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1 /* $Id: mmdbsrv.c,v 6.29 2005/01/12 22:49:13 vakatov Exp $
2 * ===========================================================================
3 *
4 * PUBLIC DOMAIN NOTICE
5 * National Center for Biotechnology Information
6 *
7 * This software/database is a "United States Government Work" under the
8 * terms of the United States Copyright Act. It was written as part of
9 * the author's official duties as a United States Government employee and
10 * thus cannot be copyrighted. This software/database is freely available
11 * to the public for use. The National Library of Medicine and the U.S.
12 * Government have not placed any restriction on its use or reproduction.
13 *
14 * Although all reasonable efforts have been taken to ensure the accuracy
15 * and reliability of the software and data, the NLM and the U.S.
16 * Government do not and cannot warrant the performance or results that
17 * may be obtained by using this software or data. The NLM and the U.S.
18 * Government disclaim all warranties, express or implied, including
19 * warranties of performance, merchantability or fitness for any particular
20 * purpose.
21 *
22 * Please cite the author in any work or product based on this material.
23 *
24 * ===========================================================================
25 *
26 * File Name: $RCSfile: mmdbsrv.c,v $
27 *
28 * Author: Christopher Hogue
29 *
30 * Version Creation Date: 6 January 1997
31 *
32 * $Revision: 6.29 $
33 *
34 * File Description:
35 * MMDB WWW-server
36 *
37 * $Log: mmdbsrv.c,v $
38 * Revision 6.29 2005/01/12 22:49:13 vakatov
39 * /htbin-post/Taxonomy/wgetorg -> /Taxonomy/Browser/wwwtax.cgi
40 *
41 * Revision 6.28 2001/12/12 20:43:38 beloslyu
42 * change the name of ftp site to ftp.ncbi.nih.gov
43 *
44 * Revision 6.27 2001/01/25 23:02:56 lewisg
45 * get rid of content-disp, add mdlLvl and maxModels args
46 *
47 * Revision 6.26 2000/08/21 16:12:42 lewisg
48 * add save=asntext option
49 *
50 * Revision 6.25 2000/06/26 18:05:26 lewisg
51 * fix another hardcoded url
52 *
53 * Revision 6.24 2000/06/23 22:35:58 lewisg
54 * get rid of hardcoded urls
55 *
56 * Revision 6.23 2000/01/31 19:59:12 lewisg
57 * fix output of date in pdb header
58 *
59 * Revision 6.22 1999/10/13 20:13:18 zimmerma
60 * DZ: Removed use of temporary files - html ouput redirected to stdout
61 *
62 * Revision 6.21 1999/06/17 14:44:09 zimmerma
63 * Added static char variable for cvsId in order to use unix "what"
64 *
65 * Revision 6.20 1999/06/15 18:15:34 addess
66 * Initialized this_uid to 0 on line 1286
67 *
68 * Revision 6.19 1999/05/13 15:51:33 kimelman
69 * bugfix: memory deallocation fixed
70 *
71 * Revision 6.19 1999/05/13 15:51:33 kimelman
72 * bugfix: memory deallocation fixed
73 *
74 * Revision 6.18 1999/05/11 23:36:34 kimelman
75 * make StrToInt4 static
76 *
77 * Revision 6.17 1999/05/11 17:50:23 kimelman
78 * style
79 *
80 * Revision 6.16 1999/04/28 21:08:30 lewisg
81 * fixed double freeing of Biostruc
82 *
83 * Revision 6.15 1999/04/28 18:26:15 kimelman
84 * exit codes changed to 0
85 *
86 * Revision 6.14 1999/04/22 01:56:44 kimelman
87 * 1. pdb reference read completely from configurstion files
88 * 2. indentaiton
89 * 3. NcbiMimeAsn1Free(mime) commented out <-- lead to core
90 * dump AFTER sending MIME (quick & dirty fix)
91 *
92 * Revision 6.13 1999/04/19 16:52:57 kimelman
93 * spelling fix
94 *
95 * Revision 6.12 1999/03/05 19:18:47 addess
96 * changed URL to link to RCSB structure explorer
97 *
98 * Revision 6.11 1998/11/06 16:25:31 addess
99 * added features for layer-1 and PDB TITLE records
100 *
101 * Revision 6.10 1998/07/17 18:45:53 madej
102 * Got rid of some unused URLs.
103 *
104 * Revision 6.9 1998/06/11 19:12:53 madej
105 * Changes in a message type for Cn3D by Yanli.
106 *
107 * Revision 6.8 1998/04/16 17:51:38 madej
108 * Tweak to print out author names in new/old format.
109 *
110 * Revision 6.7 1998/04/15 14:54:05 kimelman
111 * 1. Make retrieval unifirm from open server and sql server.
112 * 2. mmdbsrv retrival performance tuning:
113 * - size of read-in buffers
114 * - direct pdb2mmdb DB lookup instead of full loading pdb to mmdb translataion
115 * table
116 * 3. cleaning mmdblocl.* and make.mmdbsrv in order to remove obsolete code
117 *
118 * Revision 6.6 1998/04/03 20:25:24 kimelman
119 * PubStruct access code added to mmdbsrv
120 *
121 * Revision 6.5 1998/02/20 18:25:26 madej
122 * Fix using unlink to stop file dumps into /var/tmp.
123 *
124 * Revision 6.4 1997/11/25 18:27:45 madej
125 * Fix to save asn.1 files in binary.
126 *
127 * Revision 6.3 1997/11/05 19:05:16 madej
128 * Updated comments for config file.
129 *
130 * Revision 6.2 1997/11/05 15:58:57 madej
131 * Bug fix for tax names in multiple listings
132 *
133 * Revision 6.1 1997/10/31 15:29:57 madej
134 * Major reformat of structure summary page, including taxonomy links.
135 *
136 * Revision 6.0 1997/08/25 18:11:28 madden
137 * Revision changed to 6.0
138 *
139 * Revision 1.2 1997/05/16 21:25:41 hogue
140 * Added checks with vast database entries before showing vast links.
141 *
142 * Revision 1.1 1997/02/18 18:03:30 hogue
143 * Initial revision
144 *
145 *
146 * ==========================================================================
147 */
148
149 /**************
150 *mmdbsrv GET Useage:
151 *
152 *db=t&form=6&uid=1OMD&dopt=s - PDB or MMDB-ids allowed
153 *db=t&form=6&uid=1OMD&Dopt=i - launch Cn3D Mime-type - first UID only.
154 *db=t&uid=1234,2345,1254,1232&dopt=s - multiple structure summaries
155 *db=t&uid=3INS,1234,1OMD&dopt=s - mixed id types OK
156 *
157 *Optional, but if wrong, error:
158 * db=t any other is an error message
159 * form=6 4 is an error message - any other ignored
160 *
161 *Required
162 * uid=(list of MMDB ids or PDB ids)
163 *
164 *Optional dopt=
165 * 's' Structure summary
166 * 'r' PDB file
167 * 'k' Kinemage file
168 * 'i' ASN.1 file
169 * Others - error; None assumes 's'
170 *
171 *Optional - Interpreted in Context:
172 * complexity="Cn3D+Subset" ONECOORDATOM, 1
173 * "Virtual+Bond+Model" ONECOORDRES, 1
174 * "Up+to+5+Models" ALLMDL, 5
175 * "Up+to+10+Models" ALLMDL, 10
176 * "All+Models" ALLMDL, 100
177 *
178 * KinemageColor="Molecule+Number" KIN_COLOR_NUMBER
179 * "Secondary+Structure" KIN_COLOR_TYPE
180 * "Thermal+Factor" KIN_COLOR_TEMP
181 * "Element" KIN_COLOR_ATOM
182 * KinemageRender=(integer) - not seen on Struc Summary
183 * save="See"
184 * "s" - saves
185 * "m" MacSave format
186 * header="no" same as save="s"
187 * title="no" - omit title bar and bottom options
188 * html="no"
189 */
190
191
192 /*******************************************
193 MMDBSRV MIRROR installation:
194
195 This describes what you need to run MMDBSRV:
196
197 1] YOUR MMDB DATA DIRECTORIES, e.g.:
198 ...mmdb/mmdbdata/
199 ...mmdb/vastdata/
200
201 These contain the MMDB data on your local filesystem,
202 as obtained from ftp://ftp.ncbi.nih.gov/mmdb/mmdbdata
203 and updated regularly by MIRROR. You can
204 put them in the CGI-BIN or HTTP (HTML) directories
205 if you prefer. If you wish to implement a local
206 decompression/compression scheme see the source code mmdblocl.c.
207
208 2] YOUR CGI-BIN directory & URL, e.g.:
209 ...cgi-bin/mmdb/
210 ...cgi-bin/mmdb/logs/
211 ...cgi-bin/mmdb/data/
212 http://123.456.789.10/cgi-bin/mmdb/
213
214 The first contains the compiled mmdbsrv program and the
215 config file, obtained from
216 ftp://ftp.ncbi.nih.gov/mmdb/www/mmdbsrv
217 The second will contain the log files written out.
218 The third needs sshead.txt, sscode.txt, sstail.txt
219 NOTE - you must edit "sstail.txt"
220 in order to get the proper links to your local
221 copy of help documentation & server.
222
223 3] YOUR HTTP (HTML) directory & URL, e.g.:
224 ...html/mmdb
225 ...html/mmdb/mmdbgifs
226 http://123.456.789.10/mmdb/
227
228 The first contains the html files to launch mmdbsrv,
229 arrow.gif, strucsum.gif and any other gif files, and the
230 associated MMDB help files struchelp.html, cn3d.html,
231 strucinstall.html, vast.html, etc. Master copies are kept
232 at ftp://ftp.ncbi.nih.gov/mmdb/www/http
233 You must hand edit or use scripts or SED to change links from
234 NCBI's to your own in all these HTML files.
235
236 The second contains the GIF library as obtained from
237 the NCBI ftp site ftp://ftp.ncbi.nih.gov/mmdb/mmdbgifs
238
239 6] Your WWW-Server - make it aware of the following
240 new MIME-types:
241 chemical/ncbi-asn1-binary *.val
242 chemical/x-pdb *.ent; *.pdb
243 chemical/x-kinemage *.kin
244
245
246 -----------------------------
247 7]
248 MMDBSRV gets its directory structure; link URLS and CGI call names
249 from a config file.
250 Change these as required and make a config file.
251 Unix ".mmdbrc" or Win "mmdb.ini" from this example:
252
253 Don't change:
254 URLHelp, ENTREZurl, MMDBurl, PDBurl, 3DBurl
255 unless there are broken external links to these.
256
257 -------------------- cut here --------------------
258 [MMDB]
259 ;Database and Index required when local MMDB database is used.
260 ; Database = ./Junk/
261 Database = /net/dorothy/cbb3/mmdb/data/
262 Index = mmdb.idx
263
264 [MMDBSRV]
265 ; File for configuring the MMDB server.
266 ; Base Directory & URLs for HTML documents.
267 HTMLPath = /net/vaster/usr/attic/httpd.local/htdocs/Structure/
268 URLBase = http://inhouse.ncbi.nlm.nih.gov:6224/Structure/
269 URLHelp = http://www.ncbi.nlm.nih.gov/Entrez/
270 ;
271
272 ; Base Directory for CGI-BIN code, data (gifs, html text) and logs.
273 CGIPath = /net/vaster/usr/attic/httpd.local/cgi-bin/Structure/
274 URLcgi = http://inhouse.ncbi.nlm.nih.gov:6224/cgi-bin/Structure/
275 CGIname = mmdbsrv
276 DATApath = ./data/
277 LOGpath = ./logs/
278 ;
279
280 ; Base Directory for MMDB-gif set
281 GIFpath = /net/vaster/usr/attic/httpd.public/htdocs/Structure/mmdbgifs/
282 GIFurl = http://www.ncbi.nlm.nih.gov/Structure/mmdbgifs/
283 ;
284
285 ; URL's for links to Entrez, VAST.
286 ENTREZurl = http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query
287 VASTurl = http://inhouse.ncbi.nlm.nih.gov:6224/cgi-bin/Structure/vastsrv
288 MMDBurl = http://www.ncbi.nlm.nih.gov/Structure/
289 PDBurl = http://www.pdb.bnl.gov/index.html
290 TDBurl = http://www.pdb.bnl.gov/cgi-bin/opdbshort
291
292 ; Location of gunzip function.
293 Gunzip = /usr/sbin/gunzip
294
295 ;
296 MAILto = info@ncbi.nlm.nih.gov
297 ;
298 [VAST]
299 ;Database required for local VAST fetches.
300 ;Database = /net/vaster/usr/people6/madej/vastdata.binary/
301 Database = /net/dorothy/cbb3/vast/data/
302
303 ; URL for link to taxonomy database (wgetorg for retrieval)
304 [TAXLINK]
305 TAXurl = http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi
306
307 -------------------- cut here --------------------
308 ********************************************/
309
310 #include <ncbi.h>
311 #include <ncbiwww.h>
312 #include <accentr.h>
313 #include <ncbistr.h>
314 #include <miscutils.h>
315 #include <sys/resource.h>
316 #include <mmdbapi.h>
317 #include <mmdbdata.h>
318 #include <taxinc.h>
319 #include <sys/resource.h>
320
321 #include <lsqfetch.h>
322 #include <netentr.h>
323 #include <asnmime.h>
324 #include <objmime.h>
325
326 #ifdef OS_UNIX
327 #include <signal.h>
328 #include <unistd.h>
329 #define CPUTIME_MAX 120
330 #endif
331
332
333
334 #define NUM_COMPLEXITY_TYPES 6
335 static char *ComplexityDescriptions[] =
336 {"Virtual Bond Model","All Atom Model","Up to 5 Models",
337 "Up to 10 Models","All Models","Cn3D Subset"};
338
339 #define NUM_COLOR_TYPES 5
340 static char *ColorDescriptions[] =
341 {"","Molecule Number","Secondary Structure","Thermal Factor","Element"};
342
343 /* the config file DATApath is used for the location of these files */
344
345 #define HEADFILE "sshead.txt"
346 /* Structure Summary Header File */
347
348 #define TAILFILE "sstail.txt"
349 /* Structure Summary Tail File */
350
351 #define CODEFILE "sscode.txt"
352 /* Structure Summary View Code */
353
354 #define CHAIN_CHOICE_NUM 1
355 #define ORG_CHOICE_NUM 6
356
357 /* some defines needed for the taxonomy code */
358
359 #define TAX_ID_CHOICE_NUM 0
360 #define MAX_CHAINS 128
361 #define MAX_TBUFF 8192
362
363 WWWInfoPtr info = NULL;
364
365 static Boolean GlobalTitles = TRUE;
366 static Boolean GlobalNonHtmlOutput = FALSE;
367
368 static Char HTMLPath[PATH_MAX];
369 static Char URLBase[PATH_MAX];
370 static Char URLHelp[PATH_MAX];
371
372 static Char CGIPath[PATH_MAX];
373 static Char URLcgi[PATH_MAX];
374 static Char CGIName[256];
375 static Char DATApath[PATH_MAX];
376 static Char LOGpath[PATH_MAX];
377
378 static Char ENTREZurl[PATH_MAX];
379 static Char VASTurl[PATH_MAX];
380 static Char MMDBurl[PATH_MAX];
381 static Char PDBurl[PATH_MAX];
382 static Char TDBurl[PATH_MAX];
383 static Char TAXurl[PATH_MAX];
384 static Char MAILto[256];
385 static Char MAILTO[PATH_MAX];
386 static Char ARROW[PATH_MAX];
387
388 static char* cvsId_ = "@(#)$Id: mmdbsrv.c,v 6.29 2005/01/12 22:49:13 vakatov Exp $";
389
390 /*****************************************************
391 * WWWPrintFileData looks in the current CGI-BIN directory
392 * or the "data" subdirectory for the data file.
393 * and prints it out to pFile
394 */
395
396 static void WWWPrintFileData(CharPtr FName, FILE *pFile)
397 {
398
399 FILE *f = NULL;
400 Char fullpath [PATH_MAX];
401 CharPtr ptr;
402 Char pcBuf[1024];
403
404 fullpath[0] = '\0';
405 StringCpy(fullpath, DATApath); /* look in DATApath */
406 StringCat(fullpath, FName);
407 f = FileOpen (fullpath, "r");
408 if (f == NULL) {
409 f = FileOpen (FName, "r"); /* look in curent */
410 if (f == NULL) { /* look in ./data/ */
411 ProgramPath (fullpath, sizeof (fullpath) - 1);
412 ptr = StringRChr (fullpath, DIRDELIMCHR);
413 if (ptr != NULL) {
414 *ptr = '\0';
415 }
416 FileBuildPath (fullpath, "data", FName);
417 f = FileOpen (fullpath, "r");
418 if (f == NULL) {
419 return;
420 }
421 }
422 }
423
424 do {
425 pcBuf[0] = '\0';
426 ptr = fgets(pcBuf, (size_t)1024, f);
427 if (ptr) fprintf(pFile, ptr);
428 } while (ptr);
429
430 FileClose(f);
431 return;
432 }
433
434
435 static Boolean
436 StrToInt4 (CharPtr str, Int4Ptr longval)
437 {
438 Nlm_Int2 i;
439 Nlm_Int2 len;
440 Nlm_Char local [64];
441 Nlm_Boolean nodigits;
442 long int val;
443
444 if (longval != NULL) {
445 *longval = (Nlm_Int4) 0;
446 }
447 len = (Nlm_Int2) Nlm_StringLen (str);
448 if (len == 0)
449 return FALSE;
450
451 nodigits = TRUE;
452 for (i = 0; i < len; i++)
453 {
454 Nlm_Char ch;
455
456 ch = str [i];
457 if ('0' <= ch && ch <= '9')
458 nodigits = FALSE;
459 else if ( !/*!!*/ (ch == ' ' || ch == '+' || ch == '-') || nodigits==FALSE)
460 return FALSE;
461 }
462 if (nodigits)
463 return FALSE;
464 if (longval != NULL)
465 {
466 Nlm_StringNCpy (local, str, sizeof (local));
467 if (sscanf (local, "%ld", &val) == 1)
468 *longval = val;
469 }
470 return TRUE;
471 }
472
473
474 static Int4 CountUIDs(char *String)
475 {
476 Int4 count = 0;
477
478 for (;;)
479 {
480 String = SkipSet(String,", ");
481 if (*String == NULLB)
482 break;
483 count++;
484 String = SkipToSet(String,", ");
485 }
486
487 return(count);
488 }
489
490 static Int4 ConvertMMDBUID(CharPtr pcString)
491 {
492 Int4 iUID;
493 CharPtr pcTemp = NULL;
494
495 if (pcString == NULL)
496 return 0;
497
498 iUID = 0;
499 pcTemp = StringSave(pcString);
500 CleanSpaces(pcTemp);
501 if (!StrToInt4(pcTemp, &iUID))
502 {
503 iUID = MMDBEvalPDB(pcTemp);
504 }
505 MemFree(pcTemp);
506 return iUID;
507 }
508
509
510
511
512 static void MakeUIDList(CharPtr pcString, ValNodePtr PNTR ppvnUIDS)
513 {
514 CharPtr Ptr = NULL;
515 CharPtr Ptr2 = NULL;
516 Char SavedChar = NULL;
517 Int4 Uid = 0, i;
518 Int4Ptr Uids = NULL;
519
520
521 Ptr = SkipSpaces(pcString);
522 if (*Ptr == NULLB)
523 return;
524
525 while (*Ptr)
526 {
527 Ptr2 = SkipToSet(Ptr," ,");
528 SavedChar = *Ptr2;
529 *Ptr2 = NULLB;
530 Uid = 0;
531 Uid = ConvertMMDBUID(Ptr);
532 /* printf("{%s}[%ld]\n", Ptr, Uid); */
533 if (Uid != 0)
534 {
535 ValNodeAddInt(ppvnUIDS, 0, Uid);
536 }
537 *Ptr2 = SavedChar;
538 Ptr = SkipSet(Ptr2," ,");
539 }
540
541 return;
542 }
543
544
545 static Int4 GetOptionValue(CharPtr Value, Int4 NumElements, CharPtr *ElementText)
546 {
547 Int4 count, Len;
548 Int4 valnum;
549
550 if (StrToInt4(Value, &valnum))
551 return(valnum);
552
553 Len = StringLen(Value);
554 for (count = 0; count < NumElements; count++)
555 if (StrNICmp(ElementText[count],Value, Len) == 0)
556 break;
557
558 if (count == NumElements)
559 return -1;
560
561 return(count);
562 }
563
564
565
566 /* Output links from the protein and nucleotide chains to GenPept reports. */
567
568 #define EntrezLink "<A HREF=\"%s?uid=%ld&form=6&db=%c&dopt=%c\">%s</A>"
569
570 /************ Added by Ken for Layer One PDB releases ************/
571
572 static void My_StringNCpy(CharPtr str1, CharPtr str2, Int4 len)
573 {
574 StringNCpy(str1,str2,len);
575 str1[len] = '\0';
576 }
577
578 static Boolean IsLayerOne(ValNodePtr pvn)
579 {
580 Boolean Layer = FALSE;
581 CharPtr comment_txt;
582 CharPtr LayerOne = {"This is Layer 1 Release"};
583 CharPtr temp_string;
584 Int4 len;
585
586 while (pvn)
587 {
588 if (pvn->choice == BiostrucDescr_pdb_comment)
589 {
590 comment_txt = (CharPtr)pvn->data.ptrvalue;
591 temp_string = StringSave(LayerOne);
592 len = StringLen(LayerOne);
593 My_StringNCpy(temp_string, &comment_txt[18], len);
594 if (!StringICmp(temp_string, LayerOne))
595 {
596 Layer = TRUE;
597 break;
598 }
599 }
600 pvn = pvn->next;
601 }
602
603 return Layer;
604 }
605 /***** End of functions added by Ken ********************/
606 static void
607 PrintMolecularContents(PDNMS ModelStruc, FILE *gdf)
608 {
609 PMSD pmsd;
610 PDNMM pdnmm;
611 PMMD pmmd;
612 Int2 cnt;
613
614
615
616 if (ModelStruc == NULL)
617 return;
618
619 /* protein chains */
620 pmsd = (PMSD) ModelStruc->data.ptrvalue;
621
622 for (pdnmm = pmsd->pdnmmHead, cnt = 0; pdnmm != NULL; pdnmm = pdnmm->next) {
623 pmmd = (PMMD) pdnmm->data.ptrvalue;
624
625 if ((pmmd->bWhat) & AM_PROT) {
626 if (cnt++ == 0) {
627 fprintf(gdf, "<TR>\n<TD VALIGN=TOP NOWRAP>");
628 fprintf(gdf, "<strong>Protein Chains:</strong></TD>\n<TD>");
629
630 if (pmmd->pcMolName[0] == ' ')
631 fprintf(gdf, EntrezLink, ENTREZurl, (long) pmmd->iGi, 'p', 'g',
632 "(single chain)");
633 else
634 fprintf(gdf, EntrezLink, ENTREZurl, (long) pmmd->iGi, 'p', 'g',
635 pmmd->pcMolName);
636 }
637 else {
638 fprintf(gdf, ", ");
639 fprintf(gdf, EntrezLink, ENTREZurl, (long) pmmd->iGi, 'p', 'g',
640 pmmd->pcMolName);
641 }
642 }
643 }
644
645 if (cnt > 0)
646 fprintf(gdf, "</TD>\n</TR>\n");
647
648 /* nucleotide chains */
649 for (pdnmm = pmsd->pdnmmHead, cnt = 0; pdnmm != NULL; pdnmm = pdnmm->next) {
650 pmmd = (PMMD) pdnmm->data.ptrvalue;
651
652 if ((pmmd->bWhat) & (AM_DNA | AM_RNA)) {
653 if (cnt++ == 0) {
654 fprintf(gdf, "<TR>\n<TD VALIGN=TOP NOWRAP>");
655 fprintf(gdf, "<strong>Nucleotide chains:</strong></TD>\n<TD>");
656
657 if (pmmd->pcMolName[0] == ' ')
658 fprintf(gdf, EntrezLink, ENTREZurl, (long) pmmd->iGi, 'n', 'g',
659 "(single chain)");
660 else
661 fprintf(gdf, EntrezLink, ENTREZurl, (long) pmmd->iGi, 'n', 'g',
662 pmmd->pcMolName);
663 }
664 else {
665 fprintf(gdf, ", ");
666 fprintf(gdf, EntrezLink, ENTREZurl, (long) pmmd->iGi, 'n', 'g',
667 pmmd->pcMolName);
668 }
669 }
670 }
671
672 if (cnt > 0)
673 fprintf(gdf, "</TD>\n</TR>\n");
674
675 } /* end PrintMolecularContents */
676
677
678
679 static void
680 PrintStructureInfo(PDNMS ModelStruc, FILE *File, CharPtr tax_save)
681 {
682 char Name[200];
683 Int4 depyear, depday;
684 PMSD pmsdThis = NULL;
685 BiostrucSourcePtr pbssThis = NULL;
686 ValNodePtr pvnThis = NULL;
687 BiostrucHistoryPtr pbshThis = NULL;
688 CharPtr pcAuthors = NULL;
689 char Paragraph[10];
690
691 if (!ModelStruc)
692 return;
693
694 pmsdThis = (PMSD) ModelStruc->data.ptrvalue;
695 pvnThis = ValNodeFindNext(pmsdThis->pbsBS->descr,NULL,BiostrucDescr_history);
696
697 if (pvnThis) {
698 pbshThis = (BiostrucHistoryPtr) pvnThis->data.ptrvalue;
699 pbssThis = pbshThis->data_source;
700 }
701
702 /*****
703 fprintf(File, "<font size=+2>MMDB Id: %ld  ", (long) pmsdThis->iMMDBid);
704 *****/
705 fprintf(File, "<font size=+2>");
706 fprintf(File, "MMDB Id: <A HREF=\"%s%s?uid=%ld&form=6&db=t&Dopt=s\">%ld</A>  ",
707 URLcgi, CGIName, (long) pmsdThis->iMMDBid, (long) pmsdThis->iMMDBid);
708 fprintf(File, "PDB Id: <A HREF=\"%s=%s\">%s</a>\n", TDBurl,pmsdThis->pcPDBName, pmsdThis->pcPDBName);
709 if (IsLayerOne(pmsdThis->pbsBS->descr))
710 fprintf(File, " - Warning: <A HREF=\"http://www.pdb.bnl.gov/pdb-docs/what_is_LR.html\">Not validated!</A>\n");
711 fprintf(File, "</font>");
712 fprintf(File, "<BR>\n<BR>\n");
713 fprintf(File, "<TABLE>\n");
714 PrintMolecularContents(ModelStruc, File);
715 fprintf(File, "<TR>\n<TD VALIGN=TOP NOWRAP>");
716 fprintf(File, "<strong>MEDLINE</strong>:</TD>\n<TD><A HREF=\"%s?db=t&form=6&uid=", ENTREZurl);
717 fprintf(File, "%ld&Dopt=m\">PubMed</A></TD>\n</TR>\n", (long) pmsdThis->iMMDBid );
718
719 if (tax_save != NULL)
720 fprintf(File, "%s\n", tax_save);
721 else if (pmsdThis->pcPdbSource) {
722 fprintf(File, "<TR>\n<TD VALIGN=TOP NOWRAP>");
723 fprintf(File, "<strong>Source</strong>:</TD>\n<TD>%s</TD>\n</TR>\n", pmsdThis->pcPdbSource);
724 }
725
726 /* insert a blank row in the table, for spacing */
727 fprintf(File, "<TR>\n<TD VALIGN=TOP NOWRAP> </TD>\n<TD><BR></TD>\n</TR>\n");
728 pcAuthors = AuthorListPDB(pmsdThis->pbsBS);
729
730 if (pcAuthors) {
731 fprintf(File, "<TR>\n<TD VALIGN=TOP NOWRAP>");
732 fprintf(File, "<strong>PDB Authors</strong>:</TD>\n<TD>%s</TD>\n</TR>\n", pcAuthors);
733 fflush(File);
734 MemFree(pcAuthors);
735 }
736
737 if (pbssThis) {
738 depyear = pbssThis->database_entry_date->data[1];
739 depday = pbssThis->database_entry_date->data[3];
740 fprintf(File, "<TR>\n<TD VALIGN=TOP NOWRAP>");
741 fprintf(File, "<strong>PDB Deposition</strong>:</TD>\n<TD>%2d-%3s-%02d</TD>\n</TR>\n",
742 (int) depday, NCBI_months[pbssThis->database_entry_date->data[2] - 1], (int) depyear%100);
743 }
744
745 if (pmsdThis->pcPdbClass) {
746 fprintf(File, "<TR>\n<TD VALIGN=TOP NOWRAP>");
747 fprintf(File, "<strong>PDB Class</strong>:</TD>\n<TD>%s</TD>\n</TR>\n", pmsdThis->pcPdbClass);
748 }
749
750 fprintf(File, "<TR>\n<TD VALIGN=TOP NOWRAP>");
751 pvnThis = ValNodeFindNext(pmsdThis->pGraphDescr,NULL,BiomolDescr_pdb_comment);
752 if (pvnThis)
753 fprintf(File, "<strong>PDB Title</strong>:</TD>\n<TD>%s</TD>\n</TR>\n", pmsdThis->pcChemName);
754 else
755 fprintf(File, "<strong>PDB Compound</strong>:</TD>\n<TD>%s</TD>\n</TR>\n", pmsdThis->pcChemName);
756 /* insert a blank row in the table, for spacing */
757 fprintf(File, "<TR>\n<TD VALIGN=TOP NOWRAP> </TD>\n<TD><BR></TD>\n</TR>\n");
758
759 /* Note: The table continues with "Sequence Neighbors" and "Structure Neighbors". */
760 return;
761
762 }
763
764
765
766 static void
767 PrintStructureView(PDNMS ModelStruc, FILE *File)
768 {
769 PMSD pmsd;
770
771 if (ModelStruc == NULL) return;
772
773 pmsd = (PMSD) ModelStruc->data.ptrvalue;
774 fprintf(File, "<FORM METHOD=POST ACTION=\"%s%s\">\n", URLcgi, CGIName);
775 fprintf(File, "<INPUT TYPE=HIDDEN NAME=uid VALUE=%ld>\n", (long) pmsd->iMMDBid);
776 WWWPrintFileData(CODEFILE, File);
777 }
778
779
780
781 /* This routine creates the last two rows of the table started by PrintStructureInfo.
782 * These last two rows contain the links for the "Sequence Neighbors" of the chains of
783 * the structure, and for "Structure Neighbors" of the chains and domains of the
784 * structure. The first part of the code is very similar to PrintMolecularContents.
785 * The 2nd part creates the links for the VAST structure neighbors.
786 *
787 * Note there are 3 different formats for Vast neighbor links, purely for cosmetics.
788 */
789
790 #define VastLink1 "<A HREF=\"%s?uid=%ld&chaindom=%ld\">%s</A>"
791 #define VastLink2 "<A HREF=\"%s?uid=%ld&chaindom=%ld\">%s.%d</A>"
792 #define VastLink3 "<A HREF=\"%s?uid=%ld&chaindom=%ld\">%d</A>"
793
794 static void
795 PrintStructureLinks(PDNMS ModelStruc, FILE *gdf)
796 {
797 PMSD pmsd;
798 PDNMM pdnmm;
799 PMMD pmmd;
800 PDNMG pdnmg;
801 PMGD pmgd;
802 Int2 cnt, pflg;
803 Int4 uid, ichn, idom, chndom, chndom0;
804
805
806
807 if (ModelStruc == NULL)
808 return;
809
810 /* insert a blank row in the table, for spacing */
811 fprintf(gdf, "<TR>\n<TD VALIGN=TOP NOWRAP> </TD>\n<TD> </TD>\n</TR>\n");
812
813 /* protein chains */
814 pmsd = (PMSD) ModelStruc->data.ptrvalue;
815
816 for (pdnmm = pmsd->pdnmmHead, cnt = pflg = 0; pdnmm != NULL; pdnmm = pdnmm->next) {
817 pmmd = (PMMD) pdnmm->data.ptrvalue;
818
819 if ((pmmd->bWhat) & AM_PROT) {
820 if ((pmmd->iResCount <= 1) || (pmmd->iGi <= 0))
821 continue;
822
823 if (cnt++ == 0) {
824 pflg = 1;
825 fprintf(gdf, "<TR>\n<TD VALIGN=TOP NOWRAP>");
826 fprintf(gdf, "<strong>Sequence Neighbors:</strong></TD>\n<TD>");
827
828 if (pmmd->pcMolName[0] == ' ')
829 fprintf(gdf, EntrezLink, ENTREZurl, (long) pmmd->iGi, 'p', 'p',
830 "(single chain)");
831 else
832 fprintf(gdf, EntrezLink, ENTREZurl, (long) pmmd->iGi, 'p', 'p',
833 pmmd->pcMolName);
834 }
835 else {
836 fprintf(gdf, ", ");
837 fprintf(gdf, EntrezLink, ENTREZurl, (long) pmmd->iGi, 'p', 'p',
838 pmmd->pcMolName);
839 }
840 }
841 }
842
843 /* nucleotide chains */
844 for (pdnmm = pmsd->pdnmmHead; pdnmm != NULL; pdnmm = pdnmm->next) {
845 pmmd = (PMMD) pdnmm->data.ptrvalue;
846
847 if ((pmmd->bWhat) & (AM_DNA | AM_RNA)) {
848 if ((pmmd->iResCount <= 1) || (pmmd->iGi <= 0))
849 continue;
850
851 if (cnt++ == 0) {
852 fprintf(gdf, "<TR>\n<TD VALIGN=TOP NOWRAP>");
853 fprintf(gdf, "<strong>Sequence Neighbors:</strong></TD>\n<TD>");
854
855 if (pmmd->pcMolName[0] == ' ')
856 fprintf(gdf, EntrezLink, ENTREZurl, (long) pmmd->iGi, 'n', 'n',
857 "(single chain)");
858 else
859 fprintf(gdf, EntrezLink, ENTREZurl, (long) pmmd->iGi, 'n', 'n',
860 pmmd->pcMolName);
861 }
862 else {
863 fprintf(gdf, ", ");
864 fprintf(gdf, EntrezLink, ENTREZurl, (long) pmmd->iGi, 'n', 'n',
865 pmmd->pcMolName);
866 }
867 }
868 }
869
870 if (pflg)
871 fprintf(gdf, "</TD>\n</TR>\n");
872
873 if (pmsd->pdnmlModels == NULL) {
874 /* end the table */
875 fprintf(gdf, "</TABLE>\n<BR>\n");
876 return;
877 }
878
879 /* VAST neighbors: loop over protein chains */
880 uid = (Int4) pmsd->iMMDBid;
881
882 for (pdnmm = pmsd->pdnmmHead, cnt = ichn = 0; pdnmm != NULL; pdnmm = pdnmm->next) {
883 pmmd = (PMMD) pdnmm->data.ptrvalue;
884 ichn++;
885
886 if ((pmmd->bWhat) & AM_PROT) {
887 if ((pmmd->iResCount <= 1) || (pmmd->iGi <= 0))
888 continue;
889
890 chndom0 = 10000*uid + 100*(Int4) ichn;
891
892 if (cnt++ == 0) {
893 fprintf(gdf, "<TR>\n<TD VALIGN=TOP NOWRAP>");
894 fprintf(gdf, "<strong>Structure Neighbors:</strong></TD>\n<TD>");
895
896 if (pmmd->pcMolName[0] == ' ')
897 fprintf(gdf, VastLink1, VASTurl, (long) uid, (long) chndom0,
898 "(single chain)");
899 else
900 fprintf(gdf, VastLink1, VASTurl, (long) uid, (long) chndom0,
901 pmmd->pcMolName);
902 }
903 else {
904 fprintf(gdf, ", ");
905 fprintf(gdf, VastLink1, VASTurl, (long) uid, (long) chndom0,
906 pmmd->pcMolName);
907 }
908
909 /* now loop over domains */
910 idom = 0;
911
912 for (pdnmg = pmmd->pdnmgHead; pdnmg != NULL; pdnmg = pdnmg->next) {
913 pmgd = (PMGD) pdnmg->data.ptrvalue;
914
915 if (pmgd->iDomain > idom) {
916 idom = (Int4) pmgd->iDomain;
917 chndom = chndom0 + idom;
918 fprintf(gdf, ", ");
919
920 if (pmmd->pcMolName[0] == ' ')
921 fprintf(gdf, VastLink3, VASTurl, (long) uid,
922 (long) chndom, (int) idom);
923 else
924 fprintf(gdf, VastLink2, VASTurl, (long) uid,
925 (long) chndom, pmmd->pcMolName, (int) idom);
926 }
927 }
928 }
929 }
930
931 /* end the table */
932 fprintf(gdf, "</TD>\n</TR>\n</TABLE>\n");
933
934 } /* end PrintStructureLinks */
935
936
937
938 /* Utility routine needed below. Return a vector marking the distinct integers
939 * appearing in the input array. A naive algorithm is used since we never expect
940 * the array size 'n' to be large. If an entry vec[i] is 0, this means it is
941 * a duplicate. If vec[i] > 0 then this is the first occurrence of the number,
942 * and the value vec[i] is the number of times the corresponding number nums[i]
943 * appears.
944 */
945
946 static void
947 mark_distinct(Int4Ptr nums, Int2Ptr vec, Int2 n)
948 {
949 Int2 i, j, found;
950
951 if (n == 0)
952 return;
953
954 /* initialize the vector */
955 for (i = 0; i < n; i++)
956 vec[i] = 1;
957
958 for (i = 1; i < n; i++) {
959 for (j = 0; j < i; j++) {
960 if (nums[i] == nums[j]) {
961 vec[i] = 0;
962 vec[j]++;
963 break;
964 }
965 }
966 }
967
968 } /* end mark_distinct */
969
970
971
972 /* Output the taxonomy data, per chain, and also links to the taxonomy database.
973 * Return '1' in case there was a non-trivial taxonomy assignment, '0' if there
974 * was no taxonomy data found. The success or failure is passed ultimately to
975 * PrintStructureInfo, where the PDB source is displayed in case no taxonomy data
976 * was found.
977 */
978
979 static Int2
980 SaveTaxonomyInfo(BiostrucPtr bsp, CharPtr save, Int2 n, CharPtr pname)
981 {
982 MoleculeGraphPtr mgp;
983 Int4 i, j, k, cnt, txcnt, uacnt;
984 ValNodePtr descr, db;
985 CharPtr chainp, name, names[MAX_CHAINS];
986 Char chn, chns[MAX_CHAINS], org_names[MAX_TBUFF];
987 Int2 flg, name_here, cnt_vec[MAX_CHAINS];
988 BioSourcePtr bios;
989 OrgRefPtr org;
990 Int4 molecule_type, tax_id, tax_ids[MAX_CHAINS];
991
992
993
994 if ((bsp == NULL) || (save == NULL))
995 return 0;
996
997 for (i = 0; i < MAX_TBUFF; i++)
998 org_names[i] = '\0';
999
1000 name_here = 0;
1001 mgp = bsp->chemical_graph->molecule_graphs;
1002
1003 for (cnt = uacnt = 0; (mgp != NULL) && (cnt < MAX_CHAINS); mgp = mgp->next) {
1004 /* zap the OrgRefPtr, there may be no taxonomy for this chain! */
1005 org = NULL;
1006
1007 for (descr = mgp->descr; descr != NULL; descr = descr->next) {
1008 if (descr->choice == BiomolDescr_molecule_type)
1009 molecule_type = descr->data.intvalue;
1010
1011 if (descr->choice == BiomolDescr_name) {
1012 chainp = descr->data.ptrvalue;
1013 chn = *chainp;
1014 }
1015
1016 if (descr->choice == BiomolDescr_organism) {
1017 bios = descr->data.ptrvalue;
1018 org = (OrgRefPtr) bios->org;
1019 }
1020 }
1021
1022 if ((molecule_type == Molecule_type_protein) ||
1023 (molecule_type == Molecule_type_dna) ||
1024 (molecule_type == Molecule_type_rna)) {
1025
1026 /* save the chain and get the taxonomy data */
1027 chns[cnt] = (chn == ' ') ? '\n' : chn;
1028
1029 if (org != NULL) {
1030 DbtagPtr dbtag;
1031 ObjectIdPtr object_id;
1032
1033 for (db = org->db, tax_id = -1; db != NULL; db = db->next) {
1034 if (db->choice == TAX_ID_CHOICE_NUM) {
1035 dbtag = db->data.ptrvalue;
1036 tax_id = dbtag->tag->id;
1037 break;
1038 }
1039 }
1040
1041 names[cnt] = &org_names[name_here];
1042
1043 if (org->taxname != NULL) {
1044 StringCat(names[cnt], org->taxname);
1045 name_here += StrLen(org->taxname) + 1;
1046 }
1047 else if (org->common != NULL) {
1048 StringCat(names[cnt], org->common);
1049 name_here += StrLen(org->common) + 1;
1050 }
1051 else {
1052 StringCat(names[cnt], "(unassigned)");
1053 name_here += 13;
1054 }
1055
1056 tax_ids[cnt++] = tax_id;
1057 }
1058 else {
1059 /* track the number of unassigned chains */
1060 uacnt++;
1061 names[cnt] = &org_names[name_here];
1062 StringCat(names[cnt], "(unassigned)");
1063 name_here += 13;
1064 tax_ids[cnt++] = -1;
1065 }
1066 }
1067 }
1068
1069 /* zap the save area */
1070 for (i = 0; i < n; i++)
1071 save[i] = '\0';
1072
1073 /* flag the taxonomy section */
1074 sprintf(save, "<TR>\n<TD VALIGN=TOP NOWRAP><strong>Taxonomy</strong>:</TD>\n");
1075
1076 if (cnt == 0) {
1077 k = StrLen(save);
1078 sprintf(&save[k], "<TD>(unassigned)</TD>\n");
1079 return 1;
1080 }
1081
1082 /* group chains by organism type, i.e. tax id */
1083 mark_distinct(tax_ids, cnt_vec, cnt);
1084
1085 for (i = flg = 0; i < cnt; i++) {
1086 if (cnt_vec[i] == 0)
1087 continue;
1088
1089 tax_id = tax_ids[i];
1090 k = StrLen(save);
1091
1092 if (flg)
1093 sprintf(&save[k], "; ");
1094 else {
1095 sprintf(&save[k], "<TD>");
1096 flg = 1;
1097 }
1098
1099 /* collect chains with the same tax id */
1100 txcnt = cnt_vec[i];
1101 k = StrLen(save);
1102
1103 /*****
1104 if (txcnt > 1)
1105 sprintf(&save[k], "chains ");
1106 else if (chns[i] != '\n')
1107 sprintf(&save[k], "chain ");
1108 *****/
1109
1110 for (j = i; (j < cnt) && (txcnt > 0); j++) {
1111 if (tax_ids[j] != tax_id)
1112 continue;
1113
1114 k = StrLen(save);
1115
1116 if (txcnt-- > 1)
1117 sprintf(&save[k], "%c, ", chns[j]);
1118 else
1119 sprintf(&save[k], "%c", chns[j]);
1120 }
1121
1122 k = StrLen(save);
1123
1124 if (tax_id > 0) {
1125 if (chns[i] != '\n')
1126 sprintf(&save[k], "  <A HREF=\"");
1127 else
1128 sprintf(&save[k], "<A HREF=\"");
1129
1130 k = StrLen(save);
1131 sprintf(&save[k], TAXurl, tax_id);
1132 k = StrLen(save);
1133 sprintf(&save[k], "\">%s</A> ", names[i]);
1134 }
1135 else
1136 sprintf(&save[k], " (unassigned)");
1137 }
1138
1139 k = StrLen(save);
1140 sprintf(&save[k], "</TD>\n</TR>\n");
1141 return 1;
1142
1143 } /* end SaveTaxonomyInfo */
1144
1145
1146
1147 /* Old version of DumpMime, preserved for compatibility with Cn3D v1.0. */
1148
1149 static void DumpMime_v1(AsnIoPtr aip, CharPtr title, Int2 style, Int2 choice, VoidPtr datum)
1150 {
1151 NcbiMimeAsn1Ptr mime;
1152 EntrezGeneralPtr egp;
1153
1154 mime = (NcbiMimeAsn1Ptr) ValNodeNew(NULL);
1155 mime->choice = NcbiMimeAsn1_entrez;
1156 egp = EntrezGeneralNew();
1157 mime->data.ptrvalue = (VoidPtr) egp;
1158 egp->Data_data = ValNodeNew(NULL);
1159 egp->title = StringSave(title);
1160 egp->style = style;
1161 egp->Data_data->choice = choice;
1162 egp->Data_data->data.ptrvalue = datum;
1163
1164 NcbiMimeAsn1AsnWrite(mime, aip, NULL);
1165 AsnIoFlush(aip);
1166
1167 egp->Data_data->data.ptrvalue = NULL; /* for clean free */
1168 NcbiMimeAsn1Free(mime);
1169
1170 } /* end DumpMime_v1 */
1171
1172
1173
1174 /* yanli */
1175 static void DumpMime(AsnIoPtr aip, CharPtr title, VoidPtr datum)
1176 {
1177 NcbiMimeAsn1Ptr mime;
1178 EntrezGeneralPtr egp;
1179
1180 mime = (NcbiMimeAsn1Ptr) ValNodeNew(NULL);
1181 mime->choice = NcbiMimeAsn1_strucseq;
1182 mime->data.ptrvalue= datum;
1183
1184 NcbiMimeAsn1AsnWrite(mime, aip, NULL);
1185 AsnIoFlush(aip);
1186
1187 mime->data.ptrvalue=NULL ; /* for clean free */
1188 NcbiMimeAsn1Free(mime);
1189 }
1190
1191
1192
1193 #define LAUNCH_VIEWER 0
1194 #define SEE_FILE 1
1195 #define SAVE_FILE 2
1196 #define SEND_FILE 4
1197
1198 /* Handle the various View/See/Save file options. */
1199
1200 static Int4
1201 SendStructureMIME(Char Filetype, Int4 uid, Int4 Mime, Int4 Complexity,
1202 Int4 Models, Int4 Color, Int4 Render)
1203 {
1204 BiostrucPtr bsp;
1205 PDNMS ModelStruc;
1206 Int4 count, i4Sent = 0, error_flag = 0;
1207 AsnIoPtr aip;
1208
1209 /* yanli start */
1210 NcbiMimeAsn1Ptr mime;
1211 BiostrucSeqPtr bssp;
1212 BiostrucGraphPtr bsgp;
1213 MoleculeGraphPtr mgp;
1214 SeqIdPtr sip;
1215 SeqEntryPtr sep;
1216 Int2 retcode = 3;
1217 Int4 This_uid = 0;
1218
1219 if ((bsp = MMDBBiostrucGet((DocUid) uid, Complexity, Models)) == NULL) {
1220 printf("Content-type: text/html\r\n\r\n");
1221 printf("<h2>Error</h2>\n");
1222 printf("Structure with UID = %ld failed to fetch on Server<p>\n", (long) uid);
1223 printf("No such structure available on this MMDB server.\n");
1224 return 0;
1225 }
1226
1227 /*yanli*/
1228 bsgp = bsp->chemical_graph;
1229 mgp = bsgp->molecule_graphs;
1230 sip = mgp->seq_id;
1231 /* This_uid = EntrezFindSeqId(sip); */
1232 while(sip != NULL){
1233 if(sip->choice == 12) This_uid = sip->data.intvalue;
1234 sip = sip->next;
1235 }
1236 sep = EntrezSeqEntryGet(This_uid, retcode);
1237
1238 bssp = BiostrucSeqNew();
1239 bssp->structure = bsp;
1240 ValNodeLink(&(bssp->sequences), sep);
1241
1242 mime = (NcbiMimeAsn1Ptr) ValNodeNew(NULL); /* yanli */
1243 mime->choice = NcbiMimeAsn1_strucseq;
1244 mime->data.ptrvalue = bssp;
1245 /*---yanli*/
1246
1247 /* the following headers are format-independent */
1248 switch (Mime) {
1249 case SAVE_FILE:
1250 printf("Content-type: application/octet-stream\r\n\r\n");
1251 break;
1252 case SEE_FILE:
1253 printf ("Content-type: text/html\r\n\r\n");
1254 printf ("<HTML><PRE>\r\n");
1255 break;
1256 case SEND_FILE:
1257 printf ("Content-type: text/html\r\n\r\n");
1258 break;
1259 }
1260
1261 if (Filetype == 'j') {
1262 /* Cn3D v2.0 asn.1 format */
1263 switch (Mime) {
1264 case LAUNCH_VIEWER:
1265 printf ("Content-type: chemical/ncbi-asn1-binary\r\n\r\n");
1266 aip = AsnIoNew(ASNIO_BIN_OUT, stdout, NULL, NULL, NULL);
1267 DumpMime(aip, "MIME", bssp);
1268 break;
1269 case SAVE_FILE:
1270 aip = AsnIoNew(ASNIO_BIN_OUT, stdout, NULL, NULL, NULL);
1271 NcbiMimeAsn1AsnWrite(mime, aip, NULL);
1272 break;
1273 case SEE_FILE:
1274 aip = AsnIoNew(ASNIO_TEXT_OUT, stdout, NULL, NULL, NULL);
1275 NcbiMimeAsn1AsnWrite(mime, aip, NULL);
1276 break;
1277 case SEND_FILE:
1278 aip = AsnIoNew(ASNIO_TEXT_OUT, stdout, NULL, NULL, NULL);
1279 NcbiMimeAsn1AsnWrite(mime, aip, NULL);
1280 break;
1281 }
1282
1283 AsnIoReset(aip);
1284 AsnIoClose(aip);
1285 }
1286 else if (Filetype == 'i') {
1287 /* Cn3D v1.0 asn.1 format. Included for backwards compatibility, in case users
1288 * want to stick with their old Cn3D for some reason.
1289 */
1290 switch (Mime) {
1291 case LAUNCH_VIEWER:
1292 printf ("Content-type: chemical/ncbi-asn1-binary\r\n\r\n");
1293 /* printf ("Content-disposition: filename=\"%d.val\"\r\n\r\n", uid);*/
1294 aip = AsnIoNew(ASNIO_BIN_OUT, stdout, NULL, NULL, NULL);
1295 DumpMime_v1(aip, "MIME", Entrez_style_report, Data_data_structure, bsp);
1296 break;
1297 case SAVE_FILE:
1298 aip = AsnIoNew(ASNIO_BIN_OUT, stdout, NULL, NULL, NULL);
1299 BiostrucAsnWrite(bsp, aip, NULL);
1300 break;
1301 case SEE_FILE:
1302 aip = AsnIoNew(ASNIO_TEXT_OUT, stdout, NULL, NULL, NULL);
1303 BiostrucAsnWrite(bsp, aip, NULL);
1304 break;
1305 case SEND_FILE:
1306 aip = AsnIoNew(ASNIO_TEXT_OUT, stdout, NULL, NULL, NULL);
1307 BiostrucAsnWrite(bsp, aip, NULL);
1308 break;
1309 }
1310
1311 AsnIoReset(aip);
1312 AsnIoClose(aip);
1313 }
1314 else if (Filetype == 'r') {
1315 /* RasMol format */
1316 if (Mime == LAUNCH_VIEWER)
1317 printf ("Content-type: chemical/x-pdb\r\n\r\n");
1318 /* printf ("Content-disposition: filename=\"%d.pdb\"\r\n\r\n", uid);*/
1319
1320 ModelStruc = MakeAModelstruc(bsp);
1321 bssp->structure = NULL; /* already linked into modelstruc */
1322 WritePDBAllModel(ModelStruc, stdout);
1323 ClearStructures();
1324 }
1325 else if (Filetype == 'k') {
1326 /* Mage format */
1327 if (Mime == LAUNCH_VIEWER)
1328 printf ("Content-type: chemical/x-kinemage\r\n\r\n");
1329 /* printf ("Content-disposition: filename=\"%d.kin\"\r\n\r\n", uid);*/
1330
1331 ModelStruc = MakeAModelstruc(bsp);
1332 bssp->structure = NULL; /* already linked into modelstruc */
1333 WriteKinAllModel(ModelStruc, stdout, Color, Render);
1334 ClearStructures();
1335 }
1336 else {
1337 error_flag = 1;
1338 printf("Content-type: text/html\r\n\r\n");
1339 printf("<h2>Error</h2>\n");
1340 printf("Unknown file type on structure fetch.<p>\n");
1341 printf("Contact %s\n", MAILTO);
1342 }
1343
1344 if ((Mime == SEE_FILE) && (!error_flag))
1345 printf ("</PRE></HTML>\r\n");
1346
1347 NcbiMimeAsn1Free(mime); /* yanli */
1348 return 1;
1349
1350 } /* end SendStructureMIME */
1351
1352
1353 static Int4 SendSummaryPage(Int4Ptr Uids, Int4 NumToDisplay, Int4 Save)
1354 {
1355 BiostrucPtr bsp;
1356 ValNodePtr descr;
1357 PDNMS ModelStruc;
1358 Int4 uid, count, i4Sent = 0;
1359 Int2 taxret;
1360 Char tax_save[MAX_TBUFF];
1361 FILE *sendfile;
1362
1363 if (Save == 2)
1364 printf ("Content-type: application/octet-stream\n\n");
1365 else
1366 printf ("Content-type: text/html\n\n");
1367
1368 if (!GlobalNonHtmlOutput) {
1369 if (GlobalTitles)
1370 WWWPrintFileData(HEADFILE, stdout);
1371 else
1372 printf ( "<html>\n<title>MMDB Structure Summary</title><body>");
1373 }
1374 for (count = 0; count < NumToDisplay; count++)
1375 {
1376 uid = Uids[count];
1377 bsp = MMDBBiostrucGet((DocUid) uid,3,0);
1378 if (bsp == NULL)
1379 {
1380 printf ("%sNo structure found for UID %ld.%s\n",
1381 GlobalNonHtmlOutput ? "\n" : "<P><h4>",uid,
1382 GlobalNonHtmlOutput ? "\n" : "</h4><P>");
1383 if (!GlobalNonHtmlOutput)
1384 printf ("<HR SIZE=5 NOSHADE><BR>\n");
1385 continue;
1386 }
1387
1388 if (!GlobalNonHtmlOutput) {
1389 CharPtr name;
1390
1391 for (descr = bsp->descr, name = NULL; descr != NULL; descr = descr->next) {
1392 if (descr->choice == BiomolDescr_name) {
1393 name = descr->data.ptrvalue;
1394 break;
1395 }
1396 }
1397 taxret = SaveTaxonomyInfo(bsp, tax_save, MAX_TBUFF, name);
1398 }
1399
1400 ModelStruc = MakeAModelstruc(bsp);
1401 PrintStructureInfo(ModelStruc, stdout, (taxret) ? tax_save : NULL);
1402
1403 if (!GlobalNonHtmlOutput) /* Rest of View/Save stuff */
1404 {
1405 PrintStructureLinks(ModelStruc, stdout);
1406 PrintStructureView(ModelStruc, stdout);
1407 printf ("<HR SIZE=5 NOSHADE><BR>\n");
1408 }
1409
1410 ClearStructures();
1411 }
1412 if (!GlobalNonHtmlOutput)
1413 if (GlobalTitles)
1414 WWWPrintFileData(TAILFILE, stdout);
1415 else
1416 printf ("</html>");
1417
1418 return 1;
1419 } /* SendSummaryPage() */
1420
1421
1422 static void SendGetNetscape(void) {
1423
1424 printf("HTTP/1.0 200 OK\r\n");
1425 printf("MIME-Version: 1.0\r\n");
1426 printf("Content-type: text/html\r\n\r\n");
1427 printf("<BR><BR><B>Sorry, you need a <a href=\"http://home.netscape.com/\">",
1428 "Netscape</a> version 2 or higher WWW-browser "
1429 "to be able to enter this page</B><BR>\n\n");
1430 } /* SendGetNetscape */
1431
1432
1433
1434
1435 static Boolean InitMMDBSrv(void)
1436 {
1437 Int2 i;
1438
1439 HTMLPath[0] = '\0';
1440 URLBase[0] = '\0';
1441 URLHelp[0] = '\0';
1442 CGIPath[0] = '\0';
1443 URLcgi[0] = '\0';
1444 CGIName[0] = '\0';
1445 DATApath[0] = '\0';
1446 LOGpath[0] = '\0';
1447 ENTREZurl[0] = '\0';
1448 VASTurl[0] = '\0';
1449 MMDBurl[0] = '\0';
1450 PDBurl[0] = '\0';
1451 TDBurl[0] = '\0';
1452 MAILto[0] = '\0';
1453
1454 for (i = 0; i < PATH_MAX; i++)
1455 TAXurl[i] = '\0';
1456
1457 FindPath("mmdb", "MMDBSRV", "HTMLPath", HTMLPath, PATH_MAX);
1458 if (HTMLPath[0] == '\0')
1459 {
1460 ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nMMDBSRV section no HTMLPath...\n");
1461 return FALSE;
1462 }
1463 GetAppParam("mmdb", "MMDBSRV", "URLBase", "", URLBase, PATH_MAX);
1464 if (URLBase[0] == '\0')
1465 {
1466 ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nMMDBSRV section no URLBase...\n");
1467 return FALSE;
1468 }
1469 GetAppParam("mmdb", "MMDBSRV", "URLHelp", "", URLHelp, PATH_MAX);
1470 if (URLHelp[0] == '\0')
1471 {
1472 ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nMMDBSRV section no URLHelp...\n");
1473 return FALSE;
1474 }
1475 FindPath("mmdb", "MMDBSRV", "CGIPath", CGIPath, PATH_MAX);
1476 if (CGIPath[0] == '\0')
1477 {
1478 ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nMMDBSRV section no CGIPath...\n");
1479 return FALSE;
1480 }
1481
1482 GetAppParam("mmdb", "MMDBSRV", "URLcgi", "", URLcgi, PATH_MAX);
1483 if (URLcgi[0] == '\0')
1484 {
1485 ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nMMDBSRV section no URLcgi...\n");
1486 return FALSE;
1487 }
1488 GetAppParam("mmdb", "MMDBSRV", "CGIName", "", CGIName, (size_t) 256 * sizeof(char));
1489 if (CGIName[0] == '\0')
1490 {
1491 ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nMMDBSRV section no CGIName...\n");
1492 return FALSE;
1493 }
1494 FindPath("mmdb", "MMDBSRV", "DATApath", DATApath, PATH_MAX);
1495 if (DATApath[0] == '\0')
1496 {
1497 ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nMMDBSRV section no DATApath...\n");
1498 return FALSE;
1499 }
1500 ARROW[0] = '\0';
1501 sprintf(ARROW, "<IMG alt=\"o\" SRC=\"%sarrow.gif\" ALT=\"o\" BORDER=0>\n", URLBase);
1502
1503 FindPath("mmdb", "MMDBSRV", "LOGpath", LOGpath, PATH_MAX);
1504 if (LOGpath[0] == '\0')
1505 {
1506 ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nMMDBSRV section no LOGpath...\n");
1507 return FALSE;
1508 }
1509 GetAppParam("mmdb", "MMDBSRV", "ENTREZurl", "", ENTREZurl, PATH_MAX);
1510 if (ENTREZurl[0] == '\0')
1511 {
1512 ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nMMDBSRV section no ENTREZurl...\n");
1513 return FALSE;
1514 }
1515 GetAppParam("mmdb", "MMDBSRV", "VASTurl", "", VASTurl, PATH_MAX);
1516 if (VASTurl[0] == '\0')
1517 {
1518 ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nMMDBSRV section no VASTurl...\n");
1519 return FALSE;
1520 }
1521 GetAppParam("mmdb", "MMDBSRV", "MMDBurl", "", MMDBurl, PATH_MAX);
1522 if (MMDBurl[0] == '\0')
1523 {
1524 ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nMMDBSRV section no MMDBurl...\n");
1525 return FALSE;
1526 }
1527 GetAppParam("mmdb", "MMDBSRV", "PDBurl", "", PDBurl, PATH_MAX);
1528 if (PDBurl[0] == '\0')
1529 {
1530 ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nMMDBSRV section no PDBurl...\n");
1531 return FALSE;
1532 }
1533 GetAppParam("mmdb", "MMDBSRV", "TDBurl", "", TDBurl, PATH_MAX);
1534 if (TDBurl[0] == '\0')
1535 {
1536 ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nMMDBSRV section no TDBurl...\n");
1537 return FALSE;
1538 }
1539 GetAppParam("mmdb", "TAXLINK", "TAXurl", "", TAXurl, PATH_MAX);
1540 if (TAXurl[0] == '\0')
1541 {
1542 ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nTAXLINK section no TAXurl...\n");
1543 return FALSE;
1544 }
1545 StringCat(TAXurl, "?id=%d&lvl=0");
1546 GetAppParam("mmdb", "MMDBSRV", "MAILto", "", MAILto, PATH_MAX);
1547 if (MAILto[0] == '\0')
1548 {
1549 ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nMMDBSRV section no Mailto...\n");
1550 return FALSE;
1551 }
1552
1553 MAILTO[0] = '\0';
1554 sprintf(MAILTO, "< <a href=\"%s\">%s</a> >", MAILto, MAILto);
1555
1556 return TRUE;
1557 }
1558
1559
1560
1561 /************************************************************************
1562 *
1563 * Int2 Main() - main function
1564 *
1565 ***********************************************************************/
1566
1567
1568
1569 Int2 Main ()
1570 {
1571 Boolean Netscape2_OK = FALSE;
1572 time_t time_now;
1573 CharPtr TimeNowStr = NULL;
1574 WWWErrorCode error;
1575 Int4 IndexArgs = -1;
1576 Int4 Complex = 0;
1577 Int4 MaxModels = 1;
1578 Int4 KinColor = 0;
1579 Int4 KinRender = 0;
1580 Int4 Save = 0;
1581 Char DispOpt = '\0';
1582 Int4 Form = 0;
1583 CharPtr pcThis = NULL, pcName = NULL;
1584 CharPtr Uids; /* (list of MMDB ids or PDB ids) */
1585 Int4Ptr MMDBids = NULL; /* (list of MMDB ids ) */
1586 Int4 iMMDBids = 0;
1587 Int4 iCount = 0;
1588 Int4 iBytes = 0;
1589 Int4 NumEntries = 0;
1590 ValNodePtr pvnUIDS = NULL, pvnThis = NULL;
1591
1592 /* this sets up the unix time limit */
1593
1594 #ifdef OS_UNIX
1595 {
1596 struct rlimit rl;
1597 getrlimit(RLIMIT_CPU, &rl);
1598 rl.rlim_max = rl.rlim_cur = CPUTIME_MAX;
1599 setrlimit(RLIMIT_CPU, &rl);
1600 }
1601 #endif
1602
1603 if (!InitMMDBSrv()) {
1604 printf("Content-type: text/html\r\n\r\n");
1605 printf("<H2>MMDBSRV Error</H2>\n - Unable to Open Server Configuration File.<p>\n");
1606 printf("Contact the MMDBSRV administrator for this site.<p>\n");
1607 exit(1);
1608 }
1609
1610 StringCat(LOGpath, "mmdbsrv.log");
1611 if( !ErrSetLogfile (LOGpath, ELOG_APPEND) ) {
1612 printf("Content-type: text/html\r\n\r\n");
1613 printf("<H2>MMDBSRV Error</H2>\n - Unable to Open Log.<p>\n");
1614 printf("Contact MMDBSRV administrator for this site: %s<p>\n", MAILTO);
1615 exit(1);
1616 }
1617
1618 ErrSetLogLevel(SEV_MAX);
1619 ErrSetOpts (ERR_CONTINUE, ERR_LOG_ON);
1620
1621
1622
1623 if((error = WWWGetArgs(&info)) != WWWErrOk) {
1624 printf("Content-type: text/html\r\n\r\n");
1625 printf("<H2>MMDBSRV Error</H2>\n Failed to Process Posting - Check your GET/POST syntax\n");
1626 goto earlyout;
1627 }
1628
1629
1630 /* if(WWWGetBrowser(info) != NETSCAPE) {
1631 SendGetNetscape();
1632 exit(1);
1633 } */
1634
1635 if ((!OpenMMDBAPI(0, NULL)) || (!MMDBInit()))
1636 {
1637 ErrLogPrintf("#MMDB Database Access Failed to Initialize.\n");
1638 printf("Content-type: text/html\r\n\r\n");
1639 printf("<H2>MMDBSRV Error</H2>\n - Unable to Open MMDB Database on Server.<p>");
1640 printf("Contact MMDBSRV administrator for this site: %s<p>\n", MAILTO);
1641 exit(1);
1642 }
1643 /* yanli */
1644 if (EntrezInit("mmdbsrv", NULL, FALSE) == FALSE)
1645 {
1646 printf("Content-type: text/html\n\n");
1647 printf("<h2>Error</h2>\n");
1648 printf("MMDBSERV: EntrezInit Failed.<p>\n");
1649 return;
1650 }
1651 /* yanli */
1652 /*if( !BioseqFetchInit(TRUE))
1653 {
1654 ErrLogPrintf("BioseqFetchInit failed! \n");
1655 printf("Content-type: text/html\r\n\r\n");
1656 printf("<H2>MMDBSRV Error</H2>\n - BioseqFetchInit failed! <p>");
1657 printf("Contact MMDBSRV administrator for this site: %s<p>\n", MAILTO);
1658 exit(1);
1659 } */
1660
1661 SeqAsnLoad();
1662 objmimeAsnLoad();
1663
1664 IndexArgs = -1;
1665 if ((IndexArgs = WWWFindName(info,"db")) >= 0)
1666 {
1667 pcThis = WWWGetValueByIndex(info,IndexArgs);
1668 DispOpt = pcThis[0];
1669 if ((DispOpt != 't') && (DispOpt != 'T'))
1670 {
1671 printf("Content-type: text/html\r\n\r\n");
1672 printf("<H2>MMDBSRV Error</H2>\n - Wrong Database Type db=%c.<p>\n", DispOpt );
1673 printf("Try <a href=\"%s\">WWW-Entrez</a> for this<p>\n", URLHelp);
1674 goto cleanout;
1675 }
1676 }
1677
1678 IndexArgs = -1;
1679 if ((IndexArgs = WWWFindName(info, "form")) >= 0)
1680 {
1681 pcThis = WWWGetValueByIndex(info,IndexArgs);
1682 if ((!StrToInt4(pcThis,&Form)) || (Form != 6))
1683 {
1684 printf("Content-type: text/html\r\n\r\n");
1685 printf("<H2>MMDBSRV Error</H2>\n - Wrong Form Type form=%s.<p>\n", pcThis );
1686 printf("<pre>Only supports form=6</pre><p>\n");
1687 printf("Try <a href=\"%s\">WWW-Entrez</a> for this<p>\n", URLHelp);
1688 goto cleanout;
1689 }
1690 }
1691
1692
1693
1694
1695 IndexArgs = -1;
1696 if ((IndexArgs = WWWFindName(info, "uid")) < 0)
1697 {
1698 printf("Content-type: text/html\r\n\r\n");
1699 printf("<H2>MMDBSRV Error</H2>\n - No Identifier specified:<p>\n<pre>Missing uid=</pre><p>\n");
1700 goto cleanout;
1701 }
1702 else
1703 {
1704 /* loop over entire set of tag=value entries and add all the UID's found together */
1705 /* must handle uid=1234&uid=1OMD&uid=1234,2345,2134&dopt=s&uid=3INS */
1706 NumEntries = WWWGetNumEntries(info);
1707 for (IndexArgs = 0; IndexArgs < NumEntries; IndexArgs++)
1708 {
1709 pcName = WWWGetNameByIndex(info, IndexArgs);
1710 pcThis = WWWGetValueByIndex(info, IndexArgs);
1711
1712 if (StrICmp(pcName, "uid") == 0)
1713 {
1714 /* printf("[%s][%s]\n", pcThis, pcName); */
1715 MakeUIDList(pcThis, &pvnUIDS);
1716 }
1717 }
1718 if (pvnUIDS == NULL)
1719 {
1720 printf("Content-type: text/html\r\n\r\n");
1721 printf("<H2>MMDBSRV Error</H2>\n - UID specified does not match an MMDB-ID or PDB-Code:<p>\n");
1722 goto cleanout;
1723 }
1724 pvnThis = pvnUIDS;
1725 while (pvnThis)
1726 {
1727 iMMDBids++;
1728 pvnThis = pvnThis->next;
1729 }
1730 MMDBids = (Int4Ptr) MemNew((size_t) (sizeof(Int4) * iMMDBids));
1731 pvnThis = pvnUIDS;
1732 iCount = 0;
1733 while (pvnThis)
1734 {
1735 MMDBids[iCount] = (Int4) pvnThis->data.intvalue;
1736 /* printf("%ld \n",(long) MMDBids[iCount]); */
1737 pvnThis = pvnThis->next;
1738 iCount++;
1739 }
1740 }
1741
1742 DispOpt = ' ';
1743 IndexArgs = -1;
1744 if ((IndexArgs = WWWFindName(info, "dopt")) >= 0)
1745 {
1746 pcThis = WWWGetValueByIndex(info,IndexArgs);
1747 switch (pcThis[0])
1748 {
1749 case 's':
1750 case 'S':
1751 DispOpt = 's';
1752 break;
1753 case 'r':
1754 case 'R':
1755 DispOpt = 'r';
1756 break;
1757 case 'i':
1758 case 'I':
1759 DispOpt = 'i';
1760 break;
1761 case 'j':
1762 case 'J':
1763 DispOpt = 'j';
1764 break;
1765 case 'k':
1766 case 'K':
1767 DispOpt = 'k';
1768 break;
1769 case 'a':
1770 case 'A':
1771 DispOpt = 'a';
1772 Save = 1;
1773 break;
1774 default:
1775 {
1776 printf("Content-type: text/html\r\n\r\n");
1777 printf("<H2>MMDBSRV Error</H2>\n - Wrong Display Option Type: dopt=%s.<p>\n", pcThis);
1778 printf("<pre>dopt supports:\n's' Structure summary\n");
1779 printf("'r' RasMol(PDB) format\n'k' Kinemage format\n'i', 'j', or 'a' ASN.1</pre><p>\n");
1780 goto cleanout2;
1781 }
1782 }
1783 }
1784 else
1785 {
1786 DispOpt = 's'; /* structure summary is default when no dopt supplied */
1787 }
1788
1789
1790 IndexArgs = -1;
1791 if ((IndexArgs = WWWFindName(info, "Complexity")) >= 0)
1792 {
1793 pcThis = WWWGetValueByIndex(info,IndexArgs);
1794
1795
1796 for (iCount = 0; iCount < NUM_COMPLEXITY_TYPES; iCount++)
1797 if (StrICmp(pcThis,ComplexityDescriptions[iCount]) == 0)
1798 break;
1799
1800 Complex = ALLMDL;
1801 MaxModels = 1;
1802
1803 switch (iCount)
1804 {
1805 case 0 :
1806 Complex = ONECOORDRES;
1807 break;
1808 case 1:
1809 Complex = ONECOORDATOM;
1810 break;
1811 case 2:
1812 MaxModels = 5;
1813 break;
1814 case 3 :
1815 MaxModels = 10;
1816 break;
1817 case 4 :
1818 MaxModels = INT2_MAX;
1819 break;
1820 case 5:
1821 Complex = ONECOORDATOM;
1822 break;
1823 default:
1824 {
1825 printf("Content-type: text/html\r\n\r\n");
1826 printf("<H2>MMDBSRV Error</H2>\n - Wrong Complexity Type: Complexity=%s.<p>\n", pcThis );
1827 goto cleanout2;
1828 }
1829 }
1830 }
1831
1832 IndexArgs = -1;
1833 if ((IndexArgs = WWWFindName(info, "mdlLvl")) >= 0)
1834 {
1835 pcThis = WWWGetValueByIndex(info, IndexArgs);
1836 Complex = atoi(pcThis);
1837 }
1838
1839 IndexArgs = -1;
1840 if ((IndexArgs = WWWFindName(info, "maxModels")) >= 0)
1841 {
1842 pcThis = WWWGetValueByIndex(info, IndexArgs);
1843 MaxModels = atoi(pcThis);
1844 }
1845
1846 IndexArgs = -1;
1847 if ((IndexArgs = WWWFindName(info, "KinemageColor")) >= 0)
1848 {
1849 pcThis = WWWGetValueByIndex(info, IndexArgs);
1850 KinColor = GetOptionValue(pcThis, NUM_COLOR_TYPES, ColorDescriptions);
1851 }
1852
1853
1854
1855 IndexArgs = -1;
1856 if ((IndexArgs = WWWFindName(info, "KinemageRender")) >= 0)
1857 {
1858 pcThis = WWWGetValueByIndex(info,IndexArgs);
1859 StrToInt4(pcThis, &KinRender);
1860 }
1861
1862 IndexArgs = -1;
1863 if ((IndexArgs = WWWFindName(info, "save")) >= 0)
1864 { /* these don't affect structure summaries */
1865 pcThis = WWWGetValueByIndex(info,IndexArgs);
1866 if (StrICmp(pcThis, "See") == 0)
1867 {
1868 Save = 1; /* sends MIMED-type files to view in ascii-readable form */
1869 }
1870 else if (StrICmp(pcThis, "Save") == 0)
1871 {
1872 Save = 2; /* sends MIMED-type files in raw save form */
1873 }
1874 else if (StrICmp(pcThis, "M") == 0)
1875 {
1876 Save = 3; /* MacSave - not implemented */
1877 }
1878 else if (StrICmp(pcThis, "asntext") == 0)
1879 {
1880 Save = SEND_FILE; /* writes out asn text without the html header */
1881 }
1882 }
1883
1884 IndexArgs = -1;
1885 if ((IndexArgs = WWWFindName(info, "header")) >= 0)
1886 {
1887 pcThis = WWWGetValueByIndex(info,IndexArgs);
1888 if (StrICmp(pcThis, "no") == 0)
1889 {
1890 Save = 2;
1891 }
1892 }
1893
1894
1895 IndexArgs = -1;
1896 if ((IndexArgs = WWWFindName(info, "title")) >= 0)
1897 {
1898 pcThis = WWWGetValueByIndex(info,IndexArgs);
1899 if (StrICmp(pcThis, "no") == 0)
1900 {
1901
1902 GlobalTitles = FALSE;
1903 }
1904 }
1905
1906 IndexArgs = -1;
1907 if ((IndexArgs = WWWFindName(info, "html")) >= 0)
1908 {
1909 pcThis = WWWGetValueByIndex(info,IndexArgs);
1910 if (StrICmp(pcThis, "no") == 0)
1911 {
1912 GlobalNonHtmlOutput = TRUE;
1913 GlobalTitles = FALSE;
1914 }
1915 }
1916
1917
1918
1919 /* call the pertinent Page Sender */
1920
1921 if (DispOpt == 's')
1922 {
1923 iBytes = SendSummaryPage(MMDBids, iMMDBids, Save);
1924 }
1925 else
1926 {
1927 iBytes = SendStructureMIME(DispOpt, MMDBids[0], Save ,
1928 Complex, MaxModels, KinColor, KinRender);
1929 }
1930
1931
1932 MemFree(MMDBids);
1933
1934 /* log first MMDB-id, number of id's asked for, number of bytes sent */
1935 time_now = GetSecs();
1936 TimeNowStr = ctime(&time_now);
1937 TimeNowStr[24] = '\0';
1938 ErrLogPrintf("\n%s|%s|%s|%s|Do %c|Id %ld|No %ld|By %ld|Sv %ld|Cp %ld|Md %ld|Kc %ld|Kr %ld",
1939 WWWGetAddress(info), WWWGetHost(info), WWWGetAgent(info), TimeNowStr,
1940 (char) DispOpt,
1941 (long) MMDBids[0], (long) iMMDBids, (long)iBytes, (long) Save,
1942 (long) Complex, (long) MaxModels, (long) KinColor, (long) KinRender);
1943
1944
1945 CloseMMDBAPI();
1946 MMDBFini();
1947 fflush(stdout);
1948 exit(0);
1949
1950 cleanout2:
1951 MemFree(MMDBids);
1952 CloseMMDBAPI();
1953 MMDBFini();
1954 /* log first MMDB-id, number of id's asked for, number of bytes sent */
1955 time_now = GetSecs();
1956 TimeNowStr = ctime(&time_now);
1957 TimeNowStr[24] = '\0';
1958 ErrLogPrintf("\n#Syntax Error %s|%s|%s|%s|%ld",
1959 WWWGetAddress(info), WWWGetHost(info), WWWGetAgent(info), TimeNowStr,
1960 (long)iBytes);
1961 fflush(stdout);
1962 exit(0);
1963
1964 cleanout:
1965 CloseMMDBAPI();
1966 MMDBFini();
1967 /* log first MMDB-id, number of id's asked for, number of bytes sent */
1968 time_now = GetSecs();
1969 TimeNowStr = ctime(&time_now);
1970 TimeNowStr[24] = '\0';
1971 ErrLogPrintf("\n#Query Not Supported %s|%s|%s|%s|%ld",
1972 WWWGetAddress(info), WWWGetHost(info), WWWGetAgent(info), TimeNowStr,
1973 (long)iBytes);
1974 fflush(stdout);
1975 exit(0);
1976
1977 earlyout:
1978 time_now = GetSecs();
1979 TimeNowStr = ctime(&time_now);
1980 TimeNowStr[24] = '\0';
1981 ErrLogPrintf("\n#Get/Post Error %s|%s|%s|%s|%ld",
1982 WWWGetAddress(info), WWWGetHost(info), WWWGetAgent(info), TimeNowStr,
1983 (long)iBytes);
1984
1985
1986 fflush(stdout);
1987 exit(0);
1988 }
1989
1990 |
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