Filter cohorts and concepts by permission (#2245)

.gitignore

@@ -1,3 +1,4 @@
+Makefile
 WebAPIConfig/
 *application.properties
 .idea/
@@ -12,6 +13,7 @@ sandbox/
 /nbactions*.xml
 *~
 .DS_Store
+.factorypath
 
 ### Developer's personal properties ###
 **/resources/config/application*-dev-*.properties

Makefile

@@ -1,56 +1,21 @@
 compile:
-	mvn clean
-	mvn compile -Pwebapi-postgresql-laertes
+	mvn clean compile -DskipUnitTests -DskipITtests -s WebAPIConfig/settings.xml -P webapi-postgresql
 
 package: compile
-	mvn package -Pwebapi-postgresql-laertes
+	mvn package -DskipUnitTests -DskipITtests -s WebAPIConfig/settings.xml -P webapi-postgresql
 
-deploy: package 
-	sudo service tomcat7 stop
-	sleep 4
-	sudo rm -rf /var/lib/tomcat7/webapps/WebAPI*
-	sudo cp -r target/WebAPI.war  /var/lib/tomcat7/webapps/
-	sudo chown tomcat7 /var/lib/tomcat7/webapps/WebAPI.war
-	sudo chgrp tomcat7 /var/lib/tomcat7/webapps/WebAPI.war
-	sudo service tomcat7 start
+deploy: package
+	/home/ubuntu/Downloads/apache-tomcat-8.5.84-DEV/bin/shutdown.sh 
+	mv /home/ubuntu/Downloads/apache-tomcat-8.5.84-DEV/webapps/WebAPI /mnt/disk1/webapi-dev-tmp/WebAPI-FOLDER-`date +%m%d%H%S`
+	mv /home/ubuntu/Downloads/apache-tomcat-8.5.84-DEV/webapps/WebAPI.war /mnt/disk1/webapi-dev-tmp/WebAPI.war-`date +%m%d%H%S`
+	mv target/WebAPI.war /home/ubuntu/Downloads/apache-tomcat-8.5.84-DEV/webapps/
+	echo "Now run /home/ubuntu/Downloads/apache-tomcat-8.5.84-DEV/bin/startup.sh"
 
 git-push:
-	git push myfork master
+	git push
 
 test:
-	wget -O tests/test-general-evidence.json "http://localhost:8080/WebAPI/LAERTES_CDM/evidence/752061"
-	wget -O tests/test-drug-hoi.json "http://localhost:8080/WebAPI/LAERTES_CDM/evidence/drughoi/752061-374013"
-	wget -O tests/test-drug.json "http://localhost:8080/WebAPI/LAERTES_CDM/evidence/drug/752061"
-	wget -O tests/test-hoi.json "http://localhost:8080/WebAPI/LAERTES_CDM/evidence/hoi/320073"
-	wget -O tests/test-info.json "http://localhost:8080/WebAPI/LAERTES_CDM/evidence/info"
-	wget -O tests/test-drug-hoi-eu-spc.json "http://localhost:8080/WebAPI/LAERTES_CDM/evidence/drughoi/904351-4190045" 
-	wget -O tests/test-drug-hoi-splicer.json "http://localhost:8080/WebAPI/LAERTES_CDM/evidence/drughoi/19133853-195588"
-	wget -O tests/test-drug-hoi-faers-counts-and-signals.json "http://localhost:8080/WebAPI/LAERTES_CDM/evidence/drughoi/1154343-433031"
-	wget -O tests/test-drug-hoi-pubmed-mesh-cr.json "http://localhost:8080/WebAPI/LAERTES_CDM/evidence/drughoi/1154343-433031" 
-	wget -O tests/test-drug-hoi-pubmed-mesh-clin-trial.json "http://localhost:8080/WebAPI/LAERTES_CDM/evidence/drughoi/789578-378144"
-	wget -O tests/test-drug-hoi-pubmed-mesh-other.json "http://localhost:8080/WebAPI/LAERTES_CDM/evidence/drughoi/19010482-316866"
-	wget -O tests/test-drug-hoi-semmed-cr.json "http://localhost:8080/WebAPI/LAERTES_CDM/evidence/drughoi/1112807-441202"
-	wget -O tests/test-drug-hoi-semmed-clin-trial.json "http://localhost:8080/WebAPI/LAERTES_CDM/evidence/drughoi/19059744-381591"
-	wget -O tests/test-drug-rollup-ingredient.json "http://localhost:8080/WebAPI/LAERTES_CDM/evidence/drugrollup/ingredient/1000632"
-	wget -O tests/test-drug-rollup-clin-drug.json "http://localhost:8080/WebAPI/LAERTES_CDM/evidence/drugrollup/clinicaldrug/19074181"
-	wget -O tests/test-drug-rollup-branded-drug.json "http://localhost:8080/WebAPI/LAERTES_CDM/evidence/drugrollup/brandeddrug/1000640"
-	wget -O tests/test-rdf-evidencesummary.json "http://localhost:8080/WebAPI/LAERTES_CDM/evidence/evidencesummary?conditionID=139900&drugID=1115008&evidenceGroup=Literature"
-	wget -O tests/test-rdf-evidencedetails.json "http://localhost:8080/WebAPI/LAERTES_CDM/evidence/evidencedetails?conditionID=24134&drugID=1115008&evidenceType=SPL_SPLICER_ADR"
+	wget -O /tmp/tests/test-drug-rollup-branded-drug.json "http://api.ohdsi.org/WebAPI/CS1/evidence/drugrollup/brandeddrug/1000640"
 
 test-public:
-	wget -O tests/test-general-evidence.json "http://api.ohdsi.org/WebAPI/CS1/evidence/1000640"
-	wget -O /tmp/tests/test-drug-hoi.json "http://api.ohdsi.org/WebAPI/CS1/evidence/drughoi/1000640-137682"
-	wget -O /tmp/tests/test-drug.json "http://api.ohdsi.org/WebAPI/CS1/evidence/drug/1000640"
-	wget -O /tmp/tests/test-hoi.json "http://api.ohdsi.org/WebAPI/CS1/evidence/hoi/320073"
-	wget -O /tmp/tests/test-info.json "http://api.ohdsi.org/WebAPI/CS1/evidence/info"
-	wget -O /tmp/tests/test-drug-hoi-eu-spc.json "http://api.ohdsi.org/WebAPI/CS1/evidence/drughoi/40239056-75053" 
-	wget -O /tmp/tests/test-drug-hoi-splicer.json "http://api.ohdsi.org/WebAPI/CS1/evidence/drughoi/19133853-195588"
-	wget -O /tmp/tests/test-drug-hoi-faers-counts-and-signals.json "http://api.ohdsi.org/WebAPI/CS1/evidence/drughoi/1154343-433031"
-	wget -O /tmp/tests/test-drug-hoi-pubmed-mesh-cr.json "http://api.ohdsi.org/WebAPI/CS1/evidence/drughoi/1154343-433031" 
-	wget -O /tmp/tests/test-drug-hoi-pubmed-mesh-clin-trial.json "http://api.ohdsi.org/WebAPI/CS1/evidence/drughoi/789578-378144"
-	wget -O /tmp/tests/test-drug-hoi-pubmed-mesh-other.json "http://api.ohdsi.org/WebAPI/CS1/evidence/drughoi/19010482-316866"
-	wget -O /tmp/tests/test-drug-hoi-semmed-cr.json "http://api.ohdsi.org/WebAPI/CS1/evidence/drughoi/1782521-45612000"
-	wget -O /tmp/tests/test-drug-hoi-semmed-clin-trial.json "http://api.ohdsi.org/WebAPI/CS1/evidence/drughoi/1303425-45616736"
-	wget -O /tmp/tests/test-drug-rollup-ingredient.json "http://api.ohdsi.org/WebAPI/CS1/evidence/drugrollup/ingredient/1000632"
-	wget -O /tmp/tests/test-drug-rollup-clin-drug.json "http://api.ohdsi.org/WebAPI/CS1/evidence/drugrollup/clinicaldrug/19074181"
 	wget -O /tmp/tests/test-drug-rollup-branded-drug.json "http://api.ohdsi.org/WebAPI/CS1/evidence/drugrollup/brandeddrug/1000640"

pom.xml

@@ -192,6 +192,11 @@
     <spring.datasource.hikari.register-mbeans>true</spring.datasource.hikari.register-mbeans>
     <spring.datasource.hikari.mbean-name>authDataSource</spring.datasource.hikari.mbean-name>
 
+    <!-- If defaultGlobalReadPermissions is set to true (default), then all users can see every artifact.  -->
+    <!-- If it is set to false, WebAPI will filter out the artifacts that a user does not explicitly have -->
+    <!-- read permissions to -->
+    <security.defaultGlobalReadPermissions>true</security.defaultGlobalReadPermissions>	
+
     <!-- EMBEDDED SERVER CONFIGURATION (ServerProperties) -->
     <server.port>8080</server.port>
     <server.ssl.key-store></server.ssl.key-store>

src/main/java/org/ohdsi/webapi/cohortcharacterization/CcController.java

@@ -42,9 +42,11 @@
 import org.ohdsi.webapi.versioning.dto.VersionUpdateDTO;
 import org.springframework.core.convert.ConversionService;
 import org.springframework.data.domain.Page;
+import org.springframework.data.domain.PageImpl;
 import org.springframework.data.domain.Pageable;
 import org.springframework.stereotype.Controller;
 import org.springframework.transaction.annotation.Transactional;
+import org.springframework.beans.factory.annotation.Value;
 import org.springframework.web.bind.annotation.RequestBody;
 
 import javax.ws.rs.Consumes;
@@ -63,6 +65,7 @@
 import java.io.ByteArrayOutputStream;
 import java.io.IOException;
 import java.io.StringWriter;
+import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
 import java.util.Map;
@@ -151,11 +154,12 @@ public CohortCharacterizationDTO copy(@PathParam("id") final Long id) {
     @Produces(MediaType.APPLICATION_JSON)
     @Consumes(MediaType.APPLICATION_JSON)
     public Page<CcShortDTO> list(@Pagination Pageable pageable) {
-        return service.getPage(pageable).map(entity -> {
-            CcShortDTO dto = convertCcToShortDto(entity);
-            permissionService.fillWriteAccess(entity, dto);
-            return dto;
-        });
+      return service.getPage(pageable).map(entity -> {
+          CcShortDTO dto = convertCcToShortDto(entity);
+          permissionService.fillWriteAccess(entity, dto);
+          permissionService.fillReadAccess(entity, dto);
+          return dto;
+      });
     }
 
     /**
@@ -168,7 +172,12 @@ public Page<CcShortDTO> list(@Pagination Pageable pageable) {
     @Produces(MediaType.APPLICATION_JSON)
     @Consumes(MediaType.APPLICATION_JSON)
     public Page<CohortCharacterizationDTO> listDesign(@Pagination Pageable pageable) {
-        return service.getPageWithLinkedEntities(pageable).map(this::convertCcToDto);
+        return service.getPageWithLinkedEntities(pageable).map(entity -> {
+          CohortCharacterizationDTO dto = convertCcToDto(entity);
+          permissionService.fillWriteAccess(entity, dto);
+          permissionService.fillReadAccess(entity, dto);
+          return dto;
+      });
     }
 
     /**

src/main/java/org/ohdsi/webapi/cohortcharacterization/CcServiceImpl.java

@@ -133,6 +133,9 @@
 import static org.ohdsi.webapi.Constants.Params.JOB_AUTHOR;
 import static org.ohdsi.webapi.Constants.Params.JOB_NAME;
 import static org.ohdsi.webapi.Constants.Params.SOURCE_ID;
+import org.ohdsi.webapi.security.PermissionService;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.data.domain.PageImpl;
 
 @Service
 @Transactional
@@ -207,7 +210,12 @@ public class CcServiceImpl extends AbstractDaoService implements CcService, Gene
     private final GenericConversionService genericConversionService;
     private final VocabularyService vocabularyService;
     private VersionService<CharacterizationVersion> versionService;
+
+    private PermissionService permissionService;
 
+    @Value("#{'${security.defaultGlobalReadPermissions}'.equals(false)}")
+    private boolean defaultGlobalReadPermissions;
+
     private final Environment env;
 
     public CcServiceImpl(
@@ -231,6 +239,7 @@ public CcServiceImpl(
             final JobInvalidator jobInvalidator,
             final VocabularyService vocabularyService,
             final VersionService<CharacterizationVersion> versionService,
+            final PermissionService permissionService,
             @Qualifier("conversionService") final GenericConversionService genericConversionService,
             Environment env) {
         this.repository = ccRepository;
@@ -251,6 +260,7 @@ public CcServiceImpl(
         this.eventPublisher = eventPublisher;
         this.jobInvalidator = jobInvalidator;
         this.vocabularyService = vocabularyService;
+        this.permissionService = permissionService;
         this.genericConversionService = genericConversionService;
         this.versionService = versionService;
         this.env = env;
@@ -531,12 +541,24 @@ public CohortCharacterization findDesignByGenerationId(@CcGenerationId final Lon
 
     @Override
     public Page<CohortCharacterizationEntity> getPageWithLinkedEntities(final Pageable pageable) {
-        return repository.findAll(pageable, defaultEntityGraph);
+      return repository.findAll(pageable, defaultEntityGraph);
+
     }
 
     @Override
     public Page<CohortCharacterizationEntity> getPage(final Pageable pageable) {
-        return repository.findAll(pageable);
+      List<CohortCharacterizationEntity> ccList = repository.findAll()
+              .stream().filter(!defaultGlobalReadPermissions ? entity -> permissionService.hasReadAccess(entity) : entity -> true)
+              .collect(Collectors.toList());
+      return getPageFromResults(pageable, ccList);
+    }
+
+    private Page<CohortCharacterizationEntity> getPageFromResults(Pageable pageable, List<CohortCharacterizationEntity> results) {
+      // Calculate the start and end indices for the current page
+      int startIndex = pageable.getPageNumber() * pageable.getPageSize();
+      int endIndex = Math.min(startIndex + pageable.getPageSize(), results.size());      
+
+      return new PageImpl<>(results.subList(startIndex, endIndex), pageable, results.size());
     }
 
     @Override

src/main/java/org/ohdsi/webapi/estimation/EstimationController.java

@@ -22,6 +22,7 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Value;
 import org.springframework.core.convert.support.GenericConversionService;
 import org.springframework.stereotype.Controller;
 
@@ -70,7 +71,10 @@ public class EstimationController {
   private final ScriptExecutionService executionService;
   private EstimationChecker checker;
   private PermissionService permissionService;
-
+
+  @Value("#{'${security.defaultGlobalReadPermissions}'.equals(false)}")
+  private boolean defaultGlobalReadPermissions;
+
   public EstimationController(EstimationService service,
                               GenericConversionService conversionService,
                               CommonGenerationSensitiveInfoService sensitiveInfoService,
@@ -97,11 +101,12 @@ public EstimationController(EstimationService service,
   @Path("/")
   @Produces(MediaType.APPLICATION_JSON)
   public List<EstimationShortDTO> getAnalysisList() {
-
     return StreamSupport.stream(service.getAnalysisList().spliterator(), false)
+            .filter(!defaultGlobalReadPermissions ? entity -> permissionService.hasReadAccess(entity) : entity -> true)
             .map(analysis -> {
               EstimationShortDTO dto = conversionService.convert(analysis, EstimationShortDTO.class);
               permissionService.fillWriteAccess(analysis, dto);
+              permissionService.fillReadAccess(analysis, dto);
               return dto;
             })
             .collect(Collectors.toList());

src/main/java/org/ohdsi/webapi/pathway/PathwayController.java

@@ -25,15 +25,18 @@
 import org.ohdsi.webapi.versioning.dto.VersionDTO;
 import org.ohdsi.webapi.versioning.dto.VersionUpdateDTO;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Value;
 import org.springframework.core.convert.ConversionService;
 import org.springframework.data.domain.Page;
+import org.springframework.data.domain.PageImpl;
 import org.springframework.data.domain.Pageable;
 import org.springframework.stereotype.Controller;
 import org.springframework.web.bind.annotation.RequestBody;
 
 import javax.transaction.Transactional;
 import javax.ws.rs.*;
 import javax.ws.rs.core.MediaType;
+import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
 import java.util.Map;
@@ -156,13 +159,14 @@ public PathwayAnalysisDTO importAnalysis(final PathwayAnalysisExportDTO dto) {
 	@Consumes(MediaType.APPLICATION_JSON)
 	@Transactional
 	public Page<PathwayAnalysisDTO> list(@Pagination Pageable pageable) {
-
 		return pathwayService.getPage(pageable).map(pa -> {
 			PathwayAnalysisDTO dto = conversionService.convert(pa, PathwayAnalysisDTO.class);
 			permissionService.fillWriteAccess(pa, dto);
+			permissionService.fillReadAccess(pa, dto);
 			return dto;
 		});
 	}
+
 
 	/**
 	 * Check that a pathway analysis name exists.

src/main/java/org/ohdsi/webapi/pathway/PathwayServiceImpl.java

@@ -96,6 +96,10 @@
 import static org.ohdsi.webapi.Constants.Params.JOB_NAME;
 import static org.ohdsi.webapi.Constants.Params.PATHWAY_ANALYSIS_ID;
 import static org.ohdsi.webapi.Constants.Params.SOURCE_ID;
+import org.ohdsi.webapi.cohortcharacterization.domain.CohortCharacterizationEntity;
+import org.ohdsi.webapi.security.PermissionService;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.data.domain.PageImpl;
 
 @Service
 @Transactional
@@ -116,6 +120,11 @@ public class PathwayServiceImpl extends AbstractDaoService implements PathwaySer
 	private final CohortDefinitionService cohortDefinitionService;
 	private final VersionService<PathwayVersion> versionService;
 
+	private PermissionService permissionService;
+
+	@Value("#{'${security.defaultGlobalReadPermissions}'.equals(false)}")
+	private boolean defaultGlobalReadPermissions;
+
 	private final List<String> STEP_COLUMNS = Arrays.asList(new String[]{"step_1", "step_2", "step_3", "step_4", "step_5", "step_6", "step_7", "step_8", "step_9", "step_10"});
 
 	private final EntityGraph defaultEntityGraph = EntityUtils.fromAttributePaths(
@@ -142,7 +151,8 @@ public PathwayServiceImpl(
 					@Qualifier("conversionService") GenericConversionService genericConversionService,
 					StepBuilderFactory stepBuilderFactory,
 					CohortDefinitionService cohortDefinitionService,
-					VersionService<PathwayVersion> versionService) {
+					VersionService<PathwayVersion> versionService,
+					PermissionService permissionService) {
 
 		this.pathwayAnalysisRepository = pathwayAnalysisRepository;
 		this.pathwayAnalysisGenerationRepository = pathwayAnalysisGenerationRepository;
@@ -159,6 +169,7 @@ public PathwayServiceImpl(
 		this.stepBuilderFactory = stepBuilderFactory;
 		this.cohortDefinitionService = cohortDefinitionService;
 		this.versionService = versionService;
+		this.permissionService = permissionService;
 
 		SerializedPathwayAnalysisToPathwayAnalysisConverter.setConversionService(conversionService);
 	}
@@ -218,8 +229,18 @@ public PathwayAnalysisEntity importAnalysis(PathwayAnalysisEntity toImport) {
 
 	@Override
 	public Page<PathwayAnalysisEntity> getPage(final Pageable pageable) {
+		List<PathwayAnalysisEntity> pathwayList = pathwayAnalysisRepository.findAll(defaultEntityGraph)
+						.stream().filter(!defaultGlobalReadPermissions ? entity -> permissionService.hasReadAccess(entity) : entity -> true)
+						.collect(Collectors.toList());
+		return getPageFromResults(pageable, pathwayList);
+	}
+
+	private Page<PathwayAnalysisEntity> getPageFromResults(Pageable pageable, List<PathwayAnalysisEntity> results) {
+		// Calculate the start and end indices for the current page
+		int startIndex = pageable.getPageNumber() * pageable.getPageSize();
+		int endIndex = Math.min(startIndex + pageable.getPageSize(), results.size());
 
-		return pathwayAnalysisRepository.findAll(pageable, defaultEntityGraph);
+		return new PageImpl<>(results.subList(startIndex, endIndex), pageable, results.size());
 	}
 
 	@Override

src/main/java/org/ohdsi/webapi/prediction/PredictionController.java

@@ -21,6 +21,7 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Value;
 import org.springframework.core.convert.support.GenericConversionService;
 import org.springframework.stereotype.Controller;
 
@@ -67,6 +68,9 @@ public class PredictionController {
 
   private PermissionService permissionService;
 
+  @Value("#{'${security.defaultGlobalReadPermissions}'.equals(false)}")
+  private boolean defaultGlobalReadPermissions;
+
   @Autowired
   public PredictionController(PredictionService service,
                               GenericConversionService conversionService,
@@ -94,24 +98,26 @@ public PredictionController(PredictionService service,
   @Path("/")
   @Produces(MediaType.APPLICATION_JSON)
   public List<CommonAnalysisDTO> getAnalysisList() {
-
     return StreamSupport
             .stream(service.getAnalysisList().spliterator(), false)
+            .filter(!defaultGlobalReadPermissions ? entity -> permissionService.hasReadAccess(entity) : entity -> true)
             .map(analysis -> {
               CommonAnalysisDTO dto = conversionService.convert(analysis, CommonAnalysisDTO.class);
               permissionService.fillWriteAccess(analysis, dto);
+              permissionService.fillReadAccess(analysis, dto);
               return dto;
             })
             .collect(Collectors.toList());
   }
 
   /**
    * Check to see if a prediction design exists by name
-   * 
+   *
    * @summary Prediction design exists by name
    * @param id The prediction design id
    * @param name The prediction design name
-   * @return 1 if a prediction design with the given name and id exist in WebAPI and 0 otherwise
+   * @return 1 if a prediction design with the given name and id exist in WebAPI
+   * and 0 otherwise
    */
   @GET
   @Path("/{id}/exists")