lots of little changes

.gitignore

@@ -31,5 +31,5 @@ Icon?
 Thumbs.db
 
 # tmp folders
-eoliphone/tmp/
+eoliphone/tmp/*
 blast/tmp/

blast/ncbi_blast.php

@@ -58,7 +58,7 @@ function send_blast_job($gi)
 	"MEGABLAST"		=> "yes"
 	);
 
-	$html = post('http://blast.ncbi.nlm.nih.gov/Blast.cgi', $cmds);
+	$html = post('https://blast.ncbi.nlm.nih.gov/Blast.cgi', $cmds);
 
 	if (preg_match('/^    RID = (?<rid>.*)$/m', $html, $m))
 	{
@@ -68,6 +68,11 @@ function send_blast_job($gi)
 	{
 		$job->rtoe = $m['rtoe'];
 	}
+
+	if ($job->rtoe > 100)
+	{
+		$job->rtoe =20;
+	}
 
 	return $job;
 }
@@ -82,7 +87,7 @@ function get_results($rid)
 	{
 		sleep(5);
 
-		$url = "http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Get&RID=$rid";
+		$url = "https://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Get&RID=$rid";
 
 		$html = get($url);
 
@@ -109,7 +114,7 @@ function get_results($rid)
 		}
 	}
 
-	$url = "http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Get&RID=$rid&FORMAT_TYPE=XML";
+	$url = "https://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Get&RID=$rid&FORMAT_TYPE=XML";
 	$result = get($url);
 
 	return $result;
@@ -138,7 +143,7 @@ function get_results($rid)
 	"QUERY" 		=> $gi
 	);
 
-	$html = post('http://www.ncbi.nlm.nih.gov/blast/Blast.cgi', $cmds);
+	$html = post('https://www.ncbi.nlm.nih.gov/blast/Blast.cgi', $cmds);
 
 	//echo $html;
 

course/geography/index.html

@@ -45,7 +45,7 @@ <h2><a name="background"/>Background</h2>
 
 <h2><a name="lecture"/>Lecture</h2>
 
-<div style="width:425px" id="__ss_11253521"><strong style="display:block;margin:12px 0 4px"><a href="http://www.slideshare.net/rdmpage/geography-11253521" title="Geography">Geography</a></strong><object id="__sse11253521" width="425" height="355"><param name="movie" value="http://static.slidesharecdn.com/swf/ssplayer2.swf?doc=geography-120125080546-phpapp02&stripped_title=geography-11253521&userName=rdmpage" /><param name="allowFullScreen" value="true"/><param name="allowScriptAccess" value="always"/><param name="wmode" value="transparent"/><embed name="__sse11253521" src="http://static.slidesharecdn.com/swf/ssplayer2.swf?doc=geography-120125080546-phpapp02&stripped_title=geography-11253521&userName=rdmpage" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" wmode="transparent" width="425" height="355"></embed></object><div style="padding:5px 0 12px">View more <a href="http://www.slideshare.net/">presentations</a> from <a href="http://www.slideshare.net/rdmpage">Roderic Page</a>.</div></div>
+<iframe src="//www.slideshare.net/slideshow/embed_code/key/IHNZrYvjwYXhAJ" width="595" height="485" frameborder="0" marginwidth="0" marginheight="0" scrolling="no" style="border:1px solid #CCC; border-width:1px; margin-bottom:5px; max-width: 100%;" allowfullscreen> </iframe> <div style="margin-bottom:5px"> <strong> <a href="//www.slideshare.net/rdmpage/geography-11253521" title="Geography" target="_blank">Geography</a> </strong> from <strong><a target="_blank" href="//www.slideshare.net/rdmpage">Roderic Page</a></strong> </div>
 
 <h2><a name="maps"/>Maps</h2>
 
@@ -171,7 +171,7 @@ <h2><a name="other"/>Other uses for maps</h2>
 
 <h3>Maps and timelines</h3>
 
-<p>Maps display data in space, but that spatial arrangement may change over time. There are a number of tools we can use to explore this. Google Earth itself supports timelines, as we can see with the avian flu example. Another useful tool is timemap, which creates a linked timeline and map display. For an example see the <a href="http://www.oe-files.de/gmaps/eqmashup.html" target="new">Live Earthquake Maship</a>.</p>
+<p>Maps display data in space, but that spatial arrangement may change over time. There are a number of tools we can use to explore this. Google Earth itself supports timelines, as we can see with the avian flu example. Another useful tool is timemap, which creates a linked timeline and map display. For an example see the <a href="http://www.oe-files.de/gmaps/eqmashup.html" target="new">Live Earthquake Mashup</a>.</p>
 
 <p>As an example, below is a timemap for swine flu. By scrolling through the timeline you can see the changes in geographic distribution of this disease.</p>
 

course/introduction/index.html

@@ -54,7 +54,7 @@ <h2>Background reading</h2>
 
 <h2><a name="lecture"/>Lecture</h2>
 
-<div style="width:425px" id="__ss_11218799"><strong style="display:block;margin:12px 0 4px"><a href="http://www.slideshare.net/rdmpage/phyloinformatics-introduction" title="Phyloinformatics: Introduction">Phyloinformatics: Introduction</a></strong><object id="__sse11218799" width="425" height="355"><param name="movie" value="http://static.slidesharecdn.com/swf/ssplayer2.swf?doc=introduction-120123103847-phpapp02&stripped_title=phyloinformatics-introduction&userName=rdmpage" /><param name="allowFullScreen" value="true"/><param name="allowScriptAccess" value="always"/><param name="wmode" value="transparent"/><embed name="__sse11218799" src="http://static.slidesharecdn.com/swf/ssplayer2.swf?doc=introduction-120123103847-phpapp02&stripped_title=phyloinformatics-introduction&userName=rdmpage" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" wmode="transparent" width="425" height="355"></embed></object><div style="padding:5px 0 12px">View more <a href="http://www.slideshare.net/">presentations</a> from <a href="http://www.slideshare.net/rdmpage">Roderic Page</a>.</div></div>
+<iframe src="//www.slideshare.net/slideshow/embed_code/key/nWKi1FNn7Jg0K7" width="595" height="485" frameborder="0" marginwidth="0" marginheight="0" scrolling="no" style="border:1px solid #CCC; border-width:1px; margin-bottom:5px; max-width: 100%;" allowfullscreen> </iframe> <div style="margin-bottom:5px"> <strong> <a href="//www.slideshare.net/rdmpage/phyloinformatics-introduction" title="Phyloinformatics: Introduction" target="_blank">Phyloinformatics: Introduction</a> </strong> from <strong><a target="_blank" href="//www.slideshare.net/rdmpage">Roderic Page</a></strong> </div>
 
 <p><a href="introduction.pptx">Slides</a></p>
 
@@ -167,6 +167,10 @@ <h3>RSS feeds</h3>
 <img src="images/gmaps.png" />
 </div>
 
+<div class="warning">
+Google has now disabled the old classic view. Based on an example <a href="https://developers.google.com/maps/documentation/javascript/examples/layer-georss">provided by Google</a> I've created a <a href="georss.html" target="_new">simple web page to display GeoRSS feeds</a>.
+</div>
+
 <div class="example">
 <iframe src="http://player.vimeo.com/video/35517980?title=0&amp;byline=0&amp;portrait=0" width="398" height="403" frameborder="0" webkitAllowFullScreen mozallowfullscreen allowFullScreen></iframe>
 </div>

course/taxonomy/index.html

@@ -16,6 +16,15 @@
 		background-color: rgb(222,222,222);
 		-webkit-border-radius: 10px;
 	}
+
+	.warning
+	{
+		margin:20px;
+		padding:20px;
+		background-color: #FFECAC;
+		border: 2px solid orange;
+		-webkit-border-radius: 10px;
+	}	
 </style>
 <title>Taxonomy</title>
 </head>
@@ -30,7 +39,7 @@ <h1>Taxonomy</h1>
 <li><a href="#names">Names</a></li>
 <li><a href="#classification">Classifications</a></li>
 <li><a href="#next">Where next?</a></li>
-<li><a href="#barcodes">Beyond names: DNA batcodes</a></li>
+<li><a href="#barcodes">Beyond names: DNA barcodes</a></li>
 
 </ul>
 
@@ -91,7 +100,7 @@ <h3><i>Drosophila melanogaster</i></h3>
 <li>Restrict <i>Drosophila</i> to a monophyletic group that includes the type species (<i>D. funebris</i>)<br/>
 (means <i>Drosophila melanogaster</i> can’t be <i>Drosophila melanogaster</i>)
 <li>Change the type species to be <i>Drosophila melanogaster</i><br/>
-(But nomenclature is not taxonomy, and ICZN said "no")</li>
+(But nomenclature is not taxonomy, and ICZN said "no", see <a href="http://dx.doi.org/10.21805/bzn.v67i1.a14">doi:10.21805/bzn.v67i1.a14</a>)</li>
 </ol>
 
 <p>At core of argument is notion that Linnean names have to match phylogeny.</p>
@@ -141,6 +150,8 @@ <h3>Synonyms</h3>
 
 <iframe width="560" height="315" src="//www.youtube.com/embed/xPqJkG2XhQ8?rel=0" frameborder="0" allowfullscreen></iframe>
 
+
+<div class="warning">Synynyms is offline [2017]</div>
 <div class="example">
 
 <p>Ryan Schenk's <a href="http://synynyms.com/" target="_new">http://synynyms.com</a> tool displays the frequency of usage of taxonomic names in literature scanned by the <a href="http://www.biodiversitylibrary.org" target="_new">Biodiversity Heritage Library (BHL)</a>, and was inspired by Google's <a href="http://books.google.com/ngrams" target="_new">Ngram viewer</a>.</p>
@@ -242,6 +253,9 @@ <h3>Visualing classifications</h3>
 
 <iframe src="http://player.vimeo.com/video/35704473?title=0&amp;byline=0&amp;portrait=0" width="398" height="333" frameborder="0" webkitAllowFullScreen mozallowfullscreen allowFullScreen></iframe>
 
+
+<div class="warning">EOL Treemap is offline [2017]</div>
+
 <p>For a prettier verson see the <a href="http://synthesis.eol.org/media/treemap" target="_new">EOL Treemap</a>.</p>
 
 <img src="images/eol.png" width="400"/>
@@ -272,6 +286,8 @@ <h3>Visualing classifications</h3>
 
 <h3>Rates of discovery of new species over time</h3>
 
+<div class="warning">Taxatoy is offline [2017]</div>
+
 <p>There are various tools for viewing the rate of discovery of new species (more correctly, the rate at which new taxonomic names are published) over time, such as <a href="http://taxatoy.ubio.org/" target="_new">Taxatoy</a> described below. BioNames also has a timeline feature, which we can use to explore rates of new taxa being described.</p>
 
 <div class="example">
@@ -323,6 +339,19 @@ <h2><a name="barcodes"/>Beyond names: DNA barcodes</h2>
 <li><a href="http://bins.boldsystems.org" target="_new">Barcode of Life Database (BOLD)</a></li>
 </ul>
 
+<div class="example">
+<b>Barcodes in GenBank</b>
+<img src="images/image.png" />
+<p>Below are two DNA barcodes that are also in GenBank. Look at each barcode, does Genbank treat them the same? If not, why not?</p>
+
+<ul>
+<li><a href="http://www.ncbi.nlm.nih.gov/nucleotide/HQ918292" target="_new">HQ918292</a></li>
+<li><a href="http://www.ncbi.nlm.nih.gov/nucleotide/HQ918313" target="_new">HQ918313</a></li>
+</ul>
+
+</div>
+
+
 
 <h3>Reading</h3>
 
@@ -347,6 +376,10 @@ <h3>Reading</h3>
 <a href="http://blogs.scientificamerican.com/tetrapod-zoology/taxonomic-vandalism-and-hoser/">Taxonomic vandalism and the Raymond Hoser problem</a>
 </li>
 
+<li>
+Opinion 2245 (Case 3407) Drosophila Fallén, 1823 (Insecta, Diptera): Drosophila funebris Fabricius, 1787 is maintained as the type species. (2010). The Bulletin of Zoological Nomenclature, 67(1), 106–115. <a href="http://dx.doi.org/10.21805/bzn.v67i1.a14" target="_new">doi:10.21805/bzn.v67i1.a14</a>
+</li>
+
 
 </ul>
 

rss/barcode.php

@@ -38,7 +38,7 @@ function uuid($prefix = '')
 	$taxon_id = $_GET['taxon_id'];
 }
 
-$url = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nucleotide&term=barcode[keyword]+txid' . $taxon_id . '[Organism:exp]&retmax=10'; //&reldate=365&datetype=mdat';
+$url = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nucleotide&term=barcode[keyword]+txid' . $taxon_id . '[Organism:exp]&retmax=10'; //&reldate=365&datetype=mdat';
 
 
 $xml = get($url);

rss/genbank_fetch.php

@@ -223,6 +223,8 @@ function process_locality(&$sequence)
 
 		if (isset($sequence->source->locality))
 		{
+			$matched = false;
+
 			// AY249471 Palmer Archipelago 64deg51.0'S, 63deg34.0'W 
 			if (preg_match("/(?<latitude_degrees>[0-9]{1,2})deg(?<latitude_minutes>[0-9]{1,2}(\.\d+)?)'\s*(?<latitude_hemisphere>[S|N]),\s*(?<longitude_degrees>[0-9]{1,3})deg(?<longitude_minutes>[0-9]{1,2}(\.\d+)?)'\s*(?<longitude_hemisphere>[W|E])/", $sequence->source->locality, $matches))
 			{	
@@ -372,7 +374,7 @@ function fetch_sequence($id)
 	$genbank_sequence = null;
 
 	// Query URL	
-	$url = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id='
+	$url = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id='
 		. $id
 		. '&rettype=gb&retmode=xml';
 
@@ -615,6 +617,8 @@ function fetch_sequence($id)
 
 	}
 
+	//print_r($genbank_sequence);
+
 	return $genbank_sequence;
 }
 
@@ -629,7 +633,7 @@ function fetch_one($id)
 	//print_r($sequence);
 }
 
-if (0)
+if (1)
 {
 	$id = 'DQ502910';
 

rss/nameparse.php

@@ -89,7 +89,7 @@ function	parse_name($fullname) {
 					}
 
 				if(in_array_norm($curr,$prefices)) {
-					if($out['last']) {
+					if(isset($out['last'])) {
 						$out['last']	.=	" $curr";
 						}
 					else {
@@ -99,7 +99,7 @@ function	parse_name($fullname) {
 					}
 
 				if($next == 'y' || $next == 'Y') {
-					if($out['last']) {
+					if(isset($out['last'])) {
 						$out['last']	.=	" $curr";
 						}
 					else {
@@ -108,12 +108,12 @@ function	parse_name($fullname) {
 					continue;
 					}
 
-				if($out['last']) {
+				if(isset($out['last'])) {
 					$out['last']	.=	" $curr";
 					continue;
 					}
 
-				if($out['middle']) {
+				if(isset($out['middle'])) {
 					$out['middle']		.=	" $curr";
 					}
 				else {
@@ -128,14 +128,23 @@ function	parse_name($fullname) {
 						$n_subp	=	count($subp);
 						for($i = 0; $i < $n_subp; $i++) {
 							$curr				=	trim($subp[$i]);
-							$next				=	trim($subp[$i+1]);
+							//$next				=	trim($subp[$i+1]);
+							if ($i < $n_subp - 1)
+							{
+								$next				=	trim($subp[$i+1]);
+							}
+							else
+							{
+								$next = '';
+							}
+
 
 							if($i == 0 && in_array_norm($curr,$titles)) {
 								$out['title']	=	$curr;
 								continue;
 								}
 
-							if(!$out['first']) {
+							if(!isset($out['first'])) {
 								$out['first']	=	$curr;
 								continue;
 								}
@@ -170,12 +179,12 @@ function	parse_name($fullname) {
 								continue;
 								}
 
-							if($out['last']) {
+							if(isset($out['last'])) {
 								$out['last']	.=	" $curr";
 								continue;
 								}
 
-							if($out['middle']) {
+							if(isset($out['middle'])) {
 								$out['middle']		.=	" $curr";
 								}
 							else {
@@ -189,15 +198,16 @@ function	parse_name($fullname) {
 						$n_subp	=	count($subp);
 						for($i = 0; $i < $n_subp; $i++) {
 							$curr				=	trim($subp[$i]);
-							//$next				=	trim($subp[$i+1]);
+							//$next				=	trim($subp[$i+1]);							
 							if ($i < $n_subp - 1)
 							{
 								$next				=	trim($subp[$i+1]);
 							}
 							else
 							{
 								$next = '';
-							}							
+							}
+
 
 							if($i == 0 && in_array_norm($curr,$titles)) {
 								$out['title']	=	$curr;
@@ -211,7 +221,7 @@ function	parse_name($fullname) {
 
 						if($i == $n_subp-2 && $next &&
 							in_array_norm($next,$suffices)) {
-							if($out['middle']) {
+							if(isset($out['middle'])) {
 								$out['middle']	.=	" $curr";
 								}
 							else {
@@ -226,7 +236,7 @@ function	parse_name($fullname) {
 							continue;
 							}
 
-						if($out['middle']) {
+						if(isset($out['middle'])) {
 							$out['middle']		.=	" $curr";
 							}
 						else {

services/reconciliation_worms.php

@@ -111,6 +111,23 @@ function OneQuery($query_key, $text, $limit = 1, $properties = null)
 					$hit->match = ($hit->score == 100);					
 					$hit->id 	= $worms_result[0][$i]['AphiaID'];
 					$hit->name 	= $worms_result[0][$i]['scientificname'];
+
+
+					if (isset($worms_result[0][$i]['authority']))
+					{
+						$hit->authority 	= $worms_result[0][$i]['authority'];
+					}
+
+					$keys = array('kingdom','phylum','class','order','family','genus');
+
+					foreach ($keys as $k)
+					{
+						if (isset($worms_result[0][$i][$k]))
+						{
+							$hit->{$k} = $worms_result[0][$i][$k];
+						}
+					}
+
 					$this->StoreHit($query_key, $hit); 
 				}
 			}