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validation: add compute backend validation
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,161 @@ | ||
| # -*- coding: utf-8 -*- | ||
| # | ||
| # This file is part of REANA. | ||
| # Copyright (C) 2022 CERN. | ||
| # | ||
| # REANA is free software; you can redistribute it and/or modify it | ||
| # under the terms of the MIT License; see LICENSE file for more details. | ||
|
|
||
| """REANA client compute backend validation.""" | ||
|
|
||
| import sys | ||
| from typing import Dict, List, Optional | ||
|
|
||
| from reana_client.printer import display_message | ||
|
|
||
|
|
||
| def validate_compute_backends( | ||
| reana_yaml: Dict, supported_backends: Optional[List[str]] | ||
| ) -> None: | ||
| """Validate compute backends in REANA specification file according to workflow type. | ||
| :param reana_yaml: dictionary which represents REANA specification file. | ||
| :param supported_backends: a list of the supported compute backends. | ||
| """ | ||
|
|
||
| def build_validator(workflow: Dict) -> None: | ||
| workflow_type = workflow["type"] | ||
| if workflow_type == "serial": | ||
| workflow_steps = workflow["specification"]["steps"] | ||
| return SerialComputeBackendValidator( | ||
| workflow_steps=workflow_steps, supported_backends=supported_backends | ||
| ) | ||
| if workflow_type == "yadage": | ||
| workflow_steps = workflow["specification"]["stages"] | ||
| return YadageComputeBackendValidator( | ||
| workflow_steps=workflow_steps, supported_backends=supported_backends | ||
| ) | ||
| if workflow_type == "cwl": | ||
| workflow_steps = workflow.get("specification", {}).get("$graph", workflow) | ||
| return CWLComputeBackendValidator( | ||
| workflow_steps=workflow_steps, supported_backends=supported_backends | ||
| ) | ||
| if workflow_type == "snakemake": | ||
| workflow_steps = workflow["specification"]["steps"] | ||
| return SnakemakeComputeBackendValidator( | ||
| workflow_steps=workflow_steps, supported_backends=supported_backends | ||
| ) | ||
|
|
||
| workflow = reana_yaml["workflow"] | ||
| validator = build_validator(workflow) | ||
| validator.validate() | ||
| display_message( | ||
| "Workflow compute backends appear to be valid.", | ||
| msg_type="success", | ||
| indented=True, | ||
| ) | ||
|
|
||
|
|
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| class ComputeBackendValidatorBase: | ||
| """REANA workflow compute backend validation base class.""" | ||
|
|
||
| def __init__( | ||
| self, | ||
| workflow_steps: Optional[List[Dict]] = None, | ||
| supported_backends: Optional[List[str]] = [], | ||
| ): | ||
| """Validate compute backends in REANA workflow steps. | ||
| :param workflow_steps: list of dictionaries which represents different steps involved in workflow. | ||
| :param supported_backends: a list of the supported compute backends. | ||
| """ | ||
| self.workflow_steps = workflow_steps | ||
| self.supported_backends = supported_backends | ||
| self.messages = [] | ||
|
|
||
| def validate(self) -> None: | ||
| """Validate compute backends in REANA workflow.""" | ||
| raise NotImplementedError | ||
|
|
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| def display_error_message(self, compute_backend: str, step_name: str) -> None: | ||
| """Display validation error message and exit.""" | ||
| message = ( | ||
| f'Compute backend "{compute_backend}" found in step "{step_name}" is not supported. ' | ||
| f'List of supported compute backends: "{", ".join(self.supported_backends)}"' | ||
| ) | ||
| display_message(message, msg_type="error", indented=True) | ||
| sys.exit(1) | ||
|
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||
|
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| class SerialComputeBackendValidator(ComputeBackendValidatorBase): | ||
| """REANA serial workflow compute backend validation.""" | ||
|
|
||
| def validate(self) -> None: | ||
| """Validate compute backends in REANA serial workflow.""" | ||
| for step in self.workflow_steps: | ||
| backend = step.get("compute_backend") | ||
| if backend and backend not in self.supported_backends: | ||
| self.display_error_message(backend, step.get("name")) | ||
|
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||
|
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| class YadageComputeBackendValidator(ComputeBackendValidatorBase): | ||
| """REANA Yadage workflow compute backend validation.""" | ||
|
|
||
| def validate(self) -> None: | ||
| """Validate compute backends in REANA Yadage workflow.""" | ||
|
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| def parse_stages(stages: Optional[List[Dict]]) -> None: | ||
| """Extract compute backends in Yadage workflow steps.""" | ||
| for stage in stages: | ||
| if "workflow" in stage["scheduler"]: | ||
| nested_stages = stage["scheduler"]["workflow"].get("stages", {}) | ||
| parse_stages(nested_stages) | ||
| else: | ||
| environment = stage["scheduler"]["step"]["environment"] | ||
| backend = next( | ||
| ( | ||
| resource["compute_backend"] | ||
| for resource in environment.get("resources", []) | ||
| if "compute_backend" in resource | ||
| ), | ||
| None, | ||
| ) | ||
| if backend and backend not in self.supported_backends: | ||
| self.display_error_message(backend, stage["name"]) | ||
|
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||
| return parse_stages(self.workflow_steps) | ||
|
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|
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| class CWLComputeBackendValidator(ComputeBackendValidatorBase): | ||
| """REANA CWL workflow compute backend validation.""" | ||
|
|
||
| def validate(self) -> None: | ||
| """Validate compute backends in REANA CWL workflow.""" | ||
|
|
||
| def _validate_compute_backends(workflow: Dict) -> None: | ||
| """Validate compute backends in REANA CWL workflow steps.""" | ||
| steps = workflow.get("steps", []) | ||
| for step in steps: | ||
| hints = step.get("hints", [{}]).pop() | ||
| backend = hints.get("compute_backend") | ||
| if backend and backend not in self.supported_backends: | ||
| self.display_error_message(backend, step.get("id")) | ||
|
|
||
| workflow = self.workflow_steps | ||
| if isinstance(workflow, dict): | ||
| _validate_compute_backends(workflow) | ||
| elif isinstance(workflow, list): | ||
| for wf in workflow: | ||
| _validate_compute_backends(wf) | ||
|
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||
|
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| class SnakemakeComputeBackendValidator(ComputeBackendValidatorBase): | ||
| """REANA Snakemake workflow compute backend validation.""" | ||
|
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| def validate(self) -> None: | ||
| """Validate compute backends in REANA Snakemake workflow.""" | ||
| for idx, step in enumerate(self.workflow_steps): | ||
| backend = step.get("compute_backend") | ||
| if backend and backend not in self.supported_backends: | ||
| step_name = step.get("name", str(idx)) | ||
| self.display_error_message(backend, step_name) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,42 @@ | ||
| # -*- coding: utf-8 -*- | ||
| # | ||
| # This file is part of REANA. | ||
| # Copyright (C) 2022 CERN. | ||
| # | ||
| # REANA is free software; you can redistribute it and/or modify it | ||
| # under the terms of the MIT License; see LICENSE file for more details. | ||
|
|
||
| """REANA client workspace validation.""" | ||
|
|
||
| import sys | ||
| from typing import List, Optional | ||
|
|
||
| from reana_commons.errors import REANAValidationError | ||
| from reana_commons.validation import validate_workspace | ||
|
|
||
| from reana_client.printer import display_message | ||
|
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||
|
|
||
| def _validate_workspace( | ||
| root_path: str, available_workspaces: Optional[List[str]] | ||
| ) -> None: | ||
| """Validate workspace in REANA specification file. | ||
| :param root_path: workspace root path to be validated. | ||
| :param available_workspaces: a list of the available workspaces. | ||
| :raises ValidationError: Given workspace in REANA spec file does not validate against | ||
| allowed workspaces. | ||
| """ | ||
| if root_path: | ||
| display_message( | ||
| "Verifying workspace in REANA specification file...", msg_type="info", | ||
| ) | ||
| try: | ||
| validate_workspace(root_path, available_workspaces) | ||
| display_message( | ||
| "Workflow workspace appears valid.", msg_type="success", indented=True, | ||
| ) | ||
| except REANAValidationError as e: | ||
| display_message(e.message, msg_type="error") | ||
| sys.exit(1) |
Oops, something went wrong.