Weekly Update

Last Week:

• Finished Delete branch query for PhyMod
• Added subtree export to PhyExport
• Began PhyQry
• Been reading Perl Best Practices .. good book
  

This Week:

• Finish PhyQry with basic database and tree overview information
• Add (--usage,--help, and --man) options to the command line
  

RapidSVN and GSoC Survery

I installed RapidSVN today. It looks like this will really make working with svn a bit easier. I have been doing most of my SVN work from the command line and I like being able to have a nice visual overview of how everything stands. This was really easy to install from the RPMs that I found online.

I have uploaded the code that I wanted on google at this time so I feel like I am pretty much on track to get this project done by the end of the summer. I went ahead and did the GSoC survey too.

After reading "Perl Best Practices (PBP)" I plan on going back and doing some editing of the command line options from the programs. I really think I should change the way the help works, this currently just kicks into perldoc. The PBP book suggests a much better way to do this by having separate options:

• --usage
  Short usage statement.
  
• --help
  Short usage statement with one liners describing the required arguments and options . This will be the default to go to when the user enters incorrect information at the command line.
  
• --man
  This will print the perldoc POD documentation

I will also be adding additional information to the POD doc as suggested by PBP.

PhyExport: Subtree export

Subtree export is now included in PhyExport using the --parent-node variable. This was actually pretty easy to implement. I just need to add some code to make sure that users can not try to use the parent-node variable when they are exporting all of the trees in the database. The node ids from the database can also be exported now using the --db-node-id boolean.

A test tree image

The current test tree is above. Node labels indicated by letters, node_id from the database indicated by numbers. This image is mainly for me to reference later when working with phyexort and phymod. I added the ability to include the database node_id in PhyExport so that it is easier to reference a given node by the identifier it has in the database.

PhyMod: Delete Query Available

A version of PhyMod that can do a delete query is now available from the project SVN. I ended up using the nested set values after tinkering with the transitive closure data. I will probably recode the SQL in these to avoid using nested SQL. The delete query is simply a cut at the command line where a paste is not indicated. The code will count the number of records that will be deleted from the tables and warns the user before wreaking havoc.