ckp

libdispatch/dinstance_intern.c

@@ -20,6 +20,7 @@ Currently two operations are defined:
 #include "nc4dispatch.h"
 #include "ncoffsets.h"
 #include "ncbytes.h"
+#include "nclog.h"
 
 #undef REPORT
 #undef DEBUG
@@ -76,8 +77,11 @@ NC_reclaim_data(NC* nc, nc_type xtype, void* memory, size_t count)
     NC_TYPE_INFO_T* utype = NULL;
 
     assert(nc != NULL);
-    assert((memory == NULL && count == 0) || (memory != NULL || count > 0));
+    /* If memory is NULL, ignore count */
+    assert(memory == NULL || (memory != NULL && count > 0));
 
+    if(memory == NULL) goto done;
+
     /* Process atomic types */
 
     /* Optimize: Vector of fixed size atomic types (always the case for netcdf-3)*/
@@ -118,7 +122,7 @@ NC_reclaim_data(NC* nc, nc_type xtype, void* memory, size_t count)
 #endif
 
 done:
-    return stat;
+    return NCTHROW(stat);
 }
 
 #ifdef USE_NETCDF4
@@ -128,7 +132,8 @@ NC_reclaim_data(NC* nc, nc_type xtype, void* memory, size_t count)
 static int
 reclaim_datar(NC_FILE_INFO_T* file, NC_TYPE_INFO_T* utype, Position instance)
 {
-    int i,stat = NC_NOERR;
+    int stat = NC_NOERR;
+    int i;
     nc_type basetypeid;
     NC_TYPE_INFO_T* basetype = NULL;
     size_t nfields;
@@ -154,7 +159,7 @@ reclaim_datar(NC_FILE_INFO_T* file, NC_TYPE_INFO_T* utype, Position instance)
 	if(basetypeid == NC_STRING) {
             if(vlen->len > 0 && vlen->p != NULL) {
 	        char** slist = (char**)vlen->p; /* vlen instance is a vector of string pointers */
-		for(i=0;i<vlen->len;i++) {if(slist[i] != NULL) {free(slist[i]);slist[i] = NULL;}}
+		for(i=0;i<(int)vlen->len;i++) {if(slist[i] != NULL) {free(slist[i]);slist[i] = NULL;}}
 	    }
 	    goto out;
 	}
@@ -167,7 +172,7 @@ reclaim_datar(NC_FILE_INFO_T* file, NC_TYPE_INFO_T* utype, Position instance)
         if((stat = NC_type_alignment_internal(file,basetypeid,basetype,&alignment))) goto done;;
         vinstance.memory = (char*)vlen->p; /* use char* so we can do pointer arithmetic */
         vinstance.memory = (void*)NC_read_align((uintptr_t)vinstance.memory,alignment);
-        for(i=0;i<vlen->len;i++) {
+        for(i=0;i<(int)vlen->len;i++) {
             if((stat=reclaim_datar(file,basetype,vinstance))) goto done; /* reclaim one basetype instance */
 	    vinstance.memory += basetype->size; /* move to next base instance */
         }
@@ -217,7 +222,7 @@ reclaim_datar(NC_FILE_INFO_T* file, NC_TYPE_INFO_T* utype, Position instance)
     } else {stat = NC_EBADTYPE; goto done;}
 
 done:
-    return stat;
+    return NCTHROW(stat);
 }
 #endif
 
@@ -323,7 +328,7 @@ NC_copy_data(NC* nc, nc_type xtype, const void* memory, size_t count, void* copy
 #endif
 
 done:
-    return stat;
+    return NCTHROW(stat);
 }
 
 #ifdef USE_NETCDF4
@@ -380,7 +385,7 @@ copy_datar(NC_FILE_INFO_T* file, NC_TYPE_INFO_T* utype, Position src, Position d
     	    char** dststrvec = NULL;
 	    if((dststrvec = (void*)malloc(copycount))==NULL) {stat = NC_ENOMEM; goto done;}
     	    dstvlens->p = (void*)dststrvec;
-	    for(i=0;i<srcvlens->len;i++) {
+	    for(i=0;i<(int)srcvlens->len;i++) {
 		if((dststrvec[i] = strdup(srcstrvec[i]))==NULL) {stat = NC_ENOMEM; goto done;}
 	    }
 	    goto done;
@@ -406,7 +411,7 @@ copy_datar(NC_FILE_INFO_T* file, NC_TYPE_INFO_T* utype, Position src, Position d
         dstvlens->p = vdst.memory; /* don't lose it */
         vsrc.memory = (void*)NC_read_align((uintptr_t)vsrc.memory,alignment);
 	vdst.memory = (void*)NC_read_align((uintptr_t)vdst.memory,alignment);
-        for(i=0;i<srcvlens->len;i++) {
+        for(i=0;i<(int)srcvlens->len;i++) {
             if((stat=copy_datar(file,basetype,vsrc,vdst))) goto done;
 	    vsrc.memory += basetype->size;
 	    vdst.memory += basetype->size;
@@ -441,7 +446,7 @@ copy_datar(NC_FILE_INFO_T* file, NC_TYPE_INFO_T* utype, Position src, Position d
 	    if(field->nc_typeid == NC_STRING) {
 	        char** srcstrvec = (char**)src.memory;
 	        char** dststrvec = (char**)dst.memory;
-		for(i=0;i<arraycount;i++) 
+		for(i=0;i<(int)arraycount;i++) 
 		    {if(srcstrvec[i] != NULL) {dststrvec[i] = strdup(srcstrvec[i]);} else {dststrvec[i] = NULL;}}
 		continue; /* move to next field */
 	    }
@@ -454,7 +459,7 @@ copy_datar(NC_FILE_INFO_T* file, NC_TYPE_INFO_T* utype, Position src, Position d
 	    }
 
 	    /* Remaining case; field type is variable type */
-            for(i=0;i<arraycount;i++) {
+            for(i=0;i<(int)arraycount;i++) {
                 if((stat = copy_datar(file, basetype, fsrc, fdst))) goto done;
 		fsrc.memory += basetype->size;
 		fdst.memory += basetype->size;
@@ -465,7 +470,7 @@ copy_datar(NC_FILE_INFO_T* file, NC_TYPE_INFO_T* utype, Position src, Position d
     } else {stat = NC_EBADTYPE; goto done;}
 
 done:
-    return stat;
+    return NCTHROW(stat);
 }
 #endif
 
@@ -531,7 +536,7 @@ NC_type_alignment_internal(NC_FILE_INFO_T* file, nc_type xtype, NC_TYPE_INFO_T*
 Why was this here?
     if(stat == NC_NOERR && align == 0) stat = NC_EINVAL;
 #endif
-    return stat;
+    return NCTHROW(stat);
 }
 #endif
 
@@ -546,11 +551,15 @@ NC_reclaim_data_all(NC* nc, nc_type xtypeid, void* memory, size_t count)
     int stat = NC_NOERR;
 
     assert(nc != NULL);
+    /* If memory is NULL, ignore count */
+    assert(memory == NULL || (memory != NULL && count > 0));
 
+    if(memory == NULL) goto done;
     stat = NC_reclaim_data(nc,xtypeid,memory,count);
     if(stat == NC_NOERR && memory != NULL)
         {free(memory); memory = NULL;}
-    return stat;
+done:
+    return NCTHROW(stat);
 }
 
 /* Alternate entry point: includes recovering the top-level memory */
@@ -597,7 +606,7 @@ NC_copy_data_all(NC* nc, nc_type xtype, const void* memory, size_t count, void**
 #endif
     if(copyp) {*copyp = copy; copy = NULL;}
 done:
-    return stat;
+    return NCTHROW(stat);
 }
 
 /* Alternate entry point: includes recovering the top-level memory */

libnczarr/Makefile.am

@@ -55,6 +55,7 @@ ztype.c \
 zutil.c \
 zvar.c \
 zwalk.c \
+znc4.c \
 zdebug.c \
 zformat.h \
 zarr.h \

libnczarr/zarr.h

@@ -97,7 +97,7 @@ EXTERNL void NCZ_setatts_read(NC_OBJ* container);
 EXTERNL int NCZ_decodesizet64vec(const NCjson* jshape, size_t* rankp, size64_t* shapes);
 EXTERNL int NCZ_decodesizetvec(const NCjson* jshape, size_t* rankp, size_t* shapes);
 EXTERNL int NCZ_uniquedimname(NC_FILE_INFO_T* file, NC_GRP_INFO_T* parent, NCZ_DimInfo* dimdata, NC_DIM_INFO_T** dimp, NCbytes* dimname);
-EXTERNL int NCZ_computeattrdata(NC_FILE_INFO_T* file, struct NCZ_AttrInfo* att);
+EXTERNL int NCZ_computeattrdata(NC_FILE_INFO_T* file, const NCjson* jdata, struct NCZ_AttrInfo* att);
 EXTERNL int NCZ_dictgetalt(const NCjson* jdict, const NCjson** jvaluep, ...);
 EXTERNL int NCZ_dictgetalt2(const NCjson* jdict, const NCjson** jvaluep, const char* name1, const char* name2); /* common case */
 EXTERNL int NCZ_getnczarrkey(NC_FILE_INFO_T* file, struct ZOBJ* jsonz, const char* name, const NCjson** jncxxxp);

libnczarr/zattr.c

@@ -908,9 +908,9 @@ NCZ_set_dual_obj_data(NC_FILE_INFO_T* file, NC_OBJ* object, const char* name, Du
         switch(which) {
         case DA_FILLVALUE:
 	    assert(len == 1);	    
-            if((stat = NC_reclaim_data_all(file->controller,tid,var->fill_value,1))) goto done;
+            if((stat = NC_reclaim_data_all(file->controller,tid,var->fill_value,len))) goto done;
             var->fill_value = NULL;
-            if((stat = NC_copy_data_all(file->controller,tid,data,1,&var->fill_value))) goto done;
+            if((stat = NC_copy_data_all(file->controller,tid,data,len,&var->fill_value))) goto done;
             break;
         case DA_MAXSTRLEN:
 	    assert(len == 1);
@@ -970,16 +970,15 @@ This is essentially Version 2|3 agnostic because the
 data part of an attribute is (currently) the same for both versions.
 */
 int
-NCZ_computeattrdata(NC_FILE_INFO_T* file, struct NCZ_AttrInfo* ainfo)
+NCZ_computeattrdata(NC_FILE_INFO_T* file, const NCjson* jdata, struct NCZ_AttrInfo* ainfo)
 {
     int stat = NC_NOERR;
     NCbytes* buf = ncbytesnew();
     NCjson* jtext = NULL;
     int isjson = 0; /* 1 => attribute value is neither scalar nor array of scalars */
     int reclaimvalues = 0;
-    const NCjson* jdata = ainfo->jdata;
 
-    ZTRACE(3,"typehint=%d typeid=%d values=|%s|",ainfo->typehint,ainfo->nctype,NCJtotext(ainfo->jdata));
+    ZTRACE(3,"typehint=%d typeid=%d values=|%s|",ainfo->typehint,ainfo->nctype,NCJtotext(jdata));
 
     /* See if this is a simple vector (or scalar) of atomic types vs more complex json */
     isjson = (ainfo->nctype == NC_JSON || NCZ_iscomplexjson(ainfo->name,jdata));

libnczarr/zfill.c

@@ -43,72 +43,6 @@ static struct DFALTFILL {
 /**************************************************/
 /**************************************************/
 
-#if 0
-/* (over-) write the NC_VAR_INFO_T.fill_value; always make copy of fillvalue argument.
-   Takes no_fill flag into account. Sync with attribute
-*/
-int
-NCZ_set_fill_value(NC_FILE_INFO_T* file, NC_VAR_INFO_T* var, int no_fill, const void* fillvalue)
-{
-    int stat = NC_NOERR;
-    size_t size;
-    nc_type tid = var->type_info->hdr.id;
-
-    if(no_fill) {
-	stat = NCZ_disable_fill(file,var);
-	goto done;
-    }
-
-    if ((stat = nc4_get_typelen_mem(file, tid, &size))) goto done;
-    assert(size);
-
-    /* Reclaim any existing var->fill_value */
-    if(var->fill_value != NULL) {
-	if((stat = NC_reclaim_data_all(file->controller,tid,var->fill_value,1))) goto done;
-        var->fill_value = NULL;
-    }
-    if(fillvalue == NULL) {/* use default fill value */
-	/* initialize the fill_value to the default */
-	if((stat = NCZ_set_fill_value(file,var,var->no_fill,NCZ_getdfaltfillvalue(var->type_info->hdr.id)))) goto done;
-        var->fill_val_changed = 0;
-    } else {
-        /* overwrite the fill value */
-	assert(var->fill_value == NULL);
-        if((stat = NC_copy_data_all(file->controller,tid,fillvalue,1,&var->fill_value))) goto done;
-	var->fill_val_changed = 1;
-    }
-    var->no_fill = NC_FILL;
-
-    stat = NCZ_reclaim_fill_chunk(((NCZ_VAR_INFO_T*)var->format_var_info)->cache); /* Reclaim any existing fill_chunk */
-
-done:
-    return THROW(stat);
-}
-
-/* (over-) write/create the _FillValue attribute; always makes copy of NC_VAR_INFO_T.fill_value.
-   Takes no_fill flag into account. Does not sync with NC_VAR_INFO_T.fill_value.
-*/
-int
-NCZ_set_fill_att(NC_FILE_INFO_T* file, NC_VAR_INFO_T* var, NC_ATT_INFO_T* att, int no_fill, const void* fillvalue)
-{
-    int stat = NC_NOERR;
-    if(no_fill) {
-	stat = NCZ_fillvalue_disable(file,var);
-    } else {
-	if(att == NULL) {
-	    int isnew = 0;
-	    if((stat = NCZ_getattr(file, (NC_OBJ*)var, NC_FillValue, var->type_info->hdr.id, &att, &isnew))) goto done;
-	}    
-        assert(att != NULL && strcmp(att->hdr.name,NC_FillValue)==0); /* Verify */
-        if((stat = NCZ_sync_dual_att(file,(NC_OBJ*)var,NC_FillValue,DA_FILLVALUE,FIXATT))) goto done;
-	var->no_fill = NC_FALSE;
-	var->fill_val_changed = 1;
-    }
-
-done:
-    return THROW(stat);
-}
-#endif
 
 /* Turn off var.no_fill and var.fill_value. Sync with attribute */
 int

libnczarr/zformat2.c

@@ -102,7 +102,7 @@ static int ZF2_encode_xarray(NC_FILE_INFO_T* file, size_t rank, NC_DIM_INFO_T**
 static int decode_grp_dims(NC_FILE_INFO_T* file, NC_GRP_INFO_T* grp, const NCjson* jdims, NClist* dimdefs);
 static int dtype2nctype(NC_FILE_INFO_T* file, const char* dtype, int isattr, nc_type* nctypep, int* endianp, size_t* typelenp);
 static int nctype2dtype(NC_FILE_INFO_T* file, nc_type nctype, int endianness, size_t typesize, char** dtypep, char** dattrtypep);
-static int computeattrinfo(NC_FILE_INFO_T* file, nc_type typehint, const char* aname, const NCjson* jtypes, const NCjson* jainfo, struct NCZ_AttrInfo* ainfo);
+static int computeattrinfo(NC_FILE_INFO_T* file, nc_type typehint, const char* aname, const NCjson* jtypes, const NCjson* jdata, struct NCZ_AttrInfo* ainfo);
 
 /**************************************************/
 /* Format dispatch table */
@@ -517,17 +517,14 @@ ZF2_decode_var(NC_FILE_INFO_T* file, NC_VAR_INFO_T* var, struct ZOBJ* zobj, NCli
 	    NCZ_clearAttrInfo(file,&ainfo);
 	    ainfo.name = NC_FillValue;
 	    ainfo.nctype = vtype;
-	    ainfo.jdata = jvalue;
-	    if((stat = NCZ_computeattrdata(file,&ainfo))) goto done;
+	    if((stat = NCZ_computeattrdata(file,jvalue,&ainfo))) goto done;
 	    /* Create var->fill_value */
 	    assert(ainfo.nctype == vtype);
 	    if((stat = NCZ_set_dual_obj_data(file,(NC_OBJ*)var,NC_FillValue,DA_FILLVALUE,ainfo.datalen,ainfo.data))) goto done;	
 	    /* propagate to _FillValue attribute */
 	    if((stat = NCZ_sync_dual_att(file,(NC_OBJ*)var,NC_FillValue,DA_FILLVALUE,FIXATT))) goto done;
-	    /* reclaim ainfo.data */
-	    if((stat = NC_reclaim_data_all(file->controller,ainfo.nctype,ainfo.data,ainfo.datalen))) goto done;
-	    ainfo.datalen = 0;
-	    ainfo.data = NULL;
+	    /* clear+reclaim ainfo */
+	    NCZ_clearAttrInfo(file,&ainfo);
 	}
     }
 
@@ -1656,7 +1653,7 @@ dtype2nctype(NC_FILE_INFO_T* file, const char* dtype, int isattr, nc_type* nctyp
 Extract type and data for an attribute from json
 */
 static int
-computeattrinfo(NC_FILE_INFO_T* file, nc_type typehint, const char* aname, const NCjson* jtypes, const NCjson* jainfo, struct NCZ_AttrInfo* ainfo)
+computeattrinfo(NC_FILE_INFO_T* file, nc_type typehint, const char* aname, const NCjson* jtypes, const NCjson* jdata, struct NCZ_AttrInfo* ainfo)
 {
     int stat = NC_NOERR;
     int purezarr = 0;
@@ -1670,13 +1667,11 @@ computeattrinfo(NC_FILE_INFO_T* file, nc_type typehint, const char* aname, const
     TESTPUREZARR;
 
     ainfo->name = aname;
-    /* Save the attribute data */
-    ainfo->jdata = jainfo;
 
     /* Infer the attribute data's type */
     if(purezarr || jtypes == NULL) {
         ainfo->nctype = NC_NAT;
-        if((stat = NCZ_inferattrtype(ainfo->name,typehint,ainfo->jdata,&ainfo->nctype))) goto done;
+        if((stat = NCZ_inferattrtype(ainfo->name,typehint,jdata,&ainfo->nctype))) goto done;
     } else {
         /* Search the jtypes for the type of this attribute */
         ainfo->nctype = NC_NAT;
@@ -1685,7 +1680,7 @@ computeattrinfo(NC_FILE_INFO_T* file, nc_type typehint, const char* aname, const
         if((stat=dtype2nctype(file,NCJstring(jatype),ISATTR,&ainfo->nctype,&ainfo->endianness,&ainfo->typelen))) goto done;
         if(ainfo->nctype >= N_NCZARR_TYPES) {stat = NC_EINTERNAL; goto done;}
     }
-    if((stat = NCZ_computeattrdata(file,ainfo))) goto done;
+    if((stat = NCZ_computeattrdata(file,jdata,ainfo))) goto done;
 
 done:
     return ZUNTRACEX(THROW(stat),"typeid=%d typelen=%d len=%u",ainfo->nctype,ainfo->typelen,ainfo->len);

libnczarr/zinternal.c

@@ -312,11 +312,11 @@ NCZ_ensure_fill_value(NC_VAR_INFO_T *var)
         return NC_NOERR;
 
     /* If the user has set a fill_value for this var, use, otherwise find the default fill value. */
-    assert(var->no_fill == NC_FILL);
     if(var->fill_value == NULL) {
 	NC_FILE_INFO_T* file = var->container->nc4_info;
 	nc_type vartid = var->type_info->hdr.id;
-	if((stat = NC_copy_data_all(file->controller,vartid,NCZ_getdfaltfillvalue(vartid),1,&var->fill_value))) goto done;
+	void* dfalt = NCZ_getdfaltfillvalue(vartid);
+	if((stat = NCZ_set_dual_obj_data(file,(NC_OBJ*)var,NC_FillValue,DA_FILLVALUE,1,dfalt))) goto done;
 	/* synchronize to attribute */
 	if((stat = NCZ_sync_dual_att(file,(NC_OBJ*)var,NC_FillValue,DA_FILLVALUE,FIXATT))) goto done;
     }

libnczarr/zinternal.h

@@ -358,7 +358,6 @@ typedef struct NCZ_DimDecl {
 /* Parsed Attribute info */
 struct NCZ_AttrInfo {
     const char* name;
-    const NCjson* jdata;
     nc_type nctype;
     size_t typelen;
     int endianness;