Merge pull request #4 from qbicsoftware/feature/data-options

allows to list existing and upload new datasets

pom.xml

@@ -11,8 +11,7 @@
     <description>A client software written in Java to query openBIS</description>
     <packaging>jar</packaging>
   <properties>
-    <maven.compiler.source>11</maven.compiler.source>
-    <maven.compiler.target>11</maven.compiler.target>
+    <java.version>11</java.version>
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
     <spring.version>5.3.31</spring.version>
   </properties>
@@ -138,6 +137,14 @@
       </execution>
     </executions>
   </plugin>
+    <plugin>
+      <groupId>org.apache.maven.plugins</groupId>
+      <artifactId>maven-compiler-plugin</artifactId>
+      <configuration>
+        <source>${java.version}</source>
+        <target>${java.version}</target>
+      </configuration>
+    </plugin>
   </plugins>
   </build>
 </project>

src/main/java/life/qbic/App.java

@@ -1,8 +1,8 @@
 package life.qbic;
 
+import ch.ethz.sis.openbis.generic.OpenBIS;
 import life.qbic.io.commandline.CommandLineOptions;
 import life.qbic.model.Configuration;
-import life.qbic.model.download.Authentication;
 import life.qbic.model.download.AuthenticationException;
 import life.qbic.model.download.ConnectionException;
 import org.apache.logging.log4j.LogManager;
@@ -35,30 +35,36 @@ private static Boolean isNotNullOrEmpty(String envVariableCommandLineParameter)
   }
 
   /**
-   * Logs into OpenBIS asks for and verifies password.
+   * Logs into OpenBIS, asks for and verifies password.
    *
    * @return An instance of the Authentication class.
    */
-  public static Authentication loginToOpenBIS(
-      char[] password, String user, String as_url) {
+  public static OpenBIS loginToOpenBIS(
+      char[] password, String user, String url) {
+    setupLog();
 
-    // Ensure 'logs' folder is created
-    File logFolder = new File(Configuration.LOG_PATH.toAbsolutePath().toString());
-    if (!logFolder.exists()) {
-      boolean logFolderCreated = logFolder.mkdirs();
-      if (!logFolderCreated) {
-        LOG.error("Could not create log folder '" + logFolder.getAbsolutePath() + "'");
-        System.exit(1);
-      }
-    }
+    OpenBIS authentication = new OpenBIS(url);
+
+    return tryLogin(authentication, user, password);
+  }
+
+  /**
+   * Logs into OpenBIS, asks for and verifies password, includes Datastore Server connection.
+   *
+   * @return An instance of the Authentication class.
+   */
+  public static OpenBIS loginToOpenBIS(
+      char[] password, String user, String url, String dssUrl) {
+    setupLog();
+
+    OpenBIS authentication = new OpenBIS(url, dssUrl);
+
+    return tryLogin(authentication, user, password);
+  }
 
-    Authentication authentication =
-            new Authentication(
-                    user,
-                    new String(password),
-                    as_url);
+  private static OpenBIS tryLogin(OpenBIS authentication, String user, char[] password) {
     try {
-      authentication.login();
+      authentication.login(user, new String(password));
     } catch (ConnectionException e) {
       LOG.error(e.getMessage(), e);
       LOG.error("Could not connect to QBiC's data source. Have you requested access to the "
@@ -70,4 +76,16 @@ public static Authentication loginToOpenBIS(
     }
     return authentication;
   }
+
+  private static void setupLog() {
+    // Ensure 'logs' folder is created
+    File logFolder = new File(Configuration.LOG_PATH.toAbsolutePath().toString());
+    if (!logFolder.exists()) {
+      boolean logFolderCreated = logFolder.mkdirs();
+      if (!logFolderCreated) {
+        LOG.error("Could not create log folder '" + logFolder.getAbsolutePath() + "'");
+        System.exit(1);
+      }
+    }
+  }
 }

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

@@ -3,7 +3,13 @@
 import static java.util.Objects.nonNull;
 import static picocli.CommandLine.ArgGroup;
 
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
 import java.util.StringJoiner;
+import java.util.TreeMap;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import picocli.CommandLine;
@@ -14,17 +20,49 @@ public class AuthenticationOptions {
 
   @Option(
       names = {"-u", "--user"},
-      required = true,
       description = "openBIS user name")
-  public String user;
+  private String user;
   @ArgGroup(multiplicity = "1") // ensures the password is provided once with at least one of the possible options.
   PasswordOptions passwordOptions;
 
   @Option(
       names = {"-as", "-as_url"},
       description = "ApplicationServer URL",
       scope = CommandLine.ScopeType.INHERIT)
-  public String as_url;
+  private String as_url;
+
+  @Option(
+      names = {"-dss", "-dss_url"},
+      description = "DatastoreServer URL",
+      scope = CommandLine.ScopeType.INHERIT)
+  private String dss_url;
+
+  @Option(
+      names = {"-config", "-config_file"},
+      description = "Config file path to provide openbis server information.",
+      scope = CommandLine.ScopeType.INHERIT)
+  public String configPath;
+
+  public String getUser() {
+    if(user == null & configPath!=null && !configPath.isBlank()) {
+      user = ReadProperties.getProperties(configPath).get("user");
+    }
+    return user;
+  }
+
+  public String getDSS() {
+    if(dss_url == null & configPath!=null && !configPath.isBlank()) {
+      dss_url = ReadProperties.getProperties(configPath).get("dss");
+    }
+    return dss_url;
+  }
+
+  public String getAS() {
+    if(as_url == null & configPath!=null && !configPath.isBlank()) {
+      as_url = ReadProperties.getProperties(configPath).get("as");
+    }
+    return as_url;
+  }
 
   public char[] getPassword() {
     return passwordOptions.getPassword();
@@ -76,4 +114,40 @@ public String toString() {
         .toString();
     //ATTENTION: do not expose the password here!
   }
+
+  public static class ReadProperties {
+
+    public static TreeMap<String, String> getProperties(String infile) {
+
+      TreeMap<String, String> properties = new TreeMap<>();
+      BufferedReader  bfr = null;
+      try {
+        bfr = new BufferedReader(new FileReader(new File(infile)));
+      } catch (FileNotFoundException e) {
+        throw new RuntimeException(e);
+      }
+
+      String line;
+      while (true) {
+        try {
+          if ((line = bfr.readLine()) == null)
+            break;
+        } catch (IOException e) {
+          throw new RuntimeException(e);
+        }
+        if (!line.startsWith("#") && !line.isEmpty()) {
+          String[] property = line.trim().split("=");
+          properties.put(property[0].trim(), property[1].trim());
+        }
+      }
+
+      try {
+        bfr.close();
+      } catch (IOException e) {
+        throw new RuntimeException(e);
+      }
+
+      return(properties);
+    }
+  }
 }

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

@@ -8,17 +8,17 @@
 
 // main command with format specifiers for the usage help message
 @Command(name = "openbis-scripts",
-        subcommands = { SampleHierarchyCommand.class },
+        subcommands = { SampleHierarchyCommand.class, FindDatasetsCommand.class, UploadDatasetCommand.class },
         description = "A client software for querying openBIS.",
-        mixinStandardHelpOptions = true)
+        mixinStandardHelpOptions = true, versionProvider = ManifestVersionProvider.class)
 public class CommandLineOptions {
   private static final Logger LOG = LogManager.getLogger(CommandLineOptions.class);
 
   @Option(names = {"-V", "--version"},
           versionHelp = true,
           description = "print version information",
           scope = CommandLine.ScopeType.INHERIT)
-  boolean versionRequested;
+  boolean versionRequested = false;
 
   @Option(
           names = {"-h", "--help"},

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

@@ -0,0 +1,68 @@
+package life.qbic.io.commandline;
+
+import ch.ethz.sis.openbis.generic.OpenBIS;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.DataSet;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.person.Person;
+import java.text.SimpleDateFormat;
+import java.time.Instant;
+import java.time.LocalDateTime;
+import java.time.ZoneOffset;
+import java.time.format.DateTimeFormatter;
+import java.util.ArrayList;
+import java.util.Comparator;
+import java.util.List;
+import java.util.stream.Collectors;
+import life.qbic.App;
+import life.qbic.model.download.OpenbisConnector;
+import picocli.CommandLine.Command;
+import picocli.CommandLine.Mixin;
+import picocli.CommandLine.Option;
+import picocli.CommandLine.Parameters;
+
+@Command(name = "list-data",
+    description = "lists datasets and their details for a given experiment code")
+public class DownloadDatasetCommand implements Runnable {
+
+  @Parameters(arity = "1", paramLabel = "experiment", description = "The code of the experiment data is attached to")
+  private String experimentCode;
+  @Option(arity = "1", paramLabel = "<space>", description = "Optional openBIS spaces to filter results", names = {"-s", "--space"})
+  private String space;
+  @Mixin
+  AuthenticationOptions auth = new AuthenticationOptions();
+
+    @Override
+    public void run() {
+      List<String> spaces = new ArrayList<>();
+      if (space != null) {
+        System.out.println("Querying experiment in space: " + space + "...");
+        spaces.add(space);
+      } else {
+        System.out.println("Querying experiment in all available spaces...");
+      }
+      OpenBIS authentication = App.loginToOpenBIS(auth.getPassword(), auth.getUser(), auth.getAS());
+      OpenbisConnector openbis = new OpenbisConnector(authentication);
+      List<DataSet> datasets = openbis.listDatasetsOfExperiment(spaces, experimentCode).stream()
+          .sorted(Comparator.comparing(
+              (DataSet d) -> d.getExperiment().getProject().getSpace().getCode())).collect(
+              Collectors.toList());
+      int datasetIndex = 0;
+      for (DataSet dataSet : datasets) {
+        datasetIndex++;
+        System.out.println("["+datasetIndex+"]");
+        System.out.println(dataSet.getExperiment().getIdentifier());
+        System.out.println(dataSet.getCode());
+        System.out.println(dataSet.getType().getCode());
+        System.out.println(dataSet.getRegistrationDate());
+        System.out.println(new SimpleDateFormat("MM-dd-yyyy").format(dataSet.getRegistrationDate()));
+        Person person = dataSet.getRegistrator();
+        System.out.println(person.getFirstName() + " " + person.getLastName());
+        System.out.println();
+      }
+    }
+
+    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);
+    }
+}

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

@@ -0,0 +1,70 @@
+package life.qbic.io.commandline;
+
+import ch.ethz.sis.openbis.generic.OpenBIS;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.DataSet;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.person.Person;
+import java.text.SimpleDateFormat;
+import java.time.Instant;
+import java.time.LocalDateTime;
+import java.time.ZoneOffset;
+import java.time.format.DateTimeFormatter;
+import java.util.ArrayList;
+import java.util.Comparator;
+import java.util.List;
+import java.util.stream.Collectors;
+import life.qbic.App;
+import life.qbic.model.download.OpenbisConnector;
+import picocli.CommandLine.Command;
+import picocli.CommandLine.Mixin;
+import picocli.CommandLine.Option;
+import picocli.CommandLine.Parameters;
+
+@Command(name = "list-data",
+    description = "lists datasets and their details for a given experiment code")
+public class FindDatasetsCommand implements Runnable {
+
+  @Parameters(arity = "1", paramLabel = "experiment", description = "The code of the experiment data is attached to")
+  private String experimentCode;
+  @Option(arity = "1", paramLabel = "<space>", description = "Optional openBIS spaces to filter samples", names = {"-s", "--space"})
+  private String space;
+  @Mixin
+  AuthenticationOptions auth = new AuthenticationOptions();
+
+    @Override
+    public void run() {
+      List<String> spaces = new ArrayList<>();
+      if (space != null) {
+        System.out.println("Querying experiment in space: " + space + "...");
+        spaces.add(space);
+      } else {
+        System.out.println("Querying experiment in all available spaces...");
+      }
+      OpenBIS authentication = App.loginToOpenBIS(auth.getPassword(), auth.getUser(), auth.getAS());
+      OpenbisConnector openbis = new OpenbisConnector(authentication);
+      List<DataSet> datasets = openbis.listDatasetsOfExperiment(spaces, experimentCode).stream()
+          .sorted(Comparator.comparing(
+              (DataSet d) -> d.getExperiment().getProject().getSpace().getCode())).collect(
+              Collectors.toList());
+      int datasetIndex = 0;
+      System.out.println();
+      System.out.printf("Found %s datasets for experiment %s:%n", datasets.size(), experimentCode);
+      for (DataSet dataSet : datasets) {
+        datasetIndex++;
+        System.out.println("["+datasetIndex+"]");
+        System.out.printf("ID: %s (%s)%n", dataSet.getCode(), dataSet.getExperiment().getIdentifier());
+        System.out.println("Type: "+dataSet.getType().getCode());
+        Person person = dataSet.getRegistrator();
+        String simpleTime = new SimpleDateFormat("MM-dd-yy HH:mm:ss").format(dataSet.getRegistrationDate());
+        String name = person.getFirstName() +" "+ person.getLastName();
+        String uploadedBy = "Uploaded by "+name+" ("+simpleTime+")";
+        System.out.println(uploadedBy);
+        System.out.println();
+      }
+    }
+
+    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);
+    }
+}