[AIRAVATA-2994] Experiment input editors: transformations

• Type: Sub-task
• Status: Open
• Priority: Major
• Resolution: Unresolved
• Component/s: Django Portal
• Assignee: Marcus Christie
• Reporter: Marcus Christie
• Created: 07/Mar/19 22:52
• Updated: 07/Mar/19 22:52

Description

Add the ability to add transformations to input editors through input metadata, validations (AIRAVATA-2762) and dependencies (AIRAVATA-2761).

 The schema I'm thinking of is

{
  "editor": {
    "transformations": [
      {
        "type": "regex-replace",
        "value": ["\s+", "", ""]
      },
      ...
    ]
  }
}

A list of transformations can be specified. They will be applied in order to the input value whenever it changes.

The type must be implemented by a Transformation class (something like how the ValidatorFactory works).

Example: transform

>101M:A|PDBID|CHAIN|SEQUENCE
MVLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRVKHLKTEAEMKASEDLKKHGVTVLTALGAILKKK
GHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHPGNFGADAQGAMNKALELFRKDIAAKYKELGYQG

into

MVLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRVKHLKTEAEMKASEDLKKHGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHPGNFGADAQGAMNKALELFRKDIAAKYKELGYQG

That is, remove the initial header line and remove all newlines.

Other notes:

• transformations should be applied before validations
• need to add a transform(value) method to InputDataObjectType. transform() should apply transformations and return the transformed value. If there are no transformations then transform() should just return the given value