fractal-server 2.3.4__tar.gz → 2.3.6__tar.gz

{fractal_server-2.3.4 → fractal_server-2.3.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fractal-server
-Version: 2.3.4
+Version: 2.3.6
 Summary: Server component of the Fractal analytics platform
 Home-page: https://github.com/fractal-analytics-platform/fractal-server
 License: BSD-3-Clause
@@ -33,7 +33,7 @@ Requires-Dist: psycopg[binary] (>=3.1.0,<4.0.0) ; extra == "postgres-psycopg-bin
 Requires-Dist: pydantic (>=1.10.8,<2)
 Requires-Dist: python-dotenv (>=1.0.0,<2.0.0)
 Requires-Dist: sqlalchemy[asyncio] (>=2.0.23,<2.1)
-Requires-Dist: sqlmodel (>=0.0.19,<0.0.20)
+Requires-Dist: sqlmodel (>=0.0.21,<0.0.22)
 Requires-Dist: uvicorn (>=0.29.0,<0.30.0)
 Project-URL: Changelog, https://github.com/fractal-analytics-platform/fractal-server/blob/main/CHANGELOG.md
 Project-URL: Documentation, https://fractal-analytics-platform.github.io/fractal-server

fractal_server-2.3.6/fractal_server/__init__.py

@@ -0,0 +1 @@
+__VERSION__ = "2.3.6"

fractal_server-2.3.6/fractal_server/app/models/v2/task.py

@@ -0,0 +1,41 @@
+from typing import Any
+from typing import Optional
+
+from pydantic import HttpUrl
+from sqlalchemy import Column
+from sqlalchemy.types import JSON
+from sqlmodel import Field
+from sqlmodel import SQLModel
+
+
+class TaskV2(SQLModel, table=True):
+
+    id: Optional[int] = Field(default=None, primary_key=True)
+    name: str
+
+    type: str
+    command_non_parallel: Optional[str] = None
+    command_parallel: Optional[str] = None
+    source: str = Field(unique=True)
+
+    meta_non_parallel: dict[str, Any] = Field(
+        sa_column=Column(JSON, server_default="{}", default={}, nullable=False)
+    )
+    meta_parallel: dict[str, Any] = Field(
+        sa_column=Column(JSON, server_default="{}", default={}, nullable=False)
+    )
+
+    owner: Optional[str] = None
+    version: Optional[str] = None
+    args_schema_non_parallel: Optional[dict[str, Any]] = Field(
+        sa_column=Column(JSON), default=None
+    )
+    args_schema_parallel: Optional[dict[str, Any]] = Field(
+        sa_column=Column(JSON), default=None
+    )
+    args_schema_version: Optional[str]
+    docs_info: Optional[str] = None
+    docs_link: Optional[HttpUrl] = None
+
+    input_types: dict[str, bool] = Field(sa_column=Column(JSON), default={})
+    output_types: dict[str, bool] = Field(sa_column=Column(JSON), default={})

{fractal_server-2.3.4 → fractal_server-2.3.6}/fractal_server/app/routes/api/v2/_aux_functions.py

@@ -422,6 +422,8 @@ async def _workflow_insert_task(
 
     # Get task from db, and extract default arguments via a Task property
     # method
+    # NOTE: this logic remains there for V1 tasks only. When we deprecate V1
+    # tasks, we can simplify this block
     if is_legacy_task is True:
         db_task = await db.get(Task, task_id)
         if db_task is None:
@@ -439,12 +441,8 @@ async def _workflow_insert_task(
             raise ValueError(f"TaskV2 {task_id} not found.")
         task_type = db_task.type
 
-        final_args_non_parallel = (
-            db_task.default_args_non_parallel_from_args_schema.copy()
-        )
-        final_args_parallel = (
-            db_task.default_args_parallel_from_args_schema.copy()
-        )
+        final_args_non_parallel = {}
+        final_args_parallel = {}
         final_meta_parallel = (db_task.meta_parallel or {}).copy()
         final_meta_non_parallel = (db_task.meta_non_parallel or {}).copy()
 

{fractal_server-2.3.4 → fractal_server-2.3.6}/fractal_server/app/routes/api/v2/workflowtask.py

@@ -186,34 +186,17 @@ async def update_workflowtask(
                 default_args = (
                     db_wf_task.task_legacy.default_args_from_args_schema
                 )
+                actual_args = deepcopy(default_args)
+                if value is not None:
+                    for k, v in value.items():
+                        actual_args[k] = v
             else:
-                default_args = (
-                    db_wf_task.task.default_args_parallel_from_args_schema
-                )
-            # Override default_args with args value items
-            actual_args = deepcopy(default_args)
-            if value is not None:
-                for k, v in value.items():
-                    actual_args[k] = v
+                actual_args = deepcopy(value)
             if not actual_args:
                 actual_args = None
             setattr(db_wf_task, key, actual_args)
         elif key == "args_non_parallel":
-            # Get default arguments via a Task property method
-            if db_wf_task.is_legacy_task:
-                # This is only needed so that we don't have to modify the rest
-                # of this block, but legacy task cannot take any non-parallel
-                # args (see checks above).
-                default_args = {}
-            else:
-                default_args = deepcopy(
-                    db_wf_task.task.default_args_non_parallel_from_args_schema
-                )
-            # Override default_args with args value items
-            actual_args = default_args.copy()
-            if value is not None:
-                for k, v in value.items():
-                    actual_args[k] = v
+            actual_args = deepcopy(value)
             if not actual_args:
                 actual_args = None
             setattr(db_wf_task, key, actual_args)

{fractal_server-2.3.4 → fractal_server-2.3.6}/fractal_server/app/runner/executors/slurm/_slurm_config.py

@@ -62,6 +62,8 @@ class _SlurmConfigSet(BaseModel, extra=Extra.forbid):
     time: Optional[str]
     account: Optional[str]
     extra_lines: Optional[list[str]]
+    pre_submission_commands: Optional[list[str]]
+    gpus: Optional[str]
 
 
 class _BatchingConfigSet(BaseModel, extra=Extra.forbid):
@@ -219,6 +221,7 @@ class SlurmConfig(BaseModel, extra=Extra.forbid):
         constraint: Corresponds to SLURM option.
         gres: Corresponds to SLURM option.
         account: Corresponds to SLURM option.
+        gpus: Corresponds to SLURM option.
         time: Corresponds to SLURM option (WARNING: not fully supported).
         prefix: Prefix of configuration lines in SLURM submission scripts.
         shebang_line: Shebang line for SLURM submission scripts.
@@ -240,6 +243,8 @@ class SlurmConfig(BaseModel, extra=Extra.forbid):
             Key-value pairs to be included as `export`-ed variables in SLURM
             submission script, after prepending values with the user's cache
             directory.
+        pre_submission_commands: List of commands to be prepended to the sbatch
+            command.
     """
 
     # Required SLURM parameters (note that the integer attributes are those
@@ -254,6 +259,7 @@ class SlurmConfig(BaseModel, extra=Extra.forbid):
     job_name: Optional[str] = None
     constraint: Optional[str] = None
     gres: Optional[str] = None
+    gpus: Optional[str] = None
     time: Optional[str] = None
     account: Optional[str] = None
 
@@ -274,6 +280,8 @@ class SlurmConfig(BaseModel, extra=Extra.forbid):
     target_num_jobs: int
     max_num_jobs: int
 
+    pre_submission_commands: list[str] = Field(default_factory=list)
+
     def _sorted_extra_lines(self) -> list[str]:
         """
         Return a copy of `self.extra_lines`, where lines starting with
@@ -340,7 +348,14 @@ class SlurmConfig(BaseModel, extra=Extra.forbid):
             f"{self.prefix} --cpus-per-task={self.cpus_per_task}",
             f"{self.prefix} --mem={mem_per_job_MB}M",
         ]
-        for key in ["job_name", "constraint", "gres", "time", "account"]:
+        for key in [
+            "job_name",
+            "constraint",
+            "gres",
+            "gpus",
+            "time",
+            "account",
+        ]:
             value = getattr(self, key)
             if value is not None:
                 # Handle the `time` parameter

{fractal_server-2.3.4 → fractal_server-2.3.6}/fractal_server/app/runner/executors/slurm/ssh/executor.py

@@ -869,9 +869,22 @@ class FractalSlurmSSHExecutor(SlurmExecutor):
 
         # Submit job to SLURM, and get jobid
         sbatch_command = f"sbatch --parsable {job.slurm_script_remote}"
-        sbatch_stdout = self.fractal_ssh.run_command(
-            cmd=sbatch_command,
-        )
+        pre_submission_cmds = job.slurm_config.pre_submission_commands
+        if len(pre_submission_cmds) == 0:
+            sbatch_stdout = self.fractal_ssh.run_command(cmd=sbatch_command)
+        else:
+            logger.debug(f"Now using {pre_submission_cmds=}")
+            script_lines = pre_submission_cmds + [sbatch_command]
+            script_content = "\n".join(script_lines)
+            script_content = f"{script_content}\n"
+            script_path_remote = (
+                f"{job.slurm_script_remote.as_posix()}_wrapper.sh"
+            )
+            self.fractal_ssh.write_remote_file(
+                path=script_path_remote, content=script_content
+            )
+            cmd = f"bash {script_path_remote}"
+            sbatch_stdout = self.fractal_ssh.run_command(cmd=cmd)
 
         # Extract SLURM job ID from stdout
         try:
@@ -881,7 +894,9 @@ class FractalSlurmSSHExecutor(SlurmExecutor):
             error_msg = (
                 f"Submit command `{sbatch_command}` returned "
                 f"`{stdout=}` which cannot be cast to an integer "
-                f"SLURM-job ID. Original error:\n{str(e)}"
+                f"SLURM-job ID.\n"
+                f"Note that {pre_submission_cmds=}.\n"
+                f"Original error:\n{str(e)}"
             )
             logger.error(error_msg)
             raise JobExecutionError(info=error_msg)

{fractal_server-2.3.4 → fractal_server-2.3.6}/fractal_server/app/runner/executors/slurm/sudo/executor.py

@@ -1121,6 +1121,12 @@ class FractalSlurmExecutor(SlurmExecutor):
             slurm_err_path=str(job.slurm_stderr),
         )
 
+        # Print warning for ignored parameter
+        if len(job.slurm_config.pre_submission_commands) > 0:
+            logger.warning(
+                f"Ignoring {job.slurm_config.pre_submission_commands=}."
+            )
+
         # Submit job via sbatch, and retrieve jobid
 
         # Write script content to a job.slurm_script

{fractal_server-2.3.4 → fractal_server-2.3.6}/fractal_server/app/runner/v2/__init__.py

@@ -36,8 +36,8 @@ from ._local import process_workflow as local_process_workflow
 from ._local_experimental import (
     process_workflow as local_experimental_process_workflow,
 )
-from ._slurm import process_workflow as slurm_sudo_process_workflow
 from ._slurm_ssh import process_workflow as slurm_ssh_process_workflow
+from ._slurm_sudo import process_workflow as slurm_sudo_process_workflow
 from .handle_failed_job import assemble_filters_failed_job
 from .handle_failed_job import assemble_history_failed_job
 from .handle_failed_job import assemble_images_failed_job

{fractal_server-2.3.4/fractal_server/app/runner/v2/_slurm_ssh → fractal_server-2.3.6/fractal_server/app/runner/v2/_slurm_common}/get_slurm_config.py

@@ -18,8 +18,6 @@ from fractal_server.app.runner.executors.slurm._slurm_config import (
 
 def get_slurm_config(
     wftask: WorkflowTaskV2,
-    workflow_dir_local: Path,
-    workflow_dir_remote: Path,
     which_type: Literal["non_parallel", "parallel"],
     config_path: Optional[Path] = None,
 ) -> SlurmConfig:
@@ -43,13 +41,6 @@ def get_slurm_config(
         wftask:
             WorkflowTask for which the SLURM configuration is is to be
             prepared.
-        workflow_dir_local:
-            Server-owned directory to store all task-execution-related relevant
-            files (inputs, outputs, errors, and all meta files related to the
-            job execution). Note: users cannot write directly to this folder.
-        workflow_dir_remote:
-            User-side directory with the same scope as `workflow_dir_local`,
-            and where a user can write.
         config_path:
             Path of a Fractal SLURM configuration file; if `None`, use
             `FRACTAL_SLURM_CONFIG_FILE` variable from settings.
@@ -99,13 +90,13 @@ def get_slurm_config(
     # 1. This block of definitions takes priority over other definitions from
     #    slurm_env which are not under the `needs_gpu` subgroup
     # 2. This block of definitions has lower priority than whatever comes next
-    #    (i.e. from WorkflowTask.meta).
+    #    (i.e. from WorkflowTask.meta_parallel).
     if wftask_meta is not None:
         needs_gpu = wftask_meta.get("needs_gpu", False)
     else:
         needs_gpu = False
     logger.debug(f"[get_slurm_config] {needs_gpu=}")
-    if needs_gpu and slurm_env.gpu_slurm_config is not None:  # FIXME
+    if needs_gpu:
         for key, value in slurm_env.gpu_slurm_config.dict(
             exclude_unset=True, exclude={"mem"}
         ).items():
@@ -143,9 +134,9 @@ def get_slurm_config(
             )
             logger.error(error_msg)
             raise SlurmConfigError(error_msg)
-        for key in ["time", "gres", "constraint"]:
+        for key in ["time", "gres", "gpus", "constraint"]:
             value = wftask_meta.get(key, None)
-            if value:
+            if value is not None:
                 slurm_dict[key] = value
     if wftask_meta is not None:
         extra_lines = wftask_meta.get("extra_lines", [])

{fractal_server-2.3.4 → fractal_server-2.3.6}/fractal_server/app/runner/v2/_slurm_ssh/_submit_setup.py

@@ -17,8 +17,10 @@ from pathlib import Path
 from typing import Literal
 
 from ...task_files import get_task_file_paths
-from .get_slurm_config import get_slurm_config
 from fractal_server.app.models.v2 import WorkflowTaskV2
+from fractal_server.app.runner.v2._slurm_common.get_slurm_config import (
+    get_slurm_config,
+)
 
 
 def _slurm_submit_setup(
@@ -62,8 +64,6 @@ def _slurm_submit_setup(
     # Get SlurmConfig object
     slurm_config = get_slurm_config(
         wftask=wftask,
-        workflow_dir_local=workflow_dir_local,
-        workflow_dir_remote=workflow_dir_remote,
         which_type=which_type,
     )
 

{fractal_server-2.3.4/fractal_server/app/runner/v2/_slurm → fractal_server-2.3.6/fractal_server/app/runner/v2/_slurm_sudo}/_submit_setup.py

@@ -17,8 +17,10 @@ from pathlib import Path
 from typing import Literal
 
 from ...task_files import get_task_file_paths
-from .get_slurm_config import get_slurm_config
 from fractal_server.app.models.v2 import WorkflowTaskV2
+from fractal_server.app.runner.v2._slurm_common.get_slurm_config import (
+    get_slurm_config,
+)
 
 
 def _slurm_submit_setup(
@@ -62,8 +64,6 @@ def _slurm_submit_setup(
     # Get SlurmConfig object
     slurm_config = get_slurm_config(
         wftask=wftask,
-        workflow_dir_local=workflow_dir_local,
-        workflow_dir_remote=workflow_dir_remote,
         which_type=which_type,
     )
 

{fractal_server-2.3.4 → fractal_server-2.3.6}/fractal_server/ssh/_fabric.py

@@ -306,6 +306,28 @@ class FractalSSH(object):
             cmd = f"rm -r {folder}"
             self.run_command(cmd=cmd)
 
+    def write_remote_file(
+        self,
+        *,
+        path: str,
+        content: str,
+        lock_timeout: Optional[float] = None,
+    ) -> None:
+        """
+        Open a remote file via SFTP and write it.
+
+        Args:
+            path: Absolute path
+            contents: File contents
+            lock_timeout:
+        """
+        actual_lock_timeout = self.default_lock_timeout
+        if lock_timeout is not None:
+            actual_lock_timeout = lock_timeout
+        with self.acquire_timeout(timeout=actual_lock_timeout):
+            with self.sftp().open(filename=path, mode="w") as f:
+                f.write(content)
+
 
 def get_ssh_connection(
     *,

{fractal_server-2.3.4 → fractal_server-2.3.6}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "fractal-server"
-version = "2.3.4"
+version = "2.3.6"
 description = "Server component of the Fractal analytics platform"
 authors = [
     "Tommaso Comparin <tommaso.comparin@exact-lab.it>",
@@ -27,7 +27,7 @@ exclude = [
 python = "^3.9"
 python-dotenv = "^1.0.0"
 fastapi = "^0.110.0"
-sqlmodel = "^0.0.19"
+sqlmodel = "^0.0.21"
 sqlalchemy = {extras = ["asyncio"], version = ">=2.0.23,<2.1"}
 aiosqlite = "^0.19.0"
 fastapi-users = {extras = ["oauth"], version = "^12.1.0"}
@@ -91,7 +91,7 @@ filterwarnings = [
 ]
 
 [tool.bumpver]
-current_version = "2.3.4"
+current_version = "2.3.6"
 version_pattern = "MAJOR.MINOR.PATCH[PYTAGNUM]"
 commit_message = "bump version {old_version} -> {new_version}"
 commit = true

fractal_server-2.3.4/fractal_server/__init__.py

@@ -1 +0,0 @@
-__VERSION__ = "2.3.4"

fractal_server-2.3.4/fractal_server/app/models/v2/task.py

@@ -1,93 +0,0 @@
-import json
-import logging
-from typing import Any
-from typing import Optional
-
-from pydantic import HttpUrl
-from sqlalchemy import Column
-from sqlalchemy.types import JSON
-from sqlmodel import Field
-from sqlmodel import SQLModel
-
-
-class TaskV2(SQLModel, table=True):
-
-    id: Optional[int] = Field(default=None, primary_key=True)
-    name: str
-
-    type: str
-    command_non_parallel: Optional[str] = None
-    command_parallel: Optional[str] = None
-    source: str = Field(unique=True)
-
-    meta_non_parallel: dict[str, Any] = Field(
-        sa_column=Column(JSON, server_default="{}", default={}, nullable=False)
-    )
-    meta_parallel: dict[str, Any] = Field(
-        sa_column=Column(JSON, server_default="{}", default={}, nullable=False)
-    )
-
-    owner: Optional[str] = None
-    version: Optional[str] = None
-    args_schema_non_parallel: Optional[dict[str, Any]] = Field(
-        sa_column=Column(JSON), default=None
-    )
-    args_schema_parallel: Optional[dict[str, Any]] = Field(
-        sa_column=Column(JSON), default=None
-    )
-    args_schema_version: Optional[str]
-    docs_info: Optional[str] = None
-    docs_link: Optional[HttpUrl] = None
-
-    input_types: dict[str, bool] = Field(sa_column=Column(JSON), default={})
-    output_types: dict[str, bool] = Field(sa_column=Column(JSON), default={})
-
-    @property
-    def default_args_non_parallel_from_args_schema(self) -> dict[str, Any]:
-        """
-        Extract default arguments from args_schema
-        """
-        # Return {} if there is no args_schema
-        if self.args_schema_non_parallel is None:
-            return {}
-        # Try to construct default_args
-        try:
-            default_args = {}
-            properties = self.args_schema_non_parallel["properties"]
-            for prop_name, prop_schema in properties.items():
-                default_value = prop_schema.get("default", None)
-                if default_value is not None:
-                    default_args[prop_name] = default_value
-            return default_args
-        except KeyError as e:
-            logging.warning(
-                "Cannot set default_args from args_schema_non_parallel="
-                f"{json.dumps(self.args_schema_non_parallel)}\n"
-                f"Original KeyError: {str(e)}"
-            )
-            return {}
-
-    @property
-    def default_args_parallel_from_args_schema(self) -> dict[str, Any]:
-        """
-        Extract default arguments from args_schema
-        """
-        # Return {} if there is no args_schema
-        if self.args_schema_parallel is None:
-            return {}
-        # Try to construct default_args
-        try:
-            default_args = {}
-            properties = self.args_schema_parallel["properties"]
-            for prop_name, prop_schema in properties.items():
-                default_value = prop_schema.get("default", None)
-                if default_value is not None:
-                    default_args[prop_name] = default_value
-            return default_args
-        except KeyError as e:
-            logging.warning(
-                "Cannot set default_args from args_schema_parallel="
-                f"{json.dumps(self.args_schema_parallel)}\n"
-                f"Original KeyError: {str(e)}"
-            )
-            return {}