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netcdf-c/libhdf5/nc4info.c
Dennis Heimbigner 2ea1cf5f1b There was a request to extend the provenance information 
stored in the _NCProperties attribute to allow two things:
1. capture of additional library dependencies (over and above
   hdf5)
2. Recognition of non-netcdf libraries that create netcdf-4 format
   files.

To this end, the _NCProperties format has been extended to be
and arbitrary set of key=value pairs separated by commas.
This new format has version = 2, and uses commas as the pair separator.
Thus the general form is:
    _NCProperties = "version=2,key1=value,key2=value2..." ;

This new version is accompanied by a new ./configure option of the form
    --with-ncproperties="key1=value1,key2=value2..."
that specifies pairs to add to the _NCProperties attribute for all
files created with that netcdf library.

At this point, what is missing is some programmatic way to
specify either all the pairs or additional pairs
to the _NCProperties attribute. Not sure of the best way
to do this.

Builders using non-netcdf libraries can specify
whatever they want in the key value pairs (as long
as the version=2 is specified first).

By convention, the primary library is expected to be the
the first pair after the leading version=2 pair, but this
is convention only and is neither required nor enforced.

Related changes:
1. Fixed the tests that check _NCProperties to properly operate with version=2.
2. When reading a version 1 _NCProperties attribute, convert it to look
   like a version 2 attribute.
2. Added some version 2 tests to ncdump/tst_fileinfo.c and
   ncdump/tst_fileinfo.sh

Misc Changes:
1. Fix minor problem in ncdap_test/testurl.sh where a parameter to
   buildurl needed to be quoted.
2. Minor fix to ncgen to swap switches -H and -h to be consistent
   with other utilities.
3. Document the -M flag in nccopy usage() and the nccopy man page.
4. Modify a test case to use the nccopy -M flag.
2018-08-25 21:44:41 -06:00

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/**
* @file
* @internal Add provenance info for netcdf-4 files.
*
* Copyright 2010, UCAR/Unidata See netcdf/COPYRIGHT file for copying
* and redistribution conditions.
* @author Dennis Heimbigner
*/
#include "config.h"
#include "nc4internal.h"
#include "hdf5internal.h"
#include "nclist.h"
#include "ncbytes.h"
/* Various Constants */
#define NCPROPS_MAX_NAME 1024 /* max key name size */
#define NCPROPS_MAX_VALUE 1024 /* max value size */
#define HDF5_MAX_NAME 1024 /**< HDF5 max name. */
#define ESCAPECHARS "\\=|,"
/** @internal Check NetCDF return code. */
#define NCHECK(expr) {if((expr)!=NC_NOERR) {goto done;}}
/** @internal Check HDF5 return code. */
#define HCHECK(expr) {if((expr)<0) {ncstat = NC_EHDFERR; goto done;}}
static int globalpropinitialized = 0;
struct NCPROPINFO globalpropinfo; /**< Global property info. */
/* Forward */
static int properties_parse(const char* text0, NClist* pairs);
/**
* @internal Initialize default provenance info
* This will only be used for newly created files
* or for opened files that do not contain an _NCProperties
* attribute.
*
* @return ::NC_NOERR No error.
* @author Dennis Heimbigner
*/
int
NC4_provenance_init(void)
{
int stat = NC_NOERR;
int i;
NClist* other = NULL;
char* name = NULL;
char* value = NULL;
unsigned major,minor,release;
if(globalpropinitialized)
return stat;
/* Build _NCProperties info */
/* Initialize globalpropinfo */
memset((void*)&globalpropinfo,0,sizeof(globalpropinfo));
globalpropinfo.version = NCPROPS_VERSION;
globalpropinfo.properties = nclistnew();
if(globalpropinfo.properties == NULL)
{stat = NC_ENOMEM; goto done;}
/* Insert primary library version as first entry */
if((value = strdup(PACKAGE_VERSION)) == NULL)
{stat = NC_ENOMEM; goto done;}
if((name = strdup(NCPNCLIB2)) == NULL)
{stat = NC_ENOMEM; goto done;}
nclistpush(globalpropinfo.properties,name);
name = NULL;
nclistpush(globalpropinfo.properties,value);
value = NULL;
/* Insert the HDF5 as underlying storage format library */
stat = NC4_hdf5get_libversion(&major,&minor,&release);
if(stat) goto done;
{
char sversion[64];
snprintf(sversion,sizeof(sversion),"%1u.%1u.%1u",major,minor,release);
if((value = strdup(sversion)) == NULL)
{stat = NC_ENOMEM; goto done;}
}
if((name = strdup(NCPHDF5LIB2)) == NULL)
{stat = NC_ENOMEM; goto done;}
nclistpush(globalpropinfo.properties,name);
name = NULL;
nclistpush(globalpropinfo.properties,value);
value = NULL;
/* Add any extra fields */
/*Parse them into an NClist */
other = nclistnew();
if(other == NULL) {stat = NC_ENOMEM; goto done;}
#ifdef NCPROPERTIES
stat = properties_parse(NCPROPERTIES_EXTRA,other);
if(stat) goto done;
#endif
/* merge into the properties list */
for(i=0;i<nclistlength(other);i++)
nclistpush(globalpropinfo.properties,strdup(nclistget(other,i)));
done:
if(name != NULL) free(name);
if(value != NULL) free(value);
if(other != NULL)
nclistfreeall(other);
if(stat && globalpropinfo.properties != NULL) {
nclistfreeall(globalpropinfo.properties);
globalpropinfo.properties = NULL;
}
if(stat == NC_NOERR)
globalpropinitialized = 1; /* avoid repeating it */
return stat;
}
/* Locate a specific character and return its pointer
or EOS if not found
take \ escapes into account */
static char*
locate(char* p, char tag)
{
char* next;
int c;
assert(p != NULL);
for(next = p;(c = *next);next++) {
if(c == tag)
return next;
else if(c == '\\' && next[1] != '\0')
next++; /* skip escaped char */
}
return next; /* not found */
}
/**
* @internal Parse file properties.
*
* @param properties list of parsed (key,value) pairs
* @param text Text properties.
*
* @return ::NC_NOERR No error.
* @author Dennis Heimbigner
*/
static int
properties_parse(const char* text0, NClist* pairs)
{
int ret = NC_NOERR;
char* p;
char* q;
char* text = NULL;
if(text0 == NULL || strlen(text0) == 0)
goto done;
text = strdup(text0);
if(text == NULL) return NC_ENOMEM;
/* For back compatibility with version 1, translate '|' -> ',' */
for(p=text;*p;p++) {
if(*p == NCPROPSSEP1)
*p = NCPROPSSEP2;
}
/* Walk and fill in ncinfo */
p = text;
while(*p) {
char* name = p;
char* value = NULL;
char* next = NULL;
/* Delimit whole (key,value) pair */
q = locate(p,NCPROPSSEP2);
if(*q != '\0') /* Never go beyond the final nul term */
*q++ = '\0';
next = q;
/* split key and value */
q = locate(p,'=');
name = p;
*q++ = '\0';
value = q;
/* Set up p for next iteration */
p = next;
nclistpush(pairs,strdup(name));
nclistpush(pairs,strdup(value));
}
done:
if(text) free(text);
return ret;
}
/* Utility to transfer a string to a buffer with escaping */
static void
escapify(NCbytes* buffer, const char* s)
{
const char* p;
for(p=s;*p;p++) {
if(strchr(ESCAPECHARS,*p) != NULL)
ncbytesappend(buffer,'\\');
ncbytesappend(buffer,*p);
}
}
/* Utility to copy contents of the dfalt into an NCPROPINFO object */
static int
propinfo_default(struct NCPROPINFO* dst, const struct NCPROPINFO* dfalt)
{
int i;
if(dst->properties == NULL) {
dst->properties = nclistnew();
if(dst->properties == NULL) return NC_ENOMEM;
}
dst->version = dfalt->version;
for(i=0;i<nclistlength(dfalt->properties);i++) {
char* s = nclistget(dfalt->properties,i);
s = strdup(s);
if(s == NULL) return NC_ENOMEM;
nclistpush(dst->properties,s);
}
return NC_NOERR;
}
/**
* @internal Build _NCProperties attribute value.
*
* Convert a NCPROPINFO instance to a single string.
*
* @param info Properties info.
* @param propdatap Pointer that gets properties string.
*
* @return ::NC_NOERR No error.
* @return ::NC_EINVAL failed.
* @author Dennis Heimbigner
*/
int
NC4_buildpropinfo(struct NCPROPINFO* info, char** propdatap)
{
int stat = NC_NOERR;
int i;
NCbytes* buffer = NULL;
char sversion[64];
if(info == NULL || info->version == 0 || propdatap == NULL)
{stat = NC_EINVAL; goto done;}
*propdatap = NULL;
buffer = ncbytesnew();
if(!buffer) {stat = NC_ENOMEM; goto done;}
/* start with version */
ncbytescat(buffer,NCPVERSION);
ncbytesappend(buffer,'=');
snprintf(sversion,sizeof(sversion),"%d",info->version);
ncbytescat(buffer,sversion);
for(i=0;i<nclistlength(info->properties);i+=2) {
char* value, *name;
name = nclistget(info->properties,i);
if(name == NULL) continue;
value = nclistget(info->properties,i+1);
ncbytesappend(buffer,NCPROPSSEP2); /* terminate last entry */
escapify(buffer,name);
ncbytesappend(buffer,'=');
escapify(buffer,value);
}
/* Force null termination */
ncbytesnull(buffer);
*propdatap = ncbytesextract(buffer);
done:
if(buffer != NULL) ncbytesfree(buffer);
return stat;
}
#if 0
/**
* @internal Write the properties attribute to file.
*
* @param h5 Pointer to HDF5 file info struct.
*
* @return ::NC_NOERR No error.
* @author Dennis Heimbigner
*/
int
NC4_put_ncproperties(NC_FILE_INFO_T* file)
{
int ncstat = NC_NOERR;
char* text = NULL;
/* Get root group */
grp = h5->root_grp->hdf_grpid; /* get root group */
/* See if the NCPROPS attribute exists */
if(H5Aexists(grp,NCPROPS) <= 0) { /* Does not exist */
ncstat = NC4_buildpropinfo(&h5->fileinfo->propattr,&text);
if(text == NULL || ncstat != NC_NOERR) {
goto done;
}
/* Create a datatype to refer to. */
HCHECK((atype = H5Tcopy(H5T_C_S1)));
HCHECK((H5Tset_cset(atype, H5T_CSET_ASCII)));
HCHECK((H5Tset_size(atype, strlen(text)+1))); /*keep nul term */
HCHECK((aspace = H5Screate(H5S_SCALAR)));
HCHECK((attid = H5Acreate(grp, NCPROPS, atype, aspace, H5P_DEFAULT)));
HCHECK((H5Awrite(attid, atype, text)));
}
done:
if(text != NULL) {
free(text);
text = NULL;
}
if(attid >= 0) HCHECK((H5Aclose(attid)));
if(aspace >= 0) HCHECK((H5Sclose(aspace)));
if(atype >= 0) HCHECK((H5Tclose(atype)));
return ncstat;
}
#endif
/**
* @internal
*
* Construct the provenance information for a newly created file
* using dfalt as the default.
* Note that creation of the _NCProperties attribute is deferred
* to the sync_netcdf4_file function.
*
* @param file Pointer to file object.
* @param dfalt
*
* @return ::NC_NOERR No error.
* [Note: other errors are reported via LOG()]
* @author Dennis Heimbigner
*/
int
NC4_set_provenance(NC_FILE_INFO_T* file, const struct NCPROPINFO* dfalt)
{
int ncstat = NC_NOERR;
struct NCPROVENANCE* provenance = NULL;
int superblock = -1;
assert(file->provenance == NULL);
provenance = calloc(1,sizeof(struct NCPROVENANCE));
if(provenance == NULL) {ncstat = NC_ENOMEM; goto done;}
/* Initialize from the default */
provenance->propattr.version = globalpropinfo.version;
provenance->propattr.properties = nclistnew();
if(provenance->propattr.properties == NULL)
{ncstat = NC_ENOMEM; goto done;}
/* Get the superblock number */
if((ncstat = NC4_hdf5get_superblock(file,&superblock)))
goto done;
provenance->superblockversion = superblock;
/* add in the dfalt values */
if(dfalt != NULL) {
int i;
for(i=0;i<nclistlength(dfalt->properties);i++) {
nclistpush(provenance->propattr.properties,nclistget(dfalt->properties,i));
}
}
done:
if(ncstat) {
LOG((0,"Could not create _NCProperties attribute"));
(void)NC4_free_provenance(provenance);
} else
file->provenance = provenance;
return NC_NOERR;
}
/**
* @internal
*
* Construct the provenance information for a newly opened file
* Using the specified _NCProperties value. If NULL, then
* initialize using dfalt.
*
* @param file Pointer to file object.
* @param propstring The contents of _NCProperties
* @param dfalt
*
* @return ::NC_NOERR No error.
* @return ::NC_ENOMEM
* @return ::NC_EINVAL
* @author Dennis Heimbigner
*/
int
NC4_get_provenance(NC_FILE_INFO_T* file, const char* propstring, const struct NCPROPINFO* dfalt)
{
int ncstat = NC_NOERR;
struct NCPROVENANCE* provenance;
char *name = NULL;
char *value = NULL;
int v = 0;
int superblock = -1;
assert(file->provenance == NULL);
if((file->provenance = calloc(1,sizeof(struct NCPROVENANCE))) == NULL)
{ncstat = NC_ENOMEM; goto done;}
provenance = file->provenance;
if((provenance->propattr.properties = nclistnew()) == NULL)
{ncstat = NC_ENOMEM; goto done;}
/* Set the superblock */
if((ncstat = NC4_hdf5get_superblock(file,&superblock)))
goto done;
provenance->superblockversion = superblock;
if(propstring == NULL) {
/* Use dfalt */
if((ncstat=propinfo_default(&provenance->propattr,dfalt)))
goto done;
} else {
NClist* list = provenance->propattr.properties;
if((ncstat=properties_parse(propstring,list)))
goto done;
/* Check the version and remove from properties list*/
if(nclistlength(list) < 2)
{ncstat = NC_EINVAL; goto done;} /* bad _NCProperties attribute */
/* Extract the purported version=... */
name = nclistremove(list,0);
value = nclistremove(list,0);
if(strcmp(name,NCPVERSION) == 0) {
if(sscanf(value,"%d",&v) != 1)
{ncstat = NC_EINVAL; goto done;} /* illegal version */
if(v <= 0 || v > NCPROPS_VERSION)
{ncstat = NC_EINVAL; goto done;} /* unknown version */
provenance->propattr.version = v;
} else
{ncstat = NC_EINVAL; goto done;} /* bad _NCProperties attribute */
#if 0
/* Now, rebuild from version 1 to version 2 if necessary */
if(provenance->propattr.version == 1) {
int i;
for(i=0;i<nclistlength(list);i+=2) {
char* newname = NULL;
name = nclistget(list,i);
if(name == NULL) continue; /* ignore */
if(strcmp(name,NCPNCLIB1) == 0)
newname = NCPNCLIB2; /* change name */
else if(strcmp(name,NCPHDF5LIB1) == 0)
newname = NCPHDF5LIB2;
else continue; /* ignore */
/* Do any rename */
nclistset(list,i,strdup(newname));
if(name) free(name);
}
}
#endif
}
done:
if(name != NULL) free(name);
if(value != NULL) free(value);
return ncstat;
}
/**
* @internal
*
* Free the NCPROVENANCE object
* @param prov Pointer to provenance object
*
* @return ::NC_NOERR No error.
* @author Dennis Heimbigner
*/
int
NC4_free_provenance(struct NCPROVENANCE* prov)
{
if(prov == NULL) return NC_NOERR;
if(prov->propattr.properties)
nclistfreeall(prov->propattr.properties);
free(prov);
return NC_NOERR;
}
/* HDF5 Specific attribute read/write of _NCProperties */
int
NC4_read_ncproperties(NC_FILE_INFO_T* h5)
{
int retval = NC_NOERR;
hid_t hdf5grpid = -1;
hid_t attid = -1;
hid_t aspace = -1;
hid_t atype = -1;
hid_t ntype = -1;
char* text = NULL;
H5T_class_t t_class;
hsize_t size;
hdf5grpid = h5->root_grp->hdf_grpid;
if(H5Aexists(hdf5grpid,NCPROPS) <= 0) { /* Does not exist */
/* File did not contain a _NCProperties attribute */
retval=NC4_get_provenance(h5,NULL,&globalpropinfo);
goto done;
}
/* NCPROPS Attribute exists, make sure it is legitimate */
attid = H5Aopen_name(hdf5grpid, NCPROPS);
assert(attid > 0);
aspace = H5Aget_space(attid);
atype = H5Aget_type(attid);
/* Verify atype and size */
t_class = H5Tget_class(atype);
if(t_class != H5T_STRING)
{retval = NC_EINVAL; goto done;}
size = H5Tget_size(atype);
if(size == 0)
{retval = NC_EINVAL; goto done;}
text = (char*)malloc(1+(size_t)size);
if(text == NULL)
{retval = NC_ENOMEM; goto done;}
if((ntype = H5Tget_native_type(atype, H5T_DIR_DEFAULT)) < 0)
{retval = NC_EHDFERR; goto done;}
if((H5Aread(attid, ntype, text)) < 0)
{retval = NC_EHDFERR; goto done;}
/* Make sure its null terminated */
text[(size_t)size] = '\0';
/* Process the _NCProperties value */
if((retval = NC4_get_provenance(h5, text, &globalpropinfo)))
goto done;
done:
if(text != NULL) free(text);
/* Close out the HDF5 objects */
if(attid > 0 && H5Aclose(attid) < 0) retval = NC_EHDFERR;
if(aspace > 0 && H5Sclose(aspace) < 0) retval = NC_EHDFERR;
if(atype > 0 && H5Tclose(atype) < 0) retval = NC_EHDFERR;
if(ntype > 0 && H5Tclose(ntype) < 0) retval = NC_EHDFERR;
/* For certain errors, actually fail, else log that attribute was invalid and ignore */
if(retval != NC_ENOMEM && retval != NC_EHDFERR) {
LOG((0,"Invalid _NCProperties attribute"));
retval = NC_NOERR;
}
return retval;
}
int
NC4_write_ncproperties(NC_FILE_INFO_T* h5)
{
int retval = NC_NOERR;
hid_t hdf5grpid = -1;
hid_t attid = -1;
hid_t aspace = -1;
hid_t atype = -1;
char* text = NULL;
size_t len = 0;
/* If the file is read-only, return an error. */
if (h5->no_write)
{retval = NC_EPERM; goto done;}
hdf5grpid = h5->root_grp->hdf_grpid;
if(H5Aexists(hdf5grpid,NCPROPS) > 0) /* Already exists, no overwrite */
goto done;
/* Build the attribute string */
if((retval = NC4_buildpropinfo(&h5->provenance->propattr,&text)))
goto done;
/* Build the HDF5 string type */
if ((atype = H5Tcopy(H5T_C_S1)) < 0)
{retval = NC_EHDFERR; goto done;}
if (H5Tset_strpad(atype, H5T_STR_NULLTERM) < 0)
{retval = NC_EHDFERR; goto done;}
if(H5Tset_cset(atype, H5T_CSET_ASCII) < 0)
{retval = NC_EHDFERR; goto done;}
/* Create NCPROPS attribute */
len = strlen(text);
if(H5Tset_size(atype, len) < 0)
{retval = NC_EFILEMETA; goto done;}
if((aspace = H5Screate(H5S_SCALAR)) < 0)
{retval = NC_EFILEMETA; goto done;}
if ((attid = H5Acreate(hdf5grpid, NCPROPS, atype, aspace, H5P_DEFAULT)) < 0)
{retval = NC_EFILEMETA; goto done;}
if (H5Awrite(attid, atype, text) < 0)
{retval = NC_EFILEMETA; goto done;}
done:
if(text != NULL) free(text);
/* Close out the HDF5 objects */
if(attid > 0 && H5Aclose(attid) < 0) retval = NC_EHDFERR;
if(aspace > 0 && H5Sclose(aspace) < 0) retval = NC_EHDFERR;
if(atype > 0 && H5Tclose(atype) < 0) retval = NC_EHDFERR;
/* For certain errors, actually fail, else log that attribute was invalid and ignore */
switch (retval) {
case NC_ENOMEM:
case NC_EHDFERR:
case NC_EPERM:
case NC_EFILEMETA:
case NC_NOERR:
break;
default:
LOG((0,"Invalid _NCProperties attribute"));
retval = NC_NOERR;
break;
}
return retval;
}
/* Debugging */
void
ncprintpropinfo(struct NCPROPINFO* info)
{
int i;
fprintf(stderr,"[%p] version=%d\n",info,info->version);
for(i=0;i<nclistlength(info->properties);i+=2) {
char* name = nclistget(info->properties,i);
char* value = nclistget(info->properties,i+1);
fprintf(stderr,"\t[%d] name=|%s| value=|%s|\n",i,name,value);
}
}
void
ncprintprovenance(struct NCPROVENANCE* prov)
{
fprintf(stderr,"[%p] superblockversion=%d\n",prov,prov->superblockversion);
ncprintpropinfo(&prov->propattr);
}
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