fixed an edge case for incremental run failures on cloud filesystems

pipelines/common/src/main/java/com/google/fhir/analytics/DwhFiles.java

@@ -35,7 +35,9 @@
 import java.nio.file.FileAlreadyExistsException;
 import java.time.Instant;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Collections;
+import java.util.Comparator;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
@@ -72,6 +74,8 @@ public class DwhFiles {
 
   private static final String INCREMENTAL_DIR = "incremental_run";
 
+  static final String TIMESTAMP_PREFIX = "_TIMESTAMP_";
+
   // TODO: It is probably better if we build all DWH files related operations using Beam's
   //  filesystem API such that when a new filesystem is registered, it automatically works
   //  everywhere in our code. Note that currently we have hardcoded the valid schema in some places,
@@ -121,6 +125,10 @@ static DwhFiles forRoot(String dwhRoot, FhirContext fhirContext) {
     return new DwhFiles(dwhRoot, fhirContext);
   }
 
+  public static String safeTimestampSuffix() {
+    return Instant.now().toString().replace(":", "-").replace("-", "_").replace(".", "_");
+  }
+
   public String getRoot() {
     return dwhRoot;
   }
@@ -145,50 +153,75 @@ public String getFilePattern(String resourceType) {
         "%s*%s", getResourcePath(resourceType).toString(), ParquetUtil.PARQUET_EXTENSION);
   }
 
+  // TODO: Move this to a util class and make it non-static.
   /**
-   * This returns the default incremental run path; each incremental run is relative to a full path,
-   * hence we put this directory under the full-run root.
+   * Returns all the child directories under the given base directory which are 1-level deep. Note
+   * in many cloud/distributed file-systems, we do not have "directories"; there are only buckets
+   * and files in those buckets. We use file-seprators (e.g., `/`) to simulate the concept of
+   * directories. So for example, this method returns an empty set if `baseDir` is `bucket/test` and
+   * the only file in that bucket is `bucket/test/dir1/dir2/file.txt`. If `baseDir` is
+   * `bucket/test/dir1`, in the above example, `dir2` is returned.
    *
-   * @return the default incremental run path
+   * @param baseDir the path under which "directories" are looked for.
+   * @return The list of all child directories under the base directory
+   * @throws IOException
    */
-  public ResourceId getIncrementalRunPath() {
-    return FileSystems.matchNewResource(getRoot(), true)
-        .resolve(INCREMENTAL_DIR, StandardResolveOptions.RESOLVE_DIRECTORY);
-  }
-
-  /** This is used when we want to keep a backup of the old incremental run output. */
-  public ResourceId getIncrementalRunPathWithTimestamp() {
-    return FileSystems.matchNewResource(getRoot(), true)
-        .resolve(
-            String.format("%s_old_%d", INCREMENTAL_DIR, System.currentTimeMillis()),
-            StandardResolveOptions.RESOLVE_DIRECTORY);
+  static Set<ResourceId> getAllChildDirectories(String baseDir) throws IOException {
+    String fileSeparator = getFileSeparatorForDwhFiles(baseDir);
+    // Avoid using ResourceId.resolve(..) method to resolve the files when the path contains glob
+    // expressions with multiple special characters like **, */* etc as this api only supports
+    // single special characters like `*` or `..`. Rather use the FileSystems.match(..) if the path
+    // contains glob expressions.
+    List<MatchResult> matchResultList =
+        FileSystems.match(
+            List.of(
+                getPathEndingWithFileSeparator(baseDir, fileSeparator)
+                    + "*"
+                    + fileSeparator
+                    + "*"));
+    Set<ResourceId> childDirectories = new HashSet<>();
+    for (MatchResult matchResult : matchResultList) {
+      if (matchResult.status() == Status.OK && !matchResult.metadata().isEmpty()) {
+        for (Metadata metadata : matchResult.metadata()) {
+          childDirectories.add(metadata.resourceId().getCurrentDirectory());
+        }
+      } else if (matchResult.status() == Status.ERROR) {
+        String errorMessage = String.format("Error matching files under directory %s", baseDir);
+        log.error(errorMessage);
+        throw new IOException(errorMessage);
+      }
+    }
+    log.info("Child directories of {} are {}", baseDir, childDirectories);
+    return childDirectories;
   }
 
   /**
-   * Similar to {@link #getIncrementalRunPath} but also checks if that directory exists and if so,
-   * moves it to {@link #getIncrementalRunPathWithTimestamp()}.
-   *
-   * @return same as {@link #getIncrementalRunPath()}
-   * @throws IOException if the directory move fails
+   * Also see {@link #newIncrementalRunPath()}
+   * @return the current incremental run path if one found; null otherwise.
    */
-  public ResourceId newIncrementalRunPath() throws IOException {
-    ResourceId incPath = getIncrementalRunPath();
-    if (hasIncrementalDir()) {
-      ResourceId movePath = getIncrementalRunPathWithTimestamp();
-      log.info("Moving the old {} directory to {}", INCREMENTAL_DIR, movePath);
-      FileSystems.rename(Collections.singletonList(incPath), Collections.singletonList(movePath));
-    }
-    return incPath;
+  @Nullable
+  public ResourceId getIncrementalRunPath() throws IOException {
+    List<ResourceId> dirs =
+        getAllChildDirectories(getRoot()).stream()
+            .filter(dir -> dir.getFilename().contains(INCREMENTAL_DIR + TIMESTAMP_PREFIX))
+            .collect(Collectors.toList());
+    if (dirs.isEmpty()) return null;
+
+    Collections.sort(dirs, Comparator.comparing(ResourceId::toString));
+    return dirs.get(dirs.size() - 1);
   }
 
   /**
-   * @return true iff there is already an incremental run subdirectory in this DWH.
+   * This returns a new incremental-run path based on the current timestamp. Note that each
+   * incremental-run is relative to a full-run, hence we put this directory under the full-run root.
+   *
+   * @return a new incremental run path based on the current timestamp.
    */
-  public boolean hasIncrementalDir() throws IOException {
-    List<MatchResult> matches =
-        FileSystems.matchResources(Collections.singletonList(getIncrementalRunPath()));
-    MatchResult matchResult = Iterables.getOnlyElement(matches);
-    return matchResult.status() == Status.OK;
+  public ResourceId newIncrementalRunPath() {
+    return FileSystems.matchNewResource(getRoot(), true)
+        .resolve(
+            String.format("%s%s%s", INCREMENTAL_DIR, TIMESTAMP_PREFIX, safeTimestampSuffix()),
+            StandardResolveOptions.RESOLVE_DIRECTORY);
   }
 
   public Set<String> findNonEmptyResourceDirs() throws IOException {

pipelines/common/src/test/java/com/google/fhir/analytics/GcsDwhFilesTest.java

@@ -17,6 +17,7 @@
 
 import static org.hamcrest.MatcherAssert.assertThat;
 import static org.hamcrest.Matchers.equalTo;
+import static org.hamcrest.Matchers.startsWith;
 
 import ca.uhn.fhir.context.FhirContext;
 import com.google.api.services.storage.model.Objects;
@@ -92,7 +93,9 @@ public void newIncrementalRunPathTest() throws IOException {
     Mockito.when(mockGcsUtil.getObjects(Mockito.anyList())).thenReturn(items);
 
     ResourceId resourceId = dwhFiles.newIncrementalRunPath();
-    assertThat(resourceId.toString(), equalTo("gs://testbucket/testdirectory/incremental_run/"));
+    assertThat(
+        resourceId.toString(),
+        startsWith("gs://testbucket/testdirectory/incremental_run" + DwhFiles.TIMESTAMP_PREFIX));
   }
 
   @Test
@@ -244,4 +247,41 @@ private StorageObject createStorageObject(String gcsFilename, long fileSize) {
         .setName(gcsPath.getObject())
         .setSize(size);
   }
+
+  @Test
+  public void testGetAllChildDirectoriesOneLevelDeep() throws IOException {
+    Objects modelObjects = new Objects();
+    List<StorageObject> items = new ArrayList<>();
+    // Files within the directory
+    items.add(
+        createStorageObject(
+            "gs://testbucket/testdirectory/Patient/patient.parquet", 1L /* fileSize */));
+    items.add(
+        createStorageObject(
+            "gs://testbucket/testdirectory/Observation/observation.parquet", 2L /* fileSize */));
+    // This is not returned in this case of GCS because there is no files right "under" TEST1.
+    // Note in GCS we do not have "directories", we are just simulating them by `/` separators.
+    items.add(
+        createStorageObject(
+            "gs://testbucket/testdirectory/TEST1/TEST2/file.txt", 2L /* fileSize */));
+    modelObjects.setItems(items);
+
+    Mockito.when(
+            mockGcsUtil.listObjects(
+                Mockito.eq("testbucket"), Mockito.anyString(), Mockito.isNull()))
+        .thenReturn(modelObjects);
+
+    Set<ResourceId> childDirectories =
+        DwhFiles.getAllChildDirectories("gs://testbucket/testdirectory");
+
+    assertThat(childDirectories.size(), equalTo(2));
+    assertThat(
+        childDirectories.contains(
+            FileSystems.matchNewResource("gs://testbucket/testdirectory/Patient", true)),
+        equalTo(true));
+    assertThat(
+        childDirectories.contains(
+            FileSystems.matchNewResource("gs://testbucket/testdirectory/Observation", true)),
+        equalTo(true));
+  }
 }

pipelines/common/src/test/java/com/google/fhir/analytics/LocalDwhFilesTest.java

@@ -17,6 +17,7 @@
 
 import static org.hamcrest.MatcherAssert.assertThat;
 import static org.hamcrest.Matchers.equalTo;
+import static org.hamcrest.Matchers.startsWith;
 
 import ca.uhn.fhir.context.FhirContext;
 import com.google.common.io.Resources;
@@ -33,6 +34,8 @@
 import java.util.List;
 import java.util.Set;
 import java.util.stream.Collectors;
+import org.apache.beam.sdk.io.FileSystems;
+import org.apache.beam.sdk.io.fs.ResolveOptions.StandardResolveOptions;
 import org.apache.beam.sdk.io.fs.ResourceId;
 import org.apache.commons.lang3.SystemUtils;
 import org.junit.Assert;
@@ -54,12 +57,31 @@ public void getResourcePathTestWindows() {
     assertThat(dwhFiles.getResourcePath("Patient").toString(), equalTo("C:\\tmp\\Patient\\"));
   }
 
+  @Test
+  public void getIncrementalRunPathTest() throws IOException {
+    Assume.assumeFalse(SystemUtils.IS_OS_WINDOWS);
+    DwhFiles instance = new DwhFiles("/tmp", FhirContext.forR4Cached());
+    ResourceId incrementalRunPath1 = instance.newIncrementalRunPath();
+    ResourceId file1 =
+        incrementalRunPath1.resolve("file1.txt", StandardResolveOptions.RESOLVE_FILE);
+    FileSystems.create(file1, "test");
+    ResourceId incrementalRunPath2 = instance.newIncrementalRunPath();
+    ResourceId file2 =
+        incrementalRunPath2.resolve("file2.txt", StandardResolveOptions.RESOLVE_FILE);
+    FileSystems.create(file2, "test");
+    // making sure that the last incremental path is returned
+    assertThat(
+        instance.getIncrementalRunPath().toString(), equalTo(incrementalRunPath2.toString()));
+  }
+
   @Test
   public void newIncrementalRunPathTestNonWindows() throws IOException {
     Assume.assumeFalse(SystemUtils.IS_OS_WINDOWS);
     DwhFiles instance = new DwhFiles("/tmp", FhirContext.forR4Cached());
     ResourceId incrementalRunPath = instance.newIncrementalRunPath();
-    assertThat(incrementalRunPath.toString(), equalTo("/tmp/incremental_run/"));
+    assertThat(
+        incrementalRunPath.toString(),
+        startsWith("/tmp/incremental_run" + DwhFiles.TIMESTAMP_PREFIX));
   }
 
   @Test
@@ -242,4 +264,34 @@ public void passWindowsLocalPathDwhRootPrefix_returnsFileSeparator() {
   private void createFile(Path path, byte[] bytes) throws IOException {
     Files.write(path, bytes);
   }
+
+  @Test
+  public void testGetAllChildDirectoriesOneLevelDeep() throws IOException {
+    Path rootDir = Files.createTempDirectory("DWH_FILES_TEST");
+    Path childDir1 = Paths.get(rootDir.toString(), "childDir1");
+    Files.createDirectories(childDir1);
+    Path fileAtChildDir1 = Path.of(childDir1.toString(), "file1.txt");
+    createFile(fileAtChildDir1, "SAMPLE TEXT".getBytes(StandardCharsets.UTF_8));
+    Path childDir2 = Paths.get(rootDir.toString(), "childDir2");
+    Files.createDirectories(childDir2);
+    Path fileAtChildDir2 = Path.of(childDir2.toString(), "file2.txt");
+    createFile(fileAtChildDir2, "SAMPLE TEXT".getBytes(StandardCharsets.UTF_8));
+
+    // The following directory should not appear in the results of `getAllChildDirectories`
+    // because only dirs at one-level deep should be returned.
+    Path childDir21 = Paths.get(childDir2.toString(), "childDir21");
+    Files.createDirectories(childDir21);
+    Path fileAtChildDir21 = Path.of(childDir21.toString(), "file3.txt");
+    createFile(fileAtChildDir21, "SAMPLE TEXT".getBytes(StandardCharsets.UTF_8));
+
+    Set<ResourceId> childDirectories = DwhFiles.getAllChildDirectories(rootDir.toString());
+
+    assertThat(childDirectories.size(), equalTo(2));
+    assertThat(
+        childDirectories.contains(FileSystems.matchNewResource(childDir1.toString(), true)),
+        equalTo(true));
+    assertThat(
+        childDirectories.contains(FileSystems.matchNewResource(childDir2.toString(), true)),
+        equalTo(true));
+  }
 }

pipelines/controller/src/main/java/com/google/fhir/analytics/DataProperties.java

@@ -20,7 +20,6 @@
 import com.google.common.base.Strings;
 import java.lang.reflect.InvocationTargetException;
 import java.lang.reflect.Method;
-import java.time.Instant;
 import java.util.ArrayList;
 import java.util.Comparator;
 import java.util.List;
@@ -53,8 +52,6 @@ public class DataProperties {
 
   private static final Logger logger = LoggerFactory.getLogger(DataProperties.class.getName());
 
-  static final String TIMESTAMP_PREFIX = "_TIMESTAMP_";
-
   private static final String GET_PREFIX = "get";
 
   private static final Set<String> EXCLUDED_ARGS =
@@ -212,17 +209,16 @@ PipelineConfig createBatchOptions() {
     }
 
     // Using underscore for suffix as hyphens are discouraged in hive table names.
-    String timestampSuffix =
-        Instant.now().toString().replace(":", "-").replace("-", "_").replace(".", "_");
-    options.setOutputParquetPath(dwhRootPrefix + TIMESTAMP_PREFIX + timestampSuffix);
+    String timestampSuffix = DwhFiles.safeTimestampSuffix();
+    options.setOutputParquetPath(dwhRootPrefix + DwhFiles.TIMESTAMP_PREFIX + timestampSuffix);
 
     PipelineConfig.PipelineConfigBuilder pipelineConfigBuilder = addFlinkOptions(options);
 
     // Get hold of thrift server parquet directory from dwhRootPrefix config.
     String thriftServerParquetPathPrefix =
         dwhRootPrefix.substring(dwhRootPrefix.lastIndexOf("/") + 1, dwhRootPrefix.length());
     pipelineConfigBuilder.thriftServerParquetPath(
-        thriftServerParquetPathPrefix + TIMESTAMP_PREFIX + timestampSuffix);
+        thriftServerParquetPathPrefix + DwhFiles.TIMESTAMP_PREFIX + timestampSuffix);
     pipelineConfigBuilder.timestampSuffix(timestampSuffix);
 
     return pipelineConfigBuilder.build();

pipelines/controller/src/main/java/com/google/fhir/analytics/DwhFilesManager.java

@@ -140,7 +140,7 @@ private void purgeDwhFiles() {
     try {
       String prefix = getPrefix(dwhRootPrefix);
       List<ResourceId> paths =
-          getAllChildDirectories(baseDir).stream()
+          DwhFiles.getAllChildDirectories(baseDir).stream()
               .filter(dir -> dir.getFilename().startsWith(prefix))
               .collect(Collectors.toList());
 
@@ -336,7 +336,7 @@ String getPrefix(String dwhRootPrefix) {
   }
 
   List<String> findExistingResources(String dwhRoot) throws IOException {
-    Set<ResourceId> childPaths = getAllChildDirectories(dwhRoot);
+    Set<ResourceId> childPaths = DwhFiles.getAllChildDirectories(dwhRoot);
     Set<String> configuredSet =
         new HashSet<>(Arrays.asList(dataProperties.getResourceList().split(",")));
     return childPaths.stream()
@@ -345,42 +345,6 @@ List<String> findExistingResources(String dwhRoot) throws IOException {
         .collect(Collectors.toList());
   }
 
-  /**
-   * Returns all the child directories under the given base directory which are 1-level deep.
-   *
-   * @param baseDir
-   * @return The list of all child directories under the base directory
-   * @throws IOException
-   */
-  Set<ResourceId> getAllChildDirectories(String baseDir) throws IOException {
-    String fileSeparator = DwhFiles.getFileSeparatorForDwhFiles(baseDir);
-    // Avoid using ResourceId.resolve(..) method to resolve the files when the path contains glob
-    // expressions with multiple special characters like **, */* etc as this api only supports
-    // single special characters like `*` or `..`. Rather use the FileSystems.match(..) if the path
-    // contains glob expressions.
-    List<MatchResult> matchResultList =
-        FileSystems.match(
-            List.of(
-                DwhFiles.getPathEndingWithFileSeparator(baseDir, fileSeparator)
-                    + "*"
-                    + fileSeparator
-                    + "*"));
-    Set<ResourceId> childDirectories = new HashSet<>();
-    for (MatchResult matchResult : matchResultList) {
-      if (matchResult.status() == Status.OK && !matchResult.metadata().isEmpty()) {
-        for (Metadata metadata : matchResult.metadata()) {
-          childDirectories.add(metadata.resourceId().getCurrentDirectory());
-        }
-      } else if (matchResult.status() == Status.ERROR) {
-        String errorMessage = String.format("Error matching files under directory %s", baseDir);
-        logger.error(errorMessage);
-        throw new IOException(errorMessage);
-      }
-    }
-    logger.info("Child directories : {}", childDirectories);
-    return childDirectories;
-  }
-
   private int getLastIndexOfSlash(String dwhRootPrefix) {
     CloudPath cloudPath = DwhFiles.parsePath(dwhRootPrefix);
     int index = -1;