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biosamples_csv.py
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biosamples_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.biosamples import Biosamples
with open("files/headers/biosamples.txt", "r") as txt_file:
list_of_headers=txt_file.read().splitlines()
with open('files/deref_schemas/biosamples.json') as json_file:
dict_properties = json.load(json_file)
csv_filename = sys.argv[1]
output_path = sys.argv[2]
def commas(prova):
length_iter=0
array_of_newdicts=[]
for key, value in prova.items():
if isinstance(value, str):
valuesplitted = value.split('|')
length_iter=len(valuesplitted)
elif isinstance(value, dict):
for kval, vval in value.items():
if isinstance(vval, str):
valsplitted = vval.split('|')
length_iter=len(valsplitted)
if length_iter > 0:
i=0
while i < length_iter:
newdict={}
for key, value in prova.items():
if isinstance(value, str):
valuesplitted = value.split('|')
if valuesplitted[i]!='' or valuesplitted[i]!={}:
newdict[key]=valuesplitted[i]
elif isinstance(value, int):
valuesplitted = value.split('|')
if valuesplitted[i]!='' or valuesplitted[i]!={}:
newdict[key]=valuesplitted[i]
elif isinstance(value, dict):
newdict[key]={}
for k, v in value.items():
if isinstance(v, str):
vsplitted = v.split('|')
try:
if vsplitted[i]!='' or vsplitted[i]!={}:
newdict[key][k]=float(vsplitted[i])
except Exception:
if vsplitted[i]!='' or vsplitted[i]!={}:
newdict[key][k]=vsplitted[i]
elif isinstance(v, int):
newdict[key][k]=v
elif isinstance(v, dict):
newdict[key][k]={}
for k1, v1 in v.items():
if isinstance(v1, str):
v1splitted = v1.split('|')
try:
if v1splitted[i]!='' or v1splitted[i]!={} and len(v1splitted[i])!=0:
newdict[key][k][k1]=v1splitted[i]
except Exception:
pass
if newdict[key][k]=={} or newdict[key][k]=="":
del newdict[key]
array_of_newdicts.append(newdict)
i+=1
else:
array_of_newdicts.append(prova)
return(array_of_newdicts)
def generate(dict_properties, list_of_headers):
#csv_filename = conf.csv_filename
with open(csv_filename, 'r' ) as theFile:
reader = csv.DictReader(theFile)
num_rows = sum(1 for row in reader)
total_dict =[]
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
property_value=property_value.replace('\ufeff', '')
valor = vline
if property_value not in list_of_headers:
raise Exception(('the header {} is not allowed. Please, take a look at files/headers/biosamples.txt to check the headers allowed.').format(property_value))
if i > 0:
if valor is not None and valor != '':
list_of_filled_items.append(property_value)
if valor:
dict_of_properties[property_value]=valor
#print(dict_properties)
#print(dict_of_properties)
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:
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:
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:
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:
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:
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:
vi_dict[ki1][ki2]=propv
if vi_dict != {}:
vivilist=[]
for kivi, vivi in vi_dict.items():
if vivi != {}:
vivilist.append(vivi)
for vivitem in vivilist:
if vivitem != {}:
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:
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:
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 != []:
for itemvl in value_list:
list_to_def=commas(itemvl)
for itemldf in list_to_def:
try:
if itemldf not in definitivedict[key]:
if key == 'pedigrees':
for k, v in itemldf.items():
if k == 'members':
list_members=[]
list_members.append(v)
try:
itemldf['members']=list_members
except Exception:
pass
definitivedict[key].append(itemldf)
except Exception:
definitivedict[key]=[]
definitivedict[key].append(itemldf)
else:
for itemvl in value_list:
definitivedict[key].append(itemvl)
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):
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:
value_dict[kd]={}
value_dict[kd][kd1]={}
value_dict[kd][kd1][kd2]=propv
else:
new_item = ""
new_item = key + "|" + kd + "|" + kd1
for propk, propv in dict_of_properties.items():
if propk == new_item:
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]=[]
value_dict[kd].append(dicty)
n+=1
else:
dicty[kd1]=propv
arrayofkdvs=[]
for kdv, vdv in value_dict.items():
arrayofkdvs.append(kdv)
if kd not in arrayofkdvs:
value_dict[kd]=[]
if dicty not in value_dict[kd]:
value_dict[kd].append(dicty)
if value_dict != {}:
if value_dict not in vd_list:
vd_list.append(value_dict)
if vd_list != []:
definitivedict[key]=vd_list
elif isinstance(vd, dict):
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:
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:
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:
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:
value_dict[kd]=propv
definitivedict[key]=value_dict
if value == {}:
new_item = ""
new_item = key
for propk, propv in dict_of_properties.items():
if propk == new_item:
propv = re.sub(r'\s', '', propv)
respropv = json.loads(propv)
definitivedict[key]=respropv
else:
new_item = ""
new_item = key
for propk, propv in dict_of_properties.items():
if propk == new_item:
definitivedict[key]=propv
Biosamples(**definitivedict)
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 + 'biosamples.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)