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

FIxes to get the synced build working

This commit is contained in:
jamesagnew 2018-05-13 08:08:34 -04:00
parent 23a01b5f18
commit ccb859fdbe
43 changed files with 42270 additions and 42000 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/i18n/HapiLocalizer.java
View File

@ -7,6 +7,7 @@ import java.util.*;
import java.util.concurrent.ConcurrentHashMap;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.trim;
/*
* #%L
@ -70,6 +71,7 @@ public class HapiLocalizer {
for (ResourceBundle nextBundle : myBundle) {
if (nextBundle.containsKey(theQualifiedKey)) {
formatString = nextBundle.getString(theQualifiedKey);
formatString = trim(formatString);
}
if (isNotBlank(formatString)) {
break;

4
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/ValidateUtil.java
View File

@ -9,9 +9,9 @@ package ca.uhn.fhir.util;
* 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.

2
hapi-fhir-base/src/main/resources/ca/uhn/fhir/i18n/hapi-messages.properties
View File

@ -58,6 +58,7 @@ ca.uhn.fhir.validation.ValidationResult.noIssuesDetected=No issues detected duri
# JPA Messages
ca.uhn.fhir.jpa.config.HapiFhirHibernateJpaDialect.resourceVersionConstraintFailure=The operation has failed with a version constraint failure. This generally means that two clients/threads were trying to update the same resource at the same time, and this request was chosen as the failing request.
ca.uhn.fhir.jpa.config.HapiFhirHibernateJpaDialect.resourceIndexedCompositeStringUniqueConstraintFailure=The operation has failed with a unique index constraint failure. This probably means that the operation was trying to create/update a resource that would have resulted in a duplicate value for a unique index.
ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.externalReferenceNotAllowed=Resource contains external reference to URL "{0}" but this server is not configured to allow external references
ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.incomingNoopInTransaction=Transaction contains resource with operation NOOP. This is only valid as a response operation, not in a request
@ -67,6 +68,7 @@ ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.invalidMatchUrlMultipleMatches=Invalid match
ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.transactionOperationWithMultipleMatchFailure=Failed to {0} resource with match URL "{1}" because this search matched {2} resources
ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.transactionOperationFailedNoId=Failed to {0} resource in transaction because no ID was provided
ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.transactionOperationFailedUnknownId=Failed to {0} resource in transaction because no resource could be found with ID {1}
ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.uniqueIndexConflictFailure=Can not create resource of type {0} as it would create a duplicate index matching query: {1} (existing index belongs to {2})
ca.uhn.fhir.jpa.dao.BaseHapiFhirSystemDao.transactionContainsMultipleWithDuplicateId=Transaction bundle contains multiple resources with ID: {0}
ca.uhn.fhir.jpa.dao.BaseHapiFhirSystemDao.transactionEntryHasInvalidVerb=Transaction bundle entry has missing or invalid HTTP Verb specified in Bundle.entry({1}).request.method. Found value: "{0}"

20
hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/AbstractImportExportCsvConceptMapCommand.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.cli;
/*-
* #%L
* HAPI FHIR - Command Line Client - API
* %%
* Copyright (C) 2014 - 2018 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 ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.rest.client.api.IGenericClient;

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

@ -9,9 +9,9 @@ package ca.uhn.fhir.cli;
* 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.

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

@ -9,9 +9,9 @@ package ca.uhn.fhir.cli;
* 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.

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

@ -9,9 +9,9 @@ package ca.uhn.fhir.cli;
* 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.

35
hapi-fhir-converter/src/main/java/org/hl7/fhir/convertors/VersionConvertorConstants.java
View File

@ -1,7 +1,28 @@
package org.hl7.fhir.convertors;
public class VersionConvertorConstants {
public final static String MODIFIER_REASON_EXTENSION = "http://hl7.org/fhir/tooling/StructureDefinition/r4ModifierReason";
public final static String MODIFIER_REASON_LEGACY = "No Modifier Reason provideed in previous versions of FHIR";
}
package org.hl7.fhir.convertors;
/*-
* #%L
* HAPI FHIR - Converter
* %%
* Copyright (C) 2014 - 2018 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%
*/
public class VersionConvertorConstants {
public final static String MODIFIER_REASON_EXTENSION = "http://hl7.org/fhir/tooling/StructureDefinition/r4ModifierReason";
public final static String MODIFIER_REASON_LEGACY = "No Modifier Reason provideed in previous versions of FHIR";
}

24415
hapi-fhir-converter/src/main/java/org/hl7/fhir/convertors/VersionConvertor_10_40.java
View File

File diff suppressed because it is too large Load Diff

14569
hapi-fhir-converter/src/main/java/org/hl7/fhir/convertors/VersionConvertor_14_40.java
View File

File diff suppressed because it is too large Load Diff

44805
hapi-fhir-converter/src/main/java/org/hl7/fhir/convertors/VersionConvertor_30_40.java
View File

File diff suppressed because it is too large Load Diff

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

@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.config;
* 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.

32
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/HapiFhirHibernateJpaDialect.java
View File

@ -1,14 +1,38 @@
package ca.uhn.fhir.jpa.config;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2018 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 ca.uhn.fhir.i18n.HapiLocalizer;
import ca.uhn.fhir.jpa.entity.ResourceHistoryTable;
import ca.uhn.fhir.jpa.entity.ResourceIndexedCompositeStringUnique;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
import org.hibernate.HibernateException;
import org.hibernate.exception.ConstraintViolationException;
import org.springframework.dao.DataAccessException;
import org.springframework.data.mapping.PreferredConstructor;
import org.springframework.orm.jpa.vendor.HibernateJpaDialect;
import static org.apache.commons.lang3.StringUtils.defaultString;
public class HapiFhirHibernateJpaDialect extends HibernateJpaDialect {
private HapiLocalizer myLocalizer;
@ -23,8 +47,12 @@ public class HapiFhirHibernateJpaDialect extends HibernateJpaDialect {
@Override
protected DataAccessException convertHibernateAccessException(HibernateException theException) {
if (theException instanceof ConstraintViolationException) {
if (ResourceHistoryTable.IDX_RESVER_ID_VER.equals(((ConstraintViolationException) theException).getConstraintName())) {
throw new ResourceVersionConflictException(myLocalizer.getMessage(HapiFhirHibernateJpaDialect.class, "resourceVersionConstraintFailure"));
String constraintName = ((ConstraintViolationException) theException).getConstraintName();
switch (defaultString(constraintName)) {
case ResourceHistoryTable.IDX_RESVER_ID_VER:
throw new ResourceVersionConflictException(myLocalizer.getMessage(HapiFhirHibernateJpaDialect.class, "resourceVersionConstraintFailure"));
case ResourceIndexedCompositeStringUnique.IDX_IDXCMPSTRUNIQ_STRING:
throw new ResourceVersionConflictException(myLocalizer.getMessage(HapiFhirHibernateJpaDialect.class, "resourceIndexedCompositeStringUniqueConstraintFailure"));
}
}

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/dstu3/BaseDstu3Config.java
View File

@ -37,9 +37,9 @@ import org.springframework.transaction.annotation.EnableTransactionManagement;
* 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.

15
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
View File

@ -297,12 +297,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
return toExpungeOutcome(theExpungeOptions, remainingCount);
}
private void doExpungeEverythingQuery(String theQuery) {
StopWatch sw = new StopWatch();
int outcome = myEntityManager.createQuery(theQuery).executeUpdate();
ourLog.info("Query affected {} rows in {}: {}", outcome, sw.toString(), theQuery);
}
private void doExpungeEverything() {
ourLog.info("** BEGINNING GLOBAL $expunge **");
@ -368,6 +362,12 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
ourLog.info("** COMPLETED GLOBAL $expunge **");
}
private void doExpungeEverythingQuery(String theQuery) {
StopWatch sw = new StopWatch();
int outcome = myEntityManager.createQuery(theQuery).executeUpdate();
ourLog.info("Query affected {} rows in {}: {}", outcome, sw.toString(), theQuery);
}
private void expungeCurrentVersionOfResource(Long theResourceId) {
ResourceTable resource = myResourceTableDao.findOne(theResourceId);
@ -2081,7 +2081,8 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
if (myConfig.isUniqueIndexesCheckedBeforeSave()) {
ResourceIndexedCompositeStringUnique existing = myResourceIndexedCompositeStringUniqueDao.findByQueryString(next.getIndexString());
if (existing != null) {
throw new PreconditionFailedException("Can not create resource of type " + theEntity.getResourceType() + " as it would create a duplicate index matching query: " + next.getIndexString() + " (existing index belongs to " + existing.getResource().getIdDt().toUnqualifiedVersionless().getValue() + ")");
String msg = getContext().getLocalizer().getMessage(BaseHapiFhirDao.class, "uniqueIndexConflictFailure", theEntity.getResourceType(), next.getIndexString(), existing.getResource().getIdDt().toUnqualifiedVersionless().getValue());
throw new PreconditionFailedException(msg);
}
}
ourLog.debug("Persisting unique index: {}", next);

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

@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.dao;
* 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.

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

@ -17,9 +17,9 @@ import java.util.Optional;
* 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.

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

@ -15,9 +15,9 @@ import org.springframework.data.repository.query.Param;
* 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.

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

@ -15,9 +15,9 @@ import org.springframework.data.repository.query.Param;
* 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.

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

@ -15,9 +15,9 @@ import org.springframework.data.repository.query.Param;
* 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.

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoConceptMapDstu3.java
View File

@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.dao.dstu3;
* 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.

20
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptMap.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.jpa.entity;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2018 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 org.apache.commons.lang3.builder.ToStringBuilder;
import org.apache.commons.lang3.builder.ToStringStyle;

20
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptMapGroup.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.jpa.entity;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2018 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 org.apache.commons.lang3.builder.ToStringBuilder;
import org.apache.commons.lang3.builder.ToStringStyle;

20
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptMapGroupElement.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.jpa.entity;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2018 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 org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.HashCodeBuilder;
import org.apache.commons.lang3.builder.ToStringBuilder;

20
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptMapGroupElementTarget.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.jpa.entity;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2018 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 org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.HashCodeBuilder;
import org.apache.commons.lang3.builder.ToStringBuilder;

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

@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.search;
* 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.

12
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImpl.java
View File

@ -104,7 +104,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
for (SearchTask next : myIdToSearchTask.values()) {
next.requestImmediateAbort();
try {
next.getCompletionLatch().await();
next.getCompletionLatch().await(30, TimeUnit.SECONDS);
} catch (InterruptedException e) {
ourLog.warn("Failed to wait for completion", e);
}
@ -559,11 +559,13 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
saveSearch();
}
} finally {
myIdToSearchTask.remove(mySearch.getUuid());
myInitialCollectionLatch.countDown();
myCompletionLatch.countDown();
myIdToSearchTask.remove(mySearch.getUuid());
myInitialCollectionLatch.countDown();
myCompletionLatch.countDown();
}
return null;
}

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcDstu3.java
View File

@ -40,9 +40,9 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
* 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.

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

@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.term;
* 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.

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

@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.term;
* 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.

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

@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.term;
* 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.

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

@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.term;
* 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.

20
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/DerbyTenSevenHapiFhirDialect.java
View File

@ -1,5 +1,25 @@
package ca.uhn.fhir.jpa.util;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2018 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 org.hibernate.dialect.DerbyTenSevenDialect;
import org.hibernate.exception.spi.TemplatedViolatedConstraintNameExtracter;
import org.hibernate.exception.spi.ViolatedConstraintNameExtracter;

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

@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.util;
* 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.

7
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDaoTest.java
View File

@ -17,6 +17,7 @@ import ca.uhn.fhir.model.dstu2.resource.Observation;
import ca.uhn.fhir.model.primitive.DateTimeDt;
import ca.uhn.fhir.rest.param.ReferenceParam;
import ca.uhn.fhir.util.TestUtil;
import org.springframework.transaction.PlatformTransactionManager;
public class BaseHapiFhirDaoTest extends BaseJpaTest {
@ -61,5 +62,9 @@ public class BaseHapiFhirDaoTest extends BaseJpaTest {
protected FhirContext getContext() {
return ourCtx;
}
@Override
protected PlatformTransactionManager getTxManager() {
return null;
}
}

42
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/BaseJpaTest.java
View File

@ -30,6 +30,11 @@ import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Rule;
import org.mockito.Mockito;
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 java.io.IOException;
import java.io.InputStream;
@ -44,8 +49,6 @@ import static org.mockito.Mockito.when;
public abstract class BaseJpaTest {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseJpaTest.class);
protected static final String CM_URL = "http://example.com/my_concept_map";
protected static final String CS_URL = "http://example.com/my_code_system";
protected static final String CS_URL_2 = "http://example.com/my_code_system2";
@ -53,14 +56,13 @@ public abstract class BaseJpaTest {
protected static final String CS_URL_4 = "http://example.com/my_code_system4";
protected static final String VS_URL = "http://example.com/my_value_set";
protected static final String VS_URL_2 = "http://example.com/my_value_set2";
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseJpaTest.class);
@Rule
public LoggingRule myLoggingRule = new LoggingRule();
protected ServletRequestDetails mySrd;
protected ArrayList<IServerInterceptor> myServerInterceptorList;
protected IRequestOperationCallback myRequestOperationCallback = mock(IRequestOperationCallback.class);
@Rule
public LoggingRule myLoggingRule = new LoggingRule();
@After
public final void afterPerformCleanup() {
BaseHapiFhirResourceDao.setDisableIncrementOnUpdateForUnitTest(false);
@ -76,8 +78,31 @@ public abstract class BaseJpaTest {
when(mySrd.getHeaders(eq(JpaConstants.HEADER_META_SNAPSHOT_MODE))).thenReturn(new ArrayList<>());
}
@Before
public void beforeRandomizeLocale() {
randomizeLocale();
}
protected abstract FhirContext getContext();
protected abstract PlatformTransactionManager getTxManager();
public TransactionTemplate newTxTemplate() {
TransactionTemplate retVal = new TransactionTemplate(getTxManager());
retVal.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRES_NEW);
retVal.afterPropertiesSet();
return retVal;
}
public void runInTransaction(Runnable theRunnable) {
newTxTemplate().execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
theRunnable.run();
}
});
}
/**
* Sleep until at least 1 ms has elapsed
*/
@ -239,11 +264,6 @@ public abstract class BaseJpaTest {
return retVal.toArray(new String[retVal.size()]);
}
@Before
public void beforeRandomizeLocale() {
randomizeLocale();
}
@AfterClass
public static void afterClassClearContext() throws Exception {
TestUtil.clearAllStaticFieldsForUnitTest();

5
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/BaseJpaDstu2Test.java
View File

@ -211,6 +211,11 @@ public abstract class BaseJpaDstu2Test extends BaseJpaTest {
return myFhirCtx;
}
@Override
protected PlatformTransactionManager getTxManager() {
return myTxManager;
}
protected <T extends IBaseResource> T loadResourceFromClasspath(Class<T> type, String resourceName) throws IOException {
InputStream stream = FhirResourceDaoDstu2SearchNoFtTest.class.getResourceAsStream(resourceName);
if (stream == null) {

5
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/BaseJpaDstu3Test.java
View File

@ -301,6 +301,11 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
return myFhirCtx;
}
@Override
protected PlatformTransactionManager getTxManager() {
return myTxManager;
}
protected <T extends IBaseResource> T loadResourceFromClasspath(Class<T> type, String resourceName) throws IOException {
InputStream stream = FhirResourceDaoDstu2SearchNoFtTest.class.getResourceAsStream(resourceName);
if (stream == null) {

92
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3SearchWithLuceneDisabledTest.java
View File

@ -1,22 +1,5 @@
package ca.uhn.fhir.jpa.dao.dstu3;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.fail;
import javax.persistence.EntityManager;
import org.hl7.fhir.dstu3.hapi.ctx.IValidationSupport;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.*;
import org.junit.runner.RunWith;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.test.context.ContextConfiguration;
import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.annotation.Transactional;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.config.TestDstu3WithoutLuceneConfig;
import ca.uhn.fhir.jpa.dao.*;
@ -26,15 +9,40 @@ import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.TestUtil;
import org.hl7.fhir.dstu3.hapi.ctx.IValidationSupport;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.test.context.ContextConfiguration;
import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
import org.springframework.transaction.PlatformTransactionManager;
import javax.persistence.EntityManager;
import static org.junit.Assert.*;
// @RunWith(SpringJUnit4ClassRunner.class)
// @ContextConfiguration(classes= {TestDstu3WithoutLuceneConfig.class})
// @SuppressWarnings("unchecked")
@RunWith(SpringJUnit4ClassRunner.class)
@ContextConfiguration(classes = { TestDstu3WithoutLuceneConfig.class })
@ContextConfiguration(classes = {TestDstu3WithoutLuceneConfig.class})
public class FhirResourceDaoDstu3SearchWithLuceneDisabledTest extends BaseJpaTest {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoDstu3SearchWithLuceneDisabledTest.class);
@Autowired
protected DaoConfig myDaoConfig;
@Autowired
protected PlatformTransactionManager myTxManager;
@Autowired
protected ISearchParamPresenceSvc mySearchParamPresenceSvc;
@Autowired
protected ISearchCoordinatorSvc mySearchCoordinatorSvc;
@Autowired
protected ISearchParamRegistry mySearchParamRegistry;
@Autowired
@Qualifier("myAllergyIntoleranceDaoDstu3")
private IFhirResourceDao<AllergyIntolerance> myAllergyIntoleranceDao;
@ -63,8 +71,6 @@ public class FhirResourceDaoDstu3SearchWithLuceneDisabledTest extends BaseJpaTes
@Qualifier("myConditionDaoDstu3")
private IFhirResourceDao<Condition> myConditionDao;
@Autowired
protected DaoConfig myDaoConfig;
@Autowired
@Qualifier("myDeviceDaoDstu3")
private IFhirResourceDao<Device> myDeviceDao;
@Autowired
@ -135,24 +141,15 @@ public class FhirResourceDaoDstu3SearchWithLuceneDisabledTest extends BaseJpaTes
@Autowired
@Qualifier("mySystemProviderDstu3")
private JpaSystemProviderDstu3 mySystemProvider;
@Autowired
protected PlatformTransactionManager myTxManager;
@Autowired
protected ISearchParamPresenceSvc mySearchParamPresenceSvc;
@Autowired
@Qualifier("myJpaValidationSupportChainDstu3")
private IValidationSupport myValidationSupport;
@Autowired
protected ISearchCoordinatorSvc mySearchCoordinatorSvc;
@Autowired
protected ISearchParamRegistry mySearchParamRegistry;
@Before
@Transactional()
public void beforePurgeDatabase() {
purgeDatabase(myDaoConfig, mySystemDao, mySearchParamPresenceSvc, mySearchCoordinatorSvc, mySearchParamRegistry);
runInTransaction(() -> {
purgeDatabase(myDaoConfig, mySystemDao, mySearchParamPresenceSvc, mySearchCoordinatorSvc, mySearchParamRegistry);
});
}
@Before
@ -167,18 +164,9 @@ public class FhirResourceDaoDstu3SearchWithLuceneDisabledTest extends BaseJpaTes
return myFhirCtx;
}
@Test
public void testSearchWithRegularParam() throws Exception {
String methodName = "testEverythingIncludesBackReferences";
Organization org = new Organization();
org.setName(methodName);
IIdType orgId = myOrganizationDao.create(org, mySrd).getId().toUnqualifiedVersionless();
SearchParameterMap map = new SearchParameterMap();
map.add(Organization.SP_NAME, new StringParam(methodName));
myOrganizationDao.search(map);
@Override
protected PlatformTransactionManager getTxManager() {
return myTxManager;
}
@Test
@ -199,6 +187,20 @@ public class FhirResourceDaoDstu3SearchWithLuceneDisabledTest extends BaseJpaTes
}
}
@Test
public void testSearchWithRegularParam() throws Exception {
String methodName = "testEverythingIncludesBackReferences";
Organization org = new Organization();
org.setName(methodName);
IIdType orgId = myOrganizationDao.create(org, mySrd).getId().toUnqualifiedVersionless();
SearchParameterMap map = new SearchParameterMap();
map.add(Organization.SP_NAME, new StringParam(methodName));
myOrganizationDao.search(map);
}
@Test
public void testSearchWithText() throws Exception {
String methodName = "testEverythingIncludesBackReferences";

17
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseJpaR4Test.java
View File

@ -324,20 +324,9 @@ public abstract class BaseJpaR4Test extends BaseJpaTest {
return newJsonParser.parseResource(type, string);
}
public TransactionTemplate newTxTemplate() {
TransactionTemplate retVal = new TransactionTemplate(myTxManager);
retVal.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRES_NEW);
retVal.afterPropertiesSet();
return retVal;
}
public void runInTransaction(Runnable theRunnable) {
newTxTemplate().execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
theRunnable.run();
}
});
@Override
protected PlatformTransactionManager getTxManager() {
return myTxManager;
}
@AfterClass

5
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchWithLuceneDisabledTest.java
View File

@ -103,6 +103,11 @@ public class FhirResourceDaoR4SearchWithLuceneDisabledTest extends BaseJpaTest {
myDaoConfig.setIncludeLimit(2000);
}
@Override
protected PlatformTransactionManager getTxManager() {
return myTxManager;
}
@Override
protected FhirContext getContext() {
return myFhirCtx;

10
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4UniqueSearchParamTest.java
View File

@ -10,6 +10,7 @@ import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.param.DateParam;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
import ca.uhn.fhir.util.TestUtil;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.*;
@ -18,7 +19,6 @@ import org.junit.After;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Test;
import org.springframework.orm.jpa.JpaSystemException;
import org.springframework.test.context.TestPropertySource;
import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.support.TransactionCallbackWithoutResult;
@ -316,7 +316,7 @@ public class FhirResourceDaoR4UniqueSearchParamTest extends BaseJpaR4Test {
List<JpaRuntimeSearchParam> params = mySearchParamRegsitry.getActiveUniqueSearchParams("Patient");
assertEquals(1, params.size());
assertEquals(params.get(0).isUnique(), true);
assertTrue(params.get(0).isUnique());
assertEquals(2, params.get(0).getCompositeOf().size());
// Should be alphabetical order
assertEquals("birthdate", params.get(0).getCompositeOf().get(0).getName());
@ -484,8 +484,8 @@ public class FhirResourceDaoR4UniqueSearchParamTest extends BaseJpaR4Test {
try {
myPatientDao.create(pt1).getId().toUnqualifiedVersionless();
fail();
} catch (JpaSystemException e) {
// good
} catch (ResourceVersionConflictException e) {
assertEquals("The operation has failed with a unique index constraint failure. This probably means that the operation was trying to create/update a resource that would have resulted in a duplicate value for a unique index.", e.getMessage());
}
}
@ -788,7 +788,7 @@ public class FhirResourceDaoR4UniqueSearchParamTest extends BaseJpaR4Test {
assertEquals(searchId, results.getUuid());
assertThat(toUnqualifiedVersionlessIdValues(results), containsInAnyOrder(id1));
// Null because we just reuse the last search
assertEquals(null, SearchBuilder.getLastHandlerMechanismForUnitTest());
assertNull(SearchBuilder.getLastHandlerMechanismForUnitTest());
SearchBuilder.resetLastHandlerMechanismForUnitTest();
params = new SearchParameterMap();

4
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/method/OperationParameter.java
View File

@ -41,9 +41,9 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
* 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.