Generate yaml file with metadata from simulation output for research data management
Problem to solve with the new feature
We would like to extract the simulation setup parameters from the parameter.par file to a yaml file, which then can be loaded in Python as a dictionary.
Intended users
People using openCARP for simulations that want to store their output data in a way that in the future, it can be easily assessed what the intention and setup of the simulation was; or they want to search for all simulations that obey a certain setup.
Further details
Nowadays there is a strong tendency to make your research data FAIR (Findable, Accessible, Interoperability, Reusable). Within openCARP, there is already the initiative of making a bundle out of a simulation to make it ready to publish. This bundle includes the scripts and commandos to run the simulation. This definitely makes the output Reusable.
Our institution has a simulation data repository based on irods where research data can be annotated with metadata. The system allows to search for certain keyword-value pairs, hence the data is Findable. For that, we would like to extract certain desired and crucial describing parameters from openCARP simulation output. It seems that the parameter.par
file is particularly feasible for this, however it is not straightforward how to extract the parameters with their values.
Proposal
A simple Python parser function or module would suffice. However, the parameter.par
file has a specific structure that needs to be taken into account.
Testing
There are no risks involved since it is a postprocessing function.
Links / references
This issue has been discussed during the hacky hour on the openCARP user's meeting 2023. First efforts in coding this up have been done by @tomas.stary .