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/* vastlocl.c
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information (NCBI)
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government do not place any restriction on its use or reproduction.
* We would, however, appreciate having the NCBI and the author cited in
* any work or product based on this material
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* ===========================================================================
*
* File Name: vastlocl.c
*
* Author: Christopher Hogue
*
* Version Creation Date: 21 February 97
*
* $Revision: 6.6 $
*
* File Description: Used to provide VAST data to MMDB-API when
* VAST files are on a local filesystem in standard VAST ftp-site format.
*
* Modifications:
* --------------------------------------------------------------------------
* $Log: vastlocl.c,v $
* Revision 6.6 2000/06/21 21:40:07 lewisg
* change to using gzip
*
* Revision 6.5 1998/07/27 16:07:40 madej
* Pipe the results of gunzip when we get a BAS.
*
* Revision 6.4 1998/05/19 20:13:21 madej
* Gunzip needed to run vastsrv on Suns.
*
* Revision 6.3 1998/03/30 19:28:55 madej
* Changes to enable subset filtering.
*
* Revision 6.2 1998/03/16 15:41:34 lewisg
* got rid of gunzip in config file
*
* Revision 6.1 1998/03/06 01:14:12 lewisg
* merge
*
*
*
* ==========================================================================
*/
/******** NOTE - .mmdbrc (UNIX) mmdb.ini (Win) mmdb.cnf (Mac) required *******/
/* containing paths to database VAST *****/
/*
[VAST]
Database = /net/dorothy/export/home/hogue/mmdb/Oct96/vastdata/
*/
#include <ncbi.h>
#include <mmdbapi1.h>
#include "vastlocl.h"
#ifdef OS_UNIX
#define MMDB_UNIXCOMPRESSED 1
#endif
static Char database[PATH_MAX];
static Char gunzip[PATH_MAX];
BiostrucAnnotSetPtr LIBCALL VASTBsAnnotSetGet (Int4 uid)
{
AsnIoPtr aip = NULL;
AsnTypePtr atp = NULL;
Char path[PATH_MAX];
Char compath[PATH_MAX];
Char tempfile[PATH_MAX];
Char pcId[20];
Int2 iFileExists = 0;
BiostrucAnnotSetPtr pbsa = NULL;
int iAvail = 1;
FILE *pipe;
sprintf(pcId, "%ld", (long) uid);
path[0] = '\0';
StringCpy(path, database);
StringCat(path, pcId);
StringCat(path, ".bas");
#ifdef MMDB_UNIXCOMPRESSED
compath[0] = '\0';
sprintf(compath, "%s -d -c %s.gz ", gunzip, path);
pipe = popen(compath, "rb");
if (pipe == NULL) {
ErrPostEx(SEV_FATAL,0,0, "VASTBsAnnotSetGet failed: Can't find gunzip in path.\n");
return NULL;
}
aip = AsnIoNew(ASNIO_BIN_IN, pipe, NULL, NULL, NULL);
#else
iFileExists = FileLength(path);
if (iFileExists == 0)
{
return NULL;
}
aip = AsnIoOpen(path, "rb");
#endif
if (aip)
{
pbsa = BiostrucAnnotSetAsnRead(aip, NULL);
AsnIoClose (aip);
}
#ifdef MMDB_UNIXCOMPRESSED
pclose(pipe);
#endif
if (!pbsa) return NULL;
return pbsa;
}
Boolean LIBCALL IsVASTData(Int4 uid)
{
AsnIoPtr aip = NULL;
AsnTypePtr atp = NULL;
Char path[PATH_MAX];
Char pcId[30];
sprintf(pcId, "%ld", (long) uid);
path[0] = '\0';
StringCpy(path, database);
StringCat(path, pcId);
StringCat(path, ".bas");
#ifdef MMDB_UNIXCOMPRESSED
StringCat(path, ".gz");
if (FileLength(path) != 0)
return TRUE;
#else
if (FileLength(path) != 0)
return TRUE;
#endif
return FALSE;
}
#ifndef _lygmerge
Boolean LIBCALL VASTInit (void)
{
Char fname[PATH_MAX];
database[0] = gunzip[0] = '\0';
GetAppParam("vast", "VASTSRV", "Database", "", database, PATH_MAX);
if (database[0] == '\0')
{
ErrPostEx(SEV_FATAL,0,0, "MMDB config file / path to VAST data missing.\n");
return FALSE;
}
GetAppParam("vast", "VASTSRV", "Gunzip", "", gunzip, (size_t) 256 * (sizeof(char)));
if (gunzip[0] == '\0')
{
ErrPostEx(SEV_FATAL,0,0, "VASTInit failed: gunzip path missing.\n");
return FALSE;
}
GetAppParam("vast", "VASTSRV", "SubsetFile", "", fname, PATH_MAX);
if (fname[0] == '\0') {
ErrPostEx(SEV_FATAL, 0, 0, "VASTInit failed: no subset file name.\n");
return FALSE;
}
if (LoadSubsetTable(fname) != 1) {
ErrPostEx(SEV_FATAL, 0, 0, "VASTInit failed: can't load subset table.\n");
return FALSE;
}
return TRUE;
}
#else
Boolean LIBCALL VASTInit (void)
{
GetAppParam("mmdb", "VAST", "Database", "", database, PATH_MAX);
if (database[0] == NULL)
{
ErrPostEx(SEV_FATAL,0,0, "MMDB config file / path to VAST data missing.\n");
return FALSE;
}
return TRUE;
}
#endif
void LIBCALL VASTFini (void)
{
return;
}
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