@bedroesb @cpommier what is 'study' object (in Sample Name) referring to in the ISA Study Sample table?

Also, out of curiosity, is the file d_POPYOMICS-POP2-F_VIRTUAL_TRIAL.txt served by the GENPIS server ? if so, could this a be resolveable URI?

This is something I would like to discuss too.

@proccaserra take a look at this issue and the replies.

To reiterate: The idea behind this is that, sometimes, you have observations only on the study level. For example, a temperature sensor produces measurements that you consider applicable to the whole field.

This translates to a single observation unit, with observation level/type study. The challenge was that the study file must list all biological materials (ISA sources) for each observation unit (ISA sample) too, which would very often lead to redundancy and be unnecessarily time-consuming: In most cases these materials will be described again in the study file, as they will each be connected to their specific observation unit(s).

We thought that it might be a good idea to define a study keyword, for use in the ISA Source column in the study file, to indicate that all materials in the study are connected to that unit. Then the unit with all those materials may be used in the Assay table too.
Note the other decision that we have discussed: each assay file will be about exactly one observation level! And by definition, the level of an observation unit that refers to the whole study would be study too. So it cannot be put in the same assay file as observation units of other levels, which is what the example above indicates.

In my opinion also it doesn't make sense to create this unit unless you have study-level data (i.e. a measurement belonging not to a specific plant, plot or pot in the study, but to the study as a whole), because that's the purpose of the Assay file.

Otherwise, if you want to provide a data file or link for the whole study, you can do so using the equivalent to MIAPPE's data file link section: the comment fields (Comment[Study Data File Link], Comment[Study Data File Description], Comment[Study Data File Version]) in the Study section of the investigation file.

Does this make sense?

thx @PapoutsoglouE. I see where you are coming from, I am concerned with validating such a representation. @bedroesb is there a test study on one of the server that would have such layout?
It would be interesting to test a few things (e.g. validation with ISA (and MIAPPE ISAconfiguration) + conversion to ISA-JSON).

@proccaserra I use always following endpoints to test my scripts:

python brapi_to_isa.py -t all -e https://pippa.psb.ugent.be/BrAPIPPA/brapi/v1/
python brapi_to_isa.py -s RIGW1 -e https://urgi.versailles.inra.fr/gnpis-core-srv/brapi/v1/
python brapi_to_isa.py -t 24 -e https://urgi.versailles.inra.fr/gnpis-core-srv/brapi/v1/
This last one has the data file links.

and a really big one that contains treatments (I terminate most of the time within the process):

python brapi_to_isa.py -t 6 -e https://urgi.versailles.inra.fr/gnpis-core-srv/brapi/v1/

in my last PR #44 I fixed btw the docker file problem and is implemented in the refactoring branch now.
Isa validation is outputted in a json file for every trial together with the ISA json.