[svn-r7842] Purpose:

    Bug fix

Description:
    Variable length strings and sequences with NULL pointers were not handled
by library, causing problems access the data.  This also affected fill values
for variable-length datatypes.

Solution:
    Address the issues in the library by detecting NULL sequences/strings
and avoid trying to convert them.

    Patched up dumper to display NULL sequences/strings.

Platforms tested:
    FreeBSD 4.9 (sleipnir)
    h5committest

13 files changed, 243 insertions, 55 deletions

diff --git a/tools/h5dump/h5dump.c b/tools/h5dump/h5dump.c
index 77ce159..d79f4ee 100644
--- a/tools/h5dump/h5dump.c
+++ b/tools/h5dump/h5dump.c
@@ -4846,7 +4846,8 @@ xml_print_strs(hid_t did, int source)
     for (i = 0; i < ssiz; i++) {
         if(is_vlstr) {
             onestring = *(char **)bp;
-            str_size = (size_t)strlen(onestring);
+            if(onestring)
+                str_size = (size_t)strlen(onestring);
         } else {    
     	    strncpy(onestring, bp, tsiz);
             str_size = tsiz;
@@ -4854,7 +4855,7 @@ xml_print_strs(hid_t did, int source)
 	indentation(indent + COL);
 
 	if (!onestring) {
-	    printf("\"%s\"\n", "NULL");
+	    printf("NULL\n");
 	} else {
             char *t_onestring = xml_escape_the_string(onestring, (int)str_size);
 
diff --git a/tools/h5dump/h5dumpgentest.c b/tools/h5dump/h5dumpgentest.c
index 0356b2b..901f427 100644
--- a/tools/h5dump/h5dumpgentest.c
+++ b/tools/h5dump/h5dumpgentest.c
@@ -68,6 +68,7 @@
 #define FILE40  "tattr2.h5"
 #define FILE41  "tcompound_complex.h5"
 #define FILE42  "tnamed_dtype_attr.h5"
+#define FILE43 "tvldtypes5.h5"
 
 
 /* prototypes */
@@ -145,6 +146,10 @@ typedef struct s1_t {
 #define F42_TYPENAME "Datatype"
 #define F42_ATTRNAME "Attribute"
 
+/* "File 43" macros */
+/* Name of dataset to create in datafile                              */
+#define F43_DSETNAME "Dataset"
+
 static void gent_group(void)
 {
     hid_t fid, group;
@@ -2196,6 +2201,67 @@ static void gent_vldatatypes4(void)
     assert(ret>=0);
 }
 
+/* Generate a variable-length dataset with NULL values in it */
+static void gent_vldatatypes5(void)
+{
+    hvl_t wdata [SPACE1_DIM1];
+    hid_t		fid1;		      
+    hid_t		dataset;	    
+    hid_t		sid1;
+    hid_t		tid1;
+    hsize_t		dims1[] = {SPACE1_DIM1};
+    int                 i,j;          /* counting variable */
+    herr_t		ret;		/* Generic return value  */
+
+    /* initialize data for dataset */
+    for(i=0; i<SPACE1_DIM1; i++) {
+        if(i%2) {
+            wdata[i].len=0;
+            wdata[i].p=NULL;
+        } /* end if */
+        else {
+            wdata[i].len=i+5;
+            wdata[i].p=malloc(sizeof(unsigned)*(i+5));
+            for(j=0; j<i+5; j++)
+                ((unsigned *)wdata[i].p)[j]=j*2;
+        } /* end else */
+    } /* end for */
+
+    /* Create file */
+    fid1 = H5Fcreate (FILE43, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+    assert(fid1>0);
+
+    /* Create dataspace for datasets */
+    sid1 = H5Screate_simple (SPACE1_RANK, dims1, NULL);
+    assert(sid1>0);
+
+    /* Create a datatype to refer to */
+    tid1 = H5Tvlen_create (H5T_NATIVE_UINT);
+    assert(tid1>0);
+
+    /* Create a dataset */
+    dataset = H5Dcreate (fid1, F43_DSETNAME, tid1, sid1, H5P_DEFAULT);
+    assert(dataset>0);
+
+    ret = H5Dwrite (dataset, tid1, H5S_ALL, H5S_ALL, H5P_DEFAULT, wdata);
+    assert(ret>=0);
+
+    ret = H5Dclose (dataset);
+    assert(ret>=0);
+
+    ret = H5Dvlen_reclaim (tid1, sid1, H5P_DEFAULT, wdata);
+    assert(ret>=0);
+
+    ret = H5Tclose (tid1);
+    assert(ret>=0);
+
+    ret = H5Sclose (sid1);
+    assert(ret>=0);
+
+    ret = H5Fclose (fid1);
+    assert(ret>=0);
+}
+
 static void gent_array1(void)
 {
     int wdata[SPACE1_DIM1][ARRAY1_DIM1];   /* Information to write */
@@ -2884,8 +2950,8 @@ static void gent_vlstr(void)
     const char *wdata[SPACE1_DIM1]= {
         "Four score and seven years ago our forefathers brought forth on this continent a new nation,",
         "conceived in liberty and dedicated to the proposition that all men are created equal.",
-        "Now we are engaged in a great civil war,",
-        "testing whether that nation or any nation so conceived and so dedicated can long endure."
+        "",
+        NULL
         };   /* Information to write */
     const char *string_att= "This is the string for the attribute";
     hid_t  fid1;  /* HDF5 File IDs  */
@@ -4288,6 +4354,7 @@ int main(void)
     gent_vldatatypes2();
     gent_vldatatypes3();
     gent_vldatatypes4();
+    gent_vldatatypes5();
 
     gent_array1();
     gent_array2();
diff --git a/tools/h5dump/testh5dump.sh b/tools/h5dump/testh5dump.sh
index 2e214d8..c0b5165 100755
--- a/tools/h5dump/testh5dump.sh
+++ b/tools/h5dump/testh5dump.sh
@@ -147,6 +147,7 @@ TOOLTEST tvldtypes1.ddl tvldtypes1.h5
 TOOLTEST tvldtypes2.ddl tvldtypes2.h5
 TOOLTEST tvldtypes3.ddl tvldtypes3.h5
 TOOLTEST tvldtypes4.ddl tvldtypes4.h5
+TOOLTEST tvldtypes5.ddl tvldtypes5.h5
 
 #test for file with variable length string data
 TOOLTEST tvlstr.ddl tvlstr.h5
diff --git a/tools/h5dump/testh5dumpxml.sh b/tools/h5dump/testh5dumpxml.sh
index b7c6f54..d5e3ad5 100755
--- a/tools/h5dump/testh5dumpxml.sh
+++ b/tools/h5dump/testh5dumpxml.sh
@@ -126,6 +126,8 @@ TOOLTEST tarray7.h5.xml --xml tarray7.h5
 TOOLTEST tvldtypes1.h5.xml --xml tvldtypes1.h5
 TOOLTEST tvldtypes2.h5.xml --xml tvldtypes2.h5
 TOOLTEST tvldtypes3.h5.xml --xml tvldtypes3.h5
+TOOLTEST tvldtypes4.h5.xml --xml tvldtypes4.h5
+TOOLTEST tvldtypes5.h5.xml --xml tvldtypes5.h5
 TOOLTEST tvlstr.h5.xml --xml tvlstr.h5
 TOOLTEST tsaf.h5.xml --xml tsaf.h5
 TOOLTEST tempty.h5.xml --xml tempty.h5
diff --git a/tools/lib/h5tools_str.c b/tools/lib/h5tools_str.c
index de1bf72..b3ee8e3 100644
--- a/tools/lib/h5tools_str.c
+++ b/tools/lib/h5tools_str.c
@@ -510,8 +510,8 @@ char *
 h5tools_str_sprint(h5tools_str_t *str, const h5dump_t *info, hid_t container,
                    hid_t type, void *vp, h5tools_context_t *ctx)
 {
-    size_t         n, offset, size, nelmts, start;
-    char          *name, quote = '\0';
+    size_t         n, offset, size=0, nelmts, start;
+    char          *name;
     unsigned char *ucp_vp = (unsigned char *)vp;
     char          *cp_vp = (char *)vp;
     hid_t          memb, obj, region;
@@ -567,6 +567,7 @@ h5tools_str_sprint(h5tools_str_t *str, const h5dump_t *info, hid_t container,
         h5tools_print_char(str, info, (unsigned char)(*ucp_vp));
     } else if (H5T_STRING == H5Tget_class(type)) {
         unsigned int i;
+        char quote = '\0';
         char *s;
 
         quote = '\0';
@@ -574,64 +575,71 @@ h5tools_str_sprint(h5tools_str_t *str, const h5dump_t *info, hid_t container,
             /* cp_vp is the pointer into the struct where a `char*' is stored. So we have
              * to dereference the pointer to get the `char*' to pass to HDstrlen(). */
             s = *(char**)cp_vp;
-            size = HDstrlen(s);
+            if(s!=NULL)
+                size = HDstrlen(s);
         } else {
             s = cp_vp;
             size = H5Tget_size(type);
         }
         pad = H5Tget_strpad(type);
 
-        for (i=0; i<size && (s[i] || pad!=H5T_STR_NULLTERM); i++) {
-            int j = 1;
-
-            /*
-             * Count how many times the next character repeats. If the
-             * threshold is zero then that means it can repeat any number
-             * of times.
-             */
-            if (info->str_repeat > 0)
-                while (i + j < size && s[i] == s[i + j])
-                    j++;
-            
-            /*
-             * Print the opening quote.  If the repeat count is high enough to
-             * warrant printing the number of repeats instead of enumerating
-             * the characters, then make sure the character to be repeated is
-             * in it's own quote.
-             */
-            if (info->str_repeat > 0 && j > info->str_repeat) {
-                if (quote)
-                    h5tools_str_append(str, "%c", quote);
-
-                quote = '\'';
-                h5tools_str_append(str, "%s%c", i ? " " : "", quote);
-            } else if (!quote) {
-                quote = '"';
-                h5tools_str_append(str, "%s%c", i ? " " : "", quote);
-            }
+        /* Check for NULL pointer for string */
+        if(s==NULL) {
+            h5tools_str_append(str, "NULL");
+        }
+        else {
+            for (i=0; i<size && (s[i] || pad!=H5T_STR_NULLTERM); i++) {
+                int j = 1;
+
+                /*
+                 * Count how many times the next character repeats. If the
+                 * threshold is zero then that means it can repeat any number
+                 * of times.
+                 */
+                if (info->str_repeat > 0)
+                    while (i + j < size && s[i] == s[i + j])
+                        j++;
                 
-            /* Print the character */
-            h5tools_print_char(str, info, (unsigned char)(s[i]));
-            
-            /* Print the repeat count */
-            if (info->str_repeat && j > info->str_repeat) {
+                /*
+                 * Print the opening quote.  If the repeat count is high enough to
+                 * warrant printing the number of repeats instead of enumerating
+                 * the characters, then make sure the character to be repeated is
+                 * in it's own quote.
+                 */
+                if (info->str_repeat > 0 && j > info->str_repeat) {
+                    if (quote)
+                        h5tools_str_append(str, "%c", quote);
+
+                    quote = '\'';
+                    h5tools_str_append(str, "%s%c", i ? " " : "", quote);
+                } else if (!quote) {
+                    quote = '"';
+                    h5tools_str_append(str, "%s%c", i ? " " : "", quote);
+                }
+                    
+                /* Print the character */
+                h5tools_print_char(str, info, (unsigned char)(s[i]));
+                
+                /* Print the repeat count */
+                if (info->str_repeat && j > info->str_repeat) {
 #ifdef REPEAT_VERBOSE
-                h5tools_str_append(str, "%c repeats %d times", quote, j - 1);
+                    h5tools_str_append(str, "%c repeats %d times", quote, j - 1);
 #else
-                h5tools_str_append(str, "%c*%d", quote, j - 1);
+                    h5tools_str_append(str, "%c*%d", quote, j - 1);
 #endif  /* REPEAT_VERBOSE */
-                quote = '\0';
-                i += j - 1;
-            }
+                    quote = '\0';
+                    i += j - 1;
+                }
 
-        }
+            }
 
-        if (quote)
-            h5tools_str_append(str, "%c", quote);
+            if (quote)
+                h5tools_str_append(str, "%c", quote);
 
-        if (i == 0)
-            /*empty string*/
-            h5tools_str_append(str, "\"\"");
+            if (i == 0)
+                /*empty string*/
+                h5tools_str_append(str, "\"\"");
+        } /* end else */
     } else if (H5Tequal(type, H5T_NATIVE_INT)) {
         memcpy(&tempint, vp, sizeof(int));
         h5tools_str_append(str, OPT(info->fmt_int, "%d"), tempint);
diff --git a/tools/testfiles/tvldtypes4.h5 b/tools/testfiles/tvldtypes4.h5
index 87aa5f9..ae5f967 100644
--- a/tools/testfiles/tvldtypes4.h5
+++ b/tools/testfiles/tvldtypes4.h5
diff --git a/tools/testfiles/tvldtypes4.h5.xml b/tools/testfiles/tvldtypes4.h5.xml
new file mode 100644
index 0000000..6a31194
--- /dev/null
+++ b/tools/testfiles/tvldtypes4.h5.xml
@@ -0,0 +1,55 @@
+#############################
+Expected output for 'h5dump --xml tvldtypes4.h5'
+#############################
+<?xml version="1.0" encoding="UTF-8"?>
+<hdf5:HDF5-File xmlns:hdf5="http://hdf.ncsa.uiuc.edu/DTDs/HDF5-File" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://hdf.ncsa.uiuc.edu/DTDs/HDF5File http://hdf.ncsa.uiuc.edu/DTDs/HDF5-File.xsd">
+<hdf5:RootGroup OBJ-XID="xid_928" H5Path="/">
+   <hdf5:Dataset Name="Dataset1" OBJ-XID="xid_976" H5Path= "/Dataset1" Parents="xid_928" H5ParentPaths="/">
+      <hdf5:StorageLayout>
+         <hdf5:ContiguousLayout/>
+      </hdf5:StorageLayout>
+         <hdf5:FillValueInfo FillTime="FillOnAlloc" AllocationTime="Late">
+         <hdf5:FillValue>
+               <hdf5:Data>
+                  <!-- VL fill not yet implemented. -->
+                  <hdf5:NoData />
+               </hdf5:Data>
+         </hdf5:FillValue>
+      </hdf5:FillValueInfo>
+      <hdf5:Dataspace>
+         <hdf5:SimpleDataspace Ndims="1">
+            <hdf5:Dimension  DimSize="4" MaxDimSize="4"/>
+         </hdf5:SimpleDataspace>
+      </hdf5:Dataspace>
+      <hdf5:DataType>
+         <hdf5:VLType>
+            <hdf5:DataType>
+               <hdf5:CompoundType>
+                  <hdf5:Field FieldName="i">
+                     <hdf5:DataType>
+                        <hdf5:AtomicType>
+                           <hdf5:IntegerType ByteOrder="LE" Sign="true" Size="4" />
+                        </hdf5:AtomicType>
+                     </hdf5:DataType>
+                  </hdf5:Field>
+                  <hdf5:Field FieldName="f">
+                     <hdf5:DataType>
+                        <hdf5:AtomicType>
+                           <hdf5:FloatType ByteOrder="LE" Size="4" SignBitLocation="31" ExponentBits="8" ExponentLocation="23" MantissaBits="23" MantissaLocation="0" />
+                        </hdf5:AtomicType>
+                     </hdf5:DataType>
+                  </hdf5:Field>
+               </hdf5:CompoundType>
+            </hdf5:DataType>
+         </hdf5:VLType>
+      </hdf5:DataType>
+<!-- Note: format of VL data not specified -->
+      <hdf5:Data>
+         <hdf5:DataFromFile>
+          0 0  10 6.66667 11 7  20 13.3333 21 13.6667 22 14
+          30 20 31 20.3333 32 20.6667 33 21
+         </hdf5:DataFromFile>
+      </hdf5:Data>
+   </hdf5:Dataset>
+</hdf5:RootGroup>
+</hdf5:HDF5-File>
diff --git a/tools/testfiles/tvldtypes5.ddl b/tools/testfiles/tvldtypes5.ddl
new file mode 100644
index 0000000..d199037
--- /dev/null
+++ b/tools/testfiles/tvldtypes5.ddl
@@ -0,0 +1,14 @@
+#############################
+Expected output for 'h5dump tvldtypes5.h5'
+#############################
+HDF5 "tvldtypes5.h5" {
+GROUP "/" {
+   DATASET "Dataset" {
+      DATATYPE  H5T_VLEN { H5T_STD_U32LE}
+      DATASPACE  SIMPLE { ( 4 ) / ( 4 ) }
+      DATA {
+         (0, 2, 4, 6, 8), (), (0, 2, 4, 6, 8, 10, 12), ()
+      }
+   }
+}
+}
diff --git a/tools/testfiles/tvldtypes5.h5 b/tools/testfiles/tvldtypes5.h5
new file mode 100644
index 0000000..702e45b
--- /dev/null
+++ b/tools/testfiles/tvldtypes5.h5
diff --git a/tools/testfiles/tvldtypes5.h5.xml b/tools/testfiles/tvldtypes5.h5.xml
new file mode 100644
index 0000000..f2452a7
--- /dev/null
+++ b/tools/testfiles/tvldtypes5.h5.xml
@@ -0,0 +1,41 @@
+#############################
+Expected output for 'h5dump --xml tvldtypes5.h5'
+#############################
+<?xml version="1.0" encoding="UTF-8"?>
+<hdf5:HDF5-File xmlns:hdf5="http://hdf.ncsa.uiuc.edu/DTDs/HDF5-File" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://hdf.ncsa.uiuc.edu/DTDs/HDF5File http://hdf.ncsa.uiuc.edu/DTDs/HDF5-File.xsd">
+<hdf5:RootGroup OBJ-XID="xid_928" H5Path="/">
+   <hdf5:Dataset Name="Dataset" OBJ-XID="xid_976" H5Path= "/Dataset" Parents="xid_928" H5ParentPaths="/">
+      <hdf5:StorageLayout>
+         <hdf5:ContiguousLayout/>
+      </hdf5:StorageLayout>
+         <hdf5:FillValueInfo FillTime="FillOnAlloc" AllocationTime="Late">
+         <hdf5:FillValue>
+               <hdf5:Data>
+                  <!-- VL fill not yet implemented. -->
+                  <hdf5:NoData />
+               </hdf5:Data>
+         </hdf5:FillValue>
+      </hdf5:FillValueInfo>
+      <hdf5:Dataspace>
+         <hdf5:SimpleDataspace Ndims="1">
+            <hdf5:Dimension  DimSize="4" MaxDimSize="4"/>
+         </hdf5:SimpleDataspace>
+      </hdf5:Dataspace>
+      <hdf5:DataType>
+         <hdf5:VLType>
+            <hdf5:DataType>
+               <hdf5:AtomicType>
+                  <hdf5:IntegerType ByteOrder="LE" Sign="false" Size="4" />
+               </hdf5:AtomicType>
+            </hdf5:DataType>
+         </hdf5:VLType>
+      </hdf5:DataType>
+<!-- Note: format of VL data not specified -->
+      <hdf5:Data>
+         <hdf5:DataFromFile>
+          0 2 4 6 8    0 2 4 6 8 10 12  
+         </hdf5:DataFromFile>
+      </hdf5:Data>
+   </hdf5:Dataset>
+</hdf5:RootGroup>
+</hdf5:HDF5-File>
diff --git a/tools/testfiles/tvlstr.ddl b/tools/testfiles/tvlstr.ddl
index 2487984..aa19d89 100644
--- a/tools/testfiles/tvlstr.ddl
+++ b/tools/testfiles/tvlstr.ddl
@@ -21,8 +21,7 @@ GROUP "/" {
       DATA {
          "Four score and seven years ago our forefathers brought forth on this continent a new nation,",
          "conceived in liberty and dedicated to the proposition that all men are created equal.",
-         "Now we are engaged in a great civil war,",
-         "testing whether that nation or any nation so conceived and so dedicated can long endure."
+         "", NULL
       }
    }
    DATATYPE "vl_string_type"       H5T_STRING {
diff --git a/tools/testfiles/tvlstr.h5 b/tools/testfiles/tvlstr.h5
index f2bf9e4..c00defc 100644
--- a/tools/testfiles/tvlstr.h5
+++ b/tools/testfiles/tvlstr.h5
diff --git a/tools/testfiles/tvlstr.h5.xml b/tools/testfiles/tvlstr.h5.xml
index d6f31df..7d9fb5b 100644
--- a/tools/testfiles/tvlstr.h5.xml
+++ b/tools/testfiles/tvlstr.h5.xml
@@ -48,8 +48,8 @@ Expected output for 'h5dump --xml tvlstr.h5'
          <hdf5:DataFromFile>
          "Four score and seven years ago our forefathers brought forth on this continent a new nation,"
          "conceived in liberty and dedicated to the proposition that all men are created equal."
-         "Now we are engaged in a great civil war,"
-         "testing whether that nation or any nation so conceived and so dedicated can long endure."
+         ""
+         NULL
          </hdf5:DataFromFile>
       </hdf5:Data>
    </hdf5:Dataset>