1 /*
2 * $Id: mmdbsrv.c,v 1.7 2003/01/31 16:05:11 chenj Exp $
3 *
4 *
5 * ===========================================================================
6 *
7 * PUBLIC DOMAIN NOTICE
8 * National Center for Biotechnology Information
9 *
10 * This software/database is a "United States Government Work" under the
11 * terms of the United States Copyright Act. It was written as part of
12 * the author's official duties as a United States Government employee and
13 * thus cannot be copyrighted. This software/database is freely available
14 * to the public for use. The National Library of Medicine and the U.S.
15 * Government have not placed any restriction on its use or reproduction.
16 *
17 * Although all reasonable efforts have been taken to ensure the accuracy
18 * and reliability of the software and data, the NLM and the U.S.
19 * Government do not and cannot warrant the performance or results that
20 * may be obtained by using this software or data. The NLM and the U.S.
21 * Government disclaim all warranties, express or implied, including
22 * warranties of performance, merchantability or fitness for any particular
23 * purpose.
24 *
25 * Please cite the author in any work or product based on this material.
26 *
27 * ===========================================================================
28 *
29 *
30 * Author: Jie Chen
31 *
32 *
33 * $Log: mmdbsrv.c,v $
34 * Revision 1.7 2003/01/31 16:05:11 chenj
35 * minor changes
36 *
37 * Revision 1.6 2003/01/29 19:51:12 chenj
38 * minor changes
39 *
40 * Revision 1.5 2003/01/23 20:51:06 chenj
41 * fixed bug in dealing with obsolete structure
42 *
43 * Revision 1.4 2003/01/22 17:04:45 chenj
44 * change Cn3D 4.0 to 4.1
45 *
46 * Revision 1.3 2003/01/15 17:54:59 chenj
47 * bugs in view of an obsolete structure was fixed
48 *
49 * Revision 1.2 2003/01/15 16:12:04 chenj
50 * Change the font color (replaced by)
51 *
52 * Revision 1.1.1.1 2002/12/04 21:12:07 chenj
53 * Imported sources
54 *
55 *
56 *
57 * This file with others: mmdbgraph.c mmdbutil.c, is used to created new
58 * version of mmdbsrv.cgi which displays the structure features and annotations
59 * with graphics.
60 *
61 * ==========================================================================
62 */
63
64 /**************
65 *mmdbsrv GET Useage:
66 *
67 *db=t&form=6&uid=1OMD&dopt=s - PDB or MMDB-ids allowed
68 *db=t&form=6&uid=1OMD&Dopt=i - launch Cn3D Mime-type - first UID only.
69 *db=t&uid=1234,2345,1254,1232&dopt=s - multiple structure summaries
70 *db=t&uid=3INS,1234,1OMD&dopt=s - mixed id types OK
71 *
72 *Optional, but if wrong, error:
73 * db=t any other is an error message
74 * form=6 4 is an error message - any other ignored
75 *
76 *Required
77 * uid=(list of MMDB ids or PDB ids)
78 *
79 *Optional dopt=
80 * 's' Structure summary
81 * 'r' PDB file
82 * 'k' Kinemage file
83 * 'i' ASN.1 file
84 * Others - error; None assumes 's'
85 *
86 *Optional - Interpreted in Context:
87 * complexity="Cn3D+Subset" ONECOORDATOM, 1
88 * "Virtual+Bond+Model" ONECOORDRES, 1
89 * "Up+to+5+Models" ALLMDL, 5
90 * "Up+to+10+Models" ALLMDL, 10
91 * "All+Models" ALLMDL, 100
92 *
93 * KinemageColor="Molecule+Number" KIN_COLOR_NUMBER
94 * "Secondary+Structure" KIN_COLOR_TYPE
95 * "Thermal+Factor" KIN_COLOR_TEMP
96 * "Element" KIN_COLOR_ATOM
97 * KinemageRender=(integer) - not seen on Struc Summary
98 * save="See"
99 * "s" - saves
100 * "m" MacSave format
101 * header="no" same as save="s"
102 * title="no" - omit title bar and bottom options
103 * html="no"
104 */
105
106
107 /*******************************************
108 MMDBSRV MIRROR installation:
109
110 This describes what you need to run MMDBSRV:
111
112 1] YOUR MMDB DATA DIRECTORIES, e.g.:
113 ...mmdb/mmdbdata/
114 ...mmdb/vastdata/
115
116 These contain the MMDB data on your local filesystem,
117 as obtained from ftp://ncbi.nlm.nih.gov/mmdb/mmdbdata
118 and updated regularly by MIRROR. You can
119 put them in the CGI-BIN or HTTP (HTML) directories
120 if you prefer. If you wish to implement a local
121 decompression/compression scheme see the source code mmdblocl.c.
122
123 2] YOUR CGI-BIN directory & URL, e.g.:
124 ...cgi-bin/mmdb/
125 ...cgi-bin/mmdb/logs/
126 ...cgi-bin/mmdb/data/
127 http://123.456.789.10/cgi-bin/mmdb/
128
129 The first contains the compiled mmdbsrv program and the
130 config file, obtained from
131 ftp://ncbi.nlm.nih.gov/mmdb/www/mmdbsrv
132 The second will contain the log files written out.
133 The third needs sshead.txt, sscode.txt, sstail.txt
134 NOTE - you must edit "sstail.txt"
135 in order to get the proper links to your local
136 copy of help documentation & server.
137
138 3] YOUR HTTP (HTML) directory & URL, e.g.:
139 ...html/mmdb
140 ...html/mmdb/mmdbgifs
141 http://123.456.789.10/mmdb/
142
143 The first contains the html files to launch mmdbsrv,
144 arrow.gif, strucsum.gif and any other gif files, and the
145 associated MMDB help files struchelp.html, cn3d.html,
146 strucinstall.html, vast.html, etc. Master copies are kept
147 at ftp://ncbi.nlm.nih.gov/mmdb/www/http
148 You must hand edit or use scripts or SED to change links from
149 NCBI's to your own in all these HTML files.
150
151 The second contains the GIF library as obtained from
152 the NCBI ftp site ftp://ncbi.nlm.nih.gov/mmdb/mmdbgifs
153
154 6] Your WWW-Server - make it aware of the following
155 new MIME-types:
156 chemical/ncbi-asn1-binary *.val
157 chemical/x-pdb *.ent; *.pdb
158 chemical/x-kinemage *.kin
159
160
161 -----------------------------
162 7]
163 MMDBSRV gets its directory structure; link URLS and CGI call names
164 from a config file.
165 Change these as required and make a config file.
166 Unix ".mmdbrc" or Win "mmdb.ini" from this example:
167
168 Don't change:
169 URLHelp, ENTREZurl, MMDBurl, PDBurl, 3DBurl
170 unless there are broken external links to these.
171
172 -------------------- cut here --------------------
173 [MMDB]
174 ;Database and Index required when local MMDB database is used.
175 ; Database = ./Junk/
176 Database = /net/dorothy/cbb3/mmdb/data/
177 Index = mmdb.idx
178
179 [MMDBSRV]
180 ; File for configuring the MMDB server.
181 ; Base Directory & URLs for HTML documents.
182 HTMLPath = /net/vaster/usr/attic/httpd.local/htdocs/Structure/
183 URLBase = http://inhouse.ncbi.nlm.nih.gov:6224/Structure/
184 URLHelp = http://www.ncbi.nlm.nih.gov/Entrez/
185 ;
186
187 ; Base Directory for CGI-BIN code, data (gifs, html text) and logs.
188 CGIPath = /net/vaster/usr/attic/httpd.local/cgi-bin/Structure/
189 URLcgi = http://inhouse.ncbi.nlm.nih.gov:6224/cgi-bin/Structure/
190 CGIname = mmdbsrv
191 DATApath = ./data/
192 LOGpath = ./logs/
193 ;
194
195 ; Base Directory for MMDB-gif set
196 GIFpath = /net/vaster/usr/attic/httpd.public/htdocs/Structure/mmdbgifs/
197 GIFurl = http://www.ncbi.nlm.nih.gov/Structure/mmdbgifs/
198 ;
199
200 ; URL's for links to Entrez, VAST.
201 ; ENTREZurl = http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query
202 ENTREZurl = http://www.ncbi.nlm.nih.gov/entrez/query.fcgi
203 VASTurl = http://inhouse.ncbi.nlm.nih.gov:6224/cgi-bin/Structure/vastsrv
204 MMDBurl = http://www.ncbi.nlm.nih.gov/Structure/
205 PDBurl = http://www.pdb.bnl.gov/index.html
206 TDBurl = http://www.pdb.bnl.gov/cgi-bin/opdbshort
207
208 ; Location of gunzip function.
209 Gunzip = /usr/sbin/gunzip
210
211 ;
212 MAILto = info@ncbi.nlm.nih.gov
213 ;
214 [VAST]
215 ;Database required for local VAST fetches.
216 ;Database = /net/vaster/usr/people6/madej/vastdata.binary/
217 Database = /net/dorothy/cbb3/vast/data/
218
219 ; URL for link to taxonomy database (wgetorg for retrieval)
220 [TAXLINK]
221 TAXurl = http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg
222
223 [CD]
224 DARTdatabase = CDart
225 LOGINname = lewisg
226 PASSwd = lewisg
227 INITpath = /netopt/structure/ini/.odbc.sassy.ini
228 LIBpath = /opt/machine/merant/lib
229 CDDurl = http://scarecrow:5701/Structure/cdd/cddsrv.cgi
230
231 -------------------- cut here --------------------
232 ********************************************/
233
234 #include <ncbi.h>
235 #include <ncbiwww.h>
236 #include <sys/resource.h>
237 #include <mmdbapi.h>
238 #include <objmime.h>
239 #include "mmdbuti.h"
240 #include <sys/utsname.h>
241
242 #ifdef OS_UNIX
243 #include <signal.h>
244 #include <unistd.h>
245 #define CPUTIME_MAX 120
246 #endif
247
248
249 #define NUM_COMPLEXITY_TYPES 6
250 static char *ComplexityDescriptions[] =
251 {"Virtual Bond Model","All Atom Model","Up to 5 Models",
252 "Up to 10 Models","All Models","Cn3D Subset"};
253
254 #define NUM_COLOR_TYPES 5
255 static char *ColorDescriptions[] =
256 {"","Molecule Number","Secondary Structure","Thermal Factor","Element"};
257
258 /* the config file DATApath is used for the location of these files */
259
260 #define HEADFILE "sshead.txt" /* Structure Summary Header File */
261
262 #define TAILFILE "sstail.txt" /* Structure Summary Tail File */
263
264 #define CHAIN_CHOICE_NUM 1
265 #define ORG_CHOICE_NUM 6
266
267 /* some defines needed for the taxonomy code */
268
269 #define TAX_ID_CHOICE_NUM 0
270 #define MAX_CHAINS 128
271
272 static WWWInfoPtr info = NULL;
273
274 static Boolean GlobalTitles = TRUE;
275 static Boolean GlobalNonHtmlOutput = FALSE;
276
277 static Char HTMLPath[PATH_MAX];
278 static Char URLBase[PATH_MAX];
279 static Char URLHelp[PATH_MAX];
280 static Char HELPname[PATH_MAX];
281 Char Database[PATH_MAX];
282
283 static Char CGIPath[PATH_MAX];
284 static Char URLcgi[PATH_MAX];
285 static Char URLcgi_absolute_path[PATH_MAX];
286 static Char CGIName[256];
287 static Char DATApath[PATH_MAX];
288 static Char LOGpath[PATH_MAX];
289
290 Char ENTREZurl[PATH_MAX];
291 Char VASTurl[PATH_MAX];
292 static Char MMDBurl[PATH_MAX];
293 static Char PDBurl[PATH_MAX];
294 static Char TDBurl[PATH_MAX];
295 static Char TAXurl[PATH_MAX];
296 static Char MAILto[256];
297 Char MAILTO[PATH_MAX];
298 static Char ARROW[PATH_MAX];
299
300 static Char DART[PATH_MAX];
301 static Char LOGIN[PATH_MAX];
302 static Char PASSWD[PATH_MAX];
303 static Char INITpath[PATH_MAX];
304 static Char LIBpath[PATH_MAX];
305 Char CDDurl[PATH_MAX];
306
307
308 /* Global Variables defined by J. Chen */
309
310 Boolean psok = TRUE;
311 Dart_Connect *dartcon;
312
313 extern Int4 ModelMapOrImg(Boolean ismap, gdImagePtr im, Int4 uid, PMSD pmsd,
314 Int4 chain1, Int4 chain2, IntervalHead **DomHead, Int4Ptr DomIdx, FILE *File);
315
316 /*****************************************************
317 * WWWPrintFileData looks in the current CGI-BIN directory
318 * or the "data" subdirectory for the data file.
319 * and prints it out to pFile
320 */
321
WWWPrintFileData(CharPtr FName,FILE * pFile)322 static void WWWPrintFileData(CharPtr FName, FILE *pFile)
323 {
324
325 FILE *f = NULL;
326 Char fullpath [PATH_MAX];
327 CharPtr ptr;
328 Char pcBuf[1024];
329
330 fullpath[0] = '\0';
331 StringCpy(fullpath, DATApath); /* look in DATApath */
332 StringCat(fullpath, FName);
333 f = FileOpen (fullpath, "r");
334 if (f == NULL) {
335 f = FileOpen (FName, "r"); /* look in curent */
336 if (f == NULL) { /* look in ./data/ */
337 ProgramPath (fullpath, sizeof (fullpath) - 1);
338 ptr = StringRChr (fullpath, DIRDELIMCHR);
339 if (ptr != NULL) {
340 *ptr = '\0';
341 }
342 FileBuildPath (fullpath, "data", FName);
343 f = FileOpen (fullpath, "r");
344 if (f == NULL) {
345 return;
346 }
347 }
348 }
349
350 do {
351 pcBuf[0] = '\0';
352 ptr = fgets(pcBuf, (size_t)1024, f);
353 if (ptr) fprintf(pFile, ptr);
354 } while (ptr);
355
356 FileClose(f);
357 return;
358 }
359
360
361 static Boolean
StrToInt4(CharPtr str,Int4Ptr longval)362 StrToInt4 (CharPtr str, Int4Ptr longval)
363 {
364 Nlm_Int2 i;
365 Nlm_Int2 len;
366 Nlm_Char local [64];
367 Nlm_Boolean nodigits;
368 long int val;
369
370 if (longval != NULL) {
371 *longval = (Nlm_Int4) 0;
372 }
373 len = (Nlm_Int2) Nlm_StringLen (str);
374 if (len == 0)
375 return FALSE;
376
377 nodigits = TRUE;
378 for (i = 0; i < len; i++)
379 {
380 Nlm_Char ch;
381
382 ch = str [i];
383 if ('0' <= ch && ch <= '9')
384 nodigits = FALSE;
385 else if ( !/*!!*/ (ch == ' ' || ch == '+' || ch == '-') || nodigits==FALSE)
386 return FALSE;
387 }
388 if (nodigits)
389 return FALSE;
390 if (longval != NULL)
391 {
392 Nlm_StringNCpy (local, str, sizeof (local));
393 if (sscanf (local, "%ld", &val) == 1)
394 *longval = val;
395 }
396 return TRUE;
397 }
398
399
400
ConvertMMDBUID(CharPtr pcString)401 static Int4 ConvertMMDBUID(CharPtr pcString)
402 {
403 Int4 iUID;
404 unsigned i;
405 CharPtr pcTemp = NULL;
406
407 if (pcString == NULL)
408 return 0;
409
410 iUID = 0;
411 pcTemp = StringSave(pcString);
412
413 for (i=0; i< StrLen(pcTemp); i++) pcTemp[i] = toupper(pcTemp[i]);
414 CleanSpaces(pcTemp);
415 if (!StrToInt4(pcTemp, &iUID))
416 iUID = constructLiveOrDeadMmdbIdForPdbId(pcTemp, &psok, Database);
417
418 MemFree(pcTemp);
419 return iUID;
420 } /* ConvertMMDBUID() */
421
422
MakeUIDList(CharPtr pcString,ValNodePtr PNTR ppvnUIDS)423 static void MakeUIDList(CharPtr pcString, ValNodePtr PNTR ppvnUIDS)
424 {
425 CharPtr Ptr = NULL;
426 CharPtr Ptr2 = NULL, Ptr3 = NULL;
427 Char SavedChar = NULL, SavedChar3 = NULL;
428 Int4 Uid = 0, Uid1, Uid2, tmpuid1, tmpuid2;
429
430 Ptr = SkipSpaces(pcString);
431 if (*Ptr == NULLB)
432 return;
433
434 while (*Ptr)
435 {
436 Ptr2 = SkipToSet(Ptr," ,");
437 SavedChar = *Ptr2;
438 *Ptr2 = NULLB;
439
440 Ptr3 = SkipToSet(Ptr, " -");
441 if (*Ptr3 != NULLB) {
442 SavedChar3 = *Ptr3;
443 *Ptr3 = NULLB;
444 Uid1 = 0;
445 Uid1 = ConvertMMDBUID(Ptr);
446 if (Uid1 <0) tmpuid1 = -Uid1;
447 else tmpuid1 = Uid1;
448 *Ptr3 = SavedChar3;
449 Ptr = SkipSet(Ptr3, " -");
450 Uid2 = 0;
451 Uid2 = ConvertMMDBUID(Ptr);
452 if (Uid2<0) tmpuid2 = -Uid2;
453 else tmpuid2 = Uid2;
454 for (Uid = tmpuid1; Uid <= tmpuid2; Uid++) {
455 if (Uid == -Uid1) Uid = Uid1;
456 if (Uid == -Uid2) Uid = Uid2;
457 if (Uid) ValNodeAddInt(ppvnUIDS, 0, Uid);
458 }
459 }
460 else {
461 Uid = ConvertMMDBUID(Ptr);
462 if (Uid) ValNodeAddInt(ppvnUIDS, 0, Uid);
463 }
464
465 *Ptr2 = SavedChar;
466 Ptr = SkipSet(Ptr2," ,");
467 }
468
469 return;
470 }
471
472
GetOptionValue(CharPtr Value,Int4 NumElements,CharPtr * ElementText)473 static Int4 GetOptionValue(CharPtr Value, Int4 NumElements, CharPtr *ElementText)
474 {
475 Int4 count, Len;
476 Int4 valnum;
477
478 if (StrToInt4(Value, &valnum))
479 return(valnum);
480
481 Len = StringLen(Value);
482 for (count = 0; count < NumElements; count++)
483 if (StrNICmp(ElementText[count],Value, Len) == 0)
484 break;
485
486 if (count == NumElements)
487 return -1;
488
489 return(count);
490 }
491
492
493 /* J. Chen (begin) */
494
495
496 static void
PrintStrucViewNew_page(Int4 uid,FILE * File)497 PrintStrucViewNew_page(Int4 uid, FILE *File)
498 {
499
500 fprintf(File, "<table border=0 cellpadding=0 cellspacing=0>\n");
501 fprintf(File, "<FORM METHOD=post ACTION=\"%s%s\">\n", URLcgi,CGIName);
502 fprintf(File, "<tr>\n");
503 fprintf(File, "<TD class=SMALL1>\n");
504
505 fprintf(File, "<strong>");
506 fprintf(File, "<INPUT TYPE=submit NAME= submit VALUE=\"View 3D Structure\">");
507 fprintf(File, " of </strong>\n");
508
509 fprintf(File, "<SELECT NAME=Complexity>\n");
510 fprintf(File, "<OPTION VALUE=\"Cn3D Subset\">Best Model\n");
511 fprintf(File, "<OPTION VALUE=\"Virtual Bond Model\">Virtual Bond\n");
512 fprintf(File, "<OPTION VALUE=\"All Models\">All Models\n");
513 fprintf(File, "</SELECT>\n");
514
515 fprintf(File, "<strong> with </strong>\n");
516
517 fprintf(File, "<SELECT NAME=dopt>\n");
518 fprintf(File, "<OPTION VALUE=j>Cn3D\n");
519 fprintf(File, "<OPTION VALUE=r>RasMol\n");
520 fprintf(File, "<OPTION VALUE=k>Mage\n");
521 fprintf(File, "</SELECT>\n");
522
523 fprintf(File, "<SELECT NAME=save>\n");
524 fprintf(File, "<OPTION VALUE=Viewer>Display\n");
525 fprintf(File, "<OPTION VALUE=See>See File\n");
526 fprintf(File, "<OPTION VALUE=Save>Save File\n");
527 fprintf(File, "</SELECT>\n");
528
529 fprintf(File, "<img src=\"/Structure/new.gif\" alt=\"New\">\n");
530 fprintf(File, "<a href=\"/Structure/CN3D/cn3d.shtml\">");
531 fprintf(File, "<B><I>Get Cn3D 4.1!</I></B></a>");
532
533 if (uid <0) uid = -uid;
534 fprintf(File, "<INPUT TYPE=HIDDEN NAME=uid VALUE=%d>\n", uid);
535 fprintf(File, "<INPUT TYPE=HIDDEN NAME=form VALUE=6>\n");
536 fprintf(File, "<INPUT TYPE=HIDDEN NAME=db VALUE=t>\n");
537 fprintf(File, "<INPUT TYPE=HIDDEN NAME=KinemageColor VALUE=\"Molecule Number\">\n");
538 fprintf(File, "<INPUT TYPE=HIDDEN NAME=KinemageRender VALUE=63>\n");
539
540 fprintf(File, "</td>\n</tr>\n");
541 fprintf(File, "</FORM>\n");
542 fprintf(File, "</table>\n");
543
544 } /* end PrintStrucViewNew_page */
545
546
547
548
549 #define MMDBOpt "SUBMIT=y&db=structure&orig_db=structure&term="
550
551 static void
PrintStrucInfoNew(PDNMS ModelStruc,Int4 LiveUid,unsigned short Live,CharPtr tax_save,Int4 uid,FILE * File)552 PrintStrucInfoNew(PDNMS ModelStruc, Int4 LiveUid, unsigned short Live,
553 CharPtr tax_save, Int4 uid, FILE *File)
554 {
555 Int2 chaincnt;
556 Int4 depyear, depday;
557 PMSD pmsdThis = NULL;
558 BiostrucSourcePtr pbssThis = NULL;
559 ValNodePtr pvnThis = NULL;
560 BiostrucHistoryPtr pbshThis = NULL;
561 CharPtr pcAuthors = NULL;
562
563 if (!ModelStruc)
564 return;
565
566 pmsdThis = (PMSD) ModelStruc->data.ptrvalue;
567 pvnThis =ValNodeFindNext(pmsdThis->pbsBS->descr,NULL,BiostrucDescr_history);
568
569 if (pvnThis) {
570 pbshThis = (BiostrucHistoryPtr) pvnThis->data.ptrvalue;
571 pbssThis = pbshThis->data_source;
572 }
573
574
575 fprintf(File, "\n<!-- Structure Info table -->\n");
576 fprintf(File, "<TABLE width=800 BORDER=0 CELLPADDING=3 CELLSPACING=0 bgcolor=#FFFFCC>\n\n");
577
578 fprintf(File, "<TR>\n");
579 fprintf(File, "<TD>\n");
580
581 fprintf(File, "<table> <!-- 1st subtable, in the first layer -->\n\n");
582
583 /* insert a blank row in the table, for spacing */
584 fprintf(File, "<tr>\n<td VALIGN=TOP NOWRAP> </td>\n</tr>\n\n");
585
586 fprintf(File, "<tr>\n");
587 fprintf(File, "<td VALIGN=TOP NOWRAP ALIGN=RIGHT class=H4>\n");
588 pvnThis =ValNodeFindNext(pmsdThis->pGraphDescr,NULL,BiomolDescr_pdb_comment);
589 chaincnt = ChainCount(pmsdThis);
590 fprintf(File, "<strong>Description:</strong></td>\n");
591 fprintf(File, "<td class=\"TEXT\">%s.",pmsdThis->pcChemName);
592
593 if (!chaincnt) {
594 fprintf(File, "<br><font color=red>");
595 fprintf(File, "There is no protein and nucleotide chains in this structure.</font></br>\n");
596 }
597 fprintf(File, "</td>\n</tr>\n\n");
598
599
600 pcAuthors = AuthorListPDB(pmsdThis->pbsBS);
601 if (pcAuthors) {
602 fprintf(File, "<tr>\n");
603 fprintf(File, "<td VALIGN=TOP NOWRAP ALIGN=RIGHT class=H4>");
604 fprintf(File, "<strong>Deposition:</strong></td>\n");
605 fprintf(File, "<td class=\"TEXT\">%s, ", pcAuthors);
606
607 depyear = pbssThis->database_entry_date->data[1];
608 depday = pbssThis->database_entry_date->data[3];
609 fprintf(File, "%2d-%3s-%02d</td>\n",(int) depday,
610 NCBI_months[pbssThis->database_entry_date->data[2] - 1],
611 (int) depyear%100);
612
613 fprintf(File, "</tr>\n\n");
614 fflush(File);
615 MemFree(pcAuthors);
616 }
617 else {
618 fprintf(File, "<tr>\n");
619 fprintf(File, "<td><H2>");
620 fprintf(File, "No Authors' information -- Contact structure group.");
621 fprintf(File, "</H2></td>\n</tr>\n");
622 fprintf(File, "</table>\n");
623 exit(1);
624 }
625
626
627 if (tax_save != NULL) fprintf(File, "%s", tax_save);
628 else if (pmsdThis->pcPdbSource) {
629 fprintf(File, "<tr>\n");
630 fprintf(File, "<td NOWRAP class=H4>");
631 fprintf(File, "<strong>Source</strong>:</td>\n");
632 fprintf(File, "<td class=\"TEXT\">%s</td>\n</tr>\n",
633 pmsdThis->pcPdbSource);
634 }
635
636 fprintf(File, "<tr>\n");
637 fprintf(File, "<td VALIGN=TOP NOWRAP ALIGN=RIGHT class=H4>");
638 fprintf(File, "<strong>Reference:</strong></td>\n");
639 fprintf(File, "<td class=TEXT>\n");
640 fprintf(File, "<A HREF=\"%s?db=structure&cmd=Display&dopt=structure_pubmed&from_uid=%ld\">PubMed</A>\n",
641 ENTREZurl, (long) pmsdThis->iMMDBid );
642 if (!Live && (pmsdThis->iMMDBid == LiveUid)) {
643 fprintf(File, "<font class=H4><strong> MMDB:</strong></font>\n\n");
644 fprintf(File, "<A HREF=\"%s?%s%s\">%d</A>",
645 ENTREZurl, MMDBOpt, pmsdThis->pcPDBName, pmsdThis->iMMDBid);
646 }
647 else {
648 fprintf(File, "</td>\n</tr>\n\n");
649 fprintf(File, "<tr>\n");
650 fprintf(File, "<td VALIGN=TOP NOWRAP ALIGN=RIGHT class=H4>");
651 fprintf(File, "<strong>MMDB:</strong></td>\n");
652 fprintf(File, "<td class=TEXT>\n");
653 fprintf(File, "<A HREF=\"%s?%s%s\">%d</A>",
654 ENTREZurl, MMDBOpt, pmsdThis->pcPDBName, pmsdThis->iMMDBid);
655
656 /* J. Chen, for an obsolete or removed model */
657 if (psok && Live) {
658 fprintf(File, "\n<FONT color=MAROON>(</FONT>");
659 fprintf(File, "<a href=\"%s%s#ObsoNbr\">", URLBase, HELPname);
660 fprintf(File, "<FONT color=MAROON>obsolete, from archive</FONT></a>");
661 fprintf(File, "<FONT color=MAROON>)</FONT>\n");
662 }
663 else if (psok && pmsdThis->iMMDBid != LiveUid) {
664 fprintf(File, "\n<FONT color=red>(</FONT>");
665 fprintf(File, "<a href=\"%s%s#ObsoNbr\">", URLBase, HELPname);
666 fprintf(File, "<FONT color=MAROON>replaced by:</FONT></a> ");
667 fprintf(File, "<A HREF=\"%s%s?uid=%d&form=6&db=t&Dopt=s\">",
668 URLcgi, CGIName, LiveUid);
669 fprintf(File, "<FONT COLOR=RED>%d</FONT></a>", LiveUid);
670 fprintf(File, "<FONT color=red>)</FONT>\n");
671 }
672 }
673
674 fprintf(File, "<font class=H4>");
675 fprintf(File, "<strong> PDB:</strong></font>\n<spacer size=4>\n");
676 fprintf(File, "<A HREF=\"%s=%s\">%s</A>\n",
677 TDBurl, pmsdThis->pcPDBName, pmsdThis->pcPDBName);
678
679 fprintf(File, "</td>\n</tr>\n");
680
681 /* insert a blank row in the table, for spacing */
682 fprintf(File, "\n<tr>\n");
683 fprintf(File, "<td VALIGN=TOP NOWRAP><BR></td>\n");
684 fprintf(File, "</tr>\n");
685 fprintf(File, "</table> <!-- end of first subtable -->\n");
686
687 fprintf(File, "</TD>\n</TR>\n\n");
688 fprintf(File, "<TR>\n<TD>\n\n <!-- 2nd subtable -->\n");
689 PrintStrucViewNew_page(uid, File);
690 fprintf(File, " <!-- end of 3rd subtable -->\n");
691 fprintf(File, "\n</TD>\n</TR>\n");
692
693 /* J. Chen: close the TABLE */
694 fprintf(File, "</TABLE>\n");
695
696 return;
697
698 } /* end PrintStrucInfoNew */
699
700
701
702
703 static void
PrintChainsMap(BiostrucPtr bsp,PDNMS ModelStruc,Int2 chain1,FILE * File)704 PrintChainsMap (BiostrucPtr bsp, PDNMS ModelStruc, Int2 chain1, FILE *File)
705 {
706 BiostrucFeaturePtr domain_bfp = NULL;
707 Boolean hasDomain = FALSE;
708 Int4 uid, imgsize = 0, *DomIdx;
709 Int2 i, y, cnt=0, chain2;
710 PMSD pmsd;
711 PDNMM pdnmm, pdnmm1;
712 IntervalHead **DomHead;
713
714 pmsd = (PMSD) ModelStruc->data.ptrvalue;
715 pdnmm = pmsd->pdnmmHead;
716 if (pdnmm == NULL) return;
717 cnt = ChainCount(pmsd);
718 if (!cnt) return;
719
720 DomHead = (IntervalHead **) MemNew (cnt * sizeof(IntervalHead *));
721 for (i=0; i< cnt; i++) DomHead[i] = NULL;
722
723 CalDomIdx(pdnmm, &DomIdx);
724 GetDomFeaPtr(bsp, &hasDomain, &domain_bfp);
725 CheckDomColIdx(domain_bfp, pdnmm, DomHead,DomIdx,NULL,hasDomain,FALSE);
726
727 GroupingChains(pmsd);
728
729 pdnmm = pmsd->pdnmmHead;
730 pdnmm1 = PdnmmforChainX(pdnmm, chain1);
731 pdnmm = pdnmm1;
732
733 uid = (Int4)pmsd->iMMDBid;
734 chain2 = MIN(cnt, chain1+ChainPerImg-1);
735
736 fprintf(File, "<map name=chain_map>\n");
737 y =ModelMapOrImg(TRUE,NULL,uid,pmsd,chain1,chain2,DomHead,DomIdx,File);
738 imgsize = y + FontBH + 80;
739
740 fprintf(File, "</map>\n");
741 /*
742 {
743 struct utsname name;
744 char *chp = getenv("SERVER_NAME");
745
746 uname(&name);
747 if (!strcmp(chp,"web.ncbi.nlm.nih.gov") &&
748 !strcmp(name.nodename, "rosencrantz"))
749 strcpy(URLcgi_absolute_path,
750 "http://rosencrantz.nlm.nih.gov:2441/Structure/mmdb/");
751 else if (!strcmp(chp, "web.ncbi.nlm.nih.gov") &&
752 !strcmp(name.nodename, "guildenstern"))
753 strcpy(URLcgi_absolute_path,
754 "http://guildenstern.nlm.nih.gov:2441/Structure/mmdb/");
755 else if (!strcmp(chp, "www.ncbi.nlm.nih.gov") &&
756 !strcmp(name.nodename, "rosencrantz"))
757 strcpy(URLcgi_absolute_path,
758 "http://rosencrantz.nlm.nih.gov:80/Structure/mmdb/");
759 else if (!strcmp(chp, "www.ncbi.nlm.nih.gov") &&
760 !strcmp(name.nodename, "guildenstern"))
761 strcpy(URLcgi_absolute_path,
762 "http://guildenstern.nlm.nih.gov:80/Structure/mmdb/");
763 else strcpy(URLcgi_absolute_path, URLcgi);
764
765 }
766 */
767
768 strcpy(URLcgi_absolute_path, URLcgi);
769
770
771 fprintf(File, "<img src=\"%s%s?cmd=graph&uid=%d&chbeg=%d&chend=%d&imgsize=%d\" usemap=#chain_map border=0 ismap>\n",
772 URLcgi_absolute_path, CGIName, uid, chain1, chain2, imgsize);
773
774 MemFree(DomIdx);
775
776 } /* end PrintChainsMap */
777
778
779
780
PrintPageView(Int4 UidNum,Int4Ptr Uids,Int4 TotalPg,Int2 PageCur,FILE * File)781 static void PrintPageView(Int4 UidNum, Int4Ptr Uids, Int4 TotalPg, Int2 PageCur,FILE *File)
782 {
783 Int2 i, tmpuid;
784
785 if (TotalPg == 1) return;
786
787 fprintf(File, "<FORM name=pagequery method=post action=\"%s%s\">\n",
788 URLcgi, CGIName);
789 if (UidNum == 1) {
790 if (Uids[0] <0) tmpuid = -Uids[0];
791 else tmpuid = Uids[0];
792 fprintf(File,"<INPUT TYPE=HIDDEN NAME=uid VALUE=%d>\n",tmpuid);
793 }
794 else {
795 if (Uids[0] <0) tmpuid = -Uids[0];
796 else tmpuid = Uids[0];
797 fprintf(File, "<INPUT TYPE=HIDDEN NAME=uid VALUE=%d",tmpuid);
798 for (i=1; i< UidNum; i++) {
799 if (Uids[i] <0) tmpuid = -Uids[i];
800 else tmpuid = Uids[i];
801 fprintf(File, ",%d", Uids[i]);
802 }
803 fprintf(File, ">\n");
804 }
805 fprintf(File, "<INPUT TYPE=HIDDEN NAME=form VALUE=6>\n");
806 fprintf(File, "<INPUT TYPE=HIDDEN NAME=db VALUE=t>\n");
807 fprintf(File, "<input type=hidden name=page VALUE=%d>\n", PageCur);
808 fprintf(File, "</FORM>\n");
809
810 fprintf(File, "<table>\n<tr>\n");
811 fprintf(File, "<td width=\"270\" align=right class=H4><strong>Summary page:</strong></td>\n");
812 fprintf(File, "<td width=\"60\" class=TEXT>");
813 if (PageCur == 1)
814 fprintf(File, "Previous</td>\n");
815 else
816 fprintf(File, "<a href=\"about:\" onClick=\"pageview(\'%d\'); return false\">Previous</a></td>\n",
817 PageCur-1);
818 for (i = 1; i<= TotalPg; i++)
819 {
820 if (i==PageCur)
821 fprintf(File, "<td width=\"20\" class=TEXT><strong>%d</strong></td>\n",i);
822
823 else {
824 fprintf(File, "<td width=\"20\" class=TEXT>");
825 fprintf(File, "<a href=\"about:\" onClick=\"pageview(\'%d\'); return false;\">%d</a></td>\n", i, i);
826 }
827 }
828
829 fprintf(File, "<td width=\"60\" class=TEXT>");
830 if (PageCur == TotalPg)
831 fprintf(File, "Next</td>\n");
832 else
833 fprintf(File, "<a href=\"about:\" onClick=\"pageview(\'%d\'); return false\">Next</a></td>\n",
834 PageCur+1);
835 fprintf(File, "</tr>\n</table>\n");
836
837 fprintf(File, "<script>\n");
838 fprintf(File, "function pageview(page)\n");
839 fprintf(File, "{\n");
840 fprintf(File, "document.pagequery.reset();\n");
841 fprintf(File, "document.pagequery.page.value=page;\n");
842 fprintf(File, "document.pagequery.submit();\n");
843 fprintf(File, "}\n");
844 fprintf(File, "</script>\n");
845
846 }
847
848
849
850
851
852 /* J. Chen (end) */
853
854
855 /* Utility routine needed below. Return a vector marking the distinct integers
856 * appearing in the input array. A naive algorithm is used since we never expect
857 * the array size 'n' to be large. If an entry vec[i] is 0, this means it is
858 * a duplicate. If vec[i] > 0 then this is the first occurrence of the number,
859 * and the value vec[i] is the number of times the corresponding number nums[i]
860 * appears.
861 */
862
863 static void
mark_distinct(Int4Ptr nums,Int2Ptr vec,Int2 n)864 mark_distinct(Int4Ptr nums, Int2Ptr vec, Int2 n)
865 {
866 Int2 i, j;
867
868 if (n == 0)
869 return;
870
871 /* initialize the vector */
872 for (i = 0; i < n; i++)
873 vec[i] = 1;
874
875 for (i = 1; i < n; i++) {
876 for (j = 0; j < i; j++) {
877 if (nums[i] == nums[j]) {
878 vec[i] = 0;
879 vec[j]++;
880 break;
881 }
882 }
883 }
884
885 } /* end mark_distinct */
886
887
888 /* Old version of DumpMime, preserved for compatibility with Cn3D v1.0. */
889
DumpMime_v1(AsnIoPtr aip,CharPtr title,Int2 style,Int2 choice,VoidPtr datum)890 static void DumpMime_v1(AsnIoPtr aip, CharPtr title, Int2 style, Int2 choice, VoidPtr datum)
891 {
892 NcbiMimeAsn1Ptr mime;
893 EntrezGeneralPtr egp;
894
895 mime = (NcbiMimeAsn1Ptr) ValNodeNew(NULL);
896 mime->choice = NcbiMimeAsn1_entrez;
897 egp = EntrezGeneralNew();
898 mime->data.ptrvalue = (VoidPtr) egp;
899 egp->Data_data = ValNodeNew(NULL);
900 egp->title = StringSave(title);
901 egp->style = style;
902 egp->Data_data->choice = choice;
903 egp->Data_data->data.ptrvalue = datum;
904
905 NcbiMimeAsn1AsnWrite(mime, aip, NULL);
906 AsnIoFlush(aip);
907
908 egp->Data_data->data.ptrvalue = NULL; /* for clean free */
909 NcbiMimeAsn1Free(mime);
910
911 } /* end DumpMime_v1 */
912
913
914
915 /* yanli */
DumpMime(AsnIoPtr aip,CharPtr title,VoidPtr datum)916 static void DumpMime(AsnIoPtr aip, CharPtr title, VoidPtr datum)
917 {
918 NcbiMimeAsn1Ptr mime;
919
920 mime = (NcbiMimeAsn1Ptr) ValNodeNew(NULL);
921 mime->choice = NcbiMimeAsn1_strucseq;
922 mime->data.ptrvalue= datum;
923
924 NcbiMimeAsn1AsnWrite(mime, aip, NULL);
925 AsnIoFlush(aip);
926
927 mime->data.ptrvalue=NULL ; /* for clean free */
928 NcbiMimeAsn1Free(mime);
929 }
930
931
932 #define LAUNCH_VIEWER 0
933 #define SEE_FILE 1
934 #define SAVE_FILE 2
935 #define SEND_FILE 4
936
937 /* Handle the various View/See/Save file options. */
938
939 static Int4
SendStructureMIME(Char Filetype,Int4 uid,Int4 Mime,Int4 Complexity,Int4 Models,Int4 Color,Int4 Render)940 SendStructureMIME(Char Filetype, Int4 uid, Int4 Mime, Int4 Complexity,
941 Int4 Models, Int4 Color, Int4 Render)
942 {
943 BiostrucPtr bsp;
944 PDNMS ModelStruc;
945 Int4 error_flag = 0;
946 AsnIoPtr aip;
947
948 /* yanli start */
949 NcbiMimeAsn1Ptr mime;
950 BiostrucSeqPtr bssp;
951 SeqEntryPtr sep;
952
953 bsp = (BiostrucPtr) openBSP(uid, Complexity, Models, TRUE, FALSE, FALSE,
954 &psok, Database);
955
956 if (bsp == NULL) {
957 char str[10];
958
959 sprintf(str, "%d", uid);
960 PrtMes(NULL, "MMDBSRV",
961 "No such structure available on this MMDB server: uid=", str, TRUE);
962
963 return 0;
964 }
965
966 sep = (SeqEntryPtr) constructSeqEntryForMmdbId(uid, TRUE, Database);
967 if (sep == NULL) {
968 char str[10];
969
970 sprintf(str, "%d", uid);
971 PrtMes(NULL, "MMDBSRV",
972 "No sequence information available on this MMDB server, maybe an obsolete structure: uid=", str, TRUE);
973
974 return 0;
975 }
976
977 bssp = BiostrucSeqNew();
978 bssp->structure = bsp;
979 ValNodeLink(&(bssp->sequences), sep);
980
981 mime = (NcbiMimeAsn1Ptr) ValNodeNew(NULL); /* yanli */
982 mime->choice = NcbiMimeAsn1_strucseq;
983 mime->data.ptrvalue = bssp;
984
985 /* the following headers are format-independent */
986 switch (Mime) {
987 case SAVE_FILE:
988 printf("Content-type: application/octet-stream\r\n\r\n");
989 break;
990 case SEE_FILE:
991 printf ("Content-type: text/html\r\n\r\n");
992 printf ("<HTML><PRE>\r\n");
993 break;
994 case SEND_FILE:
995 printf ("Content-type: text/html\r\n\r\n");
996 break;
997 }
998
999
1000 if (Filetype == 'j') {
1001 /* Cn3D v2.0 asn.1 format */
1002 switch (Mime) {
1003 case LAUNCH_VIEWER:
1004 printf ("Content-type: chemical/ncbi-asn1-binary\r\n\r\n");
1005 aip = AsnIoNew(ASNIO_BIN_OUT, stdout, NULL, NULL, NULL);
1006 DumpMime(aip, "MIME", bssp);
1007 break;
1008 case SAVE_FILE:
1009 aip = AsnIoNew(ASNIO_BIN_OUT, stdout, NULL, NULL, NULL);
1010 NcbiMimeAsn1AsnWrite(mime, aip, NULL);
1011 break;
1012 case SEE_FILE:
1013 aip = AsnIoNew(ASNIO_TEXT_OUT, stdout, NULL, NULL, NULL);
1014 NcbiMimeAsn1AsnWrite(mime, aip, NULL);
1015 break;
1016 case SEND_FILE:
1017 aip = AsnIoNew(ASNIO_TEXT_OUT, stdout, NULL, NULL, NULL);
1018 NcbiMimeAsn1AsnWrite(mime, aip, NULL);
1019 break;
1020 }
1021
1022 AsnIoReset(aip);
1023 AsnIoClose(aip);
1024 ClearStructures();
1025
1026 }
1027 else if (Filetype == 'i') {
1028 /* Cn3D v1.0 asn.1 format. Included for backwards compatibility, in case users
1029 * want to stick with their old Cn3D for some reason. */
1030 switch (Mime) {
1031 case LAUNCH_VIEWER:
1032 printf ("Content-type: chemical/ncbi-asn1-binary\r\n\r\n");
1033 /* printf ("Content-disposition: filename=\"%d.val\"\r\n\r\n", uid);*/
1034 aip = AsnIoNew(ASNIO_BIN_OUT, stdout, NULL, NULL, NULL);
1035 DumpMime_v1(aip, "MIME", Entrez_style_report, Data_data_structure, bsp);
1036 break;
1037 case SAVE_FILE:
1038 aip = AsnIoNew(ASNIO_BIN_OUT, stdout, NULL, NULL, NULL);
1039 BiostrucAsnWrite(bsp, aip, NULL);
1040 break;
1041 case SEE_FILE:
1042 aip = AsnIoNew(ASNIO_TEXT_OUT, stdout, NULL, NULL, NULL);
1043 BiostrucAsnWrite(bsp, aip, NULL);
1044 break;
1045 case SEND_FILE:
1046 aip = AsnIoNew(ASNIO_TEXT_OUT, stdout, NULL, NULL, NULL);
1047 BiostrucAsnWrite(bsp, aip, NULL);
1048 break;
1049 }
1050
1051 AsnIoReset(aip);
1052 AsnIoClose(aip);
1053 ClearStructures();
1054
1055 }
1056 else if (Filetype == 'r') {
1057 /* RasMol format */
1058 if (Mime == LAUNCH_VIEWER)
1059 printf ("Content-type: chemical/x-pdb\r\n\r\n");
1060
1061 ModelStruc = MakeAModelstruc(bsp);
1062 bssp->structure = NULL; /* already linked into modelstruc */
1063 WritePDBAllModel(ModelStruc, stdout);
1064 ClearStructures();
1065 }
1066 else if (Filetype == 'k') {
1067 /* Mage format */
1068 if (Mime == LAUNCH_VIEWER)
1069 printf ("Content-type: chemical/x-kinemage\r\n\r\n");
1070
1071 ModelStruc = MakeAModelstruc(bsp);
1072 bssp->structure = NULL; /* already linked into modelstruc */
1073 WriteKinAllModel(ModelStruc, stdout, Color, Render);
1074 ClearStructures();
1075 }
1076 else {
1077 error_flag = 1;
1078 PrtMes(MAILTO, "MMDBSRV","Unknown file type on structure fetch.",NULL,TRUE);
1079 }
1080
1081 if ((Mime == SEE_FILE) && (!error_flag))
1082 printf ("</PRE></HTML>\r\n");
1083
1084 NcbiMimeAsn1Free(mime); /* yanli */
1085 return 1;
1086
1087 } /* end SendStructureMIME */
1088
1089
1090
1091 /* Output the taxonomy data, per chain, and also links to the taxonomy database.
1092 * Return '1' in case there was a non-trivial taxonomy assignment, '0' if there
1093 * was no taxonomy data found. The success or failure is passed ultimately to
1094 * PrintStructureInfo, where the PDB source is displayed in case no taxonomy data
1095 * was found.
1096 */
1097
1098 static Int2
SaveTaxonomyInfoNew(PDNMS ModelStruc,CharPtr save,Int2 n,CharPtr pname)1099 SaveTaxonomyInfoNew(PDNMS ModelStruc, CharPtr save, Int2 n, CharPtr pname)
1100 {
1101 PMSD pmsd;
1102 PDNMM pdnmm;
1103 PMMD pmmd;
1104 Int4 i, j, k, cnt, txcnt, uacnt;
1105 ValNodePtr descr, db;
1106 CharPtr chainp, names[MAX_CHAINS];
1107 Char chn, chns[MAX_CHAINS], org_names[MAX_TBUFF];
1108 Int2 flg, name_here, cnt_vec[MAX_CHAINS];
1109 BioSourcePtr bios;
1110 OrgRefPtr org;
1111 Int4 molecule_type, tax_id, tax_ids[MAX_CHAINS];
1112
1113 if ((ModelStruc == NULL) || (save == NULL))
1114 return 0;
1115
1116 for (i = 0; i < MAX_TBUFF; i++)
1117 org_names[i] = '\0';
1118
1119 pmsd = (PMSD) ModelStruc->data.ptrvalue;
1120 pdnmm = (PDNMM) pmsd->pdnmmHead;
1121
1122 name_here = 0;
1123
1124 for (cnt = uacnt = 0; (pdnmm != NULL) && (cnt < MAX_CHAINS); pdnmm = pdnmm->next) {
1125 /* zap the OrgRefPtr, there may be no taxonomy for this chain! */
1126 pmmd = pdnmm->data.ptrvalue;
1127 org = NULL;
1128
1129 for (descr = pmmd->pMolDescr; descr != NULL; descr = descr->next) {
1130 if (descr->choice == BiomolDescr_molecule_type)
1131 molecule_type = descr->data.intvalue;
1132
1133 if (descr->choice == BiomolDescr_name) {
1134 chainp = descr->data.ptrvalue;
1135 chn = *chainp;
1136 }
1137
1138 if (descr->choice == BiomolDescr_organism) {
1139 bios = descr->data.ptrvalue;
1140 org = (OrgRefPtr) bios->org;
1141 }
1142 }
1143
1144 if ((molecule_type == Molecule_type_protein) ||
1145 (molecule_type == Molecule_type_dna) ||
1146 (molecule_type == Molecule_type_rna)) {
1147
1148 /* save the chain and get the taxonomy data */
1149 chns[cnt] = (chn == ' ') ? '\n' : chn;
1150
1151 if (org != NULL) {
1152 DbtagPtr dbtag;
1153
1154 for (db = org->db, tax_id = -1; db != NULL; db = db->next) {
1155 if (db->choice == TAX_ID_CHOICE_NUM) {
1156 dbtag = db->data.ptrvalue;
1157 tax_id = dbtag->tag->id;
1158 break;
1159 }
1160 }
1161
1162 names[cnt] = &org_names[name_here];
1163
1164 if (org->taxname != NULL) {
1165 StringCat(names[cnt], org->taxname);
1166 name_here += StrLen(org->taxname) + 1;
1167 }
1168 else if (org->common != NULL) {
1169 StringCat(names[cnt], org->common);
1170 name_here += StrLen(org->common) + 1;
1171 }
1172 else {
1173 StringCat(names[cnt], "(unassigned)");
1174 name_here += 13;
1175 }
1176
1177 tax_ids[cnt++] = tax_id;
1178 }
1179 else {
1180 /* track the number of unassigned chains */
1181 uacnt++;
1182 names[cnt] = &org_names[name_here];
1183 StringCat(names[cnt], "(unassigned)");
1184 name_here += 13;
1185 tax_ids[cnt++] = -1;
1186 }
1187 }
1188 }
1189
1190 /* zap the save area */
1191 for (i = 0; i < n; i++)
1192 save[i] = '\0';
1193
1194 /* flag the taxonomy section */
1195 sprintf(save, "<tr bgcolor=#FFFFCC>\n");
1196 k = StrLen(save);
1197 sprintf(&save[k], "<td VALIGN=TOP NOWRAP ALIGN=RIGHT class=H4>");
1198 k = StrLen(save);
1199 sprintf(&save[k], "<strong>Taxonomy:</strong></td>\n");
1200
1201 if (cnt == 0) {
1202 k = StrLen(save);
1203 sprintf(&save[k], "<td class=\"TEXT\">(unassigned)</td>\n");
1204 return 1;
1205 }
1206
1207 /* group chains by organism type, i.e. tax id */
1208 mark_distinct(tax_ids, cnt_vec, cnt);
1209
1210 for (i = flg = 0; i < cnt; i++) {
1211 if (cnt_vec[i] == 0)
1212 continue;
1213
1214 tax_id = tax_ids[i];
1215 k = StrLen(save);
1216
1217 if (flg)
1218 sprintf(&save[k], "; ");
1219 else {
1220 sprintf(&save[k], "<td class=\"TEXT\">");
1221 flg = 1;
1222 }
1223
1224 /* collect chains with the same tax id */
1225 txcnt = cnt_vec[i];
1226 k = StrLen(save);
1227
1228 /*****
1229 if (txcnt > 1)
1230 sprintf(&save[k], "chains ");
1231 else if (chns[i] != '\n')
1232 sprintf(&save[k], "chain ");
1233 *****/
1234
1235 for (j = i; (j < cnt) && (txcnt > 0); j++) {
1236 if (tax_ids[j] != tax_id)
1237 continue;
1238
1239 if (txcnt < cnt) {
1240 k = StrLen(save);
1241
1242 if (txcnt-- > 1)
1243 sprintf(&save[k], "%c, ", chns[j]);
1244 else
1245 sprintf(&save[k], "%c", chns[j]);
1246 }
1247 }
1248
1249 k = StrLen(save);
1250
1251 if (tax_id > 0) {
1252 if (chns[i] != '\n' && txcnt < cnt)
1253 sprintf(&save[k], " <A HREF=\"");
1254 else
1255 sprintf(&save[k], "<A HREF=\"");
1256
1257 k = StrLen(save);
1258 sprintf(&save[k], TAXurl, tax_id);
1259 k = StrLen(save);
1260 sprintf(&save[k], "\">%s</A> ", names[i]);
1261 }
1262 else
1263 sprintf(&save[k], " (unassigned)");
1264 }
1265
1266 k = StrLen(save);
1267 sprintf(&save[k], "</td>\n</tr>\n");
1268 return 1;
1269
1270 } /* end SaveTaxonomyInfoNew */
1271
1272
1273
1274
SendSummaryPageNew_page_fly(Int4Ptr Uids,Int4 NumToDisplay,Int4Ptr LiveUids,unsigned short * Live,Int2 PageCur,Int4 Save)1275 static Int4 SendSummaryPageNew_page_fly(Int4Ptr Uids, Int4 NumToDisplay, Int4Ptr LiveUids, unsigned short * Live, Int2 PageCur, Int4 Save)
1276 {
1277 BiostrucPtr *bsp;
1278 Char tax_save[MAX_TBUFF];
1279 Int2 taxret, chaincnt=0, *pageThis, prepg, pgbeg, pgend;
1280 Int2 totalpg=0, chbeg;
1281 Int4 uid, count;
1282 Int4 liveuid;
1283 unsigned short live;
1284 PDNMS *ModelStruc;
1285 ValNodePtr descr;
1286
1287 if (Save == 2)
1288 printf ("Content-type: application/octet-stream\n\n");
1289 else
1290 printf ("Content-type: text/html\n\n");
1291
1292 if (!GlobalNonHtmlOutput) {
1293 if (GlobalTitles) WWWPrintFileData(HEADFILE, stdout);
1294 else
1295 printf ("<html>\n<title>MMDB Structure Summary</title><body>");
1296 }
1297
1298 bsp =(BiostrucPtr *)MemNew((size_t)(sizeof(BiostrucPtr) *NumToDisplay));
1299 ModelStruc = (PDNMS *) MemNew ((size_t)(sizeof(PDNMS) * NumToDisplay));
1300 pageThis = (Int2Ptr) MemNew ((size_t) (sizeof(Int2) * NumToDisplay));
1301
1302 prepg = 0;
1303 for (count = 0; count < NumToDisplay; count++)
1304 {
1305 uid = Uids[count];
1306 if (uid <0) uid = -uid;
1307 bsp[count] = (BiostrucPtr) openBSP(uid, 3, 0, TRUE, FALSE,
1308 FALSE, &psok, Database);
1309
1310 if (bsp[count] == NULL) pageThis[count] = prepg + 1;
1311 else {
1312 PMSD pmsd;
1313
1314 ModelStruc[count] = MakeAModelstruc(bsp[count]);
1315 pmsd = ModelStruc[count]->data.ptrvalue;
1316 chaincnt = ChainCount(pmsd);
1317
1318 /* pageThis is the last page no. of This model */
1319
1320 if (chaincnt == 0) pageThis[count] = prepg + 1;
1321 else if (chaincnt % ChainPerImg > 0)
1322 pageThis[count]=prepg + chaincnt / ChainPerImg +1;
1323 else pageThis[count] = prepg + chaincnt / ChainPerImg;
1324 }
1325
1326 prepg = pageThis[count];
1327 }
1328 totalpg += pageThis[count-1];
1329
1330 pgend = pageThis[0]; count=0;
1331 while (pgend < PageCur) pgend = pageThis[++count];
1332
1333 if (bsp[count] == NULL) {
1334 printf ("%sNo structure found for UID %d.%s\n",
1335 GlobalNonHtmlOutput ? "\n" : "<P><h4>",uid,
1336 GlobalNonHtmlOutput ? "\n" : "</h4><P>");
1337 printf("<h4>- UID specified dose not match an MMDB-ID or PDB-ID</h4>\n");
1338 }
1339 else {
1340 uid = Uids[count];
1341 liveuid = LiveUids[count];
1342 live = Live[count];
1343
1344 if (!GlobalNonHtmlOutput) { /* ? */
1345 CharPtr name;
1346
1347 for (descr = bsp[count]->descr, name = NULL; descr != NULL; descr = descr->next) {
1348 if (descr->choice == BiomolDescr_name) {
1349 name = descr->data.ptrvalue;
1350 break;
1351 }
1352 }
1353 taxret = SaveTaxonomyInfoNew(ModelStruc[count],tax_save,
1354 MAX_TBUFF, name);
1355 }
1356
1357 PrintStrucInfoNew(ModelStruc[count], liveuid, live,
1358 (taxret) ? tax_save : NULL, uid, stdout);
1359
1360 if (!count) pgbeg = 1;
1361 else pgbeg = pageThis[count - 1] + 1;
1362 chbeg = (PageCur - pgbeg) * ChainPerImg + 1;
1363
1364 PrintChainsMap(bsp[count], ModelStruc[count], chbeg, stdout);
1365 PrintPageView(NumToDisplay, Uids, totalpg, PageCur, stdout);
1366 }
1367
1368 printf("<BR><HR SIZE=5 NOSHADE><BR>\n");
1369
1370 if (!GlobalNonHtmlOutput)
1371 if (GlobalTitles)
1372 WWWPrintFileData(TAILFILE, stdout);
1373 else {
1374 printf ("</body>\n");
1375 printf ("</html>");
1376 }
1377
1378 for (count = 0; count < NumToDisplay; count++) {
1379 ClearStructures();
1380 MemFree(bsp[count]);
1381 MemFree(ModelStruc[count]);
1382 }
1383
1384 MemFree(bsp);
1385 MemFree(ModelStruc);
1386 MemFree(pageThis);
1387
1388 return 1;
1389
1390 } /* end SendSummaryPageNew */
1391
1392
1393
InitMMDBSrv(void)1394 static Boolean InitMMDBSrv(void)
1395 {
1396 Int2 i;
1397
1398 HTMLPath[0] = URLBase[0] = URLHelp[0] = HELPname[0] = CGIPath[0] = URLcgi[0]
1399 = CGIName[0] = DATApath[0] = LOGpath[0] = ENTREZurl[0] = VASTurl[0]
1400 = MMDBurl[0] = PDBurl[0] = TDBurl[0] = MAILto[0] = DART[0] = Database[0]
1401 = LOGIN[0] = PASSWD[0] = INITpath[0] = LIBpath[0] = CDDurl[0] = '\0';
1402
1403
1404 for (i = 0; i < PATH_MAX; i++)
1405 TAXurl[i] = '\0';
1406
1407 GetAppParam("mmdb", "MMDB", "Database", "", Database, PATH_MAX);
1408 if (Database[0] == '\0')
1409 {
1410 ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nMMDBSRV section no Database...\n");
1411 return FALSE;
1412 }
1413
1414 FindPath("mmdb", "MMDBSRV", "HTMLPath", HTMLPath, PATH_MAX);
1415 if (HTMLPath[0] == '\0')
1416 {
1417 ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nMMDBSRV section no HTMLPath...\n");
1418 return FALSE;
1419 }
1420 GetAppParam("mmdb", "MMDBSRV", "URLBase", "", URLBase, PATH_MAX);
1421 if (URLBase[0] == '\0')
1422 {
1423 ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nMMDBSRV section no URLBase...\n");
1424 return FALSE;
1425 }
1426 GetAppParam("mmdb", "MMDBSRV", "URLHelp", "", URLHelp, PATH_MAX);
1427 if (URLHelp[0] == '\0')
1428 {
1429 ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nMMDBSRV section no URLHelp...\n");
1430 return FALSE;
1431 }
1432 GetAppParam("mmdb", "MMDBSRV", "HELPname", "", HELPname, PATH_MAX);
1433 if (HELPname[0] == '\0')
1434 {
1435 ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nMMDBSRV section no HELPname...\n");
1436 return FALSE;
1437 }
1438 FindPath("mmdb", "MMDBSRV", "CGIPath", CGIPath, PATH_MAX);
1439 if (CGIPath[0] == '\0')
1440 {
1441 ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nMMDBSRV section no CGIPath...\n");
1442 return FALSE;
1443 }
1444
1445 GetAppParam("mmdb", "MMDBSRV", "URLcgi", "", URLcgi, PATH_MAX);
1446 if (URLcgi[0] == '\0')
1447 {
1448 ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nMMDBSRV section no URLcgi...\n");
1449 return FALSE;
1450 }
1451 GetAppParam("mmdb", "MMDBSRV", "CGIName", "", CGIName, (size_t) 256 * sizeof(char));
1452 if (CGIName[0] == '\0')
1453 {
1454 ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nMMDBSRV section no CGIName...\n");
1455 return FALSE;
1456 }
1457 FindPath("mmdb", "MMDBSRV", "DATApath", DATApath, PATH_MAX);
1458 if (DATApath[0] == '\0')
1459 {
1460 ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nMMDBSRV section no DATApath...\n");
1461 return FALSE;
1462 }
1463 ARROW[0] = '\0';
1464 sprintf(ARROW, "<IMG alt=\"o\" SRC=\"%sarrow.gif\" ALT=\"o\" BORDER=0>\n", URLBase);
1465
1466 FindPath("mmdb", "MMDBSRV", "LOGpath", LOGpath, PATH_MAX);
1467 if (LOGpath[0] == '\0')
1468 {
1469 ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nMMDBSRV section no LOGpath...\n");
1470 return FALSE;
1471 }
1472 GetAppParam("mmdb", "MMDBSRV", "ENTREZurl", "", ENTREZurl, PATH_MAX);
1473 if (ENTREZurl[0] == '\0')
1474 {
1475 ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nMMDBSRV section no ENTREZurl...\n");
1476 return FALSE;
1477 }
1478 GetAppParam("mmdb", "MMDBSRV", "VASTurl", "", VASTurl, PATH_MAX);
1479 if (VASTurl[0] == '\0')
1480 {
1481 ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nMMDBSRV section no VASTurl...\n");
1482 return FALSE;
1483 }
1484 GetAppParam("mmdb", "MMDBSRV", "MMDBurl", "", MMDBurl, PATH_MAX);
1485 if (MMDBurl[0] == '\0')
1486 {
1487 ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nMMDBSRV section no MMDBurl...\n");
1488 return FALSE;
1489 }
1490 GetAppParam("mmdb", "MMDBSRV", "PDBurl", "", PDBurl, PATH_MAX);
1491 if (PDBurl[0] == '\0')
1492 {
1493 ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nMMDBSRV section no PDBurl...\n");
1494 return FALSE;
1495 }
1496 GetAppParam("mmdb", "MMDBSRV", "TDBurl", "", TDBurl, PATH_MAX);
1497 if (TDBurl[0] == '\0')
1498 {
1499 ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nMMDBSRV section no TDBurl...\n");
1500 return FALSE;
1501 }
1502 GetAppParam("mmdb", "TAXLINK", "TAXurl", "", TAXurl, PATH_MAX);
1503 if (TAXurl[0] == '\0')
1504 {
1505 ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nTAXLINK section no TAXurl...\n");
1506 return FALSE;
1507 }
1508 StringCat(TAXurl, "?id=%d&lvl=0");
1509 GetAppParam("mmdb", "MMDBSRV", "MAILto", "", MAILto, PATH_MAX);
1510 if (MAILto[0] == '\0')
1511 {
1512 ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nMMDBSRV section no Mailto...\n");
1513 return FALSE;
1514 }
1515
1516 MAILTO[0] = '\0';
1517 sprintf(MAILTO, "< <a href=\"%s\">%s</a> >", MAILto, MAILto);
1518
1519 GetAppParam("mmdb", "CD", "DARTdatabase", "", DART, PATH_MAX);
1520 if (DART[0] == '\0') {
1521 ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nCD section no DARTdatabase\n");
1522 return FALSE;
1523 }
1524
1525 GetAppParam("mmdb", "CD", "LOGINname", "", LOGIN, PATH_MAX);
1526 if (LOGIN[0] == '\0') {
1527 ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nCD section no LOGINname\n");
1528 return FALSE;
1529 }
1530
1531 GetAppParam("mmdb", "CD", "PASSwd", "", PASSWD, PATH_MAX);
1532 if (PASSWD[0] == '\0') {
1533 ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nCD section no PASSwd\n");
1534 return FALSE;
1535 }
1536
1537 GetAppParam("mmdb", "CD", "INITpath", "", INITpath, PATH_MAX);
1538 if (INITpath[0] == '\0') {
1539 ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nCD section no INITpath\n");
1540 return FALSE;
1541 }
1542
1543 GetAppParam("mmdb", "CD", "LIBpath", "", LIBpath, PATH_MAX);
1544 if (LIBpath[0] == '\0') {
1545 ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nCD section no LIBpath\n");
1546 return FALSE;
1547 }
1548
1549 GetAppParam("mmdb", "CD", "CDDurl", "", CDDurl, PATH_MAX);
1550 if (CDDurl[0] == '\0') {
1551 ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nCD section no CDDurl\n");
1552 return FALSE;
1553 }
1554
1555
1556 return TRUE;
1557 }
1558
1559
1560
1561 /************************************************************************
1562 *
1563 * Int2 Main() - main function
1564 *
1565 ***********************************************************************/
1566
1567
1568
Main()1569 Int2 Main ()
1570 {
1571 time_t time_now;
1572 Char DispOpt = '\0';
1573 CharPtr TimeNowStr = NULL, pcThis = NULL, pcName = NULL;
1574 Int4 IndexArgs = -1, Complex = 0, MaxModels = 1;
1575 Int4 KinColor = 0, KinRender = 0, Save = 0, Form = 0;
1576 Int4Ptr MMDBids = NULL; /* (list of MMDB ids ) */
1577 Int4 iMMDBids = 0, iCount = 0, iBytes = 0, NumEntries = 0;
1578 ValNodePtr pvnUIDS = NULL, pvnThis = NULL;
1579 WWWErrorCode error;
1580
1581 /* J. Chen */
1582 Int4Ptr LiveMMDBids = NULL; /* list of live MMDB ids */
1583 unsigned short * Live = NULL; /* state of live or non-live */
1584 CharPtr Cmd = NULL, pcThis2 = NULL, pcThis3 = NULL;
1585 Int2 PageNo=1, i, chain1, chain2, imgsize;
1586 Char ODBCInitStr[100], LIBPathStr[100];
1587
1588
1589 /* this sets up the unix time limit */
1590
1591 #ifdef OS_UNIX
1592 {
1593 struct rlimit rl;
1594 getrlimit(RLIMIT_CPU, &rl);
1595 rl.rlim_max = rl.rlim_cur = CPUTIME_MAX;
1596 setrlimit(RLIMIT_CPU, &rl);
1597 }
1598 #endif
1599
1600 if (!InitMMDBSrv())
1601 PrtMes(MAILTO, "MMDBSRV", "Unable to Open Server Configuration File.",
1602 NULL, FALSE);
1603
1604 sprintf(ODBCInitStr, "ODBCINI=%s", INITpath);
1605 putenv(ODBCInitStr);
1606
1607 sprintf(LIBPathStr, "LD_LIBRARY_PATH=%s", LIBpath);
1608 putenv(LIBPathStr);
1609
1610 if ((dartcon = Dart_Init2(DART, LOGIN, PASSWD)) == NULL)
1611 PrtMes(MAILTO, "MMDBSRV", "Dart Initialization failed", NULL, FALSE);
1612
1613 StringCat(LOGpath, "mmdbsrv.log");
1614 if( !ErrSetLogfile (LOGpath, ELOG_APPEND) )
1615 PrtMes(MAILTO, "MMDBSRV", "Unable to Open Log. LOGpath = ",
1616 LOGpath, FALSE);
1617
1618 ErrSetLogLevel(SEV_MAX);
1619 ErrSetOpts (ERR_CONTINUE, ERR_LOG_ON);
1620
1621 if((error = WWWGetArgs(&info)) != WWWErrOk) {
1622 PrtMes(NULL, "MMDBSRV",
1623 "Failed to Process Posting - Check your GET/POST syntax",
1624 NULL, TRUE);
1625 goto earlyout;
1626 }
1627
1628
1629 if (!OpenMMDBAPI(0, NULL)) {
1630 ErrLogPrintf("#OpenMMDBAPI failed.\n");
1631 PrtMes(MAILTO, "MMDBSRV Error", " - Unable OpenMMDBAPI.", NULL, FALSE);
1632 }
1633
1634 SeqAsnLoad();
1635 objmimeAsnLoad();
1636
1637 if (!MmdbSrvInitialize()) {
1638 psok = FALSE;
1639 ErrLogPrintf("#MMDB Database Access Failed to Initialize.\n");
1640 PrtMes(MAILTO, "MMDBSRV",
1641 "Unable to Open MMDB Database on Server.", NULL, FALSE);
1642 }
1643
1644
1645 IndexArgs = -1;
1646 if ((IndexArgs = WWWFindName(info,"db")) >= 0)
1647 {
1648 pcThis = WWWGetValueByIndex(info,IndexArgs);
1649 DispOpt = pcThis[0];
1650 if ((DispOpt != 't') && (DispOpt != 'T'))
1651 {
1652 printf("Content-type: text/html\r\n\r\n");
1653 printf("<H2>MMDBSRV Error</H2>\n - Wrong Database Type db=%c.<p>\n", DispOpt );
1654 printf("Try <a href=\"%s\">WWW-Entrez</a> for this<p>\n", URLHelp);
1655 goto cleanout;
1656 }
1657 }
1658
1659
1660 IndexArgs = -1;
1661 if ((IndexArgs = WWWFindName(info, "form")) >= 0)
1662 {
1663 pcThis = WWWGetValueByIndex(info,IndexArgs);
1664 if ((!StrToInt4(pcThis,&Form)) || (Form != 6))
1665 {
1666 printf("Content-type: text/html\r\n\r\n");
1667 printf("<H2>MMDBSRV Error</H2>\n - Wrong Form Type form=%s.<p>\n", pcThis );
1668 printf("<pre>Only supports form=6</pre><p>\n");
1669 printf("Try <a href=\"%s\">WWW-Entrez</a> for this<p>\n", URLHelp);
1670 goto cleanout;
1671 }
1672 }
1673
1674
1675 IndexArgs = -1;
1676 if ((IndexArgs = WWWFindName(info, "uid")) < 0)
1677 PrtMes(NULL, "MMDBSRV", "No Identifier specified: missing uid",
1678 NULL, TRUE);
1679 else
1680 {
1681 /* loop over entire set of tag=value entries and add all the UID's found together */
1682 /* must handle uid=1234&uid=1OMD&uid=1234,2345,2134&dopt=s&uid=3INS */
1683 NumEntries = WWWGetNumEntries(info);
1684 for (IndexArgs = 0; IndexArgs < NumEntries; IndexArgs++)
1685 {
1686 pcName = WWWGetNameByIndex(info, IndexArgs);
1687 pcThis = WWWGetValueByIndex(info, IndexArgs);
1688
1689 if (StrICmp(pcName, "uid") == 0) MakeUIDList(pcThis, &pvnUIDS);
1690 }
1691 if (pvnUIDS == NULL) {
1692 PrtMes(NULL, "MMDBSRV",
1693 "No structure found for this UID: UID specified is not a MMDB_ID or PDB_ID", NULL, TRUE);
1694 goto cleanout;
1695 }
1696 pvnThis = pvnUIDS;
1697 while (pvnThis)
1698 {
1699 iMMDBids++;
1700 pvnThis = pvnThis->next;
1701 }
1702 MMDBids = (Int4Ptr) MemNew((size_t) (sizeof(Int4) * iMMDBids));
1703
1704 LiveMMDBids = (Int4Ptr) MemNew ((size_t) (sizeof(Int4) * iMMDBids));
1705 Live = (unsigned short *) MemNew ((size_t)(sizeof(unsigned short)*iMMDBids));
1706
1707 for (i=0; i< iMMDBids; i++) Live[i] = 0;
1708
1709 pvnThis = pvnUIDS;
1710 iCount = 0;
1711 while (pvnThis)
1712 {
1713 MMDBids[iCount] = (Int4) pvnThis->data.intvalue;
1714
1715 LiveMMDBids[iCount] = MMDBids[iCount];
1716 if (psok)
1717 i =constructLiveMmdbId(&(LiveMMDBids[iCount]),&(Live[iCount]));
1718 pvnThis = pvnThis->next;
1719 iCount++;
1720 }
1721
1722 }
1723
1724 DispOpt = ' ';
1725 IndexArgs = -1;
1726 if ((IndexArgs = WWWFindName(info, "dopt")) >= 0)
1727 {
1728 pcThis = WWWGetValueByIndex(info,IndexArgs);
1729 switch (pcThis[0])
1730 {
1731 case 's':
1732 case 'S':
1733 DispOpt = 's';
1734 break;
1735 case 'r':
1736 case 'R':
1737 DispOpt = 'r';
1738 break;
1739 case 'i':
1740 case 'I':
1741 DispOpt = 'i';
1742 break;
1743 case 'j':
1744 case 'J':
1745 DispOpt = 'j';
1746 break;
1747 case 'k':
1748 case 'K':
1749 DispOpt = 'k';
1750 break;
1751 case 'a':
1752 case 'A':
1753 DispOpt = 'a';
1754 Save = 1;
1755 break;
1756 default:
1757 {
1758 printf("Content-type: text/html\r\n\r\n");
1759 printf("<H2>MMDBSRV Error</H2>\n - Wrong Display Option Type: dopt=%s.<p>\n", pcThis);
1760 printf("<pre>dopt supports:\n's' Structure summary\n");
1761 printf("'r' RasMol(PDB) format\n'k' Kinemage format\n'i', 'j', or 'a' ASN.1</pre><p>\n");
1762 goto cleanout2;
1763 }
1764 }
1765 }
1766 else DispOpt = 's'; /* structure summary is default when no dopt supplied */
1767
1768 IndexArgs = -1;
1769 if ((IndexArgs = WWWFindName(info, "Complexity")) >= 0)
1770 {
1771 pcThis = WWWGetValueByIndex(info,IndexArgs);
1772
1773
1774 for (iCount = 0; iCount < NUM_COMPLEXITY_TYPES; iCount++)
1775 if (StrICmp(pcThis,ComplexityDescriptions[iCount]) == 0)
1776 break;
1777
1778 Complex = ALLMDL;
1779 MaxModels = 1;
1780
1781 switch (iCount)
1782 {
1783 case 0 :
1784 Complex = ONECOORDRES;
1785 break;
1786 case 4 :
1787 MaxModels = INT2_MAX;
1788 break;
1789 case 5:
1790 Complex = ONECOORDATOM;
1791 break;
1792 default:
1793 {
1794 if (DispOpt != 's') {
1795 PrtMes(NULL, "MMDBSRV",
1796 "Wrong Complexity Type: Complexity = ", pcThis, TRUE);
1797 goto cleanout2;
1798 }
1799 }
1800 }
1801 }
1802
1803 IndexArgs = -1;
1804 if ((IndexArgs = WWWFindName(info, "mdlLvl")) >= 0)
1805 {
1806 pcThis = WWWGetValueByIndex(info, IndexArgs);
1807 Complex = atoi(pcThis);
1808 }
1809
1810 IndexArgs = -1;
1811 if ((IndexArgs = WWWFindName(info, "maxModels")) >= 0)
1812 {
1813 pcThis = WWWGetValueByIndex(info, IndexArgs);
1814 MaxModels = atoi(pcThis);
1815 }
1816
1817 IndexArgs = -1;
1818 if ((IndexArgs = WWWFindName(info, "KinemageColor")) >= 0)
1819 {
1820 pcThis = WWWGetValueByIndex(info, IndexArgs);
1821 KinColor = GetOptionValue(pcThis, NUM_COLOR_TYPES, ColorDescriptions);
1822 }
1823
1824
1825
1826 IndexArgs = -1;
1827 if ((IndexArgs = WWWFindName(info, "KinemageRender")) >= 0)
1828 {
1829 pcThis = WWWGetValueByIndex(info,IndexArgs);
1830 StrToInt4(pcThis, &KinRender);
1831 }
1832
1833 IndexArgs = -1;
1834 if ((IndexArgs = WWWFindName(info, "save")) >= 0)
1835 { /* these don't affect structure summaries */
1836 pcThis = WWWGetValueByIndex(info,IndexArgs);
1837 if (StrICmp(pcThis, "See") == 0)
1838 {
1839 Save = 1; /* sends MIMED-type files to view in ascii-readable form */
1840 }
1841 else if (StrICmp(pcThis, "Save") == 0)
1842 {
1843 Save = 2; /* sends MIMED-type files in raw save form */
1844 }
1845 else if (StrICmp(pcThis, "M") == 0)
1846 {
1847 Save = 3; /* MacSave - not implemented */
1848 }
1849 else if (StrICmp(pcThis, "asntext") == 0)
1850 {
1851 Save = SEND_FILE; /* writes out asn text without the html header */
1852 }
1853 }
1854
1855 IndexArgs = -1;
1856 if ((IndexArgs = WWWFindName(info, "header")) >= 0)
1857 {
1858 pcThis = WWWGetValueByIndex(info,IndexArgs);
1859 if (StrICmp(pcThis, "no") == 0)
1860 {
1861 Save = 2;
1862 }
1863 }
1864
1865
1866 IndexArgs = -1;
1867 if ((IndexArgs = WWWFindName(info, "title")) >= 0)
1868 {
1869 pcThis = WWWGetValueByIndex(info,IndexArgs);
1870 if (StrICmp(pcThis, "no") == 0)
1871 {
1872
1873 GlobalTitles = FALSE;
1874 }
1875 }
1876
1877 IndexArgs = -1;
1878 if ((IndexArgs = WWWFindName(info, "html")) >= 0)
1879 {
1880 pcThis = WWWGetValueByIndex(info,IndexArgs);
1881 if (StrICmp(pcThis, "no") == 0)
1882 {
1883 GlobalNonHtmlOutput = TRUE;
1884 GlobalTitles = FALSE;
1885 }
1886 }
1887
1888
1889 /* J. Chen */
1890
1891 IndexArgs = -1;
1892 PageNo = 1; /* default */
1893 if ((IndexArgs = WWWFindName(info, "page")) >=0)
1894 {
1895 pcThis = WWWGetValueByIndex(info, IndexArgs);
1896 for (i = 0; i< StrLen(pcThis); i++)
1897 if (!isdigit(pcThis[i])) break;
1898 if (i == StrLen(pcThis))
1899 PageNo = (Int2) atoi(pcThis);
1900 else {
1901 PrtMes(NULL, "MMDBSRV", "Non-numeric Page type: page = ",
1902 pcThis, TRUE);
1903 goto cleanout;
1904 }
1905 }
1906
1907 IndexArgs = -1;
1908 if ((IndexArgs = WWWFindName(info, "cmd")) >=0)
1909 {
1910 pcThis = WWWGetValueByIndex(info, IndexArgs);
1911 Cmd = pcThis;
1912
1913 if (!StrICmp(Cmd, "graph"))
1914 {
1915 IndexArgs = -1;
1916 if ((IndexArgs = WWWFindName(info, "chbeg")) >=0)
1917 pcThis = WWWGetValueByIndex(info, IndexArgs);
1918 else {
1919 PrtMes(NULL, "MMDBSRV", "Missing first chain id",
1920 NULL, TRUE);
1921 goto cleanout;
1922 }
1923
1924 IndexArgs = -1;
1925 if ((IndexArgs = WWWFindName(info, "chend")) >=0)
1926 pcThis2 = WWWGetValueByIndex(info,IndexArgs);
1927 else {
1928 PrtMes(NULL, "MMDBSRV", "Missing last chain id",
1929 NULL, TRUE);
1930 goto cleanout;
1931 }
1932
1933 IndexArgs = -1;
1934 if ((IndexArgs = WWWFindName(info, "imgsize")) >=0)
1935 pcThis3 = WWWGetValueByIndex(info,IndexArgs);
1936 else {
1937 PrtMes(NULL, "MMDBSRV", "Missing image size",
1938 NULL, TRUE);
1939 goto cleanout;
1940 }
1941
1942
1943 for (i = 0; i < StrLen(pcThis); i++)
1944 if (!isdigit(pcThis[i])) break;
1945
1946 if (i == StrLen(pcThis)) chain1 = atoi(pcThis);
1947 else {
1948 PrtMes(NULL, "MMDBSRV",
1949 "Non-numeric chain id: chbeg = ", pcThis, TRUE);
1950 goto cleanout;
1951 }
1952
1953 for (i = 0; i < StrLen(pcThis2); i++)
1954 if (!isdigit(pcThis2[i])) break;
1955 if (i == StrLen(pcThis2)) chain2 = atoi(pcThis2);
1956 else {
1957 PrtMes(NULL, "MMDBSRV",
1958 "Non-numeric chain id: chend = ", pcThis, TRUE);
1959 goto cleanout;
1960 }
1961
1962 for (i = 0; i < StrLen(pcThis3); i++)
1963 if (!isdigit(pcThis3[i])) break;
1964 if (i == StrLen(pcThis3)) imgsize = atoi(pcThis3);
1965 else {
1966 PrtMes(NULL, "MMDBSRV",
1967 "Non-numeric image size: imgsize = ", pcThis,
1968 TRUE);
1969 goto cleanout;
1970 }
1971
1972 }
1973
1974 }
1975
1976
1977
1978 /* J. Chen (end) */
1979
1980 if (DispOpt == 's') {
1981 if ((Cmd != NULL) && !StrICmp(Cmd, "graph"))
1982 iBytes = DrawImg(MMDBids, chain1, chain2, imgsize);
1983 else
1984 iBytes = SendSummaryPageNew_page_fly(MMDBids, iMMDBids,
1985 LiveMMDBids, Live, PageNo,Save);
1986 }
1987 else
1988 iBytes = SendStructureMIME(DispOpt, MMDBids[0], Save ,
1989 Complex, MaxModels, KinColor, KinRender);
1990
1991 MemFree(MMDBids);
1992 MemFree(LiveMMDBids);
1993 MemFree(Live);
1994
1995 /* log first MMDB-id, number of id's asked for, number of bytes sent */
1996 time_now = GetSecs();
1997 TimeNowStr = ctime(&time_now);
1998 TimeNowStr[24] = '\0';
1999 ErrLogPrintf("\n%s|%s|%s|%s|Do %c|Id %ld|No %ld|By %ld|Sv %ld|Cp %ld|Md %ld|Kc %ld|Kr %ld",
2000 WWWGetAddress(info), WWWGetHost(info), WWWGetAgent(info), TimeNowStr,
2001 (char) DispOpt,
2002 (long) MMDBids[0], (long) iMMDBids, (long)iBytes, (long) Save,
2003 (long) Complex, (long) MaxModels, (long) KinColor, (long) KinRender);
2004
2005
2006 CloseMMDBAPI();
2007 fflush(stdout);
2008 Dart_Fini(dartcon);
2009 if (psok) MmdbSrvFinish();
2010 /* else MMDBFini(); */
2011 exit(0);
2012
2013 cleanout2:
2014 MemFree(MMDBids);
2015 CloseMMDBAPI();
2016 if (psok) MmdbSrvFinish();
2017 /* else MMDBFini(); */
2018 Dart_Fini(dartcon);
2019 /* log first MMDB-id, number of id's asked for, number of bytes sent */
2020 time_now = GetSecs();
2021 TimeNowStr = ctime(&time_now);
2022 TimeNowStr[24] = '\0';
2023 ErrLogPrintf("\n#Syntax Error %s|%s|%s|%s|%ld",
2024 WWWGetAddress(info), WWWGetHost(info), WWWGetAgent(info), TimeNowStr,
2025 (long)iBytes);
2026 fflush(stdout);
2027 exit(0);
2028
2029 cleanout:
2030 CloseMMDBAPI();
2031 if (psok) MmdbSrvFinish();
2032 /* else MMDBFini();*/
2033 Dart_Fini(dartcon);
2034
2035 /* log first MMDB-id, number of id's asked for, number of bytes sent */
2036 time_now = GetSecs();
2037 TimeNowStr = ctime(&time_now);
2038 TimeNowStr[24] = '\0';
2039 ErrLogPrintf("\n#Query Not Supported %s|%s|%s|%s|%ld",
2040 WWWGetAddress(info), WWWGetHost(info), WWWGetAgent(info), TimeNowStr,
2041 (long)iBytes);
2042
2043 fflush(stdout);
2044 exit(0);
2045
2046 earlyout:
2047 time_now = GetSecs();
2048 TimeNowStr = ctime(&time_now);
2049 TimeNowStr[24] = '\0';
2050 ErrLogPrintf("\n#Get/Post Error %s|%s|%s|%s|%ld",
2051 WWWGetAddress(info), WWWGetHost(info), WWWGetAgent(info), TimeNowStr,
2052 (long)iBytes);
2053
2054
2055 fflush(stdout);
2056 exit(0);
2057 }
2058
2059
