Removed .close() call from container-managed entity manager

gradle.properties

@@ -1,3 +1,3 @@
-jpacrepo.version=2023.07
+jpacrepo.version=2023.10.04
 
-lys.version=2023.07.28
+lys.version=2023.10.01

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,7 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.2.1-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.3-bin.zip
+networkTimeout=10000
+validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

gradlew

@@ -55,7 +55,7 @@
 #       Darwin, MinGW, and NonStop.
 #
 #   (3) This script is generated from the Groovy template
-#       https://github.com/gradle/gradle/blob/master/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
+#       https://github.com/gradle/gradle/blob/HEAD/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
 #       within the Gradle project.
 #
 #       You can find Gradle at https://github.com/gradle/gradle/.
@@ -80,13 +80,10 @@ do
     esac
 done
 
-APP_HOME=$( cd "${APP_HOME:-./}" && pwd -P ) || exit
+# This is normally unused
-
+# shellcheck disable=SC2034
-APP_NAME="Gradle"
 APP_BASE_NAME=${0##*/}
-
+APP_HOME=$( cd "${APP_HOME:-./}" && pwd -P ) || exit
-# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
 
 # Use the maximum available, or set MAX_FD != -1 to use that value.
 MAX_FD=maximum
@@ -133,22 +130,29 @@ location of your Java installation."
     fi
 else
     JAVACMD=java
-    which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+    if ! command -v java >/dev/null 2>&1
+    then
+        die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
 
 Please set the JAVA_HOME variable in your environment to match the
 location of your Java installation."
+    fi
 fi
 
 # Increase the maximum file descriptors if we can.
 if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then
     case $MAX_FD in #(
       max*)
+        # In POSIX sh, ulimit -H is undefined. That's why the result is checked to see if it worked.
+        # shellcheck disable=SC3045
         MAX_FD=$( ulimit -H -n ) ||
             warn "Could not query maximum file descriptor limit"
     esac
     case $MAX_FD in  #(
       '' | soft) :;; #(
       *)
+        # In POSIX sh, ulimit -n is undefined. That's why the result is checked to see if it worked.
+        # shellcheck disable=SC3045
         ulimit -n "$MAX_FD" ||
             warn "Could not set maximum file descriptor limit to $MAX_FD"
     esac
@@ -193,6 +197,10 @@ if "$cygwin" || "$msys" ; then
     done
 fi
 
+
+# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
+
 # Collect all arguments for the java command;
 #   * $DEFAULT_JVM_OPTS, $JAVA_OPTS, and $GRADLE_OPTS can contain fragments of
 #     shell script including quotes and variable substitutions, so put them in

gradlew.bat

@@ -26,6 +26,7 @@ if "%OS%"=="Windows_NT" setlocal
 
 set DIRNAME=%~dp0
 if "%DIRNAME%"=="" set DIRNAME=.
+@rem This is normally unused
 set APP_BASE_NAME=%~n0
 set APP_HOME=%DIRNAME%
 

src/main/java/net/woggioni/jpacrepo/service/PacmanServiceEJB.java

@@ -96,74 +96,70 @@ public class PacmanServiceEJB implements PacmanServiceLocal {
     @TransactionAttribute(TransactionAttributeType.REQUIRED)
     @Schedule(hour = "4", minute = "00", persistent = false)
     public void syncDB() {
-        try {
+        logger.info("Starting repository cleanup");
-            logger.info("Starting repository cleanup");
+        //Removes from DB the packages that have been deleted from filesystem
-            //Removes from DB the packages that have been deleted from filesystem
+        logger.info("Searching for packages that are no more in the filesystem");
-            logger.info("Searching for packages that are no more in the filesystem");
+        List<String> resultList = Queries.listAllPackageFiles(em)
-            List<String> resultList = Queries.listAllPackageFiles(em)
+                .getResultList();
-                    .getResultList();
+        logger.info("Got list of filenames from db");
-            logger.info("Got list of filenames from db");
+        Set<String> knownPkg = resultList.stream().filter(fileName -> {
-            Set<String> knownPkg = resultList.stream().filter(fileName -> {
+            Path file = ctx.getFile(fileName);
-                Path file = ctx.getFile(fileName);
+            boolean result = Files.exists(file);
-                boolean result = Files.exists(file);
+            if (!result) {
-                if (!result) {
+                logger.info("Removing package {} which was not found in filesystem", file.getFileName());
-                    logger.info("Removing package {} which was not found in filesystem", file.getFileName());
+                Queries.getPackageByFileName(em, file.getFileName().toString())
-                    Queries.getPackageByFileName(em, file.getFileName().toString())
+                        .getResultList()
-                            .getResultList()
+                        .forEach(pkgData -> deletePkgData(em, pkgData));
-                            .forEach(pkgData -> deletePkgData(em, pkgData));
+            }
-                }
+            return result;
-                return result;
+        }).collect(Collectors.toUnmodifiableSet());
-            }).collect(Collectors.toUnmodifiableSet());
+        logger.info("Searching for new packages or packages that were modified after being added to the database");
-            logger.info("Searching for new packages or packages that were modified after being added to the database");
+        CompletionService<PkgData> completionService = new ExecutorCompletionService<>(executor);
-            CompletionService<PkgData> completionService = new ExecutorCompletionService<>(executor);
+        final Set<Future<PkgData>> inProgress = new HashSet<>();
-            final Set<Future<PkgData>> inProgress = new HashSet<>();
+        final int maxInProgress = Runtime.getRuntime().availableProcessors() * 5;
-            final int maxInProgress = Runtime.getRuntime().availableProcessors() * 5;
+        Sup<Stream<Path>> fileListStreamSupplier = () -> Files.list(ctx.getRepoFolder()).filter((Path file) -> {
-            Sup<Stream<Path>> fileListStreamSupplier = () -> Files.list(ctx.getRepoFolder()).filter((Path file) -> {
+            String name = file.getFileName().toString();
-                String name = file.getFileName().toString();
+            return name.endsWith(".pkg.tar.xz") || name.endsWith(".pkg.tar.zst") || name.endsWith(".pkg.tar.gz");
-                return name.endsWith(".pkg.tar.xz") || name.endsWith(".pkg.tar.zst") || name.endsWith(".pkg.tar.gz");
+        });
-            });
+        long[] count = new long[]{0};
-            long[] count = new long[] {0};
+        long totalPackages = fileListStreamSupplier.get().count();
-            long totalPackages = fileListStreamSupplier.get().count();
 
-            Con<Boolean> persistPackages = (Boolean drain) -> {
+        Con<Boolean> persistPackages = (Boolean drain) -> {
-                while ((drain && inProgress.size() > 0) || inProgress.size() > maxInProgress) {
+            while ((drain && inProgress.size() > 0) || inProgress.size() > maxInProgress) {
-                    Optional.ofNullable(completionService.poll(1, TimeUnit.SECONDS))
+                Optional.ofNullable(completionService.poll(1, TimeUnit.SECONDS))
-                            .ifPresent((Con<Future<PkgData>>) future -> {
+                        .ifPresent((Con<Future<PkgData>>) future -> {
-                        inProgress.remove(future);
+                            inProgress.remove(future);
-                        PkgData pkgData;
+                            PkgData pkgData;
-                        try {
+                            try {
-                            pkgData = future.get();
+                                pkgData = future.get();
-                        } catch (ExecutionException ee) {
+                            } catch (ExecutionException ee) {
-                            throw ee.getCause();
+                                throw ee.getCause();
-                        }
+                            }
-                        persistPackage(em, pkgData, ++count[0], totalPackages);
+                            persistPackage(em, pkgData, ++count[0], totalPackages);
-                    });
+                        });
-                }
+            }
-            };
+        };
-            fileListStreamSupplier.get().forEach((Con<Path>) file -> {
+        fileListStreamSupplier.get().forEach((Con<Path>) file -> {
-                if (!knownPkg.contains(file.getFileName().toString()) || ((Sup<Boolean>) () -> {
+            if (!knownPkg.contains(file.getFileName().toString()) || ((Sup<Boolean>) () -> {
-                    Instant result = Queries.getUpdateTimestampByFileName(em, file.getFileName().toString()).getSingleResult();
+                Instant result = Queries.getUpdateTimestampByFileName(em, file.getFileName().toString()).getSingleResult();
-                    return Files.getLastModifiedTime(file).toMillis() > result.toEpochMilli();
+                return Files.getLastModifiedTime(file).toMillis() > result.toEpochMilli();
-                }).get()) {
+            }).get()) {
-                    inProgress.add(completionService.submit(() -> {
+                inProgress.add(completionService.submit(() -> {
-                        try {
+                    try {
-                            return PkgDataImpl.parseFile(file, CompressionFormatImpl.guess(file));
+                        return PkgDataImpl.parseFile(file, CompressionFormatImpl.guess(file));
-                        } catch (Exception ex) {
+                    } catch (Exception ex) {
-                            logger.error(String.format("Error parsing '%s'", file.toAbsolutePath()), ex);
+                        logger.error(String.format("Error parsing '%s'", file.toAbsolutePath()), ex);
-                            throw ex;
+                        throw ex;
-                        }
+                    }
-                    }));
+                }));
-                }
+            }
-                persistPackages.accept(false);
+            persistPackages.accept(false);
-            });
+        });
-            persistPackages.accept(true);
+        persistPackages.accept(true);
-            logger.info("Removing obsolete packages");
+        logger.info("Removing obsolete packages");
-            deleteOld(em);
+        deleteOld(em);
-            logger.info("Repository cleanup completed successfully");
+        logger.info("Repository cleanup completed successfully");
-            packageCache.invalidateCache();
+        packageCache.invalidateCache();
-        } finally {
-            em.close();
-        }
     }
 
     private void persistPackage(EntityManager em, PkgData pkgData, long count, long totalPackages) {
@@ -194,6 +190,7 @@ public class PacmanServiceEJB implements PacmanServiceLocal {
         em.remove(pkg);
         Files.delete(ctx.getFile(pkg));
     }
+
     private void deleteOld(EntityManager em) {
         Instant cutoff = Instant.now().minus(365 * 3, ChronoUnit.DAYS);
         Queries.getOldPackages2Delete(em, cutoff, 3L)
@@ -266,7 +263,7 @@ public class PacmanServiceEJB implements PacmanServiceLocal {
     public Set<String> missingFiles(Collection<String> fileNames) {
         Stream<String> result = fileNames.stream();
         Set<String> existing = Queries.getExistingFiles(em, fileNames)
-            .getResultStream().collect(CollectionUtils.toUnmodifiableTreeSet());
+                .getResultStream().collect(CollectionUtils.toUnmodifiableTreeSet());
         return result.filter(JWO.not(existing::contains))
                 .collect(CollectionUtils.toUnmodifiableTreeSet());
     }
@@ -281,18 +278,19 @@ public class PacmanServiceEJB implements PacmanServiceLocal {
             PkgId pkgId = tuple.get(0, PkgId.class);
             String filename = tuple.get(1, String.class);
             long size = tuple.get(2, Long.class);
-            String md5sum = tuple.get(3, String.class);;
+            String md5sum = tuple.get(3, String.class);
+            ;
             PkgTuple pkgTuple = new PkgTuple();
             pkgTuple.setFileName(filename);
             pkgTuple.setSize(size);
             pkgTuple.setMd5sum(md5sum);
             return Tuple2.newInstance(pkgId, pkgTuple);
         }).collect(
-            CollectionUtils.toUnmodifiableTreeMap(
+                CollectionUtils.toUnmodifiableTreeMap(
-                Tuple2<PkgId, PkgTuple>::get_1,
+                        Tuple2<PkgId, PkgTuple>::get_1,
-                Tuple2<PkgId, PkgTuple>::get_2,
+                        Tuple2<PkgId, PkgTuple>::get_2,
-                PkgIdComparator.getComparator()
+                        PkgIdComparator.getComparator()
-            )
+                )
         );
     }
 
@@ -308,12 +306,12 @@ public class PacmanServiceEJB implements PacmanServiceLocal {
         List<PkgData> savedFiles = searchByFileName(fileName);
         if (savedFiles.size() > 0) return false;
         else {
-            try(OutputStream output = Files.newOutputStream(file)) {
+            try (OutputStream output = Files.newOutputStream(file)) {
                 JWO.copy(input, output, 0x10000);
                 PkgData pkg = PkgDataImpl.parseFile(file,
-                    CompressionFormatImpl.guess(Paths.get(fileName)));
+                        CompressionFormatImpl.guess(Paths.get(fileName)));
                 pkg.setFileName(fileName);
-                Optional.ofNullable(em.find(PkgData.class, pkg.getId())).ifPresent((Con<PkgData>) (pkgData ->  {
+                Optional.ofNullable(em.find(PkgData.class, pkg.getId())).ifPresent((Con<PkgData>) (pkgData -> {
                     em.remove(pkgData);
                     Files.delete(ctx.getRepoFolder().resolve(pkgData.getFileName()));
                 }));
@@ -324,7 +322,7 @@ public class PacmanServiceEJB implements PacmanServiceLocal {
                 return true;
             } catch (Throwable t) {
                 Files.delete(file);
-                throw  t;
+                throw t;
             }
         }
     }