def add_prices(csvtext, drug_dict):
# adds prices from a CSV file (the date is the str csvtext arg) to each drug in a given drug dictionary.
# for drugs in the dictionary but not in the file, the function adds None as the price.
# this function passes on drugs in the CSV but not in the drug_dict.
date = csvtext[-8:]
count = 1
headers = which_headers(date)
drug_list = [drug for drug in drug_dict]
with open(csvtext+".csv", "r") as drugcsv:
drugreader = csv.reader(drugcsv)
for line in drugreader:
if count < 5:
pass
else:
drug = {}
for i in range(len(headers)):
drug[headers[i]] = line[i]
price = drug["Price"]
if drug["NDC"] in drug_dict:
Drug.add_price(drug_dict[drug["NDC"]], date, price)
drug_list.remove(drug["NDC"])
else:
pass
count += 1
drugcsv.close()
for drug in drug_list:
Drug.add_price(drug_dict[drug], date, None)
return drug_dict
def builder(csvtext):
# The function that takes a given CSV filename/date and creates a dictionary of drugs.
# Their key is the drug NDC, and their value is the Drug object.
date = csvtext[-8:]
drug_dict = {}
count = 1
headers = which_headers(date)
with open(csvtext+".csv", "r") as drugcsv:
drugreader = csv.reader(drugcsv)
for line in drugreader:
if count < 5:
pass
else:
drug = {}
for i in range(len(headers)):
drug[headers[i]] = line[i]
price = drug["Price"]
this_drug = Drug(drug["Name"], drug["NDC"], drug["Pricing Unit"],
drug["OTC or Not"], drug["Brand or Generic"], "NADAC")
Drug.add_price(this_drug, date, price)
drug_dict[drug["NDC"]] = this_drug
count += 1
drugcsv.close()
return drug_dict
def mine_drug_register():
drugs = []
print("Fetching drug data...")
response = requests.get(DRUG_REGISTER_URL)
print("Done.")
if not response.ok:
print("Failed to fetch data.")
return
print("Setting up data...")
drug_register_html = response.content
drug_register = BeautifulSoup(drug_register_html, 'html.parser')
for line_break in drug_register.find_all('br'):
line_break.extract()
data_table = drug_register.find(id="tablepress-42").tbody
rows = data_table.find_all('tr')
print("Done.")
print("Parsing...")
for row in rows:
data = [str(item.string) for item in row.find_all('td')]
drug = Drug(*data)
drugs.append(drug)
print("Done.")
print("Writing to file...")
drug_data = '\n'.join([drug.to_csv() for drug in drugs])
headers = "identifier, nda_reg_number, license_holder, local_technical_rep, name_of_drug, manufacturer, country_of_manufacture, dosage_form, pack_size"
drug_data = headers + "\n" + drug_data
with open("data/drugs.csv", 'w') as file:
file.write(drug_data)
print("Done.")
print("Complete!")
print("\n")
def update(csvtext, drug_dict):
# accesses a one-date CSV file (date given as str csvtext) and adds prices for drugs in the given drug dictionary.
# if a drug is not in the drug dict, this function adds the drug and its info to the dictionary.
date = csvtext[-8:]
count = 1
headers = which_headers(date)
with open(csvtext+".csv", "r") as drugcsv:
drugreader = csv.reader(drugcsv)
for line in drugreader:
if count < 5:
pass
else:
drug = {}
for i in range(len(headers)):
drug[headers[i]] = line[i]
price = drug["Price"]
if drug["NDC"] in drug_dict:
Drug.add_price(drug_dict[drug["NDC"]], date, price)
else:
if int(date) < 20130215:
drug["Pricing Unit"] = "Unknown"
drug["Brand or Generic"] = "Unknown"
this_drug = Drug(drug["Name"], drug["NDC"], drug["Pricing Unit"],
drug["OTC or Not"], drug["Brand or Generic"], "NADAC")
Drug.add_price(this_drug, date, price)
drug_dict[drug["NDC"]] = this_drug
count += 1
drugcsv.close()
return drug_dict
def get_desired_data(filename):
with open(filename, encoding="utf-8") as f:
parser = BeautifulSoup(f.read(), "html.parser")
drug = parser.find("drug")
if drug:
id = drug.find("drugbank-id")
# Gradaully setting Drug db object...
new_drug = Drug(id=(id.string or ""))
name = drug.find("name")
# setting up drug db object
new_drug.name = name.string or ""
groups_wrapper = drug.find("groups")
if groups_wrapper is not None:
groups = groups_wrapper.find_all("group")
gp_str = ""
for group in groups:
gp_str += (group.string or "")
# setting up drug db object
new_drug.group = gp_str
toxicity = drug.find("toxicity")
if toxicity:
# setting up drug db object
new_drug.toxicity = (toxicity.string or "")
db.session.add(new_drug)
external_identifiers_wr = drug.find("external-identifiers")
if external_identifiers_wr:
external_identifiers = external_identifiers_wr.find_all("external-identifier")
for ext_id in external_identifiers:
resource = (ext_id.find("resource").string or "")
identifier = (ext_id.find("identifier").string or "")
# setting up ExternalIdentifier db object
new_external_identifier = ExternalIdentifier(resource=resource, name=identifier, drug_id=new_drug.id)
db.session.add(new_external_identifier)
food_interactions_wrapper = drug.find("food-interactions")
if food_interactions_wrapper:
food_interactions = food_interactions_wrapper.find_all("food-interaction")
for food_int in food_interactions:
food_interaction_description = (food_int.string or "")
# Setting up FoodInteraction db object
new_food_interaction = FoodInteraction(drug_id=new_drug.id, description=food_interaction_description)
db.session.add(new_food_interaction)
# Commit all changes to DB!
db.session.commit()
def create_network():
p = create_test_protein()
cancer = Cancer(name='Ovarian', code='OV')
known_interactor_of_x = create_test_kinase('Kinase Y', 'NM_0009')
kinase_mutation = Mutation(position=1,
alt='T',
meta_MC3=[MC3Mutation(cancer=cancer)])
known_interactor_of_x.protein.mutations = [kinase_mutation]
drug = Drug(
name='Drug targeting ' + known_interactor_of_x.name,
drug_bank_id='DB01',
target_genes=[known_interactor_of_x.protein.gene],
# by default only approved drugs are shown
groups={DrugGroup(name='approved')})
group = KinaseGroup(name='Group of kinases', )
s = Site(position=1,
type='phosphorylation',
residue='T',
kinases=[known_interactor_of_x],
kinase_groups=[group])
s2 = Site(position=2,
type='phosphorylation',
residue='R',
kinase_groups=[group])
p.sites = [s, s2]
predicted_interactor = create_test_kinase('Kinase Z', 'NM_0002')
protein_mutation = Mutation(position=2,
alt='T',
meta_MC3=[MC3Mutation(cancer=cancer)],
meta_MIMP=[
MIMPMutation(
pwm=known_interactor_of_x.name,
effect='loss',
site=s,
probability=0.1,
position_in_motif=1),
MIMPMutation(pwm=predicted_interactor.name,
effect='gain',
site=s,
probability=0.1,
position_in_motif=1)
])
p.mutations = [protein_mutation]
db.session.add_all([p, drug, predicted_interactor])
db.session.commit()
# a new cancer was added, reload is necessary (this should not happen during normal app usage)
from website.views.filters import cached_queries
cached_queries.reload()
def addStock(drugNum):
# 判断用户是否登录
user_id = session.get('user_id')
if user_id:
user = User.query.filter(User.id == user_id).first()
if user:
# 判断是否是POST
if request.method == 'GET':
drug = Drug.query.filter(Drug.num == drugNum).first()
return render_template('addStock.html', drug=drug)
else:
num = request.form.get('num')
name = request.form.get('name')
type = request.form.get('type')
count = request.form.get('count')
price = request.form.get('price')
desc = request.form.get('desc')
try:
count = int(count)
except Exception:
raise ValueError('count value is error!')
# 查找数据库类别表
drugType = DrugType.query.filter(DrugType.name == type).first()
if drugType:
drugTypeId = drugType.id
for index in range(0, count):
drug = Drug(num=num,
name=name,
desc=desc,
stockPrice=price,
drugTypeId=drugTypeId)
drug.drugType = drugType
db.session.add(drug)
db.session.flush() # 主要是这里，写入数据库，但是不提交
db.session.commit()
return redirect(url_for('addStockHome'))
return redirect(url_for('login'))
def addDrug():
# 判断用户是否登录
user_id = session.get('user_id')
if user_id:
user = User.query.filter(User.id == user_id).first()
if user:
if request.method == 'GET':
return render_template('addDrug.html')
else:
# 当前时间
nowDate = time.strftime("%Y-%m-%d %H:%M:%S", time.localtime())
num = request.form.get('num')
name = request.form.get('name')
type = request.form.get('type')
count = request.form.get('count')
price = request.form.get('price')
desc = request.form.get('desc')
try:
count = int(count)
except Exception:
raise ValueError('count value is error!')
# 查找数据库类别表
drugType = DrugType.query.filter(DrugType.name == type).first()
if drugType:
drugTypeId = drugType.id
for index in range(0, count):
drug = Drug(num=num,
name=name,
desc=desc,
stockDate=nowDate,
stockPrice=price,
drugTypeId=drugTypeId)
drug.drugType = drugType
db.session.add(drug)
db.session.flush() # 主要是这里，写入数据库，但是不提交
else:
drugType = DrugType(name=type)
db.session.add(drugType)
db.session.commit()
drugTypeId = drugType.id
for index in range(0, count):
drug = Drug(num=num,
name=name,
desc=desc,
stockDate=nowDate,
stockPrice=price,
drugTypeId=drugTypeId)
drug.drugType = drugType
db.session.add(drug)
db.session.flush() # 主要是这里，写入数据库，但是不提交
db.session.commit()
return redirect(url_for('home'))
return redirect(url_for('login'))
def create_tables():
db.create_all()
for a in drug_classes.keys():
new_drug_class = Drugclass(name=a,
beers_criteria=drug_classes[a][0],
stopp_start_criteria=drug_classes[a][1])
try:
db.session.add(new_drug_class)
db.session.commit()
except:
pass
for a in medications.keys():
new_med = Drug(name=a,
beers_criteria=medications[a][0],
stopp_start_criteria=medications[a][1],
drug_class_id=medications[a][2])
try:
db.session.add(new_med)
db.session.commit()
except:
pass
def add_FDA_info(drug_dict):
# this function supplies drug and vendor names via NDCs from the FDA's official database.
# sadly the FDA and NADAC have a slightly different format for NDCs, so it's not perfect.
# It is very unlikely to assign an incorrect NDC -- rather, it will pass on drugs it cannot find a match for.
name_file = "FDA-20160118.csv"
headers = ["PRODUCTID", "PRODUCTNDC", "PRODUCTTYPENAME", "PROPRIETARYNAME", "PROPRIETARYNAMESUFFIX",
"NONPROPRIETARYNAME", "DOSAGEFORMNAME", "ROUTENAME", "STARTMARKETINGDATE", "ENDMARKETINGDATE",
"MARKETINGCATEGORYNAME", "APPLICATIONNUMBER", "LABELERNAME", "SUBSTANCENAME",
"ACTIVE_NUMERATOR_STRENGTH", "ACTIVE_INGRED_UNIT", "PHARM_CLASSES", "DEASCHEDULE"]
count = 1
current_list = [key for key in drug_dict]
with open(name_file, "r") as namecsv:
csvreader = csv.reader(namecsv)
for line in csvreader:
if count == 1:
pass
else:
drug = {}
for i in range(len(headers)):
if headers [i] == "PRODUCTNDC":
drug["NDC"] = line[i].translate(None,"-")
templist = line[i].split("-")
templist[0] = templist[0] + "0"
drug["NDC2"] = "".join(templist)
else:
drug[headers[i]] = line[i]
findings = [item for item in current_list if ( drug["NDC"] in item ) or ( drug["NDC2"] in item )]
if len(findings) == 1:
this_drug = drug_dict[findings[0]]
Drug.add_vendor(this_drug, drug["LABELERNAME"])
Drug.add_sci_name(this_drug, drug["NONPROPRIETARYNAME"])
Drug.add_desc(this_drug, drug["PHARM_CLASSES"])
current_list.remove(findings[0])
print "%i drugs left to ID..." % len(current_list)
elif len(findings) == 0:
pass
else:
findings_as_drugs = [drug_dict[key] for key in findings] #converts list of keys into list of Drugs
findings = multiple_results(drug, findings_as_drugs) #list of Drugs
for finding in findings: #finding is a Drug
Drug.add_vendor(finding, drug["LABELERNAME"])
Drug.add_sci_name(finding, drug["NONPROPRIETARYNAME"])
Drug.add_desc(finding, drug["PHARM_CLASSES"])
current_list.remove(finding.id)
print "%i drugs left to ID..." % len(current_list)
# BECAUSE THE FDA NDCS ARE ONLY EIGHT DIGITS LONG, THIS SEARCH OFTEN RETURNS 2+ RESULTS.
# TODO: write a function to check other info to figure out which is the correct one.
# or, worst-case scenario, prompt user to choose which looks right, maybe?
count += 1
return drug_dict
def addDrug():
# 判断用户是否登录
user_id = session.get('user_id')
if user_id:
user = User.query.filter(User.id == user_id).first()
if user:
if request.method == 'GET':
return render_template('addDrug.html')
else:
num = request.form.get('num')
name = request.form.get('name')
type = request.form.get('type')
count = request.form.get('count')
price = request.form.get('price')
desc = request.form.get('desc')
# 首先查找药品是否存在
drug = Drug.query.filter(Drug.num == num).first()
# 如果存在
if drug:
# 库存量增加
Drug.query.filter(Drug.id == drug.id).update(
{Drug.count: int(drug.count) + int(count)})
stock = Stock(stockPrice=price,
stockCount=count,
stockMoney=int(count) * float(price),
drugId=drug.id,
userId=user_id)
db.session.add(stock)
db.session.commit()
else:
# 判断类别
drugType = DrugType.query.filter(
DrugType.name == type).first()
# 存在
if drugType:
drug = Drug(num=num,
name=name,
count=count,
price=price,
desc=desc,
drugTypeId=drugType.id)
else:
drugType = DrugType(name=type)
db.session.add(drugType)
db.session.commit()
drugType = DrugType.query.filter(
DrugType.name == type).first()
drug = Drug(num=num,
name=name,
count=count,
price=price,
desc=desc,
drugTypeId=drugType.id)
db.session.add(drug)
db.session.commit()
drug = Drug.query.filter(Drug.num == num).first()
stock = Stock(stockPrice=price,
stockCount=count,
stockMoney=int(count) * float(price),
drugId=drug.id,
userId=user_id)
db.session.add(stock)
db.session.commit()
return redirect(url_for('home'))
return redirect(url_for('login'))
from app import app
from models import db, Drug, Pharmacy
db.drop_all()
db.create_all()
def create_drugs():
"""Function for creating drugs for database"""
drug_list = []
for num in range(232):
print(f'd{num} = (name="{TOP_200[num]}"", price={prices[num]})')
d0 = Drug(name="Lexapro", price=5)
d1 = Drug(name="Vicodin", price=65)
d2 = Drug(name="Prinivil", price=55)
d3 = Drug(name="Qbrelis", price=89)
d4 = Drug(name="Zocor", price=80)
d5 = Drug(name="Synthroid", price=7)
d6 = Drug(name="Amoxil", price=70)
d7 = Drug(name="Trimox", price=15)
d8 = Drug(name="Zithromax", price=69)
d9 = Drug(name="Microzide", price=8)
d10 = Drug(name="Aquazide", price=20)
d11 = Drug(name="Norvasc", price=66)
d12 = Drug(name="Xanax", price=43)
d13 = Drug(name="Glucophage", price=34)
d14 = Drug(name="Lipitor", price=22)
d15 = Drug(name="Prilosec", price=94)
d16 = Drug(name="Cipro", price=87)