Jwoodlee Week 12

Individual Journal Assignment

Milestone 1: Version Control Setup

1. Get a GitHub account and pass it to Dr. Dionisio so that you can be added as a developer of the XMLPipeDB project on GitHub.
   • Once you are set up as a developer, you can clone and push your GenMAPP Builder source code.
2. Create a GitHub branch of xmlpipedb for your team.
   • The easiest way to do this is via the Branch dropdown menu on the GitHub project website for XMLPipeDB.
3. (with QA) Commit and push relevant source data to the GenMAPP Gene Databases folder of your GitHub branch
   • You can always verify what is publicly visible on your branch by visiting the XMLPipeDB GitHub website, choosing your branch from the Branch dropdown menu, then inspecting the code that is visible there.

Milestone 2: “Developer Rig” Setup and Initial As-Is Build

1. Install core software for developing, building, and testing prototype versions of GenMAPP Builder:
   • Java developer tools: JDK 8 (which, at this writing, is JDK 8u65)
   • A git client (for interacting with GitHub)
   • Any tool that can unpack .gz and .zip files (we are using 7-zip on the Seaver 120 machines)
   • XMLPipeDB Match utility
   • Development environment: while any will do, Eclipse is the specific one that most XMLPipeDB developers have used:
     • Download and install Eclipse from its download web site. Either Eclipse IDE for Java Developers or Eclipse IDE for Java EE Developers will work.
     • Eclipse includes ant so you do not need a separate ant installation unless you plan to build GenMAPP Builder outside of Eclipse
     • If you want to use ant outside Eclipse, please visit http://ant.apache.org.
2. Follow the instructions in the GenMAPP Builder Project Setup and Initial Build section of this wiki page in order to:
   • Set up a functioning Eclipse development environment for your branch of GenMAPP Builder.
   • Build your own copy of GenMAPP Builder from scratch.
3. (with QA) Get a full import-export cycle done.
4. (with QA) Decide on a file/version management scheme/system.

As needed, coders may arrange for a walkthrough or other help session with Dr. Dionisio if there are any issues with the procedures on this guild page.

Milestone 3: Species Profile Creation

Follow the instructions in the Adding a Species Profile to GenMAPP Builder section of this wiki page in order to:

• Add a species profile to the GenMAPP Builder code base.
• Customize the species profile with the species name in the OrderedLocusNames record of the Systems table.
• Customize the Link field in the OrderedLocusNames record of the Systems table to hold a URL query with ~ standing in for the gene ID.
  • (with QA) The URL would need to be determined first, of course.

Milestone 4: Species Export Customization

1. 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.
2. Implement this export behavior.
3. As needed, commit and push your work to your GitHub branch.
4. Additional milestones will depend on how the rest of the project goes, and the bugs/features generated by that work.
5. Document/log all work done, problems encountered, and how they were resolved.
6. When your work is complete, issue a GitHub pull request to merge your branch into the main development line.

BIOL 367, Fall 2015, User Page, Team Page

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