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cohorts_csv.py
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import json
import re
from tqdm import tqdm
import conf.conf as conf
import csv
import sys
from validators.cohorts import Cohorts
csv_filename = sys.argv[1]
output_path = sys.argv[2]
with open("files/headers/cohorts.txt", "r") as txt_file:
list_of_headers=txt_file.read().splitlines()
with open('files/deref_schemas/cohorts.json') as json_file:
dict_properties = json.load(json_file)
def generate(dict_properties, list_of_headers):
#csv_filename = conf.csv_filename
total_dict =[]
with open(csv_filename, 'r' ) as theFile:
reader = csv.DictReader(theFile)
num_rows = sum(1 for row in reader)
k=0
pbar = tqdm(total = num_rows)
with open(csv_filename, 'r' ) as theFile:
reader = csv.DictReader(theFile)
i=1
for line in reader:
dict_of_properties={}
list_of_filled_items=[]
for kline, vline in line.items():
property_value = kline
valor = vline
property_value=property_value.replace('\ufeff', '')
if property_value not in list_of_headers:
raise Exception(('the header {} is not allowed. Please, take a look at files/headers/cohorts.txt to check the headers allowed.').format(property_value))
if i > 0:
if valor != '':
list_of_filled_items.append(property_value)
if valor:
dict_of_properties[property_value]=valor
definitivedict={}
for key, value in dict_properties.items():
if isinstance(value, list):
value_list=[]
for item in value:
if isinstance(item, dict):
item_dict={}
for ki, vi in item.items():
if isinstance(vi, list):
vi_list=[]
for subitem in vi:
if isinstance(subitem, dict):
subitem_dict={}
for k, v in subitem.items():
if isinstance(v, dict):
for k1, v1 in v.items():
if isinstance(v1, dict):
for k2, v2 in v1.items():
if isinstance(v2, dict):
for k3, v3 in v2.items():
new_item = ""
new_item = key + "|" + ki + "|" + k + "|" + k1 + "|" + k2 + "|" + k3
for propk, propv in dict_of_properties.items():
if propk == new_item:
#print(propk)
subitem_dict[k][k1]={}
subitem_dict[k][k1][k2]={}
subitem_dict[k][k1][k2][k3]=propv
else:
new_item = ""
new_item = key + "|" + ki + "|" + k + "|" + k1 + "|" + k2
for propk, propv in dict_of_properties.items():
if propk == new_item:
#print(propk)
subitem_dict[k][k1]={}
subitem_dict[k][k1][k2]=propv
else:
new_item = ""
new_item = key + "|" + ki + "|" + k + "|" + k1
for propk, propv in dict_of_properties.items():
if propk == new_item:
#print(propk)
if subitem_dict == {}:
subitem_dict[k]={}
subitem_dict[k][k1]=propv
else:
new_item = ""
new_item = key + "|" + ki + "|" + k
for propk, propv in dict_of_properties.items():
if propk == new_item:
#print(propk)
subitem_dict[k]=propv
if subitem_dict != {} and subitem_dict[k] != {}:
if subitem_dict not in vi_list:
vi_list.append(subitem_dict)
item_dict[ki]=vi_list[0]
elif isinstance(vi, dict):
vi_dict={}
for ki1, vi1 in vi.items():
if isinstance(vi1, dict):
vi_dict={}
vi_dict[ki1]={}
if vi1 == {}:
new_item = ""
new_item = key + "|" + ki + "|" + ki1
for propk, propv in dict_of_properties.items():
if propk == new_item:
#print(propk)
propv = re.sub(r'\s', '', propv)
respropv = json.loads(propv)
item_dict[ki][ki1]=respropv
else:
for ki2, vi2 in vi1.items():
new_item = ""
new_item = key + "|" + ki + "|" + ki1 + "|" + ki2
for propk, propv in dict_of_properties.items():
if propk == new_item:
#print(propk)
vi_dict[ki1][ki2]=propv
if vi_dict != {}:
item_dict[ki]=vi_dict
else:
new_item = ""
new_item = key + "|" + ki + "|" + ki1
for propk, propv in dict_of_properties.items():
if propk == new_item:
#print(propk)
if propk.endswith('availability'):
vi_dict[ki1]=bool(propv)
item_dict[ki]=vi_dict
elif propk.endswith('availabilityCount'):
vi_dict[ki1]=int(propv)
item_dict[ki]=vi_dict
else:
vi_dict[ki1]=propv
item_dict[ki]=vi_dict
else:
new_item = ""
new_item = key + "|" + ki
for propk, propv in dict_of_properties.items():
if propk == new_item:
#print(propk)
item_dict[ki]=propv
if item_dict != {} and item_dict != [{}]:
if item_dict not in value_list:
value_list.append(item_dict)
if value_list != []:
itemdict={}
definitivedict[key]=[]
v_array=[]
v1_array=[]
v2_array=[]
v1_keys = []
v2_keys=[]
kv2dict={}
kvl2dict={}
v1_bigkeys=[]
v2_bigkeys=[]
v3_bigkeys=[]
for itemvl in value_list:
for kvl, vvl in itemvl.items():
if isinstance(vvl, str):
if '|' in vvl:
v_array = vvl.split('|')
for vitem in v_array:
v1_array.append(vitem)
if kvl not in v1_bigkeys:
v1_bigkeys.append(kvl)
elif isinstance(vvl, dict):
itemdict[kvl]={}
for kvl1, vvl1 in vvl.items():
itemdict[kvl][kvl1]={}
if isinstance(vvl1, str) and '|' in vvl1:
vvl1_array = vvl1.split('|')
for vvlitem in vvl1_array:
v1_array.append(vvlitem)
if kvl not in v1_bigkeys:
v1_bigkeys.append(kvl)
if kvl1 not in v1_keys:
v1_keys.append(kvl1)
elif isinstance(vvl1, dict):
if kvl1 not in v2_bigkeys:
v2_bigkeys.append(kvl1)
if v1_keys != []:
n=0
list_to_def=[]
newdict={}
for v1bigkey in v1_bigkeys:
newdict[v1bigkey]={}
if v1bigkey == 'measurementValue':
newdict[v1bigkey][v2_bigkeys[0]]={}
newdict[v1bigkey][v2_bigkeys[0]][v3_bigkeys[0]]=''
newdict[v1bigkey][v2_bigkeys[0]][v3_bigkeys[1]]=''
elif v1bigkey == 'assayCode':
newdict[v1bigkey][v1_keys[0]]=""
while n < len(v_array):
num=int(n+len(v_array)-1)
num2=int(n+len(v_array))
num4=int(n+(len(v_array)*2))
num6=int(n+(len(v_array)*3))
for v1bigkey in v1_bigkeys:
if v1bigkey == 'measurementValue':
newdict[v1bigkey][v2_bigkeys[0]][v3_bigkeys[0]]=v2_array[n]
newdict[v1bigkey][v2_bigkeys[0]][v3_bigkeys[1]]=v2_array[num2]
newdict[v1bigkey][v1_keys[3]]=v1_array[num6]
elif v1bigkey == 'assayCode':
newdict[v1bigkey][v1_keys[0]]=v1_array[n]
newdict[v1bigkey][v1_keys[1]]=v1_array[num2]
elif v1bigkey == 'date':
newdict[v1bigkey]=v1_array[num4]
list_to_def.append(newdict)
n +=1
for itemldf in list_to_def:
definitivedict[key].append(itemldf)
else:
for itemvl in value_list:
definitivedict[key].append(itemvl)
elif isinstance(value, dict):
value_dict={}
for kd, vd in value.items():
if isinstance(vd, list):
vd_list=[]
if isinstance(vd[0], dict):
value_dict[kd]={}
dicty={}
propv_splitted_id=[]
propv_splitted_label=[]
arrayofkdvs=[]
for kd1, vd1 in vd[0].items():
if isinstance(vd1, dict):
for kd2, vd2 in vd1.items():
new_item = ""
new_item = key + "|" + kd + "|" + kd1 + "|" + kd2
for propk, propv in dict_of_properties.items():
if propk == new_item:
#print(propk)
try:
value_dict[kd][0][kd1][kd2]=propv
except Exception:
try:
value_dict[kd][0][kd1]={}
value_dict[kd][0][kd1][kd2]=propv
except Exception:
value_dict[kd][kd1]={}
value_dict[kd][kd1][kd2]=propv
try:
vdictitem=value_dict[kd][0]
value_dict[kd]=[vdictitem]
except Exception:
pass
elif isinstance(vd1, list):
arrayofkdvs=[]
new_item = ""
new_item = key + "|" + kd + "|" + kd1
for propk, propv in dict_of_properties.items():
if propk == new_item:
#print(propk)
if '|' in propv:
if propv_splitted_id != [] and propv_splitted_label != []:
propv_splitted_version = propv.split(',')
elif propv_splitted_id != []:
propv_splitted_label = propv.split(',')
else:
propv_splitted_id = propv.split(',')
if propv_splitted_version != []:
n=0
while n < len(propv_splitted_id):
dicty={}
dicty['id']=propv_splitted_id[n]
dicty['label']=propv_splitted_label[n]
dicty['version']=propv_splitted_version[n]
for kdv, vdv in value_dict.items():
arrayofkdvs.append(kdv)
if kd not in arrayofkdvs:
value_dict[kd]=[]
value_dict[kd].append(dicty)
n+=1
else:
try:
jsonedpropv=json.loads(propv)
if kd1 == 'ageOfOnset':
dicty[kd1]=jsonedpropv
elif kd1 == 'onset':
dicty[kd1]=jsonedpropv
elif kd1 == 'resolution':
dicty[kd1]=jsonedpropv
else:
dicty[kd1]=[jsonedpropv]
if dicty not in arrayofkdvs:
arrayofkdvs.append(dicty)
value_dict[kd]=arrayofkdvs
except Exception:
jsonedpropv=propv
dicty[kd1]=jsonedpropv
if dicty not in arrayofkdvs:
arrayofkdvs.append(dicty)
value_dict[kd]=arrayofkdvs
else:
new_item = ""
new_item = key + "|" + kd + "|" + kd1
for propk, propv in dict_of_properties.items():
if propk == new_item:
#print(propk)
if '|' in propv:
if propv_splitted_id != []:
propv_splitted_label = propv.split('|')
else:
propv_splitted_id = propv.split('|')
if propv_splitted_label != []:
n=0
while n < len(propv_splitted_id):
dicty={}
dicty['id']=propv_splitted_id[n]
dicty['label']=propv_splitted_label[n]
for kdv, vdv in value_dict.items():
arrayofkdvs.append(kdv)
if kd not in arrayofkdvs:
value_dict[kd]=[]
if value_dict[kd]=={}:
value_dict[kd]=[]
value_dict[kd].append(dicty)
n+=1
else:
if propv == 'TRUE' or propv == 'true' or propv == 'FALSE' or propv == 'false':
propv = bool(propv)
dicty[kd1]=propv
arrayofkdvs=[]
for kdv, vdv in value_dict.items():
arrayofkdvs.append(kdv)
if kd not in arrayofkdvs:
value_dict[kd]=[]
try:
if dicty not in value_dict[kd]:
if dicty != {}:
value_dict[kd].append(dicty)
except Exception:
if key == 'inclusionCriteria' or key == 'exclusionCriteria':
try:
if dicty != {}:
value_dict[kd].append(dicty)
except Exception:
if dicty != {}:
value_dict[kd]=[]
value_dict[kd].append(dicty)
else:
value_dict[kd]=dicty
if value_dict != {}:
if value_dict not in vd_list:
vd_list.append(value_dict)
if vd_list != []:
definitive_vd_dict={}
for kdv,vdv in vd_list[0].items():
if vdv == {}:
pass
else:
definitive_vd_dict[kdv]=vdv
if definitive_vd_dict!={}:
definitivedict[key]=definitive_vd_dict
elif isinstance(vd, dict):
value_dict[kd]={}
for kd1, vd1 in vd.items():
if isinstance(vd1, dict):
for kd2, vd2 in vd1.items():
new_item = ""
new_item = key + "|" + kd + "|" + kd1 + "|" + kd2
for propk, propv in dict_of_properties.items():
if propk == new_item:
#print(propk)
if value_dict == {}:
value_dict[kd]={}
value_dict[kd][kd1]={}
value_dict[kd][kd1][kd2]=propv
definitivedict[key]=value_dict
else:
new_item = ""
new_item = key + "|" + kd + "|" + kd1
for propk, propv in dict_of_properties.items():
if propk == new_item:
#print(propk)
value_dict[kd][kd1]=propv
definitivedict[key]=value_dict
else:
new_item = ""
new_item = key + "|" + kd
for propk, propv in dict_of_properties.items():
if propk == new_item:
#print(propk)
value_dict[kd]=propv
definitivedict[key]=value_dict
else:
new_item = ""
new_item = key + "|" + kd
for propk, propv in dict_of_properties.items():
if propk == new_item:
#print(propk)
value_dict[kd]=propv
if key == 'cohortDataTypes':
definitivedict[key]=[value_dict]
else:
definitivedict[key]=value_dict
if value == {}:
new_item = ""
new_item = key
for propk, propv in dict_of_properties.items():
if propk == new_item:
#print(propk)
propvalue={}
propvalue_splitted = propv.split(':')
propvalue[propvalue_splitted[0]]=propvalue_splitted[1]
print(key)
print(value)
definitivedict[key]=propvalue
else:
new_item = ""
new_item = key
for propk, propv in dict_of_properties.items():
if propk == new_item:
try:
propv = int(propv)
except Exception:
propv = propv
#print(key)
#print(propv)
definitivedict[key]=propv
#print(definitivedict)
Cohorts(**definitivedict)
definitivedict["datasetId"]=conf.datasetId
total_dict.append(definitivedict)
pbar.update(1)
if i > num_rows:
break
i+=1
pbar.close()
return total_dict, i
dict_generado, total_i=generate(dict_properties, list_of_headers)
output = conf.output_docs_folder + 'cohorts.json'
if total_i-1 > 0:
print('Successfully converted {} registries into {}'.format(total_i-1, output))
else:
print('No registries found.')
with open(output, 'w') as f:
json.dump(dict_generado, f)