run

libnczarr/zattr.c

@@ -1249,7 +1249,6 @@ NCZ_computeattrdata(nc_type typehint, nc_type* typeidp, const NCjson* values, si
     size_t typelen;
     nc_type typeid = NC_NAT;
     NCjson* jtext = NULL;
-    int reclaimvalues = 0;
     int isjson = 0; /* 1 => json valued attribute */
     int count = 0; /* no. of attribute values */
 
@@ -1270,24 +1269,24 @@ NCZ_computeattrdata(nc_type typehint, nc_type* typeidp, const NCjson* values, si
 	/* Apply the JSON attribute convention and convert to JSON string */
 	typeid = NC_CHAR;
 	if((stat = NCZ_json_convention_read(values,&jtext))) goto done;
-	values = jtext; jtext = NULL;
-	reclaimvalues = 1;
+        /* Convert the JSON attribute values to the actual netcdf attribute bytes */
+        if((stat = NCZ_attr_convert(jtext,typeid,typelen,&count,buf))) goto done;
+    } else {
+        /* Convert the JSON attribute values to the actual netcdf attribute bytes */
+        if((stat = NCZ_attr_convert(values,typeid,typelen,&count,buf))) goto done;
     }
 
     if((stat = NC4_inq_atomic_type(typeid, NULL, &typelen)))
 	goto done;
 
-    /* Convert the JSON attribute values to the actual netcdf attribute bytes */
-    if((stat = NCZ_attr_convert(values,typeid,typelen,&count,buf))) goto done;
-
     if(typelenp) *typelenp = typelen;
     if(typeidp) *typeidp = typeid; /* return possibly inferred type */
     if(countp) *countp = count;
     if(datap) *datap = ncbytesextract(buf);
 
 done:
     ncbytesfree(buf);
-    if(reclaimvalues) NCJreclaim((NCjson*)values); /* we created it */
+    NCJreclaim(jtext); /* we created it */
     return ZUNTRACEX(THROW(stat),"typelen=%d count=%u",(typelenp?*typelenp:0),(countp?*countp:-1));
 }
 

libnczarr/zformat2.c

@@ -27,7 +27,7 @@ static int ZF2_codec2hdf(const NC_FILE_INFO_T* file, const NC_VAR_INFO_T* var, c
 static int write_grp(NC_FILE_INFO_T* file, NCZ_FILE_INFO_T* zfile, NCZMAP* map, NC_GRP_INFO_T* grp);
 static int write_var_meta(NC_FILE_INFO_T* file, NCZ_FILE_INFO_T* zfile, NCZMAP* map, NC_VAR_INFO_T* var);
 static int write_var(NC_FILE_INFO_T* file, NCZ_FILE_INFO_T* zfile, NCZMAP* map, NC_VAR_INFO_T* var);
-static int build_atts(NC_FILE_INFO_T* file, NCZ_FILE_INFO_T* zfile, NCZMAP* map, NC_OBJ* container, NCindex* attlist, NCjson**, NCjson**);
+static int build_atts(NC_FILE_INFO_T* file, NCZ_FILE_INFO_T* zfile, NCZMAP* map, NC_OBJ* container, NCindex* attlist, NCjson**);
 
 static int read_superblock(NC_FILE_INFO_T* file, int* nczarrvp);
 static int read_grp(NC_FILE_INFO_T* file, NC_GRP_INFO_T* grp);
@@ -143,7 +143,6 @@ write_grp(NC_FILE_INFO_T* file, NCZ_FILE_INFO_T* zfile, NCZMAP* map, NC_GRP_INFO
     NCjson* jsuper = NULL;
     NCjson* jtmp = NULL;
     NCjson* jatts = NULL;
-    NCjson* jtypes = NULL;
 
     ZTRACE(3,"file=%s grp=%s isclose=%d",file->controller->path,grp->hdr.name,isclose);
 
@@ -218,7 +217,7 @@ write_grp(NC_FILE_INFO_T* file, NCZ_FILE_INFO_T* zfile, NCZMAP* map, NC_GRP_INFO
 
     /* Build and write the Z2ATTRS object */
     assert(grp->att);
-    if((stat = build_atts(file,zfile,map,(NC_OBJ*)grp, grp->att,&jatts,&jtypes)))goto done;
+    if((stat = build_atts(file,zfile,map,(NC_OBJ*)grp, grp->att,&jatts)))goto done;
     /* write .zattrs path */
     if((stat = nczm_concat(fullpath,Z2ATTRS,&key))) goto done;
     /* Write to map */
@@ -276,7 +275,6 @@ write_var_meta(NC_FILE_INFO_T* file, NCZ_FILE_INFO_T* zfile, NCZMAP* map, NC_VAR
     NCjson* jtmp = NULL;
     NCjson* jfill = NULL;
     NCjson* jatts = NULL;
-    NCjson* jtypes = NULL;
     char* dtypename = NULL;
     int purezarr = 0;
     size64_t shape[NC_MAX_VAR_DIMS];
@@ -505,7 +503,7 @@ write_var_meta(NC_FILE_INFO_T* file, NCZ_FILE_INFO_T* zfile, NCZMAP* map, NC_VAR
 
     /* Build and write .zattrs object */
     assert(var->att);
-    if((stat = build_atts(file,zfile,map,(NC_OBJ*)var, var->att,&jatts,&jtypes)))goto done;
+    if((stat = build_atts(file,zfile,map,(NC_OBJ*)var, var->att,&jatts)))goto done;
     /* write .zattrs path */
     if((stat = nczm_concat(fullpath,Z2ATTRS,&key))) goto done;
     /* Write to map */
@@ -567,7 +565,7 @@ write_var(NC_FILE_INFO_T* file, NCZ_FILE_INFO_T* zfile, NCZMAP* map, NC_VAR_INFO
  * @author Dennis Heimbigner
  */
 static int
-build_atts(NC_FILE_INFO_T* file, NCZ_FILE_INFO_T* zfile, NCZMAP* map, NC_OBJ* container, NCindex* attlist, NCjson** jattsp, NCjson** jtypesp)
+build_atts(NC_FILE_INFO_T* file, NCZ_FILE_INFO_T* zfile, NCZMAP* map, NC_OBJ* container, NCindex* attlist, NCjson** jattsp)
 {
     int i,stat = NC_NOERR;
     NCjson* jatts = NULL;
@@ -744,7 +742,7 @@ build_atts(NC_FILE_INFO_T* file, NCZ_FILE_INFO_T* zfile, NCZMAP* map, NC_OBJ* co
     }
 
     if(jattsp) {*jattsp = jatts; jatts = NULL;}
-    if(jtypesp) {*jtypesp = jtypes; jtypes = NULL;}
+//    if(jtypesp) {*jtypesp = jtypes; jtypes = NULL;}
 done:
     nullfree(fullpath);
     nullfree(key);

libnczarr/zformat3.c

@@ -825,6 +825,7 @@ ZF3_readmeta(NC_FILE_INFO_T* file)
 	goto done;
 
 done:
+    NCJreclaim(jrootgrp);
     nullfree(rootkey);
     nclistfreeall(paths);
     return ZUNTRACE(THROW(stat));
@@ -865,8 +866,8 @@ ZF3_readattrs(NC_FILE_INFO_T* file, NC_OBJ* container, const NCjson* jatts, cons
 	jkey = NCJdictkey(jatts,i);
 	assert(jkey != NULL && NCJisatomic(jkey));
 	jvalue = NCJdictvalue(jatts,i);
-	ainfo[i].name = NCJstring(jkey);
-	ainfo[i].values = jvalue;
+	ainfo[i].name = strdup(NCJstring(jkey));
+	NCJcheck(NCJclone(jvalue,&ainfo[i].values));
 	ainfo[i].nctype = NC_NAT; /* not yet known */
     }
 
@@ -1056,7 +1057,7 @@ read_grp(NC_FILE_INFO_T* file, NC_GRP_INFO_T* grp)
     /* Pull out lists about groups and vars */
     if(purezarr)
 	{if((stat = subobjects_pure(zfile,grp,subvars,subgrps))) goto done;}
-    else
+    else if(jnczgrp != NULL)
 	{if((stat = subobjects(zfile,grp,jnczgrp,subvars,subgrps))) goto done;}
 
     /* Define vars */
@@ -1770,6 +1771,7 @@ subobjects(NCZ_FILE_INFO_T* zfile, NC_GRP_INFO_T* parent, const NCjson* jnczgrp,
     const NCjson* jsubgrps = NULL;
     const NCjson* jarrays = NULL;
 
+    assert(jnczgrp != NULL);
     NCJcheck(NCJdictget(jnczgrp,"arrays",&jarrays));
     NCJcheck(NCJdictget(jnczgrp,"subgroups",&jsubgrps));
 
@@ -2297,16 +2299,20 @@ getnextlevel(NCZ_FILE_INFO_T* zfile, NC_GRP_INFO_T* parent, NClist* varnames, NC
 	const NCjson* jnodetype;
 	if(strcmp(name,Z3OBJECT)==0) {continue;}
         /* See if name/zarr.json exists */
+        nullfree(subkey); subkey = NULL;
         if((stat = nczm_concat(grpkey,name,&subkey))) goto done;
+	nullfree(zobject); zobject = NULL;
         if((stat = nczm_concat(subkey,Z3OBJECT,&zobject))) goto done;
         switch(stat = nczmap_len(zfile->map,zobject,&zjlen)) {
 	case NC_NOERR: break;
 	case NC_ENOOBJECT: nclistpush(subgrpnames,name); continue; /* assume a virtual group */
 	default: goto done;
 	}
+	nullfree(content); content = NULL;
 	if((content = malloc(zjlen))==NULL) {stat = NC_ENOMEM; goto done;}
         if((stat = nczmap_read(zfile->map,zobject,0,zjlen,content))) goto done; /* read the zarr.json */
 	/* parse it */
+	NCJreclaim(jzarrjson); jzarrjson = NULL;
 	NCJcheck(NCJparsen((size_t)zjlen,(char*)content,0,&jzarrjson));
 	if(jzarrjson == NULL) {stat = NC_ENOTZARR; goto done;}
 	/* See what the node_type says */

libsrc4/nc4internal.c

@@ -795,8 +795,10 @@ nc4_var_set_ndims(NC_VAR_INFO_T *var, int ndims)
     /* Allocate space for dimension information. */
     if (ndims)
     {
+	if(var->dim != NULL) free(var->dim);
 	if (!(var->dim = calloc(ndims, sizeof(NC_DIM_INFO_T *))))
             return NC_ENOMEM;
+	if(var->dimids != NULL) free(var->dimids);
         if (!(var->dimids = calloc(ndims, sizeof(int))))
             return NC_ENOMEM;
 

nczarr_test/Makefile.am

@@ -8,14 +8,14 @@ BUILT_SOURCES =
 EXTRA_DIST =
 DISTCLEANFILES =
 TESTS =
+check_PROGRAMS =
 
 include $(top_srcdir)/nczarr_test/Makefile.files
 
 BUILT_SOURCES += ${ALLBUILTSCRIPTS}
 
-
 # V2 specific files
-EXTRA_DIST = CMakeLists.txt Makefile.core Makefile.files ${ALLV2BASELINE} ${ALLV2SCRIPTS}
+EXTRA_DIST += CMakeLists.txt Makefile.core Makefile.files ${ALLV2BASELINE} ${ALLV2SCRIPTS}
 
 include $(top_srcdir)/nczarr_test/Makefile.core
 

nczarr_test/ref_tst_nans.dmp

@@ -0,0 +1,16 @@
+netcdf ref_tst_nans {
+dimensions:
+	dim = 3 ;
+variables:
+	float fvar(dim) ;
+		fvar:_FillValue = NaNf ;
+		fvar:att = -Infinityf, NaNf, Infinityf ;
+	double dvar(dim) ;
+		dvar:_FillValue = NaN ;
+		dvar:att = -Infinity, NaN, Infinity ;
+data:
+
+ fvar = -Infinityf, _, Infinityf ;
+
+ dvar = -Infinity, _, Infinity ;
+}

nczarr_test/run_nan.sh

@@ -19,7 +19,7 @@ set -e
 
 # Location constants
 cdl="$srcdir/../ncdump/cdl"
-expected="$srcdir/../ncdump/expected"
+expected="$srcdir"
 
 # Functions