Merge pull request #296 from madgik/bug/bad_user_input_exception_on_s…

…ame_variables

Added more cases as Bad User Input Exception.

Exareme-Docker/src/exareme/exareme-master/src/main/java/madgik/exareme/master/engine/iterations/handler/IterationsHandler.java

@@ -10,6 +10,7 @@
 import madgik.exareme.master.engine.iterations.state.IterationsStateManager;
 import madgik.exareme.master.engine.iterations.state.IterationsStateManagerImpl;
 import madgik.exareme.master.engine.iterations.state.IterativeAlgorithmState;
+import madgik.exareme.master.gateway.async.handler.HBP.Exceptions.BadUserInputException;
 import madgik.exareme.master.queryProcessor.HBP.AlgorithmProperties;
 import madgik.exareme.master.queryProcessor.HBP.Composer;
 import madgik.exareme.master.queryProcessor.HBP.Exceptions.ComposerException;
@@ -65,7 +66,7 @@ public static IterationsHandler getInstance() {
      */
     public IterativeAlgorithmState handleNewIterativeAlgorithmRequest(
             AdpDBManager adpDBManager, String algorithmKey,
-            AlgorithmProperties algorithmProperties, ContainerProxy[] usedContainerProxies) {
+            AlgorithmProperties algorithmProperties, ContainerProxy[] usedContainerProxies) throws BadUserInputException {
 
         // Generate the AdpDBClient for this iterative algorithm that will be used to execute all the phases' queries
         AdpDBClient adpDBClient;

Exareme-Docker/src/exareme/exareme-master/src/main/java/madgik/exareme/master/gateway/async/handler/HBP/Exceptions/BadUserInputException.java

@@ -0,0 +1,7 @@
+package madgik.exareme.master.gateway.async.handler.HBP.Exceptions;
+
+public class BadUserInputException extends Exception{
+    public BadUserInputException(String message) {
+        super(message);
+    }
+}

Exareme-Docker/src/exareme/exareme-master/src/main/java/madgik/exareme/master/gateway/async/handler/HBP/HBPQueryHandler.java

@@ -14,7 +14,7 @@
 import madgik.exareme.master.engine.iterations.state.IterativeAlgorithmState;
 import madgik.exareme.master.gateway.ExaremeGatewayUtils;
 import madgik.exareme.master.gateway.async.handler.HBP.Exceptions.RequestException;
-import madgik.exareme.master.gateway.async.handler.HBP.Exceptions.UserException;
+import madgik.exareme.master.gateway.async.handler.HBP.Exceptions.BadUserInputException;
 import madgik.exareme.master.gateway.async.handler.entity.NQueryResultEntity;
 import madgik.exareme.master.queryProcessor.HBP.AlgorithmProperties;
 import madgik.exareme.master.queryProcessor.HBP.Algorithms;
@@ -167,7 +167,7 @@ private void handleHBPAlgorithmExecution(HttpRequest request, HttpResponse respo
                 response.setStatusCode(HttpStatus.SC_OK);
                 response.setEntity(entity);
             }
-        } catch (UserException e) {
+        } catch (BadUserInputException e) {
             log.error(e.getMessage());
             String errorType = HBPQueryHelper.ErrorResponse.ErrorResponseTypes.user_error;
             response.setStatusCode(HttpStatus.SC_OK);

Exareme-Docker/src/exareme/exareme-master/src/main/java/madgik/exareme/master/gateway/async/handler/HBP/HBPQueryHelper.java

@@ -2,7 +2,7 @@
 
 import com.google.gson.Gson;
 import madgik.exareme.master.gateway.async.handler.HBP.Exceptions.ConsulException;
-import madgik.exareme.master.gateway.async.handler.HBP.Exceptions.UserException;
+import madgik.exareme.master.gateway.async.handler.HBP.Exceptions.BadUserInputException;
 import madgik.exareme.worker.art.container.ContainerProxy;
 import madgik.exareme.worker.art.registry.ArtRegistryLocator;
 import org.apache.http.HttpEntity;
@@ -88,12 +88,12 @@ public static HashMap<String, String> getAlgorithmParameters(HttpRequest request
      * @param algorithmParameters are used to get the dataset/pathology
      * @return the containers on which the algorithm should run
      * @throws ConsulException if consul is unreachable
-     * @throws UserException   if dataset's node is inactive or doesn't exist in the pathology
+     * @throws BadUserInputException   if dataset's node is inactive or doesn't exist in the pathology
      *                         or if the pathology is not available or not provided
      * @throws RemoteException if the Exareme Registry is unreachable
      */
     public static ContainerProxy[] getAlgorithmNodes(HashMap<String, String> algorithmParameters)
-            throws ConsulException, UserException, RemoteException {
+            throws ConsulException, BadUserInputException, RemoteException {
         ConsulNodesPathologiesAndDatasetsInfo consulNodesPathologiesAndDatasetsInfo =
                 new ConsulNodesPathologiesAndDatasetsInfo();
 
@@ -139,7 +139,7 @@ public static ContainerProxy[] getAlgorithmNodes(HashMap<String, String> algorit
 
         } else {
             // If an algorithm parameter exists, a pathology should be provided.
-            throw new UserException(pathologyNotProvided);
+            throw new BadUserInputException(pathologyNotProvided);
         }
     }
 
@@ -151,14 +151,14 @@ public static ContainerProxy[] getAlgorithmNodes(HashMap<String, String> algorit
      * @param datasets                              of the algorithm
      * @param consulNodesPathologiesAndDatasetsInfo are the consul information needed
      * @return the containers to run the algorithm
-     * @throws UserException   if dataset's node is inactive or doesn't exist in the pathology
+     * @throws BadUserInputException   if dataset's node is inactive or doesn't exist in the pathology
      * @throws RemoteException if the Exareme Registry is unreachable
      */
     private static ContainerProxy[] getAlgorithmNodes(
             String pathology,
             ArrayList<String> datasets,
             ConsulNodesPathologiesAndDatasetsInfo consulNodesPathologiesAndDatasetsInfo
-    ) throws RemoteException, UserException {
+    ) throws RemoteException, BadUserInputException {
 
         HashMap<String, ArrayList<String>> algorithmNodeIPsAndDatasets = consulNodesPathologiesAndDatasetsInfo.getNodeDatasets(pathology, datasets);
         ArrayList<String> algorithmNodes = new ArrayList<>(algorithmNodeIPsAndDatasets.keySet());
@@ -179,7 +179,7 @@ private static ContainerProxy[] getAlgorithmNodes(
                 }
             }
         }
-        throw new UserException(
+        throw new BadUserInputException(
                 String.format(
                         datasetsXYZAreInactive,
                         String.join(", ", inactiveDatasets)
@@ -191,25 +191,25 @@ private static void validatePathologyAndDatasets(
             String pathology,
             ArrayList<String> datasets,
             ConsulNodesPathologiesAndDatasetsInfo nodesInformation
-    ) throws UserException {
+    ) throws BadUserInputException {
 
         if (pathology != null) {
             log.debug("Available pathologies: " + nodesInformation.getAllAvailablePathologies());
             if (!nodesInformation.getAllAvailablePathologies().contains(pathology)) {
-                throw new UserException(String.format(pathologyXNotAvailable, pathology));
+                throw new BadUserInputException(String.format(pathologyXNotAvailable, pathology));
             }
 
             if (datasets != null) {
                 ArrayList<String> datasetsOfPathology = nodesInformation.getDatasetsOfPathology(pathology);
                 for (String dataset : datasets) {
                     if (!datasetsOfPathology.contains(dataset)) {
-                        throw new UserException(String.format(datasetXDoesNotExistInPathologyY, dataset, pathology));
+                        throw new BadUserInputException(String.format(datasetXDoesNotExistInPathologyY, dataset, pathology));
                     }
                 }
             }
         } else {
             if (datasets != null) {
-                throw new UserException(pathologyNotProvided);
+                throw new BadUserInputException(pathologyNotProvided);
             }
         }
     }

Exareme-Docker/src/exareme/exareme-master/src/main/java/madgik/exareme/master/gateway/control/handler/HttpAsyncCheckWorker.java

@@ -10,7 +10,7 @@
 import madgik.exareme.master.engine.AdpDBManagerLocator;
 import madgik.exareme.master.gateway.ExaremeGatewayUtils;
 import madgik.exareme.master.gateway.async.handler.HBP.Exceptions.RequestException;
-import madgik.exareme.master.gateway.async.handler.HBP.Exceptions.UserException;
+import madgik.exareme.master.gateway.async.handler.HBP.Exceptions.BadUserInputException;
 import madgik.exareme.master.gateway.async.handler.entity.NQueryResultEntity;
 import madgik.exareme.master.queryProcessor.HBP.AlgorithmProperties;
 import madgik.exareme.master.queryProcessor.HBP.Algorithms;
@@ -55,7 +55,7 @@ public void handle(
         HttpResponse response = httpexchange.getResponse();
         try {
             handleInternal(request, response, context);
-        } catch (AlgorithmException | CDEsMetadataException | ComposerException | UserException | RequestException e) {
+        } catch (AlgorithmException | CDEsMetadataException | ComposerException | BadUserInputException | RequestException e) {
             e.printStackTrace();
         }
         httpexchange.submitResponse(new BasicAsyncResponseProducer(response));
@@ -65,7 +65,7 @@ private void handleInternal(
             final HttpRequest request,
             final HttpResponse response,
             final HttpContext context
-    ) throws HttpException, IOException, AlgorithmException, CDEsMetadataException, ComposerException, UserException, RequestException {
+    ) throws HttpException, IOException, AlgorithmException, CDEsMetadataException, ComposerException, BadUserInputException, RequestException {
 
         String method = request.getRequestLine().getMethod().toUpperCase(Locale.ENGLISH);
         if (!method.equals("GET") && !method.equals("HEAD") && !method.equals("POST")) {

Exareme-Docker/src/exareme/exareme-master/src/main/java/madgik/exareme/master/queryProcessor/HBP/AlgorithmProperties.java

@@ -1,9 +1,8 @@
 package madgik.exareme.master.queryProcessor.HBP;
 
-import madgik.exareme.master.gateway.async.handler.HBP.Exceptions.UserException;
+import madgik.exareme.master.gateway.async.handler.HBP.Exceptions.BadUserInputException;
 import madgik.exareme.master.queryProcessor.HBP.Exceptions.AlgorithmException;
 import madgik.exareme.master.queryProcessor.HBP.Exceptions.CDEsMetadataException;
-import madgik.exareme.master.queryProcessor.HBP.Exceptions.ComposerException;
 import org.codehaus.jettison.json.JSONArray;
 import org.codehaus.jettison.json.JSONException;
 import org.codehaus.jettison.json.JSONObject;
@@ -114,13 +113,13 @@ public String getParameterValue(String parameterName) {
      * @param parameterName     the name of a parameter
      * @param newParameterValue the new value of the parameter
      */
-    public void setParameterValue(String parameterName, String newParameterValue) throws ComposerException {
+    public void setParameterValue(String parameterName, String newParameterValue) throws BadUserInputException {
         String allowedDynamicParameters = ComposerConstants.dbIdentifierKey;
 
         // Not all parameters are allowed to be changed.
         // This is a safety check
         if (!allowedDynamicParameters.contains(parameterName)) {
-            throw new ComposerException("The value of the parameter " + parameterName + " should not be set manually.");
+            throw new BadUserInputException("The value of the parameter " + parameterName + " should not be set manually.");
         }
 
         for (ParameterProperties parameter : parameters) {
@@ -129,7 +128,7 @@ public void setParameterValue(String parameterName, String newParameterValue) th
                 return;
             }
         }
-        throw new ComposerException("The parameter " + parameterName + " does not exist.");
+        throw new BadUserInputException("The parameter " + parameterName + " does not exist.");
     }
 
     /**
@@ -140,7 +139,7 @@ public void setParameterValue(String parameterName, String newParameterValue) th
      * @throws AlgorithmException when algorithm's properties do not match the algorithmParameters
      */
     public void mergeWithAlgorithmParameters(HashMap<String, String> algorithmParameters)
-            throws AlgorithmException, CDEsMetadataException, UserException {
+            throws AlgorithmException, CDEsMetadataException, BadUserInputException {
         if (algorithmParameters == null)
             return;
 
@@ -151,15 +150,15 @@ public void mergeWithAlgorithmParameters(HashMap<String, String> algorithmParame
             if (value != null && !value.equals("")) {
                 if (!parameterProperties.getValueMultiple() && value.contains(",")
                         && !parameterProperties.getValueType().equals(ParameterProperties.ParameterValueType.json)) {
-                    throw new UserException("The value of the parameter '" + parameterProperties.getName()
+                    throw new BadUserInputException("The value of the parameter '" + parameterProperties.getName()
                             + "' should contain only one value.");
                 }
                 validateAlgorithmParameterValueType(name, value, parameterProperties);
                 validateAlgorithmParameterType(value, parameterProperties, pathology);
 
             } else {            // if value not given or it is blank
                 if (parameterProperties.getValueNotBlank()) {
-                    throw new UserException(
+                    throw new BadUserInputException(
                             "The value of the parameter '" + parameterProperties.getName() + "' should not be blank.");
                 }
 
@@ -184,7 +183,7 @@ private static void validateAlgorithmParameterType(
             String value,
             ParameterProperties parameterProperties,
             String pathology
-    ) throws CDEsMetadataException, UserException {
+    ) throws CDEsMetadataException, BadUserInputException {
         // First we split in case we have multiple values.
         String[] values = value.split(",");
         for (String singleValue : values) {
@@ -199,17 +198,17 @@ else if (parameterProperties.getType().equals(ParameterProperties.ParameterType.
                 if (parameterProperties.getValueType().equals(ParameterProperties.ParameterValueType.integer)
                         || parameterProperties.getValueType().equals(ParameterProperties.ParameterValueType.real)) {
                     if (parameterProperties.getValueMin() != null && Double.parseDouble(singleValue) < parameterProperties.getValueMin())
-                        throw new UserException("The value(s) of the parameter '" + parameterProperties.getName()
+                        throw new BadUserInputException("The value(s) of the parameter '" + parameterProperties.getName()
                                 + "' should be greater than " + parameterProperties.getValueMin() + " .");
                     if (parameterProperties.getValueMax() != null && Double.parseDouble(singleValue) > parameterProperties.getValueMax())
-                        throw new UserException("The value(s) of the parameter '" + parameterProperties.getName()
+                        throw new BadUserInputException("The value(s) of the parameter '" + parameterProperties.getName()
                                 + "' should be less than " + parameterProperties.getValueMax() + " .");
                 } else if (parameterProperties.getValueType().equals(ParameterProperties.ParameterValueType.string)) {
                     if (parameterProperties.getValueEnumerations() == null)
                         return;
                     List<String> enumerations = Arrays.asList(parameterProperties.getValueEnumerations());
                     if (!enumerations.contains(singleValue))
-                        throw new UserException("The value '" + singleValue + "' of the parameter '" + parameterProperties.getName()
+                        throw new BadUserInputException("The value '" + singleValue + "' of the parameter '" + parameterProperties.getName()
                                 + "' is not included in the valueEnumerations " + Arrays.toString(parameterProperties.getValueEnumerations()) + " .");
                 }
             }
@@ -229,24 +228,24 @@ private static void validateCDEVariables(
             String[] variables,
             ParameterProperties parameterProperties,
             String pathology
-    ) throws CDEsMetadataException, UserException {
+    ) throws CDEsMetadataException, BadUserInputException {
         CDEsMetadata.PathologyCDEsMetadata metadata = CDEsMetadata.getInstance().getPathologyCDEsMetadata(pathology);
         for (String curValue : variables) {
             if (!metadata.columnExists(curValue)) {
-                throw new UserException("The CDE '" + curValue + "' does not exist.");
+                throw new BadUserInputException("The CDE '" + curValue + "' does not exist.");
             }
 
             String allowedSQLTypeValues = parameterProperties.getColumnValuesSQLType();
             String columnValuesSQLType = metadata.getColumnValuesSQLType(curValue);
             if (!allowedSQLTypeValues.contains(columnValuesSQLType) && !allowedSQLTypeValues.equals("")) {
-                throw new UserException("The CDE '" + curValue + "' does not have one of the allowed SQL Types '"
+                throw new BadUserInputException("The CDE '" + curValue + "' does not have one of the allowed SQL Types '"
                         + allowedSQLTypeValues + "' for the algorithm.");
             }
 
             String allowedIsCategoricalValue = parameterProperties.getColumnValuesIsCategorical();
             String columnValuesIsCategorical = metadata.getColumnValuesIsCategorical(curValue);
             if (!allowedIsCategoricalValue.equals(columnValuesIsCategorical) && !allowedIsCategoricalValue.equals("")) {
-                throw new UserException("The CDE '" + curValue + "' does not match the categorical value '"
+                throw new BadUserInputException("The CDE '" + curValue + "' does not match the categorical value '"
                         + allowedIsCategoricalValue + "' specified for the algorithm.");
             }
         }
@@ -263,7 +262,7 @@ private static void validateAlgorithmParameterValueType(
             String algorithmName,
             String value,
             ParameterProperties parameterProperties
-    ) throws AlgorithmException, UserException {
+    ) throws AlgorithmException, BadUserInputException {
         if (parameterProperties.getValueType().equals(ParameterProperties.ParameterValueType.json)) {
             try {
                 new JSONObject(value);
@@ -285,19 +284,19 @@ private static void validateAlgorithmParameterValueType(
                 try {
                     Double.parseDouble(curValue);
                 } catch (NumberFormatException nfe) {
-                    throw new UserException(
+                    throw new BadUserInputException(
                             "The value of the parameter '" + parameterProperties.getName() + "' should be a real number.");
                 }
             } else if (parameterProperties.getValueType().equals(ParameterProperties.ParameterValueType.integer)) {
                 try {
                     Integer.parseInt(curValue);
                 } catch (NumberFormatException e) {
-                    throw new UserException(
+                    throw new BadUserInputException(
                             "The value of the parameter '" + parameterProperties.getName() + "' should be an integer.");
                 }
             } else if (parameterProperties.getValueType().equals(ParameterProperties.ParameterValueType.string)) {
                 if (curValue.equals("")) {
-                    throw new UserException(
+                    throw new BadUserInputException(
                             "The value of the parameter '" + parameterProperties.getName()
                                     + "' contains an empty string.");
                 }