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1 /*
2 * $Id: cVSMmdbcmd.cpp,v 1.1 2005/07/26 17:11:46 chenj Exp $
3 *
4 * ===========================================================================
5 *
6 * PUBLIC DOMAIN NOTICE
7 * National Center for Biotechnology Information (NCBI)
8 *
9 * This software/database is a "United States Government Work" under the
10 * terms of the United States Copyright Act. It was written as part of
11 * the author's official duties as a United States Government employee and
12 * thus cannot be copyrighted. This software/database is freely available
13 * to the public for use. The National Library of Medicine and the U.S.
14 * Government do not place any restriction on its use or reproduction.
15 * We would, however, appreciate having the NCBI and the author cited in
16 * any work or product based on this material
17 *
18 * Although all reasonable efforts have been taken to ensure the accuracy
19 * and reliability of the software and data, the NLM and the U.S.
20 * Government do not and cannot warrant the performance or results that
21 * may be obtained by using this software or data. The NLM and the U.S.
22 * Government disclaim all warranties, express or implied, including
23 * warranties of performance, merchantability or fitness for any particular
24 * purpose.
25 *
26 * ===========================================================================
27 *
28 * Author: Jie Chen
29 * Source file for VSMmdb.cgi
30 *
31 * $Log: cVSMmdbcmd.cpp,v $
32 * Revision 1.1 2005/07/26 17:11:46 chenj
33 * Making linux VSMmdb.cgi
34 *
35 *
36 *
37 */
38
39
40 #include <corelib/ncbiexec.hpp>
41 #include <corelib/ncbifile.hpp>
42 #include <serial/objostr.hpp>
43
44 #include "hVSMmdbapp.hpp"
45 #include "hVSMmdbcmd.hpp"
46 #include "VastSrchUti.hpp"
47 #include "SHGlobal.hpp"
48 #include "mmdbuti.hpp"
49 #include "rdpdb.hpp"
50 #include "qmuti.hpp"
51 #include "SendSummary.hpp"
52
53 #include <sstream>
54
55 #include <objmime.h>
56
57 #include <string.h>
58 #include <sys/time.h>
59 #include <math.h>
60
61
62 // #include "../../newVSch/mmdbdep.h"
63 // #include "../../newVSch/mmdbapi.h"
64
65
66 // Initialization
67
68 string DataInfo::JobID;
69 string DataInfo::JobType;
70 string DataInfo::subset;
71 stringstream DataInfo::PDB_ios;
72 stringstream DataInfo::PDB_chk;
73 QmReqID DataInfo::ReqID = 0;
74 QmGrpID DataInfo::GrpID = 0;
75
76
77 using namespace SHProjNS;
78 using namespace ncbi;
79
80 static ostringstream output;
81
82 CVSMmdbCommand::CVSMmdbCommand(CNcbiResource& resource) : CNcbiCommand(resource)
83 {};
84
85 string CVSMmdbCommand::GetEntry() const
86 {
87 return string("cmdVSMmdb");
88 }
89
90
91
92 // CVSMmdbSubmitCommand
93
94 CVSMmdbSubmitCommand :: CVSMmdbSubmitCommand(CNcbiResource& resource) : CVSMmdbCommand(resource)
95 {};
96
97 CNcbiCommand* CVSMmdbSubmitCommand :: Clone(void) const
98 {
99 return new CVSMmdbSubmitCommand(GetVSMmdbResource());
100 }
101
102 string CVSMmdbSubmitCommand :: GetName() const
103 {
104 return string("Submit");
105 }
106
107
108 string CVSMmdbSubmitCommand :: ReadReqAndPDBSubmission(CCgiContext& ctx)
109 {
110
111 string HeadValue = "HEADER";
112 string Remark = "REMARK 1";
113 string molname = "QUERY PROTEIN";
114
115 CCgiRequest& req = ctx.GetRequest();
116 CCgiResponse& resp = ctx.GetResponse();
117
118 static DataInfo Dinfo;
119 static VSMmdbConf thisConf;
120
121 string date = GetTodaysDate();
122
123 /* Write the contents of the pdb text area to buffer */
124
125 string pdbdata = req.GetEntry("pdbfile").GetValue();
126 if (pdbdata.empty()) {
127 PrtMes::PrintErrorHeader(&resp, "VastSrch", 1);
128 PrtMes::PrintMsgWithoutTail(&resp,
129 "<h3>Missing Required PDB File:</h3><p>\nPlease submit a file.\n");
130
131
132 resp.out() << "<HR align=left width=800><br>\n"
133 << "<a href=\"" << thisConf.HomePage
134 << "\">Back</a> to the HomePage\n"
135 << "</body>\n</html>";
136 exit(1);
137 }
138
139 if (pdbdata.size() > PDBMAXLEN) {
140
141 PrtMes::PrintErrorHeader(&resp, "VastSrch", 1);
142 PrtMes::PrintMsgWithTail(&resp,
143 "<h2>You cannot submit a file greater than 5MB!</h2><p>\nIf this is a problem, please notify info@ncbi.nlm.nih.gov\n");
144
145 THROWS("input file too bigger");
146 }
147
148 unsigned pos = pdbdata.find(HeadValue);
149 if (pos == string::npos) {
150
151 Dinfo.PDB_ios.setf(ios::left);
152 Dinfo.PDB_ios << setw(10) << HeadValue << setw(40) << molname;
153 Dinfo.PDB_ios.unsetf(ios::left);
154 Dinfo.PDB_ios << date;
155 Dinfo.PDB_ios << setw(7) << Dinfo.JobID.substr(0,4)<< "\n";
156 Dinfo.PDB_ios.setf(ios::left);
157 Dinfo.PDB_ios << pdbdata;
158 }
159 else {
160 if (pos) pdbdata = pdbdata.substr(pos);
161 char data_line[100];
162 istringstream strm_tmp(pdbdata);
163
164 strm_tmp.getline(data_line, 100);
165 string strtmp = data_line;
166 unsigned siz = strtmp.size();
167 if (siz < 59)
168 {
169 for (unsigned i= siz; i < 59; i++) strtmp += ' ';
170 strtmp.replace(50, 9, date);
171 Dinfo.PDB_ios << strtmp << "\n"
172 << pdbdata.substr(siz+1);
173 }
174 else {
175
176 pdbdata.replace(50, 9, date);
177 Dinfo.PDB_ios << pdbdata;
178 }
179 }
180
181 Dinfo.subset = req.GetEntry("dataset").GetValue();
182 if (Dinfo.subset.empty()) {
183
184 PrtMes::PrintErrorHeader(&resp, "VastSrch", 1);
185 PrtMes::PrintMsgWithoutTail(&resp,
186 "<h3>No search set provided. ");
187 PrtMes::PrintMsgWithoutTail(&resp, Dinfo.subset);
188 PrtMes::PrintMsgWithTail(&resp,
189 "Please select 'All' or 'Nonredundant' search set\n");
190 exit(1);
191 }
192
193 return date;
194
195 } // end of ReadReqAndPDBSubmission
196
197
198
199 void CVSMmdbSubmitCommand :: Execute(CCgiContext& ctx)
200 {
201
202 CCgiResponse& resp = ctx.GetResponse();
203 static DataInfo Dinfo;
204
205 int iJobId = GetJobID_DB();
206 Dinfo.JobID = "VS" + ToString(iJobId);
207
208 string date = ReadReqAndPDBSubmission(ctx);
209
210 string headerStr = Dinfo.PDB_ios.str().substr(10, 39);
211 if (headerStr.find_first_not_of(" ") == string::npos)
212 headerStr = "NULL";
213 UploadReqInfo(Dinfo.subset, iJobId, date, headerStr);
214
215
216 //if (!UploadAllPdbOnly(Dinfo.JobID, Dinfo.PDB_ios.str(), Dinfo.PDB_chk.str())) {
217 if (!UploadOriPdbOnly(Dinfo.JobID, Dinfo.PDB_ios.str())) {
218
219 THROWS("UploadAllPdb failed");
220 }
221 // return;
222
223 static VSMmdbConf thisConf;
224
225 if (!sqmInit()) {
226
227 resp.WriteHeader();
228 resp.out() << "<html>\n<body>\n"
229 << "<h1>VastSch Error: </h1>\n<br><br>\n"
230 << "Can't Initialize QM\n"
231 << "</body>\n</html>\n\n";
232
233 ERR_POST("Can't Initialize QM.");
234 throw exception();
235 }
236
237 Dinfo.ReqID = sqmSubmit(thisConf.QMqueStrName.c_str(), 0, 0);
238 if (!Dinfo.ReqID) {
239
240
241 resp.WriteHeader();
242
243 resp.out() << "<html>\n<body>\n"
244 << "<h1>VSchSrv Erro:</h1>\n<br><br>\n"
245 << "ReqId1 = 0\n"
246 << "</body>\n</html>\n\n";
247
248 ERR_POST("Got 0 as reqId from QM");
249 THROWS("Got 0 as reqId from QM");
250 // throw exception();
251
252 }
253
254 // sqmSetAction(Dinfo.ReqID, qmReqActionRun);
255
256 /*
257 char *IP = getenv("REMOTE_ADDR");
258 if (!IP) {
259
260 resp.WriteHeader();
261
262 resp.out() << "<html>\n<body>\n"
263 << "<h1>VachSrv Error: </h1>\n<br><br>\n"
264 << "No IP information.\n"
265 << "</body>\n</html>\n";
266
267 ERR_POST("No IP information.\n");
268 throw exception();
269 }
270
271 sqmSetIP(Dinfo.ReqID, IP);
272 */
273
274 Dinfo.GrpID = sqmSetGroup(Dinfo.ReqID, 0);
275 ChkGrpId(ctx, 0, Dinfo.GrpID);
276
277 UploadQMIdsAndSetPdbLoaded(Dinfo.ReqID, Dinfo.GrpID, iJobId);
278
279 if (!sqmFree()) {
280
281 resp.WriteHeader();
282 resp.out() << "<html>\n<body>\n"
283 << "<h1>VastSch Error: </h1>\n<br><br>\n"
284 << "Can't close QM\n"
285 << "</body>\n</html>\n\n";
286
287 ERR_POST("Can't close QM.");
288 throw exception();
289
290 };
291
292 string UrlStr = thisConf.MonitUrl + thisConf.MonitCgi
293 + "?cmdSch=Status&ReqId=" + ReqId2Str(Dinfo.ReqID)
294 + "&GrpId=" + ReqId2Str(Dinfo.GrpID)
295 + "&QMQue=" + thisConf.QMqueStrName;
296
297 resp.WriteHeader();
298 resp.out() << "<html>\n"
299 << "<meta http-equiv=refresh content=0;url=\""
300 << UrlStr
301 << "\">\n</html>\n";
302
303
304 } // CVSMmdbSubmitCommand :: Execute()
305
306
307
308
309 // CVSMmdbStrTextCommand
310
311 CVSMmdbStrTextCommand :: CVSMmdbStrTextCommand(CNcbiResource& resource)
312 : CVSMmdbCommand(resource)
313 {};
314
315 string CVSMmdbStrTextCommand :: GetName() const
316 {
317
318 return string("StrText"); // cmdVSMmdb=StrText,
319 };
320
321
322 CNcbiCommand* CVSMmdbStrTextCommand :: Clone(void) const
323 {
324 return new CVSMmdbStrTextCommand(GetVSMmdbResource());
325 };
326
327
328 void CVSMmdbStrTextCommand :: Execute(CCgiContext& ctx)
329 {
330
331 CCgiResponse& resp = ctx.GetResponse();
332 CCgiRequest& req = ctx.GetRequest();
333 static DataInfo Dinfo;
334 static VSMmdbConf thisConf;
335 static ImgInfo Iinfo;
336 string strtmp;
337
338 string value = req.GetEntry("grpid").GetValue();
339 Dinfo.GrpID = atoll(value.c_str());
340 if (!Dinfo.GrpID) {
341
342 output.str("");
343 output << "<h3>Missing request_id the request_id provided is 0.</h3><p>\n"
344 << "Please input a request_id.\n";
345 PrtMes::PrintErrorHeader(&resp, "VastSrch", 1);
346 PrtMes::PrintMsgWithoutTail(&resp, output.str());
347
348 resp.out() << "<HR align=left width=800><br>\n"
349 << "<a href=\"" << thisConf.HomePage
350 << "\">Back</a> to the HomePage\n"
351 << "</body>\n</html>";
352 exit(1);
353
354 }
355 Iinfo.id = GrpId2JobId(Dinfo.GrpID);
356 if (!Iinfo.id) {
357
358 output.str("");
359 output << "<h3>Invalid request_id.</h3><p>\n"
360 << "You provided either an invalid request_id, "
361 << "or your request_id has expired since the search results are kept only for 10 days.<p>\n"
362 << "Please check your request_id carefully, or you may resubmit your file to start a new search.\n";
363
364 PrtMes::PrintErrorHeader(&resp, "VastSrch", 1);
365 PrtMes::PrintMsgWithoutTail(&resp, output.str());
366
367 resp.out() << "<HR align=left width=800><br>\n"
368 << "<a href=\"" << thisConf.HomePage
369 << "\">Back</a> to the HomePage\n"
370 << "</body>\n</html>";
371 exit(1);
372
373
374 }
375 Dinfo.JobID = "VS" + ToString(Iinfo.id);
376
377 Dinfo.ReqID = JobId2ReqId(Iinfo.id);
378
379 if (!VSMmdbJobDone(Iinfo.id)) {
380
381 string errmsg, wmsg, wmsgH;
382 DownloadErrWarnMsgs( (long long)Dinfo.GrpID, errmsg, wmsg, wmsgH);
383 if ( errmsg.empty() && wmsg.empty() && wmsgH.empty() ) {
384
385 // redirect
386
387 string UrlStr = thisConf.MonitUrl + thisConf.MonitCgi
388 + "?cmdSch=Status&ReqId=" + ReqId2Str(Dinfo.ReqID)
389 + "&GrpId=" + ReqId2Str(Dinfo.GrpID)
390 + "&QMQue=" + thisConf.QMqueStrName;
391
392 resp.WriteHeader();
393 resp.out() << "<html>\n"
394 << "<meta http-equiv=refresh content=0;url=\""
395 << UrlStr
396 << "\">\n</html>\n";
397 }
398 else {
399
400 resp.WriteHeader();
401 resp.out() << "<html>\n<head>\n"
402 << "<title>VAST Search Error Report</title>\n";
403 PrintFileData(resp, thisConf.HtmlDir + thisConf.HeadFName);
404
405 resp.out() << "<pre><HR align=left width=800><br>\n";
406 if ( !errmsg.empty() ) {
407
408 resp.out()
409 << "<font class=H2>Errors in the submitted file:</font><br>\n"
410 << errmsg << "<br><br>\n\n";
411 }
412
413 if ( !wmsg.empty() ) {
414
415 resp.out()
416 << "\n<font class=H2>Warning: the following chains may have no structure neighbors due to missing Ca atoms.</font><br>\n"
417 << wmsg << "<br><br>\n\n";
418 }
419
420 if ( !wmsgH.empty() ) {
421
422 resp.out() << "\n<font class=H2>Warning: the following HETATM records interpreted as modified residues, changed to ATOM records in the submitted file.</font><br>\n"
423 << wmsgH << "<br><br>\n\n";
424 }
425
426 resp.out() << "<a href=\"" << thisConf.HomePage
427 << "\">Back</a> to the HomePage\n";
428
429 }
430
431 return;
432 }
433
434
435 Dinfo.subset = GetSubsetName4Job(Iinfo.id);
436 if ( Dinfo.subset == "NULL" ) {
437 ERR_POST("GetSubsetName4Job() failed");
438 throw exception();
439 }
440
441 resp.WriteHeader();
442 resp.out() << "<html>\n<head>\n"
443 << "<title>VAST Search Structure Summary: "
444 << GetTodaysDate()
445 << "; ReqId: "
446 << Dinfo.GrpID
447 << "</title>\n";
448
449 PrintFileData(resp, thisConf.HtmlDir + thisConf.HeadFName);
450
451 string curtime;
452 value= req.GetEntry("ViewNbr").GetValue();
453 if (value.empty()) {
454
455 if (!VSNbrStarted(Iinfo.id)) Dinfo.JobType = "Biostr";
456 else Dinfo.JobType = "Nbr";
457 }
458 else if (value == "No") Dinfo.JobType = "Biostr";
459 else if (value=="Yes" || value=="Show") Dinfo.JobType = "Nbr";
460
461 curtime = CTime(CTime::eCurrent).AsString();
462 fprintf(stderr, "SendSummaryPageText curtime %s\n", curtime.c_str());
463
464 if (Dinfo.JobType == "Biostr") {
465
466 SendSummaryPageText(ctx, 0, 0);
467
468 curtime = CTime(CTime::eCurrent).AsString();
469 fprintf(stderr, "after SendSummaryPageText curtime %s\n", curtime.c_str());
470
471 }
472 else if (Dinfo.JobType == "Nbr") {
473
474 if (VSJobDone(Iinfo.id)) {
475 SendSummaryPageText(ctx, 1);
476 }
477 else {
478
479 SendSummaryPageText(ctx, 1, 0);
480 exit(0);
481 }
482 }
483 else {
484 THROWS("ViewNbr input incorrect");
485 }
486
487
488 ctx.GetResponse().out() << "</body>\n</html>\n\n";
489
490 return;
491
492 }; // end of CVSMmdbStrCommand :: Execute()
493
494
495
496
497
498 // CVSMmdbStrImgCommand
499 CVSMmdbStrImgCommand :: CVSMmdbStrImgCommand(CNcbiResource& resource)
500 : CVSMmdbCommand(resource)
501 {};
502
503
504 string CVSMmdbStrImgCommand :: GetName() const
505 {
506 return string("StrImg");
507 };
508
509
510 CNcbiCommand* CVSMmdbStrImgCommand :: Clone(void) const
511 {
512 return new CVSMmdbStrImgCommand(GetVSMmdbResource());
513 };
514
515
516
517 void CVSMmdbStrImgCommand :: Execute(CCgiContext& ctx)
518 {
519 CCgiRequest& req = ctx.GetRequest();
520 static DataInfo Dinfo;
521 static ImgInfo Iinfo;
522
523 string value = req.GetEntry("grpid").GetValue();
524 if (value.empty()) {
525
526 ERR_POST("No grpid");
527 throw exception();
528
529 }
530 Dinfo.GrpID = atoll(value.c_str());
531 if (!Dinfo.GrpID) {
532 ERR_POST("Grp ID is 0, from CVSMmdbStrImgCommand :: Execute");
533 throw exception();
534 }
535
536 Iinfo.id = GrpId2JobId(Dinfo.GrpID);
537 Dinfo.JobID = "VS" + ToString(Iinfo.id);
538
539 value = req.GetEntry("chbeg").GetValue();
540 if (value.empty()) THROWS("NO chbeg");
541 Iinfo.chbeg = atoi(value.c_str());
542
543 value = req.GetEntry("chend").GetValue();
544 if (value.empty()) THROWS("NO chend");
545 Iinfo.chend = atoi(value.c_str());
546
547 value = req.GetEntry("imgsize").GetValue();
548 if (value.empty()) THROWS("NO chend");
549 Iinfo.imgsize = atoi(value.c_str());
550
551 /*
552 value = req.GetEntry("ViewNbr").GetValue();
553 if (value == "Yes" || value=="Show")
554 DrawImg(ctx, 1); // 1 or 0 VastLink
555 else DrawImg(ctx, 0);
556 */
557
558 DrawImg(ctx);
559
560 } // CVSMmdbSubmitStrImgCommand :: Execute
561
562
563
564 // CVSMmdbViewCommand
565
566 CVSMmdbViewCommand :: CVSMmdbViewCommand(CNcbiResource& resource) : CVSMmdbCommand(resource)
567 {};
568
569 CNcbiCommand* CVSMmdbViewCommand :: Clone(void) const
570 {
571 return new CVSMmdbViewCommand(GetVSMmdbResource());
572 }
573
574 string CVSMmdbViewCommand :: GetName() const
575 {
576 return string("View3D");
577 }
578
579
580
581 void CVSMmdbViewCommand :: SendStructureMIME(char Filetype, int Mime,
582 int Complexity, int Models, CCgiContext& ctx)
583 {
584
585 static DataInfo Dinfo;
586 CCgiResponse& resp = ctx.GetResponse();
587
588 int iJobId = atoi(Dinfo.JobID.substr(2).c_str());
589
590 BiostrucPtr bsp;
591 SeqEntryPtr sep;
592 NcbiMimeAsn1Ptr mime;
593 BiostrucSeqPtr bssp;
594
595 /* Save or View = add appropriate MIME header */
596
597 // bsp = FetchBS((char*)bFile.c_str(), 1, Complexity, Models, POWER_VIEW);
598
599 bsp = VSOpenBSP(iJobId, Complexity, Models);
600 if (bsp == NULL) {
601
602 string strtmp = "Missing Biostruc data for reqid = "
603 + ReqId2Str(Dinfo.GrpID)
604 + ". Please inform chenj@ncbi.nlm.nih.gov for this problem. Thanks!";
605 PrtMes::PrintErrorHeader(&resp, "VastSrch", 1);
606 PrtMes::PrintMsgWithTail(&resp, strtmp);
607
608 exit(1);
609 }
610
611 bssp = BiostrucSeqNew();
612 bssp->structure = bsp;
613
614 sep = GetSeqEntryForJobId(iJobId, 0, NULL);
615
616 if (sep == NULL) {
617
618 string strtmp = "Missing SeqEntry data for reqid = "
619 + ReqId2Str(Dinfo.GrpID)
620 + ". Please inform chenj@ncbi.nlm.nih.gov for this problem. Thanks!";
621
622 PrtMes::PrintErrorHeader(&resp, "VastSrch", 1);
623 PrtMes::PrintMsgWithTail(&resp, strtmp);
624
625 exit(1);
626 }
627
628 if (sep->choice == 2) { // BioseqSet, multiple chains
629
630 BioseqSetPtr seps = (BioseqSetPtr) sep->data.ptrvalue;
631 SeqEntryPtr subsep = (SeqEntryPtr) seps->seq_set;
632 SeqIdPtr sid;
633 int ori_gi=0;
634
635 while (subsep != NULL) {
636
637 sid = (SeqIdPtr) ((BioseqPtr)subsep->data.ptrvalue)->id;
638 while (sid != NULL) {
639
640 if (sid->choice == SEQID_GI) {
641
642 sid->data.intvalue = ori_gi++;
643 break;
644 }
645 sid=sid->next;
646 }
647
648 subsep = subsep->next;
649 }
650
651 }
652
653 ValNodeLink(&(bssp->sequences), sep);
654
655 mime = (NcbiMimeAsn1Ptr) ValNodeNew(NULL); /* yanli */
656 mime->choice = NcbiMimeAsn1_strucseq;
657 mime->data.ptrvalue = bssp;
658
659 /* the following headers are format-independent */
660
661 ESerialDataFormat dataformat;
662 // if (Filetype == 'i') { BiostrucAsnWrite()
663 if (Filetype == 'j') {
664 /* Cn3D asn.1 format */
665 if (Mime == LAUNCH_VIEWER || Mime == SAVE_FILE)
666 dataformat = eSerial_AsnBinary;
667 else dataformat = eSerial_AsnText;
668
669 auto_ptr <CObjectOStream> oos
670 (CObjectOStream::Open(dataformat, resp.out()));
671 CObjectOStream::AsnIo aip(*oos, "Ncbi-mime-asn1");
672
673 switch (Mime) {
674 case LAUNCH_VIEWER:
675 resp.SetContentType("chemical/ncbi-asn1-binary");
676 resp.WriteHeader();
677 NcbiMimeAsn1AsnWrite(mime, aip, NULL);
678 break;
679
680 case SAVE_FILE:
681 resp.SetContentType("application/octet-stream");
682 resp.WriteHeader();
683 NcbiMimeAsn1AsnWrite(mime, aip, NULL);
684 break;
685
686 case SEE_FILE:
687 resp.SetContentType("text/html");
688 resp.WriteHeader();
689 resp.out() << "<HTML><PRE>\r\n";
690 NcbiMimeAsn1AsnWrite(mime, aip, NULL);
691 break;
692 }
693
694 aip.End();
695 }
696 if (Mime == SEE_FILE)
697 resp.out() << "</PRE></HTML>\r\n";
698
699 // CExec::System((string("rm -r ") + dir).c_str());
700
701 } // end of SendStructureMIME()
702
703
704
705 void CVSMmdbViewCommand :: Execute(CCgiContext& ctx)
706 {
707
708 fprintf(stderr, "CVSMmdbViewCommand :: Execute()\n");
709
710
711 CCgiRequest& req = ctx.GetRequest();
712 CCgiResponse& resp = ctx.GetResponse();
713 static DataInfo Dinfo;
714
715 string value = req.GetEntry("grpid").GetValue();
716 if (value.empty()) {
717 THROWS("No GrpId");
718 }
719 Dinfo.GrpID = atoll(value.c_str());
720
721 Dinfo.JobID = "VS" + ToString(GrpId2JobId(Dinfo.GrpID));
722 if (Dinfo.JobID.empty()) {
723 ERR_POST("No JobID");
724 throw exception();
725 }
726
727 string View = req.GetEntry("dopt").GetValue();
728 if (View.empty()) {
729
730 PrtMes::PrintErrorHeader(&resp, "VastSrch", 1);
731 PrtMes::PrintMsgWithoutTail(&resp,
732 " Wrong Display Option Type: dopt= ");
733 PrtMes::PrintMsgWithoutTail(&resp, View);
734 PrtMes::PrintMsgWithTail(&resp, ".<p>\n<pre>dopt supports: 'i' or 'a' ASN.1</pre><p>\n");
735
736 ERR_POST("No dopt provided");
737 throw exception();
738
739 }
740
741 char DispOpt = '\0';
742 int Save = 0;
743 switch (View[0])
744 {
745 case 'i':
746 DispOpt = 'i';
747 break;
748 case 'a':
749 DispOpt = 'a';
750 Save = 1;
751 break;
752 case 'j':
753 DispOpt = 'j';
754 break;
755 }
756
757 string com_value = req.GetEntry("Complexity").GetValue();
758 if (com_value.empty()) {
759 PrtMes::PrintErrorHeader(&resp, "VastSrch", 1);
760 PrtMes::PrintMsgWithTail(&resp, "Can't find value of Complexity.\n");
761 ERR_POST("No complexity provided");
762 throw exception();
763 }
764
765 int iCount = -1;
766 vector<string> ComplexityDescriptions;
767 ComplexityDescriptions.push_back("Virtual Bond Model");
768 ComplexityDescriptions.push_back("All Atom Model");
769 ComplexityDescriptions.push_back("Up to 5 Models");
770 ComplexityDescriptions.push_back("Up to 10 Models");
771 ComplexityDescriptions.push_back("All Models");
772 ComplexityDescriptions.push_back("Cn3D Subset");
773
774 for (int i=0; i< (int)ComplexityDescriptions.size(); i++)
775 if (com_value.find(ComplexityDescriptions[i]) !=string::npos) {
776 iCount = i;
777 break;
778 }
779
780 if (iCount < 0) {
781
782 string strtmp = "Wrong Complexity Type\nPlease select one from: "
783 + ComplexityDescriptions[5] + ", "
784 + ComplexityDescriptions[0] + ", and "
785 + ComplexityDescriptions[4] + ".";
786 PrtMes::PrintErrorHeader(&resp, "VastSrch", 1);
787 PrtMes::PrintMsgWithTail(&resp, strtmp);
788
789 THROWS("Wrong Complexity type");
790 }
791
792 int MaxModels = 1;
793 int Complex = ALLMDL;
794 switch (iCount)
795 {
796 case 0 :
797 Complex = ONECOORDRES;
798 break;
799 case 1:
800 Complex = ONECOORDATOM;
801 break;
802 case 2:
803 MaxModels = 5;
804 break;
805 case 3 :
806 MaxModels = 10;
807 break;
808 case 4 :
809 MaxModels = INT2_MAX;
810 break;
811 case 5:
812 Complex = ONECOORDATOM;
813 break;
814 }
815
816 string SaveChoice = req.GetEntry("save").GetValue();
817
818 if (SaveChoice.find("See") != string::npos)
819 Save = 1; /* sends MIMED-type files to view in ascii*/
820 else if (SaveChoice.find("Save") != string::npos)
821 Save = 2; /* sends MIMED-type files in raw save form */
822
823 SendStructureMIME(DispOpt, Save, Complex, MaxModels, ctx);
824
825
826 } // end of CVSMmdbViewCommand :: Execute()
827
828
829
830
831
832 // CVSMmdbSearchCommand
833
834 CVSMmdbSearchCommand::CVSMmdbSearchCommand(CNcbiResource& resource):CVSMmdbCommand(resource)
835 {};
836
837
838 CNcbiCommand* CVSMmdbSearchCommand :: Clone(void) const
839 {
840 return new CVSMmdbSearchCommand(GetVSMmdbResource());
841 }
842
843 string CVSMmdbSearchCommand :: GetName() const
844 {
845 return string("Search");
846 }
847
848 void CVSMmdbSearchCommand :: Execute(CCgiContext& ctx)
849 {
850 static DataInfo Dinfo;
851 static VSMmdbConf thisConf;
852 CCgiRequest& req = ctx.GetRequest();
853 CCgiResponse& resp= ctx.GetResponse();
854
855
856 string value = req.GetEntry("grpid").GetValue();
857 if (value.empty())
858 ERR_POST("No reqid in CVSMmdbSearchCommand :: Execute");
859 Dinfo.GrpID = atoll(value.c_str());
860
861 if ( SetupDoitInDB(Dinfo.GrpID) ) {
862
863 if (!sqmInit()) {
864
865 resp.WriteHeader();
866
867 resp.out() << "<html>\n<body>\n"
868 << "<h1>VastSch Error: </h1>\n<br><br>\n"
869 << "Can't Initialize QM\n"
870 << "</body>\n</html>\n\n";
871
872 ERR_POST("Can't Initialize QM.");
873 throw exception();
874 }
875
876 Dinfo.ReqID = sqmSubmit(thisConf.QMqueNbrName.c_str(), 0, 0);
877 if (!Dinfo.ReqID) {
878
879 resp.WriteHeader();
880
881 resp.out() << "<html>\n<body>\n"
882 << "<h1>VSchSrv Erro:</h1>\n<br><br>\n"
883 << "ReqId2 = 0\n"
884 << "</body>\n</html>\n\n";
885
886 ERR_POST("Got 0 as reqId from QM");
887 throw exception();
888
889 }
890
891 // sqmSetAction(Dinfo.ReqID, qmReqActionRun);
892
893 QmReqID grpid = sqmSetGroup(Dinfo.ReqID, Dinfo.GrpID);
894 ChkGrpId(ctx, Dinfo.GrpID, grpid);
895
896 UpdateReqIdOfGrpId(Dinfo.GrpID, Dinfo.ReqID);
897
898 /*
899 char *IP = getenv("REMOTE_ADDR");
900 if (!IP) {
901
902 resp.WriteHeader();
903
904 resp.out() << "<html>\n<body>\n"
905 << "<h1>VachSrv Error: </h1>\n<br><br>\n"
906 << "No IP information.\n"
907 << "</body>\n</html>\n";
908
909 ERR_POST("No IP information.\n");
910 throw exception();
911 }
912
913 sqmSetIP(Dinfo.ReqID, IP);
914 */
915
916
917 if (!sqmFree()) {
918
919 resp.WriteHeader();
920 resp.out() << "<html>\n<body>\n"
921 << "<h1>VastSch Error: </h1>\n<br><br>\n"
922 << "Can't close QM\n"
923 << "</body>\n</html>\n\n";
924
925 ERR_POST("Can't close QM.");
926 throw exception();
927
928 };
929
930 }
931
932 /*
933
934 output << thisConf.MonitUrl << thisConf.MonitCgi
935 << "?cmdSch=Status&ReqId=" << Dinfo.ReqID
936 << "&GrpId=" << Dinfo.GrpID
937 << "&QMQue=" << thisConf.QMqueNbrName;
938 */
939
940 output.str("");
941 output << thisConf.BaseUrl << thisConf.CgiName
942 << "?cmdVSMmdb=StrText&grpid=" << Dinfo.GrpID
943 << "&ViewNbr=Yes";
944
945 resp.WriteHeader();
946 resp.out() << "<html>\n"
947 << "<meta http-equiv=refresh content=0;url=\""
948 << output.str()
949 << "\">\n</html>\n";
950
951
952
953 } // CVSMmdbSearchCommand :: Execute()
954
955
956
957 // CVSMmdbChkErrCommand
958
959 CVSMmdbChkErrCommand :: CVSMmdbChkErrCommand(CNcbiResource& resource):CVSMmdbCommand(resource)
960 {};
961
962 CNcbiCommand* CVSMmdbChkErrCommand :: Clone(void) const
963 {
964 return new CVSMmdbChkErrCommand(GetVSMmdbResource());
965 }
966
967 string CVSMmdbChkErrCommand :: GetName() const
968 {
969 return string("ChkErr");
970 }
971
972 void CVSMmdbChkErrCommand :: Execute(CCgiContext& ctx)
973 {
974
975 CCgiResponse& resp = ctx.GetResponse();
976 CCgiRequest& req = ctx.GetRequest();
977 static DataInfo Dinfo;
978 static VSMmdbConf thisConf;
979
980 string errmsg, wmsg, wmsgH;
981 string value = req.GetEntry("Jobid").GetValue();
982 if ( !value.empty() )
983 DownloadErrWarnMsgs((unsigned)atoi(value.c_str()), errmsg, wmsg, wmsgH);
984 else {
985
986 value = req.GetEntry("grpid").GetValue();
987 if ( !value.empty() )
988 DownloadErrWarnMsgs((long long)atoll(value.c_str()), errmsg,
989 wmsg, wmsgH);
990 else throw exception();
991 }
992
993 resp.WriteHeader();
994 resp.out() << "<html>\n<head>\n"
995 << "<title>VAST Search Error Report</title>\n";
996 PrintFileData(resp, thisConf.HtmlDir + thisConf.HeadFName);
997
998 resp.out() << "<pre><HR align=left width=800><br>\n";
999 if ( !errmsg.empty() ) {
1000
1001 resp.out()
1002 << "<font class=H2>Errors in the submitted file:</font><br>\n"
1003 << errmsg << "<br><br>\n\n";
1004 }
1005
1006 if ( !wmsg.empty() ) {
1007
1008 resp.out() << "\n<font class=H2>Warning: the following chains may have no structure neighbors due to missing Ca atoms.</font><br>\n"
1009 << wmsg << "<br><br>\n\n";
1010 }
1011
1012 if ( !wmsgH.empty() ) {
1013
1014 resp.out() << "\n<font class=H2>Warning: the following HETATM records interpreted as modified residues, changed to ATOM records in the submitted file.</font><br>\n"
1015 << wmsgH << "<br><br>\n\n";
1016 }
1017
1018 resp.out() << "<HR align=left width=800><br>\n"
1019 << "<a href=# onclick=\"self.close();return false;\">"
1020 << "Close Window</a>"
1021 << "<br>\n</pre>\n</body>\n</html>\n\n";
1022
1023 /*
1024 << "<a href=\"" << thisConf.HomePage
1025 << "\">Back</a> to the HomePage\n"
1026 */
1027
1028 }
1029
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