Merge for AIM-AHEAD 2024-03-14-Release (#187)

## Features

- **Search by CA ID**
  - Enabled search functionality by common area (CA) ID in addition to the existing uuid-based query system, enhancing the platform's search capabilities and covering more use cases.

## Bugs

- **Visualization Fixes**
  - Resolved an issue where the Open Access StatViz did not display the "Other" category, ensuring complete data visualization.
  - Addressed a bug in the resources table by removing an obsolete stack column, improving data management and presentation consistency.

## Enhancements

- **Key Length Handling in Visualization**
  - Improved the `limitKeySize` method in `VisualizationUtil` to ensure key uniqueness while handling keys longer than 45 characters, enhancing data integrity in visualizations.
  - Added `VisualizationUtilTests` to validate the functionality and adjustments made to the key shortening logic, ensuring robustness and accuracy.
  - Refined empty return conditions in `DataProcessingService` to better account for data scenarios where min and max values are 0, optimizing data processing logic.

- **Persistence and Resource Management**
  - Added `persistence.xml` to the visualization resource to resolve startup errors related to persistence unit injection, ensuring the smooth operation of visualization resources.

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/ResourceRepository.java

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

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-resources/pic-sure-visualization-resource/src/main/java/edu/harvard/hms/dbmi/avillach/resource/visualization/service/DataProcessingService.java

@@ -158,8 +158,8 @@ private static Map<String, Integer> bucketData(Map<String, Integer> originalMap)
         int numBins = calcNumBins(data);
         double min = data.keySet().stream().min(Double::compareTo).orElse(0.0);
         double max = data.keySet().stream().max(Double::compareTo).orElse(0.0);
-
-        if ((min == 0.0 && max == 0.0) || numBins == 0) return new HashMap<>();
+        // The min and max can both be 0, but we could still have a numBins of 1 if there are values in the data.
+        if (min == 0.0 && max == 0.0 && numBins == 0) return new HashMap<>();
 
         int binSize = (int) Math.ceil((max - min) / numBins);