finish tests; fix f order; implement nested store

Author: haileyajohnson

cdm/core/src/main/java/ucar/nc2/iosp/IospHelper.java

@@ -306,6 +306,9 @@ public static Object readData(LayoutBB layout, DataType dataType, Object arr) {
       while (layout.hasNext()) {
         LayoutBB.Chunk chunk = layout.next();
         ByteBuffer bb = chunk.getByteBuffer();
+        if (!bb.hasRemaining()) {
+          continue;
+        }
         bb.position(chunk.getSrcElem());
         int pos = (int) chunk.getDestElem();
         for (int i = 0; i < chunk.getNelems(); i++)
@@ -314,18 +317,19 @@ public static Object readData(LayoutBB layout, DataType dataType, Object arr) {
       // return (dataType == DataType.CHAR) ? convertByteToChar(pa) : pa;
       if (dataType == DataType.CHAR) {
         return convertByteToChar(pa);
-      }
-      else if (dataType == DataType.BOOLEAN) {
+      } else if (dataType == DataType.BOOLEAN) {
         return convertByteToBoolean(pa);
-      }
-      else
+      } else
         return pa;
 
     } else if (dataType.getPrimitiveClassType() == short.class) {
       short[] pa = (short[]) arr;
       while (layout.hasNext()) {
         LayoutBB.Chunk chunk = layout.next();
         ShortBuffer buff = chunk.getShortBuffer();
+        if (!buff.hasRemaining()) {
+          continue;
+        }
         buff.position(chunk.getSrcElem());
         int pos = (int) chunk.getDestElem();
         for (int i = 0; i < chunk.getNelems(); i++)
@@ -338,6 +342,9 @@ else if (dataType == DataType.BOOLEAN) {
       while (layout.hasNext()) {
         LayoutBB.Chunk chunk = layout.next();
         IntBuffer buff = chunk.getIntBuffer();
+        if (!buff.hasRemaining()) {
+          continue;
+        }
         buff.position(chunk.getSrcElem());
         int pos = (int) chunk.getDestElem();
         for (int i = 0; i < chunk.getNelems(); i++)
@@ -350,6 +357,9 @@ else if (dataType == DataType.BOOLEAN) {
       while (layout.hasNext()) {
         LayoutBB.Chunk chunk = layout.next();
         FloatBuffer buff = chunk.getFloatBuffer();
+        if (!buff.hasRemaining()) {
+          continue;
+        }
         buff.position(chunk.getSrcElem());
         int pos = (int) chunk.getDestElem();
         for (int i = 0; i < chunk.getNelems(); i++)
@@ -362,6 +372,9 @@ else if (dataType == DataType.BOOLEAN) {
       while (layout.hasNext()) {
         LayoutBB.Chunk chunk = layout.next();
         DoubleBuffer buff = chunk.getDoubleBuffer();
+        if (!buff.hasRemaining()) {
+          continue;
+        }
         buff.position(chunk.getSrcElem());
         int pos = (int) chunk.getDestElem();
         for (int i = 0; i < chunk.getNelems(); i++)
@@ -374,6 +387,9 @@ else if (dataType == DataType.BOOLEAN) {
       while (layout.hasNext()) {
         LayoutBB.Chunk chunk = layout.next();
         LongBuffer buff = chunk.getLongBuffer();
+        if (!buff.hasRemaining()) {
+          continue;
+        }
         buff.position(chunk.getSrcElem());
         int pos = (int) chunk.getDestElem();
         for (int i = 0; i < chunk.getNelems(); i++)
@@ -387,6 +403,9 @@ else if (dataType == DataType.BOOLEAN) {
       while (layout.hasNext()) {
         LayoutBB.Chunk chunk = layout.next();
         ByteBuffer bb = chunk.getByteBuffer();
+        if (!bb.hasRemaining()) {
+          continue;
+        }
         bb.position(chunk.getSrcElem() * recsize);
         int pos = (int) chunk.getDestElem() * recsize;
         for (int i = 0; i < chunk.getNelems() * recsize; i++)
@@ -399,12 +418,15 @@ else if (dataType == DataType.BOOLEAN) {
       while (layout.hasNext()) {
         LayoutBB.Chunk chunk = layout.next();
         ByteBuffer bb = chunk.getByteBuffer();
+        if (!bb.hasRemaining()) {
+          continue;
+        }
         bb.position(chunk.getSrcElem() * recsize);
         int pos = (int) chunk.getDestElem();
         for (int i = 0; i < chunk.getNelems(); i++) {
           char[] ch = new char[dataType.getSize()];
-          for ( int j = 0; j < ch.length; j++) {
-            ch[j] = (char)bb.get();
+          for (int j = 0; j < ch.length; j++) {
+            ch[j] = (char) bb.get();
           }
           pa[pos++] = new String(ch);
         }

cdm/zarr/src/main/java/ucar/nc2/iosp/zarr/ZArray.java

@@ -181,7 +181,7 @@ public ZArray deserialize(JsonParser p, DeserializationContext ctxt) throws IOEx
         fill = fillValueNode.longValue();
       } else if (fillValueNode.isFloat()) {
         fill = fillValueNode.floatValue();
-      }  else if (fillValueNode.isNumber()){
+      } else if (fillValueNode.isNumber()) {
         fill = fillValueNode.asDouble();
       } else {
         fill = fillValueNode.asText("");

cdm/zarr/src/main/java/ucar/nc2/iosp/zarr/ZarrFormatException.java

@@ -19,4 +19,7 @@ public ZarrFormatException(String invalidField, String value) {
     super(String.format(customExceptionMessageFormat, invalidField, value));
   }
 
+  public ZarrFormatException(String msg) {
+    super(msg);
+  }
 }