Release 0.2.0

Release 0.2.0

README.md

@@ -130,7 +130,9 @@ Here is an example of the provenance file:
 {
   "origin": "/Users/myuser/registration",
   "user": "/Users/myuser",
-  "measurementId": "QTEST001AE-1234512312",
+  "measurementId": "NGSQTEST001AE-1234512312",
+  "datasetFiles" : [ "file1_1.fastq.gz", "file1_2.fastq.gz" ],
+  "taskId": "74c5d26f-b756-42c3-b6f4-2b4825670a2d",
   "history": [
     "/opt/scanner-app/scanner-processing-dir/74c5d26f-b756-42c3-b6f4-2b4825670a2d"
   ]
@@ -146,6 +148,10 @@ Here is an example of the provenance file:
 >
 > `measurementId`: any valid QBiC measurement ID that has been found in the dataset (this might
 > be `null`) in case the evaluation has not been done yet.
+> 
+> `datasetFiles`: a list of relative file paths belonging to the dataset
+> 
+> `taskId`: a unique task ID assigned by the application to track the dataset registration progress
 >
 > `history`: a list of history items, which steps have been performed. The list is ordered by first
 > processing steps being at the start and the latest at the end.
@@ -157,12 +163,14 @@ perform checksum validation. Feel free to use it as template for subsequent proc
 
 ### Evaluation
 
-Last but not least, this step looks for any present QBiC measurement ID in the dataset name. If none
-is given, the registration cannot be executed.
+Last but not least, this step validates the QBiC measurement ID via a [configurable](#evaluation-step-config) regex pattern.
+
+In case of invalid measurement ID formats, the process moves the task directory into the user's home error folder.
+After the user has provided a valid QBiC measurement id, they can move the dataset into registration again.
 
-In this case the process moves the task directory into the user's home error folder. After the user
-has
-provided a valid QBiC measurement id, they can move the dataset into registration again.
+In case of a successful ID validation, the dataset will be moved to the configured destination folder.
+If multiple destination folders are provided in the [configuration](#evaluation-step-config), the assignment of the next target directory is based
+on a round-robin approach, to balance any downstream task load (e.g. openBIS dropbox registration).
 
 ## Configuration
 
@@ -218,7 +226,8 @@ finished tasks are moved to after successful operation.
 #----------------
 # Settings for the registration worker threads
 #----------------
-registration.threads=2
+registration.threads=${REGISTRATION_THREADS:2}
+registration.metadata.filename=metadata.txt
 registration.working.dir=${WORKING_DIR:}
 registration.target.dir=${PROCESSING_DIR:}
 ```
@@ -233,7 +242,7 @@ finished tasks are moved to after successful operation.
 # Settings for the 1. processing step
 # Proper packaging and provenance data, some simple checks
 #------------------------------------
-processing.threads=2
+processing.threads=${PROCESSING_THREADS:2}
 processing.working.dir=${PROCESSING_DIR}
 processing.target.dir=${EVALUATION_DIR}
 ```
@@ -248,7 +257,7 @@ finished tasks are moved to after successful operation.
 # Setting for the 2. processing step:
 # Measurement ID evaluation
 # ---------------------------------
-evaluations.threads=2
+evaluations.threads=${EVALUATION_THREADS:2}
 evaluation.working.dir=${EVALUATION_DIR}
 # Define one or more target directories here
 # Example single target dir:

src/main/java/life/qbic/data/processing/AppConfig.java

@@ -52,20 +52,17 @@ RegistrationConfiguration registrationConfiguration(
 
   @Bean
   EvaluationWorkersConfig evaluationWorkersConfig(
-      @Value("${evaluations.threads}") int amountOfWorkers,
+      @Value("${evaluation.threads}") int amountOfWorkers,
       @Value("${evaluation.working.dir}") String workingDirectory,
-      @Value("${evaluation.target.dirs}") String[] targetDirectory,
-      @Value("${evaluation.measurement-id.pattern}") String measurementIdPattern) {
-    return new EvaluationWorkersConfig(amountOfWorkers, workingDirectory,
-        measurementIdPattern, Arrays.stream(targetDirectory).toList());
+      @Value("${evaluation.target.dirs}") String[] targetDirectory) {
+    return new EvaluationWorkersConfig(amountOfWorkers, workingDirectory, Arrays.stream(targetDirectory).toList());
   }
 
   @Bean
   EvaluationConfiguration evaluationConfiguration(EvaluationWorkersConfig evaluationWorkersConfig,
       GlobalConfig globalConfig) {
     return new EvaluationConfiguration(evaluationWorkersConfig.workingDirectory().toString(),
-        evaluationWorkersConfig.targetDirectories(),
-        evaluationWorkersConfig.measurementIdPattern().toString(), globalConfig);
+        evaluationWorkersConfig.targetDirectories(), globalConfig);
   }
 
   @Bean
@@ -86,8 +83,9 @@ ProcessingConfiguration processingConfiguration(ProcessingWorkersConfig processi
   @Bean
   GlobalConfig globalConfig(
       @Value("${users.error.directory.name}") String usersErrorDirectoryName,
-      @Value("${users.registration.directory.name}") String usersRegistrationDirectoryName) {
-    return new GlobalConfig(usersErrorDirectoryName, usersRegistrationDirectoryName);
+      @Value("${users.registration.directory.name}") String usersRegistrationDirectoryName,
+      @Value("${qbic.measurement-id.pattern}") String measurementIdPattern) {
+    return new GlobalConfig(usersErrorDirectoryName, usersRegistrationDirectoryName, measurementIdPattern);
   }
 
 }

src/main/java/life/qbic/data/processing/GlobalConfig.java

@@ -2,22 +2,29 @@
 
 import java.nio.file.Path;
 import java.nio.file.Paths;
+import java.util.regex.Pattern;
 
 public class GlobalConfig {
 
   private final Path usersErrorDirectoryName;
 
   private final Path usersDirectoryRegistrationName;
 
-  public GlobalConfig(String usersErrorDirectoryName, String usersRegistrationDirectoryName) {
+  private final Pattern qbicMeasurementIdPattern;
+
+  public GlobalConfig(String usersErrorDirectoryName, String usersRegistrationDirectoryName, String qbicMeasurementIdPattern) {
     if (usersErrorDirectoryName == null || usersErrorDirectoryName.isBlank()) {
       throw new IllegalArgumentException("usersErrorDirectoryName cannot be null or empty");
     }
     if (usersRegistrationDirectoryName == null || usersRegistrationDirectoryName.isBlank()) {
       throw new IllegalArgumentException("usersRegistrationDirectoryName cannot be null or empty");
     }
+    if (qbicMeasurementIdPattern == null || qbicMeasurementIdPattern.isBlank()) {
+      throw new IllegalArgumentException("qbicMeasurementIdPattern cannot be null or empty");
+    }
     this.usersErrorDirectoryName = Paths.get(usersErrorDirectoryName);
     this.usersDirectoryRegistrationName = Paths.get(usersRegistrationDirectoryName);
+    this.qbicMeasurementIdPattern = Pattern.compile(qbicMeasurementIdPattern);
   }
 
   public Path usersErrorDirectory() {
@@ -28,4 +35,8 @@ public Path usersDirectoryRegistration() {
     return this.usersDirectoryRegistrationName;
   }
 
+  public Pattern qbicMeasurementIdPattern() {
+    return this.qbicMeasurementIdPattern;
+  }
+
 }

src/main/java/life/qbic/data/processing/Provenance.java

@@ -47,6 +47,9 @@ public class Provenance {
   @JsonProperty("datasetFiles")
   public List<String> datasetFiles;
 
+  @JsonProperty("taskId")
+  public String taskId;
+
   /**
    * A list of ordered processing folder stops the dataset has traversed and passed successfully.
    * <p>

src/main/java/life/qbic/data/processing/config/EvaluationWorkersConfig.java

@@ -10,9 +10,8 @@ public class EvaluationWorkersConfig {
   private final int threads;
   private final Path workingDirectory;
   private final Collection<Path> targetDirectories;
-  private final Pattern measurementIdPattern;
 
-  public EvaluationWorkersConfig(int threads, String workingDirectory, String measurementIdPattern,
+  public EvaluationWorkersConfig(int threads, String workingDirectory,
       Collection<String> targetDirectories) {
     if (threads < 1) {
       throw new IllegalArgumentException(
@@ -32,10 +31,6 @@ public EvaluationWorkersConfig(int threads, String workingDirectory, String meas
       throw new IllegalArgumentException(
           "Evaluation target directory '%s' does not exist".formatted(path));
     });
-    if (measurementIdPattern.isBlank()) {
-      throw new IllegalArgumentException("Measurement id pattern cannot be blank");
-    }
-    this.measurementIdPattern = Pattern.compile(measurementIdPattern);
   }
 
   public int threads() {
@@ -49,8 +44,4 @@ public Path workingDirectory() {
   public Collection<Path> targetDirectories() {
     return targetDirectories;
   }
-
-  public Pattern measurementIdPattern() {
-    return measurementIdPattern;
-  }
 }

src/main/java/life/qbic/data/processing/evaluation/EvaluationConfiguration.java

@@ -18,12 +18,10 @@ public class EvaluationConfiguration {
 
   private final Path workingDirectory;
   private final Collection<Path> targetDirectories;
-  private final Pattern measurementIdPattern;
   private final Path usersErrorDirectory;
   private final RoundRobinDraw<Path> targetDirectoriesRoundRobinDraw;
 
   public EvaluationConfiguration(String workingDirectory, Collection<Path> targetDirectories,
-      String measurementIdPattern,
       GlobalConfig globalConfig) {
     this.workingDirectory = Paths.get(workingDirectory);
     if (!this.workingDirectory.toFile().exists()) {
@@ -35,11 +33,7 @@ public EvaluationConfiguration(String workingDirectory, Collection<Path> targetD
           "Evaluation target directory '%s' does not exist".formatted(path));
     });
     this.targetDirectoriesRoundRobinDraw = RoundRobinDraw.create(targetDirectories);
-    if (measurementIdPattern.isBlank()) {
-      throw new IllegalArgumentException("Measurement id pattern cannot be blank");
-    }
     this.usersErrorDirectory = globalConfig.usersErrorDirectory();
-    this.measurementIdPattern = Pattern.compile(measurementIdPattern);
   }
 
   public Path workingDirectory() {
@@ -50,10 +44,6 @@ public RoundRobinDraw<Path> targetDirectories() {
     return targetDirectoriesRoundRobinDraw;
   }
 
-  public Pattern measurementIdPattern() {
-    return measurementIdPattern;
-  }
-
   public Path usersErrorDirectory() {
     return usersErrorDirectory;
   }

src/main/java/life/qbic/data/processing/evaluation/EvaluationRequest.java

@@ -50,17 +50,15 @@ public class EvaluationRequest extends Thread {
   private final AtomicBoolean active = new AtomicBoolean(false);
   private final AtomicBoolean terminated = new AtomicBoolean(false);
   private final Path workingDirectory;
-  private final Pattern measurementIdPattern;
   private final Path usersErrorDirectory;
   private final RoundRobinDraw<Path> targetDirectories;
   private Path assignedTargetDirectory;
 
   public EvaluationRequest(Path workingDirectory, RoundRobinDraw<Path> targetDirectories,
-      Pattern measurementIdPattern, Path usersErrorDirectory) {
+     Path usersErrorDirectory) {
     this.setName(THREAD_NAME.formatted(nextThreadNumber()));
     this.workingDirectory = workingDirectory;
     this.targetDirectories = targetDirectories;
-    this.measurementIdPattern = measurementIdPattern;
     if (!workingDirectory.resolve(INTERVENTION_DIRECTORY).toFile().mkdir()
         && !workingDirectory.resolve(
         INTERVENTION_DIRECTORY).toFile().exists()) {
@@ -73,7 +71,6 @@ public EvaluationRequest(Path workingDirectory, RoundRobinDraw<Path> targetDirec
 
   public EvaluationRequest(EvaluationConfiguration evaluationConfiguration) {
     this(evaluationConfiguration.workingDirectory(), evaluationConfiguration.targetDirectories(),
-        evaluationConfiguration.measurementIdPattern(),
         evaluationConfiguration.usersErrorDirectory());
   }
 
@@ -185,10 +182,6 @@ private boolean createMarkerFile(Path targetDirectory, String name) throws IOExc
     return targetDirectory.resolve(markerFileName).toFile().createNewFile();
   }
 
-  private Optional<File> findDataset(File taskDir) {
-    return Arrays.stream(taskDir.listFiles()).filter(File::isDirectory).findFirst();
-  }
-
   private void moveToSystemIntervention(File taskDir, String reason) {
     try {
       var errorFile = taskDir.toPath().resolve("error.txt").toFile();

src/main/java/life/qbic/data/processing/registration/ErrorCode.java

@@ -9,5 +9,5 @@
  */
 public enum ErrorCode {
   METADATA_FILE_NOT_FOUND,
-  INCOMPLETE_METADATA, FILE_NOT_FOUND, MISSING_FILE_ENTRY, IO_EXCEPTION
+  INCOMPLETE_METADATA, FILE_NOT_FOUND, MISSING_FILE_ENTRY, INVALID_MEASUREMENT_ID_FORMAT, IO_EXCEPTION
 }

src/main/java/life/qbic/data/processing/registration/ProcessRegistrationRequest.java

@@ -17,6 +17,7 @@
 import java.util.Optional;
 import java.util.UUID;
 import java.util.concurrent.atomic.AtomicBoolean;
+import java.util.regex.Pattern;
 import java.util.stream.Collectors;
 import life.qbic.data.processing.ConcurrentRegistrationQueue;
 import life.qbic.data.processing.GlobalConfig;
@@ -53,6 +54,7 @@ public class ProcessRegistrationRequest extends Thread {
   private final Path targetDirectory;
   private final String metadataFileName;
   private final Path userErrorDirectory;
+  private final Pattern measurementIdPattern;
   private AtomicBoolean active = new AtomicBoolean(false);
 
   public ProcessRegistrationRequest(@NonNull ConcurrentRegistrationQueue registrationQueue,
@@ -63,6 +65,7 @@ public ProcessRegistrationRequest(@NonNull ConcurrentRegistrationQueue registrat
     this.targetDirectory = configuration.targetDirectory();
     this.metadataFileName = configuration.metadataFileName();
     this.userErrorDirectory = globalConfig.usersErrorDirectory();
+    this.measurementIdPattern = globalConfig.qbicMeasurementIdPattern();
   }
 
   private static int nextThreadNumber() {
@@ -179,6 +182,7 @@ private void writeProvenanceInformation(Path taskDir, Path newLocation,
     provenance.history.add(newLocation.toString());
     provenance.userWorkDirectoryPath = String.valueOf(request.userPath());
     provenance.qbicMeasurementID = measurementId;
+    provenance.taskId = taskDir.toFile().getName();
     provenance.addDatasetFiles(datasetFiles);
     ObjectMapper mapper = new ObjectMapper();
     mapper.writerWithDefaultPrettyPrinter()
@@ -221,6 +225,8 @@ public void run() {
         var registrationMetadata = findAndParseMetadata(workingTargetDir);
         validateFileEntries(registrationMetadata, workingTargetDir);
 
+        validateMeasurementIds(registrationMetadata);
+
         var aggregatedFilesByMeasurementId = registrationMetadata.stream().collect(
             Collectors.groupingBy(RegistrationMetadata::measurementId));
 
@@ -244,6 +250,24 @@ public void run() {
     }
   }
 
+  private void validateMeasurementIds(List<RegistrationMetadata> registrationMetadata)
+      throws ValidationException {
+    registrationMetadata.stream().map(RegistrationMetadata::measurementId)
+        .filter(this::isMeasurementIdInvalid).findAny().ifPresent(invalidEntry -> {
+          throw new ValidationException(
+              "Invalid measurement ID format found: %s".formatted(invalidEntry),
+              ErrorCode.INVALID_MEASUREMENT_ID_FORMAT);
+        });
+  }
+
+  private boolean isMeasurementIdInvalid(String measurementId) {
+    return !isMeasurementIdValid(measurementId);
+  }
+
+  private boolean isMeasurementIdValid(String measurementId) {
+    return measurementIdPattern.matcher(measurementId).matches();
+  }
+
   private void processAll(Map<String, List<RegistrationMetadata>> aggregatedFilesByMeasurementId,
       Path workingTargetDir, RegistrationRequest request) throws IOException {
     for (String measurementId : aggregatedFilesByMeasurementId.keySet()) {

src/main/resources/application.properties

@@ -13,6 +13,7 @@ users.error.directory.name=error
 # Needs to be present in the users' home folders
 # e.g. /home/<user1>/registration
 users.registration.directory.name=registration
+qbic.measurement-id.pattern=^(MS|NGS)Q[A-Z0-9]{4}[0-9]{3}[A-Z0-9]{2}-[0-9]*
 
 #--------------------------------------
 # Settings for the data scanning thread
@@ -30,7 +31,7 @@ scanner.interval=1000
 #----------------
 # Settings for the registration worker threads
 #----------------
-registration.threads=2
+registration.threads=${REGISTRATION_THREADS:2}
 registration.metadata.filename=metadata.txt
 registration.working.dir=${WORKING_DIR:}
 registration.target.dir=${PROCESSING_DIR:}
@@ -39,23 +40,22 @@ registration.target.dir=${PROCESSING_DIR:}
 # Settings for the 1. processing step
 # Proper packaging and provenance data, some simple checks
 #------------------------------------
-processing.threads=2
+processing.threads=${PROCESSING_THREADS:2}
 processing.working.dir=${PROCESSING_DIR}
 processing.target.dir=${EVALUATION_DIR}
 
 #----------------------------------
 # Setting for the 2. processing step:
 # Measurement ID evaluation
 # ---------------------------------
-evaluations.threads=2
+evaluation.threads=${EVALUATION_THREADS:2}
 evaluation.working.dir=${EVALUATION_DIR}
 # Define one or more target directories here
 # Example single target dir:
 #    evaluation.target.dirs=/my/example/target/dir
 # Example multiple target dir:
 #   evaluation.target.dirs=/my/example/target/dir1,/my/example/target/dir2,/my/example/target/dir3
 evaluation.target.dirs=${OPENBIS_ETL_DIRS}
-evaluation.measurement-id.pattern=^(MS|NGS)Q[A-Z0-9]{4}[0-9]{3}[A-Z0-9]{2}-[0-9]*
 
 # ----------------
 # Logging settings