Merge pull request #425 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10 to hdf5_1_10

* commit 'b03e41146a3e15c7a287ab98f1963bf7944719a8':
  Skip tests for page buffering in test/fheap.c for parallel build Skip the two tests for page buffering in test/fheap.c because this feature is disabled in parallel. Activate full testing when this feature is re-enabled in the future for parallel build.
  Due to HDFVIEW-19 add read VL as string function
  Fix URL name
  updated with README changes
  DAILYTEST-250 change test props to reduce timeout
  Combined the README_DEVEL and README, and removed out-dated README material
  Fix for H5Dset_extent test failure with extensive array indexing (HDFFV-9771) 1) Calculate chunk index for extensive array index based on swizzled max chunks when unlim_dim > 0 2) Minor fixes to test/fheap.c that somehow were missed from last check in.  See pull request #396 review comments.

3 files changed, 103 insertions, 0 deletions

diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java
index e47ba76..48b2402 100644
--- a/java/src/hdf/hdf5lib/H5.java
+++ b/java/src/hdf/hdf5lib/H5.java
@@ -1798,6 +1798,9 @@ public class H5 implements java.io.Serializable {
         return H5Dread_short(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true);
     }
 
+    public synchronized static native int H5DreadVL(long dataset_id, long mem_type_id, long mem_space_id,
+            long file_space_id, long xfer_plist_id, Object[] buf) throws HDF5LibraryException, NullPointerException;
+
     public synchronized static native int H5Dread_string(long dataset_id, long mem_type_id, long mem_space_id,
             long file_space_id, long xfer_plist_id, String[] buf) throws HDF5LibraryException, NullPointerException;
 
diff --git a/java/src/jni/h5dImp.c b/java/src/jni/h5dImp.c
index 9765dc8..0bb015e 100644
--- a/java/src/jni/h5dImp.c
+++ b/java/src/jni/h5dImp.c
@@ -55,6 +55,7 @@ extern jobject visit_callback;
 /* Local Prototypes */
 /********************/
 
+static herr_t H5DreadVL_asstr (JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid, hid_t xfer_plist_id, jobjectArray buf);
 static herr_t H5DreadVL_str (JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid, hid_t xfer_plist_id, jobjectArray buf);
 static herr_t H5DreadVL_array (JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid, hid_t xfer_plist_id, jobjectArray buf);
 static herr_t H5DwriteVL_str (JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid, hid_t xfer_plist_id, jobjectArray buf);
@@ -994,6 +995,96 @@ Java_hdf_hdf5lib_H5_H5Dwrite_1double
 
 /*
  * Class:     hdf_hdf5lib_H5
+ * Method:    H5DreadVL
+ * Signature: (JJJJJ[Ljava/lang/String;)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5DreadVL
+    (JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id, jlong mem_space_id,
+          jlong file_space_id, jlong xfer_plist_id, jobjectArray buf)
+{
+    herr_t  status = -1;
+    htri_t  isVlenStr=0;
+
+    if (buf == NULL) {
+        h5nullArgument(env, "H5DreadVL:  buf is NULL");
+    } /* end if */
+    else {
+        isVlenStr = H5Tdetect_class((hid_t)mem_type_id, H5T_STRING);
+
+        if (isVlenStr)
+            h5badArgument(env, "H5DreadVL: type is not variable length non-string");
+        else
+            status = H5DreadVL_asstr(env, (hid_t)dataset_id, (hid_t)mem_type_id,
+                                        (hid_t)mem_space_id, (hid_t)file_space_id,
+                                        (hid_t)xfer_plist_id, buf);
+    } /* end else */
+
+    return (jint)status;
+} /* end Java_hdf_hdf5lib_H5_H5Dread_1VLStrings */
+
+herr_t
+H5DreadVL_asstr
+    (JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid, hid_t xfer_plist_id, jobjectArray buf)
+{
+    jint    i;
+    jint    n;
+    jstring jstr;
+    h5str_t h5str;
+    hvl_t  *rdata;
+    size_t  size;
+    size_t  max_len = 0;
+    herr_t  status = -1;
+
+    n = ENVPTR->GetArrayLength(ENVPAR buf);
+    rdata = (hvl_t*)HDcalloc((size_t)n, sizeof(hvl_t));
+    if (rdata == NULL) {
+        h5JNIFatalError(env, "H5DreadVL_notstr:  failed to allocate buff for read");
+    } /* end if */
+    else {
+        status = H5Dread(did, tid, mem_sid, file_sid, xfer_plist_id, rdata);
+
+        if (status < 0) {
+            H5Dvlen_reclaim(tid, mem_sid, xfer_plist_id, rdata);
+            HDfree(rdata);
+            h5JNIFatalError(env, "H5DreadVL_notstr: failed to read data");
+        } /* end if */
+        else {
+            max_len = 1;
+            for (i=0; i < n; i++) {
+                if ((rdata + i)->len > max_len)
+                    max_len = (rdata + i)->len;
+            }
+
+            size = H5Tget_size(tid) * max_len;
+            HDmemset(&h5str, 0, sizeof(h5str_t));
+            h5str_new(&h5str, 4 * size);
+
+            if (h5str.s == NULL) {
+                H5Dvlen_reclaim(tid, mem_sid, xfer_plist_id, rdata);
+                HDfree(rdata);
+                h5JNIFatalError(env, "H5DreadVL_notstr:  failed to allocate buf");
+            } /* end if */
+            else {
+                for (i=0; i < n; i++) {
+                    h5str.s[0] = '\0';
+                    h5str_sprintf(&h5str, did, tid, rdata+i, 0);
+                    jstr = ENVPTR->NewStringUTF(ENVPAR h5str.s);
+                    ENVPTR->SetObjectArrayElement(ENVPAR buf, i, jstr);
+                } /* end for */
+                h5str_free(&h5str);
+
+                H5Dvlen_reclaim(tid, mem_sid, xfer_plist_id, rdata);
+                HDfree(rdata);
+            } /* end else */
+        } /* end else */
+    } /* end else */
+
+    return status;
+}
+
+/*
+ * Class:     hdf_hdf5lib_H5
  * Method:    H5Dread_string
  * Signature: (JJJJJ[Ljava/lang/String;)I
  */
diff --git a/java/src/jni/h5dImp.h b/java/src/jni/h5dImp.h
index eb26265..e79c590 100644
--- a/java/src/jni/h5dImp.h
+++ b/java/src/jni/h5dImp.h
@@ -206,6 +206,15 @@ Java_hdf_hdf5lib_H5_H5Dwrite_1double
 
 /*
  * Class:     hdf_hdf5lib_H5
+ * Method:    H5DreadVL
+ * Signature: (JJJJJ[Ljava/lang/String;)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5DreadVL
+(JNIEnv*, jclass, jlong, jlong, jlong, jlong, jlong, jobjectArray);
+
+/*
+ * Class:     hdf_hdf5lib_H5
  * Method:    H5Dread_string
  * Signature: (JJJJJ[Ljava/lang/String;)I
  */