NP_PubMed/trunk/pubmed/template.php

   1 <?php\r
   2 \r
   3 class PUBMED_TEMPLATE_BASE {\r
   4         /*\r
   5          * This class must be inhelited by PUBMED_TEMPLATE class.\r
   6          * Note that PHP 5 is needed.\r
   7          */\r
   8         /* \r
   9          * Default methods follow.\r
  10          * These methods will be overrided in PUBMED_TEMPLATE class.\r
  11          */\r
  12         public function manualSort(){\r
  13                 // If the order of manuscript is manually sorted (PNAS etc),\r
  14                 // this method must return true.\r
  15                 return false;\r
  16         }\r
  17         public function sortPapers(){\r
  18                 $this->sortByAuthorName();\r
  19         }\r
  20         public function parse_header(){\r
  21                 return '<br />';\r
  22         }\r
  23         public function parse_footer(){\r
  24                 return '<br />';\r
  25         }\r
  26         public function parse($num,$pmid,$xml,$authors,$year,$journal,$volume,$pages,$title){\r
  27                 return <<<END\r
  28 \r
  29 <p>{$this->parse_authors($authors)} ({$year})<br />\r
  30 <i>{$journal}</i> <b>{$volume}</b>, {$pages}<br />\r
  31 {$title}</p>\r
  32 \r
  33 END;\r
  34         }\r
  35         public function parse_authors($authors, $and=', and '){\r
  36                 $num=count($authors);\r
  37                 switch($num){\r
  38                         case 1:\r
  39                                 $result=$this->parse_author($authors[0]);\r
  40                                 break;\r
  41                         case 2:\r
  42                                 $result=$this->parse_author($authors[0]).$and.$this->parse_author($authors[1]);\r
  43                                 break;\r
  44                         default:\r
  45                                 $result=$this->parse_author($authors[0]);\r
  46                                 for($i=1;$i<$num;$i++){\r
  47                                         if ($i==1) $result.=', ';\r
  48                                         elseif ($i==$num-1) $result.=$and;\r
  49                                         $result.=$this->parse_author($authors[$i]);\r
  50                                 }\r
  51                                 break;\r
  52                 }\r
  53                 return htmlspecialchars($result);\r
  54         }\r
  55         public function parse_author($author){\r
  56                 $result=$author->LastName.', ';\r
  57                 $initials=$author->Initials;\r
  58                 for($i=0;$i<strlen($initials);$i++) $result.=substr($initials,$i,1).'.';\r
  59                 return $result;\r
  60         }\r
  61         /*\r
  62          * Following methods shouldn't be overrided.\r
  63          */\r
  64         protected $sortdata=array(),$data=array();\r
  65         public static final function getTemplate($template){\r
  66                 // Static method.\r
  67                 // Define PUBLED_TEMPLATE class\r
  68                 if (!preg_match('/^[a-z0-9A-Z_]+$/',$template)) exit('Bad template name!');\r
  69                 $file=dirname(__FILE__)."/templates/{$template}.php";\r
  70                 if (!file_exists($file)) return false;\r
  71                 require_once($file);\r
  72                 $obj = new PUBMED_TEMPLATE;\r
  73                 return $obj;\r
  74         }\r
  75         public final function setData($more,$sort){\r
  76                 // $more is the $item->more.\r
  77                 if (!preg_match('#<MedlineCitation[^>]*>([\s\S]*?)</MedlineCitation>#',$more,$m)) return;\r
  78                 $xml="<?xml version='1.0'?>\r\n<document>\r\n$m[1]\r\n</document>";\r
  79                 $xml=simplexml_load_string($xml);\r
  80                 $pmid=(int)$xml->PMID;\r
  81                 $this->data[$pmid]=$xml;\r
  82                 if (!isset($this->sortdata[$sort])) $this->sortdata[$sort]=$pmid;\r
  83                 else $this->sortdata[]=$pmid;\r
  84         }\r
  85         public final function parse_all(){\r
  86                 echo $this->parse_header();\r
  87                 $num=0;\r
  88                 $sortdata=$this->sortdata;\r
  89                 ksort($sortdata);\r
  90                 foreach($sortdata as $pmid) {\r
  91                         $xml=$this->data[$pmid];\r
  92                         $num++;\r
  93                         // Get year\r
  94                         $year=$xml->Article->Journal->JournalIssue->PubDate->Year;\r
  95                         // Get journal name\r
  96                         $journal=$xml->Article->Journal->ISOAbbreviation;\r
  97                         // Get volume\r
  98                         $volume=$xml->Article->Journal->JournalIssue->Volume;\r
  99                         // Get paper title\r
 100                         $title=$xml->Article->ArticleTitle;\r
 101                         if (substr($title,-1,1)!=='.') $title.='.';\r
 102                         // Get the start and end pages\r
 103                         $pages=explode('-',(string)$xml->Article->Pagination->MedlinePgn);\r
 104                         $pages=$pages[0].'-'.substr($pages[0],0,strlen($pages[0])-strlen($pages[1])).$pages[1];\r
 105                         // Let's parse the citation\r
 106                         echo $this->parse( (int)$num,(int)$pmid,$xml,$xml->Article->AuthorList->Author\r
 107                                 ,htmlspecialchars($year) // Don't use (int) because it may be like 2008a\r
 108                                 ,htmlspecialchars($journal)\r
 109                                 ,(int)$volume\r
 110                                 ,htmlspecialchars($pages)\r
 111                                 ,htmlspecialchars($title)\r
 112                                 );\r
 113                 }\r
 114                 echo $this->parse_footer();\r
 115         }\r
 116         /* Sort methods follow.\r
 117          * note that these methods will be called from "sortPapers" method\r
 118          */\r
 119         public final function sortByAuthorName(){\r
 120                 $citations=array();\r
 121                 $papers=array();\r
 122                 $i=0;\r
 123                 foreach($this->data as $pmid=>&$xml){\r
 124                         $i++;\r
 125                         // Get date\r
 126                         $year=(int)$xml->Article->Journal->JournalIssue->PubDate->Year;\r
 127                         $month=(string)$xml->Article->Journal->JournalIssue->PubDate->Month;\r
 128                         $month=$this->month($month);\r
 129                         $month=$month<10 ? "0$month" : "$month";\r
 130                         $day=(int)$xml->Article->Journal->JournalIssue->PubDate->Day;\r
 131                         $day=$day<10 ? "0$day" : "$day";\r
 132                         $date="$year-$month-$day";\r
 133                         // Get Authors\r
 134                         $authors=$xml->Article->AuthorList->Author;\r
 135                         $firstauthor=$authors[0]->LastName.', '.$authors[0]->Initials;\r
 136                         $authornum=count($authors);\r
 137                         switch($authornum){\r
 138                                 case 1:\r
 139                                         $citation=$authors[0]->LastName.", $year";\r
 140                                         break;\r
 141                                 case 2:\r
 142                                         $citation=$authors[0]->LastName.' and '.$authors[1]->LastName.", $year";\r
 143                                         break;\r
 144                                 default:\r
 145                                         $citation=$authors[0]->LastName." et al., $year";\r
 146                                         break;\r
 147                         }\r
 148                         if (!isset($citations[$citation])) $citations[$citation]=array();\r
 149                         $citations[$citation][]=$pmid;\r
 150                         // Construct the sort key and cache data\r
 151                         $key="$firstauthor $year $citation $date $i";\r
 152                         $papers[$key]=$pmid;\r
 153                 }\r
 154                 // Modify Year (for example, 2008 => 2008a, 2008b, etc.\r
 155                 $abc='abcdefghijklmnopqrstuvwxyz';\r
 156                 foreach($citations as $key=>$value){\r
 157                         if (count($value)<2) continue;\r
 158                         for ($i=0;$i<count($value);$i++){\r
 159                                 $pmid=$value[$i];\r
 160                                 $year=(int)$this->data[$pmid]->Article->Journal->JournalIssue->PubDate->Year;\r
 161                                 $this->data[$pmid]->Article->Journal->JournalIssue->PubDate->Year=(string)$year.substr($abc,$i,1);\r
 162                         }\r
 163                 }\r
 164                 // Sort the data\r
 165                 ksort($papers);\r
 166                 // Let's get the result.\r
 167                 $result=array();\r
 168                 foreach($papers as $pmid) $result[]=$pmid;\r
 169                 $this->sortdata=$result;\r
 170         }\r
 171         protected final function month($month){\r
 172                 if (is_numeric($month)) return (int)$month;\r
 173                 switch(strtolower($month)){\r
 174                         case 'january':\r
 175                         case 'jan': return 1;\r
 176                         case 'february':\r
 177                         case 'feb': return 2;\r
 178                         case 'march':\r
 179                         case 'mar': return 3;\r
 180                         case 'april':\r
 181                         case 'apr': return 4;\r
 182                         case 'may': return 5;\r
 183                         case 'june':\r
 184                         case 'jun': return 6;\r
 185                         case 'july':\r
 186                         case 'jul': return 7;\r
 187                         case 'august':\r
 188                         case 'aug': return 8;\r
 189                         case 'september':\r
 190                         case 'sep': return 9;\r
 191                         case 'october':\r
 192                         case 'oct': return 10;\r
 193                         case 'november':\r
 194                         case 'nov': return 11;\r
 195                         case 'december':\r
 196                         case 'dec': return 12;\r
 197                         default: return 0;\r
 198                 }\r
 199         }\r
 200         \r
 201 }