Merge pull request #12 from pgdurand/prepV5

Prep v5

src/bzh/plealog/dbmirror/main/Annotate.java

@@ -46,13 +46,14 @@
  * 
  * @author Patrick G. Durand
  */
-public class Annotate {
+@BdmTool(command="annotate", description="annotate a BLAST XML formatted file")
+public class Annotate implements BdmToolApi {
 
   /**
    * Setup the valid command-line of the application.
    */
   @SuppressWarnings("static-access")
-  private static Options getCmdLineOptions() {
+  private Options getCmdLineOptions() {
     Options opts;
 
     Option type = OptionBuilder
@@ -95,7 +96,8 @@ private static Options getCmdLineOptions() {
     return opts;
   }
 
-  public static boolean doJob(String[] args){
+  @Override
+  public boolean execute(String[] args){
     PAnnotateBlastResult annotator;
     CommandLine cmdLine;
     String input, output, writer, type;
@@ -121,10 +123,4 @@ public static boolean doJob(String[] args){
 
     return annotator.annotate(input, output, writer, type, includeBC);
   }
-
-  public static void main(String[] args) {
-    if (!doJob(args)){
-      System.exit(1);// exit code=1 : do this to report error to calling app
-    }
-  }
 }

src/bzh/plealog/dbmirror/main/AutoCheckDescriptors.java

@@ -66,6 +66,7 @@
  * 
  * @author Patrick G. Durand
  */
+@BdmTool(command="check", description="check whether or not a descriptor is still ok (URL not broken, etc)")
 public class AutoCheckDescriptors {
   private static final Log LOGGER = LogFactory.getLog(
       DBMSAbstractConfig.KDMS_ROOTLOG_CATEGORY + ".DSCChecker");

src/bzh/plealog/dbmirror/main/BdmTool.java

@@ -0,0 +1,37 @@
+/* Copyright (C) 2022 Patrick G. Durand
+ *
+ *  This program is free software: you can redistribute it and/or modify
+ *  it under the terms of the GNU Affero General Public License as published by
+ *  the Free Software Foundation, either version 3 of the License, or
+ *  (at your option) any later version.
+ *
+ *  You may obtain a copy of the License at
+ *
+ *     https://www.gnu.org/licenses/agpl-3.0.txt
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU Affero General Public License for more details.
+ */
+package bzh.plealog.dbmirror.main;
+
+import java.lang.annotation.Retention;
+import java.lang.annotation.RetentionPolicy;
+
+/**
+ * Annotation aims at marking a class as a BeeDeeM command-line tool.
+ * 
+ * @author Patrick G. Durand
+ */
+@Retention(RetentionPolicy.RUNTIME)
+public @interface BdmTool {
+  /**
+   * Name of command.
+   */
+  String command();
+  /**
+   * Description of command.
+   */
+  String description();
+}

src/bzh/plealog/dbmirror/main/BdmToolApi.java

@@ -0,0 +1,33 @@
+/* Copyright (C) 2022 Patrick G. Durand
+ *
+ *  This program is free software: you can redistribute it and/or modify
+ *  it under the terms of the GNU Affero General Public License as published by
+ *  the Free Software Foundation, either version 3 of the License, or
+ *  (at your option) any later version.
+ *
+ *  You may obtain a copy of the License at
+ *
+ *     https://www.gnu.org/licenses/agpl-3.0.txt
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU Affero General Public License for more details.
+ */
+package bzh.plealog.dbmirror.main;
+
+/**
+ * Defines API a BeeDeeM command-line tool must implement.
+ * 
+ * @author Patrick G. Durand
+ */
+public interface BdmToolApi {
+  /**
+   * Execute business logic of a tool.
+   * 
+   * @param args command-line arguments
+   * 
+   * @return true whether execution is ok, false otherwise.
+   */
+  public boolean execute(String[] args);
+}

src/bzh/plealog/dbmirror/main/BeeDeeMain.java

@@ -16,8 +16,17 @@
  */
 package bzh.plealog.dbmirror.main;
 
+import java.io.BufferedReader;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.lang.reflect.Method;
 import java.util.Arrays;
+import java.util.Collections;
+import java.util.Hashtable;
+import java.util.List;
 import java.util.Properties;
+import java.util.Set;
+import java.util.stream.Collectors;
 
 import bzh.plealog.dbmirror.ui.resources.DBMSMessages;
 
@@ -35,31 +44,54 @@
  * @author Patrick G. Durand
  */
 public class BeeDeeMain {
-
-  private static final String[] TOOL_LIST= {
-      "Annotate",
-      "DeleteBank",
-      "Dump",
-      "Install",
-      "Query",
-      "UiInstall"};
-
+
+  /** Code from: https://www.baeldung.com/java-find-all-classes-in-package*/
+  public static Set<Class<?>> findAllClassesUsingClassLoader(
+      String packageName) {
+    InputStream stream = ClassLoader.getSystemClassLoader()
+        .getResourceAsStream(packageName.replaceAll("[.]", "/"));
+    BufferedReader reader = new BufferedReader(new InputStreamReader(stream));
+    return reader.lines().filter(line -> line.endsWith(".class"))
+        .map(line -> getClass(line, packageName)).collect(Collectors.toSet());
+  }
+  private static Class<?> getClass(String className, String packageName) {
+    try {
+      return Class.forName(packageName + "."
+          + className.substring(0, className.lastIndexOf('.')));
+    } catch (ClassNotFoundException e) {
+      System.err.println(e);
+    }
+    return null;
+  }
+  /** */
+
   private static void dumpHelp() {
     Properties props = StarterUtils.getVersionProperties();
     System.out.print(props.getProperty("prg.app.name"));
     System.out.print(" ");
     System.out.println(DBMSMessages.getString("Tool.Master.intro"));
-    for (String tName : TOOL_LIST) {
+    Hashtable<String, String> tools = new Hashtable<String, String>();
+    Set<Class<?>> clazz = findAllClassesUsingClassLoader(new BeeDeeMain().getClass().getPackage().getName());
+    for(Class<?> c : clazz) {
+      BdmTool bdmT = c.getAnnotation(BdmTool.class); 
+      if (bdmT != null) {
+        tools.put(bdmT.command(), bdmT.description());
+      }
+    }
+    List<String> sortedTools = Collections.list(tools.keys());
+    Collections.sort(sortedTools);
+    for(String tName : sortedTools) {
       System.out.print("  bmd ");
-      System.out.print(DBMSMessages.getString("Tool."+tName+".cmd"));
-      if (tName.equals("UiInstall")) {
+      System.out.print(tName);
+      if (tName.equals("ui")) {
         System.out.print(": ");
       }
       else {
         System.out.print(" [options]: ");
       }
-      System.out.println(DBMSMessages.getString("Tool."+tName+".desc"));
+      System.out.println(tools.get(tName));
     }
+
     StringBuffer buf = new StringBuffer();
     System.out.println(DBMSMessages.getString("Tool.Master.more"));
     buf.append("--\n");
@@ -92,33 +124,42 @@ public static void main(String[] args) {
       args = Arrays.copyOfRange(args, 1, args.length);
     }
 
-    switch(cmd) {
-      case "annotate":
-        Annotate.main(args);
-        break;
-      case "delete":
-        DeleteBank.main(args);
-        break;
-      case "help":
-        dumpHelp();
-        break;
-      case "info":
-        DumpBankList.main(args);
-        break;
-      case "install":
-        CmdLineInstaller.main(args);
-        break;
-      case "query":
-        CmdLineQuery.main(args);
-        break;
-      case "ui":
-        UiInstaller.main(args);
-        break;
-      default:
+    if (cmd.equalsIgnoreCase("help") || 
+        cmd.equalsIgnoreCase("-h") || 
+        cmd.equalsIgnoreCase("--help")) {
+      dumpHelp();
+    }
+    else {
+      // Get all classes from current package
+      // to locate ones being annotated as BdmTool classes
+      boolean cmdOk = false;
+      Set<Class<?>> clazz = findAllClassesUsingClassLoader(new BeeDeeMain().getClass().getPackage().getName());
+      for(Class<?> c : clazz) {
+        BdmTool bdmT = c.getAnnotation(BdmTool.class); 
+        String bdmTCmd = bdmT != null ? bdmT.command() : "-" ;
+        if (bdmT != null && cmd.equalsIgnoreCase(bdmTCmd)) {
+          cmdOk = true;
+          try {
+            Method method = c.getDeclaredMethod("execute", String[].class);
+            Object bRet = method.invoke(c.newInstance(), new Object[] {args});
+            if ( ! bRet.toString().equalsIgnoreCase("true") ) {
+              System.exit(1);
+            }
+          } catch (Exception e) {
+            System.err.print(DBMSMessages.getString("Tool.Master.err2.cmd"));
+            System.err.println(cmd);
+            System.err.println(e.getMessage());
+            System.exit(1);
+          }
+        }
+      }
+      // unknown command
+      if (!cmdOk) {
         System.err.print(DBMSMessages.getString("Tool.Master.err.cmd"));
         System.err.print(": ");
         System.err.println(cmd);
         System.exit(1);
+      }
     }
   }
 }

src/bzh/plealog/dbmirror/main/CmdLineInstaller.java

@@ -69,17 +69,18 @@
  * 
  * @author Patrick G. Durand
  */
-public class CmdLineInstaller {
+@BdmTool(command="install", description="install bank(s)")
+public class CmdLineInstaller implements BdmToolApi {
 
   private File prepareListOfBanks(String bankListFormat){
     File f=null;
     FileOutputStream fos=null;
-
+    boolean bRet = false;
     try {
       f = File.createTempFile("bdm-list-of-banks", ".txt");
       fos = new FileOutputStream(f);
       DumpBankList dbl = new DumpBankList();
-      dbl.doJob(fos, "all", bankListFormat, "?");
+      bRet=dbl.doJob(fos, "all", bankListFormat, "?");
       fos.flush();
       fos.close();
       if (f.length()==0){
@@ -90,7 +91,7 @@ private File prepareListOfBanks(String bankListFormat){
       //for now, hide this msg, not really bad
     }
 
-    return f;
+    return bRet ? f : null;
   }
   private void sendTerminationMail(PFTPLoaderDescriptor fDescriptor, String bankListFormat) {
     PMailer mailer;
@@ -241,13 +242,14 @@ private boolean startApplication(
    * Options are defined in CmdLineInstallerOptions utility class. Use -h or -help
    * option to get software command-line description.
    */
-  public static void main(String[] args) {
+  @Override
+  public boolean execute(String[] args) {
     // convert the array of strings into an appropriate object
     CommandLine cmd = CmdLineInstallerOptions.handleArguments(args);
 
     // nothing to do, exit!
     if (cmd==null){
-      return;
+      return false;
     }
 
     // do we have a global descriptor name? (first and second cases described above)
@@ -274,7 +276,10 @@ public static void main(String[] args) {
     //go, go, go...
     CmdLineInstaller mirror = new CmdLineInstaller();
     if (!mirror.startApplication(globalDesc, fDescCmd, bankListFormat, fof)) {
-      System.exit(1);
+      return false;
+    }
+    else {
+      return true;
     }
   }
 

src/bzh/plealog/dbmirror/main/CmdLineQuery.java

@@ -55,7 +55,8 @@
  * 
  * @author Patrick G. Durand
  */
-public class CmdLineQuery {
+@BdmTool(command="query", description="query bank repository to fetch entry(ies) given ID(s)")
+public class CmdLineQuery implements BdmToolApi {
   private static final String DATABASE = "d";
   private static final String SEQID    = "i";
   private static final String FORMAT   = "f";
@@ -65,7 +66,7 @@ public class CmdLineQuery {
    * Setup the valid command-line of the application.
    */
   @SuppressWarnings("static-access")
-  private static Options getCmdLineOptions() {
+  private Options getCmdLineOptions() {
     Options opts;
 
     Option repo = OptionBuilder
@@ -101,7 +102,8 @@ private static Options getCmdLineOptions() {
     return opts;
   }
 
-  public static boolean doJob(String[] args) {
+  @Override
+  public boolean execute(String[] args) {
     PQueryMirrorBase qm;
     Hashtable<String, String> values;
     CommandLine cmdLine;
@@ -144,10 +146,4 @@ public static boolean doJob(String[] args) {
       return true;
     }
   }
-
-  public static void main(String[] args) {
-    if (!doJob(args)){
-      System.exit(1);
-    }
-  }
 }