| 1 |
7876
|
aaronmk
|
<?php
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| 2 |
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require_once dirname(__FILE__)."/util.php";
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| 3 |
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|
| 4 |
7956
|
aaronmk
|
$self_dir = ensure_suffix("/", dirname($_SERVER["SCRIPT_NAME"]));
|
| 5 |
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|
|
| 6 |
7876
|
aaronmk
|
function by_prefix($url, $main_url=null)
|
| 7 |
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{
|
| 8 |
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if (!isset($main_url)) $main_url = $url;
|
| 9 |
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|
| 10 |
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return function($path) use($url, $main_url)
|
| 11 |
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{
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| 12 |
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return $path ? $url.$path : $main_url;
|
| 13 |
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};
|
| 14 |
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}
|
| 15 |
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|
| 16 |
13613
|
aaronmk
|
function user2path($user) # multiple @ and nested . OK: a@b.c@host -> host?b.c.a
|
| 17 |
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{ return implode(".", array_reverse(explode("@", $user))); }
|
| 18 |
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|
| 19 |
13612
|
aaronmk
|
# redirect subpath@host? -> host?subpath (one type of prefix redirect)
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| 20 |
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# better than subpath.host because case is preserved and special chars allowed
|
| 21 |
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# must require trailing ? , to avoid needing login to view the page itself
|
| 22 |
13613
|
aaronmk
|
# subpath prefix: see format in user2path()
|
| 23 |
13612
|
aaronmk
|
if (substr($_SERVER["REQUEST_URI"], -1/*last char*/) === "?")
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| 24 |
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{
|
| 25 |
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if (!isset($_SERVER["PHP_AUTH_USER"])) # browser first omits Authorization
|
| 26 |
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{
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| 27 |
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header('WWW-Authenticate: Basic realm="please leave username/password blank or as filled in"');
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| 28 |
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}
|
| 29 |
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elseif ($_SERVER["PHP_AUTH_USER"] !== "")
|
| 30 |
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{
|
| 31 |
13613
|
aaronmk
|
header("Location: ?".user2path($_SERVER["PHP_AUTH_USER"]));
|
| 32 |
13612
|
aaronmk
|
exit;
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| 33 |
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}
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| 34 |
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# otherwise, user empty so just display page
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| 35 |
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}
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| 36 |
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| 37 |
7904
|
aaronmk
|
$h_level = 5;
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| 38 |
9601
|
aaronmk
|
$root = $_SERVER["SERVER_NAME"].rm_suffix("/", $self_dir)."?";
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| 39 |
7953
|
aaronmk
|
# instead of PATH_INFO, to support the Apache ErrorDocument directive
|
| 40 |
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$rel_fs_path = rm_prefix($self_dir, $_SERVER["REQUEST_URI"]);
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| 41 |
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$path = parse_dot_path($rel_fs_path);
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| 42 |
7939
|
aaronmk
|
$ns = strtolower($path->head);
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| 43 |
7876
|
aaronmk
|
|
| 44 |
7939
|
aaronmk
|
function add_ns($name, $path_pat, $url_func)
|
| 45 |
7876
|
aaronmk
|
{
|
| 46 |
7967
|
aaronmk
|
global $root, $h_level, $path, $ns;
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| 47 |
7876
|
aaronmk
|
if (is_string($url_func)) $url_func = by_prefix($url_func);
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| 48 |
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|
| 49 |
7967
|
aaronmk
|
print("<h".$h_level.' id="'.$name.'">'.$root.'<big><a href="http://'.$root
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| 50 |
7938
|
aaronmk
|
.$name.'">'.$name."</a></big><i>".$path_pat."</i></h".$h_level.">\n");
|
| 51 |
7939
|
aaronmk
|
if ($ns === strtolower($name)) # found match, so redirect
|
| 52 |
7876
|
aaronmk
|
{
|
| 53 |
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header("Location: ".strip_url($url_func($path->tail)));
|
| 54 |
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ob_end_flush();
|
| 55 |
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exit;
|
| 56 |
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}
|
| 57 |
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}
|
| 58 |
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| 59 |
7937
|
aaronmk
|
function custom_separator($url, $sep, $main_url=null)
|
| 60 |
7910
|
aaronmk
|
{
|
| 61 |
7914
|
aaronmk
|
if (!isset($main_url)) $main_url = $url;
|
| 62 |
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|
| 63 |
|
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return function($path) use($url, $sep, $main_url)
|
| 64 |
7910
|
aaronmk
|
{
|
| 65 |
7914
|
aaronmk
|
if ($path === "") return $main_url;
|
| 66 |
7910
|
aaronmk
|
$path = parse_dot_path($path);
|
| 67 |
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return $url.join_non_empty($sep, array($path->head, $path->tail));
|
| 68 |
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};
|
| 69 |
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}
|
| 70 |
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|
| 71 |
7876
|
aaronmk
|
function fragment_override($url, $fragment=null)
|
| 72 |
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{
|
| 73 |
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return function($path) use($url, $fragment)
|
| 74 |
|
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{
|
| 75 |
|
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if (!isset($fragment))
|
| 76 |
|
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{
|
| 77 |
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$path = parse_dot_path($path);
|
| 78 |
|
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$fragment = $path->head;
|
| 79 |
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$path = $path->tail;
|
| 80 |
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}
|
| 81 |
7902
|
aaronmk
|
if ($path !== "") $url .= "?".$path;
|
| 82 |
7876
|
aaronmk
|
return $url."#".$fragment;
|
| 83 |
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};
|
| 84 |
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}
|
| 85 |
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|
| 86 |
7934
|
aaronmk
|
function phpPgAdmin($url, $table=null)
|
| 87 |
7876
|
aaronmk
|
{
|
| 88 |
7934
|
aaronmk
|
return function($path) use($url, $table)
|
| 89 |
7876
|
aaronmk
|
{
|
| 90 |
7934
|
aaronmk
|
$path = join_non_empty(".", array($table, $path));
|
| 91 |
7876
|
aaronmk
|
$path = parse_dot_path($path);
|
| 92 |
7886
|
aaronmk
|
$subject = "schema";
|
| 93 |
7902
|
aaronmk
|
if ($path->head !== "")
|
| 94 |
7876
|
aaronmk
|
{
|
| 95 |
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$url .= "&table=".$path->head;
|
| 96 |
7902
|
aaronmk
|
if ($path->tail !== "")
|
| 97 |
7886
|
aaronmk
|
{
|
| 98 |
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$url .= "&column=".$path->tail;
|
| 99 |
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$subject = "column";
|
| 100 |
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}
|
| 101 |
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else $subject = "table";
|
| 102 |
7876
|
aaronmk
|
}
|
| 103 |
7895
|
aaronmk
|
$url .= "&subject=".$subject;
|
| 104 |
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return $url;
|
| 105 |
7876
|
aaronmk
|
};
|
| 106 |
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}
|
| 107 |
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|
| 108 |
7934
|
aaronmk
|
function phpMyAdmin($url, $table=null)
|
| 109 |
7893
|
aaronmk
|
{
|
| 110 |
7934
|
aaronmk
|
return function($path) use($url, $table)
|
| 111 |
7893
|
aaronmk
|
{
|
| 112 |
7934
|
aaronmk
|
$path = join_non_empty(".", array($table, $path));
|
| 113 |
7893
|
aaronmk
|
$path = parse_dot_path($path);
|
| 114 |
|
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$target = "db_structure";
|
| 115 |
7902
|
aaronmk
|
if ($path->head !== "")
|
| 116 |
7893
|
aaronmk
|
{
|
| 117 |
|
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$url .= "&table=".$path->head;
|
| 118 |
7902
|
aaronmk
|
if ($path->tail !== "") $url .= "&column=".$path->tail;
|
| 119 |
7899
|
aaronmk
|
$target = "tbl_structure";
|
| 120 |
7893
|
aaronmk
|
}
|
| 121 |
7896
|
aaronmk
|
$url .= "&target=".$target.".php";
|
| 122 |
7895
|
aaronmk
|
return $url;
|
| 123 |
7893
|
aaronmk
|
};
|
| 124 |
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}
|
| 125 |
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|
| 126 |
7876
|
aaronmk
|
ob_start(); // delay output in case there is a redirect
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| 127 |
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?>
|
| 128 |
9613
|
aaronmk
|
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
| 129 |
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<html xmlns="http://www.w3.org/1999/xhtml">
|
| 130 |
7876
|
aaronmk
|
<head>
|
| 131 |
7881
|
aaronmk
|
<title>VegPath</title>
|
| 132 |
8033
|
aaronmk
|
<link rel="stylesheet" type="text/css" href="/main.css" />
|
| 133 |
7876
|
aaronmk
|
<style type="text/css">
|
| 134 |
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h1 {color: green;}
|
| 135 |
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</style>
|
| 136 |
8033
|
aaronmk
|
<script type="text/javascript" src="/util.js"></script>
|
| 137 |
7876
|
aaronmk
|
</head>
|
| 138 |
|
|
<body>
|
| 139 |
7951
|
aaronmk
|
<h1>VegPath <small><a href="http://en.wikipedia.org/wiki/PURL">persistent URLs</a> for vegetation resources</small></h1>
|
| 140 |
7923
|
aaronmk
|
<div>Supported URL patterns: <small>(elements in <i>italics</i> are optional)</small></div>
|
| 141 |
7876
|
aaronmk
|
<?php
|
| 142 |
|
|
# add and list URLs
|
| 143 |
7920
|
aaronmk
|
|
| 144 |
7924
|
aaronmk
|
$Redmine = "https://projects.nceas.ucsb.edu/nceas/projects/bien";
|
| 145 |
7928
|
aaronmk
|
$Redmine_svn = $Redmine."/repository/raw";
|
| 146 |
7924
|
aaronmk
|
|
| 147 |
7920
|
aaronmk
|
$nimoy = "http://nimoy.nceas.ucsb.edu/phpmyadmin/index.php";
|
| 148 |
7921
|
aaronmk
|
function nimoy_db($db) { global $nimoy; return phpMyAdmin($nimoy."?db=".$db); }
|
| 149 |
7936
|
aaronmk
|
|
| 150 |
|
|
$IH_db = phpMyAdmin($nimoy."?db=bien3_adb", "ih");
|
| 151 |
7944
|
aaronmk
|
|
| 152 |
|
|
$SALVIAS = "http://salvias.net/Documents/salvias_data_dictionary.html";
|
| 153 |
7931
|
aaronmk
|
?>
|
| 154 |
|
|
<table border="0" cellspacing="0" cellpadding="0">
|
| 155 |
|
|
<tr valign="top">
|
| 156 |
|
|
<td nowrap="nowrap"><h2>Terms</h2></td>
|
| 157 |
8044
|
aaronmk
|
<td nowrap="nowrap"><h2> </h2></td>
|
| 158 |
7931
|
aaronmk
|
<td nowrap="nowrap"><h2>Data</h2></td>
|
| 159 |
|
|
</tr>
|
| 160 |
|
|
<tr valign="top">
|
| 161 |
|
|
<td nowrap="nowrap">
|
| 162 |
|
|
<?php
|
| 163 |
|
|
print("<blockquote>\n");
|
| 164 |
|
|
print("<h3>Exchange schemas</h3>");
|
| 165 |
7876
|
aaronmk
|
{
|
| 166 |
|
|
print("<blockquote>\n");
|
| 167 |
7939
|
aaronmk
|
add_ns("VegCore", ".term", "https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCore#");
|
| 168 |
|
|
add_ns("DwC", ".term", "http://rs.tdwg.org/dwc/terms/#");
|
| 169 |
7876
|
aaronmk
|
{
|
| 170 |
7931
|
aaronmk
|
print("<blockquote>\n"); $h_level++;
|
| 171 |
8050
|
aaronmk
|
add_ns("DwC.history", ".term", "http://rs.tdwg.org/dwc/terms/history/#");
|
| 172 |
7931
|
aaronmk
|
print("</blockquote>\n"); $h_level--;
|
| 173 |
7876
|
aaronmk
|
}
|
| 174 |
7942
|
aaronmk
|
add_ns("TCS", "#/XPath", "http://www.tdwg.org/standards/117/download/#/v101.xsd");
|
| 175 |
|
|
add_ns("VegX", "#/XPath", "http://wiki.tdwg.org/twiki/pub/Vegetation/WebHome/VegX_Schema_1.5.3_proposed.zip#/veg.xsd");
|
| 176 |
7931
|
aaronmk
|
print("</blockquote>\n");
|
| 177 |
|
|
}
|
| 178 |
|
|
print("<h3>Aggregators</h3>");
|
| 179 |
|
|
{
|
| 180 |
|
|
print("<blockquote>\n");
|
| 181 |
7939
|
aaronmk
|
add_ns("VegBank", ".table.column", custom_separator("http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&entity=dba_tabledescription&where=where_tablename&wparam=",
|
| 182 |
7931
|
aaronmk
|
"#", "http://vegbank.org/get/index/dba_tabledescription"));
|
| 183 |
7945
|
aaronmk
|
add_ns("SALVIAS", ".table.column", by_prefix($SALVIAS."#Plot_", $SALVIAS));
|
| 184 |
7876
|
aaronmk
|
{
|
| 185 |
7931
|
aaronmk
|
print("<blockquote>\n"); $h_level++;
|
| 186 |
8050
|
aaronmk
|
add_ns("SALVIAS.db", ".table.column", nimoy_db("salvias_plots"));
|
| 187 |
|
|
add_ns("SALVIAS.users", ".table.column", nimoy_db("salvias_users"));
|
| 188 |
7931
|
aaronmk
|
print("</blockquote>\n"); $h_level--;
|
| 189 |
7876
|
aaronmk
|
}
|
| 190 |
7939
|
aaronmk
|
add_ns("BIEN2", "", $nimoy."?target=server_databases.php");
|
| 191 |
7876
|
aaronmk
|
{
|
| 192 |
7931
|
aaronmk
|
print("<blockquote>\n"); $h_level++;
|
| 193 |
8050
|
aaronmk
|
add_ns("BIEN2.web", ".table.column", nimoy_db("bien_web"));
|
| 194 |
|
|
add_ns("BIEN2.core", ".table.column", nimoy_db("bien2"));
|
| 195 |
|
|
add_ns("BIEN2.geoscrub", ".table.column", nimoy_db("geoscrub"));
|
| 196 |
|
|
add_ns("BIEN2.staging", ".table.column", nimoy_db("bien2_staging"));
|
| 197 |
7931
|
aaronmk
|
print("</blockquote>\n"); $h_level--;
|
| 198 |
7876
|
aaronmk
|
}
|
| 199 |
7939
|
aaronmk
|
add_ns("VegBIEN", ".table.column", phpPgAdmin("http://vegbiendev.nceas.ucsb.edu/phppgadmin/redirect.php?server=localhost%3A5432%3Aallow&database=vegbien&schema=public"));
|
| 200 |
7931
|
aaronmk
|
print("</blockquote>\n");
|
| 201 |
|
|
}
|
| 202 |
|
|
print("<h3>Primary databases</h3>");
|
| 203 |
|
|
{
|
| 204 |
|
|
print("<blockquote>\n");
|
| 205 |
7939
|
aaronmk
|
add_ns("TNRS", ".term", fragment_override("http://tnrs.iplantcollaborative.org/instructions.html", "download_results"));
|
| 206 |
7961
|
aaronmk
|
add_ns("CTFS", "", $Redmine."/wiki/CTFS");
|
| 207 |
7929
|
aaronmk
|
{
|
| 208 |
7931
|
aaronmk
|
print("<blockquote>\n"); $h_level++;
|
| 209 |
8050
|
aaronmk
|
add_ns("CTFS.schema", ".table.column", $Redmine_svn."/inputs/CTFS/_archive/DBv5.txt#");
|
| 210 |
|
|
add_ns("CTFS.tables", ".table", fragment_override($Redmine."/wiki/CTFS", "Tables"));
|
| 211 |
|
|
add_ns("CTFS.terms", ".term", $Redmine_svn."/inputs/CTFS/_src/ctfs-comments_worksheet.xls#");
|
| 212 |
7931
|
aaronmk
|
print("</blockquote>\n"); $h_level--;
|
| 213 |
7929
|
aaronmk
|
}
|
| 214 |
8050
|
aaronmk
|
add_ns("IH.db", ".term", $IH_db);
|
| 215 |
7876
|
aaronmk
|
print("</blockquote>\n");
|
| 216 |
|
|
}
|
| 217 |
7931
|
aaronmk
|
print("<h3>People</h3>");
|
| 218 |
7876
|
aaronmk
|
{
|
| 219 |
|
|
print("<blockquote>\n");
|
| 220 |
8042
|
aaronmk
|
add_ns("Brad", "", "mailto:bboyleATemail.arizona.edu");
|
| 221 |
7931
|
aaronmk
|
{
|
| 222 |
|
|
print("<blockquote>\n"); $h_level++;
|
| 223 |
|
|
$Brad_Boyle_VegCore = $Redmine_svn."/schemas/VegCore/Brad_Boyle";
|
| 224 |
8050
|
aaronmk
|
add_ns("Brad.data-provenance", ".term", $Brad_Boyle_VegCore."/BIEN%20database%20entities%20related%20to%20data%20provenance%20and%20ownership.docx#");
|
| 225 |
|
|
add_ns("Brad.DwC-IDs.2013-2-7", ".term", $Brad_Boyle_VegCore."/vegbien_identifiers.xlsx#");
|
| 226 |
|
|
add_ns("Brad.DwC-IDs.2013-1-31", ".term", $Brad_Boyle_VegCore."/vegbien_identifier_examples.xlsx#");
|
| 227 |
7931
|
aaronmk
|
print("</blockquote>\n"); $h_level--;
|
| 228 |
|
|
}
|
| 229 |
7876
|
aaronmk
|
print("</blockquote>\n");
|
| 230 |
|
|
}
|
| 231 |
7931
|
aaronmk
|
print("</blockquote>\n");
|
| 232 |
|
|
?>
|
| 233 |
|
|
</td>
|
| 234 |
8044
|
aaronmk
|
<td nowrap="nowrap"></td>
|
| 235 |
7931
|
aaronmk
|
<td nowrap="nowrap">
|
| 236 |
|
|
<?php
|
| 237 |
|
|
print("<blockquote>\n");
|
| 238 |
7932
|
aaronmk
|
print("<h3>Institutions</h3>");
|
| 239 |
|
|
{
|
| 240 |
|
|
print("<blockquote>\n");
|
| 241 |
7939
|
aaronmk
|
add_ns("IH", ".herbarium_code", by_prefix("http://sweetgum.nybg.org/ih/herbarium_list.php?QueryName=DetailedQuery&Restriction=NamPartyType+%3D+%27IH+Herbarium%27&col_NamOrganisationAcronym=",
|
| 242 |
7931
|
aaronmk
|
"http://sweetgum.nybg.org/ih/"));
|
| 243 |
7932
|
aaronmk
|
print("</blockquote>\n");
|
| 244 |
|
|
}
|
| 245 |
7931
|
aaronmk
|
print("</blockquote>\n");
|
| 246 |
|
|
?>
|
| 247 |
|
|
</td>
|
| 248 |
|
|
</tr>
|
| 249 |
|
|
</table>
|
| 250 |
|
|
<?php
|
| 251 |
7967
|
aaronmk
|
if (ends_with($root, '#')) # URL shortener requires fragment redirect
|
| 252 |
7922
|
aaronmk
|
{
|
| 253 |
7876
|
aaronmk
|
?>
|
| 254 |
7931
|
aaronmk
|
<script type="text/javascript">
|
| 255 |
7876
|
aaronmk
|
var loc = document.location
|
| 256 |
8365
|
aaronmk
|
if (loc.hash) document.location = '?'+rm_prefix('#', loc.hash)
|
| 257 |
7931
|
aaronmk
|
</script>
|
| 258 |
7922
|
aaronmk
|
<?php
|
| 259 |
|
|
}
|
| 260 |
9607
|
aaronmk
|
?>
|
| 261 |
|
|
<p> </p>
|
| 262 |
|
|
<?php
|
| 263 |
7876
|
aaronmk
|
ob_end_flush();
|
| 264 |
9605
|
aaronmk
|
|
| 265 |
|
|
# full directory index
|
| 266 |
13305
|
aaronmk
|
# to fix bug, only display if invoked as "__.org/", not "__.org/index.php"
|
| 267 |
|
|
if (substr($_SERVER["SCRIPT_URI"], -1) === '/')
|
| 268 |
13611
|
aaronmk
|
fpassthru(fopen($_SERVER["SCRIPT_URI"]."all?".$_SERVER["HTTP_AUTHORIZATION"], "r"));
|
| 269 |
9606
|
aaronmk
|
?>
|
| 270 |
|
|
</body>
|
| 271 |
|
|
</html>
|
