Added fix for File.toURI regression

Base/src/main/java/io/deephaven/base/FileUtils.java

@@ -8,6 +8,9 @@
 import org.jetbrains.annotations.Nullable;
 
 import java.io.*;
+import java.net.URI;
+import java.net.URISyntaxException;
+import java.nio.file.Path;
 import java.util.ArrayList;
 
 public class FileUtils {
@@ -249,4 +252,72 @@ public boolean accept(File pathname) {
                     || (pathname.isFile() && (normalFileFilter == null || normalFileFilter.accept(pathname)));
         }
     }
+
+    /**
+     * Take the file source path or URI string and convert it to a URI object.
+     *
+     * @param source The file source path or URI
+     * @param isDirectory Whether the source is a directory
+     * @return The URI object
+     */
+    public static URI convertToURI(final String source, final boolean isDirectory) {
+        if (source.isEmpty()) {
+            throw new IllegalArgumentException("Cannot convert empty source to URI");
+        }
+        final URI uri;
+        try {
+            uri = new URI(source);
+        } catch (final URISyntaxException e) {
+            // If the URI is invalid, assume it's a file path
+            return convertToURI(new File(source), isDirectory);
+        }
+        if (uri.getScheme() == null) {
+            // Convert to a "file" URI
+            return convertToURI(new File(source), isDirectory);
+        }
+        return uri;
+    }
+
+    /**
+     * Takes a file and convert it to a URI object with {@code "file"} scheme. This method is preferred instead of
+     * {@link File#toURI()} because {@link File#toURI()} internally calls {@link File#isDirectory()}, which typically
+     * invokes the {@code stat} system call, resulting in filesystem metadata access.
+     *
+     * @param file The file
+     * @param isDirectory Whether the source file is a directory
+     * @return The URI object
+     */
+    public static URI convertToURI(final File file, final boolean isDirectory) {
+        String absPath = file.getAbsolutePath();
+        if (File.separatorChar != '/') {
+            absPath = absPath.replace(File.separatorChar, '/');
+        }
+        if (absPath.charAt(0) != '/') {
+            absPath = "/" + absPath;
+        }
+        if (isDirectory && absPath.charAt(absPath.length() - 1) != '/') {
+            absPath = absPath + "/";
+        }
+        if (absPath.startsWith("//")) {
+            absPath = "//" + absPath;
+        }
+        try {
+            return new URI("file", null, absPath, null);
+        } catch (final URISyntaxException e) {
+            throw new IllegalStateException("Failed to convert file to URI: " + file, e);
+        }
+    }
+
+    /**
+     * Takes a path and convert it to a URI object with {@code "file"} scheme. This method is preferred instead of
+     * {@link Path#toUri()} because {@link Path#toUri()} internally invokes the {@code stat} system call, resulting in
+     * filesystem metadata access.
+     *
+     * @param path The path
+     * @param isDirectory Whether the file is a directory
+     * @return The URI object
+     */
+    public static URI convertToURI(final Path path, final boolean isDirectory) {
+        return convertToURI(path.toFile(), isDirectory);
+    }
 }

Util/channel/src/main/java/io/deephaven/util/channel/SeekableChannelsProvider.java

@@ -6,43 +6,22 @@
 import io.deephaven.util.SafeCloseable;
 import org.jetbrains.annotations.NotNull;
 
-import java.io.File;
 import java.io.IOException;
 import java.io.InputStream;
 import java.net.URI;
-import java.net.URISyntaxException;
 import java.nio.channels.SeekableByteChannel;
 import java.nio.file.Path;
 import java.nio.file.Paths;
 
-public interface SeekableChannelsProvider extends SafeCloseable {
+import static io.deephaven.base.FileUtils.convertToURI;
 
-    /**
-     * Take the file source path or URI and convert it to a URI object.
-     *
-     * @param source The file source path or URI
-     * @return The URI object
-     */
-    static URI convertToURI(final String source) {
-        final URI uri;
-        try {
-            uri = new URI(source);
-        } catch (final URISyntaxException e) {
-            // If the URI is invalid, assume it's a file path
-            return new File(source).toURI();
-        }
-        if (uri.getScheme() == null) {
-            // Need to convert to a "file" URI
-            return new File(source).toURI();
-        }
-        return uri;
-    }
+public interface SeekableChannelsProvider extends SafeCloseable {
 
     /**
      * Wraps {@link SeekableChannelsProvider#getInputStream(SeekableByteChannel)} to ensure the channel's position is
      * incremented the exact amount that has been consumed from the resulting input stream. To remain valid, the caller
      * must ensure that the resulting input stream isn't re-wrapped by any downstream code in a way that would adversely
-     * effect the position (such as re-wrapping the resulting input stream with buffering).
+     * affect the position (such as re-wrapping the resulting input stream with buffering).
      *
      * <p>
      * Equivalent to {@code ChannelPositionInputStream.of(ch, provider.getInputStream(ch))}.
@@ -79,7 +58,7 @@ default SeekableChannelContext makeSingleUseContext() {
 
     default SeekableByteChannel getReadChannel(@NotNull SeekableChannelContext channelContext, @NotNull String uriStr)
             throws IOException {
-        return getReadChannel(channelContext, convertToURI(uriStr));
+        return getReadChannel(channelContext, convertToURI(uriStr, false));
     }
 
     SeekableByteChannel getReadChannel(@NotNull SeekableChannelContext channelContext, @NotNull URI uri)

extensions/parquet/base/src/main/java/io/deephaven/parquet/base/ColumnChunkReaderImpl.java

@@ -32,6 +32,7 @@
 import java.util.NoSuchElementException;
 import java.util.function.Function;
 
+import static io.deephaven.base.FileUtils.convertToURI;
 import static io.deephaven.parquet.base.ParquetFileReader.FILE_URI_SCHEME;
 import static org.apache.parquet.format.Encoding.PLAIN_DICTIONARY;
 import static org.apache.parquet.format.Encoding.RLE_DICTIONARY;
@@ -120,7 +121,7 @@ private URI getURI() {
             return uri;
         }
         if (columnChunk.isSetFile_path() && FILE_URI_SCHEME.equals(rootURI.getScheme())) {
-            return uri = Path.of(rootURI).resolve(columnChunk.getFile_path()).toUri();
+            return uri = convertToURI(Path.of(rootURI).resolve(columnChunk.getFile_path()), false);
         } else {
             // TODO(deephaven-core#5066): Add support for reading metadata files from non-file URIs
             return uri = rootURI;

extensions/parquet/base/src/main/java/io/deephaven/parquet/base/ParquetFileReader.java

@@ -10,15 +10,15 @@
 import org.apache.parquet.format.Type;
 import org.apache.parquet.schema.*;
 
+import java.io.File;
 import java.io.IOException;
 import java.io.InputStream;
 import java.net.URI;
 import java.nio.channels.SeekableByteChannel;
 import java.nio.charset.StandardCharsets;
-import java.nio.file.Path;
 import java.util.*;
 
-import static io.deephaven.util.channel.SeekableChannelsProvider.convertToURI;
+import static io.deephaven.base.FileUtils.convertToURI;
 
 /**
  * Top level accessor for a parquet file which can read both from a file path string or a CLI style file URI,
@@ -39,17 +39,29 @@ public class ParquetFileReader {
     private final URI rootURI;
     private final MessageType type;
 
+    /**
+     * Create a new ParquetFileReader for the provided source.
+     *
+     * @param source The source path or URI for the parquet file or the parquet metadata file
+     * @param channelsProvider The {@link SeekableChannelsProvider} to use for reading the file
+     */
     public ParquetFileReader(final String source, final SeekableChannelsProvider channelsProvider)
             throws IOException {
-        this(convertToURI(source), channelsProvider);
+        this(convertToURI(source, false), channelsProvider);
     }
 
+    /**
+     * Create a new ParquetFileReader for the provided source.
+     *
+     * @param parquetFileURI The URI for the parquet file or the parquet metadata file
+     * @param channelsProvider The {@link SeekableChannelsProvider} to use for reading the file
+     */
     public ParquetFileReader(final URI parquetFileURI, final SeekableChannelsProvider channelsProvider)
             throws IOException {
         this.channelsProvider = channelsProvider;
         if (!parquetFileURI.getRawPath().endsWith(".parquet") && FILE_URI_SCHEME.equals(parquetFileURI.getScheme())) {
             // Construct a new file URI for the parent directory
-            rootURI = Path.of(parquetFileURI).getParent().toUri();
+            rootURI = convertToURI(new File(parquetFileURI).getParentFile(), true);
         } else {
             // TODO(deephaven-core#5066): Add support for reading metadata files from non-file URIs
             rootURI = parquetFileURI;

extensions/parquet/table/src/main/java/io/deephaven/parquet/table/ParquetTableWriter.java

@@ -45,7 +45,7 @@
 import java.nio.file.Paths;
 import java.util.*;
 
-import static io.deephaven.util.channel.SeekableChannelsProvider.convertToURI;
+import static io.deephaven.base.FileUtils.convertToURI;
 
 /**
  * API for writing DH tables in parquet format
@@ -314,7 +314,7 @@ private static ParquetFileWriter getParquetFileWriter(
         final Map<String, String> extraMetaData = new HashMap<>(tableMeta);
         extraMetaData.put(METADATA_KEY, tableInfoBuilder.build().serializeToJSON());
         return new ParquetFileWriter(path,
-                SeekableChannelsProviderLoader.getInstance().fromServiceLoader(convertToURI(path), null),
+                SeekableChannelsProviderLoader.getInstance().fromServiceLoader(convertToURI(path, false), null),
                 writeInstructions.getTargetPageSize(),
                 new HeapByteBufferAllocator(), mappedSchema.getParquetSchema(),
                 writeInstructions.getCompressionCodecName(), extraMetaData);

extensions/parquet/table/src/main/java/io/deephaven/parquet/table/ParquetTools.java

@@ -54,8 +54,8 @@
 import java.nio.file.attribute.BasicFileAttributes;
 import java.util.*;
 
+import static io.deephaven.base.FileUtils.convertToURI;
 import static io.deephaven.parquet.base.ParquetFileReader.FILE_URI_SCHEME;
-import static io.deephaven.util.channel.SeekableChannelsProvider.convertToURI;
 import static io.deephaven.parquet.table.ParquetTableWriter.PARQUET_FILE_EXTENSION;
 import static io.deephaven.util.type.TypeUtils.getUnboxedTypeIfBoxed;
 
@@ -97,7 +97,7 @@ private ParquetTools() {}
      * @see ParquetFlatPartitionedLayout
      */
     public static Table readTable(@NotNull final String source) {
-        return readTableInternal(convertToURI(source), ParquetInstructions.EMPTY);
+        return readTableInternal(convertParquetSourceToURI(source), ParquetInstructions.EMPTY);
     }
 
     /**
@@ -128,7 +128,7 @@ public static Table readTable(@NotNull final String source) {
     public static Table readTable(
             @NotNull final String source,
             @NotNull final ParquetInstructions readInstructions) {
-        return readTableInternal(convertToURI(source), readInstructions);
+        return readTableInternal(convertParquetSourceToURI(source), readInstructions);
     }
 
     /**
@@ -186,6 +186,19 @@ public static Table readTable(
         return readTableInternal(sourceFile, readInstructions);
     }
 
+    /**
+     * Convert a parquet source to a URI.
+     *
+     * @param source The path or URI of parquet file or directory to examine
+     * @return The URI
+     */
+    private static URI convertParquetSourceToURI(@NotNull final String source) {
+        if (source.endsWith(".parquet")) {
+            return convertToURI(source, false);
+        }
+        return convertToURI(source, true);
+    }
+
     /**
      * Write a table to a file.
      *
@@ -961,7 +974,7 @@ public static Table readFlatPartitionedTable(
     public static Table readSingleFileTable(
             @NotNull final File file,
             @NotNull final ParquetInstructions readInstructions) {
-        return readSingleFileTable(file.toURI(), readInstructions);
+        return readSingleFileTable(convertToURI(file, false), readInstructions);
     }
 
     /**
@@ -980,7 +993,7 @@ public static Table readSingleFileTable(
     public static Table readSingleFileTable(
             @NotNull final String source,
             @NotNull final ParquetInstructions readInstructions) {
-        return readSingleFileTable(convertToURI(source), readInstructions);
+        return readSingleFileTable(convertToURI(source, false), readInstructions);
     }
 
     private static Table readSingleFileTable(
@@ -1007,7 +1020,7 @@ public static Table readSingleFileTable(
             @NotNull final File file,
             @NotNull final ParquetInstructions readInstructions,
             @NotNull final TableDefinition tableDefinition) {
-        return readSingleFileTable(file.toURI(), readInstructions, tableDefinition);
+        return readSingleFileTable(convertToURI(file, false), readInstructions, tableDefinition);
     }
 
     /**
@@ -1025,7 +1038,7 @@ public static Table readSingleFileTable(
             @NotNull final String source,
             @NotNull final ParquetInstructions readInstructions,
             @NotNull final TableDefinition tableDefinition) {
-        return readSingleFileTable(convertToURI(source), readInstructions, tableDefinition);
+        return readSingleFileTable(convertToURI(source, false), readInstructions, tableDefinition);
     }
 
     private static Table readSingleFileTable(
@@ -1105,7 +1118,7 @@ private static ParquetSchemaReader.ColumnDefinitionConsumer makeSchemaReaderCons
      * Make a {@link ParquetFileReader} for the supplied {@link File}. Wraps {@link IOException} as
      * {@link TableDataException}.
      *
-     * @param parquetFile The {@link File} to read
+     * @param parquetFile The parquet file or the parquet metadata file
      * @param readInstructions the instructions for customizations while reading
      * @return The new {@link ParquetFileReader}
      */
@@ -1122,7 +1135,7 @@ public static ParquetFileReader getParquetFileReader(@NotNull final File parquet
      * Make a {@link ParquetFileReader} for the supplied {@link URI}. Wraps {@link IOException} as
      * {@link TableDataException}.
      *
-     * @param parquetFileURI The {@link URI} to read
+     * @param parquetFileURI The URI for the parquet file or the parquet metadata file
      * @param readInstructions the instructions for customizations while reading
      * @return The new {@link ParquetFileReader}
      */
@@ -1138,20 +1151,20 @@ public static ParquetFileReader getParquetFileReader(@NotNull final URI parquetF
     /**
      * Make a {@link ParquetFileReader} for the supplied {@link File}.
      *
-     * @param parquetFile The {@link File} to read
+     * @param parquetFile The parquet file or the parquet metadata file
      * @return The new {@link ParquetFileReader}
      * @throws IOException if an IO exception occurs
      */
     public static ParquetFileReader getParquetFileReaderChecked(
             @NotNull final File parquetFile,
             @NotNull final ParquetInstructions readInstructions) throws IOException {
-        return getParquetFileReaderChecked(parquetFile.toURI(), readInstructions);
+        return getParquetFileReaderChecked(convertToURI(parquetFile, false), readInstructions);
     }
 
     /**
      * Make a {@link ParquetFileReader} for the supplied {@link URI}.
      *
-     * @param parquetFileURI The {@link URI} to read
+     * @param parquetFileURI The URI for the parquet file or the parquet metadata file
      * @return The new {@link ParquetFileReader}
      * @throws IOException if an IO exception occurs
      */

extensions/parquet/table/src/main/java/io/deephaven/parquet/table/location/ParquetTableLocationKey.java

@@ -23,6 +23,8 @@
 import java.util.Map;
 import java.util.stream.IntStream;
 
+import static io.deephaven.base.FileUtils.convertToURI;
+
 /**
  * {@link TableLocationKey} implementation for use with data stored in the parquet format.
  */
@@ -70,7 +72,7 @@ public ParquetTableLocationKey(@NotNull final URI parquetFileUri, final int orde
     }
 
     private static URI validateParquetFile(@NotNull final File file) {
-        return validateParquetFile(file.toURI());
+        return validateParquetFile(convertToURI(file, false));
     }
 
     private static URI validateParquetFile(@NotNull final URI parquetFileUri) {
@@ -189,7 +191,7 @@ public synchronized int[] getRowGroupIndices() {
             // we're not expecting that in this code path. To support it, discovery tools should figure out
             // the row groups for a partition themselves and call setRowGroupReaders.
             final String filePath = rowGroups.get(rgi).getColumns().get(0).getFile_path();
-            return filePath == null || new File(filePath).getAbsoluteFile().toURI().equals(uri);
+            return filePath == null || convertToURI(filePath, false).equals(uri);
         }).toArray();
     }