Difference between revisions of "Jwoodlee Week 12"

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(→‎Milestone 2: “Developer Rig” Setup and Initial As-Is Build: added more procedure)
(→‎Initial Build: added procedure)
 
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* I clicked Yes when Eclipse asked if I wanted to open the Java perspective.
 
* I clicked Yes when Eclipse asked if I wanted to open the Java perspective.
  
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# If the ''gmbuilder'' project folder icon shows a red ''x'' icon, do the following:
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==== Initial Build of GenMAPP Builder in Eclipse====
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#* Right-click on the ''gmbuilder'' item and choose '''Properties''' from the menu that appears.
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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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#* Click on the ''Java Compiler'' item. ''Click on the item name itself, not its triangle.''
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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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#* You should see that ''Compiler compliance level:'' is set to ''1.6''. If so, uncheck the ''Enable project specific settings'' checkbox.
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#* Click the ''Apply'' button. If Eclipse asks you whether it is OK to rebuild the project, click ''Yes''.
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#* Click on ''OK'' to dismiss the ''Properties'' dialog.
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#* See if the red ''x'' icon has disappeared.
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# If the red ''x'' icon persists, please show your setup to fellow guild members or Dr. Dionisio for troubleshooting.
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==== Initial Build ====
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{{ Build Instructions }}
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=== Milestone 3: Species Profile Creation ===
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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:
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* Add a ''species profile'' to the GenMAPP Builder code base.
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* 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.
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** ''(with QA)'' The URL would need to be determined first, of course.
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=== Milestone 4: Species Export Customization ===
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# 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.
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# Implement this export behavior.
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# As needed, commit and push your work to your GitHub branch.
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# Additional milestones will depend on how the rest of the project goes, and the bugs/features generated by that work.
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# Document/log all work done, problems encountered, and how they were resolved.
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# When your work is complete, issue a GitHub ''pull request'' to merge your branch into the main development line.
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{{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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