New Tools Framework

[j-coll]

OpenCGA Tools

Every tool will extend the class OpenCgaTool, which provides some utility methods. These tools must be annotated with the annotation @Tool to indicate the tool ID, type and description.

ToolExecutor

Tools will have, potentially, multiple ToolExecutors, depending on the data input source and the available frameworks. The main OpenCgaTool class will have some methods to make the discovery of compatible ToolExecutors in the classpath.

ExecutionResult

The Tool will produce an ExecutionResult with the information of the execution status, the generated files, the list of steps, and the progress. This ExecutionResult will be written always to disk, as a <tool-id>.result.yml file in the output directory.

ExecutionResult Model

• ExecutorInfo
  • String id
  • ObjectMap params
  • Source source
  • Framework framework
  • Class<? extends OpenCgaExecutor> clazz
• Date start
• Date end
• Status status
  • enum name [PENDING, RUNNING, ERROR, DONE]
  • String step
  • Date date
• List events
• List moveFiles
  • String source
  • FileTarget
    • String catalogPath
    • String uri (optional)
• List steps
  • String id
  • Date start
  • Date end
  • enum status [PENDING, RUNNING, ERROR, DONE]
  • ObjectMap attributes

Discarded elements from the ExecutionResult:

• ObjectMap params
• List outputFiles
  • String name
  • FileType type

Tasks

• [x] Fill the issue description
• [x] Add the AnalysisResultManager
• [x] Use Source and Frameworks to decide automatically the Executor

[j-coll]

Rename Analysis Framework to Tools Framework