Merge branch 'refs/heads/development' into feature/provide-pattern-ma…

…tching # Conflicts: # src/main/java/life/qbic/qpostman/list/ListCommand.java
qbicsoftware · Jul 11, 2024 · 5c8dcab · 5c8dcab
2 parents ea99800 + 3557137
commit 5c8dcab
Show file tree

Hide file tree

Showing 7 changed files with 150 additions and 90 deletions.
diff --git a/pom.xml b/pom.xml
@@ -5,7 +5,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>life.qbic</groupId>
     <artifactId>postman-cli</artifactId>
-    <version>2.1.0</version>
+    <version>2.1.1</version>
     <name>Postman cli</name>
     <url>https://github.com/qbicsoftware/postman-cli</url>
     <description>A client software written in Java for dataset downloads from QBiC's data management system openBIS </description>

diff --git a/src/main/java/life/qbic/App.java b/src/main/java/life/qbic/App.java
@@ -1,6 +1,7 @@
 package life.qbic;
 
 import java.util.Arrays;
+import life.qbic.qpostman.common.DefaultExceptionHandler;
 import life.qbic.qpostman.common.PostmanCommand;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
@@ -16,6 +17,7 @@ public class App {
   public static void main(String[] args) {
     LOG.debug("command line arguments: " + Arrays.deepToString(args));
     CommandLine cmd = new CommandLine(new PostmanCommand());
+    cmd.setExecutionExceptionHandler(new DefaultExceptionHandler());
     int exitCode = cmd.execute(args);
     System.exit(exitCode);
   }

diff --git a/src/main/java/life/qbic/qpostman/common/DefaultExceptionHandler.java b/src/main/java/life/qbic/qpostman/common/DefaultExceptionHandler.java
@@ -0,0 +1,65 @@
+package life.qbic.qpostman.common;
+
+import java.nio.file.Path;
+import java.util.Optional;
+import life.qbic.qpostman.common.options.AuthenticationOptions.NoPasswordException;
+import life.qbic.qpostman.common.options.SampleIdentifierOptions.IdentityFileEmptyException;
+import life.qbic.qpostman.common.options.SampleIdentifierOptions.IdentityFileNotFoundException;
+import life.qbic.qpostman.common.options.SampleIdentifierOptions.IdentityFileNotReadableException;
+import life.qbic.qpostman.common.options.SampleIdentifierOptions.SampleInput.ToShortSampleIdsException;
+import life.qbic.qpostman.openbis.ConnectionException;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.springframework.remoting.RemoteAccessException;
+import picocli.CommandLine;
+import picocli.CommandLine.IExecutionExceptionHandler;
+import picocli.CommandLine.ParseResult;
+
+/**
+ * The exception handler to use for exceptions within commands.
+ */
+public class DefaultExceptionHandler implements IExecutionExceptionHandler {
+  private static final Logger log = LogManager.getLogger(DefaultExceptionHandler.class);
+  private static final String LOG_PATH = Optional.ofNullable(System.getProperty("log.path"))
+      .orElse("logs");
+
+  private void logError(RuntimeException e) {
+    if (e instanceof RemoteAccessException remoteAccessException) {
+      log.error(
+          "Failed to connect to OpenBis: " + remoteAccessException.getCause().getMessage());
+      log.debug(remoteAccessException.getMessage(), remoteAccessException);
+    } else if (e instanceof AuthenticationException authenticationException) {
+      log.error(
+          "Could not authenticate user %s. Please make sure to provide the correct password.".formatted(
+              authenticationException.username()));
+      log.debug(authenticationException.getMessage(), authenticationException);
+    } else if (e instanceof ConnectionException) {
+      log.error("Could not connect to QBiC's data source. Have you requested access to the "
+          + "server? If not please write to [email protected]");
+      log.debug(e.getMessage(), e);
+    } else if (e instanceof NoPasswordException) {
+      log.error("No password provided. Please provide your password.");
+    } else if (e instanceof IdentityFileEmptyException identityFileException) {
+      log.error(identityFileException.getFile().getAbsolutePath() + " does not contain any identifiers.");
+    } else if (e instanceof IdentityFileNotFoundException identityFileNotFoundException) {
+      log.error("File not found: " + identityFileNotFoundException.getFile());
+    } else if (e instanceof IdentityFileNotReadableException identityFileNotReadableException) {
+      log.error("Not allowed to read file " + identityFileNotReadableException.getFile());
+    } else if (e instanceof ToShortSampleIdsException toShortSampleIdsException) {
+      log.error(
+          "Please provide at least 5 letters for your sample identifiers. The following sample identifiers are to short: "
+              + toShortSampleIdsException.getIdentifiers());
+    } else {
+      log.error("Something went wrong. For more detailed output see " + Path.of(LOG_PATH, "postman.log").toAbsolutePath());
+      log.debug(e.getMessage(), e);
+    }
+  }
+
+  @Override
+  public int handleExecutionException(Exception e, CommandLine commandLine, ParseResult parseResult)
+      throws Exception {
+    logError((RuntimeException) e);
+    commandLine.usage(commandLine. getErr());
+    return commandLine.getCommandSpec().exitCodeOnExecutionException();
+  }
+}
diff --git a/src/main/java/life/qbic/qpostman/common/options/AuthenticationOptions.java b/src/main/java/life/qbic/qpostman/common/options/AuthenticationOptions.java
@@ -4,14 +4,11 @@
 import static picocli.CommandLine.ArgGroup;
 
 import java.util.StringJoiner;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
 import picocli.CommandLine.Option;
 
 public class AuthenticationOptions {
-    private static final Logger log = LogManager.getLogger(AuthenticationOptions.class);
 
-    @Option(
+  @Option(
             names = {"-u", "--user"},
             required = true,
             description = "openBIS user name")
@@ -55,11 +52,11 @@ char[] getPassword() {
             if (nonNull(environmentVariable) && !environmentVariable.isBlank()) {
                 return environmentVariable.toCharArray();
             }
-            log.error("No password provided. Please provide your password.");
-            System.exit(2);
-            return null; // not reachable due to System.exit in previous line
+            throw new NoPasswordException();
         }
+    }
 
+    public static class NoPasswordException extends RuntimeException {
     }
 
     @Override

diff --git a/src/main/java/life/qbic/qpostman/common/options/SampleIdentifierOptions.java b/src/main/java/life/qbic/qpostman/common/options/SampleIdentifierOptions.java
@@ -1,5 +1,6 @@
 package life.qbic.qpostman.common.options;
 
+import static java.util.Objects.requireNonNull;
 import static picocli.CommandLine.ArgGroup;
 import static picocli.CommandLine.Option;
 import static picocli.CommandLine.Parameters;
@@ -12,13 +13,9 @@
 import java.util.List;
 import java.util.StringJoiner;
 import java.util.stream.Collectors;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
 
 public class SampleIdentifierOptions {
 
-  private static final Logger log = LogManager.getLogger(SampleIdentifierOptions.class);
-
   @ArgGroup(multiplicity = "1")
   public SampleInput sampleInput;
 
@@ -35,28 +32,67 @@ public String toString() {
 
   static class IdentityFileParser {
 
+    private IdentityFileParser() {
+
+    }
     public static List<String> parseIdentityFile(Path path) {
       File file = path.toFile();
       if (!file.exists()) {
-        log.error("File not found: " + file);
-        System.exit(2);
+        throw new IdentityFileNotFoundException(file);
       }
       if (!file.canRead()) {
-        log.error("Not allowed to read file " + file);
-        System.exit(2);
+        throw new IdentityFileNotReadableException(file);
       }
       try {
-        return Files.readAllLines(path).stream()
+        List<String> readIdentifiers = Files.readAllLines(path).stream()
             .filter(it -> !it.isBlank())
             .filter(it -> !it.startsWith("#"))
             .map(String::strip)
             .collect(Collectors.toList());
+        if (readIdentifiers.isEmpty()) {
+          throw new IdentityFileEmptyException(file);
+        }
+        return readIdentifiers;
       } catch (IOException e) {
         throw new RuntimeException(e);
       }
     }
   }
 
+  public static class IdentityFileParsingException extends RuntimeException {
+    protected final File file;
+
+    public IdentityFileParsingException(File file) {
+      this.file = file;
+    }
+
+    public File getFile() {
+      return file;
+    }
+  }
+
+  public static class IdentityFileNotFoundException extends IdentityFileParsingException {
+
+    public IdentityFileNotFoundException(File file) {
+      super(file);
+    }
+  }
+
+  public static class IdentityFileNotReadableException extends IdentityFileParsingException {
+
+
+    public IdentityFileNotReadableException(File file) {
+      super(file);
+    }
+  }
+
+  public static class IdentityFileEmptyException extends IdentityFileParsingException {
+
+    public IdentityFileEmptyException(File file) {
+      super(file);
+    }
+  }
+
   public static class SampleInput {
 
     @Option(
@@ -69,17 +105,38 @@ public static class SampleInput {
     public List<String> ids = new ArrayList<>();
 
     public List<String> getIds() {
-      if (ids.isEmpty()) {
-        List<String> identities = IdentityFileParser.parseIdentityFile(filePath).stream()
-            .filter(it -> !it.isBlank()).toList();
+      var identifiers = ids.isEmpty()
+          ? parseIdentifiers()
+          : ids;
+      // we want to prevent matching to something shorter than a project code.
+      List<String> toShortSampleIds = identifiers.stream()
+          .filter(it -> !it.matches("^\\w{5,}"))
+          .toList();
+      if (!toShortSampleIds.isEmpty()) {
+        throw new ToShortSampleIdsException(toShortSampleIds);
+      }
+      return identifiers;
+    }
 
-        if (identities.isEmpty()) {
-          log.error(filePath.toString() + " does not contain any identifiers.");
-          System.exit(2);
-        }
-        return identities;
+    public static class SampleIdParsingException extends RuntimeException {
+    }
+
+    public static class ToShortSampleIdsException extends SampleIdParsingException {
+      protected final List<String> identifiers;
+
+      public ToShortSampleIdsException(List<String> identifiers) {
+        this.identifiers = requireNonNull(identifiers, "identifiers must not be null");
       }
-      return ids;
+
+      public List<String> getIdentifiers() {
+        return identifiers;
+      }
+    }
+
+    private List<String> parseIdentifiers() {
+      return IdentityFileParser.parseIdentityFile(filePath).stream()
+          .filter(it -> !it.isBlank())
+          .toList();
     }
 
 

diff --git a/src/main/java/life/qbic/qpostman/download/DownloadCommand.java b/src/main/java/life/qbic/qpostman/download/DownloadCommand.java
@@ -8,8 +8,6 @@
 import java.nio.file.Path;
 import java.util.Collection;
 import java.util.List;
-import java.util.Optional;
-import life.qbic.qpostman.common.AuthenticationException;
 import life.qbic.qpostman.common.FileSizeFormatter;
 import life.qbic.qpostman.common.functions.FileFilter;
 import life.qbic.qpostman.common.functions.FindSourceSample;
@@ -25,19 +23,15 @@
 import life.qbic.qpostman.common.structures.DataSetWrapper;
 import life.qbic.qpostman.common.structures.FileSize;
 import life.qbic.qpostman.download.WriteFileToDisk.DownloadReport;
-import life.qbic.qpostman.openbis.ConnectionException;
 import life.qbic.qpostman.openbis.OpenBisSessionProvider;
 import life.qbic.qpostman.openbis.ServerFactory;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
-import org.springframework.remoting.RemoteAccessException;
 
 @Command(name = "download",
         description = "Download data from QBiC.")
 public class DownloadCommand implements Runnable {
     private static final Logger log = LogManager.getLogger(DownloadCommand.class);
-    private static final String LOG_PATH = Optional.ofNullable(System.getProperty("log.path"))
-        .orElse("logs");
     @Mixin
     AuthenticationOptions authenticationOptions;
     @Mixin
@@ -51,7 +45,7 @@ public class DownloadCommand implements Runnable {
 
     @Override
     public void run() {
-        try {
+
             Functions functions = functions();
 
             Collection<DataFile> dataSetFiles = functions.searchDataSets()
@@ -85,28 +79,6 @@ public void run() {
             if (!failedDownloads.isEmpty()) {
                 log.warn("Failed to download %s / %s files.".formatted(failedDownloads.size(), downloadReports.size()));
             }
-
-
-        } catch (RemoteAccessException remoteAccessException) {
-            log.error(
-                "Failed to connect to OpenBis: " + remoteAccessException.getCause().getMessage());
-            log.debug(remoteAccessException.getMessage(), remoteAccessException);
-            System.exit(1);
-        } catch (AuthenticationException authenticationException) {
-            log.error(
-                "Could not authenticate user %s. Please make sure to provide the correct password.".formatted(
-                    authenticationException.username()));
-            log.debug(authenticationException.getMessage(), authenticationException);
-            System.exit(1);
-        }  catch (ConnectionException e) {
-            log.error("Could not connect to QBiC's data source. Have you requested access to the "
-                + "server? If not please write to [email protected]");
-            log.debug(e.getMessage(), e);
-            System.exit(1);
-        } catch (RuntimeException e) {
-            log.error("Something went wrong. For more detailed output see " + Path.of(LOG_PATH, "postman.log").toAbsolutePath());
-            log.debug(e.getMessage(), e);
-        }
     }
 
     private SearchFiles searchFiles(Collection<DataSetWrapper> it) {