Jwoodlee Week 14

• What worked?
  • Almost every procedural action I took from Dondi worked. The only hiccup I had was in regard to Eclipse and navigating the directories.

• What didn't work?
  • In Eclipse, my edits to the GenMAPP builder source code were causing red error marks, but after selecting "Organize Imports" from the source menu the errors were fixed easily and the proper classes were imported. Also I had difficulty navigating to the dist file in my Temp drive, however I traced this back within Eclipse and was able to make a zip that I could hand off to Trixie for export.

• What will I do next week to fix what didn't work?
  • It seems to me that there wasn't a whole lot that went wrong with my procedure. What wasn't working I already fixed. Currently Trixie and I are running an export that will take 4 hours with the new additions in the property files, so there may be some new hiccups when that export is finished but we will have to wait and see.

The following is what I did this week.

Milestone 3: Species Profile Creation

Majority of the procedure was from here.

Adding a Species Profile to GenMAPP Builder

In the Java perspective within Eclipse(change perspective on the top right), the following was executed.

Create the Species Profile

1. I exposed the contents of the src folder in my gmbuilder project.
2. Right-clicked on the edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles package and chose New > Class from the popup menu.
3. In the dialog that appears, I entered the following:
   • Name: ShigellaflexneriUniProtSpeciesProfile
   • Superclass: edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles.UniProtSpeciesProfile
4. Clicked Finish. A new .java file within the edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles package was created.

Customize the Species Profile

• I opened the file that I just created.
• I added the following constructor block right below the public class line in the new file.

public ShigellaflexneriUniProtSpeciesProfile() {
    super("Shigella flexneri",
        623,
        "This profile customizes the GenMAPP Builder export for " +
            "Shigella flexneri" +
            " data loaded from a UniProt XML file.");
}

• 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://www.mgc.ac.cn/cgi-bin/ShiBASE/ShiBASE_query.cgi?synonym=~" }
    });

    return tableManager;
}

• I chose Organize Imports from the Source menu to make sure I had everything imported.

Add the Species Profile to the Catalog of Known Species Profiles

• Under edu.lmu.xmlpipedb.gmbuilder.databasetoolkit.profiles, I opened UniProtDatabaseProfile.java.
• Near the top of the file is a block that looks like this:

super("org.uniprot.uniprot.Uniprot",
    "This profile defines the requirements "
        + "for any UniProt centric gene database.",
    new SpeciesProfile[] {
    new EscherichiaColiUniProtSpeciesProfile(),
    new ArabidopsisThalianaUniProtSpeciesProfile(),
    new PlasmodiumFalciparumUniProtSpeciesProfile(),
    new VibrioCholeraeUniprotSpeciesProfile() });

• I added the species profile that I created to the block.

super("org.uniprot.uniprot.Uniprot",
    "This profile defines the requirements "
        + "for any UniProt centric gene database.",
    new SpeciesProfile[] {
    new EscherichiaColiUniProtSpeciesProfile(),
    new ArabidopsisThalianaUniProtSpeciesProfile(),
    new PlasmodiumFalciparumUniProtSpeciesProfile(),
    new VibrioCholeraeUniprotSpeciesProfile(),
    new ShigellaflexneriUniProtSpeciesProfile() });

• I saved changes and selected Organize Imports.

Build, Test, and Possibly Commit

1. I created a new distribution of GenMAPP Builder.
   • Expanded the custom project, scrolled down the build.xml and right clicked it. In the menu that appeared I clicked on Ant Build... (with ellipses). Now in the menu that appeared I deselected dist, and selected clean, dist in that order. The build order was now clean, dist so it will wipe the current version of genmappbuilder and create a new distribution. I clicked run.
2. With Trixie, we performed a new export run with this custom version of GenMAPP Builder. A new .gdb was created.
3. I checked the Systems table in the resulting .gdb with Microsoft Access and verified that it contained the custom information:
   • The record OrderedLocusNames was there with the species name under the Species column and our link URL under the Link column.
4. Opened up a gene in GenMAPP with the custom .gdb created to make sure the link that I inserted was working properly.
5. I then committed the custom version of GenMAPP builder to our GitHub branch.

Milestone 4: Species Export Customization

1. Trixie noticed that the microarray data has IDs that have CP#### and SF####.# not the typical SF####, which will need to accounted for.
2. This week, we edited the gmbuilder.properties file in eclipse as found in the Quality Assurance guild page. We added lines for our species.

BIOL 367, Fall 2015, User Page, Team Page

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