Difference between revisions of "Jwoodlee Week 12"

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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].
 
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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# Follow the instructions in the  section of this wiki page in order to:
 
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#* Set up a functioning Eclipse development environment for your branch of GenMAPP Builder.
 
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#* Build your own copy of GenMAPP Builder from scratch.
 
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# ''(with QA)'' Get a full import-export cycle done.
 
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# ''(with QA)'' Decide on a file/version management scheme/system.
 
  
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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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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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==== Eclipse Workspace Setup ====
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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.
  
 
[[Image:Initial-eclipse-workspace.png|thumb]]
 
[[Image:Initial-eclipse-workspace.png|thumb]]
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# Run Eclipse.
 
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# When Eclipse asks you to select a workspace, click the ''Browse…'' and navigate to your repository clone folder. Select it and click on ''Open''.
 
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# Verify that your repository clone folder is what is listed as the ''Workspace:''. Click on ''OK''.
 
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# You will see an introductory display with assorted menu items. Click the ''Workbench'' button (upper-right corner, with a 3D arrow for an icon).
 
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# If everything went well, you should now see an empty developer area, showing your repository clone folder in the window title with a ''Project Explorer'' tab on the left (see screenshot for an example).
 
  
 
==== Java Project Setup ====
 
==== 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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# Right-click anywhere within the empty ''Project Explorer'' tab and choose '''New > Project…''' from the menu that appears.
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==== Initial Build of GenMAPP Builder in Eclipse====
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# Choose ''Java Project'' from the list of “wizards” and click on the ''Next >'' button.
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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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# On the next panel, enter <code>gmbuilder</code> as the ''Project name:''. Note how the ''Location:'' field underneath, although disabled, should show your cloned repository folder location with ''/gmbuilder'' appended to it.
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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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# Verify that the ''JRE'' section is showing Java 8 or 1.8. If not, talk to Dr. Dionisio.
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# Click on the ''Finish'' button (yes, there is no need for further configuration).
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# If Eclipse asks you whether you want to open the “Java perspective,” respond with ''Yes''. You may check the ''Remember my decision'' checkbox if you wish.
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# You should now see a ''gmbuilder'' project folder in the ''Project Explorer'' tab.
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# If the ''gmbuilder'' project folder icon shows a red ''x'' icon, do the following:
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#* Right-click on the ''gmbuilder'' item and choose '''Properties''' from the menu that appears.
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#* Click on the ''Java Compiler'' item. ''Click on the item name itself, not its triangle.''
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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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