AjBool gHttpGetBinS(AjPStr url, AjPFile* outf)
{
AjPFile file = NULL;
AjPStr line = NULL;
AjPStr host = NULL;
AjPStr path = NULL;
AjPStr get = NULL;
ajint port = 80;
ajuint http = 0;
FILE *fp;
AjPRegexp crlf = NULL;
char buf[8];
AjOSysSocket sock;
get = ajStrNew();
ajHttpUrlDeconstruct(url, &port, &host, &path);
while(file==NULL || gHttpRedirect(file, &host, &port, &path))
{
if(ajStrGetCharFirst(path) != '/')
ajStrInsertK(&path, 0, '/');
ajFmtPrintS(&get, "GET http://%S:%d%S HTTP/1.1\r\n", host, port, path);
fp = ajHttpOpen(NULL, host, port, get, &sock);
file = ajFileNewFromCfile(fp);
if(!file)
return ajFalse;
}
ajStrDel(&get);
crlf = ajRegCompC("^\r?\n$");
while(ajReadline(file, &line))
{
if(ajRegExec(crlf, line))
break;
}
while(ajReadbinBinary(file, 1, 1, buf))
{
ajWritebinBinary(*outf, 1, 1, buf);
}
ajFileClose(outf);
ajFileClose(&file);
return ajTrue;
}
AjBool gFilebuffURLS(AjPStr url, AjPFilebuff* buff){
AjPStr line = NULL;
AjPStr host = NULL;
AjPStr path = NULL;
ajint port = 80;
ajHttpUrlDeconstruct(url, &port, &host, &path);
*buff = ajHttpRead(NULL, NULL, NULL, host, port, path);
if(!*buff)
return ajFalse;
ajFilebuffHtmlNoheader(*buff);
return ajTrue;
}
int main(int argc, char **argv)
{
AjPDasServer server = NULL;
AjPDasSource source = NULL;
AjPDasSegment segment = NULL;
AjPStr host = NULL;
AjPStr path = NULL;
AjPFile outf = NULL;
ajint port = 80;
AjBool sequencesourcesonly;
AjBool entrypoints;
AjBool showtestqueries;
AjBool runtestqueries = ajTrue;
AjBool quickexit = ajFalse;
ajint itest=0;
ajint j=0;
ajint maxtests=0;
ajint maxfeatures=0;
ajint maxsegments=0;
AjIList iter = NULL;
AjIList coordsi = NULL;
AjIList itereps = NULL;
AjPFilebuff buff = NULL;
AjPUrlref uo = NULL;
AjPList segments = NULL;
AjPStr ffname = NULL;
AjPStr url = NULL;
AjPStr dbhttpver = ajStrNew();
AjPStr dbname = ajStrNew();
AjPStr dbproxy = ajStrNew();
AjPStr servername = NULL;
AjPTable titlecount = NULL;
const ajuint* count;
int k=0;
embInit("dastest", argc, argv);
host = ajAcdGetString("host");
path = ajAcdGetString("path");
port = ajAcdGetInt("port");
sequencesourcesonly = ajAcdGetBoolean("sequencesourcesonly");
entrypoints = ajAcdGetBoolean("entrypoints");
showtestqueries = ajAcdGetBoolean("showtestqueries");
runtestqueries = ajAcdGetBoolean("runtestqueries");
servername = ajAcdGetString("servername");
outf = ajAcdGetOutfile("outfile");
maxtests = ajAcdGetInt("maxtests");
maxfeatures = ajAcdGetInt("maxfeatures");
maxsegments = ajAcdGetInt("maxsegments");
server = ajDasServerNew();
if(runtestqueries)
{
url = ajStrNew();
if(!ajNamServer(servername))
{
ajWarn("following das server is required to be defined "
"for test queries...");
ajWarn("\nSERVER %S [\n"
" type: \"sequence\"\n"
" method: \"das\"\n"
" url: \"http://%S%S\"\n"
"]\n",servername, host,path);
ajWarn("ignoring -runtestqueries option...");
runtestqueries = ajFalse;
}
else
{
ajNamSvrGetUrl(servername, &url);
ajHttpUrlDeconstruct(url, &port, &host, &path);
ajStrDel(&url);
}
}
ajDasServerSethostS(server,host);
ajDasServerSetport(server,port);
if(ajStrGetCharLast(path)!='/')
ajStrAppendK(&path,'/');
ajStrAppendC(&path,"sources");
ajDasServerSetpathS(server,path);
ajFmtPrintF(outf,"host = %S\npath = %S\nport = %d\n",
server->host, server->path, server->port);
/*
* TODO: stop using http-read but instead use
* ajNamSvrListListDatabases(svrname, dbnames);
*/
buff = ajHttpRead(dbhttpver, dbname, dbproxy, host, port, path);
if(!buff)
ajExitAbort();
ajFilebuffHtmlNoheader(buff);
ajDasParseRegistry(buff, server->sources);
ajFmtPrintF(outf,"DAS sources and descriptions\n\n");
titlecount = dastestGetTitleCount(server);
iter = ajListIterNew(server->sources);
while(!ajListIterDone(iter) && !quickexit)
{
source = ajListIterGet(iter);
if ((sequencesourcesonly && !source->sequence)
|| ajStrMatchC(source->title,"cath") || k++ <50)
continue;
ajFmtPrintF(outf,"%-30S %-50S\n%S\n",source->uri,source->title,
source->description);
if(entrypoints && source->entry_points)
{
uo = ajHttpUrlrefNew();
ajHttpUrlrefParseC(&uo, ajStrGetPtr(source->entry_points_uri));
if(ajStrGetLen(uo->Port))
ajStrToInt(uo->Port, &port);
else
port = 80;
ajFilebuffDel(&buff);
buff = ajHttpRead(dbhttpver, dbname, dbproxy,
uo->Host, port, uo->Absolute);
ajHttpUrlrefDel(&uo);
if(!buff)
continue;
ajFilebuffHtmlNoheader(buff);
segments = ajListNew();
ajDasParseEntrypoints(buff, segments);
itereps = ajListIterNew(segments);
ajFmtPrintF(outf, "Number of entry points %d\n",
ajListGetLength(segments));
j=0;
while(!ajListIterDone(itereps))
{
segment = ajListIterGet(itereps);
if (j++ < maxsegments)
ajFmtPrintF(outf,
"segment id:%S orientation:%S start:%d stop:%d\n",
segment->id,
segment->orientation,
segment->start, segment->stop);
ajDasSegmentDel(&segment);
}
ajListIterDel(&itereps);
ajListFree(&segments);
}
if(showtestqueries || runtestqueries)
{
AjPDasCoordinate coord;
coordsi = ajListIterNew(source->coordinates);
while(!ajListIterDone(coordsi) && !quickexit)
{
coord = ajListIterGet(coordsi);
ajDebug("coordinate uri:%S taxid:%S source:%S test_range:%S\n",
coord->uri,
coord->taxid,
coord->source,
coord->test_range);
if(showtestqueries)
{
if(source->sequence)
ajFmtPrintF(outf,
"example/test entry = '%S?segment=%S'\n",
source->sequence_query_uri,coord->test_range);
if(source->features)
ajFmtPrintF(outf,
"example/test entry = '%S?segment=%S'\n",
source->features_query_uri,coord->test_range);
}
if(runtestqueries)
{
AjPStr idqry = ajStrNew();
AjPStr entry = NULL;
AjPSeq seq = NULL;
ajint ibegin = 0;
ajint iend = 0;
AjPStr example = NULL;
example = ajDasTestrangeParse(coord->test_range,
&entry, &ibegin, &iend);
if(ajStrGetLen(entry))
{
count = ajTableFetchS(titlecount, source->title);
dbname = ajDasSourceGetDBname(source, *count>1);
if (source->features)
{
AjPStr qpath=NULL;
uo = ajHttpUrlrefNew();
ajFmtPrintS(&idqry,"dasgff::%S:%S:%S",
servername,
dbname,
entry);
ajFmtPrintF(outf,
"feature query: %S start:%d end:%d\n",
idqry,
ibegin, iend);
ajHttpUrlrefParseC(&uo,
ajStrGetPtr(source->features_query_uri));
ajHttpUrlrefSplitPort(uo);
ajFmtPrintS(&qpath,"%S?segment=%S",
uo->Absolute,entry);
if(iend>0)
ajFmtPrintAppS(&qpath,":%d,%d",ibegin, iend);
if(ajStrGetLen(uo->Port))
ajStrToInt(uo->Port, &port);
else
port = 80;
ajDebug("calling ajHttpRead to get the raw"
" output; host:%S port:%d path:%S\n",
uo->Host, port, qpath);
ajFilebuffDel(&buff);
buff = ajHttpRead(dbhttpver, dbname, dbproxy,
uo->Host, port, qpath);
if(buff)
{
AjPFeattable ft;
ajFmtPrintS(&ffname, "%S.%S", source->uri,
entry);
ajFilebuffHtmlNoheader(buff);
dastestSaveRawFeatures(buff, ffname);
ajDebug("now using EMBOSS feature queries\n");
ft = dastestFeatureQuery(idqry,
ibegin, iend);
dastestSaveMappedFeatures(ft, ffname,
outf, maxfeatures);
ajStrDel(&ffname);
ajFeattableDel(&ft);
}
ajHttpUrlrefDel(&uo);
ajStrDel(&qpath);
if(++itest>=maxtests)
quickexit = ajTrue;
}
else if(source->sequence)
{
seq = ajSeqNewRes(iend-ibegin+1);
ajFmtPrintS(&idqry,"%S:%S:%S",
servername, dbname, entry);
ajFmtPrintF(outf,
"sequence query: %S start:%d end:%d\n",
idqry,
ibegin, iend);
ajSeqGetFromUsaRange(idqry, ajFalse, ibegin, iend,
seq);
ajFmtPrintF(outf,
"length of sequence returned: %d\n",
ajSeqGetLen(seq));
if(ajSeqGetLen(seq)>0)
ajFmtPrintF(outf,
"sequence returned (first 100 bases):"
" %-100.100s\n",
ajSeqGetSeqC(seq));
ajSeqDel(&seq);
}
ajStrDel(&dbname);
}
ajStrDel(&entry);
ajStrDel(&idqry);
ajStrDel(&example);
}
}
ajListIterDel(&coordsi);
}
}
ajListIterDel(&iter);
ajDasServerDel(&server);
ajFilebuffDel(&buff);
ajStrDel(&host);
ajStrDel(&path);
ajStrDel(&servername);
ajStrDel(&dbhttpver);
ajStrDel(&dbname);
ajStrDel(&dbproxy);
ajFileClose(&outf);
ajTableDelValdel(&titlecount, ajMemFree);
embExit();
return 0;
}
AjBool gHttpRedirect(AjPFile file, AjPStr* host, ajint* port, AjPStr* path)
{
AjPFilebuff buff = NULL;
AjPRegexp httpexp = NULL;
AjPRegexp nullexp = NULL;
AjPRegexp redirexp = NULL;
AjPStr codestr = NULL;
AjPStr newurl = NULL;
AjPStr newhost = NULL;
AjPStr currline = NULL;
ajuint httpcode = 0;
AjBool isheader = ajFalse;
AjBool ret = ajFalse;
httpexp = ajRegCompC("^HTTP/\\S+\\s+(\\d+)");
ajReadline(file, &currline);
ajDebug("gHttpRedirect: First line: '%S'\n", currline);
if(ajRegExec(httpexp, currline))
{
isheader = ajTrue;
ajRegSubI(httpexp, 1, &codestr);
ajStrToUint(codestr, &httpcode);
ajDebug("Header: codestr '%S' code '%u'\n", codestr, httpcode);
ajStrDel(&codestr);
}
if(isheader)
{
if(httpcode == 301 || httpcode == 302 || httpcode==307)
{
redirexp = ajRegCompC("^Location: (\\S+)");
nullexp = ajRegCompC("^\r?\n?$");
while( ajReadline(file, &currline) &&
!ajRegExec(nullexp, currline))
{
ajDebug("gHttpRedirect: header line: '%S'\n", currline);
if(ajRegExec(redirexp, currline))
{
ajRegSubI(redirexp, 1, &newurl);
ajHttpUrlDeconstruct(newurl, port, &newhost, path);
if(ajStrGetLen(newhost))
ajStrAssignS(host, newhost);
ajStrDel(&newurl);
ajStrDel(&newhost);
ret = ajTrue;
break;
}
}
ajRegFree(&redirexp);
ajRegFree(&nullexp);
}
}
ajRegFree(&httpexp);
ajStrDel(&currline);
return ret;
}
AjPFilebuff gHttpPostFileSS(AjPStr url, AjPStr filename)
{
AjPFilebuff buff = NULL;
AjPFile file = NULL;
AjPStr line = NULL;
AjPStr cont = NULL;
AjPStr host = NULL;
AjPStr path = NULL;
AjPStr post = NULL;
AjPStr body = NULL;
ajint port = 80;
ajuint http = 0;
FILE *fp;
char crlf[] = "\015\021";
AjOSysSocket sock;
AjOSysTimeout timo;
post = ajStrNew();
body = ajStrNew();
cont = ajStrNew();
file = ajFileNewInNameS(filename);
while(ajReadline(file, &line))
{
ajStrAppendS(&cont, line);
}
ajHttpUrlDeconstruct(url, &port, &host, &path);
while(buff==NULL || ajHttpRedirect(buff, &host, &port, &path, &http))
{
if(ajStrGetCharFirst(path) != '/')
ajStrInsertK(&path, 0, '/');
ajFmtPrintS(
&body,
"--xYzZY\015\012"
"Content-Disposition: form-data; name=\"file\";"
" filename=\"%S\"\015\012"
"Content-Type: text/plain\015\012"
"%S\015\012"
"\015\012--xYzZY--\015\012",
filename, cont
);
ajFmtPrintS(
&post,
"POST http://%S%S\n"
"Content-Length: %d\n"
"Content-Type: multipart/form-data; boundary=xYzZY\n\n"
"%S",
host, path,
ajStrGetLen(body), body
);
ajFmtPrint("%S", post);
fp = ajHttpOpen(NULL, host, port, post, &sock);
buff = ajFilebuffNewFromCfile(fp);
if(!buff)
return NULL;
}
ajStrDel(&post);
timo.seconds = 180;
ajSysTimeoutSet(&timo);
ajFilebuffLoadAll(buff);
ajSysTimeoutUnset(&timo);
return buff;
}
