我正在尝试从巴西健康数据存储库这里获取健康数据。我正在尝试获取 2018 年至 2024 年、每个性别(男/女)以及 22 个不同年龄组的每个月因焦虑/抑郁而去看医生的次数。我有 A/D 代码列表 (54),并且想分别查看每个代码的访问次数。我有一个数据框,其中每一行都是这些变量的组合(54 个代码 X 2 个性别 X 22 个年龄组 X 7 年):
combns = pd.read_csv("/.../data/Anxiety_Depression_combinations.csv")
code year sex codeType agelower ageupper
0 F32 2018 2 CID 0 200
1 F320 2018 2 CID 0 200
2 F321 2018 2 CID 0 200
3 F322 2018 2 CID 0 200
4 F323 2018 2 CID 0 200
... ... ... ... ... ... ...
16627 P01 2024 3 CIAP 100 200
16628 P02 2024 3 CIAP 100 200
16629 P74 2024 3 CIAP 100 200
16630 P79 2024 3 CIAP 100 200
16631 P82 2024 3 CIAP 100 200
16632 rows × 6 columns
对于数据框中的每一行,我更改设置,然后抓取生成的 html 表格并将其保存为 Excel 文件。我有这段代码可以在无头模式下打开网络浏览器,并选择一些常用设置:
url = "https://sisab.saude.gov.br/paginas/acessoRestrito/relatorio/federal/saude/RelSauProducao.xhtml"
DRIVER_PATH = '/home/kvemuri/.local/share/binman_chromedriver/linux64/128.0.6613.119/chromedriver'
options = webdriver.ChromeOptions()
options.add_argument("--headless=new")
driver = webdriver.Chrome(executable_path=DRIVER_PATH,options=options)
#driver.quit()
# Open browser and navigate to SISAB website.
#DRIVER_PATH = '/home/kvemuri/.local/share/binman_chromedriver/linux64/127.0.6533.119/chromedriver'
#driver = webdriver.Chrome(executable_path=DRIVER_PATH)
#url = "https://sisab.saude.gov.br/paginas/acessoRestrito/relatorio/federal/saude/RelSauProducao.xhtml"
driver.get(url)
# Set type of service - Individual
driver.find_element(By.ID,"tpProducao").send_keys('Atendimento Individual')
# Set column to month (Competencia)
driver.find_element(By.XPATH,'//*[@id="selectLinha"]/optgroup[1]/option[6]').click()
# Set Type of team
driver.find_element(By.XPATH,'//*[@id="filtroEquipeProf"]/div[1]').click()
driver.find_element(By.XPATH,'//*[@id="filtroEquipeProf"]/div[1]/ul/li[2]/a/label/input').click()
driver.find_element(By.XPATH,'//*[@id="filtroEquipeProf"]/div[1]/ul/li[5]/a/label/input').click()
driver.find_element(By.XPATH,'//*[@id="filtroEquipeProf"]/div[1]/ul/li[9]/a/label/input').click()
driver.find_element(By.XPATH,'//*[@id="filtroEquipeProf"]/div[1]').click()
# Set place of service
driver.find_element(By.XPATH,'//*[@id="filtrosLocalTipoEstabelecimento"]/div/button').click()
driver.find_element(By.XPATH,'//*[@id="filtrosLocalTipoEstabelecimento"]/div/ul/li[2]/a/label/input').click()
driver.find_element(By.XPATH,'//*[@id="filtrosLocalTipoEstabelecimento"]/div/button').click()
# Set type of service - Individual
driver.find_element(By.ID,"tpProducao").send_keys('Atendimento Individual')
# Set type of attendance - select all
driver.find_element(By.XPATH,'//*[@id="divTipoAtendimento"]/div/button/span').click()
driver.find_element(By.XPATH,'//*[@id="divTipoAtendimento"]/div/ul/li[1]/a/label').click()
driver.find_element(By.XPATH,'//*[@id="divTipoAtendimento"]/div/button/span').click()
# Set type of professional
driver.find_element(By.XPATH,'//*[@id="filtroEquipeProf"]/div[2]/button/span').click()
driver.find_element(By.XPATH,'//*[@id="filtroEquipeProf"]/div[2]/ul/li[12]/a/label').click()
driver.find_element(By.XPATH,'//*[@id="filtroEquipeProf"]/div[2]/ul/li[19]/a/label').click()
driver.find_element(By.XPATH,'//*[@id="filtroEquipeProf"]/div[2]/button/span').click()
# Select 'years' button for age
driver.find_element(By.XPATH,'//*[@id="tpIdade:2"]').click()
我有以下功能:
def createXpathPattern(code,codeType):
if codeType == 'CID':
codeXpath = '//*[@id="cid-{}-1"]'.format(code)
#code = code
else:
codeXpath = '//*[@id="cid-{}-4"]'.format(code)
def setDxCode(code, codeType):
if codeType == 'CID':
codeXpath = '//*[@id="cid-{}-1"]'.format(code)
#code = code
else:
codeXpath = '//*[@id="cid-{}-4"]'.format(code)
#codeXpath = '//*[@id="cid-{}"]'.format(code)
#codeXpath = createXpathPattern(code = code, codeType = codeType)
driver.find_element(By.ID,"btnAddCid").click()
time.sleep(1)
searchBox = driver.find_element(By.XPATH,'//*[@id="dtBasicExample_filter"]/label/input')
searchBox.clear()
searchBox.send_keys(code)
#time.sleep(1)
driver.find_element(By.XPATH,codeXpath).click()
searchBox.clear()
#time.sleep(1)
driver.find_element(By.XPATH,'//*[@id="modal-default-cid"]/div/div/div[2]/button[2]/span').click()
# function to set age group and sex
def setAgeLimit(agelower, ageupper):
"""Selects the upper and lower age limit in years, and the sex for which data is to be output"""
#Set lower age limit
agelim1 = driver.find_element(By.XPATH,'//*[@id="idadeInicio"]')
agelim1.clear()
agelim1.send_keys(str(agelower))
#Set uper age limit
agelim2 = driver.find_element(By.XPATH,'//*[@id="idadeFim"]')
agelim2.clear()
agelim2.send_keys(str(ageupper))
def setSex(sex = 1):
# Set Sex
sexXpath = '//*[@id="filtrosCaracteristicaUsuario"]/div/ul/li[{}]/a/label'.format(sex)
driver.find_element(By.XPATH,'//*[@id="filtrosCaracteristicaUsuario"]/div/button/span').click() #//*[@id="filtrosCaracteristicaUsuario"]/div/button
driver.find_element(By.XPATH,sexXpath).click() # //*[@id="filtrosCaracteristicaUsuario"]/div/ul/li[2]/a/label/input
driver.find_element(By.XPATH,'//*[@id="filtrosCaracteristicaUsuario"]/div/button/span').click()
# Get list of all months in the months column in the webpage
monthBoxes = driver.find_elements(By.CSS_SELECTOR,"#competencia > div > ul > li > a> label > input")
yearMonth = []
for i in range(len(monthBoxes)):
yearMonth.append(monthBoxes[i].get_attribute("value"))
def getMonthsforYear(year):
year = str(year)
boolMonth = [year in i for i in yearMonth]
return(list(compress(yearMonth,boolMonth)))
def ClickMonthCheckbox(monthsList):
driver.find_element(By.XPATH,'//*[@id="competencia"]/div/button/span').click()
for month in monthsList:
monthIdx = str(yearMonth.index(month) + 1)
monthxpath = '//*[@id="competencia"]/div/ul/li[{}]/a/label/input'.format(monthIdx)
driver.find_element(By.XPATH,monthxpath).click()
def SelectAllMonthsInaYear(year):
TmpMonthsList = getMonthsforYear(year)
ClickMonthCheckbox(TmpMonthsList)
driver.find_element(By.XPATH,'//*[@id="competencia"]/div/button/span').click()
def checkboxIsSelected(monthsList):
driver.find_element(By.XPATH,'//*[@id="competencia"]/div/button/span').click()
for month in monthsList:
monthIdx = str(yearMonth.index(month) + 1)
monthxpath = '//*[@id="competencia"]/div/ul/li[{}]/a/label/input'.format(monthIdx)
checkbox = driver.find_element(By.XPATH,monthxpath)
print(checkbox.is_selected())
def checkboxYearIsSelected(year):
driver.find_element(By.XPATH,'//*[@id="competencia"]/div/button/span').click()
TmpMonthsList = getMonthsforYear(year)
checkboxIsSelected(TmpMonthsList)
driver.find_element(By.XPATH,'//*[@id="competencia"]/div/button/span').click()
def getHTMLtable():
driver.find_element(By.XPATH,'//*[@id="j_idt44"]/div[3]/div[1]/div/div[2]/div[2]/div[5]/div/div/div[1]/label').click() # Click on submit button
driver.find_element(By.XPATH,'//*[@id="tabela_length"]/label/select').send_keys('100') # Set number of rows in table to 100
t = driver.find_element(By.XPATH,'//*[@id="tabela"]').get_attribute('outerHTML') # //*[@id="tabela"]/tbody
table = pd.read_html(t,thousands ='.')
table_dt = pd.concat(table)
#table_dt['sex'] = 'Female'
#table_dt['agelower'] = 5
#table_dt['ageupper'] = 9
return(table_dt)
def SetParametersAndGetTable(agemin,agemax,sex,year, code, codeType):
if sex == 1:
sexL = "Both sexes"
elif sex == 2:
sexL = "Males"
else:
sexL = "Females"
dlCode = code + "." + str(year) + "." + sexL + "." + str(agemin) + "." + str(agemax)
setAgeLimit(agelower = agemin,ageupper = agemax)
SelectAllMonthsInaYear(year)
setSex(sex = sex)
setDxCode(code = code, codeType = codeType)
time.sleep(1)
try:
table_dt = getHTMLtable()
table_dt['code'] = code
table_dt['sex'] = sexL
table_dt['agelower'] = agemin
table_dt['ageupper'] = agemax
table_dt = table_dt[['code','sex', 'agelower', 'ageupper','Competência','Atendimento Individual']]
table_dt.rename(columns = {'Competência':"YearMonth",'Atendimento Individual':"individual.visits",
'code':'code','sex':"sex",'agelower':"agelower",'ageupper':"ageupper"},inplace= True)
table_dt['YearMonth'] = pd.to_datetime(table_dt['YearMonth'], format = "%Y%m").dt.strftime('%Y-%m')
setDxCode(code = code, codeType = codeType) # Unselect code
time.sleep(1)
setSex(sex = sex) # Unselect Sex
SelectAllMonthsInaYear(year) # Unselect yearMonth parameters
return(table_dt)
except:
print(f'Table not found for {dlCode}')
setDxCode(code = code, codeType = codeType) # Unselect code
time.sleep(1)
setSex(sex = sex) # Unselect Sex
SelectAllMonthsInaYear(year) # Unselect yearMonth parameters
def ApplyRows(row):
year = row['year']
sex = row['sex']
agelower = row['agelower']
ageupper = row['ageupper']
code = row['code']
codeType = row['codeType']
if sex == 1:
sexL = "Both sexes"
elif sex == 2:
sexL = "Males"
else:
sexL = "Females"
anx_dep_key = code + "." + str(year) + "." + str(sex) + "." + str(agelower) + "." + str(ageupper)
print(anx_dep_key)
table_name = "~/sisab/data/anxiety_depression_with_codes/sisab_anx_dep_code_{}_{}_{}_{}_to_{}.xlsx".format(code,str(year),sexL,str(agelower),str(ageupper))
print(table_name)
try:
print("Scraping code {}, year {}, for {} in age range {} to {}".format(code,str(year),sexL,str(agelower),str(ageupper)))
table_dt = SetParametersAndGetTable(agemin = agelower,agemax = ageupper,sex = sex,year = year, code = code, codeType = codeType)
table_dt.to_excel(table_name,index = False,header = True)
Anx_Dep_dict[anx_dep_key] = table_dt
except:
notRun = {'Code':code,'codeType':codeType,'Year':year,'Sex':sex,'agelower':agelower,'ageupper':ageupper}
noRun.append(notRun)
然后将 ApplyRows() 函数应用于组合数据帧的每一行。
noRun = []
Anx_Dep_dict = {}
combns.apply(ApplyRows, axis = 1)
我的问题是,每行运行大约需要 20 秒,大约 17000 行,这意味着如果没有问题的话,所有行需要 3 天以上才能完成运行。
我想看看是否有办法将其与 Dask 并行化。我不确定是否需要使用 Dask.dataframe 或 dask.delayed 或两者,以及如何使用它们。我正在寻找有关如何执行此操作的任何指示,并且希望得到任何帮助。
非常感谢!!
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