From 817dc805ce681fb621c76e805a33aafb66bacf6d Mon Sep 17 00:00:00 2001 From: AlexGherardelli Date: Thu, 7 May 2026 15:31:42 +0200 Subject: [PATCH 01/16] chore: update ODBC driver to 18 --- README.md | 2 +- datalibrary/extract.py | 2 +- datalibrary/load.py | 2 +- datalibrary/transform.py | 118 +-------------------------------------- 4 files changed, 4 insertions(+), 120 deletions(-) diff --git a/README.md b/README.md index 0828d53..3f6f46b 100644 --- a/README.md +++ b/README.md @@ -21,7 +21,7 @@ This is a Python CLI tool to query the [WFP Data Library API](https://datalib.va - Packages listed in `requirements.txt` ## Documentation -For more details on the Data Library API endpoints, see the [API documentation](http://docs.ckan.org/en/2.9/api/). +For more details on the Data Library API endpoints, see the [API documentation](http://docs.ckan.org/en/2.11/api/). ## Contributing Contributions to add more API querying/exporting functionality are welcome! diff --git a/datalibrary/extract.py b/datalibrary/extract.py index c2fe2eb..2cd3707 100644 --- a/datalibrary/extract.py +++ b/datalibrary/extract.py @@ -70,7 +70,7 @@ def help(self): info = k.replace("_", " ").capitalize() print(f'{info} on endpoint {BASE_URL + v}') - print("\n---\n For documentation visit: http://docs.ckan.org/en/2.9/api/\n---\n") + print("\n---\n For documentation visit: http://docs.ckan.org/en/2.11/api/\n---\n") def get_users(self): """Get list of users""" diff --git a/datalibrary/load.py b/datalibrary/load.py index 0a76d4f..62350a7 100644 --- a/datalibrary/load.py +++ b/datalibrary/load.py @@ -14,7 +14,7 @@ USERNAME = os.getenv("DB_USERNAME") PASSWORD = os.getenv("DB_PASSWORD") -conn_str = f'mssql+pyodbc://{USERNAME}:{PASSWORD}@{SERVER}/{DATABASE}?driver=ODBC+Driver+17+for+SQL+Server&Encrypt=yes&TrustServerCertificate=yes' +conn_str = f'mssql+pyodbc://{USERNAME}:{PASSWORD}@{SERVER}/{DATABASE}?driver=ODBC+Driver+18+for+SQL+Server&Encrypt=yes&TrustServerCertificate=yes' engine = create_engine(conn_str) class ExcelExportError(Exception): diff --git a/datalibrary/transform.py b/datalibrary/transform.py index 39ff114..e2a20f5 100644 --- a/datalibrary/transform.py +++ b/datalibrary/transform.py @@ -1,118 +1,3 @@ -<<<<<<< HEAD -import pandas as pd -import json - - -SURVEY_COLUMNS_SELECTION = ['assessment_status', 'collection_method', 'creator_user_id', 'data_collector', 'description', 'end_date', 'id', 'metadata_created', 'metadata_modified', 'month', 'name', 'num_resources', 'organization_id', 'organization_title', 'organization_description', 'organization_created', 'owner_org', 'private', 'progress_status', 'start_date', 'survey_attributes', 'survey_category', 'survey_type', 'title', 'year', 'resources'] - -SURVEY_COLUMNS_RENAMING = {"id": "survey_id", "organization_id": "container_id", - "organization_title": "container_name", - "organization_description": "container_description", - "organization_created": "container_created", - "data_collector": "organization", "owner_org": "parent_container_id", - "title": "survey_title"} - -RESOURCES_COLUMNS_TO_DROP = ["resources", "restricted", "cache_last_updated", "cache_url", "revision_id", "url_type", "state", "resource_type", "mimetype_inner", "hash", "package_id"] - -def clean_column_names(df): - """Rename columns to be more readable""" - df.columns = df.columns.str.replace('.', '_') - return df - -def flatten_response(df: pd.DataFrame, col: str, _id: str) -> pd.DataFrame: - flat_list = [] - for _, row in df.iterrows(): - for r in row[col]: - flat_dict = {_id : row[_id]} - flat_dict.update(r) - flat_list.append(flat_dict) - - df = pd.DataFrame(flat_list) - return df - -def flatten_resources(df): - resources = df[["resources", "organization_id", "survey_id"]] - flat_resources = flatten_response(resources, "resources", "survey_id") - return flat_resources - -def normalize_restrictions(df): - """Normalize restricted column""" - try: - df['restricted'] = df['restricted'].apply(json.loads) - except TypeError: - pass - - restricted = pd.json_normalize(df["restricted"]) - return restricted - -def user_data_transform(df): - # Remove unnecessary columns from users table - users_columns_to_drop = ["apikey", "display_name", "about", "state", "image_url", "image_display_url"] - df = df.drop(columns=users_columns_to_drop) - return df - -def survey_data_transform(df): - df = clean_column_names(df) - df = df[SURVEY_COLUMNS_SELECTION] - df = df.rename(columns=SURVEY_COLUMNS_RENAMING) - return df - -def member_data_transform(df): - df = df.rename(columns={0: "user_id", 1: "type", 2: "capacity"}) - df = df[df.type.isin(["user"])] - df = df[["user_id", "capacity", "container_id"]] - return df - - -def transform(data: tuple) -> tuple: - """ - Transforms the input data tuple into a new tuple. - - Args: - data (tuple): A tuple containing the data to be transformed. - - Returns: - tuple: The transformed data. - """ - surveys, users, members = data - - surveys = survey_data_transform(surveys) - - # Flatten resources - resources = surveys[["resources", "container_id", "survey_id"]] - flat_resources = flatten_response(resources, "resources", "survey_id") - - # Remove unnecessary columns from survey table - surveys.drop(columns=["resources"], inplace=True) - full_resources = pd.merge(resources, flat_resources, on="survey_id") - - # Normalize restricted datasets - restricted = normalize_restrictions(full_resources) - full_resources = full_resources.join(restricted) - - - # Remove unnecessary columns from resource table - full_resources.drop(columns=RESOURCES_COLUMNS_TO_DROP, inplace=True) - - # Rename resource columns - resources_cols_renaming = { - "restricted-level": "access_level", - 'restricted-allowed_users': "allowed_users" - } - full_resources = full_resources.rename(columns=resources_cols_renaming) - - - # User table transformations - users = user_data_transform(users) - - # Member DF - members = member_data_transform(members) - - - return (surveys, full_resources, users, members) - -if __name__ == "__main__": -======= import pandas as pd import json @@ -161,7 +46,7 @@ def normalize_restrictions(df): def user_data_transform(df): # Remove unnecessary columns from users table - users_columns_to_drop = ["display_name", "about", "state", "image_url", "image_display_url"] + users_columns_to_drop = ["apikey", "display_name", "about", "state", "image_url", "image_display_url"] df = df.drop(columns=users_columns_to_drop) return df @@ -226,5 +111,4 @@ def transform(data: tuple) -> tuple: return (surveys, full_resources, users, members) if __name__ == "__main__": ->>>>>>> master pass \ No newline at end of file From 79fe96f6adc8a1fcfd113679ce11b3ea34cd81c5 Mon Sep 17 00:00:00 2001 From: AlexGherardelli Date: Mon, 1 Jun 2026 14:03:56 +0200 Subject: [PATCH 02/16] chore: update dependencies and add Dockerfile --- Dockerfile | 31 +++++++++++++++++++ docker-compose.yml | 14 +++++++++ pyproject.toml | 4 ++- uv.lock | 77 +++++++++++++++++++++++++++++++++++++++++++++- 4 files changed, 124 insertions(+), 2 deletions(-) create mode 100644 Dockerfile create mode 100644 docker-compose.yml diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 0000000..d78ee29 --- /dev/null +++ b/Dockerfile @@ -0,0 +1,31 @@ +# syntax=docker/dockerfile:1 +FROM python:3.11-slim + +# Install uv from official image +COPY --from=ghcr.io/astral-sh/uv:latest /uv /uvx /bin/ + +# System dependencies + SQL Server ODBC driver +RUN apt-get update && \ + apt-get install -y --no-install-recommends curl gnupg2 ca-certificates unixodbc-dev && \ + curl -fsSL https://packages.microsoft.com/keys/microsoft.asc | gpg --dearmor -o /usr/share/keyrings/microsoft-prod.gpg && \ + echo "deb [signed-by=/usr/share/keyrings/microsoft-prod.gpg] https://packages.microsoft.com/debian/12/prod bookworm main" > /etc/apt/sources.list.d/mssql-release.list && \ + apt-get update && \ + ACCEPT_EULA=Y apt-get install -y --no-install-recommends msodbcsql17 && \ + DRIVER_PATH="$(ls /opt/microsoft/msodbcsql17/lib64/libmsodbcsql-17*.so* | head -n 1)" && \ + printf "[SQL Server]\nDescription=Microsoft ODBC Driver 17 for SQL Server (alias)\nDriver=%s\nUsageCount=1\n" "$DRIVER_PATH" >> /etc/odbcinst.ini && \ + rm -rf /var/lib/apt/lists/* + +WORKDIR /app + +# Install dependencies first for better layer caching +COPY pyproject.toml ./ +COPY uv.lock* ./ +RUN uv sync --frozen --no-dev + +# Copy project files +COPY . . + +# Runtime default environment for main.py arg +ENV APP_ENV=hpc_dev + +CMD ["sh", "-c", "uv run python main.py ${APP_ENV}"] diff --git a/docker-compose.yml b/docker-compose.yml new file mode 100644 index 0000000..4c6db48 --- /dev/null +++ b/docker-compose.yml @@ -0,0 +1,14 @@ +services: + ipcch-pipeline: #CHANGE THIS + build: + context: . + dockerfile: Dockerfile + image: ipcch-pipeline:latest + environment: + APP_ENV: ${APP_ENV:-dev} + ipc_api_key: ${ipc_api_key:-} + # REPORTINGdev_DB_ADMNAME: ${REPORTINGdev_DB_ADMNAME:-} + REPORTINGdev_DB_ADMPWD: ${REPORTINGdev_DB_ADMPWD:-} + REPORTING_DB_ADMNAME: ${REPORTING_DB_ADMNAME:-} + REPORTING_DB_ADMPWD: ${REPORTING_DB_ADMPWD:-} + command: ["sh", "-c", "uv run python main.py ${APP_ENV:-dev}"] \ No newline at end of file diff --git a/pyproject.toml b/pyproject.toml index 55ab7d0..933ba52 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [project] name = "datalibrary-pipeline" -version = "0.1.0" +version = "1.0.0" description = "Add your description here" readme = "README.md" requires-python = ">=3.12" @@ -13,6 +13,8 @@ dependencies = [ "numpy==1.26.4", "pandas==2.2.2", "pip==24.0", + "polars>=1.41.2", + "pyarrow>=24.0.0", "pyodbc==5.1.0", "pysocks==1.7.1", "python-dateutil==2.9.0", diff --git a/uv.lock b/uv.lock index 3c5167c..3955e44 100644 --- a/uv.lock +++ b/uv.lock @@ -75,7 +75,7 @@ wheels = [ [[package]] name = "datalibrary-pipeline" -version = "0.1.0" +version = "1.0.0" source = { virtual = "." } dependencies = [ { name = "brotli" }, @@ -86,6 +86,8 @@ dependencies = 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-COPY uv.lock* ./ -RUN uv sync --frozen --no-dev +COPY uv.lock ./ +RUN uv sync --frozen # Copy project files COPY . . @@ -28,4 +31,4 @@ COPY . . # Runtime default environment for main.py arg ENV APP_ENV=hpc_dev -CMD ["sh", "-c", "uv run python main.py ${APP_ENV}"] +CMD ["sh", "-c", "uv run python main.py --db"] diff --git a/docker-compose.yml b/docker-compose.yml index 4c6db48..2f633fa 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -1,14 +1,20 @@ + services: - ipcch-pipeline: #CHANGE THIS + data-library-pipeline: # you can rename this to your new pipeline name build: context: . dockerfile: Dockerfile - image: ipcch-pipeline:latest + + image: data-library-pipeline:latest # just a name for the built image + environment: APP_ENV: ${APP_ENV:-dev} - ipc_api_key: ${ipc_api_key:-} - # REPORTINGdev_DB_ADMNAME: ${REPORTINGdev_DB_ADMNAME:-} - REPORTINGdev_DB_ADMPWD: ${REPORTINGdev_DB_ADMPWD:-} - REPORTING_DB_ADMNAME: ${REPORTING_DB_ADMNAME:-} - REPORTING_DB_ADMPWD: ${REPORTING_DB_ADMPWD:-} - command: ["sh", "-c", "uv run python main.py ${APP_ENV:-dev}"] \ No newline at end of file + + # ✅ Your new required variables + DATALIB_API_KEY: ${DATALIB_API_KEY:-} + SERVER: ${SERVER:-} + DB_NAME: ${DB_NAME:-} + DB_USERNAME: ${DB_USERNAME:-} + DB_PASSWORD: ${DB_PASSWORD:-} + + command: ["sh", "-c", "uv run python main.py --db"] diff --git a/main.py b/main.py index 8fadd67..a2f5a98 100644 --- a/main.py +++ b/main.py @@ -6,7 +6,7 @@ from datalibrary.transform import transform from datalibrary.load import save_to_excel, load_to_db -load_dotenv() # take environment variables from .env. +# load_dotenv() # take environment variables from .env. def main(): """ diff --git a/pyproject.toml b/pyproject.toml index 933ba52..b0dba39 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -3,7 +3,7 @@ name = "datalibrary-pipeline" version = "1.0.0" description = "Add your description here" readme = "README.md" -requires-python = ">=3.12" +requires-python = ">=3.11" 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c652b4d9c52251d534cd5aea6081d719916a7a1b Mon Sep 17 00:00:00 2001 From: AlexGherardelli Date: Mon, 1 Jun 2026 17:00:38 +0200 Subject: [PATCH 04/16] fix: reinstate load_dotenv() --- main.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/main.py b/main.py index a2f5a98..8fadd67 100644 --- a/main.py +++ b/main.py @@ -6,7 +6,7 @@ from datalibrary.transform import transform from datalibrary.load import save_to_excel, load_to_db -# load_dotenv() # take environment variables from .env. +load_dotenv() # take environment variables from .env. def main(): """ From b0c042d79077d7127356b6393e27a148a51ecec8 Mon Sep 17 00:00:00 2001 From: AlexGherardelli Date: Tue, 2 Jun 2026 14:41:40 +0200 Subject: [PATCH 05/16] fix: typo in docker-compose --- docker-compose.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/docker-compose.yml b/docker-compose.yml index 2f633fa..fdeb910 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -8,9 +8,8 @@ services: image: data-library-pipeline:latest # just a name for the built image environment: - APP_ENV: ${APP_ENV:-dev} + APP_ENV: ${APP_ENV:-} - # ✅ Your new required variables DATALIB_API_KEY: ${DATALIB_API_KEY:-} SERVER: ${SERVER:-} DB_NAME: ${DB_NAME:-} From 139bd6b70b31b357df550668c3f90b30781b3094 Mon Sep 17 00:00:00 2001 From: AlexGherardelli Date: Tue, 2 Jun 2026 14:50:39 +0200 Subject: [PATCH 06/16] chore: add Makefile with tooling, run codestyle and fix Python package action --- .github/workflows/python-package.yml | 51 +++--- Makefile | 101 ++++++++++++ datalibrary/__init__.py | 10 +- datalibrary/extract.py | 121 ++++++++------- datalibrary/load.py | 29 ++-- datalibrary/transform.py | 105 ++++++++++--- main.py | 23 +-- pyproject.toml | 10 ++ uv.lock | 223 +++++++++++++++++++++++++++ 9 files changed, 538 insertions(+), 135 deletions(-) create mode 100644 Makefile diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 96cb87b..7e54daf 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -1,40 +1,31 @@ -# This workflow will install Python dependencies, run tests and lint with a variety of Python versions -# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python - +--- name: Python package - on: - push: - branches: [ "master" ] pull_request: - branches: [ "master" ] + branches: + - master + +permissions: + contents: write jobs: build: - runs-on: ubuntu-latest strategy: - fail-fast: false matrix: - python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"] - + python-version: + - "3.11" + - "3.12" + - "3.13" + - "3.14" steps: - - uses: actions/checkout@v4 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v3 - with: - python-version: ${{ matrix.python-version }} - - name: Install dependencies - run: | - python -m pip install --upgrade pip - python -m pip install flake8 pytest - if [ -f requirements.txt ]; then pip install -r requirements.txt; fi - - name: Lint with flake8 - run: | - # stop the build if there are Python syntax errors or undefined names - flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics - # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide - flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics - - name: Test with pytest - run: | - pytest + - uses: actions/checkout@v6 + - name: Install uv and set Python version + uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b + with: + python-version: ${{ matrix.python-version }} + - name: Install dependencies + run: uv sync --dev + - name: Lint with Ruff + run: | + uv run ruff check . --fix diff --git a/Makefile b/Makefile new file mode 100644 index 0000000..1727ced --- /dev/null +++ b/Makefile @@ -0,0 +1,101 @@ +#* Variables +SHELL := /usr/bin/env bash +PYTHON := python +PYTHONPATH := `pwd`/src + +#* INSTALL + +#* Install dependencies and package +.PHONY: install +install: + uv sync --all-extras --dev --frozen + +#* LINTING + +#* Check formatting +.PHONY: check-codestyle +check-codestyle: + uv run isort --diff --check-only --settings-path pyproject.toml ./ + uv run black --diff --check --config pyproject.toml ./ + uv run ruff check . + +#* Fix formatting +.PHONY: codestyle +codestyle: + uv run isort --settings-path pyproject.toml ./ + uv run black --fast --config pyproject.toml ./ + uv run ruff check . --fix + +# .PHONY: test +# test: +# uv run pytest tests/unit --cov=data_bridges_knots --cov-report=html +# uv run coverage-badge -o assets/images/coverage.svg -f + +#* Typing +.PHONY: mypy +mypy: + uv run mypy --config-file pyproject.toml ./ + +# .PHONY: check-safety +# check-safety: +# uv run bandit -r src + +#* All in one +.PHONY: lint +lint: test check-codestyle mypy + +#* DOCS + +# #* Documentation +# # Test +# .PHONY: docs-test +# docs-test: +# uv run python -m doctest data_bridges_knots/client.py + +#* DOCKER + +# Example: make docker-build VERSION=latest +# Example: make docker-build IMAGE=some_name VERSION=0.1.0 +.PHONY: docker-build +docker-build: + @echo Building docker $(IMAGE):$(VERSION) ... + docker build \ + -t $(IMAGE):$(VERSION) . \ + -f ./docker/Dockerfile --no-cache + +# Example: make docker-remove VERSION=latest +# Example: make docker-remove IMAGE=some_name VERSION=0.1.0 +.PHONY: docker-remove +docker-remove: + @echo Removing docker $(IMAGE):$(VERSION) ... + docker rmi -f $(IMAGE):$(VERSION) + + +#* CLEANING + +.PHONY: pycache-remove +pycache-remove: + find . | grep -E "(__pycache__|\.pyc|\.pyo$$)" | xargs rm -rf + +.PHONY: dsstore-remove +dsstore-remove: + find . | grep -E ".DS_Store" | xargs rm -rf + +.PHONY: mypycache-remove +mypycache-remove: + find . | grep -E ".mypy_cache" | xargs rm -rf + +.PHONY: ipynbcheckpoints-remove +ipynbcheckpoints-remove: + find . | grep -E ".ipynb_checkpoints" | xargs rm -rf + +.PHONY: pytestcache-remove +pytestcache-remove: + find . | grep -E ".pytest_cache" | xargs rm -rf + +.PHONY: build-remove +build-remove: + rm -rf build/ + +.PHONY: cleanup +cleanup: pycache-remove dsstore-remove mypycache-remove ipynbcheckpoints-remove pytestcache-remove \ No newline at end of file diff --git a/datalibrary/__init__.py b/datalibrary/__init__.py index f839c6c..599de80 100644 --- a/datalibrary/__init__.py +++ b/datalibrary/__init__.py @@ -1,3 +1,9 @@ -from .extract import DataLibrary, get_survey_data, get_user_data, get_member_data, get_data +from .extract import ( + DataLibrary, + get_data, + get_member_data, + get_survey_data, + get_user_data, +) -__all__ = ["DataLibrary"] \ No newline at end of file +__all__ = ["DataLibrary"] diff --git a/datalibrary/extract.py b/datalibrary/extract.py index 2cd3707..6024a32 100644 --- a/datalibrary/extract.py +++ b/datalibrary/extract.py @@ -1,40 +1,42 @@ -import requests import json import logging + import pandas as pd +import requests logger = logging.getLogger(__name__) BASE_URL = "https://datalib.vam.wfp.org/api/3/" ENDPOINTS = { -'users': 'action/user_list', -'all_surveys_information': 'action/current_package_list_with_resources', -'all_surveys_code': 'action/package_list', -'member_list': 'action/member_list', + "users": "action/user_list", + "all_surveys_information": "action/current_package_list_with_resources", + "all_surveys_code": "action/package_list", + "member_list": "action/member_list", } + class DataLibrary: """Class to query WFP Data Library API. -Attributes: - api_key (str): API key for authentication + Attributes: + api_key (str): API key for authentication -Methods: - get_users: Get list of Data Library users - get_surveys: Get list of survey codes - get_survey_info: Get info on all surveys - """ + Methods: + get_users: Get list of Data Library users + get_surveys: Get list of survey codes + get_survey_info: Get info on all surveys + """ def __init__(self, api_key): """Initialize DataLibrary instance. Args: api_key (str): API key for authentication - """ + """ self.api_key = api_key self.session = requests.Session() self._ua = "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:147.0) Gecko/20100101 Firefox/147.0" - + def get_response(self, url, params=None): """Send API request. @@ -45,14 +47,14 @@ def get_response(self, url, params=None): Returns: dict: API response """ - headers = {'Authorization': f'{self.api_key}', 'User-Agent': self._ua} + headers = {"Authorization": f"{self.api_key}", "User-Agent": self._ua} if params is None: params = {} elif isinstance(params, int): - params = {'limit': params} + params = {"limit": params} - logger.info(f'Querying {url} with params {params}') + logger.info(f"Querying {url} with params {params}") r = self.session.get(url, headers=headers, params=params) if r.status_code == 200: @@ -64,36 +66,40 @@ def get_response(self, url, params=None): def help(self): """Get basic information on the usage of the API.""" - print(f'\n---\n This library helps RAM users to query the Data Library API:{BASE_URL}\n') - print('You can get information about the following:') + print( + f"\n---\n This library helps RAM users to query the Data Library API:{BASE_URL}\n" + ) + print("You can get information about the following:") for k, v in ENDPOINTS.items(): info = k.replace("_", " ").capitalize() - print(f'{info} on endpoint {BASE_URL + v}') + print(f"{info} on endpoint {BASE_URL + v}") - print("\n---\n For documentation visit: http://docs.ckan.org/en/2.11/api/\n---\n") + print( + "\n---\n For documentation visit: http://docs.ckan.org/en/2.11/api/\n---\n" + ) def get_users(self): """Get list of users""" - url = BASE_URL + ENDPOINTS['users'] - response = self.get_response(url) + url = BASE_URL + ENDPOINTS["users"] + response = self.get_response(url) data = response["result"] return data def get_survey_list(self, limit=None): """Get package list""" - url = BASE_URL + ENDPOINTS['all_surveys_code'] - response = self.get_response(url, params=limit) + url = BASE_URL + ENDPOINTS["all_surveys_code"] + response = self.get_response(url, params=limit) data = response["result"] return data def get_surveys_with_resources(self, limit=None): """Get all surveys with country, type of survey and description""" - url = BASE_URL + ENDPOINTS['all_surveys_information'] - response = self.get_response(url, params=limit) + url = BASE_URL + ENDPOINTS["all_surveys_information"] + response = self.get_response(url, params=limit) data = response["result"] return data - + def get_member_list(self, id=None, object_type=None, capacity=None, limit=None): """Get list of members of a group. @@ -106,34 +112,35 @@ def get_member_list(self, id=None, object_type=None, capacity=None, limit=None): Returns: list: List of tuples containing (id, type, capacity) for each member. """ - url = BASE_URL + ENDPOINTS['member_list'] - params = {'id': id, 'object_type': object_type, 'limit': limit} + url = BASE_URL + ENDPOINTS["member_list"] + params = {"id": id, "object_type": object_type, "limit": limit} response = self.get_response(url, params=params) data = response.get("result", []) return data - + def __repr__(self): - return f'DataLibraryData({self.api_key})' + return f"DataLibraryData({self.api_key})" def __str__(self): - return f'The API key used in this DataLibraryData is {self.api_key}' + return f"The API key used in this DataLibraryData is {self.api_key}" def get_survey_data(client): - survey_list = client.get_survey_list() - total_surveys = len(survey_list) + survey_list = client.get_survey_list() + total_surveys = len(survey_list) - all_surveys = client.get_surveys_with_resources(limit=total_surveys) - all_surveys_df = pd.json_normalize(all_surveys) + all_surveys = client.get_surveys_with_resources(limit=total_surveys) + all_surveys_df = pd.json_normalize(all_surveys) - return all_surveys_df + return all_surveys_df def get_user_data(client): - users = client.get_users() - users_df = pd.DataFrame(users) + users = client.get_users() + users_df = pd.DataFrame(users) + + return users_df - return users_df def get_member_data(client, id=None): members = client.get_member_list(id=id) @@ -142,21 +149,23 @@ def get_member_data(client, id=None): def get_data(client): - survey_df = get_survey_data(client) - user_df = get_user_data(client) - - result = [] - container_ids = set(survey_df['organization.id']) - for container_id in container_ids: - container_members = get_member_data(client, id=container_id) - if container_members is not None: - container_members.insert(3, "container_id", container_id) # Check if container_members is not None - result.append(container_members) - # BUG: container id should be included as column, along with user_id - member_df = pd.concat(result, ignore_index=True) - - return survey_df, user_df, member_df + survey_df = get_survey_data(client) + user_df = get_user_data(client) + + result = [] + container_ids = set(survey_df["organization.id"]) + for container_id in container_ids: + container_members = get_member_data(client, id=container_id) + if container_members is not None: + container_members.insert( + 3, "container_id", container_id + ) # Check if container_members is not None + result.append(container_members) + # BUG: container id should be included as column, along with user_id + member_df = pd.concat(result, ignore_index=True) + + return survey_df, user_df, member_df if __name__ == "__main__": - pass \ No newline at end of file + pass diff --git a/datalibrary/load.py b/datalibrary/load.py index 62350a7..fc170d0 100644 --- a/datalibrary/load.py +++ b/datalibrary/load.py @@ -1,10 +1,10 @@ -import os -import pandas as pd -from sqlalchemy import create_engine -from dotenv import load_dotenv import logging +import os from datetime import date +from dotenv import load_dotenv +from sqlalchemy import create_engine + logger = logging.getLogger(__name__) load_dotenv() # take environment variables from .env. @@ -14,20 +14,25 @@ USERNAME = os.getenv("DB_USERNAME") PASSWORD = os.getenv("DB_PASSWORD") -conn_str = f'mssql+pyodbc://{USERNAME}:{PASSWORD}@{SERVER}/{DATABASE}?driver=ODBC+Driver+18+for+SQL+Server&Encrypt=yes&TrustServerCertificate=yes' +conn_str = f"mssql+pyodbc://{USERNAME}:{PASSWORD}@{SERVER}/{DATABASE}?driver=ODBC+Driver+18+for+SQL+Server&Encrypt=yes&TrustServerCertificate=yes" engine = create_engine(conn_str) + class ExcelExportError(Exception): pass -def load_data(data, table_name = 'table'): + +def load_data(data, table_name="table"): try: - data.to_sql(name=table_name, con=engine, if_exists='replace') + data.to_sql(name=table_name, con=engine, if_exists="replace") except Exception as e: logger.error(f"Error {e} when populating {table_name}") -def load_to_db(data: tuple, table_names = ("DL_Surveys", "DL_Resources", "DL_Users", "DL_Members")): - try: + +def load_to_db( + data: tuple, table_names=("DL_Surveys", "DL_Resources", "DL_Users", "DL_Members") +): + try: for df, table_name in zip(data, table_names): logger.info("Loading data to database") load_data(df, table_name) @@ -35,19 +40,19 @@ def load_to_db(data: tuple, table_names = ("DL_Surveys", "DL_Resources", "DL_Use logger.error(f"Error loading data: {e}") -def save_to_excel(data: tuple, filenames = ("surveys", "resources", "users", "members")): +def save_to_excel(data: tuple, filenames=("surveys", "resources", "users", "members")): # export survey list, survey information with resources and user list as csv folder = "output" today = str(date.today()).replace("-", "_") - for df, filename in zip(data, filenames): path = f"{folder}/{today}_{filename}.csv" try: df.to_csv(path) - except Exception as e: + except Exception: logger.error(f"Error saving {filename} to excel") continue + if __name__ == "__main__": pass diff --git a/datalibrary/transform.py b/datalibrary/transform.py index e2a20f5..ba739da 100644 --- a/datalibrary/transform.py +++ b/datalibrary/transform.py @@ -1,54 +1,110 @@ -import pandas as pd import json +import pandas as pd -SURVEY_COLUMNS_SELECTION = ['assessment_status', 'collection_method', 'creator_user_id', 'data_collector', 'description', 'end_date', 'id', 'metadata_created', 'metadata_modified', 'month', 'name', 'num_resources', 'organization_id', 'organization_title', 'organization_description', 'organization_created', 'owner_org', 'private', 'progress_status', 'start_date', 'survey_attributes', 'survey_category', 'survey_type', 'title', 'year', 'resources'] - -SURVEY_COLUMNS_RENAMING = {"id": "survey_id", "organization_id": "container_id", - "organization_title": "container_name", - "organization_description": "container_description", - "organization_created": "container_created", - "data_collector": "organization", "owner_org": "parent_container_id", - "title": "survey_title"} +SURVEY_COLUMNS_SELECTION = [ + "assessment_status", + "collection_method", + "creator_user_id", + "data_collector", + "description", + "end_date", + "id", + "metadata_created", + "metadata_modified", + "month", + "name", + "num_resources", + "organization_id", + "organization_title", + "organization_description", + "organization_created", + "owner_org", + "private", + "progress_status", + "start_date", + "survey_attributes", + "survey_category", + "survey_type", + "title", + "year", + "resources", +] + +SURVEY_COLUMNS_RENAMING = { + "id": "survey_id", + "organization_id": "container_id", + "organization_title": "container_name", + "organization_description": "container_description", + "organization_created": "container_created", + "data_collector": "organization", + "owner_org": "parent_container_id", + "title": "survey_title", +} + +RESOURCES_COLUMNS_TO_DROP = [ + "resources", + "restricted", + "cache_last_updated", + "cache_url", + "revision_id", + "url_type", + "state", + "resource_type", + "mimetype_inner", + "hash", + "package_id", +] -RESOURCES_COLUMNS_TO_DROP = ["resources", "restricted", "cache_last_updated", "cache_url", "revision_id", "url_type", "state", "resource_type", "mimetype_inner", "hash", "package_id"] def clean_column_names(df): """Rename columns to be more readable""" - df.columns = df.columns.str.replace('.', '_') + df.columns = df.columns.str.replace(".", "_") return df + def flatten_response(df: pd.DataFrame, col: str, _id: str) -> pd.DataFrame: flat_list = [] for _, row in df.iterrows(): for r in row[col]: - flat_dict = {_id : row[_id]} + flat_dict = {_id: row[_id]} flat_dict.update(r) flat_list.append(flat_dict) - + df = pd.DataFrame(flat_list) return df + def flatten_resources(df): resources = df[["resources", "organization_id", "survey_id"]] flat_resources = flatten_response(resources, "resources", "survey_id") return flat_resources + def normalize_restrictions(df): """Normalize restricted column""" try: - df['restricted'] = df['restricted'].apply(json.loads) + df["restricted"] = df["restricted"].apply(json.loads) except TypeError: pass - + restricted = pd.json_normalize(df["restricted"]) return restricted + def user_data_transform(df): - # Remove unnecessary columns from users table - users_columns_to_drop = ["apikey", "display_name", "about", "state", "image_url", "image_display_url"] + # Remove unnecessary columns from users table + users_columns_to_drop = [ + "apikey", + "display_name", + "about", + "state", + "image_url", + "image_display_url", + ] df = df.drop(columns=users_columns_to_drop) - return df + return df + def survey_data_transform(df): df = clean_column_names(df) @@ -56,6 +112,7 @@ def survey_data_transform(df): df = df.rename(columns=SURVEY_COLUMNS_RENAMING) return df + def member_data_transform(df): df = df.rename(columns={0: "user_id", 1: "type", 2: "capacity"}) df = df[df.type.isin(["user"])] @@ -82,33 +139,31 @@ def transform(data: tuple) -> tuple: flat_resources = flatten_response(resources, "resources", "survey_id") # Remove unnecessary columns from survey table - surveys.drop(columns=["resources"], inplace=True) + surveys.drop(columns=["resources"], inplace=True) full_resources = pd.merge(resources, flat_resources, on="survey_id") # Normalize restricted datasets restricted = normalize_restrictions(full_resources) full_resources = full_resources.join(restricted) - # Remove unnecessary columns from resource table full_resources.drop(columns=RESOURCES_COLUMNS_TO_DROP, inplace=True) # Rename resource columns resources_cols_renaming = { "restricted-level": "access_level", - 'restricted-allowed_users': "allowed_users" + "restricted-allowed_users": "allowed_users", } full_resources = full_resources.rename(columns=resources_cols_renaming) - - # User table transformations + # User table transformations users = user_data_transform(users) # Member DF members = member_data_transform(members) - return (surveys, full_resources, users, members) + if __name__ == "__main__": - pass \ No newline at end of file + pass diff --git a/main.py b/main.py index 8fadd67..f26bc1a 100644 --- a/main.py +++ b/main.py @@ -1,13 +1,15 @@ -import pdb -from dotenv import load_dotenv -import os import argparse +import os + +from dotenv import load_dotenv + from datalibrary.extract import DataLibrary, get_data +from datalibrary.load import load_to_db, save_to_excel from datalibrary.transform import transform -from datalibrary.load import save_to_excel, load_to_db load_dotenv() # take environment variables from .env. + def main(): """ Executes the ETL (Extract, Transform, Load) process to fetch data from VAM Data Library, process the data, and load it into a database and/or save it to an Excel file. @@ -21,9 +23,11 @@ def main(): processed_data = transform(dl_api_data) # Parse command-line arguments - parser = argparse.ArgumentParser(description='Export Data Library data to CSV or database.') - parser.add_argument('--csv', action='store_true', help='Export data to CSV files') - parser.add_argument('--db', action='store_true', help='Upload data to a database') + parser = argparse.ArgumentParser( + description="Export Data Library data to CSV or database." + ) + parser.add_argument("--csv", action="store_true", help="Export data to CSV files") + parser.add_argument("--db", action="store_true", help="Upload data to a database") args = parser.parse_args() if args.csv: @@ -37,7 +41,6 @@ def main(): if not args.csv and not args.db: print("No action specified. 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599de80..5115f55 100644 --- a/datalibrary/__init__.py +++ b/datalibrary/__init__.py @@ -6,4 +6,10 @@ get_user_data, ) -__all__ = ["DataLibrary"] +__all__ = [ + "DataLibrary", + "get_data", + "get_member_data", + "get_survey_data", + "get_user_data", +] From 2074a5e577534ff9f1f736d9e7a8edb51cd315e0 Mon Sep 17 00:00:00 2001 From: AlexGherardelli Date: Thu, 11 Jun 2026 12:25:32 +0200 Subject: [PATCH 08/16] fix: add ODBC dependencies to GHA --- .github/workflows/python-package.yml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 7e54daf..6bcb246 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -20,6 +20,12 @@ jobs: - "3.14" steps: - uses: actions/checkout@v6 + + - name: Install ODBC dependencies + run: | + sudo apt-get update + sudo apt-get install -y unixodbc-dev + - name: Install uv and set Python version uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b with: From d305763221f6d7e35b2a63fecd0297402cfdb797 Mon Sep 17 00:00:00 2001 From: AlexGherardelli Date: Thu, 11 Jun 2026 12:30:42 +0200 Subject: [PATCH 09/16] fix: add ODBC dependencies to GHA --- .github/workflows/python-package.yml | 31 ++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 6bcb246..84bae96 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -8,6 +8,28 @@ on: permissions: contents: write +jobs: + build: + runs-on: ubuntu-latest + strategy: + matrix: + python-version: + - "3.11" + - "3.12" + - "3.13" + - "3.14" + steps: + - uses: actions/checkout@v6 + --- +name: Python package +on: + pull_request: + branches: + - master + +permissions: + contents: write + jobs: build: runs-on: ubuntu-latest @@ -25,6 +47,15 @@ jobs: run: | sudo apt-get update sudo apt-get install -y unixodbc-dev + - name: Install uv and set Python version + uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b + with: + python-version: ${{ matrix.python-version }} + - name: Install dependencies + run: uv sync --dev + - name: Lint with Ruff + run: | + uv run ruff check . --fix - name: Install uv and set Python version uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b From 7aa8272107cbcc2743e267f70dae56911874a803 Mon Sep 17 00:00:00 2001 From: AlexGherardelli Date: Thu, 11 Jun 2026 12:33:15 +0200 Subject: [PATCH 10/16] fix: add ODBC dependencies to GHA --- .github/workflows/python-package.yml | 38 +++------------------------- 1 file changed, 3 insertions(+), 35 deletions(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 84bae96..7d72d51 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -20,42 +20,10 @@ jobs: - "3.14" steps: - uses: actions/checkout@v6 - --- -name: Python package -on: - pull_request: - branches: - - master - -permissions: - contents: write - -jobs: - build: - runs-on: ubuntu-latest - strategy: - matrix: - python-version: - - "3.11" - - "3.12" - - "3.13" - - "3.14" - steps: - - uses: actions/checkout@v6 - - - name: Install ODBC dependencies - run: | - sudo apt-get update - sudo apt-get install -y unixodbc-dev - - name: Install uv and set Python version - uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b - with: - python-version: ${{ matrix.python-version }} - - name: Install dependencies - run: uv sync --dev - - name: Lint with Ruff + - name: Install ODBC dependencies run: | - uv run ruff check . --fix + sudo apt-get update + sudo apt-get install -y unixodbc-dev - name: Install uv and set Python version uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b From 4f964c7de0052d8a551c686c265297aab9a4f442 Mon Sep 17 00:00:00 2001 From: AlexGherardelli Date: Thu, 11 Jun 2026 12:43:36 +0200 Subject: 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