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    1. <?php
    2.  
    3. $filename = substr($_SERVER['argv'][1], 11);
    4. $lines = file($filename);
    5.  
    6. // Are we in an h4 tag?
    7. $in_section = false;
    8. // h4?
    9. $in_sub_section = false;
    10. // Title for the section <h3>
    11. $title = '';
    12. // <h4> title
    13. $sub_title = '';
    14. // In the html body?
    15. $in_html_body = false;
    16. // References???
    17. $found_reference = false;
    18. $in_list = false;
    19. // Tables?
    20. $tables_count = 0;
    21.  
    22. $front = array(
    23. 	'article_id' => 0,
    24. 	'publication' => 0,
    25. 	'column' => '',
    26. 	'volume' => '',
    27. 	'issue' => '',
    28. 	'pages' => '',
    29. 	'date' => array(
    30. 		'day' => date('d'),
    31. 		'month' => date('m'),
    32. 		'year' => date('Y'),
    33. 	),
    34. 	'pub_abbr' => '',
    35. );
    36. $back = array(
    37. 	'references' => array(),
    38. 	'ack' => '',
    39. 	'financial' => '',
    40. 	'conflict' => '',
    41. 	'abbr' => '',
    42. 	'reprint' => '',
    43. 	'sidebar' => array(),
    44. );
    45.  
    46. $sections = array();
    47. foreach ($lines as $key => $line)
    48. {
    49. 	// Clean spaces.
    50. 	$line = trim($line);
    51.  
    52. 	// No blank lines.
    53. 	if (empty($line))
    54. 		continue;
    55.  
    56. 	// Skip the head matter.
    57. 	if (!$in_html_body && $line != '<body>')
    58. 		continue;
    59. 	elseif (!$in_html_body && $line == '<body>')
    60. 	{
    61. 		$in_html_body = true;
    62. 		continue;
    63. 	}
    64.  
    65. 	// We just end here.  We don't parse the table and image stuff just yet.
    66. 	if (in_array($line, array('</body>', '</html>')))
    67. 		break;
    68.  
    69. 	// We continue with these.
    70. 	if (in_array($line, array('<!--', '-->')))
    71. 		continue;
    72.  
    73. 	// Lets just do the head stuff first since it's usually on top.
    74. 	if (substr($line, 0, 11) == 'Article ID:')
    75. 	{
    76. 		$front['article_id'] = trim(substr($line, 11));
    77. 		continue;
    78. 	}
    79. 	elseif (substr($line, 0, 15) == 'Publication ID:')
    80. 	{
    81. 		$front['publication'] = trim(substr($line, 15));
    82. 		continue;
    83. 	}
    84. 	elseif (substr($line, 0, 18) == 'Section/Column ID:')
    85. 	{
    86. 		$front['column'] = trim(substr($line, 18));
    87. 		continue;
    88. 	}
    89. 	elseif (substr($line, 0, 7) == 'Volume:')
    90. 	{
    91. 		$front['volume'] = trim(substr($line, 7));
    92. 		continue;
    93. 	}
    94. 	elseif (substr($line, 0, 6) == 'Issue:')
    95. 	{
    96. 		$front['issue'] =  trim(substr($line, 6));
    97. 		continue;
    98. 	}
    99. 	elseif (substr($line, 0, 6) == 'Pages:')
    100. 	{
    101. 		$front['pages'] = trim(substr($line, 6));
    102. 		continue;
    103. 	}
    104. 	elseif (substr($line, 0, 9) == 'Pub Date:')
    105. 	{
    106. 		list ($month, $day, $year) = explode('/', trim(substr($line, 9)));
    107. 		$front['date']['month'] = empty($month) ? date('m') : $month;
    108. 		$front['date']['day'] = empty($day) ? date('d') : $day;
    109. 		$front['date']['year'] = empty($year) ? date('Y') : $year;
    110. 		continue;
    111. 	}
    112. 	elseif (substr($line, 0, 8) == 'Surname:')
    113. 	{
    114. 		$front['surname'] = trim(substr($line, 8));
    115. 		continue;
    116. 	}
    117. 	elseif (substr($line, 0, 11) == 'Disclosure:')
    118. 	{
    119. 		$front['disclosure'] = trim(substr($line, 11));
    120. 		continue;
    121. 	}
    122. 	elseif (substr($line, 0, 4) == 'Bio:')
    123. 	{
    124. 		$front['bio'] = trim(substr($line, 4));
    125. 		continue;
    126. 	}
    127. 	elseif (substr($line, 0, 7) == 'Images:')
    128. 	{
    129. 		$front['has_images'] = trim(substr($line, 7)) == 'true' ? true : false;
    130. 		continue;
    131. 	}
    132. 	elseif (substr($line, 0, 9) == 'Pub Abbr:')
    133. 	{
    134. 		$front['pub_abbr'] = trim(substr($line, 9));
    135. 		continue;
    136. 	}
    137. 	elseif (substr($line, 0, 4) == 'Ack:')
    138. 	{
    139. 		$back['ack'] = trim(substr($line, 4));
    140. 		continue;
    141. 	}
    142. 	elseif (substr($line, 0, 10) == 'Financial:' || substr($line, 0, 8) == 'Funding:')
    143. 	{
    144. 		$back['financial'] = trim(substr($line, substr($line, 0, 10) == 'Financial:' ? 10 : 8));
    145. 		continue;
    146. 	}
    147. 	elseif (substr($line, 0, 9) == 'Conflict:')
    148. 	{
    149. 		$back['conflict'] = trim(substr($line, 9));
    150. 		continue;
    151. 	}
    152. 	elseif (substr($line, 0, 5) == 'Abbr:')
    153. 	{
    154. 		$back['abbr'] = trim(substr($line, 5));
    155. 		continue;
    156. 	}
    157. 	elseif (substr($line, 0, 8) == 'Reprint:')
    158. 	{
    159. 		$back['reprint'] = trim(substr($line, 8));
    160. 		continue;
    161. 	}
    162.  
    163. 	// References here.
    164. 	if (trim($line) == '<h3>References</h3>')
    165. 	{
    166. 		$found_reference = true;
    167. 		continue;
    168. 	}
    169.  
    170. 	// In a first level section and we already in one.  Just go to the new one.
    171. 	if ($in_section && !$found_reference && substr($line, 0, 3) == '<h3')
    172. 	{
    173. 		$in_section = false;
    174. 		$in_sub_section = false;
    175. 		$title = '';
    176. 		$sub_title = '';
    177. 		$section_type = '';
    178. 	}
    179.  
    180. 	// A section?
    181. 	if (!$in_section && !$found_reference && preg_match('~^<h3(?:\s*id="([a-zA-Z0-9_]+)")?>(.+?)</h3>$~', $line, $matches))
    182. 	{
    183. 		$in_section = true;
    184. 		$title = count($matches) == 2 ? trim($matches[1]) : trim($matches[2]);
    185.  
    186. 		// Clean title.
    187. 		$clean_title = strtolower(substr($title, 0, 50));
    188.  
    189. 		// We start a new section in the array.
    190. 		$sections[$clean_title] = array(
    191. 			'title' => $title == '.' ? '' : $title,
    192. 			'sub_section' => array(),
    193. 		);
    194.  
    195. 		if (count($matches) == 3)
    196. 			$sections[$clean_title]['type'] = trim($matches[1]);
    197.  
    198. 		// NEXT...
    199. 		continue;
    200. 	}
    201.  
    202. 	// First lets check if we even doing references yet then check for list.
    203. 	if ($found_reference && ($line == '<ol>' || $line == '<ul>'))
    204. 	{
    205. 		$in_list = true;
    206. 		$reference_ordered = $line == '<ol>' ? true : false;
    207. 		continue;
    208. 	}
    209.  
    210. 	if ($in_list && $found_reference && substr(trim($line), 0, 4) == '<li>')
    211. 	{
    212. 		$back['references'][] = htmlspecialchars_uni(substr(trim($line), 4, -5));
    213. 		continue;
    214. 	}
    215.  
    216. 	if ($in_list && $found_reference && ($line == '</ol>' || $line == '</ul>'))
    217. 	{
    218. 		$found_reference = false;
    219. 		$in_list = false;
    220. 		continue;
    221. 	}
    222.  
    223. 	// In a sub section and another one just pops up? We no longer in the other one then.  One section at a time.
    224. 	if ($in_section && $in_sub_section && substr($line, 0, 3) == '<h4')
    225. 		$in_sub_section = false;
    226.  
    227. 	// Sub section.
    228. 	if ($in_section && !$in_sub_section && preg_match('~^<h4(?:\s*id="([a-zA-Z0-9_]+)")?>(.+?)</h4>$~', $line, $matches))
    229. 	{
    230. 		$in_sub_section = true;
    231. 		$sub_title = count($matches) == 2 ? trim($matches[1]) : trim($matches[2]);
    232.  
    233. 		// Clean sub title.
    234. 		$clean_sub_title = strtolower(substr($sub_title, 0, 50));
    235.  
    236. 		// Type?
    237. 		$section_type = '';
    238. 		if (count($matches) == 3)
    239. 			$section_type = trim($matches[1]);
    240.  
    241. 		// We don't need any more data from this line so... NEXT!!!
    242. 		continue;
    243. 	}
    244. 	elseif ($in_section && !$in_sub_section)
    245. 	{
    246. 		$in_sub_section = true;
    247. 		$clean_sub_title = 'no_title_' . substr(md5(time()), 0, 5);
    248. 	}
    249.  
    250. 	if (isset($sections[$clean_title]) && !isset($sections[$clean_title]['sub_section'][$clean_sub_title]))
    251. 		$sections[$clean_title]['sub_section'][$clean_sub_title] = array(
    252. 			'title' => $sub_title,
    253. 			'type' => $section_type,
    254. 			'data' => array(),
    255. 		);
    256.  
    257. 	// Now for the data.
    258. 	$sections[$clean_title]['sub_section'][$clean_sub_title]['data'][] = $line;
    259. }
    260.  
    261. $body = '
    262. 	<body>';
    263.  
    264. foreach ($sections as $id => $section)
    265. {
    266. 	// Sidebar?  They go in the back.
    267. 	if (isset($section['type']) && $section['type'] == 'sidebar')
    268. 	{
    269. 		$back['sidebar'][] = $section;
    270. 		continue;
    271. 	}
    272.  
    273. 	// First level?  Then it's a page.
    274. 	$body .= '
    275. 		<sec sec-type="page">
    276. 			' . (empty($section['title']) ? '<title/>' : '<title>' . htmlspecialchars_uni($section['title']) . '</title>');
    277.  
    278. 	// Ok we move on grass hoppa.
    279. 	foreach ($section['sub_section'] as $name => $sub_section)
    280. 	{
    281. 		$body .= '
    282. 			<sec sec-type="' . (empty($sub_section['type']) ? 'content' : $sub_section['type']) . '">
    283. 				' . (empty($sub_section['title']) ? '<title/>' : '<title>' . htmlspecialchars_uni($sub_section['title']) . '</title>');
    284.  
    285. 		// Now the data.
    286. 		$body .= parse_content($sub_section['data']);
    287.  
    288. 		$body .= '
    289. 			</sec>';
    290. 	}
    291.  
    292. 	$body .= '
    293. 		</sec>';
    294. }
    295.  
    296. $body .= '
    297. 	</body>';
    298.  
    299. // Generate the front section
    300. $front_xml = generate_front($front);
    301. // References
    302. $back_xml = generate_back($back);
    303.  
    304. $xml = '<?xml version="1.0" encoding="UTF-8"?>
    305. <!DOCTYPE article SYSTEM "/content/journal-publishing-dtd-1.1/journalpublishing.dtd">
    306. <article>' . $front_xml . $body . $back_xml . '
    307. </article>';
    308.  
    309. // Emails
    310. $xml = preg_replace('~([0-9A-Za-z=_+\-/][0-9A-Za-z=_\'+\-/\.]*@[\w\-]+(\.[\w\-]+)*(\.[\w]{2,6}))~', '<ext-link ext-link-type="mailto" xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="\1" xlink:title="\1"/>', $xml);
    311.  
    312. echo $xml;
    313.  
    314. $fp = fopen(dirname($filename) . '/' . basename($filename, '.html') . '.xml', 'w+');
    315. if (fwrite($fp, $xml))
    316. 	echo "\nWROTE AND SAVED FILE";
    317. fclose($fp);
    318.  
    319. function xml_replacement($data)
    320. {
    321. 	global $front;
    322.  
    323. 	$data = preg_replace('~(Table|Exhibit|Box) (\d+)~', '<xref ref-type="table" rid="T\2">\1 \2</xref>', $data);
    324.  
    325. 	// Images now?
    326. 	if (isset($front['pub_abbr']) && preg_match('~\[\[(InlineFigure|Figure)\|\^\|\d+\|\^\|.+?\]\]~', $data, $matches))
    327. 	{
    328. 		if (trim($matches[1]) == 'InlineFigure')
    329. 			$data = preg_replace('~\[\[InlineFigure\|\^\|(\d+)\|\^\|(.+?)\]\]~', "
    330. 				<inline-graphic xmlns:xlink=\"http://www.w3.org/1999/xlink\" xlink:href=\"/images/" . substr($front['article_id'], 0, 3) . "/" . substr($front['article_id'], -3) . "/art-" . $front['pub_abbr'] . $front['article_id'] . ".equation$1.gif\">
    331. 					<alt-text>Equation</alt-text>
    332. 				</inline-graphic>
    333. 				", $data);
    334. 		else
    335. 			$data = preg_replace('~\[\[Figure\|\^\|(\d+)\|\^\|(.+?)\]\]~', "
    336. 				<fig id=\"F\$1\">
    337. 					<label>Figure \$1.</label>
    338. 					<caption>