Concept Set Snapshots/Locking/Unlocking feature implementation

Author: oleg-odysseus

.github/workflows/ci.yaml

@@ -30,7 +30,7 @@ jobs:
             java-version: 8
 
       - name: Maven cache
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
             # Cache gradle directories
             path: ~/.m2
@@ -57,7 +57,7 @@ jobs:
       - uses: actions/checkout@v2
 
       - name: Cache Docker layers
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
           path: /tmp/.buildx-cache
           key: ${{ runner.os }}-buildx-${{ github.sha }}

.github/workflows/release.yaml

@@ -26,7 +26,7 @@ jobs:
           java-version: 8
 
       - name: Maven cache
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
           # Cache gradle directories
           path: ~/.m2

pom.xml

@@ -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_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 -->

src/main/java/org/ohdsi/webapi/service/ConceptSetService.java

@@ -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;
@@ -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;
@@ -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;
@@ -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.
@@ -145,6 +170,8 @@ public void customize(CacheManager cacheManager) {
     @Autowired
     private ObjectMapper mapper;
 
+    @Autowired
+    private ConceptSetLockingService conceptSetLockingService;
 
     @Value("${security.defaultGlobalReadPermissions}")
     private boolean defaultGlobalReadPermissions;
@@ -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) {
 
@@ -1030,4 +1126,4 @@ public Response deleteConceptSetAnnotation(@PathParam("conceptSetId") final int
             return Response.ok().build();
         } else throw new NotFoundException("Concept set annotation not found");
     }
-}
+}