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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((name = strdup(NCPNCLIB2)) == NULL)
{stat = NC_ENOMEM; goto done;}
nclistpush(globalpropinfo.properties,name);
name = NULL; /* Avoid multiple free() */
if((value = strdup(PACKAGE_VERSION)) == NULL)
{stat = NC_ENOMEM; goto done;}
nclistpush(globalpropinfo.properties,value);
value = NULL;
/* Insert the HDF5 as underlying storage format library */
if((name = strdup(NCPHDF5LIB2)) == NULL)
{stat = NC_ENOMEM; goto done;}
nclistpush(globalpropinfo.properties,name);
name = NULL;
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;}
}
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)));
nclistfreeall(other);
other = NULL;
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 finalize default provenance info
*
* @return ::NC_NOERR No error.
* @author Dennis Heimbigner
*/
int
NC4_provenance_finalize(void)
{
nclistfreeall(globalpropinfo.properties);
return NC_NOERR;
}
/**
* @internal Parse file properties.
*
* @param text0 Text properties.
* @param pairs list of parsed (key,value) pairs
*
* @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 = ((NC_HDF5_GRP_INFO_T *)(h5->root_grp->format_grp_info))->hdf_grpid;
/* 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;
/* Get the superblock number */
if((ncstat = NC4_hdf5get_superblock(file,&superblock)))
goto done;
provenance->superblockversion = superblock;
/* Capture properties */
provenance->propattr.properties = nclistnew();
if(provenance->propattr.properties == NULL)
{ncstat = NC_ENOMEM; goto done;}
/* add in the dfalt values */
if(dfalt != NULL) {
int i;
for(i=0;i<nclistlength(dfalt->properties);i++) {
char* prop = nclistget(dfalt->properties,i);
if(prop != NULL) {
prop = strdup(prop);
if(prop == NULL) {ncstat = NC_ENOMEM; goto done;}
nclistpush(provenance->propattr.properties,prop);
}
}
}
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 != NULL)
nclistfreeall(prov->propattr.properties);
prov->propattr.properties = NULL;
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 = ((NC_HDF5_GRP_INFO_T *)(h5->root_grp->format_grp_info))->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 = ((NC_HDF5_GRP_INFO_T *)(h5->root_grp->format_grp_info))->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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