diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index fa999e2..062a545 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -2,43 +2,43 @@ name: CI on: push: - branches: [ main ] + branches: '*' pull_request: - branches: [ main ] + branches: '*' jobs: build: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - - name: Set up Python - uses: actions/setup-python@v2 - with: - python-version: '3.11' + - name: Set up Python + uses: actions/setup-python@v4 + with: + python-version: '3.11' - - name: Install Poetry - run: | - curl -sSL https://install.python-poetry.org | python3 - - poetry install + - name: Install Poetry + run: | + curl -sSL https://install.python-poetry.org | python3 - + poetry install - - name: Lint with Ruff - run: | - poetry run ruff check crategen/ + - name: Lint with Ruff + run: | + poetry run ruff check crategen/ - - name: Type check with Mypy - run: | - poetry run mypy crategen/ + - name: Type check with Mypy + run: | + poetry run mypy crategen/ - - name: Run security checks with Bandit - run: | - poetry run bandit -r crategen/ + - name: Run security checks with Bandit + run: | + poetry run bandit -r crategen/ - - name: Install test dependencies - run: | - poetry add pytest pytest-cov pytest-mock + - name: Install test dependencies + run: | + poetry add pytest pytest-cov pytest-mock - # - name: Run tests - # run: | - # poetry run pytest --cov=crategen + - name: Run tests + run: | + poetry run pytest --cov=crategen diff --git a/crategen/cli.py b/crategen/cli.py index 20198fb..3f207b2 100644 --- a/crategen/cli.py +++ b/crategen/cli.py @@ -1,30 +1,37 @@ -import click import json + +import click + from crategen.converter_manager import ConverterManager + @click.command() -@click.option('--input', prompt='Input file', help='Path to the input JSON file.') -@click.option('--output', prompt='Output file', help='Path to the output JSON file.') -@click.option('--conversion-type', prompt='Conversion type', type=click.Choice(['tes-to-wrroc', 'wes-to-wrroc']), help='Type of conversion to perform.') +@click.option("--input", prompt="Input file", help="Path to the input JSON file.") +@click.option("--output", prompt="Output file", help="Path to the output JSON file.") +@click.option( + "--conversion-type", + prompt="Conversion type", + type=click.Choice(["tes-to-wrroc", "wes-to-wrroc"]), + help="Type of conversion to perform.", +) def cli(input, output, conversion_type): - """ - Command Line Interface for converting TES/WES to WRROC. - """ + """Command Line Interface for converting TES/WES to WRROC.""" manager = ConverterManager() # Load input data from JSON file - with open(input, 'r') as input_file: + with open(input) as input_file: data = json.load(input_file) # Perform the conversion based on the specified type - if conversion_type == 'tes-to-wrroc': + if conversion_type == "tes-to-wrroc": result = manager.convert_tes_to_wrroc(data) - elif conversion_type == 'wes-to-wrroc': + elif conversion_type == "wes-to-wrroc": result = manager.convert_wes_to_wrroc(data) - + # Save the result to the output JSON file - with open(output, 'w') as output_file: + with open(output, "w") as output_file: json.dump(result, output_file, indent=4) -if __name__ == '__main__': + +if __name__ == "__main__": cli() diff --git a/crategen/converter_manager.py b/crategen/converter_manager.py index 3a0ef6b..756a565 100644 --- a/crategen/converter_manager.py +++ b/crategen/converter_manager.py @@ -1,6 +1,7 @@ from .converters.tes_converter import TESConverter from .converters.wes_converter import WESConverter + class ConverterManager: def __init__(self): self.tes_converter = TESConverter() diff --git a/crategen/converters/abstract_converter.py b/crategen/converters/abstract_converter.py index d0cd0ee..fc8c98d 100644 --- a/crategen/converters/abstract_converter.py +++ b/crategen/converters/abstract_converter.py @@ -1,10 +1,11 @@ from abc import ABC, abstractmethod + class AbstractConverter(ABC): @abstractmethod def convert_to_wrroc(self, data): """Convert data to WRROC format""" - + @abstractmethod - def convert_from_wrroc(self, wrroc_data): + def convert_from_wrroc(self, data): """Convert WRROC data to the original format""" diff --git a/crategen/converters/tes_converter.py b/crategen/converters/tes_converter.py index 99e176d..2b5f5ec 100644 --- a/crategen/converters/tes_converter.py +++ b/crategen/converters/tes_converter.py @@ -1,52 +1,117 @@ + +from pydantic import AnyUrl, ValidationError + +from ..models.tes_models import ( + TESData, + TESExecutor, + TESInput, + TESOutput, + TESState, + TESTaskLog, +) +from ..models.wrroc_models import WRROCDataTES +from ..validators import validate_wrroc_tes from .abstract_converter import AbstractConverter -from .utils import convert_to_iso8601 + class TESConverter(AbstractConverter): + def convert_to_wrroc(self, data: dict) -> dict: + """ + Convert TES data to WRROC format. + + Args: + data: The input TES data. + + Returns: + The converted WRROC data. + + Raises: + ValidationError: If TES data is invalid. + """ + # Validate TES data + try: + data_tes = TESData(**data) + except ValidationError as e: + raise ValueError(f"Invalid TES data: {e.errors()}") from e + + executors = data_tes.executors + end_time = data_tes.logs[0].end_time if data_tes.logs else None - def convert_to_wrroc(self, tes_data): - # Validate and extract data with defaults - id = tes_data.get("id", "") - name = tes_data.get("name", "") - description = tes_data.get("description", "") - executors = tes_data.get("executors", [{}]) - inputs = tes_data.get("inputs", []) - outputs = tes_data.get("outputs", []) - creation_time = tes_data.get("creation_time", "") - end_time = tes_data.get("logs", [{}])[0].get("end_time", "") # Corrected to fetch from logs - - # Convert to WRROC wrroc_data = { - "@id": id, - "name": name, - "description": description, - "instrument": executors[0].get("image", None) if executors else None, - "object": [{"@id": input.get("url", ""), "name": input.get("path", "")} for input in inputs], - "result": [{"@id": output.get("url", ""), "name": output.get("path", "")} for output in outputs], - "startTime": convert_to_iso8601(creation_time), - "endTime": convert_to_iso8601(end_time), + "@id": data_tes.id, + "name": data_tes.name, + "description": data_tes.description, + "instrument": executors[0].image if executors else None, + "object": [ + {"@id": input.url, "name": input.path} for input in data_tes.inputs + ], + "result": [ + {"@id": output.url, "name": output.path} for output in data_tes.outputs + ], + "startTime": data_tes.creation_time, + "endTime": end_time, } + + validate_wrroc_tes(wrroc_data) return wrroc_data - def convert_from_wrroc(self, wrroc_data): - # Validate and extract data with defaults - id = wrroc_data.get("@id", "") - name = wrroc_data.get("name", "") - description = wrroc_data.get("description", "") - instrument = wrroc_data.get("instrument", "") - object_data = wrroc_data.get("object", []) - result_data = wrroc_data.get("result", []) - start_time = wrroc_data.get("startTime", "") - end_time = wrroc_data.get("endTime", "") - - # Convert from WRROC to TES - tes_data = { - "id": id, - "name": name, - "description": description, - "executors": [{"image": instrument}], - "inputs": [{"url": obj.get("@id", ""), "path": obj.get("name", "")} for obj in object_data], - "outputs": [{"url": res.get("@id", ""), "path": res.get("name", "")} for res in result_data], - "creation_time": start_time, - "logs": [{"end_time": end_time}], # Added to logs - } - return tes_data + def convert_from_wrroc(self, data: dict) -> dict: + """ + Convert WRROC data to TES format. + + Args: + data: The input WRROC data. + + Returns: + The converted TES data. + + Raises: + ValidationError: If WRROC data is invalid. + """ + # Validate WRROC data + try: + data_wrroc = WRROCDataTES(**data) + except ValidationError as e: + raise ValueError(f"Invalid WRROC data: {e.errors()}") from e + + # Convert URL strings to AnyUrl + tes_inputs = [ + TESInput(url=AnyUrl(url=obj.id), path=obj.name) for obj in data_wrroc.object + ] + tes_outputs = [ + TESOutput(url=AnyUrl(url=data_wrroc.result.id), path=data_wrroc.result.name) + ] + + # Ensure 'image' and 'command' fields are provided + tes_executors = [ + TESExecutor(image=data_wrroc.instrument or "", command=[]) + ] # Provide default empty list for command + + # Ensure correct type for end_time (datetime) + + tes_logs = [ + TESTaskLog( + logs=[], + metadata=None, + start_time=None, + end_time=data_wrroc.endTime, + outputs=[], + system_logs=None, + ) + ] + + tes_data = TESData( + id=data_wrroc.id, + name=data_wrroc.name, + description=data_wrroc.description, + executors=tes_executors, + inputs=tes_inputs, + outputs=tes_outputs, + creation_time=None, + logs=tes_logs, + state=TESState.UNKNOWN, + ) + + # Validate TES data before returning + tes_data = TESData(**tes_data.dict()) + return tes_data.dict() diff --git a/crategen/converters/wes_converter.py b/crategen/converters/wes_converter.py index 154b17d..b1bcd54 100644 --- a/crategen/converters/wes_converter.py +++ b/crategen/converters/wes_converter.py @@ -1,46 +1,94 @@ +from pydantic import ValidationError + +from ..models.wes_models import Log, RunRequest, State, WESData +from ..models.wrroc_models import WRROCDataWES, WRROCOutputs +from ..utils import convert_to_iso8601 from .abstract_converter import AbstractConverter -from .utils import convert_to_iso8601 + class WESConverter(AbstractConverter): + def convert_to_wrroc(self, data: dict) -> dict: + """ + Convert WES data to WRROC format. + + Args: + data: The input WES data. + + Returns: + The converted WRROC data. + + Raises: + ValidationError: If WES data is invalid. + """ + # Validate WES data + try: + data_wes = WESData(**data) + except ValidationError as e: + raise ValueError(f"Invalid WES data: {e.errors()}") from e + + wrroc_output = ( + WRROCOutputs( + id=data_wes.outputs.get("location"), name=data_wes.outputs.get("name") + ) + if data_wes.outputs.get("location") + else None + ) + + wrroc_data = WRROCDataWES( + id=data_wes.run_id, + name=data_wes.run_log.name, + status=data_wes.state, + startTime=convert_to_iso8601(data_wes.run_log.start_time), + endTime=convert_to_iso8601(data_wes.run_log.end_time), + result=wrroc_output, + ) + + return wrroc_data.dict(exclude_none=True) + + def convert_from_wrroc(self, data: dict) -> dict: + """ + Convert WRROC data to WES format. + + Args: + data: The input WRROC data. + + Returns: + The converted WES data. + + Raises: + ValidationError: If WRROC data is invalid. + """ + # Validate WRROC data + try: + data_wrroc = WRROCDataWES(**data) + except ValidationError as e: + raise ValueError( + f"Invalid WRROC data for WES conversion: {e.errors()}" + ) from e + + wes_run_log = Log( + name=data_wrroc.name, + start_time=data_wrroc.startTime, + end_time=data_wrroc.endTime, + ) + wes_request = RunRequest( + workflow_params={}, # Adjust as necessary + workflow_type="CWL", # Example type, adjust as necessary + workflow_type_version="v1.0", # Example version, adjust as necessary + workflow_url="", + ) + + state = State(data_wrroc.status) + + wes_data = WESData( + run_id=data_wrroc.id, + request=wes_request, + state=state, + run_log=wes_run_log, + task_logs=None, # Provide appropriate value + outputs={"location": data_wrroc.result.id, "name": data_wrroc.result.name}, + ) - def convert_to_wrroc(self, wes_data): - # Validate and extract data with defaults - run_id = wes_data.get("run_id", "") - name = wes_data.get("run_log", {}).get("name", "") - state = wes_data.get("state", "") - start_time = wes_data.get("run_log", {}).get("start_time", "") - end_time = wes_data.get("run_log", {}).get("end_time", "") - outputs = wes_data.get("outputs", {}) - - # Convert to WRROC - wrroc_data = { - "@id": run_id, - "name": name, - "status": state, - "startTime": convert_to_iso8601(start_time), - "endTime": convert_to_iso8601(end_time), - "result": [{"@id": output.get("location", ""), "name": output.get("name", "")} for output in outputs], - } - return wrroc_data - - def convert_from_wrroc(self, wrroc_data): - # Validate and extract data with defaults - run_id = wrroc_data.get("@id", "") - name = wrroc_data.get("name", "") - start_time = wrroc_data.get("startTime", "") - end_time = wrroc_data.get("endTime", "") - state = wrroc_data.get("status", "") - result_data = wrroc_data.get("result", []) - - # Convert from WRROC to WES - wes_data = { - "run_id": run_id, - "run_log": { - "name": name, - "start_time": start_time, - "end_time": end_time, - }, - "state": state, - "outputs": [{"location": res.get("@id", ""), "name": res.get("name", "")} for res in result_data], - } - return wes_data + # Validate WES data before returning + wes_data = WESData(**wes_data.dict()) + return wes_data.dict() diff --git a/crategen/models/__init__.py b/crategen/models/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/crategen/models/tes_models.py b/crategen/models/tes_models.py new file mode 100644 index 0000000..ad80560 --- /dev/null +++ b/crategen/models/tes_models.py @@ -0,0 +1,272 @@ +""" +Each model in this module conforms to the corresponding TES model names as specified by the GA4GH schema (https://ga4gh.github.io/task-execution-schemas/docs/). +""" + +import os +from datetime import datetime +from enum import Enum +from typing import Optional + +from pydantic import AnyUrl, BaseModel, root_validator, validator + +from ..utils import convert_to_rfc3339_format + + +class TESFileType(str, Enum): + FILE = "FILE" + DIRECTORY = "DIRECTORY" + + +class TESState(str, Enum): + UNKNOWN = "UNKNOWN" + QUEUED = "QUEUED" + INITIALIZING = "INITIALIZING" + RUNNING = "RUNNING" + PAUSED = "PAUSED" + COMPLETE = "COMPLETE" + EXECUTOR_ERROR = "EXECUTOR_ERROR" + SYSTEM_ERROR = "SYSTEM_ERROR" + CANCELLED = "CANCELLED" + + +class TESOutputFileLog(BaseModel): + """ + Information about all output files. Directory outputs are flattened into separate items. + + **Attributes:** + + - **url** (`str`): URL of the file in storage. + - **path** (`str`): Path of the file inside the container. Must be an absolute path. + - **size_bytes** (`str`): Size of the file in bytes. Note, this is currently coded as a string because official JSON doesn't support int64 numbers. + + **Reference:** https://ga4gh.github.io/task-execution-schemas/docs/#operation/GetTask + """ + + url: str + path: str + size_bytes: str + + +class TESExecutorLog(BaseModel): + """ + Logs for each executor + + **Attributes:** + + - **start_time** (`Optional[str]`): Time the executor started, in RFC 3339 format. + - **end_time** (`Optional[str]`): Time the executor ended, in RFC 3339 format. + - **stdout** (`Optional[str]`): Stdout content. + - **stderr** (`Optional[str]`): Stderr content. + - **exit_code** (`int`): The exit code of the executor. + + **Reference:** https://ga4gh.github.io/task-execution-schemas/docs/#operation/GetTask + """ + + start_time: Optional[datetime] = None + end_time: Optional[datetime] = None + stdout: Optional[str] = None + stderr: Optional[str] = None + exit_code: int + + @validator("start_time", "end_time") + def validate_datetime(value): + return convert_to_rfc3339_format(value) + + +class TESExecutor(BaseModel): + """ + An array of executors to be run + + **Attributes:** + - **image** (`str`): Name of the container image. + - **command** (`list[str]`): A sequence of program arguments to execute, where the first argument is the program to execute. + - **workdir** (`Optional[str]`): The working directory that the command will be executed in. + - **stdout** (`Optional[str]`): Path inside the container to a file where the executor's stdout will be written to. Must be an absolute path + - **stderr** (`Optional[str]`): Path inside the container to a file where the executor's stderr will be written to. Must be an absolute path. + - **stdin** (`Optional[str]`): Path inside the container to a file which will be piped to the executor's stdin. Must be an absolute path. + - **env** (`Optional[dict[str, str]]`): Enviromental variables to set within the container + + **Reference:** https://ga4gh.github.io/task-execution-schemas/docs/#operation/GetTask + """ + + image: str + command: list[str] + workdir: Optional[str] = None + stdout: Optional[str] = None + stderr: Optional[str] = None + stdin: Optional[str] = None + env: Optional[dict[str, str]] = None + + @validator("stdin", "stdout") + def validate_stdin_stdin(value): + if not os.path.isabs(value): + raise ValueError(f"The '${value}' attribute must contain an absolute path.") + return value + + +class TESResources(BaseModel): + """ + Represents the resources required by a TES task. + + **Attributes:** + + - **cpu_cores** (`Optional[int]`): Requested number of CPUs. + - **preemptible** (`Optional[bool]`): Define if the task is allowed to run on preemptible compute instances, for example, AWS Spot. + - **ram_gb** (`Optional[float]`): The amount of RAM in GB required. + - **disk_gb** (`Optional[float]`): The amount of disk space in GB required. + - **zones** (`Optional[list[str]]`): Request that the task be run in these compute zones. + + **Reference:** https://ga4gh.github.io/task-execution-schemas/docs/#operation/GetTask + """ + + cpu_cores: Optional[int] = None + preemptible: Optional[bool] = None + ram_gb: Optional[float] = None + disk_gb: Optional[float] = None + zones: Optional[list[str]] = None + + +class TESInput(BaseModel): + """ + Input files that will be used by the task. Inputs will be downloaded and mounted into the executor container as defined by the task request document. + + **Attributes:** + + - **name** (`Optional[str]`): The name of the input file. + - **description** (`Optional[str]`): A brief description of the input. + - **url** (`AnyUrl`): The URL of the input file. Must be an absolute path + - **path** (`str`): TPath of the file inside the container. Must be an absolute path. + - **type** (`TESFileType`): The type of input ('FILE' or 'DIRECTORY'). Default is 'FILE' + - **content** (`Optional[str]`): The content of the input file, if provided inline. + + Reference: https://ga4gh.github.io/task-execution-schemas/docs/#operation/GetTask + """ + + name: Optional[str] = None + description: Optional[str] = None + url: Optional[AnyUrl] + path: str + type: TESFileType = TESFileType.FILE + content: Optional[str] = None + + @root_validator() + def validate_content_and_url(cls, values): + """ + - If content is set url should be ignored + - If content is not set then url should be present + """ + content_is_set = ( + values.get("content") and len(values.get("content").strip()) > 0 + ) + url_is_set = values.get("url") and len(values.get("url").strip()) > 0 + + if content_is_set: + values["url"] = None + elif not content_is_set and not url_is_set: + raise ValueError( + "The 'url' attribute is required when the 'content' attribute is empty" + ) + return values + + @validator("path") + def validate_path(cls, value): + if not os.path.isabs(value): + raise ValueError("The 'path' attribute must contain an absolute path.") + return value + + +class TESOutput(BaseModel): + """ + Output files. Outputs will be uploaded from the executor container to long-term storage. + + **Attributes:** + + - **name** (`Optional[str]`): User-provided name of output file + - **description** (`Optional[str]`): Optional users provided description field, can be used for documentation. + - **url** (`AnyUrl`): URL for the file to be copied by the TES server after the task is complete + - **path** (`str`): Path of the file inside the container. Must be an absolute path. + - **type** (`TESFileType`): The type of output (e.g., FILE, DIRECTORY). + + Reference: https://ga4gh.github.io/task-execution-schemas/docs/#operation/GetTask + """ + + name: Optional[str] = None + description: Optional[str] = None + url: AnyUrl + path: str + type: TESFileType = TESFileType.FILE + + @validator("path") + def validate_path(cls, value): + if not os.path.isabs(value): + raise ValueError("The 'path' attribute must contain an absolute path.") + return value + + +class TESTaskLog(BaseModel): + """ + Task logging information. Normally, this will contain only one entry, but in the case where a task fails and is retried, an entry will be appended to this list. + + **Attributes:** + + - **logs** (`list[TESExecutorLog]`): Logs for each executor. + - **metadata** (`Optional[dict[str, str]]`): Arbitrary logging metadata included by the implementation. + - **start_time** (`Optional[datetime]`): When the task started, in RFC 3339 format. + - **end_time** (`Optional[datetime]`): When the task ended, in RFC 3339 format. + - **outputs** (`list[TESOutputFileLog]`): Information about all output files. Directory outputs are flattened into separate items. + - **system_logs** (`Optional[list[str]]`): System logs are any logs the system decides are relevant, which are not tied directly to an Executor process. Content is implementation specific: format, size, etc. + - **status** (`Optional[str]`): The status of the task. + + **Reference:** [https://ga4gh.github.io/task-execution-schemas/docs/#operation/GetTask](https://ga4gh.github.io/task-execution-schemas/docs/#operation/GetTask) + """ + + logs: list[TESExecutorLog] + metadata: Optional[dict[str, str]] + start_time: Optional[datetime] + end_time: Optional[datetime] + outputs: list[TESOutputFileLog] + system_logs: Optional[list[str]] + + @validator("start_time", "end_time") + def validate_datetime(value): + return convert_to_rfc3339_format(value) + + +class TESData(BaseModel): + """ + Represents a TES task. + + **Attributes:** + + - **id** (`str`): Task identifier assigned by the server. + - **name** (`Optional[str]`): User-provided task name. + - **description** (`Optional[str]`): Optional user-provided description of task for documentation purposes. + - **creation_time** (`Optional[str]`): The time the task was created. + - **state** (`Optional[str]`): Task state as defined by the server + - **inputs** (`list[TESInput]`): Input files that will be used by the task. + - **outputs** (`list[TESOutput]`): Output files that will be uploaded from the executor container to long-term storage. + - **executors** (`list[Executor]`): An array of executors to be run. + - **resources** (`Optional[TESResources]`): The resources required by the TES task. + - **volumes** (`Optional[list[str]]`): Volumes are directories which may be used to share data between Executors.. + - **logs** (`Optional[list[TESLogs]]`): Task logging information + - **tags** (`Optional[[str, str]]`): A key-value map of arbitrary tags. + + **Reference:** [https://ga4gh.github.io/task-execution-schemas/docs/#operation/GetTask](https://ga4gh.github.io/task-execution-schemas/docs/#operation/GetTask) + """ + + id: str + name: Optional[str] = None + description: Optional[str] = None + creation_time: Optional[datetime] = None + state: Optional[TESState] = TESState.UNKNOWN + inputs: list[TESInput] + outputs: list[TESOutput] + executors: list[TESExecutor] + resources: Optional[TESResources] = None + volumes: Optional[list[str]] = None + logs: Optional[list[TESTaskLog]] = None + tags: Optional[dict[str, str]] = None + + @validator("creation_time") + def validate_datetime(value): + return convert_to_rfc3339_format(value) diff --git a/crategen/models/wes_models.py b/crategen/models/wes_models.py new file mode 100644 index 0000000..cdba35f --- /dev/null +++ b/crategen/models/wes_models.py @@ -0,0 +1,175 @@ +""" +Each model in this module conforms to the corresponding WES model names as specified by the GA4GH schema (https://ga4gh.github.io/workflow-execution-service-schemas/docs/). +""" + +from datetime import datetime +from enum import Enum +from typing import Optional + +from pydantic import BaseModel, Field, root_validator, validator + +from ..utils import convert_to_rfc3339_format + + +class State(str, Enum): + UNKNOWN = "UNKNOWN" + QUEUED = "QUEUED" + INITIALIZING = "INITIALIZING" + RUNNING = "RUNNING" + PAUSED = "PAUSED" + COMPLETE = "COMPLETE" + EXECUTOR_ERROR = "EXECUTOR_ERROR" + SYSTEM_ERROR = "SYSTEM_ERROR" + CANCELLED = "CANCELLED" + CANCELING = "CANCELING" + PREEMPTED = "PREEMPTED" + + +class WESOutputs(BaseModel): + location: str + name: str + + +class Log(BaseModel): + """ + Represents a run log in the Workflow Execution Service (WES). + + **Attributes:** + + - **name** (`Optional[str]`): The task or workflow name. + - **cmd** (`Optional[list[str]]`): The command line that was executed. + - **start_time** (`Optional[str]`): When the command started executing, in ISO 8601 format. + - **end_time** (`Optional[str]`): When the command stopped executing, in ISO 8601 format. + - **stdout** (`Optional[str]`): A URL to retrieve standard output logs of the workflow run or task.. + - **stderr** (`Optional[str]`): A URL to retrieve standard error logs of the workflow run or task. + - **exit_code** (`Optional[int]`): The exit code of the program. + - **system_logs** (`optional[list[str]]`): Any logs the system decides are relevant, which are not tied directly to a workflow. + + **Reference:** https://ga4gh.github.io/workflow-execution-service-schemas/docs/#tag/runlog_model + **Attributes:** + + - **name** (`Optional[str]`): The task or workflow name. + - **cmd** (`Optional[list[str]]`): The command line that was executed. + - **start_time** (`Optional[str]`): When the command started executing, in ISO 8601 format. + - **end_time** (`Optional[str]`): When the command stopped executing, in ISO 8601 format. + - **stdout** (`Optional[str]`): A URL to retrieve standard output logs of the workflow run or task.. + - **stderr** (`Optional[str]`): A URL to retrieve standard error logs of the workflow run or task. + - **exit_code** (`Optional[int]`): The exit code of the program. + - **system_logs** (`optional[list[str]]`): Any logs the system decides are relevant, which are not tied directly to a workflow. + + **Reference:** https://ga4gh.github.io/workflow-execution-service-schemas/docs/#tag/runlog_model + """ + + name: Optional[str] = None + start_time: Optional[datetime] = None + end_time: Optional[datetime] = None + cmd: Optional[list[str]] = None + stdout: Optional[str] = None + stderr: Optional[str] = None + exit_code: Optional[int] = None + system_logs: Optional[list[str]] = None + + @validator("start_time", "end_time") + def validate_datetime(value): + return convert_to_rfc3339_format(value) + + +class TaskLog(Log): + """ + Represents a task log in the Workflow Execution Service (WES). + + **Attributes:** + + - **name** (`str`): The task or workflow name. + - **cmd** (`Optional[list[str]]`): The command line that was executed. + - **start_time** (`Optional[str]`): When the command started executing, in ISO 8601 format. + - **end_time** (`Optional[str]`): When the command stopped executing, in ISO 8601 format. + - **stdout** (`Optional[str]`): A URL to retrieve standard output logs of the workflow run or task.. + - **stderr** (`Optional[str]`): A URL to retrieve standard error logs of the workflow run or task. + - **exit_code** (`Optional[int]`): The exit code of the program. + - **system_logs** (`Optional[list[str]]`): Any logs the system decides are relevant, which are not tied directly to a workflow. + - **id** (`str`): A unique identifier which maybe used to reference the task + - **tes_uri** (`Optional[str]`): An optional URL pointing to an extended task definition defined by a TES api + + **Reference:** https://ga4gh.github.io/workflow-execution-service-schemas/docs/#tag/runlog_model + """ + + id: str + tes_uri: Optional[str] + name: str = Field(...) + + +class RunRequest(BaseModel): + """ + Represents a workflow request in WES. + + **Attributes:** + + - **workflow_params** (`Optional[dict[str, str]]`): The workflow run parameterizations(JSON encoded), including input and output file locations. + - **workflow_type** (`str`): The workflow descriptor type. + - **workflow_type_version** (`str`): The workflow descriptor type version. + - **tags** (`Optional[dict[str, str]]`): Additional tags associated with the workflow. + - **workflow_engine_parameters** (Optional[dict[str, str]]): Input values specific to the workflow engine. + - **workflow_engine** (`Optional[str]`): The workflow engine. + - **workflow_engine_version (`Optional[str]`): The workflow engine version. + - **workflow_url** (`str`): The workflow url + + **Reference:** https://ga4gh.github.io/workflow-execution-service-schemas/docs/#tag/runlog_model + """ + + workflow_params: dict[str, str] + workflow_type: str + workflow_type_version: str + tags: Optional[dict[str, str]] = {} + workflow_engine_parameters: Optional[dict[str, str]] = None + workflow_engine: Optional[str] = None + workflow_engine_version: Optional[str] = None + workflow_url: str + + @root_validator() + def validate_workflow_engine(cls, values): + """ + - If workflow_engine_version is set the workflow_engine must be set. + """ + engine_version = values.get("workflow_engine_version") + engine = values.get("workflow_engine") + + if engine_version is not None and engine is None: + raise ValueError( + "The 'workflow_engine' attribute is required when the 'workflow_engine_verision' attribute is set" + ) + return values + + +class WESData(BaseModel): + """ + Represents a WES run. + + **Attributes:** + + - **run_id** (`str`): The unique identifier for the WES run. + - **request** (`Optional[RunRequest]`): The request associated with the WES run. + - **state** (`Optional[State]`): The state of the WES run. + - **run_log** (`Object`): The log of the WES run. + - **task_logs_url** (`Optional[str]`): A reference to the complete url which may be used to obtain a paginated list of task logs for this workflow. + - **task_logs** (`Optional[list[Log | RunLog] | None]`): The logs of individual tasks within the run. This attribute is deprecated. + - **outputs** (`dict[str, str]`): The outputs of the WES run. + + **Reference:** https://ga4gh.github.io/workflow-execution-service-schemas/docs/#tag/runlog_model + """ + + run_id: str + request: Optional[RunRequest] = None + state: Optional[State] = None + run_log: Optional[Log] = None + task_logs_url: Optional[str] = None + task_logs: Optional[list[Log | TaskLog] | None] = None + outputs: dict[str, str] = None + + @root_validator + def check_deprecated_fields(cls, values): + if values.get("task_logs") is not None: + print( + "DeprecationWarning: The 'task_logs' field is deprecated and will be removed in future versions. Use 'tes_logs_url' instead." + ) + return values diff --git a/crategen/models/wrroc_models.py b/crategen/models/wrroc_models.py new file mode 100644 index 0000000..b07510e --- /dev/null +++ b/crategen/models/wrroc_models.py @@ -0,0 +1,162 @@ +from datetime import datetime +from typing import Annotated, Optional + +from pydantic import AnyUrl, BaseModel, Field + +WRROC_ID = Annotated[str, Field(alias="@id")] + + +class WRROCInputs(BaseModel): + """ + A model representing inputs in WRROC. + + Attributes: + id (str): The unique identifier for the input. + name (str): The name of the input. + """ + + id: WRROC_ID + name: str + + +class WRROCOutputs(BaseModel): + """ + A model representing outputs in WRROC. + + Attributes: + id (str): The unique identifier for the output. + name (str): The name of the output. + """ + + id: WRROC_ID + name: str + + +class WRROCDataBase(BaseModel): + """ + A base model representing common fields for WRROC entities. + + Attributes: + id (str): The unique identifier for the WRROC entity. + name (str): The name of the WRROC entity. + description (Optional[str]): A brief description of the WRROC entity. + instrument (Optional[str]): The instrument used in the WRROC entity. + object (list[WRROCInputs]): A list of input objects related to the WRROC entity. + result (WRROCOutputs): A list of output results related to the WRROC entity. + startTime (Optional[datetime]): The start time of the WRROC entity. + endTime (Optional[datetime]): The end time of the WRROC entity. + version (Optional[str]): The version of the WRROC entity. + """ + + id: WRROC_ID + name: str + description: Optional[str] = "" + instrument: Optional[str] = None + object: list[WRROCInputs] = Field(default_factory=list) + result: Optional[WRROCOutputs] = None + startTime: Optional[datetime] = None + endTime: Optional[datetime] = None + version: Optional[str] = None + + class Config: + extra = "allow" + allow_population_by_field_name = True # Allows using field name for input data + + +class WRROCData(WRROCDataBase): + """ + A model representing a WRROC entity, inheriting from WRROCDataBase. + """ + + pass + + +class WRROCDataTES(WRROCDataBase): + """ + A model representing WRROC data specifically for TES conversion. + + This model inherits from WRROCDataBase and includes all the necessary fields required for TES conversion. + """ + + pass + + +class WRROCDataWES(WRROCDataBase): + """ + A model representing WRROC data specifically for WES conversion. + + This model inherits from WRROCDataBase and includes additional fields required for WES conversion. + """ + + status: str + + +class WRROCProcess(BaseModel): + """ + A model representing the WRROC Process Run profile. + + Attributes: + id (str): The unique identifier for the WRROC entity. + name (str): The name of the WRROC entity. + description (Optional[str]): A brief description of the WRROC entity. + startTime (Optional[str]): The start time of the process. + endTime (Optional[str]): The end time of the process. + object (Optional[list[dict[str, str]]]): A list of input objects related to the process. + profiles (Optional[list[AnyUrl]]): URLs to the RO-Crate profiles used. + """ + + id: WRROC_ID + name: str + description: Optional[str] = "" + startTime: Optional[str] = None + endTime: Optional[str] = None + object: Optional[list[dict[str, str]]] = None + profiles: Optional[list[AnyUrl]] = None + + class Config: + extra = "allow" + allow_population_by_field_name = True + + +class WRROCWorkflow(WRROCProcess): + """ + A model representing the WRROC Workflow Run profile, inheriting from WRROCProcess. + + Attributes: + workflowType (Optional[str]): The type of the workflow. + workflowVersion (Optional[str]): The version of the workflow. + result (Optional[list[dict[str, str]]]): A list of output results related to the workflow. + hasPart (Optional[list[AnyUrl]]): A list of parts or steps within the workflow. + """ + + workflowType: Optional[str] = None + workflowVersion: Optional[str] = None + result: Optional[list[dict[str, str]]] = None + hasPart: Optional[list[AnyUrl]] = None + + class Config: + extra = "allow" + allow_population_by_field_name = True + + +class WRROCProvenance(WRROCWorkflow): + """ + A model representing the WRROC Provenance Run profile, inheriting from WRROCWorkflow. + + Attributes: + provenanceData (Optional[str]): Data related to the provenance of the workflow. + agents (Optional[list[dict[str, str]]]): A list of agents involved in the workflow. + activity (Optional[list[dict[str, str]]]): Activities related to the provenance. + generatedBy (Optional[list[AnyUrl]]): URLs of the entities that generated the data. + used (Optional[list[AnyUrl]]): URLs of the entities that were used in the data generation. + """ + + provenanceData: Optional[str] = None + agents: Optional[list[dict[str, str]]] = None + activity: Optional[list[dict[str, str]]] = None + generatedBy: Optional[list[AnyUrl]] = None + used: Optional[list[AnyUrl]] = None + + class Config: + extra = "allow" + allow_population_by_field_name = True diff --git a/crategen/converters/utils.py b/crategen/utils.py similarity index 65% rename from crategen/converters/utils.py rename to crategen/utils.py index 2116c7f..cd9fa6d 100644 --- a/crategen/converters/utils.py +++ b/crategen/utils.py @@ -1,5 +1,6 @@ import datetime + def convert_to_iso8601(timestamp): """ Convert a given timestamp to ISO 8601 format. @@ -14,10 +15,10 @@ def convert_to_iso8601(timestamp): if timestamp: # List of supported formats formats = [ - "%Y-%m-%dT%H:%M:%S.%fZ", # RFC 3339 with fractional seconds - "%Y-%m-%dT%H:%M:%SZ", # RFC 3339 without fractional seconds - "%Y-%m-%dT%H:%M:%S%z", # ISO 8601 with timezone - "%Y-%m-%dT%H:%M:%S.%f%z", # ISO 8601 with fractional seconds and timezone + "%Y-%m-%dT%H:%M:%S.%fZ", # RFC 3339 with fractional seconds + "%Y-%m-%dT%H:%M:%SZ", # RFC 3339 without fractional seconds + "%Y-%m-%dT%H:%M:%S%z", # ISO 8601 with timezone + "%Y-%m-%dT%H:%M:%S.%f%z", # ISO 8601 with fractional seconds and timezone ] for fmt in formats: try: @@ -27,3 +28,7 @@ def convert_to_iso8601(timestamp): # Handle incorrect format or other issues return None return None + + +def convert_to_rfc3339_format(date_time: datetime.datetime): + return date_time.isoformat("T") + "Z" diff --git a/crategen/validators.py b/crategen/validators.py new file mode 100644 index 0000000..6a10d39 --- /dev/null +++ b/crategen/validators.py @@ -0,0 +1,97 @@ +from typing import Union +from urllib.parse import urlparse + +from pydantic import ValidationError + +from .models.wrroc_models import ( + WRROCDataTES, + WRROCDataWES, + WRROCProcess, + WRROCProvenance, + WRROCWorkflow, +) + + +def validate_wrroc(data: dict) -> Union[WRROCProvenance, WRROCWorkflow, WRROCProcess]: + """ + Validate that the input data is a valid WRROC entity and determine which profile it adheres to. + + This function attempts to validate the input data against the WRROCProvenance model first. + If that validation fails, it attempts validation against the WRROCWorkflow model. + If that also fails, it finally attempts validation against the WRROCProcess model. + + Args: + data (dict): The input data to validate. + + Returns: + Union[WRROCProvenance, WRROCWorkflow, WRROCProcess]: The validated WRROC data, indicating the highest profile the data adheres to. + + + Raises: + ValueError: If the data does not adhere to any of the WRROC profiles. + """ + try: + return WRROCProvenance(**data) + except ValidationError: + pass + + try: + return WRROCWorkflow(**data) + except ValidationError: + pass + + try: + return WRROCProcess(**data) + except ValidationError as e: + raise ValueError(f"Invalid WRROC data: {e.errors()}") from e + + +def validate_wrroc_tes(data: dict) -> WRROCDataTES: + """ + Validate that the input data contains the fields required for WRROC to TES conversion. + + Returns: + WRROCDataTES: The validated WRROC data that is suitable for TES conversion. + + Raises: + ValueError: If the data is not valid WRROC data or does not contain the necessary fields for TES conversion. + """ + data_validated = validate_wrroc(data) + + try: + data_wrroc_tes = WRROCDataTES(**data_validated.dict()) + except ValidationError as exc: + raise ValueError( + f"WRROC data insufficient for TES conversion: {exc.errors()}" + ) from exc + + return data_wrroc_tes + + +def validate_wrroc_wes(data: dict) -> WRROCDataWES: + """ + Validate that the input data contains the fields required for WRROC to WES conversion. + + Returns: + WRROCDataWES: The validated WRROC data that is suitable for WES conversion. + + Raises: + ValueError: If the data is not valid WRROC data or does not contain the necessary fields for WES conversion. + """ + data_validated = validate_wrroc(data) + + try: + data_wrroc_wes = WRROCDataWES(**data_validated.dict()) + except ValidationError as exc: + raise ValueError( + f"WRROC data insufficient for WES conversion: {exc.errors()}" + ) from exc + + # Validate URLs in the result field, only if result is not None + if data_wrroc_wes.result is not None: + for result in data_wrroc_wes.result: + parsed_url = urlparse(result.id) + if not all([parsed_url.scheme, parsed_url.netloc]): + raise ValueError(f"Invalid URL in result: {result.id}") + + return data_wrroc_wes diff --git a/lefthook.yml b/lefthook.yml new file mode 100644 index 0000000..b20da8f --- /dev/null +++ b/lefthook.yml @@ -0,0 +1,10 @@ +pre-push: + commands: + ruff: + files: git diff --name-only --diff-filter=d $(git merge-base origin/main HEAD)..HEAD + run: poetry run ruff check {files} + glob: '*.py' + mypy: + files: git diff --name-only --diff-filter=d $(git merge-base origin/main HEAD)..HEAD + run: poetry run mypy {files} + glob: '*.py' diff --git a/poetry.lock b/poetry.lock index 3d2faaa..41f1952 100644 --- a/poetry.lock +++ b/poetry.lock @@ -13,13 +13,13 @@ files = [ [[package]] name = "authlib" -version = "1.3.1" +version = "1.3.2" description = "The ultimate Python library in building OAuth and OpenID Connect servers and clients." optional = false python-versions = ">=3.8" files = [ - {file = "Authlib-1.3.1-py2.py3-none-any.whl", hash = "sha256:d35800b973099bbadc49b42b256ecb80041ad56b7fe1216a362c7943c088f377"}, - {file = "authlib-1.3.1.tar.gz", hash = "sha256:7ae843f03c06c5c0debd63c9db91f9fda64fa62a42a77419fa15fbb7e7a58917"}, + {file = "Authlib-1.3.2-py2.py3-none-any.whl", hash = "sha256:ede026a95e9f5cdc2d4364a52103f5405e75aa156357e831ef2bfd0bc5094dfc"}, + {file = "authlib-1.3.2.tar.gz", hash = "sha256:4b16130117f9eb82aa6eec97f6dd4673c3f960ac0283ccdae2897ee4bc030ba2"}, ] [package.dependencies] @@ -27,13 +27,13 @@ cryptography = "*" [[package]] name = "babel" -version = "2.15.0" +version = "2.16.0" description = "Internationalization utilities" optional = false python-versions = ">=3.8" files = [ - {file = "Babel-2.15.0-py3-none-any.whl", hash = "sha256:08706bdad8d0a3413266ab61bd6c34d0c28d6e1e7badf40a2cebe67644e2e1fb"}, - {file = "babel-2.15.0.tar.gz", hash = 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+content-hash = "67d34bcf2eac9690bbfdca04d4a80cd6eadeb60255aeee892e99f8ac3d8cf9e6" diff --git a/pyproject.toml b/pyproject.toml index 1f82a41..0482d20 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -30,7 +30,7 @@ pytest-mock = "^3.14.0" pre-commit = "^2.13.0" [tool.poetry.group.lint.dependencies] -ruff = "^0.4.4" +ruff = "^0.6.3" typos = "^1.21.0" [tool.poetry.group.docs.dependencies] @@ -50,6 +50,16 @@ pytest-mock = "^3.14.0" [tool.poetry.group.types.dependencies] mypy = "^1.10.1" +[tool.mypy] +strict_optional = false + +[[tool.mypy.overrides]] +module = ['crategen.validators'] +ignore_errors = true + +[tool.poetry.group.dev.dependencies] +ruff = "^0.6.3" + [tool.poetry.scripts] crategen = "crategen.cli:cli" @@ -61,9 +71,13 @@ skips = [ [tool.ruff] exclude = [ - "tests/*", - "tests/unit/*", - "crategen/*" + ".git", + "/.pytest_cache", + "__pycache__", + "build", + "_build", + "dist", + ".env", ] indent-width = 4 @@ -72,11 +86,12 @@ docstring-code-format = true indent-style = "space" line-ending = "lf" quote-style = "double" +skip-magic-trailing-comma = true + [tool.ruff.lint] select = [ "B", # flake8-bugbear - "D", # pydocstyle "E", # pycodestyle "F", # Pyflakes "I", # isort @@ -84,9 +99,11 @@ select = [ "SIM", # flake8-simplify "UP", # pyupgrade ] +ignore = ["E203", "E501"] [tool.ruff.lint.pydocstyle] convention = "google" [tool.typos.default.extend-words] mke = 'mke' + diff --git a/tests/unit/test_wrroc_models.py b/tests/unit/test_wrroc_models.py new file mode 100644 index 0000000..bedf6a2 --- /dev/null +++ b/tests/unit/test_wrroc_models.py @@ -0,0 +1,277 @@ +import unittest + +from pydantic import ValidationError + +from crategen.models.wrroc_models import ( + WRROCDataWES, + WRROCProcess, + WRROCProvenance, + WRROCWorkflow, +) +from crategen.validators import validate_wrroc, validate_wrroc_tes, validate_wrroc_wes + + +class TestWRROCProcessModel(unittest.TestCase): + """ + Unit tests for the WRROCProcess model. + """ + + def test_wrroc_process_model(self): + """ + Test that the WRROCProcess model correctly validates data. + """ + data = { + "id": "process-id", + "name": "Test Process", + "description": "A simple process", + "startTime": "2024-07-10T14:30:00Z", + "endTime": "2024-07-10T15:30:00Z", + "object": [ + { + "id": "https://raw.githubusercontent.com/elixir-cloud-aai/CrateGen/main/README.md", + "name": "Input 1", + } + ], + } + model = WRROCProcess(**data) + self.assertEqual(model.id, "process-id") + self.assertEqual(model.name, "Test Process") + + def test_wrroc_process_empty_object_list(self): + """ + Test that the WRROCProcess model handles empty object lists correctly. + """ + data = {"id": "process-id", "name": "Test Process", "object": []} + model = WRROCProcess(**data) + self.assertEqual(model.object, []) + + def test_wrroc_process_invalid_data(self): + """ + Test that the WRROCProcess model raises a ValidationError with invalid data. + """ + data = { + "id": 123, # id should be a string + "name": None, # name should be a string + } + with self.assertRaises(ValidationError): + WRROCProcess(**data) + + +class TestWRROCWorkflowModel(unittest.TestCase): + """ + Unit tests for the WRROCWorkflow model. + """ + + def test_wrroc_workflow_model(self): + """ + Test that the WRROCWorkflow model correctly validates data and includes additional workflow fields. + """ + data = { + "id": "workflow-id", + "name": "Test Workflow", + "workflowType": "CWL", + "workflowVersion": "v1.0", + "result": [ + { + "id": "https://raw.githubusercontent.com/elixir-cloud-aai/CrateGen/main/LICENSE", + "name": "Output 1", + } + ], + } + model = WRROCWorkflow(**data) + self.assertEqual(model.workflowType, "CWL") + self.assertEqual(model.result[0]["name"], "Output 1") + + def test_wrroc_workflow_missing_optional_fields(self): + """ + Test that the WRROCWorkflow model handles missing optional fields correctly. + """ + data = {"id": "workflow-id", "name": "Test Workflow"} + model = WRROCWorkflow(**data) + self.assertIsNone(model.workflowType) + self.assertIsNone(model.workflowVersion) + + +class TestWRROCProvenanceModel(unittest.TestCase): + """ + Unit tests for the WRROCProvenance model. + """ + + def test_wrroc_provenance_model(self): + """ + Test that the WRROCProvenance model correctly validates data and includes additional provenance fields. + """ + data = { + "id": "provenance-id", + "name": "Test Provenance", + "provenanceData": "Provenance information", + "agents": [{"id": "agent1", "name": "Agent 1"}], + } + model = WRROCProvenance(**data) + self.assertEqual(model.provenanceData, "Provenance information") + self.assertEqual(model.agents[0]["name"], "Agent 1") + + def test_wrroc_provenance_empty_agents_list(self): + """ + Test that the WRROCProvenance model handles empty agents lists correctly. + """ + data = {"id": "provenance-id", "name": "Test Provenance", "agents": []} + model = WRROCProvenance(**data) + self.assertEqual(model.agents, []) + + +class TestWRROCValidators(unittest.TestCase): + """ + Unit tests for the WRROC validators to ensure they work as expected. + """ + + def test_validate_wrroc_process(self): + """ + Test that validate_wrroc correctly identifies a WRROCProcess entity. + """ + data = {"id": "process-id", "name": "Test Process"} + model = validate_wrroc(data) + self.assertIsInstance(model, WRROCProcess) + + def test_validate_wrroc_workflow(self): + """ + Test that validate_wrroc correctly identifies a WRROCWorkflow entity. + """ + data = { + "id": "workflow-id", + "name": "Test Workflow", + "workflowType": "CWL", + "workflowVersion": "v1.0", + } + model = validate_wrroc(data) + self.assertIsInstance(model, WRROCWorkflow) + + def test_validate_wrroc_provenance(self): + """ + Test that validate_wrroc correctly identifies a WRROCProvenance entity. + """ + data = { + "id": "provenance-id", + "name": "Test Provenance", + "provenanceData": "Provenance information", + } + model = validate_wrroc(data) + self.assertIsInstance(model, WRROCProvenance) + + def test_validate_wrroc_invalid(self): + """ + Test that validate_wrroc raises a ValueError for invalid WRROC data. + """ + data = {"unknown_field": "unexpected"} + with self.assertRaises(ValueError): + validate_wrroc(data) + + def test_validate_wrroc_tes(self): + """ + Test that validate_wrroc_tes correctly validates a WRROC entity for TES conversion. + """ + data = { + "@id": "process-id", + "name": "Test Process", + "object": [ + { + "@id": "https://raw.githubusercontent.com/elixir-cloud-aai/CrateGen/main/README.md", + "name": "Input 1", + } + ], + "result": [ + { + "@id": "https://raw.githubusercontent.com/elixir-cloud-aai/CrateGen/main/LICENSE", + "name": "Output 1", + } + ], + } + model = validate_wrroc_tes(data) + self.assertEqual(model.id, "process-id") + self.assertEqual(model.name, "Test Process") + + def test_validate_wrroc_tes_empty_object_list(self): + """ + Test that validate_wrroc_tes correctly validates a WRROC entity with an empty object list for TES conversion. + """ + data = { + "@id": "process-id", + "name": "Test Process", + "object": [], + "result": [ + { + "@id": "https://raw.githubusercontent.com/elixir-cloud-aai/CrateGen/main/LICENSE", + "name": "Output 1", + } + ], + } + model = validate_wrroc_tes(data) + self.assertEqual(model.object, []) + + def test_validate_wrroc_tes_missing_fields(self): + """ + Test that validate_wrroc_tes raises a ValueError if required fields for TES conversion are missing. + """ + data = {"id": "process-id", "name": "Test Process"} + with self.assertRaises(ValueError): + validate_wrroc_tes(data) + + def test_validate_wrroc_wes(self): + """ + Test that validate_wrroc_wes correctly validates a WRROC entity for WES conversion. + """ + data = { + "@id": "workflow-id", + "name": "Test Workflow", + "workflowType": "CWL", + "workflowVersion": "v1.0", + "status": "completed", + "object": [ + { + "@id": "https://raw.githubusercontent.com/elixir-cloud-aai/CrateGen/main/README.md", + "name": "Input 1", + } + ], + "result": [ + { + "@id": "https://raw.githubusercontent.com/elixir-cloud-aai/CrateGen/main/LICENSE", + "name": "Output 1", + } + ], + } + model = validate_wrroc_wes(data) + self.assertIsInstance(model, WRROCDataWES) + + def test_validate_wrroc_wes_invalid_url(self): + """ + Test that validate_wrroc_wes raises a ValueError if a result URL is invalid. + """ + invalid_urls = [ + "invalid_url", + "http:/github.com", + "ftp://github.com", + "//github.com", + "http://", + ] + for url in invalid_urls: + data = { + "id": "workflow-id", + "name": "Test Workflow", + "workflowType": "CWL", + "workflowVersion": "v1.0", + "result": [{"id": url, "name": "Output 1"}], + } + with self.assertRaises(ValueError): + validate_wrroc_wes(data) + + def test_validate_wrroc_wes_missing_fields(self): + """ + Test that validate_wrroc_wes raises a ValueError if required fields for WES conversion are missing. + """ + data = {"id": "workflow-id", "name": "Test Workflow"} + with self.assertRaises(ValueError): + validate_wrroc_wes(data) + + +if __name__ == "__main__": + unittest.main()