add more user friendly reporting

qbicsoftware · Mar 11, 2024 · 16cc00b · 16cc00b
1 parent ac10137
commit 16cc00b
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Showing 4 changed files with 68 additions and 26 deletions.
diff --git a/src/main/java/life/qbic/io/commandline/SampleHierarchyCommand.java b/src/main/java/life/qbic/io/commandline/SampleHierarchyCommand.java
@@ -1,12 +1,22 @@
 package life.qbic.io.commandline;
 
+import java.io.IOException;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.time.Instant;
+import java.time.LocalDateTime;
+import java.time.ZoneOffset;
+import java.time.format.DateTimeFormatter;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
 import java.util.Map.Entry;
 import life.qbic.App;
+import life.qbic.model.Configuration;
 import life.qbic.model.SampleTypeConnection;
 import life.qbic.model.download.Authentication;
+import life.qbic.model.download.FileSystemWriter;
+import life.qbic.model.download.ModelReporter;
 import life.qbic.model.download.OpenbisConnector;
 import picocli.CommandLine.Command;
 import picocli.CommandLine.Mixin;
@@ -18,20 +28,48 @@ public class SampleHierarchyCommand implements Runnable {
 
   @Option(arity = "1", paramLabel = "<space>", description = "optional openBIS spaces to filter samples", names = {"-s", "--space"})
   private String space;
+  @Option(arity = "1", paramLabel = "<output file path>", description = "optional output path", names = {"-o", "--out"})
+  private String outpath;
   @Mixin
   AuthenticationOptions auth = new AuthenticationOptions();
 
     @Override
     public void run() {
-        List<String> spaces = new ArrayList<>();
+      List<String> summary = new ArrayList<>();
+      List<String> spaces = new ArrayList<>();
         if(space!=null) {
+          summary.add("Querying samples in space: "+space+"...\n");
           spaces.add(space);
+        } else {
+          summary.add("Querying samples in all available spaces...\n");
         }
         Authentication authentication = App.loginToOpenBIS(auth.getPassword(), auth.user, auth.as_url);
-        OpenbisConnector openbis = new OpenbisConnector(auth.as_url, authentication.getSessionToken(), "/Users/afriedrich/Downloads/");
-        Map<SampleTypeConnection, Integer> hierarchy =     openbis.queryFullSampleHierarchy(spaces);
+        OpenbisConnector openbis = new OpenbisConnector(auth.as_url, authentication.getSessionToken());
+        Map<SampleTypeConnection, Integer> hierarchy = openbis.queryFullSampleHierarchy(spaces);
+
         hierarchy.entrySet().stream()
             .sorted(Entry.comparingByValue())
-            .forEach(entry -> System.err.println(entry.getKey()+" ("+entry.getValue()+")"));
+            .forEach(entry -> summary.add(entry.getKey()+" ("+entry.getValue()+")"));
+
+      for(String s : summary) {
+        System.out.println(s);
+      }
+      Path outputPath = Paths.get(Configuration.LOG_PATH.toString(),
+          "summary_model_"+getTimeStamp()+".txt");
+      if(outpath!=null) {
+        outputPath = Paths.get(outpath);
+      }
+      ModelReporter modelReporter = new FileSystemWriter(outputPath);
+      try {
+        modelReporter.reportSummary(summary);
+      } catch (IOException e) {
+        throw new RuntimeException("Could not write summary file.");
+      }
+    }
+
+    private String getTimeStamp() {
+      final String PATTERN_FORMAT = "YYYY-MM-dd_HHmmss";
+      DateTimeFormatter formatter = DateTimeFormatter.ofPattern(PATTERN_FORMAT);
+      return LocalDateTime.ofInstant(Instant.now(), ZoneOffset.UTC).format(formatter).toString();
     }
 }
diff --git a/src/main/java/life/qbic/model/download/FileSystemWriter.java b/src/main/java/life/qbic/model/download/FileSystemWriter.java
@@ -1,6 +1,9 @@
 package life.qbic.model.download;
 
+import java.io.BufferedWriter;
 import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
 import java.nio.file.Path;
 import java.util.List;
 
@@ -11,29 +14,40 @@
  *
  * @author: Sven Fillinger, Andreas Friedrich
  */
-class FileSystemWriter implements ModelReporter {
+public class FileSystemWriter implements ModelReporter {
 
   /**
    * File that stores the summary report content for valid checksums.
    */
-  final private File matchingSummaryFile;
+  final private File summaryFile;
 
 
   /**
-   * FileSystemWriter constructor with the paths for the summary files.     *
+   * FileSystemWriter constructor with the paths for the summary files.
    *
-   * @param matchingSummaryFile The path where to write the summary
+   * @param summaryFile The path where to write the summary
    */
-  FileSystemWriter(Path matchingSummaryFile) {
-    this.matchingSummaryFile = new File(matchingSummaryFile.toString());
+  public FileSystemWriter(Path summaryFile) {
+    this.summaryFile = new File(summaryFile.toString());
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
-  public void reportSummary(List<String> summary) {
-    //TODO
+  public void reportSummary(List<String> summary) throws IOException {
+    if (!summaryFile.exists()) {
+      summaryFile.createNewFile();
+      //file exists or could not be created
+      if (!summaryFile.exists()) {
+        throw new IOException("The file " + summaryFile.getAbsoluteFile() + " could not be created.");
+      }
+    }
+    BufferedWriter writer = new BufferedWriter(new FileWriter(summaryFile, true));
+    for(String line : summary) {
+      writer.append(line+"\n");
+    }
+    writer.close();
   }
 
 }
diff --git a/src/main/java/life/qbic/model/download/ModelReporter.java b/src/main/java/life/qbic/model/download/ModelReporter.java
@@ -1,10 +1,11 @@
 package life.qbic.model.download;
 
+import java.io.IOException;
 import java.net.URL;
 import java.nio.file.Path;
 import java.util.List;
 
-interface ModelReporter {
+public interface ModelReporter {
 
-  void reportSummary(List<String> summary);
+  void reportSummary(List<String> summary) throws IOException;
 }
diff --git a/src/main/java/life/qbic/model/download/OpenbisConnector.java b/src/main/java/life/qbic/model/download/OpenbisConnector.java
@@ -10,14 +10,10 @@
 import ch.ethz.sis.openbis.generic.asapi.v3.dto.space.fetchoptions.SpaceFetchOptions;
 import ch.ethz.sis.openbis.generic.asapi.v3.dto.space.search.SpaceSearchCriteria;
 import ch.systemsx.cisd.common.spring.HttpInvokerUtils;
-import java.nio.file.Paths;
-import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.stream.Collectors;
-import life.qbic.App;
-import life.qbic.model.Configuration;
 import life.qbic.model.SampleTypeConnection;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
@@ -27,11 +23,6 @@ public class OpenbisConnector {
   private static final Logger LOG = LogManager.getLogger(OpenbisConnector.class);
   private final IApplicationServerApi applicationServer;
   private final String sessionToken;
-  private final String outputPath;
-
-  private final ModelReporter modelReporter = new FileSystemWriter(
-      Paths.get(Configuration.LOG_PATH.toString(), "summary_model.txt"));
-
   /**
    * Constructor for a QBiCDataDownloader instance
    *
@@ -40,10 +31,8 @@ public class OpenbisConnector {
    */
   public OpenbisConnector(
           String AppServerUri,
-          String sessionToken,
-          String outputPath) {
+          String sessionToken) {
     this.sessionToken = sessionToken;
-    this.outputPath = outputPath;
 
     if (!AppServerUri.isEmpty()) {
       applicationServer =