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create_dict_of_samples.py
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"""
Create a dictionary of samples from the Harmonized Data "Merged Sheet".
Each key for output dict is a new row from the sheet.
If a term exists in the ontology, a valid value must be chosen, otherwise
accept the text as a string.
"""
import pandas as pd
import sys
import datetime
import re
import copy
def create_dict_of_samples(xls, ontology_terms_and_values,antimicrobian_agent_names_ids):
def isNaN(string):
return string != string
def reading_file(sheet):
fields = pd.read_excel(xls,sheet_name=sheet,na_values=[datetime.time(0, 0),"1900-01-00","Missing","missing","Not Applicable [GENEPIO:0001619]"],keep_default_na=False, header=1)
#fields_sheet_filtered = fields_sheet[fields_sheet["Ontology ID"].str.contains("GENEPIO")==True]
if "AMR" not in sheet:
fields_noNA=fields.dropna(axis=0, subset=['sample_collector_sample_ID'])
else:
fields_noNA=fields.dropna(axis=0, subset=['isolate_ID'])
fields_sheet =fields_noNA
fields_sheet.fillna(0, inplace = True)
return(fields_sheet)
sample_sheet =reading_file("Sample Collection & Processing")
isolate_sheet = reading_file("Strain and Isolate Information")
sequence_sheet = reading_file("Sequence Information")
amr_sheet = reading_file("AMR Phenotypic Test Information")
risk_sheet = reading_file("Risk Assessment")
#print (sample_sheet)
xl = pd.ExcelFile(xls)
new_ont_terms = copy.deepcopy(ontology_terms_and_values)
dict_terms_file={'sample':{},'host':{},'isolate':{},'sequence':{},'publicRep':{},'AMR':{},'risk':{}}
terms_to_fix={}
terms_accepting_multiple_values =["environmental_site","weather_type","available_data_types","animal_or_plant_population",
"environmental_material","anatomical_material","body_product","anatomical_part","food_product",
"food_product_properties","animal_source_of_food","food_packaging","purpose_of_sequencing","experimental_intervention",
"pre_sampling_activity","purpose_of_sampling"]
if len(xl.sheet_names) > 8:
temp_dict={}
#print (ontology_terms_and_values)
#
host_sheet = reading_file("Host Information")
publicRep_sheet = reading_file("Public Repository Information")
array_sheet = [sample_sheet,host_sheet,isolate_sheet,sequence_sheet,publicRep_sheet,amr_sheet,risk_sheet]
#dict_terms_file={'sample':{},'host':{},'isolate':{},'sequence':{},'publicRep':{},'AMR':{},'risk':{}}
sample_id = ""
sample_flagged_list =[]
for index_sheet,sheet_from_array in enumerate(array_sheet):
if(not sheet_from_array.empty):
for index, row in sheet_from_array.iterrows():
for i in row.index:
if (row[i] != 0 and not isNaN(row[i]) and row[i] ):
key = i.strip()
key2 = key
print ("begin with",key2)
for abs in antimicrobian_agent_names_ids.keys():
if abs == "nalidixic acid":
abs = "nalidixic_acid"
if abs == "oxolinic acid":
abs = "oxolinic-acid"
if abs in key:
substrL= re.match(abs+"_(.+)",key)
#print (key)
key2 = "antimicrobial_"+substrL.groups()[0]
#print(key2)
#sys.exit()
if (key == 'AMR_laboratory_typing_method'):
key2 = "antimicrobial_laboratory_typing_method"
if (key == 'production_stream'):
key2 ="food_product_production_stream"
cell=""
if key2 in terms_accepting_multiple_values:
print(row[i],"ready to split")
cell_prov=row[i].split(";")
print(cell_prov)
cell=[]
for sub in cell_prov:
if isinstance(sub,str):
cell_sub=sub.strip()
cell.append(cell_sub)
else:
cell = row[i]
if isinstance(cell,str):
cell=cell.strip()
print("Here_",cell)
if key2 == "sample_collector_sample_ID" :
sample_id = cell
if key2 in ontology_terms_and_values.keys():
print("Here", key2)
if "terms" in ontology_terms_and_values[key2].keys():
if key2 in terms_accepting_multiple_values:
for index,cell_sub in enumerate(cell):
flag = 0;
pseudoid=""
if(":" in cell_sub and "[" not in cell_sub):
wanted = cell_sub.split(":")
cell_sub = wanted[0]
pseudoid = wanted[1]
# print(ontology_terms_and_values[key]["terms"])
for item in ontology_terms_and_values[key2]["terms"]:
print(item)
if type(item) != dict:
if cell_sub == item:
flag+=1;
else:
for keyI in item.keys():
#print(type(keyI))
if cell_sub in keyI:
# print(cell,keyI)
flag+=1;
cell[index]= item[keyI]["term"]+"//"+item[keyI]["term_id"]
#print("added //",cell)
#sys.exit()
if flag == 0:
#print("diferent term: ",cell," with id: ",pseudoid," in field:",key)
if sample_id not in sample_flagged_list:
sample_flagged_list.append(sample_id)
if ( cell_sub in terms_to_fix.keys()):
if (key in terms_to_fix[cell].keys()):
terms_to_fix[cell_sub][key] += 1
else:
terms_to_fix[cell_sub] = {}
terms_to_fix[cell_sub] [key] = 1
##Provisory adding terms to the ontology_terms
new_ont_terms[key]['terms'].append({cell_sub+"//"+pseudoid:{'term': cell, 'term_id': pseudoid}})
#print(cell,ontology_terms_and_values[key])
cell[index]= cell_sub+"//"+pseudoid
else:
flag = 0;
pseudoid=""
if(":" in cell and "[" not in cell):
wanted = cell.split(":")
cell = wanted[0]
pseudoid = wanted[1]
# print(ontology_terms_and_values[key]["terms"])
for item in ontology_terms_and_values[key2]["terms"]:
#print(item.keys())
if type(item) != dict:
if cell == item:
flag+=1;
else:
for keyI in item.keys():
#print(type(keyI))
if cell in keyI:
# print(cell,keyI)
flag+=1;
cell= item[keyI]["term"]+"//"+item[keyI]["term_id"]
#print("added //",cell)
#sys.exit()
if flag == 0:
if sample_id not in sample_flagged_list:
sample_flagged_list.append(sample_id)
#print("diferent term: ",cell," with id: ",pseudoid," in field:",key)
if ( cell in terms_to_fix.keys()):
if (key in terms_to_fix[cell].keys()):
terms_to_fix[cell][key] += 1
else:
terms_to_fix[cell] = {}
terms_to_fix[cell] [key] = 1
##Provisory adding terms to the ontology_terms
new_ont_terms[key]['terms'].append({cell+"//"+pseudoid:{'term': cell, 'term_id': pseudoid}})
#print(cell,ontology_terms_and_values[key])
cell= cell+"//"+pseudoid
if 'date' in key:
last_part_of_key = key.split("_")[-1]
if "date" in last_part_of_key:
#print (type(cell))
print(cell,"before if")
currentDateWithoutTime = ""
if ("/" in cell):
print("has /",cell)
date_obj = datetime.datetime.strptime(cell, "%d/%m/%Y")
currentDateWithoutTime = date_obj.strftime("%Y-%m-%d")
elif("-" in cell):
hyphen_count = cell.count("-")
if hyphen_count == 1:
datetime_object = datetime.datetime.strptime(cell, '%Y-%m')
currentDateWithoutTime = datetime_object.strftime('%Y-%m')
elif hyphen_count == 2:
datetime_object = datetime.datetime.strptime(cell, '%Y-%m-%d')
currentDateWithoutTime = datetime_object.strftime('%Y-%m-%d')
else:
print("int",cell)
int_value = int(cell)
currentDateWithoutTime = datetime.date(int_value, 1, 1)
cell = currentDateWithoutTime
#print('after',cell)
print ("temp_creating",key,cell)
temp_dict[key]=cell
#checking duplications
flag_dup =0
if index_sheet == 0:
# print ("checando...")
for index2 in dict_terms_file['sample']:
# print (index2,dict_terms_file['sample'][index2])
# print(temp_dict)
if dict_terms_file['sample'][index2]['sample_collector_sample_ID'] == temp_dict['sample_collector_sample_ID']:
print ("sample table duplicated:","in row:",index2,"term:",dict_terms_file['sample'][index2]['sample_collector_sample_ID']," and ","in row:",index,"term:",temp_dict['sample_collector_sample_ID'])
flag_dup =1
# print("come on:",flag_dup)
if (flag_dup == 0 ):
# print ("chegou aqui")
dict_terms_file['sample'][index]=temp_dict
elif index_sheet == 1:
for index2 in dict_terms_file['host']:
# print (index2,dict_terms_file['sample'][index2])
# print(temp_dict)
if dict_terms_file['host'][index2]['sample_collector_sample_ID'] == temp_dict['sample_collector_sample_ID']:
print ("host table duplicated:","in row:",index2,"term:",dict_terms_file['host'][index2]['sample_collector_sample_ID']," and ","in row:",index,"term:",temp_dict['sample_collector_sample_ID'])
flag_dup =1
# print("come on:",flag_dup)
if (flag_dup == 0 ):
# print ("chegou aqui")
dict_terms_file['host'][index]=temp_dict
elif index_sheet == 2:
for index2 in dict_terms_file['isolate']:
if dict_terms_file['isolate'][index2]['isolate_ID'] == temp_dict['isolate_ID']:
print ("isolate table duplicated:","in row:",index2,"term:",dict_terms_file['isolate'][index2]['isolate_ID']," and ","in row:",index,"term:",temp_dict['isolate_ID'])
flag_dup =1
if (flag_dup == 0 ):
dict_terms_file['isolate'][index]=temp_dict
elif index_sheet == 3:
subflag_dup =0
index_save = "y"
for index2 in dict_terms_file['sequence']:
if dict_terms_file['sequence'][index2]['isolate_ID'] == temp_dict['isolate_ID'] :
for keys_temp in temp_dict:
if temp_dict[keys_temp] != dict_terms_file['sequence'][index2][keys_temp]:
subflag_dup = 1
else:
flag_dup = 1
index_save = index2
if subflag_dup == 1:
flag_dup =0
else:
if (index_save != "y"):
print ("sequence table duplication:","in row:",index_save,"term:",dict_terms_file['sequence'][index_save]['isolate_ID']," and ","in row:",index,"term:",temp_dict['isolate_ID'])
if flag_dup ==0:
dict_terms_file['sequence'][index]=temp_dict
elif index_sheet == 4:
subflag_dup =0
index_save = "y"
for index2 in dict_terms_file['publicRep']:
if dict_terms_file['publicRep'][index2]['isolate_ID'] == temp_dict['isolate_ID'] :
for keys_temp in temp_dict:
if temp_dict[keys_temp] != dict_terms_file['publicRep'][index2][keys_temp]:
subflag_dup = 1
else:
flag_dup = 1
index_save = index2
if subflag_dup == 1:
flag_dup =0
else:
if (index_save != "y"):
print ("public rep table duplication:","in row:",index_save,"term:",dict_terms_file['publicRep'][index_save]['isolate_ID']," and ","in row:",index,"term:",temp_dict['isolate_ID'])
if flag_dup ==0:
dict_terms_file['publicRep'][index]=temp_dict
elif index_sheet == 5:
subflag_dup =0
index_save = "y"
for index2 in dict_terms_file['AMR']:
if dict_terms_file['AMR'][index2]['isolate_ID'] == temp_dict['isolate_ID']:
for keys_temp in temp_dict:
if temp_dict[keys_temp] != dict_terms_file['AMR'][index2][keys_temp]:
subflag_dup = 1
else:
flag_dup = 1
index_save = index2
if subflag_dup == 1:
flag_dup =0
else:
if (index_save != "y"):
print ("AMR table duplication:","in row:",index_save,"term:",dict_terms_file['AMR'][index_save]['isolate_ID']," and ","in row:",index,"term:",temp_dict['isolate_ID'])
if flag_dup ==0:
dict_terms_file['AMR'][index]=temp_dict
elif index_sheet == 6:
subflag_dup =0
index_save = "y"
for index2 in dict_terms_file['risk']:
if dict_terms_file['risk'][index2]['isolate_ID'] == temp_dict['isolate_ID'] :
for keys_temp in temp_dict:
if temp_dict[keys_temp] != dict_terms_file['risk'][index2][keys_temp]:
subflag_dup = 1
else:
flag_dup = 1
index_save = index2
if subflag_dup == 1:
flag_dup =0
else:
if (index_save != "y"):
print ("Risk table duplication:","in row:",index_save,"term:",dict_terms_file['risk'][index_save]['isolate_ID']," and ","in row:",index,"term:",temp_dict['isolate_ID'])
if flag_dup ==0:
dict_terms_file['risk'][index]=temp_dict
print(temp_dict)
temp_dict ={}
#print(dict_terms_file)
#sys.exit()
else:
temp_dict={}
#print("here")
#sys.exit()
array_sheet = [sample_sheet,isolate_sheet,sequence_sheet,amr_sheet,risk_sheet]
#print (ontology_terms_and_values)
# sys.exit()
#={'sample':{},'host':{},'isolate':{},'sequence':{},'publicRep':{},'AMR':{},'risk':{}}
#dict_terms_file={'sample':{},'isolate':{},'sequence':{},'AMR':{},'risk':{}}
sample_id = ""
sample_flagged_list =[]
for index_sheet,sheet_from_array in enumerate(array_sheet):
if(not sheet_from_array.empty):
for index, row in sheet_from_array.iterrows():
#print(index, "number row")
#print(row.index)
#sys.exit()
for i in row.index:
if (row[i] != 0 and not isNaN(row[i]) and row[i] ):
key = i.strip()
if ("geo_loc (country)" in key):
key = "geo_loc_name (country)"
if ("geo_loc (state/province/region)" in key):
key = "geo_loc_name (state/province/region)"
if ("sample_processing" in key):
key = "specimen_processing"
key2 = key
for abs in antimicrobian_agent_names_ids.keys():
if abs == "nalidixic acid":
abs = "nalidixic_acid"
if abs == "oxolinic acid":
abs = "oxolinic-acid"
if abs in key:
substrL= re.match(abs+"_(.+)",key)
#print (key)
key2 = "antimicrobial_"+substrL.groups()[0]
#print(key2)
#sys.exit()
if (key == 'AMR_laboratory_typing_method'):
key2 = "antimicrobial_laboratory_typing_method"
if (key == 'production_stream'):
key2 ="food_product_production_stream"
cell=""
#print("debugging_here")
#print (key,row[i])
if key2 in terms_accepting_multiple_values:
cell_prov=row[i].split(";")
# print(cell_prov)
cell=[]
for sub in cell_prov:
if isinstance(sub,str):
cell_sub=sub.strip()
cell.append(cell_sub)
else:
cell = row[i]
if isinstance(cell,str):
cell=cell.strip()
#print(cell,"here")
flag_to_discard = 0
#print (ontology_terms_and_values)
#sys.exit()
if key2 == "sample_collector_sample_ID" :
sample_id = cell
if key2 in ontology_terms_and_values.keys():
if "terms" in ontology_terms_and_values[key2].keys():
if key2 in terms_accepting_multiple_values:
for index3,cell_sub in enumerate(cell):
flag = 0;
pseudoid=""
if(":" in cell_sub and "[" not in cell_sub):
wanted = cell_sub.split(":")
cell_sub = wanted[0]
pseudoid = wanted[1]
# print(ontology_terms_and_values[key]["terms"])
for item in ontology_terms_and_values[key2]["terms"]:
#print(item.keys())
if type(item) != dict:
if cell_sub == item:
flag+=1;
else:
for keyI in item.keys():
#print(type(keyI))
if cell_sub in keyI:
# print(cell,keyI)
flag+=1;
# print(item[keyI])
cell[index3]=item[keyI]["term"]+"//"+item[keyI]["term_id"]
#print("added //",cell)
#sys.exit()
if flag == 0:
flag2 = 0
if flag2 == 0:
flag_to_discard += 1
if ( cell_sub in terms_to_fix.keys()):
if (key in terms_to_fix[cell_sub].keys()):
terms_to_fix[cell_sub][key] += 1
if sample_id not in sample_flagged_list:
sample_flagged_list.append(sample_id)
else:
terms_to_fix[cell_sub] = {}
terms_to_fix[cell_sub] [key] = 1
if sample_id not in sample_flagged_list:
sample_flagged_list.append(sample_id)
##Provisory adding terms to the ontology_terms
new_ont_terms[key2]['terms'].append({cell_sub+"//"+pseudoid:{'term': cell_sub, 'term_id': pseudoid}})
#print(cell,ontology_terms_and_values[key])
cell[index3]=cell_sub+"//"+pseudoid
else:
flag = 0;
pseudoid=""
if(":" in cell and "[" not in cell):
wanted = cell.split(":")
cell = wanted[0]
pseudoid = wanted[1]
# print(ontology_terms_and_values[key]["terms"])
for item in ontology_terms_and_values[key2]["terms"]:
#print(item.keys())
if type(item) != dict:
if cell == item:
flag+=1;
else:
for keyI in item.keys():
#print(type(keyI))
if cell in keyI:
# print(cell,keyI)
flag+=1;
# print(item[keyI])
cell= item[keyI]["term"]+"//"+item[keyI]["term_id"]
#print("added //",cell)
#sys.exit()
if flag == 0:
flag2 = 0
if flag2 == 0:
flag_to_discard += 1
if ( cell in terms_to_fix.keys()):
if (key in terms_to_fix[cell].keys()):
terms_to_fix[cell][key] += 1
if sample_id not in sample_flagged_list:
sample_flagged_list.append(sample_id)
else:
terms_to_fix[cell] = {}
terms_to_fix[cell] [key] = 1
if sample_id not in sample_flagged_list:
sample_flagged_list.append(sample_id)
##Provisory adding terms to the ontology_terms
new_ont_terms[key2]['terms'].append({cell+"//"+pseudoid:{'term': cell, 'term_id': pseudoid}})
#print(cell,ontology_terms_and_values[key])
cell= cell+"//"+pseudoid
if 'date' in key:
#print (type(cell))
# print(cell, "here?")
if 'precision' not in key:
#print (cell)
currentDateWithoutTime = cell.strftime('%Y-%m-%d')
# print(cell)
cell = currentDateWithoutTime
#print('after',cell)
if flag_to_discard == 0:
# print(cell)
temp_dict[key]=cell
#keeping also terms not in the voc.
else:
temp_dict[key]=cell
#checking duplications
flag_dup =0
if index_sheet == 0:
# print ("checando...")
for index2 in dict_terms_file['sample']:
# print (index2,dict_terms_file['sample'][index2])
# print(temp_dict)
if dict_terms_file['sample'][index2]['sample_collector_sample_ID'] == temp_dict['sample_collector_sample_ID']:
print ("sample table duplicated:","in row:",index2,"term:",dict_terms_file['sample'][index2]['sample_collector_sample_ID']," and ","in row:",index,"term:",temp_dict['sample_collector_sample_ID'])
flag_dup =1
# print("come on:",flag_dup)
if (flag_dup == 0 ):
#print ("chegou aqui",index)
dict_terms_file['sample'][index]=temp_dict
dict_terms_file['host'][index]=temp_dict
elif index_sheet == 1:
for index2 in dict_terms_file['isolate']:
if dict_terms_file['isolate'][index2]['isolate_ID'] == temp_dict['isolate_ID']:
print ("isolate table duplicated:","in row:",index2,"term:",dict_terms_file['isolate'][index2]['isolate_ID']," and ","in row:",index,"term:",temp_dict['isolate_ID'])
flag_dup =1
if (flag_dup == 0 ):
dict_terms_file['isolate'][index]=temp_dict
elif index_sheet == 2:
subflag_dup =0
index_save = "y"
for index2 in dict_terms_file['sequence']:
if dict_terms_file['sequence'][index2]['isolate_ID'] == temp_dict['isolate_ID'] :
for keys_temp in temp_dict:
if temp_dict[keys_temp] != dict_terms_file['sequence'][index2][keys_temp]:
subflag_dup = 1
else:
flag_dup = 1
index_save = index2
if subflag_dup == 1:
flag_dup =0
else:
if (index_save != "y"):
print ("sequence table duplication:","in row:",index_save,"term:",dict_terms_file['sequence'][index_save]['isolate_ID']," and ","in row:",index,"term:",temp_dict['isolate_ID'])
if flag_dup ==0:
dict_terms_file['sequence'][index]=temp_dict
dict_terms_file['publicRep'][index]=temp_dict
elif index_sheet == 3:
subflag_dup =0
index_save = "y"
for index2 in dict_terms_file['AMR']:
if dict_terms_file['AMR'][index2]['isolate_ID'] == temp_dict['isolate_ID']:
for keys_temp in temp_dict:
if temp_dict[keys_temp] != dict_terms_file['AMR'][index2][keys_temp]:
subflag_dup = 1
else:
flag_dup = 1
index_save = index2
if subflag_dup == 1:
flag_dup =0
else:
if (index_save != "y"):
print ("AMR table duplication:","in row:",index_save,"term:",dict_terms_file['AMR'][index_save]['isolate_ID']," and ","in row:",index,"term:",temp_dict['isolate_ID'])
if flag_dup ==0:
dict_terms_file['AMR'][index]=temp_dict
elif index_sheet == 4:
subflag_dup =0
index_save = "y"
for index2 in dict_terms_file['risk']:
if dict_terms_file['risk'][index2]['sample_collector_sample_ID'] == temp_dict['sample_collector_sample_ID'] :
for keys_temp in temp_dict:
if temp_dict[keys_temp] != dict_terms_file['risk'][index2][keys_temp]:
subflag_dup = 1
else:
flag_dup = 1
index_save = index2
if subflag_dup == 1:
flag_dup =0
else:
if (index_save != "y"):
print ("Risk table duplication:","in row:",index_save,"term:",dict_terms_file['risk'][index_save]['sample_collector_sample_ID']," and ","in row:",index,"term:",temp_dict['sample_collector_sample_ID'])
if flag_dup ==0:
dict_terms_file['risk'][index]=temp_dict
#if(dict_terms_file['AMR']):
# print (dict_terms_file)
# sys.exit()
temp_dict ={}
countEvents =0
if terms_to_fix:
for termE in terms_to_fix:
for fieldE in terms_to_fix[termE]:
print ("The term:",termE," in the field:",fieldE," is different from the vocabulary and appears ",terms_to_fix[termE][fieldE]," times")
countEvents+=1
print("A total of terms different from the vocabulary:",countEvents)
print('done dict of terms')
#print(dict_terms_file)
#sys.exit()
#print(dict_terms_file['sample'])
#sys.exit()
return(dict_terms_file,new_ont_terms,terms_accepting_multiple_values,sample_flagged_list)