/*
* $Id: vastuti.cpp,v 1.1 2005/07/26 17:12:50 chenj Exp $
*
*
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* 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 have not placed any restriction on its use or reproduction.
*
* 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.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
*
* Author: Jie Chen
*
*
* $Log: vastuti.cpp,v $
* Revision 1.1 2005/07/26 17:12:50 chenj
* Making linux VSNbr.cgi
*
* Revision 1.1.1.1 2002/12/06 20:17:21 chenj
* Imported Scouces
*
*
*
*
* This is the utility program file.
*
* ==========================================================================
*/
#include "hUtilib.hpp"
#include "vastuti.hpp"
extern Uint1 numSubsets;
extern SubsetNameData subsetNames[5];
extern string MAILto;
extern char DATApath[MAX_TBUFF], VSPATH[MAX_TBUFF];
extern char URLcgi[MAX_TBUFF], CGIname[MAX_TBUFF];
extern bool SubsetInfoLoaded;
extern string JobID, Passwd;
void PrtMesC(string MAILto, CharPtr str1, CharPtr str2, CharPtr str3, bool ret)
{
printf("Content-type: text/html\n\n");
printf("\n");
printf("
%s
\n", str1);
if (str2) {
printf("
%s", str2);
if (str3) printf("\"%s\".
\n", str3);
else printf("
\n");
}
if (MAILto != "")
printf("
Please alert \"%s\" of this problem.
\n",
MAILto);
if (!ret) exit(1);
}
void loadSubsetInfo(void)
{
numSubsets = 0;
numSubsets = constructSubsetNames(subsetNames, 10);
if(numSubsets <= 0)
PrtMesC(MAILto, "VASTSRV", "loadSubsetInfo() failed.", "", false);
SubsetInfoLoaded = true;
} /* loadSubsetInfo() */
string GetSubsetName_DB(unsigned subsetId)
{
Uint1 i = 0;
if(SubsetInfoLoaded == false) loadSubsetInfo();
for(i = 0; i < numSubsets; i++)
if(subsetNames[i].subId == (Uint1) subsetId)
return (string)subsetNames[i].subName;
PrtMesC(MAILto, "VASTSRV", "GetSubsetName_DB() failed.", "", false);
return ("");
} /* GetSubsetName_DB() */
/************************** DZ: extracted from mmdbsrv.c **********************
* WWWPrintFileData looks in the current CGI-BIN directory, or the "data"
* subdirectory for the data file and prints it out to pFile.
*/
void WWWPrintFileData(char *FName, FILE *pFile)
{
FILE *f = NULL;
char fullpath [PATH_MAX], pcBuf[1024];
char *ptr;
fullpath[0] = '\0';
StringCpy(fullpath, DATApath); /* look in DATApath */
StringCat(fullpath, FName);
f = FileOpen (fullpath, "r");
if (f == NULL) {
f = FileOpen (FName, "r"); /* look in curent */
if (f == NULL) { /* look in ./data/ */
ProgramPath (fullpath, sizeof (fullpath) - 1);
ptr = StringRChr (fullpath, DIRDELIMCHR);
if (ptr != NULL) {
*ptr = '\0';
}
FileBuildPath (fullpath, (char *)"data", FName);
f = FileOpen (fullpath, (char *)"r");
if (f == NULL) {
return;
}
}
}
do {
pcBuf[0] = '\0';
ptr = fgets(pcBuf, (size_t)1024, f);
if (ptr) fprintf(pFile, ptr);
} while (ptr);
FileClose(f);
} /* WWWPrintFileData() */
/* Note: A lot of this common html text could be put into a header file,
* read in, and then spewed out.
* Cf. the way this is done in mmdbsrv with WWWPrintFile.
* Sometime I'll take the time to write a more general version of the latter
* function that can be used for this purpose. T.M.
*/
/* DZ: most of the HTML file URLs are inside the new VAST subdirectory, and
* references to these are interwoven with many query-specific references.
* Becasue of this interleaving, using WWWPrintFileData would require several
* invocations and corresponding text files. Instead, WWWPrintFileData is only
* used to define the new path to CN3D, and all vast html references are now
* prefixed with the VASTpath string. This variable has been added to .vastrc
* and to the list of parameters to be extracted using GetVastParams.
*/
BiostrucAnnotSetPtr LIBCALL
LocalGetBiostrucAnnotSet(unsigned mmdbid)
{
AsnIoPtr aip = NULL;
BiostrucAnnotSetPtr pbsa = NULL;
char path[PATH_MAX];
char pcId[20];
unsigned iFileExists = 0;
sprintf(pcId, "/%ld", (long) mmdbid);
StringCpy(path, VSPATH);
StringCat(path, JobID.c_str());
StringCat(path, pcId);
StringCat(path, ".bas");
iFileExists = FileLength(path);
if (iFileExists == 0)
return NULL;
aip = AsnIoOpen(path, (char *)"r");
pbsa = BiostrucAnnotSetAsnRead(aip, NULL);
AsnIoClose (aip);
if (!pbsa) return NULL;
return pbsa;
} /* LocalGetBiostrucAnnotSet() */
/*
BiostrucAnnotSetPtr LIBCALL
LocalGetFeatureSet(unsigned mmdbid, unsigned feature_set_id)
{
BiostrucAnnotSetPtr basp2 = NULL;
BiostrucFeatureSetPtr pbsfs = NULL;
BiostrucAnnotSetPtr basp = NULL;
BiostrucFeatureSetPtr pbsfsLast = NULL;
if (IsVASTData(mmdbid))
basp = VASTBsAnnotSetGet(mmdbid);
else if (IsVASTData(feature_set_id)) {
basp = VASTBsAnnotSetGet(feature_set_id);
if (basp != NULL) return basp;
}
else
if (JobID != "")
basp = LocalGetBiostrucAnnotSet(mmdbid);
if (basp == NULL)
return NULL;
pbsfs = basp->features;
pbsfsLast = NULL;
basp2 = NULL;
while (pbsfs)
{
if (pbsfs->id == feature_set_id)
{
basp2 = BiostrucAnnotSetNew();
basp2->id = basp->id;
basp->id = NULL; // unlink the id valnode from basp object
basp2->descr = basp->descr;
basp->descr = NULL; // unlink the descr from basp object
basp2->features = pbsfs;
if (pbsfsLast) // relink next to prev
pbsfsLast->next = pbsfs->next;
else
basp->features = pbsfs->next;
basp2->features->next = NULL;
BiostrucAnnotSetFree(basp);
return basp2;
}
pbsfsLast = pbsfs;
pbsfs = pbsfs->next;
}
BiostrucAnnotSetFree(basp);
return basp2;
} // LocalGetFeatureSet */
BiostrucAnnotSetPtr LIBCALL BiostrucAnnotSetGetByFid (
BiostrucAnnotSetPtr basp, int feature_id, int feature_set_id)
{
BiostrucAnnotSetPtr basp2 = NULL;
BiostrucFeatureSetPtr pbsfs = NULL;
BiostrucFeaturePtr pbsf = NULL;
if (basp == NULL)
return NULL;
pbsfs = basp->features;
while (pbsfs) {
if (pbsfs->id == feature_set_id) {
pbsf = pbsfs->features;
while(pbsf) {
if (pbsf->id == feature_id) { /* found it */
basp2 = BiostrucAnnotSetNew();
basp2->id = basp->id;
basp->id = NULL; /* unlink the id valnode from basp object */
basp2->descr = basp->descr;
basp->descr = NULL; /* unlink the descr from basp object */
basp2->features = BiostrucFeatureSetNew();
basp2->features->id = pbsfs->id;
basp2->features->descr = pbsfs->descr;
pbsfs->descr = NULL; /* unlink */
basp2->features->features = BiostrucFeatureNew();
basp2->features->features->id = pbsf->id;
basp2->features->features->name = StringSave(pbsf->name);
basp2->features->features->type = pbsf->type;
basp2->features->features->Property_property=pbsf->Property_property;
pbsf->Property_property = NULL; /* unlink */
basp2->features->features->Location_location=pbsf->Location_location;
pbsf->Location_location = NULL; /* unlink */
BiostrucAnnotSetFree(basp);
return basp2;
}
pbsf = pbsf->next;
}
}
pbsfs = pbsfs->next;
}
BiostrucAnnotSetFree(basp);
return basp2;
} /* BiostrucAnnotSetGetByFid() */
short LIBCALL Check_VastSearch_Password()
{
char pcPassFile[24];
char PassPath[PATH_MAX];
FILE *passwdfile;
char * pcPassOld;
unsigned iPassLen;
iPassLen = StringLen(Passwd.c_str());
pcPassOld = StringSave(Passwd.c_str());
sprintf(pcPassFile, "/%s.passwd", JobID.c_str());
PassPath[0]='\0';
StringCpy(PassPath, VSPATH);
StringCat(PassPath, JobID.c_str());
StringCat(PassPath, pcPassFile);
if ((passwdfile = FileOpen(PassPath, "r")) == NULL) {
char str[100];
sprintf(str, (char *)"%s", JobID.c_str());
PrtMesC(NULL, (char *)"VASTSRV",
(char *)"Password file doesn't exist for JobId = ", str, true);
return 2;
}
fscanf(passwdfile, "%s", pcPassOld);
FileClose(passwdfile);
if (!StringNCmp(pcPassOld, Passwd.c_str(), iPassLen))
return 1;
else
return 0;
} /* end of Check_VastSearch_Password */
/* new Prune */
BiostrucAnnotSetPtr PruneBiostrucAnnotHits(
BiostrucAnnotSetPtr basp, unsigned FSID, ValNodePtr pvnFids)
{
BiostrucAnnotSetPtr basp2 = NULL;
BiostrucFeatureSetPtr pbsfs = NULL;
BiostrucFeaturePtr pbsf = NULL, pre_pbsf = NULL;
BiostrucFeaturePtr pbsfHold = NULL;
BiostrucFeaturePtr pbsf2 = NULL;
bool found = false;
if ((basp == NULL) || (pvnFids == NULL) || (FSID == 0))
return NULL;
pbsfs = basp->features;
while (pbsfs) {
if (pbsfs->id == FSID) {
basp2 = BiostrucAnnotSetNew();
basp2->id = basp->id;
basp->id = NULL; /* unlink the id valnode from basp object */
basp2->descr = basp->descr;
basp->descr = NULL; /* unlink the descr from basp object */
basp2->features = BiostrucFeatureSetNew();
basp2->features->id = pbsfs->id;
pbsfs->id = NULL;
basp2->features->descr = pbsfs->descr;
pbsfs->descr = NULL; /* unlink */
pbsfHold = pbsfs->features;
pbsfs->features = NULL;
BiostrucAnnotSetFree(basp);
pbsfs = NULL;
while (pvnFids) {
found = false;
pbsf = pbsfHold;
pre_pbsf = NULL;
while (pbsf) {
if ((unsigned) pvnFids->data.intvalue == pbsf->id) {
found = true;
break;
}
pre_pbsf = pbsf;
pbsf = pbsf->next;
}
if (found) {
if (!pre_pbsf) pbsfHold = pbsf->next;
else pre_pbsf->next = pbsf->next;
if (!basp2->features->features) {
basp2->features->features = pbsf;
pbsf2 = basp2->features->features;
}
else {
pbsf2->next = pbsf;
pbsf2 = pbsf;
}
}
pvnFids = pvnFids->next;
} /* while pvbFids */
pbsf2->next = NULL;
}
if(pbsfs) pbsfs = pbsfs->next;
}
return basp2;
} /* PruneBiostrucAnnotHits() */
void MakeNbrList(char * nbrString, char * *(*SelNames), unsigned **SelSds,
unsigned *iCount, unsigned ischar)
{
char SavedChar = NULLB;
char *Ptr=NULL, *Ptr2=NULL;
unsigned i, j;
Ptr2 = Ptr = SkipSpaces(nbrString);
if (*Ptr == NULLB) return;
*iCount = 0;
while (*Ptr) {
if (*Ptr != ',') (*iCount)++;
Ptr = SkipToSet(Ptr, (char *)" ,");
Ptr = SkipSet(Ptr, (char *)" ,");
}
if (!(*iCount)) return;
if (ischar) {
*SelNames = new char* [*iCount];
for (i=0; i< *iCount; i++) (*SelNames)[i] = new char [100];
}
else *SelSds = new unsigned [*iCount];
Ptr = Ptr2;
i = 0;
while (*Ptr) {
Ptr2 = SkipToSet(Ptr, (char *)" ,");
SavedChar = *Ptr2;
*Ptr2 = NULLB;
if (ischar && Ptr[0] != '\0') {
for (j=0; j< StrLen(Ptr); j++) Ptr[j] = toupper(Ptr[j]);
if (Ptr[4] == '.') Ptr[4] = ' ';
strcpy((*SelNames)[i++], Ptr);
}
else if (!ischar) {
if ( isInt(Ptr) ) (*SelSds)[i++] = atoi(Ptr);
else {
PrtMesC("", "VASTSRV", "Please use numbers as 3D-Domain ids, but not this: ", Ptr, false);
}
}
*Ptr2 = SavedChar;
Ptr = SkipSet(Ptr2, (char *)" ,");
}
*iCount = i;
} /* end of MakeNbrList */
void
OrderCopyVpp(VastPageDataPtr vpptmp, VastPageDataPtr vpp, unsigned iKept, unsigned * KepId)
{
unsigned i, j, k;
for (i=0; i< iKept; i++) {
j=0;
while (j