cli:getObjectAsJSON completo #TASK-5160

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

@@ -1,5 +1,5 @@
 /*
-* Copyright 2015-2023-10-27 OpenCB
+* Copyright 2015-2023-11-02 OpenCB
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.

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

@@ -1,5 +1,5 @@
 /*
-* Copyright 2015-2023-10-27 OpenCB
+* Copyright 2015-2023-11-02 OpenCB
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.

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

@@ -48,7 +48,7 @@
  */
 public class AnalysisAlignmentCommandExecutor extends OpencgaCommandExecutor {
 
-    public String categoryName = "analysisAlignment";
+    public String categoryName = "alignment";
     public AnalysisAlignmentCommandOptions analysisAlignmentCommandOptions;
 
     public AnalysisAlignmentCommandExecutor(AnalysisAlignmentCommandOptions analysisAlignmentCommandOptions) throws CatalogAuthenticationException {

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

@@ -80,7 +80,7 @@
  */
 public class AnalysisClinicalCommandExecutor extends OpencgaCommandExecutor {
 
-    public String categoryName = "analysisClinical";
+    public String categoryName = "clinical";
     public AnalysisClinicalCommandOptions analysisClinicalCommandOptions;
 
     public AnalysisClinicalCommandExecutor(AnalysisClinicalCommandOptions analysisClinicalCommandOptions) throws CatalogAuthenticationException {

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

@@ -76,7 +76,7 @@
  */
 public class AnalysisVariantCommandExecutor extends OpencgaCommandExecutor {
 
-    public String categoryName = "analysisVariant";
+    public String categoryName = "variant";
     public AnalysisVariantCommandOptions analysisVariantCommandOptions;
 
     public AnalysisVariantCommandExecutor(AnalysisVariantCommandOptions analysisVariantCommandOptions) throws CatalogAuthenticationException {

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

@@ -44,7 +44,7 @@
  */
 public class DiseasePanelsCommandExecutor extends OpencgaCommandExecutor {
 
-    public String categoryName = "diseasePanels";
+    public String categoryName = "panels";
     public DiseasePanelsCommandOptions diseasePanelsCommandOptions;
 
     public DiseasePanelsCommandExecutor(DiseasePanelsCommandOptions diseasePanelsCommandOptions) throws CatalogAuthenticationException {

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

@@ -225,34 +225,97 @@ public OpencgaCommandExecutor setOpenCGAClient(OpenCGAClient openCGAClient) {
     }
 
     public String getObjectAsJSON(String objectCategory, String objectPath) throws Exception {
-        String jsonInString = "";
+        String jsonInString = "\n";
         try {
             ObjectMap queryParams = new ObjectMap();
-            queryParams.putIfNotEmpty("category", String.valueOf(objectCategory));
+            queryParams.putIfNotEmpty("category", objectCategory);
             RestResponse<List> response = openCGAClient.getMetaClient().api(queryParams);
             ObjectMapper jsonObjectMapper = new ObjectMapper();
            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())){
-                            for (RestParameter parameter:endpoint.getParameters()){
+                    for (RestEndpoint endpoint : category.getEndpoints()) {
+                        if (objectPath.equals(endpoint.getPath())) {
+                            boolean enc = false;
+                            for (RestParameter parameter : endpoint.getParameters()) {
                                 //jsonInString += parameter.getName()+":"+parameter.getAllowedValues()+"\n";
-                                jsonInString += parameter.toString()+"\n";
+                                if (parameter.getData() != null) {
+                                    enc = true;
+                                    jsonInString += printBody(parameter.getData(), "");
+                                }
+                            }
+                            if (!enc) {
+                                jsonInString += "No model available";
                             }
                             //
                         }
                     }
                 }
-            }
-            //  jsonInString = DataModelsUtils.dataModelToJsonString(o.getClass());
+           }
         } catch (Exception e) {
             jsonInString = "Data model not found.";
             CommandLineUtils.error(e);
         }
         return jsonInString;
     }
 
+    private String printBody(List<RestParameter> data, String tabs) {
+        String res = "";
+        res += "{\n";
+        String tab = "    " + tabs;
+        for (RestParameter parameter : data) {
+            if (parameter.getData() == null) {
+                res += printParameter(parameter, tab);
+            } else {
+                res += tab + parameter.getName() + "\"" + ": [" + printBody(parameter.getData(), tab) + "],\n";
+            }
+        }
+        res += tabs + "}";
+        return res;
+
+    }
+
+    private String printParameter(RestParameter parameter, String tab) {
+
+        return tab + "\"" + parameter.getName() + "\"" + ":" + printParameterValue(parameter) + ",\n";
+    }
+
+    private String printParameterValue(RestParameter parameter) {
+
+        if(!StringUtils.isEmpty(parameter.getAllowedValues())){
+            return parameter.getAllowedValues().replace(" ", "|");
+        }
+        switch (parameter.getType()) {
+            case "Boolean":
+            case "java.lang.Boolean":
+                return "false";
+            case "Long":
+            case "Float":
+            case "Double":
+            case "Integer":
+            case "int":
+            case "double":
+            case "float":
+            case "long":
+                return "0";
+            case "List":
+                return "[\"\"]";
+            case "Date":
+                return "\"dd/mm/yyyy\"";
+            case "Map":
+                return "{\"key\": \"value\"}";
+            case "String":
+                return "\"\"";
+            default:
+                return "\"-\"";
+        }
+    }
+
+    private boolean isNumeric(String type) {
+
+        return "int".equals(type) || "Long".equals(type) || "Float".equals(type) || "double".equals(type);
+    }
+
     public RestResponse<AuthenticationResponse> saveSession(String user, AuthenticationResponse response) throws ClientException, IOException {
         RestResponse<AuthenticationResponse> res = new RestResponse<>();
         if (response != null) {

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

@@ -61,7 +61,7 @@
  */
 public class OperationsVariantStorageCommandExecutor extends OpencgaCommandExecutor {
 
-    public String categoryName = "operationsVariantStorage";
+    public String categoryName = "operation";
     public OperationsVariantStorageCommandOptions operationsVariantStorageCommandOptions;
 
     public OperationsVariantStorageCommandExecutor(OperationsVariantStorageCommandOptions operationsVariantStorageCommandOptions) throws CatalogAuthenticationException {

opencga-client/src/main/R/R/Admin-methods.R

@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-10-27
+#    Autogenerated on: 2023-11-02
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.

opencga-client/src/main/R/R/Alignment-methods.R

@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-10-27
+#    Autogenerated on: 2023-11-02
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.

opencga-client/src/main/R/R/AllGenerics.R

@@ -1,21 +1,21 @@
 # ##############################################################################
 ## UserClient
-setGeneric("userClient", function(OpencgaR, user, filterId, users, endpointName, params=NULL, ...)
+setGeneric("userClient", function(OpencgaR, filterId, user, users, endpointName, params=NULL, ...)
     standardGeneric("userClient"))
 
 # ##############################################################################
 ## ProjectClient
-setGeneric("projectClient", function(OpencgaR, projects, project, endpointName, params=NULL, ...)
+setGeneric("projectClient", function(OpencgaR, project, projects, endpointName, params=NULL, ...)
     standardGeneric("projectClient"))
 
 # ##############################################################################
 ## StudyClient
-setGeneric("studyClient", function(OpencgaR, templateId, variableSet, study, group, studies, members, endpointName, params=NULL, ...)
+setGeneric("studyClient", function(OpencgaR, group, members, studies, study, templateId, variableSet, endpointName, params=NULL, ...)
     standardGeneric("studyClient"))
 
 # ##############################################################################
 ## FileClient
-setGeneric("fileClient", function(OpencgaR, files, file, folder, annotationSet, members, endpointName, params=NULL, ...)
+setGeneric("fileClient", function(OpencgaR, files, file, members, annotationSet, folder, endpointName, params=NULL, ...)
     standardGeneric("fileClient"))
 
 # ##############################################################################
@@ -25,7 +25,7 @@ setGeneric("jobClient", function(OpencgaR, jobs, members, job, endpointName, par
 
 # ##############################################################################
 ## SampleClient
-setGeneric("sampleClient", function(OpencgaR, sample, samples, members, annotationSet, endpointName, params=NULL, ...)
+setGeneric("sampleClient", function(OpencgaR, samples, members, sample, annotationSet, endpointName, params=NULL, ...)
     standardGeneric("sampleClient"))
 
 # ##############################################################################
@@ -35,7 +35,7 @@ setGeneric("individualClient", function(OpencgaR, individual, members, individua
 
 # ##############################################################################
 ## FamilyClient
-setGeneric("familyClient", function(OpencgaR, annotationSet, members, family, families, endpointName, params=NULL, ...)
+setGeneric("familyClient", function(OpencgaR, members, family, families, annotationSet, endpointName, params=NULL, ...)
     standardGeneric("familyClient"))
 
 # ##############################################################################
@@ -60,7 +60,7 @@ setGeneric("variantClient", function(OpencgaR, endpointName, params=NULL, ...)
 
 # ##############################################################################
 ## ClinicalClient
-setGeneric("clinicalClient", function(OpencgaR, clinicalAnalysis, clinicalAnalyses, interpretations, members, interpretation, endpointName, params=NULL, ...)
+setGeneric("clinicalClient", function(OpencgaR, clinicalAnalysis, members, interpretation, interpretations, clinicalAnalyses, endpointName, params=NULL, ...)
     standardGeneric("clinicalClient"))
 
 # ##############################################################################

opencga-client/src/main/R/R/Clinical-methods.R

@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-10-27
+#    Autogenerated on: 2023-11-02
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.
@@ -58,7 +58,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("clinicalClient", "OpencgaR", function(OpencgaR, clinicalAnalysis, clinicalAnalyses, interpretations, members, interpretation, endpointName, params=NULL, ...) {
+setMethod("clinicalClient", "OpencgaR", function(OpencgaR, clinicalAnalysis, members, interpretation, interpretations, clinicalAnalyses, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/analysis/clinical/acl/{members}/update:

opencga-client/src/main/R/R/Cohort-methods.R

@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-10-27
+#    Autogenerated on: 2023-11-02
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.

opencga-client/src/main/R/R/Family-methods.R

@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-10-27
+#    Autogenerated on: 2023-11-02
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.
@@ -38,7 +38,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("familyClient", "OpencgaR", function(OpencgaR, annotationSet, members, family, families, endpointName, params=NULL, ...) {
+setMethod("familyClient", "OpencgaR", function(OpencgaR, members, family, families, annotationSet, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/families/acl/{members}/update:

opencga-client/src/main/R/R/File-methods.R

@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-10-27
+#    Autogenerated on: 2023-11-02
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.
@@ -54,7 +54,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("fileClient", "OpencgaR", function(OpencgaR, files, file, folder, annotationSet, members, endpointName, params=NULL, ...) {
+setMethod("fileClient", "OpencgaR", function(OpencgaR, files, file, members, annotationSet, folder, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/files/acl/{members}/update:

opencga-client/src/main/R/R/GA4GH-methods.R

@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-10-27
+#    Autogenerated on: 2023-11-02
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.

opencga-client/src/main/R/R/Individual-methods.R

@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-10-27
+#    Autogenerated on: 2023-11-02
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.

opencga-client/src/main/R/R/Job-methods.R

@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-10-27
+#    Autogenerated on: 2023-11-02
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.

opencga-client/src/main/R/R/Meta-methods.R

@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-10-27
+#    Autogenerated on: 2023-11-02
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.

opencga-client/src/main/R/R/Operation-methods.R

@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-10-27
+#    Autogenerated on: 2023-11-02
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.

opencga-client/src/main/R/R/Panel-methods.R

@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-10-27
+#    Autogenerated on: 2023-11-02
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.

opencga-client/src/main/R/R/Project-methods.R

@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-10-27
+#    Autogenerated on: 2023-11-02
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.
@@ -34,7 +34,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("projectClient", "OpencgaR", function(OpencgaR, projects, project, endpointName, params=NULL, ...) {
+setMethod("projectClient", "OpencgaR", function(OpencgaR, project, projects, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/projects/create:

opencga-client/src/main/R/R/Sample-methods.R

@@ -2,7 +2,7 @@
 # WARNING: AUTOGENERATED CODE
 #
 #    This code was generated by a tool.
-#    Autogenerated on: 2023-10-27
+#    Autogenerated on: 2023-11-02
 #    
 #    Manual changes to this file may cause unexpected behavior in your application.
 #    Manual changes to this file will be overwritten if the code is regenerated.
@@ -39,7 +39,7 @@
 #' [*]: Required parameter
 #' @export
 
-setMethod("sampleClient", "OpencgaR", function(OpencgaR, sample, samples, members, annotationSet, endpointName, params=NULL, ...) {
+setMethod("sampleClient", "OpencgaR", function(OpencgaR, samples, members, sample, annotationSet, endpointName, params=NULL, ...) {
     switch(endpointName,
 
         #' @section Endpoint /{apiVersion}/samples/acl/{members}/update: