fractal-server 1.4.2a5__py3-none-any.whl → 1.4.3a1__py3-none-any.whl

fractal_server/app/schemas/task_collection.py

@@ -15,15 +15,7 @@ __all__ = (
 )
 
 
-class _TaskCollectBase(BaseModel):
-    """
-    Base class for `TaskCollectPip`.
-    """
-
-    pass
-
-
-class TaskCollectPip(_TaskCollectBase):
+class TaskCollectPip(BaseModel):
     """
     TaskCollectPip class
 
@@ -89,7 +81,7 @@ class TaskCollectPip(_TaskCollectBase):
         return v
 
 
-class TaskCollectStatus(_TaskCollectBase):
+class TaskCollectStatus(BaseModel):
     """
     TaskCollectStatus class
 

fractal_server/app/schemas/user.py

@@ -118,9 +118,13 @@ class UserCreate(schemas.BaseUserCreate):
 
     # Validators
 
-    _slurm_accounts = validator("slurm_accounts", allow_reuse=True)(
-        val_unique_list("slurm_accounts")
-    )
+    @validator("slurm_accounts")
+    def slurm_accounts_validator(cls, value):
+        for i, element in enumerate(value):
+            value[i] = valstr(attribute=f"slurm_accounts[{i}]")(element)
+        val_unique_list("slurm_accounts")(value)
+        return value
+
     _slurm_user = validator("slurm_user", allow_reuse=True)(
         valstr("slurm_user")
     )

fractal_server/app/schemas/workflow.py

@@ -1,3 +1,4 @@
+from datetime import datetime
 from enum import Enum
 from typing import Any
 from typing import Optional
@@ -131,6 +132,7 @@ class WorkflowRead(_WorkflowBase):
     project_id: int
     task_list: list[WorkflowTaskRead]
     project: ProjectRead
+    timestamp_created: datetime
 
 
 class WorkflowCreate(_WorkflowBase):

fractal_server/app/security/__init__.py

@@ -56,7 +56,7 @@ from sqlmodel import select
 
 from ...config import get_settings
 from ...syringe import Inject
-from ..db import get_db
+from ..db import get_async_db
 from ..models.security import OAuthAccount
 from ..models.security import UserOAuth as User
 from fractal_server.app.models.security import UserOAuth
@@ -175,7 +175,7 @@ class SQLModelUserDatabaseAsync(Generic[UP, ID], BaseUserDatabase[UP, ID]):
 
 
 async def get_user_db(
-    session: AsyncSession = Depends(get_db),
+    session: AsyncSession = Depends(get_async_db),
 ) -> AsyncGenerator[SQLModelUserDatabaseAsync, None]:
     yield SQLModelUserDatabaseAsync(session, User, OAuthAccount)
 
@@ -247,7 +247,7 @@ current_active_superuser = fastapi_users.current_user(
     active=True, superuser=True
 )
 
-get_async_session_context = contextlib.asynccontextmanager(get_db)
+get_async_session_context = contextlib.asynccontextmanager(get_async_db)
 get_user_db_context = contextlib.asynccontextmanager(get_user_db)
 get_user_manager_context = contextlib.asynccontextmanager(get_user_manager)
 

fractal_server/config.py

@@ -360,6 +360,14 @@ class Settings(BaseSettings):
                 raise FractalConfigurationError(
                     "POSTGRES_DB cannot be None when DB_ENGINE=postgres."
                 )
+            try:
+                import psycopg2  # noqa: F401
+                import asyncpg  # noqa: F401
+            except ModuleNotFoundError:
+                raise FractalConfigurationError(
+                    "DB engine is `postgres` but `psycopg2` or `asyncpg` "
+                    "are not available"
+                )
         else:
             if not self.SQLITE_PATH:
                 raise FractalConfigurationError(
@@ -375,6 +383,12 @@ class Settings(BaseSettings):
 
         info = f"FRACTAL_RUNNER_BACKEND={self.FRACTAL_RUNNER_BACKEND}"
         if self.FRACTAL_RUNNER_BACKEND == "slurm":
+            try:
+                import cfut  # noqa: F401
+            except ModuleNotFoundError:
+                raise FractalConfigurationError(
+                    f"{info} but `clusterfutures` is not available"
+                )
             if not self.FRACTAL_SLURM_CONFIG_FILE:
                 raise FractalConfigurationError(
                     f"Must set FRACTAL_SLURM_CONFIG_FILE when {info}"

fractal_server/migrations/versions/4cedeb448a53_workflowtask_foreign_keys_not_nullables.py

@@ -0,0 +1,42 @@
+"""WorkflowTask foreign keys not nullables
+
+Revision ID: 4cedeb448a53
+Revises: efa89c30e0a4
+Create Date: 2024-01-16 13:57:47.891931
+
+"""
+import sqlalchemy as sa
+from alembic import op
+
+
+# revision identifiers, used by Alembic.
+revision = "4cedeb448a53"
+down_revision = "efa89c30e0a4"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("workflowtask", schema=None) as batch_op:
+        batch_op.alter_column(
+            "workflow_id", existing_type=sa.INTEGER(), nullable=False
+        )
+        batch_op.alter_column(
+            "task_id", existing_type=sa.INTEGER(), nullable=False
+        )
+
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("workflowtask", schema=None) as batch_op:
+        batch_op.alter_column(
+            "task_id", existing_type=sa.INTEGER(), nullable=True
+        )
+        batch_op.alter_column(
+            "workflow_id", existing_type=sa.INTEGER(), nullable=True
+        )
+
+    # ### end Alembic commands ###

fractal_server/migrations/versions/9fd26a2b0de4_add_workflow_timestamp_created.py

@@ -0,0 +1,60 @@
+"""add Workflow.timestamp_created and Dataset.timestamp_created
+
+Revision ID: 9fd26a2b0de4
+Revises: efa89c30e0a4
+Create Date: 2024-01-11 09:31:20.950090
+
+"""
+from datetime import datetime
+from datetime import timezone
+
+import sqlalchemy as sa
+from alembic import op
+
+
+# revision identifiers, used by Alembic.
+revision = "9fd26a2b0de4"
+down_revision = "4cedeb448a53"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("workflow", schema=None) as batch_op:
+        batch_op.add_column(
+            sa.Column(
+                "timestamp_created",
+                sa.DateTime(timezone=True),
+                nullable=False,
+                server_default=str(datetime(2000, 1, 1, tzinfo=timezone.utc)),
+            )
+        )
+
+    with op.batch_alter_table("workflow", schema=None) as batch_op:
+        batch_op.alter_column("timestamp_created", server_default=None)
+
+    with op.batch_alter_table("dataset", schema=None) as batch_op:
+        batch_op.add_column(
+            sa.Column(
+                "timestamp_created",
+                sa.DateTime(timezone=True),
+                nullable=False,
+                server_default=str(datetime(2000, 1, 1, tzinfo=timezone.utc)),
+            )
+        )
+
+    with op.batch_alter_table("dataset", schema=None) as batch_op:
+        batch_op.alter_column("timestamp_created", server_default=None)
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("dataset", schema=None) as batch_op:
+        batch_op.drop_column("timestamp_created")
+
+    with op.batch_alter_table("workflow", schema=None) as batch_op:
+        batch_op.drop_column("timestamp_created")
+
+    # ### end Alembic commands ###

fractal_server/tasks/_TaskCollectPip.py

@@ -0,0 +1,103 @@
+from pathlib import Path
+from typing import Optional
+
+from pydantic import root_validator
+
+from fractal_server.app.schemas import ManifestV1
+from fractal_server.app.schemas import TaskCollectPip
+
+
+class _TaskCollectPip(TaskCollectPip):
+    """
+    Internal TaskCollectPip schema
+
+    Differences with its parent class (`TaskCollectPip`):
+
+        1. We check if the package corresponds to a path in the filesystem, and
+           whether it exists (via new validator `check_local_package`, new
+           method `is_local_package` and new attribute `package_path`).
+        2. We include an additional `package_manifest` attribute.
+        3. We expose an additional attribute `package_name`, which is filled
+           during task collection.
+    """
+
+    package_name: Optional[str] = None
+    package_path: Optional[Path] = None
+    package_manifest: Optional[ManifestV1] = None
+
+    @property
+    def is_local_package(self) -> bool:
+        return bool(self.package_path)
+
+    @root_validator(pre=True)
+    def check_local_package(cls, values):
+        """
+        Checks if package corresponds to an existing path on the filesystem
+
+        In this case, the user is providing directly a package file, rather
+        than a remote one from PyPI. We set the `package_path` attribute and
+        get the actual package name and version from the package file name.
+        """
+        if "/" in values["package"]:
+            package_path = Path(values["package"])
+            if not package_path.is_absolute():
+                raise ValueError("Package path must be absolute")
+            if package_path.exists():
+                values["package_path"] = package_path
+                (
+                    values["package"],
+                    values["version"],
+                    *_,
+                ) = package_path.name.split("-")
+            else:
+                raise ValueError(f"Package {package_path} does not exist.")
+        return values
+
+    @property
+    def package_source(self) -> str:
+        """
+        NOTE: As of PR #1188 in `fractal-server`, the attribute
+        `self.package_name` is normalized; this means e.g. that `_` is
+        replaced by `-`. To guarantee backwards compatibility with
+        `Task.source` attributes created before this change, we still replace
+        `-` with `_` upon generation of the `source` attribute, in this
+        method.
+        """
+        if not self.package_name or not self.package_version:
+            raise ValueError(
+                "Cannot construct `package_source` property with "
+                f"{self.package_name=} and {self.package_version=}."
+            )
+        if self.is_local_package:
+            collection_type = "pip_local"
+        else:
+            collection_type = "pip_remote"
+
+        package_extras = self.package_extras or ""
+        if self.python_version:
+            python_version = f"py{self.python_version}"
+        else:
+            python_version = ""  # FIXME: can we allow this?
+
+        source = ":".join(
+            (
+                collection_type,
+                self.package_name.replace("-", "_"),  # see method docstring
+                self.package_version,
+                package_extras,
+                python_version,
+            )
+        )
+        return source
+
+    def check(self):
+        """
+        Verify that the package has all attributes that are needed to continue
+        with task collection
+        """
+        if not self.package_name:
+            raise ValueError("`package_name` attribute is not set")
+        if not self.package_version:
+            raise ValueError("`package_version` attribute is not set")
+        if not self.package_manifest:
+            raise ValueError("`package_manifest` attribute is not set")

fractal_server/tasks/__init__.py

@@ -2,5 +2,7 @@
 `tasks` module
 
 Submodules:
-    * [task collection](collection)
+    * [Endpoint functions](background_operations)
+    * [Background-task functions](endpoint_operations)
+    * [Auxiliary functions](utils)
 """