app: The cli-usage.yml now is in the jar #TASK-5055

opencb · Oct 31, 2023 · 8e2d0e9 · 8e2d0e9
1 parent 769f964
commit 8e2d0e9
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Showing 3 changed files with 30 additions and 13 deletions.
diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml
@@ -138,13 +138,21 @@
         <sourceDirectory>src/main/java</sourceDirectory>
 
         <resources>
+<!--            <resource>-->
+<!--                <directory>src/main/resources</directory>-->
+<!--                <filtering>true</filtering>-->
+<!--                <targetPath>${project.basedir}/target/clients/R</targetPath>-->
+<!--                <includes>-->
+<!--                    <include>compileR.sh</include>-->
+<!--                </includes>-->
+<!--            </resource>-->
             <resource>
                 <directory>src/main/resources</directory>
                 <filtering>true</filtering>
-                <targetPath>${project.basedir}/target/clients/R</targetPath>
                 <includes>
-                    <include>compileR.sh</include>
+                    <include>cli-usage.yml</include>
                 </includes>
+                <targetPath>${project.basedir}/target/classes</targetPath>
             </resource>
             <resource>
                 <directory>app/cloud/docker/compose</directory>
@@ -346,7 +354,7 @@
                                     <arg value="${project.basedir}/../opencga-core/target/classes/log4j2.internal.xml"/>
                                     <arg value="${project.basedir}/../opencga-storage/opencga-storage-core/target/classes/storage-configuration.yml"/>
                                     <arg value="${project.basedir}/../opencga-client/target/classes/client-configuration.yml"/>
-                                    <arg value="${project.basedir}/src/main/resources/usage.yml"/>
+<!--                                    <arg value="${project.basedir}/src/main/resources/usage.yml"/>-->
                                     <arg value="${build.dir}/conf"/>
                                 </exec>
 

diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/config/CliConfiguration.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/config/CliConfiguration.java
@@ -2,11 +2,13 @@
 
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.fasterxml.jackson.dataformat.yaml.YAMLFactory;
+import org.apache.commons.io.FileUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import java.io.File;
 import java.io.IOException;
+import java.util.Scanner;
 
 public class CliConfiguration {
 
@@ -23,7 +25,7 @@ public class CliConfiguration {
     /**
      * FILENAME is the file location of the configuration yml file
      */
-    public static final String CLI_USAGE_FILENAME = "cli-usage.yml";
+    private String cliUsageFileName = "cli-usage.yml";
 
     /**
      * LOGGER is an instance of the Logger class so that we can do proper
@@ -38,12 +40,10 @@ public static CliConfiguration getInstance() {
         return CliConfiguration.instance;
     }
 
-    private static CliUsage loadConfiguration() throws IOException {
+    private CliUsage loadConfiguration() throws IOException {
         // Loading the YAML file from the /conf folder
-        String appHome = System.getProperty("app.home", System.getenv("OPENCGA_HOME"));
-        String conf = appHome + "/conf";
-        File file = new File(conf + File.separator + CLI_USAGE_FILENAME);
-
+        File file = new File(cliUsageFileName);
+        FileUtils.copyURLToFile(getClass().getClassLoader().getResource(cliUsageFileName),file);
         // Mapping the config from the YAML file to the Configuration class
         logger.info("Loading CLI configuration from: " + file.getAbsolutePath());
         ObjectMapper yamlObjectMapper = new ObjectMapper(new YAMLFactory());
@@ -53,18 +53,27 @@ private static CliUsage loadConfiguration() throws IOException {
     /*
      * We keep an instance of cliUsage for the Shell
      */
-    public static CliUsage getUsage() {
+    public CliUsage getUsage() {
         if (cliUsage == null) {
             try {
                 cliUsage = loadConfiguration();
             } catch (IOException e) {
-                logger.error("Loading CLI configuration from: " + CLI_USAGE_FILENAME + " Failed");
+                logger.error("Loading CLI configuration from: " + cliUsageFileName + " Failed");
+                System.err.println("Loading CLI configuration from: " + cliUsageFileName + " Failed");
             }
         }
         return cliUsage;
     }
 
-    public static void setUsage(CliUsage cliUsage) {
+    public void setUsage(CliUsage cliUsage) {
         CliConfiguration.cliUsage = cliUsage;
     }
+
+    public String getCliUsageFileName() {
+        return cliUsageFileName;
+    }
+
+    public void setCliUsageFileName(String cliUsageFileName) {
+        this.cliUsageFileName = cliUsageFileName;
+    }
 }
diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/custom/CustomCliOptionsParser.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/custom/CustomCliOptionsParser.java
@@ -108,7 +108,7 @@ private String getPrefix() {
      */
     @Override
     protected void printMainUsage() {
-        CliUsage cliUsage = CliConfiguration.getUsage();
+        CliUsage cliUsage = CliConfiguration.getInstance().getUsage();
         CliCategory[] categories = cliUsage.getCategories();
         for (CliCategory cliCategory : categories) {
             String[] options = cliCategory.getOptions();