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BaseHapiFhirDao.java
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BaseHapiFhirDao.java
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package ca.uhn.fhir.jpa.dao;
/*
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2015 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import java.io.UnsupportedEncodingException;
import java.net.URI;
import java.net.URISyntaxException;
import java.text.Normalizer;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.Comparator;
import java.util.Date;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import javax.persistence.EntityManager;
import javax.persistence.NoResultException;
import javax.persistence.PersistenceContext;
import javax.persistence.PersistenceContextType;
import javax.persistence.Tuple;
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 org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.apache.http.NameValuePair;
import org.apache.http.client.utils.URLEncodedUtils;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.support.TransactionCallback;
import org.springframework.transaction.support.TransactionTemplate;
import com.google.common.base.Function;
import com.google.common.collect.ArrayListMultimap;
import com.google.common.collect.Collections2;
import com.google.common.collect.Lists;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.jpa.entity.BaseHasResource;
import ca.uhn.fhir.jpa.entity.BaseResourceIndexedSearchParam;
import ca.uhn.fhir.jpa.entity.BaseTag;
import ca.uhn.fhir.jpa.entity.ForcedId;
import ca.uhn.fhir.jpa.entity.ResourceEncodingEnum;
import ca.uhn.fhir.jpa.entity.ResourceHistoryTable;
import ca.uhn.fhir.jpa.entity.ResourceHistoryTag;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamCoords;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamDate;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamNumber;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamQuantity;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamString;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamToken;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamUri;
import ca.uhn.fhir.jpa.entity.ResourceLink;
import ca.uhn.fhir.jpa.entity.ResourceTable;
import ca.uhn.fhir.jpa.entity.ResourceTag;
import ca.uhn.fhir.jpa.entity.TagDefinition;
import ca.uhn.fhir.jpa.entity.TagTypeEnum;
import ca.uhn.fhir.jpa.util.StopWatch;
import ca.uhn.fhir.model.api.IQueryParameterAnd;
import ca.uhn.fhir.model.api.IResource;
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.base.composite.BaseCodingDt;
import ca.uhn.fhir.model.base.composite.BaseResourceReferenceDt;
import ca.uhn.fhir.model.dstu2.composite.MetaDt;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.model.primitive.InstantDt;
import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import ca.uhn.fhir.rest.method.MethodUtil;
import ca.uhn.fhir.rest.method.QualifiedParamList;
import ca.uhn.fhir.rest.method.RestSearchParameterTypeEnum;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.server.Constants;
import ca.uhn.fhir.rest.server.IBundleProvider;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
import ca.uhn.fhir.util.FhirTerser;
public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
public static final long INDEX_STATUS_INDEXED = Long.valueOf(1L);
public static final long INDEX_STATUS_INDEXING_FAILED = Long.valueOf(2L);
public static final String NS_JPA_PROFILE = "https://github.com/jamesagnew/hapi-fhir/ns/jpa/profile";
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseHapiFhirDao.class);
private static final Map<FhirVersionEnum, FhirContext> ourRetrievalContexts = new HashMap<FhirVersionEnum, FhirContext>();
public static final String UCUM_NS = "http://unitsofmeasure.org";
@Autowired(required = true)
private DaoConfig myConfig;
private FhirContext myContext;
// @PersistenceContext(name = "FHIR_UT", type = PersistenceContextType.TRANSACTION, unitName = "FHIR_UT")
@PersistenceContext(type = PersistenceContextType.TRANSACTION)
private EntityManager myEntityManager;
private List<IDaoListener> myListeners = new ArrayList<IDaoListener>();
@Autowired
private PlatformTransactionManager myPlatformTransactionManager;
@Autowired
private List<IFhirResourceDao<?>> myResourceDaos;
private Map<Class<? extends IBaseResource>, IFhirResourceDao<?>> myResourceTypeToDao;
private ISearchParamExtractor mySearchParamExtractor;
protected void createForcedIdIfNeeded(ResourceTable entity, IIdType id) {
if (id.isEmpty() == false && id.hasIdPart()) {
if (isValidPid(id)) {
return;
}
ForcedId fid = new ForcedId();
fid.setForcedId(id.getIdPart());
fid.setResource(entity);
entity.setForcedId(fid);
}
}
InstantDt createHistoryToTimestamp() {
// final InstantDt end = new InstantDt(DateUtils.addSeconds(DateUtils.truncate(new Date(), Calendar.SECOND),
// -1));
return InstantDt.withCurrentTime();
}
protected List<ResourceLink> extractResourceLinks(ResourceTable theEntity, IResource theResource) {
ArrayList<ResourceLink> retVal = new ArrayList<ResourceLink>();
RuntimeResourceDefinition def = getContext().getResourceDefinition(theResource);
for (RuntimeSearchParam nextSpDef : def.getSearchParams()) {
if (nextSpDef.getParamType() != RestSearchParameterTypeEnum.REFERENCE) {
continue;
}
String nextPathsUnsplit = nextSpDef.getPath();
if (isBlank(nextPathsUnsplit)) {
continue;
}
boolean multiType = false;
if (nextPathsUnsplit.endsWith("[x]")) {
multiType = true;
}
for (Object nextObject : extractValues(nextPathsUnsplit, theResource)) {
if (nextObject == null) {
continue;
}
ResourceLink nextEntity;
if (nextObject instanceof BaseResourceReferenceDt) {
BaseResourceReferenceDt nextValue = (BaseResourceReferenceDt) nextObject;
if (nextValue.isEmpty()) {
continue;
}
if (nextValue.getReference().isEmpty() || nextValue.getReference().getValue().startsWith("#")) {
// This is a blank or contained resource reference
continue;
}
String typeString = nextValue.getReference().getResourceType();
if (isBlank(typeString)) {
throw new InvalidRequestException("Invalid resource reference found at path[" + nextPathsUnsplit + "] - Does not contain resource type - " + nextValue.getReference().getValue());
}
Class<? extends IBaseResource> type = getContext().getResourceDefinition(typeString).getImplementingClass();
String id = nextValue.getReference().getIdPart();
if (StringUtils.isBlank(id)) {
continue;
}
IFhirResourceDao<?> dao = getDao(type);
if (dao == null) {
StringBuilder b = new StringBuilder();
b.append("This server (version ");
b.append(myContext.getVersion().getVersion());
b.append(") is not able to handle resources of type[");
b.append(nextValue.getReference().getResourceType());
b.append("] - Valid resource types for this server: ");
b.append(myResourceTypeToDao.keySet().toString());
throw new InvalidRequestException(b.toString());
}
Long valueOf;
try {
valueOf = translateForcedIdToPid(nextValue.getReference());
} catch (ResourceNotFoundException e) {
String resName = getContext().getResourceDefinition(type).getName();
throw new InvalidRequestException("Resource " + resName + "/" + id + " not found, specified in path: " + nextPathsUnsplit);
}
ResourceTable target = myEntityManager.find(ResourceTable.class, valueOf);
if (target == null) {
String resName = getContext().getResourceDefinition(type).getName();
throw new InvalidRequestException("Resource " + resName + "/" + id + " not found, specified in path: " + nextPathsUnsplit);
}
nextEntity = new ResourceLink(nextPathsUnsplit, theEntity, target);
} else {
if (!multiType) {
throw new ConfigurationException("Search param " + nextSpDef.getName() + " is of unexpected datatype: " + nextObject.getClass());
} else {
continue;
}
}
if (nextEntity != null) {
retVal.add(nextEntity);
}
}
}
theEntity.setHasLinks(retVal.size() > 0);
return retVal;
}
protected List<ResourceIndexedSearchParamDate> extractSearchParamDates(ResourceTable theEntity, IResource theResource) {
return mySearchParamExtractor.extractSearchParamDates(theEntity, theResource);
}
protected List<ResourceIndexedSearchParamNumber> extractSearchParamNumber(ResourceTable theEntity, IResource theResource) {
return mySearchParamExtractor.extractSearchParamNumber(theEntity, theResource);
}
protected List<ResourceIndexedSearchParamUri> extractSearchParamUri(ResourceTable theEntity, IResource theResource) {
return mySearchParamExtractor.extractSearchParamUri(theEntity, theResource);
}
protected List<ResourceIndexedSearchParamCoords> extractSearchParamCoords(ResourceTable theEntity, IResource theResource) {
return mySearchParamExtractor.extractSearchParamCoords(theEntity, theResource);
}
protected List<ResourceIndexedSearchParamQuantity> extractSearchParamQuantity(ResourceTable theEntity, IResource theResource) {
return mySearchParamExtractor.extractSearchParamQuantity(theEntity, theResource);
}
protected List<ResourceIndexedSearchParamString> extractSearchParamStrings(ResourceTable theEntity, IResource theResource) {
return mySearchParamExtractor.extractSearchParamStrings(theEntity, theResource);
}
protected List<BaseResourceIndexedSearchParam> extractSearchParamTokens(ResourceTable theEntity, IResource theResource) {
return mySearchParamExtractor.extractSearchParamTokens(theEntity, theResource);
}
private List<Object> extractValues(String thePaths, IResource theResource) {
List<Object> values = new ArrayList<Object>();
String[] nextPathsSplit = thePaths.split("\\|");
FhirTerser t = getContext().newTerser();
for (String nextPath : nextPathsSplit) {
String nextPathTrimmed = nextPath.trim();
try {
values.addAll(t.getValues(theResource, nextPathTrimmed));
} catch (Exception e) {
RuntimeResourceDefinition def = myContext.getResourceDefinition(theResource);
ourLog.warn("Failed to index values from path[{}] in resource type[{}]: ", new Object[] { nextPathTrimmed, def.getName(), e.toString() });
}
}
return values;
}
private void findMatchingTagIds(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"), translateForcedIdToPid(theResourceId)));
} else {
cq.where(typePredicate);
}
}
TypedQuery<Tuple> query = myEntityManager.createQuery(cq);
for (Tuple next : query.getResultList()) {
tagIds.add(next.get(0, Long.class));
}
}
}
protected void notifyInterceptors(RestOperationTypeEnum operationType, ActionRequestDetails requestDetails) {
if (requestDetails.getId() != null && requestDetails.getId().hasResourceType() && isNotBlank(requestDetails.getResourceType())) {
if (requestDetails.getId().getResourceType().equals(requestDetails.getResourceType()) == false) {
throw new InternalErrorException("Inconsistent server state - Resource types don't match: " + requestDetails.getId().getResourceType() + " / " + requestDetails.getResourceType());
}
}
List<IServerInterceptor> interceptors = getConfig().getInterceptors();
if (interceptors == null) {
return;
}
for (IServerInterceptor next : interceptors) {
next.incomingRequestPreHandled(operationType, requestDetails);
}
}
protected DaoConfig getConfig() {
return myConfig;
}
public FhirContext getContext() {
return myContext;
}
public FhirContext getContext(FhirVersionEnum theVersion) {
FhirVersionEnum ver = theVersion != null ? theVersion : FhirVersionEnum.DSTU1;
synchronized (ourRetrievalContexts) {
FhirContext retVal = ourRetrievalContexts.get(ver);
if (retVal == null) {
retVal = new FhirContext(ver);
ourRetrievalContexts.put(ver, retVal);
}
return retVal;
}
}
@SuppressWarnings("unchecked")
protected <R extends IBaseResource> IFhirResourceDao<R> getDao(Class<R> theType) {
if (myResourceTypeToDao == null) {
myResourceTypeToDao = new HashMap<Class<? extends IBaseResource>, IFhirResourceDao<?>>();
for (IFhirResourceDao<?> next : myResourceDaos) {
myResourceTypeToDao.put(next.getResourceType(), next);
}
if (this instanceof IFhirResourceDao<?>) {
IFhirResourceDao<?> thiz = (IFhirResourceDao<?>) this;
myResourceTypeToDao.put(thiz.getResourceType(), thiz);
}
}
return (IFhirResourceDao<R>) myResourceTypeToDao.get(theType);
}
protected TagDefinition getTag(TagTypeEnum theTagType, String theScheme, String theTerm, String theLabel) {
CriteriaBuilder builder = myEntityManager.getCriteriaBuilder();
CriteriaQuery<TagDefinition> cq = builder.createQuery(TagDefinition.class);
Root<TagDefinition> from = cq.from(TagDefinition.class);
//@formatter:off
if (isNotBlank(theScheme)) {
cq.where(
builder.and(
builder.equal(from.get("myTagType"), theTagType),
builder.equal(from.get("mySystem"), theScheme),
builder.equal(from.get("myCode"), theTerm))
);
} else {
cq.where(
builder.and(
builder.equal(from.get("myTagType"), theTagType),
builder.isNull(from.get("mySystem")),
builder.equal(from.get("myCode"), theTerm))
);
}
//@formatter:on
TypedQuery<TagDefinition> q = myEntityManager.createQuery(cq);
try {
return q.getSingleResult();
} catch (NoResultException e) {
TagDefinition retVal = new TagDefinition(theTagType, theScheme, theTerm, theLabel);
myEntityManager.persist(retVal);
return retVal;
}
}
protected TagList getTags(Class<? extends IResource> theResourceType, IIdType theResourceId) {
String resourceName = null;
if (theResourceType != null) {
resourceName = toResourceName(theResourceType);
if (theResourceId != null && theResourceId.hasVersionIdPart()) {
IFhirResourceDao<? extends IResource> dao = getDao(theResourceType);
BaseHasResource entity = dao.readEntity(theResourceId);
TagList retVal = new TagList();
for (BaseTag next : entity.getTags()) {
retVal.add(next.getTag().toTag());
}
return retVal;
}
}
Set<Long> tagIds = new HashSet<Long>();
findMatchingTagIds(resourceName, theResourceId, tagIds, ResourceTag.class);
findMatchingTagIds(resourceName, theResourceId, tagIds, ResourceHistoryTag.class);
if (tagIds.isEmpty()) {
return new TagList();
}
{
CriteriaBuilder builder = myEntityManager.getCriteriaBuilder();
CriteriaQuery<TagDefinition> cq = builder.createQuery(TagDefinition.class);
Root<TagDefinition> from = cq.from(TagDefinition.class);
cq.where(from.get("myId").in(tagIds));
cq.orderBy(builder.asc(from.get("mySystem")), builder.asc(from.get("myCode")));
TypedQuery<TagDefinition> q = myEntityManager.createQuery(cq);
q.setMaxResults(getConfig().getHardTagListLimit());
TagList retVal = new TagList();
for (TagDefinition next : q.getResultList()) {
retVal.add(next.toTag());
}
return retVal;
}
}
protected IBundleProvider history(String theResourceName, Long theId, Date theSince) {
final List<HistoryTuple> tuples = new ArrayList<HistoryTuple>();
final InstantDt end = createHistoryToTimestamp();
StopWatch timer = new StopWatch();
int limit = 10000;
// Get list of IDs
searchHistoryCurrentVersion(theResourceName, theId, theSince, end.getValue(), limit, tuples);
ourLog.info("Retrieved {} history IDs from current versions in {} ms", tuples.size(), timer.getMillisAndRestart());
searchHistoryHistory(theResourceName, theId, theSince, end.getValue(), limit, tuples);
ourLog.info("Retrieved {} history IDs from previous versions in {} ms", tuples.size(), timer.getMillisAndRestart());
// Sort merged list
Collections.sort(tuples, Collections.reverseOrder());
assert tuples.size() < 2 || !tuples.get(tuples.size() - 2).getUpdated().before(tuples.get(tuples.size() - 1).getUpdated()) : tuples.toString();
return new IBundleProvider() {
@Override
public InstantDt getPublished() {
return end;
}
@Override
public List<IBaseResource> getResources(final int theFromIndex, final int theToIndex) {
final StopWatch timer = new StopWatch();
TransactionTemplate template = new TransactionTemplate(myPlatformTransactionManager);
return template.execute(new TransactionCallback<List<IBaseResource>>() {
@Override
public List<IBaseResource> doInTransaction(TransactionStatus theStatus) {
List<BaseHasResource> resEntities = Lists.newArrayList();
List<HistoryTuple> tupleSubList = tuples.subList(theFromIndex, theToIndex);
searchHistoryCurrentVersion(tupleSubList, resEntities);
ourLog.info("Loaded history from current versions in {} ms", timer.getMillisAndRestart());
searchHistoryHistory(tupleSubList, resEntities);
ourLog.info("Loaded history from previous versions in {} ms", timer.getMillisAndRestart());
Collections.sort(resEntities, new Comparator<BaseHasResource>() {
@Override
public int compare(BaseHasResource theO1, BaseHasResource theO2) {
return theO2.getUpdated().getValue().compareTo(theO1.getUpdated().getValue());
}
});
int limit = theToIndex - theFromIndex;
if (resEntities.size() > limit) {
resEntities = resEntities.subList(0, limit);
}
ArrayList<IBaseResource> retVal = new ArrayList<IBaseResource>();
for (BaseHasResource next : resEntities) {
RuntimeResourceDefinition type;
try {
type = myContext.getResourceDefinition(next.getResourceType());
} catch (DataFormatException e) {
if (next.getFhirVersion() != getContext().getVersion().getVersion()) {
ourLog.info("Ignoring history resource of type[{}] because it is not compatible with version[{}]", next.getResourceType(), getContext().getVersion().getVersion());
continue;
}
throw e;
}
IResource resource = (IResource) toResource(type.getImplementingClass(), next);
retVal.add(resource);
}
return retVal;
}
});
}
@Override
public int size() {
return tuples.size();
}
@Override
public Integer preferredPageSize() {
return null;
}
};
}
protected boolean isValidPid(IIdType theId) {
String idPart = theId.getIdPart();
for (int i = 0; i < idPart.length(); i++) {
char nextChar = idPart.charAt(i);
if (nextChar < '0' || nextChar > '9') {
return false;
}
}
return true;
}
protected List<IBaseResource> loadResourcesById(Set<? extends IIdType> theIncludePids) {
Set<Long> pids = new HashSet<Long>();
for (IIdType next : theIncludePids) {
if (next.isIdPartValidLong()) {
pids.add(next.getIdPartAsLong());
} else {
try {
pids.add(translateForcedIdToPid(next));
} catch (ResourceNotFoundException e) {
ourLog.warn("Failed to translate forced ID [{}] to PID", next.getValue());
}
}
}
if (pids.isEmpty()) {
return new ArrayList<IBaseResource>();
}
CriteriaBuilder builder = myEntityManager.getCriteriaBuilder();
CriteriaQuery<ResourceTable> cq = builder.createQuery(ResourceTable.class);
Root<ResourceTable> from = cq.from(ResourceTable.class);
// cq.where(builder.equal(from.get("myResourceType"),
// getContext().getResourceDefinition(myResourceType).getName()));
// if (theIncludePids != null) {
cq.where(from.get("myId").in(pids));
// }
TypedQuery<ResourceTable> q = myEntityManager.createQuery(cq);
ArrayList<IBaseResource> retVal = new ArrayList<IBaseResource>();
for (ResourceTable next : q.getResultList()) {
IResource resource = (IResource) toResource(next);
retVal.add(resource);
}
return retVal;
}
protected void notifyWriteCompleted() {
for (IDaoListener next : myListeners) {
next.writeCompleted();
}
}
protected void populateResourceIntoEntity(IResource theResource, ResourceTable theEntity) {
if (theEntity.getPublished().isEmpty()) {
theEntity.setPublished(new Date());
}
theEntity.setUpdated(new Date());
theEntity.setResourceType(toResourceName(theResource));
List<BaseResourceReferenceDt> refs = myContext.newTerser().getAllPopulatedChildElementsOfType(theResource, BaseResourceReferenceDt.class);
for (BaseResourceReferenceDt nextRef : refs) {
if (nextRef.getReference().isEmpty() == false) {
if (nextRef.getReference().hasVersionIdPart()) {
nextRef.setReference(nextRef.getReference().toUnqualifiedVersionless());
}
}
}
String encoded = myConfig.getResourceEncoding().newParser(myContext).encodeResourceToString(theResource);
ResourceEncodingEnum encoding = myConfig.getResourceEncoding();
theEntity.setEncoding(encoding);
theEntity.setFhirVersion(myContext.getVersion().getVersion());
try {
switch (encoding) {
case JSON:
theEntity.setResource(encoded.getBytes("UTF-8"));
break;
case JSONC:
theEntity.setResource(GZipUtil.compress(encoded));
break;
}
} catch (UnsupportedEncodingException e) {
throw new InternalErrorException(e);
}
Set<TagDefinition> allDefs = new HashSet<TagDefinition>();
TagList tagList = ResourceMetadataKeyEnum.TAG_LIST.get(theResource);
if (tagList != null) {
for (Tag next : tagList) {
TagDefinition tag = getTag(TagTypeEnum.TAG, next.getScheme(), next.getTerm(), next.getLabel());
allDefs.add(tag);
theEntity.addTag(tag);
theEntity.setHasTags(true);
}
}
List<BaseCodingDt> securityLabels = ResourceMetadataKeyEnum.SECURITY_LABELS.get(theResource);
if (securityLabels != null) {
for (BaseCodingDt next : securityLabels) {
TagDefinition tag = getTag(TagTypeEnum.SECURITY_LABEL, next.getSystemElement().getValue(), next.getCodeElement().getValue(), next.getDisplayElement().getValue());
allDefs.add(tag);
theEntity.addTag(tag);
theEntity.setHasTags(true);
}
}
List<IdDt> profiles = ResourceMetadataKeyEnum.PROFILES.get(theResource);
if (profiles != null) {
for (IIdType next : profiles) {
TagDefinition tag = getTag(TagTypeEnum.PROFILE, NS_JPA_PROFILE, next.getValue(), null);
allDefs.add(tag);
theEntity.addTag(tag);
theEntity.setHasTags(true);
}
}
for (ResourceTag next : new ArrayList<ResourceTag>(theEntity.getTags())) {
TagDefinition nextDef = next.getTag();
if (!allDefs.contains(nextDef)) {
theEntity.getTags().remove(next);
}
}
if (theEntity.getTags().size() == 0) {
theEntity.setHasTags(false);
}
String title = ResourceMetadataKeyEnum.TITLE.get(theResource);
if (title != null && title.length() > BaseHasResource.MAX_TITLE_LENGTH) {
title = title.substring(0, BaseHasResource.MAX_TITLE_LENGTH);
}
theEntity.setTitle(title);
}
protected <R extends IResource> Set<Long> processMatchUrl(String theMatchUrl, Class<R> theResourceType) {
RuntimeResourceDefinition resourceDef = getContext().getResourceDefinition(theResourceType);
SearchParameterMap paramMap = translateMatchUrl(theMatchUrl, resourceDef);
IFhirResourceDao<R> dao = getDao(theResourceType);
Set<Long> ids = dao.searchForIdsWithAndOr(paramMap);
return ids;
}
static SearchParameterMap translateMatchUrl(String theMatchUrl, RuntimeResourceDefinition resourceDef) {
SearchParameterMap paramMap = new SearchParameterMap();
List<NameValuePair> parameters;
try {
String matchUrl = theMatchUrl;
if (matchUrl.indexOf('?') == -1) {
throw new InvalidRequestException("Failed to parse match URL[" + theMatchUrl + "] - Error was: URL does not contain any parameters ('?' not detected)");
}
matchUrl = matchUrl.replace("|", "%7C");
matchUrl = matchUrl.replace("=>=", "=%3E%3D");
matchUrl = matchUrl.replace("=<=", "=%3C%3D");
matchUrl = matchUrl.replace("=>", "=%3E");
matchUrl = matchUrl.replace("=<", "=%3C");
parameters = URLEncodedUtils.parse(new URI(matchUrl), "UTF-8");
} catch (URISyntaxException e) {
throw new InvalidRequestException("Failed to parse match URL[" + theMatchUrl + "] - Error was: " + e.toString());
}
ArrayListMultimap<String, QualifiedParamList> nameToParamLists = ArrayListMultimap.create();
for (NameValuePair next : parameters) {
String paramName = next.getName();
String qualifier = null;
for (int i = 0; i < paramMap.size(); i++) {
switch (paramName.charAt(i)) {
case '.':
case ':':
qualifier = paramName.substring(i);
paramName = paramName.substring(0, i);
i = Integer.MAX_VALUE;
break;
}
}
QualifiedParamList paramList = QualifiedParamList.splitQueryStringByCommasIgnoreEscape(qualifier, next.getValue());
nameToParamLists.put(paramName, paramList);
}
for (String nextParamName : nameToParamLists.keySet()) {
List<QualifiedParamList> paramList = nameToParamLists.get(nextParamName);
if (Constants.PARAM_LASTUPDATED.equals(nextParamName)) {
if (paramList != null && paramList.size() > 0) {
if (paramList.size() > 2) {
throw new InvalidRequestException("Failed to parse match URL[" + theMatchUrl + "] - Can not have more than 2 " + Constants.PARAM_LASTUPDATED + " parameter repetitions");
} else {
DateRangeParam p1 = new DateRangeParam();
p1.setValuesAsQueryTokens(paramList);
paramMap.setLastUpdated(p1);
}
}
continue;
}
if (Constants.PARAM_COUNT.equals(nextParamName)) {
if (paramList.size() > 0 && paramList.get(0).size() > 0) {
String intString = paramList.get(0).get(0);
try {
paramMap.setCount(Integer.parseInt(intString));
} catch (NumberFormatException e) {
throw new InvalidRequestException("Invalid " + Constants.PARAM_COUNT + " value: " + intString);
}
}
continue;
}
RuntimeSearchParam paramDef = resourceDef.getSearchParam(nextParamName);
if (paramDef == null) {
throw new InvalidRequestException("Failed to parse match URL[" + theMatchUrl + "] - Resource type " + resourceDef.getName() + " does not have a parameter with name: " + nextParamName);
}
IQueryParameterAnd<?> param = MethodUtil.parseQueryParams(paramDef, nextParamName, paramList);
paramMap.add(nextParamName, param);
}
return paramMap;
}
@Override
public void registerDaoListener(IDaoListener theListener) {
Validate.notNull(theListener, "theListener");
myListeners.add(theListener);
}
private void searchHistoryCurrentVersion(List<HistoryTuple> theTuples, List<BaseHasResource> theRetVal) {
Collection<HistoryTuple> tuples = Collections2.filter(theTuples, new com.google.common.base.Predicate<HistoryTuple>() {
@Override
public boolean apply(HistoryTuple theInput) {
return theInput.isHistory() == false;
}
});
Collection<Long> ids = Collections2.transform(tuples, new Function<HistoryTuple, Long>() {
@Override
public Long apply(HistoryTuple theInput) {
return theInput.getId();
}
});
if (ids.isEmpty()) {
return;
}
CriteriaBuilder builder = myEntityManager.getCriteriaBuilder();
CriteriaQuery<ResourceTable> cq = builder.createQuery(ResourceTable.class);
Root<ResourceTable> from = cq.from(ResourceTable.class);
cq.where(from.get("myId").in(ids));
cq.orderBy(builder.desc(from.get("myUpdated")));
TypedQuery<ResourceTable> q = myEntityManager.createQuery(cq);
for (ResourceTable next : q.getResultList()) {
theRetVal.add(next);
}
}
private void searchHistoryCurrentVersion(String theResourceName, Long theId, Date theSince, Date theEnd, Integer theLimit, List<HistoryTuple> tuples) {
CriteriaBuilder builder = myEntityManager.getCriteriaBuilder();
CriteriaQuery<Tuple> cq = builder.createTupleQuery();
Root<?> from = cq.from(ResourceTable.class);
cq.multiselect(from.get("myId").as(Long.class), from.get("myUpdated").as(Date.class));
List<Predicate> predicates = new ArrayList<Predicate>();
if (theSince != null) {
Predicate low = builder.greaterThanOrEqualTo(from.<Date> get("myUpdated"), theSince);
predicates.add(low);
}
Predicate high = builder.lessThan(from.<Date> get("myUpdated"), theEnd);
predicates.add(high);
if (theResourceName != null) {
predicates.add(builder.equal(from.get("myResourceType"), theResourceName));
}
if (theId != null) {
predicates.add(builder.equal(from.get("myId"), theId));
}
cq.where(builder.and(predicates.toArray(new Predicate[0])));
cq.orderBy(builder.desc(from.get("myUpdated")));
TypedQuery<Tuple> q = myEntityManager.createQuery(cq);
if (theLimit != null && theLimit < myConfig.getHardSearchLimit()) {
q.setMaxResults(theLimit);
} else {
q.setMaxResults(myConfig.getHardSearchLimit());
}
for (Tuple next : q.getResultList()) {
long id = next.get(0, Long.class);
Date updated = next.get(1, Date.class);
tuples.add(new HistoryTuple(false, updated, id));
}
}
private void searchHistoryHistory(List<HistoryTuple> theTuples, List<BaseHasResource> theRetVal) {
Collection<HistoryTuple> tuples = Collections2.filter(theTuples, new com.google.common.base.Predicate<HistoryTuple>() {
@Override
public boolean apply(HistoryTuple theInput) {
return theInput.isHistory() == true;
}
});
Collection<Long> ids = Collections2.transform(tuples, new Function<HistoryTuple, Long>() {
@Override
public Long apply(HistoryTuple theInput) {
return (Long) theInput.getId();
}
});
if (ids.isEmpty()) {
return;
}
ourLog.info("Retrieving {} history elements from ResourceHistoryTable", ids.size());
CriteriaBuilder builder = myEntityManager.getCriteriaBuilder();
CriteriaQuery<ResourceHistoryTable> cq = builder.createQuery(ResourceHistoryTable.class);
Root<ResourceHistoryTable> from = cq.from(ResourceHistoryTable.class);
cq.where(from.get("myId").in(ids));
cq.orderBy(builder.desc(from.get("myUpdated")));
TypedQuery<ResourceHistoryTable> q = myEntityManager.createQuery(cq);
for (ResourceHistoryTable next : q.getResultList()) {
theRetVal.add(next);
}
}
private void searchHistoryHistory(String theResourceName, Long theResourceId, Date theSince, Date theEnd, Integer theLimit, List<HistoryTuple> tuples) {
CriteriaBuilder builder = myEntityManager.getCriteriaBuilder();
CriteriaQuery<Tuple> cq = builder.createTupleQuery();
Root<?> from = cq.from(ResourceHistoryTable.class);
cq.multiselect(from.get("myId").as(Long.class), from.get("myUpdated").as(Date.class));
List<Predicate> predicates = new ArrayList<Predicate>();
if (theSince != null) {
Predicate low = builder.greaterThanOrEqualTo(from.<Date> get("myUpdated"), theSince);
predicates.add(low);
}
Predicate high = builder.lessThan(from.<Date> get("myUpdated"), theEnd);
predicates.add(high);
if (theResourceName != null) {
predicates.add(builder.equal(from.get("myResourceType"), theResourceName));
}
if (theResourceId != null) {
predicates.add(builder.equal(from.get("myResourceId"), theResourceId));
}
cq.where(builder.and(predicates.toArray(new Predicate[0])));
cq.orderBy(builder.desc(from.get("myUpdated")));
TypedQuery<Tuple> q = myEntityManager.createQuery(cq);
if (theLimit != null && theLimit < myConfig.getHardSearchLimit()) {
q.setMaxResults(theLimit);
} else {
q.setMaxResults(myConfig.getHardSearchLimit());
}
for (Tuple next : q.getResultList()) {
Long id = next.get(0, Long.class);
Date updated = (Date) next.get(1);
tuples.add(new HistoryTuple(true, updated, id));
}
}
protected MetaDt toMetaDt(List<TagDefinition> tagDefinitions) {
MetaDt retVal = new MetaDt();
for (TagDefinition next : tagDefinitions) {
switch (next.getTagType()) {
case PROFILE:
retVal.addProfile(next.getCode());
break;
case SECURITY_LABEL:
retVal.addSecurity().setSystem(next.getSystem()).setCode(next.getCode()).setDisplay(next.getDisplay());
break;
case TAG:
retVal.addTag().setSystem(next.getSystem()).setCode(next.getCode()).setDisplay(next.getDisplay());
break;
}
}
return retVal;
}
public void setContext(FhirContext theContext) {
myContext = theContext;
switch (myContext.getVersion().getVersion()) {
case DSTU2:
mySearchParamExtractor = new SearchParamExtractorDstu2(theContext);
break;
case DSTU1:
mySearchParamExtractor = new SearchParamExtractorDstu1(theContext);
break;
case DSTU2_HL7ORG:
case DEV:
throw new IllegalStateException("Don't know how to handle version: " + myContext.getVersion().getVersion());
}
}
protected ResourceTable toEntity(IResource theResource) {
ResourceTable retVal = new ResourceTable();
populateResourceIntoEntity(theResource, retVal);
return retVal;
}
protected IBaseResource toResource(BaseHasResource theEntity) {
RuntimeResourceDefinition type = myContext.getResourceDefinition(theEntity.getResourceType());
return toResource(type.getImplementingClass(), theEntity);
}
protected <R extends IBaseResource> R toResource(Class<R> theResourceType, BaseHasResource theEntity) {
String resourceText = null;
switch (theEntity.getEncoding()) {
case JSON:
try {
resourceText = new String(theEntity.getResource(), "UTF-8");
} catch (UnsupportedEncodingException e) {
throw new Error("Should not happen", e);
}
break;
case JSONC:
resourceText = GZipUtil.decompress(theEntity.getResource());
break;
}
IParser parser = theEntity.getEncoding().newParser(getContext(theEntity.getFhirVersion()));
R retVal;
try {
retVal = parser.parseResource(theResourceType, resourceText);
} catch (Exception e) {
StringBuilder b = new StringBuilder();
b.append("Failed to parse database resource[");
b.append(theResourceType);
b.append("/");
b.append(theEntity.getIdDt().getIdPart());
b.append(" (pid ");
b.append(theEntity.getId());
b.append(", version ");
b.append(myContext.getVersion().getVersion());
b.append("): ");
b.append(e.getMessage());
String msg = b.toString();
ourLog.error(msg, e);
throw new DataFormatException(msg, e);
}
IResource res = (IResource) retVal;
res.setId(theEntity.getIdDt());
ResourceMetadataKeyEnum.VERSION.put(res, Long.toString(theEntity.getVersion()));
ResourceMetadataKeyEnum.PUBLISHED.put(res, theEntity.getPublished());
ResourceMetadataKeyEnum.UPDATED.put(res, theEntity.getUpdated());
if (theEntity.getTitle() != null) {
ResourceMetadataKeyEnum.TITLE.put(res, theEntity.getTitle());
}
if (theEntity.getDeleted() != null) {
ResourceMetadataKeyEnum.DELETED_AT.put(res, new InstantDt(theEntity.getDeleted()));
}
Collection<? extends BaseTag> tags = theEntity.getTags();
if (theEntity.isHasTags()) {