From e7016f06609595475139b77862460b9743bb8ba5 Mon Sep 17 00:00:00 2001 From: folhesgabriel Date: Wed, 6 Dec 2023 16:35:20 -0300 Subject: [PATCH 01/44] feat: add new poetry depencies --- pipelines/datasets/br_ms_cnes/tasks.py | 27 +- poetry.lock | 2918 ++++++++++++++++++++---- pyproject.toml | 1 + 3 files changed, 2433 insertions(+), 513 deletions(-) diff --git a/pipelines/datasets/br_ms_cnes/tasks.py b/pipelines/datasets/br_ms_cnes/tasks.py index 8428b8a9b..b3f8712e1 100644 --- a/pipelines/datasets/br_ms_cnes/tasks.py +++ b/pipelines/datasets/br_ms_cnes/tasks.py @@ -11,6 +11,7 @@ import rpy2.robjects.packages as rpackages import wget from prefect import task +from pyreaddbc import read_dbc from rpy2.robjects.packages import importr from pipelines.constants import constants @@ -136,20 +137,22 @@ def read_dbc_save_csv(file_list: list, path: str, table: str) -> str: """ log(f"wrangling {table} data") # import R's utility package - utils = rpackages.importr("utils") + # utils = rpackages.importr("utils") # select a mirror for R packages - utils.chooseCRANmirror(ind=1) + # utils.chooseCRANmirror(ind=1) - log("installing read.dbc package") - utils.install_packages("read.dbc") - readdbc = importr("read.dbc") + # log("installing read.dbc package") + # utils.install_packages("read.dbc") + # readdbc = importr("read.dbc") # list files for file in file_list: log(f"the file {file} is being converted to csv") # read dbc - dbc_file = readdbc.read_dbc(file) + # dbc_file = readdbc.read_dbc(file) + dbc_file = read_dbc(file, encoding="iso-8859-1") + # convert from r to pandas # https://rpy2.github.io/doc/latest/html/generated_rst/pandas.html#from-r-to-pandas @@ -166,11 +169,17 @@ def read_dbc_save_csv(file_list: list, path: str, table: str) -> str: log(f"{file} 1 saved") # salvar df - dbc_file.to_csvfile( + # dbc_file.to_csvfile( + # output_file, + # sep=",", + # na="", + # row_names=False, + # ) + dbc_file.to_csv( output_file, sep=",", - na="", - row_names=False, + na_rep="", + index=False, ) # delete dbc file os.system(f"rm {file}") diff --git a/poetry.lock b/poetry.lock index ac2f11dfb..99f30309d 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,41 +1,69 @@ +# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. + [[package]] name = "async-timeout" version = "4.0.3" description = "Timeout context manager for asyncio programs" -category = "main" optional = false python-versions = ">=3.7" +files = [ + {file = "async-timeout-4.0.3.tar.gz", hash = "sha256:4640d96be84d82d02ed59ea2b7105a0f7b33abe8703703cd0ab0bf87c427522f"}, + {file = "async_timeout-4.0.3-py3-none-any.whl", hash = "sha256:7405140ff1230c310e51dc27b3145b9092d659ce68ff733fb0cefe3ee42be028"}, +] [[package]] name = "attrs" version = "23.1.0" description = "Classes Without Boilerplate" -category = "main" optional = false python-versions = ">=3.7" +files = [ + {file = "attrs-23.1.0-py3-none-any.whl", hash = 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mapping tools" -category = "main" optional = false python-versions = "*" +files = [ + {file = "zict-2.0.0-py3-none-any.whl", hash = "sha256:26aa1adda8250a78dfc6a78d200bfb2ea43a34752cf58980bca75dde0ba0c6e9"}, + {file = "zict-2.0.0.tar.gz", hash = "sha256:8e2969797627c8a663575c2fc6fcb53a05e37cdb83ee65f341fc6e0c3d0ced16"}, +] [package.dependencies] heapdict = "*" @@ -2224,187 +4303,18 @@ heapdict = "*" name = "zipp" version = "3.17.0" description = "Backport of pathlib-compatible object wrapper for zip files" -category = "main" optional = false python-versions = ">=3.8" +files = [ + {file = "zipp-3.17.0-py3-none-any.whl", hash = "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31"}, + {file = "zipp-3.17.0.tar.gz", hash = "sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0"}, +] [package.extras] -docs = ["sphinx (>=3.5)", "sphinx (<7.2.5)", "jaraco.packaging (>=9.3)", "rst.linker (>=1.9)", "furo", "sphinx-lint", "jaraco.tidelift (>=1.4)"] -testing 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-redis-pal = [] -requests = [] -requests-oauthlib = [] -requests-toolbelt = [] -rpy2 = [] -rsa = [] -"ruamel.yaml" = [] -"ruamel.yaml.clib" = [] -scipy = [] -seaborn = [] -selenium = [] -setuptools-scm = [] -shapely = [] -six = [] -sniffio = [] -sortedcontainers = [] -soupsieve = [] -tabulate = [] -tblib = [] -text-unidecode = [] -toml = [] -tomli = [] -tomlkit = [] -toolz = [] -tornado = [] -tqdm = [] -trio = [] -trio-websocket = [] -tweepy = [] -typing-extensions = [] -tzdata = [] -tzlocal = [] -unidecode = [] -uritemplate = [] -urllib3 = [] -virtualenv = [] -webdriver-manager = [] -websocket-client = [] -wget = [] -win32-setctime = [] -wsproto = [] -xlrd = [] -yarl = [] -zict = [] -zipp = [] +content-hash = "77920c0bf4329d528cb429d287bc3c9a6154fb11b55d7863f5c70b7eb4730e00" diff --git a/pyproject.toml b/pyproject.toml index c859cf707..78d33d031 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -108,6 +108,7 @@ geopandas = "0.13.2" shapely = "2.0.1" webdriver-manager = "^4.0.1" xlrd=">=2.0.1" +pyreaddbc = { version = "^1.2.0", python = ">=3.9" } [tool.poetry.dev-dependencies] pytest_cov = "^3.0.0" From 71b9e8bde1b9090e37bcb537740fc9cb04f7c99f Mon Sep 17 00:00:00 2001 From: folhesgabriel Date: Wed, 6 Dec 2023 16:48:35 -0300 Subject: [PATCH 02/44] re register flow --- pipelines/datasets/br_ms_cnes/tasks.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pipelines/datasets/br_ms_cnes/tasks.py b/pipelines/datasets/br_ms_cnes/tasks.py index b3f8712e1..977d55ef4 100644 --- a/pipelines/datasets/br_ms_cnes/tasks.py +++ b/pipelines/datasets/br_ms_cnes/tasks.py @@ -8,10 +8,10 @@ from datetime import timedelta import pandas as pd +import pyreaddbc as dbcreader import rpy2.robjects.packages as rpackages import wget from prefect import task -from pyreaddbc import read_dbc from rpy2.robjects.packages import importr from pipelines.constants import constants @@ -151,7 +151,7 @@ def read_dbc_save_csv(file_list: list, path: str, table: str) -> str: log(f"the file {file} is being converted to csv") # read dbc # dbc_file = readdbc.read_dbc(file) - dbc_file = read_dbc(file, encoding="iso-8859-1") + dbc_file = dbcreader.read_dbc(file, encoding="iso-8859-1") # convert from r to pandas # https://rpy2.github.io/doc/latest/html/generated_rst/pandas.html#from-r-to-pandas From 1f63455820a995236590c7719f1ed6dc82304077 Mon Sep 17 00:00:00 2001 From: folhesgabriel Date: Wed, 6 Dec 2023 17:33:59 -0300 Subject: [PATCH 03/44] re register flow --- pipelines/datasets/br_ms_cnes/tasks.py | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/pipelines/datasets/br_ms_cnes/tasks.py b/pipelines/datasets/br_ms_cnes/tasks.py index 977d55ef4..78c1907ce 100644 --- a/pipelines/datasets/br_ms_cnes/tasks.py +++ b/pipelines/datasets/br_ms_cnes/tasks.py @@ -8,11 +8,11 @@ from datetime import timedelta import pandas as pd -import pyreaddbc as dbcreader -import rpy2.robjects.packages as rpackages + +# import rpy2.robjects.packages as rpackages import wget from prefect import task -from rpy2.robjects.packages import importr +from pyreaddbc import read_dbc as dbcreader from pipelines.constants import constants from pipelines.datasets.br_ms_cnes.constants import constants as cnes_constants @@ -26,6 +26,8 @@ from pipelines.utils.metadata.utils import get_api_most_recent_date from pipelines.utils.utils import log +# from rpy2.robjects.packages import importr + @task def check_files_to_parse( From 0ad8bc04507a4ea6520d58d086c729b6b0b34065 Mon Sep 17 00:00:00 2001 From: folhesgabriel Date: Wed, 6 Dec 2023 17:38:48 -0300 Subject: [PATCH 04/44] feat: change pyreadbc version config in pyproject.toml --- poetry.lock | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/poetry.lock b/poetry.lock index 99f30309d..3872e4697 100644 --- a/poetry.lock +++ b/poetry.lock @@ -4317,4 +4317,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p [metadata] lock-version = "2.0" python-versions = ">=3.8,<3.11" -content-hash = "77920c0bf4329d528cb429d287bc3c9a6154fb11b55d7863f5c70b7eb4730e00" +content-hash = "cdfc2637a6d71e4c104a44d47e4072d3c78ed944ae83d9e88dda4752526f6d71" diff --git a/pyproject.toml b/pyproject.toml index 78d33d031..174dd7b09 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -108,7 +108,7 @@ geopandas = "0.13.2" shapely = "2.0.1" webdriver-manager = "^4.0.1" xlrd=">=2.0.1" -pyreaddbc = { version = "^1.2.0", python = ">=3.9" } +pyreaddbc = { version = "1.2.0", python = ">=3.9" } [tool.poetry.dev-dependencies] pytest_cov = "^3.0.0" From 799392cc80010c45f4b1c88e643dbcbea09bb1e4 Mon Sep 17 00:00:00 2001 From: folhesgabriel Date: Tue, 19 Dec 2023 13:46:40 -0300 Subject: [PATCH 05/44] feat: test new cnes crawler --- pipelines/datasets/br_ms_cnes/tasks.py | 7 +- poetry.lock | 1089 ++++++++++++------------ pyproject.toml | 1 + 3 files changed, 552 insertions(+), 545 deletions(-) diff --git a/pipelines/datasets/br_ms_cnes/tasks.py b/pipelines/datasets/br_ms_cnes/tasks.py index 78c1907ce..1b82e20f8 100644 --- a/pipelines/datasets/br_ms_cnes/tasks.py +++ b/pipelines/datasets/br_ms_cnes/tasks.py @@ -11,8 +11,10 @@ # import rpy2.robjects.packages as rpackages import wget + +# from pyreaddbc import read_dbc as dbcreader +from datasus import read_dbc from prefect import task -from pyreaddbc import read_dbc as dbcreader from pipelines.constants import constants from pipelines.datasets.br_ms_cnes.constants import constants as cnes_constants @@ -153,7 +155,8 @@ def read_dbc_save_csv(file_list: list, path: str, table: str) -> str: log(f"the file {file} is being converted to csv") # read dbc # dbc_file = readdbc.read_dbc(file) - dbc_file = dbcreader.read_dbc(file, encoding="iso-8859-1") + # dbc_file = dbcreader.read_dbc(file, encoding="iso-8859-1") + dbc_file = pd.DataFrame(read_dbc(file)) # convert from r to pandas # https://rpy2.github.io/doc/latest/html/generated_rst/pandas.html#from-r-to-pandas diff --git a/poetry.lock 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folhesgabriel Date: Tue, 19 Dec 2023 14:09:42 -0300 Subject: [PATCH 06/44] feat: add git to Dockerfile --- Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/Dockerfile b/Dockerfile index 706fb43ab..07d5f8c4c 100644 --- a/Dockerfile +++ b/Dockerfile @@ -33,6 +33,7 @@ RUN apt-get update && \ python3-dev \ traceroute \ wget \ + git \ && \ apt-get install -y r-base && \ apt-get clean && \ From 39aa1baa34d81ab136ded99273210346c5d75fb1 Mon Sep 17 00:00:00 2001 From: folhesgabriel Date: Thu, 1 Feb 2024 14:13:35 -0300 Subject: [PATCH 07/44] feat: and new task --- .../br_ms_cnes/adapted_convert2dbf.sh | 24 + pipelines/datasets/br_ms_cnes/flows.py | 86 ++-- pipelines/datasets/br_ms_cnes/tasks.py | 116 ++--- pipelines/datasets/br_ms_cnes/utils.py | 20 +- poetry.lock | 423 +++++++++++------- pyproject.toml | 6 +- 6 files changed, 407 insertions(+), 268 deletions(-) create mode 100755 pipelines/datasets/br_ms_cnes/adapted_convert2dbf.sh diff --git a/pipelines/datasets/br_ms_cnes/adapted_convert2dbf.sh b/pipelines/datasets/br_ms_cnes/adapted_convert2dbf.sh new file mode 100755 index 000000000..b7d57f91e --- /dev/null +++ b/pipelines/datasets/br_ms_cnes/adapted_convert2dbf.sh @@ -0,0 +1,24 @@ +#!/bin/bash + +# Clone blast-dbf and build it +git clone https://github.com/eaglebh/blast-dbf +cd blast-dbf +make +blast=$(readlink -f blast-dbf) +echo $blast +cd .. + +# Set path to the directory with .dbc files +files=("$@") + +# Iterate over the provided file paths +for file in "${files[@]}" +do + # Check if the file has a .dbc extension + if [[ $file == *.dbc ]]; then + # Execute blast-dbf on the file + $blast $file "${file/.dbc/.dbf}" + else + echo "Skipping non-DBC file: $file" + fi +done \ No newline at end of file diff --git a/pipelines/datasets/br_ms_cnes/flows.py b/pipelines/datasets/br_ms_cnes/flows.py index 63cb98e22..94fab7858 100644 --- a/pipelines/datasets/br_ms_cnes/flows.py +++ b/pipelines/datasets/br_ms_cnes/flows.py @@ -30,8 +30,9 @@ from pipelines.datasets.br_ms_cnes.tasks import ( access_ftp_donwload_files, check_files_to_parse, + decompress_dbc, + decompress_dbf, is_empty, - read_dbc_save_csv, ) from pipelines.utils.constants import constants as utils_constants from pipelines.utils.decorators import Flow @@ -82,11 +83,13 @@ table=br_ms_cnes_constants.TABLE.value[0], ) - filepath = read_dbc_save_csv( + dbf_files = decompress_dbc(file_list=dbc_files) + + filepath = decompress_dbf( file_list=dbc_files, path=br_ms_cnes_constants.PATH.value[1], table=br_ms_cnes_constants.TABLE.value[0], - upstream_tasks=[files_path, dbc_files], + upstream_tasks=[dbf_files, dbc_files], ) wait_upload_table = create_table_and_upload_to_gcs( @@ -181,18 +184,19 @@ "Os dados do FTP CNES-ST ainda não foram atualizados para o ano/mes mais recente" ) - with case(is_empty(files_path), False): dbc_files = access_ftp_donwload_files( file_list=files_path, path=br_ms_cnes_constants.PATH.value[0], table=br_ms_cnes_constants.TABLE.value[1], ) - filepath = read_dbc_save_csv( + dbf_files = decompress_dbc(file_list=dbc_files) + + filepath = decompress_dbf( file_list=dbc_files, path=br_ms_cnes_constants.PATH.value[1], table=br_ms_cnes_constants.TABLE.value[1], - upstream_tasks=[files_path, dbc_files], + upstream_tasks=[dbf_files, dbc_files], ) wait_upload_table = create_table_and_upload_to_gcs( @@ -288,11 +292,13 @@ table=br_ms_cnes_constants.TABLE.value[4], ) - filepath = read_dbc_save_csv( + dbf_files = decompress_dbc(file_list=dbc_files) + + filepath = decompress_dbf( file_list=dbc_files, path=br_ms_cnes_constants.PATH.value[1], table=br_ms_cnes_constants.TABLE.value[4], - upstream_tasks=[files_path, dbc_files], + upstream_tasks=[dbf_files, dbc_files], ) wait_upload_table = create_table_and_upload_to_gcs( @@ -388,11 +394,13 @@ table=br_ms_cnes_constants.TABLE.value[3], ) - filepath = read_dbc_save_csv( + dbf_files = decompress_dbc(file_list=dbc_files) + + filepath = decompress_dbf( file_list=dbc_files, path=br_ms_cnes_constants.PATH.value[1], table=br_ms_cnes_constants.TABLE.value[3], - upstream_tasks=[files_path, dbc_files], + upstream_tasks=[dbf_files, dbc_files], ) wait_upload_table = create_table_and_upload_to_gcs( @@ -493,11 +501,13 @@ table=br_ms_cnes_constants.TABLE.value[2], ) - filepath = read_dbc_save_csv( + dbf_files = decompress_dbc(file_list=dbc_files) + + filepath = decompress_dbf( file_list=dbc_files, path=br_ms_cnes_constants.PATH.value[1], table=br_ms_cnes_constants.TABLE.value[2], - upstream_tasks=[files_path, dbc_files], + upstream_tasks=[dbf_files, dbc_files], ) wait_upload_table = create_table_and_upload_to_gcs( @@ -593,11 +603,13 @@ table=br_ms_cnes_constants.TABLE.value[5], ) - filepath = read_dbc_save_csv( + dbf_files = decompress_dbc(file_list=dbc_files) + + filepath = decompress_dbf( file_list=dbc_files, path=br_ms_cnes_constants.PATH.value[1], table=br_ms_cnes_constants.TABLE.value[5], - upstream_tasks=[files_path, dbc_files], + upstream_tasks=[dbf_files, dbc_files], ) wait_upload_table = create_table_and_upload_to_gcs( @@ -694,11 +706,13 @@ table=br_ms_cnes_constants.TABLE.value[6], ) - filepath = read_dbc_save_csv( + dbf_files = decompress_dbc(file_list=dbc_files) + + filepath = decompress_dbf( file_list=dbc_files, path=br_ms_cnes_constants.PATH.value[1], table=br_ms_cnes_constants.TABLE.value[6], - upstream_tasks=[files_path, dbc_files], + upstream_tasks=[dbf_files, dbc_files], ) wait_upload_table = create_table_and_upload_to_gcs( @@ -797,11 +811,13 @@ table=br_ms_cnes_constants.TABLE.value[7], ) - filepath = read_dbc_save_csv( + dbf_files = decompress_dbc(file_list=dbc_files) + + filepath = decompress_dbf( file_list=dbc_files, path=br_ms_cnes_constants.PATH.value[1], table=br_ms_cnes_constants.TABLE.value[7], - upstream_tasks=[files_path, dbc_files], + upstream_tasks=[dbf_files, dbc_files], ) wait_upload_table = create_table_and_upload_to_gcs( @@ -902,11 +918,13 @@ table=br_ms_cnes_constants.TABLE.value[8], ) - filepath = read_dbc_save_csv( + dbf_files = decompress_dbc(file_list=dbc_files) + + filepath = decompress_dbf( file_list=dbc_files, path=br_ms_cnes_constants.PATH.value[1], table=br_ms_cnes_constants.TABLE.value[8], - upstream_tasks=[files_path, dbc_files], + upstream_tasks=[dbf_files, dbc_files], ) wait_upload_table = create_table_and_upload_to_gcs( @@ -1002,11 +1020,13 @@ table=br_ms_cnes_constants.TABLE.value[9], ) - filepath = read_dbc_save_csv( + dbf_files = decompress_dbc(file_list=dbc_files) + + filepath = decompress_dbf( file_list=dbc_files, path=br_ms_cnes_constants.PATH.value[1], table=br_ms_cnes_constants.TABLE.value[9], - upstream_tasks=[files_path, dbc_files], + upstream_tasks=[dbf_files, dbc_files], ) wait_upload_table = create_table_and_upload_to_gcs( @@ -1104,11 +1124,13 @@ table=br_ms_cnes_constants.TABLE.value[10], ) - filepath = read_dbc_save_csv( + dbf_files = decompress_dbc(file_list=dbc_files) + + filepath = decompress_dbf( file_list=dbc_files, path=br_ms_cnes_constants.PATH.value[1], table=br_ms_cnes_constants.TABLE.value[10], - upstream_tasks=[files_path, dbc_files], + upstream_tasks=[dbf_files, dbc_files], ) wait_upload_table = create_table_and_upload_to_gcs( @@ -1202,14 +1224,16 @@ dbc_files = access_ftp_donwload_files( file_list=files_path, path=br_ms_cnes_constants.PATH.value[0], - table=br_ms_cnes_constants.TABLE.value[11], + table=br_ms_cnes_constants.TABLE.value[12], ) - filepath = read_dbc_save_csv( + dbf_files = decompress_dbc(file_list=dbc_files) + + filepath = decompress_dbf( file_list=dbc_files, path=br_ms_cnes_constants.PATH.value[1], - table=br_ms_cnes_constants.TABLE.value[11], - upstream_tasks=[files_path, dbc_files], + table=br_ms_cnes_constants.TABLE.value[12], + upstream_tasks=[dbf_files, dbc_files], ) wait_upload_table = create_table_and_upload_to_gcs( @@ -1308,11 +1332,13 @@ table=br_ms_cnes_constants.TABLE.value[12], ) - filepath = read_dbc_save_csv( + dbf_files = decompress_dbc(file_list=dbc_files) + + filepath = decompress_dbf( file_list=dbc_files, path=br_ms_cnes_constants.PATH.value[1], table=br_ms_cnes_constants.TABLE.value[12], - upstream_tasks=[files_path, dbc_files], + upstream_tasks=[dbf_files, dbc_files], ) wait_upload_table = create_table_and_upload_to_gcs( diff --git a/pipelines/datasets/br_ms_cnes/tasks.py b/pipelines/datasets/br_ms_cnes/tasks.py index 1b82e20f8..b63ec1d2a 100644 --- a/pipelines/datasets/br_ms_cnes/tasks.py +++ b/pipelines/datasets/br_ms_cnes/tasks.py @@ -5,16 +5,20 @@ import os +import subprocess from datetime import timedelta +from glob import glob import pandas as pd # import rpy2.robjects.packages as rpackages import wget +from datasus import decompress # from pyreaddbc import read_dbc as dbcreader -from datasus import read_dbc from prefect import task +from simpledbf import Dbf5 +from tqdm import tqdm from pipelines.constants import constants from pipelines.datasets.br_ms_cnes.constants import constants as cnes_constants @@ -53,6 +57,10 @@ def check_files_to_parse( year = str(last_date.year) month = last_date.month + # download files to compare + year = "2023" + month = 7 + if month <= 11: month = month + 1 else: @@ -102,97 +110,95 @@ def access_ftp_donwload_files(file_list: list, path: str, table: str) -> list[st log(f"wrangling {table} data") - for file in file_list: + for file in tqdm(file_list): # build partition dirs - year_month_sigla_uf = year_month_sigla_uf_parser(file=file) + try: + + year_month_sigla_uf = year_month_sigla_uf_parser(file=file) - log(f"the file {file} was parsed to {year_month_sigla_uf}") - input_path = path + table + "/" + year_month_sigla_uf + input_path = path + table + "/" + year_month_sigla_uf - os.system(f"mkdir -p {input_path}") - os.system(f"find {input_path} -type f -delete") + os.system(f"mkdir -p {input_path}") + os.system(f"find {input_path} -type f -delete") - log(f"created input dir {path + table + '/' + year_month_sigla_uf}") + log(f"created input dir {path + table + '/' + year_month_sigla_uf}") - url = f"ftp://ftp.datasus.gov.br/{file}" - # access ftp - wget.download(url, out=input_path) + url = f"ftp://ftp.datasus.gov.br/{file}" + # access ftp + wget.download(url, out=input_path) - # list downloaded files - dbc_file = os.listdir(input_path) + # list downloaded files + dbc_file = os.listdir(input_path) - # append to list - complete_path = input_path + "/" + dbc_file[0] - log(f"The complete path is -- {complete_path}") + # append to list + complete_path = input_path + "/" + dbc_file[0] - dbc_files_path_list.append(complete_path) + dbc_files_path_list.append(complete_path) - log(f"The file {dbc_file} is in {input_path}") + except Exception as e: + log(f"An error occurred while downloading {file} from DATASUS FTP: {e}") + raise e return dbc_files_path_list +@task +def decompress_dbc(file_list: list) -> None: + + log(f"==== curent env {os. getcwd()}") + + # ? Tive que dar um grant pra exucutar bash na pipeline + # ? chmod +x adapted_convert2dbf.sh + subprocess.run( + ["/home/gabri/pipelines/pipelines/datasets/br_ms_cnes/adapted_convert2dbf.sh"] + + file_list + ) + + # task to convert dbc to csv and save to a partitioned dir @task -def read_dbc_save_csv(file_list: list, path: str, table: str) -> str: +def decompress_dbf(file_list: list, path: str, table: str) -> str: """ Convert dbc to csv """ log(f"wrangling {table} data") - # import R's utility package - # utils = rpackages.importr("utils") - - # select a mirror for R packages - # utils.chooseCRANmirror(ind=1) - - # log("installing read.dbc package") - # utils.install_packages("read.dbc") - # readdbc = importr("read.dbc") # list files - for file in file_list: - log(f"the file {file} is being converted to csv") - # read dbc - # dbc_file = readdbc.read_dbc(file) - # dbc_file = dbcreader.read_dbc(file, encoding="iso-8859-1") - dbc_file = pd.DataFrame(read_dbc(file)) + for file in tqdm(file_list): + log(f"---------- {file}") + dbf_file = ".".join([file.split(".")[0], "dbf"]) - # convert from r to pandas - # https://rpy2.github.io/doc/latest/html/generated_rst/pandas.html#from-r-to-pandas + log(f"-------- reading .dbf {dbf_file}") + dbf = Dbf5(dbf_file, codec="iso-8859-1") - # parse year month sigla_uf year_month_sigla_uf = year_month_sigla_uf_parser(file=file) + log(f"year_month_sigla_uf of {file} parsed") output_path = path + table + "/" + year_month_sigla_uf os.system(f"mkdir -p {output_path}") - log(f"created output partition dir {path + table + '/'+ year_month_sigla_uf}") output_file = output_path + "/" + table + ".csv" - log(f"{file} 1 saved") - # salvar df - # dbc_file.to_csvfile( - # output_file, - # sep=",", - # na="", - # row_names=False, - # ) - dbc_file.to_csv( - output_file, - sep=",", - na_rep="", - index=False, - ) + + # filesd='.'.join([dbf_file.split('.')[0], "csv"]) + log(f"-------- saving to .csv {output_file}") + dbf.to_csv(output_file) + # delete dbc file - os.system(f"rm {file}") + folder_path = file.split(".")[0] + files_to_remove = glob(os.path.join(folder_path, "*.dbc")) + glob( + os.path.join(folder_path, "*.dbf") + ) + # Remove each file + for file in files_to_remove: + os.system(f"rm {file}") # ler df - log("file 2 being read") - df = pd.read_csv(output_file, dtype=str, encoding="latin1") + df = pd.read_csv(output_file, dtype=str, encoding="iso-8859-1") # tratar list_columns_to_delete = [ diff --git a/pipelines/datasets/br_ms_cnes/utils.py b/pipelines/datasets/br_ms_cnes/utils.py index 902da1d95..f897ab4ec 100644 --- a/pipelines/datasets/br_ms_cnes/utils.py +++ b/pipelines/datasets/br_ms_cnes/utils.py @@ -43,18 +43,20 @@ def year_month_sigla_uf_parser(file: str) -> str: Returns: (str): """ - # todo: implement a check to make sure the result is right - # parse file name last 8 digits before .DBC - file = file[-10:-4] + try: + # parse file name last 8 digits before .DBC + file = file[-10:-4] - # parse and build year 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files to CSV, DataFrames, HDF5 tables, and SQL tables. 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+content-hash = "d54b646a9fde265ae67d4e33129fe4162939598d4d0fd54e8b4e7e7863f05c39" + +[metadata.files] +anyio = [] +arrow = [] +async-timeout = [] +attrs = [] +backoff = [] +basedosdados = [] +beautifulsoup4 = [] +binaryornot = [] +cachetools = [] +certifi = [] +cffi = [] +chardet = [] +charset-normalizer = [] +ckanapi = [] +click = [] +click-plugins = [] +cligj = [] +cloudpickle = [] +colorama = [] +contourpy = [] +cookiecutter = [] +coverage = [] +cramjam = [] +croniter = [] +cycler = [] +dask = [] +db-dtypes = [] +dbt-client = [] +dill = [] +distributed = [] +docker = [] +docopt = [] +et-xmlfile = [] +exceptiongroup = [] +fake-useragent = [] +fastavro = [] +fastparquet = [] +fiona = [] +fonttools = [] +fsspec = [] +geopandas = [] +google-analytics-data = [] +google-api-core = [] +google-api-python-client = [] +google-auth = [] +google-auth-httplib2 = [] +google-auth-oauthlib = [] +google-cloud-bigquery = [] +google-cloud-bigquery-connection = [] +google-cloud-bigquery-storage = [] +google-cloud-core = [] +google-cloud-storage = [] +google-crc32c = [] +google-resumable-media = [] +googleapis-common-protos = [] +gql = [] +graphql-core = [] +grpc-google-iam-v1 = [] +grpcio = [] +grpcio-status = [] +h11 = [] +heapdict = [] +httpcore = [] +httplib2 = [] +httpx = [] +hvac = [] +idna = [] +iniconfig = [] +ipeadatapy = [] +jinja2 = [] +jinja2-time = [] +kiwisolver = [] +levenshtein = [] +locket = [] +loguru = [] +lxml = [] +markupsafe = [] +marshmallow = [] +marshmallow-oneofschema = [] +matplotlib = [] +msgpack = [] +multidict = [] +mypy-extensions = [] +numpy = [] +oauth2client = [] +oauthlib = [] +openpyxl = [] +outcome = [] +packaging = [] +pandas = [] +pandas-gbq = [] +pandavro = [] +partd = [] +pendulum = [] +pillow = [] +pluggy = [] +polars = [] +poyo = [] +prefect = [] +proto-plus = [] +protobuf = [] +psutil = [] +pyaml = [] +pyarrow = [] +pyasn1 = [] +pyasn1-modules = [] +pycparser = [] +pydata-google-auth = [] +pymssql = [] +pyparsing = [] +pyproj = [] +pysocks = [] +pytest = [] +pytest-cov = [] +python-box = [] +python-dateutil = [] +python-dotenv = [] +python-levenshtein = [] +python-slugify = [] +python-string-utils = [] +pytz = [] +pytzdata = [] +pywin32 = [] +pyyaml = [] +rapidfuzz = [] +rarfile = [] +redis = [] +redis-pal = [] +requests = [] +requests-oauthlib = [] +requests-toolbelt = [] +rpy2 = [] +rsa = [] +"ruamel.yaml" = [] +"ruamel.yaml.clib" = [] +scipy = [] +seaborn = [] +selenium = [] +shapely = [] +simpledbf = [] +six = [] +sniffio = [] +sortedcontainers = [] +soupsieve = [] +tabulate = [] +tblib = [] +text-unidecode = [] +toml = [] +tomli = [] +tomlkit = [] +toolz = [] +tornado = [] +tqdm = [] +trio = [] +trio-websocket = [] +tweepy = [] +typer = [] +types-python-dateutil = [] +typing-extensions = [] +tzdata = [] +tzlocal = [] +unidecode = [] +uritemplate = [] +urllib3 = [] +webdriver-manager = [] +websocket-client = [] +wget = [] +win32-setctime = [] +wsproto = [] +xlrd = [] +yarl = [] +zict = [] diff --git a/pyproject.toml b/pyproject.toml index 47a541550..d3b5ad0a0 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -124,8 +124,8 @@ pytest_cov = "^3.0.0" [tool.poetry.scripts] lint = "scripts.lint:main" -[tool.poetry.group.dev.dependencies] -pre-commit = "^3.6.0" +#[tool.poetry.group.dev.dependencies] +#pre-commit = "^3.6.0" [tool.black] exclude = "pipelines/{{cookiecutter.project_name}}" From 44e7801bc7a06eee9bcd56f5274ddb1c48e9ccd2 Mon Sep 17 00:00:00 2001 From: folhesgabriel Date: Thu, 1 Feb 2024 14:33:25 -0300 Subject: [PATCH 09/44] feat: fix ci lint python action --- poetry.lock | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/poetry.lock b/poetry.lock index c489002b8..0f0573e3e 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2287,7 +2287,7 @@ heapdict = "*" [metadata] lock-version = "1.1" python-versions = ">=3.10,<3.11" -content-hash = "d54b646a9fde265ae67d4e33129fe4162939598d4d0fd54e8b4e7e7863f05c39" +content-hash = "4390fa9e0d6d569741081270ef6eaf1143e3c4fa38239de81ce6d2d27efe188b" [metadata.files] anyio = [] diff --git a/pyproject.toml b/pyproject.toml index d3b5ad0a0..fd9243cca 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -104,7 +104,7 @@ polars = "^0.19.0" selenium = "^4.11.2" fastparquet = "^2023.7.0" rarfile = "^4.0" -setuptools = "^68.1.2" +setuptools = ">=69.0.0" python-string-utils = {git = "https://github.com/daveoncode/python-string-utils.git", rev = "master"} geopandas = "0.13.2" shapely = "2.0.1" From 89dd0e96f0436843c8730f55f56aa67d6678234b Mon Sep 17 00:00:00 2001 From: folhesgabriel Date: Thu, 1 Feb 2024 14:47:29 -0300 Subject: [PATCH 10/44] feat: remove unnused modules --- pipelines/datasets/br_ms_cnes/tasks.py | 1 - 1 file changed, 1 deletion(-) diff --git a/pipelines/datasets/br_ms_cnes/tasks.py b/pipelines/datasets/br_ms_cnes/tasks.py index b63ec1d2a..9c17abb3f 100644 --- a/pipelines/datasets/br_ms_cnes/tasks.py +++ b/pipelines/datasets/br_ms_cnes/tasks.py @@ -13,7 +13,6 @@ # import rpy2.robjects.packages as rpackages import wget -from datasus import decompress # from pyreaddbc import read_dbc as dbcreader from prefect import task From 27e6648d33ca1d970807e6234e5578137e3c61f6 Mon Sep 17 00:00:00 2001 From: folhesgabriel Date: Thu, 1 Feb 2024 18:57:02 -0300 Subject: [PATCH 11/44] feat: fix bash path --- pipelines/datasets/br_ms_cnes/tasks.py | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/pipelines/datasets/br_ms_cnes/tasks.py b/pipelines/datasets/br_ms_cnes/tasks.py index 9c17abb3f..393084dfb 100644 --- a/pipelines/datasets/br_ms_cnes/tasks.py +++ b/pipelines/datasets/br_ms_cnes/tasks.py @@ -145,14 +145,11 @@ def access_ftp_donwload_files(file_list: list, path: str, table: str) -> list[st @task def decompress_dbc(file_list: list) -> None: - log(f"==== curent env {os. getcwd()}") + log(f"==== curent env {os.getcwd()}") # ? Tive que dar um grant pra exucutar bash na pipeline # ? chmod +x adapted_convert2dbf.sh - subprocess.run( - ["/home/gabri/pipelines/pipelines/datasets/br_ms_cnes/adapted_convert2dbf.sh"] - + file_list - ) + subprocess.run(["/app/adapted_convert2dbf.sh"] + file_list) # task to convert dbc to csv and save to a partitioned dir From ad883a6d962cb2aa38c24ed09ca1b1fac9b4a7e2 Mon Sep 17 00:00:00 2001 From: folhesgabriel Date: Fri, 2 Feb 2024 09:37:50 -0300 Subject: [PATCH 12/44] re-register flow --- pipelines/datasets/br_ms_cnes/tasks.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/pipelines/datasets/br_ms_cnes/tasks.py b/pipelines/datasets/br_ms_cnes/tasks.py index 393084dfb..bb53d6b20 100644 --- a/pipelines/datasets/br_ms_cnes/tasks.py +++ b/pipelines/datasets/br_ms_cnes/tasks.py @@ -31,6 +31,8 @@ from pipelines.utils.metadata.utils import get_api_most_recent_date from pipelines.utils.utils import log +# from pipelines.datasets.br_ms_cnes import adap + # from rpy2.robjects.packages import importr @@ -147,8 +149,8 @@ def decompress_dbc(file_list: list) -> None: log(f"==== curent env {os.getcwd()}") - # ? Tive que dar um grant pra exucutar bash na pipeline - # ? chmod +x adapted_convert2dbf.sh + # Tive que dar um grant pra exucutar bash na pipeline + # chmod +x adapted_convert2dbf.sh subprocess.run(["/app/adapted_convert2dbf.sh"] + file_list) From 7f4b14d6e815358640404bfc6e64a128fa3f1548 Mon Sep 17 00:00:00 2001 From: folhesgabriel Date: Mon, 5 Feb 2024 08:23:52 -0300 Subject: [PATCH 13/44] fix: decompress_dbc task --- pipelines/datasets/br_ms_cnes/tasks.py | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/pipelines/datasets/br_ms_cnes/tasks.py b/pipelines/datasets/br_ms_cnes/tasks.py index bb53d6b20..78605c6f7 100644 --- a/pipelines/datasets/br_ms_cnes/tasks.py +++ b/pipelines/datasets/br_ms_cnes/tasks.py @@ -20,6 +20,7 @@ from tqdm import tqdm from pipelines.constants import constants +from pipelines.datasets.br_ms_cnes import adap from pipelines.datasets.br_ms_cnes.constants import constants as cnes_constants from pipelines.datasets.br_ms_cnes.utils import ( check_and_create_column, @@ -31,8 +32,6 @@ from pipelines.utils.metadata.utils import get_api_most_recent_date from pipelines.utils.utils import log -# from pipelines.datasets.br_ms_cnes import adap - # from rpy2.robjects.packages import importr @@ -149,9 +148,9 @@ def decompress_dbc(file_list: list) -> None: log(f"==== curent env {os.getcwd()}") - # Tive que dar um grant pra exucutar bash na pipeline - # chmod +x adapted_convert2dbf.sh - subprocess.run(["/app/adapted_convert2dbf.sh"] + file_list) + # ? Tive que dar um grant pra exucutar bash na pipeline + # ? chmod +x adapted_convert2dbf.sh + subprocess.run(["pipelines/datasets/br_ms_cnes/adapted_convert2dbf.sh"] + file_list) # task to convert dbc to csv and save to a partitioned dir From 50d43ed738b9d66d8692d774bd977f528bb96fc0 Mon Sep 17 00:00:00 2001 From: folhesgabriel Date: Mon, 5 Feb 2024 08:31:11 -0300 Subject: [PATCH 14/44] fix: ci action --- pipelines/datasets/br_ms_cnes/tasks.py | 1 - 1 file changed, 1 deletion(-) diff --git a/pipelines/datasets/br_ms_cnes/tasks.py b/pipelines/datasets/br_ms_cnes/tasks.py index 78605c6f7..7884439d8 100644 --- a/pipelines/datasets/br_ms_cnes/tasks.py +++ b/pipelines/datasets/br_ms_cnes/tasks.py @@ -20,7 +20,6 @@ from tqdm import tqdm from pipelines.constants import constants -from pipelines.datasets.br_ms_cnes import adap from pipelines.datasets.br_ms_cnes.constants import constants as cnes_constants from pipelines.datasets.br_ms_cnes.utils import ( check_and_create_column, From fa7f844216b11f3aed6f3ff2a2b7996d2876f657 Mon Sep 17 00:00:00 2001 From: folhesgabriel Date: Mon, 5 Feb 2024 09:04:34 -0300 Subject: [PATCH 15/44] fix: upstream tasks --- pipelines/datasets/br_ms_cnes/flows.py | 2 +- pipelines/datasets/br_ms_cnes/tasks.py | 12 +++++++++--- 2 files changed, 10 insertions(+), 4 deletions(-) diff --git a/pipelines/datasets/br_ms_cnes/flows.py b/pipelines/datasets/br_ms_cnes/flows.py index 94fab7858..42a5ec5df 100644 --- a/pipelines/datasets/br_ms_cnes/flows.py +++ b/pipelines/datasets/br_ms_cnes/flows.py @@ -83,7 +83,7 @@ table=br_ms_cnes_constants.TABLE.value[0], ) - dbf_files = decompress_dbc(file_list=dbc_files) + dbf_files = decompress_dbc(file_list=dbc_files, upstream_tasks=[dbc_files]) filepath = decompress_dbf( file_list=dbc_files, diff --git a/pipelines/datasets/br_ms_cnes/tasks.py b/pipelines/datasets/br_ms_cnes/tasks.py index 7884439d8..cafd14766 100644 --- a/pipelines/datasets/br_ms_cnes/tasks.py +++ b/pipelines/datasets/br_ms_cnes/tasks.py @@ -109,6 +109,8 @@ def access_ftp_donwload_files(file_list: list, path: str, table: str) -> list[st log(f"wrangling {table} data") + file_list = file_list[1:5] + for file in tqdm(file_list): # build partition dirs @@ -149,7 +151,12 @@ def decompress_dbc(file_list: list) -> None: # ? Tive que dar um grant pra exucutar bash na pipeline # ? chmod +x adapted_convert2dbf.sh - subprocess.run(["pipelines/datasets/br_ms_cnes/adapted_convert2dbf.sh"] + file_list) + # + # pipelines/datasets/br_ms_cnes/adapted_convert2dbf.sh + + subprocess.run( + ["/pipelines/datasets/br_ms_cnes/adapted_convert2dbf.sh"] + file_list + ) # task to convert dbc to csv and save to a partitioned dir @@ -162,9 +169,8 @@ def decompress_dbf(file_list: list, path: str, table: str) -> str: # list files for file in tqdm(file_list): - log(f"---------- {file}") - dbf_file = ".".join([file.split(".")[0], "dbf"]) + dbf_file = ".".join([file.split(".")[0], "dbf"]) log(f"-------- reading .dbf {dbf_file}") dbf = Dbf5(dbf_file, codec="iso-8859-1") From 176d63a85cd6f2f99feb6657c3dcd8076815d6c9 Mon Sep 17 00:00:00 2001 From: folhesgabriel Date: Mon, 5 Feb 2024 10:13:33 -0300 Subject: [PATCH 16/44] check folder tree --- pipelines/datasets/br_ms_cnes/tasks.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/pipelines/datasets/br_ms_cnes/tasks.py b/pipelines/datasets/br_ms_cnes/tasks.py index cafd14766..0064c21ed 100644 --- a/pipelines/datasets/br_ms_cnes/tasks.py +++ b/pipelines/datasets/br_ms_cnes/tasks.py @@ -154,6 +154,10 @@ def decompress_dbc(file_list: list) -> None: # # pipelines/datasets/br_ms_cnes/adapted_convert2dbf.sh + os.system("ls pipelines/datasets/br_ms_cnes/") + # subprocess.run( + # ["chmod", "+x", "/home/gabri/pipelines/pipelines/datasets/br_ms_cnes/adapted_convert2dbf.sh"]) + subprocess.run( ["/pipelines/datasets/br_ms_cnes/adapted_convert2dbf.sh"] + file_list ) From f7077d6d1d5d71200a37b2e9c561d6f84d326aec Mon Sep 17 00:00:00 2001 From: folhesgabriel Date: Mon, 5 Feb 2024 10:25:58 -0300 Subject: [PATCH 17/44] feat: add logs --- pipelines/datasets/br_ms_cnes/tasks.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipelines/datasets/br_ms_cnes/tasks.py b/pipelines/datasets/br_ms_cnes/tasks.py index 0064c21ed..9462787d6 100644 --- a/pipelines/datasets/br_ms_cnes/tasks.py +++ b/pipelines/datasets/br_ms_cnes/tasks.py @@ -154,7 +154,7 @@ def decompress_dbc(file_list: list) -> None: # # pipelines/datasets/br_ms_cnes/adapted_convert2dbf.sh - os.system("ls pipelines/datasets/br_ms_cnes/") + log(os.system("ls pipelines/datasets/br_ms_cnes/")) # subprocess.run( # ["chmod", "+x", "/home/gabri/pipelines/pipelines/datasets/br_ms_cnes/adapted_convert2dbf.sh"]) From c76a6ab985cf93b80b85d300a50341728a06b3e8 Mon Sep 17 00:00:00 2001 From: folhesgabriel Date: Mon, 5 Feb 2024 10:38:42 -0300 Subject: [PATCH 18/44] feat: refactor convert2dbf.sh into a series of cli comands --- pipelines/datasets/br_ms_cnes/tasks.py | 54 ++++++++++++++++++-------- 1 file changed, 38 insertions(+), 16 deletions(-) diff --git a/pipelines/datasets/br_ms_cnes/tasks.py b/pipelines/datasets/br_ms_cnes/tasks.py index 9462787d6..0bde05105 100644 --- a/pipelines/datasets/br_ms_cnes/tasks.py +++ b/pipelines/datasets/br_ms_cnes/tasks.py @@ -5,9 +5,9 @@ import os -import subprocess from datetime import timedelta from glob import glob +from pathlib import Path import pandas as pd @@ -144,23 +144,45 @@ def access_ftp_donwload_files(file_list: list, path: str, table: str) -> list[st return dbc_files_path_list -@task -def decompress_dbc(file_list: list) -> None: - - log(f"==== curent env {os.getcwd()}") - - # ? Tive que dar um grant pra exucutar bash na pipeline - # ? chmod +x adapted_convert2dbf.sh - # - # pipelines/datasets/br_ms_cnes/adapted_convert2dbf.sh +# @task +# def decompress_dbc(file_list: list) -> None: +# +# log(f"==== curent env {os.getcwd()}") +# +# # ? Tive que dar um grant pra exucutar bash na pipeline +# # ? chmod +x adapted_convert2dbf.sh +# # +# # pipelines/datasets/br_ms_cnes/adapted_convert2dbf.sh +# +# log(os.system("ls pipelines/datasets/br_ms_cnes/")) +# # subprocess.run( +# # ["chmod", "+x", "/home/gabri/pipelines/pipelines/datasets/br_ms_cnes/adapted_convert2dbf.sh"]) +# +# subprocess.run( +# ["/pipelines/datasets/br_ms_cnes/adapted_convert2dbf.sh"] + file_list +# ) - log(os.system("ls pipelines/datasets/br_ms_cnes/")) - # subprocess.run( - # ["chmod", "+x", "/home/gabri/pipelines/pipelines/datasets/br_ms_cnes/adapted_convert2dbf.sh"]) - subprocess.run( - ["/pipelines/datasets/br_ms_cnes/adapted_convert2dbf.sh"] + file_list - ) +@task +def decompress_dbc(file_list: list) -> None: + log(f"==== current env {os.getcwd()}") + + # Clone blast-dbf and build it + os.system("git clone https://github.com/eaglebh/blast-dbf") + os.chdir("blast-dbf") + os.system("make") + blast_path = str(Path.cwd().resolve()) + log(f"Blast-dbf path: {blast_path}") + os.chdir("..") + + # Iterate over the provided file paths + for file in file_list: + # Check if the file has a .dbc extension + if file.endswith(".dbc"): + # Execute blast-dbf on the file + os.system(f"{blast_path}/blast-dbf {file} {file.replace('.dbc', '.dbf')}") + else: + log(f"Skipping non-DBC file: {file}") # task to convert dbc to csv and save to a partitioned dir From e9fc590c758910af39faf8a90e8a1bd0887e6605 Mon Sep 17 00:00:00 2001 From: folhesgabriel Date: Mon, 5 Feb 2024 10:59:58 -0300 Subject: [PATCH 19/44] fix: agora vai --- pipelines/datasets/br_ms_cnes/flows.py | 4 +++- pipelines/datasets/br_ms_cnes/tasks.py | 9 ++++----- 2 files changed, 7 insertions(+), 6 deletions(-) diff --git a/pipelines/datasets/br_ms_cnes/flows.py b/pipelines/datasets/br_ms_cnes/flows.py index 42a5ec5df..bd5383f72 100644 --- a/pipelines/datasets/br_ms_cnes/flows.py +++ b/pipelines/datasets/br_ms_cnes/flows.py @@ -184,13 +184,15 @@ "Os dados do FTP CNES-ST ainda não foram atualizados para o ano/mes mais recente" ) + with case(is_empty(files_path), False): + dbc_files = access_ftp_donwload_files( file_list=files_path, path=br_ms_cnes_constants.PATH.value[0], table=br_ms_cnes_constants.TABLE.value[1], ) - dbf_files = decompress_dbc(file_list=dbc_files) + dbf_files = decompress_dbc(file_list=dbc_files, upstream_tasks=[dbc_files]) filepath = decompress_dbf( file_list=dbc_files, diff --git a/pipelines/datasets/br_ms_cnes/tasks.py b/pipelines/datasets/br_ms_cnes/tasks.py index 0bde05105..82cb13a2b 100644 --- a/pipelines/datasets/br_ms_cnes/tasks.py +++ b/pipelines/datasets/br_ms_cnes/tasks.py @@ -7,7 +7,6 @@ import os from datetime import timedelta from glob import glob -from pathlib import Path import pandas as pd @@ -167,11 +166,11 @@ def access_ftp_donwload_files(file_list: list, path: str, table: str) -> list[st def decompress_dbc(file_list: list) -> None: log(f"==== current env {os.getcwd()}") - # Clone blast-dbf and build it - os.system("git clone https://github.com/eaglebh/blast-dbf") - os.chdir("blast-dbf") + # Clone blast-dbf to /tmp/br_ms_cnes and build it + blast_path = "/tmp/br_ms_cnes/blast-dbf" + os.system(f"git clone https://github.com/eaglebh/blast-dbf {blast_path}") + os.chdir(blast_path) os.system("make") - blast_path = str(Path.cwd().resolve()) log(f"Blast-dbf path: {blast_path}") os.chdir("..") From 6002b2f38a6490a81c18e4648e40497458b201bf Mon Sep 17 00:00:00 2001 From: folhesgabriel Date: Mon, 5 Feb 2024 11:29:57 -0300 Subject: [PATCH 20/44] fix: hopeless --- pipelines/datasets/br_ms_cnes/tasks.py | 1 + 1 file changed, 1 insertion(+) diff --git a/pipelines/datasets/br_ms_cnes/tasks.py b/pipelines/datasets/br_ms_cnes/tasks.py index 82cb13a2b..61f8b543c 100644 --- a/pipelines/datasets/br_ms_cnes/tasks.py +++ b/pipelines/datasets/br_ms_cnes/tasks.py @@ -168,6 +168,7 @@ def decompress_dbc(file_list: list) -> None: # Clone blast-dbf to /tmp/br_ms_cnes and build it blast_path = "/tmp/br_ms_cnes/blast-dbf" + os.system(f"mkdir -p {blast_path}") os.system(f"git clone https://github.com/eaglebh/blast-dbf {blast_path}") os.chdir(blast_path) os.system("make") From 9769f4ba08a12562ab2b6358b48e81bf3a102401 Mon Sep 17 00:00:00 2001 From: folhesgabriel Date: Mon, 5 Feb 2024 12:22:03 -0300 Subject: [PATCH 21/44] fix: is it blasting or not? --- pipelines/datasets/br_ms_cnes/tasks.py | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/pipelines/datasets/br_ms_cnes/tasks.py b/pipelines/datasets/br_ms_cnes/tasks.py index 61f8b543c..7b29d46c0 100644 --- a/pipelines/datasets/br_ms_cnes/tasks.py +++ b/pipelines/datasets/br_ms_cnes/tasks.py @@ -57,7 +57,7 @@ def check_files_to_parse( # download files to compare year = "2023" - month = 7 + month = 10 if month <= 11: month = month + 1 @@ -108,7 +108,7 @@ def access_ftp_donwload_files(file_list: list, path: str, table: str) -> list[st log(f"wrangling {table} data") - file_list = file_list[1:5] + file_list = file_list[1:3] for file in tqdm(file_list): # build partition dirs @@ -171,15 +171,14 @@ def decompress_dbc(file_list: list) -> None: os.system(f"mkdir -p {blast_path}") os.system(f"git clone https://github.com/eaglebh/blast-dbf {blast_path}") os.chdir(blast_path) + log(f"==== current env {os.getcwd()}") os.system("make") log(f"Blast-dbf path: {blast_path}") os.chdir("..") - - # Iterate over the provided file paths - for file in file_list: - # Check if the file has a .dbc extension + log(f"==== current env {os.getcwd()}") + for file in tqdm(file_list): + log(f"Blasting: {file}") if file.endswith(".dbc"): - # Execute blast-dbf on the file os.system(f"{blast_path}/blast-dbf {file} {file.replace('.dbc', '.dbf')}") else: log(f"Skipping non-DBC file: {file}") From 8d81aa49c4fdaefc2a3b2e7d0e54519418751b7a Mon Sep 17 00:00:00 2001 From: folhesgabriel Date: Mon, 5 Feb 2024 13:07:39 -0300 Subject: [PATCH 22/44] fix: debug decompress_dbc --- pipelines/datasets/br_ms_cnes/tasks.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/pipelines/datasets/br_ms_cnes/tasks.py b/pipelines/datasets/br_ms_cnes/tasks.py index 7b29d46c0..3b144693a 100644 --- a/pipelines/datasets/br_ms_cnes/tasks.py +++ b/pipelines/datasets/br_ms_cnes/tasks.py @@ -180,6 +180,9 @@ def decompress_dbc(file_list: list) -> None: log(f"Blasting: {file}") if file.endswith(".dbc"): os.system(f"{blast_path}/blast-dbf {file} {file.replace('.dbc', '.dbf')}") + a = file.split("/")[:-1] + directory_path = "/".join(a) + log(f"----- files {os.listdir(directory_path)}") else: log(f"Skipping non-DBC file: {file}") From 4970af5585a87593209566743d8d8cb1caf81bb4 Mon Sep 17 00:00:00 2001 From: folhesgabriel Date: Tue, 6 Feb 2024 11:02:02 -0300 Subject: [PATCH 23/44] feat: test prefect ShellTask --- pipelines/datasets/br_ms_cnes/tasks.py | 87 ++++++++++++++++++++------ 1 file changed, 67 insertions(+), 20 deletions(-) diff --git a/pipelines/datasets/br_ms_cnes/tasks.py b/pipelines/datasets/br_ms_cnes/tasks.py index 3b144693a..c84dc5c93 100644 --- a/pipelines/datasets/br_ms_cnes/tasks.py +++ b/pipelines/datasets/br_ms_cnes/tasks.py @@ -15,6 +15,7 @@ # from pyreaddbc import read_dbc as dbcreader from prefect import task +from prefect.tasks.shell import ShellTask from simpledbf import Dbf5 from tqdm import tqdm @@ -57,7 +58,7 @@ def check_files_to_parse( # download files to compare year = "2023" - month = 10 + month = 11 if month <= 11: month = month + 1 @@ -162,29 +163,75 @@ def access_ftp_donwload_files(file_list: list, path: str, table: str) -> list[st # ) +# Define a ShellTask to create the directory +create_dir_task = ShellTask( + name="Create Directory", + command="mkdir -p /tmp/br_ms_cnes/blast-dbf", + return_all=True, + log_stderr=True, +) + +# Define a ShellTask to clone the git repository +clone_repo_task = ShellTask( + name="Clone Repository", + command="git clone https://github.com/eaglebh/blast-dbf /tmp/br_ms_cnes/blast-dbf", + return_all=True, + log_stderr=True, +) + +# Define a ShellTask to build the blast-dbf +compile_blast_dbf = ShellTask( + name="Build blast-dbf", + command="cd /tmp/br_ms_cnes/blast-dbf && make", + return_all=True, + log_stderr=True, +) + + @task def decompress_dbc(file_list: list) -> None: - log(f"==== current env {os.getcwd()}") - - # Clone blast-dbf to /tmp/br_ms_cnes and build it - blast_path = "/tmp/br_ms_cnes/blast-dbf" - os.system(f"mkdir -p {blast_path}") - os.system(f"git clone https://github.com/eaglebh/blast-dbf {blast_path}") - os.chdir(blast_path) - log(f"==== current env {os.getcwd()}") - os.system("make") - log(f"Blast-dbf path: {blast_path}") - os.chdir("..") - log(f"==== current env {os.getcwd()}") - for file in tqdm(file_list): - log(f"Blasting: {file}") + create_dir_task.run() + clone_repo_task.run() + compile_blast_dbf.run() + + for file in file_list: + # Check if the file has a .dbc extension if file.endswith(".dbc"): - os.system(f"{blast_path}/blast-dbf {file} {file.replace('.dbc', '.dbf')}") - a = file.split("/")[:-1] - directory_path = "/".join(a) - log(f"----- files {os.listdir(directory_path)}") + # Execute blast-dbf on the file + decompress_task = ShellTask( + name=f"Decompress {file}", + command=f"/tmp/br_ms_cnes/blast-dbf/blast-dbf {file} {file.replace('.dbc', '.dbf')}", + return_all=True, + log_stderr=True, + ) + decompress_task.run() else: - log(f"Skipping non-DBC file: {file}") + print(f"Skipping non-DBC file: {file}") + + +# @task +# def decompress_dbc(file_list: list) -> None: +# log(f"==== current env {os.getcwd()}") +# +# # Clone blast-dbf to /tmp/br_ms_cnes and build it +# blast_path = "/tmp/br_ms_cnes/blast-dbf" +# os.system(f"mkdir -p {blast_path}") +# os.system(f"git clone https://github.com/eaglebh/blast-dbf {blast_path}") +# os.chdir(blast_path) +# log(f"----- current dir {os.getcwd()}") +# os.system("make") +# log(f"Blast-dbf path: {blast_path}") +# os.chdir("..") +# log(f"==== current env {os.getcwd()}") +# for file in tqdm(file_list): +# log(f"Blasting: {file}") +# if file.endswith(".dbc"): +# os.system(f"{blast_path}/blast-dbf {file} {file.replace('.dbc', '.dbf')}") +# a = file.split("/")[:-1] +# directory_path = "/".join(a) +# log(f"----- files {os.listdir(directory_path)}") +# else: +# log(f"Skipping non-DBC file: {file}") # task to convert dbc to csv and save to a partitioned dir From 2e42f3f53178dd75110dc74e212736bc119c6a0a Mon Sep 17 00:00:00 2001 From: folhesgabriel Date: Tue, 6 Feb 2024 11:20:57 -0300 Subject: [PATCH 24/44] feat: add git to Dockerfile --- Dockerfile | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 0e56d502c..12f796bac 100644 --- a/Dockerfile +++ b/Dockerfile @@ -14,7 +14,7 @@ ENV PYTHONUNBUFFERED 1 ARG PREFECT_VERSION=0.15.9 ENV PREFECT_VERSION $PREFECT_VERSION -# Install gcc, Google Chrome, CLI tools and R +# Install gcc, Google Chrome, CLI tools, git and R RUN apt-get update && \ apt-get install --no-install-recommends -y wget gnupg && \ wget -q -O - https://dl-ssl.google.com/linux/linux_signing_key.pub | apt-key add - && \ @@ -33,6 +33,7 @@ RUN apt-get update && \ python3-dev \ traceroute \ wget \ + git \ && \ apt-get install -y r-base && \ apt-get clean && \ From 5e3f6290cfcdb9276d9f7277d9696a9735532c3a Mon Sep 17 00:00:00 2001 From: folhesgabriel Date: Tue, 6 Feb 2024 12:23:48 -0300 Subject: [PATCH 25/44] feat: add refactored decompress_dbc task --- pipelines/datasets/br_ms_cnes/flows.py | 30 ++++++------ pipelines/datasets/br_ms_cnes/tasks.py | 68 ++++++++++++++------------ 2 files changed, 53 insertions(+), 45 deletions(-) diff --git a/pipelines/datasets/br_ms_cnes/flows.py b/pipelines/datasets/br_ms_cnes/flows.py index bd5383f72..3780a8843 100644 --- a/pipelines/datasets/br_ms_cnes/flows.py +++ b/pipelines/datasets/br_ms_cnes/flows.py @@ -9,6 +9,7 @@ from prefect.run_configs import KubernetesRun from prefect.storage import GCS from prefect.tasks.prefect import create_flow_run, wait_for_flow_run +from prefect.tasks.shell import ShellTask from pipelines.constants import constants from pipelines.datasets.br_ms_cnes.constants import constants as br_ms_cnes_constants @@ -294,7 +295,7 @@ table=br_ms_cnes_constants.TABLE.value[4], ) - dbf_files = decompress_dbc(file_list=dbc_files) + dbf_files = decompress_dbc(file_list=dbc_files, upstream_tasks=[dbc_files]) filepath = decompress_dbf( file_list=dbc_files, @@ -390,13 +391,14 @@ ) with case(is_empty(files_path), False): + dbc_files = access_ftp_donwload_files( file_list=files_path, path=br_ms_cnes_constants.PATH.value[0], table=br_ms_cnes_constants.TABLE.value[3], ) - dbf_files = decompress_dbc(file_list=dbc_files) + dbf_files = decompress_dbc(file_list=dbc_files, upstream_tasks=[dbc_files]) filepath = decompress_dbf( file_list=dbc_files, @@ -495,15 +497,13 @@ ) with case(is_empty(files_path), False): - # task para veficiar se for nula - # e deliberar dbc_files = access_ftp_donwload_files( file_list=files_path, path=br_ms_cnes_constants.PATH.value[0], table=br_ms_cnes_constants.TABLE.value[2], ) - dbf_files = decompress_dbc(file_list=dbc_files) + dbf_files = decompress_dbc(file_list=dbc_files, upstream_tasks=[dbc_files]) filepath = decompress_dbf( file_list=dbc_files, @@ -605,7 +605,7 @@ table=br_ms_cnes_constants.TABLE.value[5], ) - dbf_files = decompress_dbc(file_list=dbc_files) + dbf_files = decompress_dbc(file_list=dbc_files, upstream_tasks=[dbc_files]) filepath = decompress_dbf( file_list=dbc_files, @@ -708,7 +708,7 @@ table=br_ms_cnes_constants.TABLE.value[6], ) - dbf_files = decompress_dbc(file_list=dbc_files) + dbf_files = decompress_dbc(file_list=dbc_files, upstream_tasks=[dbc_files]) filepath = decompress_dbf( file_list=dbc_files, @@ -813,7 +813,7 @@ table=br_ms_cnes_constants.TABLE.value[7], ) - dbf_files = decompress_dbc(file_list=dbc_files) + dbf_files = decompress_dbc(file_list=dbc_files, upstream_tasks=[dbc_files]) filepath = decompress_dbf( file_list=dbc_files, @@ -920,7 +920,7 @@ table=br_ms_cnes_constants.TABLE.value[8], ) - dbf_files = decompress_dbc(file_list=dbc_files) + dbf_files = decompress_dbc(file_list=dbc_files, upstream_tasks=[dbc_files]) filepath = decompress_dbf( file_list=dbc_files, @@ -1022,7 +1022,7 @@ table=br_ms_cnes_constants.TABLE.value[9], ) - dbf_files = decompress_dbc(file_list=dbc_files) + dbf_files = decompress_dbc(file_list=dbc_files, upstream_tasks=[dbc_files]) filepath = decompress_dbf( file_list=dbc_files, @@ -1126,7 +1126,7 @@ table=br_ms_cnes_constants.TABLE.value[10], ) - dbf_files = decompress_dbc(file_list=dbc_files) + dbf_files = decompress_dbc(file_list=dbc_files, upstream_tasks=[dbc_files]) filepath = decompress_dbf( file_list=dbc_files, @@ -1229,7 +1229,7 @@ table=br_ms_cnes_constants.TABLE.value[12], ) - dbf_files = decompress_dbc(file_list=dbc_files) + dbf_files = decompress_dbc(file_list=dbc_files, upstream_tasks=[dbc_files]) filepath = decompress_dbf( file_list=dbc_files, @@ -1331,15 +1331,15 @@ dbc_files = access_ftp_donwload_files( file_list=files_path, path=br_ms_cnes_constants.PATH.value[0], - table=br_ms_cnes_constants.TABLE.value[12], + table=br_ms_cnes_constants.TABLE.value[13], ) - dbf_files = decompress_dbc(file_list=dbc_files) + dbf_files = decompress_dbc(file_list=dbc_files, upstream_tasks=[dbc_files]) filepath = decompress_dbf( file_list=dbc_files, path=br_ms_cnes_constants.PATH.value[1], - table=br_ms_cnes_constants.TABLE.value[12], + table=br_ms_cnes_constants.TABLE.value[13], upstream_tasks=[dbf_files, dbc_files], ) diff --git a/pipelines/datasets/br_ms_cnes/tasks.py b/pipelines/datasets/br_ms_cnes/tasks.py index c84dc5c93..4795ccae8 100644 --- a/pipelines/datasets/br_ms_cnes/tasks.py +++ b/pipelines/datasets/br_ms_cnes/tasks.py @@ -163,35 +163,36 @@ def access_ftp_donwload_files(file_list: list, path: str, table: str) -> list[st # ) -# Define a ShellTask to create the directory -create_dir_task = ShellTask( - name="Create Directory", - command="mkdir -p /tmp/br_ms_cnes/blast-dbf", - return_all=True, - log_stderr=True, -) - -# Define a ShellTask to clone the git repository -clone_repo_task = ShellTask( - name="Clone Repository", - command="git clone https://github.com/eaglebh/blast-dbf /tmp/br_ms_cnes/blast-dbf", - return_all=True, - log_stderr=True, -) +@task +def decompress_dbc(file_list: list) -> None: + # ShellTask to create the blast-dbf directory + create_dir_task = ShellTask( + name="Create blast-dbf Directory", + command="mkdir -p /tmp/br_ms_cnes/blast-dbf", + return_all=True, + log_stderr=True, + ) -# Define a ShellTask to build the blast-dbf -compile_blast_dbf = ShellTask( - name="Build blast-dbf", - command="cd /tmp/br_ms_cnes/blast-dbf && make", - return_all=True, - log_stderr=True, -) + # Define a ShellTask to clone the blast-dbf repository + clone_repo_task = ShellTask( + name="Clone blast-dbf Repository", + command="git clone https://github.com/eaglebh/blast-dbf /tmp/br_ms_cnes/blast-dbf", + return_all=True, + log_stderr=True, + ) + # Define a ShellTask to build the blast-dbf repository + compile_blast_dbf = ShellTask( + name="Build blast-dbf", + command="cd /tmp/br_ms_cnes/blast-dbf && make", + return_all=True, + log_stderr=True, + ) -@task -def decompress_dbc(file_list: list) -> None: create_dir_task.run() + log("------ Cloning blast-dbf repository") clone_repo_task.run() + log("------ Compiling blast-dbf repository") compile_blast_dbf.run() for file in file_list: @@ -204,6 +205,7 @@ def decompress_dbc(file_list: list) -> None: return_all=True, log_stderr=True, ) + log(f"Decompressing {file}") decompress_task.run() else: print(f"Skipping non-DBC file: {file}") @@ -215,18 +217,23 @@ def decompress_dbc(file_list: list) -> None: # # # Clone blast-dbf to /tmp/br_ms_cnes and build it # blast_path = "/tmp/br_ms_cnes/blast-dbf" -# os.system(f"mkdir -p {blast_path}") -# os.system(f"git clone https://github.com/eaglebh/blast-dbf {blast_path}") +# clone_exit_code = os.system(f"git clone https://github.com/eaglebh/blast-dbf {blast_path}") +# log(f"Command CLONE exited with code {clone_exit_code}") +# # os.chdir(blast_path) # log(f"----- current dir {os.getcwd()}") -# os.system("make") +# make_exit_code = os.system("make") +# log(f"Command MAKE exited with code {make_exit_code}") +# # log(f"Blast-dbf path: {blast_path}") # os.chdir("..") # log(f"==== current env {os.getcwd()}") # for file in tqdm(file_list): # log(f"Blasting: {file}") # if file.endswith(".dbc"): -# os.system(f"{blast_path}/blast-dbf {file} {file.replace('.dbc', '.dbf')}") +# blast_command = f"{blast_path}/blast-dbf {file} {file.replace('.dbc', '.dbf')}" +# blast_exit_code = os.system(blast_command) +# log(f"Command '{blast_command}' exited with code {blast_exit_code}") # a = file.split("/")[:-1] # directory_path = "/".join(a) # log(f"----- files {os.listdir(directory_path)}") @@ -251,11 +258,11 @@ def decompress_dbf(file_list: list, path: str, table: str) -> str: year_month_sigla_uf = year_month_sigla_uf_parser(file=file) - log(f"year_month_sigla_uf of {file} parsed") + # log(f"year_month_sigla_uf of {file} parsed") output_path = path + table + "/" + year_month_sigla_uf os.system(f"mkdir -p {output_path}") - log(f"created output partition dir {path + table + '/'+ year_month_sigla_uf}") + # log(f"created output partition dir {path + table + '/'+ year_month_sigla_uf}") output_file = output_path + "/" + table + ".csv" log(f"{file} 1 saved") @@ -271,6 +278,7 @@ def decompress_dbf(file_list: list, path: str, table: str) -> str: ) # Remove each file for file in files_to_remove: + log(f"---- Removing file {file}") os.system(f"rm {file}") # ler df From 5a60b2b28c3f28f5bd69740b980fed9f2b6d2eba Mon Sep 17 00:00:00 2001 From: folhesgabriel Date: Tue, 6 Feb 2024 12:29:13 -0300 Subject: [PATCH 26/44] fix: ci action --- pipelines/datasets/br_ms_cnes/flows.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/pipelines/datasets/br_ms_cnes/flows.py b/pipelines/datasets/br_ms_cnes/flows.py index 3780a8843..a448717cb 100644 --- a/pipelines/datasets/br_ms_cnes/flows.py +++ b/pipelines/datasets/br_ms_cnes/flows.py @@ -1226,7 +1226,7 @@ dbc_files = access_ftp_donwload_files( file_list=files_path, path=br_ms_cnes_constants.PATH.value[0], - table=br_ms_cnes_constants.TABLE.value[12], + table=br_ms_cnes_constants.TABLE.value[11], ) dbf_files = decompress_dbc(file_list=dbc_files, upstream_tasks=[dbc_files]) @@ -1234,7 +1234,7 @@ filepath = decompress_dbf( file_list=dbc_files, path=br_ms_cnes_constants.PATH.value[1], - table=br_ms_cnes_constants.TABLE.value[12], + table=br_ms_cnes_constants.TABLE.value[11], upstream_tasks=[dbf_files, dbc_files], ) @@ -1331,7 +1331,7 @@ dbc_files = access_ftp_donwload_files( file_list=files_path, path=br_ms_cnes_constants.PATH.value[0], - table=br_ms_cnes_constants.TABLE.value[13], + table=br_ms_cnes_constants.TABLE.value[12], ) dbf_files = decompress_dbc(file_list=dbc_files, upstream_tasks=[dbc_files]) @@ -1339,7 +1339,7 @@ filepath = decompress_dbf( file_list=dbc_files, path=br_ms_cnes_constants.PATH.value[1], - table=br_ms_cnes_constants.TABLE.value[13], + table=br_ms_cnes_constants.TABLE.value[12], upstream_tasks=[dbf_files, dbc_files], ) From c9f7c22bd5b0a677204bc2c7f0a8b32a26c791ba Mon Sep 17 00:00:00 2001 From: folhesgabriel Date: Wed, 7 Feb 2024 08:09:53 -0300 Subject: [PATCH 27/44] fix: final modifications --- .../br_ms_cnes/adapted_convert2dbf.sh | 24 ------ pipelines/datasets/br_ms_cnes/tasks.py | 74 ++----------------- 2 files changed, 7 insertions(+), 91 deletions(-) delete mode 100755 pipelines/datasets/br_ms_cnes/adapted_convert2dbf.sh diff --git a/pipelines/datasets/br_ms_cnes/adapted_convert2dbf.sh b/pipelines/datasets/br_ms_cnes/adapted_convert2dbf.sh deleted file mode 100755 index b7d57f91e..000000000 --- a/pipelines/datasets/br_ms_cnes/adapted_convert2dbf.sh +++ /dev/null @@ -1,24 +0,0 @@ -#!/bin/bash - -# Clone blast-dbf and build it -git clone https://github.com/eaglebh/blast-dbf -cd blast-dbf -make -blast=$(readlink -f blast-dbf) -echo $blast -cd .. - -# Set path to the directory with .dbc files -files=("$@") - -# Iterate over the provided file paths -for file in "${files[@]}" -do - # Check if the file has a .dbc extension - if [[ $file == *.dbc ]]; then - # Execute blast-dbf on the file - $blast $file "${file/.dbc/.dbf}" - else - echo "Skipping non-DBC file: $file" - fi -done \ No newline at end of file diff --git a/pipelines/datasets/br_ms_cnes/tasks.py b/pipelines/datasets/br_ms_cnes/tasks.py index 4795ccae8..65ddd1bce 100644 --- a/pipelines/datasets/br_ms_cnes/tasks.py +++ b/pipelines/datasets/br_ms_cnes/tasks.py @@ -9,11 +9,7 @@ from glob import glob import pandas as pd - -# import rpy2.robjects.packages as rpackages import wget - -# from pyreaddbc import read_dbc as dbcreader from prefect import task from prefect.tasks.shell import ShellTask from simpledbf import Dbf5 @@ -31,8 +27,6 @@ from pipelines.utils.metadata.utils import get_api_most_recent_date from pipelines.utils.utils import log -# from rpy2.robjects.packages import importr - @task def check_files_to_parse( @@ -58,12 +52,14 @@ def check_files_to_parse( # download files to compare year = "2023" - month = 11 + month = 12 if month <= 11: month = month + 1 else: month = 1 + year = int(year) + 1 + year = str(year) # 3. buildar no formato do ftp YYMM year = year[2:4] @@ -109,8 +105,6 @@ def access_ftp_donwload_files(file_list: list, path: str, table: str) -> list[st log(f"wrangling {table} data") - file_list = file_list[1:3] - for file in tqdm(file_list): # build partition dirs @@ -144,27 +138,12 @@ def access_ftp_donwload_files(file_list: list, path: str, table: str) -> list[st return dbc_files_path_list -# @task -# def decompress_dbc(file_list: list) -> None: -# -# log(f"==== curent env {os.getcwd()}") -# -# # ? Tive que dar um grant pra exucutar bash na pipeline -# # ? chmod +x adapted_convert2dbf.sh -# # -# # pipelines/datasets/br_ms_cnes/adapted_convert2dbf.sh -# -# log(os.system("ls pipelines/datasets/br_ms_cnes/")) -# # subprocess.run( -# # ["chmod", "+x", "/home/gabri/pipelines/pipelines/datasets/br_ms_cnes/adapted_convert2dbf.sh"]) -# -# subprocess.run( -# ["/pipelines/datasets/br_ms_cnes/adapted_convert2dbf.sh"] + file_list -# ) - - @task def decompress_dbc(file_list: list) -> None: + """ + Convert dbc to dbf format + """ + # ShellTask to create the blast-dbf directory create_dir_task = ShellTask( name="Create blast-dbf Directory", @@ -211,37 +190,6 @@ def decompress_dbc(file_list: list) -> None: print(f"Skipping non-DBC file: {file}") -# @task -# def decompress_dbc(file_list: list) -> None: -# log(f"==== current env {os.getcwd()}") -# -# # Clone blast-dbf to /tmp/br_ms_cnes and build it -# blast_path = "/tmp/br_ms_cnes/blast-dbf" -# clone_exit_code = os.system(f"git clone https://github.com/eaglebh/blast-dbf {blast_path}") -# log(f"Command CLONE exited with code {clone_exit_code}") -# -# os.chdir(blast_path) -# log(f"----- current dir {os.getcwd()}") -# make_exit_code = os.system("make") -# log(f"Command MAKE exited with code {make_exit_code}") -# -# log(f"Blast-dbf path: {blast_path}") -# os.chdir("..") -# log(f"==== current env {os.getcwd()}") -# for file in tqdm(file_list): -# log(f"Blasting: {file}") -# if file.endswith(".dbc"): -# blast_command = f"{blast_path}/blast-dbf {file} {file.replace('.dbc', '.dbf')}" -# blast_exit_code = os.system(blast_command) -# log(f"Command '{blast_command}' exited with code {blast_exit_code}") -# a = file.split("/")[:-1] -# directory_path = "/".join(a) -# log(f"----- files {os.listdir(directory_path)}") -# else: -# log(f"Skipping non-DBC file: {file}") - - -# task to convert dbc to csv and save to a partitioned dir @task def decompress_dbf(file_list: list, path: str, table: str) -> str: """ @@ -356,11 +304,3 @@ def decompress_dbf(file_list: list, path: str, table: str) -> str: ) return path + table - - -@task -def is_empty(lista): - if len(lista) == 0: - return True - else: - return False From b9c66fa5e219ae54a1dfffe31b92f04ab4a56cfe Mon Sep 17 00:00:00 2001 From: folhesgabriel Date: Wed, 7 Feb 2024 08:15:08 -0300 Subject: [PATCH 28/44] fix: unnused imports --- pipelines/datasets/br_ms_cnes/flows.py | 1 - pipelines/datasets/br_ms_cnes/tasks.py | 14 +++++++++++++- 2 files changed, 13 insertions(+), 2 deletions(-) diff --git a/pipelines/datasets/br_ms_cnes/flows.py b/pipelines/datasets/br_ms_cnes/flows.py index a448717cb..7f425a4e7 100644 --- a/pipelines/datasets/br_ms_cnes/flows.py +++ b/pipelines/datasets/br_ms_cnes/flows.py @@ -9,7 +9,6 @@ from prefect.run_configs import KubernetesRun from prefect.storage import GCS from prefect.tasks.prefect import create_flow_run, wait_for_flow_run -from prefect.tasks.shell import ShellTask from pipelines.constants import constants from pipelines.datasets.br_ms_cnes.constants import constants as br_ms_cnes_constants diff --git a/pipelines/datasets/br_ms_cnes/tasks.py b/pipelines/datasets/br_ms_cnes/tasks.py index 65ddd1bce..c3661cd62 100644 --- a/pipelines/datasets/br_ms_cnes/tasks.py +++ b/pipelines/datasets/br_ms_cnes/tasks.py @@ -27,6 +27,8 @@ from pipelines.utils.metadata.utils import get_api_most_recent_date from pipelines.utils.utils import log +# from rpy2.robjects.packages import importr + @task def check_files_to_parse( @@ -52,7 +54,7 @@ def check_files_to_parse( # download files to compare year = "2023" - month = 12 + month = 11 if month <= 11: month = month + 1 @@ -105,6 +107,8 @@ def access_ftp_donwload_files(file_list: list, path: str, table: str) -> list[st log(f"wrangling {table} data") + # file_list = file_list[1:3] + for file in tqdm(file_list): # build partition dirs @@ -304,3 +308,11 @@ def decompress_dbf(file_list: list, path: str, table: str) -> str: ) return path + table + + +@task +def is_empty(lista): + if len(lista) == 0: + return True + else: + return False From 42bea6ed96c1fee28f34c6d88d7434366e8fa9b5 Mon Sep 17 00:00:00 2001 From: folhesgabriel Date: Thu, 8 Feb 2024 12:53:04 -0300 Subject: [PATCH 29/44] feat: requested changes --- poetry.lock | 393 ++++++++++++++++++------------------------------- pyproject.toml | 2 - 2 files changed, 144 insertions(+), 251 deletions(-) diff --git a/poetry.lock b/poetry.lock index 906366e69..87d5da1c2 100644 --- a/poetry.lock +++ b/poetry.lock @@ -22,25 +22,6 @@ doc = ["Sphinx (>=7)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphin test = ["anyio[trio]", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)"] trio = ["trio (>=0.23)"] -[[package]] -name = "arrow" -version = "1.3.0" -description = "Better dates & times for Python" -optional = false -python-versions = ">=3.8" -files = [ - {file = 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Based on Python type hints." -optional = false -python-versions = ">=3.6" -files = [ - {file = "typer-0.4.0-py3-none-any.whl", hash = "sha256:d81169725140423d072df464cad1ff25ee154ef381aaf5b8225352ea187ca338"}, - {file = "typer-0.4.0.tar.gz", hash = "sha256:63c3aeab0549750ffe40da79a1b524f60e08a2cbc3126c520ebf2eeaf507f5dd"}, -] - -[package.dependencies] -click = ">=7.1.1,<9.0.0" - -[package.extras] -all = ["colorama (>=0.4.3,<0.5.0)", "shellingham (>=1.3.0,<2.0.0)"] -dev = ["autoflake (>=1.3.1,<2.0.0)", "flake8 (>=3.8.3,<4.0.0)"] -doc = ["markdown-include (>=0.5.1,<0.6.0)", "mkdocs (>=1.1.2,<2.0.0)", "mkdocs-material (>=5.4.0,<6.0.0)"] -test = ["black (>=19.10b0,<20.0b0)", "coverage (>=5.2,<6.0)", "isort (>=5.0.6,<6.0.0)", "mypy (==0.910)", "pytest (>=4.4.0,<5.4.0)", "pytest-cov (>=2.10.0,<3.0.0)", "pytest-sugar (>=0.9.4,<0.10.0)", "pytest-xdist (>=1.32.0,<2.0.0)", "shellingham (>=1.3.0,<2.0.0)"] - -[[package]] -name = "types-python-dateutil" -version = "2.8.19.20240106" -description = "Typing stubs for python-dateutil" -optional = false -python-versions = ">=3.8" -files = [ - {file = "types-python-dateutil-2.8.19.20240106.tar.gz", hash = "sha256:1f8db221c3b98e6ca02ea83a58371b22c374f42ae5bbdf186db9c9a76581459f"}, - {file = "types_python_dateutil-2.8.19.20240106-py3-none-any.whl", hash = "sha256:efbbdc54590d0f16152fa103c9879c7d4a00e82078f6e2cf01769042165acaa2"}, -] - [[package]] name = "typing-extensions" version = "4.9.0" @@ -4406,4 +4301,4 @@ heapdict = "*" [metadata] lock-version = "2.0" python-versions = ">=3.10,<3.11" -content-hash = "f7898efdf990c8c167f08857ab39d73334c77cd65e055222d8643290b962de78" +content-hash = "0c25996bca26cd03d06f955843f0729bc54420fe02440389699f2f8adc3d434e" diff --git a/pyproject.toml b/pyproject.toml index 5fdf4d801..baa76b8f0 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -114,8 +114,6 @@ httpx = "^0.26.0" cffi = "^1.16.0" pendulum = "^3.0.0" simpledbf = "^0.2.6" -cookiecutter = "<=1.7.3" -typer = "<=0.4.0" [tool.poetry.dev-dependencies] From 9f076b1ff555bfe7194481a279fea19922b3e231 Mon Sep 17 00:00:00 2001 From: folhesgabriel Date: Thu, 15 Feb 2024 14:32:51 -0300 Subject: [PATCH 30/44] feat: add datasus deepcopy flow --- pipelines/datasets/br_ms_cnes/flows.py | 1392 +----------------- pipelines/utils/crawler_datasus/__init__.py | 0 pipelines/utils/crawler_datasus/constants.py | 292 ++++ pipelines/utils/crawler_datasus/flows.py | 142 ++ pipelines/utils/crawler_datasus/tasks.py | 291 ++++ pipelines/utils/crawler_datasus/utils.py | 272 ++++ poetry.lock | 107 +- pyproject.toml | 1 + 8 files changed, 1117 insertions(+), 1380 deletions(-) create mode 100644 pipelines/utils/crawler_datasus/__init__.py create mode 100644 pipelines/utils/crawler_datasus/constants.py create mode 100644 pipelines/utils/crawler_datasus/flows.py create mode 100644 pipelines/utils/crawler_datasus/tasks.py create mode 100644 pipelines/utils/crawler_datasus/utils.py diff --git a/pipelines/datasets/br_ms_cnes/flows.py b/pipelines/datasets/br_ms_cnes/flows.py index 7f425a4e7..3232da0c1 100644 --- a/pipelines/datasets/br_ms_cnes/flows.py +++ b/pipelines/datasets/br_ms_cnes/flows.py @@ -2,16 +2,14 @@ """ Flows for br_ms_cnes """ -# pylint: disable=invalid-name -from datetime import timedelta +# pylint: disable=C0103, E1123, invalid-name + +from copy import deepcopy -from prefect import Parameter, case from prefect.run_configs import KubernetesRun from prefect.storage import GCS -from prefect.tasks.prefect import create_flow_run, wait_for_flow_run from pipelines.constants import constants -from pipelines.datasets.br_ms_cnes.constants import constants as br_ms_cnes_constants from pipelines.datasets.br_ms_cnes.schedules import ( schedule_br_ms_cnes_dados_complementares, schedule_br_ms_cnes_equipamento, @@ -24,1376 +22,102 @@ schedule_br_ms_cnes_incentivos, schedule_br_ms_cnes_leito, schedule_br_ms_cnes_profissional, - schedule_br_ms_cnes_regra_contratual, schedule_br_ms_cnes_servico_especializado, ) -from pipelines.datasets.br_ms_cnes.tasks import ( - access_ftp_donwload_files, - check_files_to_parse, - decompress_dbc, - decompress_dbf, - is_empty, -) -from pipelines.utils.constants import constants as utils_constants -from pipelines.utils.decorators import Flow -from pipelines.utils.execute_dbt_model.constants import constants as dump_db_constants -from pipelines.utils.metadata.flows import update_django_metadata -from pipelines.utils.tasks import ( - create_table_and_upload_to_gcs, - get_current_flow_labels, - log_task, - rename_current_flow_run_dataset_table, -) - -with Flow( - name="br_ms_cnes.estabelecimento", code_owners=["Gabriel Pisa"] -) as br_ms_cnes_estabelecimento: - # Parameters - dataset_id = Parameter("dataset_id", default="br_ms_cnes", required=True) - table_id = Parameter("table_id", default="estabelecimento", required=True) - update_metadata = Parameter("update_metadata", default=False, required=False) - materialization_mode = Parameter( - "materialization_mode", default="dev", required=False - ) - materialize_after_dump = Parameter( - "materialize after dump", default=True, required=False - ) - dbt_alias = Parameter("dbt_alias", default=False, required=False) - - rename_flow_run = rename_current_flow_run_dataset_table( - prefix="Dump: ", dataset_id=dataset_id, table_id=table_id, wait=table_id - ) - - files_path = check_files_to_parse( - dataset_id=dataset_id, - table_id=table_id, - cnes_database="CNES", - cnes_group_file=br_ms_cnes_constants.DATABASE_GROUPS.value["CNES"][0], - ) - - with case(is_empty(files_path), True): - log_task( - "Os dados do FTP CNES-ST ainda não foram atualizados para o ano/mes mais recente" - ) - - with case(is_empty(files_path), False): - dbc_files = access_ftp_donwload_files( - file_list=files_path, - path=br_ms_cnes_constants.PATH.value[0], - table=br_ms_cnes_constants.TABLE.value[0], - ) - - dbf_files = decompress_dbc(file_list=dbc_files, upstream_tasks=[dbc_files]) - - filepath = decompress_dbf( - file_list=dbc_files, - path=br_ms_cnes_constants.PATH.value[1], - table=br_ms_cnes_constants.TABLE.value[0], - upstream_tasks=[dbf_files, dbc_files], - ) - - wait_upload_table = create_table_and_upload_to_gcs( - data_path=filepath, - dataset_id=dataset_id, - table_id=table_id, - dump_mode="append", - wait=filepath, - ) - - # estabelecimento - with case(materialize_after_dump, True): - # Trigger DBT flow run - current_flow_labels = get_current_flow_labels() - materialization_flow = create_flow_run( - flow_name=utils_constants.FLOW_EXECUTE_DBT_MODEL_NAME.value, - project_name=constants.PREFECT_DEFAULT_PROJECT.value, - parameters={ - "dataset_id": dataset_id, - "table_id": table_id, - "mode": materialization_mode, - "dbt_alias": dbt_alias, - }, - labels=current_flow_labels, - run_name=f"Materialize {dataset_id}.{table_id}", - ) - - wait_for_materialization = wait_for_flow_run( - materialization_flow, - stream_states=True, - stream_logs=True, - raise_final_state=True, - ) - wait_for_materialization.max_retries = ( - dump_db_constants.WAIT_FOR_MATERIALIZATION_RETRY_ATTEMPTS.value - ) - wait_for_materialization.retry_delay = timedelta( - seconds=dump_db_constants.WAIT_FOR_MATERIALIZATION_RETRY_INTERVAL.value - ) - - with case(update_metadata, True): - update_django_metadata( - dataset_id=dataset_id, - table_id=table_id, - date_column_name={"year": "ano", "month": "mes"}, - date_format="%Y-%m", - coverage_type="part_bdpro", - time_delta={"months": 6}, - prefect_mode=materialization_mode, - bq_project="basedosdados", - upstream_tasks=[wait_for_materialization], - ) +from pipelines.utils.crawler_datasus.flows import flow_datasus +br_ms_cnes_profissional = deepcopy(flow_datasus) +br_ms_cnes_profissional.name = "br_ms_cnes.profissional" +br_ms_cnes_profissional.code_owners = ["equipe_pipelines"] +br_ms_cnes_profissional.storage = GCS(constants.GCS_FLOWS_BUCKET.value) +br_ms_cnes_profissional.run_config = KubernetesRun(image=constants.DOCKER_IMAGE.value) +# br_ms_cnes_profissional.schedule = schedule_br_ms_cnes_profissional +br_ms_cnes_estabelecimento = deepcopy(flow_datasus) +br_ms_cnes_estabelecimento.name = "br_ms_cnes.estabelecimento" +br_ms_cnes_estabelecimento.code_owners = ["equipe_pipelines"] br_ms_cnes_estabelecimento.storage = GCS(constants.GCS_FLOWS_BUCKET.value) br_ms_cnes_estabelecimento.run_config = KubernetesRun( image=constants.DOCKER_IMAGE.value ) # br_ms_cnes_estabelecimento.schedule = schedule_br_ms_cnes_estabelecimento - -# profissional -with Flow( - name="br_ms_cnes.profissional", code_owners=["Gabriel Pisa"] -) as br_ms_cnes_profissional: - # Parameters - dataset_id = Parameter("dataset_id", default="br_ms_cnes", required=True) - table_id = Parameter("table_id", default="profissional", required=True) - update_metadata = Parameter("update_metadata", default=False, required=False) - - materialization_mode = Parameter( - "materialization_mode", default="dev", required=False - ) - materialize_after_dump = Parameter( - "materialize after dump", default=True, required=False - ) - dbt_alias = Parameter("dbt_alias", default=False, required=False) - - rename_flow_run = rename_current_flow_run_dataset_table( - prefix="Dump: ", dataset_id=dataset_id, table_id=table_id, wait=table_id - ) - - files_path = check_files_to_parse( - dataset_id=dataset_id, - table_id=table_id, - cnes_database="CNES", - cnes_group_file=br_ms_cnes_constants.DATABASE_GROUPS.value["CNES"][1], - ) - - with case(is_empty(files_path), True): - log_task( - "Os dados do FTP CNES-ST ainda não foram atualizados para o ano/mes mais recente" - ) - - with case(is_empty(files_path), False): - - dbc_files = access_ftp_donwload_files( - file_list=files_path, - path=br_ms_cnes_constants.PATH.value[0], - table=br_ms_cnes_constants.TABLE.value[1], - ) - - dbf_files = decompress_dbc(file_list=dbc_files, upstream_tasks=[dbc_files]) - - filepath = decompress_dbf( - file_list=dbc_files, - path=br_ms_cnes_constants.PATH.value[1], - table=br_ms_cnes_constants.TABLE.value[1], - upstream_tasks=[dbf_files, dbc_files], - ) - - wait_upload_table = create_table_and_upload_to_gcs( - data_path=filepath, - dataset_id=dataset_id, - table_id=table_id, - dump_mode="append", - wait=filepath, - ) - - # estabelecimento - with case(materialize_after_dump, True): - # Trigger DBT flow run - current_flow_labels = get_current_flow_labels() - materialization_flow = create_flow_run( - flow_name=utils_constants.FLOW_EXECUTE_DBT_MODEL_NAME.value, - project_name=constants.PREFECT_DEFAULT_PROJECT.value, - parameters={ - "dataset_id": dataset_id, - "table_id": table_id, - "mode": materialization_mode, - "dbt_alias": dbt_alias, - }, - labels=current_flow_labels, - run_name=f"Materialize {dataset_id}.{table_id}", - ) - - wait_for_materialization = wait_for_flow_run( - materialization_flow, - stream_states=True, - stream_logs=True, - raise_final_state=True, - ) - wait_for_materialization.max_retries = ( - dump_db_constants.WAIT_FOR_MATERIALIZATION_RETRY_ATTEMPTS.value - ) - wait_for_materialization.retry_delay = timedelta( - seconds=dump_db_constants.WAIT_FOR_MATERIALIZATION_RETRY_INTERVAL.value - ) - - with case(update_metadata, True): - update_django_metadata( - dataset_id=dataset_id, - table_id=table_id, - date_column_name={"year": "ano", "month": "mes"}, - date_format="%Y-%m", - coverage_type="part_bdpro", - time_delta={"months": 6}, - prefect_mode=materialization_mode, - bq_project="basedosdados", - upstream_tasks=[wait_for_materialization], - ) - -br_ms_cnes_profissional.storage = GCS(constants.GCS_FLOWS_BUCKET.value) -br_ms_cnes_profissional.run_config = KubernetesRun(image=constants.DOCKER_IMAGE.value) -# br_ms_cnes_profissional.schedule = schedule_br_ms_cnes_profissional - -# equipe -with Flow(name="br_ms_cnes.equipe", code_owners=["Gabriel Pisa"]) as br_ms_cnes_equipe: - # Parameters - dataset_id = Parameter("dataset_id", default="br_ms_cnes", required=True) - table_id = Parameter("table_id", default="equipe", required=True) - update_metadata = Parameter("update_metadata", default=False, required=False) - - materialization_mode = Parameter( - "materialization_mode", default="dev", required=False - ) - materialize_after_dump = Parameter( - "materialize after dump", default=True, required=False - ) - dbt_alias = Parameter("dbt_alias", default=False, required=False) - - rename_flow_run = rename_current_flow_run_dataset_table( - prefix="Dump: ", dataset_id=dataset_id, table_id=table_id, wait=table_id - ) - - files_path = check_files_to_parse( - dataset_id=dataset_id, - table_id=table_id, - cnes_database="CNES", - cnes_group_file=br_ms_cnes_constants.DATABASE_GROUPS.value["CNES"][4], - ) - - with case(is_empty(files_path), True): - log_task( - "Os dados do FTP CNES-ST ainda não foram atualizados para o ano/mes mais recente" - ) - - with case(is_empty(files_path), False): - dbc_files = access_ftp_donwload_files( - file_list=files_path, - path=br_ms_cnes_constants.PATH.value[0], - table=br_ms_cnes_constants.TABLE.value[4], - ) - - dbf_files = decompress_dbc(file_list=dbc_files, upstream_tasks=[dbc_files]) - - filepath = decompress_dbf( - file_list=dbc_files, - path=br_ms_cnes_constants.PATH.value[1], - table=br_ms_cnes_constants.TABLE.value[4], - upstream_tasks=[dbf_files, dbc_files], - ) - - wait_upload_table = create_table_and_upload_to_gcs( - data_path=filepath, - dataset_id=dataset_id, - table_id=table_id, - dump_mode="append", - wait=filepath, - ) - - with case(materialize_after_dump, True): - # Trigger DBT flow run - current_flow_labels = get_current_flow_labels() - materialization_flow = create_flow_run( - flow_name=utils_constants.FLOW_EXECUTE_DBT_MODEL_NAME.value, - project_name=constants.PREFECT_DEFAULT_PROJECT.value, - parameters={ - "dataset_id": dataset_id, - "table_id": table_id, - "mode": materialization_mode, - "dbt_alias": dbt_alias, - }, - labels=current_flow_labels, - run_name=f"Materialize {dataset_id}.{table_id}", - ) - - wait_for_materialization = wait_for_flow_run( - materialization_flow, - stream_states=True, - stream_logs=True, - raise_final_state=True, - ) - wait_for_materialization.max_retries = ( - dump_db_constants.WAIT_FOR_MATERIALIZATION_RETRY_ATTEMPTS.value - ) - wait_for_materialization.retry_delay = timedelta( - seconds=dump_db_constants.WAIT_FOR_MATERIALIZATION_RETRY_INTERVAL.value - ) - - with case(update_metadata, True): - update_django_metadata( - dataset_id=dataset_id, - table_id=table_id, - date_column_name={"year": "ano", "month": "mes"}, - date_format="%Y-%m", - coverage_type="part_bdpro", - time_delta={"months": 6}, - prefect_mode=materialization_mode, - bq_project="basedosdados", - upstream_tasks=[wait_for_materialization], - ) - - -br_ms_cnes_equipe.storage = GCS(constants.GCS_FLOWS_BUCKET.value) -br_ms_cnes_equipe.run_config = KubernetesRun(image=constants.DOCKER_IMAGE.value) -# br_ms_cnes_equipe.schedule = schedule_br_ms_cnes_equipe - -# leito -with Flow(name="br_ms_cnes.leito", code_owners=["Gabriel Pisa"]) as br_ms_cnes_leito: - # Parameters - dataset_id = Parameter("dataset_id", default="br_ms_cnes", required=True) - table_id = Parameter("table_id", default="leito", required=True) - update_metadata = Parameter("update_metadata", default=False, required=False) - - materialization_mode = Parameter( - "materialization_mode", default="dev", required=False - ) - materialize_after_dump = Parameter( - "materialize after dump", default=True, required=False - ) - dbt_alias = Parameter("dbt_alias", default=False, required=False) - - rename_flow_run = rename_current_flow_run_dataset_table( - prefix="Dump: ", dataset_id=dataset_id, table_id=table_id, wait=table_id - ) - - files_path = check_files_to_parse( - dataset_id=dataset_id, - table_id=table_id, - cnes_database="CNES", - cnes_group_file=br_ms_cnes_constants.DATABASE_GROUPS.value["CNES"][3], - ) - - with case(is_empty(files_path), True): - log_task( - "Os dados do FTP CNES-ST ainda não foram atualizados para o ano/mes mais recente" - ) - - with case(is_empty(files_path), False): - - dbc_files = access_ftp_donwload_files( - file_list=files_path, - path=br_ms_cnes_constants.PATH.value[0], - table=br_ms_cnes_constants.TABLE.value[3], - ) - - dbf_files = decompress_dbc(file_list=dbc_files, upstream_tasks=[dbc_files]) - - filepath = decompress_dbf( - file_list=dbc_files, - path=br_ms_cnes_constants.PATH.value[1], - table=br_ms_cnes_constants.TABLE.value[3], - upstream_tasks=[dbf_files, dbc_files], - ) - - wait_upload_table = create_table_and_upload_to_gcs( - data_path=filepath, - dataset_id=dataset_id, - table_id=table_id, - dump_mode="append", - wait=filepath, - ) - - with case(materialize_after_dump, True): - # Trigger DBT flow run - current_flow_labels = get_current_flow_labels() - materialization_flow = create_flow_run( - flow_name=utils_constants.FLOW_EXECUTE_DBT_MODEL_NAME.value, - project_name=constants.PREFECT_DEFAULT_PROJECT.value, - parameters={ - "dataset_id": dataset_id, - "table_id": table_id, - "mode": materialization_mode, - "dbt_alias": dbt_alias, - }, - labels=current_flow_labels, - run_name=f"Materialize {dataset_id}.{table_id}", - ) - - wait_for_materialization = wait_for_flow_run( - materialization_flow, - stream_states=True, - stream_logs=True, - raise_final_state=True, - ) - wait_for_materialization.max_retries = ( - dump_db_constants.WAIT_FOR_MATERIALIZATION_RETRY_ATTEMPTS.value - ) - wait_for_materialization.retry_delay = timedelta( - seconds=dump_db_constants.WAIT_FOR_MATERIALIZATION_RETRY_INTERVAL.value - ) - - with case(update_metadata, True): - update_django_metadata( - dataset_id=dataset_id, - table_id=table_id, - date_column_name={"year": "ano", "month": "mes"}, - date_format="%Y-%m", - coverage_type="part_bdpro", - time_delta={"months": 6}, - prefect_mode=materialization_mode, - bq_project="basedosdados", - upstream_tasks=[wait_for_materialization], - ) - - +br_ms_cnes_leito = deepcopy(flow_datasus) +br_ms_cnes_leito.name = "br_ms_cnes.leito" +br_ms_cnes_leito.code_owners = ["equipe_pipelines"] br_ms_cnes_leito.storage = GCS(constants.GCS_FLOWS_BUCKET.value) br_ms_cnes_leito.run_config = KubernetesRun(image=constants.DOCKER_IMAGE.value) # br_ms_cnes_leito.schedule = schedule_br_ms_cnes_leito -# equipamento -with Flow( - name="br_ms_cnes.equipamento", code_owners=["Gabriel Pisa"] -) as br_ms_cnes_equipamento: - # Parameters - dataset_id = Parameter("dataset_id", default="br_ms_cnes", required=True) - table_id = Parameter("table_id", default="equipamento", required=True) - update_metadata = Parameter("update_metadata", default=False, required=False) - - materialization_mode = Parameter( - "materialization_mode", default="dev", required=False - ) - materialize_after_dump = Parameter( - "materialize after dump", default=True, required=False - ) - dbt_alias = Parameter("dbt_alias", default=False, required=False) - - rename_flow_run = rename_current_flow_run_dataset_table( - prefix="Dump: ", dataset_id=dataset_id, table_id=table_id, wait=table_id - ) - - files_path = check_files_to_parse( - dataset_id=dataset_id, - table_id=table_id, - cnes_database="CNES", - # mudar no aqui pra 1 - cnes_group_file=br_ms_cnes_constants.DATABASE_GROUPS.value["CNES"][2], - ) - - with case(is_empty(files_path), True): - log_task( - "Os dados do FTP CNES-ST ainda não foram atualizados para o ano/mes mais recente" - ) - - with case(is_empty(files_path), False): - dbc_files = access_ftp_donwload_files( - file_list=files_path, - path=br_ms_cnes_constants.PATH.value[0], - table=br_ms_cnes_constants.TABLE.value[2], - ) - - dbf_files = decompress_dbc(file_list=dbc_files, upstream_tasks=[dbc_files]) - - filepath = decompress_dbf( - file_list=dbc_files, - path=br_ms_cnes_constants.PATH.value[1], - table=br_ms_cnes_constants.TABLE.value[2], - upstream_tasks=[dbf_files, dbc_files], - ) - - wait_upload_table = create_table_and_upload_to_gcs( - data_path=filepath, - dataset_id=dataset_id, - table_id=table_id, - dump_mode="append", - wait=filepath, - ) - - with case(materialize_after_dump, True): - # Trigger DBT flow run - current_flow_labels = get_current_flow_labels() - materialization_flow = create_flow_run( - flow_name=utils_constants.FLOW_EXECUTE_DBT_MODEL_NAME.value, - project_name=constants.PREFECT_DEFAULT_PROJECT.value, - parameters={ - "dataset_id": dataset_id, - "table_id": table_id, - "mode": materialization_mode, - "dbt_alias": dbt_alias, - }, - labels=current_flow_labels, - run_name=f"Materialize {dataset_id}.{table_id}", - ) - - wait_for_materialization = wait_for_flow_run( - materialization_flow, - stream_states=True, - stream_logs=True, - raise_final_state=True, - ) - wait_for_materialization.max_retries = ( - dump_db_constants.WAIT_FOR_MATERIALIZATION_RETRY_ATTEMPTS.value - ) - wait_for_materialization.retry_delay = timedelta( - seconds=dump_db_constants.WAIT_FOR_MATERIALIZATION_RETRY_INTERVAL.value - ) - - with case(update_metadata, True): - update_django_metadata( - dataset_id=dataset_id, - table_id=table_id, - date_column_name={"year": "ano", "month": "mes"}, - date_format="%Y-%m", - coverage_type="part_bdpro", - time_delta={"months": 6}, - prefect_mode=materialization_mode, - bq_project="basedosdados", - upstream_tasks=[wait_for_materialization], - ) - +br_ms_cnes_equipamento = deepcopy(flow_datasus) +br_ms_cnes_equipamento.name = "br_ms_cnes.equipamento" +br_ms_cnes_equipamento.code_owners = ["equipe_pipelines"] br_ms_cnes_equipamento.storage = GCS(constants.GCS_FLOWS_BUCKET.value) br_ms_cnes_equipamento.run_config = KubernetesRun(image=constants.DOCKER_IMAGE.value) # br_ms_cnes_equipamento.schedule = schedule_br_ms_cnes_equipamento +br_ms_cnes_equipe = deepcopy(flow_datasus) +br_ms_cnes_equipe.name = "br_ms_cnes.equipe" +br_ms_cnes_equipe.code_owners = ["equipe_pipelines"] +br_ms_cnes_equipe.storage = GCS(constants.GCS_FLOWS_BUCKET.value) +br_ms_cnes_equipe.run_config = KubernetesRun(image=constants.DOCKER_IMAGE.value) +# br_ms_cnes_equipe.schedule = schedule_br_ms_cnes_equipe -with Flow( - name="br_ms_cnes.estabelecimento_ensino", code_owners=["Gabriel Pisa"] -) as br_ms_cnes_estabelecimento_ensino: - # Parameters - dataset_id = Parameter("dataset_id", default="br_ms_cnes", required=True) - table_id = Parameter("table_id", default="estabelecimento_ensino", required=True) - update_metadata = Parameter("update_metadata", default=False, required=False) - materialization_mode = Parameter( - "materialization_mode", default="dev", required=False - ) - materialize_after_dump = Parameter( - "materialize after dump", default=True, required=False - ) - dbt_alias = Parameter("dbt_alias", default=False, required=False) - - rename_flow_run = rename_current_flow_run_dataset_table( - prefix="Dump: ", dataset_id=dataset_id, table_id=table_id, wait=table_id - ) - - files_path = check_files_to_parse( - dataset_id=dataset_id, - table_id=table_id, - cnes_database="CNES", - cnes_group_file=br_ms_cnes_constants.DATABASE_GROUPS.value["CNES"][5], - ) - - with case(is_empty(files_path), True): - log_task( - "Os dados do FTP CNES-ST ainda não foram atualizados para o ano/mes mais recente" - ) - - with case(is_empty(files_path), False): - dbc_files = access_ftp_donwload_files( - file_list=files_path, - path=br_ms_cnes_constants.PATH.value[0], - table=br_ms_cnes_constants.TABLE.value[5], - ) - - dbf_files = decompress_dbc(file_list=dbc_files, upstream_tasks=[dbc_files]) - - filepath = decompress_dbf( - file_list=dbc_files, - path=br_ms_cnes_constants.PATH.value[1], - table=br_ms_cnes_constants.TABLE.value[5], - upstream_tasks=[dbf_files, dbc_files], - ) - - wait_upload_table = create_table_and_upload_to_gcs( - data_path=filepath, - dataset_id=dataset_id, - table_id=table_id, - dump_mode="append", - wait=filepath, - ) - - with case(materialize_after_dump, True): - # Trigger DBT flow run - current_flow_labels = get_current_flow_labels() - materialization_flow = create_flow_run( - flow_name=utils_constants.FLOW_EXECUTE_DBT_MODEL_NAME.value, - project_name=constants.PREFECT_DEFAULT_PROJECT.value, - parameters={ - "dataset_id": dataset_id, - "table_id": table_id, - "mode": materialization_mode, - "dbt_alias": dbt_alias, - }, - labels=current_flow_labels, - run_name=f"Materialize {dataset_id}.{table_id}", - ) - - wait_for_materialization = wait_for_flow_run( - materialization_flow, - stream_states=True, - stream_logs=True, - raise_final_state=True, - ) - wait_for_materialization.max_retries = ( - dump_db_constants.WAIT_FOR_MATERIALIZATION_RETRY_ATTEMPTS.value - ) - wait_for_materialization.retry_delay = timedelta( - seconds=dump_db_constants.WAIT_FOR_MATERIALIZATION_RETRY_INTERVAL.value - ) - - with case(update_metadata, True): - update_django_metadata( - dataset_id=dataset_id, - table_id=table_id, - date_column_name={"year": "ano", "month": "mes"}, - date_format="%Y-%m", - coverage_type="part_bdpro", - time_delta={"months": 6}, - prefect_mode=materialization_mode, - bq_project="basedosdados", - upstream_tasks=[wait_for_materialization], - ) - -br_ms_cnes_estabelecimento_ensino.storage = GCS(constants.GCS_FLOWS_BUCKET.value) -br_ms_cnes_estabelecimento_ensino.run_config = KubernetesRun( - image=constants.DOCKER_IMAGE.value -) -# br_ms_cnes_estabelecimento_ensino.schedule = schedule_br_ms_cnes_estabelecimento_ensino - -with Flow( - name="br_ms_cnes.dados_complementares", code_owners=["Gabriel Pisa"] -) as br_ms_cnes_dados_complementares: - # Parameters - dataset_id = Parameter("dataset_id", default="br_ms_cnes", required=True) - table_id = Parameter("table_id", default="dados_complementares", required=True) - update_metadata = Parameter("update_metadata", default=False, required=False) - materialization_mode = Parameter( - "materialization_mode", default="dev", required=False - ) - materialize_after_dump = Parameter( - "materialize after dump", default=True, required=False - ) - dbt_alias = Parameter("dbt_alias", default=False, required=False) - - rename_flow_run = rename_current_flow_run_dataset_table( - prefix="Dump: ", dataset_id=dataset_id, table_id=table_id, wait=table_id - ) - - files_path = check_files_to_parse( - dataset_id=dataset_id, - table_id=table_id, - cnes_database="CNES", - cnes_group_file=br_ms_cnes_constants.DATABASE_GROUPS.value["CNES"][6], - ) - - with case(is_empty(files_path), True): - log_task( - "Os dados do FTP CNES-ST ainda não foram atualizados para o ano/mes mais recente" - ) - - with case(is_empty(files_path), False): - dbc_files = access_ftp_donwload_files( - file_list=files_path, - path=br_ms_cnes_constants.PATH.value[0], - table=br_ms_cnes_constants.TABLE.value[6], - ) - - dbf_files = decompress_dbc(file_list=dbc_files, upstream_tasks=[dbc_files]) - - filepath = decompress_dbf( - file_list=dbc_files, - path=br_ms_cnes_constants.PATH.value[1], - table=br_ms_cnes_constants.TABLE.value[6], - upstream_tasks=[dbf_files, dbc_files], - ) - - wait_upload_table = create_table_and_upload_to_gcs( - data_path=filepath, - dataset_id=dataset_id, - table_id=table_id, - dump_mode="append", - wait=filepath, - ) - - with case(materialize_after_dump, True): - # Trigger DBT flow run - current_flow_labels = get_current_flow_labels() - materialization_flow = create_flow_run( - flow_name=utils_constants.FLOW_EXECUTE_DBT_MODEL_NAME.value, - project_name=constants.PREFECT_DEFAULT_PROJECT.value, - parameters={ - "dataset_id": dataset_id, - "table_id": table_id, - "mode": materialization_mode, - "dbt_alias": dbt_alias, - }, - labels=current_flow_labels, - run_name=f"Materialize {dataset_id}.{table_id}", - ) - - wait_for_materialization = wait_for_flow_run( - materialization_flow, - stream_states=True, - stream_logs=True, - raise_final_state=True, - ) - wait_for_materialization.max_retries = ( - dump_db_constants.WAIT_FOR_MATERIALIZATION_RETRY_ATTEMPTS.value - ) - wait_for_materialization.retry_delay = timedelta( - seconds=dump_db_constants.WAIT_FOR_MATERIALIZATION_RETRY_INTERVAL.value - ) - - with case(update_metadata, True): - update_django_metadata( - dataset_id=dataset_id, - table_id=table_id, - date_column_name={"year": "ano", "month": "mes"}, - date_format="%Y-%m", - coverage_type="part_bdpro", - time_delta={"months": 6}, - prefect_mode=materialization_mode, - bq_project="basedosdados", - upstream_tasks=[wait_for_materialization], - ) +br_ms_cnes_dados_complementares = deepcopy(flow_datasus) +br_ms_cnes_dados_complementares.name = "br_ms_cnes.dados_complementares" +br_ms_cnes_dados_complementares.code_owners = ["equipe_pipelines"] br_ms_cnes_dados_complementares.storage = GCS(constants.GCS_FLOWS_BUCKET.value) br_ms_cnes_dados_complementares.run_config = KubernetesRun( image=constants.DOCKER_IMAGE.value ) # br_ms_cnes_dados_complementares.schedule = schedule_br_ms_cnes_dados_complementares -with Flow( - name="br_ms_cnes.estabelecimento_filantropico", code_owners=["Gabriel Pisa"] -) as br_ms_cnes_estabelecimento_filantropico: - # Parameters - dataset_id = Parameter("dataset_id", default="br_ms_cnes", required=True) - table_id = Parameter( - "table_id", default="estabelecimento_filantropico", required=True - ) - update_metadata = Parameter("update_metadata", default=False, required=False) - materialization_mode = Parameter( - "materialization_mode", default="dev", required=False - ) - materialize_after_dump = Parameter( - "materialize after dump", default=True, required=False - ) - dbt_alias = Parameter("dbt_alias", default=False, required=False) - - rename_flow_run = rename_current_flow_run_dataset_table( - prefix="Dump: ", dataset_id=dataset_id, table_id=table_id, wait=table_id - ) - - files_path = check_files_to_parse( - dataset_id=dataset_id, - table_id=table_id, - cnes_database="CNES", - cnes_group_file=br_ms_cnes_constants.DATABASE_GROUPS.value["CNES"][7], - ) - - with case(is_empty(files_path), True): - log_task( - "Os dados do FTP CNES-ST ainda não foram atualizados para o ano/mes mais recente" - ) - - with case(is_empty(files_path), False): - dbc_files = access_ftp_donwload_files( - file_list=files_path, - path=br_ms_cnes_constants.PATH.value[0], - table=br_ms_cnes_constants.TABLE.value[7], - ) - dbf_files = decompress_dbc(file_list=dbc_files, upstream_tasks=[dbc_files]) - - filepath = decompress_dbf( - file_list=dbc_files, - path=br_ms_cnes_constants.PATH.value[1], - table=br_ms_cnes_constants.TABLE.value[7], - upstream_tasks=[dbf_files, dbc_files], - ) - - wait_upload_table = create_table_and_upload_to_gcs( - data_path=filepath, - dataset_id=dataset_id, - table_id=table_id, - dump_mode="append", - wait=filepath, - ) - - with case(materialize_after_dump, True): - # Trigger DBT flow run - current_flow_labels = get_current_flow_labels() - materialization_flow = create_flow_run( - flow_name=utils_constants.FLOW_EXECUTE_DBT_MODEL_NAME.value, - project_name=constants.PREFECT_DEFAULT_PROJECT.value, - parameters={ - "dataset_id": dataset_id, - "table_id": table_id, - "mode": materialization_mode, - "dbt_alias": dbt_alias, - }, - labels=current_flow_labels, - run_name=f"Materialize {dataset_id}.{table_id}", - ) - - wait_for_materialization = wait_for_flow_run( - materialization_flow, - stream_states=True, - stream_logs=True, - raise_final_state=True, - ) - wait_for_materialization.max_retries = ( - dump_db_constants.WAIT_FOR_MATERIALIZATION_RETRY_ATTEMPTS.value - ) - wait_for_materialization.retry_delay = timedelta( - seconds=dump_db_constants.WAIT_FOR_MATERIALIZATION_RETRY_INTERVAL.value - ) - - with case(update_metadata, True): - update_django_metadata( - dataset_id=dataset_id, - table_id=table_id, - date_column_name={"year": "ano", "month": "mes"}, - date_format="%Y-%m", - coverage_type="part_bdpro", - time_delta={"months": 6}, - prefect_mode=materialization_mode, - bq_project="basedosdados", - upstream_tasks=[wait_for_materialization], - ) - - -br_ms_cnes_estabelecimento_filantropico.storage = GCS(constants.GCS_FLOWS_BUCKET.value) -br_ms_cnes_estabelecimento_filantropico.run_config = KubernetesRun( +br_ms_cnes_servico_especializado = deepcopy(flow_datasus) +br_ms_cnes_servico_especializado.name = "br_ms_cnes.servico_especializado" +br_ms_cnes_servico_especializado.code_owners = ["equipe_pipelines"] +br_ms_cnes_servico_especializado.storage = GCS(constants.GCS_FLOWS_BUCKET.value) +br_ms_cnes_servico_especializado.run_config = KubernetesRun( image=constants.DOCKER_IMAGE.value ) -# br_ms_cnes_estabelecimento_filantropico.schedule = ( -# schedule_br_ms_cnes_estabelecimento_filantropico -# ) - -# gestao_metas -with Flow( - name="br_ms_cnes.gestao_metas", code_owners=["Gabriel Pisa"] -) as br_ms_cnes_gestao_metas: - # Parameters - dataset_id = Parameter("dataset_id", default="br_ms_cnes", required=True) - table_id = Parameter("table_id", default="gestao_metas", required=True) - update_metadata = Parameter("update_metadata", default=False, required=False) - materialization_mode = Parameter( - "materialization_mode", default="dev", required=False - ) - materialize_after_dump = Parameter( - "materialize after dump", default=True, required=False - ) - dbt_alias = Parameter("dbt_alias", default=False, required=False) - - rename_flow_run = rename_current_flow_run_dataset_table( - prefix="Dump: ", dataset_id=dataset_id, table_id=table_id, wait=table_id - ) - - files_path = check_files_to_parse( - dataset_id=dataset_id, - table_id=table_id, - cnes_database="CNES", - cnes_group_file=br_ms_cnes_constants.DATABASE_GROUPS.value["CNES"][8], - ) - - with case(is_empty(files_path), True): - log_task( - "Os dados do FTP CNES-ST ainda não foram atualizados para o ano/mes mais recente" - ) - - with case(is_empty(files_path), False): - dbc_files = access_ftp_donwload_files( - file_list=files_path, - path=br_ms_cnes_constants.PATH.value[0], - table=br_ms_cnes_constants.TABLE.value[8], - ) - - dbf_files = decompress_dbc(file_list=dbc_files, upstream_tasks=[dbc_files]) - - filepath = decompress_dbf( - file_list=dbc_files, - path=br_ms_cnes_constants.PATH.value[1], - table=br_ms_cnes_constants.TABLE.value[8], - upstream_tasks=[dbf_files, dbc_files], - ) - - wait_upload_table = create_table_and_upload_to_gcs( - data_path=filepath, - dataset_id=dataset_id, - table_id=table_id, - dump_mode="append", - wait=filepath, - ) - - with case(materialize_after_dump, True): - # Trigger DBT flow run - current_flow_labels = get_current_flow_labels() - materialization_flow = create_flow_run( - flow_name=utils_constants.FLOW_EXECUTE_DBT_MODEL_NAME.value, - project_name=constants.PREFECT_DEFAULT_PROJECT.value, - parameters={ - "dataset_id": dataset_id, - "table_id": table_id, - "mode": materialization_mode, - "dbt_alias": dbt_alias, - }, - labels=current_flow_labels, - run_name=f"Materialize {dataset_id}.{table_id}", - ) - - wait_for_materialization = wait_for_flow_run( - materialization_flow, - stream_states=True, - stream_logs=True, - raise_final_state=True, - ) - wait_for_materialization.max_retries = ( - dump_db_constants.WAIT_FOR_MATERIALIZATION_RETRY_ATTEMPTS.value - ) - wait_for_materialization.retry_delay = timedelta( - seconds=dump_db_constants.WAIT_FOR_MATERIALIZATION_RETRY_INTERVAL.value - ) - - with case(update_metadata, True): - update_django_metadata( - dataset_id=dataset_id, - table_id=table_id, - date_column_name={"year": "ano", "month": "mes"}, - date_format="%Y-%m", - coverage_type="part_bdpro", - time_delta={"months": 6}, - prefect_mode=materialization_mode, - bq_project="basedosdados", - upstream_tasks=[wait_for_materialization], - ) - -br_ms_cnes_gestao_metas.storage = GCS(constants.GCS_FLOWS_BUCKET.value) -br_ms_cnes_gestao_metas.run_config = KubernetesRun(image=constants.DOCKER_IMAGE.value) -# br_ms_cnes_gestao_metas.schedule = schedule_br_ms_cnes_gestao_metas - -# habilitacao -with Flow( - name="br_ms_cnes.habilitacao", code_owners=["Gabriel Pisa"] -) as br_ms_cnes_habilitacao: - # Parameters - dataset_id = Parameter("dataset_id", default="br_ms_cnes", required=True) - table_id = Parameter("table_id", default="habilitacao", required=True) - update_metadata = Parameter("update_metadata", default=False, required=False) - materialization_mode = Parameter( - "materialization_mode", default="dev", required=False - ) - materialize_after_dump = Parameter( - "materialize after dump", default=True, required=False - ) - dbt_alias = Parameter("dbt_alias", default=False, required=False) - - rename_flow_run = rename_current_flow_run_dataset_table( - prefix="Dump: ", dataset_id=dataset_id, table_id=table_id, wait=table_id - ) - - files_path = check_files_to_parse( - dataset_id=dataset_id, - table_id=table_id, - cnes_database="CNES", - cnes_group_file=br_ms_cnes_constants.DATABASE_GROUPS.value["CNES"][9], - ) - - with case(is_empty(files_path), True): - log_task( - "Os dados do FTP CNES-ST ainda não foram atualizados para o ano/mes mais recente" - ) - - with case(is_empty(files_path), False): - dbc_files = access_ftp_donwload_files( - file_list=files_path, - path=br_ms_cnes_constants.PATH.value[0], - table=br_ms_cnes_constants.TABLE.value[9], - ) - - dbf_files = decompress_dbc(file_list=dbc_files, upstream_tasks=[dbc_files]) - - filepath = decompress_dbf( - file_list=dbc_files, - path=br_ms_cnes_constants.PATH.value[1], - table=br_ms_cnes_constants.TABLE.value[9], - upstream_tasks=[dbf_files, dbc_files], - ) - - wait_upload_table = create_table_and_upload_to_gcs( - data_path=filepath, - dataset_id=dataset_id, - table_id=table_id, - dump_mode="append", - wait=filepath, - ) - - with case(materialize_after_dump, True): - # Trigger DBT flow run - current_flow_labels = get_current_flow_labels() - materialization_flow = create_flow_run( - flow_name=utils_constants.FLOW_EXECUTE_DBT_MODEL_NAME.value, - project_name=constants.PREFECT_DEFAULT_PROJECT.value, - parameters={ - "dataset_id": dataset_id, - "table_id": table_id, - "mode": materialization_mode, - "dbt_alias": dbt_alias, - }, - labels=current_flow_labels, - run_name=f"Materialize {dataset_id}.{table_id}", - ) - - wait_for_materialization = wait_for_flow_run( - materialization_flow, - stream_states=True, - stream_logs=True, - raise_final_state=True, - ) - wait_for_materialization.max_retries = ( - dump_db_constants.WAIT_FOR_MATERIALIZATION_RETRY_ATTEMPTS.value - ) - wait_for_materialization.retry_delay = timedelta( - seconds=dump_db_constants.WAIT_FOR_MATERIALIZATION_RETRY_INTERVAL.value - ) - - with case(update_metadata, True): - update_django_metadata( - dataset_id=dataset_id, - table_id=table_id, - date_column_name={"year": "ano", "month": "mes"}, - date_format="%Y-%m", - coverage_type="part_bdpro", - time_delta={"months": 6}, - prefect_mode=materialization_mode, - bq_project="basedosdados", - upstream_tasks=[wait_for_materialization], - ) - +# br_ms_cnes_servico_especializado.schedule = schedule_br_ms_cnes_servico_especializado +br_ms_cnes_habilitacao = deepcopy(flow_datasus) +br_ms_cnes_habilitacao.name = "br_ms_cnes.habilitacao" +br_ms_cnes_habilitacao.code_owners = ["equipe_pipelines"] br_ms_cnes_habilitacao.storage = GCS(constants.GCS_FLOWS_BUCKET.value) br_ms_cnes_habilitacao.run_config = KubernetesRun(image=constants.DOCKER_IMAGE.value) # br_ms_cnes_habilitacao.schedule = schedule_br_ms_cnes_habilitacao +br_ms_cnes_gestao_metas = deepcopy(flow_datasus) +br_ms_cnes_gestao_metas.name = "br_ms_cnes.gestao_metas" +br_ms_cnes_gestao_metas.code_owners = ["equipe_pipelines"] +br_ms_cnes_gestao_metas.storage = GCS(constants.GCS_FLOWS_BUCKET.value) +br_ms_cnes_gestao_metas.run_config = KubernetesRun(image=constants.DOCKER_IMAGE.value) +# br_ms_cnes_gestao_metas.schedule = schedule_br_ms_cnes_gestao_metas -# incentivos -with Flow( - name="br_ms_cnes.incentivos", code_owners=["Gabriel Pisa"] -) as br_ms_cnes_incentivos: - # Parameters - dataset_id = Parameter("dataset_id", default="br_ms_cnes", required=True) - table_id = Parameter("table_id", default="incentivos", required=True) - update_metadata = Parameter("update_metadata", default=False, required=False) - materialization_mode = Parameter( - "materialization_mode", default="dev", required=False - ) - materialize_after_dump = Parameter( - "materialize after dump", default=True, required=False - ) - dbt_alias = Parameter("dbt_alias", default=False, required=False) - - rename_flow_run = rename_current_flow_run_dataset_table( - prefix="Dump: ", dataset_id=dataset_id, table_id=table_id, wait=table_id - ) - - files_path = check_files_to_parse( - dataset_id=dataset_id, - table_id=table_id, - cnes_database="CNES", - cnes_group_file=br_ms_cnes_constants.DATABASE_GROUPS.value["CNES"][10], - ) - - with case(is_empty(files_path), True): - log_task( - "Os dados do FTP CNES-ST ainda não foram atualizados para o ano/mes mais recente" - ) - - with case(is_empty(files_path), False): - dbc_files = access_ftp_donwload_files( - file_list=files_path, - path=br_ms_cnes_constants.PATH.value[0], - table=br_ms_cnes_constants.TABLE.value[10], - ) - - dbf_files = decompress_dbc(file_list=dbc_files, upstream_tasks=[dbc_files]) - - filepath = decompress_dbf( - file_list=dbc_files, - path=br_ms_cnes_constants.PATH.value[1], - table=br_ms_cnes_constants.TABLE.value[10], - upstream_tasks=[dbf_files, dbc_files], - ) - - wait_upload_table = create_table_and_upload_to_gcs( - data_path=filepath, - dataset_id=dataset_id, - table_id=table_id, - dump_mode="append", - wait=filepath, - ) - - with case(materialize_after_dump, True): - # Trigger DBT flow run - current_flow_labels = get_current_flow_labels() - materialization_flow = create_flow_run( - flow_name=utils_constants.FLOW_EXECUTE_DBT_MODEL_NAME.value, - project_name=constants.PREFECT_DEFAULT_PROJECT.value, - parameters={ - "dataset_id": dataset_id, - "table_id": table_id, - "mode": materialization_mode, - "dbt_alias": dbt_alias, - }, - labels=current_flow_labels, - run_name=f"Materialize {dataset_id}.{table_id}", - ) - - wait_for_materialization = wait_for_flow_run( - materialization_flow, - stream_states=True, - stream_logs=True, - raise_final_state=True, - ) - wait_for_materialization.max_retries = ( - dump_db_constants.WAIT_FOR_MATERIALIZATION_RETRY_ATTEMPTS.value - ) - wait_for_materialization.retry_delay = timedelta( - seconds=dump_db_constants.WAIT_FOR_MATERIALIZATION_RETRY_INTERVAL.value - ) - - with case(update_metadata, True): - update_django_metadata( - dataset_id=dataset_id, - table_id=table_id, - date_column_name={"year": "ano", "month": "mes"}, - date_format="%Y-%m", - coverage_type="part_bdpro", - time_delta={"months": 6}, - prefect_mode=materialization_mode, - bq_project="basedosdados", - upstream_tasks=[wait_for_materialization], - ) - - +br_ms_cnes_incentivos = deepcopy(flow_datasus) +br_ms_cnes_incentivos.name = "br_ms_cnes.incentivos" +br_ms_cnes_incentivos.code_owners = ["equipe_pipelines"] br_ms_cnes_incentivos.storage = GCS(constants.GCS_FLOWS_BUCKET.value) br_ms_cnes_incentivos.run_config = KubernetesRun(image=constants.DOCKER_IMAGE.value) # br_ms_cnes_incentivos.schedule = schedule_br_ms_cnes_incentivos -# regra_contratual -with Flow( - name="br_ms_cnes.regra_contratual", code_owners=["Gabriel Pisa"] -) as br_ms_cnes_regra_contratual: - # Parameters - dataset_id = Parameter("dataset_id", default="br_ms_cnes", required=True) - table_id = Parameter("table_id", default="regra_contratual", required=True) - update_metadata = Parameter("update_metadata", default=False, required=False) - materialization_mode = Parameter( - "materialization_mode", default="dev", required=False - ) - materialize_after_dump = Parameter( - "materialize after dump", default=True, required=False - ) - dbt_alias = Parameter("dbt_alias", default=False, required=False) - - rename_flow_run = rename_current_flow_run_dataset_table( - prefix="Dump: ", dataset_id=dataset_id, table_id=table_id, wait=table_id - ) - - files_path = check_files_to_parse( - dataset_id=dataset_id, - table_id=table_id, - cnes_database="CNES", - cnes_group_file=br_ms_cnes_constants.DATABASE_GROUPS.value["CNES"][11], - ) - - with case(is_empty(files_path), True): - log_task( - "Os dados do FTP CNES-ST ainda não foram atualizados para o ano/mes mais recente" - ) - - with case(is_empty(files_path), False): - dbc_files = access_ftp_donwload_files( - file_list=files_path, - path=br_ms_cnes_constants.PATH.value[0], - table=br_ms_cnes_constants.TABLE.value[11], - ) - - dbf_files = decompress_dbc(file_list=dbc_files, upstream_tasks=[dbc_files]) - - filepath = decompress_dbf( - file_list=dbc_files, - path=br_ms_cnes_constants.PATH.value[1], - table=br_ms_cnes_constants.TABLE.value[11], - upstream_tasks=[dbf_files, dbc_files], - ) - - wait_upload_table = create_table_and_upload_to_gcs( - data_path=filepath, - dataset_id=dataset_id, - table_id=table_id, - dump_mode="append", - wait=filepath, - ) - - with case(materialize_after_dump, True): - # Trigger DBT flow run - current_flow_labels = get_current_flow_labels() - materialization_flow = create_flow_run( - flow_name=utils_constants.FLOW_EXECUTE_DBT_MODEL_NAME.value, - project_name=constants.PREFECT_DEFAULT_PROJECT.value, - parameters={ - "dataset_id": dataset_id, - "table_id": table_id, - "mode": materialization_mode, - "dbt_alias": dbt_alias, - }, - labels=current_flow_labels, - run_name=f"Materialize {dataset_id}.{table_id}", - ) - - wait_for_materialization = wait_for_flow_run( - materialization_flow, - stream_states=True, - stream_logs=True, - raise_final_state=True, - ) - wait_for_materialization.max_retries = ( - dump_db_constants.WAIT_FOR_MATERIALIZATION_RETRY_ATTEMPTS.value - ) - wait_for_materialization.retry_delay = timedelta( - seconds=dump_db_constants.WAIT_FOR_MATERIALIZATION_RETRY_INTERVAL.value - ) - - with case(update_metadata, True): - update_django_metadata( - dataset_id=dataset_id, - table_id=table_id, - date_column_name={"year": "ano", "month": "mes"}, - date_format="%Y-%m", - coverage_type="part_bdpro", - time_delta={"months": 6}, - prefect_mode=materialization_mode, - bq_project="basedosdados", - upstream_tasks=[wait_for_materialization], - ) - - -br_ms_cnes_regra_contratual.storage = GCS(constants.GCS_FLOWS_BUCKET.value) -br_ms_cnes_regra_contratual.run_config = KubernetesRun( +br_ms_cnes_estabelecimento_ensino = deepcopy(flow_datasus) +br_ms_cnes_estabelecimento_ensino.name = "br_ms_cnes.estabelecimento_ensino" +br_ms_cnes_estabelecimento_ensino.code_owners = ["equipe_pipelines"] +br_ms_cnes_estabelecimento_ensino.storage = GCS(constants.GCS_FLOWS_BUCKET.value) +br_ms_cnes_estabelecimento_ensino.run_config = KubernetesRun( image=constants.DOCKER_IMAGE.value ) -# br_ms_cnes_regra_contratual.schedule = schedule_br_ms_cnes_regra_contratual - -# regra_contratual -with Flow( - name="br_ms_cnes.servico_especializado", code_owners=["Gabriel Pisa"] -) as br_ms_cnes_servico_especializado: - # Parameters - dataset_id = Parameter("dataset_id", default="br_ms_cnes", required=True) - table_id = Parameter("table_id", default="servico_especializado", required=True) - update_metadata = Parameter("update_metadata", default=False, required=False) - materialization_mode = Parameter( - "materialization_mode", default="dev", required=False - ) - materialize_after_dump = Parameter( - "materialize after dump", default=True, required=False - ) - dbt_alias = Parameter("dbt_alias", default=False, required=False) - - rename_flow_run = rename_current_flow_run_dataset_table( - prefix="Dump: ", dataset_id=dataset_id, table_id=table_id, wait=table_id - ) - - files_path = check_files_to_parse( - dataset_id=dataset_id, - table_id=table_id, - cnes_database="CNES", - cnes_group_file=br_ms_cnes_constants.DATABASE_GROUPS.value["CNES"][12], - ) - - with case(is_empty(files_path), True): - log_task( - "Os dados do FTP CNES-ST ainda não foram atualizados para o ano/mes mais recente" - ) - - with case(is_empty(files_path), False): - dbc_files = access_ftp_donwload_files( - file_list=files_path, - path=br_ms_cnes_constants.PATH.value[0], - table=br_ms_cnes_constants.TABLE.value[12], - ) - - dbf_files = decompress_dbc(file_list=dbc_files, upstream_tasks=[dbc_files]) - - filepath = decompress_dbf( - file_list=dbc_files, - path=br_ms_cnes_constants.PATH.value[1], - table=br_ms_cnes_constants.TABLE.value[12], - upstream_tasks=[dbf_files, dbc_files], - ) - - wait_upload_table = create_table_and_upload_to_gcs( - data_path=filepath, - dataset_id=dataset_id, - table_id=table_id, - dump_mode="append", - wait=filepath, - ) - - with case(materialize_after_dump, True): - # Trigger DBT flow run - current_flow_labels = get_current_flow_labels() - materialization_flow = create_flow_run( - flow_name=utils_constants.FLOW_EXECUTE_DBT_MODEL_NAME.value, - project_name=constants.PREFECT_DEFAULT_PROJECT.value, - parameters={ - "dataset_id": dataset_id, - "table_id": table_id, - "mode": materialization_mode, - "dbt_alias": dbt_alias, - }, - labels=current_flow_labels, - run_name=f"Materialize {dataset_id}.{table_id}", - ) - - wait_for_materialization = wait_for_flow_run( - materialization_flow, - stream_states=True, - stream_logs=True, - raise_final_state=True, - ) - wait_for_materialization.max_retries = ( - dump_db_constants.WAIT_FOR_MATERIALIZATION_RETRY_ATTEMPTS.value - ) - wait_for_materialization.retry_delay = timedelta( - seconds=dump_db_constants.WAIT_FOR_MATERIALIZATION_RETRY_INTERVAL.value - ) - - with case(update_metadata, True): - update_django_metadata( - dataset_id=dataset_id, - table_id=table_id, - date_column_name={"year": "ano", "month": "mes"}, - date_format="%Y-%m", - coverage_type="part_bdpro", - time_delta={"months": 6}, - prefect_mode=materialization_mode, - bq_project="basedosdados", - upstream_tasks=[wait_for_materialization], - ) +# br_ms_cnes_estabelecimento_ensino.schedule = schedule_br_ms_cnes_estabelecimento_ensino -br_ms_cnes_servico_especializado.storage = GCS(constants.GCS_FLOWS_BUCKET.value) -br_ms_cnes_servico_especializado.run_config = KubernetesRun( +br_ms_cnes_estabelecimento_filantropico = deepcopy(flow_datasus) +br_ms_cnes_estabelecimento_filantropico.name = "br_ms_cnes.estabelecimento_filantropico" +br_ms_cnes_estabelecimento_filantropico.code_owners = ["equipe_pipelines"] +br_ms_cnes_estabelecimento_filantropico.storage = GCS(constants.GCS_FLOWS_BUCKET.value) +br_ms_cnes_estabelecimento_filantropico.run_config = KubernetesRun( image=constants.DOCKER_IMAGE.value ) -# br_ms_cnes_servico_especializado.schedule = schedule_br_ms_cnes_servico_especializado +# br_ms_cnes_estabelecimento_filantropico.schedule = schedule_br_ms_cnes_estabelecimento_filantropico diff --git a/pipelines/utils/crawler_datasus/__init__.py b/pipelines/utils/crawler_datasus/__init__.py new file mode 100644 index 000000000..e69de29bb diff --git a/pipelines/utils/crawler_datasus/constants.py b/pipelines/utils/crawler_datasus/constants.py new file mode 100644 index 000000000..66c340ef2 --- /dev/null +++ b/pipelines/utils/crawler_datasus/constants.py @@ -0,0 +1,292 @@ +# -*- coding: utf-8 -*- +""" +Constant values for the datasets projects +""" + + +from enum import Enum + + +class constants(Enum): # pylint: disable=c0103 + """ + Constant values for the crawler_datasus project + """ + + # to build paths + PATH = [ + "/tmp/br_ms_cnes/input/", + "/tmp/br_ms_cnes/output/", + ] + + # to download files from datasus FTP server + DATASUS_DATABASE = { + "br_ms_cnes": "CNES", + } + + DATASUS_DATABASE_TABLE = { + "estabelecimento": "ST", + "profissional": "PF", + "equipamento": "EQ", + "leito": "LT", + "equipe": "EP", + "estabelecimento_ensino": "EE", + "dados_complementares": "DC", + "estabelecimento_filantropico": "EF", + "gestao_metas": "GM", + "habilitacao": "HB", + "incentivos": "IN", + "regra_contratual": "RC", + "servico_especializado": "SR", + } + + COLUMNS_TO_KEEP = { + # equipamento + "EP": [ + "CODUFMUN", + "CNES", + "TIPEQUIP", + "CODEQUIP", + "QT_EXIST", + "QT_USO", + "IND_SUS", + "IND_NSUS", + ], + # leito + "LT": ["CNES", "TP_LEITO", "CODLEITO", "QT_EXIST", "QT_CONTR", "QT_SUS"], + # equipe + "EQ": [ + "CODUFMUN", + "CNES", + "ID_EQUIPE", + "TIPO_EQP", + "NOME_EQP", + "ID_AREA", + "NOMEAREA", + "ID_SEGM", + "DESCSEGM", + "TIPOSEGM", + "DT_ATIVA", + "DT_DESAT", + "MOTDESAT", + "TP_DESAT", + "QUILOMBO", + "ASSENTAD", + "POPGERAL", + "ESCOLA", + "INDIGENA", + "PRONASCI", + ], + # profissional + "PF": [ + "COMPETEN", + "CNES", + "UFMUNRES", + "NOMEPROF", + "CNS_PROF", + "CBO", + "REGISTRO", + "CONSELHO", + "TERCEIRO", + "VINCULAC", + "VINCUL_C", + "VINCUL_A", + "VINCUL_N", + "PROF_SUS", + "PROFNSUS", + "HORAOUTR", + "HORAHOSP", + "HORA_AMB", + ], + # estabelecimento_ensino + "EE": [ + "CODUFMUN", + "CNES", + "CMPT_INI", + "CMPT_FIM", + "SGRUPHAB", + "DTPORTAR", + "PORTARIA", + "MAPORTAR", + ], + # estabelecimento_filantropico + "EF": [ + "CODUFMUN", + "CNES", + "CMPT_INI", + "CMPT_FIM", + "SGRUPHAB", + "DTPORTAR", + "PORTARIA", + "MAPORTAR", + ], + # gestao_metas + "GM": [ + "CODUFMUN", + "CNES", + "CMPT_INI", + "CMPT_FIM", + "SGRUPHAB", + "DTPORTAR", + "PORTARIA", + "MAPORTAR", + ], + # habilitacao + "HB": [ + "CODUFMUN", + "CNES", + "NAT_JUR", + "NULEITOS", + "SGRUPHAB", + "CMPT_INI", + "CMPT_FIM", + "DTPORTAR", + "PORTARIA", + "MAPORTAR", + ], + # incentivos + "IN": [ + "CODUFMUN", + "CNES", + "CMPT_INI", + "CMPT_FIM", + "SGRUPHAB", + "DTPORTAR", + "PORTARIA", + "MAPORTAR", + ], + # regra_contratual + "RC": [ + "CODUFMUN", + "CNES", + "CMPT_INI", + "CMPT_FIM", + "SGRUPHAB", + "DTPORTAR", + "PORTARIA", + "MAPORTAR", + ], + # servico_especializado + "SR": [ + "CODUFMUN", + "CNES", + "SERV_ESP", + "CLASS_SR", + "SRVUNICO", + "CARACTER", + "AMB_NSUS", + "AMB_SUS", + "HOSP_NSUS", + "HOSP_SUS", + "CONTSRVU", + "CNESTERC", + ], + # dados complementares + "DC": [ + "CODUFMUN", + "CNES", + "S_HBSAGP", + "S_HBSAGN", + "S_DPI", + "S_DPAC", + "S_REAGP", + "S_REAGN", + "S_REHCV", + "MAQ_PROP", + "MAQ_OUTR", + "F_AREIA", + "F_CARVAO", + "ABRANDAD", + "DEIONIZA", + "OSMOSE_R", + "OUT_TRAT", + "CNS_NEFR", + "DIALISE", + "SIMUL_RD", + "PLANJ_RD", + "ARMAZ_FT", + "CONF_MAS", + "SALA_MOL", + "BLOCOPER", + "S_ARMAZE", + "S_PREPAR", + "S_QCDURA", + "S_QLDURA", + "S_CPFLUX", + "S_SIMULA", + "S_ACELL6", + "S_ALSEME", + "S_ALCOME", + "ORTV1050", + "ORV50150", + "OV150500", + "UN_COBAL", + "EQBRBAIX", + "EQBRMEDI", + "EQBRALTA", + "EQ_MAREA", + "EQ_MINDI", + "EQSISPLN", + "EQDOSCLI", + "EQFONSEL", + "CNS_ADM", + "CNS_OPED", + "CNS_CONC", + "CNS_OCLIN", + "CNS_MRAD", + "CNS_FNUC", + "QUIMRADI", + "S_RECEPC", + "S_TRIHMT", + "S_TRICLI", + "S_COLETA", + "S_AFERES", + "S_PREEST", + "S_PROCES", + "S_ESTOQU", + "S_DISTRI", + "S_SOROLO", + "S_IMUNOH", + "S_PRETRA", + "S_HEMOST", + "S_CONTRQ", + "S_BIOMOL", + "S_IMUNFE", + "S_TRANSF", + "S_SGDOAD", + "QT_CADRE", + "QT_CENRE", + "QT_REFSA", + "QT_CONRA", + "QT_EXTPL", + "QT_FRE18", + "QT_FRE30", + "QT_AGIPL", + "QT_SELAD", + "QT_IRRHE", + "QT_AGLTN", + "QT_MAQAF", + "QT_REFRE", + "QT_REFAS", + "QT_CAPFL", + "CNS_HMTR", + "CNS_HMTL", + "CNS_CRES", + "CNS_RTEC", + "HEMOTERA", + ], + } + + GENERATE_MONTH_TO_PARSE = { + 12: "11", + 1: "12", + 2: "01", + 3: "02", + 4: "03", + 5: "04", + 6: "05", + 7: "06", + 8: "07", + 9: "08", + 10: "09", + 11: "10", + } diff --git a/pipelines/utils/crawler_datasus/flows.py b/pipelines/utils/crawler_datasus/flows.py new file mode 100644 index 000000000..0f00ceb06 --- /dev/null +++ b/pipelines/utils/crawler_datasus/flows.py @@ -0,0 +1,142 @@ +# -*- coding: utf-8 -*- +""" +Flows for br_ms_cnes +""" +# pylint: disable=invalid-name + +from datetime import timedelta + +from prefect import Parameter, case +from prefect.run_configs import KubernetesRun +from prefect.storage import GCS +from prefect.tasks.prefect import create_flow_run, wait_for_flow_run + +from pipelines.constants import constants +from pipelines.utils.constants import constants as utils_constants +from pipelines.utils.crawler_datasus.constants import constants as br_datasus_constants +from pipelines.utils.crawler_datasus.tasks import ( + access_ftp_download_files_async, + check_files_to_parse, + decompress_dbc, + decompress_dbf, + is_empty, + pre_process_files, +) +from pipelines.utils.decorators import Flow +from pipelines.utils.execute_dbt_model.constants import constants as dump_db_constants +from pipelines.utils.metadata.flows import update_django_metadata +from pipelines.utils.tasks import ( + create_table_and_upload_to_gcs, + get_current_flow_labels, + log_task, + rename_current_flow_run_dataset_table, +) +from pipelines.utils.to_download.tasks import to_download + +with Flow(name="BD Template - DATASUS", code_owners=["Gabriel Pisa"]) as flow_datasus: + # Parameters + dataset_id = Parameter("dataset_id", default=False, required=True) + table_id = Parameter("table_id", default=False, required=True) + update_metadata = Parameter("update_metadata", default=False, required=False) + materialization_mode = Parameter( + "materialization_mode", default="dev", required=False + ) + materialize_after_dump = Parameter( + "materialize_after_dump", default=True, required=False + ) + dbt_alias = Parameter("dbt_alias", default=False, required=False) + + rename_flow_run = rename_current_flow_run_dataset_table( + prefix="Dump: ", dataset_id=dataset_id, table_id=table_id, wait=table_id + ) + + ftp_files = check_files_to_parse( + dataset_id=dataset_id, + table_id=table_id, + ) + + with case(is_empty(ftp_files), True): + log_task( + "Os dados do FTP CNES-ST ainda não foram atualizados para o ano/mes mais recente" + ) + + with case(is_empty(ftp_files), False): + + dbc_files = access_ftp_download_files_async( + file_list=ftp_files, + dataset_id=dataset_id, + table_id=table_id, + ) + + dbf_files = decompress_dbc( + file_list=dbc_files, dataset_id=dataset_id, upstream_tasks=[dbc_files] + ) + + csv_files = decompress_dbf( + file_list=dbc_files, + dataset_id=dataset_id, + table_id=table_id, + upstream_tasks=[dbf_files, dbc_files], + ) + + files_path = pre_process_files( + file_list=csv_files, + dataset_id=dataset_id, + table_id=table_id, + upstream_tasks=[csv_files, dbf_files, dbc_files], + ) + + wait_upload_table = create_table_and_upload_to_gcs( + data_path=files_path, + dataset_id=dataset_id, + table_id=table_id, + dump_mode="append", + wait=files_path, + ) + + # estabelecimento + with case(materialize_after_dump, True): + # Trigger DBT flow run + current_flow_labels = get_current_flow_labels() + materialization_flow = create_flow_run( + flow_name=utils_constants.FLOW_EXECUTE_DBT_MODEL_NAME.value, + project_name=constants.PREFECT_DEFAULT_PROJECT.value, + parameters={ + "dataset_id": dataset_id, + "table_id": table_id, + "mode": materialization_mode, + "dbt_alias": dbt_alias, + }, + labels=current_flow_labels, + run_name=f"Materialize {dataset_id}.{table_id}", + ) + + wait_for_materialization = wait_for_flow_run( + materialization_flow, + stream_states=True, + stream_logs=True, + raise_final_state=True, + ) + wait_for_materialization.max_retries = ( + dump_db_constants.WAIT_FOR_MATERIALIZATION_RETRY_ATTEMPTS.value + ) + wait_for_materialization.retry_delay = timedelta( + seconds=dump_db_constants.WAIT_FOR_MATERIALIZATION_RETRY_INTERVAL.value + ) + + with case(update_metadata, True): + update_django_metadata( + dataset_id=dataset_id, + table_id=table_id, + date_column_name={"year": "ano", "month": "mes"}, + date_format="%Y-%m", + coverage_type="part_bdpro", + time_delta={"months": 6}, + prefect_mode=materialization_mode, + bq_project="basedosdados", + upstream_tasks=[wait_for_materialization], + ) + + +flow_datasus.storage = GCS(constants.GCS_FLOWS_BUCKET.value) +flow_datasus.run_config = KubernetesRun(image=constants.DOCKER_IMAGE.value) diff --git a/pipelines/utils/crawler_datasus/tasks.py b/pipelines/utils/crawler_datasus/tasks.py new file mode 100644 index 000000000..d4665d60d --- /dev/null +++ b/pipelines/utils/crawler_datasus/tasks.py @@ -0,0 +1,291 @@ +# -*- coding: utf-8 -*- +""" +Tasks for br_ms_cnes +""" + + +import asyncio +import os +from datetime import timedelta + +import aioftp +import pandas as pd +import wget +from prefect import task +from prefect.tasks.shell import ShellTask +from simpledbf import Dbf5 +from tqdm import tqdm + +from pipelines.constants import constants +from pipelines.utils.crawler_datasus.constants import constants as datasus_constants +from pipelines.utils.crawler_datasus.utils import ( + download_files, + list_all_cnes_dbc_files, + post_process_dados_complementares, + post_process_equipamento, + post_process_equipe, + post_process_estabelecimento, + post_process_estabelecimento_ensino, + post_process_estabelecimento_filantropico, + post_process_gestao_metas, + post_process_habilitacao, + post_process_incentivos, + post_process_leito, + post_process_profissional, + post_process_regra_contratual, + post_process_servico_especializado, + year_month_sigla_uf_parser, +) +from pipelines.utils.metadata.utils import get_api_most_recent_date +from pipelines.utils.utils import log + + +@task +def check_files_to_parse( + dataset_id: str, + table_id: str, +) -> list[str]: + log(f"extracting last date from api for {dataset_id}.{table_id}") + # 1. extrair data mais atual da api + last_date = get_api_most_recent_date( + dataset_id=dataset_id, + table_id=table_id, + date_format="%Y-%m", + ) + log("building next year/month to parse") + # 2. adicionar mais um no mes ou transformar pra 1 se for 12 + # para ver se o mês seguinte já está disponível no FTP + # eg. last_date = 2023-04-01 + + year = str(last_date.year) + month = last_date.month + + # download files to compare + year = "2023" + month = 11 + + if month <= 11: + month = month + 1 + else: + month = 1 + year = int(year) + 1 + year = str(year) + # 3. buildar no formato do ftp YYMM + year = year[2:4] + + if month <= 9: + month = "0" + str(month) + else: + month = str(month) + + year_month_to_parse = year + month + log(f"year_month_to_parse (YYMM) is {year_month_to_parse}") + # 4. ver se o arquivo existe + + # 5. converter para dabase que se deseja usar + datasus_database = datasus_constants.DATASUS_DATABASE.value[dataset_id] + datasus_database_table = datasus_constants.DATASUS_DATABASE_TABLE.value[table_id] + + available_dbs = list_all_cnes_dbc_files( + datasus_database=datasus_database, datasus_database_table=datasus_database_table + ) + + list_files = [file for file in available_dbs if file[-8:-4] == year_month_to_parse] + # list_files = [file for file in available_dbs if file[-10:-8] == 'SP' and file[-8:-6] in ['22', '23']] + + # filtra pra ver se acha e retorna a lista + # for file in available_dbs: + # if file[-10:-8] == 'SP': + # list_files.append(file) + # final + log(f"the following files were selected fom DATASUS FTP: {list_files}") + + return list_files + + +@task( + max_retries=constants.TASK_MAX_RETRIES.value, + retry_delay=timedelta(seconds=constants.TASK_RETRY_DELAY.value), +) +def access_ftp_download_files_async( + file_list: list, dataset_id: str, table_id: str +) -> list[str]: + """This function receives a list of files and + downloads them from DATASUS FTP server asynchronously. + + Args: + file_list (list): a file list extracted with the function choose_latest_cnes_dbc_files + dataset_id (str): identifier for the dataset + table_id (str): identifier for the table + + Returns: + list[str]: a list with the downloaded files' paths + """ + + input_path = os.path.join("/tmp", dataset_id, "input", table_id) + log(f"------created input dir {input_path}") + os.makedirs(input_path, exist_ok=True) + + log(f"------dowloading {table_id} files from DATASUS FTP") + asyncio.run(download_files(files=file_list, output_dir=input_path)) + + dbc_files_path_list = [ + os.path.join( + input_path, year_month_sigla_uf_parser(file=file), file.split("/")[-1] + ) + for file in file_list + ] + + return dbc_files_path_list + + +@task +def decompress_dbc(file_list: list, dataset_id: str) -> None: + """ + Convert dbc to dbf format + """ + + # ShellTask to create the blast-dbf directory + create_dir_task = ShellTask( + name="Create blast-dbf Directory", + command=f"mkdir -p /tmp/{dataset_id}/blast-dbf", + return_all=True, + log_stderr=True, + ) + + # Define a ShellTask to clone the blast-dbf repository + clone_repo_task = ShellTask( + name="Clone blast-dbf Repository", + command=f"git clone https://github.com/eaglebh/blast-dbf /tmp/{dataset_id}/blast-dbf", + return_all=True, + log_stderr=True, + ) + + # Define a ShellTask to build the blast-dbf repository + compile_blast_dbf = ShellTask( + name="Build blast-dbf", + command=f"cd /tmp/{dataset_id}/blast-dbf && make", + return_all=True, + log_stderr=True, + ) + + create_dir_task.run() + log("------ Cloning blast-dbf repository") + clone_repo_task.run() + log("------ Compiling blast-dbf repository") + compile_blast_dbf.run() + + for file in file_list: + # Check if the file has a .dbc extension + if file.endswith(".dbc"): + # Execute blast-dbf on the file + decompress_task = ShellTask( + name=f"Decompress {file}", + command=f"/tmp/{dataset_id}/blast-dbf/blast-dbf {file} {file.replace('.dbc', '.dbf')}", + return_all=True, + log_stderr=True, + ) + log(f"Decompressing {file}") + decompress_task.run() + else: + print(f"Skipping non-DBC file: {file}") + + log("------ Removing dbc files") + + for file in file_list: + if file.endswith(".dbc"): + os.system(f"rm {file}") + + +@task +def decompress_dbf(file_list: list, dataset_id: str, table_id: str) -> str: + """ + Convert dbc to csv + """ + log(f"--------- Decompressing {table_id} files") + + csv_file_list = list() + + dbf_file_list = [file.replace(".dbc", ".dbf") for file in file_list] + + for file in tqdm(dbf_file_list): + + # replace .csv with .dbf + log(f"-------- reading {file}") + dbf = Dbf5(file, codec="iso-8859-1") + + # remove cnes default file name + path_parts = file.split("/")[:-1] + output_path = os.path.join(*path_parts) + os.system(f"mkdir -p {output_path}") + + output_file = os.path.join(output_path, f"{table_id}.csv") + log(f"-------- saving {file.split('/')[-1]} to .csv ") + + dbf.to_csv(output_file) + csv_file_list.append(output_file) + + log("------ Removing dbf files") + + for file in dbf_file_list: + if file.endswith(".dbf"): + os.system(f"rm {file}") + + return csv_file_list + + +@task +def pre_process_files(file_list: list, dataset_id: str, table_id: str) -> str: + + log("Post-processing CSV files") + + # todo: colocar em constants + post_process_functions = { + "estabelecimento": post_process_estabelecimento, + "profissional": post_process_profissional, + "equipamento": post_process_equipamento, + "dados_complementares": post_process_dados_complementares, + "equipe": post_process_equipe, + "estabelecimento_ensino": post_process_estabelecimento_ensino, + "leito": post_process_leito, + "estabelecimento_filantropico": post_process_estabelecimento_filantropico, + "gestao_metas": post_process_gestao_metas, + "habilitacao": post_process_habilitacao, + "incentivos": post_process_incentivos, + "regra_contratual": post_process_regra_contratual, + "servico_especializado": post_process_servico_especializado, + } + + try: + post_process_function = post_process_functions.get(table_id) + + except Exception as e: + log( + f"The error {e} occured. It problably indicates that none post-processing function was found for table_id: {table_id}" + ) + + for file in tqdm(file_list): + + log(f"-------- reading {file}") + + df = pd.read_csv(file, dtype=str, encoding="iso-8859-1") + df = post_process_function(df) + + # df.to_csv(output_path, sep=",", na_rep="", index=False, encoding="utf-8") + + output_path = file.replace(".csv", ".parquet") + df.to_parquet(output_path, index=None) + + log("Post-processing complete") + + parquet_files = [file.replace(".csv", ".parquet") for file in file_list] + + return parquet_files + + +@task +def is_empty(lista): + if len(lista) == 0: + return True + else: + return False diff --git a/pipelines/utils/crawler_datasus/utils.py b/pipelines/utils/crawler_datasus/utils.py new file mode 100644 index 000000000..c2f201a24 --- /dev/null +++ b/pipelines/utils/crawler_datasus/utils.py @@ -0,0 +1,272 @@ +# -*- coding: utf-8 -*- +""" +General purpose functions for the br_ms_cnes project +""" + +import asyncio +from datetime import datetime +from ftplib import FTP + +import aioftp +import pandas as pd + +from pipelines.utils.crawler_datasus.constants import constants as datasus_constants + + +def list_all_cnes_dbc_files( + datasus_database: str, + datasus_database_table: str = None, +) -> list: + # todo: insert fcodeco link reference + """ + Enters FTP server and lists all DBCs files found for a + a given datasus_database. + """ + available_dbs = list() + ftp = FTP("ftp.datasus.gov.br") + ftp.login() + + # se datasus_database tiver diferentes URL em virtude de + # variados anos de inicio mudar abaixo + cnes_path = ["dissemin/publicos/CNES/200508_/Dados"] + + for path in cnes_path: + try: + # Adicionar aqui eventuais caminhos de databse + if datasus_database == "CNES": + if not datasus_database_table: + raise ValueError("No group assigned to CNES_group") + available_dbs.extend(ftp.nlst(f"{path}/{datasus_database_table}/*.DBC")) + except Exception as e: + raise e + ftp.close() + return available_dbs + + +async def download_files(files: list, output_dir: str): + tasks = [ + download_file(file, f"{output_dir}/{year_month_sigla_uf_parser(file=file)}") + for file in files + ] + await asyncio.gather(*tasks) + + +async def download_file(file: str, output_path: str): + try: + async with aioftp.Client.context( + host="ftp.datasus.gov.br", + parse_list_line_custom=line_file_parser, + # max wait time for data to be received from the server, if it fails trigger a + socket_timeout=30, + ) as client: + await client.download(file, output_path) + except aioftp.StatusCodeError as e: + print(e.expected_codes, e.received_codes, e.info) + + +def line_file_parser(file_line): + line = file_line.decode("utf-8") + info = {} + if "" in line: + date, time, _, *name = line.strip().split() + info["size"] = 0 + info["type"] = "dir" + name = " ".join(name) + else: + date, time, size, name = 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 name, info + + +def year_month_sigla_uf_parser(file: str) -> str: + """receives a DATASUS CNES ST file and parse year, month and sigla_uf + to create proper partitions + + Returns: + (str): partition string + """ + try: + # parse file name last 8 digits before .DBC + file = file[-10:-4] + + # parse and build year + year = "20" + file[2:4] + + # parse and build month + month = int(file[4:6]) + + # parse and build state + sigla_uf = file[:2] + + except IndexError: + raise ValueError("Unable to parse month and year from file") + + return f"ano={year}/mes={month}/sigla_uf={sigla_uf}" + + +def pre_cleaning_to_utf8(df: pd.DataFrame): + """This function is used to pre-clean the data to convert its encoding + from latin1 to utf-8 + + Args: + df (pd.Dataframe): a df + """ + + colums_to_clean = [ + "REGSAUDE", + "MICR_REG", + "DISTRSAN", + "DISTRADM", + "PF_PJ", + "NIV_DEP", + "COD_IR", + "ESFERA_A", + "ATIVIDAD", + "TP_UNID", + "TURNO_AT", + "NIV_HIER", + "TP_PREST", + "ORGEXPED", + "AV_ACRED", + "AV_PNASS", + ] + + for column in colums_to_clean: + df[column] = df[column].str.replace(",", "") + df[column] = df[column].str.replace("¿", "") + df[column] = df[column].str.rstrip("ª") + df[column] = df[column].str.rstrip("º") + df[column] = df[column].str.lstrip("0") + + return df + + +def check_and_create_column(df: pd.DataFrame, col_name: str) -> pd.DataFrame: + """ + Check if a column exists in a Pandas DataFrame. If it doesn't, create a new column with the given name + and fill it with NaN values. If it does exist, do nothing. + + Parameters: + df (Pandas DataFrame): The DataFrame to check. + col_name (str): The name of the column to check for or create. + + Returns: + Pandas DataFrame: The modified DataFrame. + """ + if col_name not in df.columns: + df[col_name] = "" + return df + + +def if_column_exist_delete(df: pd.DataFrame, col_list: str): + """Some columns present in cnes st files from 2019 onwards only contain blank values and are not + registred in any metadata file + https://cnes.datasus.gov.br/pages/downloads/documentacao.jsp + It checkes if one of those columns are present in the dataframe and deletes it + + Args: + df (pd.DataFrame): a cnes st group dataframe + col_list (str): list of cnes st group dataframe columns to delete + + Returns: + df (pd.DataFrame): withut the columns in col_list + """ + + for col in col_list: + if col in df.columns: + del df[col] + + return df + + +def post_process_estabelecimento(df: pd.DataFrame) -> pd.DataFrame: + list_columns_to_delete = [ + "AP01CV07", + "AP02CV07", + "AP03CV07", + "AP04CV07", + "AP05CV07", + "AP06CV07", + "AP07CV07", + ] + + df = pre_cleaning_to_utf8(df) + df = if_column_exist_delete(df=df, col_list=list_columns_to_delete) + df = check_and_create_column(df=df, col_name="NAT_JUR") + + return df + + +def post_process_profissional(df: pd.DataFrame) -> pd.DataFrame: + df = df[datasus_constants.COLUMNS_TO_KEEP.value["PF"]] + return df + + +def post_process_leito(df: pd.DataFrame) -> pd.DataFrame: + df = df[datasus_constants.COLUMNS_TO_KEEP.value["LT"]] + return df + + +def post_process_equipamento(df: pd.DataFrame) -> pd.DataFrame: + df = df[datasus_constants.COLUMNS_TO_KEEP.value["EP"]] + return df + + +def post_process_equipe(df: pd.DataFrame) -> pd.DataFrame: + standardize_colums = { + "IDEQUIPE": "ID_EQUIPE", + "AREA_EQP": "ID_AREA", + } + + df.rename(columns=standardize_colums, inplace=True) + + df = df[datasus_constants.COLUMNS_TO_KEEP.value["EQ"]] + + return df + + +def post_process_estabelecimento_ensino(df: pd.DataFrame) -> pd.DataFrame: + df = df[datasus_constants.COLUMNS_TO_KEEP.value["EE"]] + return df + + +def post_process_dados_complementares(df: pd.DataFrame) -> pd.DataFrame: + df = df[datasus_constants.COLUMNS_TO_KEEP.value["DC"]] + + return df + + +def post_process_estabelecimento_filantropico(df: pd.DataFrame) -> pd.DataFrame: + df = df[datasus_constants.COLUMNS_TO_KEEP.value["EF"]] + return df + + +def post_process_gestao_metas(df: pd.DataFrame) -> pd.DataFrame: + df = df[datasus_constants.COLUMNS_TO_KEEP.value["GM"]] + return df + + +def post_process_habilitacao(df: pd.DataFrame) -> pd.DataFrame: + df = check_and_create_column(df=df, col_name="NAT_JUR") + df = df[datasus_constants.COLUMNS_TO_KEEP.value["HB"]] + return df + + +def post_process_incentivos(df: pd.DataFrame) -> pd.DataFrame: + df = df[datasus_constants.COLUMNS_TO_KEEP.value["IN"]] + return df + + +def post_process_regra_contratual(df: pd.DataFrame) -> pd.DataFrame: + df = 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["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "packaging (>=23.1)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"] [[package]] @@ -3941,13 +3956,13 @@ files = [ [[package]] name = "tqdm" -version = "4.66.1" +version = "4.66.2" description = "Fast, Extensible Progress Meter" optional = false python-versions = ">=3.7" files = [ - {file = "tqdm-4.66.1-py3-none-any.whl", hash = "sha256:d302b3c5b53d47bce91fea46679d9c3c6508cf6332229aa1e7d8653723793386"}, - {file = "tqdm-4.66.1.tar.gz", hash = "sha256:d88e651f9db8d8551a62556d3cff9e3034274ca5d66e93197cf2490e2dcb69c7"}, + {file = "tqdm-4.66.2-py3-none-any.whl", hash = "sha256:1ee4f8a893eb9bef51c6e35730cebf234d5d0b6bd112b0271e10ed7c24a02bd9"}, + {file = "tqdm-4.66.2.tar.gz", hash = "sha256:6cd52cdf0fef0e0f543299cfc96fec90d7b8a7e88745f411ec33eb44d5ed3531"}, ] [package.dependencies] @@ -4029,13 +4044,13 @@ files = [ [[package]] name = "tzdata" -version = "2023.4" +version = "2024.1" description = "Provider of IANA time zone data" optional = false python-versions = ">=2" files = [ - {file = "tzdata-2023.4-py2.py3-none-any.whl", hash = "sha256:aa3ace4329eeacda5b7beb7ea08ece826c28d761cda36e747cfbf97996d39bf3"}, - {file = "tzdata-2023.4.tar.gz", hash = "sha256:dd54c94f294765522c77399649b4fefd95522479a664a0cec87f41bebc6148c9"}, + {file = "tzdata-2024.1-py2.py3-none-any.whl", hash = "sha256:9068bc196136463f5245e51efda838afa15aaeca9903f49050dfa2679db4d252"}, + {file = "tzdata-2024.1.tar.gz", hash = "sha256:2674120f8d891909751c38abcdfd386ac0a5a1127954fbc332af6b5ceae07efd"}, ] [[package]] @@ -4301,4 +4316,4 @@ heapdict = "*" [metadata] lock-version = "2.0" python-versions = ">=3.10,<3.11" -content-hash = "0c25996bca26cd03d06f955843f0729bc54420fe02440389699f2f8adc3d434e" +content-hash = "089052a2961d797479fe6ad5f94592a669925f696e5d981e2fcc9183e2a257a2" diff --git a/pyproject.toml b/pyproject.toml index baa76b8f0..74eb9805a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -114,6 +114,7 @@ httpx = "^0.26.0" cffi = "^1.16.0" pendulum = "^3.0.0" simpledbf = "^0.2.6" +aioftp = "^0.22.3" [tool.poetry.dev-dependencies] From 7ec9de3ba9be26136f8224b7039b63af2dba15c5 Mon Sep 17 00:00:00 2001 From: folhesgabriel Date: Fri, 16 Feb 2024 15:32:54 -0300 Subject: [PATCH 31/44] feat: add final modifications --- pipelines/utils/crawler_datasus/flows.py | 1 - pipelines/utils/crawler_datasus/tasks.py | 45 +++++++++++++----------- 2 files changed, 24 insertions(+), 22 deletions(-) diff --git a/pipelines/utils/crawler_datasus/flows.py b/pipelines/utils/crawler_datasus/flows.py index 0f00ceb06..5998da9ed 100644 --- a/pipelines/utils/crawler_datasus/flows.py +++ b/pipelines/utils/crawler_datasus/flows.py @@ -74,7 +74,6 @@ csv_files = decompress_dbf( file_list=dbc_files, - dataset_id=dataset_id, table_id=table_id, upstream_tasks=[dbf_files, dbc_files], ) diff --git a/pipelines/utils/crawler_datasus/tasks.py b/pipelines/utils/crawler_datasus/tasks.py index d4665d60d..f8fee026e 100644 --- a/pipelines/utils/crawler_datasus/tasks.py +++ b/pipelines/utils/crawler_datasus/tasks.py @@ -93,12 +93,7 @@ def check_files_to_parse( list_files = [file for file in available_dbs if file[-8:-4] == year_month_to_parse] # list_files = [file for file in available_dbs if file[-10:-8] == 'SP' and file[-8:-6] in ['22', '23']] - # filtra pra ver se acha e retorna a lista - # for file in available_dbs: - # if file[-10:-8] == 'SP': - # list_files.append(file) - # final - log(f"the following files were selected fom DATASUS FTP: {list_files}") + log(f"The following files were selected fom DATASUS FTP: {list_files}") return list_files @@ -126,6 +121,7 @@ def access_ftp_download_files_async( log(f"------created input dir {input_path}") os.makedirs(input_path, exist_ok=True) + # https://github.com/AlertaDengue/PySUS/blob/main/pysus/ftp/__init__.py#L156 log(f"------dowloading {table_id} files from DATASUS FTP") asyncio.run(download_files(files=file_list, output_dir=input_path)) @@ -185,7 +181,7 @@ def decompress_dbc(file_list: list, dataset_id: str) -> None: return_all=True, log_stderr=True, ) - log(f"Decompressing {file}") + log(f"Decompressing {file.split('/')[-1]} file") decompress_task.run() else: print(f"Skipping non-DBC file: {file}") @@ -194,15 +190,15 @@ def decompress_dbc(file_list: list, dataset_id: str) -> None: for file in file_list: if file.endswith(".dbc"): - os.system(f"rm {file}") + os.system(f"rm -f {file}") @task -def decompress_dbf(file_list: list, dataset_id: str, table_id: str) -> str: +def decompress_dbf(file_list: list, table_id: str) -> str: """ Convert dbc to csv """ - log(f"--------- Decompressing {table_id} files") + log(f"--------- Decompressing {table_id} .DBF files") csv_file_list = list() @@ -211,16 +207,17 @@ def decompress_dbf(file_list: list, dataset_id: str, table_id: str) -> str: for file in tqdm(dbf_file_list): # replace .csv with .dbf - log(f"-------- reading {file}") + log(f"-------- Reading {file}") dbf = Dbf5(file, codec="iso-8859-1") # remove cnes default file name + file = file.replace("input", "output") path_parts = file.split("/")[:-1] - output_path = os.path.join(*path_parts) - os.system(f"mkdir -p {output_path}") + output_path = os.path.join("/", *path_parts) + os.makedirs(output_path, exist_ok=True) output_file = os.path.join(output_path, f"{table_id}.csv") - log(f"-------- saving {file.split('/')[-1]} to .csv ") + log(f"-------- Saving {file.split('/')[-1]} to {table_id}.csv ") dbf.to_csv(output_file) csv_file_list.append(output_file) @@ -229,7 +226,7 @@ def decompress_dbf(file_list: list, dataset_id: str, table_id: str) -> str: for file in dbf_file_list: if file.endswith(".dbf"): - os.system(f"rm {file}") + os.system(f"rm -f {file}") return csv_file_list @@ -238,7 +235,7 @@ def decompress_dbf(file_list: list, dataset_id: str, table_id: str) -> str: def pre_process_files(file_list: list, dataset_id: str, table_id: str) -> str: log("Post-processing CSV files") - + log(f"-------- {file_list}") # todo: colocar em constants post_process_functions = { "estabelecimento": post_process_estabelecimento, @@ -261,20 +258,26 @@ def pre_process_files(file_list: list, dataset_id: str, table_id: str) -> str: except Exception as e: log( - f"The error {e} occured. It problably indicates that none post-processing function was found for table_id: {table_id}" + f"The error {e} occurred. It probably indicates that no post-processing function was found for table_id: {table_id}" ) for file in tqdm(file_list): log(f"-------- reading {file}") + # Initialize an empty DataFrame to store concatenated results + concatenated_df = pd.DataFrame() - df = pd.read_csv(file, dtype=str, encoding="iso-8859-1") - df = post_process_function(df) + for chunk_df in pd.read_csv( + file, dtype=str, encoding="iso-8859-1", chunksize=100000 + ): + concatenated_df = pd.concat([concatenated_df, chunk_df]) - # df.to_csv(output_path, sep=",", na_rep="", index=False, encoding="utf-8") + processed_df = post_process_function(concatenated_df) output_path = file.replace(".csv", ".parquet") - df.to_parquet(output_path, index=None) + processed_df.to_parquet(output_path, index=None) + + os.system(f"rm -f {file}") log("Post-processing complete") From efc21b7346075e4ccaa263bebb3fb966cfdc0f44 Mon Sep 17 00:00:00 2001 From: folhesgabriel Date: Fri, 16 Feb 2024 18:49:58 -0300 Subject: [PATCH 32/44] fix: crawler_datasus template flow parameters --- pipelines/utils/crawler_datasus/flows.py | 4 ++-- pipelines/utils/crawler_datasus/tasks.py | 1 - 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/pipelines/utils/crawler_datasus/flows.py b/pipelines/utils/crawler_datasus/flows.py index 5998da9ed..44b23aca1 100644 --- a/pipelines/utils/crawler_datasus/flows.py +++ b/pipelines/utils/crawler_datasus/flows.py @@ -35,8 +35,8 @@ with Flow(name="BD Template - DATASUS", code_owners=["Gabriel Pisa"]) as flow_datasus: # Parameters - dataset_id = Parameter("dataset_id", default=False, required=True) - table_id = Parameter("table_id", default=False, required=True) + dataset_id = Parameter("dataset_id", required=True) + table_id = Parameter("table_id", required=True) update_metadata = Parameter("update_metadata", default=False, required=False) materialization_mode = Parameter( "materialization_mode", default="dev", required=False diff --git a/pipelines/utils/crawler_datasus/tasks.py b/pipelines/utils/crawler_datasus/tasks.py index f8fee026e..9534ee367 100644 --- a/pipelines/utils/crawler_datasus/tasks.py +++ b/pipelines/utils/crawler_datasus/tasks.py @@ -60,7 +60,6 @@ def check_files_to_parse( year = str(last_date.year) month = last_date.month - # download files to compare year = "2023" month = 11 From b7c80c5044322d06f9757d39ddc896b080907044 Mon Sep 17 00:00:00 2001 From: folhesgabriel Date: Fri, 16 Feb 2024 19:08:22 -0300 Subject: [PATCH 33/44] feat: delete old tasks & utils --- pipelines/datasets/br_ms_cnes/tasks.py | 318 ------------------------- pipelines/datasets/br_ms_cnes/utils.py | 136 ----------- 2 files changed, 454 deletions(-) delete mode 100644 pipelines/datasets/br_ms_cnes/tasks.py delete mode 100644 pipelines/datasets/br_ms_cnes/utils.py diff --git a/pipelines/datasets/br_ms_cnes/tasks.py b/pipelines/datasets/br_ms_cnes/tasks.py deleted file mode 100644 index c3661cd62..000000000 --- a/pipelines/datasets/br_ms_cnes/tasks.py +++ /dev/null @@ -1,318 +0,0 @@ -# -*- coding: utf-8 -*- -""" -Tasks for br_ms_cnes -""" - - -import os -from datetime import timedelta -from glob import glob - -import pandas as pd -import wget -from prefect import task -from prefect.tasks.shell import ShellTask -from simpledbf import Dbf5 -from tqdm import tqdm - -from pipelines.constants import constants -from pipelines.datasets.br_ms_cnes.constants import constants as cnes_constants -from pipelines.datasets.br_ms_cnes.utils import ( - check_and_create_column, - if_column_exist_delete, - list_all_cnes_dbc_files, - pre_cleaning_to_utf8, - year_month_sigla_uf_parser, -) -from pipelines.utils.metadata.utils import get_api_most_recent_date -from pipelines.utils.utils import log - -# from rpy2.robjects.packages import importr - - -@task -def check_files_to_parse( - dataset_id: str, - table_id: str, - cnes_database: str, - cnes_group_file: str, -) -> list[str]: - log(f"extracting last date from api for {dataset_id}.{table_id}") - # 1. extrair data mais atual da api - last_date = get_api_most_recent_date( - dataset_id=dataset_id, - table_id=table_id, - date_format="%Y-%m", - ) - log("building next year/month to parse") - # 2. adicionar mais um no mes ou transformar pra 1 se for 12 - # para ver se o mês seguinte já está disponível no FTP - # eg. last_date = 2023-04-01 - - year = str(last_date.year) - month = last_date.month - - # download files to compare - year = "2023" - month = 11 - - if month <= 11: - month = month + 1 - else: - month = 1 - year = int(year) + 1 - year = str(year) - # 3. buildar no formato do ftp YYMM - year = year[2:4] - - if month <= 9: - month = "0" + str(month) - else: - month = str(month) - - year_month_to_parse = year + month - log(f"year_month_to_parse (YYMM) is {year_month_to_parse}") - # 4. ver se o arquivo existe - available_dbs = list_all_cnes_dbc_files( - database=cnes_database, CNES_group=cnes_group_file - ) - - list_files = [] - - # filtra pra ver se acha e retorna a lista - for file in available_dbs: - if file[-8:-4] == year_month_to_parse: - list_files.append(file) - # final - log(f"the following files were selected fom DATASUS FTP: {list_files}") - - return list_files - - -@task( - max_retries=constants.TASK_MAX_RETRIES.value, - retry_delay=timedelta(seconds=constants.TASK_RETRY_DELAY.value), -) -def access_ftp_donwload_files(file_list: list, path: str, table: str) -> list[str]: - """This function recives a list of files and - download them from DATASUS FTP server - - Args: - file_list (list): a file list extracted with the function choose_latest_cnes_dbc_files - - Returns: - pd.DataFrame: a list with the downloaded files paths - """ - dbc_files_path_list = list() - - log(f"wrangling {table} data") - - # file_list = file_list[1:3] - - for file in tqdm(file_list): - # build partition dirs - - try: - - year_month_sigla_uf = year_month_sigla_uf_parser(file=file) - - input_path = path + table + "/" + year_month_sigla_uf - - os.system(f"mkdir -p {input_path}") - os.system(f"find {input_path} -type f -delete") - - log(f"created input dir {path + table + '/' + year_month_sigla_uf}") - - url = f"ftp://ftp.datasus.gov.br/{file}" - # access ftp - wget.download(url, out=input_path) - - # list downloaded files - dbc_file = os.listdir(input_path) - - # append to list - complete_path = input_path + "/" + dbc_file[0] - - dbc_files_path_list.append(complete_path) - - except Exception as e: - log(f"An error occurred while downloading {file} from DATASUS FTP: {e}") - raise e - - return dbc_files_path_list - - -@task -def decompress_dbc(file_list: list) -> None: - """ - Convert dbc to dbf format - """ - - # ShellTask to create the blast-dbf directory - create_dir_task = ShellTask( - name="Create blast-dbf Directory", - command="mkdir -p /tmp/br_ms_cnes/blast-dbf", - return_all=True, - log_stderr=True, - ) - - # Define a ShellTask to clone the blast-dbf repository - clone_repo_task = ShellTask( - name="Clone blast-dbf Repository", - command="git clone https://github.com/eaglebh/blast-dbf /tmp/br_ms_cnes/blast-dbf", - return_all=True, - log_stderr=True, - ) - - # Define a ShellTask to build the blast-dbf repository - compile_blast_dbf = ShellTask( - name="Build blast-dbf", - command="cd /tmp/br_ms_cnes/blast-dbf && make", - return_all=True, - log_stderr=True, - ) - - create_dir_task.run() - log("------ Cloning blast-dbf repository") - clone_repo_task.run() - log("------ Compiling blast-dbf repository") - compile_blast_dbf.run() - - for file in file_list: - # Check if the file has a .dbc extension - if file.endswith(".dbc"): - # Execute blast-dbf on the file - decompress_task = ShellTask( - name=f"Decompress {file}", - command=f"/tmp/br_ms_cnes/blast-dbf/blast-dbf {file} {file.replace('.dbc', '.dbf')}", - return_all=True, - log_stderr=True, - ) - log(f"Decompressing {file}") - decompress_task.run() - else: - print(f"Skipping non-DBC file: {file}") - - -@task -def decompress_dbf(file_list: list, path: str, table: str) -> str: - """ - Convert dbc to csv - """ - log(f"wrangling {table} data") - - # list files - for file in tqdm(file_list): - - dbf_file = ".".join([file.split(".")[0], "dbf"]) - log(f"-------- reading .dbf {dbf_file}") - dbf = Dbf5(dbf_file, codec="iso-8859-1") - - year_month_sigla_uf = year_month_sigla_uf_parser(file=file) - - # log(f"year_month_sigla_uf of {file} parsed") - output_path = path + table + "/" + year_month_sigla_uf - - os.system(f"mkdir -p {output_path}") - # log(f"created output partition dir {path + table + '/'+ year_month_sigla_uf}") - - output_file = output_path + "/" + table + ".csv" - log(f"{file} 1 saved") - - # filesd='.'.join([dbf_file.split('.')[0], "csv"]) - log(f"-------- saving to .csv {output_file}") - dbf.to_csv(output_file) - - # delete dbc file - folder_path = file.split(".")[0] - files_to_remove = glob(os.path.join(folder_path, "*.dbc")) + glob( - os.path.join(folder_path, "*.dbf") - ) - # Remove each file - for file in files_to_remove: - log(f"---- Removing file {file}") - os.system(f"rm {file}") - - # ler df - log("file 2 being read") - df = pd.read_csv(output_file, dtype=str, encoding="iso-8859-1") - - # tratar - list_columns_to_delete = [ - "AP01CV07", - "AP02CV07", - "AP03CV07", - "AP04CV07", - "AP05CV07", - "AP06CV07", - "AP07CV07", - ] - - if table == "estabelecimento": - df = pre_cleaning_to_utf8(df) - df = if_column_exist_delete(df=df, col_list=list_columns_to_delete) - df = check_and_create_column(df=df, col_name="NAT_JUR") - - elif table == "profissional": - df = df[cnes_constants.COLUMNS_TO_KEEP.value["PF"]] - - elif table == "leito": - df = df[cnes_constants.COLUMNS_TO_KEEP.value["LT"]] - - elif table == "equipamento": - df = df[cnes_constants.COLUMNS_TO_KEEP.value["EP"]] - - elif table == "equipe": - # equipe - # the EQ table has different names for same variables across the years - # this is a workaround to standardize the names - standardize_colums = { - "IDEQUIPE": "ID_EQUIPE", - "AREA_EQP": "ID_AREA", - } - - df.rename(columns=standardize_colums, inplace=True) - - df = df[cnes_constants.COLUMNS_TO_KEEP.value["EQ"]] - - elif table == "estabelecimento_ensino": - df = df[cnes_constants.COLUMNS_TO_KEEP.value["EE"]] - - elif table == "dados_complementares": - df = df[cnes_constants.COLUMNS_TO_KEEP.value["DC"]] - - elif table == "estabelecimento_filantropico": - df = df[cnes_constants.COLUMNS_TO_KEEP.value["EF"]] - - elif table == "gestao_metas": - df = df[cnes_constants.COLUMNS_TO_KEEP.value["GM"]] - - elif table == "habilitacao": - df = check_and_create_column(df=df, col_name="NAT_JUR") - df = df[cnes_constants.COLUMNS_TO_KEEP.value["HB"]] - - elif table == "incentivos": - df = df[cnes_constants.COLUMNS_TO_KEEP.value["IN"]] - - elif table == "regra_contratual": - df = df[cnes_constants.COLUMNS_TO_KEEP.value["RC"]] - - elif table == "servico_especializado": - df = df[cnes_constants.COLUMNS_TO_KEEP.value["SR"]] - - # salvar de novo - df.to_csv(output_file, sep=",", na_rep="", index=False, encoding="utf-8") - - log( - f"The file {file} was converted to csv and saved at {output_path + file + '.csv'}" - ) - - return path + table - - -@task -def is_empty(lista): - if len(lista) == 0: - return True - else: - return False diff --git a/pipelines/datasets/br_ms_cnes/utils.py b/pipelines/datasets/br_ms_cnes/utils.py deleted file mode 100644 index f897ab4ec..000000000 --- a/pipelines/datasets/br_ms_cnes/utils.py +++ /dev/null @@ -1,136 +0,0 @@ -# -*- coding: utf-8 -*- -""" -General purpose functions for the br_ms_cnes project -""" - -from ftplib import FTP - -import pandas as pd - - -def list_all_cnes_dbc_files( - database: str, - CNES_group: str = None, -) -> list: - # todo: insert fcodeco link reference - """ - Enters FTP server and lists all DBCs files found for a - CNES-ST database group. - """ - available_dbs = list() - ftp = FTP("ftp.datasus.gov.br") - ftp.login() - - cnes_path = ["dissemin/publicos/CNES/200508_/Dados"] - - for path in cnes_path: - try: - # CNES - if database == "CNES": - if not CNES_group: - raise ValueError("No group assigned to CNES_group") - available_dbs.extend(ftp.nlst(f"{path}/{CNES_group}/*.DBC")) - except Exception as e: - raise e - ftp.close() - return available_dbs - - -def year_month_sigla_uf_parser(file: str) -> str: - """receives a DATASUS CNES ST file and parse year, month and sigla_uf - to create proper partitions - - Returns: - (str): - """ - try: - # parse file name last 8 digits before .DBC - file = file[-10:-4] - - # parse and build year - year = "20" + file[2:4] - - # parse and build month - month = int(file[4:6]) - - # parse and build state - sigla_uf = file[:2] - except IndexError: - raise ValueError("Unable to parse month and year from file") - - return f"ano={year}/mes={month}/sigla_uf={sigla_uf}" - - -def pre_cleaning_to_utf8(df: pd.DataFrame): - """This function is used to pre-clean the data to convert its encoding - from latin1 to utf-8 - - Args: - df (pd.Dataframe): a df - """ - - colums_to_clean = [ - "REGSAUDE", - "MICR_REG", - "DISTRSAN", - "DISTRADM", - "PF_PJ", - "NIV_DEP", - "COD_IR", - "ESFERA_A", - "ATIVIDAD", - "TP_UNID", - "TURNO_AT", - "NIV_HIER", - "TP_PREST", - "ORGEXPED", - "AV_ACRED", - "AV_PNASS", - ] - - for column in colums_to_clean: - df[column] = df[column].str.replace(",", "") - df[column] = df[column].str.replace("¿", "") - df[column] = df[column].str.rstrip("ª") - df[column] = df[column].str.rstrip("º") - df[column] = df[column].str.lstrip("0") - - return df - - -def check_and_create_column(df: pd.DataFrame, col_name: str) -> pd.DataFrame: - """ - Check if a column exists in a Pandas DataFrame. If it doesn't, create a new column with the given name - and fill it with NaN values. If it does exist, do nothing. - - Parameters: - df (Pandas DataFrame): The DataFrame to check. - col_name (str): The name of the column to check for or create. - - Returns: - Pandas DataFrame: The modified DataFrame. - """ - if col_name not in df.columns: - df[col_name] = "" - return df - - -def if_column_exist_delete(df: pd.DataFrame, col_list: str): - """Some columns present in cnes st files from 2019 onwards only contain blank values and are not - registred in any metadata file - https://cnes.datasus.gov.br/pages/downloads/documentacao.jsp - It checkes if one of those columns are present in the dataframe and deletes it - - Args: - df (pd.DataFrame): a cnes st group dataframe - col_list (str): list of cnes st group dataframe columns to delete - - Returns: - df (pd.DataFrame): withut the columns in col_list - """ - - for col in col_list: - if col in df.columns: - del df[col] - - return df From 5523a0eb2a87f1f1f856a8c9996544bf14329a79 Mon Sep 17 00:00:00 2001 From: folhesgabriel Date: Sat, 17 Feb 2024 13:00:37 -0300 Subject: [PATCH 34/44] fix: pre_process_files output to next task --- pipelines/utils/crawler_datasus/tasks.py | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/pipelines/utils/crawler_datasus/tasks.py b/pipelines/utils/crawler_datasus/tasks.py index 9534ee367..e4bf39759 100644 --- a/pipelines/utils/crawler_datasus/tasks.py +++ b/pipelines/utils/crawler_datasus/tasks.py @@ -234,7 +234,7 @@ def decompress_dbf(file_list: list, table_id: str) -> str: def pre_process_files(file_list: list, dataset_id: str, table_id: str) -> str: log("Post-processing CSV files") - log(f"-------- {file_list}") + # todo: colocar em constants post_process_functions = { "estabelecimento": post_process_estabelecimento, @@ -262,27 +262,31 @@ def pre_process_files(file_list: list, dataset_id: str, table_id: str) -> str: for file in tqdm(file_list): - log(f"-------- reading {file}") + log(f"-------- wrangling {file.split('/')[-1]} and saving to parquet") # Initialize an empty DataFrame to store concatenated results concatenated_df = pd.DataFrame() for chunk_df in pd.read_csv( - file, dtype=str, encoding="iso-8859-1", chunksize=100000 + file, dtype=str, encoding="iso-8859-1", chunksize=50000 ): concatenated_df = pd.concat([concatenated_df, chunk_df]) processed_df = post_process_function(concatenated_df) + output_path = file.replace(".csv", ".parquet") - processed_df.to_parquet(output_path, index=None) + processed_df.to_parquet(output_path, index=None, compression='gzip') os.system(f"rm -f {file}") log("Post-processing complete") - parquet_files = [file.replace(".csv", ".parquet") for file in file_list] + #parquet_files = [file.replace(".csv", ".parquet") for file in file_list] + + path_parts = file.split("/")[:5] + output_path = os.path.join("/", *path_parts) - return parquet_files + return output_path @task From 4de4623f0f9641b11e73c809eda9d4d98471f750 Mon Sep 17 00:00:00 2001 From: folhesgabriel Date: Sun, 18 Feb 2024 15:02:20 -0300 Subject: [PATCH 35/44] feat: add sequential chunks to control requests made to datasus ftp --- pipelines/datasets/br_ms_cnes/flows.py | 2 +- pipelines/utils/crawler_datasus/tasks.py | 19 +++++++--- pipelines/utils/crawler_datasus/utils.py | 46 +++++++++++++++++++----- 3 files changed, 52 insertions(+), 15 deletions(-) diff --git a/pipelines/datasets/br_ms_cnes/flows.py b/pipelines/datasets/br_ms_cnes/flows.py index 3232da0c1..1f52177a3 100644 --- a/pipelines/datasets/br_ms_cnes/flows.py +++ b/pipelines/datasets/br_ms_cnes/flows.py @@ -9,6 +9,7 @@ from prefect.run_configs import KubernetesRun from prefect.storage import GCS +from pipelines.utils.crawler_datasus.flows import flow_datasus from pipelines.constants import constants from pipelines.datasets.br_ms_cnes.schedules import ( schedule_br_ms_cnes_dados_complementares, @@ -24,7 +25,6 @@ schedule_br_ms_cnes_profissional, schedule_br_ms_cnes_servico_especializado, ) -from pipelines.utils.crawler_datasus.flows import flow_datasus br_ms_cnes_profissional = deepcopy(flow_datasus) br_ms_cnes_profissional.name = "br_ms_cnes.profissional" diff --git a/pipelines/utils/crawler_datasus/tasks.py b/pipelines/utils/crawler_datasus/tasks.py index e4bf39759..e6d333a4f 100644 --- a/pipelines/utils/crawler_datasus/tasks.py +++ b/pipelines/utils/crawler_datasus/tasks.py @@ -10,7 +10,6 @@ import aioftp import pandas as pd -import wget from prefect import task from prefect.tasks.shell import ShellTask from simpledbf import Dbf5 @@ -19,7 +18,7 @@ from pipelines.constants import constants from pipelines.utils.crawler_datasus.constants import constants as datasus_constants from pipelines.utils.crawler_datasus.utils import ( - download_files, + download_chunks, list_all_cnes_dbc_files, post_process_dados_complementares, post_process_equipamento, @@ -94,7 +93,7 @@ def check_files_to_parse( log(f"The following files were selected fom DATASUS FTP: {list_files}") - return list_files + return available_dbs @task( @@ -102,7 +101,7 @@ def check_files_to_parse( retry_delay=timedelta(seconds=constants.TASK_RETRY_DELAY.value), ) def access_ftp_download_files_async( - file_list: list, dataset_id: str, table_id: str + file_list: list, dataset_id: str, table_id: str, max_parallel: int = 10, chunk_size: int = 20 ) -> list[str]: """This function receives a list of files and downloads them from DATASUS FTP server asynchronously. @@ -122,7 +121,17 @@ def access_ftp_download_files_async( # https://github.com/AlertaDengue/PySUS/blob/main/pysus/ftp/__init__.py#L156 log(f"------dowloading {table_id} files from DATASUS FTP") - asyncio.run(download_files(files=file_list, output_dir=input_path)) + + + + asyncio.run( + download_chunks( + files=file_list, + output_dir=input_path, + max_parallel=max_parallel, + chunk_size=chunk_size, + ) + ) dbc_files_path_list = [ os.path.join( diff --git a/pipelines/utils/crawler_datasus/utils.py b/pipelines/utils/crawler_datasus/utils.py index c2f201a24..ea771fb68 100644 --- a/pipelines/utils/crawler_datasus/utils.py +++ b/pipelines/utils/crawler_datasus/utils.py @@ -9,8 +9,9 @@ import aioftp import pandas as pd - +from typing import List, Dict, Tuple from pipelines.utils.crawler_datasus.constants import constants as datasus_constants +from pipelines.utils.utils import log def list_all_cnes_dbc_files( @@ -42,17 +43,35 @@ def list_all_cnes_dbc_files( ftp.close() return available_dbs +async def download_chunks(files: List[str], output_dir: str, chunk_size: int, max_parallel: int): + """This function is used to sequentially control the number of concurrent downloads + #OSError: [Errno 24] Too many open files -async def download_files(files: list, output_dir: str): - tasks = [ - download_file(file, f"{output_dir}/{year_month_sigla_uf_parser(file=file)}") - for file in files - ] - await asyncio.gather(*tasks) + Args: + files (List[str]): list of files to download + output_dir (str): savepath + chunk_size (int): size of the chunk + max_parallel (int): number of concurrent downloads + """ + + for i in range(0, len(files), chunk_size): + chunk = files[i:i + chunk_size] + await download_files(files=chunk, output_dir=output_dir, max_parallel=max_parallel) + + +async def download_files(files: list, output_dir: str, max_parallel: int): + semaphore = asyncio.Semaphore(max_parallel) + async with semaphore: + tasks = [ + download_file(file, f"{output_dir}/{year_month_sigla_uf_parser(file=file)}") + for file in files + ] + await asyncio.gather(*tasks) async def download_file(file: str, output_path: str): try: + log(f"------- Downloading {file} ") async with aioftp.Client.context( host="ftp.datasus.gov.br", parse_list_line_custom=line_file_parser, @@ -61,10 +80,19 @@ async def download_file(file: str, output_path: str): ) as client: await client.download(file, output_path) except aioftp.StatusCodeError as e: - print(e.expected_codes, e.received_codes, e.info) + log(e.expected_codes, e.received_codes, e.info) -def line_file_parser(file_line): +def line_file_parser(file_line)-> Tuple[List, Dict]: + """This function is used to parse the file line from the FTP server + + Args: + file_line (_type_): + + Returns: + _type_: + """ + line = file_line.decode("utf-8") info = {} if "" in line: From a020f70ced554cf12cd7a9342b15da716c6ea2ca Mon Sep 17 00:00:00 2001 From: folhesgabriel Date: Mon, 19 Feb 2024 11:39:47 -0300 Subject: [PATCH 36/44] feat: goodbye --- pipelines/datasets/br_ms_cnes/constants.py | 308 ------------------- pipelines/datasets/br_ms_cnes/flows.py | 24 +- pipelines/datasets/br_ms_cnes/schedules.py | 52 ++-- pipelines/utils/crawler_datasus/constants.py | 1 + pipelines/utils/crawler_datasus/tasks.py | 40 +-- pipelines/utils/crawler_datasus/utils.py | 134 +++++++- 6 files changed, 179 insertions(+), 380 deletions(-) delete mode 100644 pipelines/datasets/br_ms_cnes/constants.py diff --git a/pipelines/datasets/br_ms_cnes/constants.py b/pipelines/datasets/br_ms_cnes/constants.py deleted file mode 100644 index 249d958ba..000000000 --- a/pipelines/datasets/br_ms_cnes/constants.py +++ /dev/null @@ -1,308 +0,0 @@ -# -*- coding: utf-8 -*- -""" -Constant values for the datasets projects -""" - - -from enum import Enum - - -class constants(Enum): # pylint: disable=c0103 - """ - Constant values for the br_ms_cnes project - """ - - # to build paths - PATH = [ - "/tmp/br_ms_cnes/input/", - "/tmp/br_ms_cnes/output/", - ] - - # to build paths - TABLE = [ - "estabelecimento", - "profissional", - "equipamento", - "leito", - "equipe", - "estabelecimento_ensino", - "dados_complementares", - "estabelecimento_filantropico", - "gestao_metas", - "habilitacao", - "incentivos", - "regra_contratual", - "servico_especializado", - ] - - # to download files from datasus FTP server - DATABASE_GROUPS = { - # group: table name - "CNES": [ - "ST", - "PF", - "EQ", - "LT", - "EP", - "EE", - "DC", - "EF", - "GM", - "HB", - "IN", - "RC", - "SR", - ], - } - - COLUMNS_TO_KEEP = { - # equipamento - "EP": [ - "CODUFMUN", - "CNES", - "TIPEQUIP", - "CODEQUIP", - "QT_EXIST", - "QT_USO", - "IND_SUS", - "IND_NSUS", - ], - # leito - "LT": ["CNES", "TP_LEITO", "CODLEITO", "QT_EXIST", "QT_CONTR", "QT_SUS"], - # equipe - "EQ": [ - "CODUFMUN", - "CNES", - "ID_EQUIPE", - "TIPO_EQP", - "NOME_EQP", - "ID_AREA", - "NOMEAREA", - "ID_SEGM", - "DESCSEGM", - "TIPOSEGM", - "DT_ATIVA", - "DT_DESAT", - "MOTDESAT", - "TP_DESAT", - "QUILOMBO", - "ASSENTAD", - "POPGERAL", - "ESCOLA", - "INDIGENA", - "PRONASCI", - ], - # profissional - "PF": [ - "COMPETEN", - "CNES", - "UFMUNRES", - "NOMEPROF", - "CNS_PROF", - "CBO", - "REGISTRO", - "CONSELHO", - "TERCEIRO", - "VINCULAC", - "VINCUL_C", - "VINCUL_A", - "VINCUL_N", - "PROF_SUS", - "PROFNSUS", - "HORAOUTR", - "HORAHOSP", - "HORA_AMB", - ], - # estabelecimento_ensino - "EE": [ - "CODUFMUN", - "CNES", - "CMPT_INI", - "CMPT_FIM", - "SGRUPHAB", - "DTPORTAR", - "PORTARIA", - "MAPORTAR", - ], - # estabelecimento_filantropico - "EF": [ - "CODUFMUN", - "CNES", - "CMPT_INI", - "CMPT_FIM", - "SGRUPHAB", - "DTPORTAR", - "PORTARIA", - "MAPORTAR", - ], - # gestao_metas - "GM": [ - "CODUFMUN", - "CNES", - "CMPT_INI", - "CMPT_FIM", - "SGRUPHAB", - "DTPORTAR", - "PORTARIA", - "MAPORTAR", - ], - # habilitacao - "HB": [ - "CODUFMUN", - "CNES", - "NAT_JUR", - "NULEITOS", - "SGRUPHAB", - "CMPT_INI", - "CMPT_FIM", - "DTPORTAR", - "PORTARIA", - "MAPORTAR", - ], - # incentivos - "IN": [ - "CODUFMUN", - "CNES", - "CMPT_INI", - "CMPT_FIM", - "SGRUPHAB", - "DTPORTAR", - "PORTARIA", - "MAPORTAR", - ], - # regra_contratual - "RC": [ - "CODUFMUN", - "CNES", - "CMPT_INI", - "CMPT_FIM", - "SGRUPHAB", - "DTPORTAR", - "PORTARIA", - "MAPORTAR", - ], - # servico_especializado - "SR": [ - "CODUFMUN", - "CNES", - "SERV_ESP", - "CLASS_SR", - "SRVUNICO", - "CARACTER", - "AMB_NSUS", - "AMB_SUS", - "HOSP_NSUS", - "HOSP_SUS", - "CONTSRVU", - "CNESTERC", - ], - # dados complementares - "DC": [ - "CODUFMUN", - "CNES", - "S_HBSAGP", - "S_HBSAGN", - "S_DPI", - "S_DPAC", - "S_REAGP", - "S_REAGN", - "S_REHCV", - "MAQ_PROP", - "MAQ_OUTR", - "F_AREIA", - "F_CARVAO", - "ABRANDAD", - "DEIONIZA", - "OSMOSE_R", - "OUT_TRAT", - "CNS_NEFR", - "DIALISE", - "SIMUL_RD", - "PLANJ_RD", - "ARMAZ_FT", - "CONF_MAS", - "SALA_MOL", - "BLOCOPER", - "S_ARMAZE", - "S_PREPAR", - "S_QCDURA", - "S_QLDURA", - "S_CPFLUX", - "S_SIMULA", - "S_ACELL6", - "S_ALSEME", - "S_ALCOME", - "ORTV1050", - "ORV50150", - "OV150500", - "UN_COBAL", - "EQBRBAIX", - "EQBRMEDI", - "EQBRALTA", - "EQ_MAREA", - "EQ_MINDI", - "EQSISPLN", - "EQDOSCLI", - "EQFONSEL", - "CNS_ADM", - "CNS_OPED", - "CNS_CONC", - "CNS_OCLIN", - "CNS_MRAD", - "CNS_FNUC", - "QUIMRADI", - "S_RECEPC", - "S_TRIHMT", - "S_TRICLI", - "S_COLETA", - "S_AFERES", - "S_PREEST", - "S_PROCES", - "S_ESTOQU", - "S_DISTRI", - "S_SOROLO", - "S_IMUNOH", - "S_PRETRA", - "S_HEMOST", - "S_CONTRQ", - "S_BIOMOL", - "S_IMUNFE", - "S_TRANSF", - "S_SGDOAD", - "QT_CADRE", - "QT_CENRE", - "QT_REFSA", - "QT_CONRA", - "QT_EXTPL", - "QT_FRE18", - "QT_FRE30", - "QT_AGIPL", - "QT_SELAD", - "QT_IRRHE", - "QT_AGLTN", - "QT_MAQAF", - "QT_REFRE", - "QT_REFAS", - "QT_CAPFL", - "CNS_HMTR", - "CNS_HMTL", - "CNS_CRES", - "CNS_RTEC", - "HEMOTERA", - ], - } - - GENERATE_MONTH_TO_PARSE = { - 12: "11", - 1: "12", - 2: "01", - 3: "02", - 4: "03", - 5: "04", - 6: "05", - 7: "06", - 8: "07", - 9: "08", - 10: "09", - 11: "10", - } diff --git a/pipelines/datasets/br_ms_cnes/flows.py b/pipelines/datasets/br_ms_cnes/flows.py index 1f52177a3..60627c4fd 100644 --- a/pipelines/datasets/br_ms_cnes/flows.py +++ b/pipelines/datasets/br_ms_cnes/flows.py @@ -31,7 +31,7 @@ br_ms_cnes_profissional.code_owners = ["equipe_pipelines"] br_ms_cnes_profissional.storage = GCS(constants.GCS_FLOWS_BUCKET.value) br_ms_cnes_profissional.run_config = KubernetesRun(image=constants.DOCKER_IMAGE.value) -# br_ms_cnes_profissional.schedule = schedule_br_ms_cnes_profissional +br_ms_cnes_profissional.schedule = schedule_br_ms_cnes_profissional br_ms_cnes_estabelecimento = deepcopy(flow_datasus) br_ms_cnes_estabelecimento.name = "br_ms_cnes.estabelecimento" @@ -40,28 +40,28 @@ br_ms_cnes_estabelecimento.run_config = KubernetesRun( image=constants.DOCKER_IMAGE.value ) -# br_ms_cnes_estabelecimento.schedule = schedule_br_ms_cnes_estabelecimento +br_ms_cnes_estabelecimento.schedule = schedule_br_ms_cnes_estabelecimento br_ms_cnes_leito = deepcopy(flow_datasus) br_ms_cnes_leito.name = "br_ms_cnes.leito" br_ms_cnes_leito.code_owners = ["equipe_pipelines"] br_ms_cnes_leito.storage = GCS(constants.GCS_FLOWS_BUCKET.value) br_ms_cnes_leito.run_config = KubernetesRun(image=constants.DOCKER_IMAGE.value) -# br_ms_cnes_leito.schedule = schedule_br_ms_cnes_leito +br_ms_cnes_leito.schedule = schedule_br_ms_cnes_leito br_ms_cnes_equipamento = deepcopy(flow_datasus) br_ms_cnes_equipamento.name = "br_ms_cnes.equipamento" br_ms_cnes_equipamento.code_owners = ["equipe_pipelines"] br_ms_cnes_equipamento.storage = GCS(constants.GCS_FLOWS_BUCKET.value) br_ms_cnes_equipamento.run_config = KubernetesRun(image=constants.DOCKER_IMAGE.value) -# br_ms_cnes_equipamento.schedule = schedule_br_ms_cnes_equipamento +br_ms_cnes_equipamento.schedule = schedule_br_ms_cnes_equipamento br_ms_cnes_equipe = deepcopy(flow_datasus) br_ms_cnes_equipe.name = "br_ms_cnes.equipe" br_ms_cnes_equipe.code_owners = ["equipe_pipelines"] br_ms_cnes_equipe.storage = GCS(constants.GCS_FLOWS_BUCKET.value) br_ms_cnes_equipe.run_config = KubernetesRun(image=constants.DOCKER_IMAGE.value) -# br_ms_cnes_equipe.schedule = schedule_br_ms_cnes_equipe +br_ms_cnes_equipe.schedule = schedule_br_ms_cnes_equipe br_ms_cnes_dados_complementares = deepcopy(flow_datasus) @@ -71,7 +71,7 @@ br_ms_cnes_dados_complementares.run_config = KubernetesRun( image=constants.DOCKER_IMAGE.value ) -# br_ms_cnes_dados_complementares.schedule = schedule_br_ms_cnes_dados_complementares +br_ms_cnes_dados_complementares.schedule = schedule_br_ms_cnes_dados_complementares br_ms_cnes_servico_especializado = deepcopy(flow_datasus) @@ -81,28 +81,28 @@ br_ms_cnes_servico_especializado.run_config = KubernetesRun( image=constants.DOCKER_IMAGE.value ) -# br_ms_cnes_servico_especializado.schedule = schedule_br_ms_cnes_servico_especializado +br_ms_cnes_servico_especializado.schedule = schedule_br_ms_cnes_servico_especializado br_ms_cnes_habilitacao = deepcopy(flow_datasus) br_ms_cnes_habilitacao.name = "br_ms_cnes.habilitacao" br_ms_cnes_habilitacao.code_owners = ["equipe_pipelines"] br_ms_cnes_habilitacao.storage = GCS(constants.GCS_FLOWS_BUCKET.value) br_ms_cnes_habilitacao.run_config = KubernetesRun(image=constants.DOCKER_IMAGE.value) -# br_ms_cnes_habilitacao.schedule = schedule_br_ms_cnes_habilitacao +br_ms_cnes_habilitacao.schedule = schedule_br_ms_cnes_habilitacao br_ms_cnes_gestao_metas = deepcopy(flow_datasus) br_ms_cnes_gestao_metas.name = "br_ms_cnes.gestao_metas" br_ms_cnes_gestao_metas.code_owners = ["equipe_pipelines"] br_ms_cnes_gestao_metas.storage = GCS(constants.GCS_FLOWS_BUCKET.value) br_ms_cnes_gestao_metas.run_config = KubernetesRun(image=constants.DOCKER_IMAGE.value) -# br_ms_cnes_gestao_metas.schedule = schedule_br_ms_cnes_gestao_metas +br_ms_cnes_gestao_metas.schedule = schedule_br_ms_cnes_gestao_metas br_ms_cnes_incentivos = deepcopy(flow_datasus) br_ms_cnes_incentivos.name = "br_ms_cnes.incentivos" br_ms_cnes_incentivos.code_owners = ["equipe_pipelines"] br_ms_cnes_incentivos.storage = GCS(constants.GCS_FLOWS_BUCKET.value) br_ms_cnes_incentivos.run_config = KubernetesRun(image=constants.DOCKER_IMAGE.value) -# br_ms_cnes_incentivos.schedule = schedule_br_ms_cnes_incentivos +br_ms_cnes_incentivos.schedule = schedule_br_ms_cnes_incentivos br_ms_cnes_estabelecimento_ensino = deepcopy(flow_datasus) br_ms_cnes_estabelecimento_ensino.name = "br_ms_cnes.estabelecimento_ensino" @@ -111,7 +111,7 @@ br_ms_cnes_estabelecimento_ensino.run_config = KubernetesRun( image=constants.DOCKER_IMAGE.value ) -# br_ms_cnes_estabelecimento_ensino.schedule = schedule_br_ms_cnes_estabelecimento_ensino +br_ms_cnes_estabelecimento_ensino.schedule = schedule_br_ms_cnes_estabelecimento_ensino br_ms_cnes_estabelecimento_filantropico = deepcopy(flow_datasus) br_ms_cnes_estabelecimento_filantropico.name = "br_ms_cnes.estabelecimento_filantropico" @@ -120,4 +120,4 @@ br_ms_cnes_estabelecimento_filantropico.run_config = KubernetesRun( image=constants.DOCKER_IMAGE.value ) -# br_ms_cnes_estabelecimento_filantropico.schedule = schedule_br_ms_cnes_estabelecimento_filantropico +br_ms_cnes_estabelecimento_filantropico.schedule = schedule_br_ms_cnes_estabelecimento_filantropico diff --git a/pipelines/datasets/br_ms_cnes/schedules.py b/pipelines/datasets/br_ms_cnes/schedules.py index ae234d1ae..4e1fc629e 100644 --- a/pipelines/datasets/br_ms_cnes/schedules.py +++ b/pipelines/datasets/br_ms_cnes/schedules.py @@ -14,7 +14,7 @@ clocks=[ CronClock( cron="0 9 * * *", # every day at 9:00 - start_date=datetime(2023, 9, 1, 0, 0), + start_date=datetime(2024, 1, 1, 0, 0), labels=[ constants.BASEDOSDADOS_PROD_AGENT_LABEL.value, ], @@ -24,7 +24,7 @@ "materialization_mode": "prod", "materialize_after_dump": True, "update_metadata": True, - "dbt_alias": False, + "dbt_alias": True, }, ) ], @@ -37,7 +37,7 @@ clocks=[ CronClock( cron="30 6 * * *", # every day at 18:30 - start_date=datetime(2023, 9, 1, 0, 0), + start_date=datetime(2024, 1, 1, 0, 0), labels=[ constants.BASEDOSDADOS_PROD_AGENT_LABEL.value, ], @@ -47,7 +47,7 @@ "materialization_mode": "prod", "materialize_after_dump": True, "update_metadata": True, - "dbt_alias": False, + "dbt_alias": True, }, ) ], @@ -60,7 +60,7 @@ clocks=[ CronClock( cron="30 9 * * *", # every day 9:30 - start_date=datetime(2023, 9, 1, 0, 0), + start_date=datetime(2024, 1, 1, 0, 0), labels=[ constants.BASEDOSDADOS_PROD_AGENT_LABEL.value, ], @@ -70,7 +70,7 @@ "materialization_mode": "prod", "materialize_after_dump": True, "update_metadata": True, - "dbt_alias": False, + "dbt_alias": True, }, ) ], @@ -82,7 +82,7 @@ clocks=[ CronClock( cron="0 10 * * *", # every day at 10:00 - start_date=datetime(2023, 9, 1, 0, 0), + start_date=datetime(2024, 1, 1, 0, 0), labels=[ constants.BASEDOSDADOS_PROD_AGENT_LABEL.value, ], @@ -92,7 +92,7 @@ "materialization_mode": "prod", "materialize_after_dump": True, "update_metadata": True, - "dbt_alias": False, + "dbt_alias": True, }, ) ], @@ -104,7 +104,7 @@ clocks=[ CronClock( cron="30 10 * * *", # every day at 10:30 - start_date=datetime(2023, 9, 1, 0, 0), + start_date=datetime(2024, 1, 1, 0, 0), labels=[ constants.BASEDOSDADOS_PROD_AGENT_LABEL.value, ], @@ -114,7 +114,7 @@ "materialization_mode": "prod", "materialize_after_dump": True, "update_metadata": True, - "dbt_alias": False, + "dbt_alias": True, }, ) ], @@ -126,7 +126,7 @@ clocks=[ CronClock( cron="45 10 * * *", # every day at 10:45 - start_date=datetime(2023, 9, 1, 0, 0), + start_date=datetime(2024, 1, 1, 0, 0), labels=[ constants.BASEDOSDADOS_PROD_AGENT_LABEL.value, ], @@ -136,7 +136,7 @@ "materialization_mode": "prod", "materialize_after_dump": True, "update_metadata": True, - "dbt_alias": False, + "dbt_alias": True, }, ) ], @@ -148,7 +148,7 @@ clocks=[ CronClock( cron="0 11 * * *", # every day 11:00 - start_date=datetime(2023, 9, 1, 0, 0), + start_date=datetime(2024, 1, 1, 0, 0), labels=[ constants.BASEDOSDADOS_PROD_AGENT_LABEL.value, ], @@ -158,7 +158,7 @@ "materialization_mode": "prod", "materialize_after_dump": True, "update_metadata": True, - "dbt_alias": False, + "dbt_alias": True, }, ) ], @@ -170,7 +170,7 @@ clocks=[ CronClock( cron="15 11 * * *", # every day at 11:15 - start_date=datetime(2023, 9, 1, 0, 0), + start_date=datetime(2024, 1, 1, 0, 0), labels=[ constants.BASEDOSDADOS_PROD_AGENT_LABEL.value, ], @@ -180,7 +180,7 @@ "materialization_mode": "prod", "materialize_after_dump": True, "update_metadata": True, - "dbt_alias": False, + "dbt_alias": True, }, ) ], @@ -191,7 +191,7 @@ clocks=[ CronClock( cron="30 11 * * *", # every day at 11:30 - start_date=datetime(2023, 9, 1, 0, 0), + start_date=datetime(2024, 1, 1, 0, 0), labels=[ constants.BASEDOSDADOS_PROD_AGENT_LABEL.value, ], @@ -201,7 +201,7 @@ "materialization_mode": "prod", "materialize_after_dump": True, "update_metadata": True, - "dbt_alias": False, + "dbt_alias": True, }, ) ], @@ -214,7 +214,7 @@ clocks=[ CronClock( cron="45 11 * * *", # every day at 11:45 - start_date=datetime(2023, 9, 1, 0, 0), + start_date=datetime(2024, 1, 1, 0, 0), labels=[ constants.BASEDOSDADOS_PROD_AGENT_LABEL.value, ], @@ -224,7 +224,7 @@ "materialization_mode": "prod", "materialize_after_dump": True, "update_metadata": True, - "dbt_alias": False, + "dbt_alias": True, }, ) ], @@ -236,7 +236,7 @@ clocks=[ CronClock( cron="45 11 * * *", # every day at 11:45 - start_date=datetime(2023, 9, 1, 0, 0), + start_date=datetime(2024, 1, 1, 0, 0), labels=[ constants.BASEDOSDADOS_PROD_AGENT_LABEL.value, ], @@ -246,7 +246,7 @@ "materialization_mode": "prod", "materialize_after_dump": True, "update_metadata": True, - "dbt_alias": False, + "dbt_alias": True, }, ) ], @@ -258,7 +258,7 @@ clocks=[ CronClock( cron="0 12 * * *", # every day at 12:00 - start_date=datetime(2023, 9, 1, 0, 0), + start_date=datetime(2024, 1, 1, 0, 0), labels=[ constants.BASEDOSDADOS_PROD_AGENT_LABEL.value, ], @@ -268,7 +268,7 @@ "materialization_mode": "prod", "materialize_after_dump": True, "update_metadata": True, - "dbt_alias": False, + "dbt_alias": True, }, ) ], @@ -281,7 +281,7 @@ clocks=[ CronClock( cron="30 12 * * *", # every day at 12:30 - start_date=datetime(2023, 9, 1, 0, 0), + start_date=datetime(2024, 1, 1, 0, 0), labels=[ constants.BASEDOSDADOS_PROD_AGENT_LABEL.value, ], @@ -291,7 +291,7 @@ "materialization_mode": "prod", "materialize_after_dump": True, "update_metadata": True, - "dbt_alias": False, + "dbt_alias": True, }, ) ], diff --git a/pipelines/utils/crawler_datasus/constants.py b/pipelines/utils/crawler_datasus/constants.py index 66c340ef2..a099a1ba3 100644 --- a/pipelines/utils/crawler_datasus/constants.py +++ b/pipelines/utils/crawler_datasus/constants.py @@ -39,6 +39,7 @@ class constants(Enum): # pylint: disable=c0103 "servico_especializado": "SR", } + COLUMNS_TO_KEEP = { # equipamento "EP": [ diff --git a/pipelines/utils/crawler_datasus/tasks.py b/pipelines/utils/crawler_datasus/tasks.py index e6d333a4f..94051e759 100644 --- a/pipelines/utils/crawler_datasus/tasks.py +++ b/pipelines/utils/crawler_datasus/tasks.py @@ -44,23 +44,20 @@ def check_files_to_parse( dataset_id: str, table_id: str, ) -> list[str]: - log(f"extracting last date from api for {dataset_id}.{table_id}") + log(f"------- Extracting last date from api for {dataset_id}.{table_id}") # 1. extrair data mais atual da api last_date = get_api_most_recent_date( dataset_id=dataset_id, table_id=table_id, date_format="%Y-%m", ) - log("building next year/month to parse") - # 2. adicionar mais um no mes ou transformar pra 1 se for 12 - # para ver se o mês seguinte já está disponível no FTP - # eg. last_date = 2023-04-01 + + log("------- Building next year/month to parse") + year = str(last_date.year) month = last_date.month - year = "2023" - month = 11 if month <= 11: month = month + 1 @@ -68,7 +65,7 @@ def check_files_to_parse( month = 1 year = int(year) + 1 year = str(year) - # 3. buildar no formato do ftp YYMM + year = year[2:4] if month <= 9: @@ -77,10 +74,9 @@ def check_files_to_parse( month = str(month) year_month_to_parse = year + month - log(f"year_month_to_parse (YYMM) is {year_month_to_parse}") - # 4. ver se o arquivo existe + log(f"------- The year_month_to_parse (YYMM) is {year_month_to_parse}") - # 5. converter para dabase que se deseja usar + #Convert datasus database names to Basedosdados database names datasus_database = datasus_constants.DATASUS_DATABASE.value[dataset_id] datasus_database_table = datasus_constants.DATASUS_DATABASE_TABLE.value[table_id] @@ -91,7 +87,7 @@ def check_files_to_parse( list_files = [file for file in available_dbs if file[-8:-4] == year_month_to_parse] # list_files = [file for file in available_dbs if file[-10:-8] == 'SP' and file[-8:-6] in ['22', '23']] - log(f"The following files were selected fom DATASUS FTP: {list_files}") + log(f"------- The following files were selected fom DATASUS FTP: {list_files}") return available_dbs @@ -103,16 +99,17 @@ def check_files_to_parse( def access_ftp_download_files_async( file_list: list, dataset_id: str, table_id: str, max_parallel: int = 10, chunk_size: int = 20 ) -> list[str]: - """This function receives a list of files and - downloads them from DATASUS FTP server asynchronously. + """This task access Datasus FTP server and download a list of files asynchronously Args: - file_list (list): a file list extracted with the function choose_latest_cnes_dbc_files - dataset_id (str): identifier for the dataset - table_id (str): identifier for the table + file_list (list): datasus FTP file list + dataset_id (str): Basedosdados dataset id + table_id (str): Basedosdados table id + max_parallel (int, optional): Max concurrent downloads. Defaults to 10. + chunk_size (int, optional): Sequentially define max concurrent downloads. Defaults to 20. Returns: - list[str]: a list with the downloaded files' paths + list[str]: Path to downloaded files """ input_path = os.path.join("/tmp", dataset_id, "input", table_id) @@ -157,7 +154,7 @@ def decompress_dbc(file_list: list, dataset_id: str) -> None: log_stderr=True, ) - # Define a ShellTask to clone the blast-dbf repository + # ShellTask to clone the blast-dbf repository clone_repo_task = ShellTask( name="Clone blast-dbf Repository", command=f"git clone https://github.com/eaglebh/blast-dbf /tmp/{dataset_id}/blast-dbf", @@ -165,7 +162,7 @@ def decompress_dbc(file_list: list, dataset_id: str) -> None: log_stderr=True, ) - # Define a ShellTask to build the blast-dbf repository + # ShellTask to build the blast-dbf repository compile_blast_dbf = ShellTask( name="Build blast-dbf", command=f"cd /tmp/{dataset_id}/blast-dbf && make", @@ -272,7 +269,6 @@ def pre_process_files(file_list: list, dataset_id: str, table_id: str) -> str: for file in tqdm(file_list): log(f"-------- wrangling {file.split('/')[-1]} and saving to parquet") - # Initialize an empty DataFrame to store concatenated results concatenated_df = pd.DataFrame() for chunk_df in pd.read_csv( @@ -290,8 +286,6 @@ def pre_process_files(file_list: list, dataset_id: str, table_id: str) -> str: log("Post-processing complete") - #parquet_files = [file.replace(".csv", ".parquet") for file in file_list] - path_parts = file.split("/")[:5] output_path = os.path.join("/", *path_parts) diff --git a/pipelines/utils/crawler_datasus/utils.py b/pipelines/utils/crawler_datasus/utils.py index ea771fb68..34828e79b 100644 --- a/pipelines/utils/crawler_datasus/utils.py +++ b/pipelines/utils/crawler_datasus/utils.py @@ -18,7 +18,7 @@ def list_all_cnes_dbc_files( datasus_database: str, datasus_database_table: str = None, ) -> list: - # todo: insert fcodeco link reference + """ Enters FTP server and lists all DBCs files found for a a given datasus_database. @@ -44,7 +44,7 @@ def list_all_cnes_dbc_files( return available_dbs async def download_chunks(files: List[str], output_dir: str, chunk_size: int, max_parallel: int): - """This function is used to sequentially control the number of concurrent downloads + """This function is used to sequentially control the number of concurrent downloads to avoid #OSError: [Errno 24] Too many open files Args: @@ -59,7 +59,15 @@ async def download_chunks(files: List[str], output_dir: str, chunk_size: int, ma await download_files(files=chunk, output_dir=output_dir, max_parallel=max_parallel) -async def download_files(files: list, output_dir: str, max_parallel: int): +async def download_files(files: list, output_dir: str, max_parallel: int)-> None: + """Download files asynchronously and save them in the given output directory + + Args: + files (list): List of files to download + output_dir (str): output directory + max_parallel (int): number of max parallel downloads + """ + semaphore = asyncio.Semaphore(max_parallel) async with semaphore: tasks = [ @@ -69,13 +77,22 @@ async def download_files(files: list, output_dir: str, max_parallel: int): await asyncio.gather(*tasks) -async def download_file(file: str, output_path: str): +async def download_file(file: str, output_path: str)-> None: + """Create connection with DATASUS FTP server using AIOFTP which supports + Asynchronous download within FTP servers + + Args: + file (str): A file path to download + output_path (str): output path to save + """ + + try: log(f"------- Downloading {file} ") async with aioftp.Client.context( host="ftp.datasus.gov.br", parse_list_line_custom=line_file_parser, - # max wait time for data to be received from the server, if it fails trigger a + # max wait time for data to be received from the server socket_timeout=30, ) as client: await client.download(file, output_path) @@ -86,11 +103,8 @@ async def download_file(file: str, output_path: str): def line_file_parser(file_line)-> Tuple[List, Dict]: """This function is used to parse the file line from the FTP server - Args: - file_line (_type_): - Returns: - _type_: + Tupple: A tuple containing a list and a dictionary """ line = file_line.decode("utf-8") @@ -138,8 +152,7 @@ def year_month_sigla_uf_parser(file: str) -> str: def pre_cleaning_to_utf8(df: pd.DataFrame): - """This function is used to pre-clean the data to convert its encoding - from latin1 to utf-8 + """This function is used to remove latin1 characters Args: df (pd.Dataframe): a df @@ -213,6 +226,8 @@ def if_column_exist_delete(df: pd.DataFrame, col_list: str): def post_process_estabelecimento(df: pd.DataFrame) -> pd.DataFrame: + + list_columns_to_delete = [ "AP01CV07", "AP02CV07", @@ -231,21 +246,54 @@ def post_process_estabelecimento(df: pd.DataFrame) -> pd.DataFrame: def post_process_profissional(df: pd.DataFrame) -> pd.DataFrame: + """Apply custom post-process to the profissional table + + Args: + df (pd.DataFrame): a pd.DataFrame + + Returns: + pd.DataFrame: a pd.DataFrame + """ + df = df[datasus_constants.COLUMNS_TO_KEEP.value["PF"]] return df def post_process_leito(df: pd.DataFrame) -> pd.DataFrame: + """Apply custom post-process to the leito table + + Args: + df (pd.DataFrame): a pd.DataFrame + + Returns: + pd.DataFrame: a pd.DataFrame + """ df = df[datasus_constants.COLUMNS_TO_KEEP.value["LT"]] return df def post_process_equipamento(df: pd.DataFrame) -> pd.DataFrame: + """Apply custom post-process to the equipamento table + + Args: + df (pd.DataFrame): a pd.DataFrame + + Returns: + pd.DataFrame: a pd.DataFrame + """ df = df[datasus_constants.COLUMNS_TO_KEEP.value["EP"]] return df def post_process_equipe(df: pd.DataFrame) -> pd.DataFrame: + """Apply custom post-process to the equipe table + + Args: + df (pd.DataFrame): a pd.DataFrame + + Returns: + pd.DataFrame: a pd.DataFrame + """ standardize_colums = { "IDEQUIPE": "ID_EQUIPE", "AREA_EQP": "ID_AREA", @@ -259,42 +307,106 @@ def post_process_equipe(df: pd.DataFrame) -> pd.DataFrame: def post_process_estabelecimento_ensino(df: pd.DataFrame) -> pd.DataFrame: + """Apply custom post-process to the estabelecimento_ensino table + + Args: + df (pd.DataFrame): a pd.DataFrame + + Returns: + pd.DataFrame: a pd.DataFrame + """ df = df[datasus_constants.COLUMNS_TO_KEEP.value["EE"]] return df def post_process_dados_complementares(df: pd.DataFrame) -> pd.DataFrame: + """Apply custom post-process to the dados_complementares table + + Args: + df (pd.DataFrame): a pd.DataFrame + + Returns: + pd.DataFrame: a pd.DataFrame + """ df = df[datasus_constants.COLUMNS_TO_KEEP.value["DC"]] return df def post_process_estabelecimento_filantropico(df: pd.DataFrame) -> pd.DataFrame: + """Apply custom post-process to the estabelecimento_filantropico table + + Args: + df (pd.DataFrame): a pd.DataFrame + + Returns: + pd.DataFrame: a pd.DataFrame + """ df = df[datasus_constants.COLUMNS_TO_KEEP.value["EF"]] return df def post_process_gestao_metas(df: pd.DataFrame) -> pd.DataFrame: + """Apply custom post-process to the gestao_metas table + + Args: + df (pd.DataFrame): a pd.DataFrame + + Returns: + pd.DataFrame: a pd.DataFrame + """ df = df[datasus_constants.COLUMNS_TO_KEEP.value["GM"]] return df def post_process_habilitacao(df: pd.DataFrame) -> pd.DataFrame: + """Apply custom post-process to the habilitacao table + + Args: + df (pd.DataFrame): a pd.DataFrame + + Returns: + pd.DataFrame: a pd.DataFrame + """ df = check_and_create_column(df=df, col_name="NAT_JUR") df = df[datasus_constants.COLUMNS_TO_KEEP.value["HB"]] return df def post_process_incentivos(df: pd.DataFrame) -> pd.DataFrame: + """Apply custom post-process to the incentivos table + + Args: + df (pd.DataFrame): a pd.DataFrame + + Returns: + pd.DataFrame: a pd.DataFrame + """ df = df[datasus_constants.COLUMNS_TO_KEEP.value["IN"]] return df def post_process_regra_contratual(df: pd.DataFrame) -> pd.DataFrame: + """Apply custom post-process to the regra_contratual table + + Args: + df (pd.DataFrame): a pd.DataFrame + + Returns: + pd.DataFrame: a pd.DataFrame + """ df = df[datasus_constants.COLUMNS_TO_KEEP.value["RC"]] return df def post_process_servico_especializado(df: pd.DataFrame) -> pd.DataFrame: + """Apply custom post-process to the servico_especializado table + + Args: + df (pd.DataFrame): a pd.DataFrame + + Returns: + pd.DataFrame: a pd.DataFrame + """ df = df[datasus_constants.COLUMNS_TO_KEEP.value["SR"]] return df From 30f84acb4e5576da42c54a04f6e5c9ab2eb097b9 Mon Sep 17 00:00:00 2001 From: folhesgabriel Date: Mon, 19 Feb 2024 12:03:26 -0300 Subject: [PATCH 37/44] fix: check_files_to_parse return task --- pipelines/utils/crawler_datasus/tasks.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipelines/utils/crawler_datasus/tasks.py b/pipelines/utils/crawler_datasus/tasks.py index 94051e759..ff6ce90d5 100644 --- a/pipelines/utils/crawler_datasus/tasks.py +++ b/pipelines/utils/crawler_datasus/tasks.py @@ -89,7 +89,7 @@ def check_files_to_parse( log(f"------- The following files were selected fom DATASUS FTP: {list_files}") - return available_dbs + return list_files @task( From c3d52872f037925e23f39a176f5db3ab5e52f33a Mon Sep 17 00:00:00 2001 From: folhesgabriel Date: Wed, 28 Feb 2024 15:47:50 -0300 Subject: [PATCH 38/44] feat: add sia flow --- pipelines/datasets/br_ms_sia/flows.py | 23 ++++ pipelines/datasets/br_ms_sia/schedules.py | 33 ++++++ pipelines/utils/crawler_datasus/constants.py | 4 + pipelines/utils/crawler_datasus/flows.py | 113 ++++++++++++++++++- pipelines/utils/crawler_datasus/tasks.py | 65 ++++++++--- pipelines/utils/crawler_datasus/utils.py | 109 ++++++++++++++++-- 6 files changed, 319 insertions(+), 28 deletions(-) create mode 100644 pipelines/datasets/br_ms_sia/flows.py create mode 100644 pipelines/datasets/br_ms_sia/schedules.py diff --git a/pipelines/datasets/br_ms_sia/flows.py b/pipelines/datasets/br_ms_sia/flows.py new file mode 100644 index 000000000..51f2e8bc9 --- /dev/null +++ b/pipelines/datasets/br_ms_sia/flows.py @@ -0,0 +1,23 @@ +# -*- coding: utf-8 -*- +""" +Flows for br_ms_sia +""" +# pylint: disable=C0103, E1123, invalid-name + +from copy import deepcopy + +from prefect.run_configs import KubernetesRun +from prefect.storage import GCS + +from pipelines.utils.crawler_datasus.flows import flow_sia +from pipelines.constants import constants +from pipelines.datasets.br_ms_sia.schedules import ( + schedule_br_ms_sia_producao_ambulatorial, +) + +br_ms_sia_producao_ambulatorial = deepcopy(flow_sia) +br_ms_sia_producao_ambulatorial.name = "br_ms_sia.producao_ambulatorial" +br_ms_sia_producao_ambulatorial.code_owners = ["Gabriel Pisa"] +br_ms_sia_producao_ambulatorial.storage = GCS(constants.GCS_FLOWS_BUCKET.value) +br_ms_sia_producao_ambulatorial.run_config = KubernetesRun(image=constants.DOCKER_IMAGE.value) +br_ms_sia_producao_ambulatorial.schedule = schedule_br_ms_sia_producao_ambulatorial \ No newline at end of file diff --git a/pipelines/datasets/br_ms_sia/schedules.py b/pipelines/datasets/br_ms_sia/schedules.py new file mode 100644 index 000000000..77021804d --- /dev/null +++ b/pipelines/datasets/br_ms_sia/schedules.py @@ -0,0 +1,33 @@ +# -*- coding: utf-8 -*- +""" +Schedules for br_ms_sia +""" + +from datetime import datetime + +from prefect.schedules import Schedule, adjustments, filters +from prefect.schedules.clocks import CronClock + +from pipelines.constants import constants + +schedule_br_ms_sia_producao_ambulatorial = Schedule( + clocks=[ + CronClock( + cron="0 9 * * *", # every day at 9:00 + start_date=datetime(2024, 1, 1, 0, 0), + labels=[ + constants.BASEDOSDADOS_PROD_AGENT_LABEL.value, + ], + parameter_defaults={ + "dataset_id": "br_ms_sia", + "table_id": "producao_ambulatorial", + "materialization_mode": "prod", + "materialize_after_dump": True, + "update_metadata": True, + "dbt_alias": True, + }, + ) + ], + filters=[filters.is_weekday], + adjustments=[adjustments.next_weekday], +) diff --git a/pipelines/utils/crawler_datasus/constants.py b/pipelines/utils/crawler_datasus/constants.py index a099a1ba3..3e1a8baee 100644 --- a/pipelines/utils/crawler_datasus/constants.py +++ b/pipelines/utils/crawler_datasus/constants.py @@ -21,9 +21,11 @@ class constants(Enum): # pylint: disable=c0103 # to download files from datasus FTP server DATASUS_DATABASE = { "br_ms_cnes": "CNES", + "br_ms_sia": "SIA" } DATASUS_DATABASE_TABLE = { + #CNES "estabelecimento": "ST", "profissional": "PF", "equipamento": "EQ", @@ -37,6 +39,8 @@ class constants(Enum): # pylint: disable=c0103 "incentivos": "IN", "regra_contratual": "RC", "servico_especializado": "SR", + #SIA + "producao_ambulatorial": "PA", } diff --git a/pipelines/utils/crawler_datasus/flows.py b/pipelines/utils/crawler_datasus/flows.py index 44b23aca1..6481ffe15 100644 --- a/pipelines/utils/crawler_datasus/flows.py +++ b/pipelines/utils/crawler_datasus/flows.py @@ -21,6 +21,7 @@ decompress_dbf, is_empty, pre_process_files, + read_dbf_save_parquet_chunks, ) from pipelines.utils.decorators import Flow from pipelines.utils.execute_dbt_model.constants import constants as dump_db_constants @@ -33,7 +34,7 @@ ) from pipelines.utils.to_download.tasks import to_download -with Flow(name="BD Template - DATASUS", code_owners=["Gabriel Pisa"]) as flow_datasus: +with Flow(name="BD Template - DATASUS-CNES", code_owners=["Gabriel Pisa"]) as flow_datasus: # Parameters dataset_id = Parameter("dataset_id", required=True) table_id = Parameter("table_id", required=True) @@ -63,9 +64,9 @@ with case(is_empty(ftp_files), False): dbc_files = access_ftp_download_files_async( - file_list=ftp_files, - dataset_id=dataset_id, - table_id=table_id, + file_list=ftp_files, + dataset_id=dataset_id, + table_id=table_id, ) dbf_files = decompress_dbc( @@ -139,3 +140,107 @@ flow_datasus.storage = GCS(constants.GCS_FLOWS_BUCKET.value) flow_datasus.run_config = KubernetesRun(image=constants.DOCKER_IMAGE.value) + + + + +with Flow(name="BD Template - DATASUS-SIA", code_owners=["Gabriel Pisa"]) as flow_sia: + # Parameters + dataset_id = Parameter("dataset_id", required=True) + table_id = Parameter("table_id", required=True) + update_metadata = Parameter("update_metadata", default=False, required=False) + materialization_mode = Parameter( + "materialization_mode", default="dev", required=False + ) + materialize_after_dump = Parameter( + "materialize_after_dump", default=True, required=False + ) + dbt_alias = Parameter("dbt_alias", default=False, required=False) + + rename_flow_run = rename_current_flow_run_dataset_table( + prefix="Dump: ", dataset_id=dataset_id, table_id=table_id, wait=table_id + ) + + ftp_files = check_files_to_parse( + dataset_id=dataset_id, + table_id=table_id, + ) + + with case(is_empty(ftp_files), True): + log_task( + "Os dados do FTP CNES-ST ainda não foram atualizados para o ano/mes mais recente" + ) + + with case(is_empty(ftp_files), False): + + dbc_files = access_ftp_download_files_async( + file_list=ftp_files, + dataset_id=dataset_id, + table_id=table_id, + ) + + dbf_files = decompress_dbc( + file_list=dbc_files, dataset_id=dataset_id, upstream_tasks=[dbc_files] + ) + + + files_path = read_dbf_save_parquet_chunks( + file_list=dbc_files, + table_id=table_id, + upstream_tasks=[dbc_files,dbf_files], + ) + + wait_upload_table = create_table_and_upload_to_gcs( + data_path=files_path, + dataset_id=dataset_id, + table_id=table_id, + dump_mode="append", + wait=files_path, + ) + + # estabelecimento + with case(materialize_after_dump, True): + # Trigger DBT flow run + current_flow_labels = get_current_flow_labels() + materialization_flow = create_flow_run( + flow_name=utils_constants.FLOW_EXECUTE_DBT_MODEL_NAME.value, + project_name=constants.PREFECT_DEFAULT_PROJECT.value, + parameters={ + "dataset_id": dataset_id, + "table_id": table_id, + "mode": materialization_mode, + "dbt_alias": dbt_alias, + }, + labels=current_flow_labels, + run_name=f"Materialize {dataset_id}.{table_id}", + ) + + wait_for_materialization = wait_for_flow_run( + materialization_flow, + stream_states=True, + stream_logs=True, + raise_final_state=True, + ) + wait_for_materialization.max_retries = ( + dump_db_constants.WAIT_FOR_MATERIALIZATION_RETRY_ATTEMPTS.value + ) + wait_for_materialization.retry_delay = timedelta( + seconds=dump_db_constants.WAIT_FOR_MATERIALIZATION_RETRY_INTERVAL.value + ) + + with case(update_metadata, True): + update_django_metadata( + dataset_id=dataset_id, + table_id=table_id, + date_column_name={"year": "ano", "month": "mes"}, + date_format="%Y-%m", + coverage_type="part_bdpro", + time_delta={"months": 6}, + prefect_mode=materialization_mode, + bq_project="basedosdados", + upstream_tasks=[wait_for_materialization], + ) + + +flow_datasus.storage = GCS(constants.GCS_FLOWS_BUCKET.value) +flow_datasus.run_config = KubernetesRun(image=constants.DOCKER_IMAGE.value) diff --git a/pipelines/utils/crawler_datasus/tasks.py b/pipelines/utils/crawler_datasus/tasks.py index ff6ce90d5..01211269a 100644 --- a/pipelines/utils/crawler_datasus/tasks.py +++ b/pipelines/utils/crawler_datasus/tasks.py @@ -19,7 +19,9 @@ from pipelines.utils.crawler_datasus.constants import constants as datasus_constants from pipelines.utils.crawler_datasus.utils import ( download_chunks, - list_all_cnes_dbc_files, + list_datasus_dbc_files, + year_month_sigla_uf_parser, + dbf_to_parquet, post_process_dados_complementares, post_process_equipamento, post_process_equipe, @@ -33,12 +35,13 @@ post_process_profissional, post_process_regra_contratual, post_process_servico_especializado, - year_month_sigla_uf_parser, + ) from pipelines.utils.metadata.utils import get_api_most_recent_date from pipelines.utils.utils import log + @task def check_files_to_parse( dataset_id: str, @@ -80,12 +83,12 @@ def check_files_to_parse( datasus_database = datasus_constants.DATASUS_DATABASE.value[dataset_id] datasus_database_table = datasus_constants.DATASUS_DATABASE_TABLE.value[table_id] - available_dbs = list_all_cnes_dbc_files( + available_dbs = list_datasus_dbc_files( datasus_database=datasus_database, datasus_database_table=datasus_database_table ) + log(year_month_to_parse) + list_files = [file for file in available_dbs if file.split('/')[-1][4:8] == year_month_to_parse] - list_files = [file for file in available_dbs if file[-8:-4] == year_month_to_parse] - # list_files = [file for file in available_dbs if file[-10:-8] == 'SP' and file[-8:-6] in ['22', '23']] log(f"------- The following files were selected fom DATASUS FTP: {list_files}") @@ -134,7 +137,7 @@ def access_ftp_download_files_async( os.path.join( input_path, year_month_sigla_uf_parser(file=file), file.split("/")[-1] ) - for file in file_list + for file in tqdm(file_list) ] return dbc_files_path_list @@ -176,7 +179,7 @@ def decompress_dbc(file_list: list, dataset_id: str) -> None: log("------ Compiling blast-dbf repository") compile_blast_dbf.run() - for file in file_list: + for file in tqdm(file_list): # Check if the file has a .dbc extension if file.endswith(".dbc"): # Execute blast-dbf on the file @@ -186,16 +189,18 @@ def decompress_dbc(file_list: list, dataset_id: str) -> None: return_all=True, log_stderr=True, ) - log(f"Decompressing {file.split('/')[-1]} file") + log(f"------ Decompressing {file.split('/')[-1]} file") decompress_task.run() + log(f"------ Removing {file.split('/')[-1]} file") + os.system(f"rm -f {file}") + else: - print(f"Skipping non-DBC file: {file}") + log(f"Skipping non-DBC file: {file}") log("------ Removing dbc files") - for file in file_list: - if file.endswith(".dbc"): - os.system(f"rm -f {file}") + + @task @@ -227,15 +232,18 @@ def decompress_dbf(file_list: list, table_id: str) -> str: dbf.to_csv(output_file) csv_file_list.append(output_file) - log("------ Removing dbf files") - - for file in dbf_file_list: if file.endswith(".dbf"): + file = file.replace("output", "input") + log(f"------ Removing {file.split('/')[-1]}") os.system(f"rm -f {file}") return csv_file_list + + + + @task def pre_process_files(file_list: list, dataset_id: str, table_id: str) -> str: @@ -261,7 +269,7 @@ def pre_process_files(file_list: list, dataset_id: str, table_id: str) -> str: try: post_process_function = post_process_functions.get(table_id) - except Exception as e: + except: #Exception as e: log( f"The error {e} occurred. It probably indicates that no post-processing function was found for table_id: {table_id}" ) @@ -278,7 +286,7 @@ def pre_process_files(file_list: list, dataset_id: str, table_id: str) -> str: processed_df = post_process_function(concatenated_df) - + processed_df = processed_df.astype(str) output_path = file.replace(".csv", ".parquet") processed_df.to_parquet(output_path, index=None, compression='gzip') @@ -292,9 +300,32 @@ def pre_process_files(file_list: list, dataset_id: str, table_id: str) -> str: return output_path + + @task def is_empty(lista): if len(lista) == 0: return True else: return False + + + + +@task +def read_dbf_save_parquet_chunks(file_list: list, table_id: str) -> str: + """ + Convert dbc to csv + """ + log(f"--------- Decompressing {table_id} .DBF files") + + + dbf_file_list = [file.replace(".dbc", ".dbf") for file in file_list] + + for file in tqdm(dbf_file_list): + + # replace .csv with .dbf + log(f"-------- Reading {file}") + result_path = dbf_to_parquet(dbf=file) + + return f'tmp/br_ms_sia/output/{table_id}' diff --git a/pipelines/utils/crawler_datasus/utils.py b/pipelines/utils/crawler_datasus/utils.py index 34828e79b..e3eb8122d 100644 --- a/pipelines/utils/crawler_datasus/utils.py +++ b/pipelines/utils/crawler_datasus/utils.py @@ -6,15 +6,95 @@ import asyncio from datetime import datetime from ftplib import FTP - +import pyarrow as pa +from pathlib import Path +import pyarrow.parquet as pq +from dbfread import DBF import aioftp import pandas as pd +import os from typing import List, Dict, Tuple from pipelines.utils.crawler_datasus.constants import constants as datasus_constants from pipelines.utils.utils import log -def list_all_cnes_dbc_files( +#----------------------------- +#Utils to handle dbf and dbf + +def stream_dbf(dbf, chunk_size=400000): + """Fetches records in parquet chunks to preserve memory""" + data = [] + i = 0 + for records in dbf: + data.append(records) + i += 1 + if i == chunk_size: + yield data + data = [] + i = 0 + else: + yield data + +def decode_column(value): + """ + Decodes binary data to str + """ + if isinstance(value, bytes): + return value.decode(encoding="iso-8859-1").replace("\x00", "") + + if isinstance(value, str): + return str(value).replace("\x00", "") + return value + +def dbf_to_parquet(dbf: str) -> str: + """ + Parses DBF file into parquet to preserve memory + """ + + + path = Path(dbf) + if path.suffix.lower() != ".dbf": + raise ValueError(f"Not a DBF file: {path}") + + #TODO: adaptar no flow do cnes para trocar sufixos de arquivos + parquet = path.with_suffix(".parquet") + print(parquet) + approx_final_size = ( + os.path.getsize(path)/1000 + ) # TODO: possibly use it to decide upon number of chunks + print(approx_final_size) + + + #cira diretório de output + dbf = dbf.replace("input", "output") + path_parts = dbf.split("/")[:-1] + output_path = os.path.join("/", *path_parts) + os.makedirs(output_path, exist_ok=True) + + try: + #chunk_size = 30_000 + #chunk_size = 100_000 + for chunk in stream_dbf( + #dbf5 no lugar de DBF + DBF(path, encoding="iso-8859-1", raw=True) + ): + chunk_df = pd.DataFrame(chunk) + #TODO: INSERT SCHEMA FOR CNES TABLES + #NOTE: applymap is deprecated on pandas=2.1 onwards; basedosdados uses 2.0.1 + table = pa.Table.from_pandas(chunk_df.applymap(decode_column)) + #TypeError: __init__() got multiple values for argument 'schema' when set schema + pq.write_to_dataset(table, root_path=str(output_path)) + except struct.error as err: + + Path(path).unlink() + raise err + + + path.unlink() + + return str(parquet) + +def list_datasus_dbc_files( datasus_database: str, datasus_database_table: str = None, ) -> list: @@ -22,6 +102,9 @@ def list_all_cnes_dbc_files( """ Enters FTP server and lists all DBCs files found for a a given datasus_database. + + NOTE: It currently supports CNES and SIA databases groups; + CIHA, SIH, SIM, SINAN, SINASC and PNI are not implemented yet. """ available_dbs = list() ftp = FTP("ftp.datasus.gov.br") @@ -29,7 +112,10 @@ def list_all_cnes_dbc_files( # se datasus_database tiver diferentes URL em virtude de # variados anos de inicio mudar abaixo - cnes_path = ["dissemin/publicos/CNES/200508_/Dados"] + cnes_path = [ + "dissemin/publicos/CNES/200508_/Dados", + "dissemin/publicos/SIASUS/200801_/Dados" + ] for path in cnes_path: try: @@ -37,7 +123,14 @@ def list_all_cnes_dbc_files( if datasus_database == "CNES": if not datasus_database_table: raise ValueError("No group assigned to CNES_group") + print(f"{path}/{datasus_database_table}/*.DBC") available_dbs.extend(ftp.nlst(f"{path}/{datasus_database_table}/*.DBC")) + + if datasus_database == "SIA": + print("SIA database") + if not datasus_database_table: + raise ValueError("No group assigned to SIA_group") + available_dbs.extend(ftp.nlst(f"{path}/{datasus_database_table}*.DBC")) except Exception as e: raise e ftp.close() @@ -134,16 +227,18 @@ def year_month_sigla_uf_parser(file: str) -> str: """ try: # parse file name last 8 digits before .DBC - file = file[-10:-4] + #file = file[-10:-4] + file = file.split('/')[-1] + # parse and build year - year = "20" + file[2:4] + year = "20" + file[4:6] # parse and build month - month = int(file[4:6]) + month = int(file[6:8]) # parse and build state - sigla_uf = file[:2] + sigla_uf = file[2:4] except IndexError: raise ValueError("Unable to parse month and year from file") From 9cf9416ecc5fdf125ed91f826388b6860a61cb77 Mon Sep 17 00:00:00 2001 From: folhesgabriel Date: Wed, 28 Feb 2024 16:30:52 -0300 Subject: [PATCH 39/44] fix: add dependencies --- pipelines/utils/crawler_datasus/utils.py | 1 + poetry.lock | 24 +++++++++++++++++++++++- pyproject.toml | 2 ++ 3 files changed, 26 insertions(+), 1 deletion(-) diff --git a/pipelines/utils/crawler_datasus/utils.py b/pipelines/utils/crawler_datasus/utils.py index e3eb8122d..ddf0529d4 100644 --- a/pipelines/utils/crawler_datasus/utils.py +++ b/pipelines/utils/crawler_datasus/utils.py @@ -10,6 +10,7 @@ from pathlib import Path import pyarrow.parquet as pq from dbfread import DBF +import struct import aioftp import pandas as pd import os diff --git a/poetry.lock b/poetry.lock index 050c53baa..b6c61cba9 100644 --- a/poetry.lock +++ b/poetry.lock @@ -681,6 +681,17 @@ packaging = ">=17.0" pandas = ">=0.24.2" pyarrow = ">=3.0.0" +[[package]] +name = "dbfread" +version = "2.0.7" +description = "Read DBF Files with Python" +optional = false +python-versions = "*" +files = [ + {file = "dbfread-2.0.7-py2.py3-none-any.whl", hash = "sha256:f604def58c59694fa0160d7be5d0b8d594467278d2bb6a47d46daf7162c84cec"}, + {file = "dbfread-2.0.7.tar.gz", hash = "sha256:07c8a9af06ffad3f6f03e8fe91ad7d2733e31a26d2b72c4dd4cfbae07ee3b73d"}, +] + [[package]] name = "dbt-client" version = "0.1.3" @@ -2699,6 +2710,17 @@ toolz = "*" [package.extras] complete = ["blosc", "numpy (>=1.9.0)", "pandas (>=0.19.0)", "pyzmq"] +[[package]] +name = "pathlib" +version = "1.0.1" +description = "Object-oriented filesystem paths" +optional = false +python-versions = "*" +files = [ + {file = "pathlib-1.0.1-py3-none-any.whl", hash = "sha256:f35f95ab8b0f59e6d354090350b44a80a80635d22efdedfa84c7ad1cf0a74147"}, + {file = "pathlib-1.0.1.tar.gz", hash = "sha256:6940718dfc3eff4258203ad5021090933e5c04707d5ca8cc9e73c94a7894ea9f"}, +] + [[package]] name = "pendulum" version = "3.0.0" @@ -4818,4 +4840,4 @@ heapdict = "*" [metadata] lock-version = "2.0" python-versions = ">=3.10,<3.11" -content-hash = "ca2361fadc10ad55e6d7760c2436fe11bdb4e090d5257b16f200db212cefc977" +content-hash = "9dabdbe4673edf09636d5b96e6a43bc72fcd51c34b76aa169223ea9e001327ba" diff --git a/pyproject.toml b/pyproject.toml index f581d817b..d05bb6a3d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -116,6 +116,8 @@ cffi = "^1.16.0" pendulum = "^3.0.0" simpledbf = "^0.2.6" aioftp = "^0.22.3" +pathlib = "^1.0.1" +dbfread = "^2.0.7" [tool.poetry.group.dev] From 75585ee5d5367f6700e586df75863409701c77f0 Mon Sep 17 00:00:00 2001 From: folhesgabriel Date: Wed, 28 Feb 2024 16:51:42 -0300 Subject: [PATCH 40/44] fix: concrete flow names --- pipelines/utils/crawler_datasus/flows.py | 20 ++++++++------------ pipelines/utils/crawler_datasus/utils.py | 2 +- 2 files changed, 9 insertions(+), 13 deletions(-) diff --git a/pipelines/utils/crawler_datasus/flows.py b/pipelines/utils/crawler_datasus/flows.py index 6481ffe15..b5cd42c40 100644 --- a/pipelines/utils/crawler_datasus/flows.py +++ b/pipelines/utils/crawler_datasus/flows.py @@ -32,9 +32,9 @@ log_task, rename_current_flow_run_dataset_table, ) -from pipelines.utils.to_download.tasks import to_download -with Flow(name="BD Template - DATASUS-CNES", code_owners=["Gabriel Pisa"]) as flow_datasus: + +with Flow(name="BD Template - DATASUS-CNES", code_owners=["Gabriel Pisa"]) as flow_cnes: # Parameters dataset_id = Parameter("dataset_id", required=True) table_id = Parameter("table_id", required=True) @@ -58,7 +58,7 @@ with case(is_empty(ftp_files), True): log_task( - "Os dados do FTP CNES-ST ainda não foram atualizados para o ano/mes mais recente" + "Os dados do FTP CNES ainda não foram atualizados para o ano/mes mais recente" ) with case(is_empty(ftp_files), False): @@ -136,10 +136,8 @@ bq_project="basedosdados", upstream_tasks=[wait_for_materialization], ) - - -flow_datasus.storage = GCS(constants.GCS_FLOWS_BUCKET.value) -flow_datasus.run_config = KubernetesRun(image=constants.DOCKER_IMAGE.value) +flow_cnes.storage = GCS(constants.GCS_FLOWS_BUCKET.value) +flow_cnes.run_config = KubernetesRun(image=constants.DOCKER_IMAGE.value) @@ -168,7 +166,7 @@ with case(is_empty(ftp_files), True): log_task( - "Os dados do FTP CNES-ST ainda não foram atualizados para o ano/mes mais recente" + "Os dados do FTP SIA ainda não foram atualizados para o ano/mes mais recente" ) with case(is_empty(ftp_files), False): @@ -240,7 +238,5 @@ bq_project="basedosdados", upstream_tasks=[wait_for_materialization], ) - - -flow_datasus.storage = GCS(constants.GCS_FLOWS_BUCKET.value) -flow_datasus.run_config = KubernetesRun(image=constants.DOCKER_IMAGE.value) +flow_sia.storage = GCS(constants.GCS_FLOWS_BUCKET.value) +flow_sia.run_config = KubernetesRun(image=constants.DOCKER_IMAGE.value) diff --git a/pipelines/utils/crawler_datasus/utils.py b/pipelines/utils/crawler_datasus/utils.py index ddf0529d4..2d4465469 100644 --- a/pipelines/utils/crawler_datasus/utils.py +++ b/pipelines/utils/crawler_datasus/utils.py @@ -21,7 +21,7 @@ #----------------------------- #Utils to handle dbf and dbf - +#https://github.com/AlertaDengue/PySUS/blob/main/pysus/data/__init__.py def stream_dbf(dbf, chunk_size=400000): """Fetches records in parquet chunks to preserve memory""" data = [] From 80a9e4001a975994509130a82b473f5485b87eea Mon Sep 17 00:00:00 2001 From: folhesgabriel Date: Wed, 28 Feb 2024 17:16:24 -0300 Subject: [PATCH 41/44] feat: br_ms_cnes --- pipelines/datasets/br_ms_cnes/flows.py | 38 ++++++++++++++++---------- 1 file changed, 24 insertions(+), 14 deletions(-) diff --git a/pipelines/datasets/br_ms_cnes/flows.py b/pipelines/datasets/br_ms_cnes/flows.py index 60627c4fd..32e08e9d4 100644 --- a/pipelines/datasets/br_ms_cnes/flows.py +++ b/pipelines/datasets/br_ms_cnes/flows.py @@ -9,7 +9,7 @@ from prefect.run_configs import KubernetesRun from prefect.storage import GCS -from pipelines.utils.crawler_datasus.flows import flow_datasus +from pipelines.utils.crawler_datasus.flows import flow_cnes from pipelines.constants import constants from pipelines.datasets.br_ms_cnes.schedules import ( schedule_br_ms_cnes_dados_complementares, @@ -24,16 +24,17 @@ schedule_br_ms_cnes_leito, schedule_br_ms_cnes_profissional, schedule_br_ms_cnes_servico_especializado, + schedule_br_ms_cnes_regra_contratual, ) -br_ms_cnes_profissional = deepcopy(flow_datasus) +br_ms_cnes_profissional = deepcopy(flow_cnes) br_ms_cnes_profissional.name = "br_ms_cnes.profissional" br_ms_cnes_profissional.code_owners = ["equipe_pipelines"] br_ms_cnes_profissional.storage = GCS(constants.GCS_FLOWS_BUCKET.value) br_ms_cnes_profissional.run_config = KubernetesRun(image=constants.DOCKER_IMAGE.value) br_ms_cnes_profissional.schedule = schedule_br_ms_cnes_profissional -br_ms_cnes_estabelecimento = deepcopy(flow_datasus) +br_ms_cnes_estabelecimento = deepcopy(flow_cnes) br_ms_cnes_estabelecimento.name = "br_ms_cnes.estabelecimento" br_ms_cnes_estabelecimento.code_owners = ["equipe_pipelines"] br_ms_cnes_estabelecimento.storage = GCS(constants.GCS_FLOWS_BUCKET.value) @@ -42,21 +43,21 @@ ) br_ms_cnes_estabelecimento.schedule = schedule_br_ms_cnes_estabelecimento -br_ms_cnes_leito = deepcopy(flow_datasus) +br_ms_cnes_leito = deepcopy(flow_cnes) br_ms_cnes_leito.name = "br_ms_cnes.leito" br_ms_cnes_leito.code_owners = ["equipe_pipelines"] br_ms_cnes_leito.storage = GCS(constants.GCS_FLOWS_BUCKET.value) br_ms_cnes_leito.run_config = KubernetesRun(image=constants.DOCKER_IMAGE.value) br_ms_cnes_leito.schedule = schedule_br_ms_cnes_leito -br_ms_cnes_equipamento = deepcopy(flow_datasus) +br_ms_cnes_equipamento = deepcopy(flow_cnes) br_ms_cnes_equipamento.name = "br_ms_cnes.equipamento" br_ms_cnes_equipamento.code_owners = ["equipe_pipelines"] br_ms_cnes_equipamento.storage = GCS(constants.GCS_FLOWS_BUCKET.value) br_ms_cnes_equipamento.run_config = KubernetesRun(image=constants.DOCKER_IMAGE.value) br_ms_cnes_equipamento.schedule = schedule_br_ms_cnes_equipamento -br_ms_cnes_equipe = deepcopy(flow_datasus) +br_ms_cnes_equipe = deepcopy(flow_cnes) br_ms_cnes_equipe.name = "br_ms_cnes.equipe" br_ms_cnes_equipe.code_owners = ["equipe_pipelines"] br_ms_cnes_equipe.storage = GCS(constants.GCS_FLOWS_BUCKET.value) @@ -64,7 +65,7 @@ br_ms_cnes_equipe.schedule = schedule_br_ms_cnes_equipe -br_ms_cnes_dados_complementares = deepcopy(flow_datasus) +br_ms_cnes_dados_complementares = deepcopy(flow_cnes) br_ms_cnes_dados_complementares.name = "br_ms_cnes.dados_complementares" br_ms_cnes_dados_complementares.code_owners = ["equipe_pipelines"] br_ms_cnes_dados_complementares.storage = GCS(constants.GCS_FLOWS_BUCKET.value) @@ -74,7 +75,7 @@ br_ms_cnes_dados_complementares.schedule = schedule_br_ms_cnes_dados_complementares -br_ms_cnes_servico_especializado = deepcopy(flow_datasus) +br_ms_cnes_servico_especializado = deepcopy(flow_cnes) br_ms_cnes_servico_especializado.name = "br_ms_cnes.servico_especializado" br_ms_cnes_servico_especializado.code_owners = ["equipe_pipelines"] br_ms_cnes_servico_especializado.storage = GCS(constants.GCS_FLOWS_BUCKET.value) @@ -83,37 +84,37 @@ ) br_ms_cnes_servico_especializado.schedule = schedule_br_ms_cnes_servico_especializado -br_ms_cnes_habilitacao = deepcopy(flow_datasus) +br_ms_cnes_habilitacao = deepcopy(flow_cnes) br_ms_cnes_habilitacao.name = "br_ms_cnes.habilitacao" br_ms_cnes_habilitacao.code_owners = ["equipe_pipelines"] br_ms_cnes_habilitacao.storage = GCS(constants.GCS_FLOWS_BUCKET.value) br_ms_cnes_habilitacao.run_config = KubernetesRun(image=constants.DOCKER_IMAGE.value) br_ms_cnes_habilitacao.schedule = schedule_br_ms_cnes_habilitacao -br_ms_cnes_gestao_metas = deepcopy(flow_datasus) +br_ms_cnes_gestao_metas = deepcopy(flow_cnes) br_ms_cnes_gestao_metas.name = "br_ms_cnes.gestao_metas" br_ms_cnes_gestao_metas.code_owners = ["equipe_pipelines"] br_ms_cnes_gestao_metas.storage = GCS(constants.GCS_FLOWS_BUCKET.value) br_ms_cnes_gestao_metas.run_config = KubernetesRun(image=constants.DOCKER_IMAGE.value) br_ms_cnes_gestao_metas.schedule = schedule_br_ms_cnes_gestao_metas -br_ms_cnes_incentivos = deepcopy(flow_datasus) +br_ms_cnes_incentivos = deepcopy(flow_cnes) br_ms_cnes_incentivos.name = "br_ms_cnes.incentivos" br_ms_cnes_incentivos.code_owners = ["equipe_pipelines"] br_ms_cnes_incentivos.storage = GCS(constants.GCS_FLOWS_BUCKET.value) br_ms_cnes_incentivos.run_config = KubernetesRun(image=constants.DOCKER_IMAGE.value) br_ms_cnes_incentivos.schedule = schedule_br_ms_cnes_incentivos -br_ms_cnes_estabelecimento_ensino = deepcopy(flow_datasus) +br_ms_cnes_estabelecimento_ensino = deepcopy(flow_cnes) br_ms_cnes_estabelecimento_ensino.name = "br_ms_cnes.estabelecimento_ensino" br_ms_cnes_estabelecimento_ensino.code_owners = ["equipe_pipelines"] br_ms_cnes_estabelecimento_ensino.storage = GCS(constants.GCS_FLOWS_BUCKET.value) br_ms_cnes_estabelecimento_ensino.run_config = KubernetesRun( image=constants.DOCKER_IMAGE.value ) -br_ms_cnes_estabelecimento_ensino.schedule = schedule_br_ms_cnes_estabelecimento_ensino +#br_ms_cnes_estabelecimento_ensino.schedule = schedule_br_ms_cnes_estabelecimento_ensino -br_ms_cnes_estabelecimento_filantropico = deepcopy(flow_datasus) +br_ms_cnes_estabelecimento_filantropico = deepcopy(flow_cnes) br_ms_cnes_estabelecimento_filantropico.name = "br_ms_cnes.estabelecimento_filantropico" br_ms_cnes_estabelecimento_filantropico.code_owners = ["equipe_pipelines"] br_ms_cnes_estabelecimento_filantropico.storage = GCS(constants.GCS_FLOWS_BUCKET.value) @@ -121,3 +122,12 @@ image=constants.DOCKER_IMAGE.value ) br_ms_cnes_estabelecimento_filantropico.schedule = schedule_br_ms_cnes_estabelecimento_filantropico + +br_ms_cnes_regra_contratual = deepcopy(flow_cnes) +br_ms_cnes_regra_contratual.name = "br_ms_cnes.estabelecimento_filantropico" +br_ms_cnes_regra_contratual.code_owners = ["equipe_pipelines"] +br_ms_cnes_regra_contratual.storage = GCS(constants.GCS_FLOWS_BUCKET.value) +br_ms_cnes_regra_contratual.run_config = KubernetesRun( + image=constants.DOCKER_IMAGE.value +) +#br_ms_cnes_regra_contratual.schedule = schedule.schedule_br_ms_cnes_regra_contratual From 1f85fa15286342732137a96124f8c3539fe95aed Mon Sep 17 00:00:00 2001 From: folhesgabriel Date: Wed, 28 Feb 2024 17:18:31 -0300 Subject: [PATCH 42/44] add: deactivate regra_contratual schedule --- pipelines/datasets/br_ms_cnes/flows.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipelines/datasets/br_ms_cnes/flows.py b/pipelines/datasets/br_ms_cnes/flows.py index 32e08e9d4..b0b16b2b7 100644 --- a/pipelines/datasets/br_ms_cnes/flows.py +++ b/pipelines/datasets/br_ms_cnes/flows.py @@ -124,7 +124,7 @@ br_ms_cnes_estabelecimento_filantropico.schedule = schedule_br_ms_cnes_estabelecimento_filantropico br_ms_cnes_regra_contratual = deepcopy(flow_cnes) -br_ms_cnes_regra_contratual.name = "br_ms_cnes.estabelecimento_filantropico" +br_ms_cnes_regra_contratual.name = "br_ms_cnes.br_ms_cnes_regra_contratual" br_ms_cnes_regra_contratual.code_owners = ["equipe_pipelines"] br_ms_cnes_regra_contratual.storage = GCS(constants.GCS_FLOWS_BUCKET.value) br_ms_cnes_regra_contratual.run_config = KubernetesRun( From 60980b09ada154f3d5655c24f2f02fc221788733 Mon Sep 17 00:00:00 2001 From: folhesgabriel Date: Wed, 28 Feb 2024 17:33:26 -0300 Subject: [PATCH 43/44] feat: standardize flow names --- pipelines/utils/crawler_datasus/flows.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pipelines/utils/crawler_datasus/flows.py b/pipelines/utils/crawler_datasus/flows.py index b5cd42c40..e167d08ba 100644 --- a/pipelines/utils/crawler_datasus/flows.py +++ b/pipelines/utils/crawler_datasus/flows.py @@ -34,7 +34,7 @@ ) -with Flow(name="BD Template - DATASUS-CNES", code_owners=["Gabriel Pisa"]) as flow_cnes: +with Flow(name="DATASUS-CNES", code_owners=["Gabriel Pisa"]) as flow_cnes: # Parameters dataset_id = Parameter("dataset_id", required=True) table_id = Parameter("table_id", required=True) @@ -142,7 +142,7 @@ -with Flow(name="BD Template - DATASUS-SIA", code_owners=["Gabriel Pisa"]) as flow_sia: +with Flow(name="DATASUS-SIA", code_owners=["Gabriel Pisa"]) as flow_sia: # Parameters dataset_id = Parameter("dataset_id", required=True) table_id = Parameter("table_id", required=True) From 31819017d5d5bd7ce97513b60d8eeb09fbd219d8 Mon Sep 17 00:00:00 2001 From: folhesgabriel Date: Wed, 28 Feb 2024 19:52:57 -0300 Subject: [PATCH 44/44] feat: final modifications --- pipelines/datasets/br_ms_sia/flows.py | 2 +- pipelines/utils/crawler_datasus/utils.py | 41 +++++++++--------------- 2 files changed, 16 insertions(+), 27 deletions(-) diff --git a/pipelines/datasets/br_ms_sia/flows.py b/pipelines/datasets/br_ms_sia/flows.py index 51f2e8bc9..c7dc0953e 100644 --- a/pipelines/datasets/br_ms_sia/flows.py +++ b/pipelines/datasets/br_ms_sia/flows.py @@ -20,4 +20,4 @@ br_ms_sia_producao_ambulatorial.code_owners = ["Gabriel Pisa"] br_ms_sia_producao_ambulatorial.storage = GCS(constants.GCS_FLOWS_BUCKET.value) br_ms_sia_producao_ambulatorial.run_config = KubernetesRun(image=constants.DOCKER_IMAGE.value) -br_ms_sia_producao_ambulatorial.schedule = schedule_br_ms_sia_producao_ambulatorial \ No newline at end of file +#br_ms_sia_producao_ambulatorial.schedule = schedule_br_ms_sia_producao_ambulatorial \ No newline at end of file diff --git a/pipelines/utils/crawler_datasus/utils.py b/pipelines/utils/crawler_datasus/utils.py index 2d4465469..4aecf3b24 100644 --- a/pipelines/utils/crawler_datasus/utils.py +++ b/pipelines/utils/crawler_datasus/utils.py @@ -57,9 +57,8 @@ def dbf_to_parquet(dbf: str) -> str: if path.suffix.lower() != ".dbf": raise ValueError(f"Not a DBF file: {path}") - #TODO: adaptar no flow do cnes para trocar sufixos de arquivos parquet = path.with_suffix(".parquet") - print(parquet) + approx_final_size = ( os.path.getsize(path)/1000 ) # TODO: possibly use it to decide upon number of chunks @@ -73,8 +72,6 @@ def dbf_to_parquet(dbf: str) -> str: os.makedirs(output_path, exist_ok=True) try: - #chunk_size = 30_000 - #chunk_size = 100_000 for chunk in stream_dbf( #dbf5 no lugar de DBF DBF(path, encoding="iso-8859-1", raw=True) @@ -111,29 +108,21 @@ def list_datasus_dbc_files( ftp = FTP("ftp.datasus.gov.br") ftp.login() - # se datasus_database tiver diferentes URL em virtude de - # variados anos de inicio mudar abaixo - cnes_path = [ - "dissemin/publicos/CNES/200508_/Dados", - "dissemin/publicos/SIASUS/200801_/Dados" - ] + try: + # Adicionar aqui eventuais caminhos de databse + if datasus_database == "CNES": + if not datasus_database_table: + raise ValueError("No group assigned to CNES_group") + available_dbs.extend(ftp.nlst(f"dissemin/publicos/CNES/200508_/Dados/{datasus_database_table}/*.DBC")) + + if datasus_database == "SIA": + if not datasus_database_table: + raise ValueError("No group assigned to SIA_group") + available_dbs.extend(ftp.nlst(f"dissemin/publicos/SIASUS/200801_/Dados/{datasus_database_table}*.DBC")) + + except Exception as e: + raise e - for path in cnes_path: - try: - # Adicionar aqui eventuais caminhos de databse - if datasus_database == "CNES": - if not datasus_database_table: - raise ValueError("No group assigned to CNES_group") - print(f"{path}/{datasus_database_table}/*.DBC") - available_dbs.extend(ftp.nlst(f"{path}/{datasus_database_table}/*.DBC")) - - if datasus_database == "SIA": - print("SIA database") - if not datasus_database_table: - raise ValueError("No group assigned to SIA_group") - available_dbs.extend(ftp.nlst(f"{path}/{datasus_database_table}*.DBC")) - except Exception as e: - raise e ftp.close() return available_dbs