diff --git a/.build-constraints.txt b/.build-constraints.txt index 68b1167..ca77717 100644 --- a/.build-constraints.txt +++ b/.build-constraints.txt @@ -13,7 +13,7 @@ pluggy==1.6.0 \ --hash=sha256:7dcc130b76258d33b90f61b658791dede3486c3e6bfb003ee5c9bfb396dd22f3 \ --hash=sha256:e920276dd6813095e9377c0bc5566d94c932c33b27a3e3945d8389c374dd4746 # via hatchling -trove-classifiers==2026.4.28.13 \ - --hash=sha256:8f4b1eb4e16296b57d612965444f87a83861cc989a0451ac97fe4265ddef03b8 \ - --hash=sha256:c85bb8a53c3de7330d1699b844ed9fb809a602a09ac15dc79ad6d1a509be0676 +trove-classifiers==2026.5.7.17 \ + --hash=sha256:5ec0800de5e2ddbd7c663cb4c0c15328f132dc168813897c18866c5c7b93db33 \ + --hash=sha256:a04a48f8f0a787cb996514d3969ac7608aa3c60cb15d073c1e02801e60533e80 # via hatchling diff --git a/.github/workflows/publish.yaml b/.github/workflows/publish.yaml deleted file mode 100644 index 824c3ec..0000000 --- a/.github/workflows/publish.yaml +++ /dev/null @@ -1,438 +0,0 @@ -name: publish - -on: - push: - branches: [ main, preview ] - workflow_dispatch: - -permissions: - contents: read - pages: write - id-token: write - -concurrency: - group: "pages" - cancel-in-progress: false - -jobs: - publish: - runs-on: html_publisher - environment: - name: ${{ github.ref_name == 'main' && 'github-pages' || 'preview' }} - url: ${{ steps.deployment.outputs.page_url }} - steps: - - - name: Checkout project - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd - - - name: Set up Python - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 - with: - python-version: "3.12" - - - name: Install dependencies - run: | - pip install --upgrade pip - pip install nbconvert jupyter-book sphinx markdown beautifulsoup4 - - - name: Convert notebooks and create single-page app - run: | - mkdir -p site - - # Convert .ipynb notebooks to HTML fragments (body content only) - for notebook in */*.ipynb; do - if [ -f "$notebook" ]; then - jupyter nbconvert "$notebook" --to html \ - --template classic --HTMLExporter.theme=light \ - --no-prompt --stdout > "temp_$(basename "$notebook" .ipynb).html" - fi - done - - # Convert .py Databricks notebooks to HTML fragments - chmod +x .github/scripts/convert_notebooks.py - python3 .github/scripts/convert_notebooks.py - - # Create single-page application with embedded content - python3 << 'EOF' - import os - import json - import markdown - import re - import glob - from bs4 import BeautifulSoup - - # Read README.md - readme_content = "" - if os.path.exists('README.md'): - with open('README.md', 'r') as f: - readme_content = markdown.markdown(f.read()) - - # Get repository name and format title - repo_name = os.environ.get('GITHUB_REPOSITORY', '').split('/')[-1] - title = ' '.join(word.capitalize() for word in repo_name.split('-')) + ' Accelerator' - - # Collect all notebook content - notebooks = {} - - # Read .py notebook fragments - if os.path.exists('notebook_fragments.json'): - with open('notebook_fragments.json', 'r') as f: - py_notebooks = json.load(f) - notebooks.update(py_notebooks) - - # Read .ipynb notebook content (extract body from temp files) - for temp_file in glob.glob('temp_*.html'): - if 'fragment' not in temp_file: # These are the nbconvert outputs - name = temp_file.replace('temp_', '').replace('.html', '') - with open(temp_file, 'r') as f: - content = f.read() - # Extract body content - soup = BeautifulSoup(content, 'html.parser') - body = soup.find('body') - if body: - # Find the notebook container - container = body.find('div', class_='container') - if container: - notebooks[name] = str(container) - else: - notebooks[name] = str(body) - - # Create single-page application - html = f''' - - - {title} - - - - - - - -
- -
{title}
- View on GitHub -
- -
-
-

📚 Documentation

-
Overview
''' - - # Add notebook navigation - if notebooks: - html += '\n

📓 Notebooks

' - for name in sorted(notebooks.keys()): - display_name = name.replace('_', ' ').title() - html += f'\n
📓 {display_name}
' - - html += f''' -
- -
- -
- {readme_content} -
''' - - # Add notebook sections - for name, content in notebooks.items(): - html += f''' - -
- {content} -
''' - - html += f''' -
-
- - - - - - ''' - - # Write the single-page application - with open('site/index.html', 'w') as f: - f.write(html) - - print(f"Created single-page application with {len(notebooks)} notebooks") - - # Clean up temporary files - for temp_file in glob.glob('temp_*.html'): - os.remove(temp_file) - if os.path.exists('notebook_fragments.json'): - os.remove('notebook_fragments.json') - EOF - - - name: Upload artifact - uses: actions/upload-pages-artifact@7b1f4a764d45c48632c6b24a0339c27f5614fb0b - with: - path: 'site' - - - name: Deploy to GitHub Pages - id: deployment - uses: actions/deploy-pages@d6db90164ac5ed86f2b6aed7e0febac5b3c0c03e diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml new file mode 100644 index 0000000..3494226 --- /dev/null +++ b/.github/workflows/publish.yml @@ -0,0 +1,68 @@ +name: publish + +on: + push: + branches: [ main, preview ] + workflow_dispatch: + +permissions: + contents: read + +concurrency: + group: "pages" + cancel-in-progress: false + +jobs: + build: + name: Build Docusaurus + runs-on: html_publisher + + steps: + - name: Checkout + uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + with: + fetch-depth: 0 + + - name: Setup uv + uses: astral-sh/setup-uv@5a095e7a2014a4212f075830d4f7277575a9d098 # v7.3.1 + with: + version: "0.11.2" + enable-cache: true + cache-dependency-glob: "**/uv.lock" + + - name: Setup Node.js + uses: actions/setup-node@53b83947a5a98c8d113130e565377fae1a50d02f # v6.3.0 + with: + node-version: 22 + cache: yarn + cache-dependency-path: docs/python-data-sources/yarn.lock + + - name: Install docs dependencies + run: make docs-install + + - name: Build website + run: make docs-build + + - name: Upload Build Artifact + uses: actions/upload-pages-artifact@7b1f4a764d45c48632c6b24a0339c27f5614fb0b # v4.0.0 + with: + path: docs/python-data-sources/build + + deploy: + name: Deploy to GitHub Pages + needs: build + + permissions: + pages: write + id-token: write + + environment: + name: ${{ github.ref_name == 'main' && 'github-pages' || 'preview' }} + url: ${{ steps.deployment.outputs.page_url }} + + runs-on: html_publisher + + steps: + - name: Deploy to GitHub Pages + id: deployment + uses: actions/deploy-pages@d6db90164ac5ed86f2b6aed7e0febac5b3c0c03e # v4.0.5 diff --git a/Makefile b/Makefile index cac5de3..58f4a7d 100644 --- a/Makefile +++ b/Makefile @@ -1,4 +1,4 @@ -.PHONY: all clean dev fmt lint test coverage lock-dependencies verify-lock build +.PHONY: all clean dev fmt lint test coverage lock-dependencies verify-lock build docs-install docs-build docs-serve docs-serve-dev docs-clean all: clean lint fmt test @@ -6,7 +6,7 @@ export UV_FROZEN := 1 UV_RUN := uv run --exact --all-extras -clean: +clean: docs-clean rm -fr .venv clean htmlcov .pytest_cache .ruff_cache .coverage coverage.xml dist find . -name '__pycache__' -print0 | xargs -0 rm -fr @@ -29,7 +29,7 @@ verify-lock: if [ -n "$$bad" ]; then \ echo "uv.lock contains non-public registry URLs:"; \ echo "$$bad"; \ - echo "Run 'make lock' to regenerate and sanitize."; \ + echo "Run 'make lock-dependencies' to regenerate and sanitize."; \ exit 1; \ fi @@ -55,3 +55,21 @@ coverage: e2e: $(UV_RUN) pytest -rs --timeout 30 tests/e2e + +docs-install: + yarn --cwd docs/python-data-sources install --frozen-lockfile + +docs-build: + uv run --group docs pydoc-markdown + yarn --cwd docs/python-data-sources build + +docs-serve-dev: + uv run --group docs pydoc-markdown + yarn --cwd docs/python-data-sources start + +docs-serve: docs-build + yarn --cwd docs/python-data-sources serve + +docs-clean: + rm -rf docs/python-data-sources/build docs/python-data-sources/.docusaurus docs/python-data-sources/.cache + find docs/python-data-sources/docs/reference/api -mindepth 1 -not -name 'index.mdx' -exec rm -rf {} + diff --git a/docs/python-data-sources/.gitignore b/docs/python-data-sources/.gitignore new file mode 100644 index 0000000..2f584ae --- /dev/null +++ b/docs/python-data-sources/.gitignore @@ -0,0 +1,23 @@ +# Dependencies +/node_modules + +# Production +/build + +# Generated files +.docusaurus +.cache-loader + +# Generated API reference (pydoc-markdown output) +/docs/reference/api/python_data_sources/ + +# Misc +.DS_Store +.env.local +.env.development.local +.env.test.local +.env.production.local + +npm-debug.log* +yarn-debug.log* +yarn-error.log* diff --git a/docs/python-data-sources/docs/demos.mdx b/docs/python-data-sources/docs/demos.mdx new file mode 100644 index 0000000..c87d316 --- /dev/null +++ b/docs/python-data-sources/docs/demos.mdx @@ -0,0 +1,14 @@ +--- +sidebar_position: 3 +--- + +# Demos + +This project contains example notebooks in [`examples/`](https://github.com/databricks-industry-solutions/python-data-sources/tree/main/examples) +for you to work with custom data sources. + +* [`examples/zipdcm/zip-dicom-demo.ipynb`](https://github.com/databricks-industry-solutions/python-data-sources/blob/main/examples/zipdcm/zip-dicom-demo.ipynb) shows how to register a `zipdcm` data source, read a zipped archive of DICOM files, and access the pixel arrays. + +## Contributing a new demo + +New example notebooks are welcome. Place the notebook under `examples//` and reference it from this page. diff --git a/docs/python-data-sources/docs/installation.mdx b/docs/python-data-sources/docs/installation.mdx new file mode 100644 index 0000000..75c2c36 --- /dev/null +++ b/docs/python-data-sources/docs/installation.mdx @@ -0,0 +1,55 @@ +--- +sidebar_position: 2 +--- + +import Admonition from '@theme/Admonition'; +import Tabs from '@theme/Tabs'; +import TabItem from '@theme/TabItem'; + +# Installation + +Data sources can be installed from PyPI using `pip` commands. Each data source is packaged as an optional extra module. You can +limit installation of data sources and their dependencies to only the sources you need. + + +Installing Python Data Sources from this library requires Spark 4.0+. Each data source includes its required Python dependencies. + + +## Installing data sources + +List required data sources when installing using `pip` commands. + +```bash +pip install "python-data-sources[mcap]" # MCAP robotics logs +pip install "python-data-sources[mqtt]" # MQTT streaming +pip install "python-data-sources[zipdcm]" # DICOM in ZIP +pip install "python-data-sources[mcap,mqtt]" # Both MCAP and MQTT +pip install "python-data-sources[all]" # Installs all data sources +``` + + +Each data source requires its own dependencies. Because new data sources may be added to the project over time, it is best to +limit installation to sources required for your workloads. + + +## Registering data sources + +Data sources must be registered to be used in an active `SparkSession`. Once data sources are registered, you can reference them +using their data source name (e.g. "mcap" for the MCAP data source). See the [API reference](/docs/reference) for the full list of +registered data sources and their options. + +```python +from pyspark.sql import SparkSession +from python_data_sources.mcap import McapDataSource + +# Register the data source +spark = SparkSession.builder.getOrCreate() +spark.dataSource.register(McapDataSource) + +# Get the data source name +mcap_source_name = McapDataSource.name() # 'mcap' + +# Read MCAP data using the registered data source +df = spark.read.format("mcap").load("/path/to/logs/") +df.show() +``` diff --git a/docs/python-data-sources/docs/motivation.mdx b/docs/python-data-sources/docs/motivation.mdx new file mode 100644 index 0000000..f2d4514 --- /dev/null +++ b/docs/python-data-sources/docs/motivation.mdx @@ -0,0 +1,25 @@ +--- +sidebar_position: 1 +--- + +# Motivation + +Apache Spark ships native data sources commonly used in analytics workloads. The long tail of data sources is not covered by +standard Spark capabilities and is served by a patchwork of Java libraries or user-defined functions that are difficult to maintain. + +The [PySpark DataSource API](https://spark.apache.org/docs/latest/api/python/reference/pyspark.sql/datasource.html) allows users to implement and register Spark data source formats using `spark.read.format(...)`. +Sources that implement `DataSourceReader` and `DataSourceWriter` contracts can be used to read or write data with Spark. + +**python-data-sources** is a collection of Python-native connectors for formats and protocols that don't have a built-in Spark reader. + +## Connectors + +| Connector | Read | Write | Notes | +|-----------|------|--------|----------------------------------------------------------------| +| `mcap` | ✓ | — | MCAP container format used for robotics, AV, and ROS bag logs. | +| `mqtt` | ✓ | — | MQTT broker as a Structured Streaming source. | +| `zipdcm` | ✓ | — | DICOM medical images packaged inside ZIP archives. | + +## Contributing + +If you need a connector that isn't provided as a Python Data Source, [open a GitHub issue](https://github.com/databricks-industry-solutions/python-data-sources/issues). diff --git a/docs/python-data-sources/docs/reference/api/common/range_partition.md b/docs/python-data-sources/docs/reference/api/common/range_partition.md new file mode 100644 index 0000000..9b9f224 --- /dev/null +++ b/docs/python-data-sources/docs/reference/api/common/range_partition.md @@ -0,0 +1,13 @@ +--- +sidebar_label: range_partition +title: python_data_sources.common.range_partition +--- + +## RangePartition Objects + +```python +class RangePartition(InputPartition) +``` + +This DataSource InputPartition class provides tracking of ranges within a list + diff --git a/docs/python-data-sources/docs/reference/api/index.mdx b/docs/python-data-sources/docs/reference/api/index.mdx new file mode 100644 index 0000000..c2888a2 --- /dev/null +++ b/docs/python-data-sources/docs/reference/api/index.mdx @@ -0,0 +1,9 @@ +--- +sidebar_position: 1 +--- + +# API Reference + +The module-by-module API reference is generated by `pydoc-markdown` from the docstrings under `src/python_data_sources/`. Run `make docs-build` to regenerate the surrounding pages. + +If you're reading this in a freshly cloned tree, the per-module pages aren't here yet — they're written into this directory the first time `make docs-build` runs. diff --git a/docs/python-data-sources/docs/reference/api/mcap/mcap_datasource.md b/docs/python-data-sources/docs/reference/api/mcap/mcap_datasource.md new file mode 100644 index 0000000..e8c675c --- /dev/null +++ b/docs/python-data-sources/docs/reference/api/mcap/mcap_datasource.md @@ -0,0 +1,117 @@ +--- +sidebar_label: mcap_datasource +title: python_data_sources.mcap.mcap_datasource +--- + +### path\_handler + +```python +def path_handler(path: str, + glob_pattern: str, + recursive: bool = False) -> list +``` + +Discover files matching the glob pattern in the given path. + +**Arguments**: + +- `path` - Path to search for files +- `glob_pattern` - Glob pattern to match files (e.g., "*.mcap") +- `recursive` - If True, recursively search subdirectories using rglob + + +**Returns**: + + List of file paths matching the pattern + +### decode\_protobuf\_message + +```python +def decode_protobuf_message(message, schema, _reader) +``` + +Decode protobuf messages. + +### decode\_json\_message + +```python +def decode_json_message(message, _schema, _reader) +``` + +Decode JSON messages. + +### decode\_fallback + +```python +def decode_fallback(message, _schema, _reader) +``` + +Fallback decoder for unknown formats. + +## MCAPDataSourceReader Objects + +```python +class MCAPDataSourceReader(DataSourceReader) +``` + +Facilitate reading MCAP (ROS 2 bag) files. + +### partitions + +```python +def partitions() -> Sequence[RangePartition] +``` + +Compute 'splits' of the data to read. + +**Returns**: + + List of RangePartition objects + +### read + +```python +def read(partition: InputPartition) -> Iterator[tuple] +``` + +Executor level method, performs read by Range Partition. + +**Arguments**: + +- `partition` - The partition to read + + +**Returns**: + + Iterator of tuples (sequence, topic, schema, encoding, log_time, data_json) + +## MCAPDataSource Objects + +```python +class MCAPDataSource(DataSource) +``` + +A data source for batch query over MCAP (ROS 2 bag) files. + +Usage: + # Read all topics + df = spark.read.format("mcap").option("path", "/path/to/mcap/files").load() + + # Filter by specific topic at read time (more efficient than DataFrame filter) + df = spark.read.format("mcap") .option("path", "/path/to/mcap/files") .option("topicFilter", "pose") .load() + +Options: + - path: Path to MCAP file(s) or directory (required) + - pathGlobFilter: Glob pattern for file matching (default: "*.mcap") + - numPartitions: Number of partitions to split files across (default: 4) + - recursiveFileLookup: Recursively search subdirectories (default: false) + - topicFilter: Filter messages by topic name (optional). Use "*" or omit to read all topics. + +Schema: + - sequence: BIGINT - The message sequence number from MCAP + - topic: STRING - The message topic + - schema: STRING - The schema name + - encoding: STRING - The encoding type (protobuf, json, etc.) + - log_time: BIGINT - The message timestamp in nanoseconds + - data: STRING - JSON string containing all message fields + diff --git a/docs/python-data-sources/docs/reference/api/mqtt/mqtt_streaming.md b/docs/python-data-sources/docs/reference/api/mqtt/mqtt_streaming.md new file mode 100644 index 0000000..a6682d1 --- /dev/null +++ b/docs/python-data-sources/docs/reference/api/mqtt/mqtt_streaming.md @@ -0,0 +1,157 @@ +--- +sidebar_label: mqtt_streaming +title: python_data_sources.mqtt.mqtt_streaming +--- + +## MqttDataSource Objects + +```python +class MqttDataSource(DataSource) +``` + +A PySpark DataSource for reading MQTT messages from a broker. + +This data source allows you to stream MQTT messages into Spark DataFrames, +supporting various MQTT broker configurations including authentication, +SSL/TLS encryption, and different quality of service levels. + +Input validation is performed on critical parameters to ensure connection reliability. + +Supported options: +- broker_address: MQTT broker hostname or IP address (required, validated) +* Must be a valid hostname or IP address format +* Cannot be None, empty, or whitespace-only +- port: Broker port number (default: 8883, validated) +* Must be an integer in range 1-65535 +- username: Authentication username (optional) +- password: Authentication password (optional) +- topic: MQTT topic to subscribe to (default: "#" for all topics) +- qos: Quality of Service level 0-2 (default: 0, validated) +* Must be 0, 1, or 2 (standard MQTT QoS levels) +- require_tls: Enable SSL/TLS encryption (default: true) +- keepalive: Keep alive interval in seconds (default: 60) + +Example usage: +spark.readStream.format("mqtt_pub_sub") +.option("broker_address", "mqtt.example.com") +.option("topic", "sensors/+/temperature") +.option("username", "user") +.option("password", "pass") +.load() + +**Raises**: + +- `ValueError` - If broker_address, port, clean_session, or qos parameters are invalid. + +### name + +```python +@classmethod +def name(cls) +``` + +Returns the name of the data source. + +### \_\_init\_\_ + +```python +def __init__(options) +``` + +Initialize the MQTT data source with configuration options. + +**Arguments**: + +- `options` _dict_ - Configuration options for the MQTT connection. + See class docstring for supported options. + +### schema + +```python +def schema() +``` + +Define the schema of the data source. + +**Returns**: + +- `StructType` - The schema of the data source. + +### streamReader + +```python +def streamReader(schema: StructType) +``` + +Create and return a stream reader for MQTT data. + +**Arguments**: + +- `schema` _StructType_ - The schema for the streaming data. + + +**Returns**: + +- `MqttSimpleStreamReader` - A stream reader instance configured for MQTT. + +## MqttSimpleStreamReader Objects + +```python +class MqttSimpleStreamReader(SimpleDataSourceStreamReader) +``` + +### \_\_init\_\_ + +```python +def __init__(_schema, options) +``` + +Initialize the MQTT simple stream reader with configuration options. + +**Arguments**: + +- `_schema` _StructType_ - The schema for the streaming data. +- `options` _dict_ - Configuration options for the MQTT connection. + See class docstring for supported options. + +### latestOffset + +```python +def latestOffset() -> dict +``` + +Returns the current latest offset that the next microbatch will read to. + +### partitions + +```python +def partitions(start: dict, end: dict) +``` + +Plans the partitioning of the current microbatch defined by start and end offset. It +needs to return a sequence of :class:`InputPartition` objects. + +### read + +```python +def read(_) +``` + +Read MQTT messages from the broker. + +**Returns**: + +- `Iterator[list]` - An iterator of lists containing the MQTT message data. + The list contains the following elements: + - received_time: The time the message was received. + - topic: The topic of the message. + - message: The payload of the message. + - is_duplicate: Whether the message is a duplicate. + - qos: The quality of service level of the message. + - is_retained: Whether the message is retained. + + +**Raises**: + +- `Exception` - If the connection to the broker fails. + diff --git a/docs/python-data-sources/docs/reference/api/sidebar.json b/docs/python-data-sources/docs/reference/api/sidebar.json new file mode 100644 index 0000000..97ab080 --- /dev/null +++ b/docs/python-data-sources/docs/reference/api/sidebar.json @@ -0,0 +1,41 @@ +{ + "items": [ + { + "items": [ + { + "items": [ + "reference/api/python_data_sources/common/range_partition" + ], + "label": "python_data_sources.common", + "type": "category" + }, + { + "items": [ + "reference/api/python_data_sources/mcap/mcap_datasource" + ], + "label": "python_data_sources.mcap", + "type": "category" + }, + { + "items": [ + "reference/api/python_data_sources/mqtt/mqtt_streaming" + ], + "label": "python_data_sources.mqtt", + "type": "category" + }, + { + "items": [ + "reference/api/python_data_sources/zipdcm/zip_dcm_ds", + "reference/api/python_data_sources/zipdcm/zip_dcm_utils" + ], + "label": "python_data_sources.zipdcm", + "type": "category" + } + ], + "label": "python_data_sources", + "type": "category" + } + ], + "label": "Reference", + "type": "category" +} \ No newline at end of file diff --git a/docs/python-data-sources/docs/reference/api/zipdcm/zip_dcm_ds.md b/docs/python-data-sources/docs/reference/api/zipdcm/zip_dcm_ds.md new file mode 100644 index 0000000..6bdba5c --- /dev/null +++ b/docs/python-data-sources/docs/reference/api/zipdcm/zip_dcm_ds.md @@ -0,0 +1,40 @@ +--- +sidebar_label: zip_dcm_ds +title: python_data_sources.zipdcm.zip_dcm_ds +--- + +## ZipDCMDataSourceReader Objects + +```python +class ZipDCMDataSourceReader(DataSourceReader) +``` + +Facilitate reading Zipfiles full of DCM (DICOM) files. + +### partitions + +```python +def partitions() -> Sequence[RangePartition] +``` + +Compute 'splits' of the data to read + self.paths is the list of files discovered and now need to be partitioned. + +### read + +```python +def read( + partition: InputPartition +) -> Iterator[tuple] | Iterator["RecordBatch"] +``` + +Executor level method, performs read by Range Partition + +## ZipDCMDataSource Objects + +```python +class ZipDCMDataSource(DataSource) +``` + +A data source for batch query over zipped DICOM files the `ZipFile` and `PyDicom` libraries. + diff --git a/docs/python-data-sources/docs/reference/api/zipdcm/zip_dcm_utils.md b/docs/python-data-sources/docs/reference/api/zipdcm/zip_dcm_utils.md new file mode 100644 index 0000000..a80db0f --- /dev/null +++ b/docs/python-data-sources/docs/reference/api/zipdcm/zip_dcm_utils.md @@ -0,0 +1,45 @@ +--- +sidebar_label: zip_dcm_utils +title: python_data_sources.zipdcm.zip_dcm_utils +--- + +### readzipdcm + +```python +def readzipdcm(partition: RangePartition, paths: list, + dicom_keys_filter: list[str]) -> Iterator[list[Any]] +``` + +Generator function to extract DICOM metadata from .dcm files within ZIP archives. + +Iterates over a partitioned list of ZIP file paths, opens each ZIP file, and processes files +with a '.dcm' extension. For each DICOM file, reads the header metadata, removes specified +large keys from the metadata dictionary, computes a SHA-1 hash of the pixel data, and yields +the results as a list. + +**Arguments**: + +- `partition` _RangePartition_ - An object with 'start' and 'end' attributes specifying the range of paths to process. +- `paths` _list_ - List of ZIP file paths to process. +- `dicom_keys_filter` _list_ - List of metadata keys to remove from the extracted DICOM metadata. + + +**Yields**: + +- `list` - A list containing: + - rowid (int): Unique row identifier. + - Either concatenation of: + - zip_file_path (str): Path to the ZIP file. + - '/' + - name_in_zip (str): Name of the DICOM file within the ZIP archive. + Or: + - dcm_file_path (str): Path to the dcm file. + - meta (dict): Filtered DICOM metadata dictionary with an added 'pixel_hash' key. + + +**Notes**: + + - Assumes that the DICOM files can be read directly from the ZIP archive without extraction. + - The 'pixel_hash' is computed using SHA-1 on the pixel array of the DICOM file. + - Logging is performed at various steps for debugging purposes. + diff --git a/docs/python-data-sources/docs/reference/index.mdx b/docs/python-data-sources/docs/reference/index.mdx new file mode 100644 index 0000000..00d130e --- /dev/null +++ b/docs/python-data-sources/docs/reference/index.mdx @@ -0,0 +1,11 @@ +--- +sidebar_position: 4 +--- + +# Reference + +This section is the technical reference for `python-data-sources`. + +- [**API reference**](/docs/reference/api) — auto-generated module-by-module documentation for every public class and function in `src/python_data_sources`. Generated from docstrings by [`pydoc-markdown`](https://github.com/NiklasRosenstein/pydoc-markdown). + +If something is missing or wrong, the source of truth is the docstring in the code — fix it there and the next docs build will pick it up. See [`CONTRIBUTING.md`](https://github.com/databricks-industry-solutions/python-data-sources/blob/main/CONTRIBUTING.md) for how to rebuild the docs locally. diff --git a/docs/python-data-sources/docusaurus.config.ts b/docs/python-data-sources/docusaurus.config.ts new file mode 100644 index 0000000..2229bdf --- /dev/null +++ b/docs/python-data-sources/docusaurus.config.ts @@ -0,0 +1,203 @@ +import path from 'path'; +import { themes as prismThemes } from 'prism-react-renderer'; +import type { Config } from '@docusaurus/types'; +import type * as Preset from '@docusaurus/preset-classic'; + +// This runs in Node.js - Don't use client-side code here (browser APIs, JSX...) + +const config: Config = { + title: 'Python Data Sources', + tagline: 'A collection of custom PySpark data source connectors for various formats.', + favicon: 'img/logo.svg', + + url: 'https://databricks-industry-solutions.github.io', + baseUrl: '/python-data-sources/', + trailingSlash: true, + + organizationName: 'databricks-industry-solutions', + projectName: 'python-data-sources', + + onBrokenLinks: 'throw', + onDuplicateRoutes: 'throw', + onBrokenAnchors: 'throw', + + markdown: { + mermaid: true, + hooks: { + onBrokenMarkdownLinks: 'throw', + }, + }, + themes: ['@docusaurus/theme-mermaid'], + + i18n: { + defaultLocale: 'en', + locales: ['en'], + }, + + plugins: [ + async () => ({ + name: 'fix-vscode-languageserver-types-resolution', + configureWebpack() { + // theme-mermaid → mermaid → langium → vscode-languageserver-types. + // vscode-languageserver-types defaults to UMD (main.js) which triggers + // "Critical dependency: require function is used in a way in which + // dependencies cannot be statically extracted". Force ESM build instead. + const vscodeTypesPath = path.join( + __dirname, + 'node_modules/vscode-languageserver-types/lib/esm/main.js', + ); + return { + resolve: { + alias: { + 'vscode-languageserver-types': vscodeTypesPath, + }, + }, + }; + }, + }), + async (context, options) => { + return { + name: 'docusaurus-plugin-tailwindcss', + configurePostCss(postcssOptions) { + postcssOptions.plugins = [ + require('tailwindcss'), + require('autoprefixer'), + ]; + return postcssOptions; + }, + }; + }, + 'docusaurus-plugin-image-zoom', + 'docusaurus-lunr-search', + [ + // TODO: pinned to pre-release alpha; revisit when a stable 2.0.0 is published + // https://www.npmjs.com/package/@signalwire/docusaurus-plugin-llms-txt + '@signalwire/docusaurus-plugin-llms-txt', + { + markdown: { + enableFiles: true, + relativePaths: true, + includeBlog: false, + includePages: true, + includeDocs: true, + includeVersionedDocs: false, + excludeRoutes: [], + }, + llmsTxt: { + enableLlmsFullTxt: true, + includeBlog: false, + includePages: true, + includeDocs: true, + excludeRoutes: [], + + siteTitle: 'Python Data Sources', + siteDescription: 'A collection of custom PySpark data source connectors for various formats.', + + autoSectionDepth: 1, + autoSectionPosition: 100, + + sections: [ + { + id: 'getting-started', + name: 'Getting Started', + description: 'Installation and motivation for Python Data Sources', + position: 1, + routes: [ + { route: '/python-data-sources/docs/installation' }, + { route: '/python-data-sources/docs/motivation' }, + ], + }, + { + id: 'reference', + name: 'Reference', + description: 'API reference and technical documentation', + position: 2, + routes: [ + { route: '/python-data-sources/docs/reference/**' }, + ], + }, + { + id: 'demos', + name: 'Demos', + description: 'Example notebooks and demos', + position: 3, + routes: [ + { route: '/python-data-sources/docs/demos' }, + ], + }, + { + id: 'home', + name: 'Home', + description: 'Python Data Sources homepage', + position: 0, + routes: [ + { route: '/python-data-sources/' }, + { route: '/python-data-sources/index' }, + ], + }, + ], + }, + }, + ], + ], + + presets: [ + [ + 'classic', + { + docs: { + sidebarPath: './sidebars.ts', + editUrl: + 'https://github.com/databricks-industry-solutions/python-data-sources/tree/main/docs/python-data-sources/', + }, + blog: false, + theme: { + customCss: './src/css/custom.css', + }, + } satisfies Preset.Options, + ], + ], + + themeConfig: { + colorMode: { + defaultMode: 'dark', + respectPrefersColorScheme: false, + }, + navbar: { + title: 'Python Data Sources', + logo: { + alt: 'Python Data Sources Logo', + src: 'img/logo.svg', + }, + items: [ + { + type: 'search', + position: 'right', + }, + { + href: 'https://github.com/databricks-industry-solutions/python-data-sources', + position: 'right', + className: 'header-github-link', + 'aria-label': 'GitHub repository', + }, + ], + }, + footer: { + links: [], + copyright: `Copyright © ${new Date().getFullYear()} Databricks Industry Solutions. Docs built with Docusaurus.`, + }, + prism: { + theme: prismThemes.oneLight, + darkTheme: prismThemes.oneDark, + }, + zoom: { + selector: 'article img', + background: { + light: '#F8FAFC', + dark: '#F8FAFC', + }, + }, + } satisfies Preset.ThemeConfig, +}; + +export default config; diff --git a/docs/python-data-sources/package.json b/docs/python-data-sources/package.json new file mode 100644 index 0000000..2613bea --- /dev/null +++ b/docs/python-data-sources/package.json @@ -0,0 +1,60 @@ +{ + "name": "python-data-sources", + "version": "0.0.0", + "private": true, + "scripts": { + "docusaurus": "docusaurus", + "start": "docusaurus start", + "build": "docusaurus build", + "swizzle": "docusaurus swizzle", + "deploy": "docusaurus deploy", + "clear": "docusaurus clear", + "serve": "docusaurus serve", + "write-translations": "docusaurus write-translations", + "write-heading-ids": "docusaurus write-heading-ids", + "typecheck": "tsc" + }, + "dependencies": { + "@docusaurus/core": "^3.8.1", + "@docusaurus/preset-classic": "^3.8.1", + "@docusaurus/theme-mermaid": "^3.8.1", + "@mdx-js/react": "^3.0.0", + "@signalwire/docusaurus-plugin-llms-txt": "2.0.0-alpha.7", + "clsx": "^2.1.1", + "docusaurus-lunr-search": "3.6.1", + "docusaurus-plugin-image-zoom": "^2.0.0", + "lucide-react": "^0.471.1", + "prism-react-renderer": "^2.3.0", + "react": "^19.0.0", + "react-dom": "^19.0.0", + "tsx": "^4.20.3" + }, + "devDependencies": { + "@docusaurus/module-type-aliases": "^3.8.1", + "@docusaurus/tsconfig": "^3.8.1", + "@docusaurus/types": "^3.8.1", + "@tailwindcss/typography": "^0.5.16", + "autoprefixer": "^10.4.20", + "postcss": "^8.5.1", + "tailwindcss": "^3.4.17", + "typescript": "~5.6.2" + }, + "browserslist": { + "production": [ + ">0.5%", + "not dead", + "not op_mini all" + ], + "development": [ + "last 3 chrome version", + "last 3 firefox version", + "last 5 safari version" + ] + }, + "engines": { + "node": ">=18.0" + }, + "resolutions": { + "webpack": "~5.97.0" + } +} diff --git a/docs/python-data-sources/sidebars.ts b/docs/python-data-sources/sidebars.ts new file mode 100644 index 0000000..eb6d05c --- /dev/null +++ b/docs/python-data-sources/sidebars.ts @@ -0,0 +1,12 @@ +import type { SidebarsConfig } from '@docusaurus/plugin-content-docs'; + +// This runs in Node.js - Don't use client-side code here (browser APIs, JSX...) + +const sidebars: SidebarsConfig = { + // Generated from the docs/ folder structure + tutorialSidebar: [ + { type: 'autogenerated', dirName: '.' }, + ], +}; + +export default sidebars; diff --git a/docs/python-data-sources/src/components/Button.tsx b/docs/python-data-sources/src/components/Button.tsx new file mode 100644 index 0000000..e4c2ba7 --- /dev/null +++ b/docs/python-data-sources/src/components/Button.tsx @@ -0,0 +1,65 @@ +import React, { CSSProperties } from 'react'; +import clsx from 'clsx'; +import Link from '@docusaurus/Link'; + +type Button = { + size?: 'sm' | 'lg' | 'small' | 'medium' | 'large' | null; + outline?: boolean; + variant: 'primary' | 'secondary' | 'danger' | 'warning' | 'success' | 'info' | 'link' | string; + block?: boolean; + disabled?: boolean; + className?: string; + style?: CSSProperties; + link: string; + label: string; + linkClassName?: string; +}; + +export default function Button({ + size = null, + outline = false, + variant = 'primary', + block = false, + disabled = false, + className, + style, + link, + label, + linkClassName, +}: Button) { + const sizeMap = { + sm: 'sm', + small: 'sm', + lg: 'lg', + large: 'lg', + medium: null, + }; + const buttonSize = size ? sizeMap[size] : ''; + const sizeClass = buttonSize ? `button--${buttonSize}` : ''; + const outlineClass = outline ? 'button--outline' : ''; + const variantClass = variant ? `button--${variant}` : ''; + const blockClass = block ? 'button--block' : ''; + const disabledClass = disabled ? 'disabled' : ''; + const destination = disabled ? null : link; + return ( + + + + ); +} diff --git a/docs/python-data-sources/src/css/custom.css b/docs/python-data-sources/src/css/custom.css new file mode 100644 index 0000000..3333a17 --- /dev/null +++ b/docs/python-data-sources/src/css/custom.css @@ -0,0 +1,79 @@ +/** + * Any CSS included here will be global. The classic template + * bundles Infima by default. Infima is a CSS framework designed to + * work well for content-centric websites. + */ + +/* import fonts: DM Mono and DM Sans */ +@import url('https://fonts.googleapis.com/css2?family=DM+Mono:ital,wght@0,300;0,400;0,500;1,300;1,400;1,500&family=DM+Sans:ital,opsz,wght@0,9..40,100..1000;1,9..40,100..1000&display=swap'); + + +/* configure tailwindcss */ +@tailwind base; +@tailwind components; +@tailwind utilities; + + + +:root { + --ifm-font-family-base: 'DM Sans'; + --ifm-heading-font-family: 'DM Sans'; + --ifm-font-family-monospace: 'DM Mono', monospace; + + --ifm-code-font-size: 95%; + --docusaurus-highlighted-code-line-bg: rgba(0, 0, 0, 0.1); +} + + + +.font-mono { + font-family: "DM Mono", monospace; + font-style: normal; +} + +.font-sans { + font-family: "DM Sans", sans-serif; + font-style: normal; +} + +button { + @apply font-sans; +} + +#search_input_react { + @apply font-sans; +} + + +.header-github-link::before { + content: ''; + width: 24px; + height: 24px; + display: flex; + background-color: var(--ifm-navbar-link-color); + mask-image: url("data:image/svg+xml,%3Csvg viewBox='0 0 24 24' xmlns='http://www.w3.org/2000/svg'%3E%3Cpath d='M12 .297c-6.63 0-12 5.373-12 12 0 5.303 3.438 9.8 8.205 11.385.6.113.82-.258.82-.577 0-.285-.01-1.04-.015-2.04-3.338.724-4.042-1.61-4.042-1.61C4.422 18.07 3.633 17.7 3.633 17.7c-1.087-.744.084-.729.084-.729 1.205.084 1.838 1.236 1.838 1.236 1.07 1.835 2.809 1.305 3.495.998.108-.776.417-1.305.76-1.605-2.665-.3-5.466-1.332-5.466-5.93 0-1.31.465-2.38 1.235-3.22-.135-.303-.54-1.523.105-3.176 0 0 1.005-.322 3.3 1.23.96-.267 1.98-.399 3-.405 1.02.006 2.04.138 3 .405 2.28-1.552 3.285-1.23 3.285-1.23.645 1.653.24 2.873.12 3.176.765.84 1.23 1.91 1.23 3.22 0 4.61-2.805 5.625-5.475 5.92.42.36.81 1.096.81 2.22 0 1.606-.015 2.896-.015 3.286 0 .315.21.69.825.57C20.565 22.092 24 17.592 24 12.297c0-6.627-5.373-12-12-12'/%3E%3C/svg%3E"); + transition: background-color var(--ifm-transition-fast) + var(--ifm-transition-timing-default); +} + +.header-github-link:hover::before { + background-color: var(--ifm-navbar-link-hover-color); +} + +/* TOC sidebar header (desktop and mobile) */ +.theme-doc-toc-desktop .table-of-contents::before, +.theme-doc-toc-desktop .tableOfContents::before { + content: "📄 On this page:"; + display: block; + font-weight: 600; + margin-bottom: 0.5rem; + color: var(--ifm-color-content); +} + +.theme-doc-toc-mobile .menu__list::before { + content: "📄 On this page:"; + display: block; + font-weight: 600; + margin: 0.5rem 0 0.25rem 0.5rem; + color: var(--ifm-color-content); +} diff --git a/docs/python-data-sources/src/pages/index.tsx b/docs/python-data-sources/src/pages/index.tsx new file mode 100644 index 0000000..a747b85 --- /dev/null +++ b/docs/python-data-sources/src/pages/index.tsx @@ -0,0 +1,189 @@ +import Layout from '@theme/Layout'; +import { JSX } from 'react'; +import Button from '../components/Button'; +import { Database, Radio, Image, FileText, Cog, Zap } from 'lucide-react'; + +const Hero = () => { + return ( +
+
+ Python Data Sources Logo +
+ +

+ Python Data Sources +

+

+ Provided by{' '} + + Databricks Industry Solutions + +

+

+ A collection of custom PySpark data source connectors for formats and protocols + that don't have a built-in Spark reader. +

+ +
+
+
+ ); +}; + +const Sources = () => { + const sources = [ + { + title: 'MCAP', + description: 'Read robotics and autonomy logs (MCAP format) into Spark DataFrames.', + icon: FileText, + }, + { + title: 'MQTT', + description: 'Stream IoT telemetry from MQTT brokers as a Spark Structured Streaming source.', + icon: Radio, + }, + { + title: 'ZipDICOM', + description: 'Decode medical imaging archives (DICOM in ZIP) into queryable pixel data.', + icon: Image, + }, + ]; + + return ( +
+

+ Available Sources +

+
+ {sources.map((source, index) => { + const Icon = source.icon; + return ( +
+ +

{source.title}

+

{source.description}

+
+ ); + })} +
+
+ ); +}; + +const Capabilities = () => { + const capabilities = [ + { + title: 'Spark DataSource V2 API', + description: 'Implemented against the Python DataSource API — usable from PySpark and Databricks runtime.', + icon: Database, + }, + { + title: 'Batch & Streaming', + description: 'Both batch reads and Spark Structured Streaming sources are supported where appropriate.', + icon: Zap, + }, + { + title: 'Modular Install', + description: 'Each connector is an optional extra (mcap, mqtt, zipdcm) — install only what you need.', + icon: Cog, + }, + ]; + + return ( +
+

+ Capabilities +

+
+ {capabilities.map((capability, index) => { + const Icon = capability.icon; + return ( +
+ +

{capability.title}

+

{capability.description}

+
+ ); + })} +
+
+ ); +}; + +const CallToAction = () => { + return ( +
+

+ Plug a new source into Spark 🚀 +

+

+ Follow the installation guide to add Python Data Sources to your PySpark project. +

+
+ ); +}; + +export default function Home(): JSX.Element { + return ( + +
+
+
+ + + + +
+
+
+ + ); +} diff --git a/docs/python-data-sources/static/.nojekyll b/docs/python-data-sources/static/.nojekyll new file mode 100644 index 0000000..e69de29 diff --git a/docs/python-data-sources/static/img/logo.svg b/docs/python-data-sources/static/img/logo.svg new file mode 100644 index 0000000..615e5e3 --- /dev/null +++ b/docs/python-data-sources/static/img/logo.svg @@ -0,0 +1,7 @@ + + + + + + + diff --git a/docs/python-data-sources/tailwind.config.ts b/docs/python-data-sources/tailwind.config.ts new file mode 100644 index 0000000..0953ba0 --- /dev/null +++ b/docs/python-data-sources/tailwind.config.ts @@ -0,0 +1,17 @@ +import type { Config } from 'tailwindcss'; + +export default { + content: [ + './docs/**/*.md', + './docs/**/*.mdx', + './src/**/*.{js,jsx,ts,tsx}', + ], + darkMode: ['class', '[data-theme="dark"]'], + theme: {}, + plugins: [ + require('@tailwindcss/typography'), + ], + corePlugins: { + preflight: false, // to make headings H1-H6 work correctly + }, +} satisfies Config; diff --git a/docs/python-data-sources/tsconfig.json b/docs/python-data-sources/tsconfig.json new file mode 100644 index 0000000..920d7a6 --- /dev/null +++ b/docs/python-data-sources/tsconfig.json @@ -0,0 +1,8 @@ +{ + // This file is not used in compilation. It is here just for a nice editor experience. + "extends": "@docusaurus/tsconfig", + "compilerOptions": { + "baseUrl": "." + }, + "exclude": [".docusaurus", "build"] +} diff --git a/pyproject.toml b/pyproject.toml index 3c7ac3f..896f548 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -86,10 +86,41 @@ e2e = [ "databricks-labs-blueprint~=0.12.0", "databricks-sdk~=0.88", ] +docs = [ + "pydoc-markdown>=4.8.2,<5.0", +] [tool.uv] required-version = "~=0.11.0" +[tool.pydoc-markdown] +loaders = [ + { type = "python", search_path = [ + "./src", + ], packages = [ + "python_data_sources", + ] }, +] +processors = [ + { type = "smart" }, + { type = "crossref" }, + { type = "filter", skip_empty_modules = true }, +] +hooks = { post-render = [ + "cp -r docs/python-data-sources/docs/reference/api/python_data_sources/* docs/python-data-sources/docs/reference/api/", + "rm -rf docs/python-data-sources/docs/reference/api/python_data_sources", +] } + +[tool.pydoc-markdown.renderer] +type = "docusaurus" +docs_base_path = "docs/python-data-sources/docs" +relative_output_path = "reference/api" +relative_sidebar_path = "sidebar.json" + +# by default method and function are on level 4 which is too deep for docusaurus +# we want to move them to level 3 +markdown = { header_level_by_type = { Method = 3, Function = 3, Class = 2, Module = 1 } } + [tool.pytest.ini_options] addopts = [ "--import-mode=importlib", diff --git a/uv.lock b/uv.lock index 7e63f35..440c836 100644 --- a/uv.lock +++ b/uv.lock @@ -16,6 +16,26 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/af/0f/3b8fdc946b4d9cc8cc1e8af42c4e409468c84441b933d037e101b3d72d86/astroid-3.3.11-py3-none-any.whl", hash = "sha256:54c760ae8322ece1abd213057c4b5bba7c49818853fc901ef09719a60dbf9dec", size = 275612, upload-time = "2025-07-13T18:04:21.07Z" }, ] +[[package]] +name = "black" +version = "23.12.1" +source = { registry = "https://pypi.org/simple" } +dependencies = [ + { name = "click" }, + { name = "mypy-extensions" }, + { name 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