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

Based on observations from the GenMAPP User and QA, determine and document (as thoroughly as possible) any other modified export behavior that GenMAPP Builder will have to manifest for this species. Implement this export behavior. As needed, commit and push your work to your GitHub branch. Additional milestones will depend on how the rest of the project goes, and the bugs/features generated by that work. Document/log all work done, problems encountered, and how they were resolved. When your work is complete, issue a GitHub pull request to merge your branch into the main development line.

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