<?xml version="1.0"?>
<feed xmlns="http://www.w3.org/2005/Atom" xml:lang="en">
		<id>https://xmlpipedb.lmucs.io/biodb/fall2015/index.php?action=history&amp;feed=atom&amp;title=Bklein7_Week_9</id>
		<title>Bklein7 Week 9 - Revision history</title>
		<link rel="self" type="application/atom+xml" href="https://xmlpipedb.lmucs.io/biodb/fall2015/index.php?action=history&amp;feed=atom&amp;title=Bklein7_Week_9"/>
		<link rel="alternate" type="text/html" href="https://xmlpipedb.lmucs.io/biodb/fall2015/index.php?title=Bklein7_Week_9&amp;action=history"/>
		<updated>2026-06-08T01:35:17Z</updated>
		<subtitle>Revision history for this page on the wiki</subtitle>
		<generator>MediaWiki 1.25.1</generator>

	<entry>
		<id>https://xmlpipedb.lmucs.io/biodb/fall2015/index.php?title=Bklein7_Week_9&amp;diff=6771&amp;oldid=prev</id>
		<title>Bklein7: added apostrophe</title>
		<link rel="alternate" type="text/html" href="https://xmlpipedb.lmucs.io/biodb/fall2015/index.php?title=Bklein7_Week_9&amp;diff=6771&amp;oldid=prev"/>
				<updated>2015-11-23T22:31:08Z</updated>
		
		<summary type="html">&lt;p&gt;added apostrophe&lt;/p&gt;
&lt;table class=&#039;diff diff-contentalign-left&#039;&gt;
				&lt;col class=&#039;diff-marker&#039; /&gt;
				&lt;col class=&#039;diff-content&#039; /&gt;
				&lt;col class=&#039;diff-marker&#039; /&gt;
				&lt;col class=&#039;diff-content&#039; /&gt;
				&lt;tr style=&#039;vertical-align: top;&#039;&gt;
				&lt;td colspan=&#039;2&#039; style=&quot;background-color: white; color:black; text-align: center;&quot;&gt;← Older revision&lt;/td&gt;
				&lt;td colspan=&#039;2&#039; style=&quot;background-color: white; color:black; text-align: center;&quot;&gt;Revision as of 22:31, 23 November 2015&lt;/td&gt;
				&lt;/tr&gt;&lt;tr&gt;&lt;td colspan=&quot;2&quot; class=&quot;diff-lineno&quot; id=&quot;L126&quot; &gt;Line 126:&lt;/td&gt;
&lt;td colspan=&quot;2&quot; class=&quot;diff-lineno&quot;&gt;Line 126:&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class=&#039;diff-marker&#039;&gt;&amp;#160;&lt;/td&gt;&lt;td style=&quot;background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;===Using XMLPipeDB match to Validate the XML Results from the TallyEngine===&lt;/div&gt;&lt;/td&gt;&lt;td class=&#039;diff-marker&#039;&gt;&amp;#160;&lt;/td&gt;&lt;td style=&quot;background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;===Using XMLPipeDB match to Validate the XML Results from the TallyEngine===&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class=&#039;diff-marker&#039;&gt;&amp;#160;&lt;/td&gt;&lt;td style=&quot;background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;/td&gt;&lt;td class=&#039;diff-marker&#039;&gt;&amp;#160;&lt;/td&gt;&lt;td style=&quot;background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class=&#039;diff-marker&#039;&gt;−&lt;/td&gt;&lt;td style=&quot;color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;On the command line (&amp;#039;cmd&amp;#039;&amp;#039; on Windows), I entered the folder &amp;#039;&amp;#039;Bklein7_Week9&amp;#039;&amp;#039; to access the XML data files. The first match I ran was designed to identify matches of any ordered locus name following the pattern VC_#### in the UniProt XML file. The command sequence used is as follows:&lt;/div&gt;&lt;/td&gt;&lt;td class=&#039;diff-marker&#039;&gt;+&lt;/td&gt;&lt;td style=&quot;color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;On the command line (&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;&amp;#039;&lt;/ins&gt;&amp;#039;cmd&amp;#039;&amp;#039; on Windows), I entered the folder &amp;#039;&amp;#039;Bklein7_Week9&amp;#039;&amp;#039; to access the XML data files. The first match I ran was designed to identify matches of any ordered locus name following the pattern VC_#### in the UniProt XML file. The command sequence used is as follows:&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class=&#039;diff-marker&#039;&gt;&amp;#160;&lt;/td&gt;&lt;td style=&quot;background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;/td&gt;&lt;td class=&#039;diff-marker&#039;&gt;&amp;#160;&lt;/td&gt;&lt;td style=&quot;background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class=&#039;diff-marker&#039;&gt;&amp;#160;&lt;/td&gt;&lt;td style=&quot;background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;&amp;#160; java -jar xmlpipedb-match-1.1.1.jar &amp;quot;VC_[0-9][0-9][0-9][0-9]&amp;quot; &amp;lt; &amp;quot;uniprot-taxonomy%3A243277.xml&amp;quot; &amp;gt;&amp;#160; &amp;#160; &amp;#160;  &amp;#160;&lt;/div&gt;&lt;/td&gt;&lt;td class=&#039;diff-marker&#039;&gt;&amp;#160;&lt;/td&gt;&lt;td style=&quot;background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;&amp;#160; java -jar xmlpipedb-match-1.1.1.jar &amp;quot;VC_[0-9][0-9][0-9][0-9]&amp;quot; &amp;lt; &amp;quot;uniprot-taxonomy%3A243277.xml&amp;quot; &amp;gt;&amp;#160; &amp;#160; &amp;#160;  &amp;#160;&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;/table&gt;</summary>
		<author><name>Bklein7</name></author>	</entry>

<tr><td colspan="2" class="diff-lineno" id="L219" ><!--LINE 219--></td>
<td colspan="2" class="diff-lineno"><!--LINE 219--></td></tr>
<tr><td class='diff-marker'>&#160;</td><td class='diff-context'><div>***This ID column was analyzed in Microsoft Excel to investigate why there were 7664 entries present (as opposed to the consistent count of 3831 in SQL and XMLPipeDB Match).</div></td><td class='diff-marker'>&#160;</td><td class='diff-context'><div>***This ID column was analyzed in Microsoft Excel to investigate why there were 7664 entries present (as opposed to the consistent count of 3831 in SQL and XMLPipeDB Match).</div></td></tr>
<tr><td class='diff-marker'>&#160;</td><td class='diff-context'><div>****The analysis in Excel revealed that the variations of the the gene IDs with and without underscores were replicates of one another. Presumably, these gene IDs were duplicated during the process of exporting the gene database to account for a formatting issue pertaining to underscores. Regardless, this discovery means that only half of the 7664 entries were unique gene IDs. This leaves us with &#039;&#039;&#039;3832&#039;&#039;&#039; unique IDs, which is still one more than was expected.</div></td><td class='diff-marker'>&#160;</td><td class='diff-context'><div>****The analysis in Excel revealed that the variations of the the gene IDs with and without underscores were replicates of one another. Presumably, these gene IDs were duplicated during the process of exporting the gene database to account for a formatting issue pertaining to underscores. Regardless, this discovery means that only half of the 7664 entries were unique gene IDs. This leaves us with &#039;&#039;&#039;3832&#039;&#039;&#039; unique IDs, which is still one more than was expected.</div></td></tr>
Exception encountered, of type &quot;Error&quot;<br />
[0b752ef4] /biodb/fall2015/index.php?action=history&amp;feed=atom&amp;title=Bklein7_Week_9   Error from line 434 of /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php: Call to undefined function each()<br />
Backtrace:<br />
#0 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(544): DiffEngine-&gt;diag()<br />
#1 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(344): DiffEngine-&gt;compareSeq()<br />
#2 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(227): DiffEngine-&gt;diffLocal()<br />
#3 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(721): DiffEngine-&gt;diff()<br />
#4 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(859): Diff-&gt;__construct()<br />
#5 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(980): MappedDiff-&gt;__construct()<br />
#6 /apps/xmlpipedb/biodb/fall2015/includes/diff/TableDiffFormatter.php(194): WordLevelDiff-&gt;__construct()<br />
#7 /apps/xmlpipedb/biodb/fall2015/includes/diff/DiffFormatter.php(140): TableDiffFormatter-&gt;changed()<br />
#8 /apps/xmlpipedb/biodb/fall2015/includes/diff/DiffFormatter.php(82): DiffFormatter-&gt;block()<br />
#9 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(888): DiffFormatter-&gt;format()<br />
#10 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(802): DifferenceEngine-&gt;generateTextDiffBody()<br />
#11 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(733): DifferenceEngine-&gt;generateContentDiffBody()<br />
#12 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(662): DifferenceEngine-&gt;getDiffBody()<br />
#13 /apps/xmlpipedb/biodb/fall2015/includes/FeedUtils.php(155): DifferenceEngine-&gt;getDiff()<br />
#14 /apps/xmlpipedb/biodb/fall2015/includes/actions/HistoryAction.php(325): FeedUtils::formatDiffRow()<br />
#15 /apps/xmlpipedb/biodb/fall2015/includes/actions/HistoryAction.php(290): HistoryAction-&gt;feedItem()<br />
#16 /apps/xmlpipedb/biodb/fall2015/includes/actions/HistoryAction.php(130): HistoryAction-&gt;feed()<br />
#17 /apps/xmlpipedb/biodb/fall2015/includes/actions/FormlessAction.php(43): HistoryAction-&gt;onView()<br />
#18 /apps/xmlpipedb/biodb/fall2015/includes/MediaWiki.php(395): FormlessAction-&gt;show()<br />
#19 /apps/xmlpipedb/biodb/fall2015/includes/MediaWiki.php(273): MediaWiki-&gt;performAction()<br />
#20 /apps/xmlpipedb/biodb/fall2015/includes/MediaWiki.php(566): MediaWiki-&gt;performRequest()<br />
#21 /apps/xmlpipedb/biodb/fall2015/includes/MediaWiki.php(414): MediaWiki-&gt;main()<br />
#22 /apps/xmlpipedb/biodb/fall2015/index.php(44): MediaWiki-&gt;run()<br />
#23 {main}<br />

