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/* $Id: mmdbsrv.c,v 6.28 2001/12/12 20:43:38 beloslyu Exp $
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* ===========================================================================
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* National Center for Biotechnology Information
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* This software/database is a "United States Government Work" under the
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* terms of the United States Copyright Act. It was written as part of
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* the author's official duties as a United States Government employee and
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* thus cannot be copyrighted. This software/database is freely available
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* to the public for use. The National Library of Medicine and the U.S.
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* Government have not placed any restriction on its use or reproduction.
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* Although all reasonable efforts have been taken to ensure the accuracy
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* and reliability of the software and data, the NLM and the U.S.
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* Government do not and cannot warrant the performance or results that
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* may be obtained by using this software or data. The NLM and the U.S.
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* Government disclaim all warranties, express or implied, including
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* warranties of performance, merchantability or fitness for any particular
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* Please cite the author in any work or product based on this material.
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* ===========================================================================
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* File Name: $RCSfile: mmdbsrv.c,v $
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* Author: Christopher Hogue
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* Version Creation Date: 6 January 1997
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* Revision 6.28 2001/12/12 20:43:38 beloslyu
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* change the name of ftp site to ftp.ncbi.nih.gov
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* Revision 6.27 2001/01/25 23:02:56 lewisg
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* get rid of content-disp, add mdlLvl and maxModels args
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* Revision 6.26 2000/08/21 16:12:42 lewisg
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* add save=asntext option
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* Revision 6.25 2000/06/26 18:05:26 lewisg
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* fix another hardcoded url
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* Revision 6.24 2000/06/23 22:35:58 lewisg
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* get rid of hardcoded urls
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* Revision 6.23 2000/01/31 19:59:12 lewisg
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* fix output of date in pdb header
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* Revision 6.22 1999/10/13 20:13:18 zimmerma
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* DZ: Removed use of temporary files - html ouput redirected to stdout
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* Revision 6.21 1999/06/17 14:44:09 zimmerma
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* Added static char variable for cvsId in order to use unix "what"
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* Revision 6.20 1999/06/15 18:15:34 addess
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* Initialized this_uid to 0 on line 1286
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* Revision 6.19 1999/05/13 15:51:33 kimelman
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* bugfix: memory deallocation fixed
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* Revision 6.19 1999/05/13 15:51:33 kimelman
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* bugfix: memory deallocation fixed
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* Revision 6.18 1999/05/11 23:36:34 kimelman
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* make StrToInt4 static
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* Revision 6.17 1999/05/11 17:50:23 kimelman
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* Revision 6.16 1999/04/28 21:08:30 lewisg
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* fixed double freeing of Biostruc
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* Revision 6.15 1999/04/28 18:26:15 kimelman
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* exit codes changed to 0
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* Revision 6.14 1999/04/22 01:56:44 kimelman
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* 1. pdb reference read completely from configurstion files
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* 3. NcbiMimeAsn1Free(mime) commented out <-- lead to core
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* dump AFTER sending MIME (quick & dirty fix)
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* Revision 6.13 1999/04/19 16:52:57 kimelman
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* Revision 6.12 1999/03/05 19:18:47 addess
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* changed URL to link to RCSB structure explorer
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* Revision 6.11 1998/11/06 16:25:31 addess
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* added features for layer-1 and PDB TITLE records
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* Revision 6.10 1998/07/17 18:45:53 madej
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* Got rid of some unused URLs.
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* Revision 6.9 1998/06/11 19:12:53 madej
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* Changes in a message type for Cn3D by Yanli.
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* Revision 6.8 1998/04/16 17:51:38 madej
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* Tweak to print out author names in new/old format.
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* Revision 6.7 1998/04/15 14:54:05 kimelman
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* 1. Make retrieval unifirm from open server and sql server.
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* 2. mmdbsrv retrival performance tuning:
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* - size of read-in buffers
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* - direct pdb2mmdb DB lookup instead of full loading pdb to mmdb translataion
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* 3. cleaning mmdblocl.* and make.mmdbsrv in order to remove obsolete code
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* Revision 6.6 1998/04/03 20:25:24 kimelman
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* PubStruct access code added to mmdbsrv
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* Revision 6.5 1998/02/20 18:25:26 madej
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* Fix using unlink to stop file dumps into /var/tmp.
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* Revision 6.4 1997/11/25 18:27:45 madej
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* Fix to save asn.1 files in binary.
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* Revision 6.3 1997/11/05 19:05:16 madej
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* Updated comments for config file.
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* Revision 6.2 1997/11/05 15:58:57 madej
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* Bug fix for tax names in multiple listings
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* Revision 6.1 1997/10/31 15:29:57 madej
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* Major reformat of structure summary page, including taxonomy links.
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* Revision 6.0 1997/08/25 18:11:28 madden
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* Revision changed to 6.0
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* Revision 1.2 1997/05/16 21:25:41 hogue
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* Added checks with vast database entries before showing vast links.
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* Revision 1.1 1997/02/18 18:03:30 hogue
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* ==========================================================================
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*db=t&form=6&uid=1OMD&dopt=s - PDB or MMDB-ids allowed
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*db=t&form=6&uid=1OMD&Dopt=i - launch Cn3D Mime-type - first UID only.
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*db=t&uid=1234,2345,1254,1232&dopt=s - multiple structure summaries
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*db=t&uid=3INS,1234,1OMD&dopt=s - mixed id types OK
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*Optional, but if wrong, error:
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* db=t any other is an error message
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* form=6 4 is an error message - any other ignored
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* uid=(list of MMDB ids or PDB ids)
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* 's' Structure summary
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* Others - error; None assumes 's'
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*Optional - Interpreted in Context:
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* complexity="Cn3D+Subset" ONECOORDATOM, 1
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* "Virtual+Bond+Model" ONECOORDRES, 1
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* "Up+to+5+Models" ALLMDL, 5
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* "Up+to+10+Models" ALLMDL, 10
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* "All+Models" ALLMDL, 100
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* KinemageColor="Molecule+Number" KIN_COLOR_NUMBER
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* "Secondary+Structure" KIN_COLOR_TYPE
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* "Thermal+Factor" KIN_COLOR_TEMP
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* "Element" KIN_COLOR_ATOM
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* KinemageRender=(integer) - not seen on Struc Summary
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* header="no" same as save="s"
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* title="no" - omit title bar and bottom options
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/*******************************************
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MMDBSRV MIRROR installation:
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This describes what you need to run MMDBSRV:
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1] YOUR MMDB DATA DIRECTORIES, e.g.:
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These contain the MMDB data on your local filesystem,
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as obtained from ftp://ftp.ncbi.nih.gov/mmdb/mmdbdata
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and updated regularly by MIRROR. You can
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put them in the CGI-BIN or HTTP (HTML) directories
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if you prefer. If you wish to implement a local
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decompression/compression scheme see the source code mmdblocl.c.
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2] YOUR CGI-BIN directory & URL, e.g.:
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...cgi-bin/mmdb/logs/
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...cgi-bin/mmdb/data/
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http://123.456.789.10/cgi-bin/mmdb/
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The first contains the compiled mmdbsrv program and the
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config file, obtained from
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ftp://ftp.ncbi.nih.gov/mmdb/www/mmdbsrv
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The second will contain the log files written out.
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The third needs sshead.txt, sscode.txt, sstail.txt
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NOTE - you must edit "sstail.txt"
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in order to get the proper links to your local
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copy of help documentation & server.
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3] YOUR HTTP (HTML) directory & URL, e.g.:
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...html/mmdb/mmdbgifs
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http://123.456.789.10/mmdb/
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The first contains the html files to launch mmdbsrv,
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arrow.gif, strucsum.gif and any other gif files, and the
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associated MMDB help files struchelp.html, cn3d.html,
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strucinstall.html, vast.html, etc. Master copies are kept
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at ftp://ftp.ncbi.nih.gov/mmdb/www/http
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You must hand edit or use scripts or SED to change links from
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NCBI's to your own in all these HTML files.
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The second contains the GIF library as obtained from
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the NCBI ftp site ftp://ftp.ncbi.nih.gov/mmdb/mmdbgifs
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6] Your WWW-Server - make it aware of the following
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chemical/ncbi-asn1-binary *.val
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chemical/x-pdb *.ent; *.pdb
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chemical/x-kinemage *.kin
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-----------------------------
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MMDBSRV gets its directory structure; link URLS and CGI call names
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Change these as required and make a config file.
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Unix ".mmdbrc" or Win "mmdb.ini" from this example:
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URLHelp, ENTREZurl, MMDBurl, PDBurl, 3DBurl
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unless there are broken external links to these.
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-------------------- cut here --------------------
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;Database and Index required when local MMDB database is used.
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Database = /net/dorothy/cbb3/mmdb/data/
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; File for configuring the MMDB server.
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; Base Directory & URLs for HTML documents.
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HTMLPath = /net/vaster/usr/attic/httpd.local/htdocs/Structure/
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URLBase = http://inhouse.ncbi.nlm.nih.gov:6224/Structure/
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URLHelp = http://www.ncbi.nlm.nih.gov/Entrez/
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; Base Directory for CGI-BIN code, data (gifs, html text) and logs.
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CGIPath = /net/vaster/usr/attic/httpd.local/cgi-bin/Structure/
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URLcgi = http://inhouse.ncbi.nlm.nih.gov:6224/cgi-bin/Structure/
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; Base Directory for MMDB-gif set
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GIFpath = /net/vaster/usr/attic/httpd.public/htdocs/Structure/mmdbgifs/
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GIFurl = http://www.ncbi.nlm.nih.gov/Structure/mmdbgifs/
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; URL's for links to Entrez, VAST.
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ENTREZurl = http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query
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VASTurl = http://inhouse.ncbi.nlm.nih.gov:6224/cgi-bin/Structure/vastsrv
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MMDBurl = http://www.ncbi.nlm.nih.gov/Structure/
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PDBurl = http://www.pdb.bnl.gov/index.html
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TDBurl = http://www.pdb.bnl.gov/cgi-bin/opdbshort
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; Location of gunzip function.
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Gunzip = /usr/sbin/gunzip
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MAILto = info@ncbi.nlm.nih.gov
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;Database required for local VAST fetches.
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;Database = /net/vaster/usr/people6/madej/vastdata.binary/
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Database = /net/dorothy/cbb3/vast/data/
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; URL for link to taxonomy database (wgetorg for retrieval)
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TAXurl = http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wgetorg
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-------------------- cut here --------------------
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********************************************/
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#include <miscutils.h>
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#include <sys/resource.h>
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#include <mmdbdata.h>
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#include <sys/resource.h>
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#include <lsqfetch.h>
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#define CPUTIME_MAX 120
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#define NUM_COMPLEXITY_TYPES 6
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static char *ComplexityDescriptions[] =
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{"Virtual Bond Model","All Atom Model","Up to 5 Models",
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"Up to 10 Models","All Models","Cn3D Subset"};
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#define NUM_COLOR_TYPES 5
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static char *ColorDescriptions[] =
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{"","Molecule Number","Secondary Structure","Thermal Factor","Element"};
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/* the config file DATApath is used for the location of these files */
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#define HEADFILE "sshead.txt"
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/* Structure Summary Header File */
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#define TAILFILE "sstail.txt"
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/* Structure Summary Tail File */
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#define CODEFILE "sscode.txt"
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/* Structure Summary View Code */
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#define CHAIN_CHOICE_NUM 1
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#define ORG_CHOICE_NUM 6
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/* some defines needed for the taxonomy code */
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#define TAX_ID_CHOICE_NUM 0
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#define MAX_CHAINS 128
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#define MAX_TBUFF 8192
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WWWInfoPtr info = NULL;
362
static Boolean GlobalTitles = TRUE;
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static Boolean GlobalNonHtmlOutput = FALSE;
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static Char HTMLPath[PATH_MAX];
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static Char URLBase[PATH_MAX];
367
static Char URLHelp[PATH_MAX];
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static Char CGIPath[PATH_MAX];
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static Char URLcgi[PATH_MAX];
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static Char CGIName[256];
372
static Char DATApath[PATH_MAX];
373
static Char LOGpath[PATH_MAX];
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static Char ENTREZurl[PATH_MAX];
376
static Char VASTurl[PATH_MAX];
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static Char MMDBurl[PATH_MAX];
378
static Char PDBurl[PATH_MAX];
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static Char TDBurl[PATH_MAX];
380
static Char TAXurl[PATH_MAX];
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static Char MAILto[256];
382
static Char MAILTO[PATH_MAX];
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static Char ARROW[PATH_MAX];
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static char* cvsId_ = "@(#)$Id: mmdbsrv.c,v 6.28 2001/12/12 20:43:38 beloslyu Exp $";
387
/*****************************************************
388
* WWWPrintFileData looks in the current CGI-BIN directory
389
* or the "data" subdirectory for the data file.
390
* and prints it out to pFile
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static void WWWPrintFileData(CharPtr FName, FILE *pFile)
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Char fullpath [PATH_MAX];
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StringCpy(fullpath, DATApath); /* look in DATApath */
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StringCat(fullpath, FName);
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f = FileOpen (fullpath, "r");
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f = FileOpen (FName, "r"); /* look in curent */
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if (f == NULL) { /* look in ./data/ */
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ProgramPath (fullpath, sizeof (fullpath) - 1);
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ptr = StringRChr (fullpath, DIRDELIMCHR);
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FileBuildPath (fullpath, "data", FName);
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f = FileOpen (fullpath, "r");
423
ptr = fgets(pcBuf, (size_t)1024, f);
424
if (ptr) fprintf(pFile, ptr);
433
StrToInt4 (CharPtr str, Int4Ptr longval)
438
Nlm_Boolean nodigits;
441
if (longval != NULL) {
442
*longval = (Nlm_Int4) 0;
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len = (Nlm_Int2) Nlm_StringLen (str);
449
for (i = 0; i < len; i++)
454
if ('0' <= ch && ch <= '9')
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else if ( !/*!!*/ (ch == ' ' || ch == '+' || ch == '-') || nodigits==FALSE)
463
Nlm_StringNCpy (local, str, sizeof (local));
464
if (sscanf (local, "%ld", &val) == 1)
471
static Int4 CountUIDs(char *String)
477
String = SkipSet(String,", ");
478
if (*String == NULLB)
481
String = SkipToSet(String,", ");
487
static Int4 ConvertMMDBUID(CharPtr pcString)
490
CharPtr pcTemp = NULL;
492
if (pcString == NULL)
496
pcTemp = StringSave(pcString);
498
if (!StrToInt4(pcTemp, &iUID))
500
iUID = MMDBEvalPDB(pcTemp);
509
static void MakeUIDList(CharPtr pcString, ValNodePtr PNTR ppvnUIDS)
513
Char SavedChar = NULL;
518
Ptr = SkipSpaces(pcString);
524
Ptr2 = SkipToSet(Ptr," ,");
528
Uid = ConvertMMDBUID(Ptr);
529
/* printf("{%s}[%ld]\n", Ptr, Uid); */
532
ValNodeAddInt(ppvnUIDS, 0, Uid);
535
Ptr = SkipSet(Ptr2," ,");
542
static Int4 GetOptionValue(CharPtr Value, Int4 NumElements, CharPtr *ElementText)
547
if (StrToInt4(Value, &valnum))
550
Len = StringLen(Value);
551
for (count = 0; count < NumElements; count++)
552
if (StrNICmp(ElementText[count],Value, Len) == 0)
555
if (count == NumElements)
563
/* Output links from the protein and nucleotide chains to GenPept reports. */
565
#define EntrezLink "<A HREF=\"%s?uid=%ld&form=6&db=%c&dopt=%c\">%s</A>"
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/************ Added by Ken for Layer One PDB releases ************/
569
static void My_StringNCpy(CharPtr str1, CharPtr str2, Int4 len)
571
StringNCpy(str1,str2,len);
575
static Boolean IsLayerOne(ValNodePtr pvn)
577
Boolean Layer = FALSE;
579
CharPtr LayerOne = {"This is Layer 1 Release"};
585
if (pvn->choice == BiostrucDescr_pdb_comment)
587
comment_txt = (CharPtr)pvn->data.ptrvalue;
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temp_string = StringSave(LayerOne);
589
len = StringLen(LayerOne);
590
My_StringNCpy(temp_string, &comment_txt[18], len);
591
if (!StringICmp(temp_string, LayerOne))
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/***** End of functions added by Ken ********************/
604
PrintMolecularContents(PDNMS ModelStruc, FILE *gdf)
613
if (ModelStruc == NULL)
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pmsd = (PMSD) ModelStruc->data.ptrvalue;
619
for (pdnmm = pmsd->pdnmmHead, cnt = 0; pdnmm != NULL; pdnmm = pdnmm->next) {
620
pmmd = (PMMD) pdnmm->data.ptrvalue;
622
if ((pmmd->bWhat) & AM_PROT) {
624
fprintf(gdf, "<TR>\n<TD VALIGN=TOP NOWRAP>");
625
fprintf(gdf, "<strong>Protein Chains:</strong></TD>\n<TD>");
627
if (pmmd->pcMolName[0] == ' ')
628
fprintf(gdf, EntrezLink, ENTREZurl, (long) pmmd->iGi, 'p', 'g',
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fprintf(gdf, EntrezLink, ENTREZurl, (long) pmmd->iGi, 'p', 'g',
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fprintf(gdf, EntrezLink, ENTREZurl, (long) pmmd->iGi, 'p', 'g',
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fprintf(gdf, "</TD>\n</TR>\n");
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/* nucleotide chains */
646
for (pdnmm = pmsd->pdnmmHead, cnt = 0; pdnmm != NULL; pdnmm = pdnmm->next) {
647
pmmd = (PMMD) pdnmm->data.ptrvalue;
649
if ((pmmd->bWhat) & (AM_DNA | AM_RNA)) {
651
fprintf(gdf, "<TR>\n<TD VALIGN=TOP NOWRAP>");
652
fprintf(gdf, "<strong>Nucleotide chains:</strong></TD>\n<TD>");
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if (pmmd->pcMolName[0] == ' ')
655
fprintf(gdf, EntrezLink, ENTREZurl, (long) pmmd->iGi, 'n', 'g',
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fprintf(gdf, EntrezLink, ENTREZurl, (long) pmmd->iGi, 'n', 'g',
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fprintf(gdf, EntrezLink, ENTREZurl, (long) pmmd->iGi, 'n', 'g',
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fprintf(gdf, "</TD>\n</TR>\n");
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} /* end PrintMolecularContents */
677
PrintStructureInfo(PDNMS ModelStruc, FILE *File, CharPtr tax_save)
680
Int4 depyear, depday;
681
PMSD pmsdThis = NULL;
682
BiostrucSourcePtr pbssThis = NULL;
683
ValNodePtr pvnThis = NULL;
684
BiostrucHistoryPtr pbshThis = NULL;
685
CharPtr pcAuthors = NULL;
691
pmsdThis = (PMSD) ModelStruc->data.ptrvalue;
692
pvnThis = ValNodeFindNext(pmsdThis->pbsBS->descr,NULL,BiostrucDescr_history);
695
pbshThis = (BiostrucHistoryPtr) pvnThis->data.ptrvalue;
696
pbssThis = pbshThis->data_source;
700
fprintf(File, "<font size=+2>MMDB Id: %ld  ", (long) pmsdThis->iMMDBid);
702
fprintf(File, "<font size=+2>");
703
fprintf(File, "MMDB Id: <A HREF=\"%s%s?uid=%ld&form=6&db=t&Dopt=s\">%ld</A>  ",
704
URLcgi, CGIName, (long) pmsdThis->iMMDBid, (long) pmsdThis->iMMDBid);
705
fprintf(File, "PDB Id: <A HREF=\"%s=%s\">%s</a>\n", TDBurl,pmsdThis->pcPDBName, pmsdThis->pcPDBName);
706
if (IsLayerOne(pmsdThis->pbsBS->descr))
707
fprintf(File, " - Warning: <A HREF=\"http://www.pdb.bnl.gov/pdb-docs/what_is_LR.html\">Not validated!</A>\n");
708
fprintf(File, "</font>");
709
fprintf(File, "<BR>\n<BR>\n");
710
fprintf(File, "<TABLE>\n");
711
PrintMolecularContents(ModelStruc, File);
712
fprintf(File, "<TR>\n<TD VALIGN=TOP NOWRAP>");
713
fprintf(File, "<strong>MEDLINE</strong>:</TD>\n<TD><A HREF=\"%s?db=t&form=6&uid=", ENTREZurl);
714
fprintf(File, "%ld&Dopt=m\">PubMed</A></TD>\n</TR>\n", (long) pmsdThis->iMMDBid );
716
if (tax_save != NULL)
717
fprintf(File, "%s\n", tax_save);
718
else if (pmsdThis->pcPdbSource) {
719
fprintf(File, "<TR>\n<TD VALIGN=TOP NOWRAP>");
720
fprintf(File, "<strong>Source</strong>:</TD>\n<TD>%s</TD>\n</TR>\n", pmsdThis->pcPdbSource);
723
/* insert a blank row in the table, for spacing */
724
fprintf(File, "<TR>\n<TD VALIGN=TOP NOWRAP> </TD>\n<TD><BR></TD>\n</TR>\n");
725
pcAuthors = AuthorListPDB(pmsdThis->pbsBS);
728
fprintf(File, "<TR>\n<TD VALIGN=TOP NOWRAP>");
729
fprintf(File, "<strong>PDB Authors</strong>:</TD>\n<TD>%s</TD>\n</TR>\n", pcAuthors);
735
depyear = pbssThis->database_entry_date->data[1];
736
depday = pbssThis->database_entry_date->data[3];
737
fprintf(File, "<TR>\n<TD VALIGN=TOP NOWRAP>");
738
fprintf(File, "<strong>PDB Deposition</strong>:</TD>\n<TD>%2d-%3s-%02d</TD>\n</TR>\n",
739
(int) depday, NCBI_months[pbssThis->database_entry_date->data[2] - 1], (int) depyear%100);
742
if (pmsdThis->pcPdbClass) {
743
fprintf(File, "<TR>\n<TD VALIGN=TOP NOWRAP>");
744
fprintf(File, "<strong>PDB Class</strong>:</TD>\n<TD>%s</TD>\n</TR>\n", pmsdThis->pcPdbClass);
747
fprintf(File, "<TR>\n<TD VALIGN=TOP NOWRAP>");
748
pvnThis = ValNodeFindNext(pmsdThis->pGraphDescr,NULL,BiomolDescr_pdb_comment);
750
fprintf(File, "<strong>PDB Title</strong>:</TD>\n<TD>%s</TD>\n</TR>\n", pmsdThis->pcChemName);
752
fprintf(File, "<strong>PDB Compound</strong>:</TD>\n<TD>%s</TD>\n</TR>\n", pmsdThis->pcChemName);
753
/* insert a blank row in the table, for spacing */
754
fprintf(File, "<TR>\n<TD VALIGN=TOP NOWRAP> </TD>\n<TD><BR></TD>\n</TR>\n");
756
/* Note: The table continues with "Sequence Neighbors" and "Structure Neighbors". */
764
PrintStructureView(PDNMS ModelStruc, FILE *File)
768
if (ModelStruc == NULL) return;
770
pmsd = (PMSD) ModelStruc->data.ptrvalue;
771
fprintf(File, "<FORM METHOD=POST ACTION=\"%s%s\">\n", URLcgi, CGIName);
772
fprintf(File, "<INPUT TYPE=HIDDEN NAME=uid VALUE=%ld>\n", (long) pmsd->iMMDBid);
773
WWWPrintFileData(CODEFILE, File);
778
/* This routine creates the last two rows of the table started by PrintStructureInfo.
779
* These last two rows contain the links for the "Sequence Neighbors" of the chains of
780
* the structure, and for "Structure Neighbors" of the chains and domains of the
781
* structure. The first part of the code is very similar to PrintMolecularContents.
782
* The 2nd part creates the links for the VAST structure neighbors.
784
* Note there are 3 different formats for Vast neighbor links, purely for cosmetics.
787
#define VastLink1 "<A HREF=\"%s?uid=%ld&chaindom=%ld\">%s</A>"
788
#define VastLink2 "<A HREF=\"%s?uid=%ld&chaindom=%ld\">%s.%d</A>"
789
#define VastLink3 "<A HREF=\"%s?uid=%ld&chaindom=%ld\">%d</A>"
792
PrintStructureLinks(PDNMS ModelStruc, FILE *gdf)
800
Int4 uid, ichn, idom, chndom, chndom0;
804
if (ModelStruc == NULL)
807
/* insert a blank row in the table, for spacing */
808
fprintf(gdf, "<TR>\n<TD VALIGN=TOP NOWRAP> </TD>\n<TD> </TD>\n</TR>\n");
811
pmsd = (PMSD) ModelStruc->data.ptrvalue;
813
for (pdnmm = pmsd->pdnmmHead, cnt = pflg = 0; pdnmm != NULL; pdnmm = pdnmm->next) {
814
pmmd = (PMMD) pdnmm->data.ptrvalue;
816
if ((pmmd->bWhat) & AM_PROT) {
817
if ((pmmd->iResCount <= 1) || (pmmd->iGi <= 0))
822
fprintf(gdf, "<TR>\n<TD VALIGN=TOP NOWRAP>");
823
fprintf(gdf, "<strong>Sequence Neighbors:</strong></TD>\n<TD>");
825
if (pmmd->pcMolName[0] == ' ')
826
fprintf(gdf, EntrezLink, ENTREZurl, (long) pmmd->iGi, 'p', 'p',
829
fprintf(gdf, EntrezLink, ENTREZurl, (long) pmmd->iGi, 'p', 'p',
834
fprintf(gdf, EntrezLink, ENTREZurl, (long) pmmd->iGi, 'p', 'p',
840
/* nucleotide chains */
841
for (pdnmm = pmsd->pdnmmHead; pdnmm != NULL; pdnmm = pdnmm->next) {
842
pmmd = (PMMD) pdnmm->data.ptrvalue;
844
if ((pmmd->bWhat) & (AM_DNA | AM_RNA)) {
845
if ((pmmd->iResCount <= 1) || (pmmd->iGi <= 0))
849
fprintf(gdf, "<TR>\n<TD VALIGN=TOP NOWRAP>");
850
fprintf(gdf, "<strong>Sequence Neighbors:</strong></TD>\n<TD>");
852
if (pmmd->pcMolName[0] == ' ')
853
fprintf(gdf, EntrezLink, ENTREZurl, (long) pmmd->iGi, 'n', 'n',
856
fprintf(gdf, EntrezLink, ENTREZurl, (long) pmmd->iGi, 'n', 'n',
861
fprintf(gdf, EntrezLink, ENTREZurl, (long) pmmd->iGi, 'n', 'n',
868
fprintf(gdf, "</TD>\n</TR>\n");
870
if (pmsd->pdnmlModels == NULL) {
872
fprintf(gdf, "</TABLE>\n<BR>\n");
876
/* VAST neighbors: loop over protein chains */
877
uid = (Int4) pmsd->iMMDBid;
879
for (pdnmm = pmsd->pdnmmHead, cnt = ichn = 0; pdnmm != NULL; pdnmm = pdnmm->next) {
880
pmmd = (PMMD) pdnmm->data.ptrvalue;
883
if ((pmmd->bWhat) & AM_PROT) {
884
if ((pmmd->iResCount <= 1) || (pmmd->iGi <= 0))
887
chndom0 = 10000*uid + 100*(Int4) ichn;
890
fprintf(gdf, "<TR>\n<TD VALIGN=TOP NOWRAP>");
891
fprintf(gdf, "<strong>Structure Neighbors:</strong></TD>\n<TD>");
893
if (pmmd->pcMolName[0] == ' ')
894
fprintf(gdf, VastLink1, VASTurl, (long) uid, (long) chndom0,
897
fprintf(gdf, VastLink1, VASTurl, (long) uid, (long) chndom0,
902
fprintf(gdf, VastLink1, VASTurl, (long) uid, (long) chndom0,
906
/* now loop over domains */
909
for (pdnmg = pmmd->pdnmgHead; pdnmg != NULL; pdnmg = pdnmg->next) {
910
pmgd = (PMGD) pdnmg->data.ptrvalue;
912
if (pmgd->iDomain > idom) {
913
idom = (Int4) pmgd->iDomain;
914
chndom = chndom0 + idom;
917
if (pmmd->pcMolName[0] == ' ')
918
fprintf(gdf, VastLink3, VASTurl, (long) uid,
919
(long) chndom, (int) idom);
921
fprintf(gdf, VastLink2, VASTurl, (long) uid,
922
(long) chndom, pmmd->pcMolName, (int) idom);
929
fprintf(gdf, "</TD>\n</TR>\n</TABLE>\n");
931
} /* end PrintStructureLinks */
935
/* Utility routine needed below. Return a vector marking the distinct integers
936
* appearing in the input array. A naive algorithm is used since we never expect
937
* the array size 'n' to be large. If an entry vec[i] is 0, this means it is
938
* a duplicate. If vec[i] > 0 then this is the first occurrence of the number,
939
* and the value vec[i] is the number of times the corresponding number nums[i]
944
mark_distinct(Int4Ptr nums, Int2Ptr vec, Int2 n)
951
/* initialize the vector */
952
for (i = 0; i < n; i++)
955
for (i = 1; i < n; i++) {
956
for (j = 0; j < i; j++) {
957
if (nums[i] == nums[j]) {
965
} /* end mark_distinct */
969
/* Output the taxonomy data, per chain, and also links to the taxonomy database.
970
* Return '1' in case there was a non-trivial taxonomy assignment, '0' if there
971
* was no taxonomy data found. The success or failure is passed ultimately to
972
* PrintStructureInfo, where the PDB source is displayed in case no taxonomy data
977
SaveTaxonomyInfo(BiostrucPtr bsp, CharPtr save, Int2 n, CharPtr pname)
979
MoleculeGraphPtr mgp;
980
Int4 i, j, k, cnt, txcnt, uacnt;
981
ValNodePtr descr, db;
982
CharPtr chainp, name, names[MAX_CHAINS];
983
Char chn, chns[MAX_CHAINS], org_names[MAX_TBUFF];
984
Int2 flg, name_here, cnt_vec[MAX_CHAINS];
987
Int4 molecule_type, tax_id, tax_ids[MAX_CHAINS];
991
if ((bsp == NULL) || (save == NULL))
994
for (i = 0; i < MAX_TBUFF; i++)
998
mgp = bsp->chemical_graph->molecule_graphs;
1000
for (cnt = uacnt = 0; (mgp != NULL) && (cnt < MAX_CHAINS); mgp = mgp->next) {
1001
/* zap the OrgRefPtr, there may be no taxonomy for this chain! */
1004
for (descr = mgp->descr; descr != NULL; descr = descr->next) {
1005
if (descr->choice == BiomolDescr_molecule_type)
1006
molecule_type = descr->data.intvalue;
1008
if (descr->choice == BiomolDescr_name) {
1009
chainp = descr->data.ptrvalue;
1013
if (descr->choice == BiomolDescr_organism) {
1014
bios = descr->data.ptrvalue;
1015
org = (OrgRefPtr) bios->org;
1019
if ((molecule_type == Molecule_type_protein) ||
1020
(molecule_type == Molecule_type_dna) ||
1021
(molecule_type == Molecule_type_rna)) {
1023
/* save the chain and get the taxonomy data */
1024
chns[cnt] = (chn == ' ') ? '\n' : chn;
1028
ObjectIdPtr object_id;
1030
for (db = org->db, tax_id = -1; db != NULL; db = db->next) {
1031
if (db->choice == TAX_ID_CHOICE_NUM) {
1032
dbtag = db->data.ptrvalue;
1033
tax_id = dbtag->tag->id;
1038
names[cnt] = &org_names[name_here];
1040
if (org->taxname != NULL) {
1041
StringCat(names[cnt], org->taxname);
1042
name_here += StrLen(org->taxname) + 1;
1044
else if (org->common != NULL) {
1045
StringCat(names[cnt], org->common);
1046
name_here += StrLen(org->common) + 1;
1049
StringCat(names[cnt], "(unassigned)");
1053
tax_ids[cnt++] = tax_id;
1056
/* track the number of unassigned chains */
1058
names[cnt] = &org_names[name_here];
1059
StringCat(names[cnt], "(unassigned)");
1061
tax_ids[cnt++] = -1;
1066
/* zap the save area */
1067
for (i = 0; i < n; i++)
1070
/* flag the taxonomy section */
1071
sprintf(save, "<TR>\n<TD VALIGN=TOP NOWRAP><strong>Taxonomy</strong>:</TD>\n");
1075
sprintf(&save[k], "<TD>(unassigned)</TD>\n");
1079
/* group chains by organism type, i.e. tax id */
1080
mark_distinct(tax_ids, cnt_vec, cnt);
1082
for (i = flg = 0; i < cnt; i++) {
1083
if (cnt_vec[i] == 0)
1086
tax_id = tax_ids[i];
1090
sprintf(&save[k], "; ");
1092
sprintf(&save[k], "<TD>");
1096
/* collect chains with the same tax id */
1102
sprintf(&save[k], "chains ");
1103
else if (chns[i] != '\n')
1104
sprintf(&save[k], "chain ");
1107
for (j = i; (j < cnt) && (txcnt > 0); j++) {
1108
if (tax_ids[j] != tax_id)
1114
sprintf(&save[k], "%c, ", chns[j]);
1116
sprintf(&save[k], "%c", chns[j]);
1122
if (chns[i] != '\n')
1123
sprintf(&save[k], "  <A HREF=\"");
1125
sprintf(&save[k], "<A HREF=\"");
1128
sprintf(&save[k], TAXurl, tax_id);
1130
sprintf(&save[k], "\">%s</A> ", names[i]);
1133
sprintf(&save[k], " (unassigned)");
1137
sprintf(&save[k], "</TD>\n</TR>\n");
1140
} /* end SaveTaxonomyInfo */
1144
/* Old version of DumpMime, preserved for compatibility with Cn3D v1.0. */
1146
static void DumpMime_v1(AsnIoPtr aip, CharPtr title, Int2 style, Int2 choice, VoidPtr datum)
1148
NcbiMimeAsn1Ptr mime;
1149
EntrezGeneralPtr egp;
1151
mime = (NcbiMimeAsn1Ptr) ValNodeNew(NULL);
1152
mime->choice = NcbiMimeAsn1_entrez;
1153
egp = EntrezGeneralNew();
1154
mime->data.ptrvalue = (VoidPtr) egp;
1155
egp->Data_data = ValNodeNew(NULL);
1156
egp->title = StringSave(title);
1158
egp->Data_data->choice = choice;
1159
egp->Data_data->data.ptrvalue = datum;
1161
NcbiMimeAsn1AsnWrite(mime, aip, NULL);
1164
egp->Data_data->data.ptrvalue = NULL; /* for clean free */
1165
NcbiMimeAsn1Free(mime);
1167
} /* end DumpMime_v1 */
1172
static void DumpMime(AsnIoPtr aip, CharPtr title, VoidPtr datum)
1174
NcbiMimeAsn1Ptr mime;
1175
EntrezGeneralPtr egp;
1177
mime = (NcbiMimeAsn1Ptr) ValNodeNew(NULL);
1178
mime->choice = NcbiMimeAsn1_strucseq;
1179
mime->data.ptrvalue= datum;
1181
NcbiMimeAsn1AsnWrite(mime, aip, NULL);
1184
mime->data.ptrvalue=NULL ; /* for clean free */
1185
NcbiMimeAsn1Free(mime);
1190
#define LAUNCH_VIEWER 0
1195
/* Handle the various View/See/Save file options. */
1198
SendStructureMIME(Char Filetype, Int4 uid, Int4 Mime, Int4 Complexity,
1199
Int4 Models, Int4 Color, Int4 Render)
1203
Int4 count, i4Sent = 0, error_flag = 0;
1207
NcbiMimeAsn1Ptr mime;
1208
BiostrucSeqPtr bssp;
1209
BiostrucGraphPtr bsgp;
1210
MoleculeGraphPtr mgp;
1216
if ((bsp = MMDBBiostrucGet((DocUid) uid, Complexity, Models)) == NULL) {
1217
printf("Content-type: text/html\r\n\r\n");
1218
printf("<h2>Error</h2>\n");
1219
printf("Structure with UID = %ld failed to fetch on Server<p>\n", (long) uid);
1220
printf("No such structure available on this MMDB server.\n");
1225
bsgp = bsp->chemical_graph;
1226
mgp = bsgp->molecule_graphs;
1228
/* This_uid = EntrezFindSeqId(sip); */
1230
if(sip->choice == 12) This_uid = sip->data.intvalue;
1233
sep = EntrezSeqEntryGet(This_uid, retcode);
1235
bssp = BiostrucSeqNew();
1236
bssp->structure = bsp;
1237
ValNodeLink(&(bssp->sequences), sep);
1239
mime = (NcbiMimeAsn1Ptr) ValNodeNew(NULL); /* yanli */
1240
mime->choice = NcbiMimeAsn1_strucseq;
1241
mime->data.ptrvalue = bssp;
1244
/* the following headers are format-independent */
1247
printf("Content-type: application/octet-stream\r\n\r\n");
1250
printf ("Content-type: text/html\r\n\r\n");
1251
printf ("<HTML><PRE>\r\n");
1254
printf ("Content-type: text/html\r\n\r\n");
1258
if (Filetype == 'j') {
1259
/* Cn3D v2.0 asn.1 format */
1262
printf ("Content-type: chemical/ncbi-asn1-binary\r\n\r\n");
1263
aip = AsnIoNew(ASNIO_BIN_OUT, stdout, NULL, NULL, NULL);
1264
DumpMime(aip, "MIME", bssp);
1267
aip = AsnIoNew(ASNIO_BIN_OUT, stdout, NULL, NULL, NULL);
1268
NcbiMimeAsn1AsnWrite(mime, aip, NULL);
1271
aip = AsnIoNew(ASNIO_TEXT_OUT, stdout, NULL, NULL, NULL);
1272
NcbiMimeAsn1AsnWrite(mime, aip, NULL);
1275
aip = AsnIoNew(ASNIO_TEXT_OUT, stdout, NULL, NULL, NULL);
1276
NcbiMimeAsn1AsnWrite(mime, aip, NULL);
1283
else if (Filetype == 'i') {
1284
/* Cn3D v1.0 asn.1 format. Included for backwards compatibility, in case users
1285
* want to stick with their old Cn3D for some reason.
1289
printf ("Content-type: chemical/ncbi-asn1-binary\r\n\r\n");
1290
/* printf ("Content-disposition: filename=\"%d.val\"\r\n\r\n", uid);*/
1291
aip = AsnIoNew(ASNIO_BIN_OUT, stdout, NULL, NULL, NULL);
1292
DumpMime_v1(aip, "MIME", Entrez_style_report, Data_data_structure, bsp);
1295
aip = AsnIoNew(ASNIO_BIN_OUT, stdout, NULL, NULL, NULL);
1296
BiostrucAsnWrite(bsp, aip, NULL);
1299
aip = AsnIoNew(ASNIO_TEXT_OUT, stdout, NULL, NULL, NULL);
1300
BiostrucAsnWrite(bsp, aip, NULL);
1303
aip = AsnIoNew(ASNIO_TEXT_OUT, stdout, NULL, NULL, NULL);
1304
BiostrucAsnWrite(bsp, aip, NULL);
1311
else if (Filetype == 'r') {
1313
if (Mime == LAUNCH_VIEWER)
1314
printf ("Content-type: chemical/x-pdb\r\n\r\n");
1315
/* printf ("Content-disposition: filename=\"%d.pdb\"\r\n\r\n", uid);*/
1317
ModelStruc = MakeAModelstruc(bsp);
1318
bssp->structure = NULL; /* already linked into modelstruc */
1319
WritePDBAllModel(ModelStruc, stdout);
1322
else if (Filetype == 'k') {
1324
if (Mime == LAUNCH_VIEWER)
1325
printf ("Content-type: chemical/x-kinemage\r\n\r\n");
1326
/* printf ("Content-disposition: filename=\"%d.kin\"\r\n\r\n", uid);*/
1328
ModelStruc = MakeAModelstruc(bsp);
1329
bssp->structure = NULL; /* already linked into modelstruc */
1330
WriteKinAllModel(ModelStruc, stdout, Color, Render);
1335
printf("Content-type: text/html\r\n\r\n");
1336
printf("<h2>Error</h2>\n");
1337
printf("Unknown file type on structure fetch.<p>\n");
1338
printf("Contact %s\n", MAILTO);
1341
if ((Mime == SEE_FILE) && (!error_flag))
1342
printf ("</PRE></HTML>\r\n");
1344
NcbiMimeAsn1Free(mime); /* yanli */
1347
} /* end SendStructureMIME */
1350
static Int4 SendSummaryPage(Int4Ptr Uids, Int4 NumToDisplay, Int4 Save)
1355
Int4 uid, count, i4Sent = 0;
1357
Char tax_save[MAX_TBUFF];
1361
printf ("Content-type: application/octet-stream\n\n");
1363
printf ("Content-type: text/html\n\n");
1365
if (!GlobalNonHtmlOutput) {
1367
WWWPrintFileData(HEADFILE, stdout);
1369
printf ( "<html>\n<title>MMDB Structure Summary</title><body>");
1371
for (count = 0; count < NumToDisplay; count++)
1374
bsp = MMDBBiostrucGet((DocUid) uid,3,0);
1377
printf ("%sNo structure found for UID %ld.%s\n",
1378
GlobalNonHtmlOutput ? "\n" : "<P><h4>",uid,
1379
GlobalNonHtmlOutput ? "\n" : "</h4><P>");
1380
if (!GlobalNonHtmlOutput)
1381
printf ("<HR SIZE=5 NOSHADE><BR>\n");
1385
if (!GlobalNonHtmlOutput) {
1388
for (descr = bsp->descr, name = NULL; descr != NULL; descr = descr->next) {
1389
if (descr->choice == BiomolDescr_name) {
1390
name = descr->data.ptrvalue;
1394
taxret = SaveTaxonomyInfo(bsp, tax_save, MAX_TBUFF, name);
1397
ModelStruc = MakeAModelstruc(bsp);
1398
PrintStructureInfo(ModelStruc, stdout, (taxret) ? tax_save : NULL);
1400
if (!GlobalNonHtmlOutput) /* Rest of View/Save stuff */
1402
PrintStructureLinks(ModelStruc, stdout);
1403
PrintStructureView(ModelStruc, stdout);
1404
printf ("<HR SIZE=5 NOSHADE><BR>\n");
1409
if (!GlobalNonHtmlOutput)
1411
WWWPrintFileData(TAILFILE, stdout);
1416
} /* SendSummaryPage() */
1419
static void SendGetNetscape(void) {
1421
printf("HTTP/1.0 200 OK\r\n");
1422
printf("MIME-Version: 1.0\r\n");
1423
printf("Content-type: text/html\r\n\r\n");
1424
printf("<BR><BR><B>Sorry, you need a <a href=\"http://home.netscape.com/\">",
1425
"Netscape</a> version 2 or higher WWW-browser "
1426
"to be able to enter this page</B><BR>\n\n");
1427
} /* SendGetNetscape */
1432
static Boolean InitMMDBSrv(void)
1444
ENTREZurl[0] = '\0';
1451
for (i = 0; i < PATH_MAX; i++)
1454
FindPath("mmdb", "MMDBSRV", "HTMLPath", HTMLPath, PATH_MAX);
1455
if (HTMLPath[0] == '\0')
1457
ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nMMDBSRV section no HTMLPath...\n");
1460
GetAppParam("mmdb", "MMDBSRV", "URLBase", "", URLBase, PATH_MAX);
1461
if (URLBase[0] == '\0')
1463
ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nMMDBSRV section no URLBase...\n");
1466
GetAppParam("mmdb", "MMDBSRV", "URLHelp", "", URLHelp, PATH_MAX);
1467
if (URLHelp[0] == '\0')
1469
ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nMMDBSRV section no URLHelp...\n");
1472
FindPath("mmdb", "MMDBSRV", "CGIPath", CGIPath, PATH_MAX);
1473
if (CGIPath[0] == '\0')
1475
ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nMMDBSRV section no CGIPath...\n");
1479
GetAppParam("mmdb", "MMDBSRV", "URLcgi", "", URLcgi, PATH_MAX);
1480
if (URLcgi[0] == '\0')
1482
ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nMMDBSRV section no URLcgi...\n");
1485
GetAppParam("mmdb", "MMDBSRV", "CGIName", "", CGIName, (size_t) 256 * sizeof(char));
1486
if (CGIName[0] == '\0')
1488
ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nMMDBSRV section no CGIName...\n");
1491
FindPath("mmdb", "MMDBSRV", "DATApath", DATApath, PATH_MAX);
1492
if (DATApath[0] == '\0')
1494
ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nMMDBSRV section no DATApath...\n");
1498
sprintf(ARROW, "<IMG alt=\"o\" SRC=\"%sarrow.gif\" ALT=\"o\" BORDER=0>\n", URLBase);
1500
FindPath("mmdb", "MMDBSRV", "LOGpath", LOGpath, PATH_MAX);
1501
if (LOGpath[0] == '\0')
1503
ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nMMDBSRV section no LOGpath...\n");
1506
GetAppParam("mmdb", "MMDBSRV", "ENTREZurl", "", ENTREZurl, PATH_MAX);
1507
if (ENTREZurl[0] == '\0')
1509
ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nMMDBSRV section no ENTREZurl...\n");
1512
GetAppParam("mmdb", "MMDBSRV", "VASTurl", "", VASTurl, PATH_MAX);
1513
if (VASTurl[0] == '\0')
1515
ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nMMDBSRV section no VASTurl...\n");
1518
GetAppParam("mmdb", "MMDBSRV", "MMDBurl", "", MMDBurl, PATH_MAX);
1519
if (MMDBurl[0] == '\0')
1521
ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nMMDBSRV section no MMDBurl...\n");
1524
GetAppParam("mmdb", "MMDBSRV", "PDBurl", "", PDBurl, PATH_MAX);
1525
if (PDBurl[0] == '\0')
1527
ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nMMDBSRV section no PDBurl...\n");
1530
GetAppParam("mmdb", "MMDBSRV", "TDBurl", "", TDBurl, PATH_MAX);
1531
if (TDBurl[0] == '\0')
1533
ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nMMDBSRV section no TDBurl...\n");
1536
GetAppParam("mmdb", "TAXLINK", "TAXurl", "", TAXurl, PATH_MAX);
1537
if (TAXurl[0] == '\0')
1539
ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nTAXLINK section no TAXurl...\n");
1542
StringCat(TAXurl, "?id=%d&lvl=0");
1543
GetAppParam("mmdb", "MMDBSRV", "MAILto", "", MAILto, PATH_MAX);
1544
if (MAILto[0] == '\0')
1546
ErrPostEx(SEV_FATAL,0,0, "MMDB config file \nMMDBSRV section no Mailto...\n");
1551
sprintf(MAILTO, "< <a href=\"%s\">%s</a> >", MAILto, MAILto);
1558
/************************************************************************
1560
* Int2 Main() - main function
1562
***********************************************************************/
1568
Boolean Netscape2_OK = FALSE;
1570
CharPtr TimeNowStr = NULL;
1572
Int4 IndexArgs = -1;
1578
Char DispOpt = '\0';
1580
CharPtr pcThis = NULL, pcName = NULL;
1581
CharPtr Uids; /* (list of MMDB ids or PDB ids) */
1582
Int4Ptr MMDBids = NULL; /* (list of MMDB ids ) */
1586
Int4 NumEntries = 0;
1587
ValNodePtr pvnUIDS = NULL, pvnThis = NULL;
1589
/* this sets up the unix time limit */
1594
getrlimit(RLIMIT_CPU, &rl);
1595
rl.rlim_max = rl.rlim_cur = CPUTIME_MAX;
1596
setrlimit(RLIMIT_CPU, &rl);
1600
if (!InitMMDBSrv()) {
1601
printf("Content-type: text/html\r\n\r\n");
1602
printf("<H2>MMDBSRV Error</H2>\n - Unable to Open Server Configuration File.<p>\n");
1603
printf("Contact the MMDBSRV administrator for this site.<p>\n");
1607
StringCat(LOGpath, "mmdbsrv.log");
1608
if( !ErrSetLogfile (LOGpath, ELOG_APPEND) ) {
1609
printf("Content-type: text/html\r\n\r\n");
1610
printf("<H2>MMDBSRV Error</H2>\n - Unable to Open Log.<p>\n");
1611
printf("Contact MMDBSRV administrator for this site: %s<p>\n", MAILTO);
1615
ErrSetLogLevel(SEV_MAX);
1616
ErrSetOpts (ERR_CONTINUE, ERR_LOG_ON);
1620
if((error = WWWGetArgs(&info)) != WWWErrOk) {
1621
printf("Content-type: text/html\r\n\r\n");
1622
printf("<H2>MMDBSRV Error</H2>\n Failed to Process Posting - Check your GET/POST syntax\n");
1627
/* if(WWWGetBrowser(info) != NETSCAPE) {
1632
if ((!OpenMMDBAPI(0, NULL)) || (!MMDBInit()))
1634
ErrLogPrintf("#MMDB Database Access Failed to Initialize.\n");
1635
printf("Content-type: text/html\r\n\r\n");
1636
printf("<H2>MMDBSRV Error</H2>\n - Unable to Open MMDB Database on Server.<p>");
1637
printf("Contact MMDBSRV administrator for this site: %s<p>\n", MAILTO);
1641
if (EntrezInit("mmdbsrv", NULL, FALSE) == FALSE)
1643
printf("Content-type: text/html\n\n");
1644
printf("<h2>Error</h2>\n");
1645
printf("MMDBSERV: EntrezInit Failed.<p>\n");
1649
/*if( !BioseqFetchInit(TRUE))
1651
ErrLogPrintf("BioseqFetchInit failed! \n");
1652
printf("Content-type: text/html\r\n\r\n");
1653
printf("<H2>MMDBSRV Error</H2>\n - BioseqFetchInit failed! <p>");
1654
printf("Contact MMDBSRV administrator for this site: %s<p>\n", MAILTO);
1662
if ((IndexArgs = WWWFindName(info,"db")) >= 0)
1664
pcThis = WWWGetValueByIndex(info,IndexArgs);
1665
DispOpt = pcThis[0];
1666
if ((DispOpt != 't') && (DispOpt != 'T'))
1668
printf("Content-type: text/html\r\n\r\n");
1669
printf("<H2>MMDBSRV Error</H2>\n - Wrong Database Type db=%c.<p>\n", DispOpt );
1670
printf("Try <a href=\"%s\">WWW-Entrez</a> for this<p>\n", URLHelp);
1676
if ((IndexArgs = WWWFindName(info, "form")) >= 0)
1678
pcThis = WWWGetValueByIndex(info,IndexArgs);
1679
if ((!StrToInt4(pcThis,&Form)) || (Form != 6))
1681
printf("Content-type: text/html\r\n\r\n");
1682
printf("<H2>MMDBSRV Error</H2>\n - Wrong Form Type form=%s.<p>\n", pcThis );
1683
printf("<pre>Only supports form=6</pre><p>\n");
1684
printf("Try <a href=\"%s\">WWW-Entrez</a> for this<p>\n", URLHelp);
1693
if ((IndexArgs = WWWFindName(info, "uid")) < 0)
1695
printf("Content-type: text/html\r\n\r\n");
1696
printf("<H2>MMDBSRV Error</H2>\n - No Identifier specified:<p>\n<pre>Missing uid=</pre><p>\n");
1701
/* loop over entire set of tag=value entries and add all the UID's found together */
1702
/* must handle uid=1234&uid=1OMD&uid=1234,2345,2134&dopt=s&uid=3INS */
1703
NumEntries = WWWGetNumEntries(info);
1704
for (IndexArgs = 0; IndexArgs < NumEntries; IndexArgs++)
1706
pcName = WWWGetNameByIndex(info, IndexArgs);
1707
pcThis = WWWGetValueByIndex(info, IndexArgs);
1709
if (StrICmp(pcName, "uid") == 0)
1711
/* printf("[%s][%s]\n", pcThis, pcName); */
1712
MakeUIDList(pcThis, &pvnUIDS);
1715
if (pvnUIDS == NULL)
1717
printf("Content-type: text/html\r\n\r\n");
1718
printf("<H2>MMDBSRV Error</H2>\n - UID specified does not match an MMDB-ID or PDB-Code:<p>\n");
1725
pvnThis = pvnThis->next;
1727
MMDBids = (Int4Ptr) MemNew((size_t) (sizeof(Int4) * iMMDBids));
1732
MMDBids[iCount] = (Int4) pvnThis->data.intvalue;
1733
/* printf("%ld \n",(long) MMDBids[iCount]); */
1734
pvnThis = pvnThis->next;
1741
if ((IndexArgs = WWWFindName(info, "dopt")) >= 0)
1743
pcThis = WWWGetValueByIndex(info,IndexArgs);
1773
printf("Content-type: text/html\r\n\r\n");
1774
printf("<H2>MMDBSRV Error</H2>\n - Wrong Display Option Type: dopt=%s.<p>\n", pcThis);
1775
printf("<pre>dopt supports:\n's' Structure summary\n");
1776
printf("'r' RasMol(PDB) format\n'k' Kinemage format\n'i', 'j', or 'a' ASN.1</pre><p>\n");
1783
DispOpt = 's'; /* structure summary is default when no dopt supplied */
1788
if ((IndexArgs = WWWFindName(info, "Complexity")) >= 0)
1790
pcThis = WWWGetValueByIndex(info,IndexArgs);
1793
for (iCount = 0; iCount < NUM_COMPLEXITY_TYPES; iCount++)
1794
if (StrICmp(pcThis,ComplexityDescriptions[iCount]) == 0)
1803
Complex = ONECOORDRES;
1806
Complex = ONECOORDATOM;
1815
MaxModels = INT2_MAX;
1818
Complex = ONECOORDATOM;
1822
printf("Content-type: text/html\r\n\r\n");
1823
printf("<H2>MMDBSRV Error</H2>\n - Wrong Complexity Type: Complexity=%s.<p>\n", pcThis );
1830
if ((IndexArgs = WWWFindName(info, "mdlLvl")) >= 0)
1832
pcThis = WWWGetValueByIndex(info, IndexArgs);
1833
Complex = atoi(pcThis);
1837
if ((IndexArgs = WWWFindName(info, "maxModels")) >= 0)
1839
pcThis = WWWGetValueByIndex(info, IndexArgs);
1840
MaxModels = atoi(pcThis);
1844
if ((IndexArgs = WWWFindName(info, "KinemageColor")) >= 0)
1846
pcThis = WWWGetValueByIndex(info, IndexArgs);
1847
KinColor = GetOptionValue(pcThis, NUM_COLOR_TYPES, ColorDescriptions);
1853
if ((IndexArgs = WWWFindName(info, "KinemageRender")) >= 0)
1855
pcThis = WWWGetValueByIndex(info,IndexArgs);
1856
StrToInt4(pcThis, &KinRender);
1860
if ((IndexArgs = WWWFindName(info, "save")) >= 0)
1861
{ /* these don't affect structure summaries */
1862
pcThis = WWWGetValueByIndex(info,IndexArgs);
1863
if (StrICmp(pcThis, "See") == 0)
1865
Save = 1; /* sends MIMED-type files to view in ascii-readable form */
1867
else if (StrICmp(pcThis, "Save") == 0)
1869
Save = 2; /* sends MIMED-type files in raw save form */
1871
else if (StrICmp(pcThis, "M") == 0)
1873
Save = 3; /* MacSave - not implemented */
1875
else if (StrICmp(pcThis, "asntext") == 0)
1877
Save = SEND_FILE; /* writes out asn text without the html header */
1882
if ((IndexArgs = WWWFindName(info, "header")) >= 0)
1884
pcThis = WWWGetValueByIndex(info,IndexArgs);
1885
if (StrICmp(pcThis, "no") == 0)
1893
if ((IndexArgs = WWWFindName(info, "title")) >= 0)
1895
pcThis = WWWGetValueByIndex(info,IndexArgs);
1896
if (StrICmp(pcThis, "no") == 0)
1899
GlobalTitles = FALSE;
1904
if ((IndexArgs = WWWFindName(info, "html")) >= 0)
1906
pcThis = WWWGetValueByIndex(info,IndexArgs);
1907
if (StrICmp(pcThis, "no") == 0)
1909
GlobalNonHtmlOutput = TRUE;
1910
GlobalTitles = FALSE;
1916
/* call the pertinent Page Sender */
1920
iBytes = SendSummaryPage(MMDBids, iMMDBids, Save);
1924
iBytes = SendStructureMIME(DispOpt, MMDBids[0], Save ,
1925
Complex, MaxModels, KinColor, KinRender);
1931
/* log first MMDB-id, number of id's asked for, number of bytes sent */
1932
time_now = GetSecs();
1933
TimeNowStr = ctime(&time_now);
1934
TimeNowStr[24] = '\0';
1935
ErrLogPrintf("\n%s|%s|%s|%s|Do %c|Id %ld|No %ld|By %ld|Sv %ld|Cp %ld|Md %ld|Kc %ld|Kr %ld",
1936
WWWGetAddress(info), WWWGetHost(info), WWWGetAgent(info), TimeNowStr,
1938
(long) MMDBids[0], (long) iMMDBids, (long)iBytes, (long) Save,
1939
(long) Complex, (long) MaxModels, (long) KinColor, (long) KinRender);
1951
/* log first MMDB-id, number of id's asked for, number of bytes sent */
1952
time_now = GetSecs();
1953
TimeNowStr = ctime(&time_now);
1954
TimeNowStr[24] = '\0';
1955
ErrLogPrintf("\n#Syntax Error %s|%s|%s|%s|%ld",
1956
WWWGetAddress(info), WWWGetHost(info), WWWGetAgent(info), TimeNowStr,
1964
/* log first MMDB-id, number of id's asked for, number of bytes sent */
1965
time_now = GetSecs();
1966
TimeNowStr = ctime(&time_now);
1967
TimeNowStr[24] = '\0';
1968
ErrLogPrintf("\n#Query Not Supported %s|%s|%s|%s|%ld",
1969
WWWGetAddress(info), WWWGetHost(info), WWWGetAgent(info), TimeNowStr,
1975
time_now = GetSecs();
1976
TimeNowStr = ctime(&time_now);
1977
TimeNowStr[24] = '\0';
1978
ErrLogPrintf("\n#Get/Post Error %s|%s|%s|%s|%ld",
1979
WWWGetAddress(info), WWWGetHost(info), WWWGetAgent(info), TimeNowStr,
added
removed
biostruc/mmdbsrv.c
