NIH | National Cancer Institute | NCI Wiki  

Versions Compared

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

The validate method is not always implemented, but can and should be when a mechanism exists to insure that this is a correctly structured version of the source.  When source is XML formatted and has a schema or dtd document commonly available for validation, this is a relatively easy process.  However any free text files that do not have any associated java-based validation API, would rely on the developer to create validation functions.  This The validation method is not required to create a loader for LexEVS. 

In order to get loading done theory the developer could at this point implement only doLoad by mapping content to a coding scheme object and persisting it before turning control over to BaseLoader which will call the doLoad method and set default load options in its load method and kick off the processes to persist a coding scheme object to the database.  The other option is to implement doLoad and override the load method which sets up end user option choices for the loader.   Most loaders implement the load method, customizing load options to provide to the end user.  In the case of the MedDRA loader, a CUI load option is provided to the end user.

Beyond these methods, where a coding scheme object is passed to LexEVS for processing, the structuring of code is largely and necessarily left up to the developer.  However a few common patterns are fairly consistent in this implementation.  Generally speaking, there is some kind of source reading mechanism and  there is a central mapping class where the coding scheme object is built.  Other classes, when necessary, are supportive to this central class. 

...

In the lbConverter project  the edu.mayo.informatics.lexgrid.convert.directConversions.medDRA package contains the classes that do much of the work of the load.  edu.mayo.informatics.lexgrid.convert.directConversions.medDRA.MedDRA2LGMain provides a central kickoff point with some methods that can be wrapped for load and validation responsibilities down further up the execution chain. This package also contains edu.mayo.informatics.lexgrid.convert.directConversions.medDRA.MedDRAMapToLexGrid with a readMedDRAFile that reads data from a CSV file and persists it to objects defined in package edu.mayo.informatics.lexgrid.convert.directConversions.medDRA.Data.  While this data package defines some of the beans that model the content of lines read from the CSV file, it also organizes them into structures that are easier for the mapping code to user.  Once done the MedDRAMapToLexGrid  does the active mapping of can map data objects derived from the MedDRA source into a complete coding scheme object. 

So the tasks are to read the file into some kind of logical model or bean class object.  Organize these objects or make them available to be mapped into LexEVS objects, tie all objects together as a coding scheme, and pass this potentially large coding scheme object to LexEVS to be persisted to the database.  Back up the execution chaing MeDRALoaderImpl the doLoad method first calls the mapping method of the conversion class MedDRA2LGMain, then passes control of the resulting coding scheme to BaseLoader by calling this.persistCodingSchemeToDatabase method on the BaseLoader super class