https://xmlpipedb.lmucs.io/biodb/fall2013/index.php?action=history&feed=atom&title=TATK_Export_One%3A_TIGR4_Testing_Report TATK Export One: TIGR4 Testing Report - Revision history 2026-04-17T00:12:30Z Revision history for this page on the wiki MediaWiki 1.20.3 https://xmlpipedb.lmucs.io/biodb/fall2013/index.php?title=TATK_Export_One:_TIGR4_Testing_Report&diff=6053&oldid=prev Ajvree: /* Using SQL Queries to Validate the PostgreSQL Database Results from the TallyEngine */ SQL results/screenshot 2013-11-20T22:44:39Z <p>‎<span dir="auto"><span class="autocomment">Using SQL Queries to Validate the PostgreSQL Database Results from the TallyEngine: </span> SQL results/screenshot</span></p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 22:44, 20 November 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 45:</td> <td colspan="2" class="diff-lineno">Line 45:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>== Using SQL Queries to Validate the PostgreSQL Database Results from the TallyEngine==</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>== Using SQL Queries to Validate the PostgreSQL Database Results from the TallyEngine==</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">*Query used in SQL:</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">**select count(*) from genenametype where type = &#039;ordered locus&#039; and value ~ &#039;SP_[0-9][0-9][0-9][0-9]&#039;;</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">*Results were identical to that of XML match: 2126</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">[[Image:20131119 SQLcountresults tATK TIGR4 AJV.PNG]]</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">[[User:Ajvree|Ajvree]] ([[User talk:Ajvree|talk]]) 14:44, 20 November 2013 (PST)</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[How_Do_I_Count_Thee%3F_Let_Me_Count_The_Ways#SQL | Follow the instructions on this page to query the PostgreSQL Database.]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[How_Do_I_Count_Thee%3F_Let_Me_Count_The_Ways#SQL | Follow the instructions on this page to query the PostgreSQL Database.]]</div></td></tr> </table> Ajvree https://xmlpipedb.lmucs.io/biodb/fall2013/index.php?title=TATK_Export_One:_TIGR4_Testing_Report&diff=6049&oldid=prev Ajvree: /* OriginalRowCounts Comparison */ 2013-11-20T22:36:38Z <p>‎<span dir="auto"><span class="autocomment">OriginalRowCounts Comparison</span></span></p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 22:36, 20 November 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 59:</td> <td colspan="2" class="diff-lineno">Line 59:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>Benchmark: [[Image:20131119 benchmarkrowcounts tATK TIGR4 AJV.PNG]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>Benchmark: [[Image:20131119 benchmarkrowcounts tATK TIGR4 AJV.PNG]]</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Note:</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Note: <ins class="diffchange diffchange-inline">a few of the rows are missing in the benchmark screenshot- could not fit all of them on screen.</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>&#160;</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">[[User:Ajvree|Ajvree]] ([[User talk:Ajvree|talk]]) 14:36, 20 November 2013 (PST)</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>==Visual Inspection==</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>==Visual Inspection==</div></td></tr> </table> Ajvree https://xmlpipedb.lmucs.io/biodb/fall2013/index.php?title=TATK_Export_One:_TIGR4_Testing_Report&diff=6048&oldid=prev Ajvree: /* OriginalRowCounts Comparison */ ORC screenshots 2013-11-20T22:35:44Z <p>‎<span dir="auto"><span class="autocomment">OriginalRowCounts Comparison: </span> ORC screenshots</span></p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 22:35, 20 November 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 55:</td> <td colspan="2" class="diff-lineno">Line 55:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; 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font-weight: bold; text-decoration: none;">Benchmark: [[Image:20131119 benchmarkrowcounts tATK TIGR4 AJV.PNG]]</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>Note:</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>Note:</div></td></tr> </table> Ajvree https://xmlpipedb.lmucs.io/biodb/fall2013/index.php?title=TATK_Export_One:_TIGR4_Testing_Report&diff=6044&oldid=prev Ajvree: /* Using XMLPipeDB match to Validate the XML Results from the TallyEngine */ 2013-11-20T22:21:41Z <p>‎<span dir="auto"><span class="autocomment">Using XMLPipeDB match to Validate the XML Results from the TallyEngine</span></span></p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 22:21, 20 November 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 41:</td> <td colspan="2" class="diff-lineno">Line 41:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*The final count on XML match was 1 less than that of the Tally Engine results (2127 matches). 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XML match found all of the unique results, whereas the tally engine must have counted a repeated match into the total.</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">[[User:Ajvree|Ajvree]] ([[User talk:Ajvree|talk]]) 14:21, 20 November 2013 (PST)</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>== Using SQL Queries to Validate the PostgreSQL Database Results from the TallyEngine==</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>== Using SQL Queries to Validate the PostgreSQL Database Results from the TallyEngine==</div></td></tr> </table> Ajvree  
[[Image:TallyEngineTrial2.PNG]]
 
[[Image:TallyEngineTrial2.PNG]]
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Stack trace:
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#1 /apps/xmlpipedb/biodb/fall2013/includes/diff/DairikiDiff.php(291): _DiffEngine->_compareseq()
#2 /apps/xmlpipedb/biodb/fall2013/includes/diff/DairikiDiff.php(175): _DiffEngine->diff_local()
#3 /apps/xmlpipedb/biodb/fall2013/includes/diff/DairikiDiff.php(653): _DiffEngine->diff()
#4 /apps/xmlpipedb/biodb/fall2013/includes/diff/DairikiDiff.php(820): Diff->__construct()
#5 /apps/xmlpipedb/biodb/fall2013/includes/diff/DairikiDiff.php(1240): MappedDiff->__construct()
#6 /apps/xmlpipedb/biodb/fall2013/includes/diff/DairikiDiff.php(1458): WordLevelDiff->__construct()
#7 /apps/xmlpipedb/biodb/fall2013/includes/diff/DairikiDiff.php(952): TableDiffFormatter->_changed()
#8 /apps/xmlpipedb/biodb/fall2013/includes/diff/DairikiDiff.php(895): DiffFormatter->_block()
#9 /apps/xmlpipedb/biodb/fall2013/includes/diff/DifferenceEngine.php(765): DiffFormatter->format()
#10 /apps/xmlpipedb/biodb/fall2013/includes/diff/DifferenceEngine.php(655): DifferenceEngine->generateDiffBody()
#11 /apps/xmlpipedb/biodb/fall2013/includes/diff/DifferenceEngine.php(593): DifferenceEngine->getDiffBody()
#12 /apps/xmlpipedb/biodb/fall2013/includes/FeedUtils.php(147): DifferenceEngine->getDiff()
#13 /apps/xmlpipedb/biodb/fall2013/includes/actions/HistoryAction.php(303): FeedUtils::formatDiffRow()
#14 /apps/xmlpipedb/biodb/fall2013/includes/actions/HistoryAction.php(268): HistoryAction->feedItem()
#15 /apps/xmlpipedb/biodb/fall2013/includes/actions/HistoryAction.php(121): HistoryAction->feed()
#16 /apps/xmlpipedb/biodb/fall2013/includes/Action.php(541): HistoryAction->onView()
#17 /apps/xmlpipedb/biodb/fall2013/includes/Wiki.php(427): FormlessAction->show()
#18 /apps/xmlpipedb/biodb/fall2013/includes/Wiki.php(304): MediaWiki->performAction()
#19 /apps/xmlpipedb/biodb/fall2013/includes/Wiki.php(536): MediaWiki->performRequest()
#20 /apps/xmlpipedb/biodb/fall2013/includes/Wiki.php(446): MediaWiki->main()
#21 /apps/xmlpipedb/biodb/fall2013/index.php(59): MediaWiki->run()
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