mirror of
https://github.com/Unidata/netcdf-c.git
synced 2024-12-21 08:39:46 +08:00
84c69afca7
re: Github issue https://github.com/Unidata/netcdf-c/issues/1713 If nc_def_var_filter or nc_def_var_deflate or nc_def_var_szip is called multiple times with the same filter id, but possibly with different sets of parameters, then the first invocation is sticky and later invocations are ignored. The desired behavior is to have the last invocation be used. This PR implements that desired behavior, with some special cases. If you call nc_def_var_deflate multiple times, then the last invocation rule applies with respect to deflate. However, the shuffle filter, if enabled, is always applied just before applying deflate. Misc unrelated changes: 1. Make client-side filters be disabled by default 2. Fix the definition of uintptr_t and use in oc2 and libdap4 3. Add some test cases 4. modify filter order tests to use plugin filters rather than client-side filters
695 lines
18 KiB
C
695 lines
18 KiB
C
/**
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* @file
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* @internal Add provenance info for netcdf-4 files.
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*
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* Copyright 2018, UCAR/Unidata See netcdf/COPYRIGHT file for copying
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* and redistribution conditions.
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* @author Dennis Heimbigner
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*/
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#include "config.h"
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#include "nc4internal.h"
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#include "hdf5internal.h"
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#include "nc_provenance.h"
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#include "nclist.h"
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#include "ncbytes.h"
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/* Provide a hack to suppress the writing of _NCProperties attribute.
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This is for creating a file without _NCProperties for testing purposes.
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*/
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#undef SUPPRESSNCPROPS
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/* Various Constants */
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#define NCPROPS_MAX_NAME 1024 /* max key name size */
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#define NCPROPS_MAX_VALUE 1024 /* max value size */
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#define HDF5_MAX_NAME 1024 /**< HDF5 max name. */
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#define ESCAPECHARS "\\=|,"
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/** @internal Check NetCDF return code. */
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#define NCHECK(expr) {if((expr)!=NC_NOERR) {goto done;}}
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/** @internal Check HDF5 return code. */
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#define HCHECK(expr) {if((expr)<0) {ncstat = NC_EHDFERR; goto done;}}
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static int NC4_read_ncproperties(NC_FILE_INFO_T* h5, char** propstring);
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static int NC4_write_ncproperties(NC_FILE_INFO_T* h5);
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static int globalpropinitialized = 0;
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static NC4_Provenance globalprovenance;
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/**
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* @internal Initialize default provenance info
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* This will only be used for newly created files
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* or for opened files that do not contain an _NCProperties
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* attribute.
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*
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* @return ::NC_NOERR No error.
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* @author Dennis Heimbigner
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*/
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int
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NC4_provenance_init(void)
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{
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int stat = NC_NOERR;
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char* name = NULL;
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char* value = NULL;
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unsigned major,minor,release;
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NCbytes* buffer = NULL; /* for constructing the global _NCProperties */
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char printbuf[1024];
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if(globalpropinitialized)
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return stat;
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/* Build _NCProperties info */
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/* Initialize globalpropinfo */
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memset((void*)&globalprovenance,0,sizeof(NC4_Provenance));
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globalprovenance.version = NCPROPS_VERSION;
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buffer = ncbytesnew();
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/* Insert version as first entry */
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ncbytescat(buffer,NCPVERSION);
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ncbytescat(buffer,"=");
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snprintf(printbuf,sizeof(printbuf),"%d",globalprovenance.version);
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ncbytescat(buffer,printbuf);
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/* Insert the netcdf version */
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ncbytesappend(buffer,NCPROPSSEP2);
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ncbytescat(buffer,NCPNCLIB2);
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ncbytescat(buffer,"=");
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ncbytescat(buffer,PACKAGE_VERSION);
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/* Insert the HDF5 as underlying storage format library */
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ncbytesappend(buffer,NCPROPSSEP2);
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ncbytescat(buffer,NCPHDF5LIB2);
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ncbytescat(buffer,"=");
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if((stat = NC4_hdf5get_libversion(&major,&minor,&release))) goto done;
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snprintf(printbuf,sizeof(printbuf),"%1u.%1u.%1u",major,minor,release);
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ncbytescat(buffer,printbuf);
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#ifdef NCPROPERTIES_EXTRA
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{ const char* p;
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/* Add any extra fields */
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p = NCPROPERTIES_EXTRA;
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if(p[0] == NCPROPSSEP2) p++; /* If leading separator */
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ncbytesappend(buffer,NCPROPSSEP2);
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ncbytescat(buffer,p);
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}
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#endif
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ncbytesnull(buffer);
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globalprovenance.ncproperties = ncbytesextract(buffer);
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done:
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ncbytesfree(buffer);
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if(name != NULL) free(name);
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if(value != NULL) free(value);
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if(stat == NC_NOERR)
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globalpropinitialized = 1; /* avoid repeating it */
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return stat;
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}
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/**
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* @internal finalize default provenance info
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*
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* @return ::NC_NOERR No error.
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* @author Dennis Heimbigner
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*/
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int
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NC4_provenance_finalize(void)
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{
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return NC4_clear_provenance(&globalprovenance);
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}
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/**
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* @internal
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*
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* Construct the provenance information for a newly created file.
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* Note that creation of the _NCProperties attribute is deferred
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* to the sync_netcdf4_file function.
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*
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* @param file Pointer to file object.
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*
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* @return ::NC_NOERR No error.
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* [Note: other errors are reported via LOG()]
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* @author Dennis Heimbigner
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*/
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int
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NC4_new_provenance(NC_FILE_INFO_T* file)
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{
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int ncstat = NC_NOERR;
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NC4_Provenance* provenance = NULL;
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int superblock = -1;
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LOG((5, "%s: ncid 0x%x", __func__, file->root_grp->hdr.id));
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assert(file->provenance.ncproperties == NULL); /* not yet defined */
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provenance = &file->provenance;
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memset(provenance,0,sizeof(NC4_Provenance)); /* make sure */
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/* Set the version */
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provenance->version = globalprovenance.version;
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/* Set the superblock number */
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if((ncstat = NC4_hdf5get_superblock(file,&superblock))) goto done;
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provenance->superblockversion = superblock;
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if(globalprovenance.ncproperties != NULL) {
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if((provenance->ncproperties = strdup(globalprovenance.ncproperties)) == NULL)
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{ncstat = NC_ENOMEM; goto done;}
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}
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done:
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if(ncstat) {
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LOG((0,"Could not create _NCProperties attribute"));
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}
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return NC_NOERR;
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}
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/**
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* @internal
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*
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* Construct the provenance information for an existing file.
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*
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* @param file Pointer to file object.
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*
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* @return ::NC_NOERR No error.
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* [Note: other errors are reported via LOG()]
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* @author Dennis Heimbigner
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*/
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int
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NC4_read_provenance(NC_FILE_INFO_T* file)
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{
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int ncstat = NC_NOERR;
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NC4_Provenance* provenance = NULL;
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int superblock = -1;
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char* propstring = NULL;
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LOG((5, "%s: ncid 0x%x", __func__, file->root_grp->hdr.id));
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assert(file->provenance.version == 0); /* not yet defined */
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provenance = &file->provenance;
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memset(provenance,0,sizeof(NC4_Provenance)); /* make sure */
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/* Set the superblock number */
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if((ncstat = NC4_hdf5get_superblock(file,&superblock))) goto done;
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provenance->superblockversion = superblock;
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/* Read the _NCProperties value from the file */
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/* We do not return a size and assume the size is that upto the
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first nul character */
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if((ncstat = NC4_read_ncproperties(file,&propstring))) goto done;
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provenance->ncproperties = propstring;
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propstring = NULL;
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done:
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nullfree(propstring);
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if(ncstat) {
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LOG((0,"Could not create _NCProperties attribute"));
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}
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return NC_NOERR;
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}
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/**
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* @internal
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*
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* Add the provenance information to a newly created file.
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*
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* @param file Pointer to file object.
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*
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* @return ::NC_NOERR No error.
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* [Note: other errors are reported via LOG()]
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* @author Dennis Heimbigner
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*/
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int
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NC4_write_provenance(NC_FILE_INFO_T* file)
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{
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int ncstat = NC_NOERR;
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if((ncstat = NC4_write_ncproperties(file)))
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goto done;
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done:
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return ncstat;
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}
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/* HDF5 Specific attribute read/write of _NCProperties */
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static int
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NC4_read_ncproperties(NC_FILE_INFO_T* h5, char** propstring)
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{
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int retval = NC_NOERR;
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hid_t hdf5grpid = -1;
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hid_t attid = -1;
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hid_t aspace = -1;
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hid_t atype = -1;
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hid_t ntype = -1;
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char* text = NULL;
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H5T_class_t t_class;
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hsize_t size;
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LOG((5, "%s", __func__));
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hdf5grpid = ((NC_HDF5_GRP_INFO_T *)(h5->root_grp->format_grp_info))->hdf_grpid;
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if(H5Aexists(hdf5grpid,NCPROPS) <= 0) { /* Does not exist */
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/* File did not contain a _NCProperties attribute; leave empty */
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goto done;
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}
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/* NCPROPS Attribute exists, make sure it is legitimate */
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attid = H5Aopen_name(hdf5grpid, NCPROPS);
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assert(attid > 0);
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aspace = H5Aget_space(attid);
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atype = H5Aget_type(attid);
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/* Verify atype and size */
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t_class = H5Tget_class(atype);
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if(t_class != H5T_STRING)
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{retval = NC_EINVAL; goto done;}
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size = H5Tget_size(atype);
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if(size == 0)
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{retval = NC_EINVAL; goto done;}
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text = (char*)malloc(1+(size_t)size);
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if(text == NULL)
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{retval = NC_ENOMEM; goto done;}
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if((ntype = H5Tget_native_type(atype, H5T_DIR_DEFAULT)) < 0)
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{retval = NC_EHDFERR; goto done;}
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if((H5Aread(attid, ntype, text)) < 0)
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{retval = NC_EHDFERR; goto done;}
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/* Make sure its null terminated */
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text[(size_t)size] = '\0';
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if(propstring) {*propstring = text; text = NULL;}
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done:
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if(text != NULL) free(text);
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/* Close out the HDF5 objects */
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if(attid > 0 && H5Aclose(attid) < 0) retval = NC_EHDFERR;
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if(aspace > 0 && H5Sclose(aspace) < 0) retval = NC_EHDFERR;
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if(atype > 0 && H5Tclose(atype) < 0) retval = NC_EHDFERR;
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if(ntype > 0 && H5Tclose(ntype) < 0) retval = NC_EHDFERR;
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/* For certain errors, actually fail, else log that attribute was invalid and ignore */
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if(retval != NC_NOERR) {
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if(retval != NC_ENOMEM && retval != NC_EHDFERR) {
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LOG((0,"Invalid _NCProperties attribute: ignored"));
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retval = NC_NOERR;
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}
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}
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return retval;
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}
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static int
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NC4_write_ncproperties(NC_FILE_INFO_T* h5)
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{
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#ifdef SUPPRESSNCPROPERTY
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return NC_NOERR;
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#else /*!SUPPRESSNCPROPERTY*/
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int retval = NC_NOERR;
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hid_t hdf5grpid = -1;
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hid_t attid = -1;
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hid_t aspace = -1;
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hid_t atype = -1;
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size_t len = 0;
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NC4_Provenance* prov = &h5->provenance;
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LOG((5, "%s", __func__));
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/* If the file is read-only, return an error. */
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if (h5->no_write)
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{retval = NC_EPERM; goto done;}
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hdf5grpid = ((NC_HDF5_GRP_INFO_T *)(h5->root_grp->format_grp_info))->hdf_grpid;
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if(H5Aexists(hdf5grpid,NCPROPS) > 0) /* Already exists, no overwrite */
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goto done;
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/* Build the property if we have legit value */
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if(prov->ncproperties != NULL) {
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/* Build the HDF5 string type */
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if ((atype = H5Tcopy(H5T_C_S1)) < 0)
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{retval = NC_EHDFERR; goto done;}
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if (H5Tset_strpad(atype, H5T_STR_NULLTERM) < 0)
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{retval = NC_EHDFERR; goto done;}
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if(H5Tset_cset(atype, H5T_CSET_ASCII) < 0)
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{retval = NC_EHDFERR; goto done;}
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len = strlen(prov->ncproperties);
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if(H5Tset_size(atype, len) < 0)
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{retval = NC_EFILEMETA; goto done;}
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/* Create NCPROPS attribute */
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if((aspace = H5Screate(H5S_SCALAR)) < 0)
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{retval = NC_EFILEMETA; goto done;}
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if ((attid = H5Acreate(hdf5grpid, NCPROPS, atype, aspace, H5P_DEFAULT)) < 0)
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{retval = NC_EFILEMETA; goto done;}
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if (H5Awrite(attid, atype, prov->ncproperties) < 0)
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{retval = NC_EFILEMETA; goto done;}
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/* Verify */
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#if 0
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{
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hid_t spacev, typev;
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hsize_t dsize, tsize;
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typev = H5Aget_type(attid);
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spacev = H5Aget_space(attid);
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dsize = H5Aget_storage_size(attid);
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tsize = H5Tget_size(typev);
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fprintf(stderr,"dsize=%lu tsize=%lu\n",(unsigned long)dsize,(unsigned long)tsize);
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}
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#endif
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}
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done:
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/* Close out the HDF5 objects */
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if(attid > 0 && H5Aclose(attid) < 0) retval = NC_EHDFERR;
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if(aspace > 0 && H5Sclose(aspace) < 0) retval = NC_EHDFERR;
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if(atype > 0 && H5Tclose(atype) < 0) retval = NC_EHDFERR;
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/* For certain errors, actually fail, else log that attribute was invalid and ignore */
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switch (retval) {
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case NC_ENOMEM:
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case NC_EHDFERR:
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case NC_EPERM:
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case NC_EFILEMETA:
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case NC_NOERR:
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break;
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default:
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LOG((0,"Invalid _NCProperties attribute"));
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retval = NC_NOERR;
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break;
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}
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return retval;
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#endif /*!SUPPRESSNCPROPERTY*/
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}
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/**************************************************/
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/* Utilities */
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/* Debugging */
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void
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ncprintprovenance(NC4_Provenance* info)
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{
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fprintf(stderr,"[%p] version=%d superblockversion=%d ncproperties=|%s|\n",
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info,
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info->version,
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info->superblockversion,
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(info->ncproperties==NULL?"":info->ncproperties));
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}
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/**
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* @internal
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*
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* Clear the NCPROVENANCE object; do not free it
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* @param prov Pointer to provenance object
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*
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* @return ::NC_NOERR No error.
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* @author Dennis Heimbigner
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*/
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int
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NC4_clear_provenance(NC4_Provenance* prov)
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{
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LOG((5, "%s", __func__));
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if(prov == NULL) return NC_NOERR;
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nullfree(prov->ncproperties);
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memset(prov,0,sizeof(NC4_Provenance));
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return NC_NOERR;
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}
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#if 0
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/* Unused functions */
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/**
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* @internal Parse file properties.
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*
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* @param text0 Text properties.
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* @param pairs list of parsed (key,value) pairs
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*
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* @return ::NC_NOERR No error.
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* @author Dennis Heimbigner
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*/
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static int
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properties_parse(const char* text0, NClist* pairs)
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{
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int ret = NC_NOERR;
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char* p;
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char* q;
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char* text = NULL;
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if(text0 == NULL || strlen(text0) == 0)
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goto done;
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text = strdup(text0);
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if(text == NULL) return NC_ENOMEM;
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/* For back compatibility with version 1, translate '|' -> ',' */
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for(p=text;*p;p++) {
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if(*p == NCPROPSSEP1)
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*p = NCPROPSSEP2;
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}
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/* Walk and fill in ncinfo */
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p = text;
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while(*p) {
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char* name = p;
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char* value = NULL;
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char* next = NULL;
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/* Delimit whole (key,value) pair */
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q = locate(p,NCPROPSSEP2);
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if(*q != '\0') /* Never go beyond the final nul term */
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*q++ = '\0';
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next = q;
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/* split key and value */
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q = locate(p,'=');
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name = p;
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*q++ = '\0';
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value = q;
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/* Set up p for next iteration */
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p = next;
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nclistpush(pairs,strdup(name));
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nclistpush(pairs,strdup(value));
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}
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done:
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if(text) free(text);
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return ret;
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}
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/* Locate a specific character and return its pointer
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or EOS if not found
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take \ escapes into account */
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static char*
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locate(char* p, char tag)
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{
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char* next;
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int c;
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assert(p != NULL);
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for(next = p;(c = *next);next++) {
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if(c == tag)
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return next;
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else if(c == '\\' && next[1] != '\0')
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next++; /* skip escaped char */
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}
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return next; /* not found */
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}
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/* Utility to transfer a string to a buffer with escaping */
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static void
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escapify(NCbytes* buffer, const char* s)
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{
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const char* p;
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for(p=s;*p;p++) {
|
|
if(strchr(ESCAPECHARS,*p) != NULL)
|
|
ncbytesappend(buffer,'\\');
|
|
ncbytesappend(buffer,*p);
|
|
}
|
|
}
|
|
|
|
/**
|
|
* @internal Build _NCProperties attribute value.
|
|
*
|
|
* Convert a NCPROPINFO instance to a single string.
|
|
* Will always convert to current format
|
|
*
|
|
* @param version
|
|
* @param list Properties list
|
|
* @param spropp Pointer that gets properties string.
|
|
* @return ::NC_NOERR No error.
|
|
* @return ::NC_EINVAL failed.
|
|
* @author Dennis Heimbigner
|
|
*/
|
|
static int
|
|
build_propstring(int version, NClist* list, char** spropp)
|
|
{
|
|
int stat = NC_NOERR;
|
|
int i;
|
|
NCbytes* buffer = NULL;
|
|
char sversion[64];
|
|
|
|
LOG((5, "%s version=%d", __func__, version));
|
|
|
|
if(spropp != NULL) *spropp = NULL;
|
|
|
|
if(version == 0 || version > NCPROPS_VERSION) /* unknown case */
|
|
goto done;
|
|
if(list == NULL)
|
|
{stat = NC_EINVAL; goto done;}
|
|
|
|
if((buffer = ncbytesnew()) == NULL)
|
|
{stat = NC_ENOMEM; goto done;}
|
|
|
|
/* start with version */
|
|
ncbytescat(buffer,NCPVERSION);
|
|
ncbytesappend(buffer,'=');
|
|
/* Use current version */
|
|
snprintf(sversion,sizeof(sversion),"%d",NCPROPS_VERSION);
|
|
ncbytescat(buffer,sversion);
|
|
|
|
for(i=0;i<nclistlength(list);i+=2) {
|
|
char* value, *name;
|
|
name = nclistget(list,i);
|
|
if(name == NULL) continue;
|
|
value = nclistget(list,i+1);
|
|
ncbytesappend(buffer,NCPROPSSEP2); /* terminate last entry */
|
|
escapify(buffer,name);
|
|
ncbytesappend(buffer,'=');
|
|
escapify(buffer,value);
|
|
}
|
|
/* Force null termination */
|
|
ncbytesnull(buffer);
|
|
if(spropp) *spropp = ncbytesextract(buffer);
|
|
|
|
done:
|
|
if(buffer != NULL) ncbytesfree(buffer);
|
|
return stat;
|
|
}
|
|
|
|
static int
|
|
properties_getversion(const char* propstring, int* versionp)
|
|
{
|
|
int ncstat = NC_NOERR;
|
|
int version = 0;
|
|
/* propstring should begin with "version=dddd" */
|
|
if(propstring == NULL || strlen(propstring) < strlen("version=") + strlen("1"))
|
|
{ncstat = NC_EINVAL; goto done;} /* illegal version */
|
|
if(memcmp(propstring,"version=",strlen("version=")) != 0)
|
|
{ncstat = NC_EINVAL; goto done;} /* illegal version */
|
|
propstring += strlen("version=");
|
|
/* get version */
|
|
version = atoi(propstring);
|
|
if(version < 0)
|
|
{ncstat = NC_EINVAL; goto done;} /* illegal version */
|
|
if(versionp) *versionp = version;
|
|
done:
|
|
return ncstat;
|
|
}
|
|
|
|
/**
|
|
* @internal
|
|
*
|
|
* Construct the parsed provenance information
|
|
*
|
|
* @param prov Pointer to provenance object
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @return ::NC_ENOMEM
|
|
* @return ::NC_EINVAL
|
|
* @author Dennis Heimbigner
|
|
*/
|
|
static int
|
|
parse_provenance(NC4_Provenance* prov)
|
|
{
|
|
int ncstat = NC_NOERR;
|
|
char *name = NULL;
|
|
char *value = NULL;
|
|
int version = 0;
|
|
NClist* list = NULL;
|
|
|
|
LOG((5, "%s: prov 0x%x", __func__, prov));
|
|
|
|
if(prov->ncproperty == NULL || strlen(prov->ncproperty) < strlen("version="))
|
|
{ncstat = NC_EINVAL; goto done;}
|
|
if((list = nclistnew()) == NULL)
|
|
{ncstat = NC_ENOMEM; goto done;}
|
|
|
|
/* Do we understand the version? */
|
|
if(prov->version > 0 && prov->version <= NCPROPS_VERSION) {/* recognized version */
|
|
if((ncstat=properties_parse(prov->ncproperty,list)))
|
|
goto done;
|
|
/* Remove version pair from properties list*/
|
|
if(nclistlength(list) < 2)
|
|
{ncstat = NC_EINVAL; goto done;} /* bad _NCProperties attribute */
|
|
/* Throw away the purported version=... */
|
|
nclistremove(list,0); /* version key */
|
|
nclistremove(list,0); /* version value */
|
|
|
|
/* Now, rebuild to the latest version */
|
|
switch (version) {
|
|
default: break; /* do nothing */
|
|
case 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); name = NULL;}
|
|
}
|
|
} break;
|
|
} /*switch*/
|
|
}
|
|
prov->properties = list;
|
|
list = NULL;
|
|
|
|
done:
|
|
nclistfreeall(list);
|
|
if(name != NULL) free(name);
|
|
if(value != NULL) free(value);
|
|
return ncstat;
|
|
}
|
|
|
|
/**
|
|
* @internal
|
|
*
|
|
* Clear and Free the NC4_Provenance object
|
|
* @param prov Pointer to provenance object
|
|
*
|
|
* @return ::NC_NOERR No error.
|
|
* @author Dennis Heimbigner
|
|
*/
|
|
static int
|
|
NC4_free_provenance(NC4_Provenance* prov)
|
|
{
|
|
LOG((5, "%s", __func__));
|
|
|
|
if(prov == NULL) return NC_NOERR;
|
|
NC4_clear_provenance(prov);
|
|
free(prov);
|
|
return NC_NOERR;
|
|
}
|
|
|
|
/* Utility to copy contents of the dfalt into an NCPROPINFO object */
|
|
static int
|
|
propinfo_default(NC4_Properties* dst, const NC4_Properties* 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;
|
|
}
|
|
|
|
#endif /*0*/
|