Merge pull request #39 from qbicsoftware/development

Introduce path formatter (#35)

Author: KochTobi

measurement-provider/pom.xml

@@ -13,6 +13,36 @@
   <artifactId>measurement-provider</artifactId>
   <version>1.0.6</version>
   <packaging>jar</packaging>
+  <dependencies>
+    <dependency>
+      <groupId>org.spockframework</groupId>
+      <artifactId>spock-core</artifactId>
+      <version>2.4-M4-groovy-4.0</version>
+      <scope>test</scope>
+    </dependency>
+    <dependency>
+      <groupId>org.apache.groovy</groupId>
+      <artifactId>groovy-all</artifactId>
+      <version>4.0.24</version>
+      <type>pom</type>
+      <scope>test</scope>
+    </dependency>
+    <!-- JUnit Platform for Spock -->
+    <dependency>
+      <groupId>org.junit.platform</groupId>
+      <artifactId>junit-platform-launcher</artifactId>
+      <version>1.9.2</version> <!-- Ensure it's at least 1.7+ -->
+      <scope>test</scope>
+    </dependency>
+
+    <!-- Optional: For Running Spock with JUnit 5 -->
+    <dependency>
+      <groupId>org.junit.jupiter</groupId>
+      <artifactId>junit-jupiter-engine</artifactId>
+      <version>5.9.2</version>
+      <scope>test</scope>
+    </dependency>
+  </dependencies>
 
   <build>
     <plugins>

measurement-provider/src/main/java/life/qbic/data_download/measurements/api/PathFormatter.java

@@ -0,0 +1,89 @@
+package life.qbic.data_download.measurements.api;
+
+import java.nio.file.InvalidPathException;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.Objects;
+import java.util.regex.Pattern;
+
+/**
+ * PathFormatter applies filters to a given String value that represents a path.
+ *
+ * @since 1.1.0
+ */
+public class PathFormatter {
+
+  private final List<String> filter;
+
+  private PathFormatter() {
+    filter = new ArrayList<>();
+  }
+
+  private PathFormatter(Collection<String> filter) {
+    this.filter = new ArrayList<>(filter);
+  }
+
+  /**
+   * Creates a new instance of {@link PathFormatter} with a collection of filter regex expression.
+   *
+   * @param filter the terms to filter out
+   * @return a {@link PathFormatter} instance
+   * @since 1.1.0
+   */
+  public static PathFormatter with(Collection<String> filter) {
+    Objects.requireNonNull(filter);
+    return new PathFormatter(filter);
+  }
+
+  private static String apply(Path p, Collection<String> filter) {
+    Path result = p.isAbsolute() ? p.getRoot() : Paths.get("");
+
+    for (Path part : p) {
+      if (matchesAny(part.toString(), filter)) {
+        continue;
+      }
+      result = result.resolve(part);
+    }
+    return result.toString();
+  }
+
+  private static boolean matchesAny(String s, Collection<String> filter) {
+    return filter.stream().anyMatch(s::matches);
+  }
+
+  /**
+   * Applies the configured filter to the provided String.
+   * <p>
+   * The provided String is expected to be a valid {@link java.nio.file.Path}, otherwise an
+   * {@link InvalidPathException} is thrown.
+   * <p>
+   * Format iterates through every part of the path and checks them agains the configured filters.
+   * <p>
+   * The filter matching works the same as {@link Pattern#matches(String, CharSequence)}.
+   * <p>
+   * The resulting String representation of a path will be removed of any matching filter terms.
+   *
+   * <pre>
+   *   List<String> filters = Arrays.asList("removeme");
+   *   var formatter = PathFormatter.with(filters);
+   *
+   *   System.out.println(formatter("/example/removeme/path"));
+   *
+   *   // Prints out "/example/path"
+   * </pre>
+   * <p>
+   * Format has an implicit check for {@link Path#isAbsolute()} and preserves an absolute or
+   * relative path.
+   *
+   * @param s the String value to format
+   * @return the formatted new String, after the filter has been applied
+   * @throws InvalidPathException in case the String is not a valid path
+   * @since 1.1.0
+   */
+  public String format(String s) throws InvalidPathException {
+    return apply(Path.of(s), filter);
+  }
+}

measurement-provider/src/test/groovy/life/qbic/data_download/measurement/api/PathFormatterSpec.groovy

@@ -0,0 +1,45 @@
+package life.qbic.data_download.measurement.api
+
+import life.qbic.data_download.measurements.api.PathFormatter
+import spock.lang.Specification
+
+class PathFormatterSpec extends Specification {
+
+    def "Given a String with a to filtered part, the filtered part must not be part of the resulting String"() {
+        given:
+        var filter = Arrays.asList("awesome", "wehaa")
+
+        and:
+        var f = PathFormatter.with(filter)
+
+        when:
+        var result = f.format(input)
+
+        then:
+        result == expected
+
+        where:
+        input | expected
+        "/my/awesome/path/wehaa" | "/my/path"
+        "a/relative/wehaa/awesome/path" | "a/relative/path"
+    }
+
+    def "Given a String that contains a UUID-4 in its path, the formatter shall filter it out"() {
+        given:
+        var filter = Arrays.asList("^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}\$")
+
+        and:
+        var f = PathFormatter.with(filter)
+
+        when:
+        var result = f.format(input)
+
+        then:
+        result == expected
+
+        where:
+        input | expected
+        "/my/f47ac10b-58cc-4372-a567-0e02b2c3d479/path/" | "/my/path"
+        "a/relative/f47ac10b-58cc-4372-a567-0e02b2c3d479/path" | "a/relative/path"
+    }
+}

openbis-connector/src/main/java/life/qbic/data_download/openbis/DatasetFileStreamReaderImpl.java

@@ -6,22 +6,29 @@
 import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.download.DataSetFileDownload;
 import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.download.DataSetFileDownloadReader;
 import java.io.InputStream;
-import java.util.Optional;
+import java.util.List;
+import java.util.Objects;
 import life.qbic.data_download.measurements.api.DataFile;
 import life.qbic.data_download.measurements.api.FileInfo;
 import life.qbic.data_download.measurements.api.MeasurementDataReader;
+import life.qbic.data_download.measurements.api.PathFormatter;
 
 /**
  * Reads openbis data streams
  */
 public class DatasetFileStreamReaderImpl implements MeasurementDataReader {
 
   private DataSetFileDownloadReader dataSetFileDownloadReader;
-  private final String ignoredPrefix;
+
+   private final PathFormatter formatter;
+
+  private static final String UUID_REGEX = "^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$";
 
   public DatasetFileStreamReaderImpl(String ignoredPrefix) {
+    Objects.requireNonNull(ignoredPrefix);
     dataSetFileDownloadReader = null;
-    this.ignoredPrefix = Optional.ofNullable(ignoredPrefix).orElse("");
+    var filter = List.of(ignoredPrefix, UUID_REGEX);
+    this.formatter = PathFormatter.with(filter);
   }
 
 
@@ -55,7 +62,10 @@ public DataFile nextDataFile() {
         .toEpochMilli() : -1;
     long lastModifiedMillis = nonNull(dataStore) ? dataStore.getModificationDate().toInstant()
         .toEpochMilli() : -1;
-    FileInfo fileInfo = new FileInfo(fileDownload.getDataSetFile().getPath().replaceFirst(ignoredPrefix, ""),
+
+    var cleanedPath = formatter.format(fileDownload.getDataSetFile().getPath());
+
+    FileInfo fileInfo = new FileInfo(cleanedPath,
         fileDownload.getDataSetFile().getFileLength(),
         Integer.toUnsignedLong(fileDownload.getDataSetFile().getChecksumCRC32()),
         creationMillis,