TASK-5556 - OpenCGA CLI --json-data-model does not produce parseable JSONS

opencga-app/src/main/java/org/opencb/opencga/app/cli/CommandExecutor.java

@@ -45,7 +45,10 @@
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
+import java.util.Collections;
+import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 
 /**
  * Created by imedina on 19/04/16.
@@ -291,72 +294,61 @@ public CommandExecutor setSessionManager(SessionManager sessionManager) {
         return this;
     }
 
-
     public String getObjectAsJSON(String objectCategory, String objectPath, OpenCGAClient openCGAClient) throws Exception {
         StringBuilder jsonInString = new StringBuilder("\n");
         try {
             ObjectMap queryParams = new ObjectMap();
             queryParams.putIfNotEmpty("category", objectCategory);
             RestResponse<List> response = openCGAClient.getMetaClient().api(queryParams);
             ObjectMapper jsonObjectMapper = new ObjectMapper();
+            boolean found = false;
             for (List list : response.getResponses().get(0).getResults()) {
                 List<RestCategory> categories = jsonObjectMapper.convertValue(list, new TypeReference<List<RestCategory>>() {});
                 for (RestCategory category : categories) {
                     for (RestEndpoint endpoint : category.getEndpoints()) {
                         if (objectPath.equals(endpoint.getPath())) {
-                            boolean enc = false;
                             for (RestParameter parameter : endpoint.getParameters()) {
-                                //jsonInString += parameter.getName()+":"+parameter.getAllowedValues()+"\n";
                                 if (parameter.getData() != null) {
-                                    enc = true;
-                                    jsonInString.append(printBody(parameter.getData(), ""));
+                                    found = true;
+                                    Map<String, Object> map = getExampleBody(parameter.getData());
+                                    jsonInString.append(jsonObjectMapper.writerWithDefaultPrettyPrinter().writeValueAsString(map));
                                 }
                             }
-                            if (!enc) {
-                                jsonInString.append("No model available");
-                            }
-                            //
                         }
                     }
                 }
             }
+            if (!found) {
+                jsonInString.append("No model available");
+            }
         } catch (Exception e) {
             jsonInString = new StringBuilder("Data model not found.");
             CommandLineUtils.error(e);
         }
         return jsonInString.toString();
     }
 
-    private String printBody(List<RestParameter> data, String tabs) {
-        String res = "";
-        res += "{\n";
-        String tab = "    " + tabs;
+    private Map<String, Object> getExampleBody(List<RestParameter> data) {
+        Map<String, Object> result = new HashMap<>();
         for (RestParameter parameter : data) {
             if (parameter.getData() == null) {
-                res += printParameter(parameter, tab);
+                result.put(parameter.getName(), getParameterExampleValue(parameter));
             } else {
-                res += tab + "\"" +parameter.getName() + "\"" + ": [" + printBody(parameter.getData(), tab) + "],\n";
+                result.put(parameter.getName(), getExampleBody(parameter.getData()));
             }
         }
-        res += tabs + "}";
-        return res;
-
-    }
-
-    private String printParameter(RestParameter parameter, String tab) {
-
-        return tab + "\"" + parameter.getName() + "\"" + ":" + printParameterValue(parameter) + ",\n";
+       return result;
     }
 
-    private String printParameterValue(RestParameter parameter) {
-
+    private Object getParameterExampleValue(RestParameter parameter) {
         if(!StringUtils.isEmpty(parameter.getAllowedValues())){
             return parameter.getAllowedValues().replace(" ", "|");
         }
+
         switch (parameter.getType()) {
             case "Boolean":
             case "java.lang.Boolean":
-                return "false";
+                return false;
             case "Long":
             case "Float":
             case "Double":
@@ -365,21 +357,21 @@ private String printParameterValue(RestParameter parameter) {
             case "double":
             case "float":
             case "long":
-                return "0";
+                return 0;
             case "List":
-                return "[\"\"]";
+                return Collections.singletonList("");
             case "Date":
-                return "\"dd/mm/yyyy\"";
+                return "dd/mm/yyyy";
             case "Map":
-                return "{\"key\": \"value\"}";
+                return Collections.singletonMap("key", "value");
             case "String":
-                return "\"\"";
+                return "";
             default:
-                return "\"-\"";
+                logger.debug("Unknown type: " + parameter.getType() + " for parameter: " + parameter.getName());
+                return "-";
         }
     }
 
-
     public Logger getLogger() {
         return logger;
     }

opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/SamplesCommandExecutor.java

@@ -125,7 +125,6 @@ private RestResponse<SampleAclEntryList> updateAcl() throws Exception {
             queryParams.putIfNotEmpty("study", sessionManager.getSession().getCurrentStudy());
         }
 
-
         SampleAclUpdateParams sampleAclUpdateParams = null;
         if (commandOptions.jsonDataModel) {
             RestResponse<SampleAclEntryList> res = new RestResponse<>();

opencga-server/src/main/java/org/opencb/opencga/server/generator/models/RestParameter.java

@@ -99,104 +99,117 @@ public String getName() {
         return name;
     }
 
-    public void setName(String name) {
+    public RestParameter setName(String name) {
         this.name = name;
+        return this;
     }
 
     public RestParamType getParam() {
         return param;
     }
 
-    public void setParam(RestParamType param) {
+    public RestParameter setParam(RestParamType param) {
         this.param = param;
+        return this;
     }
 
     public String getParentName() {
         return parentName;
     }
 
-    public void setParentName(String parentName) {
+    public RestParameter setParentName(String parentName) {
         this.parentName = parentName;
+        return this;
     }
 
     public String getType() {
         return type;
     }
 
-    public void setType(String type) {
+    public RestParameter setType(String type) {
         this.type = type;
+        return this;
     }
 
     public String getTypeClass() {
         return typeClass;
     }
 
-    public void setTypeClass(String typeClass) {
+    public RestParameter setTypeClass(String typeClass) {
         this.typeClass = typeClass;
+        return this;
     }
 
     public boolean isRequired() {
         return required;
     }
 
-    public void setRequired(boolean required) {
+    public RestParameter setRequired(boolean required) {
         this.required = required;
+        return this;
     }
 
     public String getDefaultValue() {
         return defaultValue;
     }
 
-    public void setDefaultValue(String defaultValue) {
+    public RestParameter setDefaultValue(String defaultValue) {
         this.defaultValue = defaultValue;
+        return this;
     }
 
     public String getDescription() {
         return description;
     }
 
-    public void setDescription(String description) {
+    public RestParameter setDescription(String description) {
         this.description = description;
+        return this;
     }
 
     public List<RestParameter> getData() {
         return data;
     }
 
-    public void setData(List<RestParameter> data) {
+    public RestParameter setData(List<RestParameter> data) {
         this.data = data;
+        return this;
     }
 
     public String getAllowedValues() {
         return allowedValues;
     }
 
-    public void setAllowedValues(String allowedValues) {
+    public RestParameter setAllowedValues(String allowedValues) {
         this.allowedValues = allowedValues;
+        return this;
     }
 
     public boolean isComplex() {
         return complex;
     }
 
-    public void setComplex(boolean complex) {
+    public RestParameter setComplex(boolean complex) {
         this.complex = complex;
+        return this;
     }
 
     public String getGenericType() {
         return genericType;
     }
 
-    public void setGenericType(String genericType) {
+    public RestParameter setGenericType(String genericType) {
         this.genericType = genericType;
+        return this;
     }
 
     public boolean isInnerParam() {
         return innerParam;
     }
 
-    public void setInnerParam(boolean innerParam) {
+    public RestParameter setInnerParam(boolean innerParam) {
         this.innerParam = innerParam;
+        return this;
     }
 
     public boolean isEnum() {