feat: added pylint and pytest for etl

.gitignore

@@ -5,6 +5,7 @@ state
 .direnv
 venv
 .installed_deps
+.img_name
 
 *.egg-info
 __pycache__

docker-compose.yml

@@ -10,7 +10,7 @@ x-airflow-common:
       - ./state/dbt-data/target:/dbt/target
       - ./dags:/home/airflow/airflow/dags
       - ./data:/home/airflow/gcs/data:ro
-      - ./etl:/etl:ro
+      - ./etl/src:/etl:ro
       - ./dbt:/dbt
     environment:
       AIRFLOW__CORE__LOAD_EXAMPLES: 'false'

etl/Dockerfile

@@ -0,0 +1,9 @@
+FROM python:3.8-slim
+
+COPY requirements.txt /requirements.txt
+COPY dev-requirements.txt /dev-requirements.txt
+
+RUN pip install --upgrade pip && \
+    pip install -r /requirements.txt -r /dev-requirements.txt
+
+WORKDIR /src

etl/Makefile

@@ -0,0 +1,54 @@
+.PHONY: clean build_img
+
+PYTHON_VERSION = 3.8
+PYTHON_SUBVERSION = 3.8.12
+
+PYENV_VERSIONS = $(HOME)/.pyenv/versions
+PYTHON_BIN = $(PYENV_VERSIONS)/$(PYTHON_SUBVERSION)/bin/python$(PYTHON_VERSION)
+
+VENV = venv
+PYTHON_VENV = $(VENV)/bin/python
+PIP = $(PYTHON_VENV) -m pip
+PIP_COMPILE = venv/bin/pip-compile
+
+IMG_NAME=etl_beam_env
+
+all: oci_img .installed_deps
+
+build_img: .img_name
+
+.img_name: Dockerfile requirements.txt dev-requirements.txt
+	docker build -t $(IMG_NAME) .
+	echo $(IMG_NAME) > $@
+
+.installed_deps: requirements.txt dev-requirements.txt $(PYTHON_VENV)
+	$(PIP) install \
+		-r requirements.txt \
+		-r dev-requirements.txt
+	touch $@
+
+requirements.txt: pyproject.toml $(PIP_COMPILE)
+	$(PIP_COMPILE) \
+		--resolver=backtracking \
+		--output-file $@ \
+		$<
+
+dev-requirements.txt: pyproject.toml $(PIP_COMPILE)
+	$(PIP_COMPILE) \
+		--extra=dev \
+		--resolver=backtracking \
+		--output-file $@ \
+		$<
+
+$(PIP_COMPILE): $(PYTHON_VENV)
+	$(PIP) install pip-tools
+
+$(PYTHON_VENV): $(PYTHON_BIN)
+	virtualenv --python=$^ $(VENV)
+	$(PIP) install --upgrade pip
+
+$(PYTHON_BIN):
+	pyenv install $(PYTHON_SUBVERSION)
+
+clean:
+	rm -rf *.egg-info venv installed_deps

etl/dev-requirements.txt

@@ -1,5 +1,5 @@
 #
-# This file is autogenerated by pip-compile with Python 3.10
+# This file is autogenerated by pip-compile with Python 3.8
 # by the following command:
 #
 #    pip-compile --extra=dev --output-file=dev-requirements.txt --resolver=backtracking pyproject.toml
@@ -208,7 +208,7 @@ protobuf==4.23.3
     #   grpc-google-iam-v1
     #   grpcio-status
     #   proto-plus
-psycopg2==2.9.6
+psycopg2-binary==2.9.6
     # via beam-etl (pyproject.toml)
 pyarrow==11.0.0
     # via apache-beam
@@ -275,6 +275,8 @@ typing-extensions==4.6.3
     # via
     #   apache-beam
     #   astroid
+    #   black
+    #   pylint
 tzdata==2023.3
     # via pandas
 urllib3==1.26.16

etl/justfile

@@ -0,0 +1,16 @@
+build_img:
+    make build_img
+
+test: build_img
+    docker run \
+        -v $(pwd)/src:/src \
+        --rm \
+        -it $(cat .img_name) \
+        python -m pytest
+
+lint: build_img
+    docker run \
+        -v $(pwd)/src:/src \
+        --rm \
+        -it $(cat .img_name) \
+        pylint --init-hook "import sys; sys.path.append('/src')" /src

etl/pyproject.toml

@@ -1,7 +1,7 @@
 [project]
 name = "beam_etl"
 version = "0.1"
-dependencies = ["wheel", "apache-beam[gcp]", "pandas", "psycopg2"]
+dependencies = ["wheel", "apache-beam[gcp]", "pandas", "psycopg2-binary"]
 
 [project.optional-dependencies]
 dev = ["pytest", "pylint", "black"]

etl/requirements.txt

@@ -1,5 +1,5 @@
 #
-# This file is autogenerated by pip-compile with Python 3.10
+# This file is autogenerated by pip-compile with Python 3.8
 # by the following command:
 #
 #    pip-compile --output-file=requirements.txt --resolver=backtracking pyproject.toml
@@ -177,7 +177,7 @@ protobuf==4.23.3
     #   grpc-google-iam-v1
     #   grpcio-status
     #   proto-plus
-psycopg2==2.9.6
+psycopg2-binary==2.9.6
     # via beam-etl (pyproject.toml)
 pyarrow==11.0.0
     # via apache-beam

etl/src/helpers/data_io.py

@@ -5,6 +5,7 @@
 import io
 import logging
 import csv
+from typing import Dict
 
 import apache_beam as beam
 import psycopg2
@@ -17,9 +18,10 @@ class ReadFromCsv(beam.DoFn):
     dictionary where the row names are the keys and the cells are the values
     """
 
-    def process(self, in_file):
-        logging.info("reading from input file: %s", in_file)
-        with FileSystems.open(in_file) as file:
+    # pylint: disable=abstract-method,arguments-differ
+    def process(self, element):
+        logging.info("reading from input file: %s", element)
+        with FileSystems.open(element) as file:
             text_wrapper = io.TextIOWrapper(file)
             reader = csv.reader(text_wrapper)
             try:
@@ -33,24 +35,25 @@ class ReadFromCsv(beam.DoFn):
 class WriteToPostgreSQL(beam.DoFn):
     """DoFn to write elements to a PostgreSQL database"""
 
-    def __init__(
-        self, hostname, port, username, password, database, table, table_key=None
-    ):
-        self.connection_details = {
-            "host": hostname,
-            "port": port,
-            "user": username,
-            "password": password,
-            "database": database,
-        }
+    # pylint: disable=abstract-method
+    def __init__(self, connection_details: Dict[str, str], table, table_key=None):
+        # pylint: disable=super-init-not-called
+        self.connection_details = connection_details
         self.table = table
         self.table_key = table_key
+        self.connection = None
 
     def setup(self):
         self.connection = psycopg2.connect(**self.connection_details)
         self.connection.autocommit = True
 
-    def execute_insert(self, row, cursor):
+    def execute_insert(self, row: Dict, cursor):
+        """Given a dictionary reporesenting a row and a postgresql cursor,
+        insert the row into the database so that the dict keys are the colum
+        names and the dict values the cell values.
+        If a table_key is specified (`self.table_key` is set) handle conflicts
+        by doing nothing"""
+
         colnames = ",".join(row.keys())
         values = ",".join(["%s"] * len(row))
         sql = f"""
@@ -61,19 +64,28 @@ class WriteToPostgreSQL(beam.DoFn):
             sql = sql + f" ON CONFLICT ({ self.table_key }) DO NOTHING"
         cursor.execute(sql, list(row.values()))
 
+    # pylint: disable=arguments-differ
     def process(self, element):
-        cursor = self.connection.cursor()
-        self.execute_insert(element, cursor)
-        cursor.close()
+        if self.connection is not None:
+            cursor = self.connection.cursor()
+            self.execute_insert(element, cursor)
+            cursor.close()
 
     def teardown(self):
-        self.connection.close()
+        if self.connection is not None:
+            self.connection.close()
 
 
 class UpsertProductsToPg(WriteToPostgreSQL):
     """DoFn to write products to PostgreSQL with our upsert logic"""
 
+    # pylint: disable=abstract-method
     def execute_insert(self, row, cursor):
+        """Our upsert logic is the following:
+        When any of primary_category, packaging, origin, height, depth or with
+        has changed, update the element and set the ingestion_time value to the
+        current timestamp
+        """
         colnames = ",".join(row.keys())
         values = ",".join(["%s"] * len(row))
         sql = f"""
@@ -87,12 +99,18 @@ class UpsertProductsToPg(WriteToPostgreSQL):
                packaging = EXCLUDED.packaging,
                origin = EXCLUDED.origin,
                weight = EXCLUDED.weight,
+               height = EXCLUDED.height,
+               depth = EXCLUDED.depth,
+               width = EXCLUDED.width,
                ingestion_time = NOW()::TIMESTAMP
            WHERE
                { self.table }.primary_category != EXCLUDED.primary_category OR
                { self.table }.materials != EXCLUDED.materials OR
                { self.table }.packaging != EXCLUDED.packaging OR
                { self.table }.origin != EXCLUDED.origin OR
-               { self.table }.weight != EXCLUDED.weight
+               { self.table }.weight != EXCLUDED.weight OR
+               { self.table }.height != EXCLUDED.height OR
+               { self.table }.depth != EXCLUDED.depth OR
+               { self.table }.width != EXCLUDED.width
         """
         cursor.execute(sql, list(row.values()))

etl/src/main.py

@@ -1,4 +1,7 @@
-#!/usr/bin/env python
+"""This Apache Beam pipeline reads rows as elements from a CSV input file,
+extracts and parses relevant values, and upserts the elements to a PostgreSQL
+database
+"""
 
 import logging
 
@@ -10,9 +13,6 @@ from helpers.data_io import ReadFromCsv, UpsertProductsToPg
 from helpers.parse_row import parse_row
 
 
-#     def __init__(self, hostname, port, username, password, database):
-
-
 class SustainabilityScoreOptions(PipelineOptions):
     """Options for this pipeline"""
 
@@ -33,18 +33,23 @@ def main():
     beam_options = PipelineOptions()
     opts = beam_options.view_as(SustainabilityScoreOptions)
 
+    pg_connection_details = {
+        "host": opts.pg_hostname,
+        "port": opts.pg_port,
+        "user": opts.pg_username,
+        "password": opts.pg_password,
+        "database": opts.pg_database,
+    }
+
     with beam.Pipeline(options=beam_options) as pipeline:
         # fmt: off
+        # pylint: disable=expression-not-assigned
         pipeline \
             | beam.Create([opts.input]) \
             | beam.ParDo(ReadFromCsv()) \
             | beam.Map(parse_row) \
             | beam.ParDo(UpsertProductsToPg(
-                hostname=opts.pg_hostname,
-                port=opts.pg_port,
-                username=opts.pg_username,
-                password=opts.pg_password,
-                database=opts.pg_database,
+                connection_details=pg_connection_details,
                 table=opts.pg_table,
                 table_key="tcin",
             ))