Malverso Week 14

Milestone 3: Species Profile Creation

Creating the Species Profile

1. I exposed the contents of the src folder, right-clicked on the edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles package and chose New > Class from the popup menu.
2. In the dialog that appeared, I entered the following:
   • Name: ShewanellaOneidensisUniProtSpeciesProfile
   • Superclass: edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtSpeciesProfile
3. I clicked Finish. There was a new .java file within the edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles package.

Customizing the Species Profile

• I opened the file that I have just created.
• I found the Taxonomy ID from this link.
• I added the following constructor block right below the public class line in the file:

public ShewanellaOneidensisUniProtSpeciesProfile() {
    super("Shewanella oneidensis",
        211586,
        "This profile customizes the GenMAPP Builder export for " +
            "Shewanella oneidensis" +
            " data loaded from a UniProt XML file.");
}

• The species specific database link I found by searching for a gene on our MOD and then replacing the gene identification in the link with a '~'.
• To customize the species profile with the species name in the OrderedLocusNames record of the Systems table as well as a link query for that same record, I added the following method block right below the constructor block that I added above:

@Override
public TableManager getSystemsTableManagerCustomizations(TableManager tableManager, DatabaseProfile dbProfile) {
    super.getSystemsTableManagerCustomizations(tableManager, dbProfile);
    tableManager.submit("Systems", QueryType.update, new String[][] {
        { "SystemCode", "N" },
        { "Species", "|" + getSpeciesName() + "|" }
    });

    tableManager.submit("Systems", QueryType.update, new String[][] {
        { "SystemCode", "N" },
        { "Link", "http://bacteria.ensembl.org/shewanella_oneidensis_mr_1/Search/Results?species=Shewanella%20oneidensis%20MR-1;idx=;q=~;site=ensemblthis" }
    });

    return tableManager;
}

• My code had a red error badge at this point, and I fixed this by choosing Organize Imports from the Source menu, which imported necessary classes.

Milestone 4: Species Export Customization

• I uploaded my dist file to the wiki and gave it to Josh so that he could test it out using Microsoft Access and TallyEngine and GenMapp.

Committing My Code

• I right-clicked on the gmbuilder project folder and chose Team > Synchronize Workspace from the menu that appeared.
• I was switched to the Team Synchronization perspective.
• I saw a Synchronize tab. I commited the right-pointing gray-arrowed files by right-clicking on them and choosing Commit....
• I verified that the files I wanted to commit were checked in the ensuing Commit Changes dialog.
• I added a quick description to what I was committing.
• I chose Commit and Push.
• This will both save a version of my files and send the latest changes to GitHub.

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