[svn-r78] Checkpointing dataset code. Everything is currently working, except writing

a second dataset out to the file seems to loose the first one.

8 files changed, 206 insertions, 16 deletions

diff --git a/src/H5Aprivate.h b/src/H5Aprivate.h
index 572d3be..09371d1 100644
--- a/src/H5Aprivate.h
+++ b/src/H5Aprivate.h
@@ -63,6 +63,7 @@
 #define H5A_DATATYPEID_HASHSIZE	64
 #define H5A_DATASPACEID_HASHSIZE 64
 #define H5A_DATASETID_HASHSIZE	64
+#define H5A_OID_HASHSIZE	    64
 
 /* Atom information structure used */
 typedef struct atom_info_struct_tag {
diff --git a/src/H5D.c b/src/H5D.c
index 32eb59b..995d741 100644
--- a/src/H5D.c
+++ b/src/H5D.c
@@ -38,6 +38,7 @@ static char RcsId[] = "@(#)$Revision$";
 #include <H5Dprivate.h> /* Dataset functions */
 #include <H5Eprivate.h> /* Error handling */
 #include <H5Mprivate.h> /* Meta data */
+#include <H5Gprivate.h> /* Group headers */
 #include <H5Oprivate.h> /* Object headers */
 #include <H5MFprivate.h> /* File space allocation header */
 
@@ -67,6 +68,7 @@ static herr_t H5D_init_interface(void)
     FUNC_ENTER (H5D_init_interface, NULL, FAIL);
 
     /* Initialize the atom group for the file IDs */
+    ret_value=H5Ainit_group(H5_OID,H5A_OID_HASHSIZE,0);
     ret_value=H5Ainit_group(H5_DATASET,H5A_DATASETID_HASHSIZE,H5D_RESERVED_ATOMS);
 
     FUNC_LEAVE(ret_value);
@@ -165,18 +167,21 @@ hatom_t H5D_access(hatom_t oid)
     /* Pull information about the dataset out of the file */
     dset->file=H5Aatom_object(ohdr->fid);   /* Get the pointer to the file for the dataset */
     /* Get the dataset's name */
-    if((dset->name=H5O_read(dset->file,ohdr->ohdr,ohdr->ent,H5O_NAME,1,NULL))==NULL)
+    if((dset->name=H5O_read(dset->file,ohdr->ohdr,&ohdr->ent,H5O_NAME,0,NULL))==NULL)
         HGOTO_ERROR(H5E_OHDR, H5E_NOTFOUND, FAIL);
     dset->modified=BFALSE;       /* nothing changed yet */
     /* Get the dataset's type (currently only atomic types) */
-    if((dset->type=H5O_read(dset->file,ohdr->ohdr,ohdr->ent,H5O_SIM_DTYPE,1,NULL))==NULL)
+    if((dset->type=H5O_read(dset->file,ohdr->ohdr,&ohdr->ent,H5O_SIM_DTYPE,0,NULL))==NULL)
         HGOTO_ERROR(H5E_OHDR, H5E_NOTFOUND, FAIL);
     /* Get the dataset's dimensionality (currently only simple dataspaces) */
-    if((dset->dim=H5O_read(dset->file,ohdr->ohdr,ohdr->ent,H5O_SIM_DIM,1,NULL))==NULL)
+    if((dset->dim=HDmalloc(sizeof(H5P_dim_t)))==NULL)
+        HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL);
+    dset->dim->type=H5P_TYPE_SIMPLE;    /* for now... */
+    if((dset->dim->s=H5O_read(dset->file,ohdr->ohdr,&ohdr->ent,H5O_SIM_DIM,0,NULL))==NULL)
         HGOTO_ERROR(H5E_OHDR, H5E_NOTFOUND, FAIL);
     dset->header=ohdr->ohdr;        /* keep the object header location for later */
     /* Get the dataset's data offset (currently only standard storage) */
-    if(NULL==H5O_read(dset->file,ohdr->ohdr,ohdr->ent,H5O_STD_STORE,1,&store))
+    if(NULL==H5O_read(dset->file,ohdr->ohdr,&ohdr->ent,H5O_STD_STORE,0,&store))
         HGOTO_ERROR(H5E_OHDR, H5E_NOTFOUND, FAIL);
     dset->data=store.off;
     
@@ -197,6 +202,66 @@ done:
 
 /*--------------------------------------------------------------------------
  NAME
+    H5D_find_name
+ PURPOSE
+    Get the OID for accessing an existing HDF5 dataset object
+ USAGE
+    hoid_t H5D_find_name(grp_id, type, name)
+        hatom_t grp_id;         IN: Atom for directory to search for dataset
+        hobjtype_t type;        IN: Type of object to search for (dataset in this case)
+        const char *name;       IN: Name of the object to search for
+ RETURNS
+    Returns ID (atom) on success, FAIL on failure
+ DESCRIPTION
+        This function finds for a dataset by name in a directory.
+--------------------------------------------------------------------------*/
+hatom_t H5D_find_name(hatom_t grp_id, hobjtype_t type, const char *name)
+{
+    hdf5_file_t *file;          /* Pointer to the file-store of this object */
+    H5D_oid_t *ohdr;            /* OID for reference to dataset */
+    hatom_t ret_value = SUCCEED;
+
+    FUNC_ENTER(H5D_find_name, H5D_init_interface, FAIL);
+
+    /* Clear errors and check args and all the boring stuff. */
+    H5ECLEAR;
+
+    /* Allocate space for the dataset */
+    if((ohdr=HDmalloc(sizeof(H5D_oid_t)))==NULL)
+        HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL);
+
+    /* Get directory symbols, etc... */
+    if(H5Aatom_group(grp_id)!=H5_FILE)
+        HGOTO_ERROR(H5E_ATOM, H5E_BADTYPE, FAIL);
+    file=H5Aatom_object(grp_id);
+/* WARNING! WARNING! WARNING! */
+/* The following line explicitly uses the root symbol as the
+   current working directory.  This should be changed to something more
+   appropriate and is only hacked in here to get the prototype working. -QAK
+*/
+/* WARNING! WARNING! WARNING! */
+    if(H5G_find(file,file->root_sym,&(ohdr->dir),name,&(ohdr->ent))==FAIL)
+        HGOTO_ERROR(H5E_DATASET, H5E_NOTFOUND, FAIL);
+    ohdr->fid=grp_id;
+    ohdr->ohdr=ohdr->ent.header;
+    
+    /* Register the new OID and get an ID for it */
+    if((ret_value=H5Aregister_atom(H5_OID, (const VOIDP)ohdr))==FAIL)
+        HGOTO_ERROR(H5E_ATOM, H5E_CANTREGISTER, FAIL);
+
+done:
+  if(ret_value == FAIL)   
+    { /* Error condition cleanup */
+
+    } /* end if */
+
+    /* Normal function cleanup */
+
+    FUNC_LEAVE(ret_value);
+} /* end H5D_find_name() */
+
+/*--------------------------------------------------------------------------
+ NAME
     H5Dset_info
  PURPOSE
     Set the type and dimensionality of a dataset.
@@ -302,11 +367,79 @@ done:
 
 /*--------------------------------------------------------------------------
  NAME
+    H5Dread
+ PURPOSE
+    Read data from a dataset
+ USAGE
+    herr_t H5Dread(oid)
+        hatom_t oid;       IN: Dataset to read
+        hatom_t did;       IN: Dimensionality object to use as dataspace for I/O
+        VOIDP buf;         IN: Buffer to fill with data from the file
+ RETURNS
+    SUCCEED/FAIL
+ DESCRIPTION
+        This function reads dataset object data to the file.  The dataspace
+    ID determines the slice/hyper-slab/portion of the dataset to write.
+    H5P_SCALAR is a special value which indicates that the entire dataset is
+    to be written out.  (For datasets which have a scalar dataspace for the
+    entire dataset, this is somewhat redundant.... :-)
+--------------------------------------------------------------------------*/
+herr_t H5Dread(hatom_t oid, hatom_t did, VOIDP buf)
+{
+    H5D_dataset_t *dataset; /* dataset object to do I/O on */
+    uintn   toread;         /* number of bytes to read in */
+    herr_t  ret_value = SUCCEED;
+
+    FUNC_ENTER(H5Dread, H5D_init_interface, FAIL);
+
+    /* Clear errors and check args and all the boring stuff. */
+    H5ECLEAR;
+
+    /* Check that we've received correctly typed parameters */
+    if(H5Aatom_group(did)!=H5_DATASPACE || H5Aatom_group(oid)!=H5_DATASET)
+        HGOTO_ERROR(H5E_ATOM, H5E_BADTYPE, FAIL);
+    if(buf==NULL)
+        HGOTO_ERROR(H5E_ARGS, H5E_BADRANGE, FAIL);
+
+    /* Get the object */
+    if((dataset=H5Aatom_object(oid))==NULL)
+        HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL);
+
+    /* Check that the datatype & dataspace have already been initialized */
+    if(dataset->type==NULL || dataset->dim==NULL || dataset->data==(-1))
+        HGOTO_ERROR(H5E_FUNC, H5E_UNINITIALIZED, FAIL);
+
+    /* Compute the number of bytes to read */
+    if(did==H5P_SCALAR) /* Check if we are reading the entire dataset */
+        toread=H5T_size(dataset->type,BTRUE)*H5P_nelem(dataset->dim);
+    else
+        HGOTO_ERROR(H5E_INTERNAL, H5E_UNSUPPORTED, FAIL);
+
+/* Check memory to disk datatype conversions, etc. */
+/* DO THIS! -QAK */
+    
+    /* Write the data out to disk */
+    if(H5F_block_read(dataset->file,dataset->data,toread,buf)==FAIL)
+        HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL);
+
+done:
+  if(ret_value == FAIL)   
+    { /* Error condition cleanup */
+
+    } /* end if */
+
+    /* Normal function cleanup */
+
+    FUNC_LEAVE(ret_value);
+} /* end H5Dread() */
+
+/*--------------------------------------------------------------------------
+ NAME
     H5Dwrite
  PURPOSE
     Write data for a dataset
  USAGE
-    herr_t H5Dset_info(oid)
+    herr_t H5Dwrite(oid)
         hatom_t oid;       IN: Dataset object to modify
         hatom_t did;       IN: Dimensionality object to use as dataspace for I/O
         VOIDP buf;         IN: Buffer with data to write to the file
@@ -321,7 +454,7 @@ done:
 --------------------------------------------------------------------------*/
 herr_t H5Dwrite(hatom_t oid, hatom_t did, VOIDP buf)
 {
-    H5D_dataset_t *dataset;         /* dataset object to release */
+    H5D_dataset_t *dataset;         /* dataset object to do I/O on */
     uintn   towrite;        /* number of bytes to write out */
     herr_t        ret_value = SUCCEED;
 
@@ -331,7 +464,7 @@ herr_t H5Dwrite(hatom_t oid, hatom_t did, VOIDP buf)
     H5ECLEAR;
 
     /* Check that we've received correctly typed parameters */
-    if(did!=0 && H5Aatom_group(did)!=H5_DATASPACE)
+    if(H5Aatom_group(did)!=H5_DATASPACE || H5Aatom_group(oid)!=H5_DATASET)
         HGOTO_ERROR(H5E_ATOM, H5E_BADTYPE, FAIL);
     if(buf==NULL)
         HGOTO_ERROR(H5E_ARGS, H5E_BADRANGE, FAIL);
@@ -339,12 +472,13 @@ herr_t H5Dwrite(hatom_t oid, hatom_t did, VOIDP buf)
     /* Get the object */
     if((dataset=H5Aatom_object(oid))==NULL)
         HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL);
+        
     /* Check that the datatype & dataspace haven't already been initialized */
     if(dataset->type==NULL || dataset->dim==NULL)
         HGOTO_ERROR(H5E_FUNC, H5E_UNINITIALIZED, FAIL);
 
     /* Compute the number of bytes to write out */
-    if(did==0) /* Check if we are writing out the entire dataset */
+    if(did==H5P_SCALAR) /* Check if we are writing out the entire dataset */
         towrite=H5T_size(dataset->type,BTRUE)*H5P_nelem(dataset->dim);
     else
         HGOTO_ERROR(H5E_INTERNAL, H5E_UNSUPPORTED, FAIL);
@@ -423,6 +557,12 @@ herr_t H5D_flush(hatom_t oid)
           /*
            * Write the necessary messages to the header.
            */
+            /* Write the dataset's name */
+            if(dataset->name!=NULL)
+              {
+                if(H5O_modify(dataset->file,dataset->header,&d_sym,NULL,H5O_NAME,H5O_NEW_MESG,dataset->name)==FAIL)
+                    HGOTO_ERROR (H5E_INTERNAL, H5E_CANTCREATE, FAIL);
+              } /* end if */
             /* Check if this dataset has an "atomic" datatype */
             if(BTRUE==H5T_is_atomic(dataset->type))
               {
@@ -443,6 +583,7 @@ herr_t H5D_flush(hatom_t oid)
               { /* if it's not an atomic datatype, fail for right now */
                  HGOTO_ERROR (H5E_INTERNAL, H5E_UNSUPPORTED, FAIL);
               } /* end else */
+            /* Write the dataset's storage information */
             if(dataset->data>0)
               {
                 H5O_std_store_t store;  /* standard storage info */
@@ -559,10 +700,12 @@ herr_t H5D_release(hatom_t oid)
     if(dataset->modified==BTRUE)
         H5D_flush(oid);
 
-    /* relase the memory used for the dataset */
+    /* release the memory used for the dataset */
     if(dataset->name!=NULL)
+      {
         HDfree(dataset->name->s);
         HDfree(dataset->name);
+      } /* end if */
     HDfree(dataset);
 
     /* Delete the dataset from the atom group */
diff --git a/src/H5Dprivate.h b/src/H5Dprivate.h
index a5343d4..83a090f 100644
--- a/src/H5Dprivate.h
+++ b/src/H5Dprivate.h
@@ -32,8 +32,8 @@
 typedef struct {
     hatom_t fid;        /* File Id for object */
     haddr_t ohdr;       /* Offset of the object header */
-    H5G_entry_t *dir;   /* directory entry for the directory the object is located in */
-    H5G_entry_t *ent;   /* directory entry for the object itself */
+    H5G_entry_t dir;    /* directory entry for the directory the object is located in */
+    H5G_entry_t ent;    /* directory entry for the object itself */
   } H5D_oid_t;
 
 typedef struct {
@@ -54,6 +54,7 @@ typedef struct {
 /*-----------------_-- Local function prototypes ----------------------------*/
 hatom_t H5D_create(hatom_t owner_id, hobjtype_t type, const char *name);
 hatom_t H5D_access(hatom_t oid);
+hatom_t H5D_find_name(hatom_t owner_id, hobjtype_t type, const char *name);
 herr_t H5D_flush(hatom_t oid);
 herr_t H5D_release(hatom_t oid);
 
diff --git a/src/H5Dpublic.h b/src/H5Dpublic.h
index 5eda12b..31b3080 100644
--- a/src/H5Dpublic.h
+++ b/src/H5Dpublic.h
@@ -31,6 +31,7 @@ extern "C" {
 herr_t H5Dset_info(hatom_t oid, hatom_t tid, hatom_t did);
 herr_t H5Dget_info(hatom_t oid, hatom_t *tid, hatom_t *sid);
 herr_t H5Dwrite(hatom_t oid, hatom_t did, VOIDP buf);
+herr_t H5Dread(hatom_t oid, hatom_t did, VOIDP buf);
 
 #ifdef __cplusplus
 }
diff --git a/src/H5M.c b/src/H5M.c
index b47fd2f..f3771a2 100644
--- a/src/H5M.c
+++ b/src/H5M.c
@@ -117,7 +117,7 @@ static meta_func_t meta_func_arr[]={
         H5D_create,             /* Dataset Create */
         H5D_access,             /* Dataset Access */
         NULL,                   /* Dataset Copy */
-        NULL,                   /* Dataset FindName */
+        H5D_find_name,          /* Dataset FindName */
         NULL,                   /* Dataset NameLen */
         NULL,                   /* Dataset GetName */
         NULL,                   /* Dataset SetName */
@@ -128,6 +128,23 @@ static meta_func_t meta_func_arr[]={
         NULL,                   /* Dataset GetParent */
         NULL,                   /* Dataset GetFile */
         H5D_release             /* Dataset Release */
+    },
+    {   /* Dataset object meta-functions (defined in H5D.c) */
+        H5_OID,                 /* OID Type ID */
+        NULL,                   /* OID Create */
+        H5D_access,             /* OID Access (calls dataset access routine) */
+        NULL,                   /* OID Copy */
+        NULL,                   /* OID FindName */
+        NULL,                   /* OID NameLen */
+        NULL,                   /* OID GetName */
+        NULL,                   /* OID SetName */
+        NULL,                   /* OID Search */
+        NULL,                   /* OID Index */
+        NULL,                   /* OID Flush */
+        NULL,                   /* OID Delete */
+        NULL,                   /* OID GetParent */
+        NULL,                   /* OID GetFile */
+        NULL                    /* OID Release */
     }
   };
 
@@ -350,7 +367,9 @@ done:
 --------------------------------------------------------------------------*/
 hatom_t H5Mfind_name(hatom_t owner_id, hobjtype_t type, const char *name)
 {
+#ifdef OLD_WAY
     group_t group=H5Aatom_group(owner_id);   /* Atom group for incoming object */
+#endif /* OLD_WAY */
     intn i;         /* local counting variable */
     hatom_t        ret_value = SUCCEED;
 
@@ -358,10 +377,17 @@ hatom_t H5Mfind_name(hatom_t owner_id, hobjtype_t type, const char *name)
 
     /* Clear errors and check args and all the boring stuff. */
     H5ECLEAR;
+#ifdef OLD_WAY
     if(group<=BADGROUP || group>=MAXGROUP)
         HGOTO_ERROR(H5E_ARGS, H5E_BADRANGE, FAIL);
 
     i=H5M_find_type(group);
+#else /* OLD_WAY */
+    if(type<=BADGROUP || type>=MAXGROUP)
+        HGOTO_ERROR(H5E_ARGS, H5E_BADRANGE, FAIL);
+
+    i=H5M_find_type(type);
+#endif /* OLD_WAY */
     if(meta_func_arr[i].find_name==NULL)
         HGOTO_ERROR(H5E_INTERNAL, H5E_UNSUPPORTED, FAIL);
     ret_value=(meta_func_arr[i].find_name)(owner_id,type,name);
diff --git a/src/H5Oname.c b/src/H5Oname.c
index 5631887..cec5d34 100644
--- a/src/H5Oname.c
+++ b/src/H5Oname.c
@@ -196,7 +196,7 @@ H5O_name_size (hdf5_file_t *f, const void *_mesg)
    const H5O_name_t	*mesg = (const H5O_name_t *)_mesg;
    size_t		size;
    
-   FUNC_ENTER (H5O_stab_size, NULL, FAIL);
+   FUNC_ENTER (H5O_name_size, NULL, FAIL);
 
    /* check args */
    assert (f);
diff --git a/src/H5Osdim.c b/src/H5Osdim.c
index 56a0be7..6ab0519 100644
--- a/src/H5Osdim.c
+++ b/src/H5Osdim.c
@@ -171,16 +171,16 @@ H5O_sim_dim_encode (hdf5_file_t *f, size_t raw_size, uint8 *p, const void *mesg)
     UINT32ENCODE(p,sdim->dim_flags);
     if(sdim->rank>0)
       {
-        for(u=0; u<sdim->rank; u++);
+        for(u=0; u<sdim->rank; u++)
             UINT32ENCODE(p,sdim->size[u]);
         if(sdim->dim_flags&0x01)
           {
-            for(u=0; u<sdim->rank; u++);
+            for(u=0; u<sdim->rank; u++)
                 UINT32ENCODE(p,sdim->max[u]);
           } /* end if */
         if(sdim->dim_flags&0x02)
           {
-            for(u=0; u<sdim->rank; u++);
+            for(u=0; u<sdim->rank; u++)
                 UINT32ENCODE(p,sdim->perm[u]);
           } /* end if */
       } /* end if */
@@ -338,6 +338,23 @@ H5O_sim_dim_copy (const void *mesg, void *dest)
 
    /* copy */
    HDmemcpy(dst,src,sizeof(H5O_sim_dim_t));
+   if(src->rank>0)
+     {
+       dst->size = H5MM_xcalloc (src->rank, sizeof(uint32));
+       HDmemcpy(dst->size,src->size,src->rank*sizeof(uint32));
+       /* Check for maximum dimensions and copy those */
+       if((src->dim_flags&0x01)>0)
+         {
+           dst->max = H5MM_xcalloc (src->rank, sizeof(uint32));
+           HDmemcpy(dst->max,src->max,src->rank*sizeof(uint32));
+         } /* end if */
+       /* Check for dimension permutation and copy those */
+       if((src->dim_flags&0x02)>0)
+         {
+           dst->perm = H5MM_xcalloc (src->rank, sizeof(uint32));
+           HDmemcpy(dst->perm,src->perm,src->rank*sizeof(uint32));
+         } /* end if */
+     } /* end if */
 
    FUNC_LEAVE ((void*)dst);
 } /* end H5O_sim_dim_copy() */
diff --git a/src/H5Osdtyp.c b/src/H5Osdtyp.c
index 962b646..a4b3c04 100644
--- a/src/H5Osdtyp.c
+++ b/src/H5Osdtyp.c
@@ -102,6 +102,7 @@ H5O_sim_dtype_decode (hdf5_file_t *f, size_t raw_size, const uint8 *p)
         sdtype->len=*p++;
         sdtype->arch=*p++;
         UINT16DECODE(p,sdtype->base);
+        sdtype->base=MAKE_ATOM(H5_DATATYPE,sdtype->base);   /* convert into atomic base type */
       } /* end if */
 
     FUNC_LEAVE (sdtype);