Update references to jira to GH for the Runners (apache#21835)

* Update references to jira to GH for the Runners

* Spotless format

* Switch to urls

* Spotless apply

* Spotless apply

* Fix awkward formatting

runners/core-construction-java/src/main/java/org/apache/beam/runners/core/construction/External.java

@@ -243,7 +243,8 @@ public OutputT expand(InputT input) {
                     PValues.expandInput(PBegin.in(p)),
                     ImmutableMap.of(entry.getKey(), (PCollection<?>) entry.getValue()),
                     Impulse.create(),
-                    // TODO(BEAM-12082): Add proper support for Resource Hints with XLang.
+                    // TODO(https://github.com/apache/beam/issues/18371): Add proper support for
+                    // Resource Hints with XLang.
                     ResourceHints.create(),
                     p);
             // using fake Impulses to provide inputs

runners/core-construction-java/src/main/java/org/apache/beam/runners/core/construction/NativeTransforms.java

@@ -46,7 +46,7 @@ public class NativeTransforms {
    * Returns true if an only if the Runner understands this transform and can handle it directly.
    */
   public static boolean isNative(RunnerApi.PTransform pTransform) {
-    // TODO(BEAM-10109) Use default (context) classloader.
+    // TODO(https://github.com/apache/beam/issues/20192) Use default (context) classloader.
     Iterator<IsNativeTransform> matchers =
         ServiceLoader.load(IsNativeTransform.class, NativeTransforms.class.getClassLoader())
             .iterator();

runners/core-construction-java/src/main/java/org/apache/beam/runners/core/construction/PTransformTranslation.java

@@ -442,7 +442,8 @@ public RunnerApi.PTransform translate(
 
         // Required runner implemented transforms should not have an environment id.
         if (!RUNNER_IMPLEMENTED_TRANSFORMS.contains(spec.getUrn())) {
-          // TODO(BEAM-9309): Remove existing hacks around deprecated READ transform.
+          // TODO(https://github.com/apache/beam/issues/20094): Remove existing hacks around
+          // deprecated READ transform.
           if (spec.getUrn().equals(READ_TRANSFORM_URN)) {
             // Only assigning environment to Bounded reads. Not assigning an environment to
             // Unbounded

runners/core-construction-java/src/main/java/org/apache/beam/runners/core/construction/ParDoTranslation.java

@@ -599,7 +599,8 @@ public RunnerApi.StateSpec dispatchOrderedList(Coder<?> elementCoder) {
                 .setOrderedListSpec(
                     RunnerApi.OrderedListStateSpec.newBuilder()
                         .setElementCoderId(registerCoderOrThrow(components, elementCoder)))
-                // TODO(BEAM-10650): Update with correct protocol once the protocol is defined and
+                // TODO(https://github.com/apache/beam/issues/20486): Update with correct protocol
+                // once the protocol is defined and
                 // the SDK harness uses it.
                 .build();
           }

runners/core-construction-java/src/main/java/org/apache/beam/runners/core/construction/SplittableParDo.java

@@ -691,7 +691,8 @@ public void tearDown() {
    * PrimitiveBoundedRead} and {@link PrimitiveUnboundedRead} if either the experiment {@code
    * use_deprecated_read} or {@code beam_fn_api_use_deprecated_read} are specified.
    *
-   * <p>TODO(BEAM-10670): Remove the primitive Read and make the splittable DoFn the only option.
+   * <p>TODO(https://github.com/apache/beam/issues/20530): Remove the primitive Read and make the
+   * splittable DoFn the only option.
    */
   public static void convertReadBasedSplittableDoFnsToPrimitiveReadsIfNecessary(Pipeline pipeline) {
     if (!ExperimentalOptions.hasExperiment(pipeline.getOptions(), "use_sdf_read")
@@ -706,7 +707,8 @@ public static void convertReadBasedSplittableDoFnsToPrimitiveReadsIfNecessary(Pi
    * Converts {@link Read} based Splittable DoFn expansions to primitive reads implemented by {@link
    * PrimitiveBoundedRead} and {@link PrimitiveUnboundedRead}.
    *
-   * <p>TODO(BEAM-10670): Remove the primitive Read and make the splittable DoFn the only option.
+   * <p>TODO(https://github.com/apache/beam/issues/20530): Remove the primitive Read and make the
+   * splittable DoFn the only option.
    */
   public static void convertReadBasedSplittableDoFnsToPrimitiveReads(Pipeline pipeline) {
     pipeline.replaceAll(

runners/core-construction-java/src/main/java/org/apache/beam/runners/core/construction/graph/ProjectionProducerVisitor.java

@@ -57,7 +57,7 @@ class ProjectionProducerVisitor extends PipelineVisitor.Defaults {
   public CompositeBehavior enterCompositeTransform(Node node) {
     PTransform<?, ?> transform = node.getTransform();
 
-    // TODO(BEAM-13658) Support inputs other than PBegin.
+    // TODO(https://github.com/apache/beam/issues/21359) Support inputs other than PBegin.
     if (!node.getInputs().isEmpty()) {
       return CompositeBehavior.DO_NOT_ENTER_TRANSFORM;
     }

runners/core-construction-java/src/main/java/org/apache/beam/runners/core/construction/graph/ProjectionPushdownOptimizer.java

@@ -95,7 +95,7 @@ public static void optimize(Pipeline pipeline) {
     }
   }
 
-  // TODO(BEAM-13658) Support inputs other than PBegin.
+  // TODO(https://github.com/apache/beam/issues/21359) Support inputs other than PBegin.
   private static class PushdownOverrideFactory<
           OutputT extends POutput, TransformT extends PTransform<PBegin, OutputT>>
       implements PTransformOverrideFactory<PBegin, OutputT, TransformT> {

runners/core-construction-java/src/test/java/org/apache/beam/runners/core/construction/PTransformMatchersTest.java

@@ -83,7 +83,9 @@
 @RunWith(JUnit4.class)
 @SuppressWarnings({
   "rawtypes", // TODO(https://github.com/apache/beam/issues/20447)
-  "unused" // TODO(BEAM-13271): Remove when new version of errorprone is released (2.11.0)
+  // TODO(https://github.com/apache/beam/issues/21230): Remove when new version of
+  // errorprone is released (2.11.0)
+  "unused"
 })
 public class PTransformMatchersTest implements Serializable {
   @Rule

runners/core-construction-java/src/test/java/org/apache/beam/runners/core/construction/graph/ProjectionPushdownOptimizerTest.java

@@ -104,8 +104,8 @@ public void testIntermediateProducer() {
         FieldAccessDescriptor.withFieldNames("foo", "bar");
     p.apply(source).apply(originalT).apply(new FieldAccessTransform(downstreamFieldAccess));
 
-    // TODO(BEAM-13658) Support pushdown on intermediate transforms.
-    // For now, test that the pushdown optimizer ignores immediate transforms.
+    // TODO(https://github.com/apache/beam/issues/21359) Support pushdown on intermediate
+    // transforms. For now, test that the pushdown optimizer ignores immediate transforms.
     ProjectionPushdownOptimizer.optimize(p);
     Assert.assertTrue(pipelineHasTransform(p, originalT));
   }

runners/core-java/src/main/java/org/apache/beam/runners/core/WatermarkHold.java

@@ -73,7 +73,8 @@ StateTag<WatermarkHoldState> watermarkHoldTagForTimestampCombiner(
       StateTags.makeSystemTagInternal(
           StateTags.watermarkStateInternal("extra", TimestampCombiner.EARLIEST));
 
-  // [BEAM-420] Seems likely these should all be transient or this class should not be Serializable
+  // [https://github.com/apache/beam/issues/18014] Seems likely these should all be transient or
+  // this class should not be Serializable
   @SuppressFBWarnings("SE_BAD_FIELD")
   private final TimerInternals timerInternals;
 

runners/core-java/src/main/java/org/apache/beam/runners/core/metrics/HistogramCell.java

@@ -70,7 +70,8 @@ public void update(HistogramCell other) {
     dirty.afterModification();
   }
 
-  // TODO(BEAM-12103): Update this function to allow incrementing the infinite buckets as well.
+  // TODO(https://github.com/apache/beam/issues/20853): Update this function to allow incrementing
+  // the infinite buckets as well.
   // and remove the incTopBucketCount and incBotBucketCount methods.
   // Using 0 and length -1 as the bucketIndex.
   public void incBucketCount(int bucketIndex, long count) {

runners/core-java/src/main/java/org/apache/beam/runners/core/metrics/MetricsContainerStepMap.java

@@ -63,7 +63,8 @@ public MetricsContainerImpl getUnboundContainer() {
   /** Returns the container for the given step name. */
   public MetricsContainerImpl getContainer(String stepName) {
     if (stepName == null) {
-      // TODO(BEAM-6538): Disallow this in the future, some tests rely on an empty step name today.
+      // TODO(https://github.com/apache/beam/issues/19275): Disallow this in the future, some tests
+      // rely on an empty step name today.
       return getUnboundContainer();
     }
     return metricsContainers.computeIfAbsent(

runners/core-java/src/test/java/org/apache/beam/runners/core/SimpleDoFnRunnerTest.java

@@ -68,7 +68,9 @@
 @RunWith(JUnit4.class)
 @SuppressWarnings({
   "rawtypes", // TODO(https://github.com/apache/beam/issues/20447)
-  "unused" // TODO(BEAM-13271): Remove when new version of errorprone is released (2.11.0)
+  // TODO(https://github.com/apache/beam/issues/21230): Remove when new version of
+  // errorprone is released (2.11.0)
+  "unused"
 })
 public class SimpleDoFnRunnerTest {
   @Rule public ExpectedException thrown = ExpectedException.none();

runners/direct-java/build.gradle

@@ -249,7 +249,7 @@ task examplesIntegrationTest(type: Test) {
   testClassesDirs = files(project(":examples:java").sourceSets.test.output.classesDirs)
   useJUnit {
     filter{
-      // TODO (BEAM-14019) Fix integration Tests to run with DirectRunner: Timeout error
+      // TODO (https://github.com/apache/beam/issues/21344) Fix integration Tests to run with DirectRunner: Timeout error
       excludeTestsMatching 'org.apache.beam.examples.complete.TfIdfIT'
       excludeTestsMatching 'org.apache.beam.examples.WindowedWordCountIT.testWindowedWordCountInBatchDynamicSharding'
     }

runners/direct-java/src/main/java/org/apache/beam/runners/direct/BoundedReadEvaluatorFactory.java

@@ -65,7 +65,8 @@ final class BoundedReadEvaluatorFactory implements TransformEvaluatorFactory {
   private final EvaluationContext evaluationContext;
   private final PipelineOptions options;
 
-  // TODO: (BEAM-723) Create a shared ExecutorService for maintenance tasks in the DirectRunner.
+  // TODO: (https://github.com/apache/beam/issues/18079) Create a shared ExecutorService for
+  // maintenance tasks in the DirectRunner.
   @VisibleForTesting
   final ExecutorService executor =
       Executors.newCachedThreadPool(

runners/direct-java/src/main/java/org/apache/beam/runners/direct/DirectRunner.java

@@ -253,7 +253,8 @@ void performRewrites(Pipeline pipeline) {
     // The last set of overrides includes GBK overrides used in WriteView
     pipeline.replaceAll(groupByKeyOverrides());
 
-    // TODO(BEAM-10670): Use SDF read as default when we address performance issue.
+    // TODO(https://github.com/apache/beam/issues/20530): Use SDF read as default when we address
+    // performance issue.
     SplittableParDo.convertReadBasedSplittableDoFnsToPrimitiveReadsIfNecessary(pipeline);
   }
 

runners/direct-java/src/main/java/org/apache/beam/runners/direct/ExecutorServiceParallelExecutor.java

@@ -147,7 +147,8 @@ private RemovalListener<StepAndKey, TransformExecutorService> shutdownExecutorSe
   }
 
   @Override
-  // TODO: [BEAM-4563] Pass Future back to consumer to check for async errors
+  // TODO: [https://github.com/apache/beam/issues/18968] Pass Future back to consumer to check for
+  // async errors
   @SuppressWarnings("FutureReturnValueIgnored")
   public void start(DirectGraph graph, RootProviderRegistry rootProviderRegistry) {
     int numTargetSplits = Math.max(3, targetParallelism);

runners/direct-java/src/main/java/org/apache/beam/runners/direct/TransformExecutorServices.java

@@ -70,7 +70,8 @@ private ParallelTransformExecutor(ExecutorService executor) {
     }
 
     @Override
-    // TODO: [BEAM-4563] Pass Future back to consumer to check for async errors
+    // TODO: [https://github.com/apache/beam/issues/18968] Pass Future back to consumer to check for
+    // async errors
     @SuppressWarnings("FutureReturnValueIgnored")
     public void schedule(TransformExecutor work) {
       if (active.get()) {
@@ -154,7 +155,8 @@ public void shutdown() {
       workQueue.clear();
     }
 
-    // TODO: [BEAM-4563] Pass Future back to consumer to check for async errors
+    // TODO: [https://github.com/apache/beam/issues/18968] Pass Future back to consumer to check for
+    // async errors
     @SuppressWarnings("FutureReturnValueIgnored")
     private void updateCurrentlyEvaluating() {
       if (currentlyEvaluating.get() == null) {

runners/direct-java/src/test/java/org/apache/beam/runners/direct/StatefulParDoEvaluatorFactoryTest.java

@@ -88,7 +88,9 @@
 @RunWith(JUnit4.class)
 @SuppressWarnings({
   "rawtypes", // TODO(https://github.com/apache/beam/issues/20447)
-  "unused" // TODO(BEAM-13271): Remove when new version of errorprone is released (2.11.0)
+  // TODO(https://github.com/apache/beam/issues/21230): Remove when new version of
+  // errorprone is released (2.11.0)
+  "unused"
 })
 public class StatefulParDoEvaluatorFactoryTest implements Serializable {
   @Mock private transient EvaluationContext mockEvaluationContext;

runners/flink/flink_runner.gradle

@@ -225,7 +225,7 @@ class ValidatesRunnerConfig {
 }
 
 def sickbayTests = [
-        // TODO(BEAM-13573)
+        // TODO(https://github.com/apache/beam/issues/21306)
         'org.apache.beam.sdk.transforms.ParDoTest$TimestampTests.testOnWindowTimestampSkew',
 ]
 
@@ -358,9 +358,9 @@ tasks.register("examplesIntegrationTest", Test) {
   testClassesDirs = files(project(":examples:java").sourceSets.test.output.classesDirs)
   useJUnit {
     filter{
-      // TODO (BEAM-14019) Fix integration Tests to run with FlinkRunner: Assertion error
+      // TODO (https://github.com/apache/beam/issues/21344) Fix integration Tests to run with FlinkRunner: Assertion error
       excludeTestsMatching 'org.apache.beam.examples.WindowedWordCountIT.testWindowedWordCountInBatchDynamicSharding'
-      // TODO (BEAM-14019) Fix integration Tests to run with FlinkRunner: Error deleting table, Not found: Dataset
+      // TODO (https://github.com/apache/beam/issues/21344) Fix integration Tests to run with FlinkRunner: Error deleting table, Not found: Dataset
       excludeTestsMatching 'org.apache.beam.examples.cookbook.BigQueryTornadoesIT.testE2eBigQueryTornadoesWithStorageApiUsingQuery'
     }
   }

runners/flink/job-server/flink_job_server.gradle

@@ -193,17 +193,17 @@ def portableValidatesRunnerTask(String name, boolean streaming, boolean checkpoi
         excludeCategories 'org.apache.beam.sdk.testing.UsesPerKeyOrderInBundle'
     },
     testFilter: {
-      // TODO(BEAM-10016)
+      // TODO(https://github.com/apache/beam/issues/20269)
       excludeTestsMatching 'org.apache.beam.sdk.transforms.FlattenTest.testFlattenWithDifferentInputAndOutputCoders2'
-      // TODO(BEAM-12039)
+      // TODO(https://github.com/apache/beam/issues/20843)
       excludeTestsMatching 'org.apache.beam.sdk.testing.TestStreamTest.testDiscardingMode'
-      // TODO(BEAM-12038)
+      // TODO(https://github.com/apache/beam/issues/20844)
       excludeTestsMatching 'org.apache.beam.sdk.testing.TestStreamTest.testLateDataAccumulating'
       // TODO(BEAM-12710)
       excludeTestsMatching 'org.apache.beam.sdk.testing.TestStreamTest.testFirstElementLate'
       // TODO(BEAM-13498)
       excludeTestsMatching 'org.apache.beam.sdk.transforms.ParDoTest$TimestampTests.testProcessElementSkew'
-      // TODO(BEAM-13952)
+      // TODO(https://github.com/apache/beam/issues/21472)
       excludeTestsMatching 'org.apache.beam.sdk.transforms.GroupByKeyTest$BasicTests.testAfterProcessingTimeContinuationTriggerUsingState'
     },
   )

runners/flink/src/main/java/org/apache/beam/runners/flink/FlinkRunner.java

@@ -77,7 +77,8 @@ protected FlinkRunner(FlinkPipelineOptions options) {
   @Override
   public PipelineResult run(Pipeline pipeline) {
     // Portable flink only support SDF as read.
-    // TODO(BEAM-10670): Use SDF read as default when we address performance issue.
+    // TODO(https://github.com/apache/beam/issues/20530): Use SDF read as default when we address
+    // performance issue.
     if (!ExperimentalOptions.hasExperiment(pipeline.getOptions(), "beam_fn_api")) {
       SplittableParDo.convertReadBasedSplittableDoFnsToPrimitiveReadsIfNecessary(pipeline);
     }

runners/flink/src/main/java/org/apache/beam/runners/flink/translation/functions/FlinkExecutableStageFunction.java

@@ -173,7 +173,8 @@ public void onCompleted(ProcessBundleResponse response) {
             metricContainer.updateMetrics(stepName, response.getMonitoringInfosList());
           }
         };
-    // TODO(BEAM-11021): Support bundle finalization in portable batch.
+    // TODO(https://github.com/apache/beam/issues/19526): Support bundle finalization in portable
+    // batch.
     finalizationHandler =
         bundleId -> {
           throw new UnsupportedOperationException(

runners/flink/src/main/java/org/apache/beam/runners/flink/translation/wrappers/streaming/ExecutableStageDoFnOperator.java

@@ -708,9 +708,9 @@ public void flushData() throws Exception {
         // Manually drain processing time timers since Flink will ignore pending
         // processing-time timers when upstream operators have shut down and will also
         // shut down this operator with pending processing-time timers.
-        // TODO(BEAM-11210, FLINK-18647): It doesn't work efficiently when the watermark of upstream
-        // advances
-        // to MAX_TIMESTAMP immediately.
+        // TODO(https://github.com/apache/beam/issues/20600, FLINK-18647): It doesn't work
+        // efficiently when the watermark of upstream advances to MAX_TIMESTAMP
+        // immediately.
         if (numProcessingTimeTimers() > 0) {
           timerInternals.processPendingProcessingTimeTimers();
         }

runners/flink/src/test/java/org/apache/beam/runners/flink/FlinkRequiresStableInputTest.java

@@ -121,7 +121,7 @@ public static void afterClass() throws Exception {
    * restore the savepoint to check if we produce impotent results.
    */
   @Test(timeout = 30_000)
-  @Ignore("BEAM-13575")
+  @Ignore("https://github.com/apache/beam/issues/21333")
   public void testParDoRequiresStableInput() throws Exception {
     FlinkPipelineOptions options = FlinkPipelineOptions.defaults();
     options.setParallelism(1);

runners/flink/src/test/java/org/apache/beam/runners/flink/FlinkSavepointTest.java

@@ -84,7 +84,9 @@
  */
 @SuppressWarnings({
   "rawtypes", // TODO(https://github.com/apache/beam/issues/20447)
-  "unused" // TODO(BEAM-13271): Remove when new version of errorprone is released (2.11.0)
+  // TODO(https://github.com/apache/beam/issues/21230): Remove when new version of
+  // errorprone is released (2.11.0)
+  "unused"
 })
 public class FlinkSavepointTest implements Serializable {
 

runners/flink/src/test/java/org/apache/beam/runners/flink/FlinkStreamingPipelineTranslatorTest.java

@@ -55,7 +55,8 @@
 import org.junit.Test;
 
 /** Tests if overrides are properly applied. */
-// TODO(BEAM-13271): Remove when new version of errorprone is released (2.11.0)
+// TODO(https://github.com/apache/beam/issues/21230): Remove when new version of errorprone is
+// released (2.11.0)
 @SuppressWarnings("unused")
 public class FlinkStreamingPipelineTranslatorTest {
 

runners/flink/src/test/java/org/apache/beam/runners/flink/PortableStateExecutionTest.java

@@ -58,7 +58,8 @@
  * org.apache.beam.runners.flink.translation.wrappers.streaming.ExecutableStageDoFnOperator}.
  */
 @RunWith(Parameterized.class)
-// TODO(BEAM-13271): Remove when new version of errorprone is released (2.11.0)
+// TODO(https://github.com/apache/beam/issues/21230): Remove when new version of errorprone is
+// released (2.11.0)
 @SuppressWarnings("unused")
 public class PortableStateExecutionTest implements Serializable {
 

runners/flink/src/test/java/org/apache/beam/runners/flink/PortableTimersExecutionTest.java

@@ -71,7 +71,8 @@
  * of a given timer is run.
  */
 @RunWith(Parameterized.class)
-// TODO(BEAM-13271): Remove when new version of errorprone is released (2.11.0)
+// TODO(https://github.com/apache/beam/issues/21230): Remove when new version of errorprone is
+// released (2.11.0)
 @SuppressWarnings("unused")
 public class PortableTimersExecutionTest implements Serializable {
 

runners/flink/src/test/java/org/apache/beam/runners/flink/translation/wrappers/streaming/DoFnOperatorTest.java

@@ -117,7 +117,9 @@
 @RunWith(JUnit4.class)
 @SuppressWarnings({
   "keyfor",
-  "unused" // TODO(BEAM-13271): Remove when new version of errorprone is released (2.11.0)
+  // TODO(https://github.com/apache/beam/issues/21230): Remove when new version of
+  // errorprone is released (2.11.0)
+  "unused"
 })
 public class DoFnOperatorTest {