertors.conv40_50.CodeSystem.convertCodeSystem(theCodeSystemResource);
if (isBlank(theCodeSystemResource.getIdElement().getIdPart())) {
String matchUrl = "CodeSystem?url=" + UrlUtil.escapeUrlParam(theCodeSystemResource.getUrl());
return myCodeSystemResourceDao.update(codeSystemR4, matchUrl).getId();
} else {
return myCodeSystemResourceDao.update(codeSystemR4).getId();
}
}
@Override
public void createOrUpdateConceptMap(org.hl7.fhir.r4.model.ConceptMap theConceptMap) {
ConceptMap conceptMapR4 = org.hl7.fhir.convertors.conv40_50.ConceptMap.convertConceptMap(theConceptMap);
if (isBlank(theConceptMap.getIdElement().getIdPart())) {
String matchUrl = "ConceptMap?url=" + UrlUtil.escapeUrlParam(theConceptMap.getUrl());
myConceptMapResourceDao.update(conceptMapR4, matchUrl);
} else {
myConceptMapResourceDao.update(conceptMapR4);
}
}
@Override
public void createOrUpdateValueSet(org.hl7.fhir.r4.model.ValueSet theValueSet) {
ValueSet valueSetR4 = org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(theValueSet);
if (isBlank(theValueSet.getIdElement().getIdPart())) {
String matchUrl = "ValueSet?url=" + UrlUtil.escapeUrlParam(theValueSet.getUrl());
myValueSetResourceDao.update(valueSetR4, matchUrl);
} else {
myValueSetResourceDao.update(valueSetR4);
}
}
}

30
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/UploadStatistics.java Normal file
View File

@ -0,0 +1,30 @@
package ca.uhn.fhir.jpa.term;
import org.hl7.fhir.instance.model.api.IIdType;
public class UploadStatistics {
private final IIdType myTarget;
private int myUpdatedConceptCount;
public UploadStatistics(IIdType theTarget) {
this(0, theTarget);
}
public UploadStatistics(int theUpdatedConceptCount, IIdType theTarget) {
myUpdatedConceptCount = theUpdatedConceptCount;
myTarget = theTarget;
}
public void incrementUpdatedConceptCount() {
myUpdatedConceptCount++;
}
public int getUpdatedConceptCount() {
return myUpdatedConceptCount;
}
public IIdType getTarget() {
return myTarget;
}
}

39
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/api/ITermCodeSystemStorageSvc.java Normal file
View File

@ -0,0 +1,39 @@
package ca.uhn.fhir.jpa.term.api;
import ca.uhn.fhir.jpa.entity.TermCodeSystem;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.term.UploadStatistics;
import ca.uhn.fhir.jpa.term.custom.CustomTerminologySet;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.ValueSet;
import java.util.List;
/**
* This service handles writes to the CodeSystem/Concept tables within the terminology services
*/
public interface ITermCodeSystemStorageSvc {
void deleteCodeSystem(TermCodeSystem theCodeSystem);
void storeNewCodeSystemVersion(Long theCodeSystemResourcePid, String theSystemUri, String theSystemName, String theSystemVersionId, TermCodeSystemVersion theCodeSystemVersion, ResourceTable theCodeSystemResourceTable);
/**
* @return Returns the ID of the created/updated code system
*/
IIdType storeNewCodeSystemVersion(org.hl7.fhir.r4.model.CodeSystem theCodeSystemResource, TermCodeSystemVersion theCodeSystemVersion, RequestDetails theRequestDetails, List<ValueSet> theValueSets, List<org.hl7.fhir.r4.model.ConceptMap> theConceptMaps);
void storeNewCodeSystemVersionIfNeeded(CodeSystem theCodeSystem, ResourceTable theResourceEntity);
UploadStatistics applyDeltaCodeSystemsAdd(String theSystem, CustomTerminologySet theAdditions);
UploadStatistics applyDeltaCodeSystemsRemove(String theSystem, CustomTerminologySet theRemovals);
int saveConcept(TermConcept theNextConcept);
Long getValueSetResourcePid(IIdType theIdElement);
}

33
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/api/ITermDeferredStorageSvc.java Normal file
View File

@ -0,0 +1,33 @@
package ca.uhn.fhir.jpa.term.api;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
import org.hl7.fhir.r4.model.ConceptMap;
import org.hl7.fhir.r4.model.ValueSet;
import java.util.List;
/**
* This service handles processing "deferred" concept writes, meaning concepts that have neen
* queued for storage because there are too many of them to handle in a single transaction.
*/
public interface ITermDeferredStorageSvc {
void saveDeferred();
boolean isStorageQueueEmpty();
/**
* This is mostly for unit tests - we can disable processing of deferred concepts
* by changing this flag
*/
void setProcessDeferred(boolean theProcessDeferred);
void addConceptToStorageQueue(TermConcept theConcept);
void addConceptLinkToStorageQueue(TermConceptParentChildLink theConceptLink);
void addConceptMapsToStorageQueue(List<ConceptMap> theConceptMaps);
void addValueSetsToStorageQueue(List<ValueSet> theValueSets);
}

43
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/IHapiTerminologyLoaderSvc.java → hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/api/ITermLoaderSvc.java
View File

@ -1,4 +1,4 @@
package ca.uhn.fhir.jpa.term;
package ca.uhn.fhir.jpa.term.api;
/*
* #%L
@ -20,13 +20,18 @@ package ca.uhn.fhir.jpa.term;
* #L%
*/
import ca.uhn.fhir.jpa.term.UploadStatistics;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import org.hl7.fhir.instance.model.api.IIdType;
import java.io.ByteArrayInputStream;
import java.io.InputStream;
import java.util.List;
public interface IHapiTerminologyLoaderSvc {
/**
* This service handles bulk loading concepts into the terminology service concept tables
* using any of several predefined input formats
*/
public interface ITermLoaderSvc {
String IMGTHLA_URI = "http://www.ebi.ac.uk/ipd/imgt/hla";
String LOINC_URI = "http://loinc.org";
@ -39,9 +44,15 @@ public interface IHapiTerminologyLoaderSvc {
UploadStatistics loadSnomedCt(List<FileDescriptor> theFiles, RequestDetails theRequestDetails);
// FIXME: remove the default implementation before 4.0.0
// FIXME: remove the default implementation before 4.1.0
default UploadStatistics loadCustom(String theSystem, List<FileDescriptor> theFiles, RequestDetails theRequestDetails) { return null; };
// FIXME: remove the default implementation before 4.1.0
default UploadStatistics loadDeltaAdd(String theSystem, List<FileDescriptor> theFiles, RequestDetails theRequestDetails) { return null; };
// FIXME: remove the default implementation before 4.1.0
default UploadStatistics loadDeltaRemove(String theSystem, List<FileDescriptor> theFiles, RequestDetails theRequestDetails) { return null; };
interface FileDescriptor {
String getFilename();
@ -50,23 +61,25 @@ public interface IHapiTerminologyLoaderSvc {
}
class UploadStatistics {
private final int myConceptCount;
private final IIdType myTarget;
class ByteArrayFileDescriptor implements FileDescriptor {
public UploadStatistics(int theConceptCount, IIdType theTarget) {
myConceptCount = theConceptCount;
myTarget = theTarget;
private final String myNextUrl;
private final byte[] myNextData;
public ByteArrayFileDescriptor(String theNextUrl, byte[] theNextData) {
myNextUrl = theNextUrl;
myNextData = theNextData;
}
public int getConceptCount() {
return myConceptCount;
@Override
public String getFilename() {
return myNextUrl;
}
public IIdType getTarget() {
return myTarget;
@Override
public InputStream getInputStream() {
return new ByteArrayInputStream(myNextData);
}
}
}

54
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/IHapiTerminologySvc.java → hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/api/ITermReadSvc.java
View File

@ -1,20 +1,25 @@
package ca.uhn.fhir.jpa.term;
package ca.uhn.fhir.jpa.term.api;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult;
import ca.uhn.fhir.jpa.entity.*;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElement;
import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElementTarget;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import org.hl7.fhir.instance.model.api.*;
import ca.uhn.fhir.jpa.term.IValueSetConceptAccumulator;
import ca.uhn.fhir.jpa.term.TranslationRequest;
import ca.uhn.fhir.jpa.term.VersionIndependentConcept;
import org.hl7.fhir.instance.model.api.IBaseCoding;
import org.hl7.fhir.instance.model.api.IBaseDatatype;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.ConceptMap;
import org.hl7.fhir.r4.model.ValueSet;
import javax.annotation.Nullable;
import java.util.List;
import java.util.Optional;
import java.util.Set;
import java.util.concurrent.atomic.AtomicInteger;
/*
* #%L
@ -36,9 +41,17 @@ import java.util.concurrent.atomic.AtomicInteger;
* #L%
*/
public interface IHapiTerminologySvc {
void deleteCodeSystem(TermCodeSystem theCodeSystem);
/**
* This interface is the "read" interface for the terminology service. It handles things like
* lookups, code validations, expansions, concept mappings, etc.
* <p>
* It is intended to only handle read operations, leaving various write operations to
* other services within the terminology service APIs.
* (Note that at present, a few write operations remain here- they should be moved but haven't
* been moved yet)
* </p>
*/
public interface ITermReadSvc {
ValueSet expandValueSet(ValueSet theValueSetToExpand);
@ -74,22 +87,7 @@ public interface IHapiTerminologySvc {
List<VersionIndependentConcept> findCodesBelowUsingBuiltInSystems(String theSystem, String theCode);
void saveDeferred();
/**
* This is mostly for unit tests - we can disable processing of deferred concepts
* by changing this flag
*/
void setProcessDeferred(boolean theProcessDeferred);
void storeNewCodeSystemVersion(Long theCodeSystemResourcePid, String theSystemUri, String theSystemName, String theSystemVersionId, TermCodeSystemVersion theCodeSystemVersion, ResourceTable theCodeSystemResourceTable);
/**
* @return Returns the ID of the created/updated code system
*/
IIdType storeNewCodeSystemVersion(org.hl7.fhir.r4.model.CodeSystem theCodeSystemResource, TermCodeSystemVersion theCodeSystemVersion, RequestDetails theRequestDetails, List<org.hl7.fhir.r4.model.ValueSet> theValueSets, List<org.hl7.fhir.r4.model.ConceptMap> theConceptMaps);
void storeNewCodeSystemVersionIfNeeded(CodeSystem theCodeSystem, ResourceTable theResourceEntity);
CodeSystem getCodeSystemFromContext(String theSystem);
void deleteConceptMapAndChildren(ResourceTable theResourceTable);
@ -107,10 +105,6 @@ public interface IHapiTerminologySvc {
IFhirResourceDaoCodeSystem.SubsumesResult subsumes(IPrimitiveType<String> theCodeA, IPrimitiveType<String> theCodeB, IPrimitiveType<String> theSystem, IBaseCoding theCodingA, IBaseCoding theCodingB);
AtomicInteger applyDeltaCodesystemsAdd(String theSystem, @Nullable String theParent, CodeSystem theValue);
AtomicInteger applyDeltaCodesystemsRemove(String theSystem, CodeSystem theDelta);
void preExpandDeferredValueSetsToTerminologyTables();
/**
@ -124,4 +118,6 @@ public interface IHapiTerminologySvc {
* Version independent
*/
boolean isValueSetPreExpandedForCodeValidation(IBaseResource theValueSet);
}

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/IHapiTerminologySvcDstu3.java → hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/api/ITermReadSvcDstu3.java
View File

@ -1,4 +1,4 @@
package ca.uhn.fhir.jpa.term;
package ca.uhn.fhir.jpa.term.api;
/*
* #%L
@ -22,6 +22,6 @@ package ca.uhn.fhir.jpa.term;
import org.hl7.fhir.dstu3.hapi.ctx.IValidationSupport;
public interface IHapiTerminologySvcDstu3 extends IHapiTerminologySvc, IValidationSupport {
public interface ITermReadSvcDstu3 extends ITermReadSvc, IValidationSupport {
// nothing
}

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/IHapiTerminologySvcR4.java → hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/api/ITermReadSvcR4.java
View File

@ -1,4 +1,4 @@
package ca.uhn.fhir.jpa.term;
package ca.uhn.fhir.jpa.term.api;
/*-
* #%L
@ -22,6 +22,6 @@ package ca.uhn.fhir.jpa.term;
import org.hl7.fhir.r4.hapi.ctx.IValidationSupport;
public interface IHapiTerminologySvcR4 extends IHapiTerminologySvc, IValidationSupport {
public interface ITermReadSvcR4 extends ITermReadSvc, IValidationSupport {
// nothing
}

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/IHapiTerminologySvcR5.java → hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/api/ITermReadSvcR5.java
View File

@ -1,4 +1,4 @@
package ca.uhn.fhir.jpa.term;
package ca.uhn.fhir.jpa.term.api;
/*-
* #%L
@ -22,6 +22,6 @@ package ca.uhn.fhir.jpa.term;
import org.hl7.fhir.r5.hapi.ctx.IValidationSupport;
public interface IHapiTerminologySvcR5 extends IHapiTerminologySvc, IValidationSupport {
public interface ITermReadSvcR5 extends ITermReadSvc, IValidationSupport {
// nothing
}

7
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/api/ITermReindexingSvc.java Normal file
View File

@ -0,0 +1,7 @@
package ca.uhn.fhir.jpa.term.api;
public interface ITermReindexingSvc {
void processReindexing();
}

21
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/api/ITermVersionAdapterSvc.java Normal file
View File

@ -0,0 +1,21 @@
package ca.uhn.fhir.jpa.term.api;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.ConceptMap;
import org.hl7.fhir.r4.model.ValueSet;
/**
* This interface is used to handle differences in versions of FHIR for the terminology
* server. It is really just an internal interface used by the
* {@link ITermReadSvc terminology read service}.
*/
public interface ITermVersionAdapterSvc {
IIdType createOrUpdateCodeSystem(CodeSystem theCodeSystemResource);
void createOrUpdateConceptMap(ConceptMap theNextConceptMap);
void createOrUpdateValueSet(ValueSet theValueSet);
}

9
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/custom/ConceptHandler.java
View File

@ -20,10 +20,9 @@ package ca.uhn.fhir.jpa.term.custom;
* #L%
*/
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.term.IRecordHandler;
import ca.uhn.fhir.jpa.term.TerminologyLoaderSvcImpl;
import ca.uhn.fhir.jpa.term.TermLoaderSvcImpl;
import org.apache.commons.csv.CSVRecord;
import org.apache.commons.lang3.Validate;
import org.slf4j.Logger;
@ -40,11 +39,9 @@ public class ConceptHandler implements IRecordHandler {
public static final String CODE = "CODE";
public static final String DISPLAY = "DISPLAY";
private final Map<String, TermConcept> myCode2Concept;
private final TermCodeSystemVersion myCodeSystemVersion;
public ConceptHandler(Map<String, TermConcept> theCode2concept, TermCodeSystemVersion theCodeSystemVersion) {
public ConceptHandler(Map<String, TermConcept> theCode2concept) {
myCode2Concept = theCode2concept;
myCodeSystemVersion = theCodeSystemVersion;
}
@Override
@ -55,7 +52,7 @@ public class ConceptHandler implements IRecordHandler {
Validate.isTrue(!myCode2Concept.containsKey(code), "The code %s has appeared more than once", code);
TermConcept concept = TerminologyLoaderSvcImpl.getOrCreateConcept(myCodeSystemVersion, myCode2Concept, code);
TermConcept concept = TermLoaderSvcImpl.getOrCreateConcept(myCode2Concept, code);
concept.setCode(code);
concept.setDisplay(display);

158
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/custom/CustomTerminologySet.java Normal file
View File

@ -0,0 +1,158 @@
package ca.uhn.fhir.jpa.term.custom;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.term.IRecordHandler;
import ca.uhn.fhir.jpa.term.LoadedFileDescriptors;
import ca.uhn.fhir.jpa.term.TermLoaderSvcImpl;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import com.google.common.collect.ArrayListMultimap;
import com.google.common.collect.ListMultimap;
import com.google.common.collect.Multimaps;
import org.apache.commons.csv.QuoteMode;
import org.apache.commons.lang3.Validate;
import javax.annotation.Nonnull;
import java.util.*;
public class CustomTerminologySet {
private final int mySize;
private final ListMultimap<TermConcept, String> myUnanchoredChildConceptsToParentCodes;
private final List<TermConcept> myRootConcepts;
/**
* Constructor for an empty object
*/
public CustomTerminologySet() {
this(0, ArrayListMultimap.create(), new ArrayList<>());
}
/**
* Constructor
*/
private CustomTerminologySet(int theSize, ListMultimap<TermConcept, String> theUnanchoredChildConceptsToParentCodes, Collection<TermConcept> theRootConcepts) {
this(theSize, theUnanchoredChildConceptsToParentCodes, new ArrayList<>(theRootConcepts));
}
/**
* Constructor
*/
private CustomTerminologySet(int theSize, ListMultimap<TermConcept, String> theUnanchoredChildConceptsToParentCodes, List<TermConcept> theRootConcepts) {
mySize = theSize;
myUnanchoredChildConceptsToParentCodes = theUnanchoredChildConceptsToParentCodes;
myRootConcepts = theRootConcepts;
}
public void addRootConcept(String theCode) {
addRootConcept(theCode, null);
}
public TermConcept addRootConcept(String theCode, String theDisplay) {
Validate.notBlank(theCode, "theCode must not be blank");
Validate.isTrue(myRootConcepts.stream().noneMatch(t -> t.getCode().equals(theCode)), "Already have code %s", theCode);
TermConcept retVal = new TermConcept();
retVal.setCode(theCode);
retVal.setDisplay(theDisplay);
myRootConcepts.add(retVal);
return retVal;
}
public ListMultimap<TermConcept, String> getUnanchoredChildConceptsToParentCodes() {
return Multimaps.unmodifiableListMultimap(myUnanchoredChildConceptsToParentCodes);
}
public int getSize() {
return mySize;
}
public TermCodeSystemVersion toCodeSystemVersion() {
TermCodeSystemVersion csv = new TermCodeSystemVersion();
for (TermConcept next : myRootConcepts) {
csv.getConcepts().add(next);
}
populateVersionToChildCodes(csv, myRootConcepts);
return csv;
}
private void populateVersionToChildCodes(TermCodeSystemVersion theCsv, List<TermConcept> theConcepts) {
for (TermConcept next : theConcepts) {
next.setCodeSystemVersion(theCsv);
populateVersionToChildCodes(theCsv, next.getChildCodes());
}
}
public List<TermConcept> getRootConcepts() {
return Collections.unmodifiableList(myRootConcepts);
}
public void addUnanchoredChildConcept(String theParentCode, String theCode, String theDisplay) {
Validate.notBlank(theParentCode);
Validate.notBlank(theCode);
TermConcept code = new TermConcept()
.setCode(theCode)
.setDisplay(theDisplay);
myUnanchoredChildConceptsToParentCodes.put(code, theParentCode);
}
public void validateNoCycleOrThrowInvalidRequest() {
Set<String> codes = new HashSet<>();
validateNoCycleOrThrowInvalidRequest(codes, getRootConcepts());
for (TermConcept next : myUnanchoredChildConceptsToParentCodes.keySet()) {
validateNoCycleOrThrowInvalidRequest(codes, next);
}
}
private void validateNoCycleOrThrowInvalidRequest(Set<String> theCodes, List<TermConcept> theRootConcepts) {
for (TermConcept next : theRootConcepts) {
validateNoCycleOrThrowInvalidRequest(theCodes, next);
}
}
private void validateNoCycleOrThrowInvalidRequest(Set<String> theCodes, TermConcept next) {
if (!theCodes.add(next.getCode())) {
throw new InvalidRequestException("Cycle detected around code " + next.getCode());
}
validateNoCycleOrThrowInvalidRequest(theCodes, next.getChildCodes());
}
@Nonnull
public static CustomTerminologySet load(LoadedFileDescriptors theDescriptors, boolean theFlat) {
final Map<String, TermConcept> code2concept = new LinkedHashMap<>();
ArrayListMultimap<TermConcept, String> unanchoredChildConceptsToParentCodes = ArrayListMultimap.create();
// Concepts
IRecordHandler conceptHandler = new ConceptHandler(code2concept);
TermLoaderSvcImpl.iterateOverZipFile(theDescriptors, TermLoaderSvcImpl.CUSTOM_CONCEPTS_FILE, conceptHandler, ',', QuoteMode.NON_NUMERIC, false);
if (theFlat) {
return new CustomTerminologySet(code2concept.size(), ArrayListMultimap.create(), code2concept.values());
} else {
// Hierarchy
if (theDescriptors.hasFile(TermLoaderSvcImpl.CUSTOM_HIERARCHY_FILE)) {
IRecordHandler hierarchyHandler = new HierarchyHandler(code2concept, unanchoredChildConceptsToParentCodes);
TermLoaderSvcImpl.iterateOverZipFile(theDescriptors, TermLoaderSvcImpl.CUSTOM_HIERARCHY_FILE, hierarchyHandler, ',', QuoteMode.NON_NUMERIC, false);
}
// Find root concepts
List<TermConcept> rootConcepts = new ArrayList<>();
for (TermConcept nextConcept : code2concept.values()) {
if (nextConcept.getParents().isEmpty()) {
rootConcepts.add(nextConcept);
}
}
return new CustomTerminologySet(code2concept.size(), unanchoredChildConceptsToParentCodes, rootConcepts);
}
}
}

14
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/custom/HierarchyHandler.java
View File

@ -24,9 +24,8 @@ import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
import ca.uhn.fhir.jpa.term.IRecordHandler;
import ca.uhn.fhir.util.ValidateUtil;
import com.google.common.collect.ArrayListMultimap;
import org.apache.commons.csv.CSVRecord;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.util.Map;
@ -36,9 +35,11 @@ import static org.apache.commons.lang3.StringUtils.trim;
public class HierarchyHandler implements IRecordHandler {
private final Map<String, TermConcept> myCode2Concept;
private final ArrayListMultimap<TermConcept, String> myUnanchoredChildConceptsToParentCodes;
public HierarchyHandler(Map<String, TermConcept> theCode2concept) {
public HierarchyHandler(Map<String, TermConcept> theCode2concept, ArrayListMultimap<TermConcept, String> theunanchoredChildConceptsToParentCodes) {
myCode2Concept = theCode2concept;
myUnanchoredChildConceptsToParentCodes = theunanchoredChildConceptsToParentCodes;
}
@Override
@ -47,12 +48,15 @@ public class HierarchyHandler implements IRecordHandler {
String child = trim(theRecord.get("CHILD"));
if (isNotBlank(parent) && isNotBlank(child)) {
TermConcept parentConcept = myCode2Concept.get(parent);
ValidateUtil.isNotNullOrThrowUnprocessableEntity(parentConcept, "Parent code %s not found", parent);
TermConcept childConcept = myCode2Concept.get(child);
ValidateUtil.isNotNullOrThrowUnprocessableEntity(childConcept, "Child code %s not found", child);
TermConcept parentConcept = myCode2Concept.get(parent);
if (parentConcept == null) {
myUnanchoredChildConceptsToParentCodes.put(childConcept, parent);
} else {
parentConcept.addChild(childConcept, TermConceptParentChildLink.RelationshipTypeEnum.ISA);
}
}
}
}

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/BaseLoincTop2000LabResultsHandler.java
View File

@ -21,7 +21,7 @@ package ca.uhn.fhir.jpa.term.loinc;
*/
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
import ca.uhn.fhir.jpa.term.IRecordHandler;
import org.apache.commons.csv.CSVRecord;
import org.hl7.fhir.r4.model.ConceptMap;
@ -52,7 +52,7 @@ public class BaseLoincTop2000LabResultsHandler extends BaseLoincHandler implemen
String displayName = trim(theRecord.get("Long Common Name"));
ValueSet valueSet = getValueSet(myValueSetId, myValueSetUri, myValueSetName, null);
addCodeAsIncludeToValueSet(valueSet, IHapiTerminologyLoaderSvc.LOINC_URI, loincNumber, displayName);
addCodeAsIncludeToValueSet(valueSet, ITermLoaderSvc.LOINC_URI, loincNumber, displayName);
}
}

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincAnswerListHandler.java
View File

@ -22,7 +22,7 @@ package ca.uhn.fhir.jpa.term.loinc;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
import org.apache.commons.csv.CSVRecord;
import org.hl7.fhir.r4.model.ConceptMap;
import org.hl7.fhir.r4.model.ValueSet;
@ -96,7 +96,7 @@ public class LoincAnswerListHandler extends BaseLoincHandler {
vs
.getCompose()
.getIncludeFirstRep()
.setSystem(IHapiTerminologyLoaderSvc.LOINC_URI)
.setSystem(ITermLoaderSvc.LOINC_URI)
.addConcept()
.setCode(answerString)
.setDisplay(displayText);

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincAnswerListLinkHandler.java
View File

@ -20,18 +20,14 @@ package ca.uhn.fhir.jpa.term.loinc;
* #L%
*/
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
import ca.uhn.fhir.jpa.term.IRecordHandler;
import org.apache.commons.csv.CSVRecord;
import org.hl7.fhir.r4.model.Enumerations;
import org.hl7.fhir.r4.model.ValueSet;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincDocumentOntologyHandler.java
View File

@ -21,7 +21,7 @@ package ca.uhn.fhir.jpa.term.loinc;
*/
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
import ca.uhn.fhir.jpa.term.IRecordHandler;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import org.apache.commons.csv.CSVRecord;
@ -58,7 +58,7 @@ public class LoincDocumentOntologyHandler extends BaseLoincHandler implements IR
// RSNA Codes VS
ValueSet vs = getValueSet(DOCUMENT_ONTOLOGY_CODES_VS_ID, DOCUMENT_ONTOLOGY_CODES_VS_URI, DOCUMENT_ONTOLOGY_CODES_VS_NAME, null);
addCodeAsIncludeToValueSet(vs, IHapiTerminologyLoaderSvc.LOINC_URI, loincNumber, null);
addCodeAsIncludeToValueSet(vs, ITermLoaderSvc.LOINC_URI, loincNumber, null);
// Part Properties
String loincCodePropName;
@ -84,7 +84,7 @@ public class LoincDocumentOntologyHandler extends BaseLoincHandler implements IR
TermConcept code = myCode2Concept.get(loincNumber);
if (code != null) {
code.addPropertyCoding(loincCodePropName, IHapiTerminologyLoaderSvc.LOINC_URI, partNumber, partName);
code.addPropertyCoding(loincCodePropName, ITermLoaderSvc.LOINC_URI, partNumber, partName);
}
}

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincGroupTermsFileHandler.java
View File

@ -21,7 +21,7 @@ package ca.uhn.fhir.jpa.term.loinc;
*/
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
import ca.uhn.fhir.jpa.term.IRecordHandler;
import org.apache.commons.csv.CSVRecord;
import org.hl7.fhir.r4.model.ConceptMap;
@ -46,7 +46,7 @@ public class LoincGroupTermsFileHandler extends BaseLoincHandler implements IRec
String loincNumber = trim(theRecord.get("LoincNumber"));
ValueSet valueSet = getValueSet(groupId, LoincGroupFileHandler.VS_URI_PREFIX + groupId, null, null);
addCodeAsIncludeToValueSet(valueSet, IHapiTerminologyLoaderSvc.LOINC_URI, loincNumber, null);
addCodeAsIncludeToValueSet(valueSet, ITermLoaderSvc.LOINC_URI, loincNumber, null);
}

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincHandler.java
View File

@ -22,9 +22,9 @@ package ca.uhn.fhir.jpa.term.loinc;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
import ca.uhn.fhir.jpa.term.IRecordHandler;
import ca.uhn.fhir.jpa.term.TerminologyLoaderSvcImpl;
import ca.uhn.fhir.jpa.term.TermLoaderSvcImpl;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import org.apache.commons.csv.CSVRecord;
import org.apache.commons.lang3.Validate;
@ -58,7 +58,7 @@ public class LoincHandler implements IRecordHandler {
String longCommonName = trim(theRecord.get("LONG_COMMON_NAME"));
String shortName = trim(theRecord.get("SHORTNAME"));
String consumerName = trim(theRecord.get("CONSUMER_NAME"));
String display = TerminologyLoaderSvcImpl.firstNonBlank(longCommonName, shortName, consumerName);
String display = TermLoaderSvcImpl.firstNonBlank(longCommonName, shortName, consumerName);
TermConcept concept = new TermConcept(myCodeSystemVersion, code);
concept.setDisplay(display);
@ -117,7 +117,7 @@ public class LoincHandler implements IRecordHandler {
}
if (isNotBlank(partNumber)) {
concept.addPropertyCoding(nextPropertyName, IHapiTerminologyLoaderSvc.LOINC_URI, partNumber, nextPropertyValue);
concept.addPropertyCoding(nextPropertyName, ITermLoaderSvc.LOINC_URI, partNumber, nextPropertyValue);
} else {
String msg = "Unable to find part code with TYPE[" + key.getPartType() + "] and NAME[" + nextPropertyValue + "] (using name " + propertyValue + ")";
ourLog.warn(msg);

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincHierarchyHandler.java
View File

@ -23,7 +23,7 @@ package ca.uhn.fhir.jpa.term.loinc;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
import ca.uhn.fhir.jpa.term.IRecordHandler;
import org.apache.commons.csv.CSVRecord;
@ -56,13 +56,13 @@ public class LoincHierarchyHandler implements IRecordHandler {
parent.addPropertyCoding(
"child",
IHapiTerminologyLoaderSvc.LOINC_URI,
ITermLoaderSvc.LOINC_URI,
child.getCode(),
child.getDisplay());
child.addPropertyCoding(
"parent",
IHapiTerminologyLoaderSvc.LOINC_URI,
ITermLoaderSvc.LOINC_URI,
parent.getCode(),
parent.getDisplay());
}

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincIeeeMedicalDeviceCodeHandler.java
View File

@ -21,7 +21,7 @@ package ca.uhn.fhir.jpa.term.loinc;
*/
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
import ca.uhn.fhir.jpa.term.IRecordHandler;
import org.apache.commons.csv.CSVRecord;
import org.hl7.fhir.r4.model.ConceptMap;
@ -57,8 +57,8 @@ public class LoincIeeeMedicalDeviceCodeHandler extends BaseLoincHandler implemen
String ieeeDisplayName = trim(theRecord.get("IEEE_REFID"));
// LOINC Part -> IEEE 11073:10101 Mappings
String sourceCodeSystemUri = IHapiTerminologyLoaderSvc.LOINC_URI;
String targetCodeSystemUri = IHapiTerminologyLoaderSvc.IEEE_11073_10101_URI;
String sourceCodeSystemUri = ITermLoaderSvc.LOINC_URI;
String targetCodeSystemUri = ITermLoaderSvc.IEEE_11073_10101_URI;
addConceptMapEntry(
new ConceptMapping()
.setConceptMapId(LOINC_IEEE_CM_ID)

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincImagingDocumentCodeHandler.java
View File

@ -21,7 +21,7 @@ package ca.uhn.fhir.jpa.term.loinc;
*/
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
import ca.uhn.fhir.jpa.term.IRecordHandler;
import org.apache.commons.csv.CSVRecord;
import org.hl7.fhir.r4.model.ConceptMap;
@ -49,7 +49,7 @@ public class LoincImagingDocumentCodeHandler extends BaseLoincHandler implements
String displayName = trim(theRecord.get("LONG_COMMON_NAME"));
ValueSet valueSet = getValueSet(VS_ID, VS_URI, VS_NAME,null);
addCodeAsIncludeToValueSet(valueSet, IHapiTerminologyLoaderSvc.LOINC_URI, loincNumber, displayName);
addCodeAsIncludeToValueSet(valueSet, ITermLoaderSvc.LOINC_URI, loincNumber, displayName);
}

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincPartRelatedCodeMappingHandler.java
View File

@ -21,7 +21,7 @@ package ca.uhn.fhir.jpa.term.loinc;
*/
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
import ca.uhn.fhir.jpa.term.IRecordHandler;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import org.apache.commons.csv.CSVRecord;
@ -101,7 +101,7 @@ public class LoincPartRelatedCodeMappingHandler extends BaseLoincHandler impleme
String loincPartMapUri;
String loincPartMapName;
switch (extCodeSystem) {
case IHapiTerminologyLoaderSvc.SCT_URI:
case ITermLoaderSvc.SCT_URI:
loincPartMapId = LOINC_SCT_PART_MAP_ID;
loincPartMapUri = LOINC_SCT_PART_MAP_URI;
loincPartMapName = LOINC_SCT_PART_MAP_NAME;
@ -133,7 +133,7 @@ public class LoincPartRelatedCodeMappingHandler extends BaseLoincHandler impleme
.setConceptMapId(loincPartMapId)
.setConceptMapUri(loincPartMapUri)
.setConceptMapName(loincPartMapName)
.setSourceCodeSystem(IHapiTerminologyLoaderSvc.LOINC_URI)
.setSourceCodeSystem(ITermLoaderSvc.LOINC_URI)
.setSourceCode(partNumber)
.setSourceDisplay(partName)
.setTargetCodeSystem(extCodeSystem)

10
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincRsnaPlaybookHandler.java
View File

@ -21,7 +21,7 @@ package ca.uhn.fhir.jpa.term.loinc;
*/
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
import ca.uhn.fhir.jpa.term.IRecordHandler;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import org.apache.commons.csv.CSVRecord;
@ -98,7 +98,7 @@ public class LoincRsnaPlaybookHandler extends BaseLoincHandler implements IRecor
vs
.getCompose()
.getIncludeFirstRep()
.setSystem(IHapiTerminologyLoaderSvc.LOINC_URI)
.setSystem(ITermLoaderSvc.LOINC_URI)
.addConcept()
.setCode(loincNumber)
.setDisplay(longCommonName);
@ -167,7 +167,7 @@ public class LoincRsnaPlaybookHandler extends BaseLoincHandler implements IRecor
TermConcept code = myCode2Concept.get(loincNumber);
if (code != null) {
code.addPropertyCoding(loincCodePropName, IHapiTerminologyLoaderSvc.LOINC_URI, partNumber, partName);
code.addPropertyCoding(loincCodePropName, ITermLoaderSvc.LOINC_URI, partNumber, partName);
}
// LOINC Part -> Radlex RID code mappings
@ -177,7 +177,7 @@ public class LoincRsnaPlaybookHandler extends BaseLoincHandler implements IRecor
.setConceptMapId(LoincPartRelatedCodeMappingHandler.LOINC_PART_TO_RID_PART_MAP_ID)
.setConceptMapUri(LoincPartRelatedCodeMappingHandler.LOINC_PART_TO_RID_PART_MAP_URI)
.setConceptMapName(LoincPartRelatedCodeMappingHandler.LOINC_PART_TO_RID_PART_MAP_NAME)
.setSourceCodeSystem(IHapiTerminologyLoaderSvc.LOINC_URI)
.setSourceCodeSystem(ITermLoaderSvc.LOINC_URI)
.setSourceCode(partNumber)
.setSourceDisplay(partName)
.setTargetCodeSystem(RID_CS_URI)
@ -194,7 +194,7 @@ public class LoincRsnaPlaybookHandler extends BaseLoincHandler implements IRecor
.setConceptMapId(LoincPartRelatedCodeMappingHandler.LOINC_TERM_TO_RPID_PART_MAP_ID)
.setConceptMapUri(LoincPartRelatedCodeMappingHandler.LOINC_TERM_TO_RPID_PART_MAP_URI)
.setConceptMapName(LoincPartRelatedCodeMappingHandler.LOINC_TERM_TO_RPID_PART_MAP_NAME)
.setSourceCodeSystem(IHapiTerminologyLoaderSvc.LOINC_URI)
.setSourceCodeSystem(ITermLoaderSvc.LOINC_URI)
.setSourceCode(loincNumber)
.setSourceDisplay(longCommonName)
.setTargetCodeSystem(RPID_CS_URI)

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincUniversalOrderSetHandler.java
View File

@ -21,7 +21,7 @@ package ca.uhn.fhir.jpa.term.loinc;
*/
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
import ca.uhn.fhir.jpa.term.api.ITermLoaderSvc;
import ca.uhn.fhir.jpa.term.IRecordHandler;
import org.apache.commons.csv.CSVRecord;
import org.hl7.fhir.r4.model.ConceptMap;
@ -48,7 +48,7 @@ public class LoincUniversalOrderSetHandler extends BaseLoincHandler implements I
String orderObs = trim(theRecord.get("ORDER_OBS"));
ValueSet valueSet = getValueSet(VS_ID, VS_URI, VS_NAME, null);
addCodeAsIncludeToValueSet(valueSet, IHapiTerminologyLoaderSvc.LOINC_URI, loincNumber, displayName);
addCodeAsIncludeToValueSet(valueSet, ITermLoaderSvc.LOINC_URI, loincNumber, displayName);
}

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/snomedct/SctHandlerDescription.java
View File

@ -23,7 +23,7 @@ package ca.uhn.fhir.jpa.term.snomedct;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.term.IRecordHandler;
import ca.uhn.fhir.jpa.term.TerminologyLoaderSvcImpl;
import ca.uhn.fhir.jpa.term.TermLoaderSvcImpl;
import org.apache.commons.csv.CSVRecord;
import java.util.Map;
@ -56,9 +56,10 @@ public final class SctHandlerDescription implements IRecordHandler {
String term = theRecord.get("term");
TermConcept concept = TerminologyLoaderSvcImpl.getOrCreateConcept(myCodeSystemVersion, myId2concept, id);
TermConcept concept = TermLoaderSvcImpl.getOrCreateConcept(myId2concept, id);
concept.setCode(conceptId);
concept.setDisplay(term);
concept.setCodeSystemVersion(myCodeSystemVersion);
myCode2concept.put(conceptId, concept);
}
}

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/validation/JpaValidationSupportChainDstu3.java
View File

@ -21,7 +21,7 @@ package ca.uhn.fhir.jpa.validation;
*/
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvcDstu3;
import ca.uhn.fhir.jpa.term.api.ITermReadSvcDstu3;
import org.hl7.fhir.dstu3.hapi.ctx.DefaultProfileValidationSupport;
import org.hl7.fhir.dstu3.hapi.validation.ValidationSupportChain;
import org.hl7.fhir.dstu3.hapi.validation.SnapshotGeneratingValidationSupport;
@ -41,7 +41,7 @@ public class JpaValidationSupportChainDstu3 extends ValidationSupportChain {
@Autowired
private DefaultProfileValidationSupport myDefaultProfileValidationSupport;
@Autowired
private IHapiTerminologySvcDstu3 myTerminologyService;
private ITermReadSvcDstu3 myTerminologyService;
@Autowired
private FhirContext myFhirContext;

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/validation/JpaValidationSupportChainR4.java
View File

@ -21,7 +21,7 @@ package ca.uhn.fhir.jpa.validation;
*/
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvcR4;
import ca.uhn.fhir.jpa.term.api.ITermReadSvcR4;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.hapi.ctx.DefaultProfileValidationSupport;
import org.hl7.fhir.r4.hapi.validation.SnapshotGeneratingValidationSupport;
@ -46,7 +46,7 @@ public class JpaValidationSupportChainR4 extends ValidationSupportChain {
public ca.uhn.fhir.jpa.dao.r4.IJpaValidationSupportR4 myJpaValidationSupportR4;
@Autowired
private IHapiTerminologySvcR4 myTerminologyService;
private ITermReadSvcR4 myTerminologyService;
public JpaValidationSupportChainR4() {
super();

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/validation/JpaValidationSupportChainR5.java
View File

@ -21,7 +21,7 @@ package ca.uhn.fhir.jpa.validation;
*/
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvcR5;
import ca.uhn.fhir.jpa.term.api.ITermReadSvcR5;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r5.hapi.ctx.DefaultProfileValidationSupport;
import org.hl7.fhir.r5.hapi.validation.SnapshotGeneratingValidationSupport;
@ -46,7 +46,7 @@ public class JpaValidationSupportChainR5 extends ValidationSupportChain {
public ca.uhn.fhir.jpa.dao.r5.IJpaValidationSupportR5 myJpaValidationSupportR5;
@Autowired
private IHapiTerminologySvcR5 myTerminologyService;
private ITermReadSvcR5 myTerminologyService;
public JpaValidationSupportChainR5() {
super();

3
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/BaseJpaTest.java
View File

@ -4,6 +4,7 @@ import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.interceptor.api.IInterceptorService;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.interceptor.executor.InterceptorService;
import ca.uhn.fhir.jpa.BaseTest;
import ca.uhn.fhir.jpa.bulk.IBulkDataExportSvc;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
@ -66,7 +67,7 @@ import static org.junit.Assert.fail;
import static org.mockito.ArgumentMatchers.eq;
import static org.mockito.Mockito.when;
public abstract class BaseJpaTest {
public abstract class BaseJpaTest extends BaseTest {
protected static final String CM_URL = "http://example.com/my_concept_map";
protected static final String CS_URL = "http://example.com/my_code_system";

1
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2SearchNoFtTest.java
View File

@ -921,7 +921,6 @@ public class FhirResourceDaoDstu2SearchNoFtTest extends BaseJpaDstu2Test {
Patient patient = new Patient();
patient.addIdentifier().setSystem("urn:system").setValue("001");
patient.addName().addFamily("testSearchNameParam01Fam").addGiven("testSearchNameParam01Giv");
ResourceMetadataKeyEnum.TITLE.put(patient, "P1TITLE");
id1 = myPatientDao.create(patient, mySrd).getId();
}
{

23
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/BaseJpaDstu3Test.java
View File

@ -7,7 +7,6 @@ import ca.uhn.fhir.jpa.dao.*;
import ca.uhn.fhir.jpa.dao.data.*;
import ca.uhn.fhir.jpa.dao.dstu2.FhirResourceDaoDstu2SearchNoFtTest;
import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamString;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
@ -18,8 +17,11 @@ import ca.uhn.fhir.jpa.search.IStaleSearchDeletingSvc;
import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc;
import ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
import ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl;
import ca.uhn.fhir.jpa.term.TermDeferredStorageSvcImpl;
import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
import ca.uhn.fhir.jpa.util.ResourceCountCache;
import ca.uhn.fhir.jpa.util.ResourceProviderFactory;
import ca.uhn.fhir.jpa.validation.JpaValidationSupportChainDstu3;
@ -67,6 +69,8 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
private static JpaValidationSupportChainDstu3 ourJpaValidationSupportChainDstu3;
private static IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> ourValueSetDao;
@Autowired
protected ITermDeferredStorageSvc myTerminologyDeferredStorageSvc;
@Autowired
@Qualifier("myResourceCountsCache")
protected ResourceCountCache myResourceCountsCache;
@ -243,7 +247,7 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
@Autowired
protected ITermCodeSystemDao myTermCodeSystemDao;
@Autowired
protected IHapiTerminologySvc myTermSvc;
protected ITermReadSvc myTermSvc;
@Autowired
protected PlatformTransactionManager myTransactionMgr;
@Autowired
@ -262,6 +266,8 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
private JpaValidationSupportChainDstu3 myJpaValidationSupportChainDstu3;
@Autowired
private IBulkDataExportSvc myBulkDataExportSvc;
@Autowired
protected ITermCodeSystemStorageSvc myTermCodeSystemStorageSvc;
@After()
public void afterCleanupDao() {
@ -278,12 +284,13 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
@After
public void afterClearTerminologyCaches() {
BaseHapiTerminologySvcImpl baseHapiTerminologySvc = AopTestUtils.getTargetObject(myTermSvc);
BaseTermReadSvcImpl baseHapiTerminologySvc = AopTestUtils.getTargetObject(myTermSvc);
baseHapiTerminologySvc.clearTranslationCache();
baseHapiTerminologySvc.clearTranslationWithReverseCache();
baseHapiTerminologySvc.clearDeferred();
BaseHapiTerminologySvcImpl.clearOurLastResultsFromTranslationCache();
BaseHapiTerminologySvcImpl.clearOurLastResultsFromTranslationWithReverseCache();
BaseTermReadSvcImpl.clearOurLastResultsFromTranslationCache();
BaseTermReadSvcImpl.clearOurLastResultsFromTranslationWithReverseCache();
TermDeferredStorageSvcImpl deferredSvc = AopTestUtils.getTargetObject(myTerminologyDeferredStorageSvc);
deferredSvc.clearDeferred();
}
@After()

24
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3CodeSystemTest.java
View File

@ -1,34 +1,30 @@
package ca.uhn.fhir.jpa.dao.dstu3;
import static org.hamcrest.Matchers.greaterThan;
import static org.junit.Assert.*;
import java.nio.charset.StandardCharsets;
import ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl;
import ca.uhn.fhir.jpa.term.TermReindexingSvcImpl;
import ca.uhn.fhir.util.TestUtil;
import org.apache.commons.io.IOUtils;
import org.hl7.fhir.dstu3.model.CodeSystem;
import org.hl7.fhir.dstu3.model.Enumerations;
import org.hl7.fhir.dstu3.model.IdType;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.AfterClass;
import org.junit.Test;
import ca.uhn.fhir.util.TestUtil;
import java.nio.charset.StandardCharsets;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotEquals;
public class FhirResourceDaoDstu3CodeSystemTest extends BaseJpaDstu3Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoDstu3CodeSystemTest.class);
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
BaseHapiTerminologySvcImpl.setForceSaveDeferredAlwaysForUnitTest(false);
TermReindexingSvcImpl.setForceSaveDeferredAlwaysForUnitTest(false);
}
@Test
public void testIndexContained() throws Exception {
BaseHapiTerminologySvcImpl.setForceSaveDeferredAlwaysForUnitTest(true);
TermReindexingSvcImpl.setForceSaveDeferredAlwaysForUnitTest(true);
String input = IOUtils.toString(getClass().getResource("/dstu3_codesystem_complete.json"), StandardCharsets.UTF_8);
CodeSystem cs = myFhirCtx.newJsonParser().parseResource(CodeSystem.class, input);
@ -39,13 +35,13 @@ public class FhirResourceDaoDstu3CodeSystemTest extends BaseJpaDstu3Test {
int outcome= myResourceReindexingSvc.forceReindexingPass();
assertNotEquals(-1, outcome); // -1 means there was a failure
myTermSvc.saveDeferred();
myTerminologyDeferredStorageSvc.saveDeferred();
}
@Test
public void testDeleteCodeSystemComplete() {
BaseHapiTerminologySvcImpl.setForceSaveDeferredAlwaysForUnitTest(false);
TermReindexingSvcImpl.setForceSaveDeferredAlwaysForUnitTest(false);
// Create the code system
CodeSystem cs = new CodeSystem();

Some files were not shown because too many files have changed in this diff Show More