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elixir-europe / plant-brapi-to-isa

BSD 3-Clause "New" or "Revised" License
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Generate data file #14

Closed cpommier closed 5 years ago

cpommier commented 5 years ago

Need to add in brapi_to_isa.py: line 395

for my_study_id in STUDY_IDS:
    my_study = brapi_client.get_study(my_study_id)
    if "trialDbId" in my_study.keys() and my_study["trialDbId"]:
      TRIAL_IDS += my_study["trialDbId"]
    elif "trialDbIds" in my_study.keys() and my_study["trialDbIds"]:
       TRIAL_IDS += my_study["trialDbIds"]
cpommier commented 5 years ago

TODO:

cpommier commented 5 years ago

Germplasm : "observationUnitXref": [ { "source": "gnpis.lot", "id": "0040E" } "accessionNumber": "274Col49", "germplasmName": "Riesling B INRA-CV 813",

Levels

bedroesb commented 5 years ago

Germplasm : "observationUnitXref": [ { "source": "gnpis.lot", "id": "0040E" } "accessionNumber": "274Col49", "germplasmName": "Riesling B INRA-CV 813",

Levels

can { "source": "gnpis.lot", "id": "0040E" } be placed under a single column or separate it in observationUnitXref[source], observationUnitXref[id] columns?

cpommier commented 5 years ago

Most of the time there will be a single source. In our case there are gnpis.lot and biosample, but only lot is filled.