fix discovered bug in opaque data handling

ncdump/cdl4/ref_tst_opaque_data.cdl

@@ -1,13 +1,17 @@
 netcdf ref_tst_opaque_data {
 types:
-  opaque(11) raw_obs_t ;
+  opaque(10) raw_obs_t ;
+  opaque(3) raw_obs2_t ;
 dimensions:
 	time = 5 ;
 variables:
 	raw_obs_t raw_obs(time) ;
-		raw_obs_t raw_obs:_FillValue = 0XCAFEBABECAFEBABECAFEBA ;
+		raw_obs_t raw_obs:_FillValue = 0XCAFEBABECAFEBABECAF ;
+	raw_obs2_t raw_obs2(time) ;
+		raw_obs2_t raw_obs2:_FillValue = 0XABC;
 data:
 
- raw_obs = 0X0102030405060708090A0B, 0XAABBCCDDEEFFEEDDCCBBAA, 
-    0XFFFFFFFFFFFFFFFFFFFFFF, _, 0XCF0DEFACED0CAFE0FACADE ;
+ raw_obs = 0X02030405060708090A0B, 0XAABBCCDDEEFFEEDDC, 
+    0XFFFFFFFFFFFFFFFFFFFF, _, 0XCF0DEFACED0CAFE0FACA ;
+ raw_obs2 = 0X123, _, 0XFFF, _, 0X357 ;
 }

ncdump/expected4/ref_tst_opaque_data.dmp

@@ -1,13 +1,18 @@
 netcdf ref_tst_opaque_data {
 types:
-  opaque(11) raw_obs_t ;
+  opaque(10) raw_obs_t ;
+  opaque(3) raw_obs2_t ;
 dimensions:
 	time = 5 ;
 variables:
 	raw_obs_t raw_obs(time) ;
-		raw_obs_t raw_obs:_FillValue = 0XCAFEBABECAFEBABECAFEBA ;
+		raw_obs_t raw_obs:_FillValue = 0XCAFEBABECAFEBABECAF0 ;
+	raw_obs2_t raw_obs2(time) ;
+		raw_obs2_t raw_obs2:_FillValue = 0XABC000 ;
 data:
 
- raw_obs = 0X0102030405060708090A0B, 0XAABBCCDDEEFFEEDDCCBBAA, 
-    0XFFFFFFFFFFFFFFFFFFFFFF, _, 0XCF0DEFACED0CAFE0FACADE ;
+ raw_obs = 0X02030405060708090A0B, 0XAABBCCDDEEFFEEDDC000, 
+    0XFFFFFFFFFFFFFFFFFFFF, _, 0XCF0DEFACED0CAFE0FACA ;
+
+ raw_obs2 = 0X123000, _, 0XFFF000, _, 0X357000 ;
 }

ncgen/bindata.c

@@ -34,6 +34,7 @@ bin_constant(Generator* generator, Constant* con, Bytebuffer* buf,...)
     case NC_OPAQUE: {
         unsigned char* bytes;
         size_t len;
+	/* Assume the opaque string has been normalized */
         bytes=makebytestring(con->value.opaquev.stringv,&len);
         bbAppendn(buf,(void*)bytes,len);
         } break;

ncgen/cvt.c

@@ -49,7 +49,6 @@ convert1(Constant* src, Constant* dst)
     }
 
     if(src->nctype == NC_OPAQUE) {
-	ASSERT(src->value.opaquev.len >= 16);
         bytes = makebytestring(src->value.opaquev.stringv,&bytelen);
     }
 
@@ -524,7 +523,8 @@ case CASE(NC_OPAQUE,NC_DOUBLE):
     tmp.doublev = *(double*)bytes;
     break;
 case CASE(NC_OPAQUE,NC_OPAQUE):
-    tmp.opaquev.stringv = nulldup(src->value.opaquev.stringv);
+    tmp.opaquev.stringv = (char*)malloc(src->value.opaquev.len);
+    memcpy(tmp.opaquev.stringv,src->value.opaquev.stringv,src->value.opaquev.len);
     tmp.opaquev.len = src->value.opaquev.len;
     break;
 
@@ -543,6 +543,7 @@ case CASE(NC_OPAQUE,NC_OPAQUE):
     dst->value = tmp;
 }
 
+#ifdef IGNORE
 /* Force an Opaque or string to conform to a given length*/
 void
 setprimlength(Constant* prim, unsigned long len)
@@ -565,15 +566,16 @@ setprimlength(Constant* prim, unsigned long len)
             prim->value.stringv.len = len;
 	}
     } else if(prim->nctype == NC_OPAQUE) {
+	/* Note that expansion/contraction is in terms of whole
+           bytes = 2 nibbles */
+	ASSERT((len % 2) == 0);
         if(prim->value.opaquev.len == len) { 
 	    /* do nothing*/
         } else if(prim->value.opaquev.len > len) { /* truncate*/
-	    if((len % 2) != 0) len--;
 	    prim->value.opaquev.stringv[len] = '\0';
 	    prim->value.opaquev.len = len;
         } else {/* prim->value.opaquev.len < len => expand*/
 	    char* s;
-	    if((len % 2) != 0) len++;
 	    s = (char*)emalloc(len+1);
 	    memset(s,'0',len);
 	    memcpy(s,prim->value.opaquev.stringv,prim->value.opaquev.len);
@@ -584,6 +586,7 @@ setprimlength(Constant* prim, unsigned long len)
         }
     }
 }
+#endif
 
 Datalist*
 convertstringtochars(Constant* str)

ncgen/generate.c

@@ -80,6 +80,7 @@ generate_vardata(Symbol* vsym, Generator* generator, Writer writer, Bytebuffer*
     Dimset* dimset = &vsym->typ.dimset;
     int rank = dimset->ndims;
     Symbol* basetype = vsym->typ.basetype;
+    Datalist* filler = getfiller(vsym);
 
     if(vsym->data == NULL) return;
 
@@ -88,10 +89,10 @@ generate_vardata(Symbol* vsym, Generator* generator, Writer writer, Bytebuffer*
 
     if(rank == 0) {/*scalar case*/
 	Constant* c0 = datalistith(vsym->data,0);
-        generate_basetype(basetype,c0,code,NULL,generator);
+        generate_basetype(basetype,c0,code,filler,generator);
         writer(generator,vsym,code,0,NULL,NULL);
     } else {/*rank > 0*/
-	generate_array(vsym,code,NULL,generator,writer);
+	generate_array(vsym,code,filler,generator,writer);
     }
 }
 		
@@ -277,6 +278,8 @@ generate_arrayr(Symbol* vsym,
 		break;
 #endif
 	    if(con == NULL || con->nctype == NC_FILL) {
+		if(filler == NULL)
+		    filler = getfiller(vsym);
 	        generate_arrayr(vsym,code,filler,odom,nextunlimited,NULL,generator);
 		
 	    } else if(!islistconst(con))
@@ -418,6 +421,35 @@ generate_fieldarray(Symbol* basetype, Constant* con, Dimset* dimset,
     }
 }
 
+
+/* An opaque string value might not conform
+   to the size of the opaque to which it is being
+   assigned. Normalize it to match the required
+   opaque length (in bytes).
+   Note that the string is a sequence of nibbles (4 bits).
+*/
+static void
+normalizeopaquelength(Constant* prim, unsigned long nbytes)
+{
+    int nnibs = 2*nbytes;
+    ASSERT(prim->nctype==NC_OPAQUE);
+    if(prim->value.opaquev.len == nnibs) { 
+        /* do nothing*/
+    } else if(prim->value.opaquev.len > nnibs) { /* truncate*/
+	prim->value.opaquev.stringv[nnibs] = '\0';
+	prim->value.opaquev.len = nnibs;
+    } else {/* prim->value.opaquev.len < nnibs => expand*/
+        char* s;
+	s = (char*)emalloc(nnibs+1);
+	memset(s,'0',nnibs);
+	memcpy(s,prim->value.opaquev.stringv,prim->value.opaquev.len);
+	s[nnibs] = '\0';
+	efree(prim->value.opaquev.stringv);
+	prim->value.opaquev.stringv=s;
+	prim->value.opaquev.len = nnibs;
+    }
+}
+
 static void
 generate_primdata(Symbol* basetype, Constant* prim, Bytebuffer* codebuf,
 		  Datalist* filler, Generator* generator)
@@ -444,7 +476,7 @@ generate_primdata(Symbol* basetype, Constant* prim, Bytebuffer* codebuf,
 	    semerror(constline(prim),"Conversion to enum not supported (yet)");
 	} break;
      case NC_OPAQUE: 
-	setprimlength(&target,basetype->typ.size*2);
+	normalizeopaquelength(&target,basetype->typ.size);
 	break;
     default:
 	break;

ncgen/ncgen.y

@@ -931,11 +931,12 @@ makeprimitivetype(nc_type nctype)
     sym->objectclass=NC_TYPE;
     sym->subclass=NC_PRIM;
     sym->ncid = nctype;
-    sym->typ.basetype = NULL;
     sym->typ.typecode = nctype;
     sym->typ.size = ncsize(nctype);
     sym->typ.nelems = 1;
     sym->typ.alignment = nctypealignment(nctype);
+    /* Make the basetype circular so we can always ask for it */
+    sym->typ.basetype = sym;
     sym->prefix = listnew();
     return sym;
 }

ncgen/util.c

@@ -439,8 +439,8 @@ makebytestring(char* s, size_t* lenp)
 {
     unsigned char* bytes;
     unsigned char* b;
-    size_t slen = strlen(s);
-    size_t blen = slen/2;
+    size_t slen = strlen(s); /* # nibbles */
+    size_t blen = slen/2; /* # bytes */
     int i;
 
     ASSERT((slen%2) == 0);