Fix failings of nc_test/run_inmemory.sh

re: issue https://github.com/Unidata/netcdf-c/issues/1233

Changes:

1. remove exit that was there for testing.
2. the program tst_open_mem must be netcdf-4 only.
3. fix some diff problems
   - Change dataset name for tst_inmemory4_create to tst_inmemory4
   - Modify tst_inmemory.c to reorder the variables (somewhat major rewrite)

Minor Unrelated Fixes:
1. fix comment problem in nc_provenance.h
2. Fix memory leak in tst_open_mem.c
3. fix ncdump/bindata.c to properly compile if netcdf4 is disabled.
4. minor changes to ncgen.l

debug/README.txt

@@ -1,5 +1,6 @@
 This directory contains various scripts for debugging by Dennis
 Heimbigner @ Unidata.
+DO NOT DELETE.
 USE AT YOUR OWN PERIL.
 
 

debug/cf.cmake

@@ -97,7 +97,7 @@ NCLIB="${NCLIB}/build/liblib"
 #G="-GUnix Makefiles"
 #T="--trace-expand"
 cmake "${G}" $FLAGS ..
-if test "x$NOBUILD" == x ; then
+if test "x$NOBUILD" = x ; then
 make all
 make test
 fi

include/nc_provenance.h

@@ -1,13 +1,12 @@
 /* Copyright 2005-2018 University Corporation for Atmospheric
    Research/Unidata. */
-/**
 /**
  * @file
  * @internal Contains information for creating provenance
  * info and/or displaying provenance info.
  *
  * @author Dennis Heimbigner, Ward Fisher
-
+*/
 /**************************************************/
 /**
 

nc_test/run_inmemory.sh

@@ -16,7 +16,7 @@ CREATE3=tst_inmemory3_create
 FILE4=tst_inmemory4
 CREATE4=tst_inmemory4_create
 
-# For tst_open_mem
+# For tst_open_mem NETCDF4 only
 OMEMFILE=f03tst_open_mem.nc
 
 echo ""
@@ -26,8 +26,9 @@ HASNC4=`${top_builddir}/nc-config --has-nc4`
 
 # Execute the core of the inmemory tests
 ${execdir}/tst_inmemory
-exit
+if test "x$HASNC4" = xyes ; then
 ${execdir}/tst_open_mem ${srcdir}/${OMEMFILE}
+fi
 
 echo "**** Test ncdump of the resulting inmemory data"
 ${NCDUMP} -n "${FILE3}" ${FILE3}.nc > ${FILE3}.cdl
@@ -36,8 +37,9 @@ diff -wb ${FILE3}.cdl ${CREATE3}.cdl
 
 if test "x$HASNC4" = "xyes" ; then
 ${NCDUMP} ${FILE4}.nc > ${FILE4}.cdl
-${NCDUMP} ${CREATE4}.nc > ${CREATE4}.cdl
+${NCDUMP} -n ${FILE4} ${CREATE4}.nc > ${CREATE4}.cdl
 diff -wb ${FILE4}.cdl ${CREATE4}.cdl
+fi
 
 # cleanup
 rm -f ${FILE3}.nc ${FILE4}.nc ${CREATE3}.nc ${CREATE4}.nc

nc_test/tst_inmemory.c

@@ -61,8 +61,8 @@ extern int H5Eprint1(FILE * stream);
 
 #define NVARS0 3 /* # variables in define_metadata */
 #define VAR0_NAME "nightlife"
-#define VAR1_NAME "time"
-#define VAR2_NAME "taxi_distance"
+#define VAR1_NAME "taxi_distance"
+#define VAR2_NAME "time"
 
 /* Variable added by modify_file */
 #define VAR3_NAME "miles"
@@ -270,19 +270,19 @@ define_metadata(int ncid)
 {
     int stat = NC_NOERR;
     int dimid[MAXDIMS], varid0, varid1, varid2;
-    short short_data[DIM1_LEN];
     size_t start[1] = {0};
     size_t count[1] = {DIM1_LEN};
     int dimprod = (DIM0_LEN*DIM1_LEN);
     int i;
     float float_data;
     int nightdata[DIM0_LEN*DIM1_LEN] ;
+    short taxi_distance[DIM1_LEN] ;
 
     /* Create data to write */
     float_data = FLOATVAL;
 
     for (i = 0; i < DIM1_LEN; i++)
-        short_data[i] = i;
+        taxi_distance[i] = i;
 
     for (i = 0; i < dimprod; i++)
         nightdata[i] = (100*i);
@@ -294,13 +294,13 @@ define_metadata(int ncid)
     CHECK(nc_def_dim(ncid, DIM1_NAME, DIM1_LEN, &dimid[1]));
 
     CHECK(nc_def_var(ncid, VAR0_NAME, NC_INT, 2, dimid, &varid0));
-    CHECK(nc_def_var(ncid, VAR1_NAME, NC_FLOAT, 0, NULL, &varid1));
-    CHECK(nc_def_var(ncid, VAR2_NAME, NC_SHORT, 1, &dimid[1], &varid2));
+    CHECK(nc_def_var(ncid, VAR1_NAME, NC_SHORT, 1, &dimid[1], &varid1));
+    CHECK(nc_def_var(ncid, VAR2_NAME, NC_FLOAT, 0, NULL, &varid2));
 
     CHECK(nc_enddef(ncid));
 
-    CHECK(nc_put_vara_float(ncid, varid1, NULL, NULL, &float_data));
-    CHECK(nc_put_vara_short(ncid, varid2, start, count, short_data));
+    CHECK(nc_put_vara_short(ncid, varid1, start, count, taxi_distance));
+    CHECK(nc_put_var_float(ncid, varid2, &float_data));
 
     {
         size_t start[2] = {0,0};
@@ -407,6 +407,7 @@ verify_file(int ncid, int modified, int extra)
     float float_data_in;
     int milesdata_in[MAXDIMLEN];
     int expenses_in[MAXDIMLEN];
+    short taxi_distance_in[MAXDIMLEN];
     int dimprod = DIM0_LEN * DIM1_LEN;
 #ifdef USE_NETCDF4
     int tmp;
@@ -456,18 +457,23 @@ verify_file(int ncid, int modified, int extra)
     if (strcmp(name_in, VAR0_NAME) || type_in != NC_INT || ndims_in != NDIMS0 ||
     dimid_in[0] != 0 || dimid_in[1] != 1 || natts_in != 0) CHECK(NC_EINVAL);
     CHECK(nc_inq_var(ncid, varid[1], name_in, &type_in, &ndims_in, dimid_in, &natts_in));
-    if (strcmp(name_in, VAR1_NAME) || type_in != NC_FLOAT || ndims_in != 0 ||
-    natts_in != 0) CHECK(NC_EINVAL);
+    if (strcmp(name_in, VAR1_NAME) || type_in != NC_SHORT || ndims_in != 1 || dimid_in[0] != 1 || natts_in != 0)
+    	CHECK(NC_EINVAL);
     CHECK(nc_inq_var(ncid, varid[2], name_in, &type_in, &ndims_in, dimid_in, &natts_in));
-    if (strcmp(name_in, VAR2_NAME) || type_in != NC_SHORT || ndims_in != 1 ||
-        dimid_in[0] != 1 || natts_in != 0) CHECK(NC_EINVAL);
+    if (strcmp(name_in, VAR2_NAME) || type_in != NC_FLOAT || ndims_in != 0 || natts_in != 0)
+    	CHECK(NC_EINVAL);
 
     CHECK(nc_get_var_int(ncid, varid[0], nightdata_in));
     for(i=0;i<dimprod;i++) {
 	if(nightdata_in[i] != (100*i)) CHECK(NC_EINVAL);
     }
 
-    CHECK(nc_get_vara_float(ncid, varid[1], NULL, NULL, &float_data_in));
+    CHECK(nc_get_var_short(ncid, varid[1], taxi_distance_in));
+    for(i=0;i<DIM1_LEN;i++) {
+	if(taxi_distance_in[i] != (i)) CHECK(NC_EINVAL);
+    }
+
+    CHECK(nc_get_var_float(ncid, varid[2], &float_data_in));
     if (float_data_in != FLOATVAL) CHECK(NC_EINVAL);
 
     if(modified) {

nc_test/tst_open_mem.c

@@ -31,8 +31,12 @@ readfile(const char* path, NC_memio* memio)
 #else
     f = fopen(path,"r");
 #endif
-    if(f == NULL)
-	{status = errno; goto done;}
+    if(f == NULL) {
+	fprintf(stderr,"cannot open file: %s\n",path);
+	fflush(stderr);
+	status = errno;
+	goto done;
+    }
     /* get current filesize */
     if(fseek(f,0,SEEK_END) < 0)
 	{status = errno; goto done;}
@@ -56,6 +60,7 @@ readfile(const char* path, NC_memio* memio)
     if(memio) {
 	memio->size = (size_t)filesize;
 	memio->memory = memory;
+	memory = NULL;
     }    
 done:
     if(status != NC_NOERR && memory != NULL)
@@ -82,6 +87,8 @@ main(int argc, char** argv)
 	goto exit;
     if((retval = nc_close(ncid)))
 	goto exit;
+    if(mem.memory)
+        free(mem.memory);
     return 0;
 exit:
     fprintf(stderr,"retval=%d\n",retval);

ncgen/bindata.c

@@ -431,13 +431,15 @@ Internal equivalent of ncaux_reclaim_data.
 /* It is helpful to have a structure that contains memory and an offset */
 typedef struct Reclaim {char* memory; ptrdiff_t offset;} Reclaim;
 
-static ptrdiff_t read_alignment(ptrdiff_t offset, unsigned long alignment);
 static int bin_reclaim_datar(Symbol* tsym, Reclaim* reclaim);
+#ifdef USE_NETCDF4
+static ptrdiff_t read_alignment(ptrdiff_t offset, unsigned long alignment);
 static int bin_reclaim_usertype(Symbol* tsym, Reclaim* reclaim);
 static int bin_reclaim_compound(Symbol* tsym, Reclaim* reclaim);
 static int bin_reclaim_vlen(Symbol* tsym, Reclaim* reclaim);
 static int bin_reclaim_enum(Symbol* tsym, Reclaim* reclaim);
 static int bin_reclaim_opaque(Symbol* tsym, Reclaim* reclaim);
+#endif
 
 int
 binary_reclaim_data(Symbol* tsym, void* memory, size_t count)
@@ -493,6 +495,7 @@ bin_reclaim_datar(Symbol* tsym, Reclaim* reclaimer)
     return stat;
 }
 	
+#ifdef USE_NETCDF4
 static int
 bin_reclaim_usertype(Symbol* tsym, Reclaim* reclaimer)
 {
@@ -587,6 +590,7 @@ bin_reclaim_compound(Symbol* tsym, Reclaim* reclaimer)
 done:
     return stat;
 }
+#endif /*USE_NETCDF4*/
 
 #endif /*ENABLE_BINARY*/