static void
mapinit(char *mapfile)
{
int nf;
char *ln;
char *fields[2];
Biobuf *bp;
Map *map;
if (mapfile == nil)
return;
bp = Bopen(mapfile, OREAD);
if (bp == nil)
sysfatal("can't read %s", mapfile);
devmap = nil;
while ((ln = Brdline(bp, '\n')) != nil) {
ln[Blinelen(bp)-1] = '\0';
if (*ln == '\0' || *ln == '#')
continue;
nf = tokenize(ln, fields, nelem(fields));
if (nf != 2)
continue;
if(testconfig(fields[0]) != 0) {
print("bad `from' device %s in %s\n",
fields[0], mapfile);
continue;
}
map = malloc(sizeof *map);
map->from = strdup(fields[0]);
map->to = strdup(fields[1]);
map->fdev = iconfig(fields[0]);
map->tdev = nil;
if (access(map->to, AEXIST) < 0) {
/*
* map->to isn't an existing file, so it had better be
* a config string for a device.
*/
if(testconfig(fields[1]) == 0)
map->tdev = iconfig(fields[1]);
}
/* else map->to is the replacement file name */
map->next = devmap;
devmap = map;
}
Bterm(bp);
}
int CVecScreenApp::Run(void)
{
int status = BLAST_EXIT_SUCCESS;
try {
// Allow the fasta reader to complain on invalid sequence input
SetDiagPostLevel(eDiag_Warning);
const bool kIsProtein(false);
/*** Process the command line arguments ***/
const CArgs& args = GetArgs();
const string kDbName(args[kArgDb].AsString());
CRef<CBlastOptionsHandle> opts_hndl(CBlastOptionsFactory::Create(eVecScreen));
/*** Initialize the scope ***/
SDataLoaderConfig dlconfig(kDbName, kIsProtein);
dlconfig.OptimizeForWholeLargeSequenceRetrieval();
CBlastInputSourceConfig iconfig(dlconfig);
iconfig.SetQueryLocalIdMode();
CRef<CScope> scope = CBlastScopeSource(dlconfig).NewScope();
/*** Initialize the input stream ***/
CBlastFastaInputSource fasta(args[kArgQuery].AsInputFile(), iconfig);
CBlastInput input(&fasta, 1);
/*** Get the formatting options ***/
const CVecscreenRun::CFormatter::TOutputFormat kFmt =
args[kArgOutputFormat].AsInteger();
const bool kHtmlOutput = !args["text_output"].AsBoolean();
/*** Process the input ***/
while ( !input.End() ) {
CRef<CBlastQueryVector> query_batch(input.GetNextSeqBatch(*scope));
_ASSERT(query_batch->Size() == 1);
CRef<IQueryFactory> queries(new CObjMgr_QueryFactory(*query_batch));
CVecscreenRun vs(CRef<CSeq_loc>(const_cast<CSeq_loc*>(&*query_batch->GetQuerySeqLoc(0))),
query_batch->GetScope(0), kDbName);
CVecscreenRun::CFormatter vs_format(vs, *scope, kFmt, kHtmlOutput);
vs_format.FormatResults(args[kArgOutput].AsOutputFile(), opts_hndl);
}
} CATCH_ALL(status)
return status;
}
void
arginit(void)
{
int verb;
char *line;
char word[Maxword+1], *cp;
Filsys *fs;
if(nvrcheck() == 0) {
setconfig(conf.confdev);
if (!conf.configfirst)
return;
}
/* nvr was bad or invoker requested configuration step */
setconfig(conf.confdev);
for (;;) {
print("config: ");
if ((line = Brdline(&bin, '\n')) == nil)
return;
line[Blinelen(&bin)-1] = '\0';
cp = getwrd(word, line);
if (word[0] == '\0' || word[0] == '#')
continue;
if(strcmp(word, "end") == 0)
return;
if(strcmp(word, "halt") == 0)
exit();
if(strcmp(word, "queryjuke") == 0) {
getwrd(word, cp);
if(testconfig(word) == 0)
querychanger(iconfig(word));
continue;
}
if(strcmp(word, "allow") == 0) {
wstatallow = 1;
writeallow = 1;
continue;
}
if(strcmp(word, "copyworm") == 0) {
copyworm = 1;
continue;
}
if(strcmp(word, "copydev") == 0) {
cp = getwrd(word, cp);
if(testconfig(word))
continue;
src = strdup(word);
getwrd(word, cp);
if(testconfig(word))
continue;
dest = strdup(word);
copydev = 1;
continue;
}
if(strcmp(word, "noauth") == 0) {
noauth = !noauth;
continue;
}
if(strcmp(word, "noattach") == 0) {
noattach = !noattach;
continue;
}
if(strcmp(word, "readonly") == 0) {
readonly = 1;
continue;
}
if(strcmp(word, "ream") == 0) {
verb = FREAM;
goto gfsname;
}
if(strcmp(word, "recover") == 0) {
verb = FRECOVER;
goto gfsname;
}
if(strcmp(word, "filsys") == 0) {
verb = FEDIT;
goto gfsname;
}
if(strcmp(word, "nvram") == 0) {
getwrd(word, cp);
if(testconfig(word))
continue;
/* if it fails, it will complain */
nvrsetconfig(word);
continue;
}
if(strcmp(word, "config") == 0) {
getwrd(word, cp);
if(!testconfig(word) && nvrsetconfig(word) == 0)
f.newconf = 1;
continue;
}
if(strcmp(word, "service") == 0) {
getwrd(word, cp);
strncpy(service, word, sizeof service);
f.modconf = 1;
continue;
}
if (strcmp(word, "resetparams") == 0) {
resetparams++;
continue;
}
/*
* continue to parse obsolete keywords so that old
* configurations can still work.
*/
if (strcmp(word, "ipauth") != 0 &&
astrcmp(word, "ip") != 0 &&
astrcmp(word, "ipgw") != 0 &&
astrcmp(word, "ipmask") != 0 &&
astrcmp(word, "ipsntp") != 0) {
print("unknown config command\n");
print("\ttype end to get out\n");
continue;
}
getwrd(word, cp);
f.modconf = 1;
continue;
gfsname:
cp = getwrd(word, cp);
for(fs=filsys; fs->name; fs++)
if(strcmp(word, fs->name) == 0)
break;
if (fs->name == nil) {
memset(fs, 0, sizeof *fs);
fs->name = strdup(word);
}
switch(verb) {
case FREAM:
if(strcmp(fs->name, "main") == 0)
wstatallow = 1; /* only set, never reset */
/* fallthrough */
case FRECOVER:
fs->flags |= verb;
break;
case FEDIT:
f.modconf = 1;
getwrd(word, cp);
fs->flags |= verb;
if(word[0] == 0)
fs->conf = nil;
else if(!testconfig(word))
fs->conf = strdup(word);
break;
}
}
}
/* copy device from src to dest */
static int
dodevcopy(void)
{
Device *from, *to;
Iobuf *p;
Off a;
Devsize lim, tosize;
/*
* convert config strings into Devices.
*/
from = iconfig(src);
if(f.error || from == nil) {
print("bad src device %s\n", src);
return -1;
}
to = iconfig(dest);
if(f.error || to == nil) {
print("bad dest device %s\n", dest);
return -1;
}
/*
* initialise devices, size them, more sanity checking.
*/
devinit(from);
lim = devsize(from);
if(lim == 0)
panic("no blocks to copy on %Z", from);
devinit(to);
tosize = devsize(to);
if(tosize == 0)
panic("no blocks to copy on %Z", to);
/* use smaller of the device sizes */
if (tosize < lim)
lim = tosize;
print("copy %Z to %Z in 8 seconds\n", from, to);
delay(8000);
if (userabort("preparing to copy"))
return -1;
print("copying dev: %lld blocks from %Z to %Z\n", (Wideoff)lim,
from, to);
/*
* Copy all blocks, a block at a time.
*/
for (a = 0; a < lim; a++) {
if (userabort("copy"))
break;
p = getbuf(from, a, Brd);
/*
* if from is a real WORM device, we'll get errors trying to
* read unwritten blocks, but the unwritten blocks need not
* be contiguous.
*/
if (p == 0) {
print("%lld not written yet; can't read\n", (Wideoff)a);
continue;
}
if (to != 0 && devwrite(to, p->addr, p->iobuf) != 0) {
print("out block %lld: write error; bailing",
(Wideoff)a);
break;
}
putbuf(p);
if(a % 20000 == 0)
print("block %lld %T\n", (Wideoff)a, time(nil));
}
/*
* wrap up: sync target
*/
print("copied %lld blocks from %Z to %Z\n", (Wideoff)a, from, to);
sync("devcopy");
return 0;
}
void
sysinit(void)
{
int error;
char *cp, *ep;
Device *d;
Filsys *fs;
Fspar *fsp;
Iobuf *p;
cons.chan = fs_chaninit(Devcon, 1, 0);
start:
/*
* part 1 -- read the config file
*/
devnone = iconfig("n");
cp = nvrgetconfig();
print("config %s\n", cp);
confdev = d = iconfig(cp);
devinit(d);
if(f.newconf) {
p = getbuf(d, 0, Bmod);
memset(p->iobuf, 0, RBUFSIZE);
settag(p, Tconfig, 0);
} else
p = getbuf(d, 0, Brd|Bmod);
if(!p || checktag(p, Tconfig, 0))
panic("config io");
mergeconf(p);
if (resetparams) {
for (fsp = fspar; fsp->name != nil; fsp++)
fsp->declared = 0;
resetparams = 0;
}
for (fsp = fspar; fsp->name != nil; fsp++) {
/* supply defaults from this cwfs instance */
if (fsp->declared == 0) {
fsp->declared = fsp->actual;
f.modconf = 1;
}
/* warn if declared value is not our compiled-in value */
if (fsp->declared != fsp->actual)
print("warning: config %s %ld != compiled-in %ld\n",
fsp->name, fsp->declared, fsp->actual);
}
if(f.modconf) {
memset(p->iobuf, 0, BUFSIZE);
p->flags |= Bmod|Bimm;
cp = p->iobuf;
ep = p->iobuf + RBUFSIZE - 1;
if(service[0])
cp = seprint(cp, ep, "service %s\n", service);
for(fs=filsys; fs->name; fs++)
if(fs->conf && fs->conf[0] != '\0')
cp = seprint(cp, ep, "filsys %s %s\n", fs->name,
fs->conf);
for (fsp = fspar; fsp->name != nil; fsp++)
cp = seprint(cp, ep, "%s %ld\n",
fsp->name, fsp->declared);
putbuf(p);
f.modconf = f.newconf = 0;
print("config block written\n");
goto start;
}
putbuf(p);
print("service %s\n", service);
loop:
/*
* part 2 -- squeeze out the deleted filesystems
*/
for(fs=filsys; fs->name; fs++)
if(fs->conf == nil || fs->conf[0] == '\0') {
for(; fs->name; fs++)
*fs = *(fs+1);
goto loop;
}
if(filsys[0].name == nil)
panic("no filsys");
/*
* part 3 -- compile the device expression
*/
error = 0;
for(fs=filsys; fs->name; fs++) {
print("filsys %s %s\n", fs->name, fs->conf);
fs->dev = iconfig(fs->conf);
if(f.error) {
error = 1;
continue;
}
}
if(error)
panic("fs config");
/*
* part 4 -- initialize the devices
*/
for(fs=filsys; fs->name; fs++) {
delay(3000);
print("sysinit: %s\n", fs->name);
if(fs->flags & FREAM)
devream(fs->dev, 1);
if(fs->flags & FRECOVER)
devrecover(fs->dev);
devinit(fs->dev);
}
/*
* part 5 -- optionally copy devices or worms
*/
if (copyworm) {
dowormcopy(); /* can return if user quits early */
panic("copyworm bailed out!");
}
if (copydev)
if (dodevcopy() < 0)
panic("copydev failed!");
else
panic("copydev done.");
}
int
testconfig(char *s)
{
iconfig(s);
return f.error;
}
int CBlastDemoApplication::Run(void)
{
// Get arguments
const CArgs& args = GetArgs();
EProgram program = ProgramNameToEnum(args["program"].AsString());
bool db_is_aa = (program == eBlastp || program == eBlastx ||
program == eRPSBlast || program == eRPSTblastn);
CRef<CBlastOptionsHandle> opts(CBlastOptionsFactory::Create(program, CBlastOptions::eRemote));
ProcessCommandLineArgs(opts);
opts->Validate(); // Can throw CBlastException::eInvalidOptions for invalid option.
// This will dump the options to stderr.
// opts->GetOptions().DebugDumpText(cerr, "opts", 1);
CRef<CObjectManager> objmgr = CObjectManager::GetInstance();
if (!objmgr) {
throw std::runtime_error("Could not initialize object manager");
}
const bool is_protein =
!!Blast_QueryIsProtein(opts->GetOptions().GetProgramType());
SDataLoaderConfig dlconfig(is_protein);
CBlastInputSourceConfig iconfig(dlconfig, objects::eNa_strand_other, false,
args["parse"].AsBoolean());
CBlastFastaInputSource fasta_input(args["in"].AsInputFile(), iconfig);
CScope scope(*objmgr);
CBlastInput blast_input(&fasta_input);
TSeqLocVector query_loc = blast_input.GetAllSeqLocs(scope);
CRef<IQueryFactory> query_factory(new CObjMgr_QueryFactory(query_loc));
const CSearchDatabase target_db(args["db"].AsString(),
db_is_aa ? CSearchDatabase::eBlastDbIsProtein : CSearchDatabase::eBlastDbIsNucleotide);
CRemoteBlast blaster(query_factory, opts, target_db);
// This will dump a lot of stuff to stderr.
// blaster.SetVerbose();
bool status = blaster.SubmitSync();
if (status == false)
throw std::runtime_error("No results returned by SubmitSync");
cerr << "RID: " << blaster.GetRID() << '\n';
CSearchResultSet results = *blaster.GetResultSet();
CNcbiOstream& out = args["out"].AsOutputFile();
for (unsigned int i = 0; i < results.GetNumResults(); i++) {
CConstRef<CSeq_align_set> sas = results[i].GetSeqAlign();
out << MSerial_AsnText << *sas;
}
return 0;
}
