From 6ed2c565455ca6cd2c9470ced180bb4a700ae5c8 Mon Sep 17 00:00:00 2001
From: kmorimatsu <kmorimatsu@1ca29b6e-896d-4ea0-84a5-967f57386b96>
Date: Tue, 3 Feb 2009 20:18:10 +0000
Subject: [PATCH] NP_PubMed v0.2.2

git-svn-id: https://svn.sourceforge.jp/svnroot/nucleus-jp/plugin@896 1ca29b6e-896d-4ea0-84a5-967f57386b96
---
 NP_PubMed/trunk/NP_PubMed.php         |   6 +-
 NP_PubMed/trunk/pubmed/index.php      | 161 +++++++++++++++++++++++++++++++---
 NP_PubMed/trunk/pubmed/index.xml      | 120 +++++++++++++++++++++++++
 NP_PubMed/trunk/spring/sidebar.inc    |   6 +-
 NP_PubMed/trunk/spring/skinbackup.xml |   7 +-
 5 files changed, 283 insertions(+), 17 deletions(-)

diff --git a/NP_PubMed/trunk/NP_PubMed.php b/NP_PubMed/trunk/NP_PubMed.php
index f95451d..f8c63fe 100644
--- a/NP_PubMed/trunk/NP_PubMed.php
+++ b/NP_PubMed/trunk/NP_PubMed.php
@@ -3,7 +3,7 @@ class NP_PubMed extends NucleusPlugin {
 	function getName() { return 'NP_PubMed'; }
 	function getMinNucleusVersion() { return 330; }
 	function getAuthor()  { return 'Katsumi'; }
-	function getVersion() { return '0.2.1'; }
+	function getVersion() { return '0.2.2'; }
 	function getURL() {return 'http://japan.nucleuscms.org/wiki/plugins:authors:katsumi';}
 	function getDescription() {
 		return $this->getName().' plugin<br />'.
@@ -16,8 +16,9 @@ class NP_PubMed extends NucleusPlugin {
 	function getTableList() { return array(sql_table('plugin_pubmed_references'), sql_table('plugin_pubmed_manuscripts')); }
 	function install(){
 		global $member;
-		$this->createOption('droptable','Drop table when uninstall?','yesno','no');
 		$this->createOption('lastquerytime','hidden option','text','0','access=hidden');
+		$this->createOption('lastmanualpmid','hidden option','text','1000000000','access=hidden');
+		$this->createOption('droptable','Drop table when uninstall?','yesno','no');
 		$this->createOption('email','E-mail address to be sent to PubMed search site (set blank if not use):','text',$member->getEmail());
 		sql_query('CREATE TABLE IF NOT EXISTS '.sql_table('plugin_pubmed_references').' ('.
 			' id int(11) not null auto_increment,'.
@@ -373,6 +374,7 @@ END;
 					htmlspecialchars($text).'</a>';
 				break;
 			case 'edit':
+				if (!$member->isLoggedIn()) return;
 				$itemid=(int)$item->itemid;
 				$text=$p1?'manuscript management':htmlspecialchars($p1,ENT_QUOTES);
 				$width=(int)$p2;
diff --git a/NP_PubMed/trunk/pubmed/index.php b/NP_PubMed/trunk/pubmed/index.php
index ab0ca51..ffe7488 100644
--- a/NP_PubMed/trunk/pubmed/index.php
+++ b/NP_PubMed/trunk/pubmed/index.php
@@ -5,8 +5,8 @@ require('../../../config.php');
 // An instance will be created at the end of this file
 
 class PubMedAdmin extends BaseActions {
-	var $oPluginAdmin,$plugin;
-	var $blogid;
+	private $oPluginAdmin,$plugin;
+	private $blogid;
 	function __construct(){
 		if (method_exists($this,'BaseActions')) $this->BaseActions();
 	
@@ -19,9 +19,15 @@ class PubMedAdmin extends BaseActions {
 		if (!($this->blogid=intPostVar('blogid'))) $this->blogid=intGetVar('blogid');
 		$CONF['ItemURL']=quickQuery('SELECT burl as result FROM '.sql_table('blog'). ' WHERE bnumber='.(int)$this->blogid);
 		
-		// Check if there is right to maintain the blog by member.
-		if (!$member->isLoggedIn() || !$member->teamRights($this->blogid) || !$manager->existsBlogID($this->blogid))
-		{
+		// Check if there is right to maintain the blog or the manuscript.
+		$ok=true;
+		if (!$member->isLoggedIn()) $ok=false;
+		if (!$member->CanLogin()) $ok=false;
+		if ($this->blogid) {
+			if (!$member->teamRights($this->blogid)) $ok=false;
+			if (!$manager->existsBlogID($this->blogid)) $ok=false;
+		}
+		if (!$ok) {
 			$this->oPluginAdmin->start();
 			echo '<p>' . _ERROR_DISALLOWED . '</p>';
 			$this->oPluginAdmin->end();
@@ -30,7 +36,6 @@ class PubMedAdmin extends BaseActions {
 		
 		// If some data is/are posted, check the ticket.
 		// Therefore, POST method must be used to change important parameter(s).
-		if (!isset($_POST)) $_POST=&$HTTP_POST_VARS;
 		if (count($_POST) && !$manager->checkTicket()) {
 			$this->oPluginAdmin->start();
 			echo '<p class="error">Error: ' . _ERROR_BADTICKET . '</p>';
@@ -49,8 +54,8 @@ class PubMedAdmin extends BaseActions {
 		$this->oPluginAdmin->start();
 		switch(getVar('action')) {
 			case 'manuscriptlist':
-				echo '<h2><a href="'.$this->plugin->getAdminURL().'?blogid='.
-					(int)$this->blogid.'&amp;action=manuscriptlist">' . 
+				echo '<h2><a href="'.$this->plugin->getAdminURL().
+					'?action=manuscriptlist">' . 
 					'Manuscript management' . "</a></h2>\n";
 				break;
 			default:
@@ -340,8 +345,7 @@ class PubMedAdmin extends BaseActions {
 		$mname=$this->_checkmanuscriptname(postVar('manuscriptname'));
 		if ($mname) sql_query('INSERT INTO '.sql_table('plugin_pubmed_manuscripts').' SET'.
 				' userid='.(int)$mid.','.
-				' manuscriptname="'.addslashes($mname).'"'.
-				' sorttext="authorname"');
+				' manuscriptname="'.addslashes($mname).'"');
 		return $this->action_manuscriptlist();
 	}
 	private function _getSortMethod($tempname){
@@ -423,6 +427,143 @@ class PubMedAdmin extends BaseActions {
 		$this->contents=array('mid'=>$manuscriptid,'mname'=>$mname);
 		$this->_showUsingArray('editmanuscript',$array);
 	}
+	function action_addmanually(){
+		global $manager;
+		if (count($_POST)) {
+			// Add item with the defined PMID
+			$pmid=intPostVar('pmid');
+			// Determine author list
+			$author=requestArray('author');
+			$authorf=requestArray('authorf');
+			$authorm=requestArray('authorm');
+			$authors=array();
+			foreach($author as $key=>$value){
+				if (!strlen($value)) break;
+				$a=$author[$key];
+				$f=$authorf[$key];
+				$m=$authorm[$key];
+				$i=substr($f,0,1).substr($m,0,1);
+				$authors[$key]=array(
+					'LastName'=>$a,
+					'ForeName'=>$f,
+					'Initials'=>$i);
+			}
+			ksort($authors);
+			// Construct Article
+			if (($year=intPostVar('year'))==0) $year='???';
+			if (strlen($journalname=postVar('journal'))==0) $journalname='???';
+			if (strlen($volume=postVar('volume'))==0) $volume='???';
+			if (strlen($pages=postVar('pages'))==0) $pages='???';
+			if (strlen($title=postVar('title'))==0) $title='???';
+			if (strlen($abstract=postVar('abstract'))==0) $abstract='???';
+			$journal=array(
+				'ISOAbbreviation'=>$journalname,
+				'JournalIssue'=>array(
+					'Volume'=>$volume,
+					'PubDate'=>array('Year'=>$year)
+					)
+				);
+			$article=array(
+				'Journal'=>$journal,
+				'ArticleTitle'=>$title,
+				'Pagination'=>array('MedlinePgn'=>$pages),
+				'AuthorList'=>array('Author'=>$authors)
+				);
+			// Construct XML data as more
+			$medline=array(
+				'PMID'=>$pmid,
+				'Article'=>$article
+				);
+			$more='<span class="np_pubmed_abstract">'.htmlspecialchars($abstract).'</span>';
+			$more.="<span style=\"display:none;\"><![CDATA[\n";
+			$more.=$this->_convert2xml('MedlineCitation',$medline);
+			$more.=']]></span>';
+			// Construct body
+			$body="<!--$year--><!--PMID: $pmid-->PMID: $pmid\n";
+			$body.='<span class="np_pubmed_authors">';
+			$n=count($authors);
+			for ($i=1;$i<=$n;$i++) {
+				if (1<$i) {
+					$body.=', ';
+					if ($i==$n) $body.='and ';
+				}
+				$body.=htmlspecialchars($authors[$i]['LastName']);
+			}
+			$body.=" ($year)</span>\n";
+			$body.='<span class="np_pubmed_article"><i>'.htmlspecialchars($journalname).
+				'</i> <b>'.htmlspecialchars($volume).
+				'</b> '.htmlspecialchars($pages)."</span>\n";
+			$body.='<span class="np_pubmed_title">'.htmlspecialchars($title).'</span>';
+			// Construct title
+			switch($n){
+				case 1:
+					$title=$authors[1]['LastName'];
+					break;
+				case 2:
+					$title=$authors[1]['LastName'].' and '.$authors[2]['LastName'];
+					break;
+				default:
+					$title=$authors[1]['LastName'].' et al.';
+					break;
+			}
+			$title=htmlspecialchars($title." ($year) $journalname");
+			// Construct category options
+			$defcatid=(int)cookieVar($CONF['CookiePrefix'] . 'NP_PubMed_defcatid');
+			if (!$defcatid) {
+				$blog=$manager->getBlog($this->blogid);
+				$defcatid=$blog->getDefaultCategory();
+			}
+			$res=sql_query('SELECT * FROM '.sql_table('category').
+				' WHERE cblog='.(int)$this->blogid.' ORDER BY cname ASC');
+			$array=array();
+			while($row=mysql_fetch_assoc($res)){
+				$row['selected']= ($row['catid']==$defcatid);
+				$array[]=$row;
+			}
+			// parse
+			$this->contents=array('title'=>$title,'body'=>$body,'more'=>$more);
+			$this->_showUsingArray('addmanuallyconfirm',$array);
+			return;
+		}
+		// Decide PMID
+		$pmid=1+$this->plugin->getOption('lastmanualpmid');
+		if ($pmid<1000000000) $pmid=1000000001;
+		$i=1;
+		while(quickQuery('SELECT count(*) as result from '.sql_table('item').
+				' WHERE iblog='.(int)$this->blogid.
+				' AND ibody LIKE "%'.(int)$pmid.'%"') ){
+			$this->plugin->setOption('lastmanualpmid',$pmid);
+			$pmid+=$i;
+			$i+=rand(1,$i);
+		}
+		// Get the number of authors
+		$numauthor=intGetVar('numauthor');
+		if (!$numauthor) $numauthor=3;
+		$array=array();
+		for ($i=1;$i<=$numauthor;$i++) {
+			$array[]=array('i'=>$i);
+		}
+		// parse
+		$this->contents=array('pmid'=>$pmid,'i'=>$numauthor,'numauthor'=>$numauthor*2);
+		$this->_showUsingArray('addmanually',$array);
+	}
+	function _convert2xml($key,$value,$nest=0){
+		if (!preg_match('/^[a-zA-Z0-9_]+$/',$key)) exit;
+		if (!is_array($value)) {
+			$value=str_replace(array('<','>'),array('&gt;','&lt;'),$value);
+			return str_repeat('  ',$nest)."<$key>$value</$key>\n";
+		}
+		$xml='';
+		foreach ($value as $k=>$v) {
+			if (is_numeric($k)) $xml.=$this->_convert2xml($key,$v,$nest+1);
+			else {
+				if ($xml=='') $xml=str_repeat('  ',$nest)."<$key>\n";
+				$xml.=$this->_convert2xml($k,$v,$nest+1);
+			}
+		}
+		if (!is_numeric($k)) $xml.=str_repeat('  ',$nest)."</$key>\n";
+		return $xml;
+	}
 }
 
 new PubMedAdmin;
diff --git a/NP_PubMed/trunk/pubmed/index.xml b/NP_PubMed/trunk/pubmed/index.xml
index ccdf69c..d07376b 100644
--- a/NP_PubMed/trunk/pubmed/index.xml
+++ b/NP_PubMed/trunk/pubmed/index.xml
@@ -242,4 +242,124 @@ Are you sure?&nbsp;&nbsp;
     ]]></foot>
   </template>
 
+
+
+  <template>
+    <name>addmanually</name>
+    <head><![CDATA[
+
+<p>Add a paper that does not have PMID.</p>
+
+<form method="post" action="">
+<%ticket(hidden)%>
+<table>
+<tr>
+  <td>PMID:</td>
+  <td><input type="text" name="pmid" size="20" value="<%int(pmid)%>"/></td>
+  <td>year:</td>
+  <td colspan="3"><input type="text" name="year" size="10" value=""/></td>
+</tr><tr>
+  <td>title:</td>
+  <td colspan="5"><input type="text" name="title" size="100" value=""/></td>
+</tr><tr>
+  <td>journal name:</td>
+  <td><input type="text" name="journal" size="20" value=""/></td>
+  <td>volume:</td>
+  <td><input type="text" name="volume" size="10" value=""/></td>
+  <td>pages:</td>
+  <td><input type="text" name="pages" size="10" value=""/></td>
+</tr>
+<tr>
+  <td>author(s)</td>
+  <td colspan="5">
+
+    ]]></head>
+    <body><![CDATA[
+
+    <%int(i)%>:
+    <input type="text" name="author[<%int(i)%>]" size="20" value=""/>,
+    <input type="text" name="authorf[<%int(i)%>]" size="20" value=""/>
+    <input type="text" name="authorm[<%int(i)%>]" size="2" value=""/>.
+    <br />
+
+    ]]></body>
+    <foot><![CDATA[
+
+    <span id="np_pubmed_author<%int(i)%>">
+      <a href="<%self%>?blogid=<%blogid%>&amp;action=addmanually&amp;numauthor=<%int(numauthor)%>" onclick="np_pubmed_author(<%int(i)%>); return false;">more authors</a>
+    </span>
+  </td>
+</tr><tr>
+  <td>abstract:</td>
+  <td colspan="5"><textarea name="abstract" cols="100" rows="10"></textarea></td>
+</tr>
+</table>
+<input type="submit" value="Add this paper"/>
+</form>
+<script type="text/javascript">
+//<![CDATA[
+function np_pubmed_author(i){
+  var obj=document.getElementById('np_pubmed_author'+i);
+  i++;
+  var t=''+i+': ';
+  t+='<input type="text" name="author['+i+']" size="20" value=""/>, ';
+  t+='<input type="text" name="authorf['+i+']" size="20" value=""/> ';
+  t+='<input type="text" name="authorm['+i+']" size="2" value=""/>. ';
+  t+='<br />';
+  t+='<span id="np_pubmed_author'+i+'"><a href="" onclick="np_pubmed_author('+i+'); return false;">more authors</a></span>';
+  obj.innerHTML=t;
+}
+//]]>]]<![CDATA[>
+</script>
+
+    ]]></foot>
+
+  </template>
+
+
+
+  <template>
+    <name>addmanuallyconfirm</name>
+    <head><![CDATA[
+
+<form method="post" action="<%conf(AdminURL)%>">
+<%ticket(hidden)%>
+<input name="action" value="additem" type="hidden">
+<input name="blogid" value="<%blogid%>" type="hidden">
+<input name="draftid" value="0" type="hidden">
+<input name="closed" value="0" type="hidden">
+<input name="actiontype" value="addnow" type="hidden">
+<input value="Add this:" type="submit">
+<input name="title" value="<%hsc(title)%>" class="np_pubmed_form" type="hidden">
+<input name="body" value="<%hsc(body)%>" class="np_pubmed_form" type="hidden">
+<input name="more" value="<%hsc(more)%>" class="np_pubmed_form" type="hidden">
+
+<select name="catid" class="np_pubmed_form">
+<option value="newcat-<%blogid%>">New category</option>
+
+    ]]></head>
+    <body><![CDATA[
+
+<%if(selected)%>
+  <option value="<%int(catid)%>" selected="selected"><%stg(cname)%></option>
+<%else%>
+  <option value="<%int(catid)%>"><%stg(cname)%></option>
+<%endif%>
+
+    ]]></body>
+    <foot><![CDATA[
+
+</select>
+&nbsp;
+(<a href="<%self%>?blogid=<%blogid%>&amp;action=addmanually" onclick="history.go(-1); return false;">go back</a>)
+</form>
+
+<pre><%hsc(title)%></pre>
+<pre><%hsc(body)%></pre>
+<pre><%hsc(more)%></pre>
+
+    ]]></foot>
+  </template>
+
+
 </document>
diff --git a/NP_PubMed/trunk/spring/sidebar.inc b/NP_PubMed/trunk/spring/sidebar.inc
index 6161bb1..787330c 100644
--- a/NP_PubMed/trunk/spring/sidebar.inc
+++ b/NP_PubMed/trunk/spring/sidebar.inc
@@ -12,8 +12,10 @@
 <dt>Navigation</dt>
 <dd><a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=PubMed" onclick="window.open(this.href);return false;">NIH PubMed site</a></dd>
 <!-- admin link, only visible if logged in -->
-<%if(loggedin)%>
+<%if(admin)%>
 <dd><a href="<%adminurl%>plugins/pubmed/?blogid=<%blogsetting(id)%>">PubMed search</a></dd>
+<%endif%>
+<%if(loggedin)%>
 <dd><a href="<%adminurl%>" title="Admin Area">Admin</a></dd>
 <%endif%>
 </dl>
@@ -24,7 +26,7 @@
 <div class="sidebar">
 <dl class="sidebardl">
 <dt>Manuscripts</dt>
-<dd><a href="<%adminurl%>plugins/pubmed/?blogid=<%blogsetting(id)%>&amp;action=manuscriptlist">(manegement)</a></dd>
+<dd><a href="<%adminurl%>plugins/pubmed/?action=manuscriptlist">(manegement)</a></dd>
 <%PubMed(manuscriptlist,spring/item)%>
 </dl>
 </div>
diff --git a/NP_PubMed/trunk/spring/skinbackup.xml b/NP_PubMed/trunk/spring/skinbackup.xml
index 4b499c6..917fecd 100644
--- a/NP_PubMed/trunk/spring/skinbackup.xml
+++ b/NP_PubMed/trunk/spring/skinbackup.xml
@@ -7,7 +7,7 @@
 
 
 	<skin name="spring" type="text/html" includeMode="skindir" includePrefix="spring/">
-		<description>Nucleus CMS spring skin</description>
+		<description>NP_PubMed spring skin</description>
 		<part name="archive"><![CDATA[<%parsedinclude(head.inc)%>
 
 <!-- page header -->
@@ -141,6 +141,7 @@ body { margin: 0px; }
 <div class="content">
 <%PubMed(SearchLink)%><br /><br />
 <%PubMed(CreateNew)%>
+<a href="<%adminurl%>plugins/pubmed/?blogid=<%blogsetting(id)%>&amp;action=addmanually">Manually add paper</a>
 
 <%parsedinclude(paging.inc)%>
 
@@ -293,7 +294,7 @@ onclick="window.open(this.href);return false;"
 
 
 	<template name="spring/index">
-		<description>Nucleus CMS spring index template</description>
+		<description>NP_PubMed spring index template</description>
 		<part name="ARCHIVELIST_LISTITEM"><![CDATA[<dd>
 <a href="<%archivelink%>" title="Archive for %B, %Y">%Y-%m</a>
 </dd>]]></part>
@@ -387,7 +388,7 @@ return false;
 
 
 	<template name="spring/item">
-		<description>Nucleus CMS spring item template</description>
+		<description>NP_PubMed spring item template</description>
 		<part name="CATLIST_LISTITEM"><![CDATA[<dd>
 <a href="<%catlink%>" title="Manuscript: <%catname%>"><%catname%></a>
 </dd>]]></part>
-- 
2.11.0