[ALS-6921] Implement Open Access in PSAMA

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

@@ -8,6 +8,7 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import javax.annotation.PostConstruct;
 import javax.annotation.Resource;
 import javax.ejb.Singleton;
 import javax.enterprise.context.ApplicationScoped;
@@ -25,7 +26,23 @@ 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;
+
+    @Resource(mappedName = "java:global/openAccessEnabled")
+    private String open_access_enabled_str;
+
+    private boolean open_access_enabled;
+
+    @Resource(mappedName = "java:global/openAccessValidateUrl")
+    private String open_access_validate_url;
+
+    @PostConstruct
+    public void init() {
+        this.open_access_enabled = Boolean.parseBoolean(open_access_enabled_str);
+    }
+
+    // to be able to pre modified
     public static final ObjectMapper objectMapper = new ObjectMapper();
 
     // check the example from Apache HttpClient official website:
@@ -39,11 +56,7 @@ 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();
     }
 
 
@@ -54,4 +67,22 @@ public String getToken_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;
+    }
+
+    public boolean isOpenAccessEnabled() {
+        return open_access_enabled;
+    }
+
+    public String getOpenAccessValidateUrl() {
+        return this.open_access_validate_url;
+    }
+
 }