Merge pull request #925 from conveyal/dev

January 2024 Point Release 7.1

Author: ansoncfit

build.gradle

@@ -3,6 +3,7 @@ plugins {
     id 'application'
     id 'maven-publish'
     id 'com.palantir.git-version' version '2.0.0'
+    id 'com.github.johnrengelman.shadow' version '8.1.1'
 }
 
 group = 'com.conveyal'
@@ -19,7 +20,7 @@ jar {
     // For Java 11+ Modules, specify a module name.
     // Do not create module-info.java until all our dependencies specify a module name.
     // Main-Class BackendMain will start a local backend.
-    // Build-Jdk-Spec mimics a Maven manifest entry that helps us automatically install the right JVM.
+    // Build-Jdk-Spec mimics a Maven manifest entry that helps us automatically install or select the right JVM.
     // Implementation-X attributes are needed for ImageIO (used by Geotools) to initialize in some environments.
     manifest {
         attributes 'Automatic-Module-Name': 'com.conveyal.r5',
@@ -31,6 +32,10 @@ jar {
     }
 }
 
+shadowJar {
+    mergeServiceFiles()
+}
+
 // Allow reflective access by ObjectDiffer to normally closed Java internals. Used for round-trip testing serialization.
 // IntelliJ seems not to pass these JVM arguments when running tests from within the IDE, so the Kryo serialization
 // tests may only succeed under command line Gradle.
@@ -42,8 +47,8 @@ test {
                '--add-opens=java.base/java.lang=ALL-UNNAMED']
 }
 
-// `gradle publish` will upload both shadow and simple JAR to Github Packages
-// On GH Actions, GITHUB_ACTOR env variable is supplied without specifying it in action yml.
+// Set up publication of jar files to GitHub Packages Maven repository.
+// On GitHub Actions, GITHUB_ACTOR env variable is supplied without specifying it in action yml.
 publishing {
     repositories {
         maven {
@@ -56,10 +61,12 @@ publishing {
         }
     }
     publications {
-        // The presence of the shadow plugin somehow causes the shadow-jar to also be automatically included in this
-        // publication. Ideally we want to produce the shadow jar and upload it to S3 as a worker, but only publish the
-        // much smaller plain JAR without dependencies to Github Packages. On the other hand, we may want to publish
-        // shadow jars for tagged releases.
+        // The shadow plugin automatically creates and registers a component called "shadow" for integration with this
+        // Maven publish plugin. `gradle publish` will then upload both shadow jar and simple jar to Github Packages.
+        // See https://imperceptiblethoughts.com/shadow/getting-started/#default-java-groovy-tasks
+        // To run R5 with dependencies, Conveyal does not use shadow jars anymore, only the zip distribution or runBackend.
+        // For development builds and tests we don't need to produce a shadow jar, only publish the much smaller plain
+        // jar without dependencies to Github Packages. For now, we continue to attach shadow jars to tagged releases.
         gpr(MavenPublication) {
             from(components.java)
         }

src/main/java/com/conveyal/analysis/components/HttpApi.java

@@ -179,7 +179,7 @@ private void respondToException(Exception e, Request request, Response response,
         // Include a stack trace except when the error is known to be about unauthenticated or unauthorized access,
         // in which case we don't want to leak information about the server to people scanning it for weaknesses.
         if (type != UNAUTHORIZED && type != FORBIDDEN) {
-            body.put("stackTrace", errorEvent.stackTrace);
+            body.put("stackTrace", errorEvent.filteredStackTrace);
         }
         response.status(code);
         response.type("application/json");

src/main/java/com/conveyal/analysis/components/broker/Broker.java

@@ -177,19 +177,23 @@ public synchronized void enqueueTasksForRegionalJob (RegionalAnalysis regionalAn
             LOG.error("Someone tried to enqueue job {} but it already exists.", templateTask.jobId);
             throw new RuntimeException("Enqueued duplicate job " + templateTask.jobId);
         }
+        // Create the Job object to share with the MultiOriginAssembler, but defer adding this job to the Multimap of
+        // active jobs until we're sure the result assembler was constructed without any errors. Always add and remove
+        // the Job and corresponding MultiOriginAssembler as a unit in the same synchronized block of code (see #887).
         WorkerTags workerTags = WorkerTags.fromRegionalAnalysis(regionalAnalysis);
         Job job = new Job(templateTask, workerTags);
-        jobs.put(job.workerCategory, job);
 
         // Register the regional job so results received from multiple workers can be assembled into one file.
+        // If any parameters fail checks here, an exception may cause this method to exit early.
         // TODO encapsulate MultiOriginAssemblers in a new Component
-        // Note: if this fails with an exception we'll have a job enqueued, possibly being processed, with no assembler.
-        // That is not catastrophic, but the user may need to recognize and delete the stalled regional job.
         MultiOriginAssembler assembler = new MultiOriginAssembler(regionalAnalysis, job, fileStorage);
         resultAssemblers.put(templateTask.jobId, assembler);
 
+        // A MultiOriginAssembler was successfully put in place. It's now safe to register and start the Job.
+        jobs.put(job.workerCategory, job);
+
+        // If this is a fake job for testing, don't confuse the worker startup code below with its null graph ID.
         if (config.testTaskRedelivery()) {
-            // This is a fake job for testing, don't confuse the worker startup code below with null graph ID.
             return;
         }
 
@@ -385,14 +389,20 @@ public synchronized void markTaskCompleted (Job job, int taskId) {
     }
 
     /**
-     * When job.errors is non-empty, job.isErrored() becomes true and job.isActive() becomes false.
+     * Record an error that happened while a worker was processing a task on the given job. This method is tolerant
+     * of job being null, because it's called on a code path where any number of things could be wrong or missing.
+     * This method also ensures synchronization of writes to Jobs from any non-synchronized sections of an HTTP handler.
+     * Once job.errors is non-empty, job.isErrored() becomes true and job.isActive() becomes false.
      * The Job will stop delivering tasks, allowing workers to shut down, but will continue to exist allowing the user
      * to see the error message. User will then need to manually delete it, which will remove the result assembler.
-     * This method ensures synchronization of writes to Jobs from the unsynchronized worker poll HTTP handler.
      */
     private synchronized void recordJobError (Job job, String error) {
         if (job != null) {
-            job.errors.add(error);
+            // Limit the number of errors recorded to one.
+            // Still using a Set<String> instead of just String since the set of errors is exposed in a UI-facing API.
+            if (job.errors.isEmpty()) {
+                job.errors.add(error);
+            }
         }
     }
 
@@ -488,21 +498,23 @@ public void handleRegionalWorkResult(RegionalWorkResult workResult) {
         // Once the job is retrieved, it can be used below to requestExtraWorkersIfAppropriate without synchronization,
         // because that method only uses final fields of the job.
         Job job = null;
-        MultiOriginAssembler assembler;
         try {
+            MultiOriginAssembler assembler;
             synchronized (this) {
                 job = findJob(workResult.jobId);
+                // Record any error reported by the worker and don't pass bad results on to regional result assembly.
+                // This will mark the job as errored and not-active, stopping distribution of tasks to workers.
+                // To ensure that happens, record errors before any other conditional that could exit this method.
+                if (workResult.error != null) {
+                    recordJobError(job, workResult.error);
+                    return;
+                }
                 assembler = resultAssemblers.get(workResult.jobId);
                 if (job == null || assembler == null || !job.isActive()) {
                     // This will happen naturally for all delivered tasks after a job is deleted or it errors out.
                     LOG.debug("Ignoring result for unrecognized, deleted, or inactive job ID {}.", workResult.jobId);
                     return;
                 }
-                if (workResult.error != null) {
-                    // Record any error reported by the worker and don't pass bad results on to regional result assembly.
-                    recordJobError(job, workResult.error);
-                    return;
-                }
                 // Mark tasks completed first before passing results to the assembler. On the final result received,
                 // this will minimize the risk of race conditions by quickly making the job invisible to incoming stray
                 // results from spurious redeliveries, before the assembler is busy finalizing and uploading results.

src/main/java/com/conveyal/analysis/components/broker/Job.java

@@ -123,8 +123,11 @@ private RegionalTask makeOneTask (int taskNumber) {
     public int deliveryPass = 0;
 
     /**
-     * If any error compromises the usabilty or quality of results from any origin, it is recorded here.
+     * If any error compromises the usability or quality of results from any origin, it is recorded here.
      * This is a Set because identical errors are likely to be reported from many workers or individual tasks.
+     * The presence of an error here causes the job to be considered "errored" and "inactive" and stop delivering tasks.
+     * There is some risk here of accumulating unbounded amounts of large error messages (see #919).
+     * The field type could be changed to a single String instead of Set, but it's exposed on a UI-facing API as a Set.
      */
     public final Set<String> errors = new HashSet();
 

src/main/java/com/conveyal/analysis/components/eventbus/ErrorEvent.java

@@ -2,18 +2,20 @@
 
 import com.conveyal.r5.util.ExceptionUtils;
 
+import static com.conveyal.r5.util.ExceptionUtils.filterStackTrace;
+
 /**
  * This Event is fired each time a Throwable (usually an Exception or Error) occurs on the backend. It can then be
  * recorded or tracked in various places - the console logs, Slack, etc. This could eventually be used for errors on
  * the workers as well, but we'd have to be careful not to generate hundreds of messages at once.
  */
 public class ErrorEvent extends Event {
 
-    // We may serialize this object, so we convert the Throwable to two strings to control its representation.
+    // All Events are intended to be eligible for serialization into a log or database, so we convert the Throwable to
+    // some Strings to determine its representation in a simple way.
     // For flexibility in event handlers, it is tempting to hold on to the original Throwable instead of derived
     // Strings. Exceptions are famously slow, but it's the initial creation and filling in the stack trace that are
-    // slow. Once the instace exists, repeatedly examining its stack trace should not be prohibitively costly. Still,
-    // we do probably gain some efficiency by converting the stack trace to a String once and reusing that.
+    // slow. Once the instance exists, repeatedly examining its stack trace should not be prohibitively costly.
 
     public final String summary;
 
@@ -23,11 +25,16 @@ public class ErrorEvent extends Event {
      */
     public final String httpPath;
 
+    /** The full stack trace of the exception that occurred. */
     public final String stackTrace;
 
+    /** A minimal stack trace showing the immediate cause within Conveyal code. */
+    public final String filteredStackTrace;
+
     public ErrorEvent (Throwable throwable, String httpPath) {
         this.summary = ExceptionUtils.shortCauseString(throwable);
         this.stackTrace = ExceptionUtils.stackTraceString(throwable);
+        this.filteredStackTrace = ExceptionUtils.filterStackTrace(throwable);
         this.httpPath = httpPath;
     }
 
@@ -54,25 +61,9 @@ public String traceWithContext (boolean verbose) {
         if (verbose) {
             builder.append(stackTrace);
         } else {
-            builder.append(filterStackTrace(stackTrace));
+            builder.append(filteredStackTrace);
         }
         return builder.toString();
     }
 
-    private static String filterStackTrace (String stackTrace) {
-        if (stackTrace == null) return null;
-        final String unknownFrame = "Unknown stack frame, probably optimized out by JVM.";
-        String error = stackTrace.lines().findFirst().get();
-        String frame = stackTrace.lines()
-                .map(String::strip)
-                .filter(s -> s.startsWith("at "))
-                .findFirst().orElse(unknownFrame);
-        String conveyalFrame = stackTrace.lines()
-                .map(String::strip)
-                .filter(s -> s.startsWith("at com.conveyal."))
-                .filter(s -> !frame.equals(s))
-                .findFirst().orElse("");
-        return String.join("\n", error, frame, conveyalFrame);
-    }
-
 }

src/main/java/com/conveyal/analysis/results/CsvResultWriter.java

@@ -41,7 +41,12 @@ public abstract class CsvResultWriter extends BaseResultWriter implements Region
      */
     public abstract CsvResultType resultType ();
 
-    /** Override to provide column names for this CSV writer. */
+    /**
+     * Override to provide column names for this CSV writer.
+     * NOTE: Due to Java weirdness, subclass implementations of this method will be called by the CsvResultWriter
+     * constructor at a time when fields of the subclass remain initialized, but uninitialized final primitive
+     * fields are still readable! Do not read subclass fields in these implementations until/unless this is restructured.
+     */
     protected abstract String[] columnHeaders ();
 
     /** Override to extract row values from a single origin result. */

src/main/java/com/conveyal/analysis/results/MultiOriginAssembler.java

@@ -7,6 +7,8 @@
 import com.conveyal.file.FileStorage;
 import com.conveyal.file.FileStorageFormat;
 import com.conveyal.r5.analyst.PointSet;
+import com.conveyal.r5.analyst.cluster.PathResult;
+import com.conveyal.r5.analyst.cluster.RegionalTask;
 import com.conveyal.r5.analyst.cluster.RegionalWorkResult;
 import com.conveyal.r5.util.ExceptionUtils;
 import org.slf4j.Logger;
@@ -89,21 +91,27 @@ public MultiOriginAssembler (RegionalAnalysis regionalAnalysis, Job job, FileSto
             this.job = job;
             this.nOriginsTotal = job.nTasksTotal;
             this.originsReceived = new BitSet(job.nTasksTotal);
-            // Check that origin and destination sets are not too big for generating CSV files.
-            if (!job.templateTask.makeTauiSite &&
-                 job.templateTask.destinationPointSetKeys[0].endsWith(FileStorageFormat.FREEFORM.extension)
-            ) {
-               // This requires us to have already loaded this destination pointset instance into the transient field.
-                PointSet destinationPointSet = job.templateTask.destinationPointSets[0];
-                if ((job.templateTask.recordTimes || job.templateTask.includePathResults) && !job.templateTask.oneToOne) {
-                    if (nOriginsTotal * destinationPointSet.featureCount() > MAX_FREEFORM_OD_PAIRS ||
-                        destinationPointSet.featureCount() > MAX_FREEFORM_DESTINATIONS
-                    ) {
-                        throw new AnalysisServerException(String.format(
-                            "Freeform requests limited to %d destinations and %d origin-destination pairs.",
-                            MAX_FREEFORM_DESTINATIONS, MAX_FREEFORM_OD_PAIRS
-                        ));
-                    }
+            // If results have been requested for freeform origins, check that the origin and
+            // destination pointsets are not too big for generating CSV files.
+            RegionalTask task = job.templateTask;
+            if (!task.makeTauiSite && task.destinationPointSetKeys[0].endsWith(FileStorageFormat.FREEFORM.extension)) {
+                // This requires us to have already loaded this destination pointset instance into the transient field.
+                PointSet destinationPointSet = task.destinationPointSets[0];
+                int nDestinations = destinationPointSet.featureCount();
+                int nODPairs = task.oneToOne ? nOriginsTotal : nOriginsTotal * nDestinations;
+                if (task.recordTimes &&
+                    (nDestinations > MAX_FREEFORM_DESTINATIONS || nODPairs > MAX_FREEFORM_OD_PAIRS)) {
+                    throw AnalysisServerException.badRequest(String.format(
+                       "Travel time results limited to %d destinations and %d origin-destination pairs.",
+                       MAX_FREEFORM_DESTINATIONS, MAX_FREEFORM_OD_PAIRS
+                    ));
+                }
+                if (task.includePathResults &&
+                    (nDestinations > PathResult.MAX_PATH_DESTINATIONS || nODPairs > MAX_FREEFORM_OD_PAIRS)) {
+                    throw AnalysisServerException.badRequest(String.format(
+                        "Path results limited to %d destinations and %d origin-destination pairs.",
+                        PathResult.MAX_PATH_DESTINATIONS, MAX_FREEFORM_OD_PAIRS
+                    ));
                 }
             }
 
@@ -152,8 +160,11 @@ public MultiOriginAssembler (RegionalAnalysis regionalAnalysis, Job job, FileSto
                     regionalAnalysis.resultStorage.put(csvWriter.resultType(), csvWriter.fileName);
                 }
             }
+        } catch (AnalysisServerException e) {
+            throw e;
         } catch (Exception e) {
-            throw new RuntimeException("Exception while creating multi-origin assembler: " + ExceptionUtils.stackTraceString(e));
+            // Handle any obscure problems we don't want end users to see without context of MultiOriginAssembler.
+            throw new RuntimeException("Exception while creating multi-origin assembler: " + e.toString(), e);
         }
     }
 

src/main/java/com/conveyal/data/census/TigerLineSource.java

@@ -34,7 +34,7 @@ public void load (ShapeDataStore store) throws Exception {
         for (SimpleFeatureIterator it = sfc.features(); it.hasNext();) {
             GeobufFeature feat = new GeobufFeature(it.next());
             feat.id = null;
-            feat.numericId = Long.parseLong((String) feat.properties.get("GEOID10"));
+            feat.numericId = Long.parseLong((String) feat.properties.get("GEOID20"));
             feat.properties = new HashMap<>();
             store.add(feat);
         }

src/main/java/com/conveyal/r5/analyst/TemporalDensityResult.java

@@ -33,7 +33,8 @@ public class TemporalDensityResult {
 
     /**
      * The temporal density of opportunities. For each destination set, for each percentile, for each minute of
-     * travel from 0 to 120, the number of opportunities reached in travel times from i (inclusive) to i+1 (exclusive).
+     * travel m from 0 to 119, the number of opportunities reached in travel times from m (inclusive) to m+1
+     * (exclusive).
      */
     public final double[][][] opportunitiesPerMinute;
 
@@ -57,7 +58,7 @@ public void recordOneTarget (int target, int[] travelTimePercentilesSeconds) {
                     break; // If any percentile is unreached, all higher ones are also unreached.
                 }
                 int m = travelTimePercentilesSeconds[p] / 60;
-                if (m <= 120) {
+                if (m < 120) {
                     opportunitiesPerMinute[d][p][m] += dps.getOpportunityCount(target);
                 }
             }