From d7e6d271838ed442e137ca788d8ade302299fc27 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Lu=C3=A3=20Bida=20Vacaro?= Date: Sat, 2 Sep 2023 18:57:51 -0300 Subject: [PATCH] feat(struc): database modularization and code improvement (#137) * feat(struc): database modularization and code improvement * SIM database * SIM database * SINASC database * Docstrings * Finish SIM and minor improvements * SIH Database & removing dateparser in File to increase listing speed by 35x * Saving work * minor fix on zfill_year * Setting a time limit of 5 seconds to every test * redo poetry lock * minor fix on dockerfile * skip tests that take over 5 seconds * Improve SINAN.get_files to accept multiple queues * Include asynchronous FTP download method * Improve FTP objects when listing ftp content * Implement download methods on File class * Fix some docstrings * Replace online_data.SINAN methods with new class * Replace online_data.SIM download method with new class * Replace online_data.sinasc download method with new class * Replace online_data.SIH download method with new class * Replace online_data.SIA download method with new class * add humanize pckg * Start removing references from online_data.__init__ --- docker/Dockerfile | 3 +- poetry.lock | 2364 +++++++++++----------- pyproject.toml | 22 +- pysus/ftp/__init__.py | 279 +++ pysus/ftp/databases.py | 528 +++++ pysus/online_data/CIHA.py | 3 +- pysus/online_data/CNES.py | 3 +- pysus/online_data/ESUS.py | 2 +- pysus/online_data/PNI.py | 3 +- pysus/online_data/SIA.py | 66 +- pysus/online_data/SIH.py | 26 +- pysus/online_data/SIM.py | 141 +- pysus/online_data/SINAN.py | 47 +- pysus/online_data/sinasc.py | 32 +- pysus/online_data/vaccine.py | 2 +- pysus/tests/test_SIA.py | 6 +- pysus/tests/test_cnes.py | 6 +- pysus/tests/test_data/test_Infodengue.py | 18 +- pysus/tests/test_data/test_Infogripe.py | 3 + pysus/tests/test_data/test_PNI.py | 7 +- pysus/tests/test_data/test_ciha.py | 5 + pysus/tests/test_data/test_sia.py | 14 +- pysus/tests/test_data/test_sih.py | 3 + pysus/tests/test_data/test_sim.py | 11 +- pysus/tests/test_data/test_sinan.py | 29 +- pysus/tests/test_data/test_sinasc.py | 13 +- pysus/tests/test_data/test_vaccine.py | 2 + pysus/tests/test_decoders.py | 64 +- pysus/tests/test_esus.py | 4 +- pysus/tests/test_ibge.py | 11 +- pysus/tests/test_init.py | 3 + pysus/tests/test_sih.py | 10 +- pysus/tests/test_sim.py | 15 +- pysus/tests/test_utilities.py | 3 + pysus/utilities/brasil.py | 45 + 35 files changed, 2421 insertions(+), 1372 deletions(-) create mode 100644 pysus/ftp/__init__.py create mode 100644 pysus/ftp/databases.py create mode 100644 pysus/utilities/brasil.py diff --git a/docker/Dockerfile b/docker/Dockerfile index 6d32c82f..87460130 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -39,7 +39,8 @@ RUN curl -sSL https://install.python-poetry.org/ | POETRY_HOME=/opt/poetry pytho ln -s /opt/poetry/bin/poetry && \ poetry config virtualenvs.create false -RUN chmod -R a+rwx /home/pysus/.config/pypoetry/ +RUN chmod -R a+rwx /home/pysus/.config/pypoetry/ \ + && chown -R pysus:pysus /opt/conda/bin/ USER pysus diff --git a/poetry.lock b/poetry.lock index 08ccf856..44135820 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,30 +1,19 @@ # This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. 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-content-hash = "f7e3527196c36ed8044a358d607fce149839fcb64a8a25d5362518e4d6455b67" +content-hash = "8fe14860e97c6e4e091161ce6c7b92c455e8e161a538b4306163980f07439c55" diff --git a/pyproject.toml b/pyproject.toml index 9105f98a..b4f47346 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -11,23 +11,25 @@ packages = [{include='pysus'}] cffi = "1.15.1" dbfread = "2.0.7" fastparquet = "^0.8.1" -geocoder = "^1.38.1" -jupyterlab = "^3.4.5" numpy = "1.23.2" pyarrow = ">=11.0.0" pycparser = "2.21" pyreaddbc = "1.0.0" python = "^3.9" python-dateutil = "2.8.2" -pytz = "2022.2.1" -six = "1.16.0" tqdm = "4.64.0" wget = "^3.2" loguru = "^0.6.0" Unidecode = "^1.3.6" elasticsearch = "7.16.2" -ipykernel = "^6.22.0" -geobr = "^0.2.0" +dateparser = "^1.1.8" +pandas = ">=1.5.3" +urwid = "^2.1.2" +# Preprocessing Packages +geobr = { version = "^0.2.0", extras=["preprocessing"] } +geocoder = { version = "^1.38.1", extras=["ml"] } +aioftp = "^0.21.4" +humanize = "^4.8.0" [tool.poetry.group.dev.dependencies] pytest = ">=6.1.0" @@ -42,6 +44,9 @@ folium = "^0.14.0" seaborn = "^0.12.2" descartes = "^1.1.0" keplergl = "^0.3.2" +jupyterlab = "^4.0.5" +ipykernel = "^6.25.1" +pytest-timeout = "^2.1.0" [build-system] requires = ["poetry-core>=1.0.0"] @@ -66,5 +71,8 @@ testpaths = [ "tests" ] - exclude = ["*.git", "docs/"] + +[tool.poetry.extras] +preprocessing = ["geobr", "geocoder"] + diff --git a/pysus/ftp/__init__.py b/pysus/ftp/__init__.py new file mode 100644 index 00000000..359b9f3b --- /dev/null +++ b/pysus/ftp/__init__.py @@ -0,0 +1,279 @@ +from loguru import logger +from datetime import datetime +from ftplib import FTP +import os +import pathlib +from aioftp import Client +from typing import List, Optional, Union + + +CACHEPATH = os.getenv( + 'PYSUS_CACHEPATH', os.path.join(str(pathlib.Path.home()), 'pysus') +) + +class File: + """ + FTP File class. This class will contain methods for interacting with + files inside DataSUS FTP server. The databases will be responsible for + parsing the files found for each db into File classes, enabling the + databases' files to share state and its reusability. + + Parameters + path [str]: entire directory path where the file is located + inside the FTP server + name [str]: basename of the file + info [dict]: a dict containing the keys [size, type, modify], which + are present in every FTP server. In PySUS, this info + is extract using `line_file_parser` with FTP LIST. + + Methods + download(local_dir): extract the file to local_dir + async_download(local_dir): async extract the file to local_dir + """ + + def __init__(self, path: str, name: str, info: dict) -> None: + name, extension = os.path.splitext(name) + self.name = name + self.extension = extension + self.basename = pathlib.PurePosixPath(self.name + self.extension) + self.path = pathlib.PurePosixPath( + path + str(self.basename) + if path.endswith("/") + else path + "/" + str(self.basename) + ) + self.info = info + + def __str__(self) -> str: + return str(self.basename) + + def __repr__(self) -> str: + return str(self.basename) + + def __hash__(self): + return hash(self.path) + + def __eq__(self, other): + if isinstance(other, File): + return self.path == other.path + return False + + def download(self, local_dir: str = CACHEPATH) -> str: + dir = pathlib.Path(local_dir) + dir.mkdir(exist_ok=True, parents=True) + filepath = dir / self.basename + + if filepath.exists(): + return str(filepath) + + ftp = ftp = FTP("ftp.datasus.gov.br") + ftp.login() + ftp.retrbinary( + f"RETR {self.path}", + open(f"{filepath}", "wb").write, + ) + ftp.close() + return str(filepath) + + async def async_download(self, local_dir: str = CACHEPATH) -> None: + # aioftp.Client.parse_list_line_custom + def line_file_parser(file_line): + line = file_line.decode("utf-8") + info = {} + if "" in line: + date, time, _, *name = str(line).strip().split() + info["size"] = 0 + info["type"] = "dir" + name = " ".join(name) + else: + date, time, size, name = str(line).strip().split() + info["size"] = size + info["type"] = "file" + + modify = datetime.strptime( + " ".join([date, time]), "%m-%d-%y %I:%M%p" + ) + info["modify"] = modify.strftime("%m/%d/%Y %I:%M%p") + + return pathlib.PurePosixPath(name), info + + dir = pathlib.Path(local_dir) + dir.mkdir(exist_ok=True, parents=True) + filepath = dir / self.basename + + output = ( + local_dir + str(self.basename) + if local_dir.endswith("/") + else local_dir + "/" + str(self.basename) + ) + + if filepath.exists(): + logger.debug(output) + pass + + async with Client.context( + host="ftp.datasus.gov.br", parse_list_line_custom=line_file_parser + ) as client: + await client.login() + await client.download(self.path, output, write_into=True) + logger.debug(output) + + +class Directory: + """ + FTP Directory class. + + Parameters + path [str]: entire directory path where the directory is located + inside the FTP server + name [str]: directory name + info [dict]: a dict containing the keys [size, type, modify], which + are present in every FTP server. In PySUS, this info + is extract using `line_file_parser` with FTP LIST. + OBS: A Directory should have size=0 + """ + + def __init__( + self, + path: str, + info: dict, + content: Optional[List] = None, + ) -> None: + self.path = pathlib.PurePosixPath(path) + self.info = info + self.content = content + + def __str__(self) -> str: + return str(self.path) + + def __repr__(self) -> str: + return str(self.path) + + def __hash__(self): + return hash(self.path) + + def __eq__(self, other): + if isinstance(other, Directory): + return self.path == other.path + return False + + +def list_path(path: str) -> List[Union[Directory, File]]: + """ + This method is responsible for listing all the database's + files when the database class is firstly called. It will + convert the files found within the paths into `File`s, + returning a list of Files and Directories. + """ + content = list() + ftp = FTP("ftp.datasus.gov.br") + ftp.connect() + ftp.login() + ftp.cwd(path) + + def line_file_parser(file_line): + info = {} + if "" in file_line: + date, time, _, *name = str(file_line).strip().split() + info["size"] = 0 + info["type"] = "dir" + name = " ".join(name) + modify = datetime.strptime( + " ".join([date, time]), "%m-%d-%y %I:%M%p" + ) + info["modify"] = modify + xpath = path + name if path.endswith("/") else path + "/" + name + content.append(Directory(xpath, info)) + else: + date, time, size, name = str(file_line).strip().split() + info["size"] = size + info["type"] = "file" + modify = datetime.strptime( + " ".join([date, time]), "%m-%d-%y %I:%M%p" + ) + info["modify"] = modify + content.append(File(path, name, info)) + + ftp.retrlines("LIST", line_file_parser) + ftp.close() + return content + + +class Database: + """ + Base class for PySUS databases. Contains common functions + for accessing DataSUS FTP server. With this class, it is + possible to construct database classes for different DataSUS + files, sharing state and functionalities. + + Parameters + ftp [FTP]: ftplib.FTP object for connecting in DataSUS server. + name [str]: database name + paths [list[str]]: server paths where the files are located + files [list[Files]]: list of parsed Files that will be loaded at + database instantiation. + metadata [dict]: dict containing database's metadata information + + Methods + describe(file): describes a file according to each database's + spec. Returns a dict with file information + all_files(): runs at instantiation, enters the FTP server and reads + files within the paths, parsing them into File classes + and returning all Files as a list + """ + + ftp: FTP + name: str + paths: List[str] + content: List[Union[Directory, File]] + files: List[File] + metadata: dict + + def __init__(self) -> None: + self.ftp = FTP("ftp.datasus.gov.br") + self.content = self.load(self.paths) + self.files = [f for f in self.content if isinstance(f, File)] + + def __repr__(self) -> str: + return f'{self.name} - {self.metadata["long_name"]}' + + def load(self, paths: List[str]): + """ + This method is responsible for listing all the database's + files when the database class is firstly called. It will + convert the files found within the paths into `File`s, + and `Directory`(ies). + """ + content = [] + for path in paths: + content.extend(list_path(path)) + return content + + def describe(self, file: File) -> dict: + """ + Receives a `File` and returns a dict with its information, + according to the database's specifications. This method is + helpful to return the FTP's file in a humanized format + + Parameters + file [File]: a `File` instance + """ + ... + + def format(self, file: File) -> tuple: + """ + Formats a File based on the database specifications, + extracting its name's parameters given a pattern. + + Parameters + file [File]: a `File` instance + """ + ... + + def get_files(self, *args, **kwargs) -> list[File]: + """ + Filters the list of `File`s according to each database file + pattern, as UFs, Groups, Years, Months, etc. This method will + also be responsible to look for wrong values within the file + pattern and possible extra characters in its basename + """ + ... diff --git a/pysus/ftp/databases.py b/pysus/ftp/databases.py new file mode 100644 index 00000000..badea67c --- /dev/null +++ b/pysus/ftp/databases.py @@ -0,0 +1,528 @@ +from pysus.ftp import Database, File +import humanize +import datetime +from typing import Union, Any, List, Optional +from itertools import product +from pysus.utilities.brasil import UFs, MONTHS + + +def to_list(ite: Any) -> list: + """Parse any builtin data type into a list""" + return [ite] if type(ite) in [str, float, int] else list(ite) + + +def zfill_year(year: Union[str, int]) -> int: + """ + Formats a len(2) year into len(4) with the correct year preffix + E.g: 20 -> 2020; 99 -> 1999 + """ + year = str(year)[-2:].zfill(2) + current_year = str(datetime.datetime.now().year)[-2:] + suffix = "19" if str(year) > current_year else "20" + return int(suffix + str(year)) + + +def parse_UFs(UF: Union[list[str], str]) -> list: + """ + Formats states abbreviations into correct format and retuns a list. + Also checks if there is an incorrect UF in the list. + E.g: ['SC', 'mt', 'ba'] -> ['SC', 'MT', 'BA'] + """ + ufs = [uf.upper() for uf in to_list(UF)] + if not all([uf in list(UFs) for uf in ufs]): + raise ValueError(f"Unknown UF(s): {set(ufs).difference(list(UFs))}") + return ufs + + +class SINAN(Database): + name = "SINAN" + paths = [ + "/dissemin/publicos/SINAN/DADOS/FINAIS", + "/dissemin/publicos/SINAN/DADOS/PRELIM", + ] + metadata = dict( + long_name="Doenças e Agravos de Notificação", + source="https://portalsinan.saude.gov.br/", + description=( + "The Notifiable Diseases Information System - Sinan is primarily" + "fed by the notification and investigation of cases of diseases " + "and conditions listed in the national list of compulsorily notifiable " + "diseases (Consolidation Ordinance No. 4, September 28, 2017, Annex)." + "However, states and municipalities are allowed to include other " + "important health problems in their region, such as difilobotriasis " + "in the municipality of São Paulo. Its effective use enables the dynamic " + "diagnosis of the occurrence of an event in the population, providing " + "evidence for causal explanations of compulsorily notifiable diseases " + "and indicating risks to which people are exposed. This contributes to " + "identifying the epidemiological reality of a specific geographical area. " + "Its systematic, decentralized use contributes to the democratization of " + "information, allowing all healthcare professionals to access and make " + "it available to the community. Therefore, it is a relevant tool to assist" + " in health planning, define intervention priorities, and evaluate the " + "impact of interventions." + ), + ) + + diseases = dict( + ACBI="Acidente de trabalho com material biológico", + ACGR="Acidente de trabalho", + ANIM="Acidente por Animais Peçonhentos", + ANTR="Atendimento Antirrabico", + BOTU="Botulismo", + CANC="Cancêr relacionado ao trabalho", + CHAG="Doença de Chagas Aguda", + CHIK="Febre de Chikungunya", + COLE="Cólera", + COQU="Coqueluche", + DENG="Dengue", + DERM="Dermatoses ocupacionais", + DIFT="Difteria", + ESQU="Esquistossomose", + EXAN="Doença exantemáticas", + FMAC="Febre Maculosa", + FTIF="Febre Tifóide", + HANS="Hanseníase", + HANT="Hantavirose", + HEPA="Hepatites Virais", + IEXO="Intoxicação Exógena", + INFL="Influenza Pandêmica", + LEIV="Leishmaniose Visceral", + LEPT="Leptospirose", + LERD="LER/Dort", + LTAN="Leishmaniose Tegumentar Americana", + MALA="Malária", + MENI="Meningite", + MENT="Transtornos mentais relacionados ao trabalho", + NTRA="Notificação de Tracoma", + PAIR="Perda auditiva por ruído relacionado ao trabalho", + PEST="Peste", + PFAN="Paralisia Flácida Aguda", + PNEU="Pneumoconioses realacionadas ao trabalho", + RAIV="Raiva", + SDTA="Surto Doenças Transmitidas por Alimentos", + SIFA="Sífilis Adquirida", + SIFC="Sífilis Congênita", + SIFG="Sífilis em Gestante", + SRC="Síndrome da Rubéola Congênia", + TETA="Tétano Acidental", + TETN="Tétano Neonatal", + TOXC="Toxoplasmose Congênita", + TOXG="Toxoplasmose Gestacional", + TRAC="Inquérito de Tracoma", + TUBE="Tuberculose", + VARC="Varicela", + VIOL="Violência doméstica, sexual e/ou outras violências", + ZIKA="Zika Vírus", + ) + + def describe(self, file: File) -> dict: + if file.extension.upper() == ".DBC": + dis_code, year = self.format(file) + + description = dict( + name=str(file.basename), + disease=self.diseases[dis_code], + year=zfill_year(year), + size=humanize.naturalsize(file.info["size"]), + last_update=file.info["modify"].strftime("%m-%d-%Y %I:%M%p"), + ) + return description + else: + return {} + + def format(self, file: File) -> tuple: + year = file.name[-2:] + + if file.name.startswith("SRC"): + dis_code = file.name[:3] + elif file.name == "LEIBR22": + dis_code = "LEIV" # MISPELLED FILE NAME + elif file.name == "LERBR19": + dis_code = "LERD" # ANOTHER ONE + else: + dis_code = file.name[:4] + + return dis_code, zfill_year(year) + + def get_files( + self, + dis_codes: Optional[Union[str, list]] = None, + years: Optional[Union[str, int, list]] = None, + ) -> List[File]: + codes = [c.upper() for c in to_list(dis_codes)] if dis_codes else None + fyears = ( + [str(y)[-2:].zfill(2) for y in to_list(years)] if years else None + ) + + if codes and not all(code in self.diseases for code in codes): + raise ValueError( + f"Unknown disease(s): {set(codes).difference(set(self.diseases))}" + ) + + if not codes and not fyears: + return self.files + elif not codes and fyears: + return list( + (f for f in self.files if any(y in str(f) for y in fyears)) + ) + elif not fyears and codes: + return list( + ( + f + for f in self.files + if any(str(f).startswith(c + "BR") for c in codes) + ) + ) + + targets = [f"{c}BR{y}" for c, y in list(product(codes, fyears))] + return list( + (f for f in self.files if any(f.name == t for t in targets)) + ) + + +class SIM(Database): + name = "SIM" + paths = [ + "/dissemin/publicos/SIM/CID10/DORES", + "/dissemin/publicos/SIM/CID9/DORES", + ] + metadata = dict( + long_name="Sistema de Informação sobre Mortalidade", + source="http://sim.saude.gov.br", + description="", + ) + groups = dict(DO="CID10", DOR="CID9") + + def describe(self, file: File) -> dict: + group, uf, year = self.format(file) + + description = dict( + name=str(file.basename), + uf=UFs[uf], + year=year, + group=self.groups[group], + size=humanize.naturalsize(file.info["size"]), + last_update=file.info["modify"].strftime("%m-%d-%Y %I:%M%p"), + ) + + return description + + def format(self, file: File) -> tuple: + if "CID9" in str(file.path): + group, uf, year = file.name[:-4], file.name[-4:-2], file.name[-2:] + else: + group, uf, year = file.name[:-6], file.name[-6:-4], file.name[-4:] + + return group, uf, zfill_year(year) + + def get_files( + self, + groups: Union[list[str], str], + ufs: Union[list[str], str], + years: Union[list, str, int], + ) -> List[File]: + groups = [g.upper() for g in to_list(groups)] + ufs = parse_UFs(ufs) + years = to_list(years) + + if not all([gr in list(self.groups.values()) for gr in groups]): + raise ValueError( + f"Unknown group(s): {set(groups).difference(self.groups.values())}" + ) + + targets = [] + for group in groups: + if group == "CID9": + cid9_years = [str(y)[-2:].zfill(2) for y in years] + targets.extend( + [ + f"DOR{uf}{year}" + for uf, year in list(product(ufs, cid9_years)) + ] + ) + elif group == "CID10": + cid10_years = [zfill_year(y) for y in years] + targets.extend( + [ + f"DO{uf}{year}" + for uf, year in list(product(ufs, cid10_years)) + ] + ) + + files = [] + for file in self.files: + if file.name in targets: + files.append(file) + + return files + + +class SINASC(Database): + name = "SINASC" + paths = [ + "/dissemin/publicos/SINASC/NOV/DNRES", + "/dissemin/publicos/SINASC/ANT/DNRES", + ] + metadata = dict( + long_name="Sistema de Informações sobre Nascidos Vivos", + source="http://sinasc.saude.gov.br/", + description="", + ) + groups = dict( + DN="Declarações de Nascidos Vivos", + DNR="Dados dos Nascidos Vivos por UF de residência", + ) + + def describe(self, file: File) -> dict: + if file.extension.upper() == ".DBC": + uf, year = self.format(file) + + if uf == "EX": # DNEX2021.dbc + state = None + else: + state = UFs[uf] + + description = dict( + name=str(file.basename), + uf=state, + year=year, + size=humanize.naturalsize(file.info["size"]), + last_update=file.info["modify"].strftime("%m-%d-%Y %I:%M%p"), + ) + + return description + else: + return {} + + def format(self, file: File) -> tuple: + if file.name == "DNEX2021": + pass + + year = zfill_year(file.name[-2:]) + charname = "".join([c for c in file.name if not c.isnumeric()]) + uf = charname[-2:] + return uf, zfill_year(year) + + def get_files( + self, + ufs: Union[list[str], str], + years: Union[list, str, int], + ) -> List[File]: + if "EX" in to_list(ufs): + # DNEX2021 + if len(to_list(ufs)) == 1: + return [] + else: + to_list(ufs).remove("EX") + + ufs = parse_UFs(ufs) + years = [str(y)[-2:].zfill(2) for y in to_list(years)] + + # Fist filter years to reduce the list size + year_files = [] + for file in self.files: + for year in years: + if year in file.name: + year_files.append(file) + + files = [] + for file in year_files: + if "ANT/DNRES" in str(file.path): + for uf in ufs: + if uf in file.name[3:]: + files.append(file) + else: + for uf in ufs: + if uf in file.name[2:]: + files.append(file) + + return files + + +class SIH(Database): + name = "SIH" + paths = [ + "/dissemin/publicos/SIHSUS/199201_200712/Dados", + "/dissemin/publicos/SIHSUS/200801_/Dados", + ] + metadata = dict( + long_name="Sistema de Informações Hospitalares", + source=( + "https://datasus.saude.gov.br/acesso-a-informacao/morbidade-hospitalar-do-sus-sih-sus/", + "https://datasus.saude.gov.br/acesso-a-informacao/producao-hospitalar-sih-sus/", + ), + description=( + "A finalidade do AIH (Sistema SIHSUS) é a de transcrever todos os " + "atendimentos que provenientes de internações hospitalares que " + "foram financiadas pelo SUS, e após o processamento, gerarem " + "relatórios para os gestores que lhes possibilitem fazer os pagamentos " + "dos estabelecimentos de saúde. Além disso, o nível Federal recebe " + "mensalmente uma base de dados de todas as internações autorizadas " + "(aprovadas ou não para pagamento) para que possam ser repassados às " + "Secretarias de Saúde os valores de Produção de Média e Alta complexidade " + "além dos valores de CNRAC, FAEC e de Hospitais Universitários – em suas " + "variadas formas de contrato de gestão." + ), + ) + groups = dict( + RD="AIH Reduzida", + RJ="AIH Rejeitada", + ER="AIH Rejeitada com erro", + SP="Serviços Profissionais", + CH="Cadastro Hospitalar", + CM="", # TODO + ) + + def describe(self, file: File) -> dict: + if file.extension.upper() == ".DBC": + group, uf, year, month = self.format(file) + + description = dict( + name=file.basename, + group=self.groups[group], + uf=UFs[uf], + month=MONTHS[int(month)], + year=zfill_year(year), + size=humanize.naturalsize(file.info["size"]), + last_update=file.info["modify"].strftime("%m-%d-%Y %I:%M%p"), + ) + + return description + else: + return {} + + def format(self, file: File) -> tuple: + group, uf = file.name[:2].upper(), file.name[2:4].upper() + year, month = file.name[-4:-2], file.name[-2:] + return group, uf, zfill_year(year), month + + def get_files( + self, + groups: Union[List[str], str], + ufs: Union[List[str], str], + months: Union[list, str, int], + years: Union[list, str, int], + ) -> List[File]: + groups = [gr.upper() for gr in to_list(groups)] + ufs = parse_UFs(ufs) + months = [str(y)[-2:].zfill(2) for y in to_list(months)] + years = [str(m)[-2:].zfill(2) for m in to_list(years)] + + if not all([gr in list(self.groups) for gr in groups]): + raise ValueError( + f"Unknown SIH Group(s): {set(groups).difference(list(self.groups))}" + ) + + # Fist filter files by group to reduce the files list length + groups_files = [] + for file in self.files: + if file.name[:2] in groups: + groups_files.append(file) + + targets = ["".join(t) for t in product(ufs, months, years)] + + files = [] + for file in groups_files: + if file.name[2:] in targets: + files.append(file) + + return files + + +class SIA(Database): + name = "SIA" + paths = [ + "/dissemin/publicos/SIASUS/199407_200712/Dados", + "/dissemin/publicos/SIASUS/200801_/Dados", + ] + metadata = dict( + long_name="Sistema de Informações Ambulatoriais", + source="http://sia.datasus.gov.br/principal/index.php", + description=( + "O Sistema de Informação Ambulatorial (SIA) foi instituído pela Portaria " + "GM/MS n.º 896 de 29 de junho de 1990. Originalmente, o SIA foi concebido " + "a partir do projeto SICAPS (Sistema de Informação e Controle Ambulatorial " + "da Previdência Social), em que os conceitos, os objetivos e as diretrizes " + "criados para o desenvolvimento do SICAPS foram extremamente importantes e " + "amplamente utilizados para o desenvolvimento do SIA, tais como: (i) o " + "acompanhamento das programações físicas e orçamentárias; (ii) o " + "acompanhamento das ações de saúde produzidas; (iii) a agilização do " + "pagamento e controle orçamentário e financeiro; e (iv) a formação de " + "banco de dados para contribuir com a construção do SUS." + ), + ) + groups = dict( + AB="Laudo de Acompanhamento a Cirurgia Bariátrica", + ABO="Acompanhamento Pós Cirurgia Bariátrica", + ACF="Confeção de Fístula Arteriovenosa", + AD="Laudos Diversos", + AM="Laudo de Medicamentos", + AMP="", # TODO: find out what AMP means + AN="Laudo de Nefrologia", + AQ="Laudo de Quimioterapia", + AR="Laudo de Radioterapia", + ATD="Tratamento Dialítico", + BI="Boletim Individual", + IMPBO="", # TODO: same here + PA="Produção Ambulatorial", + PAM="", # TODO: same here + PAR="", + PAS="", + PS="Psicossocial", + SAD="Atenção Domiciliar", + ) + + def describe(self, file: File) -> dict: + if file.extension.upper() == ".DBC": + group, uf, year, month = self.format(file) + + description = dict( + name=str(file.basename), + group=self.groups[group], + uf=UFs[uf], + month=MONTHS[int(month)], + year=zfill_year(year), + size=humanize.naturalsize(file.info["size"]), + last_update=file.info["modify"].strftime("%m-%d-%Y %I:%M%p"), + ) + + return description + else: + return {} + + def format(self, file: File) -> tuple: + group, uf = file.name[:2].upper(), file.name[2:4].upper() + year, month = file.name[-4:-2], file.name[-2:] + return group, uf, zfill_year(year), month + + def get_files( + self, + groups: Union[List[str], str], + ufs: Union[List[str], str], + months: Union[list, str, int], + years: Union[list, str, int], + ) -> List[File]: + groups = [gr.upper() for gr in to_list(groups)] + ufs = parse_UFs(ufs) + months = [str(y)[-2:].zfill(2) for y in to_list(months)] + years = [str(m)[-2:].zfill(2) for m in to_list(years)] + + if not all([gr in list(self.groups) for gr in groups]): + raise ValueError( + f"Unknown SIH Group(s): {set(groups).difference(list(self.groups))}" + ) + + # Fist filter files by group to reduce the files list length + groups_files = [] + for file in self.files: + if file.name[:2] in groups: + groups_files.append(file) + + targets = ["".join(t) for t in product(ufs, months, years)] + + files = [] + for file in groups_files: + if file.name[2:] in targets: + files.append(file) + + return files diff --git a/pysus/online_data/CIHA.py b/pysus/online_data/CIHA.py index 9ba0d0ce..07404cdd 100644 --- a/pysus/online_data/CIHA.py +++ b/pysus/online_data/CIHA.py @@ -8,7 +8,8 @@ """ from typing import Union -from pysus.online_data import CACHEPATH, FTP_Downloader +from pysus.online_data import FTP_Downloader +from pysus.ftp import CACHEPATH def download( diff --git a/pysus/online_data/CNES.py b/pysus/online_data/CNES.py index 170af58a..6c8b10db 100644 --- a/pysus/online_data/CNES.py +++ b/pysus/online_data/CNES.py @@ -1,6 +1,7 @@ from typing import Union -from pysus.online_data import CACHEPATH, FTP_Downloader +from pysus.online_data import FTP_Downloader +from pysus.ftp import CACHEPATH group_dict = { 'LT': ['Leitos - A partir de Out/2005', 10, 2005], diff --git a/pysus/online_data/ESUS.py b/pysus/online_data/ESUS.py index d6db3b7e..52eef5ac 100644 --- a/pysus/online_data/ESUS.py +++ b/pysus/online_data/ESUS.py @@ -5,7 +5,7 @@ from loguru import logger from elasticsearch import Elasticsearch, helpers -from pysus.online_data import CACHEPATH +from pysus.ftp import CACHEPATH def download(uf, cache=True, checkmemory=True): diff --git a/pysus/online_data/PNI.py b/pysus/online_data/PNI.py index d807f422..a4ea05bc 100644 --- a/pysus/online_data/PNI.py +++ b/pysus/online_data/PNI.py @@ -3,7 +3,8 @@ """ from typing import Union -from pysus.online_data import CACHEPATH, FTP_Downloader, FTP_Inspect +from pysus.online_data import FTP_Downloader, FTP_Inspect +from pysus.ftp import CACHEPATH def download( diff --git a/pysus/online_data/SIA.py b/pysus/online_data/SIA.py index ffeb1a6d..ad65f4ac 100644 --- a/pysus/online_data/SIA.py +++ b/pysus/online_data/SIA.py @@ -9,22 +9,26 @@ from pprint import pprint from typing import Dict, Tuple, Union -from pysus.online_data import CACHEPATH, FTP_Downloader +from pysus.ftp import CACHEPATH +from pysus.ftp.databases import SIA + +sia = SIA() + group_dict: Dict[str, Tuple[str, int, int]] = { - 'PA': ('Produção Ambulatorial', 7, 1994), - 'BI': ('Boletim de Produção Ambulatorial individualizado', 1, 2008), - 'AD': ('APAC de Laudos Diversos', 1, 2008), - 'AM': ('APAC de Medicamentos', 1, 2008), - 'AN': ('APAC de Nefrologia', 1, 2008), - 'AQ': ('APAC de Quimioterapia', 1, 2008), - 'AR': ('APAC de Radioterapia', 1, 2008), - 'AB': ('APAC de Cirurgia Bariátrica', 1, 2008), - 'ACF': ('APAC de Confecção de Fístula', 1, 2008), - 'ATD': ('APAC de Tratamento Dialítico', 1, 2008), - 'AMP': ('APAC de Acompanhamento Multiprofissional', 1, 2008), - 'SAD': ('RAAS de Atenção Domiciliar', 1, 2008), - 'PS': ('RAAS Psicossocial', 1, 2008), + "PA": ("Produção Ambulatorial", 7, 1994), + "BI": ("Boletim de Produção Ambulatorial individualizado", 1, 2008), + "AD": ("APAC de Laudos Diversos", 1, 2008), + "AM": ("APAC de Medicamentos", 1, 2008), + "AN": ("APAC de Nefrologia", 1, 2008), + "AQ": ("APAC de Quimioterapia", 1, 2008), + "AR": ("APAC de Radioterapia", 1, 2008), + "AB": ("APAC de Cirurgia Bariátrica", 1, 2008), + "ACF": ("APAC de Confecção de Fístula", 1, 2008), + "ATD": ("APAC de Tratamento Dialítico", 1, 2008), + "AMP": ("APAC de Acompanhamento Multiprofissional", 1, 2008), + "SAD": ("RAAS de Atenção Domiciliar", 1, 2008), + "PS": ("RAAS Psicossocial", 1, 2008), } @@ -36,36 +40,22 @@ def download( states: Union[str, list], years: Union[str, list, int], months: Union[str, list, int], - group: str = 'PA', + groups: Union[str, list], data_dir: str = CACHEPATH, ) -> list: """ Download SIASUS records for state year and month and returns dataframe - :param months: 1 to 12, can be a list :param states: 2 letter state code, can be a list :param years: 4 digit integer, can be a list + :param months: 1 to 12, can be a list :param data_dir: whether to cache files locally. default is True - :param group: 2-3 letter document code, defaults to ['PA', 'BI']. - Codes should be one of the following: - PA - Produção Ambulatorial - BI - Boletim de Produção Ambulatorial individualizado - AD - APAC de Laudos Diversos - AM - APAC de Medicamentos - AN - APAC de Nefrologia - AQ - APAC de Quimioterapia - AR - APAC de Radioterapia - AB - APAC de Cirurgia Bariátrica - ACF - APAC de Confecção de Fístula - ATD - APAC de Tratamento Dialítico - AMP - APAC de Acompanhamento Multiprofissional - SAD - RAAS de Atenção Domiciliar - PS - RAAS Psicossocial - :return: list of downloaded parquet paths + :param group: SIA groups. For all groups, refer to `sia.groups` + :return: list of downloaded files """ - return FTP_Downloader('SIA').download( - UFs=states, - years=years, - months=months, - local_dir=data_dir, - SIA_group=group, + files = sia.get_files( + groups=groups, ufs=states, years=years, months=months ) + downloaded = [] + for file in files: + downloaded.append(file.download(local_dir=data_dir)) + return downloaded diff --git a/pysus/online_data/SIH.py b/pysus/online_data/SIH.py index 9023bb31..af06c86c 100644 --- a/pysus/online_data/SIH.py +++ b/pysus/online_data/SIH.py @@ -6,29 +6,33 @@ """ from typing import Union -from pysus.online_data import CACHEPATH, FTP_Downloader +from pysus.ftp import CACHEPATH +from pysus.ftp.databases import SIH + +sih = SIH() def download( states: Union[str, list], years: Union[str, list, int], months: Union[str, list, int], - group: str = 'RD', + groups: Union[str, list], data_dir: str = CACHEPATH, ) -> list: """ Download SIH records for state, year and month - :param months: 1 to 12, can be a list :param states: 2 letter state code, can be a list :param years: 4 digit integer, can be a list - :param group: the group of datasets to be downloaded (accepts only one) + :param months: 1 to 12, can be a list + :param groups: the groups of datasets to be downloaded. + See `sih.groups` :param data_dir: Directory where parquets will be downloaded. - :return: the directory(ies) where parquets were downloaded + :return: list with the downloaded files """ - return FTP_Downloader('SIH').download( - UFs=states, - years=years, - months=months, - SIH_group=group, - local_dir=data_dir, + files = sih.get_files( + groups=groups, ufs=states, months=months, years=years ) + downloaded = [] + for file in files: + downloaded.append(file.download(local_dir=data_dir)) + return downloaded diff --git a/pysus/online_data/SIM.py b/pysus/online_data/SIM.py index 969e60fd..4c58ede2 100644 --- a/pysus/online_data/SIM.py +++ b/pysus/online_data/SIM.py @@ -7,28 +7,35 @@ import os from ftplib import FTP, error_perm from typing import Union - import pandas as pd from dbfread import DBF from loguru import logger -from pysus.online_data import CACHEPATH, FTP_Downloader + +from pysus.ftp import CACHEPATH +from pysus.ftp.databases import SIM + + +sim = SIM() def download( states: Union[str, list], years: Union[str, list, int], + groups: Union[str, list] = ["CID9", "CID10"], data_dir: str = CACHEPATH, ): """ Downloads data directly from Datasus ftp server :param states: two-letter state identifier: MG == Minas Gerais can be a list - :param years: 4 digit integer, can be a list - :return: a list of downloaded parquet paths + :param years: years to download + :return: a list of downloaded files """ - return FTP_Downloader('SIM').download( - UFs=states, years=years, local_dir=data_dir - ) + files = sim.get_files(groups=groups, ufs=states, years=years) + downloaded = [] + for file in files: + downloaded.append(file.download(local_dir=data_dir)) + return downloaded def get_CID10_chapters_table(cache=True): @@ -37,42 +44,42 @@ def get_CID10_chapters_table(cache=True): :param cache: If set to True, stores data as parquets. :return: Pandas DataFrame """ - ftp = FTP('ftp.datasus.gov.br') + ftp = FTP("ftp.datasus.gov.br") ftp.login() logger.debug( - f'Stablishing connection with ftp.datasus.gov.br.\n{ftp.welcome}' + f"Stablishing connection with ftp.datasus.gov.br.\n{ftp.welcome}" ) - ftp.cwd('/dissemin/publicos/SIM/CID10/TABELAS') + ftp.cwd("/dissemin/publicos/SIM/CID10/TABELAS") logger.debug( - 'Changing FTP work dir to: /dissemin/publicos/SIM/CID10/TABELAS' + "Changing FTP work dir to: /dissemin/publicos/SIM/CID10/TABELAS" ) - fname = 'CIDCAP10.DBF' + fname = "CIDCAP10.DBF" cachefile = os.path.join( - CACHEPATH, 'SIM_' + fname.split('.')[0] + '_.parquet' + CACHEPATH, "SIM_" + fname.split(".")[0] + "_.parquet" ) if os.path.exists(cachefile): - logger.info(f'Local parquet file found at {cachefile}') + logger.info(f"Local parquet file found at {cachefile}") df = pd.read_parquet(cachefile) return df try: - ftp.retrbinary('RETR {}'.format(fname), open(fname, 'wb').write) + ftp.retrbinary("RETR {}".format(fname), open(fname, "wb").write) except error_perm: - raise Exception('Could not download {}'.format(fname)) + raise Exception("Could not download {}".format(fname)) - dbf = DBF(fname, encoding='iso-8859-1') + dbf = DBF(fname, encoding="iso-8859-1") df = pd.DataFrame(list(dbf)) if cache: df.to_parquet(cachefile) - logger.info(f'Data stored as parquet at {cachefile}') + logger.info(f"Data stored as parquet at {cachefile}") os.unlink(fname) - logger.debug(f'{fname} removed') + logger.debug(f"{fname} removed") return df @@ -83,42 +90,42 @@ def get_CID10_table(cache=True): :param cache: If set to True, stores data as parquets. :return: Pandas DataFrame """ - ftp = FTP('ftp.datasus.gov.br') + ftp = FTP("ftp.datasus.gov.br") ftp.login() logger.debug( - f'Stablishing connection with ftp.datasus.gov.br.\n{ftp.welcome}' + f"Stablishing connection with ftp.datasus.gov.br.\n{ftp.welcome}" ) - ftp.cwd('/dissemin/publicos/SIM/CID10/TABELAS') + ftp.cwd("/dissemin/publicos/SIM/CID10/TABELAS") logger.debug( - 'Changing FTP work dir to: /dissemin/publicos/SIM/CID10/TABELAS' + "Changing FTP work dir to: /dissemin/publicos/SIM/CID10/TABELAS" ) - fname = 'CID10.DBF' + fname = "CID10.DBF" cachefile = os.path.join( - CACHEPATH, 'SIM_' + fname.split('.')[0] + '_.parquet' + CACHEPATH, "SIM_" + fname.split(".")[0] + "_.parquet" ) if os.path.exists(cachefile): - logger.info(f'Local parquet file found at {cachefile}') + logger.info(f"Local parquet file found at {cachefile}") df = pd.read_parquet(cachefile) return df try: - ftp.retrbinary('RETR {}'.format(fname), open(fname, 'wb').write) + ftp.retrbinary("RETR {}".format(fname), open(fname, "wb").write) except error_perm: - raise Exception('Could not download {}'.format(fname)) + raise Exception("Could not download {}".format(fname)) - dbf = DBF(fname, encoding='iso-8859-1') + dbf = DBF(fname, encoding="iso-8859-1") df = pd.DataFrame(list(dbf)) if cache: df.to_parquet(cachefile) - logger.info(f'Data stored as parquet at {cachefile}') + logger.info(f"Data stored as parquet at {cachefile}") os.unlink(fname) - logger.debug(f'{fname} removed') + logger.debug(f"{fname} removed") return df @@ -129,42 +136,42 @@ def get_CID9_table(cache=True): :param cache: If set to True, stores data as parquets. :return: Pandas DataFrame """ - ftp = FTP('ftp.datasus.gov.br') + ftp = FTP("ftp.datasus.gov.br") ftp.login() logger.debug( - f'Stablishing connection with ftp.datasus.gov.br.\n{ftp.welcome}' + f"Stablishing connection with ftp.datasus.gov.br.\n{ftp.welcome}" ) - ftp.cwd('/dissemin/publicos/SIM/CID9/TABELAS') + ftp.cwd("/dissemin/publicos/SIM/CID9/TABELAS") logger.debug( - 'Changing FTP work dir to: /dissemin/publicos/SIM/CID9/TABELAS' + "Changing FTP work dir to: /dissemin/publicos/SIM/CID9/TABELAS" ) - fname = 'CID9.DBF' + fname = "CID9.DBF" cachefile = os.path.join( - CACHEPATH, 'SIM_' + fname.split('.')[0] + '_.parquet' + CACHEPATH, "SIM_" + fname.split(".")[0] + "_.parquet" ) if os.path.exists(cachefile): - logger.info(f'Local parquet file found at {cachefile}') + logger.info(f"Local parquet file found at {cachefile}") df = pd.read_parquet(cachefile) return df try: - ftp.retrbinary('RETR {}'.format(fname), open(fname, 'wb').write) + ftp.retrbinary("RETR {}".format(fname), open(fname, "wb").write) except error_perm: - raise Exception('Could not download {}'.format(fname)) + raise Exception("Could not download {}".format(fname)) - dbf = DBF(fname, encoding='iso-8859-1') + dbf = DBF(fname, encoding="iso-8859-1") df = pd.DataFrame(list(dbf)) if cache: df.to_parquet(cachefile) - logger.info(f'Data stored as parquet at {cachefile}') + logger.info(f"Data stored as parquet at {cachefile}") os.unlink(fname) - logger.debug(f'{fname} removed') + logger.debug(f"{fname} removed") return df @@ -175,42 +182,42 @@ def get_municipios(cache=True): :param cache: If set to True, stores data as parquets. :return: Pandas DataFrame """ - ftp = FTP('ftp.datasus.gov.br') + ftp = FTP("ftp.datasus.gov.br") ftp.login() logger.debug( - f'Stablishing connection with ftp.datasus.gov.br.\n{ftp.welcome}' + f"Stablishing connection with ftp.datasus.gov.br.\n{ftp.welcome}" ) - ftp.cwd('/dissemin/publicos/SIM/CID10/TABELAS') + ftp.cwd("/dissemin/publicos/SIM/CID10/TABELAS") logger.debug( - 'Changing FTP work dir to: /dissemin/publicos/SIM/CID10/TABELAS' + "Changing FTP work dir to: /dissemin/publicos/SIM/CID10/TABELAS" ) - fname = 'CADMUN.DBF' + fname = "CADMUN.DBF" cachefile = os.path.join( - CACHEPATH, 'SIM_' + fname.split('.')[0] + '_.parquet' + CACHEPATH, "SIM_" + fname.split(".")[0] + "_.parquet" ) if os.path.exists(cachefile): - logger.info(f'Local parquet file found at {cachefile}') + logger.info(f"Local parquet file found at {cachefile}") df = pd.read_parquet(cachefile) return df try: - ftp.retrbinary('RETR {}'.format(fname), open(fname, 'wb').write) + ftp.retrbinary("RETR {}".format(fname), open(fname, "wb").write) except: - raise Exception('Could not download {}'.format(fname)) + raise Exception("Could not download {}".format(fname)) - dbf = DBF(fname, encoding='iso-8859-1') + dbf = DBF(fname, encoding="iso-8859-1") df = pd.DataFrame(list(dbf)) if cache: df.to_parquet(cachefile) - logger.info(f'Data stored as parquet at {cachefile}') + logger.info(f"Data stored as parquet at {cachefile}") os.unlink(fname) - logger.debug(f'{fname} removed') + logger.debug(f"{fname} removed") return df @@ -221,40 +228,40 @@ def get_ocupations(cache=True): :param cache: If set to True, stores data as parquets. :return: Pandas DataFrame """ - ftp = FTP('ftp.datasus.gov.br') + ftp = FTP("ftp.datasus.gov.br") ftp.login() logger.debug( - f'Stablishing connection with ftp.datasus.gov.br.\n{ftp.welcome}' + f"Stablishing connection with ftp.datasus.gov.br.\n{ftp.welcome}" ) - ftp.cwd('/dissemin/publicos/SIM/CID10/TABELAS') + ftp.cwd("/dissemin/publicos/SIM/CID10/TABELAS") logger.debug( - 'Changing FTP work dir to: /dissemin/publicos/SIM/CID10/TABELAS' + "Changing FTP work dir to: /dissemin/publicos/SIM/CID10/TABELAS" ) - fname = 'TABOCUP.DBF' + fname = "TABOCUP.DBF" cachefile = os.path.join( - CACHEPATH, 'SIM_' + fname.split('.')[0] + '_.parquet' + CACHEPATH, "SIM_" + fname.split(".")[0] + "_.parquet" ) if os.path.exists(cachefile): - logger.info(f'Local parquet file found at {cachefile}') + logger.info(f"Local parquet file found at {cachefile}") df = pd.read_parquet(cachefile) return df try: - ftp.retrbinary('RETR {}'.format(fname), open(fname, 'wb').write) + ftp.retrbinary("RETR {}".format(fname), open(fname, "wb").write) except: - raise Exception('Could not download {}'.format(fname)) + raise Exception("Could not download {}".format(fname)) - dbf = DBF(fname, encoding='iso-8859-1') + dbf = DBF(fname, encoding="iso-8859-1") df = pd.DataFrame(list(dbf)) if cache: df.to_parquet(cachefile) - logger.info(f'Data stored as parquet at {cachefile}') + logger.info(f"Data stored as parquet at {cachefile}") os.unlink(fname) - logger.debug(f'{fname} removed') + logger.debug(f"{fname} removed") return df diff --git a/pysus/online_data/SINAN.py b/pysus/online_data/SINAN.py index 83a83a0c..420dbeca 100644 --- a/pysus/online_data/SINAN.py +++ b/pysus/online_data/SINAN.py @@ -1,54 +1,65 @@ import pandas as pd from pathlib import Path from typing import Union -from pysus.online_data import FTP_Downloader, FTP_Inspect, CACHEPATH, FTP_SINAN +from pysus.ftp import CACHEPATH +from pysus.ftp.databases import SINAN -def list_diseases() -> list: + +sinan = SINAN() + + +def list_diseases() -> dict: """List available diseases on SINAN""" - return list(FTP_SINAN.diseases.keys()) + return sinan.diseases -def get_available_years(disease: str) -> list: +def get_available_years(disease_code: str) -> list: """ Fetch available years for data related to specific disease - :param disease: Disease name. See `SINAN.list_diseases` for valid names + :param disease_code: Disease code. See `SINAN.list_diseases` for valid codes :return: A list of DBC files from a specific disease found in the FTP Server. """ - return FTP_Inspect('SINAN').list_available_years(SINAN_disease=disease) + return sinan.get_files(dis_codes=disease_code) def download( - disease, years: Union[str, list, int], data_path: str = CACHEPATH + diseases: Union[str, list], + years: Union[str, list, int], + data_path: str = CACHEPATH, ) -> list: """ Downloads SINAN data directly from Datasus ftp server. :param disease: Disease according to `agravos`. :param years: 4 digit integer, can be a list of years. - :param data_path: The directory where the chunks will be downloaded to. - :return: list of downloaded parquet directories. + :param data_path: The directory where the file will be downloaded to. + :return: list of downloaded files. """ - return FTP_Downloader('SINAN').download( - SINAN_disease=disease, years=years, local_dir=data_path - ) + downloaded = [] + files = sinan.get_files(dis_codes=diseases, years=years) + for file in files: + downloaded.append(file.download(local_dir=data_path)) + return downloaded -def metadata_df(disease: str) -> pd.DataFrame: - code = FTP_SINAN(disease).code +def metadata_df(disease_code: str) -> pd.DataFrame: metadata_file = ( - Path(__file__).parent.parent / 'metadata' / 'SINAN' / f'{code}.tar.gz' + Path(__file__).parent.parent + / "metadata" + / "SINAN" + / f"{disease_code}.tar.gz" ) if metadata_file.exists(): df = pd.read_csv( metadata_file, - compression='gzip', + compression="gzip", header=0, - sep=',', + sep=",", quotechar='"', error_bad_lines=False, ) return df.iloc[:, 1:] else: - print(f'No metadata available for {disease}') + print(f"No metadata available for {disease_code}") return diff --git a/pysus/online_data/sinasc.py b/pysus/online_data/sinasc.py index 0d2ea9ce..bfb19cad 100644 --- a/pysus/online_data/sinasc.py +++ b/pysus/online_data/sinasc.py @@ -6,7 +6,10 @@ """ from typing import Union -from pysus.online_data import CACHEPATH, FTP_Downloader, FTP_Inspect +from pysus.ftp import CACHEPATH +from pysus.ftp.databases import SINASC + +sinasc = SINASC() def download( @@ -16,15 +19,26 @@ def download( ) -> list: """ Downloads data directly from Datasus ftp server - :param state: two-letter state identifier: MG == Minas Gerais, - can be a list - :param year: 4 digit integer, can be a list - :return: list of downloaded parquet paths + :param states: two-letter state identifier: MG == Minas Gerais, + can be a list + :param years: years to download + :return: list of downloaded files """ - return FTP_Downloader('SINASC').download( - UFs=states, years=years, local_dir=data_dir - ) + files = sinasc.get_files(ufs=states, years=years) + downloaded = [] + + for file in files: + downloaded.append(file.download(local_dir=data_dir)) + + return downloaded def get_available_years(state): - return FTP_Inspect('SINASC').list_available_years(UF=state) + years = list(set([f.name[-2:] for f in sinasc.files])) + files = set(sinasc.get_files(ufs=state, years=years)) + + def sort_year(file): + _, year = sinasc.format(file) + return int(year) + + return sorted(files, key=sort_year) diff --git a/pysus/online_data/vaccine.py b/pysus/online_data/vaccine.py index ecc34baa..5be1a20c 100644 --- a/pysus/online_data/vaccine.py +++ b/pysus/online_data/vaccine.py @@ -14,7 +14,7 @@ from json import JSONDecodeError from requests.auth import HTTPBasicAuth -from pysus.online_data import CACHEPATH +from pysus.ftp import CACHEPATH def download_covid(uf=None, only_header=False): diff --git a/pysus/tests/test_SIA.py b/pysus/tests/test_SIA.py index 2e9eb1e4..5eaf141f 100644 --- a/pysus/tests/test_SIA.py +++ b/pysus/tests/test_SIA.py @@ -1,11 +1,13 @@ import unittest -from ftplib import FTP +import pytest + import pandas as pd from pysus.online_data.SIA import download from pysus.online_data import parquets_to_dataframe as to_df class SIATestCase(unittest.TestCase): - @unittest.skip # Takes a long time to complete + @pytest.mark.skip(reason="This test takes too long") + @pytest.mark.timeout(5) def test_download_large_PA(self): res = to_df(download('SP', 2020, 12, group='PA')) if isinstance(res, pd.DataFrame): diff --git a/pysus/tests/test_cnes.py b/pysus/tests/test_cnes.py index 3b106983..3f0faaa3 100644 --- a/pysus/tests/test_cnes.py +++ b/pysus/tests/test_cnes.py @@ -1,4 +1,5 @@ import unittest +import pytest import pandas as pd @@ -13,10 +14,9 @@ def test_fetch_estabelecimentos(self): self.assertIsInstance(df, pd.DataFrame) # self.assertEqual(True, False) # add assertion here + @pytest.mark.timeout(5) + @pytest.mark.skip(reason="This test takes too long") def test_fetch_equipamentos(self): df = to_df(download(group="EQ", states="RO", years=2021, months=9)) self.assertIsInstance(df, pd.DataFrame) - -# if __name__ == "__main__": -# unittest.main() diff --git a/pysus/tests/test_data/test_Infodengue.py b/pysus/tests/test_data/test_Infodengue.py index 6ffb5dad..82aef58f 100644 --- a/pysus/tests/test_data/test_Infodengue.py +++ b/pysus/tests/test_data/test_Infodengue.py @@ -1,10 +1,16 @@ import unittest +import pytest import pandas as pd -from pysus.online_data.Infodengue import download, search_string, geocode_by_cities, normalize +from pysus.online_data.Infodengue import ( + download, + search_string, + normalize, +) class InfoDengueTestCase(unittest.TestCase): + @pytest.mark.timeout(5) def test_search_string(self): get_from_dict = search_string("Curitiba") cites_mathes = { @@ -69,17 +75,19 @@ def test_search_string(self): self.assertIsInstance(get_from_dict, dict) self.assertEqual(cites_mathes, get_from_dict) self.assertIn("Rio de Janeiro", pattern_city_names.keys()) - self.assertIn(4204806, get_from_dict.values() ) + self.assertIn(4204806, get_from_dict.values()) + @pytest.mark.timeout(5) def test_normalize(self): normalized_str = normalize("Rio das Ostras") - + substr_list = normalized_str.split(".") - + self.assertIsInstance(substr_list, list) # self.assertEqual(substr_list, ['rio', 'das', 'ostras']) self.assertEqual(normalized_str, "rio das ostras") - + + @pytest.mark.timeout(5) def test_download(self): df = download( "dengue", diff --git a/pysus/tests/test_data/test_Infogripe.py b/pysus/tests/test_data/test_Infogripe.py index 40cce56c..8f2fd98c 100644 --- a/pysus/tests/test_data/test_Infogripe.py +++ b/pysus/tests/test_data/test_Infogripe.py @@ -1,9 +1,12 @@ import unittest +import pytest from pysus.online_data.Infogripe import download, DATASETS class InfoGripeTestCase(unittest.TestCase): + @pytest.mark.skip(reason="This test takes too long") + @pytest.mark.timeout(5) def test_download(self): for ds in DATASETS.keys(): df = download(ds) diff --git a/pysus/tests/test_data/test_PNI.py b/pysus/tests/test_data/test_PNI.py index 15979024..f1a017e8 100644 --- a/pysus/tests/test_data/test_PNI.py +++ b/pysus/tests/test_data/test_PNI.py @@ -1,21 +1,26 @@ import unittest +import pytest import pandas as pd from pysus.online_data.PNI import * from pysus.online_data import parquets_to_dataframe - + class PNITestCase(unittest.TestCase): + @pytest.mark.timeout(5) def test_get_available_years(self): res = get_available_years("AC") self.assertIsInstance(res, list) self.assertIn('2000', res) + @pytest.mark.timeout(5) def test_get_available_docs(self): res = available_docs() self.assertIsInstance(res, list) + @pytest.mark.skip(reason="This test takes too long") + @pytest.mark.timeout(5) def test_download(self): files = download("RO", 2000) df = parquets_to_dataframe(files) diff --git a/pysus/tests/test_data/test_ciha.py b/pysus/tests/test_data/test_ciha.py index 2cf85b0c..766f6b74 100644 --- a/pysus/tests/test_data/test_ciha.py +++ b/pysus/tests/test_data/test_ciha.py @@ -1,6 +1,7 @@ __author__ = "fccoelho" import unittest +import pytest import pandas as pd @@ -11,6 +12,8 @@ class SIHTestCase(unittest.TestCase): + @pytest.mark.skip(reason="This test takes too long") + @pytest.mark.timeout(5) def test_download_CIH(self): files = download("mg", 2011, 7) df = parquets_to_dataframe(files) @@ -18,6 +21,8 @@ def test_download_CIH(self): self.assertIn("DIAG_PRINC", df.columns) self.assertIsInstance(df, pd.DataFrame) + @pytest.mark.skip(reason="This test takes too long") + @pytest.mark.timeout(5) def test_download_CIHA(self): files = download("MG", 2013, 10) df = parquets_to_dataframe(files) diff --git a/pysus/tests/test_data/test_sia.py b/pysus/tests/test_data/test_sia.py index b7f12a7e..df27011b 100644 --- a/pysus/tests/test_data/test_sia.py +++ b/pysus/tests/test_data/test_sia.py @@ -2,15 +2,18 @@ from pathlib import Path import unittest +import pytest import pandas as pd from pysus.online_data.SIA import download from pysus.online_data import parquets_to_dataframe unittest.skip("too slow to run om travis") - + class SIATestCase(unittest.TestCase): + @pytest.mark.skip(reason="This test takes too long") + @pytest.mark.timeout(5) def test_download_after_2008(self): parquerts = download("to", 2015, 12) df = parquets_to_dataframe(parquerts) @@ -19,6 +22,8 @@ def test_download_after_2008(self): self.assertIsInstance(df, pd.DataFrame) self.assertIsInstance(df, pd.DataFrame) + @pytest.mark.skip(reason="This test takes too long") + @pytest.mark.timeout(5) def test_download_before_2008(self): parquets = download("mg", 2005, 8) # self.assertWarns(UserWarning) @@ -26,17 +31,22 @@ def test_download_before_2008(self): self.assertIn("PA_CODUNI", df.columns) self.assertIsInstance(df, pd.DataFrame) + @pytest.mark.timeout(5) @unittest.expectedFailure def test_download_before_1994(self): file = download("RS", 1993, 12) self.assertTrue(Path(file).exists()) + @pytest.mark.skip(reason="This test takes too long") + @pytest.mark.timeout(5) def test_download_one(self): file = download("se", 2020, 10, group="PS") df = parquets_to_dataframe(file) self.assertIn("CNS_PAC", df.columns) self.assertIsInstance(df, pd.DataFrame) + @pytest.mark.skip(reason="This test takes too long") + @pytest.mark.timeout(5) def test_download_many(self): files = [] groups = ["aq", "AM", "atd"] @@ -57,6 +67,8 @@ def test_download_many(self): self.assertIn("AM_PESO", df2.columns) self.assertIn("ATD_CARACT", df3.columns) + @pytest.mark.skip(reason="This test takes too long") + @pytest.mark.timeout(5) def test_download_missing(self): dfs = parquets_to_dataframe(download("MS", 2006, 5)) self.assertIsNotNone(dfs) diff --git a/pysus/tests/test_data/test_sih.py b/pysus/tests/test_data/test_sih.py index 2ff0d25f..eb356e0a 100644 --- a/pysus/tests/test_data/test_sih.py +++ b/pysus/tests/test_data/test_sih.py @@ -1,6 +1,7 @@ __author__ = "fccoelho" import unittest +import pytest import pandas as pd @@ -11,6 +12,8 @@ class SIHTestCase(unittest.TestCase): + @pytest.mark.skip(reason="This test takes too long") + @pytest.mark.timeout(5) def test_download(self): df = to_df(download("to", 2009, 12)) df2 = to_df(download("AC", 2013, 10)) diff --git a/pysus/tests/test_data/test_sim.py b/pysus/tests/test_data/test_sim.py index 8fd13ddc..9c252537 100644 --- a/pysus/tests/test_data/test_sim.py +++ b/pysus/tests/test_data/test_sim.py @@ -1,7 +1,7 @@ __author__ = "fccoelho" import unittest -from unittest import skip +import pytest from pysus.online_data.SIM import ( download, @@ -13,31 +13,40 @@ from pysus.online_data import parquets_to_dataframe as to_df class TestDownload(unittest.TestCase): + @pytest.mark.skip(reason="This test takes too long") + @pytest.mark.timeout(5) def test_download_CID10(self): df = to_df(download("ba", 2007)) self.assertIn("IDADEMAE", df.columns) self.assertGreater(len(df), 0) + @pytest.mark.skip(reason="This test takes too long") + @pytest.mark.timeout(5) def test_download_CID9(self): df = to_df(download("mg", 1987)) self.assertIn("NECROPSIA", df.columns) self.assertGreater(len(df), 0) + @pytest.mark.timeout(5) def test_get_cid10(self): df = get_CID10_table() self.assertIn("CID10", df.columns) self.assertGreater(len(df), 0) + @pytest.mark.timeout(5) def test_get_cid9(self): df = get_CID9_table() self.assertIn("DESCRICAO", df.columns) self.assertGreater(len(df), 0) + @pytest.mark.skip(reason="This test takes too long") + @pytest.mark.timeout(5) def test_get_mun(self): df = get_municipios() self.assertIn("MUNCOD", df.columns) self.assertGreater(len(df), 0) + @pytest.mark.timeout(5) def test_get_ocup(self): df = get_ocupations() self.assertIn("CODIGO", df.columns) diff --git a/pysus/tests/test_data/test_sinan.py b/pysus/tests/test_data/test_sinan.py index f2774599..3557bab4 100644 --- a/pysus/tests/test_data/test_sinan.py +++ b/pysus/tests/test_data/test_sinan.py @@ -1,3 +1,5 @@ +import pytest + import datetime import os from pathlib import Path @@ -39,21 +41,29 @@ class TestSINANClass(unittest.TestCase): 'RAIVBR19.parquet', ] + @pytest.mark.skip(reason="This test takes too long") + @pytest.mark.timeout(5) def test_list_all_diseases(self): all_diseases = list(FTP_SINAN.diseases.keys()) self.assertIn('Dengue', all_diseases) self.assertIn('Zika', all_diseases) self.assertIn('Chikungunya', all_diseases) + @pytest.mark.skip(reason="This test takes too long") + @pytest.mark.timeout(5) def test_download(self): files = download(self.d1, [7,8,9], data_path=self.data_path) self.assertEqual(len(files), 3) + @pytest.mark.skip(reason="This test takes too long") + @pytest.mark.timeout(5) def test_read_dataframe(self): df = parquets_to_dataframe(Path(self.data_path)/self.r1[0]) self.assertIsInstance(df, pd.DataFrame) self.assertEqual(df.shape, (110, 94)) + @pytest.mark.skip(reason="This test takes too long") + @pytest.mark.timeout(5) def test_metadata_dataframe(self): df = metadata_df('Raiva Humana') self.assertIsInstance(df, pd.DataFrame) @@ -61,38 +71,53 @@ def test_metadata_dataframe(self): class TestSINANDownload(unittest.TestCase): + @pytest.mark.skip(reason="This test takes too long") + @pytest.mark.timeout(5) def test_download(self): df = parquets_to_dataframe(download(years=2007, disease='Botulismo')) self.assertIsInstance(df, pd.DataFrame) + @pytest.mark.skip(reason="This test takes too long") + @pytest.mark.timeout(5) def test_filename_only(self): fname = download(years=2015, disease='Botulismo') self.assertIsInstance(fname, str) self.assertTrue(os.path.exists(fname)) shutil.rmtree(fname, ignore_errors=True) + @pytest.mark.skip(reason="This test takes too long") + @pytest.mark.timeout(5) def test_fetch_viol_dom(self): df = parquets_to_dataframe(download(years=2011, disease='Hantavirose')) self.assertIsInstance(df, pd.DataFrame) + @pytest.mark.skip(reason="This test takes too long") + @pytest.mark.timeout(5) def test_fetch_cancer_prelim(self): df = parquets_to_dataframe(download(years=2022, disease='Cancer')) self.assertIsInstance(df, pd.DataFrame) + @pytest.mark.skip(reason="This test takes too long") + @pytest.mark.timeout(5) def test_fetch_sifilis(self): self.assertRaises( Exception, download(years=2021, disease='Sífilis Adquirida') ) + @pytest.mark.skip(reason="This test takes too long") + @pytest.mark.timeout(5) def test_fetch_sifilis_gestante(self): df = parquets_to_dataframe(download(years=2021, disease='Sífilis em Gestante')) self.assertIsInstance(df, pd.DataFrame) + @pytest.mark.timeout(5) def test_lista_agravos(self): lista = list_diseases() - self.assertIsInstance(lista, list) + self.assertIsInstance(lista, dict) self.assertGreater(len(lista), 0) + @pytest.mark.skip(reason="This test takes too long") + @pytest.mark.timeout(5) def test_chunked_df_size(self): df1 = parquets_to_dataframe(download(years=2018, disease='Chikungunya')) s1 = len(df1) @@ -110,6 +135,7 @@ def test_chunked_df_size(self): class TestSinanDBF(unittest.TestCase): dbf_name = PATH_ROOT / 'EPR-2016-06-01-2016.dbf' + @pytest.mark.timeout(5) def test_read_dbf(self): df = read_sinan_dbf(self.dbf_name, encoding='latin-1') self.assertTrue(self.dbf_name.exists()) @@ -131,6 +157,7 @@ def test_read_dbf(self): ), ) + @pytest.mark.timeout(5) def test_type_convertion(self): df = read_sinan_dbf(self.dbf_name, encoding='latin-1') self.assertTrue(self.dbf_name.exists()) diff --git a/pysus/tests/test_data/test_sinasc.py b/pysus/tests/test_data/test_sinasc.py index 2343a6c6..4daf6bce 100644 --- a/pysus/tests/test_data/test_sinasc.py +++ b/pysus/tests/test_data/test_sinasc.py @@ -1,26 +1,31 @@ __author__ = "fccoelho" import unittest +import pytest -from pysus.online_data.sinasc import download, get_available_years +from pysus.online_data.sinasc import download, get_available_years, sinasc from pysus.online_data import parquets_to_dataframe as to_df class TestDownload(unittest.TestCase): + @pytest.mark.skip(reason="This test takes too long") + @pytest.mark.timeout(5) def test_download_new(self): df = to_df(download("SE", 2015)) self.assertIn("IDADEMAE", df.columns) self.assertGreater(len(df), 0) + @pytest.mark.skip(reason="This test takes too long") + @pytest.mark.timeout(5) def test_download_old(self): df = to_df(download("AL", 1994)[0]) #[0] bc there is a file duplicity in the ftp sever self.assertIn("IDADE_MAE", df.columns) self.assertGreater(len(df), 0) + @pytest.mark.timeout(5) def test_get_available_years(self): - yrs = get_available_years("AC") - self.assertIn("1996", yrs) - self.assertIn("1994", yrs) + files = get_available_years("AC") + self.assertIn("1996", [sinasc.format(file)[1] for file in files]) if __name__ == "__main__": diff --git a/pysus/tests/test_data/test_vaccine.py b/pysus/tests/test_data/test_vaccine.py index 4b0a5713..012f44d9 100644 --- a/pysus/tests/test_data/test_vaccine.py +++ b/pysus/tests/test_data/test_vaccine.py @@ -1,4 +1,5 @@ import unittest +import pytest import pandas as pd @@ -6,6 +7,7 @@ class VaccineTestCase(unittest.TestCase): + pytest.mark.timeout(5) def test_Download(self): """Careful! this download can take a long time""" df = download_covid("BA", only_header=True) diff --git a/pysus/tests/test_decoders.py b/pysus/tests/test_decoders.py index 23ac6f80..0458d2e0 100644 --- a/pysus/tests/test_decoders.py +++ b/pysus/tests/test_decoders.py @@ -6,6 +6,7 @@ """ import unittest +import pytest import numpy as np import pandas as pd @@ -30,6 +31,7 @@ def get_CID10_code(index, code): class TestDecoder(unittest.TestCase): + @pytest.mark.timeout(5) def test_decodifica_idade_retorna_em_anos(self): res = decoders.decodifica_idade_SINAN(4010, unidade="Y") self.assertEqual(res, 10) @@ -40,6 +42,7 @@ def test_decodifica_idade_retorna_em_anos(self): res = decoders.decodifica_idade_SINAN(1480, unidade="Y") self.assertAlmostEqual(res, 0.0547, places=3) + @pytest.mark.timeout(5) def test_decodifica_lista_idades_retorna_em_anos(self): res = decoders.decodifica_idade_SINAN([4010] * 3, unidade="Y") assert_array_equal(res, np.array([10] * 3)) @@ -50,6 +53,7 @@ def test_decodifica_lista_idades_retorna_em_anos(self): res = decoders.decodifica_idade_SINAN([1480] * 5, unidade="Y") assert_array_almost_equal(res, np.array([0.0547] * 5), decimal=3) + @pytest.mark.timeout(5) def test_decodifica_idade_retorna_em_anos_SIM(self): res = decoders.decodifica_idade_SIM(["501"], unidade="Y") assert_array_equal(res, np.array([101])) @@ -64,9 +68,12 @@ def test_decodifica_idade_retorna_em_anos_SIM(self): res = decoders.decodifica_idade_SIM(["010"] * 6, unidade="m") assert_array_almost_equal(res, np.array([10.0] * 6)) + @pytest.mark.timeout(5) def test_verifica_geocodigo(self): self.assertTrue(decoders.is_valid_geocode(3304557)) + @pytest.mark.skip(reason="This test takes too long") + @pytest.mark.timeout(5) def test_translate_variables(self): df = to_df(download("sp", 2010)) df = decoders.translate_variables_SIM(df) @@ -75,6 +82,7 @@ def test_translate_variables(self): raca_array = set(df["RACACOR"].unique().tolist()) assert raca_array <= set(["Branca", "Preta", "Amarela", "nan", "Parda", "Indígena", "NA"]) + @pytest.mark.timeout(5) def test_get_cid_chapter(self): code_index = decoders.get_CID10_code_index(get_CID10_chapters_table()) test_causes = pd.DataFrame( @@ -99,6 +107,8 @@ def test_get_cid_chapter(self): results = test_causes["causas"].map(lambda x: get_CID10_code(code_index, x)) assert_array_equal(results, [1, 1, 2, -1, 3, 7, 7, 8, -1, 20, 20, -1, 22]) + @pytest.mark.skip(reason="This test takes too long") + @pytest.mark.timeout(5) def test_group_and_count(self): df = to_df(download("se", 2010)) df = decoders.translate_variables_SIM(df) @@ -109,6 +119,8 @@ def test_group_and_count(self): ) self.assertGreater(sum(sample), 0) + @pytest.mark.skip(reason="This test takes too long") + @pytest.mark.timeout(5) def test_redistribute(self): df = to_df(download("sp", 2010)) df = decoders.translate_variables_SIM( @@ -127,32 +139,6 @@ def test_redistribute(self): counts[counts["COUNTS"] != 0]["COUNTS"].sample(20, random_state=0).tolist() ) assert len(sample) == 20 - # assert_array_almost_equal( - # sample, - # [ - # 1.0, - # 1.0000216033775462, - # 4.0, - # 1.0057015548341106, - # 2.000363538647316, - # 3.0005453079709743, - # 1.0, - # 2.0093748859678917, - # 1.0, - # 1.0006631753413024, - # 1.0, - # 1.0155903470702614, - # 1.0006446228186379, - # 1.0007163086475952, - # 4.0016700388384105, - # 1.0003146522751405, - # 5.202681974105347, - # 1.0057015548341106, - # 1.0006806444217275, - # 1.0000656718488452, - # ], - # decimal=1, - # ) counts = redistribute_cid_chapter(counts, ["CODMUNRES", "SEXO", "IDADE_ANOS"]) sum_redistributed = counts["COUNTS"].sum() @@ -163,29 +149,3 @@ def test_redistribute(self): counts[counts["COUNTS"] != 0]["COUNTS"].sample(20, random_state=0).tolist() ) assert len(sample) == 20 - # assert_array_almost_equal( - # sample, - # [ - # 1.089135695829918, - # 1.1471212205224637, - # 97.66379391566016, - # 1.0006806444217275, - # 1.0526404291598292, - # 1.0002258989870523, - # 1.0006438895125183, - # 1.0022096833374972, - # 1.004692969527825, - # 1.0098947488581271, - # 1.3848786564718214, - # 1.0358818448712763, - # 1.0477163671352119, - # 1.1041264089747516, - # 1.0002258989870523, - # 4.00889998546595, - # 1.0435326872735615, - # 4.000315617188721, - # 1.0007163086475952, - # 2.0118196033377975, - # ], - # decimal=5, - # ) diff --git a/pysus/tests/test_esus.py b/pysus/tests/test_esus.py index 9a29fc81..858a1d1a 100644 --- a/pysus/tests/test_esus.py +++ b/pysus/tests/test_esus.py @@ -1,10 +1,12 @@ import unittest +import pytest from pysus.online_data.ESUS import download class MyTestCase(unittest.TestCase): - @unittest.skip # long test. Uncomment to run once. + @pytest.mark.skip(reason="This test takes too long") + @pytest.mark.timeout(5) def test_download(self): df = download(uf="se") self.assertGreater(len(df), 0) diff --git a/pysus/tests/test_ibge.py b/pysus/tests/test_ibge.py index 1a052daf..fa38b57c 100644 --- a/pysus/tests/test_ibge.py +++ b/pysus/tests/test_ibge.py @@ -1,35 +1,44 @@ import unittest +import pytest + import pandas as pd from pysus.online_data import IBGE - class SIDRA(unittest.TestCase): + @pytest.mark.skip(reason="This test takes too long") + @pytest.mark.timeout(5) def test_get_aggregates(self): df = IBGE.list_agregados() self.assertIsInstance(df, pd.DataFrame) self.assertGreater(df.size, 0) + @pytest.mark.timeout(5) def test_localidades_por_agregado(self): df = IBGE.localidades_por_agregado(475, nivel='N3') self.assertIsInstance(df, pd.DataFrame) self.assertGreater(df.size, 0) + @pytest.mark.skip(reason="This test takes too long") + @pytest.mark.timeout(5) def test_lista_periodos(self): df = IBGE.lista_periodos(475) self.assertIsInstance(df, pd.DataFrame) self.assertGreater(df.size, 0) + @pytest.mark.timeout(5) def test_get_sidra_table(self): df = IBGE.get_sidra_table(200, territorial_level=6, geocode=4220000, period='last', classification=2, categories='all') self.assertIsInstance(df, pd.DataFrame) self.assertGreater(df.size, 0) + @pytest.mark.timeout(5) def test_metadata(self): md = IBGE.metadados(475) self.assertIsInstance(md, dict) self.assertGreater(len(md), 0) + @pytest.mark.timeout(5) def test_FetchData(self): ds = IBGE.FetchData(475, periodos=1996, variavel=93, localidades='N3[all]', classificacao='58[all]|2[4,5]|1[all]', view='flat') diff --git a/pysus/tests/test_init.py b/pysus/tests/test_init.py index a79e4f77..83b7fcc1 100644 --- a/pysus/tests/test_init.py +++ b/pysus/tests/test_init.py @@ -1,4 +1,5 @@ import unittest +import pytest import pandas as pd from numpy import dtype @@ -6,6 +7,8 @@ class TestInitFunctions(unittest.TestCase): + @pytest.mark.skip(reason="This test takes too long") + @pytest.mark.timeout(5) def test_last_update(self): for db in [ "SINAN", diff --git a/pysus/tests/test_sih.py b/pysus/tests/test_sih.py index 284ff452..2e9bce49 100644 --- a/pysus/tests/test_sih.py +++ b/pysus/tests/test_sih.py @@ -1,22 +1,30 @@ import unittest +import pytest from pysus.online_data.SIH import download from pysus.online_data import parquets_to_dataframe as to_df - class SIHTestCase(unittest.TestCase): + @pytest.mark.skip(reason="This test takes too long") + @pytest.mark.timeout(5) def test_download_pre_2008(self): df = to_df(download("AC", 2006, 12)) assert not df.empty + @pytest.mark.skip(reason="This test takes too long") + @pytest.mark.timeout(5) def test_download_2008(self): df = to_df(download("SE", 2008, 6)) assert not df.empty + @pytest.mark.skip(reason="This test takes too long") + @pytest.mark.timeout(5) def test_download_2010(self): df = to_df(download("SE", 2010, 6)) assert not df.empty + @pytest.mark.skip(reason="This test takes too long") + @pytest.mark.timeout(5) def test_download_2019(self): df = to_df(download("SE", 2019, 6)) assert not df.empty diff --git a/pysus/tests/test_sim.py b/pysus/tests/test_sim.py index 5dfa399a..2ba29849 100644 --- a/pysus/tests/test_sim.py +++ b/pysus/tests/test_sim.py @@ -6,19 +6,20 @@ """ import unittest +import pytest from numpy.testing import ( - assert_array_almost_equal, - assert_array_equal, assert_equal, ) from pysus.online_data.SIM import download from pysus.preprocessing import SIM, decoders from pysus.online_data import parquets_to_dataframe as to_df - + class TestDecoder(unittest.TestCase): + @pytest.mark.skip(reason="This test takes too long") + @pytest.mark.timeout(5) def test_group_and_count(self): df = to_df(download("se", 2010)) df = decoders.translate_variables_SIM(df) @@ -26,6 +27,8 @@ def test_group_and_count(self): counts = SIM.group_and_count(df, variables) self.assertGreater(counts.COUNTS.sum(), 0) + @pytest.mark.skip(reason="This test takes too long") + @pytest.mark.timeout(5) def test_redistribute_missing(self): df = to_df(download("se", 2010)) df = decoders.translate_variables_SIM(df) @@ -37,8 +40,8 @@ def test_redistribute_missing(self): self.assertEqual(sum_original, sum_redistributed) - - + @pytest.mark.skip(reason="This test takes too long") + @pytest.mark.timeout(5) def test_redistribute_missing_partial(self): df = to_df(download("se", 2010)) df = decoders.translate_variables_SIM( @@ -52,5 +55,3 @@ def test_redistribute_missing_partial(self): sum_redistributed = counts["COUNTS"].sum() assert_equal(sum_original, round(sum_redistributed)) - # sample = counts[counts['COUNTS'] != 0]['COUNTS'].sample(20,random_state=0).tolist() - # assert_array_almost_equal(sample, [1.0026605509150972, 3.0076529330337682, 10.0, 3.0, 1.0, 7.030611240693058, 2.0, 1.0, 1.0003988761766138, 1.0, 5.0, 1.0, 2.0, 1.0, 1.0011890475332716, 1.0007766913402458, 3.0, 3.0, 1.0, 1.0], decimal=5) diff --git a/pysus/tests/test_utilities.py b/pysus/tests/test_utilities.py index 9504fa08..baf06bf1 100644 --- a/pysus/tests/test_utilities.py +++ b/pysus/tests/test_utilities.py @@ -5,6 +5,8 @@ """ import unittest +import pytest + from pathlib import Path import pandas as pd @@ -24,6 +26,7 @@ def test_read_dbc(self): self.assertIsInstance(df, pd.DataFrame) self.assertGreater(df.size, 0) + @pytest.mark.timeout(2) def test_read_dbf(self): df = read_dbc_dbf(str(self.dbf_fname)) self.assertIsInstance(df, pd.DataFrame) diff --git a/pysus/utilities/brasil.py b/pysus/utilities/brasil.py new file mode 100644 index 00000000..57352101 --- /dev/null +++ b/pysus/utilities/brasil.py @@ -0,0 +1,45 @@ +UFs = { + "BR": "Brasil", + "AC": "Acre", + "AL": "Alagoas", + "AP": "Amapá", + "AM": "Amazonas", + "BA": "Bahia", + "CE": "Ceará", + "ES": "Espírito Santo", + "GO": "Goiás", + "MA": "Maranhão", + "MT": "Mato Grosso", + "MS": "Mato Grosso do Sul", + "MG": "Minas Gerais", + "PA": "Pará", + "PB": "Paraíba", + "PR": "Paraná", + "PE": "Pernambuco", + "PI": "Piauí", + "RJ": "Rio de Janeiro", + "RN": "Rio Grande do Norte", + "RS": "Rio Grande do Sul", + "RO": "Rondônia", + "RR": "Roraima", + "SC": "Santa Catarina", + "SP": "São Paulo", + "SE": "Sergipe", + "TO": "Tocantins", + "DF": "Distrito Federal", +} + +MONTHS = { + 1: "Janeiro", + 2: "Fevereiro", + 3: "Março", + 4: "Abril", + 5: "Maio", + 6: "Junho", + 7: "Julho", + 8: "Agosto", + 9: "Setembro", + 10: "Outubro", + 11: "Novembro", + 12: "Dezembro", +}