Merge branch 'main' into plistfix.dmh

Unidata · Jul 25, 2023 · 8a45d26 · 8a45d26
2 parents 65f866f + db2519c
commit 8a45d26
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diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md
@@ -8,6 +8,7 @@ This file contains a high-level description of this package's evolution. Release
 ## 4.9.3 - TBD
 
 * Fix memory leak WRT unreclaimed HDF5 plist. See [Github #????](https://github.com/Unidata/netcdf-c/pull/????).
+* Support HDF5 transient types when reading an HDF5 file.  See [Github #2724](https://github.com/Unidata/netcdf-c/pull/2724).
 * Suppress filters on variables with non-fixed-size types. See [Github #2716](https://github.com/Unidata/netcdf-c/pull/2716).
 * Provide a single option to disable all network access and testing. See [Github #2708](https://github.com/Unidata/netcdf-c/pull/2708).
 * Fix some problems with earthdata authorization and data access. See [Github #2709](https://github.com/Unidata/netcdf-c/pull/2709).

diff --git a/dap4_test/baseline/test_vlen4.nc.d4d b/dap4_test/baseline/test_vlen4.nc.d4d
@@ -8,7 +8,7 @@ types:
     v1_f1_t f1(2) ;
   }; // v1_t
 dimensions:
-	_Anonymous2 = 2 ;
+	_AnonymousDim2 = 2 ;
 variables:
 	v1_t v1 ;
 data:

diff --git a/dap4_test/baseline/test_vlen4.nc.d4m b/dap4_test/baseline/test_vlen4.nc.d4m
@@ -8,7 +8,7 @@ types:
     v1_f1_t f1(2) ;
   }; // v1_t
 dimensions:
-	_Anonymous2 = 2 ;
+	_AnonymousDim2 = 2 ;
 variables:
 	v1_t v1 ;
 }
diff --git a/dap4_test/baseline/test_vlen4.nc.d4p b/dap4_test/baseline/test_vlen4.nc.d4p
@@ -5,12 +5,12 @@
    xmlns="http://xml.opendap.org/ns/DAP/4.0#"
    xmlns:dap="http://xml.opendap.org/ns/DAP/4.0#">
   <Dimensions>
-    <Dimension name="_Anonymous2" size="2"/>
+    <Dimension name="_AnonymousDim2" size="2"/>
   </Dimensions>
   <Types>
     <Structure name="v1">
       <Seq name="f1" type="/v1_f1_t">
-        <Dim name="/_Anonymous2"/>
+        <Dim name="/_AnonymousDim2"/>
       </Sequence>
     </Structure>
     <Structure name="v1_f1_base">

diff --git a/dap4_test/baselinehyrax/amsre_20060131v5.dat.hyrax b/dap4_test/baselinehyrax/amsre_20060131v5.dat.hyrax
@@ -1,9 +1,9 @@
 netcdf amsre_20060131v5 {
 dimensions:
-	_Anonymous3 = 3 ;
-	_Anonymous6 = 6 ;
+	_AnonymousDim3 = 3 ;
+	_AnonymousDim6 = 6 ;
 variables:
-	byte time_a(_Anonymous3, _Anonymous6) ;
+	byte time_a(_AnonymousDim3, _AnonymousDim6) ;
 		string time_a:Equator_Crossing_Time = "1:30 PM" ;
 data:
 

diff --git a/dap4_test/baselineraw/test_vlen4.nc.ncdump b/dap4_test/baselineraw/test_vlen4.nc.ncdump
@@ -8,7 +8,7 @@ types:
     v1_f1_t f1(2) ;
   }; // v1_t
 dimensions:
-	_Anonymous2 = 2 ;
+	_AnonymousDim2 = 2 ;
 variables:
 	v1_t v1 ;
 data:

diff --git a/dap4_test/baselineremote/test_atomic_array.1.nc.ncdump b/dap4_test/baselineremote/test_atomic_array.1.nc.ncdump
@@ -2,13 +2,13 @@ netcdf test_atomic_array {
 types:
   opaque(16) opaque16_t ;
 dimensions:
-	_Anonymous1 = 1 ;
-	_Anonymous2 = 2 ;
+	_AnonymousDim1 = 1 ;
+	_AnonymousDim2 = 2 ;
 variables:
-	ubyte vu8(_Anonymous1, _Anonymous2) ;
-	double vd(_Anonymous1) ;
-	string vs(_Anonymous1, _Anonymous1) ;
-	opaque16_t vo(_Anonymous1, _Anonymous1) ;
+	ubyte vu8(_AnonymousDim1, _AnonymousDim2) ;
+	double vd(_AnonymousDim1) ;
+	string vs(_AnonymousDim1, _AnonymousDim1) ;
+	opaque16_t vo(_AnonymousDim1, _AnonymousDim1) ;
 
 // global attributes:
 		string :_dap4.ce = "/vu8[1][0:2:2];/vd[1];/vs[1][0];/vo[0][1]" ;

diff --git a/dap4_test/baselineremote/test_atomic_array.2.nc.ncdump b/dap4_test/baselineremote/test_atomic_array.2.nc.ncdump
@@ -1,8 +1,8 @@
 netcdf test_atomic_array {
 dimensions:
-	_Anonymous3 = 3 ;
+	_AnonymousDim3 = 3 ;
 variables:
-	short v16(_Anonymous3) ;
+	short v16(_AnonymousDim3) ;
 
 // global attributes:
 		string :_dap4.ce = "/v16[0:1,3]" ;

diff --git a/dap4_test/baselineremote/test_atomic_array.3.nc.ncdump b/dap4_test/baselineremote/test_atomic_array.3.nc.ncdump
@@ -1,8 +1,8 @@
 netcdf test_atomic_array {
 dimensions:
-	_Anonymous3 = 3 ;
+	_AnonymousDim3 = 3 ;
 variables:
-	short v16(_Anonymous3) ;
+	short v16(_AnonymousDim3) ;
 
 // global attributes:
 		string :_dap4.ce = "/v16[3,0:1]" ;

diff --git a/dap4_test/baselineremote/test_enum_array.6.nc.ncdump b/dap4_test/baselineremote/test_enum_array.6.nc.ncdump
@@ -5,9 +5,9 @@ types:
       Altocumulus = 7, Cirrostratus = 8, Cirrocumulus = 9, Cirrus = 10, 
       Missing = 127} ;
 dimensions:
-	_Anonymous2 = 2 ;
+	_AnonymousDim2 = 2 ;
 variables:
-	cloud_class_t primary_cloud(_Anonymous2) ;
+	cloud_class_t primary_cloud(_AnonymousDim2) ;
 		cloud_class_t primary_cloud:_FillValue = Missing ;
 
 // global attributes:

diff --git a/dap4_test/baselineremote/test_one_vararray.4.nc.ncdump b/dap4_test/baselineremote/test_one_vararray.4.nc.ncdump
@@ -1,8 +1,8 @@
 netcdf test_one_vararray {
 dimensions:
-	_Anonymous1 = 1 ;
+	_AnonymousDim1 = 1 ;
 variables:
-	int t(_Anonymous1) ;
+	int t(_AnonymousDim1) ;
 
 // global attributes:
 		string :_dap4.ce = "/t[1]" ;

diff --git a/dap4_test/baselineremote/test_one_vararray.5.nc.ncdump b/dap4_test/baselineremote/test_one_vararray.5.nc.ncdump
@@ -1,8 +1,8 @@
 netcdf test_one_vararray {
 dimensions:
-	_Anonymous2 = 2 ;
+	_AnonymousDim2 = 2 ;
 variables:
-	int t(_Anonymous2) ;
+	int t(_AnonymousDim2) ;
 
 // global attributes:
 		string :_dap4.ce = "/t[0:1]" ;

diff --git a/dap4_test/baselineremote/test_opaque_array.7.nc.ncdump b/dap4_test/baselineremote/test_opaque_array.7.nc.ncdump
@@ -2,10 +2,10 @@ netcdf test_opaque_array {
 types:
   opaque(16) opaque16_t ;
 dimensions:
-	_Anonymous1 = 1 ;
-	_Anonymous2 = 2 ;
+	_AnonymousDim1 = 1 ;
+	_AnonymousDim2 = 2 ;
 variables:
-	opaque16_t vo2(_Anonymous1, _Anonymous2) ;
+	opaque16_t vo2(_AnonymousDim1, _AnonymousDim2) ;
 
 // global attributes:
 		string :_dap4.ce = "/vo2[1][0:1]" ;

diff --git a/dap4_test/baselineremote/test_struct_array.8.nc.ncdump b/dap4_test/baselineremote/test_struct_array.8.nc.ncdump
@@ -5,9 +5,9 @@ types:
     int y ;
   }; // s_t
 dimensions:
-	_Anonymous2 = 2 ;
+	_AnonymousDim2 = 2 ;
 variables:
-	s_t s(_Anonymous2, _Anonymous2) ;
+	s_t s(_AnonymousDim2, _AnonymousDim2) ;
 
 // global attributes:
 		string :_dap4.ce = "/s[0:2:3][0:1]" ;

diff --git a/dap4_test/baselineremote/test_vlen4.nc.ncdump b/dap4_test/baselineremote/test_vlen4.nc.ncdump
@@ -8,7 +8,7 @@ types:
     v1_f1_t f1(2) ;
   }; // v1_t
 dimensions:
-	_Anonymous2 = 2 ;
+	_AnonymousDim2 = 2 ;
 variables:
 	v1_t v1 ;
 data:

diff --git a/dap4_test/baselinethredds/2004050300_eta_211.nc.thredds b/dap4_test/baselinethredds/2004050300_eta_211.nc.thredds
@@ -1,17 +1,17 @@
 netcdf \2004050300_eta_211 {
 dimensions:
 	record = UNLIMITED ; // (1 currently)
-	_Anonymous1 = 1 ;
-	_Anonymous4 = 4 ;
-	_Anonymous15 = 15 ;
+	_AnonymousDim1 = 1 ;
+	_AnonymousDim4 = 4 ;
+	_AnonymousDim15 = 15 ;
 variables:
 	double reftime(record) ;
 		string reftime:units = "hours since 1992-1-1" ;
 		string reftime:long_name = "reference time" ;
 	double valtime(record) ;
 		string valtime:units = "hours since 1992-1-1" ;
 		string valtime:long_name = "valid time" ;
-	float Z_sfc(_Anonymous1, _Anonymous4, _Anonymous15) ;
+	float Z_sfc(_AnonymousDim1, _AnonymousDim4, _AnonymousDim15) ;
 		string Z_sfc:navigation = "nav" ;
 		float Z_sfc:_FillValue = -9999.006f ;
 		string Z_sfc:units = "gp m" ;

diff --git a/include/hdf5internal.h b/include/hdf5internal.h
@@ -60,6 +60,7 @@ struct NCauth;
 /** Struct to hold HDF5-specific info for the file. */
 typedef struct NC_HDF5_FILE_INFO {
    hid_t hdfid;
+   unsigned transientid; /* counter for transient ids */
    NCURI* uri; /* Parse of the incoming path, if url */
 #if defined(ENABLE_BYTERANGE)
    int byterange;

diff --git a/include/netcdf_filter_hdf5_build.h b/include/netcdf_filter_hdf5_build.h
@@ -27,6 +27,10 @@
 #include "config.h"
 #endif
 
+#include <stdlib.h>
+#include <stdint.h>
+#include <stdio.h>
+
 /* Support headers */
 #include <netcdf.h>
 #include <netcdf_filter.h>
@@ -142,7 +146,7 @@ typedef const void* (*H5PL_get_plugin_info_proto)(void);
 #define H5MM_realloc realloc
 #endif
 #ifndef H5MM_xfree
-#define H5MM_xfree nullfree
+#define H5MM_xfree(x) do{if((x)!=NULL) free(x);}while(0)
 #endif
 #ifndef H5_ATTR_UNUSED
 #define H5_ATTR_UNUSED 

diff --git a/libdap4/d4parser.c b/libdap4/d4parser.c
@@ -1357,7 +1357,7 @@ makeAnonDim(NCD4parser* parser, const char* sizestr)
 
     ret = parseLL(sizestr,&size);
     if(ret) return NULL;
-    snprintf(name,NC_MAX_NAME,"/_Anonymous%lld",size);
+    snprintf(name,NC_MAX_NAME,"/_AnonymousDim%lld",size);
     /* See if it exists already */
     dim = lookupFQN(parser,name,NCD4_DIM);
     if(dim == NULL) {/* create it */

diff --git a/libhdf5/hdf5open.c b/libhdf5/hdf5open.c
@@ -245,9 +245,8 @@ get_type_info2(NC_GRP_INFO_T *h5_grp, hid_t datasetid, NC_TYPE_INFO_T **type_inf
         if (type == NULL) {
           /* If we still can't read the type, ignore it, it probably
            * means this object is a reference */
-          if (read_type(h5_grp, native_typeid, ""))
+          if (read_type(h5_grp, native_typeid, NULL))
             return NC_EBADTYPID;
-
           if((type = nc4_rec_find_hdf_type(h5, native_typeid)))
             *type_info = type;
         }
@@ -1981,7 +1980,7 @@ hdf5free(void* memory)
  *
  * @param grp Pointer to group info struct.
  * @param hdf_typeid HDF5 type ID.
- * @param type_name Pointer that gets the type name.
+ * @param type_name Pointer that gets the type name; NULL => anonymous
  *
  * @return ::NC_NOERR No error.
  * @return ::NC_EBADID Bad ncid.
@@ -1993,19 +1992,26 @@ hdf5free(void* memory)
 static int
 read_type(NC_GRP_INFO_T *grp, hid_t hdf_typeid, char *type_name)
 {
-    NC_TYPE_INFO_T *type;
-    NC_HDF5_TYPE_INFO_T *hdf5_type;
+    NC_FILE_INFO_T *h5 = NULL; 
+    NC_TYPE_INFO_T *type = NULL;
+    NC_HDF5_FILE_INFO_T *hdf5_info = NULL;
+    NC_HDF5_TYPE_INFO_T *hdf5_type = NULL;
     H5T_class_t class;
     hid_t native_typeid;
     size_t type_size;
     int nmembers;
     int retval;
+    char transientname[NC_MAX_NAME];
 
-    assert(grp && type_name);
+    assert(grp);
 
-    LOG((4, "%s: type_name %s grp->hdr.name %s", __func__, type_name,
+    LOG((4, "%s: type_name %s grp->hdr.name %s", __func__, (type_name?type_name:"NULL"),
          grp->hdr.name));
 
+    /* Get HDF5-specific object info. */
+    h5 = (NC_FILE_INFO_T *)grp->nc4_info;
+    hdf5_info = (NC_HDF5_FILE_INFO_T*)h5->format_file_info;
+
     /* What is the class of this type, compound, vlen, etc. */
     if ((class = H5Tget_class(hdf_typeid)) < 0)
         return NC_EHDFERR;
@@ -2023,6 +2029,20 @@ read_type(NC_GRP_INFO_T *grp, hid_t hdf_typeid, char *type_name)
         return NC_EHDFERR;
     LOG((5, "type_size %d", type_size));
 
+    if(type_name == NULL) {
+        /* This is a transient/anonymous type, so generate a name for it */
+	const char* suffix = NULL; /* class */
+	switch (class) {
+	case H5T_ENUM: suffix = "Enum"; break;
+	case H5T_COMPOUND: suffix = "Compound"; break;
+	case H5T_VLEN: suffix = "Vlen"; break;
+	case H5T_OPAQUE: suffix = "Opaque"; break;
+	default: suffix = "Unknown"; break;
+	}
+	snprintf(transientname,sizeof(transientname),"_Anonymous%s%u",suffix,++hdf5_info->transientid);
+	type_name = transientname;
+    }
+
     /* Add to the list for this new type, and get a local pointer to it. */
     if ((retval = nc4_type_list_add(grp, type_size, type_name, &type)))
         return retval;

diff --git a/nc_test4/tst_h_transient_types.c b/nc_test4/tst_h_transient_types.c
@@ -76,17 +76,14 @@ main()
 
   printf("*** Checking accessing file through netCDF-4 API...");
   {
-    int ncid, varid, enumid;
+    int i, ncid, varid, enumid;
     complex read_z;
-    int num_types, class;
     int *typeids;
-    nc_type base_nc_type;
     char name[NC_MAX_NAME];
-    size_t size, nfields;
     bool read_b;
+    int num_types;
 
-
-    nc_set_log_level(4);
+    nc_set_log_level(0); /* Report HDF5 errors */
     if (nc_open(FILE_NAME, NC_NOWRITE, &ncid)) ERR;
 
     /* Read known types */
@@ -97,7 +94,15 @@ main()
     typeids = (int*)malloc((size_t)num_types * sizeof(int));
     if (nc_inq_typeids(ncid, NULL, typeids)) ERR;
 
-    if (nc_inq_user_type(ncid, typeids[0], name, &size, &base_nc_type, &nfields, &class)) ERR;
+    /* Verify transient names */
+    for(i=0;i<num_types;i++) {
+        if (nc_inq_user_type(ncid, typeids[i], name, NULL, NULL, NULL, NULL)) ERR;
+	if(strlen(name) == 0) {
+            fprintf(stderr,"Transient type has no name\n");
+	    ERR;
+	}
+	fprintf(stderr,"type: %s\n",name);
+    }
     free(typeids);
 
     /* Verify that the dataset is present */

diff --git a/plugins/H5Zblosc.h b/plugins/H5Zblosc.h
@@ -27,7 +27,10 @@ extern "C" {
 #endif
 
 #include "netcdf_filter_build.h"
+
+#ifdef HAVE_BLOSC
 #include "blosc.h"
+#endif
 
 #ifdef _MSC_VER
   #ifdef DLL_EXPORT /* define when building the library */

diff --git a/plugins/H5Zzstd.h b/plugins/H5Zzstd.h
@@ -1,7 +1,9 @@
 #ifndef H5ZSTD_H
 #define H5ZSTD_H
 
+#ifdef HAVE_ZSTD
 #include "zstd.h"
+#endif
 
 #ifdef _MSC_VER
   #ifdef DLL_EXPORT /* define when building the library */