netcdf-c/plugins/H5Zmisc.c
Dennis Heimbigner 1552d894a2 Cleanup a number of issues.
re: Issue https://github.com/Unidata/netcdf-c/issues/2748

This PR fixes a number of issues and bugs.

## s3cleanup fixes
* Delete extraneous s3cleanup.sh related files.
* Remove duplicate s3cleanup.uids entries.

## Support the Google S3 API
* Add code to recognize "storage.gooleapis.com"
* Add extra code to track the kind of server being accessed: unknown, Amazon, Google.
* Add a new mode flag "gs3" (analog to "s3") to support this api.
* Modify the S3 URL code to support this case.
* Modify the listobjects result parsing because Google returns some non-standard XML elements.
* Change signature and calls for NC_s3urlrebuild.

## Handle corrupt Zarr files where shape is empty for a variable.
Modify behavior when a variable's "shape" dictionary entry.
Previously it returned an error, but now it suppresses such a variable.
This change makes it possible to read non-corrupt data from the file.
Also added a test case.

## Misc. Other Changes
* Fix the nclog level handling to suppress output by default.
* Fix de-duplicates code in ncuri.c
* Restore testing of iridl.ldeo.columbia.edu.
* Fix bug in define_vars() which did not always do a proper reclaim between variables.
2023-10-08 11:22:52 -06:00

294 lines
8.3 KiB
C

#include "config.h"
#include <stdlib.h>
#include <string.h>
#include <assert.h>
#include <stdio.h>
#include <sys/types.h>
#include "h5misc.h"
#include "netcdf_aux.h"
/* WARNING:
Starting with HDF5 version 1.10.x, the plugin code MUST be
careful when using the standard *malloc()*, *realloc()*, and
*free()* function.
In the event that the code is allocating, reallocating, for
free'ing memory that either came from or will be exported to the
calling HDF5 library, then one MUST use the corresponding HDF5
functions *H5allocate_memory()*, *H5resize_memory()*,
*H5free_memory()* [5] to avoid memory failures.
Additionally, if your filter code leaks memory, then the HDF5 library
will generate an error.
*/
#undef DEBUG
/* The C standard apparently defines all floating point constants as double;
we rely on that in this code.
*/
#define DBLVAL 12345678.12345678
static htri_t H5Z_test_can_apply(hid_t dcpl_id, hid_t type_id, hid_t space_id);
static size_t H5Z_filter_test(unsigned int flags, size_t cd_nelmts,
const unsigned int cd_values[], size_t nbytes,
size_t *buf_size, void **buf);
static int paramcheck(size_t nparams, const unsigned int* params, struct All* extracted);
static void mismatch(const char* which);
const H5Z_class2_t H5Z_TEST[1] = {{
H5Z_CLASS_T_VERS, /* H5Z_class_t version */
(H5Z_filter_t)(H5Z_FILTER_TEST), /* Filter id number */
1, /* encoder_present flag (set to true) */
1, /* decoder_present flag (set to true) */
"test", /* Filter name for debugging */
(H5Z_can_apply_func_t)H5Z_test_can_apply, /* The "can apply" callback */
NULL, /* The "set local" callback */
(H5Z_func_t)H5Z_filter_test, /* The actual filter function */
}};
/* External Discovery Functions */
DLLEXPORT
H5PL_type_t
H5PLget_plugin_type(void)
{
return H5PL_TYPE_FILTER;
}
DLLEXPORT
const void*
H5PLget_plugin_info(void)
{
return H5Z_TEST;
}
/* Make this explicit */
/*
* The "can_apply" callback returns positive a valid combination, zero for an
* invalid combination and negative for an error.
*/
static htri_t
H5Z_test_can_apply(hid_t dcpl_id, hid_t type_id, hid_t space_id)
{
return 1; /* Assume it can always apply */
}
/*
This filter does some verification
that the parameters passed to the filter
are correct. Specifically, that endian-ness
is correct. As a filter, it is the identify
function, passing input to output unchanged.
It also prints out the size of each chunk.
Test cases format:
1.The first param is the test index i.e. which test to execute.
2. The remaining parameters are those for the test chosen in #1
*/
static size_t
H5Z_filter_test(unsigned int flags, size_t cd_nelmts,
const unsigned int cd_values[], size_t nbytes,
size_t *buf_size, void **buf)
{
void* newbuf;
unsigned int testcase = 0;
size_t size = 1024 * sizeof(float) * 2;
struct All values;
if(cd_nelmts == 0)
goto fail;
testcase = cd_values[0];
switch (testcase) {
case TC_PARAMS:
if(!paramcheck(cd_nelmts,cd_values,&values))
goto fail;
break;
case TC_ODDSIZE:
/* Print out the chunk size */
fprintf(stderr,">>> nbytes = %lld chunk size = %lld\n",(long long)nbytes,(long long)*buf_size);
fflush(stderr);
break;
default: break;
}
if (flags & H5Z_FLAG_REVERSE) { /* Decompress */
if(testcase == TC_EXPANDED) {
#ifdef DEBUG
int i;
float* b = (float*)*buf;
fprintf(stderr,">>> TC_EXPANDED: decompress: nbytes=%u buf_size=%u xdata[0..8]=|",(unsigned)nbytes,(unsigned)*buf_size);
for(i=0;i<8;i++) {
fprintf(stderr," %u",(int)(b[1024+i]));
}
fprintf(stderr,"|\n");
#endif
/* Replace buffer */
newbuf = H5allocate_memory(*buf_size,0);
if(newbuf == NULL) abort();
memcpy(newbuf,*buf,*buf_size);
} else {
/* Replace buffer */
newbuf = H5allocate_memory(*buf_size,0);
if(newbuf == NULL) abort();
memcpy(newbuf,*buf,*buf_size);
}
/* reclaim old buffer */
H5free_memory(*buf);
*buf = newbuf;
} else { /* (flags & H5Z_FLAG_REVERSE) Compress */
if(testcase == TC_EXPANDED) {
int i;
float* b;
#ifdef DEBUG
fprintf(stderr,">>> TC_EXPANDED: compress: nbytes=%u buf_size=%u size=%u\n",(unsigned)nbytes,(unsigned)*buf_size,(unsigned)size);
#endif
/* Replace buffer with one that is bigger than the input size */
newbuf = H5allocate_memory(size,0);
if(newbuf == NULL) abort();
b = (float*)newbuf;
for(i=0;i<1024*2;i++) {
b[i] = (float)(17+i);
}
memcpy(newbuf,*buf,*buf_size);
*buf_size = size;
} else {
/* Replace buffer */
newbuf = H5allocate_memory(*buf_size,0);
if(newbuf == NULL) abort();
memcpy(newbuf,*buf,*buf_size);
}
/* reclaim old buffer */
H5free_memory(*buf);
*buf = newbuf;
}
return *buf_size;
fail:
return 0;
}
static void
extract1(void* field, size_t size, const unsigned int* params)
{
union {
unsigned long long ll;
unsigned char char8[8];
unsigned param[2];
} u;
unsigned char b = 0;
unsigned short s = 0;
unsigned int i = 0;
unsigned char* bp = 0;
unsigned short* sp = NULL;
unsigned int* ip = NULL;
unsigned long long* llp = NULL;
memset(&u,0,sizeof(u));
switch (size) {
case 1:
b = (unsigned char)(params[0]);
bp = (unsigned char*)field;
*bp = b;
break;
case 2:
s = (unsigned short)(params[0]);
sp = (unsigned short*)field;
*sp = s;
break;
case 4:
i = (unsigned)(params[0]);
ip = (unsigned*)field;
*ip = i;
break;
case 8:
u.param[0] = params[0];
u.param[1] = params[1];
ncaux_h5filterspec_fix8(u.char8,0);
llp = (unsigned long long*)field;
*llp = u.ll;
break;
default: fprintf(stderr,">>> insert: unexpected size: %u\n",(unsigned)size); abort();
}
}
static void
extractparams(size_t nparams, const unsigned int* params, struct All* all)
{
size_t offset = 0;
extract1(&all->tbyte,sizeof(all->tbyte),&params[offset]); offset += 1;
extract1(&all->tubyte,sizeof(all->tubyte),&params[offset]); offset += 1;
extract1(&all->tshort,sizeof(all->tshort),&params[offset]); offset += 1;
extract1(&all->tushort,sizeof(all->tushort),&params[offset]); offset += 1;
extract1(&all->tint,sizeof(all->tint),&params[offset]); offset += 1;
extract1(&all->tuint,sizeof(all->tuint),&params[offset]); offset += 1;
extract1(&all->tfloat32,sizeof(all->tfloat32),&params[offset]); offset += 1;
extract1(&all->tint64,sizeof(all->tint64),&params[offset]); offset += 2*1;
extract1(&all->tuint64,sizeof(all->tuint64),&params[offset]); offset += 2*1;
extract1(&all->tfloat64,sizeof(all->tfloat64),&params[offset]); offset += 2*1;
}
/* Verify values of the parameters */
static int
paramcheck(size_t nparams, const unsigned int* params, struct All* extracted)
{
struct All all;
memset(&all,0,sizeof(all));
if(nparams != NPARAMS) {
fprintf(stderr,">>> Incorrect number of parameters: expected=%ld sent=%ld\n",(unsigned long)NPARAMS,(unsigned long)nparams);
goto fail;
}
/* Convert numeric params to instance of struct All */
extractparams(nparams-1, &params[1], &all);
if(extracted) *extracted = all;
/* verify */
if(all.tbyte != spec.tbyte) mismatch("tbyte");
if(all.tubyte != spec.tubyte) mismatch("tubyte");
if(all.tshort != spec.tshort) mismatch("tshort");
if(all.tushort != spec.tushort) mismatch("tushort");
if(all.tint != spec.tint) mismatch("tint");
if(all.tuint != spec.tuint) mismatch("tuint");
if(all.tfloat32 != spec.tfloat32) mismatch("tfloat32");
if(all.tint64 != spec.tint64) mismatch("tint64");
if(all.tuint64 != spec.tuint64) mismatch("tuint64");
if(all.tfloat64 != spec.tfloat64) mismatch("tfloat64");
#ifdef DEBUG
{
size_t i;
fprintf(stderr,">>> nparams=%lu params=\n",nparams);
for(i=0;i<nparams;i++) {
fprintf(stderr,"[%d] %ud %d %f\n", (unsigned int)i, params[i],(signed int)params[i],*(float*)&params[i]);
}
fflush(stderr);
}
#endif
return 1;
fail:
return 0;
}
static void
mismatch(const char* which)
{
fprintf(stderr,">>> mismatch: %s\n",which);
fflush(stderr);
}