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Posted to commits@baremaps.apache.org by "bchapuis (via GitHub)" <gi...@apache.org> on 2023/11/13 13:58:01 UTC

[PR] Workflow [incubator-baremaps]

bchapuis opened a new pull request, #802:
URL: https://github.com/apache/incubator-baremaps/pull/802

   (no comment)


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Re: [PR] Improve workflow package [incubator-baremaps]

Posted by "github-advanced-security[bot] (via GitHub)" <gi...@apache.org>.
github-advanced-security[bot] commented on code in PR #802:
URL: https://github.com/apache/incubator-baremaps/pull/802#discussion_r1391283419


##########
baremaps-core/src/main/java/org/apache/baremaps/workflow/tasks/DecompressFile.java:
##########
@@ -94,13 +203,20 @@
     }
   }
 
-  public static void decompressTarBz2(Path sourcePath, Path targetPath) throws IOException {
-    try (var bufferedInputStream = new BufferedInputStream(Files.newInputStream(sourcePath));
+  /**
+   * Decompresses a tar.bz2 file.
+   * 
+   * @param source the source file
+   * @param target the target file
+   * @throws IOException if an I/O error occurs
+   */
+  protected static void decompressTarBz2(Path source, Path target) throws IOException {
+    try (var bufferedInputStream = new BufferedInputStream(Files.newInputStream(source));
         var bzip2InputStream = new BZip2CompressorInputStream(bufferedInputStream);
         var tarInputStream = new TarArchiveInputStream(bzip2InputStream)) {
       TarArchiveEntry entry;
       while ((entry = (TarArchiveEntry) tarInputStream.getNextEntry()) != null) {
-        var path = targetPath.resolve(entry.getName());
+        var path = target.resolve(entry.getName());

Review Comment:
   ## Arbitrary file access during archive extraction ("Zip Slip")
   
   Unsanitized archive entry, which may contain '..', is used in a [file system operation](1).
   Unsanitized archive entry, which may contain '..', is used in a [file system operation](2).
   Unsanitized archive entry, which may contain '..', is used in a [file system operation](3).
   
   [Show more details](https://github.com/apache/incubator-baremaps/security/code-scanning/837)



##########
baremaps-core/src/main/java/org/apache/baremaps/workflow/tasks/DecompressFile.java:
##########
@@ -57,26 +145,47 @@
     }
   }
 
-  public static void decompressBzip2(Path sourcePath, Path targetPath) throws IOException {
-    try (var bufferedInputStream = new BufferedInputStream(Files.newInputStream(sourcePath));
+  /**
+   * Decompresses a bzip2 file.
+   * 
+   * @param source the source file
+   * @param target the target file
+   * @throws IOException if an I/O error occurs
+   */
+  protected static void decompressBzip2(Path source, Path target) throws IOException {
+    try (var bufferedInputStream = new BufferedInputStream(Files.newInputStream(source));
         var bzip2InputStream = new BZip2CompressorInputStream(bufferedInputStream)) {
-      Files.copy(bzip2InputStream, targetPath, StandardCopyOption.REPLACE_EXISTING);
+      Files.copy(bzip2InputStream, target, StandardCopyOption.REPLACE_EXISTING);
     }
   }
 
-  public static void decompressGzip(Path sourcePath, Path targetPath) throws IOException {
-    try (var zis = new GZIPInputStream(new BufferedInputStream(Files.newInputStream(sourcePath)))) {
-      Files.copy(zis, targetPath, StandardCopyOption.REPLACE_EXISTING);
+  /**
+   * Decompresses a gzip file.
+   * 
+   * @param source the source file
+   * @param target the target file
+   * @throws IOException if an I/O error occurs
+   */
+  protected static void decompressGzip(Path source, Path target) throws IOException {
+    try (var zis = new GZIPInputStream(new BufferedInputStream(Files.newInputStream(source)))) {
+      Files.copy(zis, target, StandardCopyOption.REPLACE_EXISTING);
     }
   }
 
-  public static void decompressTarGz(Path sourcePath, Path targetPath) throws IOException {
-    try (var bufferedInputStream = new BufferedInputStream(Files.newInputStream(sourcePath));
+  /**
+   * Decompresses a tar.gz file.
+   * 
+   * @param source the source file
+   * @param target the target file
+   * @throws IOException if an I/O error occurs
+   */
+  protected static void decompressTarGz(Path source, Path target) throws IOException {
+    try (var bufferedInputStream = new BufferedInputStream(Files.newInputStream(source));
         var gzipInputStream = new GZIPInputStream(bufferedInputStream);
         var tarInputStream = new TarArchiveInputStream(gzipInputStream)) {
       TarArchiveEntry entry;
       while ((entry = (TarArchiveEntry) tarInputStream.getNextEntry()) != null) {
-        var path = targetPath.resolve(entry.getName());
+        var path = target.resolve(entry.getName());

Review Comment:
   ## Arbitrary file access during archive extraction ("Zip Slip")
   
   Unsanitized archive entry, which may contain '..', is used in a [file system operation](1).
   Unsanitized archive entry, which may contain '..', is used in a [file system operation](2).
   Unsanitized archive entry, which may contain '..', is used in a [file system operation](3).
   
   [Show more details](https://github.com/apache/incubator-baremaps/security/code-scanning/836)



##########
baremaps-core/src/main/java/org/apache/baremaps/workflow/tasks/DecompressFile.java:
##########
@@ -118,12 +234,19 @@
     }
   }
 
-  public static void decompressZip(Path sourcePath, Path targetPath) throws IOException {
-    try (var zipFile = new ZipFile(sourcePath.toFile())) {
+  /**
+   * Decompresses a zip file.
+   * 
+   * @param source the source file
+   * @param target the target file
+   * @throws IOException if an I/O error occurs
+   */
+  protected static void decompressZip(Path source, Path target) throws IOException {
+    try (var zipFile = new ZipFile(source.toFile())) {
       var entries = zipFile.entries();
       while (entries.hasMoreElements()) {
         var entry = entries.nextElement();
-        var path = targetPath.resolve(entry.getName());
+        var path = target.resolve(entry.getName());

Review Comment:
   ## Arbitrary file access during archive extraction ("Zip Slip")
   
   Unsanitized archive entry, which may contain '..', is used in a [file system operation](1).
   Unsanitized archive entry, which may contain '..', is used in a [file system operation](2).
   Unsanitized archive entry, which may contain '..', is used in a [file system operation](3).
   
   [Show more details](https://github.com/apache/incubator-baremaps/security/code-scanning/838)



##########
baremaps-core/src/main/java/org/apache/baremaps/workflow/tasks/DecompressFile.java:
##########
@@ -57,26 +145,47 @@
     }
   }
 
-  public static void decompressBzip2(Path sourcePath, Path targetPath) throws IOException {
-    try (var bufferedInputStream = new BufferedInputStream(Files.newInputStream(sourcePath));
+  /**
+   * Decompresses a bzip2 file.
+   * 
+   * @param source the source file
+   * @param target the target file
+   * @throws IOException if an I/O error occurs
+   */
+  protected static void decompressBzip2(Path source, Path target) throws IOException {
+    try (var bufferedInputStream = new BufferedInputStream(Files.newInputStream(source));
         var bzip2InputStream = new BZip2CompressorInputStream(bufferedInputStream)) {
-      Files.copy(bzip2InputStream, targetPath, StandardCopyOption.REPLACE_EXISTING);
+      Files.copy(bzip2InputStream, target, StandardCopyOption.REPLACE_EXISTING);
     }
   }
 
-  public static void decompressGzip(Path sourcePath, Path targetPath) throws IOException {
-    try (var zis = new GZIPInputStream(new BufferedInputStream(Files.newInputStream(sourcePath)))) {
-      Files.copy(zis, targetPath, StandardCopyOption.REPLACE_EXISTING);
+  /**
+   * Decompresses a gzip file.
+   * 
+   * @param source the source file
+   * @param target the target file
+   * @throws IOException if an I/O error occurs
+   */
+  protected static void decompressGzip(Path source, Path target) throws IOException {
+    try (var zis = new GZIPInputStream(new BufferedInputStream(Files.newInputStream(source)))) {

Review Comment:
   ## Potential input resource leak
   
   This BufferedInputStream is not always closed on method exit.
   
   [Show more details](https://github.com/apache/incubator-baremaps/security/code-scanning/839)



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Re: [PR] Improve workflow package [incubator-baremaps]

Posted by "sonarcloud[bot] (via GitHub)" <gi...@apache.org>.
sonarcloud[bot] commented on PR #802:
URL: https://github.com/apache/incubator-baremaps/pull/802#issuecomment-1815419933

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Re: [PR] Improve workflow package [incubator-baremaps]

Posted by "sonarcloud[bot] (via GitHub)" <gi...@apache.org>.
sonarcloud[bot] commented on PR #802:
URL: https://github.com/apache/incubator-baremaps/pull/802#issuecomment-1816681402

   SonarCloud Quality Gate failed.&nbsp; &nbsp; [![Quality Gate failed](https://sonarsource.github.io/sonarcloud-github-static-resources/v2/checks/QualityGateBadge/failed-16px.png 'Quality Gate failed')](https://sonarcloud.io/dashboard?id=apache_baremaps&pullRequest=802)
   
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Re: [PR] Improve workflow package [incubator-baremaps]

Posted by "github-advanced-security[bot] (via GitHub)" <gi...@apache.org>.
github-advanced-security[bot] commented on code in PR #802:
URL: https://github.com/apache/incubator-baremaps/pull/802#discussion_r1424102676


##########
baremaps-core/src/main/java/org/apache/baremaps/workflow/WorkflowContext.java:
##########
@@ -41,4 +65,45 @@
     return dataSources.computeIfAbsent(database, PostgresUtils::createDataSourceFromObject);
   }
 
+  public DataMap<Long, Coordinate> getCoordinateMap(Path path) throws IOException {
+    if (Files.size(path) > 1 << 30) {
+      return getMemoryAlignedDataMap("coordinates", new LonLatDataType());
+    } else {
+      return getMonotonicDataMap("coordinates", new LonLatDataType());
+    }
+  }
+
+  public DataMap<Long, List<Long>> getReferenceMap(Path path) throws IOException {

Review Comment:
   ## Useless parameter
   
   The parameter 'path' is never used.
   
   [Show more details](https://github.com/apache/incubator-baremaps/security/code-scanning/852)



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Re: [PR] Improve workflow package [incubator-baremaps]

Posted by "sonarcloud[bot] (via GitHub)" <gi...@apache.org>.
sonarcloud[bot] commented on PR #802:
URL: https://github.com/apache/incubator-baremaps/pull/802#issuecomment-1818006465

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Re: [PR] Improve workflow package [incubator-baremaps]

Posted by "sonarcloud[bot] (via GitHub)" <gi...@apache.org>.
sonarcloud[bot] commented on PR #802:
URL: https://github.com/apache/incubator-baremaps/pull/802#issuecomment-1816392697

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Re: [PR] Improve workflow package [incubator-baremaps]

Posted by "sonarcloud[bot] (via GitHub)" <gi...@apache.org>.
sonarcloud[bot] commented on PR #802:
URL: https://github.com/apache/incubator-baremaps/pull/802#issuecomment-1817701106

   SonarCloud Quality Gate failed.&nbsp; &nbsp; [![Quality Gate failed](https://sonarsource.github.io/sonarcloud-github-static-resources/v2/checks/QualityGateBadge/failed-16px.png 'Quality Gate failed')](https://sonarcloud.io/dashboard?id=apache_baremaps&pullRequest=802)
   
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Re: [PR] Improve workflow package [incubator-baremaps]

Posted by "sonarcloud[bot] (via GitHub)" <gi...@apache.org>.
sonarcloud[bot] commented on PR #802:
URL: https://github.com/apache/incubator-baremaps/pull/802#issuecomment-1852207423

   ## [![Quality Gate Failed](https://sonarsource.github.io/sonarcloud-github-static-resources/v2/checks/QualityGateBadge/qg-failed-20px.png 'Quality Gate Failed')](https://sonarcloud.io/dashboard?id=apache_baremaps&pullRequest=802) **Quality Gate failed**  
   Failed conditions
   
   [1 Security Hotspot](https://sonarcloud.io/project/security_hotspots?id=apache_baremaps&pullRequest=802&resolved=false&inNewCodePeriod=true)  
     
   [See analysis details on SonarCloud](https://sonarcloud.io/dashboard?id=apache_baremaps&pullRequest=802)
   
   


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Re: [PR] Improve workflow package [incubator-baremaps]

Posted by "sonarcloud[bot] (via GitHub)" <gi...@apache.org>.
sonarcloud[bot] commented on PR #802:
URL: https://github.com/apache/incubator-baremaps/pull/802#issuecomment-1808399371

   SonarCloud Quality Gate failed.&nbsp; &nbsp; [![Quality Gate failed](https://sonarsource.github.io/sonarcloud-github-static-resources/v2/checks/QualityGateBadge/failed-16px.png 'Quality Gate failed')](https://sonarcloud.io/dashboard?id=apache_baremaps&pullRequest=802)
   
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Re: [PR] Improve workflow package [incubator-baremaps]

Posted by "sonarcloud[bot] (via GitHub)" <gi...@apache.org>.
sonarcloud[bot] commented on PR #802:
URL: https://github.com/apache/incubator-baremaps/pull/802#issuecomment-1852172313

   ## [![Quality Gate Failed](https://sonarsource.github.io/sonarcloud-github-static-resources/v2/checks/QualityGateBadge/qg-failed-20px.png 'Quality Gate Failed')](https://sonarcloud.io/dashboard?id=apache_baremaps&pullRequest=802) **Quality Gate failed**  
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   [1 Security Hotspot](https://sonarcloud.io/project/security_hotspots?id=apache_baremaps&pullRequest=802&resolved=false&inNewCodePeriod=true)  
     
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Re: [PR] Improve workflow package [incubator-baremaps]

Posted by "sonarcloud[bot] (via GitHub)" <gi...@apache.org>.
sonarcloud[bot] commented on PR #802:
URL: https://github.com/apache/incubator-baremaps/pull/802#issuecomment-1853661259

   ## [![Quality Gate Failed](https://sonarsource.github.io/sonarcloud-github-static-resources/v2/checks/QualityGateBadge/qg-failed-20px.png 'Quality Gate Failed')](https://sonarcloud.io/dashboard?id=apache_baremaps&pullRequest=802) **Quality Gate failed**  
   Failed conditions
   
   [1 Security Hotspot](https://sonarcloud.io/project/security_hotspots?id=apache_baremaps&pullRequest=802&resolved=false&inNewCodePeriod=true)  
     
   [See analysis details on SonarCloud](https://sonarcloud.io/dashboard?id=apache_baremaps&pullRequest=802)
   
   


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Re: [PR] Improve workflow package [incubator-baremaps]

Posted by "bchapuis (via GitHub)" <gi...@apache.org>.
bchapuis merged PR #802:
URL: https://github.com/apache/incubator-baremaps/pull/802


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Re: [PR] Improve workflow package [incubator-baremaps]

Posted by "sonarcloud[bot] (via GitHub)" <gi...@apache.org>.
sonarcloud[bot] commented on PR #802:
URL: https://github.com/apache/incubator-baremaps/pull/802#issuecomment-1853401494

   ## [![Quality Gate Failed](https://sonarsource.github.io/sonarcloud-github-static-resources/v2/checks/QualityGateBadge/qg-failed-20px.png 'Quality Gate Failed')](https://sonarcloud.io/dashboard?id=apache_baremaps&pullRequest=802) **Quality Gate failed**  
   Failed conditions
   
   [1 Security Hotspot](https://sonarcloud.io/project/security_hotspots?id=apache_baremaps&pullRequest=802&resolved=false&inNewCodePeriod=true)  
     
   [See analysis details on SonarCloud](https://sonarcloud.io/dashboard?id=apache_baremaps&pullRequest=802)
   
   


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Re: [PR] Improve workflow package [incubator-baremaps]

Posted by "github-advanced-security[bot] (via GitHub)" <gi...@apache.org>.
github-advanced-security[bot] commented on code in PR #802:
URL: https://github.com/apache/incubator-baremaps/pull/802#discussion_r1398293238


##########
baremaps-core/src/main/java/org/apache/baremaps/workflow/WorkflowContext.java:
##########
@@ -41,4 +67,54 @@
     return dataSources.computeIfAbsent(database, PostgresUtils::createDataSourceFromObject);
   }
 
+  public DataMap<Long, Coordinate> getCoordinateMap(Path path) throws IOException {
+    if (Files.size(path) > 1 << 30) {
+      return getAlignedCoordinateMap();
+    } else {
+      return getMonotonicCoordinateMap();
+    }
+  }
+
+  public DataMap<Long, Coordinate> getAlignedCoordinateMap() throws IOException {
+    var coordinateDir = Files.createDirectories(cacheDir.resolve("coordinates"));
+    return new MemoryAlignedDataMap<>(
+        new LonLatDataType(),
+        new MemoryMappedDirectory(coordinateDir));
+  }
+
+  public DataMap<Long, Coordinate> getMonotonicCoordinateMap() throws IOException {
+    var coordinateKeysDir = Files.createDirectories(cacheDir.resolve("coordinate_keys"));
+    var coordinateValuesDir = Files.createDirectories(cacheDir.resolve("coordinate_values"));
+    return new MonotonicDataMap<>(
+        new MemoryAlignedDataList<>(
+            new PairDataType<>(new LongDataType(), new LongDataType()),
+            new MemoryMappedDirectory(coordinateKeysDir)),
+        new AppendOnlyBuffer<>(
+            new LonLatDataType(),
+            new MemoryMappedDirectory(coordinateValuesDir)));
+  }
+
+  public DataMap<Long, List<Long>> getReferenceMap(Path path) throws IOException {

Review Comment:
   ## Useless parameter
   
   The parameter 'path' is never used.
   
   [Show more details](https://github.com/apache/incubator-baremaps/security/code-scanning/844)



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Re: [PR] Improve workflow package [incubator-baremaps]

Posted by "sonarcloud[bot] (via GitHub)" <gi...@apache.org>.
sonarcloud[bot] commented on PR #802:
URL: https://github.com/apache/incubator-baremaps/pull/802#issuecomment-1816703066

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Re: [PR] Improve workflow package [incubator-baremaps]

Posted by "sonarcloud[bot] (via GitHub)" <gi...@apache.org>.
sonarcloud[bot] commented on PR #802:
URL: https://github.com/apache/incubator-baremaps/pull/802#issuecomment-1808216077

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Re: [PR] Improve workflow package [incubator-baremaps]

Posted by "sonarcloud[bot] (via GitHub)" <gi...@apache.org>.
sonarcloud[bot] commented on PR #802:
URL: https://github.com/apache/incubator-baremaps/pull/802#issuecomment-1815339923

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Re: [PR] Improve workflow package [incubator-baremaps]

Posted by "sonarcloud[bot] (via GitHub)" <gi...@apache.org>.
sonarcloud[bot] commented on PR #802:
URL: https://github.com/apache/incubator-baremaps/pull/802#issuecomment-1816675574

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