加速多个CSV文件的加载

x33g5p2x  于 2023-07-31  发布在  其他
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我正在尝试为法国的公共药物数据库(https://base-donnees-publique.medicaments.gouv.fr/)编写一个解析器/API。它由八个CSV文件(实际上是TSV,因为它们使用选项卡)组成,每个文件从几KB到4 MB,最大的有~20000行(每行代表药物及其名称,代码,价格等)。
由于这些文件可能会定期出现,我希望直接解析它们,而不是创建一个更干净的数据库(因为我可能必须定期重新创建它)。
导入这些文件花了一点时间(大约一秒钟),所以我试着加快一点速度,并对几种方法做了一些基准测试,我惊讶地看到,最基本的一种似乎也是最快的。
这是我的测试代码(很抱歉,它很长)。每个文件都与一个专用的类相关联以解析其行。基本上,这些类都是namedtuples,带有一个自定义的classmethod来解析日期、数字等

import pathlib
import enum
import datetime
from decimal import Decimal
from collections import namedtuple
import csv

def parse_date(date: str) -> datetime.datetime:
    return datetime.datetime.strptime(date, "%d/%m/%Y").date()

def parse_date_bis(date: str) -> datetime.datetime:
    return datetime.datetime.strptime(date, "%Y%m%d").date()

def parse_text(text):
    if not text:
        return ""
    return text.replace("<br>", "\n").strip()

def parse_list(raw):
    return raw.split(";")

def parse_price(price: str) -> Decimal:
    if not price:
        return None
    # Handles cases like "4,417,08".
    price = '.'.join(price.rsplit(",", 1)).replace(',', '')
    return Decimal(price)

def parse_percentage(raw: str) -> int:
    if not raw:
        return None
    return int(raw.replace("%", "").strip())

class StatutAdministratifPresentation(enum.Enum):
    ACTIVE = "Présentation active"
    ABROGEE = "Présentation abrogée"

class EtatCommercialisation(enum.Enum):
    DC = "Déclaration de commercialisation"
    S = "Déclaration de suspension de commercialisation"
    DAC = "Déclaration d'arrêt de commercialisation"
    AC = "Arrêt de commercialisation (le médicament n'a plus d'autorisation)"

class MotifAvisSMR(enum.Enum):
    INSCRIPTION = "Inscription (CT)"
    RENOUVELLEMENT = "Renouvellement d'inscription (CT)"
    EXT = "Extension d'indication"
    EXTNS = "Extension d'indication non sollicitée"
    REEV_SMR = "Réévaluation SMR"
    REEV_ASMR = "Réévaluation ASMR"
    REEV_SMR_ASMR = "Réévaluation SMR et ASMR"
    REEV_ETUDE = "Réévaluation suite à résultats étude post-inscript"
    REEV_SAISINE = "Réévaluation suite saisine Ministères (CT)"
    NOUV_EXAM = "Nouvel examen suite au dépôt de nouvelles données"
    MODIF_COND = "Modification des conditions d'inscription (CT)"
    AUTRE = "Autre demande"

class ImportanceSMR(enum.Enum):
    IMPORTANT = "Important"
    MODERE = "Modéré"
    FAIBLE = "Faible"
    INSUFFISANT = "Insuffisant"
    COMMENTAIRES = "Commentaires"
    NP = "Non précisé"

class ImportanceASMR(enum.Enum):
    COM = "Commentaires sans chiffrage de l'ASMR"
    I = "I"
    II = "II"
    III = "III"
    IV = "IV"
    V = "V"
    NP = "Non précisée"
    SO = "Sans objet"

class Specialite(namedtuple("Specialite", ("cis", "denomation", "forme", "voies_administration", "statut_amm", "type_amm", "commercialisation", "date_amm", "statut_bdm", "numero_autorisation_europeenne", "titulaire", "surveillance_renforcee"))):
    @classmethod
    def from_line(cls, line):
        line[2] = line[2].replace("  ", " ").strip()
        line[3] = parse_list(line[3])
        line[7] = parse_date(line[7])
        line[10] = line[10].strip()  # There are often leading spaces here (like ' OPELLA HEALTHCARE FRANCE').
        return cls(*line)

class Presentation(namedtuple("Specialite", ("cis", "cip7", "libelle", "statut", "commercialisation", "date_commercialisation", "cip13", "agrement_collectivites", "taux_remboursement", "prix", "prix_hors_honoraires", "montant_honoraires", "indications_remboursement"))):
    @classmethod
    def from_line(cls, line):
        if line[3] == "Présentation active":
            line[3] = StatutAdministratifPresentation.ACTIVE
        else:
            line[3] = StatutAdministratifPresentation.ABROGEE
        line[4] = {
            "Déclaration de commercialisation": EtatCommercialisation.DC,
            "Déclaration de suspension de commercialisation": EtatCommercialisation.S,
            "Déclaration d'arrêt de commercialisation": EtatCommercialisation.DAC,
            "Arrêt de commercialisation (le médicament n'a plus d'autorisation)": EtatCommercialisation.AC
        }.get(line[4])
        line[5] = parse_date(line[5])
        line[7] = True if line[7] == "oui" else False
        line[8] = parse_percentage(line[8])
        line[9] = parse_price(line[9])
        line[10] = parse_price(line[10])
        line[11] = parse_price(line[11])
        line[12] = parse_text(line[12])
        return cls(*line)

class Composition(namedtuple("Composition", ("cis", "element", "code", "substance", "dosage", "ref_dosage", "nature_composant", "cle"))):
    @classmethod
    def from_line(cls, line):
        line.pop(-1)
        return cls(*line)

class AvisSMR(namedtuple("AvisSMR", ("cis", "dossier_has", "motif", "date", "valeur", "libelle"))):
    @classmethod
    def from_line(cls, line):
        line[2] = MotifAvisSMR(line[2])
        line[3] = parse_date_bis(line[3])
        line[4] = ImportanceSMR(line[4])
        line[5] = parse_text(line[5])
        return cls(*line)

class AvisASMR(namedtuple("AvisASMR", ("cis", "dossier_has", "motif", "date", "valeur", "libelle"))):
    @classmethod
    def from_line(cls, line):
        line[2] = MotifAvisSMR(line[2])
        line[3] = parse_date_bis(line[3])
        line[4] = ImportanceASMR(line[4])
        line[5] = parse_text(line[5])
        return cls(*line)

class AvisCT(namedtuple("AvisCT", ("dossier_has", "lien"))):
    @classmethod
    def from_line(cls, line):
        return cls(*line)

FILE_MATCHES = {
    "CIS_bdpm.txt": Specialite,
    "CIS_CIP_bdpm.txt": Presentation,
    "CIS_COMPO_bdpm.txt": Composition,
    "CIS_HAS_ASMR_bdpm.txt": AvisASMR,
    "CIS_HAS_SMR_bdpm.txt": AvisSMR,
    "HAS_LiensPageCT_bdpm.txt": AvisCT
}

def sequential_import_file_data(filename, cls):
    result = {cls: []}
    with (pathlib.Path("data") / filename).open("r", encoding="latin1") as f:
        rows = csv.reader(f, delimiter="\t")
        for line in rows:
            data = cls.from_line(line)
            result[cls].append(data)
    return result

def import_data_sequential():
    results = []
    for filename, cls in FILE_MATCHES.items():
        results.append(sequential_import_file_data(filename, cls))

from multiprocessing.pool import ThreadPool

def import_data_mp_tp(n=2):
    pool = ThreadPool(n)
    results = []
    for filename, cls in FILE_MATCHES.items():
        results.append(pool.apply_async(
            sequential_import_file_data,
            (filename, cls)
        ))
    results = [r.get() for r in results]

from multiprocessing.pool import Pool

def import_data_mp_p(n=2):
    pool = Pool(n)
    results = []
    for filename, cls in FILE_MATCHES.items():
        results.append(pool.apply_async(
            sequential_import_file_data,
            (filename, cls)
        ))
    results = [r.get() for r in results]

import asyncio
import aiofiles
from aiocsv import AsyncReader

async def async_import_file_data(filename, cls):
    results = {cls: []}
    async with aiofiles.open(
        (pathlib.Path("data") / filename),
        mode="r",
        encoding="latin1"
    ) as afp:
        async for line in AsyncReader(afp, delimiter="\t"):
            data = cls.from_line(line)
            results[cls].append(data)
    return results

def import_data_async():
    results = []
    for filename, cls in FILE_MATCHES.items():
        results.append(asyncio.run(async_import_file_data(filename, cls)))

def main():
    import timeit
    print(
        "Sequential:",
        timeit.timeit(lambda: import_data_sequential(), number=10)
    )
    print(
        "Multi ThreadPool:",
        timeit.timeit(lambda: import_data_mp_tp(), number=10)
    )
    print(
        "Multi Pool:",
        timeit.timeit(lambda: import_data_mp_p(), number=10)
    )
    print(
        "Async:",
        timeit.timeit(lambda: import_data_async(), number=10)
    )

if __name__ == "__main__":
    main()

字符串
当我运行它时,我得到以下结果。

Sequential: 9.821639589001279
Multi ThreadPool: 10.137484730999859
Multi Pool: 12.531487682997977
Async: 30.953154197999538


迭代所有文件及其所有行的最基本解决方案似乎也是最快的。
我做错了什么会减慢进口的事吗?这样的时间差是正常的吗?

1cosmwyk

1cosmwyk1#

像往常一样:在代码上运行一个分析器,看看它在哪里花费了时间。(这是PyCharm的,它 Package 了stdlib cProfile
连续:7.865187874995172
x1c 0d1x的数据
嗯,好的。strptime,我可以告诉它会被datetime.datetime.strptime调用。奇怪的是getlocale...为什么我们需要在那里设置地点?点击调用图可以看到,strptime实际上是在查找当前的locale,并且有一堆锁等等--如果我们用自己的实现替换那些parse_date呢?

def parse_date(date: str) -> datetime.date:
    d, m, y = (int(x) for x in date.split("/", 2))
    return datetime.date(2000 + y, m, d)

def parse_date_bis(date: str) -> datetime.datetime:
    y = int(date[:4])
    m = int(date[4:6])
    d = int(date[6:8])
    return datetime.datetime(y, m, d)

字符串
序号:3.8978060420195106
好的,我们开始做饭了!52%的改善!



(It没有显示在这里的屏幕截图上,因为我是一个愚蠢的鹅裁剪它,但strptime在引擎盖下使用的re的东西也掉了。)
现在让我们假设有很多相同的日期,并在这些热parse_date_*函数上加载@lru_cache(maxsize=None) s(RAM灵活,无限缓存),运行代码并打印该高速缓存信息:

Sequential: 3.2240814580000006
CacheInfo(hits=358989, misses=6991, maxsize=None, currsize=6991)
CacheInfo(hits=221607, misses=513, maxsize=None, currsize=513)


我觉得不错,上一个号码再打八五折。
parse_price显然也可以使用缓存:

Sequential: 2.928746833000332
CacheInfo(hits=358989, misses=6991, maxsize=None, currsize=6991)
CacheInfo(hits=221607, misses=513, maxsize=None, currsize=513)
CacheInfo(hits=622064, misses=4096, maxsize=None, currsize=4096)


嘿,谁知道,数据中只有4096个单独的价格字符串。
如果你有足够的内存,剩下的解析函数也可以使用缓存,但是通过一点分析和解析,现在它的速度快了2.7倍[当运行所有东西10次时,这意味着这些缓存将是热的-单次运行的加速并不那么引人注目],不需要并行处理。魔法!
为了让游戏场地更加公平,这里有一个hyperfine基准测试,其中Python解释器在每次导入时都从头开始(每个解释器只运行一次导入):

$ hyperfine 'python3 so76781391-orig.py' 'python3 so76781391-opt.py' --warmup 5 --min-benchmarking-time 10
Benchmark 1: python3 so76781391-orig.py
  Time (mean ± σ):     363.0 ms ±   2.7 ms    [User: 340.8 ms, System: 20.7 ms]
  Range (min … max):   358.9 ms … 367.9 ms    27 runs

Benchmark 2: python3 so76781391-opt.py
  Time (mean ± σ):     234.1 ms ±   2.5 ms    [User: 215.6 ms, System: 17.0 ms]
  Range (min … max):   228.2 ms … 238.5 ms    42 runs

Summary
  'python3 so76781391-opt.py' ran
    1.55 ± 0.02 times faster than 'python3 so76781391-orig.py'


因此,快速查看分析器(以及一些额外的优化,例如不在from_line函数中创建Mapdicts等),速度提升了55%。

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