Merge pull request #7 from qbicsoftware/petab-feedback

allow dataset connection to sample, improve error handling

src/main/java/life/qbic/io/commandline/AuthenticationOptions.java

@@ -21,9 +21,9 @@ public class AuthenticationOptions {
   @Option(
       names = {"-u", "--user"},
       description = "openBIS user name")
-  private String user;
+  private String openbisUser;
   @ArgGroup(multiplicity = "1") // ensures the password is provided once with at least one of the possible options.
-  PasswordOptions passwordOptions;
+  PasswordOptions openbisPasswordOptions;
 
   @Option(
       names = {"-as", "-as_url"},
@@ -43,11 +43,23 @@ public class AuthenticationOptions {
       scope = CommandLine.ScopeType.INHERIT)
   public String configPath;
 
-  public String getUser() {
-    if(user == null & configPath!=null && !configPath.isBlank()) {
-      user = ReadProperties.getProperties(configPath).get("user");
+  @Option(
+      names = {"-seek-server", "-seek_url"},
+      description = "SEEK API URL",
+      scope = CommandLine.ScopeType.INHERIT)
+  private String seek_url;
+
+  public String getOpenbisUser() {
+    if(openbisUser == null & configPath!=null && !configPath.isBlank()) {
+      openbisUser = ReadProperties.getProperties(configPath).get("user");
     }
-    return user;
+    return openbisUser;
+  }
+
+  public String getSeekURL() {
+    log.error("No URL to the SEEK address provided.");
+    System.exit(2);
+    return seek_url;
   }
 
   public String getDSS() {
@@ -64,8 +76,8 @@ public String getAS() {
     return as_url;
   }
 
-  public char[] getPassword() {
-    return passwordOptions.getPassword();
+  public char[] getOpenbisPassword() {
+    return openbisPasswordOptions.getPassword();
   }
 
   /**
@@ -110,7 +122,7 @@ char[] getPassword() {
   @Override
   public String toString() {
     return new StringJoiner(", ", AuthenticationOptions.class.getSimpleName() + "[", "]")
-        .add("user='" + user + "'")
+        .add("user='" + openbisUser + "'")
         .toString();
     //ATTENTION: do not expose the password here!
   }

src/main/java/life/qbic/io/commandline/DownloadPetabCommand.java

@@ -27,7 +27,7 @@ public class DownloadPetabCommand implements Runnable {
 
     @Override
     public void run() {
-      OpenBIS authentication = App.loginToOpenBIS(auth.getPassword(), auth.getUser(), auth.getAS(), auth.getDSS());
+      OpenBIS authentication = App.loginToOpenBIS(auth.getOpenbisPassword(), auth.getOpenbisUser(), auth.getAS(), auth.getDSS());
       OpenbisConnector openbis = new OpenbisConnector(authentication);
 
       List<DataSet> datasets = openbis.findDataSets(Collections.singletonList(datasetCode));

src/main/java/life/qbic/io/commandline/FindDatasetsCommand.java

@@ -39,7 +39,7 @@ public void run() {
       } else {
         System.out.println("Querying experiment in all available spaces...");
       }
-      OpenBIS authentication = App.loginToOpenBIS(auth.getPassword(), auth.getUser(), auth.getAS());
+      OpenBIS authentication = App.loginToOpenBIS(auth.getOpenbisPassword(), auth.getOpenbisUser(), auth.getAS());
       OpenbisConnector openbis = new OpenbisConnector(authentication);
       List<DataSet> datasets = openbis.listDatasetsOfExperiment(spaces, experimentCode).stream()
           .sorted(Comparator.comparing(

src/main/java/life/qbic/io/commandline/SampleHierarchyCommand.java

@@ -43,7 +43,7 @@ public void run() {
         } else {
           summary.add("Querying samples in all available spaces...");
         }
-        OpenBIS authentication = App.loginToOpenBIS(auth.getPassword(), auth.getUser(), auth.getAS());
+        OpenBIS authentication = App.loginToOpenBIS(auth.getOpenbisPassword(), auth.getOpenbisUser(), auth.getAS());
         OpenbisConnector openbis = new OpenbisConnector(authentication);
         Map<SampleTypeConnection, Integer> hierarchy = openbis.queryFullSampleHierarchy(spaces);
 

src/main/java/life/qbic/io/commandline/SpaceStatisticsCommand.java

@@ -50,7 +50,7 @@ public void run() {
       } else {
         summary.add("Querying samples in all available spaces...");
       }
-      OpenBIS authentication = App.loginToOpenBIS(auth.getPassword(), auth.getUser(), auth.getAS());
+      OpenBIS authentication = App.loginToOpenBIS(auth.getOpenbisPassword(), auth.getOpenbisUser(), auth.getAS());
       OpenbisConnector openbis = new OpenbisConnector(authentication);
 
       if (spaces.isEmpty()) {

src/main/java/life/qbic/io/commandline/TransferDataToSeekCommand.java

@@ -0,0 +1,73 @@
+package life.qbic.io.commandline;
+
+import ch.ethz.sis.openbis.generic.OpenBIS;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.DataSet;
+import java.io.File;
+import java.util.Collections;
+import java.util.List;
+import java.util.Optional;
+import life.qbic.App;
+import life.qbic.model.DatasetWithProperties;
+import life.qbic.model.download.OpenbisConnector;
+import picocli.CommandLine.Command;
+import picocli.CommandLine.Mixin;
+import picocli.CommandLine.Option;
+import picocli.CommandLine.Parameters;
+
+@Command(name = "openbis-to-seek",
+    description = "Transfers data or metadata from openBIS to SEEK.")
+public class TransferDataToSeekCommand implements Runnable {
+
+  @Parameters(arity = "1", paramLabel = "dataset id", description = "The code of the dataset (or its metadata) to transfer. Can be found via list-data.")
+  private String datasetCode;
+  @Parameters(arity = "1", paramLabel = "seek node", description = "The node in SEEK to which to transfer the dataset.")
+  private String seekNode;
+  @Option(names = { "-d", "--data"}, usageHelp = true, description = "Transfers the data itself to SEEK along with the metadata")
+  private boolean transferData;
+  @Mixin
+  AuthenticationOptions auth = new AuthenticationOptions();
+
+    @Override
+    public void run() {
+      OpenBIS authentication = App.loginToOpenBIS(auth.getOpenbisPassword(), auth.getOpenbisUser(), auth.getAS(), auth.getDSS());
+      OpenbisConnector openbis = new OpenbisConnector(authentication);
+
+      List<DataSet> datasets = openbis.findDataSets(Collections.singletonList(datasetCode));
+
+      if(datasets.isEmpty()) {
+        System.out.println(datasetCode+" not found");
+        return;
+      }
+      DatasetWithProperties result = new DatasetWithProperties(datasets.get(0));
+      Optional<String> patientID = openbis.findPropertyInSampleHierarchy("PATIENT_DKFZ_ID",
+          result.getExperiment().getIdentifier());
+      patientID.ifPresent(s -> result.addProperty("patientID", s));
+
+      System.out.println("Found dataset, downloading.");
+      System.out.println();
+
+      final String tmpPath = "tmp/";
+
+      File downloadFolder = openbis.downloadDataset(tmpPath, datasetCode);
+
+
+
+      cleanupTemp(new File(tmpPath));
+
+      System.out.println("Done");
+    }
+
+  private void cleanupTemp(File tmpFolder) {
+    File[] files = tmpFolder.listFiles();
+    if (files != null) { //some JVMs return null for empty dirs
+      for (File f : files) {
+        if (f.isDirectory()) {
+          cleanupTemp(f);
+        } else {
+          f.delete();
+        }
+      }
+    }
+  }
+
+}

src/main/java/life/qbic/io/commandline/UploadDatasetCommand.java

@@ -4,10 +4,6 @@
 import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.id.DataSetPermId;
 import java.io.File;
 import java.nio.file.Path;
-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 life.qbic.App;
@@ -23,9 +19,9 @@ public class UploadDatasetCommand implements Runnable {
 
   @Parameters(arity = "1", paramLabel = "file/folder", description = "The path to the file or folder to upload")
   private String dataPath;
-  @Parameters(arity = "1", paramLabel = "experiment ID", description = "The full identifier of the experiment the data should be attached to. "
-      + "The identifier must be of the format: /space/project/experiment")
-  private String experimentID;
+  @Parameters(arity = "1", paramLabel = "object ID", description = "The full identifier of the experiment or sample the data should be attached to. "
+      + "The identifier must be of the format: /space/project/experiment for experiments or /space/sample for samples")
+  private String objectID;
   @Option(arity = "1..*", paramLabel = "<parent_datasets>", description = "Optional list of dataset codes to act"
       + " as parents for the upload. E.g. when this dataset has been generated using these datasets as input.", names = {"-pa", "--parents"})
   private List<String> parents = new ArrayList<>();
@@ -36,15 +32,28 @@ public class UploadDatasetCommand implements Runnable {
 
     @Override
     public void run() {
-      OpenBIS authentication = App.loginToOpenBIS(auth.getPassword(), auth.getUser(), auth.getAS(), auth.getDSS());
+      OpenBIS authentication = App.loginToOpenBIS(auth.getOpenbisPassword(), auth.getOpenbisUser(), auth.getAS(), auth.getDSS());
       openbis = new OpenbisConnector(authentication);
 
       if(!pathValid(dataPath)) {
         System.out.printf("Path %s could not be found%n", dataPath);
         return;
       }
-      if(!experimentExists(experimentID)) {
-        System.out.printf("Experiment %s could not be found%n", experimentID);
+      boolean attachToSample = OpenbisConnector.sampleIdPattern.matcher(objectID).find();
+      boolean attachToExperiment = false;
+      if(!attachToSample) {
+        attachToExperiment = OpenbisConnector.experimentIdPattern.matcher(objectID).find();
+      }
+      if(!attachToExperiment && !attachToSample) {
+        System.out.printf("%s is neither a valid experiment nor sample identifier%n", objectID);
+        return;
+      }
+      if(attachToExperiment && !experimentExists(objectID)) {
+        System.out.printf("Experiment with identifier %s could not be found%n", objectID);
+        return;
+      }
+      if(attachToSample && !sampleExists(objectID)) {
+        System.out.printf("Sample object with identifier %s could not be found%n", objectID);
         return;
       }
       if(!datasetsExist(parents)) {
@@ -54,10 +63,19 @@ public void run() {
       System.out.println();
       System.out.println("Parameters verified, uploading dataset...");
       System.out.println();
-      DataSetPermId result = openbis.registerDataset(Path.of(dataPath), experimentID, parents);
-      System.out.printf("Dataset %s was successfully created%n", result.getPermId());
+      if(attachToExperiment) {
+        DataSetPermId result = openbis.registerDatasetForExperiment(Path.of(dataPath), objectID, parents);
+        System.out.printf("Dataset %s was successfully attached to experiment%n", result.getPermId());
+      } else {
+        DataSetPermId result = openbis.registerDatasetForSample(Path.of(dataPath), objectID, parents);
+        System.out.printf("Dataset %s was successfully attached to sample%n", result.getPermId());
+      }
     }
 
+  private boolean sampleExists(String objectID) {
+      return openbis.sampleExists(objectID);
+  }
+
   private boolean datasetsExist(List<String> datasetCodes) {
       return openbis.findDataSets(datasetCodes).size() == datasetCodes.size();
   }
@@ -70,4 +88,5 @@ private boolean pathValid(String dataPath) {
       return new File(dataPath).exists();
   }
 
+
 }

src/main/java/life/qbic/io/commandline/UploadPetabResultCommand.java

@@ -33,13 +33,17 @@ public class UploadPetabResultCommand implements Runnable {
 
     @Override
     public void run() {
-      OpenBIS authentication = App.loginToOpenBIS(auth.getPassword(), auth.getUser(), auth.getAS(), auth.getDSS());
+      OpenBIS authentication = App.loginToOpenBIS(auth.getOpenbisPassword(), auth.getOpenbisUser(), auth.getAS(), auth.getDSS());
       openbis = new OpenbisConnector(authentication);
 
       if(!pathValid(dataPath)) {
         System.out.printf("Path %s could not be found%n", dataPath);
         return;
       }
+      if(!new File(dataPath).isDirectory()) {
+        System.out.printf("%s is not a directory. Please specify the PETab directory root%n", dataPath);
+        return;
+      }
       if(!experimentExists(experimentID)) {
         System.out.printf("Experiment %s could not be found%n", experimentID);
         return;
@@ -60,7 +64,7 @@ public void run() {
       }
       System.out.println("Uploading dataset...");
       //TODO copy and remove source references here
-      DataSetPermId result = openbis.registerDataset(Path.of(dataPath), experimentID, parents);
+      DataSetPermId result = openbis.registerDatasetForExperiment(Path.of(dataPath), experimentID, parents);
       System.out.printf("Dataset %s was successfully created%n", result.getPermId());
     }