fractal-server 2.3.5__tar.gz → 2.3.7__tar.gz

{fractal_server-2.3.5 → fractal_server-2.3.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fractal-server
-Version: 2.3.5
+Version: 2.3.7
 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-2.3.7/fractal_server/__init__.py

@@ -0,0 +1 @@
+__VERSION__ = "2.3.7"

fractal_server-2.3.7/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-2.3.5 → fractal_server-2.3.7}/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-2.3.5 → fractal_server-2.3.7}/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-2.3.5 → fractal_server-2.3.7}/fractal_server/app/runner/executors/slurm/ssh/_executor_wait_thread.py

@@ -7,6 +7,7 @@ from typing import Callable
 from cfut import FileWaitThread
 
 from ......logger import set_logger
+from fractal_server.app.runner.exceptions import JobExecutionError
 
 logger = set_logger(__name__)
 
@@ -48,6 +49,10 @@ class FractalSlurmWaitThread(FileWaitThread):
 
         This method is executed on the main thread.
         """
+        if self.shutdown:
+            error_msg = "Cannot call `wait` method after executor shutdown."
+            logger.warning(error_msg)
+            raise JobExecutionError(info=error_msg)
         with self.lock:
             self.active_job_ids.append(job_id)
 

{fractal_server-2.3.5 → fractal_server-2.3.7}/fractal_server/app/runner/executors/slurm/ssh/executor.py

@@ -353,6 +353,12 @@ class FractalSlurmSSHExecutor(SlurmExecutor):
             Future representing the execution of the current SLURM job.
         """
 
+        # Do not continue if auxiliary thread was shut down
+        if self.wait_thread.shutdown:
+            error_msg = "Cannot call `submit` method after executor shutdown"
+            logger.warning(error_msg)
+            raise JobExecutionError(info=error_msg)
+
         # Set defaults, if needed
         if slurm_config is None:
             slurm_config = get_default_slurm_config()
@@ -436,6 +442,12 @@ class FractalSlurmSSHExecutor(SlurmExecutor):
 
         """
 
+        # Do not continue if auxiliary thread was shut down
+        if self.wait_thread.shutdown:
+            error_msg = "Cannot call `map` method after executor shutdown"
+            logger.warning(error_msg)
+            raise JobExecutionError(info=error_msg)
+
         def _result_or_cancel(fut):
             """
             This function is based on the Python Standard Library 3.11.
@@ -867,6 +879,14 @@ class FractalSlurmSSHExecutor(SlurmExecutor):
             job: The `SlurmJob` object to submit.
         """
 
+        # Prevent calling sbatch if auxiliary thread was shut down
+        if self.wait_thread.shutdown:
+            error_msg = (
+                "Cannot call `_submit_job` method after executor shutdown"
+            )
+            logger.warning(error_msg)
+            raise JobExecutionError(info=error_msg)
+
         # Submit job to SLURM, and get jobid
         sbatch_command = f"sbatch --parsable {job.slurm_script_remote}"
         pre_submission_cmds = job.slurm_config.pre_submission_commands
@@ -1336,6 +1356,9 @@ class FractalSlurmSSHExecutor(SlurmExecutor):
         the self.wait_thread thread, see _completion.
         """
 
+        # Redudantly set thread shutdown attribute to True
+        self.wait_thread.shutdown = True
+
         logger.debug("Executor shutdown: start")
 
         # Handle all job futures

{fractal_server-2.3.5 → fractal_server-2.3.7}/fractal_server/config.py

@@ -553,6 +553,11 @@ class Settings(BaseSettings):
     Whether to include the v1 API.
     """
 
+    FRACTAL_MAX_PIP_VERSION: str = "24.0"
+    """
+    Maximum value at which to update `pip` before performing task collection.
+    """
+
     ###########################################################################
     # BUSINESS LOGIC
     ###########################################################################

{fractal_server-2.3.5 → fractal_server-2.3.7}/fractal_server/tasks/v2/_venv_pip.py

@@ -2,7 +2,9 @@ from pathlib import Path
 from typing import Optional
 
 from ..utils import COLLECTION_FREEZE_FILENAME
+from fractal_server.config import get_settings
 from fractal_server.logger import get_logger
+from fractal_server.syringe import Inject
 from fractal_server.tasks.v2._TaskCollectPip import _TaskCollectPip
 from fractal_server.tasks.v2.utils import get_python_interpreter_v2
 from fractal_server.utils import execute_command
@@ -24,6 +26,7 @@ async def _pip_install(
     Returns:
         The location of the package.
     """
+    settings = Inject(get_settings)
 
     logger = get_logger(logger_name)
 
@@ -41,7 +44,10 @@ async def _pip_install(
 
     await execute_command(
         cwd=venv_path,
-        command=f"{pip} install --upgrade pip",
+        command=(
+            f"{pip} install --upgrade "
+            f"'pip<={settings.FRACTAL_MAX_PIP_VERSION}'"
+        ),
         logger_name=logger_name,
     )
     await execute_command(

{fractal_server-2.3.5 → fractal_server-2.3.7}/fractal_server/tasks/v2/background_operations_ssh.py

@@ -174,6 +174,10 @@ def background_collect_pip_ssh(
                     ("__PACKAGE__", task_pkg.package),
                     ("__PYTHON__", python_bin),
                     ("__INSTALL_STRING__", install_string),
+                    (
+                        "__FRACTAL_MAX_PIP_VERSION__",
+                        settings.FRACTAL_MAX_PIP_VERSION,
+                    ),
                 ]
 
                 common_args = dict(

{fractal_server-2.3.5 → fractal_server-2.3.7}/fractal_server/tasks/v2/templates/_2_upgrade_pip.sh

@@ -14,7 +14,7 @@ VENVPYTHON=${PACKAGE_ENV_DIR}/bin/python
 
 # Upgrade pip
 write_log "START upgrade pip"
-"$VENVPYTHON" -m pip install pip --upgrade
+"$VENVPYTHON" -m pip install "pip<=__FRACTAL_MAX_PIP_VERSION__" --upgrade
 write_log "END   upgrade pip"
 echo
 

{fractal_server-2.3.5 → fractal_server-2.3.7}/fractal_server/tasks/v2/templates/_4_pip_freeze.sh

@@ -12,4 +12,4 @@ PACKAGE_ENV_DIR=__PACKAGE_ENV_DIR__
 
 VENVPYTHON=${PACKAGE_ENV_DIR}/bin/python
 
-"$VENVPYTHON" -m pip freeze
+"$VENVPYTHON" -m pip freeze --all

{fractal_server-2.3.5 → fractal_server-2.3.7}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "fractal-server"
-version = "2.3.5"
+version = "2.3.7"
 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 = "2.3.5"
+current_version = "2.3.7"
 version_pattern = "MAJOR.MINOR.PATCH[PYTAGNUM]"
 commit_message = "bump version {old_version} -> {new_version}"
 commit = true

fractal_server-2.3.5/fractal_server/__init__.py

@@ -1 +0,0 @@
-__VERSION__ = "2.3.5"

fractal_server-2.3.5/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 {}