Release

pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/entity/Resource.java

@@ -1,12 +1,12 @@
 package edu.harvard.dbmi.avillach.data.entity;
 
 import java.io.StringReader;
+import java.util.Optional;
 
 import javax.json.Json;
 import javax.json.JsonObject;
 import javax.json.JsonReader;
-import javax.persistence.Column;
-import javax.persistence.Entity;
+import javax.persistence.*;
 
 import com.fasterxml.jackson.annotation.JsonIgnore;
 import com.fasterxml.jackson.annotation.JsonProperty;
@@ -18,6 +18,9 @@ public class Resource extends BaseEntity{
 	@Column(length = 8192)
 	private String description;
 	private String targetURL;
+
+
+	@Convert(converter = ResourcePathConverter.class)
 	private String resourceRSPath;
 
 	@Column(length = 8192)
@@ -102,4 +105,31 @@ public String toString() {
 	            .add("metadata", metadataObj)
 	            .build().toString();
 	}
+
+	/**
+	 * This resource path converter allows resource paths to contain a reference to a specific stack that is
+	 * imputed at runtime based an an environment parameter. This allows multiple stacks to share the same database.
+	 *
+	 * The ___target_stack___ token in any resource path value will be replaced with the TARGET_STACK environment variable
+	 */
+	@Converter
+	public static class ResourcePathConverter implements AttributeConverter<String, String> {
+
+		public ResourcePathConverter() {
+		}
+
+		private static final Optional<String> targetStack = Optional.ofNullable(System.getProperty("TARGET_STACK", null));
+
+		@Override
+		public String convertToDatabaseColumn(String attribute) {
+			return attribute;
+		}
+
+		@Override
+		public String convertToEntityAttribute(String dbData) {
+			return targetStack
+					.map(stack -> dbData.replace("___target_stack___", stack))
+					.orElse(dbData);
+		}
+	}
 }

pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/repository/QueryRepository.java

@@ -3,12 +3,25 @@
 import edu.harvard.dbmi.avillach.data.entity.Query;
 
 import javax.enterprise.context.ApplicationScoped;
+import javax.persistence.PersistenceException;
 import javax.transaction.Transactional;
 import java.util.UUID;
 
 @Transactional
 @ApplicationScoped
-public class QueryRepository extends BaseRepository<Query, UUID>{
+public class QueryRepository extends BaseRepository<Query, UUID> {
 
-    protected QueryRepository() {super(Query.class);}
+    protected QueryRepository() {
+        super(Query.class);
+    }
+
+    public Query getQueryUUIDFromCommonAreaUUID(UUID caID) {
+        String caIDRegex = "%commonAreaUUID\":\"" + caID + "\"%";
+        String query = "SELECT * FROM query WHERE CONVERT(metadata USING utf8) LIKE ?";
+        try {
+            return (Query) em().createNativeQuery(query, Query.class).setParameter(1, caIDRegex).getSingleResult();
+        } catch (PersistenceException ignored) {
+            return null;
+        }
+    }
 }

pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/repository/ResourceRepository.java

@@ -15,5 +15,5 @@ protected ResourceRepository() {
 		super(Resource.class);
 	}
 
-	
+
 }

pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/PicSureWarInit.java

@@ -25,7 +25,10 @@ public class PicSureWarInit {
     @Resource(mappedName = "java:global/token_introspection_token")
     private String token_introspection_token;
 
-    //to be able to pre modified
+    @Resource(mappedName = "java:global/defaultApplicationUUID")
+    private String default_application_uuid;
+
+    // to be able to pre modified
     public static final ObjectMapper objectMapper = new ObjectMapper();
 
     // check the example from Apache HttpClient official website:
@@ -39,19 +42,23 @@ public class PicSureWarInit {
     static {
         HTTP_CLIENT_CONNECTION_MANAGER = new PoolingHttpClientConnectionManager();
         HTTP_CLIENT_CONNECTION_MANAGER.setMaxTotal(100);
-        CLOSEABLE_HTTP_CLIENT = HttpClients
-                .custom()
-                .setConnectionManager(HTTP_CLIENT_CONNECTION_MANAGER)
-                .useSystemProperties()
-                .build();
+        CLOSEABLE_HTTP_CLIENT = HttpClients.custom().setConnectionManager(HTTP_CLIENT_CONNECTION_MANAGER).useSystemProperties().build();
     }
 
-
     public String getToken_introspection_url() {
         return token_introspection_url;
     }
 
     public String getToken_introspection_token() {
         return token_introspection_token;
     }
+
+    /**
+     * This method is used to get the default application UUID. This value is either the open or auth hpds resource UUID.
+     *
+     * @return the default application UUID
+     */
+    public String getDefaultApplicationUUID() {
+        return this.default_application_uuid;
+    }
 }

pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/PicsureInfoService.java

@@ -21,55 +21,55 @@
 
 public class PicsureInfoService {
 
-	private final Logger logger = LoggerFactory.getLogger(PicsureQueryService.class);
+    private final Logger logger = LoggerFactory.getLogger(PicsureQueryService.class);
 
-	private final static ObjectMapper mapper = new ObjectMapper();
+    private final static ObjectMapper mapper = new ObjectMapper();
 
-	@Inject
-	ResourceRepository resourceRepo;
+    @Inject
+    ResourceRepository resourceRepo;
 
-	@Inject
-	ResourceWebClient resourceWebClient;
+    @Inject
+    ResourceWebClient resourceWebClient;
 
-	/**
-	 * Retrieve resource info for a specific resource.
-	 *
-	 * @param resourceId - Resource UUID
-	 * @param credentialsQueryRequest - Contains resource specific credentials map
-	 * @return a {@link edu.harvard.dbmi.avillach.domain.ResourceInfo ResourceInfo}
-	 */
-	public ResourceInfo info(UUID resourceId, QueryRequest credentialsQueryRequest, HttpHeaders headers) {
-		Resource resource = resourceRepo.getById(resourceId);
-		if (resource == null){
-			throw new ProtocolException(ProtocolException.RESOURCE_NOT_FOUND + resourceId.toString());
-		}
-		if (resource.getResourceRSPath() == null){
-			throw new ApplicationException(ApplicationException.MISSING_RESOURCE_PATH);
-		}
-		if (credentialsQueryRequest == null){
-			credentialsQueryRequest = new GeneralQueryRequest();
-		}
-		if (credentialsQueryRequest.getResourceCredentials() == null){
-			credentialsQueryRequest.setResourceCredentials(new HashMap<String, String>());
-		}
+    /**
+     * Retrieve resource info for a specific resource.
+     *
+     * @param resourceId - Resource UUID
+     * @param credentialsQueryRequest - Contains resource specific credentials map
+     * @return a {@link edu.harvard.dbmi.avillach.domain.ResourceInfo ResourceInfo}
+     */
+    public ResourceInfo info(UUID resourceId, QueryRequest credentialsQueryRequest, HttpHeaders headers) {
+        Resource resource = resourceRepo.getById(resourceId);
+        if (resource == null) {
+            throw new ProtocolException(ProtocolException.RESOURCE_NOT_FOUND + resourceId.toString());
+        }
+        if (resource.getResourceRSPath() == null) {
+            throw new ApplicationException(ApplicationException.MISSING_RESOURCE_PATH);
+        }
+        if (credentialsQueryRequest == null) {
+            credentialsQueryRequest = new GeneralQueryRequest();
+        }
+        if (credentialsQueryRequest.getResourceCredentials() == null) {
+            credentialsQueryRequest.setResourceCredentials(new HashMap<String, String>());
+        }
 
-		logger.info("path=/info/{resourceId}, resourceId={}, requestSource={}, credentialsQueryRequest={}",
-				resourceId,
-				Utilities.getRequestSourceFromHeader(headers),
-				Utilities.convertQueryRequestToString(mapper, credentialsQueryRequest)
-		);
+        logger.info(
+            "path=/info/{resourceId}, resourceId={}, requestSource={}, credentialsQueryRequest={}", resourceId,
+            Utilities.getRequestSourceFromHeader(headers), Utilities.convertQueryRequestToString(mapper, credentialsQueryRequest)
+        );
 
-		credentialsQueryRequest.getResourceCredentials().put(ResourceWebClient.BEARER_TOKEN_KEY, resource.getToken());
-		return resourceWebClient.info(resource.getResourceRSPath(), credentialsQueryRequest);
-	}
+        credentialsQueryRequest.getResourceCredentials().put(ResourceWebClient.BEARER_TOKEN_KEY, resource.getToken());
+        return resourceWebClient.info(resource.getResourceRSPath(), credentialsQueryRequest);
+    }
 
-	/**
-	 * Retrieve a list of all available resources.
-	 *
-	 * @return List containing limited metadata about all available resources and ids.
-	 */
-	public Map<UUID, String> resources(HttpHeaders headers) {
-		logger.info("path=/info/resources, requestSource={}", Utilities.getRequestSourceFromHeader(headers));
-		return resourceRepo.list().stream().collect(Collectors.toMap(Resource::getUuid, Resource::getName));
-	}
+    /**
+     * Retrieve a list of all available resources.
+     *
+     * @return List containing limited metadata about all available resources and ids.
+     */
+    public Map<UUID, String> resources(HttpHeaders headers) {
+        logger.info("path=/info/resources, requestSource={}", Utilities.getRequestSourceFromHeader(headers));
+        return resourceRepo.list().stream().filter(resource -> !resource.getHidden())
+            .collect(Collectors.toMap(Resource::getUuid, Resource::getName));
+    }
 }

pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/PicsureQueryService.java

@@ -241,6 +241,7 @@ public Response querySync(QueryRequest queryRequest, HttpHeaders headers) {
      */
     public QueryStatus queryMetadata(UUID queryId, HttpHeaders headers) {
         Query query = queryRepo.getById(queryId);
+        query = query == null ? queryRepo.getQueryUUIDFromCommonAreaUUID(queryId) : query;
         if (query == null) {
             throw new ProtocolException(ProtocolException.QUERY_NOT_FOUND + queryId.toString());
         }