1: # The LearningOnline Network with CAPA
2: # chemical equation style response
3: #
4: # $Id: chemresponse.pm,v 1.64 2006/03/09 01:12:05 albertel Exp $
5: #
6: # Copyright Michigan State University Board of Trustees
7: #
8: # This file is part of the LearningOnline Network with CAPA (LON-CAPA).
9: #
10: # LON-CAPA is free software; you can redistribute it and/or modify
11: # it under the terms of the GNU General Public License as published by
12: # the Free Software Foundation; either version 2 of the License, or
13: # (at your option) any later version.
14: #
15: # LON-CAPA is distributed in the hope that it will be useful,
16: # but WITHOUT ANY WARRANTY; without even the implied warranty of
17: # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
18: # GNU General Public License for more details.
19: #
20: # You should have received a copy of the GNU General Public License
21: # along with LON-CAPA; if not, write to the Free Software
22: # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
23: #
24: # /home/httpd/html/adm/gpl.txt
25: #
26: # http://www.lon-capa.org/
27: #
28: #
29: package Apache::chemresponse;
30: use strict;
31: use Apache::lonxml;
32: use Apache::lonnet;
33: use Apache::lonlocal;
34:
35: BEGIN {
36: &Apache::lonxml::register('Apache::chemresponse',('organicresponse','organicstructure','reactionresponse','chem'));
37: }
38:
39: sub chem_standard_order {
40: my ($reaction) = @_;
41: my ($re,$pr) = split(/->|<=>/,$reaction);
42: my @reactants = split(/\s\+/,$re);
43: my @products = split(/\s\+/,$pr);
44: foreach my $substance (@reactants,@products) {
45: $substance =~ s/(\^\d*)\s+/$1_/g; # protect superscript space
46: $substance =~ s/\s*//g; # strip whitespace
47: $substance =~ s/_/ /g; # restore superscript space
48: }
49: @reactants = sort @reactants;
50: @products = sort @products;
51: my $standard = '';
52: foreach my $substance (@reactants) {
53: $standard .= $substance;
54: $standard .= ' + ';
55: }
56: $standard =~ s/ \+ $//; # get rid of trailing plus sign
57: $standard .= ' -> ';
58: foreach my $substance (@products) {
59: $standard .= $substance;
60: $standard .= ' + ';
61: }
62: $standard =~ s/ \+ $//; # get rid of trailing plus sign
63: return $standard;
64: }
65:
66: sub separate_jme_window {
67: my ($smile_input,$jme_input,$molecule,$options,$shown_text)=@_;
68: my $smilesection;
69: if (defined($smile_input)) {
70: $smilesection=<<SMILESECTION;
71: smiles = document.applets.JME.smiles();
72: opener.document.lonhomework.$smile_input.value = smiles;
73: SMILESECTION
74: }
75: my $jmesection;
76: if (defined($jme_input)) {
77: $jmesection=<<JMESECTION;
78: jmeFile = document.applets.JME.jmeFile();
79: opener.document.lonhomework.$jme_input.value = jmeFile;
80: JMESECTION
81: }
82:
83: if ($molecule) { $molecule='<param name="jme" value="'.$molecule.'" />'; }
84: my $insert_answer;
85: if ($shown_text eq '') {
86: $insert_answer=
87: '<input type="button" name="submit" value="Insert Answer" onclick="javascript:submitSmiles();" />';
88: }
89:
90: my $body=<<CHEMPAGE;
91: <html>
92: <head>
93: <title>Molecule Editor</title>
94: <script type="text/javascript">
95: function submitSmiles() {
96: jmeFile = document.applets.JME.jmeFile();
97: if (jmeFile == "") {
98: alert("Nothing to submit");
99: } else {
100: $jmesection
101: $smilesection
102: window.close();
103: }
104: }
105: function openHelpWindow() {
106: window.open("/adm/jme/jme_help.html","","scrollbars=yes,resizable=yes,width=500,height=600");
107: }
108: function substituent(r) {document.applets.JME.setSubstituent(r);}
109: </script>
110: </head>
111: <body bgcolor="#ffffff">
112: <center>
113: <form>
114: <table width="440"><tr>
115: <td></td>
116: <td align="right">
117: <select onchange="javascript:substituent(options[selectedIndex].text)">
118: <option>Select substituent</option>
119: <option>-C(=O)OH</option>
120: <option>-C(=O)OMe</option>
121: <option>-OC(=O)Me</option>
122: <option>-CMe3</option>
123: <option>-CF3</option>
124: <option>-CCl3</option>
125: <option>-NO2</option>
126: <option>-SO2-NH2</option>
127: <option>-NH-SO2-Me</option>
128: <option>-NMe2</option>
129: <option>-C#N</option>
130: <option>-C#C-Me</option>
131: <option>-C#CH</option>
132: </select>
133: </td></tr>
134: </table>
135: <applet code="JME.class" name="JME" archive="/adm/jme/JME.jar" width="440" height="390" mayscript>
136: You have to enable Java and JavaScript on your machine.
137: $molecule
138: <param name="options" value="$options" />
139: </applet><br />
140: <font face="arial,helvetica,sans-serif" size="-1"><a href="http://www.molinspiration.com/jme/index.html">JME Editor</a> courtesy of Peter Ertl, Novartis</font>
141: <br />
142: $insert_answer
143: <br />
144: <input type="button" value=" Close " onclick = "javascript:window.close()" />
145:
146: <input type="button" value=" Help " onclick = "javascript:openHelpWindow()" />
147: </form>
148: </center>
149: </body>
150: </html>
151: CHEMPAGE
152: $body=&HTML::Entities::encode($body,'<>&"');
153: $body=~s/\n/ /g;
154: my $nothing=&Apache::lonhtmlcommon::javascript_nothing();
155: my $docopen=&Apache::lonhtmlcommon::javascript_docopen();
156: my $display=&mt('Draw Molecule');
157: if (defined($shown_text)) { $display=&mt($shown_text); }
158: my $result=<<CHEMINPUT;
159: <input type="button" value="$display" onclick="javascript:editor=window.open($nothing,'jmeedit','width=500,height=500,menubar=no,scrollbars=no,resizable=yes');editor.$docopen;editor.document.write('$body');editor.document.close();editor.focus()" />
160: CHEMINPUT
161: return $result;
162: }
163:
164: sub jme_img {
165: my ($jme,$smile,$width,$options)=@_;
166: my $id=&Apache::loncommon::get_cgi_id();
167: my $result='<img alt="'.$smile.'" src="/cgi-bin/convertjme.pl?'.$id.'"';
168: if ($options =~ /border/) { $result.= ' border="1"'; }
169: $result.=' />';
170: &Apache::lonnet::appenv('cgi.'.$id.'.JME' =>
171: &Apache::lonnet::escape($jme),
172: 'cgi.'.$id.'.PNG' => 1,
173: 'cgi.'.$id.'.WIDTH' => $width);
174: return $result;
175: }
176:
177: sub start_organicresponse {
178: my ($target,$token,$tagstack,$parstack,$parser,$safeeval,$style)=@_;
179: my $result;
180: my $partid = $Apache::inputtags::part;
181: my $id = &Apache::response::start_response($parstack,$safeeval);
182: if ($target eq 'meta') {
183: $result=&Apache::response::meta_package_write('organicresponse');
184: } elsif ($target eq 'web') {
185: my $jmeanswer=&Apache::lonxml::get_param('jmeanswer',$parstack,
186: $safeeval);
187: if ( &Apache::response::show_answer() && $jmeanswer ne '') {
188: my $options=&Apache::lonxml::get_param('options',$parstack,
189: $safeeval);
190: my $width=&Apache::lonxml::get_param('width',$parstack,
191: $safeeval);
192: my (@answers)=&Apache::lonxml::get_param_var('answer',$parstack,
193: $safeeval);
194: $result.=&jme_img($jmeanswer,$answers[0],$width,$options);
195: } else {
196: my $molecule;
197: if (defined($Apache::lonhomework::history{"resource.$partid.$id.molecule"})) {
198: $molecule=$Apache::lonhomework::history{"resource.$partid.$id.molecule"};
199: } else {
200: $molecule=&Apache::lonxml::get_param('molecule',$parstack,
201: $safeeval);
202: }
203: my $options=&Apache::lonxml::get_param('options',$parstack,
204: $safeeval);
205: my $shown_text;
206: if (&Apache::response::show_answer()) {
207: $shown_text="Show Your Last Answer";
208: }
209: $result=&separate_jme_window("HWVAL_$id","MOLECULE_$id",$molecule,
210: $options,$shown_text);
211: $result.= '<input type="hidden" name="MOLECULE_'.$id.'" value="" />';
212: }
213: } elsif ($target eq 'edit') {
214: $result .=&Apache::edit::tag_start($target,$token);
215: my $options=&Apache::lonxml::get_param('options',$parstack,
216: $safeeval);
217: if ($options !~ /multipart/) { $options.=',multipart'; }
218: $result .='<nobr>'.
219: &Apache::edit::text_arg('Starting Molecule:','molecule',
220: $token,40);
221: my $molecule=&Apache::lonxml::get_param('molecule',$parstack,
222: $safeeval);
223: $result .=&separate_jme_window(undef,
224: &Apache::edit::html_element_name('molecule'),
225: $molecule,$options);
226: $result .='</nobr><br /><nobr>';
227: $result .=&Apache::edit::text_arg('Correct Answer:','answer',
228: $token,40);
229: $result .=&Apache::edit::hidden_arg('jmeanswer',$token);
230: my $jmeanswer=&Apache::lonxml::get_param('jmeanswer',$parstack,
231: $safeeval);
232: $result .=&separate_jme_window(
233: &Apache::edit::html_element_name('answer'),
234: &Apache::edit::html_element_name('jmeanswer'),
235: $jmeanswer,$options);
236: $result .='</nobr><br />';
237: $result .=&Apache::edit::checked_arg('Options:','options',
238: [ ['autoez','Auto E,Z stereochemistry'],
239: ['multipart','Multipart Structures'],
240: ['nostereo','No stereochemistry'],
241: ['reaction','Is a reaction'],
242: ['number','Able to number atoms'] ],
243: ,$token);
244: $result .=&Apache::edit::text_arg('Width of correct answer image:',
245: 'width',$token,10);
246: $result .=&Apache::edit::end_row().&Apache::edit::start_spanning_row();
247: } elsif ($target eq 'modified') {
248: my $constructtag=&Apache::edit::get_new_args($token,$parstack,
249: $safeeval,'molecule',
250: 'answer','jmeanswer',
251: 'options','width');
252: if ($constructtag) { $result = &Apache::edit::rebuild_tag($token); }
253: }
254:
255: return $result;
256: }
257:
258: sub end_organicresponse {
259: my ($target,$token,$tagstack,$parstack,$parser,$safeeval,$style)=@_;
260: my $result;
261:
262: my $partid = $Apache::inputtags::part;
263: my $id = $Apache::inputtags::response['-1'];
264:
265: if ($target eq 'grade'
266: && &Apache::response::submitted()
267: && $Apache::lonhomework::type eq 'exam') {
268:
269: &Apache::response::scored_response($partid,$id);
270:
271: } elsif ($target eq 'grade'
272: && &Apache::response::submitted()
273: && $Apache::lonhomework::type ne 'exam') {
274:
275: &Apache::response::setup_params($$tagstack[-1],$safeeval);
276: my $response = &Apache::response::getresponse();
277: if ( $response =~ /[^\s]/) {
278: my (@answers)=&Apache::lonxml::get_param_var('answer',$parstack,$safeeval);
279: my %previous = &Apache::response::check_for_previous($response,$partid,$id);
280: $Apache::lonhomework::results{"resource.$partid.$id.submission"}=$response;
281: my $ad;
282: foreach my $answer (@answers) {
283: &Apache::lonxml::debug("submitted a $response for $answer<br \>\n");
284: if ($response eq $answer) {
285: $ad='EXACT_ANS';
286: last;
287: } else {
288: $ad='INCORRECT';
289: }
290: }
291: if ($ad && $Apache::lonhomework::type eq 'survey') {
292: $ad='SUBMITTED';
293: }
294: &Apache::response::handle_previous(\%previous,$ad);
295: $Apache::lonhomework::results{"resource.$partid.$id.awarddetail"}=$ad;
296: $Apache::lonhomework::results{"resource.$partid.$id.molecule"}=$env{"form.MOLECULE_$id"};
297: }
298: } elsif ($target eq "edit") {
299: $result.= &Apache::edit::tag_end($target,$token,'');
300: } elsif ($target eq 'answer') {
301: my (@answers)=&Apache::lonxml::get_param_var('answer',$parstack,
302: $safeeval);
303: $result.=&Apache::response::answer_header('organicresponse');
304: foreach my $answer (@answers) {
305: $result.=&Apache::response::answer_part('organicresponse',$answer);
306: }
307: $result.=&Apache::response::answer_footer('organicresponse');
308: }
309:
310: if ($target eq 'grade' || $target eq 'web' || $target eq 'answer' ||
311: $target eq 'tex' || $target eq 'analyze') {
312: &Apache::lonxml::increment_counter(&Apache::response::repetition());
313: }
314: &Apache::response::end_response();
315: return $result;
316: }
317:
318: sub start_organicstructure {
319: my ($target,$token,$tagstack,$parstack,$parser,$safeeval,$style)=@_;
320: my $result;
321: if ($target eq 'web') {
322: my $width=&Apache::lonxml::get_param('width',$parstack,$safeeval);
323: my $molecule=&Apache::lonxml::get_param('molecule',$parstack,$safeeval);
324: my $options=&Apache::lonxml::get_param('options',$parstack,$safeeval);
325: my $id=&Apache::loncommon::get_cgi_id();
326: $result="<img src='/cgi-bin/convertjme.pl?$id'";
327: if ($options =~ /border/) { $result.= ' border="1"'; }
328: $result.=' />';
329: &Apache::lonnet::appenv(
330: 'cgi.'.$id.'.JME' => &Apache::lonnet::escape($molecule),
331: 'cgi.'.$id.'.PNG' => 1,
332: 'cgi.'.$id.'.WIDTH' => $width );
333: } elsif ($target eq 'tex') {
334: my $texwidth=&Apache::lonxml::get_param('texwidth',$parstack,$safeeval,undef,1);
335: my $webwidth=&Apache::lonxml::get_param('width', $parstack, $safeeval);
336: my $webheight=&Apache::lonxml::get_param('height', $parstack, $safeeval);
337: if (!$webheight) { $webheight = $webwidth; }
338: if (!$texwidth) { $texwidth='90'; }
339: $result = "%DYNAMICIMAGE:$webwidth:$webheight:$texwidth\n";
340: my $molecule=&Apache::lonxml::get_param('molecule',$parstack,$safeeval);
341: my $options=&Apache::lonxml::get_param('options',$parstack,$safeeval);
342: my $filename = $env{'user.name'}.'_'.$env{'user.domain'}.
343: '_'.time.'_'.$$.int(rand(1000)).'_organicstructure';
344: my $id=$filename;
345: &Apache::lonnet::appenv(
346: 'cgi.'.$id.'.JME' => &Apache::lonnet::escape($molecule),
347: 'cgi.'.$id.'.PS' => 1,
348: 'cgi.'.$id.'.WIDTH' => $texwidth );
349: $id=&Apache::lonnet::escape($id);
350: &Apache::lonxml::register_ssi("/cgi-bin/convertjme.pl?$id");
351: if ($options =~ /border/) { $result.= '\fbox{'; }
352: $result .= '\graphicspath{{/home/httpd/perl/tmp/}}\includegraphics[width='.$texwidth.' mm]{'.$filename.'.eps}';
353: if ($options =~ /border/) { $result.= '} '; }
354: } elsif ($target eq 'edit') {
355: $result .=&Apache::edit::tag_start($target,$token);
356: $result .=&Apache::edit::text_arg('Width (pixels):','width',$token,5);
357: $result .=&Apache::edit::text_arg('TeXwidth (mm):','texwidth',$token,5);
358: $result .='<nobr>';
359: $result .=&Apache::edit::text_arg('Molecule:','molecule',$token,40);
360: my $molecule=&Apache::lonxml::get_param('molecule',$parstack,
361: $safeeval);
362: my $options=&Apache::lonxml::get_param('options',$parstack,
363: $safeeval);
364: if ($options !~ /reaction/) {
365: $options.= ',multipart,number';
366: }
367:
368: $result .=&separate_jme_window(undef,
369: &Apache::edit::html_element_name('molecule'),
370: $molecule,$options);
371: $result.="</nobr><br />";
372: $result .=&Apache::edit::checked_arg('Options:','options',
373: [ ['reaction','Is a reaction'],
374: ['border','Draw a border'] ],
375: $token);
376: $result .=&Apache::edit::end_row();
377: } elsif ($target eq 'modified') {
378: my $constructtag=&Apache::edit::get_new_args($token,$parstack,
379: $safeeval,'molecule',
380: 'width','texwidth',
381: 'options');
382: if ($constructtag) { $result = &Apache::edit::rebuild_tag($token); }
383: }
384: return $result;
385: }
386:
387: sub end_organicstructure {
388: my ($target,$token,$tagstack,$parstack,$parser,$safeeval,$style)=@_;
389: my $result;
390: if ($target eq "edit") {
391: $result.= &Apache::edit::tag_end($target,$token,'');
392: }
393: return $result;
394: }
395:
396: sub edit_reaction_button {
397: my ($id,$field,$reaction)=@_;
398: my $id_es=&Apache::lonnet::escape($id);
399: my $field_es=&Apache::lonnet::escape($field);
400: my $reaction_es=&Apache::lonnet::escape($reaction);
401: my $docopen=&Apache::lonhtmlcommon::javascript_docopen();
402: my $result=<<EDITREACTION;
403: <script type="text/javascript">
404: // <!--
405: function create_reaction_window_${id}_${field} () {
406: editor=window.open('','','width=500,height=270,scrollbars=no,resizable=yes');
407: editor.$docopen;
408: editor.document.writeln('<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML//EN"><html> <head><title>LON-CAPA Reaction Editor</title></head><frameset rows="30%,*" border="0"> <frame src="/res/adm/pages/reactionresponse/reaction_viewer.html?inhibitmenu=yes" name="viewer" scrolling="no" /> <frame src="/res/adm/pages/reactionresponse/reaction_editor.html?inhibitmenu=yes&reaction=$reaction_es&id=$id_es&field=$field_es" name="editor" scrolling="no" /> </frameset> </html>');
409: }
410: // -->
411: </script>
412: <input type='button' value='Edit Answer' onclick="javascript:create_reaction_window_${id}_${field}();void(0);" />
413: EDITREACTION
414: return $result;
415: }
416:
417: sub start_reactionresponse {
418: my ($target,$token,$tagstack,$parstack,$parser,$safeeval,$style)=@_;
419: my $result;
420: my $id = &Apache::response::start_response($parstack,$safeeval);
421: if ($target eq 'meta') {
422: $result=&Apache::response::meta_package_write('reactionresponse');
423: } elsif ($target eq 'web') {
424: my $partid = $Apache::inputtags::part;
425: my $id = $Apache::inputtags::response['-1'];
426: my $reaction=$Apache::lonhomework::history{"resource.$partid.$id.submission"};
427: if ($reaction eq '') { $reaction=&Apache::lonxml::get_param('initial',$parstack,$safeeval); }
428: my $status=$Apache::inputtags::status['-1'];
429: if ($status eq 'CAN_ANSWER') {
430: $result.=&edit_reaction_button($id,"HWVAL_$id",$reaction);
431: }
432: if ( &Apache::response::show_answer() ) {
433: my $ans=&Apache::lonxml::get_param('answer',$parstack,$safeeval);
434: if (!$Apache::lonxml::default_homework_loaded) {
435: &Apache::lonxml::default_homework_load($safeeval);
436: }
437: @Apache::scripttag::parser_env = @_;
438: $Apache::inputtags::answertxt{$id}=&Apache::run::run("return &chemparse(q\0$ans\0);",$safeeval);
439: }
440: } elsif ($target eq "edit") {
441: $result .=&Apache::edit::tag_start($target,$token);
442: my $answer=&Apache::lonxml::get_param('answer',$parstack,
443: $safeeval);
444: $result .='<nobr>'.
445: &Apache::edit::text_arg('Answer:','answer',$token,40);
446: $result .=&edit_reaction_button($id,&Apache::edit::html_element_name('answer'),$answer).'</nobr>';
447: my $initial=&Apache::lonxml::get_param('initial',$parstack,$safeeval);
448: $result.='<nobr>'.
449: &Apache::edit::text_arg('Initial Reaction:','initial',$token,40);
450: $result .=&edit_reaction_button($id,&Apache::edit::html_element_name('initial'),$initial).'</nobr>';
451:
452: $result .=&Apache::edit::end_row().&Apache::edit::start_spanning_row();
453: } elsif ($target eq 'modified') {
454: my $constructtag=&Apache::edit::get_new_args($token,$parstack,
455: $safeeval,'answer',
456: 'initial');
457: if ($constructtag) { $result = &Apache::edit::rebuild_tag($token); }
458: }
459: return $result;
460: }
461:
462: sub end_reactionresponse {
463: my ($target,$token,$tagstack,$parstack,$parser,$safeeval,$style)=@_;
464: my $result;
465:
466: my $partid = $Apache::inputtags::part;
467: my $id = $Apache::inputtags::response['-1'];
468:
469: if ($target eq 'grade'
470: && &Apache::response::submitted()
471: && $Apache::lonhomework::type eq 'exam') {
472:
473: &Apache::response::scored_response($partid,$id);
474:
475: } elsif ($target eq 'grade'
476: && &Apache::response::submitted()
477: && $Apache::lonhomework::type ne 'exam') {
478:
479: &Apache::response::setup_params($$tagstack[-1],$safeeval);
480: my $response = &Apache::response::getresponse();
481: if ( $response =~ /[^\s]/) {
482: my (@answers)=&Apache::lonxml::get_param_var('answer',$parstack,$safeeval);
483: my %previous = &Apache::response::check_for_previous($response,$partid,$id);
484: $Apache::lonhomework::results{"resource.$partid.$id.submission"}=$response;
485: my $ad;
486: foreach my $answer (@answers) {
487: &Apache::lonxml::debug("submitted a $response for $answer<br \>\n");
488: if (&chem_standard_order($response) eq
489: &chem_standard_order($answer)) {
490: $ad='EXACT_ANS';
491: } else {
492: $ad='INCORRECT';
493: }
494: }
495: if ($ad && $Apache::lonhomework::type eq 'survey') {
496: $ad='SUBMITTED';
497: }
498: &Apache::response::handle_previous(\%previous,$ad);
499: $Apache::lonhomework::results{"resource.$partid.$id.awarddetail"}=$ad;
500: }
501: } elsif ($target eq "edit") {
502: $result.= &Apache::edit::tag_end($target,$token,'');
503: } elsif ($target eq 'answer') {
504: my (@answers)=&Apache::lonxml::get_param_var('answer',$parstack,
505: $safeeval);
506: $result.=&Apache::response::answer_header('reactionresponse');
507: foreach my $answer (@answers) {
508: $result.=&Apache::response::answer_part('reactionresponse',
509: $answer);
510: }
511: $result.=&Apache::response::answer_footer('reactionresponse');
512: }
513:
514: if ($target eq 'grade' || $target eq 'web' || $target eq 'answer' ||
515: $target eq 'tex' || $target eq 'analyze') {
516: &Apache::lonxml::increment_counter(&Apache::response::repetition());
517: }
518: &Apache::response::end_response();
519: return $result;
520: }
521:
522: sub start_chem {
523: my ($target,$token,$tagstack,$parstack,$parser,$safeeval,$style) = @_;
524: my $result = '';
525: my $inside = &Apache::lonxml::get_all_text_unbalanced("/chem",$parser);
526: if ($target eq 'tex' || $target eq 'web') {
527: $inside=&Apache::run::evaluate($inside,$safeeval,$$parstack[-1]);
528: if (!$Apache::lonxml::default_homework_loaded) {
529: &Apache::lonxml::default_homework_load($safeeval);
530: }
531: @Apache::scripttag::parser_env = @_;
532: $result=&Apache::run::run("return &chemparse(q\0$inside\0);",$safeeval);
533: }
534: return $result;
535: }
536:
537: sub end_chem {
538: my ($target,$token,$tagstack,$parstack,$parser,$safeeval,$style) = @_;
539: my $result = '';
540: return $result;
541: }
542:
543: 1;
544: __END__
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