|
|
| | | | |
| | This is what the final customized class looks like: | | This is what the final customized class looks like: |
| | + | [[Image:FinalCustomizationsPart1.png]] |
| | | | |
| − | <code>
| + | [[Image:FinalCustomizationsPart2.png]] |
| − | package edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles;
| + | |
| | | | |
| − | import java.sql.Connection;
| |
| − | import java.sql.PreparedStatement;
| |
| − | import java.sql.ResultSet;
| |
| − | import java.sql.SQLException;
| |
| − | import java.util.Date;
| |
| | | | |
| − | import org.apache.commons.logging.Log;
| + | A further modification that was required was in the gmbuilder.properties file which we were supposed to edit to assist TallyEngine in its function, the initial customizations to this were the following lines: |
| − | import org.apache.commons.logging.LogFactory;
| + | |
| | | | |
| − | import edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.ConnectionManager;
| + | [[Image: Gmbuilder.propertiesOriginal.png]] |
| − | import edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.TableManager;
| + | |
| − | import edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.tables.TableManager.QueryType;
| + | |
| − | import edu.lmu.xmlpipedb.util.exceptions.InvalidParameterException;
| + | |
| | | | |
| − | public class ShigellaflexneriUniProtSpeciesProfile extends UniProtSpeciesProfile {
| |
| − | public ShigellaflexneriUniProtSpeciesProfile() {
| |
| − | super("Shigella flexneri",
| |
| − | 623,
| |
| − | "This profile customizes the GenMAPP Builder export for " +
| |
| − | "Shigella flexneri" +
| |
| − | " data loaded from a UniProt XML file.");
| |
| − | }
| |
| − |
| |
| − | @Override
| |
| − | public TableManager getSystemsTableManagerCustomizations(TableManager tableManager, DatabaseProfile dbProfile) {
| |
| − | super.getSystemsTableManagerCustomizations(tableManager, dbProfile);
| |
| − | tableManager.submit("Systems", QueryType.update, new String[][] {
| |
| − | { "SystemCode", "N" },
| |
| − | { "Species", "|" + getSpeciesName() + "|" }
| |
| − | });
| |
| | | | |
Exception encountered, of type "Error"
[43c8f328] /biodb/fall2015/index.php?diff=8063&oldid=7973&title=Jwoodlee_Week_15 Error from line 434 of /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php: Call to undefined function each()
Backtrace:
#0 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(544): DiffEngine->diag()
#1 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(344): DiffEngine->compareSeq()
#2 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(227): DiffEngine->diffLocal()
#3 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(721): DiffEngine->diff()
#4 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(859): Diff->__construct()
#5 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(980): MappedDiff->__construct()
#6 /apps/xmlpipedb/biodb/fall2015/includes/diff/TableDiffFormatter.php(194): WordLevelDiff->__construct()
#7 /apps/xmlpipedb/biodb/fall2015/includes/diff/DiffFormatter.php(140): TableDiffFormatter->changed()
#8 /apps/xmlpipedb/biodb/fall2015/includes/diff/DiffFormatter.php(111): DiffFormatter->block()
#9 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(888): DiffFormatter->format()
#10 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(802): DifferenceEngine->generateTextDiffBody()
#11 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(733): DifferenceEngine->generateContentDiffBody()
#12 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(662): DifferenceEngine->getDiffBody()
#13 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(632): DifferenceEngine->getDiff()
#14 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(453): DifferenceEngine->showDiff()
#15 /apps/xmlpipedb/biodb/fall2015/includes/page/Article.php(795): DifferenceEngine->showDiffPage()
#16 /apps/xmlpipedb/biodb/fall2015/includes/page/Article.php(506): Article->showDiffPage()
#17 /apps/xmlpipedb/biodb/fall2015/includes/actions/ViewAction.php(44): Article->view()
#18 /apps/xmlpipedb/biodb/fall2015/includes/MediaWiki.php(395): ViewAction->show()
#19 /apps/xmlpipedb/biodb/fall2015/includes/MediaWiki.php(273): MediaWiki->performAction()
#20 /apps/xmlpipedb/biodb/fall2015/includes/MediaWiki.php(566): MediaWiki->performRequest()
#21 /apps/xmlpipedb/biodb/fall2015/includes/MediaWiki.php(414): MediaWiki->main()
#22 /apps/xmlpipedb/biodb/fall2015/index.php(44): MediaWiki->run()
#23 {main}