Merge branch 'release-2.12.x' into TASK-5501

opencb · Jan 29, 2024 · 39da25d · 39da25d
2 parents 3f1c8f8 + 39b05ec
commit 39da25d
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Showing 6 changed files with 115 additions and 90 deletions.
diff --git a/.github/workflows/scripts/get_same_branch.sh b/.github/workflows/scripts/get_same_branch.sh
@@ -7,10 +7,6 @@ if [[ -z $BRANCH_NAME  ]]; then
   exit 1
 fi
 
-if [[ $BRANCH_NAME != "TASK-"*   ]]; then
-  echo "No need to check dependencies."
-  exit 0
-fi
 
 function install(){
   local REPO=$1

diff --git a/.github/workflows/test-analysis.yml b/.github/workflows/test-analysis.yml
@@ -27,7 +27,7 @@ jobs:
         uses: actions/setup-java@v3
         with:
           distribution: 'temurin'
-          java-version: '11'
+          java-version: '17'
           cache: 'maven'
       - name: Install dependencies branches
         run: |

diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/CommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/CommandExecutor.java
@@ -17,16 +17,25 @@
 package org.opencb.opencga.app.cli;
 
 import com.beust.jcommander.JCommander;
+import com.fasterxml.jackson.core.type.TypeReference;
+import com.fasterxml.jackson.databind.ObjectMapper;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.Level;
 import org.apache.logging.log4j.core.config.Configurator;
+import org.opencb.commons.datastore.core.ObjectMap;
 import org.opencb.commons.utils.FileUtils;
 import org.opencb.commons.utils.PrintUtils;
+import org.opencb.opencga.app.cli.main.utils.CommandLineUtils;
 import org.opencb.opencga.app.cli.session.SessionManager;
 import org.opencb.opencga.client.config.ClientConfiguration;
 import org.opencb.opencga.client.exceptions.ClientException;
+import org.opencb.opencga.client.rest.OpenCGAClient;
 import org.opencb.opencga.core.config.Configuration;
 import org.opencb.opencga.core.config.storage.StorageConfiguration;
+import org.opencb.opencga.core.response.RestResponse;
+import org.opencb.opencga.server.generator.models.RestCategory;
+import org.opencb.opencga.server.generator.models.RestEndpoint;
+import org.opencb.opencga.server.generator.models.RestParameter;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -36,6 +45,7 @@
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
+import java.util.List;
 
 /**
  * Created by imedina on 19/04/16.
@@ -281,6 +291,95 @@ 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();
+            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(), ""));
+                                }
+                            }
+                            if (!enc) {
+                                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;
+        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 "\"-\"";
+        }
+    }
+
+
     public Logger getLogger() {
         return logger;
     }

diff --git a/...a-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OpencgaCommandExecutor.java b/...a-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OpencgaCommandExecutor.java
@@ -225,90 +225,7 @@ public OpencgaCommandExecutor setOpenCGAClient(OpenCGAClient openCGAClient) {
     }
 
     public String getObjectAsJSON(String objectCategory, String objectPath) 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();
-           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(), ""));
-                                }
-                            }
-                            if (!enc) {
-                                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;
-        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 "\"-\"";
-        }
+        return super.getObjectAsJSON(objectCategory, objectPath, openCGAClient);
     }
 
     private boolean isNumeric(String type) {

diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml
@@ -252,7 +252,6 @@
         <plugins>
             <plugin>
                 <artifactId>maven-war-plugin</artifactId>
-                <version>2.6</version>
                 <configuration>
                     <warName>${opencga.war.name}</warName>
                     <!--

diff --git a/pom.xml b/pom.xml
@@ -146,6 +146,8 @@
         <servlet-api.version>2.5-20081211</servlet-api.version>
 
         <kryo.version>2.23.0</kryo.version>
+        <lombok.version>1.18.30</lombok.version>
+        <maven-war-plugin.version>3.4.0</maven-war-plugin.version>
     </properties>
 
     <scm>
@@ -987,6 +989,12 @@
                 <artifactId>grep4j</artifactId>
                 <version>${grep4j.version}</version>
             </dependency>
+            <dependency>
+                <groupId>org.projectlombok</groupId>
+                <artifactId>lombok</artifactId>
+                <version>${lombok.version}</version>
+                <scope>provided</scope>
+            </dependency>
             <dependency>
                 <groupId>org.redisson</groupId>
                 <artifactId>redisson</artifactId>
@@ -1087,6 +1095,7 @@
                 <artifactId>kryo</artifactId>
                 <version>${kryo.version}</version>
             </dependency>
+
         </dependencies>
     </dependencyManagement>
 
@@ -1111,6 +1120,11 @@
                     <artifactId>maven-surefire-report-plugin</artifactId>
                     <version>${maven-surefire-plugin.version}</version>
                 </plugin>
+                <plugin>
+                    <groupId>org.apache.maven.plugins</groupId>
+                    <artifactId>maven-war-plugin</artifactId>
+                    <version>${maven-war-plugin.version}</version>
+                </plugin>
             </plugins>
         </pluginManagement>