| Name | fairspace-pipeline JSON |
| Version |
0.1.1
JSON |
| download |
| home_page | None |
| Summary | Building blocks for creating a pipeline for Fairspace |
| upload_time | 2024-11-15 13:07:27 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.12 |
| license | Apache-2.0 |
| keywords |
fairspace
pipeline
|
| VCS |
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| bugtrack_url |
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| requirements |
No requirements were recorded.
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|
# Fairspace Pipeline
[](https://pypi.org/project/fairspace_pipeline/)
[](LICENSE)
This repository contains the Fairspace Pipeline,
a package that can be used as a base to create custom ETL pipelines for Fairspace.
## Installation
Requires Python 3.12 or newer.
### Installing from PyPI
```shell
python -m pip install fairspace-pipeline
```
### Installing from sources
```shell
git clone https://github.com/thehyve/fairspace-pipeline.git
python -m build
python -m pip install .
```
## Usage
Fairspace Pipeline cannot be used as a standalone package. It requires a custom implementation of several and specific configuration.
Sections below describe the necessary steps to create a fully-functioning custom pipeline with reusable components and interfaces implementation.
### Configuration
Create a `.env` file with the following environment variables:
```shell
# Keycloak
KEYCLOAK_CLIENT_ID="" # e.g. KEYCLOAK_CLIENT_ID="workspace-client"
KEYCLOAK_CLIENT_SECRET="" # e.g. KEYCLOAK_CLIENT_SECRET="********"
KEYCLOAK_USERNAME="" # e.g. KEYCLOAK_USERNAME="organisation-admin"
KEYCLOAK_PASSWORD="" # e.g. KEYCLOAK_PASSWORD="fairspace123"
KEYCLOAK_SERVER_URL="" # e.g. KEYCLOAK_SERVER_URL="https://my-keycloak-instance.com"
KEYCLOAK_REALM="" # e.g. KEYCLOAK_REALM="fairspace"
# Fairspace
FAIRSPACE_URL="" # e.g. FAIRSPACE_URL="https://my-fairspace-instance.com"
# Amazon S3
IS_AWS_S3=False # e.g. IS_AWS_S3=True if using AWS S3 bucket for source data
AWS_SOURCE_BUCKET_NAME="" # e.g. AWS_SOURCE_BUCKET_NAME="fairspace-metadata-source"
AWS_OUTPUT_BUCKET_NAME="" # e.g. AWS_OUTPUT_BUCKET_NAME="fairspace-metadata-output"
# Pipeline settings
TAXONOMIES_TTL_PATH="config/custom_taxonomies.ttl"
SOURCE_STUDIES_PATHS='' # e.g. '["./test_data/test_study_input1", "./test_data/test_study_input2"]'
OUTPUT_DATA_PATH="" # e.g. OUTPUT_DATA_PATH="./test_data/.output_data"
```
Next, implement a function that creates a FairspacePipelineConfig object using environment variables
```python
def get_config() -> FairspacePipelineConfig:
config = FairspacePipelineConfig()
config.source_study_prefixes = json.loads(str(os.environ.get('SOURCE_STUDIES_PREFIXES', '[""]')))
config.output_data_directory = os.environ.get('OUTPUT_DATA_PATH',
os.path.join(os.getcwd(), 'test_data/.output_data'))
config.is_aws_s3 = os.getenv("IS_AWS_S3", 'False').lower() in ('true', '1', 't')
if config.is_aws_s3:
config.source_study_directories = json.loads(os.environ.get('SOURCE_STUDIES_PATHS'))
else:
config.source_study_directories = [os.path.join(os.getcwd(), val) for val in json.loads(
os.environ.get('SOURCE_STUDIES_PATHS', '["test_data/source_data"]'))]
config.source_bucket_name = os.environ.get('AWS_SOURCE_BUCKET_NAME')
config.output_bucket_name = os.environ.get('AWS_OUTPUT_BUCKET_NAME')
config.taxonomies_directory = os.environ.get(
'TAXONOMIES_TTL_PATH',
os.path.join(pathlib.Path(__file__).parent.absolute(), "config", "taxonomies.ttl")
)
return config
```
### Taxonomies
Implement custom taxonomies graph class that extends [the `TaxonomiesGraph` class](src/fairspace_pipeline/graph/taxonomy_graph.py).
The class needs to:
- include all custom taxonomies as class attributes,
- define the TAXONOMY_PREFIX to be used in custom taxonomy terms URIs.
Sample implementation:
```python
from fairspace_pipeline.graph.taxonomy_graph import TaxonomiesGraph
TAXONOMY_PREFIX = "https://fairspace.com/custom_ontology#" # Prefix for custom taxonomies
class CustomTaxonomiesGraph(TaxonomiesGraph):
def __init__(self, taxonomies_dir):
super().__init__(taxonomies_dir, TAXONOMY_PREFIX)
self.countries = self.query_taxonomy(taxonomy_name='Country')
self.file_types = self.query_taxonomy(taxonomy_name='FileType')
self.species = self.query_taxonomy(taxonomy_name='Species')
self.gender = self.query_taxonomy(taxonomy_name='Gender')
self.study_status = self.query_taxonomy(taxonomy_name='StudyStatus')
self.study_phases = self.query_taxonomy(taxonomy_name='StudyPhase')
self.sample_treatments = self.query_taxonomy(taxonomy_name='Treatment')
```
### Mapping
Implement custom graph class that extends [the `FairspaceGraph` class](src/fairspace_pipeline/graph/fairspace_graph.py).
It is a module for mapping data to RDF graphs specific to the custom data model, e.g.:
The class needs to implement `create_graph()` and `get_file_suffix_processing_order()` methods of the `FairspaceGraph` interface.
Sample implementation:
```python
from fairspace_pipeline.graph.fairspace_graph import FairspaceGraph
CUSTOM_NS = Namespace("https://custom.com/ontology#")
class CustomGraph(FairspaceGraph):
def __init__(self, taxonomies_graph: CustomTaxonomiesGraph):
super().__init__(taxonomies_graph)
def map_study(self, study_dict: dict) -> Study:
# Implement custom study processing logic
pass
def map_sample(self, sample_dict: dict) -> Sample:
# Implement custom sample processing logic
pass
def map_subject(self, subject_dict: dict) -> Subject:
# Implement custom subject processing logic
pass
def create_study_graph(self, data: dict, prefix: str) -> Graph:
graph = self.create_new_graph()
studies = self.map_studies(data, prefix)
for study in studies:
graph.add((study.uri, RDF.type, CUSTOM_NS.Study))
if study.label is not None:
graph.add((study.uri, RDFS.label, Literal(study.label)))
if study.identifier is not None:
graph.add((study.uri, DCTERMS.identifier, Literal(study.identifier)))
...
return graph
def create_sample_graph(self, data: dict, prefix: str) -> Graph:
graph = self.create_new_graph()
samples = self.map_sample(data, prefix)
for sample in samples:
...
return graph
def create_subject_graph(self, data: dict, prefix: str) -> Graph:
graph = self.create_new_graph()
subjects = self.map_subject(data, prefix)
for subject in subjects:
...
return graph
def create_graph(self, file_path: str, data: dict, prefix: str) -> Graph:
if str(file_path).endswith(STUDY_MANIFEST_FILE_SUFFIX):
return self.create_study_graph(data, prefix)
if str(file_path).endswith(SAMPLE_INFORMATION_SUFFIX):
return self.create_sample_graph(data, prefix)
...
return self.create_subjects_data_files_graph(data, prefix)
# Define the order of processing files by file suffix in the source study directory
# e.g. ['_study.json', '_sample_information.json']
def get_file_suffix_processing_order(self) -> list[str]:
return [STUDY_MANIFEST_FILE_SUFFIX, SAMPLE_INFORMATION_SUFFIX]
```
#### IO Handler
Implement a custom IO handler class that extends [the `IOHandler` class](src/fairspace_pipeline/io/io_handler.py),
following examples of [the `LocalIOHandler` class](src/fairspace_pipeline/io/local_io_handler.py) and [the `S3IOHandler` class](src/fairspace_pipeline/io/s3_io_handler.py).
Sample implementation (extending local handler):
```python
class CustomIOHandler(LocalIOHandler):
def __init__(self, output_data_directory: str, fairspace_graph: CustomFairspaceGraph):
super().__init__(output_data_directory, fairspace_graph)
...
def process_directory(self, directory: str):
...
@override
def send_to_api(self, api: FairspaceApi, source_directories: str):
for directory, subdirectories, files in os.walk(self.output_data_directory):
full_path = os.path.join(directory, file)
try:
api.upload_metadata_by_path(full_path)
except Exception as e:
log.error(f"Error uploading file {full_path}")
log.error(e)
log.info(f"Done uploading all metadata to Fairspace.")
@override
def transform_data(self, source_directories: str, source_prefixes=None):
for source_directory in source_directories:
self.process_directory(source_directory)
```
#### Pipeline runner
Define main function to run the pipeline.
```python
from fairspace_pipeline.pipeline import FairspacePipeline, FairspacePipelineConfig
def main():
load_dotenv()
parser = argparse.ArgumentParser()
parser.add_argument("-i", "--init", action="store_true")
parser.add_argument("-p", "--process", action="store_true")
parser.add_argument("-u", "--upload", action="store_true")
parser.add_argument("-r", "--reindex", action="store_true")
parser.add_argument("-d", "--delete", action="store_true")
parser.add_argument("-c", "--compact", action="store_true")
parser.add_argument("-ms", "--maintenance_status", action="store_true")
args = parser.parse_args()
config = get_config()
taxonomies_graph = CustomTaxonomiesGraph(config.taxonomies_directory)
graph = CustomGraph(config, taxonomies_graph)
pipeline = FairspacePipeline(config, graph)
pipeline.run(args.init, args.process, args.upload, args.delete, args.reindex, args.compact, args.maintenance_status)
if __name__ == '__main__':
main()
```
## Running the complete pipeline
When all the components are implemented, the pipeline can be run with the following command:
```shell
python main.py --init --process --upload --compact
```
Include only the options that you need:
- `--init` or `-i` - prepare required roles for the configured user and upload taxonomies
- `--process` or `-p` - read the input source data, transform to Fairspace model and save to the configured output directory
- `--upload` or `-u` - upload the transform data into Fairspace
- `--reindex` or `-r` - reindex Fairspace views database
- `--compact` or `-c` - compact Fairspace Jena database to reduce the size
- `--maintenance_status` or `-ms` - get the maintenance status to see if reindexing or compacting is in progress
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"description": "# Fairspace Pipeline\n\n[](https://pypi.org/project/fairspace_pipeline/)\n\n[](LICENSE)\n\nThis repository contains the Fairspace Pipeline, \na package that can be used as a base to create custom ETL pipelines for Fairspace.\n\n## Installation\n\nRequires Python 3.12 or newer.\n\n### Installing from PyPI\n\n```shell\npython -m pip install fairspace-pipeline\n```\n\n### Installing from sources\n\n```shell\ngit clone https://github.com/thehyve/fairspace-pipeline.git\npython -m build\npython -m pip install .\n```\n\n## Usage\n\nFairspace Pipeline cannot be used as a standalone package. It requires a custom implementation of several and specific configuration.\nSections below describe the necessary steps to create a fully-functioning custom pipeline with reusable components and interfaces implementation.\n\n### Configuration\nCreate a `.env` file with the following environment variables:\n\n```shell\n# Keycloak\nKEYCLOAK_CLIENT_ID=\"\" # e.g. KEYCLOAK_CLIENT_ID=\"workspace-client\"\nKEYCLOAK_CLIENT_SECRET=\"\" # e.g. KEYCLOAK_CLIENT_SECRET=\"********\"\nKEYCLOAK_USERNAME=\"\" # e.g. KEYCLOAK_USERNAME=\"organisation-admin\"\nKEYCLOAK_PASSWORD=\"\" # e.g. KEYCLOAK_PASSWORD=\"fairspace123\"\nKEYCLOAK_SERVER_URL=\"\" # e.g. KEYCLOAK_SERVER_URL=\"https://my-keycloak-instance.com\"\nKEYCLOAK_REALM=\"\" # e.g. KEYCLOAK_REALM=\"fairspace\"\n\n# Fairspace\nFAIRSPACE_URL=\"\" # e.g. FAIRSPACE_URL=\"https://my-fairspace-instance.com\"\n\n# Amazon S3\nIS_AWS_S3=False # e.g. IS_AWS_S3=True if using AWS S3 bucket for source data\nAWS_SOURCE_BUCKET_NAME=\"\" # e.g. AWS_SOURCE_BUCKET_NAME=\"fairspace-metadata-source\"\nAWS_OUTPUT_BUCKET_NAME=\"\" # e.g. AWS_OUTPUT_BUCKET_NAME=\"fairspace-metadata-output\"\n\n# Pipeline settings\nTAXONOMIES_TTL_PATH=\"config/custom_taxonomies.ttl\"\nSOURCE_STUDIES_PATHS='' # e.g. '[\"./test_data/test_study_input1\", \"./test_data/test_study_input2\"]'\nOUTPUT_DATA_PATH=\"\" # e.g. OUTPUT_DATA_PATH=\"./test_data/.output_data\"\n```\n\nNext, implement a function that creates a FairspacePipelineConfig object using environment variables\n\n```python\ndef get_config() -> FairspacePipelineConfig:\n config = FairspacePipelineConfig()\n config.source_study_prefixes = json.loads(str(os.environ.get('SOURCE_STUDIES_PREFIXES', '[\"\"]')))\n config.output_data_directory = os.environ.get('OUTPUT_DATA_PATH',\n os.path.join(os.getcwd(), 'test_data/.output_data'))\n config.is_aws_s3 = os.getenv(\"IS_AWS_S3\", 'False').lower() in ('true', '1', 't')\n if config.is_aws_s3:\n config.source_study_directories = json.loads(os.environ.get('SOURCE_STUDIES_PATHS'))\n else:\n config.source_study_directories = [os.path.join(os.getcwd(), val) for val in json.loads(\n os.environ.get('SOURCE_STUDIES_PATHS', '[\"test_data/source_data\"]'))]\n config.source_bucket_name = os.environ.get('AWS_SOURCE_BUCKET_NAME')\n config.output_bucket_name = os.environ.get('AWS_OUTPUT_BUCKET_NAME')\n config.taxonomies_directory = os.environ.get(\n 'TAXONOMIES_TTL_PATH',\n os.path.join(pathlib.Path(__file__).parent.absolute(), \"config\", \"taxonomies.ttl\")\n )\n return config\n```\n\n\n### Taxonomies\nImplement custom taxonomies graph class that extends [the `TaxonomiesGraph` class](src/fairspace_pipeline/graph/taxonomy_graph.py).\nThe class needs to:\n- include all custom taxonomies as class attributes,\n- define the TAXONOMY_PREFIX to be used in custom taxonomy terms URIs.\n\nSample implementation:\n```python\nfrom fairspace_pipeline.graph.taxonomy_graph import TaxonomiesGraph\n\nTAXONOMY_PREFIX = \"https://fairspace.com/custom_ontology#\" # Prefix for custom taxonomies\n\nclass CustomTaxonomiesGraph(TaxonomiesGraph):\n def __init__(self, taxonomies_dir):\n super().__init__(taxonomies_dir, TAXONOMY_PREFIX)\n self.countries = self.query_taxonomy(taxonomy_name='Country')\n self.file_types = self.query_taxonomy(taxonomy_name='FileType')\n self.species = self.query_taxonomy(taxonomy_name='Species')\n self.gender = self.query_taxonomy(taxonomy_name='Gender')\n self.study_status = self.query_taxonomy(taxonomy_name='StudyStatus')\n self.study_phases = self.query_taxonomy(taxonomy_name='StudyPhase')\n self.sample_treatments = self.query_taxonomy(taxonomy_name='Treatment')\n```\n\n### Mapping\n\nImplement custom graph class that extends [the `FairspaceGraph` class](src/fairspace_pipeline/graph/fairspace_graph.py). \nIt is a module for mapping data to RDF graphs specific to the custom data model, e.g.:\n\nThe class needs to implement `create_graph()` and `get_file_suffix_processing_order()` methods of the `FairspaceGraph` interface.\n\nSample implementation:\n```python\nfrom fairspace_pipeline.graph.fairspace_graph import FairspaceGraph\n\nCUSTOM_NS = Namespace(\"https://custom.com/ontology#\")\n\nclass CustomGraph(FairspaceGraph):\n def __init__(self, taxonomies_graph: CustomTaxonomiesGraph):\n super().__init__(taxonomies_graph)\n\n def map_study(self, study_dict: dict) -> Study:\n # Implement custom study processing logic\n pass\n\n def map_sample(self, sample_dict: dict) -> Sample:\n # Implement custom sample processing logic\n pass\n\n def map_subject(self, subject_dict: dict) -> Subject:\n # Implement custom subject processing logic\n pass\n\n def create_study_graph(self, data: dict, prefix: str) -> Graph:\n graph = self.create_new_graph()\n studies = self.map_studies(data, prefix)\n for study in studies:\n graph.add((study.uri, RDF.type, CUSTOM_NS.Study))\n if study.label is not None:\n graph.add((study.uri, RDFS.label, Literal(study.label)))\n if study.identifier is not None:\n graph.add((study.uri, DCTERMS.identifier, Literal(study.identifier)))\n ...\n return graph\n\n def create_sample_graph(self, data: dict, prefix: str) -> Graph:\n graph = self.create_new_graph()\n samples = self.map_sample(data, prefix)\n for sample in samples:\n ...\n return graph\n \n def create_subject_graph(self, data: dict, prefix: str) -> Graph:\n graph = self.create_new_graph()\n subjects = self.map_subject(data, prefix)\n for subject in subjects:\n ...\n return graph\n \n def create_graph(self, file_path: str, data: dict, prefix: str) -> Graph:\n if str(file_path).endswith(STUDY_MANIFEST_FILE_SUFFIX):\n return self.create_study_graph(data, prefix)\n if str(file_path).endswith(SAMPLE_INFORMATION_SUFFIX):\n return self.create_sample_graph(data, prefix)\n ...\n return self.create_subjects_data_files_graph(data, prefix)\n\n # Define the order of processing files by file suffix in the source study directory\n # e.g. ['_study.json', '_sample_information.json']\n def get_file_suffix_processing_order(self) -> list[str]:\n return [STUDY_MANIFEST_FILE_SUFFIX, SAMPLE_INFORMATION_SUFFIX]\n```\n\n#### IO Handler\n\nImplement a custom IO handler class that extends [the `IOHandler` class](src/fairspace_pipeline/io/io_handler.py),\nfollowing examples of [the `LocalIOHandler` class](src/fairspace_pipeline/io/local_io_handler.py) and [the `S3IOHandler` class](src/fairspace_pipeline/io/s3_io_handler.py).\n\nSample implementation (extending local handler):\n```python\n\nclass CustomIOHandler(LocalIOHandler):\n def __init__(self, output_data_directory: str, fairspace_graph: CustomFairspaceGraph):\n super().__init__(output_data_directory, fairspace_graph)\n ...\n\n def process_directory(self, directory: str):\n ...\n\n @override\n def send_to_api(self, api: FairspaceApi, source_directories: str):\n for directory, subdirectories, files in os.walk(self.output_data_directory):\n full_path = os.path.join(directory, file)\n try:\n api.upload_metadata_by_path(full_path)\n except Exception as e:\n log.error(f\"Error uploading file {full_path}\")\n log.error(e)\n log.info(f\"Done uploading all metadata to Fairspace.\")\n\n @override\n def transform_data(self, source_directories: str, source_prefixes=None):\n for source_directory in source_directories:\n self.process_directory(source_directory)\n```\n\n#### Pipeline runner\n\nDefine main function to run the pipeline.\n```python\nfrom fairspace_pipeline.pipeline import FairspacePipeline, FairspacePipelineConfig\n\ndef main():\n load_dotenv()\n\n parser = argparse.ArgumentParser()\n parser.add_argument(\"-i\", \"--init\", action=\"store_true\")\n parser.add_argument(\"-p\", \"--process\", action=\"store_true\")\n parser.add_argument(\"-u\", \"--upload\", action=\"store_true\")\n parser.add_argument(\"-r\", \"--reindex\", action=\"store_true\")\n parser.add_argument(\"-d\", \"--delete\", action=\"store_true\")\n parser.add_argument(\"-c\", \"--compact\", action=\"store_true\")\n parser.add_argument(\"-ms\", \"--maintenance_status\", action=\"store_true\")\n args = parser.parse_args()\n\n config = get_config()\n\n taxonomies_graph = CustomTaxonomiesGraph(config.taxonomies_directory)\n graph = CustomGraph(config, taxonomies_graph)\n\n pipeline = FairspacePipeline(config, graph)\n pipeline.run(args.init, args.process, args.upload, args.delete, args.reindex, args.compact, args.maintenance_status)\n\n\nif __name__ == '__main__':\n main()\n```\n\n## Running the complete pipeline\n\nWhen all the components are implemented, the pipeline can be run with the following command:\n\n```shell\npython main.py --init --process --upload --compact\n```\nInclude only the options that you need:\n\n- `--init` or `-i` - prepare required roles for the configured user and upload taxonomies\n- `--process` or `-p` - read the input source data, transform to Fairspace model and save to the configured output directory\n- `--upload` or `-u` - upload the transform data into Fairspace\n- `--reindex` or `-r` - reindex Fairspace views database\n- `--compact` or `-c` - compact Fairspace Jena database to reduce the size\n- `--maintenance_status` or `-ms` - get the maintenance status to see if reindexing or compacting is in progress\n",
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