fractal-server 2.6.0a1__tar.gz → 2.6.2__tar.gz

{fractal_server-2.6.0a1 → fractal_server-2.6.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fractal-server
-Version: 2.6.0a1
+Version: 2.6.2
 Summary: Server component of the Fractal analytics platform
 Home-page: https://github.com/fractal-analytics-platform/fractal-server
 License: BSD-3-Clause

fractal_server-2.6.2/fractal_server/__init__.py

@@ -0,0 +1 @@
+__VERSION__ = "2.6.2"

{fractal_server-2.6.0a1 → fractal_server-2.6.2}/fractal_server/app/models/security.py

@@ -15,7 +15,6 @@ from typing import Optional
 from pydantic import EmailStr
 from sqlalchemy import Column
 from sqlalchemy.types import DateTime
-from sqlalchemy.types import JSON
 from sqlmodel import Field
 from sqlmodel import Relationship
 from sqlmodel import SQLModel
@@ -93,11 +92,6 @@ class UserOAuth(SQLModel, table=True):
     is_superuser: bool = Field(False, nullable=False)
     is_verified: bool = Field(False, nullable=False)
 
-    slurm_user: Optional[str]
-    slurm_accounts: list[str] = Field(
-        sa_column=Column(JSON, server_default="[]", nullable=False)
-    )
-    cache_dir: Optional[str]
     username: Optional[str]
 
     oauth_accounts: list["OAuthAccount"] = Relationship(

{fractal_server-2.6.0a1 → fractal_server-2.6.2}/fractal_server/app/schemas/_validators.py

@@ -69,14 +69,19 @@ def valint(attribute: str, min_val: int = 1):
     return val
 
 
-def val_absolute_path(attribute: str):
+def val_absolute_path(attribute: str, accept_none: bool = False):
     """
     Check that a string attribute is an absolute path
     """
 
     def val(string: Optional[str]) -> str:
         if string is None:
-            raise ValueError(f"String attribute '{attribute}' cannot be None")
+            if accept_none:
+                return string
+            else:
+                raise ValueError(
+                    f"String attribute '{attribute}' cannot be None"
+                )
         s = string.strip()
         if not s:
             raise ValueError(f"String attribute '{attribute}' cannot be empty")

{fractal_server-2.6.0a1 → fractal_server-2.6.2}/fractal_server/app/schemas/user_settings.py

@@ -47,23 +47,25 @@ class UserSettingsUpdate(BaseModel, extra=Extra.forbid):
     slurm_accounts: Optional[list[StrictStr]] = None
     cache_dir: Optional[str] = None
 
-    _ssh_host = validator("ssh_host", allow_reuse=True)(valstr("ssh_host"))
+    _ssh_host = validator("ssh_host", allow_reuse=True)(
+        valstr("ssh_host", accept_none=True)
+    )
     _ssh_username = validator("ssh_username", allow_reuse=True)(
-        valstr("ssh_username")
+        valstr("ssh_username", accept_none=True)
     )
     _ssh_private_key_path = validator(
         "ssh_private_key_path", allow_reuse=True
-    )(val_absolute_path("ssh_private_key_path"))
+    )(val_absolute_path("ssh_private_key_path", accept_none=True))
 
     _ssh_tasks_dir = validator("ssh_tasks_dir", allow_reuse=True)(
-        val_absolute_path("ssh_tasks_dir")
+        val_absolute_path("ssh_tasks_dir", accept_none=True)
     )
     _ssh_jobs_dir = validator("ssh_jobs_dir", allow_reuse=True)(
-        val_absolute_path("ssh_jobs_dir")
+        val_absolute_path("ssh_jobs_dir", accept_none=True)
     )
 
     _slurm_user = validator("slurm_user", allow_reuse=True)(
-        valstr("slurm_user")
+        valstr("slurm_user", accept_none=True)
     )
 
     @validator("slurm_accounts")
@@ -76,6 +78,8 @@ class UserSettingsUpdate(BaseModel, extra=Extra.forbid):
 
     @validator("cache_dir")
     def cache_dir_validator(cls, value):
+        if value is None:
+            return None
         validate_cmd(value)
         return val_absolute_path("cache_dir")(value)
 
@@ -90,5 +94,7 @@ class UserSettingsUpdateStrict(BaseModel, extra=Extra.forbid):
 
     @validator("cache_dir")
     def cache_dir_validator(cls, value):
+        if value is None:
+            return value
         validate_cmd(value)
         return val_absolute_path("cache_dir")(value)

{fractal_server-2.6.0a1 → fractal_server-2.6.2}/fractal_server/app/schemas/v2/task_collection.py

@@ -13,6 +13,7 @@ from .._validators import valdictkeys
 from .._validators import valstr
 from fractal_server.app.schemas._validators import valutc
 from fractal_server.app.schemas.v2 import ManifestV2
+from fractal_server.string_tools import validate_cmd
 
 
 class CollectionStatusV2(str, Enum):
@@ -144,13 +145,13 @@ class TaskCollectCustomV2(BaseModel):
         return values
 
     @validator("package_name")
-    def package_name_prevent_injection(cls, value: str):
+    def package_name_validator(cls, value: str):
         """
-        Remove all whitespace characters, and reject values containing `;`.
+        Remove all whitespace characters, then check for invalid code.
         """
         if value is not None:
-            if ";" in value:
-                raise ValueError(f"Invalid package_name: {value}")
+            validate_cmd(value)
+            value = valstr("package_name")(value)
             value = value.replace(" ", "")
         return value
 

{fractal_server-2.6.0a1 → fractal_server-2.6.2}/fractal_server/config.py

@@ -512,25 +512,6 @@ class Settings(BaseSettings):
     `JobExecutionError`.
     """
 
-    FRACTAL_SLURM_SSH_HOST: Optional[str] = None
-    """
-    SSH-reachable host where a SLURM client is available.
-    """
-    FRACTAL_SLURM_SSH_USER: Optional[str] = None
-    """
-    User on `FRACTAL_SLURM_SSH_HOST`.
-    """
-    FRACTAL_SLURM_SSH_PRIVATE_KEY_PATH: Optional[str] = None
-    """
-    Private key for connecting to `FRACTAL_SLURM_SSH_HOST` as
-    `FRACTAL_SLURM_SSH_USER`.
-    """
-    # FIXME SSH: Split this into two folders (for tasks and for jobs)
-    FRACTAL_SLURM_SSH_WORKING_BASE_DIR: Optional[str] = None
-    """
-    Remote folder on `FRACTAL_SLURM_SSH_HOST`.
-    """
-
     FRACTAL_API_SUBMIT_RATE_LIMIT: int = 2
     """
     Interval to wait (in seconds) to be allowed to call again

fractal_server-2.6.2/fractal_server/migrations/versions/94a47ea2d3ff_remove_cache_dir_slurm_user_and_slurm_.py

@@ -0,0 +1,52 @@
+"""remove cache_dir slurm_user and slurm_accounts from user
+
+Revision ID: 94a47ea2d3ff
+Revises: 9c5ae74c9b98
+Create Date: 2024-09-25 09:33:18.014831
+
+"""
+import sqlalchemy as sa
+from alembic import op
+from sqlalchemy.dialects import postgresql
+
+# revision identifiers, used by Alembic.
+revision = "94a47ea2d3ff"
+down_revision = "9c5ae74c9b98"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("user_oauth", schema=None) as batch_op:
+        batch_op.drop_column("slurm_user")
+        batch_op.drop_column("slurm_accounts")
+        batch_op.drop_column("cache_dir")
+
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("user_oauth", schema=None) as batch_op:
+        batch_op.add_column(
+            sa.Column(
+                "cache_dir", sa.VARCHAR(), autoincrement=False, nullable=True
+            )
+        )
+        batch_op.add_column(
+            sa.Column(
+                "slurm_accounts",
+                postgresql.JSON(astext_type=sa.Text()),
+                server_default=sa.text("'[]'::json"),
+                autoincrement=False,
+                nullable=False,
+            )
+        )
+        batch_op.add_column(
+            sa.Column(
+                "slurm_user", sa.VARCHAR(), autoincrement=False, nullable=True
+            )
+        )
+
+    # ### end Alembic commands ###

{fractal_server-2.6.0a1 → fractal_server-2.6.2}/fractal_server/ssh/_fabric.py

@@ -305,21 +305,21 @@ class FractalSSH(object):
             safe_root: If `folder` is not a subfolder of the absolute
                 `safe_root` path, raise an error.
         """
-        invalid_characters = {" ", "\n", ";", "$", "`"}
-
-        if (
-            not isinstance(folder, str)
-            or not isinstance(safe_root, str)
-            or len(invalid_characters.intersection(folder)) > 0
-            or len(invalid_characters.intersection(safe_root)) > 0
-            or not Path(folder).is_absolute()
-            or not Path(safe_root).is_absolute()
-            or not Path(folder).resolve().is_relative_to(safe_root)
+        validate_cmd(folder)
+        validate_cmd(safe_root)
+
+        if " " in folder:
+            raise ValueError(f"folder='{folder}' includes whitespace.")
+        elif " " in safe_root:
+            raise ValueError(f"safe_root='{safe_root}' includes whitespace.")
+        elif not Path(folder).is_absolute():
+            raise ValueError(f"{folder=} is not an absolute path.")
+        elif not Path(safe_root).is_absolute():
+            raise ValueError(f"{safe_root=} is not an absolute path.")
+        elif not (
+            Path(folder).resolve().is_relative_to(Path(safe_root).resolve())
         ):
-            raise ValueError(
-                f"{folder=} argument is invalid or it is not "
-                f"relative to {safe_root=}."
-            )
+            raise ValueError(f"{folder=} is not a subfolder of {safe_root=}.")
         else:
             cmd = f"rm -r {folder}"
             self.run_command(cmd=cmd)

{fractal_server-2.6.0a1 → fractal_server-2.6.2}/fractal_server/string_tools.py

@@ -60,6 +60,8 @@ def validate_cmd(command: str, allow_char: Optional[str] = None):
         command: command to validate.
         allow_char: chars to accept among the forbidden ones
     """
+    if not isinstance(command, str):
+        raise ValueError(f"{command=} is not a string.")
     forbidden = set(__NOT_ALLOWED_FOR_COMMANDS__)
     if allow_char is not None:
         forbidden = forbidden - set(allow_char)

{fractal_server-2.6.0a1 → fractal_server-2.6.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "fractal-server"
-version = "2.6.0a1"
+version = "2.6.2"
 description = "Server component of the Fractal analytics platform"
 authors = [
     "Tommaso Comparin <tommaso.comparin@exact-lab.it>",
@@ -92,7 +92,7 @@ filterwarnings = [
 ]
 
 [tool.bumpver]
-current_version = "2.6.0a1"
+current_version = "2.6.2"
 version_pattern = "MAJOR.MINOR.PATCH[PYTAGNUM]"
 commit_message = "bump version {old_version} -> {new_version}"
 commit = true

fractal_server-2.6.0a1/fractal_server/__init__.py

@@ -1 +0,0 @@
-__VERSION__ = "2.6.0a1"

fractal_server-2.6.0a1/fractal_server/data_migrations/2_6_0.py

@@ -1,49 +0,0 @@
-import logging
-
-from sqlalchemy import select
-
-from fractal_server.app.db import get_sync_db
-from fractal_server.app.models import UserOAuth
-from fractal_server.app.models import UserSettings
-from fractal_server.config import get_settings
-from fractal_server.data_migrations.tools import _check_current_version
-from fractal_server.syringe import Inject
-
-
-def fix_db():
-    logger = logging.getLogger("fix_db")
-    logger.warning("START execution of fix_db function")
-    _check_current_version("2.6.0")
-
-    global_settings = Inject(get_settings)
-
-    with next(get_sync_db()) as db:
-        users = db.execute(select(UserOAuth)).scalars().unique().all()
-        for user in sorted(users, key=lambda x: x.id):
-            logger.warning(f"START handling user {user.id}: '{user.email}'")
-            user_settings = UserSettings(
-                # SSH
-                ssh_host=global_settings.FRACTAL_SLURM_SSH_HOST,
-                ssh_username=global_settings.FRACTAL_SLURM_SSH_USER,
-                ssh_private_key_path=(
-                    global_settings.FRACTAL_SLURM_SSH_PRIVATE_KEY_PATH
-                ),
-                ssh_tasks_dir=(
-                    global_settings.FRACTAL_SLURM_SSH_WORKING_BASE_DIR
-                ),
-                ssh_jobs_dir=(
-                    global_settings.FRACTAL_SLURM_SSH_WORKING_BASE_DIR
-                ),
-                # SUDO
-                slurm_user=user.slurm_user,
-                slurm_accounts=user.slurm_accounts,
-                cache_dir=user.cache_dir,
-            )
-            user.settings = user_settings
-            db.add(user)
-            db.commit()
-            db.refresh(user)
-            logger.warning(f"New user {user.id} settings:\n{user.settings}")
-            logger.warning(f"END handling user {user.id}: '{user.email}'")
-
-    logger.warning("END of execution of fix_db function")