Merge pull request #1103 from NetCDF-World-Domination-Council/ejh_fun…

…c_cleanup3

Warning, coverity warning, error handling, documentation, and hdf5_set_log_level fixes, all on the path to the lazy var feature

include/hdf5internal.h

@@ -60,4 +60,8 @@ typedef struct  NC_HDF5_FILE_INFO
 int rec_detach_scales(NC_GRP_INFO_T *grp, int dimid, hid_t dimscaleid);
 int rec_reattach_scales(NC_GRP_INFO_T *grp, int dimid, hid_t dimscaleid);
 
+/* These functions are internal to the libhdf5 directory. */
+int nc4_detect_preserve_dimids(NC_GRP_INFO_T *grp, nc_bool_t *bad_coord_orderp);
+int hdf5_set_log_level();
+
 #endif /* _HDF5INTERNAL_ */

include/nc4internal.h

@@ -1,8 +1,9 @@
 /* Copyright 2005-2018 University Corporation for Atmospheric
    Research/Unidata. */
 /**
- * @file This header file contains macros, types and prototypes used
- * to build and manipulate the netCDF metadata model.
+ * @file
+ * @internal This header file contains macros, types and prototypes
+ * used to build and manipulate the netCDF metadata model.
  *
  * @author Ed Hartnett, Dennis Heimbigner, Ward Fisher
 */
@@ -77,6 +78,9 @@ typedef enum {NCNAT, NCVAR, NCDIM, NCATT, NCTYP, NCFLD, NCGRP} NC_SORT;
 /** This is the number of netCDF atomic types. */
 #define NUM_ATOMIC_TYPES (NC_MAX_ATOMIC_TYPE + 1)
 
+/** Number of parameters needed for ZLIB filter. */
+#define CD_NELEMS_ZLIB 1
+
 /* Boolean type, to make the code easier to read */
 typedef enum {NC_FALSE = 0, NC_TRUE = 1} nc_bool_t;
 
@@ -371,6 +375,8 @@ int nc4_type_free(NC_TYPE_INFO_T *type);
 int nc4_nc4f_list_add(NC *nc, const char *path, int mode);
 void nc4_file_list_del(NC *nc);
 int nc4_var_list_add(NC_GRP_INFO_T* grp, const char* name, int ndims, NC_VAR_INFO_T **var);
+int nc4_var_list_add2(NC_GRP_INFO_T* grp, const char* name, NC_VAR_INFO_T **var);
+int nc4_var_set_ndims(NC_VAR_INFO_T *var, int ndims);
 int nc4_var_list_del(NC_GRP_INFO_T* grp, NC_VAR_INFO_T *var);
 int nc4_var_free(NC_VAR_INFO_T *var);
 int nc4_dim_list_add(NC_GRP_INFO_T* grp, const char* name, size_t len, int assignedid, NC_DIM_INFO_T **dim);
@@ -386,7 +392,7 @@ int nc4_field_list_add(NC_TYPE_INFO_T* parent, const char *name,
 int nc4_att_list_add(NCindex* list, const char* name, NC_ATT_INFO_T **att);
 int nc4_att_list_del(NCindex* list, NC_ATT_INFO_T *att);
 int nc4_att_free(NC_ATT_INFO_T *att);
-int nc4_grp_list_add(NC_GRP_INFO_T *parent, char *name, NC_GRP_INFO_T **grp);
+int nc4_grp_list_add(NC_FILE_INFO_T *h5, NC_GRP_INFO_T *parent, char *name, NC_GRP_INFO_T **grp);
 int nc4_build_root_grp(NC_FILE_INFO_T* h5);
 int nc4_rec_grp_del(NC_GRP_INFO_T *grp);
 int nc4_enum_member_add(NC_TYPE_INFO_T *type, size_t size,

libhdf5/hdf5attr.c

@@ -2,20 +2,15 @@
  * Research. See COPYRIGHT file for copying and redistribution
  * conditions. */
 /**
- * @file @internal This file is part of netcdf-4, a netCDF-like
- * interface for HDF5, or a HDF5 backend for netCDF, depending on your
- * point of view.
- *
- * This file handles HDF5 attributes.
+ * @file
+ * @internal This file handles HDF5 attributes.
  *
  * @author Ed Hartnett
  */
 
 #include "config.h"
 #include "hdf5internal.h"
 
-int nc4typelen(nc_type type);
-
 /**
  * @internal Get the attribute list for either a varid or NC_GLOBAL
  *
@@ -75,6 +70,13 @@ getattlist(NC_GRP_INFO_T *grp, int varid, NC_VAR_INFO_T **varp,
  *
  * @return ::NC_NOERR No error.
  * @return ::NC_EBADID Bad ncid.
+ * @return ::NC_EMAXNAME New name too long.
+ * @return ::NC_EPERM File is read-only.
+ * @return ::NC_ENAMEINUSE New name already in use.
+ * @return ::NC_ENOTINDEFINE Classic model file not in define mode.
+ * @return ::NC_EHDFERR HDF error.
+ * @return ::NC_ENOMEM Out of memory.
+ * @return ::NC_EINTERNAL Could not rebuild list.
  * @author Ed Hartnett
  */
 int
@@ -184,45 +186,49 @@ NC4_rename_att(int ncid, int varid, const char *name, const char *newname)
  *
  * @return ::NC_NOERR No error.
  * @return ::NC_EBADID Bad ncid.
- * @author Ed Hartnett
+ * @return ::NC_ENOTATT Attribute not found.
+ * @return ::NC_EINVAL No name provided.
+ * @return ::NC_EPERM File is read only.
+ * @return ::NC_ENOTINDEFINE Classic model not in define mode.
+ * @return ::NC_EINTERNAL Could not rebuild list.
+ * @author Ed Hartnett, Dennis Heimbigner
  */
 int
 NC4_del_att(int ncid, int varid, const char *name)
 {
-   NC *nc;
    NC_GRP_INFO_T *grp;
    NC_VAR_INFO_T *var;
    NC_FILE_INFO_T *h5;
    NC_ATT_INFO_T *att;
    NCindex* attlist = NULL;
-   hid_t locid = 0, datasetid = 0;
+   hid_t locid = 0;
    int i;
    size_t deletedid;
    int retval;
 
+   /* Name must be provided. */
    if (!name)
       return NC_EINVAL;
 
-   LOG((2, "nc_del_att: ncid 0x%x varid %d name %s",
-        ncid, varid, name));
+   LOG((2, "nc_del_att: ncid 0x%x varid %d name %s", ncid, varid, name));
 
    /* Find info for this file, group, and h5 info. */
-   if ((retval = nc4_find_nc_grp_h5(ncid, &nc, &grp, &h5)))
+   if ((retval = nc4_find_grp_h5(ncid, &grp, &h5)))
       return retval;
-
    assert(h5 && grp);
 
    /* If the file is read-only, return an error. */
    if (h5->no_write)
       return NC_EPERM;
 
-   /* If it's not in define mode, forget it. */
+   /* If file is not in define mode, return error for classic model
+    * files, otherwise switch to define mode. */
    if (!(h5->flags & NC_INDEF))
    {
       if (h5->cmode & NC_CLASSIC_MODEL)
          return NC_ENOTINDEFINE;
       if ((retval = NC4_redef(ncid)))
-         BAIL(retval);
+         return retval;
    }
 
    /* Get either the global or a variable attribute list. */
@@ -235,43 +241,71 @@ NC4_del_att(int ncid, int varid, const char *name)
    else if (var->created)
       locid = var->hdf_datasetid;
 
-   /* Now find the attribute by name */
-   att = (NC_ATT_INFO_T*)ncindexlookup(attlist,name);
-
-   /* If att is NULL, we couldn't find the attribute. */
-   if (!att)
-      BAIL_QUIET(NC_ENOTATT);
+   /* Now find the attribute by name. */
+   if (!(att = (NC_ATT_INFO_T*)ncindexlookup(attlist, name)))
+      return NC_ENOTATT;
 
    /* Delete it from the HDF5 file, if it's been created. */
    if (att->created)
    {
       assert(locid);
-
-      if(H5Adelete(locid, att->hdr.name) < 0)
-         BAIL(NC_EATTMETA);
+      if (H5Adelete(locid, att->hdr.name) < 0)
+         return NC_EATTMETA;
    }
 
-
    deletedid = att->hdr.id;
 
    /* Remove this attribute in this list */
    if ((retval = nc4_att_list_del(attlist, att)))
-      BAIL(retval);
+      return retval;
 
    /* Renumber all attributes with higher indices. */
-   for(i=0;i<ncindexsize(attlist);i++) {
-      NC_ATT_INFO_T* a = (NC_ATT_INFO_T*)ncindexith(attlist,i);
-      if(a == NULL) continue;
-      if(a->hdr.id > deletedid) a->hdr.id--;
+   for (i = 0; i < ncindexsize(attlist); i++)
+   {
+      NC_ATT_INFO_T *a;
+      if (!(a = (NC_ATT_INFO_T *)ncindexith(attlist, i)))
+         continue;
+      if (a->hdr.id > deletedid)
+         a->hdr.id--;
    }
 
-   /* rebuild the index */
-   if(!ncindexrebuild(attlist))
-      BAIL(NC_EINTERNAL);
+   /* Rebuild the index. */
+   if (!ncindexrebuild(attlist))
+      return NC_EINTERNAL;
 
-exit:
-   if (datasetid > 0) H5Dclose(datasetid);
-   return retval;
+   return NC_NOERR;
+}
+
+/**
+ * @internal This will return the length of a netcdf atomic data type
+ * in bytes.
+ *
+ * @param type A netcdf atomic type.
+ *
+ * @return Type size in bytes, or -1 if type not found.
+ * @author Ed Hartnett
+ */
+static int
+nc4typelen(nc_type type)
+{
+   switch(type){
+   case NC_BYTE:
+   case NC_CHAR:
+   case NC_UBYTE:
+      return 1;
+   case NC_USHORT:
+   case NC_SHORT:
+      return 2;
+   case NC_FLOAT:
+   case NC_INT:
+   case NC_UINT:
+      return 4;
+   case NC_DOUBLE:
+   case NC_INT64:
+   case NC_UINT64:
+      return 8;
+   }
+   return -1;
 }
 
 /**

libhdf5/hdf5create.c

@@ -195,23 +195,16 @@ nc4_create_file(const char *path, int cmode, size_t initialsz,
                                             H5P_CRT_ORDER_INDEXED)) < 0)
       BAIL(NC_EHDFERR);
 
-   /* Create the file. */
 #ifdef HDF5_HAS_COLL_METADATA_OPS
-   H5Pset_all_coll_metadata_ops(fapl_id, 1 );
-   H5Pset_coll_metadata_write(fapl_id, 1);
+   /* If HDF5 supports collective metadata operations, turn them
+    * on. This is only relevant for parallel I/O builds of HDF5. */
+   if (H5Pset_all_coll_metadata_ops(fapl_id, 1) < 0)
+      BAIL(NC_EHDFERR);
+   if (H5Pset_coll_metadata_write(fapl_id, 1) < 0)
+      BAIL(NC_EHDFERR);
 #endif
 
    if(nc4_info->mem.inmemory) {
-#if 0
-      if(nc4_info->mem.memio.size == 0)
-         nc4_info->memio.size = DEFAULT_CREATE_MEMSIZE; /* last ditch fix */
-      if(nc4_info->memio.memory == NULL) { /* last ditch fix */
-         nc4_info->memio.memory = malloc(nc4_info->memio.size);
-         if(nc4_info->memio.memory == NULL)
-            BAIL(NC_ENOMEM);
-      }
-      assert(nc4_info->memio.size > 0 && nc4_info->memio.memory != NULL);
-#endif
       retval = NC4_create_image_file(nc4_info,initialsz);
       if(retval)
          BAIL(retval);
@@ -251,9 +244,11 @@ nc4_create_file(const char *path, int cmode, size_t initialsz,
    if (comm_duped) MPI_Comm_free(&nc4_info->comm);
    if (info_duped) MPI_Info_free(&nc4_info->info);
 #endif
-   if (fapl_id != H5P_DEFAULT) H5Pclose(fapl_id);
-   if(!nc4_info) return retval;
-   nc4_close_netcdf4_file(nc4_info,1,0); /* treat like abort */
+   if (fapl_id != H5P_DEFAULT)
+      H5Pclose(fapl_id);
+   if (!nc4_info)
+      return retval;
+   nc4_close_netcdf4_file(nc4_info, 1, 0); /* treat like abort */
    return retval;
 }
 
@@ -292,6 +287,12 @@ NC4_create(const char* path, int cmode, size_t initialsz, int basepe,
    if (!nc4_hdf5_initialized)
       nc4_hdf5_initialize();
 
+#ifdef LOGGING
+   /* If nc logging level has changed, see if we need to turn on
+    * HDF5's error messages. */
+   hdf5_set_log_level();
+#endif /* LOGGING */
+
    /* Check the cmode for validity. */
    if((cmode & ILLEGAL_CREATE_FLAGS) != 0)
    {res = NC_EINVAL; goto done;}