Improvements based on @michelleblom's review.

server/eclipse-project/src/main/java/au/org/democracydevelopers/corla/endpoint/AbstractAllIrvEndpoint.java

@@ -101,9 +101,9 @@ protected void reset() {
      * to the IRV ones. Although the countContest function isn't really useful or meaningful for IRV,
      * it is called here because it actually does a lot of other useful things, such as setting the
      * number of allowed winners and gathering all the results across counties.
+     * Assumption: Contest names are unique.
      * @return A list of all ContestResults for IRV contests.
      * @throws RuntimeException if it encounters contests with a mix of IRV and any other contest type.
-     * Assumption: Contest names are unique.
      */
     protected static List<ContestResult> getIRVContestResults() {
         final String prefix = "[getIRVContestResults]";

server/eclipse-project/src/main/java/au/org/democracydevelopers/corla/endpoint/EstimateSampleSizes.java

@@ -128,6 +128,9 @@ public String endpointBody(final Request the_request, final Response the_respons
 
   /**
    * Compute sample sizes for all contests for which CountyContestResults exist in the database.
+   * This method ignores manifests, instead using the count of uploaded CSVs. This means that the
+   * estimate may differ from the estimate computed by estimatedSampleSize() during the audit, if
+   * the manifest has more votes than the CVR file.
    * @return A list of string arrays containing rows with the following data: county name,
    * contest name, contest type, single or multi-jurisdictional, ballots cast, diluted margin,
    * and estimated sample size.
@@ -143,6 +146,7 @@ public String estimateSampleSizes() {
     // in a ContestResult for an IRV contest will not be used. In the call to ContestCounter
     // (countAllContests), all persisted CountyContestResults will be accessed from the database,
     // grouped by contest, and accumulated into a single ContestResult.
+    // Set the useManifests flag to false, to tell contest counter to use CVR count instead.
     final List<ContestResult> countedCRs = ContestCounter.countAllContests(false).stream().peek(cr ->
         cr.setAuditReason(AuditReason.OPPORTUNISTIC_BENEFITS)).toList();
 

server/eclipse-project/src/main/java/us/freeandfair/corla/controller/ContestCounter.java

@@ -30,10 +30,14 @@ private ContestCounter() {
   /**
    * Group all CountyContestResults by contest name and tally the votes
    * across all counties that have reported results.
-   * This only works for plurality - not valid, and not needed, for IRV.
-   *
-   * @return List<ContestResult> A high level view of contests and their
-   * participants.
+   * If 'useManifests' is true, it calculates the total universe size from the uploaded manifests -
+   * this is important for the validity of the audit step. useManifests can be false for sample-size
+   * estimation, where we expect that counties may not have uploaded valid manifests - in this case,
+   * universe size is calculated by counting the CVRs.
+   * The actual tallying is valid only for plurality - it is not valid, and not needed, for IRV.
+   * However, this function may still be useful for IRV, e.g. for gathering contests together by
+   * name and calculating their universes.
+   * @return List<ContestResult> A high level view of contests and their participants.
    */
   public static List<ContestResult> countAllContests(boolean useManifests) {
     return
@@ -82,8 +86,8 @@ public static Set<Integer> pairwiseMargins(final Set<String> winners,
    * @param countyContestResults the county-by-county contest results, which are useful for plurality.
    * @param useManifests         whether to use manifests to compute the total number of ballots. This
    *                             *must* be true when counting for audits - it can be false only when
-   *                             doing sample size estimation. In this case, it computes the total number
-   *                             of ballots based on the (untrusted) CVRs.
+   *                             doing pre-audit sample size estimation. In this case, it computes
+   *                             the total number of ballots based on the (untrusted) CVRs.
    **/
   public static ContestResult countContest(final Map.Entry<String, List<CountyContestResult>> countyContestResults,
                                                                            boolean useManifests) {
@@ -125,12 +129,13 @@ public static ContestResult countContest(final Map.Entry<String, List<CountyCont
                               .map(cr -> cr.county())
                               .collect(Collectors.toSet()));
 
-    Long ballotCount;
-    if(useManifests) {
-      ballotCount = BallotManifestInfoQueries.totalBallots(contestResult.countyIDs());
-    } else {
-      ballotCount = countCVRs(contestResult);
-    }
+    // If we are supposed to use manifests, set the ballotCount to their indicated total, otherwise
+    // count the CVRs.
+    final Long ballotCount = useManifests ?
+      BallotManifestInfoQueries.totalBallots(contestResult.countyIDs()) : countCVRs(contestResult);
+    LOGGER.debug(String.format("%s Contest %s counted %s manifests.", "[countContest]", contestName,
+        useManifests ? "with" : "without"));
+
     final Set<Integer> margins = pairwiseMargins(contestResult.getWinners(),
                                                   contestResult.getLosers(),
                                                   voteTotals);
@@ -154,12 +159,14 @@ public static ContestResult countContest(final Map.Entry<String, List<CountyCont
   }
 
   /**
-   * Calculate the size of the audit universe by counting CVRs. This is the total number
-   * of CVRs in all counties that have any votes in the contest. Used for sample-size estimation.
+   * Calculate the size of the audit universe for a given contest by counting CVRs. This is the
+   * total, over all counties that have any votes in the contest, of the total number of CVRs in the
+   * county. Used for preliminary sample-size estimation before the audit.
    * For example, if a county had 10,000 CVRs, of which only 500 contained the contest, it would
    * contribute 10,000 to the total.
-   * Note this should *not* be used for auditing, only for sample-size estimation - the audit
-   * calculation should get this value from the manifests, not the CVRs.
+   * Note this should *not* be used during auditing, only for preliminary sample-size estimation in
+   * advance of the audit. During auditing, the sample-size estimate calculation should get this
+   * value from the manifests, not the CVRs.
    * @param contestResult the contestResult for this contest.
    * @return the sum, over all counties that contain the contest, of the total number of CVRs in
    *         that county. This will be 0 if either the contestResult has no counties, or the counties

server/eclipse-project/src/main/java/us/freeandfair/corla/endpoint/StartAuditRound.java

@@ -256,6 +256,7 @@ public List<ContestResult> countAndSaveContests(final Set<ContestToAudit> cta) {
     LOGGER.debug(String.format("[countAndSaveContests: cta=%s]", cta));
     final Map<String, AuditReason> tcr = targetedContestReasons(cta);
 
+    // Count the contests, using the trusted Manifests to get the universe sizes.
     return ContestCounter.countAllContests(true).stream().map(cr -> {
       cr.setAuditReason(tcr.getOrDefault(cr.getContestName(),
                                          AuditReason.OPPORTUNISTIC_BENEFITS));

server/eclipse-project/src/test/java/au/org/democracydevelopers/corla/controller/ComparisonAuditControllerTests.java

@@ -99,7 +99,8 @@ public static void afterAll() {
   public void IRVContestMakesIRVAudit() {
     testUtils.log(LOGGER, "IRVContestMakesIRVAudit");
 
-    // Set up the contest results from the stored data.
+    // Set up the contest results from the stored data. Use manifests for this test (though it
+    // shouldn't matter because for this sample data, the manifests and CVRs have the same totals).
     List<ContestResult> results = ContestCounter.countAllContests(true);
 
     // Find all the ContestResults for TinyIRV - there should be one.

server/eclipse-project/src/test/java/au/org/democracydevelopers/corla/workflows/Workflow.java

@@ -122,15 +122,15 @@ public void setup() {
    * @param testFileName the name of the test file - must be different for each test.
    */
   protected static void runMain(final String testFileName) {
-    final String propertiesFile = tempConfigPath +testFileName+"-test.properties";
+    final String propertiesFile = tempConfigPath + testFileName + "-test.properties";
     try {
       FileOutputStream os = new FileOutputStream(propertiesFile);
       final StringWriter sw = new StringWriter();
-      config.store(sw, "Ephemeral database config for Demo1");
+      config.store(sw, "Ephemeral database config for "+testFileName);
       os.write(sw.toString().getBytes());
       os.close();
     } catch (Exception e) {
-      LOGGER.error("Couldn't write Demo1-test.properties. "+e.getMessage(), e);
+      LOGGER.error("Couldn't write " + testFileName + "-test.properties. "+e.getMessage(), e);
     }
     main(propertiesFile);
   }

server/eclipse-project/src/test/workflows/temp/Demo1-test.properties

@@ -1 +1,11 @@
-#Placeholder database config for Demo1
+#Ephemeral database config for Demo1
+#Fri Nov 15 15:26:53 AEDT 2024
+raire_url=http\://localhost\:8080
+generate_assertions_mock_port=8110
+hibernate.driver=org.postgresql.Driver
+hibernate.pass=corlasecret
+hibernate.dialect=org.hibernate.dialect.PostgreSQL9Dialect
+get_assertions_mock_port=8111
+hibernate.show_sql=false
+hibernate.user=corlaadmin
+hibernate.url=jdbc\:postgresql\://localhost\:32774/corla?loggerLevel\=OFF