def test_latest_cocos(self):
from omas.omas_utils import list_structures, omas_rcparams
from omas.omas_physics import generate_cocos_signals
with warnings.catch_warnings():
warnings.filterwarnings("ignore",
message=".*defining its COCOS transform.*")
generate_cocos_signals(list_structures(
imas_version=omas_rcparams['default_imas_version']),
threshold=0,
write=False,
verbose=False)
def extract_coordinates(imas_version=omas_rcparams['default_imas_version']):
'''
return list of strings with coordinates across all structures
:param imas_version: imas version
:return: list with coordinate
'''
from omas.omas_utils import list_structures
from omas.omas_utils import load_structure
omas_coordinates = set()
for structure in list_structures(imas_version=imas_version):
tmp = load_structure(structure, imas_version)[0]
coords = []
for item in tmp:
if 'coordinates' in tmp[item]:
coords.extend(map(i2o, tmp[item]['coordinates']))
coords = list(filter(lambda x: '...' not in x, set(coords)))
omas_coordinates.update(coords)
return sorted(list(omas_coordinates))
'''
Utility to generate the omas/omas_cocos.py file
'''
import os, sys
sys.path.insert(
0,
os.path.split(
os.path.split(os.path.split(os.path.abspath(__file__))[0])[0])[0])
from omas.omas_utils import list_structures, omas_rcparams
from omas.omas_physics import generate_cocos_signals
generate_cocos_signals(
list_structures(imas_version=omas_rcparams['default_imas_version']),
threshold=0,
write=True)
def create_html_documentation(
imas_version=omas_rcparams['default_imas_version']):
filename = os.path.abspath(
os.sep.join([
imas_json_dir,
imas_versions.get(imas_version, imas_version), 'omas_doc.html'
]))
table_header = "<table border=1, width='100%'>"
sub_table_header = '<tr>' \
'<th style="width:25%">Path</th>' \
'<th style="width:25%">Dimensions</th>' \
'<th>Type</th>' \
'<th>Units</th>' \
'<th>Description</th>' \
'</tr>'
column_style = 'style="word-wrap:break-word;word-break:break-all"'
lines = []
for structure_file in list_structures(imas_version=imas_version):
print('Adding to html documentation: ' + structure_file)
# load structure information
structure = load_structure(structure_file,
imas_version=imas_version)[0]
# idenfity coordinates in the structure
coords = []
for item in structure:
if 'coordinates' in structure[item]:
coords.extend(structure[item]['coordinates'])
coords = list(filter(lambda x: '...' not in x, set(coords)))
# generate output
lines.append('<!-- %s -->' % structure_file)
lines.append(table_header)
lines.append(sub_table_header)
for item in sorted(structure):
if not any([
item.endswith(k)
for k in ['_error_index', '_error_lower', '_error_upper']
]):
# uncertain quantities
is_uncertain = ''
if item + '_error_upper' in structure:
is_uncertain = ' (uncertain)'
# lifecycle status
status = ''
if 'lifecycle_status' in structure[item] and structure[item][
'lifecycle_status'] not in ['active']:
color_mapper = {'alpha': 'blue', 'obsolescent': 'red'}
status = '</p><p><font color="%s">(%s)</font>' % (
color_mapper.get(
structure[item]['lifecycle_status'],
'orange'), structure[item]['lifecycle_status'])
# highlight entries that are a coordinate
item_with_coordinate_highlight = item
if item in coords:
item_with_coordinate_highlight = '<strong>%s</strong>' % item
try:
lines.append(
'<tr>'
'<td {column_style}><p>{item_with_coordinate_highlight}{status}</p></td>' \
'<td {column_style}><p>{coordinates}</p></td>' \
'<td><p>{data_type}</p></td>' \
'<td><p>{units}</p></td>' \
'<td><p>{description}</p></td>'
'</tr>'.format(
item_with_coordinate_highlight=item_with_coordinate_highlight,
coordinates=re.sub('\[\]', '', re.sub('[\'\"]', '', re.sub(',', ',<br>', str(
list(map(str, structure[item].get('coordinates', ''))))))),
data_type=structure[item].get('data_type', '') + is_uncertain,
units=structure[item].get('units', ''),
description=re.sub('\n', '<br>', structure[item].get('documentation', '')),
status=status,
column_style=column_style
))
except Exception:
printe(item)
raise
lines.append('</table>')
lines.append('</table><p></p>')
with open(filename, 'w') as f:
if sys.version_info < (3, 0):
f.write('\n'.join(lines).encode('utf-8'))
else:
f.write('\n'.join(lines))
''' Utility to generate the omas/omas_cocos.py file ''' from omas.omas_utils import list_structures, omas_rcparams from omas.omas_physics import generate_cocos_signals generate_cocos_signals(list_structures(imas_version=omas_rcparams['default_imas_version']), threshold=0, write=True)