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This page is an electronic record of all the work that has been done by the team for the final project.
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{{Team H(oo)KD}}
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==November 7, 2013==
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'''Refer to the calendar on the team home page to see the milestones for this week.'''
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===Coder===
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==Coder Status Update==
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===Quality Assurance===
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*Began the gene database import export cycle:
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:*Downloaded the UniProt XML file for ''Chlamydia trachomatis'' serovar A strain HAR-13.
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:*Downloaded the GOA file for ''Chlamydia trachomatis'' serovar A.
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:*Created a PostgreSQl database for the species.
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:*I was able to import both the UniProt XML file and the GOA file for the ''C. trachomatis'' into the PostgreSQL database through gmbuilder-32bit.bat. While I was also able to import the OBO-XML file, I could not finish processing the data. After gmbuilder processed the 81000 term, I received the following error after which gmbuilder ceased the processing of the OBO-XML file:
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ERROR edu.lmu.xmlpipedb.gmbuilder.GenMAPPBuilder  - java.util.concurrent.ExecutionException: java.lang.OutOfMemoryError:
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Java heap space
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:*Per Dondi's advice, tomorrow (November 15) I will try to increase the java heap space and rerun the import/export cycle.
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*Created a custom species profile and committed it to SourceForge. However, this profile still needs work. I will need to work with the QA analyst to add to the profile a species-specific URL that returns a web page describing a gene for the species.
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Stack trace:
#0 /apps/xmlpipedb/biodb/fall2013/includes/diff/DairikiDiff.php(480): _DiffEngine->_diag()
#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(924): 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/diff/DifferenceEngine.php(566): DifferenceEngine->getDiff()
#13 /apps/xmlpipedb/biodb/fall2013/includes/diff/DifferenceEngine.php(409): DifferenceEngine->showDiff()
#14 /apps/xmlpipedb/biodb/fall2013/includes/Article.php(725): DifferenceEngine->showDiffPage()
#15 /apps/xmlpipedb/biodb/fall2013/includes/Article.php(478): Article->showDiffPage()
#16 /apps/xmlpipedb/biodb/fall2013/includes/actions/ViewAction.php(37): Article->view()
#17 /apps/xmlpipedb/biodb/fall2013/includes/Wiki.php(427): ViewAction->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()
#22 {main}