Refactor inventory management to use managed-file abstractions, part 2

* Transition GRIB collection abstractions from java.io/java.nio path
  APIs with the exception of writing GRIB Index files, which remain
  local-only for now.

Author: lesserwhirls

cdm-test/src/test/java/ucar/nc2/grib/TestGribCdmIndexUpdating.java

@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 1998-2021 University Corporation for Atmospheric Research/Unidata
+ * Copyright (c) 1998-2026 University Corporation for Atmospheric Research/Unidata
  * See LICENSE for license information.
  */
 
@@ -77,7 +77,7 @@ public static List<Object[]> getTestParameters() {
   public static void after(String dataDir, String newModel, FeatureCollectionConfig config, String varName, int orgLen,
       int remLen) {
     // cleanup index files created during test for a given parameter input
-    cleanUpIndexFiles(GribCdmIndex.getTopIndexFileFromConfig(config).getParent());
+    cleanUpIndexFiles(GribCdmIndex.getTopIndexFileFromConfig(config).getPath());
   }
 
   ///////////////////////////////////////
@@ -98,7 +98,7 @@ public TestGribCdmIndexUpdating(String dataDir, String newModel, FeatureCollecti
     this.orgLen = orgLen;
     this.remLen = remLen;
     GribCdmIndex.updateGribCollection(config, CollectionUpdateType.always, logger);
-    this.indexFile = GribCdmIndex.getTopIndexFileFromConfig(config).getAbsolutePath();
+    this.indexFile = GribCdmIndex.getTopIndexFileFromConfig(config).getPath();
   }
 
   @Test

cdm-test/src/test/java/ucar/nc2/grib/TestGribCollectionCoordinates.java

@@ -1,7 +1,8 @@
 /*
- * Copyright (c) 1998-2018 University Corporation for Atmospheric Research/Unidata
+ * Copyright (c) 1998-2026 University Corporation for Atmospheric Research/Unidata
  * See LICENSE for license information.
  */
+
 package ucar.nc2.grib;
 
 import static com.google.common.truth.Truth.assertThat;
@@ -68,7 +69,7 @@ public void testExtraCoordinates() throws IOException {
     config.gribConfig.setExcludeZero(true); // no longer the default
 
     boolean changed = GribCdmIndex.updateGribCollection(config, CollectionUpdateType.always, logger);
-    String topLevelIndex = GribCdmIndex.getTopIndexFileFromConfig(config).getAbsolutePath();
+    String topLevelIndex = GribCdmIndex.getTopIndexFileFromConfig(config).getPath();
 
     logger.debug("changed = {}", changed);
 
@@ -126,7 +127,7 @@ public void testBestReftimeMonotonic() throws IOException {
 
     boolean changed = GribCdmIndex.updateGribCollection(config, updateMode, logger);
     logger.debug("changed = {}", changed);
-    String topLevelIndex = GribCdmIndex.getTopIndexFileFromConfig(config).getAbsolutePath();
+    String topLevelIndex = GribCdmIndex.getTopIndexFileFromConfig(config).getPath();
     boolean ok = true;
 
     try (NetcdfDataset ds = NetcdfDatasets.openDataset(topLevelIndex)) {

cdm-test/src/test/java/ucar/nc2/grib/TestGribCollectionTimeUnits.java

@@ -1,7 +1,8 @@
 /*
- * Copyright (c) 1998-2022 University Corporation for Atmospheric Research/Unidata
+ * Copyright (c) 1998-2026 University Corporation for Atmospheric Research/Unidata
  * See LICENSE for license information.
  */
+
 package ucar.nc2.grib;
 
 import static com.google.common.truth.Truth.assertThat;
@@ -80,7 +81,7 @@ private void checkVariableNameAndTimeAxis(FeatureCollectionConfig config, String
       String units, double[] values) throws IOException {
     final boolean changed = GribCdmIndex.updateGribCollection(config, CollectionUpdateType.always, logger);
     assertThat(changed).isTrue();
-    final String topLevelIndex = GribCdmIndex.getTopIndexFileFromConfig(config).getAbsolutePath();
+    final String topLevelIndex = GribCdmIndex.getTopIndexFileFromConfig(config).getPath();
 
     try (NetcdfDataset netcdfDataset = NetcdfDatasets.openDataset(topLevelIndex)) {
       final Variable variable =

grib/src/main/java/ucar/nc2/grib/GribIndex.java

@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 1998-2018 John Caron and University Corporation for Atmospheric Research/Unidata
+ * Copyright (c) 1998-2026 John Caron and University Corporation for Atmospheric Research/Unidata
  * See LICENSE for license information.
  */
 
@@ -12,7 +12,6 @@
 import ucar.nc2.grib.grib1.Grib1Index;
 import ucar.nc2.grib.grib2.Grib2Index;
 import ucar.unidata.io.RandomAccessFile;
-import java.io.File;
 import java.io.IOException;
 
 /**
@@ -33,11 +32,11 @@ public boolean hasChangedSince(MFile file, long when) {
       String idxPath = file.getPath();
       if (!idxPath.endsWith(GBX9_IDX))
         idxPath += GBX9_IDX;
-      File idxFile = GribIndexCache.getExistingFileOrCache(idxPath);
+      MFile idxFile = GribIndexCache.getExistingFileOrCache(idxPath);
       if (idxFile == null)
         return true;
 
-      long idxLastModified = idxFile.lastModified();
+      long idxLastModified = idxFile.getLastModified();
       if (idxLastModified < file.getLastModified())
         return true;
       return 0 < when && when < idxLastModified;
@@ -47,13 +46,13 @@ public boolean hasntChangedSince(MFile file, long when) {
       String idxPath = file.getPath();
       if (!idxPath.endsWith(GBX9_IDX))
         idxPath += GBX9_IDX;
-      File idxFile = GribIndexCache.getExistingFileOrCache(idxPath);
+      MFile idxFile = GribIndexCache.getExistingFileOrCache(idxPath);
       if (idxFile == null)
         return true;
 
-      if (idxFile.lastModified() < file.getLastModified())
+      if (idxFile.getLastModified() < file.getLastModified())
         return true;
-      return 0 < when && idxFile.lastModified() < when;
+      return 0 < when && idxFile.getLastModified() < when;
     }
   };
   /////////////////////////////////////////////////////////////////////////

grib/src/main/java/ucar/nc2/grib/GribIndexCache.java

@@ -1,12 +1,14 @@
 /*
- * Copyright (c) 1998-2018 John Caron and University Corporation for Atmospheric Research/Unidata
+ * Copyright (c) 1998-2026 John Caron and University Corporation for Atmospheric Research/Unidata
  * See LICENSE for license information.
  */
 
 package ucar.nc2.grib;
 
 import ucar.nc2.grib.collection.Grib;
 import ucar.nc2.util.DiskCache2;
+import thredds.inventory.MFile;
+import thredds.inventory.MFiles;
 import java.io.File;
 
 /**
@@ -35,11 +37,11 @@ public static synchronized DiskCache2 getDiskCache2() {
    * @param fileLocation full path of original index filename
    * @return File, possibly in cache, may or may not exist
    */
-  public static File getFileOrCache(String fileLocation) {
-    File result = getExistingFileOrCache(fileLocation);
+  public static MFile getFileOrCache(String fileLocation) {
+    MFile result = getExistingFileOrCache(fileLocation);
     if (result != null)
       return result;
-    return getDiskCache2().getFile(fileLocation);
+    return MFiles.create(getDiskCache2().getFile(fileLocation).getPath());
   }
 
   /**
@@ -48,14 +50,14 @@ public static File getFileOrCache(String fileLocation) {
    * @param fileLocation full path of original index filename
    * @return existing file if you can find it, else null
    */
-  public static File getExistingFileOrCache(String fileLocation) {
+  public static MFile getExistingFileOrCache(String fileLocation) {
     File result = getDiskCache2().getExistingFileOrCache(fileLocation);
     if (result == null && Grib.debugGbxIndexOnly && fileLocation.endsWith(".gbx9.ncx4")) { // might create only from
                                                                                            // gbx9 for debugging
       int length = fileLocation.length();
       String maybeIndexAlreadyExists = fileLocation.substring(0, length - 10) + ".ncx4";
       result = getDiskCache2().getExistingFileOrCache(maybeIndexAlreadyExists);
     }
-    return result;
+    return result == null ? null : MFiles.create(result.getPath());
   }
 }

grib/src/main/java/ucar/nc2/grib/collection/GcMFile.java

@@ -1,21 +1,18 @@
 /*
- * Copyright (c) 1998-2018 John Caron and University Corporation for Atmospheric Research/Unidata
+ * Copyright (c) 1998-2026 John Caron and University Corporation for Atmospheric Research/Unidata
  * See LICENSE for license information.
  */
 
 package ucar.nc2.grib.collection;
 
-import java.io.FileInputStream;
 import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.OutputStream;
 import javax.annotation.Nullable;
-import thredds.filesystem.MFileOS;
 import thredds.inventory.MFile;
 import ucar.nc2.util.IO;
 import ucar.unidata.io.RandomAccessFile;
 import ucar.unidata.util.StringUtil2;
-import java.io.File;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Set;
@@ -28,7 +25,7 @@
  */
 public class GcMFile implements thredds.inventory.MFile {
 
-  static List<GcMFile> makeFiles(File directory, List<MFile> files, Set<Integer> allFileSet) {
+  static List<GcMFile> makeFiles(MFile directory, List<MFile> files, Set<Integer> allFileSet) {
     List<GcMFile> result = new ArrayList<>(files.size());
     String dirPath = StringUtil2.replace(directory.getPath(), '\\', "/");
 
@@ -47,12 +44,12 @@ static List<GcMFile> makeFiles(File directory, List<MFile> files, Set<Integer> a
   }
 
   ////////////////////////////////////////////////////////////////////////////////////////
-  public final File directory;
+  public final MFile directory;
   public final String name;
   public final long lastModified, length;
   public final int index;
 
-  GcMFile(File directory, String name, long lastModified, long length, int index) {
+  GcMFile(MFile directory, String name, long lastModified, long length, int index) {
     this.directory = directory;
     this.name = name;
     this.lastModified = lastModified;
@@ -77,8 +74,8 @@ public boolean isDirectory() {
 
   @Override
   public String getPath() {
-    String path = new File(directory, name).getPath();
-    return StringUtil2.replace(path, '\\', "/");
+    MFile file = directory.getChild(name);
+    return file == null ? null : file.getPath();
   }
 
   @Override
@@ -87,8 +84,8 @@ public String getName() {
   }
 
   @Override
-  public MFile getParent() {
-    return new MFileOS(directory);
+  public MFile getParent() throws IOException {
+    return directory;
   }
 
   @Override
@@ -105,24 +102,28 @@ public Object getAuxInfo() {
   @Override
   public void setAuxInfo(Object info) {}
 
-  public File getDirectory() {
+  public MFile getDirectory() {
     return directory;
   }
 
   @Override
   public String toString() {
-    return "GcMFile{" + "directory=" + directory + ", name='" + name + '\'' + ", lastModified=" + lastModified
+    return "GcMFile{" + "directory=" + directory.getPath() + ", name='" + name + '\'' + ", lastModified=" + lastModified
         + ", length=" + length + ", index=" + index + '}';
   }
 
   @Override
   public boolean exists() {
-    return new File(directory, name).exists();
+    MFile file = directory.getChild(name);
+    return file != null && file.exists();
   }
 
   @Override
-  public FileInputStream getInputStream() throws FileNotFoundException {
-    return new FileInputStream(new File(directory, name));
+  public java.io.InputStream getInputStream() throws FileNotFoundException {
+    MFile file = directory.getChild(name);
+    if (file == null)
+      throw new FileNotFoundException(name);
+    return file.getInputStream();
   }
 
   @Override

grib/src/main/java/ucar/nc2/grib/collection/Grib1CollectionBuilder.java

@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 1998-2018 John Caron and University Corporation for Atmospheric Research/Unidata
+ * Copyright (c) 1998-2026 John Caron and University Corporation for Atmospheric Research/Unidata
  * See LICENSE for license information.
  */
 
@@ -28,7 +28,6 @@
 import ucar.nc2.time.CalendarDateRange;
 import ucar.nc2.time.CalendarPeriod;
 import ucar.nc2.util.CloseableIterator;
-import java.io.File;
 import java.io.IOException;
 import java.util.*;
 
@@ -191,7 +190,7 @@ protected boolean writeIndex(String name, String indexFilepath, CoordinateRuntim
     List<Grib1CollectionWriter.Group> groups2 = new ArrayList<>();
     for (Object g : groups)
       groups2.add((Grib1CollectionWriter.Group) g); // why copy ?
-    File indexFileInCache = GribIndexCache.getFileOrCache(indexFilepath);
+    MFile indexFileInCache = GribIndexCache.getFileOrCache(indexFilepath);
     return writer.writeIndex(name, indexFileInCache, masterRuntime, groups2, files, type, dateRange);
   }
 

grib/src/main/java/ucar/nc2/grib/collection/Grib1CollectionWriter.java

@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 1998-2018 John Caron and University Corporation for Atmospheric Research/Unidata
+ * Copyright (c) 1998-2026 John Caron and University Corporation for Atmospheric Research/Unidata
  * See LICENSE for license information.
  */
 
@@ -9,6 +9,7 @@
 import java.nio.charset.StandardCharsets;
 import thredds.inventory.MCollection;
 import thredds.inventory.MFile;
+import thredds.inventory.MFiles;
 import ucar.nc2.grib.coord.Coordinate;
 import ucar.nc2.grib.coord.CoordinateEns;
 import ucar.nc2.grib.coord.CoordinateRuntime;
@@ -90,15 +91,18 @@ public Set<Long> getCoordinateRuntimes() {
    */
 
   // indexFile is in the cache
-  boolean writeIndex(String name, File idxFile, CoordinateRuntime masterRuntime, List<Group> groups, List<MFile> files,
+  boolean writeIndex(String name, MFile idxFile, CoordinateRuntime masterRuntime, List<Group> groups, List<MFile> files,
       GribCollectionImmutable.Type type, CalendarDateRange dateRange) throws IOException {
     Grib1Record first = null; // take global metadata from here
     boolean deleteOnClose = false;
 
     if (idxFile.exists()) {
       RandomAccessFile.eject(idxFile.getPath());
-      if (!idxFile.delete()) {
-        logger.warn(" gc1 cant delete index file {}", idxFile.getPath());
+      if (idxFile instanceof thredds.filesystem.MFileOS) {
+        File f = new File(idxFile.getPath());
+        if (!f.delete()) {
+          logger.warn(" gc1 cant delete index file {}", idxFile.getPath());
+        }
       }
     }
     logger.debug(" createIndex for {}", idxFile.getPath());
@@ -186,7 +190,7 @@ boolean writeIndex(String name, File idxFile, CoordinateRuntime masterRuntime, L
       indexBuilder.setVersion(currentVersion);
 
       // directory and mfile list
-      File directory = new File(dcm.getRoot());
+      MFile directory = MFiles.create(dcm.getRoot());
       List<GcMFile> gcmfiles = GcMFile.makeFiles(directory, files, allFileSet);
       for (GcMFile gcmfile : gcmfiles) {
         GribCollectionProto.MFile.Builder b = GribCollectionProto.MFile.newBuilder();
@@ -230,8 +234,10 @@ boolean writeIndex(String name, File idxFile, CoordinateRuntime masterRuntime, L
     } finally {
 
       // remove it on failure
-      if (deleteOnClose && !idxFile.delete()) {
-        logger.error(" gc1 cant deleteOnClose index file {}", idxFile.getPath());
+      if (deleteOnClose && idxFile instanceof thredds.filesystem.MFileOS) {
+        File f = new File(idxFile.getPath());
+        if (!f.delete())
+          logger.error(" gc1 cant deleteOnClose index file {}", idxFile.getPath());
       }
     }
   }

grib/src/main/java/ucar/nc2/grib/collection/Grib1PartitionBuilder.java

@@ -1,13 +1,13 @@
 /*
- * Copyright (c) 1998-2018 John Caron and University Corporation for Atmospheric Research/Unidata
+ * Copyright (c) 1998-2026 John Caron and University Corporation for Atmospheric Research/Unidata
  * See LICENSE for license information.
  */
 
 package ucar.nc2.grib.collection;
 
 import thredds.featurecollection.FeatureCollectionConfig;
+import thredds.inventory.MFile;
 import thredds.inventory.partition.PartitionManager;
-import java.io.File;
 
 /**
  * Builds Grib1 PartitionCollections (version 2)
@@ -18,7 +18,7 @@
 class Grib1PartitionBuilder extends GribPartitionBuilder {
   public static final String MAGIC_START = "Grib1Partition2Index"; // was Grib1Partition0Index
 
-  Grib1PartitionBuilder(String name, File directory, PartitionManager tpc, org.slf4j.Logger logger) {
+  Grib1PartitionBuilder(String name, MFile directory, PartitionManager tpc, org.slf4j.Logger logger) {
     super(name, tpc, logger);
 
     FeatureCollectionConfig config = null;