Jwoodlee Week 12 - Revision history

Jwoodlee: /* Initial Build */ added procedure

2015-11-24T05:38:07Z

‎Initial Build: added procedure

2015-11-24T05:33:11Z

‎Java Project Setup: removed unnecessary text

2015-11-24T05:31:59Z

‎Milestone 4: Species Export Customization: removed milestone 4

2015-11-24T05:31:37Z

‎Milestone 3: Species Profile Creation: removed milestone 3

2015-11-24T05:28:23Z

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

2015-11-24T04:59:29Z

‎Milestone 1: Version Control Setup: removed unnecessary line

@@ Line 21: / Line 21: @@
 * I clicked Yes when Eclipse asked if I wanted to open the Java perspective.
-==== Initial Build ====
+==== 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).
-{{ Build Instructions }}
+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.
-−
 {{Template: Jwoodlee}}

@@ Line 20: / Line 20: @@
 * 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 ====

← Older revision		Revision as of 05:31, 24 November 2015
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	{{ Build Instructions }}		{{ Build Instructions }}

−	~~=== 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}}

← Older revision		Revision as of 05:31, 24 November 2015
Line 33:		Line 33:

	{{ Build Instructions }}		{{ Build Instructions }}
−
−	~~=== 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.
−	* 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 ===		=== Milestone 4: Species Export Customization ===

@@ Line 7: / Line 7: @@
 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 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.
-==== Eclipse Workspace Setup ====
+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]]
 ==== Java Project Setup ====
 # If the ''gmbuilder'' project folder icon shows a red ''x'' icon, do the following:
 #* Right-click on the ''gmbuilder'' item and choose '''Properties''' from the menu that appears.

@@ Line 3: / Line 3: @@
 === Milestone 1: Version Control Setup ===
 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.
 === Milestone 2: “Developer Rig” Setup and Initial As-Is Build ===