Difference between revisions of "Jwoodlee Week 12"

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== Individual Journal Assignment ==
 
== Individual Journal Assignment ==
  
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* Store this journal entry as "''username'' Week 12" (i.e., this is the text to place between the square brackets when you link to this page).
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=== Milestone 1: Version Control Setup ===
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* Link from your user page to this Assignment page.
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* Link to your journal entry from your user page.
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# Get a GitHub account and pass it to Dr. Dionisio so that you can be added as a developer of the [https://github.com/lmu-bioinformatics/xmlpipedb XMLPipeDB project on GitHub].
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* Link back from your journal entry to your user page.
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#* Once you are set up as a developer, you can clone and push your GenMAPP Builder source code.
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* Don't forget to add the "Journal Entry" category to the end of your wiki page.
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# Create a GitHub branch of ''xmlpipedb'' for your team.
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**'''''Note: you can easily fulfill all of these links by adding them to your template and then using your template on your journal entry.'''''
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#* The easiest way to do this is via the ''Branch'' dropdown menu on the [https://github.com/lmu-bioinformatics/xmlpipedb GitHub project website for XMLPipeDB].
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* For your assignment this week, you will keep an '''''electronic laboratory notebook''''' on your individual journal entry page for this week.  An electronic laboratory notebook records all the manipulations you perform on the data and the answers to the questions throughout the protocol. Like a paper lab notebook found in a wet lab, it should contain enough information so that you or someone else could reproduce what you did using only the information from the notebook.
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# ''(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 [https://github.com/lmu-bioinformatics/xmlpipedb 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 ===
 +
 
 +
# Install core software for developing, building, and testing prototype versions of GenMAPP Builder:
 +
#* Java developer tools: [http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html JDK 8] (which, at this writing, is ''JDK 8u65'')
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#* A ''git'' client (for interacting with GitHub)
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#* Any tool that can unpack .gz and .zip files (we are using [http://www.7-zip.org/ 7-zip] on the Seaver 120 machines)
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#* ''XMLPipeDB Match'' utility
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#* Development environment: while any will do, [http://www.eclipse.org Eclipse] is the specific one that most XMLPipeDB developers have used:
 +
#** Download and install Eclipse from its [http://www.eclipse.org/downloads 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.
 +
# Follow the instructions in the [[#GenMAPP Builder Project Setup and Initial Build|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.
 +
# ''(with QA)'' Get a full import-export cycle done.
 +
# ''(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|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.
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* Customize the ''Link'' field in the ''OrderedLocusNames'' record of the ''Systems table'' to hold a URL query with <code>~</code> standing in for the gene ID.
 +
** ''(with QA)'' The URL would need to be determined first, of course.
 +
 
 +
=== 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.
 +
 
 
{{Template: Jwoodlee}}
 
{{Template: Jwoodlee}}

Revision as of 22:44, 21 November 2015

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.
  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

Weekly Assignments Individual Journal Pages Shared Journal Pages
Retrieved from "https://xmlpipedb.lmucs.io/biodb/fall2015/index.php?title=Jwoodlee_Week_12&oldid=6681"