fractal-server 2.9.0a10__tar.gz → 2.9.0a12__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/PKG-INFO +2 -3
- fractal_server-2.9.0a12/fractal_server/__init__.py +1 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/auth/group.py +20 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/auth/users.py +97 -99
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/executors/slurm/_slurm_config.py +0 -17
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/executors/slurm/ssh/executor.py +41 -173
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/executors/slurm/sudo/executor.py +26 -109
- fractal_server-2.9.0a12/fractal_server/app/runner/executors/slurm/utils_executors.py +58 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/schemas/user.py +16 -10
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/security/__init__.py +17 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/pyproject.toml +3 -4
- fractal_server-2.9.0a10/fractal_server/__init__.py +0 -1
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/LICENSE +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/README.md +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/__main__.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/alembic.ini +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/__init__.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/db/__init__.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/models/__init__.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/models/linkusergroup.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/models/linkuserproject.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/models/security.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/models/user_settings.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/models/v1/__init__.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/models/v1/dataset.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/models/v1/job.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/models/v1/project.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/models/v1/state.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/models/v1/task.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/models/v1/workflow.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/models/v2/__init__.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/models/v2/dataset.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/models/v2/job.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/models/v2/project.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/models/v2/task.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/models/v2/task_group.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/models/v2/workflow.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/models/v2/workflowtask.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/__init__.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/admin/__init__.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/admin/v1.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/admin/v2/__init__.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/admin/v2/job.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/admin/v2/project.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/admin/v2/task.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/admin/v2/task_group.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/admin/v2/task_group_lifecycle.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/api/__init__.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/api/v1/__init__.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/api/v1/_aux_functions.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/api/v1/dataset.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/api/v1/job.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/api/v1/project.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/api/v1/task.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/api/v1/task_collection.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/api/v1/workflow.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/api/v1/workflowtask.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/api/v2/__init__.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/api/v2/_aux_functions.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/api/v2/_aux_functions_task_lifecycle.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/api/v2/_aux_functions_tasks.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/api/v2/dataset.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/api/v2/images.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/api/v2/job.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/api/v2/project.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/api/v2/status.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/api/v2/submit.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/api/v2/task.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/api/v2/task_collection.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/api/v2/task_collection_custom.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/api/v2/task_group.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/api/v2/task_group_lifecycle.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/api/v2/workflow.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/api/v2/workflow_import.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/api/v2/workflowtask.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/auth/__init__.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/auth/_aux_auth.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/auth/current_user.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/auth/login.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/auth/oauth.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/auth/register.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/auth/router.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/aux/__init__.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/aux/_job.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/aux/_runner.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/routes/aux/validate_user_settings.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/.gitignore +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/__init__.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/async_wrap.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/components.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/compress_folder.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/exceptions.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/executors/__init__.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/executors/slurm/__init__.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/executors/slurm/_batching.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/executors/slurm/remote.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/executors/slurm/ssh/__init__.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/executors/slurm/ssh/_executor_wait_thread.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/executors/slurm/ssh/_slurm_job.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/executors/slurm/sudo/__init__.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/executors/slurm/sudo/_check_jobs_status.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/executors/slurm/sudo/_executor_wait_thread.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/executors/slurm/sudo/_subprocess_run_as_user.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/extract_archive.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/filenames.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/run_subprocess.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/set_start_and_last_task_index.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/shutdown.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/task_files.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/v1/__init__.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/v1/_common.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/v1/_local/__init__.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/v1/_local/_local_config.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/v1/_local/_submit_setup.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/v1/_local/executor.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/v1/_slurm/__init__.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/v1/_slurm/_submit_setup.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/v1/_slurm/get_slurm_config.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/v1/common.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/v1/handle_failed_job.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/v2/__init__.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/v2/_local/__init__.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/v2/_local/_local_config.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/v2/_local/_submit_setup.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/v2/_local/executor.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/v2/_local_experimental/__init__.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/v2/_local_experimental/_local_config.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/v2/_local_experimental/_submit_setup.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/v2/_local_experimental/executor.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/v2/_slurm_common/__init__.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/v2/_slurm_common/get_slurm_config.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/v2/_slurm_ssh/__init__.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/v2/_slurm_ssh/_submit_setup.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/v2/_slurm_sudo/__init__.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/v2/_slurm_sudo/_submit_setup.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/v2/deduplicate_list.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/v2/handle_failed_job.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/v2/merge_outputs.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/v2/runner.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/v2/runner_functions.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/v2/runner_functions_low_level.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/v2/task_interface.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/runner/versions.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/schemas/__init__.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/schemas/_validators.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/schemas/user_group.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/schemas/user_settings.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/schemas/v1/__init__.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/schemas/v1/applyworkflow.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/schemas/v1/dataset.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/schemas/v1/dumps.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/schemas/v1/manifest.py +0 -0
- {fractal_server-2.9.0a10 → fractal_server-2.9.0a12}/fractal_server/app/schemas/v1/project.py +0 -0
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Metadata-Version: 2.1
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Name: fractal-server
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Version: 2.9.
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Version: 2.9.0a12
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Summary: Server component of the Fractal analytics platform
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Home-page: https://github.com/fractal-analytics-platform/fractal-server
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License: BSD-3-Clause
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Classifier: Programming Language :: Python :: 3.11
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Classifier: Programming Language :: Python :: 3.12
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Requires-Dist: bcrypt (==4.0.1)
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Requires-Dist: fabric (>=3.2.2,<4.0.0)
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Requires-Dist: fastapi-users[oauth] (>=
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Requires-Dist: fastapi-users[oauth] (>=14,<15)
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__VERSION__ = "2.9.0a12"
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status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
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detail=(
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f"Cannot remove user from '{FRACTAL_DEFAULT_GROUP_NAME}' "
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),
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"""
|
75
66
|
|
76
|
-
# We prevent simultaneous editing of both user attributes and user/group
|
77
|
-
# associations
|
78
|
-
user_update_dict_without_groups = user_update.dict(
|
79
|
-
exclude_unset=True, exclude={"new_group_ids"}
|
80
|
-
)
|
81
|
-
edit_attributes = user_update_dict_without_groups != {}
|
82
|
-
edit_groups = user_update.new_group_ids is not None
|
83
|
-
if edit_attributes and edit_groups:
|
84
|
-
raise HTTPException(
|
85
|
-
status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
|
86
|
-
detail=(
|
87
|
-
"Cannot modify both user attributes and group membership. "
|
88
|
-
"Please make two independent PATCH calls"
|
89
|
-
),
|
90
|
-
)
|
91
|
-
|
92
67
|
# Check that user exists
|
93
68
|
user_to_patch = await _user_or_404(user_id, db)
|
94
69
|
|
95
|
-
|
96
|
-
|
97
|
-
|
98
|
-
|
99
|
-
|
100
|
-
|
101
|
-
|
102
|
-
|
70
|
+
# Modify user attributes
|
71
|
+
try:
|
72
|
+
user = await user_manager.update(
|
73
|
+
user_update,
|
74
|
+
user_to_patch,
|
75
|
+
safe=False,
|
76
|
+
request=None,
|
77
|
+
)
|
78
|
+
validated_user = schemas.model_validate(UserOAuth, user)
|
79
|
+
patched_user = await db.get(
|
80
|
+
UserOAuth, validated_user.id, populate_existing=True
|
81
|
+
)
|
82
|
+
except exceptions.InvalidPasswordException as e:
|
83
|
+
raise HTTPException(
|
84
|
+
status_code=status.HTTP_400_BAD_REQUEST,
|
85
|
+
detail={
|
86
|
+
"code": ErrorCode.UPDATE_USER_INVALID_PASSWORD,
|
87
|
+
"reason": e.reason,
|
88
|
+
},
|
89
|
+
)
|
90
|
+
except exceptions.UserAlreadyExists:
|
91
|
+
raise HTTPException(
|
92
|
+
status.HTTP_400_BAD_REQUEST,
|
93
|
+
detail=ErrorCode.UPDATE_USER_EMAIL_ALREADY_EXISTS,
|
103
94
|
)
|
104
|
-
res = await db.execute(stm)
|
105
|
-
number_matching_groups = res.scalar()
|
106
|
-
if number_matching_groups != len(user_update.new_group_ids):
|
107
|
-
raise HTTPException(
|
108
|
-
status_code=status.HTTP_404_NOT_FOUND,
|
109
|
-
detail=(
|
110
|
-
"Not all requested groups (IDs: "
|
111
|
-
f"{user_update.new_group_ids}) exist."
|
112
|
-
),
|
113
|
-
)
|
114
|
-
|
115
|
-
for new_group_id in user_update.new_group_ids:
|
116
|
-
link = LinkUserGroup(user_id=user_id, group_id=new_group_id)
|
117
|
-
db.add(link)
|
118
|
-
|
119
|
-
try:
|
120
|
-
await db.commit()
|
121
|
-
except IntegrityError as e:
|
122
|
-
error_msg = (
|
123
|
-
f"Cannot link groups with IDs {user_update.new_group_ids} "
|
124
|
-
f"to user {user_id}. "
|
125
|
-
"Likely reason: one of these links already exists.\n"
|
126
|
-
f"Original error: {str(e)}"
|
127
|
-
)
|
128
|
-
logger.info(error_msg)
|
129
|
-
raise HTTPException(
|
130
|
-
status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
|
131
|
-
detail=error_msg,
|
132
|
-
)
|
133
|
-
patched_user = user_to_patch
|
134
|
-
elif edit_attributes:
|
135
|
-
# Modify user attributes
|
136
|
-
try:
|
137
|
-
user_update_without_groups = UserUpdate(
|
138
|
-
**user_update_dict_without_groups
|
139
|
-
)
|
140
|
-
user = await user_manager.update(
|
141
|
-
user_update_without_groups,
|
142
|
-
user_to_patch,
|
143
|
-
safe=False,
|
144
|
-
request=None,
|
145
|
-
)
|
146
|
-
validated_user = schemas.model_validate(UserOAuth, user)
|
147
|
-
patched_user = await db.get(
|
148
|
-
UserOAuth, validated_user.id, populate_existing=True
|
149
|
-
)
|
150
|
-
except exceptions.InvalidPasswordException as e:
|
151
|
-
raise HTTPException(
|
152
|
-
status_code=status.HTTP_400_BAD_REQUEST,
|
153
|
-
detail={
|
154
|
-
"code": ErrorCode.UPDATE_USER_INVALID_PASSWORD,
|
155
|
-
"reason": e.reason,
|
156
|
-
},
|
157
|
-
)
|
158
|
-
except exceptions.UserAlreadyExists:
|
159
|
-
raise HTTPException(
|
160
|
-
status.HTTP_400_BAD_REQUEST,
|
161
|
-
detail=ErrorCode.UPDATE_USER_EMAIL_ALREADY_EXISTS,
|
162
|
-
)
|
163
|
-
else:
|
164
|
-
# Nothing to do, just continue
|
165
|
-
patched_user = user_to_patch
|
166
95
|
|
167
96
|
# Enrich user object with `group_ids_names` attribute
|
168
97
|
patched_user_with_groups = await _get_single_user_with_groups(
|
@@ -203,6 +132,75 @@ async def list_users(
|
|
203
132
|
return user_list
|
204
133
|
|
205
134
|
|
135
|
+
@router_users.post("/users/{user_id}/set-groups/", response_model=UserRead)
|
136
|
+
async def set_user_groups(
|
137
|
+
user_id: int,
|
138
|
+
user_update: UserUpdateGroups,
|
139
|
+
superuser: UserOAuth = Depends(current_active_superuser),
|
140
|
+
db: AsyncSession = Depends(get_async_db),
|
141
|
+
) -> UserRead:
|
142
|
+
|
143
|
+
# Preliminary check that all objects exist in the db
|
144
|
+
user = await _user_or_404(user_id=user_id, db=db)
|
145
|
+
target_group_ids = user_update.group_ids
|
146
|
+
stm = select(func.count(UserGroup.id)).where(
|
147
|
+
UserGroup.id.in_(target_group_ids)
|
148
|
+
)
|
149
|
+
res = await db.execute(stm)
|
150
|
+
count = res.scalar()
|
151
|
+
if count != len(target_group_ids):
|
152
|
+
raise HTTPException(
|
153
|
+
status_code=status.HTTP_404_NOT_FOUND,
|
154
|
+
detail=f"Some UserGroups in {target_group_ids} do not exist.",
|
155
|
+
)
|
156
|
+
|
157
|
+
# Check that default group is not being removed
|
158
|
+
default_group_id = await _get_default_usergroup_id(db=db)
|
159
|
+
if default_group_id not in target_group_ids:
|
160
|
+
raise HTTPException(
|
161
|
+
status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
|
162
|
+
detail=(
|
163
|
+
f"Cannot remove user from "
|
164
|
+
f"'{FRACTAL_DEFAULT_GROUP_NAME}' group.",
|
165
|
+
),
|
166
|
+
)
|
167
|
+
|
168
|
+
# Prepare lists of links to be removed
|
169
|
+
res = await db.execute(
|
170
|
+
select(LinkUserGroup)
|
171
|
+
.where(LinkUserGroup.user_id == user_id)
|
172
|
+
.where(LinkUserGroup.group_id.not_in(target_group_ids))
|
173
|
+
)
|
174
|
+
links_to_remove = res.scalars().all()
|
175
|
+
|
176
|
+
# Prepare lists of links to be added
|
177
|
+
res = await db.execute(
|
178
|
+
select(LinkUserGroup.group_id)
|
179
|
+
.where(LinkUserGroup.user_id == user_id)
|
180
|
+
.where(LinkUserGroup.group_id.in_(target_group_ids))
|
181
|
+
)
|
182
|
+
ids_links_already_in = res.scalars().all()
|
183
|
+
ids_links_to_add = set(target_group_ids) - set(ids_links_already_in)
|
184
|
+
|
185
|
+
# Remove/create links as needed
|
186
|
+
for link in links_to_remove:
|
187
|
+
logger.info(
|
188
|
+
f"Removing LinkUserGroup with {link.user_id=} "
|
189
|
+
f"and {link.group_id=}."
|
190
|
+
)
|
191
|
+
await db.delete(link)
|
192
|
+
for group_id in ids_links_to_add:
|
193
|
+
logger.info(
|
194
|
+
f"Creating new LinkUserGroup with {user_id=} " f"and {group_id=}."
|
195
|
+
)
|
196
|
+
db.add(LinkUserGroup(user_id=user_id, group_id=group_id))
|
197
|
+
await db.commit()
|
198
|
+
|
199
|
+
user_with_groups = await _get_single_user_with_groups(user, db)
|
200
|
+
|
201
|
+
return user_with_groups
|
202
|
+
|
203
|
+
|
206
204
|
@router_users.get(
|
207
205
|
"/users/{user_id}/settings/", response_model=UserSettingsRead
|
208
206
|
)
|
@@ -456,20 +456,3 @@ def _parse_mem_value(raw_mem: Union[str, int]) -> int:
|
|
456
456
|
|
457
457
|
logger.debug(f"{info}, return {mem_MB}")
|
458
458
|
return mem_MB
|
459
|
-
|
460
|
-
|
461
|
-
def get_default_slurm_config():
|
462
|
-
"""
|
463
|
-
Return a default `SlurmConfig` configuration object
|
464
|
-
"""
|
465
|
-
return SlurmConfig(
|
466
|
-
partition="main",
|
467
|
-
cpus_per_task=1,
|
468
|
-
mem_per_task_MB=100,
|
469
|
-
target_cpus_per_job=1,
|
470
|
-
max_cpus_per_job=2,
|
471
|
-
target_mem_per_job=100,
|
472
|
-
max_mem_per_job=500,
|
473
|
-
target_num_jobs=2,
|
474
|
-
max_num_jobs=4,
|
475
|
-
)
|
@@ -31,9 +31,11 @@ from ....filenames import SHUTDOWN_FILENAME
|
|
31
31
|
from ....task_files import get_task_file_paths
|
32
32
|
from ....task_files import TaskFiles
|
33
33
|
from ....versions import get_versions
|
34
|
-
from ...slurm._slurm_config import get_default_slurm_config
|
35
34
|
from ...slurm._slurm_config import SlurmConfig
|
36
35
|
from .._batching import heuristics
|
36
|
+
from ..utils_executors import get_pickle_file_path
|
37
|
+
from ..utils_executors import get_slurm_file_path
|
38
|
+
from ..utils_executors import get_slurm_script_file_path
|
37
39
|
from ._executor_wait_thread import FractalSlurmWaitThread
|
38
40
|
from fractal_server.app.runner.components import _COMPONENT_KEY_
|
39
41
|
from fractal_server.app.runner.compress_folder import compress_folder
|
@@ -223,132 +225,12 @@ class FractalSlurmSSHExecutor(SlurmExecutor):
|
|
223
225
|
with self.jobs_lock:
|
224
226
|
self.map_jobid_to_slurm_files_local.pop(jobid)
|
225
227
|
|
226
|
-
def get_input_pickle_file_path_local(
|
227
|
-
self, *, arg: str, subfolder_name: str, prefix: Optional[str] = None
|
228
|
-
) -> Path:
|
229
|
-
|
230
|
-
prefix = prefix or "cfut"
|
231
|
-
output = (
|
232
|
-
self.workflow_dir_local
|
233
|
-
/ subfolder_name
|
234
|
-
/ f"{prefix}_in_{arg}.pickle"
|
235
|
-
)
|
236
|
-
return output
|
237
|
-
|
238
|
-
def get_input_pickle_file_path_remote(
|
239
|
-
self, *, arg: str, subfolder_name: str, prefix: Optional[str] = None
|
240
|
-
) -> Path:
|
241
|
-
|
242
|
-
prefix = prefix or "cfut"
|
243
|
-
output = (
|
244
|
-
self.workflow_dir_remote
|
245
|
-
/ subfolder_name
|
246
|
-
/ f"{prefix}_in_{arg}.pickle"
|
247
|
-
)
|
248
|
-
return output
|
249
|
-
|
250
|
-
def get_output_pickle_file_path_local(
|
251
|
-
self, *, arg: str, subfolder_name: str, prefix: Optional[str] = None
|
252
|
-
) -> Path:
|
253
|
-
prefix = prefix or "cfut"
|
254
|
-
return (
|
255
|
-
self.workflow_dir_local
|
256
|
-
/ subfolder_name
|
257
|
-
/ f"{prefix}_out_{arg}.pickle"
|
258
|
-
)
|
259
|
-
|
260
|
-
def get_output_pickle_file_path_remote(
|
261
|
-
self, *, arg: str, subfolder_name: str, prefix: Optional[str] = None
|
262
|
-
) -> Path:
|
263
|
-
prefix = prefix or "cfut"
|
264
|
-
return (
|
265
|
-
self.workflow_dir_remote
|
266
|
-
/ subfolder_name
|
267
|
-
/ f"{prefix}_out_{arg}.pickle"
|
268
|
-
)
|
269
|
-
|
270
|
-
def get_slurm_script_file_path_local(
|
271
|
-
self, *, subfolder_name: str, prefix: Optional[str] = None
|
272
|
-
) -> Path:
|
273
|
-
prefix = prefix or "_temp"
|
274
|
-
return (
|
275
|
-
self.workflow_dir_local
|
276
|
-
/ subfolder_name
|
277
|
-
/ f"{prefix}_slurm_submit.sbatch"
|
278
|
-
)
|
279
|
-
|
280
|
-
def get_slurm_script_file_path_remote(
|
281
|
-
self, *, subfolder_name: str, prefix: Optional[str] = None
|
282
|
-
) -> Path:
|
283
|
-
prefix = prefix or "_temp"
|
284
|
-
return (
|
285
|
-
self.workflow_dir_remote
|
286
|
-
/ subfolder_name
|
287
|
-
/ f"{prefix}_slurm_submit.sbatch"
|
288
|
-
)
|
289
|
-
|
290
|
-
def get_slurm_stdout_file_path_local(
|
291
|
-
self,
|
292
|
-
*,
|
293
|
-
subfolder_name: str,
|
294
|
-
arg: str = "%j",
|
295
|
-
prefix: Optional[str] = None,
|
296
|
-
) -> Path:
|
297
|
-
prefix = prefix or "slurmpy.stdout"
|
298
|
-
return (
|
299
|
-
self.workflow_dir_local
|
300
|
-
/ subfolder_name
|
301
|
-
/ f"{prefix}_slurm_{arg}.out"
|
302
|
-
)
|
303
|
-
|
304
|
-
def get_slurm_stdout_file_path_remote(
|
305
|
-
self,
|
306
|
-
*,
|
307
|
-
subfolder_name: str,
|
308
|
-
arg: str = "%j",
|
309
|
-
prefix: Optional[str] = None,
|
310
|
-
) -> Path:
|
311
|
-
prefix = prefix or "slurmpy.stdout"
|
312
|
-
return (
|
313
|
-
self.workflow_dir_remote
|
314
|
-
/ subfolder_name
|
315
|
-
/ f"{prefix}_slurm_{arg}.out"
|
316
|
-
)
|
317
|
-
|
318
|
-
def get_slurm_stderr_file_path_local(
|
319
|
-
self,
|
320
|
-
*,
|
321
|
-
subfolder_name: str,
|
322
|
-
arg: str = "%j",
|
323
|
-
prefix: Optional[str] = None,
|
324
|
-
) -> Path:
|
325
|
-
prefix = prefix or "slurmpy.stderr"
|
326
|
-
return (
|
327
|
-
self.workflow_dir_local
|
328
|
-
/ subfolder_name
|
329
|
-
/ f"{prefix}_slurm_{arg}.err"
|
330
|
-
)
|
331
|
-
|
332
|
-
def get_slurm_stderr_file_path_remote(
|
333
|
-
self,
|
334
|
-
*,
|
335
|
-
subfolder_name: str,
|
336
|
-
arg: str = "%j",
|
337
|
-
prefix: Optional[str] = None,
|
338
|
-
) -> Path:
|
339
|
-
prefix = prefix or "slurmpy.stderr"
|
340
|
-
return (
|
341
|
-
self.workflow_dir_remote
|
342
|
-
/ subfolder_name
|
343
|
-
/ f"{prefix}_slurm_{arg}.err"
|
344
|
-
)
|
345
|
-
|
346
228
|
def submit(
|
347
229
|
self,
|
348
230
|
fun: Callable[..., Any],
|
349
231
|
*fun_args: Sequence[Any],
|
350
|
-
slurm_config:
|
351
|
-
task_files:
|
232
|
+
slurm_config: SlurmConfig,
|
233
|
+
task_files: TaskFiles,
|
352
234
|
**fun_kwargs: dict,
|
353
235
|
) -> Future:
|
354
236
|
"""
|
@@ -359,11 +241,9 @@ class FractalSlurmSSHExecutor(SlurmExecutor):
|
|
359
241
|
fun_args: Function positional arguments
|
360
242
|
fun_kwargs: Function keyword arguments
|
361
243
|
slurm_config:
|
362
|
-
A `SlurmConfig` object
|
363
|
-
`get_default_slurm_config()`.
|
244
|
+
A `SlurmConfig` object.
|
364
245
|
task_files:
|
365
|
-
A `TaskFiles` object
|
366
|
-
`self.get_default_task_files()`.
|
246
|
+
A `TaskFiles` object.
|
367
247
|
|
368
248
|
Returns:
|
369
249
|
Future representing the execution of the current SLURM job.
|
@@ -375,12 +255,6 @@ class FractalSlurmSSHExecutor(SlurmExecutor):
|
|
375
255
|
logger.warning(error_msg)
|
376
256
|
raise JobExecutionError(info=error_msg)
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|
|
378
|
-
# Set defaults, if needed
|
379
|
-
if slurm_config is None:
|
380
|
-
slurm_config = get_default_slurm_config()
|
381
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-
if task_files is None:
|
382
|
-
task_files = self.get_default_task_files()
|
383
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-
|
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258
|
# Set slurm_file_prefix
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|
slurm_file_prefix = task_files.file_prefix
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|
|
@@ -418,8 +292,8 @@ class FractalSlurmSSHExecutor(SlurmExecutor):
|
|
418
292
|
fn: Callable[..., Any],
|
419
293
|
iterable: list[Sequence[Any]],
|
420
294
|
*,
|
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|
-
slurm_config:
|
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|
-
task_files:
|
295
|
+
slurm_config: SlurmConfig,
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296
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+
task_files: TaskFiles,
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297
|
):
|
424
298
|
"""
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425
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|
Return an iterator with the results of several execution of a function
|
@@ -442,12 +316,9 @@ class FractalSlurmSSHExecutor(SlurmExecutor):
|
|
442
316
|
An iterable such that each element is the list of arguments to
|
443
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|
be passed to `fn`, as in `fn(*args)`.
|
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318
|
slurm_config:
|
445
|
-
A `SlurmConfig` object
|
446
|
-
`get_default_slurm_config()`.
|
319
|
+
A `SlurmConfig` object.
|
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320
|
task_files:
|
448
|
-
A `TaskFiles` object
|
449
|
-
`self.get_default_task_files()`.
|
450
|
-
|
321
|
+
A `TaskFiles` object.
|
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|
"""
|
452
323
|
|
453
324
|
# Do not continue if auxiliary thread was shut down
|
@@ -472,12 +343,6 @@ class FractalSlurmSSHExecutor(SlurmExecutor):
|
|
472
343
|
# self._exception
|
473
344
|
del fut
|
474
345
|
|
475
|
-
# Set defaults, if needed
|
476
|
-
if not slurm_config:
|
477
|
-
slurm_config = get_default_slurm_config()
|
478
|
-
if task_files is None:
|
479
|
-
task_files = self.get_default_task_files()
|
480
|
-
|
481
346
|
# Include common_script_lines in extra_lines
|
482
347
|
logger.debug(
|
483
348
|
f"Adding {self.common_script_lines=} to "
|
@@ -710,63 +575,80 @@ class FractalSlurmSSHExecutor(SlurmExecutor):
|
|
710
575
|
f"Missing folder {subfolder_path.as_posix()}."
|
711
576
|
)
|
712
577
|
|
713
|
-
# Define I/O pickle file local/remote paths
|
714
578
|
job.input_pickle_files_local = tuple(
|
715
|
-
|
579
|
+
get_pickle_file_path(
|
716
580
|
arg=job.workerids[ind],
|
581
|
+
workflow_dir=self.workflow_dir_local,
|
717
582
|
subfolder_name=job.wftask_subfolder_name,
|
583
|
+
in_or_out="in",
|
718
584
|
prefix=job.wftask_file_prefixes[ind],
|
719
585
|
)
|
720
586
|
for ind in range(job.num_tasks_tot)
|
721
587
|
)
|
588
|
+
|
722
589
|
job.input_pickle_files_remote = tuple(
|
723
|
-
|
590
|
+
get_pickle_file_path(
|
724
591
|
arg=job.workerids[ind],
|
592
|
+
workflow_dir=self.workflow_dir_remote,
|
725
593
|
subfolder_name=job.wftask_subfolder_name,
|
594
|
+
in_or_out="in",
|
726
595
|
prefix=job.wftask_file_prefixes[ind],
|
727
596
|
)
|
728
597
|
for ind in range(job.num_tasks_tot)
|
729
598
|
)
|
730
599
|
job.output_pickle_files_local = tuple(
|
731
|
-
|
600
|
+
get_pickle_file_path(
|
732
601
|
arg=job.workerids[ind],
|
602
|
+
workflow_dir=self.workflow_dir_local,
|
733
603
|
subfolder_name=job.wftask_subfolder_name,
|
604
|
+
in_or_out="out",
|
734
605
|
prefix=job.wftask_file_prefixes[ind],
|
735
606
|
)
|
736
607
|
for ind in range(job.num_tasks_tot)
|
737
608
|
)
|
738
609
|
job.output_pickle_files_remote = tuple(
|
739
|
-
|
610
|
+
get_pickle_file_path(
|
740
611
|
arg=job.workerids[ind],
|
612
|
+
workflow_dir=self.workflow_dir_remote,
|
741
613
|
subfolder_name=job.wftask_subfolder_name,
|
614
|
+
in_or_out="out",
|
742
615
|
prefix=job.wftask_file_prefixes[ind],
|
743
616
|
)
|
744
617
|
for ind in range(job.num_tasks_tot)
|
745
618
|
)
|
746
|
-
|
747
|
-
|
748
|
-
|
619
|
+
# define slurm-job file local/remote paths
|
620
|
+
job.slurm_script_local = get_slurm_script_file_path(
|
621
|
+
workflow_dir=self.workflow_dir_local,
|
749
622
|
subfolder_name=job.wftask_subfolder_name,
|
750
623
|
prefix=job.slurm_file_prefix,
|
751
624
|
)
|
752
|
-
job.slurm_script_remote =
|
625
|
+
job.slurm_script_remote = get_slurm_script_file_path(
|
626
|
+
workflow_dir=self.workflow_dir_remote,
|
753
627
|
subfolder_name=job.wftask_subfolder_name,
|
754
628
|
prefix=job.slurm_file_prefix,
|
755
629
|
)
|
756
|
-
job.slurm_stdout_local =
|
630
|
+
job.slurm_stdout_local = get_slurm_file_path(
|
631
|
+
workflow_dir=self.workflow_dir_local,
|
757
632
|
subfolder_name=job.wftask_subfolder_name,
|
633
|
+
out_or_err="out",
|
758
634
|
prefix=job.slurm_file_prefix,
|
759
635
|
)
|
760
|
-
job.slurm_stdout_remote =
|
636
|
+
job.slurm_stdout_remote = get_slurm_file_path(
|
637
|
+
workflow_dir=self.workflow_dir_remote,
|
761
638
|
subfolder_name=job.wftask_subfolder_name,
|
639
|
+
out_or_err="out",
|
762
640
|
prefix=job.slurm_file_prefix,
|
763
641
|
)
|
764
|
-
job.slurm_stderr_local =
|
642
|
+
job.slurm_stderr_local = get_slurm_file_path(
|
643
|
+
workflow_dir=self.workflow_dir_local,
|
765
644
|
subfolder_name=job.wftask_subfolder_name,
|
645
|
+
out_or_err="err",
|
766
646
|
prefix=job.slurm_file_prefix,
|
767
647
|
)
|
768
|
-
job.slurm_stderr_remote =
|
648
|
+
job.slurm_stderr_remote = get_slurm_file_path(
|
649
|
+
workflow_dir=self.workflow_dir_remote,
|
769
650
|
subfolder_name=job.wftask_subfolder_name,
|
651
|
+
out_or_err="err",
|
770
652
|
prefix=job.slurm_file_prefix,
|
771
653
|
)
|
772
654
|
|
@@ -1294,7 +1176,6 @@ class FractalSlurmSSHExecutor(SlurmExecutor):
|
|
1294
1176
|
slurm_err_path: str,
|
1295
1177
|
slurm_config: SlurmConfig,
|
1296
1178
|
):
|
1297
|
-
|
1298
1179
|
num_tasks_max_running = slurm_config.parallel_tasks_per_job
|
1299
1180
|
mem_per_task_MB = slurm_config.mem_per_task_MB
|
1300
1181
|
|
@@ -1346,19 +1227,6 @@ class FractalSlurmSSHExecutor(SlurmExecutor):
|
|
1346
1227
|
script = "\n".join(script_lines)
|
1347
1228
|
return script
|
1348
1229
|
|
1349
|
-
def get_default_task_files(self) -> TaskFiles:
|
1350
|
-
"""
|
1351
|
-
This will be called when self.submit or self.map are called from
|
1352
|
-
outside fractal-server, and then lack some optional arguments.
|
1353
|
-
"""
|
1354
|
-
task_files = TaskFiles(
|
1355
|
-
workflow_dir_local=self.workflow_dir_local,
|
1356
|
-
workflow_dir_remote=self.workflow_dir_remote,
|
1357
|
-
task_order=None,
|
1358
|
-
task_name="name",
|
1359
|
-
)
|
1360
|
-
return task_files
|
1361
|
-
|
1362
1230
|
def shutdown(self, wait=True, *, cancel_futures=False):
|
1363
1231
|
"""
|
1364
1232
|
Clean up all executor variables. Note that this function is executed on
|