fractal-server 2.17.0a4__py3-none-any.whl → 2.17.0a6__py3-none-any.whl

fractal_server/config/_email.py

@@ -1,6 +1,6 @@
 from typing import Literal
+from typing import Self
 
-from cryptography.fernet import Fernet
 from pydantic import BaseModel
 from pydantic import EmailStr
 from pydantic import Field
@@ -31,8 +31,7 @@ class PublicEmailSettings(BaseModel):
     recipients: list[EmailStr] = Field(min_length=1)
     smtp_server: str
     port: int
-    encrypted_password: SecretStr | None = None
-    encryption_key: SecretStr | None = None
+    password: SecretStr | None = None
     instance_name: str
     use_starttls: bool
     use_login: bool
@@ -53,10 +52,6 @@ class EmailSettings(BaseSettings):
     """
     Password for the OAuth-signup email sender.
     """
-    FRACTAL_EMAIL_PASSWORD_KEY: SecretStr | None = None
-    """
-    Key value for `cryptography.fernet` decrypt
-    """
     FRACTAL_EMAIL_SMTP_SERVER: str | None = None
     """
     SMTP server for the OAuth-signup emails.
@@ -81,8 +76,7 @@ class EmailSettings(BaseSettings):
     FRACTAL_EMAIL_USE_LOGIN: Literal["true", "false"] = "true"
     """
     Whether to use login when using the SMTP server.
-    If 'true', FRACTAL_EMAIL_PASSWORD and FRACTAL_EMAIL_PASSWORD_KEY must be
-    provided.
+    If 'true', FRACTAL_EMAIL_PASSWORD  must be provided.
     Accepted values: 'true', 'false'.
     """
 
@@ -93,7 +87,7 @@ class EmailSettings(BaseSettings):
     """
 
     @model_validator(mode="after")
-    def validate_email_settings(self):
+    def validate_email_settings(self: Self) -> Self:
         """
         Set `self.public`.
         """
@@ -119,49 +113,18 @@ class EmailSettings(BaseSettings):
             use_starttls = self.FRACTAL_EMAIL_USE_STARTTLS == "true"
             use_login = self.FRACTAL_EMAIL_USE_LOGIN == "true"
 
-            if use_login:
-                if self.FRACTAL_EMAIL_PASSWORD is None:
-                    raise ValueError(
-                        "'FRACTAL_EMAIL_USE_LOGIN' is 'true' but "
-                        "'FRACTAL_EMAIL_PASSWORD' is not provided."
-                    )
-                if self.FRACTAL_EMAIL_PASSWORD_KEY is None:
-                    raise ValueError(
-                        "'FRACTAL_EMAIL_USE_LOGIN' is 'true' but "
-                        "'FRACTAL_EMAIL_PASSWORD_KEY' is not provided."
-                    )
-                try:
-                    (
-                        Fernet(
-                            self.FRACTAL_EMAIL_PASSWORD_KEY.get_secret_value()
-                        )
-                        .decrypt(
-                            self.FRACTAL_EMAIL_PASSWORD.get_secret_value()
-                        )
-                        .decode("utf-8")
-                    )
-                except Exception as e:
-                    raise ValueError(
-                        "Invalid pair (FRACTAL_EMAIL_PASSWORD, "
-                        "FRACTAL_EMAIL_PASSWORD_KEY). "
-                        f"Original error: {str(e)}."
-                    )
-                password = self.FRACTAL_EMAIL_PASSWORD.get_secret_value()
-            else:
-                password = None
-
-            if self.FRACTAL_EMAIL_PASSWORD_KEY is not None:
-                key = self.FRACTAL_EMAIL_PASSWORD_KEY.get_secret_value()
-            else:
-                key = None
+            if use_login and self.FRACTAL_EMAIL_PASSWORD is None:
+                raise ValueError(
+                    "'FRACTAL_EMAIL_USE_LOGIN' is 'true' but "
+                    "'FRACTAL_EMAIL_PASSWORD' is not provided."
+                )
 
             self.public = PublicEmailSettings(
                 sender=self.FRACTAL_EMAIL_SENDER,
                 recipients=self.FRACTAL_EMAIL_RECIPIENTS.split(","),
                 smtp_server=self.FRACTAL_EMAIL_SMTP_SERVER,
                 port=self.FRACTAL_EMAIL_SMTP_PORT,
-                encrypted_password=password,
-                encryption_key=key,
+                password=self.FRACTAL_EMAIL_PASSWORD,
                 instance_name=self.FRACTAL_EMAIL_INSTANCE_NAME,
                 use_starttls=use_starttls,
                 use_login=use_login,

fractal_server/config/_main.py

@@ -1,20 +1,12 @@
 import logging
 from typing import Literal
-from typing import TypeVar
 
+from pydantic import HttpUrl
 from pydantic import SecretStr
 from pydantic_settings import BaseSettings
 from pydantic_settings import SettingsConfigDict
 
 from ._settings_config import SETTINGS_CONFIG_DICT
-from fractal_server.types import AbsolutePathStr
-
-
-class FractalConfigurationError(ValueError):
-    pass
-
-
-T = TypeVar("T")
 
 
 class Settings(BaseSettings):
@@ -26,7 +18,6 @@ class Settings(BaseSettings):
 
     model_config = SettingsConfigDict(**SETTINGS_CONFIG_DICT)
 
-    # JWT TOKEN
     JWT_EXPIRE_SECONDS: int = 180
     """
     JWT token lifetime, in seconds.
@@ -40,7 +31,6 @@ class Settings(BaseSettings):
     it.
     """
 
-    # COOKIE TOKEN
     COOKIE_EXPIRE_SECONDS: int = 86400
     """
     Cookie token lifetime, in seconds.
@@ -72,50 +62,7 @@ class Settings(BaseSettings):
     Waiting time for the shutdown phase of executors
     """
 
-    FRACTAL_VIEWER_AUTHORIZATION_SCHEME: Literal[
-        "viewer-paths", "users-folders", "none"
-    ] = "none"
-    """
-    Defines how the list of allowed viewer paths is built.
-
-    This variable affects the `GET /auth/current-user/allowed-viewer-paths/`
-    response, which is then consumed by
-    [fractal-vizarr-viewer](https://github.com/fractal-analytics-platform/fractal-vizarr-viewer).
-
-    Options:
-
-    - "viewer-paths": The list of allowed viewer paths will include the user's
-      `project_dir` along with any path defined in user groups' `viewer_paths`
-      attributes.
-    - "users-folders": The list will consist of the user's `project_dir` and a
-       user-specific folder. The user folder is constructed by concatenating
-       the base folder `FRACTAL_VIEWER_BASE_FOLDER` with the user's
-       `slurm_user`.
-    - "none": An empty list will be returned, indicating no access to
-       viewer paths. Useful when vizarr viewer is not used.
-    """
-
-    FRACTAL_VIEWER_BASE_FOLDER: AbsolutePathStr | None = None
+    FRACTAL_HELP_URL: HttpUrl | None = None
     """
-    Base path to Zarr files that will be served by fractal-vizarr-viewer;
-    This variable is required and used only when
-    FRACTAL_VIEWER_AUTHORIZATION_SCHEME is set to "users-folders".
+    The URL of an instance-specific Fractal help page.
     """
-
-    def check(self):
-        """
-        Make sure that required variables are set
-
-        This method must be called before the server starts
-        """
-        # FRACTAL_VIEWER_BASE_FOLDER is required when
-        # FRACTAL_VIEWER_AUTHORIZATION_SCHEME is set to "users-folders"
-        # and it must be an absolute path
-        if self.FRACTAL_VIEWER_AUTHORIZATION_SCHEME == "users-folders":
-            viewer_base_folder = self.FRACTAL_VIEWER_BASE_FOLDER
-            if viewer_base_folder is None:
-                raise FractalConfigurationError(
-                    "FRACTAL_VIEWER_BASE_FOLDER is required when "
-                    "FRACTAL_VIEWER_AUTHORIZATION_SCHEME is set to "
-                    "users-folders"
-                )

fractal_server/config/_oauth.py

@@ -37,7 +37,7 @@ class OAuthSettings(BaseSettings):
     """
     Secret to authorise against the identity provider.
     """
-    OAUTH_OIDC_CONFIG_ENDPOINT: str | None = None
+    OAUTH_OIDC_CONFIG_ENDPOINT: SecretStr | None = None
     """
     OpenID configuration endpoint, for autodiscovery of relevant endpoints.
     """
@@ -55,7 +55,7 @@ class OAuthSettings(BaseSettings):
             and self.OAUTH_OIDC_CONFIG_ENDPOINT is None
         ):
             raise ValueError(
-                f"{self.OAUTH_OIDC_CONFIG_ENDPOINT=} but "
+                f"self.OAUTH_OIDC_CONFIG_ENDPOINT=None but "
                 f"{self.OAUTH_CLIENT_NAME=}"
             )
         return self

fractal_server/main.py

@@ -6,6 +6,7 @@ from fastapi import FastAPI
 
 from .app.routes.aux._runner import _backend_supports_shutdown
 from .app.shutdown import cleanup_after_shutdown
+from .config import get_data_settings
 from .config import get_db_settings
 from .config import get_email_settings
 from .config import get_settings
@@ -50,16 +51,16 @@ def check_settings() -> None:
         ValidationError: If the configuration is invalid.
     """
     settings = Inject(get_settings)
-    settings.check()
     db_settings = Inject(get_db_settings)
     email_settings = Inject(get_email_settings)
-
+    data_settings = Inject(get_data_settings)
     logger = set_logger("fractal_server_settings")
     logger.debug("Fractal Settings:")
     for key, value in chain(
         db_settings.model_dump().items(),
         settings.model_dump().items(),
         email_settings.model_dump().items(),
+        data_settings.model_dump().items(),
     ):
         if any(s in key.upper() for s in ["PASSWORD", "SECRET", "KEY"]):
             value = "*****"

fractal_server/migrations/versions/f65ee53991e3_user_settings_related.py

@@ -0,0 +1,67 @@
+"""user-settings-related
+
+Revision ID: f65ee53991e3
+Revises: 90f6508c6379
+Create Date: 2025-10-22 15:16:42.217910
+
+"""
+import sqlalchemy as sa
+from alembic import op
+from sqlalchemy.dialects import postgresql
+
+# revision identifiers, used by Alembic.
+revision = "f65ee53991e3"
+down_revision = "90f6508c6379"
+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.add_column(
+            sa.Column(
+                "project_dir",
+                sa.String(),
+                server_default="/PLACEHOLDER",
+                nullable=False,
+            )
+        )
+        batch_op.add_column(
+            sa.Column(
+                "slurm_accounts",
+                postgresql.ARRAY(sa.String()),
+                server_default="{}",
+                nullable=True,
+            )
+        )
+        batch_op.drop_constraint(
+            batch_op.f("fk_user_oauth_user_settings_id_user_settings"),
+            type_="foreignkey",
+        )
+        batch_op.drop_column("user_settings_id")
+
+    # ### 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(
+                "user_settings_id",
+                sa.INTEGER(),
+                autoincrement=False,
+                nullable=True,
+            )
+        )
+        batch_op.create_foreign_key(
+            batch_op.f("fk_user_oauth_user_settings_id_user_settings"),
+            "user_settings",
+            ["user_settings_id"],
+            ["id"],
+        )
+        batch_op.drop_column("slurm_accounts")
+        batch_op.drop_column("project_dir")
+
+    # ### end Alembic commands ###

fractal_server/runner/executors/slurm_common/base_slurm_runner.py

@@ -87,7 +87,7 @@ class BaseSlurmRunner(BaseRunner):
         python_worker_interpreter: str,
         poll_interval: int,
         common_script_lines: list[str] | None = None,
-        user_cache_dir: str | None = None,  # FIXME: make required?
+        user_cache_dir: str,
         slurm_account: str | None = None,
     ):
         self.slurm_runner_type = slurm_runner_type

fractal_server/runner/executors/slurm_common/slurm_config.py

@@ -136,7 +136,7 @@ class SlurmConfig(BaseModel):
 
     def to_sbatch_preamble(
         self,
-        remote_export_dir: str | None = None,
+        remote_export_dir: str,
     ) -> list[str]:
         """
         Compile `SlurmConfig` object into the preamble of a SLURM submission
@@ -189,13 +189,10 @@ class SlurmConfig(BaseModel):
         for line in self._sorted_extra_lines():
             lines.append(line)
 
-        if self.user_local_exports != {} and remote_export_dir is None:
-            raise ValueError(
-                f"{remote_export_dir=} but {self.user_local_exports=}"
-            )
-        for key, value in self.user_local_exports.items():
-            tmp_value = str(Path(remote_export_dir) / value)
-            lines.append(f"export {key}={tmp_value}")
+        if self.user_local_exports:
+            for key, value in self.user_local_exports.items():
+                tmp_value = str(Path(remote_export_dir) / value)
+                lines.append(f"export {key}={tmp_value}")
 
         """
         FIXME export SRUN_CPUS_PER_TASK

fractal_server/runner/executors/slurm_ssh/runner.py

@@ -31,7 +31,7 @@ class SlurmSSHRunner(BaseSlurmRunner):
         # Specific
         slurm_account: str | None = None,
         profile: Profile,
-        user_cache_dir: str | None = None,
+        user_cache_dir: str,
         fractal_ssh: FractalSSH,
     ) -> None:
         """

fractal_server/runner/executors/slurm_sudo/runner.py

@@ -54,7 +54,7 @@ class SudoSlurmRunner(BaseSlurmRunner):
         resource: Resource,
         # Specific
         profile: Profile,
-        user_cache_dir: str | None = None,  # FIXME: make required?
+        user_cache_dir: str,
         slurm_account: str | None = None,
     ) -> None:
         """

fractal_server/runner/v2/_slurm_ssh.py

@@ -50,7 +50,7 @@ def process_workflow(
     fractal_ssh: FractalSSH | None = None,
     slurm_account: str | None = None,
     worker_init: str | None = None,
-    user_cache_dir: str | None = None,
+    user_cache_dir: str,
 ) -> None:
     """
     Run a workflow through a `slurm_ssh` backend.
@@ -105,6 +105,7 @@ def process_workflow(
         resource=resource,
         profile=profile,
         common_script_lines=worker_init,
+        user_cache_dir=user_cache_dir,
     ) as runner:
         execute_tasks_v2(
             wf_task_list=workflow.task_list[

fractal_server/runner/v2/_slurm_sudo.py

@@ -44,7 +44,7 @@ def process_workflow(
     user_id: int,
     resource: Resource,
     profile: Profile,
-    user_cache_dir: str | None = None,
+    user_cache_dir: str,
     slurm_account: str | None = None,
     worker_init: str | None = None,
     fractal_ssh: FractalSSH | None = None,

fractal_server/runner/v2/submit_workflow.py

@@ -52,6 +52,7 @@ class ProcessWorkflowType(Protocol):
         user_id: int,
         resource: Resource,
         profile: Profile,
+        user_cache_dir: str,
     ) -> None:
         ...
 
@@ -84,10 +85,10 @@ def submit_workflow(
     dataset_id: int,
     job_id: int,
     user_id: int,
-    worker_init: str | None = None,
-    user_cache_dir: str | None = None,  # FIXME: review this
+    user_cache_dir: str,
     resource: Resource,
     profile: Profile,
+    worker_init: str | None = None,
     fractal_ssh: FractalSSH | None = None,
 ) -> None:
     """
@@ -110,8 +111,10 @@ def submit_workflow(
             Custom executor parameters that get parsed before the execution of
             each task.
         user_cache_dir:
-            Cache directory (namely a path where the user can write); for the
-            slurm backend, this is used as a base directory for FIXME.
+            Cache directory (namely a path where the user can write). For
+            `slurm_sudo` backend, this is both a base directory for
+            `job.working_dir_user`. For `slurm_sudo` and `slurm_ssh` backends,
+            this is used for `user_local_exports`.
         resource:
             Computational resource to be used for this job (e.g. a SLURM
             cluster).
@@ -224,22 +227,18 @@ def submit_workflow(
         job_working_dir = job.working_dir
 
     try:
+        process_workflow: ProcessWorkflowType
         match resource.type:
             case ResourceType.LOCAL:
-                process_workflow: ProcessWorkflowType = local_process_workflow
+                process_workflow = local_process_workflow
                 backend_specific_kwargs = {}
             case ResourceType.SLURM_SUDO:
-                process_workflow: ProcessWorkflowType = (
-                    slurm_sudo_process_workflow
-                )
+                process_workflow = slurm_sudo_process_workflow
                 backend_specific_kwargs = dict(
                     slurm_account=job.slurm_account,
-                    user_cache_dir=user_cache_dir,
                 )
             case ResourceType.SLURM_SSH:
-                process_workflow: ProcessWorkflowType = (
-                    slurm_ssh_process_workflow
-                )
+                process_workflow = slurm_ssh_process_workflow
                 backend_specific_kwargs = dict(
                     fractal_ssh=fractal_ssh,
                     slurm_account=job.slurm_account,
@@ -260,6 +259,7 @@ def submit_workflow(
             job_type_filters=job.type_filters,
             resource=resource,
             profile=profile,
+            user_cache_dir=user_cache_dir,
             **backend_specific_kwargs,
         )
 

{fractal_server-2.17.0a4.dist-info → fractal_server-2.17.0a6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: fractal-server
-Version: 2.17.0a4
+Version: 2.17.0a6
 Summary: Backend component of the Fractal analytics platform
 License-Expression: BSD-3-Clause
 License-File: LICENSE
@@ -12,20 +12,18 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Requires-Dist: alembic (>=1.13.1,<2.0.0)
-Requires-Dist: cryptography (>=46.0.0,<47.0.0)
 Requires-Dist: fabric (>=3.2.2,<3.3.0)
-Requires-Dist: fastapi (>=0.118.0,<0.119.0)
-Requires-Dist: fastapi-users[oauth] (>=14,<15)
+Requires-Dist: fastapi (>=0.120.0,<0.121.0)
+Requires-Dist: fastapi-users[oauth] (>=15,<16)
 Requires-Dist: gunicorn (>=23.0,<24.0)
 Requires-Dist: packaging (>=25.0.0,<26.0.0)
 Requires-Dist: psycopg[binary] (>=3.1.0,<4.0.0)
 Requires-Dist: pydantic (>=2.12.0,<2.13.0)
 Requires-Dist: pydantic-settings (==2.11.0)
-Requires-Dist: python-dotenv (>=1.1.0,<1.2.0)
 Requires-Dist: sqlalchemy[asyncio] (>=2.0.23,<2.1)
 Requires-Dist: sqlmodel (==0.0.27)
 Requires-Dist: tomli_w (>=1.2.0,<1.3.0)
-Requires-Dist: uvicorn (>=0.37.0,<0.38.0)
+Requires-Dist: uvicorn (>=0.38.0,<0.39.0)
 Requires-Dist: uvicorn-worker (==0.4.0)
 Project-URL: Documentation, https://fractal-analytics-platform.github.io/fractal-server
 Project-URL: Homepage, https://github.com/fractal-analytics-platform/fractal-server