Difference between revisions of "Jwoodlee Week 12"

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== Individual Journal Assignment ==
 
== Individual Journal Assignment ==
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The "Milestones" can be found [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Coder here] on the Coder guild page.
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=== Milestone 1: Version Control Setup ===
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Since I already had a GitHub account, Dondi added me to the [https://github.com/lmu-bioinformatics/xmlpipedb XMLPipeDB project] on GitHub.  I then selected the branch dropdown menu on the project entitled "Branch:master" and typed into the create new branch field "s-flexneri".  This will allow me to make my own commits without changing the master branch.
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=== Milestone 2: “Developer Rig” Setup and Initial As-Is Build ===
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I downloaded [http://www.eclipse.org Eclipse IDE for Java EE Developers] and ran the .exe.  From there, I followed the instruction on:[https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Coder#GenMAPP_Builder_Project_Setup_and_Initial_Build GenMAPP Builder Project Setup and Initial Build].
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I installed Eclipse to the T drive on my lab computer because I decided that would be my development environment.  I also determined I wanted my Git clone to be on my T drive as well.  So I used <code>cd</code> to get into the T drive and typed the command: <code> git clone https://github.com/lmu-bioinformatics/xmlpipedb.git</code>.  I used <code> cd </code> To get into the clone folder: <code>xmlpipedb</code>.  I switched to the "s-flexneri" branch: <code> git checkout s-flexneri </code> so my commits will be in the proper branch. 
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When I first started up eclipse I selected the repository clone folder as my work space.  I then clicked the workbench button.  This setup my eclipse work space.
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[[Image:Initial-eclipse-workspace.png|thumb]]
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==== Java Project Setup ====
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*I right clicked in the Project Explorer tab and chose New > Project...
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*I then chose Java Project from the list of wizards and clicked Next.
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* On the next panel, I entered <code>gmbuilder</code> as the ''Project name:''.
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* I clicked on the ''Finish'' button with no further configuration.
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* I clicked Yes when Eclipse asked if I wanted to open the Java perspective.
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==== Initial Build of GenMAPP Builder in Eclipse====
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I opened the gmbuilder project by clicking on the little gray triangle left of its name.  I right clicked on build.xml and chose Run As > Ant Build... (including ellipses).
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I then unchecked dist and rechecked clean and dist in the Targets tab in that order. When the order of the Target execution order box saidclean, dist I clicked the Run button. Eclipse finished building the build and then I right clicked on the gmbuilder project folder and hit refresh.  This created a new dist and thus I created a personally built copy of GenMAPP Builder.
  
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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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* 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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* Link back from your journal entry to your user page.
 
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* Don't forget to add the "Journal Entry" category to the end of your wiki page.
 
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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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* 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.
 
 
{{Template: Jwoodlee}}
 
{{Template: Jwoodlee}}

Latest revision as of 05:38, 24 November 2015

Individual Journal Assignment

The "Milestones" can be found here on the Coder guild page.

Milestone 1: Version Control Setup

Since I already had a GitHub account, Dondi added me to the XMLPipeDB project on GitHub. I then selected the branch dropdown menu on the project entitled "Branch:master" and typed into the create new branch field "s-flexneri". This will allow me to make my own commits without changing the master branch.

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

I downloaded Eclipse IDE for Java EE Developers and ran the .exe. From there, I followed the instruction on:GenMAPP Builder Project Setup and Initial Build.

I installed Eclipse to the T drive on my lab computer because I decided that would be my development environment. I also determined I wanted my Git clone to be on my T drive as well. So I used cd to get into the T drive and typed the command: git clone https://github.com/lmu-bioinformatics/xmlpipedb.git. I used cd To get into the clone folder: xmlpipedb. I switched to the "s-flexneri" branch: git checkout s-flexneri so my commits will be in the proper branch.

When I first started up eclipse I selected the repository clone folder as my work space. I then clicked the workbench button. This setup my eclipse work space.

Initial-eclipse-workspace.png

Java Project Setup

  • I right clicked in the Project Explorer tab and chose New > Project...
  • I then chose Java Project from the list of wizards and clicked Next.
  • On the next panel, I entered gmbuilder as the Project name:.
  • I clicked on the Finish button with no further configuration.
  • I clicked Yes when Eclipse asked if I wanted to open the Java perspective.

Initial Build of GenMAPP Builder in Eclipse

I opened the gmbuilder project by clicking on the little gray triangle left of its name. I right clicked on build.xml and chose Run As > Ant Build... (including ellipses). I then unchecked dist and rechecked clean and dist in the Targets tab in that order. When the order of the Target execution order box saidclean, dist I clicked the Run button. Eclipse finished building the build and then I right clicked on the gmbuilder project folder and hit refresh. This created a new dist and thus I created a personally built copy of GenMAPP Builder.


BIOL 367, Fall 2015, User Page, Team Page

Weekly Assignments Individual Journal Pages Shared Journal Pages
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