extern Pointer ReadFromTPASmart (CharPtr accn, Uint2Ptr datatype, Uint2Ptr entityID)
{
Char cmmd [256];
Pointer dataptr;
FILE* fp;
Char path [PATH_MAX];
Char err_path [PATH_MAX];
if (datatype != NULL) {
*datatype = 0;
}
if (entityID != NULL) {
*entityID = 0;
}
if (StringHasNoText (accn)) return NULL;
if (tpasmartfetchcmd == NULL) {
if (GetAppParam ("SEQUIN", "TPASMART", "FETCHSCRIPT", NULL, cmmd, sizeof (cmmd))) {
tpasmartfetchcmd = StringSaveNoNull (cmmd);
}
}
if (tpasmartfetchcmd == NULL) return NULL;
TmpNam (path);
#ifdef OS_UNIX
sprintf (err_path, "%s.err", path);
sprintf (cmmd, "csh %s %s > %s 2>%s", tpasmartfetchcmd, accn, path, err_path);
system (cmmd);
#endif
#ifdef OS_MSWIN
sprintf (cmmd, "%s %s -o %s", tpasmartfetchcmd, accn, path);
system (cmmd);
#endif
fp = FileOpen (path, "r");
if (fp == NULL) {
FileRemove (path);
return NULL;
}
dataptr = ReadAsnFastaOrFlatFile (fp, datatype, entityID, FALSE, FALSE, TRUE, FALSE);
FileClose (fp);
FileRemove (path);
#ifdef OS_UNIX
FileRemove (err_path);
#endif
return dataptr;
}
void SaveAsPPM(RefPtr<Gdk::Pixbuf> pix, const char* name_prefix)
{
const char* fnam = TmpNam(0, name_prefix);
io::stream strm(fnam, iof::def|iof::trunc);
int wdh = pix->get_width();
int hgt = pix->get_height();
int rowstride = pix->get_rowstride();
RGBA::Pixel* dat = (RGBA::Pixel*)pix->get_pixels(), *cur;
BOOST_CHECK( pix->get_has_alpha() );
strm << "P6\n" << wdh << " " << hgt << "\n255\n";
for( int y=0; cur=dat, y<hgt; y++, dat = (RGBA::Pixel*)((char*)dat + rowstride) )
for( int x=0; x<wdh; x++, cur++ )
{
strm << cur->red << cur->green << cur->blue;
}
}
NLM_EXTERN Boolean VecScreenAsynchronousRequest (
CharPtr database,
BioseqPtr bsp,
VQUEUE* queue,
VecScreenResultProc resultproc,
VecScreenAnnounceProc announceproc,
VoidPtr userdata
)
{
CONN conn;
FILE *fp;
Char path [PATH_MAX];
Char str [128];
if (bsp == NULL || queue == NULL || resultproc == NULL) return FALSE;
if (StringHasNoText (database)) {
database = "UniVec";
}
sprintf (str, "db=%s", database);
conn = VecScreenOpenConnection (str);
if (conn == NULL) return FALSE;
TmpNam (path);
fp = FileOpen (path, "w");
BioseqToFasta (bsp, fp, ISA_na (bsp->mol));
FileClose (fp);
fp = FileOpen (path, "r");
QUERY_CopyFileToQuery (conn, fp);
FileClose (fp);
QUERY_SendQuery (conn);
VecScreen_AddToQueue (queue, resultproc, announceproc, userdata, conn, bsp);
FileRemove (path);
return TRUE;
}
NLM_EXTERN void ViewSortedProteins (SeqEntryPtr sep)
{
Char path [PATH_MAX];
FILE *fp;
if (sep == NULL) return;
TmpNam (path);
fp = FileOpen(path, "w");
if (fp == NULL) {
Message (MSG_ERROR, "Unable to open %s", path);
return;
}
WriteSortedProteinsToFile (fp, sep);
FileClose(fp);
LaunchGeneralTextViewer (path, "Sorted Proteins");
FileRemove (path);
}
static Int2 LIBCALLBACK TPASmartBioseqFetchFunc (Pointer data)
{
BioseqPtr bsp;
Char cmmd [256];
Pointer dataptr;
Uint2 datatype;
Uint2 entityID;
FILE* fp;
OMProcControlPtr ompcp;
ObjMgrProcPtr ompp;
Char path [PATH_MAX];
Char err_path [PATH_MAX];
SeqEntryPtr sep = NULL;
SeqIdPtr sip;
TextSeqIdPtr tsip;
ompcp = (OMProcControlPtr) data;
if (ompcp == NULL) return OM_MSG_RET_ERROR;
ompp = ompcp->proc;
if (ompp == NULL) return OM_MSG_RET_ERROR;
sip = (SeqIdPtr) ompcp->input_data;
if (sip == NULL) return OM_MSG_RET_ERROR;
if (sip->choice != SEQID_TPG) return OM_MSG_RET_ERROR;
tsip = (TextSeqIdPtr) sip->data.ptrvalue;
if (tsip == NULL || StringHasNoText (tsip->accession)) return OM_MSG_RET_ERROR;
if (tpasmartfetchcmd == NULL) {
if (GetAppParam ("SEQUIN", "TPASMART", "FETCHSCRIPT", NULL, cmmd, sizeof (cmmd))) {
tpasmartfetchcmd = StringSaveNoNull (cmmd);
}
}
if (tpasmartfetchcmd == NULL) return OM_MSG_RET_ERROR;
TmpNam (path);
#ifdef OS_UNIX
sprintf (err_path, "%s.err", path);
sprintf (cmmd, "csh %s %s > %s 2>%s", tpasmartfetchcmd, tsip->accession, path, err_path);
system (cmmd);
#endif
#ifdef OS_MSWIN
sprintf (cmmd, "%s %s -o %s", tpasmartfetchcmd, tsip->accession, path);
system (cmmd);
#endif
fp = FileOpen (path, "r");
if (fp == NULL) {
FileRemove (path);
#ifdef OS_UNIX
FileRemove (err_path);
#endif
return OM_MSG_RET_ERROR;
}
dataptr = ReadAsnFastaOrFlatFile (fp, &datatype, &entityID, FALSE, FALSE, TRUE, FALSE);
FileClose (fp);
FileRemove (path);
#ifdef OS_UNIX
FileRemove (err_path);
#endif
if (dataptr == NULL) return OM_MSG_RET_OK;
sep = GetTopSeqEntryForEntityID (entityID);
if (sep == NULL) return OM_MSG_RET_ERROR;
bsp = BioseqFindInSeqEntry (sip, sep);
ompcp->output_data = (Pointer) bsp;
ompcp->output_entityID = ObjMgrGetEntityIDForChoice (sep);
return OM_MSG_RET_DONE;
}
static BioseqPtr FetchBioseqFromSmartNotId (CharPtr accn, Uint2Ptr pEntityID)
{
BioseqPtr bsp;
Char cmmd [256];
Pointer dataptr;
Uint2 datatype;
Uint2 entityID;
FILE* fp;
OMProcControlPtr ompcp;
ObjMgrProcPtr ompp;
Char path [PATH_MAX];
Char err_path [PATH_MAX];
SeqEntryPtr sep = NULL;
SeqIdPtr sip;
TextSeqIdPtr tsip;
Int4 gi = 0;
ValNodePtr vnp;
time_t t1, t2;
if (srcchkfetchcmd == NULL) {
if (GetAppParam ("SEQUIN", "TBL_CHK", "FETCHSCRIPT", NULL, cmmd, sizeof (cmmd))) {
srcchkfetchcmd = StringSaveNoNull (cmmd);
}
}
if (srcchkfetchcmd == NULL) {
if (GetAppParam ("SEQUIN", "SMART", "FETCHSCRIPT", NULL, cmmd, sizeof (cmmd))) {
srcchkfetchcmd = StringSaveNoNull (cmmd);
}
}
if (srcchkfetchcmd == NULL) return NULL;
TmpNam (path);
t1 = time(NULL);
#ifdef OS_UNIX
sprintf (err_path, "%s.err", path);
sprintf (cmmd, "csh %s %s > %s 2>%s", srcchkfetchcmd, accn, path, err_path);
system (cmmd);
#endif
#ifdef OS_MSWIN
sprintf (cmmd, "%s %s -o %s", srcchkfetchcmd, accn, path);
system (cmmd);
#endif
fp = FileOpen (path, "r");
if (fp == NULL) {
FileRemove (path);
#ifdef OS_UNIX
FileRemove (err_path);
#endif
return OM_MSG_RET_ERROR;
}
dataptr = ReadAsnFastaOrFlatFile (fp, &datatype, &entityID, FALSE, FALSE, TRUE, FALSE);
FileClose (fp);
FileRemove (path);
#ifdef OS_UNIX
FileRemove (err_path);
#endif
if (dataptr == NULL) return NULL;
sep = GetTopSeqEntryForEntityID (entityID);
if (sep == NULL) return NULL;
sip = SmartGuessMakeId (accn);
bsp = BioseqFindInSeqEntry (sip, sep);
sip = SeqIdFree (sip);
if (debug_mode) {
t2 = time(NULL);
if (t2 - t1 > 1) {
printf("Time to download %s from SMART:%d\n", accn, t2 - t1);
}
}
if (pEntityID != NULL) {
*pEntityID = entityID;
}
return bsp;
}
static Boolean LIBCALLBACK FirstVecScreenCallback (
CONN conn,
Nlm_VoidPtr userdata,
EIO_Status status
)
{
VQueuePtr cqp;
FILE *fp;
Char line [256];
Char path [PATH_MAX];
CharPtr rid;
CharPtr rtoe;
CharPtr str;
long int val;
/* read rID or failure message */
cqp = (VQueuePtr) userdata;
TmpNam (path);
fp = FileOpen (path, "w");
QUERY_CopyResultsToFile (conn, fp);
FileClose (fp);
fp = FileOpen (path, "r");
str = ReadALine (line, sizeof (line), fp);
while (str != NULL) {
if (! StringHasNoText (line)) {
if (line [0] == '>') {
if (StringNICmp (line, ">Vector", 7) == 0) {
rid = StringStr (line, "RID: ");
if (rid != NULL) {
rid += 5;
rtoe = StringStr (rid, " RTOE: ");
if (rtoe != NULL) {
*rtoe = '\0';
rtoe += 7;
StringNCpy_0 (cqp->rid, rid, sizeof (cqp->rid));
if (sscanf (rtoe, "%ld", &val) == 1) {
cqp->estTime = (time_t) val;
cqp->secondsToWait = (Int2) val + 2;
} else {
cqp->secondsToWait = 15;
}
if (cqp->secondsToWait > 15) {
cqp->secondsToWait = 15;
}
if (cqp->announceproc != NULL) {
cqp->announceproc (rid, cqp->seqid, (Int2) val);
}
}
} else if (StringStr (line, "FAILED") != NULL) {
cqp->done = TRUE;
if (cqp->resultproc != NULL) {
cqp->resultproc (NULL, cqp->userdata, cqp->rid, cqp->seqid, FALSE);
}
}
} else if (StringNICmp (line, ">Message", 8) == 0) {
str = ReadALine (line, sizeof (line), fp);
while (str != NULL && StringNCmp (line, "//", 2) != 0) {
Message (MSG_POST, "%s\n", str);
if (StringStr (line, "FAILURE") != NULL) {
cqp->done = TRUE;
}
str = ReadALine (line, sizeof (line), fp);
}
}
}
}
str = ReadALine (line, sizeof (line), fp);
}
FileClose (fp);
FileRemove (path);
return TRUE;
}
static Boolean LIBCALLBACK SecondVecScreenCallback (
CONN conn,
Nlm_VoidPtr userdata,
EIO_Status status
)
{
VQueuePtr cqp;
FILE *fp;
Char line [256];
Char path [PATH_MAX];
CharPtr rid;
CharPtr sttus;
CharPtr str;
Boolean success = FALSE;
Boolean waiting = FALSE;
/* look for waiting, failure, or success */
cqp = (VQueuePtr) userdata;
TmpNam (path);
fp = FileOpen (path, "w");
QUERY_CopyResultsToFile (conn, fp);
FileClose (fp);
fp = FileOpen (path, "r");
str = ReadALine (line, sizeof (line), fp);
while (str != NULL) {
if (! StringHasNoText (line)) {
if (line [0] == '>') {
if (StringNICmp (line, ">Vector", 7) == 0) {
rid = StringStr (line, "RID: ");
if (rid != NULL) {
rid += 5;
sttus = StringStr (rid, " Status: ");
if (sttus != NULL) {
*sttus = '\0';
sttus += 9;
if (StringCmp (cqp->rid, rid) != 0) {
ErrPostEx (SEV_ERROR, 0, 0, "RID mismatch '%s' vs '%s'", cqp->rid, rid);
cqp->done = TRUE;
} else if (StringStr (sttus, "FAILED") != NULL) {
cqp->done = TRUE;
} else if (StringStr (sttus, "unknown") != NULL) {
ErrPostEx (SEV_ERROR, 0, 0, "RID unknown '%s'", rid);
cqp->done = TRUE;
} else if (StringStr (sttus, "SUCCESS") != NULL) {
success = TRUE;
} else if (StringStr (sttus, "WAITING") != NULL) {
waiting = TRUE;
/*
Message (MSG_POST, "WAITING");
*/
}
}
}
} else if (StringNICmp (line, ">Message", 8) == 0) {
str = ReadALine (line, sizeof (line), fp);
while (str != NULL && StringNCmp (line, "//", 2) != 0) {
Message (MSG_POST, "%s\n", str);
if (StringStr (line, "FAILURE") != NULL) {
if (! waiting) {
cqp->done = TRUE;
}
}
str = ReadALine (line, sizeof (line), fp);
}
}
}
}
str = ReadALine (line, sizeof (line), fp);
}
FileClose (fp);
if (success) {
cqp->resultproc (path, cqp->userdata, cqp->rid, cqp->seqid, success);
cqp->done = TRUE;
} else if (cqp->done) {
cqp->resultproc (NULL, cqp->userdata, cqp->rid, cqp->seqid, success);
}
FileRemove (path);
return TRUE;
}