Interface with GKDB

Use OMAS to interface with Gyro-Kinetic DataBase (GKDB) https://gitlab.com/gkdb/gkdb GKDB is a publicly accessible database of delta-f flux-tube gyro-kinetic simulations of tokamak plasmas which stores its data according to the gyrokinetic IMAS IDS https://gafusion.github.io/omas/schema/schema_gyrokinetics.html

from omas import ODS, omas_dir, omas_testdir
from pprint import pprint
import sys

# load a sample GKDB sample json file
sample_filename = omas_dir + 'samples/gkdb_linear_eigenvalue.json'
ods = ODS()
# warn about `gyrokinetics_local.fluxes_integrated_norm = []` and drop it
ods['gyrokinetics_local'].load(sample_filename, consistency_check='warn_drop')

# show content
pprint(ods.pretty_paths())

# save a copy
try:
    __file__
except NameError:
    import inspect

    __file__ = inspect.getfile(lambda: None)
filename = omas_testdir(__file__) + '/gkdb_linear_initialvalue.json'
ods['gyrokinetics_local'].save(filename)

# load the newly saved copy
ods1 = ODS()
ods1['gyrokinetics_local'].load(filename)

# look for differences between original GKDB json and OMAS json
differences = ods.diff(ods1, ignore_type=True)
if not differences:
    print('\nPrint no differences found: save/load of GKDB json file worked\n')
else:
    pprint(differences)
    raise RuntimeError('Save/Load of GKDB on json file failed')

# raise error if trying to run GKDB under Python2x
try:
    import gkdb.core.model
except ImportError as _excp:
    print('Could not import gkdb library: %s' % repr(_excp))
else:
    # Check that GKDB file written by OMAS is valid also according to GKDB
    if gkdb.core.ids_checks.check_json(filename, only_input=False):
        print('json file saved via OMAS is valid for gkdb')

    # This requires an account on the GKDB server
    if False:
        gkdb.core.model.connect_to_gkdb()
        gkdb.core.model.Ids_properties.from_json(filename)