static void ValidateOneFile (
CharPtr directory,
CharPtr base,
CharPtr suffix,
SeqEntryPtr sep
)
{
Char file [FILENAME_MAX], path [PATH_MAX];
ErrSev oldErrSev;
ValidStructPtr vsp;
StringNCpy_0 (path, directory, sizeof (path));
sprintf (file, "%s.%s", base, suffix);
FileBuildPath (path, NULL, file);
ErrSetOptFlags (EO_LOGTO_USRFILE);
ErrSetLogfile (path, ELOG_APPEND | ELOG_NOCREATE);
vsp = ValidStructNew ();
if (vsp != NULL) {
vsp->useSeqMgrIndexes = TRUE;
vsp->suppressContext = TRUE;
oldErrSev = ErrSetMessageLevel (SEV_NONE);
ValidateSeqEntry (sep, vsp);
ValidStructFree (vsp);
ErrSetMessageLevel (oldErrSev);
}
ErrSetLogfile (NULL, ELOG_APPEND | ELOG_NOCREATE);
ErrClearOptFlags (EO_LOGTO_USRFILE);
}
BEDataPtr BEMakeCLParam(void)
{
BEDataPtr pBdata;
FILE *fd;
if (!GetArgs ("qserver", NUMARGS, BE_args))
return NULL;
if(!ErrSetLogfile (BE_args[7].strvalue, ELOG_APPEND))
exit(1);
pBdata = (BEDataPtr)MemNew(sizeof(BEData));
pBdata->database = BE_args[0].intvalue;
pBdata->format = BE_args[1].intvalue;
pBdata->allset = BE_args[2].intvalue;
pBdata->html = (Uchar) BE_args[3].intvalue;
pBdata->query = StringSave(BE_args[4].strvalue);
if(BE_args[5].strvalue != NULL)
pBdata->uids = StringSave(BE_args[5].strvalue);
else if(BE_args[4].strvalue == NULL) {
fd = FileOpen(BE_args[6].strvalue, "r");
pBdata->uids = WWWReadFileInMemory(fd, 0, FALSE);
FileClose(fd);
}
pBdata->commandline = TRUE;
if(pBdata->query == NULL && pBdata->uids == NULL) {
MemFree(pBdata);
ErrPostEx(SEV_ERROR, 88, 0,
"Error in reading parameters. "
"Please check, that query string was set\n");
return NULL;
}
return pBdata;
}
int
#endif
main(int argc, char *argv[])
{
Nlm_Int2 retval;
Nlm_SetupArguments(argc, argv);
#ifdef MSC_VIRT
if ( !_vheapinit(0, 1250, _VM_ALLSWAP) )
{
ErrPost(CTX_NCBIOBJ, 1, "Can't open virtual memory");
return 1;
}
#endif
/* Initialize connection library's logger, registry and lock */
CONNECT_Init(0);
retval = Nlm_Main();
NlmThreadJoinAll();
Nlm_FreeConfigStruct();
ErrSetLogfile(NULL, 0);
Nlm_ReleaseAppContext();
#ifdef MSC_VIRT
_vheapterm();
#endif
NlmThreadDestroyAll();
#if defined(OS_MSWIN)
return retval;
#elif defined(OS_UNIX) || defined(OS_VMS)
exit( retval );
#endif
}
Int2 Main(void)
{
ValNodePtr vnp2 = NULL, vnp = NULL;
CharPtr pchar = NULL;
Int4 i = 0;
CharPtr pi = NULL;
ErrSetOptFlags(EO_LOG_SEVERITY | EO_LOG_CODES | EO_LOG_FILELINE | EO_LOG_USRFILE);
ErrSetLogfile("goquerylog", ELOG_BANNER);
ErrSetLogLevel(SEV_INFO);
ErrSetMessageLevel(SEV_MAX);
/*GODB_InitCodeBase();
GODB_OpenAllDBs();*/
if(!SHoundInit(FALSE, "goquery"))
{
printf("Cannot open SeqHound.\n");
return 1;
}
printf("Starting the query\n");
/*GODB_PrintAllRecords();*/
printf("Children of 7612\n");
vnp = SHoundGODBGetChildrenOf(7612);
PrintValNodeOfInt(vnp);
ValNodeFree(vnp);
printf("Children of 4907\n");
vnp = SHoundGODBGetChildrenOf(4907);
PrintValNodeOfInt(vnp);
ValNodeFree(vnp);
printf("Children of 5381\n");
vnp = SHoundGODBGetChildrenOf(5381);
PrintValNodeOfInt(vnp);
ValNodeFree(vnp);
printf("Parent of 5381\n");
vnp = SHoundGODBGetParentOf(5381);
PrintValNodeOfInt(vnp);
ValNodeFree(vnp);
printf("Parent of 5367\n");
vnp = SHoundGODBGetParentOf(5367);
PrintValNodeOfInt(vnp);
ValNodeFree(vnp);
printf("Parent of 16883\n");
vnp = SHoundGODBGetParentOf(16883);
PrintValNodeOfInt(vnp);
ValNodeFree(vnp);
printf("Name of 7625\n");
pchar = SHoundGODBGetNameByID(7625);
printf("%s\n", IsNullStr(pchar));
MemFree(pchar);
printf("Name of 16882\n");
pchar = SHoundGODBGetNameByID(16882);
printf("%s\n", IsNullStr(pchar));
MemFree(pchar);
printf("Name of 15412\n");
pchar = SHoundGODBGetNameByID(15412);
printf("%s\n", IsNullStr(pchar));
MemFree(pchar);
printf("All ancestors of 7627\n");
vnp2 = SHoundGODBGetAllAncestors(7627);
PrintValNodeOfInt(vnp2);
ValNodeFree(vnp2);
printf("All ancestors of 5141\n");
vnp2 = SHoundGODBGetAllAncestors(5141);
PrintValNodeOfInt(vnp2);
ValNodeFree(vnp2);
printf("All children of 7627\n");
vnp2 = SHoundGODBGetAllChildren(7627);
PrintValNodeOfInt(vnp2);
ValNodeFree(vnp2);
printf("All children of 16787\n");
vnp2 = SHoundGODBGetAllChildren(16787);
PrintValNodeOfInt(vnp2);
ValNodeFree(vnp2);
printf("Getting those records with EC\n");
vnp2 = SHoundGODBGetRecordByReference("EC");
PrintValNodeOfInt(vnp2);
ValNodeFree(vnp2);
printf("Getting those records with ISBN\n");
vnp2 = SHoundGODBGetRecordByReference("ISBN");
PrintValNodeOfInt(vnp2);
ValNodeFree(vnp2);
printf("Geting classification\n");
pi = SHoundGODBGetClassification(5935);
printf("%s\n", IsNullStr(pi));
ErrPostEx(SEV_INFO, 0, 0, "Done.");
/*GODB_InitUndoCodeBase();*/
SHoundFini();
return 0;
}
Int2 Main()
{
PMSD pmsdRoot = NULL;
static char valfilein[PATH_MAX];
Int2 iDotLen = 0;
AsnIoPtr aip=NULL;
NcbiMimeAsn1Ptr nmap=NULL;
BiostrucPtr bsp=NULL;
BiostrucSeqPtr bssp=NULL;
PDNMS pdnmsModelstruc = NULL;
ErrSev esMsg,esLog,esFatal;
PDNML pdnmlModel;
PMLD pmldThis;
Boolean isMime = FALSE;
Int4 iModels = 0, iNCBImodel = 0, iPDBmodel = 0, iAscii = 0;
/* Initialize MMDB-API */
ErrSetLogfile("error_strSummary.log", ELOG_APPEND|ELOG_BANNER);
ErrSetOptFlags(EO_SHOW_SEVERITY|EO_SHOW_CODES|EO_LOG_FILELINE|EO_SHOW_USERSTR|EO_SHOW_ERRTEXT|EO_BEEP|EO_WAIT_KEY|EO_LOGTO_USRFILE);
if (!GetArgs("strSummary reports on what is inside .val or .cn3 or .prt file to stdout.\nCaution - will not work on Biounits downloaded from NCBI, use Asymmetric Units\n",3,Rargs))
return 1;
/* we use exact filenames and extensions to avoid confusion */
StringCpy(valfilein, Rargs[0].strvalue);
if (FileLength(valfilein) == 0)
{
ErrPostEx(SEV_FATAL,13,1,"Unable to find input file %s",Rargs[0].strvalue);
return 13;
}
if (!OpenMMDBAPI(0,NULL)) {
ErrPostEx(SEV_FATAL,12,1,"Unable to open MMDBAPI, check for missing bstdt.val dictionary file.");
return 12;
}
/* load an ASN.1 file *.val or *.c3d or *.prt write out Biostruc only */
aip=AsnIoOpen(valfilein,"rb");
if (aip==NULL) {
ErrPostEx(SEV_FATAL,11,1,"Unable open ASN.1 stream in file %s",valfilein);
return 11;
}
/* first try biostruc load */
/* printf("try biostruc\n"); */
esMsg=ErrGetMessageLevel();
esLog=ErrGetLogLevel();
esFatal=ErrGetFatalLevel();
ErrSetMessageLevel(SEV_MAX);
ErrSetLogLevel(SEV_MAX);
ErrSetFatalLevel(SEV_MAX);
bsp=BiostrucAsnRead(aip,NULL);
AsnIoClose(aip);
ErrSetMessageLevel(esMsg);
ErrSetLogLevel(esLog);
ErrSetFatalLevel(esFatal);
if (bsp == NULL) { /* try ascii */
aip = AsnIoOpen(valfilein,"r");
if (aip==NULL) {
ErrPostEx(SEV_FATAL,10,1,"Unable open binary or ascii ASN.1 from file %s",valfilein);
return 10;
}
esMsg=ErrGetMessageLevel();
esLog=ErrGetLogLevel();
esFatal=ErrGetFatalLevel();
ErrSetMessageLevel(SEV_MAX);
ErrSetLogLevel(SEV_MAX);
ErrSetFatalLevel(SEV_MAX);
bsp=BiostrucAsnRead(aip,NULL);
AsnIoClose(aip);
ErrSetMessageLevel(esMsg);
ErrSetLogLevel(esLog);
ErrSetFatalLevel(esFatal);
if (bsp) iAscii = 1;
}
if (bsp==NULL) {
/* printf("try mime binary\n"); */
/* then try NCBIMime load */
aip=NULL;
aip=AsnIoOpen(valfilein,"rb");
ErrSetMessageLevel(SEV_MAX);
ErrSetLogLevel(SEV_MAX);
ErrSetFatalLevel(SEV_MAX);
nmap=NcbiMimeAsn1AsnRead(aip,NULL);
ErrSetMessageLevel(esMsg);
ErrSetLogLevel(esLog);
ErrSetFatalLevel(esFatal);
AsnIoClose(aip);
if (nmap == NULL) {
/* printf("try mime ascii\n"); */
aip=AsnIoOpen(valfilein,"r");
ErrSetMessageLevel(SEV_MAX);
ErrSetLogLevel(SEV_MAX);
ErrSetFatalLevel(SEV_MAX);
nmap=NcbiMimeAsn1AsnRead(aip,NULL);
ErrSetMessageLevel(esMsg);
ErrSetLogLevel(esLog);
ErrSetFatalLevel(esFatal);
AsnIoClose(aip);
if (nmap) iAscii = 1;
}
if (nmap!=NULL) {
/* got an NCBI mime */
if (nmap->choice!=NcbiMimeAsn1_strucseq && nmap->choice!=NcbiMimeAsn1_strucseqs) {
/* wrong MIME type */
nmap=NcbiMimeAsn1Free(nmap);
ErrPostEx(SEV_ERROR,9,1,"MIME-type wrapper is not a strucseq or strucseqs - no Biostruc to report in: %s",valfilein);
return 9;
}
isMime = TRUE;
/* unwrap the mime and leave the bsp for PDB conversion */
bssp=(BiostrucSeqPtr)(nmap->data.ptrvalue);
bsp=bssp->structure;
bssp->structure = NULL;
/* may want to report on contents of wrapper ... */
nmap=NcbiMimeAsn1Free(nmap); /* discard the wrapper */
nmap = NULL;
bssp = NULL;
}
}
if (bsp == NULL) {
ErrPostEx(SEV_ERROR,8,1,"No Biostruc in files to report in: %s",valfilein);
return 8;
}
pdnmsModelstruc=MakeAModelstruc(bsp);
if (pdnmsModelstruc==NULL) {
ErrPostEx(SEV_ERROR,7,1,"Unable to convert Biostruc to Modelstruc");
return 7;
}
pmsdRoot=(PMSD)(pdnmsModelstruc->data.ptrvalue);
if (pmsdRoot==NULL) {
ErrPostEx(SEV_ERROR,6,1,"Internal error.");
return 6;
}
/* OK, Ready to Start Reporting */
printf("Filename: %s\n", valfilein);
if (Rargs[1].intvalue == FALSE) {
if (iAscii) printf("ASCII Asn.1 (.prt) ");
else printf("Binary Asn.1 (.val) ");
if (isMime) printf("Entry Point: NCBIMime\n");
else printf("Entry Point: Biostruc\n");
if (pmsdRoot->pcPDBName != NULL) printf("PDB code: %s\n",pmsdRoot->pcPDBName);
printf("MMDB Id: %d\n", (int) pmsdRoot->iMMDBid);
printf("Name: %s\n",GetStrucStrings(pdnmsModelstruc, LONG_NAME));
printf("PDB Class: %s\n",GetStrucStrings(pdnmsModelstruc, PDB_CLASS));
printf("PDB Source: %s\n",GetStrucStrings(pdnmsModelstruc, PDB_SOURCE));
pdnmlModel=pmsdRoot->pdnmlModels;
while (pdnmlModel) {
iModels++;
pmldThis=(PMLD)(pdnmlModel->data.ptrvalue);
if (pmldThis->iType==Model_type_ncbi_all_atom) {
iNCBImodel = pdnmlModel->choice;
}
if (pmldThis->iType==Model_type_pdb_model) {
iPDBmodel = pdnmlModel->choice;
}
pdnmlModel=pdnmlModel->next;
}
printf("Number of Models: %d\n",iModels);
if(iNCBImodel) printf("NCBI All Atom Model: %d\n",iNCBImodel);
if (iPDBmodel) printf("PDB All Atom Model: %d\n",iPDBmodel);
if (pmsdRoot->pDictLocal) printf("Has Local Chemical Graph Dictionary\n");
printf("Number of Molecules: %d\n", (int) pmsdRoot->iMolCount); /* number of molecules */
printf("Number of Objects: %d\n",(int) pmsdRoot->iObjCount); /* number of objects */
printf("Number of Density Sets: %d\n",(int) pmsdRoot->iDensCount); /* number of densities */
printf("Number of Inter-Molecule Bonds: %d\n", (int) pmsdRoot->iIMBCount);
if (Rargs[2].intvalue == TRUE) {
printf("\n\nRAMACHANDRAN Angles for all Proteins:\n");
if (iNCBImodel) {
printf("NCBI All Atom Coordinate Model Number %d\n\nChain, AA, Num, Phi, Psi\n",iNCBImodel);
WriteStdoutRamaOneModel(pmsdRoot, iNCBImodel );
}
else if (iPDBmodel) {
printf("PDB All Atom Coordinate Model Number %d:\n\nChain, AA, Num, Phi, Psi\n",iPDBmodel);
WriteStdoutRamaOneModel(pmsdRoot, iPDBmodel );
}
}
}
printf("\n\n");
/* Output FASTA for each chain and dump het list - oldie but goodie code ! */
WriteFASTASeqHet(pdnmsModelstruc, stdout);
/* Shut Down MMDB-API */
/* All Modelstrucs remaining are freed in CloseMMDB-API() */
CloseMMDBAPI();
return 0;
}
Int2 Main(void)
{
WWWInfoPtr info;
WWWErrorCode error;
BEDataPtr pBdata;
Int4 count;
Uint4 *ids;
Char tmp[512];
if((error = WWWReadPosting(&info)) != WWWErrOk) {
ErrPostEx(SEV_FATAL, 88, 0, "Error in processing WWW request");
return 1;
}
if(WWWGetMethod(info) == COMMAND_LINE) {
WWWInfoFree(info);
if((pBdata = BEMakeCLParam()) == NULL)
return 1;
} else {
if(!ErrSetLogfile (QSRV_LOGFILE_STD_NAME, ELOG_APPEND))
return 1;
if((pBdata = BEMakeWWWParam(info)) == NULL) {
printf("Content-type: text/html\n\n");
printf("QSRV_STATUS 802 Invalid input parameters <PRE><BR>\n");
fflush(stdout);
ErrPostEx(SEV_ERROR, 88, 0,
"Error in reading parameters. "
"Please check, that query string was set\n");
return 1;
}
}
if(!pBdata->commandline) {
if(pBdata->savetodisk)
printf("Content-type: chemical/seq-%s-genbank\n\n",
pBdata->database == 0 ? "na" : "aa");
else {
printf("Content-type: text/html\n\n");
printf("<HTML><HEADER><TITLE>Batch Entrez results"
"</TITLE></HEADER><PRE>\n");
}
}
if (! ID1BioseqFetchEnable("Nbatch", TRUE)) {
printf("Cannot initialize ID1\n");
return 1;
}
if(pBdata->html) {
init_www(); /* initializing WWW mode */
head_tail_ff(NULL, BatchHead, BatchTail);
}
SeqEntryLoad();
switch(pBdata->request_type) {
case REQ_DEFAULT:
if(pBdata->uids == NULL) {
count = BEGetUidsFromQuery(pBdata->query, &ids,
pBdata->database == 0, /* Nucleotide ? */
FALSE);
} else {
count = BE_ReadIds(pBdata, &ids);
}
break;
case REQ_ADVANCED_QUERY:
case REQ_ORGANISM:
count = BEGetUidsFromQuery(pBdata->query, &ids,
pBdata->database == 0, /* Nucleotide ? */
FALSE);
break;
case REQ_LIST_OF_GIS:
count = BE_ReadIds(pBdata, &ids);
break;
}
pBdata->count = count;
QSRVWriteLogInfo(pBdata);
if(count < 0) {
if(pBdata->commandline)
ErrPostEx(SEV_ERROR, 0, count, "Error in searching the database");
else
printf("QSRV_STATUS %d Error in searching database\n", count);
return 1;
}
if(count == 0) {
if(pBdata->commandline)
ErrPostEx(SEV_INFO, 0,0, "No entries found");
else
printf("QSRV_STATUS 901 OK No entries found\n", count);
return 1;
}
if((count > 20000 && pBdata->format == F_GEN) ||
(count > 100000 && pBdata->format != F_GILIST)) {
if(pBdata->commandline)
ErrPostEx(SEV_WARNING, 0,0, "Number of sequences %d exceed limit",
count);
else
printf("QSRV_STATUS 803 Error Number of sequences %d "
"exceed limit\n", count);
pBdata->format = F_GILIST;
}
if(!pBdata->noheader && !pBdata->commandline)
printf("QSRV_STATUS 900 OK: %d entr%s found <PRE><BR>\n",
count, count == 1? "y" : "ies");
fflush(stdout);
/* Printing results */
BEPrintIds(pBdata, ids, count);
/* Clearing memory */
MemFree(ids);
BEFreeCLParam(pBdata);
return 0;
}
