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Concept Set Snapshots/Locking/Unlocking feature implementation
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@oleg-odysseus
oleg-odysseus committed Feb 11, 2025
1 parent df5175c commit a17099c
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Showing 20 changed files with 893 additions and 27 deletions.
8 changes: 8 additions & 0 deletions pom.xml
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Expand Up @@ -64,6 +64,14 @@
<!-- CDM properties -->
<source.name>CDM_NAME</source.name>
<cdm.version>5</cdm.version>
<!-- Snapshot datasource properties -->
<snapshot.history.source.connection>jdbc:postgresql://localhost:5432/OHDSI_AMGEN_LOCK_HISTORY</snapshot.history.source.connection>
<snapshot.history.source.schema>lock_history</snapshot.history.source.schema>
<snapshot.history.source.dialect>postgresql</snapshot.history.source.dialect>
<snapshot.history.source.username>userWithWritePrivs</snapshot.history.source.username>
<snapshot.history.source.password>password</snapshot.history.source.password>
<snapshot.history.flyway.locations>classpath:snapshots_db/migration/postgresql</snapshot.history.flyway.locations>
<snapshot.locking.enabled>true</snapshot.locking.enabled>
<!-- Person properties -->
<person.viewDates>false</person.viewDates>
<!-- Heracles properties -->
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132 changes: 114 additions & 18 deletions src/main/java/org/ohdsi/webapi/service/ConceptSetService.java
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Expand Up @@ -15,21 +15,8 @@
*/
package org.ohdsi.webapi.service;

import java.io.ByteArrayOutputStream;
import java.util.*;
import java.util.stream.Collectors;
import java.util.stream.StreamSupport;

import javax.transaction.Transactional;
import javax.ws.rs.*;
import javax.ws.rs.core.MediaType;
import javax.ws.rs.core.Response;

import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import javax.cache.CacheManager;
import javax.cache.configuration.MutableConfiguration;

import org.apache.shiro.authz.UnauthorizedException;
import org.ohdsi.circe.vocabulary.ConceptSetExpression;
import org.ohdsi.vocabulary.Concept;
Expand All @@ -40,16 +27,23 @@
import org.ohdsi.webapi.conceptset.ConceptSetGenerationInfo;
import org.ohdsi.webapi.conceptset.ConceptSetGenerationInfoRepository;
import org.ohdsi.webapi.conceptset.ConceptSetItem;
import org.ohdsi.webapi.conceptset.dto.ConceptSetVersionFullDTO;
import org.ohdsi.webapi.conceptset.annotation.ConceptSetAnnotation;
import org.ohdsi.webapi.conceptset.dto.ConceptSetVersionFullDTO;
import org.ohdsi.webapi.exception.ConceptNotExistException;
import org.ohdsi.webapi.security.PermissionService;
import org.ohdsi.webapi.service.annotations.SearchDataTransformer;
import org.ohdsi.webapi.service.dto.AnnotationDTO;
import org.ohdsi.webapi.service.dto.AnnotationDetailsDTO;
import org.ohdsi.webapi.service.dto.ConceptSetDTO;
import org.ohdsi.webapi.service.dto.SaveConceptSetAnnotationsRequest;
import org.ohdsi.webapi.service.dto.AnnotationDTO;
import org.ohdsi.webapi.service.dto.CopyAnnotationsRequest;
import org.ohdsi.webapi.service.dto.SaveConceptSetAnnotationsRequest;
import org.ohdsi.webapi.service.lock.ConceptSetLockingService;
import org.ohdsi.webapi.service.lock.dto.ConceptSetSnapshotActionRequest;
import org.ohdsi.webapi.service.lock.dto.ConceptSetSnapshotParameters;
import org.ohdsi.webapi.service.lock.dto.GetConceptSetSnapshotItemsRequest;
import org.ohdsi.webapi.service.lock.dto.GetConceptSetSnapshotItemsResponse;
import org.ohdsi.webapi.service.lock.dto.IsLockedBatchCheckRequest;
import org.ohdsi.webapi.service.lock.dto.IsLockedBatchCheckResponse;
import org.ohdsi.webapi.shiro.Entities.UserEntity;
import org.ohdsi.webapi.shiro.Entities.UserRepository;
import org.ohdsi.webapi.shiro.management.Security;
Expand All @@ -60,9 +54,9 @@
import org.ohdsi.webapi.tag.domain.HasTags;
import org.ohdsi.webapi.tag.dto.TagNameListRequestDTO;
import org.ohdsi.webapi.util.CacheHelper;
import org.ohdsi.webapi.util.ExceptionUtils;
import org.ohdsi.webapi.util.ExportUtil;
import org.ohdsi.webapi.util.NameUtils;
import org.ohdsi.webapi.util.ExceptionUtils;
import org.ohdsi.webapi.versioning.domain.ConceptSetVersion;
import org.ohdsi.webapi.versioning.domain.Version;
import org.ohdsi.webapi.versioning.domain.VersionBase;
Expand All @@ -79,6 +73,37 @@
import org.springframework.dao.EmptyResultDataAccessException;
import org.springframework.stereotype.Component;

import javax.cache.CacheManager;
import javax.cache.configuration.MutableConfiguration;
import javax.transaction.Transactional;
import javax.ws.rs.Consumes;
import javax.ws.rs.DELETE;
import javax.ws.rs.DefaultValue;
import javax.ws.rs.GET;
import javax.ws.rs.NotFoundException;
import javax.ws.rs.POST;
import javax.ws.rs.PUT;
import javax.ws.rs.Path;
import javax.ws.rs.PathParam;
import javax.ws.rs.Produces;
import javax.ws.rs.QueryParam;
import javax.ws.rs.core.MediaType;
import javax.ws.rs.core.Response;
import java.io.ByteArrayOutputStream;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.Date;
import java.util.HashMap;
import java.util.List;
import java.util.Locale;
import java.util.Map;
import java.util.Objects;
import java.util.Set;
import java.util.stream.Collectors;
import java.util.stream.StreamSupport;

/**
* Provides REST services for working with
* concept sets.
Expand Down Expand Up @@ -145,6 +170,8 @@ public void customize(CacheManager cacheManager) {
@Autowired
private ObjectMapper mapper;

@Autowired
private ConceptSetLockingService conceptSetLockingService;

@Value("${security.defaultGlobalReadPermissions}")
private boolean defaultGlobalReadPermissions;
Expand Down Expand Up @@ -564,6 +591,75 @@ public ConceptSetDTO updateConceptSet(@PathParam("id") final int id, ConceptSetD
ConceptSet conceptSet = conversionService.convert(conceptSetDTO, ConceptSet.class);
return conversionService.convert(updateConceptSet(updated, conceptSet), ConceptSetDTO.class);
}
@Path("/{id}/list-snapshots")
@GET
@Produces(MediaType.APPLICATION_JSON)
@Transactional
public List<ConceptSetSnapshotParameters> listSnapshots(@PathParam("id") final int id) throws Exception {
return conceptSetLockingService.listSnapshotsByConceptSetId(id);
}
@POST
@Path("/{id}/snapshot")
@Consumes(MediaType.APPLICATION_JSON)
@Produces(MediaType.APPLICATION_JSON)
@Transactional
public Response invokeSnapshotAction(@PathParam("id") final int id, ConceptSetSnapshotActionRequest snapshotActionRequest) {
try {
String sourceKey = snapshotActionRequest.getSourceKey();

if(snapshotActionRequest.isTakeSnapshot()) {

ConceptSetExpression conceptSetExpression = getConceptSetExpression(id, sourceKey);
Collection<Concept> includedConcepts = vocabService.executeIncludedConceptLookup(sourceKey, conceptSetExpression);
Collection<Concept> includedSourceCodes = vocabService.executeMappedLookup(sourceKey, conceptSetExpression);

conceptSetLockingService.invokeSnapshotAction(id, snapshotActionRequest, conceptSetExpression, includedConcepts, includedSourceCodes);
} else {
conceptSetLockingService.invokeSnapshotAction(id, snapshotActionRequest, null, null, null);
}
return Response.ok().entity("Snapshot action successfully invoked.").build();
} catch (Exception e) {
log.error("Invoke snapshot action failed", e);
return Response.status(Response.Status.INTERNAL_SERVER_ERROR)
.entity("Invoke snapshot action failed: " + e.getMessage())
.build();
}
}

@POST
@Path("/check-locked")
@Consumes(MediaType.APPLICATION_JSON)
@Produces(MediaType.APPLICATION_JSON)
public Response checkIsLockedBatch(IsLockedBatchCheckRequest isLockedBatchCheckRequest) {
IsLockedBatchCheckResponse response = new IsLockedBatchCheckResponse();
try {
List<Integer> ids = isLockedBatchCheckRequest.getConceptSetIds();
Map<Integer, Boolean> lockStatuses = conceptSetLockingService.areLocked(ids);
response.setLockStatus(lockStatuses);
return Response.ok(response).build();
} catch (Exception e) {
return Response.status(Response.Status.INTERNAL_SERVER_ERROR)
.entity("Error checking lock statuses: " + e.getMessage())
.build();
}
}

@POST
@Path("/get-snapshot-items")
@Consumes(MediaType.APPLICATION_JSON)
@Produces(MediaType.APPLICATION_JSON)
public Response getSnapshotItems(GetConceptSetSnapshotItemsRequest request) {
try {
List<ConceptSetExpression.ConceptSetItem> conceptSetItems = conceptSetLockingService.getConceptSetSnapshotItemsBySnapshotId(request.getSnapshotId(), request.getSnapshotItemType());
GetConceptSetSnapshotItemsResponse response = new GetConceptSetSnapshotItemsResponse();
response.setConceptSetItems(conceptSetItems);
return Response.ok(response).build();
} catch (Exception e) {
return Response.status(Response.Status.INTERNAL_SERVER_ERROR)
.entity("Error fetching snapshot items: " + e.getMessage())
.build();
}
}

private ConceptSet updateConceptSet(ConceptSet dst, ConceptSet src) {

Expand Down Expand Up @@ -1030,4 +1126,4 @@ public Response deleteConceptSetAnnotation(@PathParam("conceptSetId") final int
return Response.ok().build();
} else throw new NotFoundException("Concept set annotation not found");
}
}
}
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