def retrieve_data(arg_dict):
update_statusbar("Downloading...")
download_keys = {key: date_keys[key]["keys"] for key in selected_data}
retrieve = Retrieve(service_url=base_url)
data = retrieve.retrieve(keys=download_keys)
# Convert the JSON into Dataframes
# TODO - the returned data will be an xarray Dataset in the future
# Write a test to catch this change
for key in data:
data[key] = pd_read_json(data[key])
# Update the status bar
if data:
# update_statusbar("Download complete")
# # Create the plotting box
create_plotting_box()
else:
print("Update statusbar")
# update_statusbar("No data downloaded")
selected_data = []
def select_data(**kwargs):
selected_data.clear()
for key in kwargs:
if kwargs[key] is True:
selected_data.append(key)
# Here could update the status bar and call the download function
# download_button.on_click(retrieve_data)
out = widgets.interactive_output(select_data, arg_dict)
def make_geojson_links(ref_layer_geojson, csv_table, field_i, field_j,
field_fij, join_field):
gdf = GeoDataFrame.from_features(ref_layer_geojson["features"])
gdf.set_index(join_field, inplace=True, drop=False)
gdf.geometry = _compute_centroids(gdf.geometry)
csv_table = pd_read_json(csv_table)
csv_table = csv_table[csv_table["i"].isin(gdf.index)
& csv_table["j"].isin(gdf.index)]
geoms_loc = gdf.geometry.loc
ft_template_start = \
'''{"type":"Feature","geometry":{"type":"LineString","coordinates":['''
geojson_features = []
for n, id_i, id_j, fij in csv_table[[field_i, field_j,
field_fij]].itertuples():
# pt1, pt2 = \
# list(geoms_loc[id_i].coords)[0], list(geoms_loc[id_j].coords)[0]
pts = \
list(geoms_loc[id_i].coords)[0] + list(geoms_loc[id_j].coords)[0]
geojson_features.append(''.join([
ft_template_start, '''[{0},{1}],[{2},{3}]'''.format(*pts),
''']},"properties":{"''',
'''i":"{0}","j":"{1}","fij":"{2}"'''.format(id_i, id_j,
fij), '''}}'''
]))
return ''.join([
'''{"type":"FeatureCollection","crs":{"type":"name","properties":'''
'''{"name":"urn:ogc:def:crs:OGC:1.3:CRS84"}},"features":[''',
','.join(geojson_features), ''']}'''
]).encode()
def make_geojson_links(ref_layer_geojson, csv_table, field_i, field_j,
field_fij, join_field):
gdf = GeoDataFrame.from_features(ref_layer_geojson["features"])
gdf.loc[:, join_field] = gdf.loc[:, join_field].astype(str)
gdf.set_index(join_field, inplace=True, drop=False)
gdf.geometry = _compute_centroids(gdf.geometry)
table = pd_read_json(csv_table)
table.loc[:, (field_i, field_j)] = \
table.loc[:, (field_i, field_j)].astype(str)
table = \
table[table[field_i].isin(gdf.index) & table[field_j].isin(gdf.index)]
geoms_loc = gdf.geometry.loc
ft_template_start = \
'''{"type":"Feature","geometry":{"type":"LineString","coordinates":['''
geojson_features = []
for n, id_i, id_j, fij in table[[field_i, field_j,
field_fij]].itertuples():
pts = \
list(geoms_loc[id_i].coords)[0] + list(geoms_loc[id_j].coords)[0]
geojson_features.append(''.join([
ft_template_start, '''[{0},{1}],[{2},{3}]'''.format(*pts),
''']},"properties":{"''',
'''{0}":"{1}","{2}":"{3}","{4}":"{5}"'''.format(
field_i, id_i, field_j, id_j, field_fij, fij), '''}}'''
]))
return ''.join([
'''{"type":"FeatureCollection","features":[''',
','.join(geojson_features), ''']}'''
]).encode()
def make_geojson_links(
ref_layer_geojson, csv_table, field_i, field_j, field_fij, join_field):
gdf = GeoDataFrame.from_features(ref_layer_geojson["features"])
gdf.loc[:, join_field] = gdf.loc[:, join_field].astype(str)
gdf.set_index(join_field, inplace=True, drop=False)
gdf.geometry = _compute_centroids(gdf.geometry)
table = pd_read_json(csv_table)
table.loc[:, (field_i, field_j)] = \
table.loc[:, (field_i, field_j)].astype(str)
table = \
table[table[field_i].isin(gdf.index) & table[field_j].isin(gdf.index)]
geoms_loc = gdf.geometry.loc
ft_template_start = \
'''{"type":"Feature","geometry":{"type":"LineString","coordinates":['''
geojson_features = []
for n, id_i, id_j, fij in table[[field_i, field_j, field_fij]].itertuples():
pts = \
list(geoms_loc[id_i].coords)[0] + list(geoms_loc[id_j].coords)[0]
geojson_features.append(''.join([
ft_template_start,
'''[{0},{1}],[{2},{3}]'''.format(*pts),
''']},"properties":{"''',
'''{0}":"{1}","{2}":"{3}","{4}":"{5}"'''
.format(field_i, id_i, field_j, id_j, field_fij, fij),
'''}}'''
])
)
return ''.join([
'''{"type":"FeatureCollection","features":[''',
','.join(geojson_features),
''']}'''
]).encode()
def load(json_file=None):
import json
with open(json_file, "r") as read_file:
interrogatory_json = json.load(read_file)
if interrogatory_json[0] == '"Target"':
tmp_target = _Target()
tmp_target.card = pd_read_json(interrogatory_json[1], orient='table')
tmp_target._chembl.card = pd_read_json(interrogatory_json[2],
orient='table')
tmp_target._chembl.compounds = pd_read_json(interrogatory_json[3],
orient='table')
tmp_target._uniprot.card = pd_read_json(interrogatory_json[4],
orient='table')
tmp_target._uniprot.compounds = pd_read_json(interrogatory_json[5],
orient='table')
return tmp_target