Fix Generic ErrorProne/NullAway/JavaStyleGuide warnings

pipelines/batch/src/main/java/com/google/fhir/analytics/BulkExportApiClient.java

@@ -26,6 +26,8 @@
 import com.google.gson.Gson;
 import java.io.IOException;
 import java.io.Reader;
+import java.time.ZonedDateTime;
+import java.time.format.DateTimeFormatter;
 import java.util.Arrays;
 import java.util.Date;
 import java.util.HashMap;
@@ -95,7 +97,7 @@ public String triggerBulkExportJob(
    *
    * @param bulkExportStatusUrl the url of the bulk export job
    * @return BulkExportHttpResponse - the status and details of the bulk export job
-   * @throws IOException
+   * @throws IOException in case of any error while fetching the status of bulk export job
    */
   public BulkExportHttpResponse fetchBulkExportHttpResponse(String bulkExportStatusUrl)
       throws IOException {
@@ -104,12 +106,14 @@ public BulkExportHttpResponse fetchBulkExportHttpResponse(String bulkExportStatu
     httpResponseBuilder.httpStatus(httpResponse.getStatus());
     if (httpResponse.getHeaders(EXPIRES) != null && !httpResponse.getHeaders(EXPIRES).isEmpty()) {
       String expiresString = httpResponse.getHeaders(EXPIRES).get(0);
-      Date expires = new Date(expiresString);
+      DateTimeFormatter formatter = DateTimeFormatter.RFC_1123_DATE_TIME;
+      ZonedDateTime zonedDateTime = ZonedDateTime.parse(expiresString, formatter);
+      Date expires = Date.from(zonedDateTime.toInstant());
       httpResponseBuilder.expires(expires);
     }
     if (!CollectionUtils.isEmpty(httpResponse.getHeaders(RETRY_AFTER))) {
       String retryHeaderString = httpResponse.getHeaders(RETRY_AFTER).get(0);
-      httpResponseBuilder.retryAfter(Integer.valueOf(retryHeaderString));
+      httpResponseBuilder.retryAfter(Integer.parseInt(retryHeaderString));
     }
     if (!CollectionUtils.isEmpty(httpResponse.getHeaders(X_PROGRESS))) {
       String xProgress = httpResponse.getHeaders(X_PROGRESS).get(0);

pipelines/batch/src/main/java/com/google/fhir/analytics/BulkExportUtil.java

@@ -47,7 +47,8 @@ public class BulkExportUtil {
    * @param since - the fhir resources fetched should have updated timestamp greater than this
    * @param fhirVersionEnum - the fhir version of resource types
    * @return the BulkExportResponse
-   * @throws IOException
+   * @throws IOException in case of any error while triggering or fetching the status of bulk export
+   *     job
    */
   public BulkExportResponse triggerBulkExport(
       List<String> resourceTypes, @Nullable String since, FhirVersionEnum fhirVersionEnum)

pipelines/batch/src/main/java/com/google/fhir/analytics/ConvertResourceFn.java

@@ -26,6 +26,7 @@
 import java.sql.SQLException;
 import java.text.ParseException;
 import java.text.SimpleDateFormat;
+import java.time.Instant;
 import java.util.ArrayList;
 import java.util.Date;
 import java.util.HashMap;
@@ -121,7 +122,7 @@ public void writeResource(HapiRowDescriptor element)
       // deleted
       resource = createNewFhirResource(element.fhirVersion(), resourceType);
       ActionType removeAction = ActionType.REMOVE;
-      meta.setLastUpdated(new Date());
+      meta.setLastUpdated(Date.from(Instant.now()));
       meta.addTag(
           new Coding(removeAction.getSystem(), removeAction.toCode(), removeAction.getDisplay()));
     } else {
@@ -215,10 +216,10 @@ private Resource createNewFhirResource(String fhirVersion, String resourceType)
     try {
       // TODO create tests for this method and different versions of FHIR; casting to R4 resource
       //  does not seem right!
-      return (Resource)
-          Class.forName(getFhirBasePackageName(fhirVersion) + "." + resourceType)
-              .getConstructor()
-              .newInstance();
+      return Class.forName(getFhirBasePackageName(fhirVersion) + "." + resourceType)
+          .asSubclass(Resource.class)
+          .getConstructor()
+          .newInstance();
     } catch (InstantiationException
         | IllegalAccessException
         | ClassNotFoundException

pipelines/batch/src/main/java/com/google/fhir/analytics/FetchPatients.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2020-2024 Google LLC
+ * Copyright 2020-2025 Google LLC
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -21,8 +21,6 @@
 import com.google.fhir.analytics.view.ViewApplicationException;
 import java.io.IOException;
 import java.sql.SQLException;
-import java.util.List;
-import org.apache.avro.Schema;
 import org.apache.beam.sdk.transforms.PTransform;
 import org.apache.beam.sdk.transforms.ParDo;
 import org.apache.beam.sdk.values.KV;
@@ -40,15 +38,10 @@ public class FetchPatients extends PTransform<PCollection<KV<String, Integer>>,
 
   private final FetchSearchPageFn<KV<String, Integer>> fetchSearchPageFn;
 
-  private final Schema schema;
-
-  FetchPatients(FhirEtlOptions options, Schema schema) {
+  FetchPatients(FhirEtlOptions options) {
     Preconditions.checkState(!options.getActivePeriod().isEmpty());
-    List<String> dateRange = FhirSearchUtil.getDateRange(options.getActivePeriod());
 
     int count = options.getBatchSize();
-    this.schema = schema;
-
     fetchSearchPageFn =
         new FetchSearchPageFn<KV<String, Integer>>(options, "PatientById") {
 

pipelines/batch/src/main/java/com/google/fhir/analytics/FhirEtl.java

@@ -133,9 +133,7 @@ static void fetchPatientHistory(
     PCollection<KV<String, Integer>> flattenedPatients =
         patientIdList.apply(Flatten.pCollections());
     PCollection<KV<String, Integer>> mergedPatients = flattenedPatients.apply(Sum.integersPerKey());
-    final String patientType = "Patient";
-    FetchPatients fetchPatients =
-        new FetchPatients(options, avroConversionUtil.getResourceSchema(patientType));
+    FetchPatients fetchPatients = new FetchPatients(options);
     mergedPatients.apply(fetchPatients);
     for (String resourceType : patientAssociatedResources) {
       FetchPatientHistory fetchPatientHistory = new FetchPatientHistory(options, resourceType);

pipelines/batch/src/main/java/com/google/fhir/analytics/FhirEtlOptions.java

@@ -214,21 +214,25 @@ public interface FhirEtlOptions extends BasePipelineOptions {
   void setActivePeriod(String value);
 
   @Description(
-      "Fetch only FHIR resources that were updated after the given timestamp."
-          + "The date format follows the dateTime format in the FHIR standard, without time-zone:\n"
-          + "https://www.hl7.org/fhir/datatypes.html#dateTime\n"
-          + "This feature is currently implemented only for HAPI JDBC mode.")
+      """
+          Fetch only FHIR resources that were updated after the given timestamp.
+          The date format follows the dateTime format in the FHIR standard, without time-zone:
+          https://www.hl7.org/fhir/datatypes.html#dateTime
+          This feature is currently implemented only for HAPI JDBC mode.
+          """)
   @Default.String("")
   String getSince();
 
   void setSince(String value);
 
   @Description(
-      "Path to the sink database config; if not set, no sink DB is used.\n"
-          + "If viewDefinitionsDir is set, the output tables will be the generated views\n"
-          + "(the `name` field value will be used as the table name); if not, one table\n"
-          + "per resource type is created with the JSON content of a resource and its\n"
-          + "`id` column for each row.")
+      """
+          Path to the sink database config; if not set, no sink DB is used.
+          If viewDefinitionsDir is set, the output tables will be the generated views
+          (the `name` field value will be used as the table name); if not, one table
+          per resource type is created with the JSON content of a resource and its
+          `id` column for each row.
+          """)
   @Default.String("")
   String getSinkDbConfigPath();
 

pipelines/batch/src/main/java/com/google/fhir/analytics/ResourceTag.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2020-2023 Google LLC
+ * Copyright 2020-2025 Google LLC
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -43,12 +43,10 @@ public boolean equals(Object other) {
       return true;
     }
 
-    if (!(other instanceof ResourceTag)) {
+    if (!(other instanceof ResourceTag resourceTag)) {
       return false;
     }
 
-    ResourceTag resourceTag = (ResourceTag) other;
-
     return coding != null
         && coding.equalsDeep(resourceTag.coding)
         && StringUtils.compare(resourceId, resourceTag.getResourceId()) == 0

pipelines/batch/src/main/java/com/google/fhir/analytics/metrics/PipelineMetrics.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2020-2023 Google LLC
+ * Copyright 2020-2025 Google LLC
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -27,10 +27,6 @@ public interface PipelineMetrics {
   /** Clears all the metrics */
   void clearAllMetrics();
 
-  /**
-   * Sets the total number of resources
-   *
-   * @param totalNumOfResources
-   */
+  /** Sets the total number of resources */
   void setTotalNumOfResources(long totalNumOfResources);
 }

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

@@ -164,10 +164,11 @@ Resource convertToHapi(GenericRecord record, String resourceType) throws Profile
     AvroConverter converter = getConverter(resourceType);
     IBaseResource resource = converter.avroToResource(record);
     // TODO: fix this for other FHIR versions: https://github.com/google/fhir-data-pipes/issues/400
-    if (!(resource instanceof Resource)) {
+    if (resource instanceof Resource res) {
+      return res;
+    } else {
       throw new IllegalArgumentException("Cannot convert input record to resource!");
     }
-    return (Resource) resource;
   }
 
   /**

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

@@ -131,7 +131,7 @@ public class DwhFiles {
    * @param dwhRoot the root of the DWH
    * @param viewRoot the root of the view dir under DWH; note this should be an absolute path, but
    *     it is usually "under" `dwhRoot`.
-   * @param fhirContext
+   * @param fhirContext the FHIR Context of the FHIR version we are working with.
    */
   private DwhFiles(String dwhRoot, @Nullable String viewRoot, FhirContext fhirContext) {
     Preconditions.checkArgument(!Strings.isNullOrEmpty(dwhRoot));
@@ -199,8 +199,10 @@ public ResourceId getViewPath(String viewName) {
   }
 
   /**
-   * @param resourceType the type of the FHIR resources
-   * @return The file pattern for Parquet files of `resourceType` in this DWH.
+   * Returns the file-pattern for all Parquet files of a specific resource type.
+   *
+   * @param resourceType the type of the FHIR resources {@return The file pattern for Parquet files
+   *     of `resourceType` in this DWH.}
    */
   public String getResourceFilePattern(String resourceType) {
     return String.format(
@@ -221,14 +223,14 @@ public String getViewFilePattern(String viewName) {
   /**
    * 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
+   * and files in those buckets. We use file-separators (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.
    *
    * @param baseDir the path under which "directories" are looked for.
    * @return The list of all child directories under the base directory
-   * @throws IOException
+   * @throws IOException if there is an error accessing the base directory
    */
   static Set<ResourceId> getAllChildDirectories(String baseDir) throws IOException {
     return getAllChildDirectories(baseDir, "");
@@ -241,8 +243,8 @@ static Set<ResourceId> getAllChildDirectories(String baseDir) throws IOException
    *
    * @param baseDir the baseDir of the DWH
    * @param commonPrefix the prefix of directories under `baseDir` that we are looking for
-   * @return the list of found directory names.
-   * @throws IOException
+   * @return the set of found directory names.
+   * @throws IOException if there is an error accessing the base directory
    */
   static Set<ResourceId> getAllChildDirectories(String baseDir, String commonPrefix)
       throws IOException {
@@ -280,7 +282,7 @@ static Set<ResourceId> getAllChildDirectories(String baseDir, String commonPrefi
    *
    * @param commonPrefix the common prefix for the timestamped directories to search.
    * @return the latest directory with the `commonPrefix`.
-   * @throws IOException
+   * @throws IOException if there is an error accessing the dwhRoot directory
    */
   @Nullable
   private static ResourceId getLatestPath(String dwhRoot, String commonPrefix) throws IOException {
@@ -300,6 +302,8 @@ private static ResourceId newTimestampedPath(String dwhRoot, String commonPrefix
   }
 
   /**
+   * Gets the latest incremental-run path under the given DWH root.
+   *
    * @return the current incremental run path if one found; null otherwise.
    */
   @Nullable
@@ -435,7 +439,7 @@ public static void copyDirToDwh(String srcDwh, String dirName, String destDwh)
     }
 
     List<ResourceId> destResourceIdList = new ArrayList<>();
-    sourceResourceIdList.stream()
+    sourceResourceIdList
         .forEach(
             resourceId -> {
               if (resourceId.getFilename() != null) {
@@ -580,7 +584,7 @@ public static String getFileSeparatorForDwhFiles(String dwhRootPrefix) {
     };
   }
 
-  /** This method returns the {@code path} by appending the {@code fileseparator} if required. */
+  /** This method returns the {@code path} by appending the {@code fileSeparator} if required. */
   public static String getPathEndingWithFileSeparator(String path, String fileSeparator) {
     Preconditions.checkNotNull(path);
     Preconditions.checkNotNull(fileSeparator);

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

@@ -184,8 +184,8 @@ protected Collection<MethodOutcome> uploadBundle(
         }
 
         Resource outcome = responseComponent.getOutcome();
-        if (outcome instanceof IBaseOperationOutcome) {
-          methodOutcome.setOperationOutcome((IBaseOperationOutcome) outcome);
+        if (outcome instanceof IBaseOperationOutcome operationOutcome) {
+          methodOutcome.setOperationOutcome(operationOutcome);
         }
 
         responses.add(methodOutcome);

pipelines/common/src/main/java/com/google/fhir/analytics/view/ViewApplicator.java

@@ -291,11 +291,10 @@ FlatRow applyColumns(@Nullable IBase element, List<Column> columns)
     List<RowElement> rowElements = new ArrayList<>();
     for (Column col : columns) {
       if (GET_RESOURCE_KEY.equals(col.getPath())) {
-        if (element == null || !(element instanceof IBaseResource)) {
+        if (element == null || !(element instanceof IBaseResource baseResource)) {
           throw new ViewApplicationException(
               GET_RESOURCE_KEY + " can only be applied at the root!");
         }
-        IBaseResource baseResource = (IBaseResource) element;
         rowElements.add(
             new RowElement(
                 // TODO move all type inference to a single place outside View application.
@@ -322,11 +321,11 @@ FlatRow applyColumns(@Nullable IBase element, List<Column> columns)
           eval = evaluateFhirPath(element, fhirPathForRef);
         }
         for (IBase refElem : eval) {
-          if (!(refElem instanceof IBaseReference)) {
+          if (!(refElem instanceof IBaseReference refElemBaseReference)) {
             throw new ViewApplicationException(
                 "getReferenceKey can only be applied to Reference elements; got " + fhirPathForRef);
           }
-          IIdType ref = ((IBaseReference) refElem).getReferenceElement();
+          IIdType ref = refElemBaseReference.getReferenceElement();
           if (resType.isEmpty()) {
             refs.add(ref);
           } else {
@@ -365,7 +364,9 @@ public static class RowList {
 
     private final ImmutableList<FlatRow> rows;
 
-    private RowList(List<FlatRow> rows, LinkedHashMap<String, Column> columnInfos) {
+    private RowList(
+        List<FlatRow> rows,
+        @SuppressWarnings("NonApiType") LinkedHashMap<String, Column> columnInfos) {
       this.rows = ImmutableList.copyOf(rows);
       this.columnInfos = ImmutableMap.copyOf(columnInfos);
     }
@@ -466,6 +467,7 @@ private static Builder builder() {
     }
 
     // This can eventually be public, but currently it is not used outside this file.
+    @SuppressWarnings("EffectivelyPrivate")
     private static class Builder {
       private final LinkedHashMap<String, Column> columnInfos = new LinkedHashMap<>();
       private final List<FlatRow> rows = new ArrayList<>();

pipelines/common/src/main/java/com/google/fhir/analytics/view/ViewDefinition.java

@@ -143,6 +143,7 @@ void validateAndSetUp(boolean checkName, @Nullable String fhirVersion)
    * @return the [ordered] map of new column names and their types as string.
    * @throws ViewDefinitionException for repeated columns or other requirements not satisfied.
    */
+  @SuppressWarnings("NonApiType")
   private LinkedHashMap<String, Column> validateAndReplaceConstantsInSelects(
       @Nullable List<Select> selects, LinkedHashMap<String, Column> currentColumns)
       throws ViewDefinitionException {
@@ -157,10 +158,12 @@ private LinkedHashMap<String, Column> validateAndReplaceConstantsInSelects(
     return newCols;
   }
 
+  @SuppressWarnings("NonApiType")
   private static LinkedHashMap<String, Column> newTypeMap() {
     return new LinkedHashMap<>();
   }
 
+  @SuppressWarnings("NonApiType")
   private static LinkedHashMap<String, Column> unionTypeMaps(
       LinkedHashMap<String, Column> m1, LinkedHashMap<String, Column> m2) {
     LinkedHashMap<String, Column> u = new LinkedHashMap<>();
@@ -169,6 +172,7 @@ private static LinkedHashMap<String, Column> unionTypeMaps(
     return u;
   }
 
+  @SuppressWarnings("NonApiType")
   private LinkedHashMap<String, Column> validateAndReplaceConstantsInOneSelect(
       Select select, LinkedHashMap<String, Column> currentColumns) throws ViewDefinitionException {
     LinkedHashMap<String, Column> newCols = newTypeMap();
@@ -329,6 +333,8 @@ private String quoteString(String s) {
     }
 
     /**
+     * Converts the value of this constant to a string that can be used in FHIRPath expressions.
+     *
      * @return a string that can replace this constant in FHIRPaths.
      * @throws ViewDefinitionException if zero or more than one value is defined.
      */

pipelines/common/src/main/java/com/google/fhir/analytics/view/ViewSchema.java

@@ -100,7 +100,7 @@ public static ImmutableMap<String, JDBCType> getDbSchema(ViewDefinition view) {
    *
    * @param rowElements the input elements of the row
    * @param statement the statement on which `set*()` methods are called to write the row elements
-   * @throws SQLException
+   * @throws SQLException if an error occurs while setting values in the statement
    */
   public static void setValueInStatement(
       ImmutableList<RowElement> rowElements, PreparedStatement statement) throws SQLException {