Initial commit

.gitignore

+.coverage
+__pycache__/
+.idea/
+.env/
+*~
+uri_replacements.json
+*.log
\ No newline at end of file

.gitlab-ci.yml

+stages:
+  - lint
+  - test
+
+lint:
+  image: node
+  stage: lint
+  before_script:
+    - "npm install -g markdownlint"
+    - "npm install -g markdownlint-cli"
+  script:
+    - markdownlint '**/*.md' --ignore node_modules | tee lint.log  # Lint markdown files
+  artifacts:
+    when: always
+    paths:
+      - lint.log
+  allow_failure: true  # Continue pipeline even if markdownlint fails
+
+ruff:
+  image: python:3.10
+  stage: lint
+  before_script:
+    # Install pipx
+    - python3 -m pip install --user pipx
+    - python3 -m pipx ensurepath
+    - source ~/.bashrc
+    # Install Poetry using pipx
+    - pipx install poetry
+    # Install dependencies using Poetry
+    - poetry install
+  script:
+    - poetry run ruff check .  # Run ruff linter
+  allow_failure: true  # Continue pipeline even if ruff fails
+
+test:
+  image: python:3.10
+  stage: test
+  before_script:
+    # Install pipx
+    - python3 -m pip install --user pipx
+    - python3 -m pipx ensurepath
+    - source ~/.bashrc
+    # Install Poetry using pipx
+    - pipx install poetry
+    # Install dependencies using Poetry
+    - poetry install
+  script:
+    - poetry run coverage run -m unittest  # Run unit tests with coverage
+    - poetry run coverage report           # Output coverage report to console
+    - poetry run coverage xml           # Output coverage report to console
+  coverage: '/TOTAL.*\s+([0-9]{1,3})%/'    # Extract coverage percentage
+

.markdownlint.json

+{
+  "MD013": false,
+  "MD024": {
+    "siblings_only": true
+  }
+}
\ No newline at end of file

CHANGELOG.md

+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [1.0.0] - 2024-12-20
+
+### Added
+
+- Initial project files

Dockerfile

+FROM alpine
+
+# Install necessary system dependencies
+RUN apk add --no-cache poetry proj-util gdal-dev gcc python3-dev musl-dev geos-dev proj-dev libmagic
+
+# Set the PATH for pipx
+ENV PATH="/root/.local/bin:${PATH}"
+
+# Set the working directory inside the container
+WORKDIR /app
+
+# Copy the entire project to the container's working directory
+COPY . .
+
+# Install project dependencies with Poetry
+RUN poetry install --no-interaction --no-ansi
+
+# Make the main script executable
+RUN chmod +x dcat_catalog_check.py
+
+# Specify the entry point to run the script by default
+ENTRYPOINT ["poetry", "run", "./dcat_catalog_check.py"]

LICENSE

+EUROPEAN UNION PUBLIC LICENCE v. 1.2
+EUPL © the European Union 2007, 2016
+
+This European Union Public Licence (the ‘EUPL’) applies to the Work (as defined below) which is provided under the
+terms of this Licence. Any use of the Work, other than as authorised under this Licence is prohibited (to the extent such
+use is covered by a right of the copyright holder of the Work).
+The Work is provided under the terms of this Licence when the Licensor (as defined below) has placed the following
+notice immediately following the copyright notice for the Work:
+                          Licensed under the EUPL
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+
+1.Definitions
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+
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+— this Licence shall be governed by the law of the European Union Member State where the Licensor has his seat,
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+— this licence shall be governed by Belgian law if the Licensor has no seat, residence or registered office inside
+a European Union Member State.
+
+
+                                                         Appendix
+
+‘Compatible Licences’ according to Article 5 EUPL are:
+— GNU General Public License (GPL) v. 2, v. 3
+— GNU Affero General Public License (AGPL) v. 3
+— Open Software License (OSL) v. 2.1, v. 3.0
+— Eclipse Public License (EPL) v. 1.0
+— CeCILL v. 2.0, v. 2.1
+— Mozilla Public Licence (MPL) v. 2
+— GNU Lesser General Public Licence (LGPL) v. 2.1, v. 3
+— Creative Commons Attribution-ShareAlike v. 3.0 Unported (CC BY-SA 3.0) for works other than software
+— European Union Public Licence (EUPL) v. 1.1, v. 1.2
+— Québec Free and Open-Source Licence — Reciprocity (LiLiQ-R) or Strong Reciprocity (LiLiQ-R+).
+
+The European Commission may update this Appendix to later versions of the above licences without producing
+a new version of the EUPL, as long as they provide the rights granted in Article 2 of this Licence and protect the
+covered Source Code from exclusive appropriation.
+All other changes or additions to this Appendix require the production of a new EUPL version.

README.md

+# DCAT Catalog Check
+
+![pipeline status](https://code.schleswig-holstein.de/opendata/dcat-catalog-check/badges/main/pipeline.svg)
+![Coverage](https://code.schleswig-holstein.de/opendata/dcat-catalog-check/badges/main/coverage.svg?job=test)
+
+This project is a Python script designed to monitor and validate links in a DCAT catalog.
+
+The script is particularly useful for maintaining the integrity of distributions by ensuring that links are active and files are correctly formatted, thus helping to avoid issues related to broken links and invalid file types.
+
+## Table of Contents
+
+- [Features](#features)
+- [Installation](#installation)
+- [Usage](#usage)
+- [Configuration](#configuration)
+- [Docker](#docker)
+- [Tests](#tests)
+- [Contributing](#contributing)
+- [License](#license)
+
+## Features
+
+- Retrieves the DCAT catalog.
+- Checks if the URLs associated with the resources are alive or dead.
+- If the file has been successfully downloaded, it is checked using the **format specified in the metadata**.
+- Validates the MIME type of the distributions if no specialized check is available.
+- Logs the results.
+
+The following format checks are currently being carried out:
+
+| Format    | Check |
+| --------- | ------- |
+| `GEOJSON` | Load the file using [`GeoPandas`](https://geopandas.org). |
+| `GML`     | Load the file using [`GeoPandas`](https://geopandas.org). |
+| `JPEG`    | Load the image. |
+| `JSON`    | Is it syntactically correct JSON? If it is a *Frictionless Data Resource*, it is checked with the Frictionless Tools. |
+| `PNG`     | Load the image. |
+| `PDF`     | Load the document using [`pypdf`](https://pypi.org/project/pypdf/). |
+| `SHP`     | Load the file using [`GeoPandas`](https://geopandas.org). |
+| `WFS`     | Is it a valid well-formed `WMS_Capabilities` XML document? If the address does not contain the `request=GetCapabilities` parameter, a `GetCapabilities` request is performed. This response is then checked. |
+| `WMS`     | Is it a valid well-formed `WFS_Capabilities` XML document? If the address does not contain the `request=GetCapabilities` parameter, a `GetCapabilities` request is performed. This response is then checked.  |
+| `XML`     | Is it well-formed XML? |
+
+## Installation
+
+Follow the steps below to set up the **DCAT Catalog Check** on your local machine.
+
+### Installation with Poetry
+
+Using **Poetry** is recommended for dependency management and virtual environment handling.
+
+1. **Install Dependencies**
+
+   Navigate to the project directory and install the project’s dependencies (including development dependencies) using Poetry:
+
+   ```sh
+   poetry install
+   ```
+
+   This command will create a virtual environment and install all necessary packages as specified in the [`pyproject.toml`](./pyproject.toml) file.
+
+2. **Activating the Virtual Environment**
+
+   Poetry automatically manages virtual environments. You can activate the virtual environment with:
+
+   ```sh
+   poetry shell
+   ```
+
+   To exit the virtual environment, simply run:
+
+   ```sh
+   exit
+   ```
+
+## Usage
+
+### Parameters
+
+The **DCAT Catalog Check** script accepts several command-line arguments to customize its behavior. Below is a detailed explanation of each parameter:
+
+| Parameter | Description | Type | Default |
+| --------- | ----------- | ---- | ------- |
+| `--url` | The URL of the DCAT catalog to check. | String | Required |
+| `--log_file` | Path to the log file for storing detailed output. | String | None |
+| `--results` | File path to load results from previous runs. | String | None |
+| `--verbose` | Enable verbose logging for more detailed output. | Flag | Off |
+| `--debug` | Enable debug logging for troubleshooting purposes. | Flag | Off |
+| `--recheck` | Use the previous results (specified by `--results`) as input for rechecking only. | Flag | Off |
+| `--no-recheck` | Only check new entries from the catalog without rechecking existing results. | Flag | Off |
+| `--check-format` | Specify a single format to check (e.g., `JSON`, `JPEG`). | String | None |
+| `--force-check-format`| Force checking distributions with the specified format, regardless of previous results. | String | None |
+| `--check-http-5xx` | Recheck entries that encountered HTTP 5xx errors in previous runs. | Flag | Off |
+
+### Example Usage
+
+**Basic Run:**
+
+To check a DCAT catalog and save the results:
+
+```sh
+poetry run python dcat_catalog_check.py --url https://example.com/catalog.xml > results.jsonl
+```
+
+The catalog (including possible subsequent pages) is completely downloaded and checked. The result is written to the file `results.jsonl` in *JSON Lines text file format*.
+
+**Recheck Previous Results:**
+
+To recheck only existing results from a previous run:
+
+```sh
+poetry run python dcat_catalog_check.py --url https://example.com/catalog.xml --results results.jsonl --recheck
+```
+
+**Check New Entries Only:**
+
+To check only new entries without rechecking the existing ones:
+
+```sh
+poetry run python dcat_catalog_check.py --url https://example.com/catalog.xml --results results.jsonl --no-recheck > new.jsonl
+mv new.json results.jsonl
+```
+
+The results from a previous run from the file `result.jsonl` are used. The catalog is processed completely. Only new data records are checked. All results (new ones as well as the old ones that have not been checked again) are output to the file `new.jsonl`. Once the check is complete, the old results file is overwritten with the new one.
+
+**Debugging and Verbose Output:**
+
+To enable verbose and debug logging:
+
+```sh
+poetry run python dcat_catalog_check.py --url https://example.com/catalog.xml --verbose --debug
+```
+
+**Format-Specific Checks:**
+
+To check only a specific format (e.g., `JSON`):
+
+```sh
+poetry run python dcat_catalog_check.py --url https://example.com/catalog.xml --check-format JSON
+```
+
+**Force Format Check:**
+
+To force-check a specific format regardless of previous results:
+
+```sh
+poetry run python dcat_catalog_check.py --url https://example.com/catalog.xml --force-check-format JSON
+```
+
+## Configuration
+
+### File Formats
+
+The script reads the allowed file formats from [`resources/file_types.json`](./resources/file_types.json)
+file. This file defines the MIME types that are considered valid for each
+format and should be placed in the same directory as the script.
+
+#### Example `file_types.json`
+
+```json
+{
+  "HTML": [
+    "text/html"
+  ],
+  "JPEG": [
+    "image/jpeg"
+  ],
+  "JSON": [
+    "application/json", "text/plain"
+  ]
+}
+```
+
+### URI Replacements (optional)
+
+The `uri_replacements.json` file is an optional configuration file that provides a way to preprocess and modify URLs before they are checked by the script. This can be useful for standardizing, correcting, or transforming URLs to match specific patterns or to comply with expected formats.
+
+#### Example `uri_replacements.json`
+
+The file is a JSON array, where each element is an object containing two keys:
+
+- `regex`: A regular expression (in Python regex syntax) that matches parts of the URL that need to be replaced.
+- `replaced_by`: A string specifying the replacement value for the matched parts of the URL.
+
+Example:
+
+```json
+[
+  {
+    "regex": "http://example.com/old-path",
+    "replaced_by": "http://example.com/new-path"
+  },
+  {
+    "regex": "https://(.*)/deprecated",
+    "replaced_by": "https://\\1/updated"
+  }
+]
+```
+
+In this example:
+
+- URLs starting with `http://example.com/old-path` will be replaced with `http://example.com/new-path`.
+- Any URL containing `/deprecated` after the domain will have `/deprecated` replaced with `/updated`.
+
+#### How to Use
+
+1. Create a file named `uri_replacements.json` in the script's directory.
+2. Define the desired replacements in the JSON array format described above.
+3. Run the script as usual. If the file exists, replacements will be applied automatically.
+
+By using `uri_replacements.json`, you can streamline URL handling and ensure consistent preprocessing for your link-checking tasks.
+
+## Docker
+
+You can run the script in a Docker container. See the [Dockerfile](./Dockerfile) for more information.
+
+### Build and Run
+
+1. Build the Docker image:
+
+    ```sh
+    docker build -t dcat-catalog-check .
+    ```
+
+2. Run the Docker container:
+
+    ```sh
+    docker run --rm dcat-catalog-check --url https://example.com 
+    ```
+
+## Tests
+
+To ensure the quality of the code, we utilize **unittest** for testing and **coverage** to measure code coverage. Follow the instructions below to run the tests and generate coverage reports.
+
+### Running Tests
+
+To run the tests with coverage, you can use either of the following commands:
+
+```sh
+# Using Python directly
+python3 -m coverage run -m unittest
+```
+
+or
+
+```sh
+# Using Poetry
+poetry run coverage run -m unittest
+```
+
+### Generating a Coverage Report
+
+After running the tests, you can generate a coverage report to see which parts of your code were exercised during testing:
+
+```sh
+# Using Python directly
+python3 -m coverage report
+```
+
+or
+
+```sh
+# Using Poetry
+poetry run coverage report
+```
+
+### Code Linting
+
+For code linting, we use **ruff** to enforce style and catch potential issues. Run the following command to lint your code:
+
+```sh
+# Using Python directly
+python3 -m ruff check .
+```
+
+or
+
+```sh
+# Using Poetry
+poetry run ruff check .
+```
+
+## Contributing
+
+Contributions are welcome! Please open an issue or submit a pull request
+with your changes.
+
+## License
+
+This project is licensed under the European Union Public License 1.2.
+See the [`LICENSE`](./LICENSE) file for details.

formats/geojson_format.py

+import geopandas
+from pyogrio.errors import DataSourceError
+from shapely.errors import GEOSException
+
+
+def is_valid(resource, file):
+    """Check if the content is a readable GeoJSON file."""
+
+    with open(file.name, "rb") as f:
+        try:
+            geopandas.read_file(f)
+            return True
+        except DataSourceError:
+            return False
+        except GEOSException:
+            return False

formats/gml_format.py

+import geopandas
+from pyogrio.errors import DataSourceError
+from shapely.errors import GEOSException
+
+
+def is_valid(resource, file):
+    """Check if the content is a readable GML file."""
+
+    with open(file.name, "rb") as f:
+        try:
+            geopandas.read_file(f)
+            return True
+        except DataSourceError as e:
+            resource["error"] = str(e)
+            return False
+        except GEOSException as e:
+            resource["error"] = str(e)
+            return False
+        except Exception as e:
+            resource["error"] = str(e)
+            return False

formats/jpeg_format.py

+from PIL import Image, UnidentifiedImageError
+
+
+def is_valid(resource, file):
+    """Check if the content is a readable JPEG image."""
+
+    try:
+        with Image.open(file.name, formats=["JPEG"]):
+            return True
+    except UnidentifiedImageError:
+        return False

formats/json_format.py

+import json
+from frictionless import Resource
+
+
+def is_valid(resource, file):
+    """Check if the HTTP response is a valid JSON document."""
+
+    with open(file.name, "rb") as f:
+        try:
+            json_data = json.load(f)
+
+            if (
+                "path" in json_data
+                and "schema" in json_data
+                and (
+                    json_data.get("profile") == "tabular-data-resource"
+                    or json_data.get("type") == "table"
+                )
+            ):
+                # There is a good chance that this is a Frictionless Data Resource.
+                res = Resource(json_data)
+                resource["schema_valid"] = res.validate().valid
+                return resource["schema_valid"]
+
+            return True
+        except json.JSONDecodeError as e:
+            resource["error"] = str(e)
+            return False
+        except UnicodeDecodeError as e:
+            resource["error"] = str(e)
+            return False

formats/parquet_format.py

+import pandas as pd
+
+
+def is_valid(resource, file):
+    """Check if the content is a readable Apache Parquet file."""
+
+    try:
+        pd.read_parquet(file.name)
+        return True
+    except Exception as e:
+        resource["error"] = str(e)
+        return False

formats/pdf_format.py

+from pypdf import PdfReader
+from pypdf.errors import PyPdfError
+
+
+def is_valid(resource, file):
+    """Check if the content is a readable PDF document."""
+
+    with open(file.name, "rb") as f:
+        try:
+            PdfReader(f)
+            return True
+        except PyPdfError:
+            return False

formats/png_format.py

+from PIL import Image, UnidentifiedImageError
+
+
+def is_valid(resource, file):
+    """Check if the content is a readable PNG image."""
+
+    try:
+        with Image.open(file.name, formats=["PNG"]):
+            return True
+    except UnidentifiedImageError:
+        return False

formats/shp_format.py

+import geopandas
+from pyogrio.errors import DataSourceError
+from shapely.errors import GEOSException
+import zipfile
+
+
+def is_valid(resource, file):
+    """Check if the content is a readable shape file."""
+
+    # There are some strange 'shape files' that are actually ZIP files
+    # containing multiple SHP file.
+    try:
+        with zipfile.ZipFile(file.name, "r") as z:
+            shapefiles = [f for f in z.namelist() if f.endswith(".shp")]
+    except zipfile.BadZipFile as e:
+        resource["error"] = str(e)
+        return False
+
+    if len(shapefiles) == 0:
+        resource["error"] = "File contains no .shp file"
+        return False
+    elif (len(shapefiles) == 1) and ("/" not in shapefiles[0]):
+        #  the normal case
+        with open(file.name, "rb") as f:
+            try:
+                geopandas.read_file(f)
+            except DataSourceError as e:
+                resource["error"] = str(e)
+                return False
+            except GEOSException as e:
+                resource["error"] = str(e)
+                return False
+        return True
+    else:
+        with zipfile.ZipFile(file.name, "r") as z:
+            for shp in shapefiles:
+                with z.open(shp) as f:
+                    try:
+                        geopandas.read_file(f"zip://{file.name}!{shp}")
+                    except DataSourceError as e:
+                        resource["error"] = str(e)
+                        return False
+                    except GEOSException as e:
+                        resource["error"] = str(e)
+                        return False
+        return True

formats/wfs_srvc_format.py

+import xml.etree.ElementTree as ET
+import requests
+import tempfile
+
+
+def _load_into_file(url):
+    response = requests.get(url)
+    response.raise_for_status()
+
+    with tempfile.NamedTemporaryFile(delete=False) as temp_file:
+        temp_file.write(response.content)
+        return temp_file
+
+
+def _is_capabilites_response(file):
+    with open(file.name, "rb") as f:
+        try:
+            xml = ET.parse(f).getroot()
+
+            return (
+                xml.tag == "{http://www.opengis.net/wfs/2.0}WFS_Capabilities"
+                or xml.tag == "{http://www.opengis.net/wfs}WFS_Capabilities"
+            )
+        except ET.ParseError:
+            return False
+
+
+def is_valid(resource, file):
+    if _is_capabilites_response(file):
+        return True
+
+    # The response is not a capabilites XML files. That is allowed.
+    # Let's add the request parameters to the URL and try again.
+
+    url = resource["url"]
+    if "request=" not in url.lower():
+        if not url.endswith("?"):
+            url = url + "?"
+
+        url = url + "service=WFS&request=GetCapabilities"
+        return _is_capabilites_response(_load_into_file(url))
+    else:
+        # The URL already contains a getCapabilites request but the result was not a correct answer.
+        return False

formats/wms_srvc_format.py

+import xml.etree.ElementTree as ET
+import requests
+import tempfile
+
+
+def _load_into_file(url):
+    response = requests.get(url)
+    response.raise_for_status()
+
+    with tempfile.NamedTemporaryFile(delete=False) as temp_file:
+        temp_file.write(response.content)
+        return temp_file
+
+
+def _is_capabilites_response(file):
+    with open(file.name, "rb") as f:
+        try:
+            xml = ET.parse(f).getroot()
+
+            return xml.tag == "{http://www.opengis.net/wms}WMS_Capabilities"
+        except ET.ParseError:
+            return False
+
+
+def is_valid(resource, file):
+    if _is_capabilites_response(file):
+        return True
+
+    # The response is not a capabilites XML files. That is allowed.
+    # Let's add the request parameters to the URL and try again.
+
+    url = resource["url"]
+    if "request=" not in url.lower():
+        if not url.endswith("?"):
+            url = url + "?"
+
+        url = url + "service=WMS&request=GetCapabilities"
+        return _is_capabilites_response(_load_into_file(url))
+    else:
+        # The URL already contains a getCapabilites request but the result was not a correct answer.
+        return False

formats/xml_format.py

+import xml.etree.ElementTree as ET
+
+
+def is_valid(resource, file):
+    """Check if the HTTP response is a well-formed XML document."""
+
+    with open(file.name, "rb") as f:
+        try:
+            ET.parse(f)
+            return True
+        except ET.ParseError as e:
+            resource["error"] = str(e)
+            return False