Combination of user input parameters in --createInfoFile

[jcasadogp]

With the positional argument createInfoFile, the user can introduce 3 optional arguments: --num_studies, --num_biological_replicatesand --num_perturbations. The problem is because of the combinations that can be created with this input parameters. --num_studies is already limited to 0 or 1; only one study can be added at a time. Is --num_biological_replicates is 1, -num_perturbations can be 0, 1 or N, as all the perturbations will be added in that single new experiment. But, if -num_biological_replicates is N, the perturbations we may add after that will all be included in the last biological replicate introduced in the database. Solve this in way that is easy for the user to understand the combinations he can make.

[jcasadogp]

Possible solution. Add this into the YAML file. Modify the create_populate_file.py.

• Add the BIOLOGICAL_REPLICATE_IDENTIFIER: 1 into the BIOLOGICAL_REPLICATE part of the YAML file.
• Then, add the same identifier entry in the PERTURBATION part.
• This identifier will only be used to link user inputs (biological replicates and perturbations) but will have no effect on database's identifiers (primary keys).
• Biological replicate identifiers can be generated automatically by the code, so the user just needs to provide that number into the perturbation part of the YAML file.

Code:

BIOLOGICAL_REPLICATE:
- BIOLOGICAL_REPLICATE_IDENTIFIER: 1
  NAME:
    value: _name_
    ## description: Name of the biological replicate

PERTURBATION:
- BIOLOGICAL_REPLICATE_IDENTIFIER: _id_
    ## description: Indicate the BR name you provided before.

[hariszaf]

:+1:

[jcasadogp]

Related change to be made:

• --num_studies: I am using the argument as a boolean, so num_ is misleading