2. rPredictorDB Technical Documentation

• 1. rPredictorDB architecture
  • 1.1. rData
  • 1.2. rETL
  • 1.3. rTools
  • 1.4. rWeb
  • 1.5. rDoc
• 2. Setup
  • 2.1. Before starting
  • 2.2. Platform
  • 2.3. Programming languages
  • 2.4. Setup process overview
  • 2.5. HTTP server
  • 2.6. Nette
  • 2.7. PostgreSQL
  • 2.8. rETL
  • 2.9. rWeb
  • 2.10. Blast
  • 2.11. Cppredict
• 3. rPredictorDB data & database
  • 3.1. General information
  • 3.2. Database schema
  • 3.3. Functions
  • 3.4. Views
  • 3.5. The subversion repository
• 4. rETL: getting data
  • 4.1. Requirements
  • 4.2. Data sources
  • 4.3. ETL process phases
  • 4.4. Structure of an ETL phase
  • 4.5. Complete ETL process schema
  • 4.6. Database preparation
  • 4.7. Extracting data
  • 4.8. Importing sequences
  • 4.9. Importing qualities
  • 4.10. Importing annotations
  • 4.11. Importing predictions
  • 4.12. Finalization
  • 4.13. Sample: How to execute all database functions in correct order
• 5. rPredictorDB website
  • 5.1. Implementation overview
  • 5.2. Query processing
  • 5.3. Tools
  • 5.4. Analytical models
  • 5.5. Client side scripting
  • 5.6. Coding standards
• 6. Creating your own tool
  • 6.1. The tool class
  • 6.2. Integrating the tool into rPredictorDB
  • 6.3. rPredictorDB environmental variables
  • 6.4. Tool development best practices
• 7. Creating your own analytical model
  • 7.1. The model class
  • 7.2. The temporary files
  • 7.3. The presentation
• 8. Database queries using DbTool
  • 8.1. Access to database
  • 8.2. How does DbTool work?
  • 8.3. Miscellaneous methods

This is the technical documentation (NOT reference) of the rPredictorDB infrastructure.

Information here should cover the individual rPredictorDB components and how they fit together, on the level of why they are there.

The instruction on setting up rPredictorDB from scratch are covered by rPredictorDB setup.

2.9. RSS Channel

RSS channel functionality is in BaseModule in RssPresenter. It uses DbService for getting and manipulating data. Displaying RSS data is very straightforward - it simply loads specified amount of records from database and display them into view.latte template. Updating (inserting, editing and deleting) is done in add, edit and delete actions of the same presenter (only one template - add.latte is used for both). Updating requires user authentification which is very basic - it uses Authenticator service, which is a standard part of Nette framework. It simply checks whether user inserted correct username and password. Both username and password is stored here locally, because there is no need for having multiple users (and thus implementing a more complex authentication system).