Closed IVANDOMENZAIN closed 3 years ago
This issue has been partially addressed by PR#113 in GECKO. Model version can be parsed directly by GECKO either from the name
, id
or version
fields for non version-controlled models with an available MATLAB file.
Temporarily, for non-version controlled models, it is intended that the python runner script (for the automated pipeline) assigns a dummy version to the model.
Is there a specific reason we load the .mat
file instead of the .xml
? I'm consider of using the xml_load function in the pipeline. Does this have something to do with fetching the version?
@mihai-sysbio, not really, .xml
files be the ones that are loaded preferably, if available. Just use the importModel
function in RAVEN instead of xml_load
.
Alright, switching from .mat
to .xml
is quite straighforward. I've done a preliminary test and it seems to work. For now, I'll revert the changes. Whenever we decide to start using SBML
I can reimplement this.
The pipeline has switched to .xml
files for non version-controlled models, instead of handling .mat
files, in order to stick to standard good practices. Check script run.py
in this merge commit.
It has been agreed that all original models' structures (version controlled or not) should be loaded from their corresponding
SBML
file. Currently, the version of the model can be obtained in several ways by theecModels
pipeline (e.g. read from a MATLAB structure or provided by the user).A generalized way to read the model's version is to parse it from the
<name>
or<id>
fields in theSBML
file. As an example, the model name and Ids lines for theKmx
andiYali
models are provided here:As a solution, a python script can be developed in which the version is parsed from this file, trying it on both fields
<name>
or<id>
and, if absent a default v1.0.0 string is introduced