fractal-server 2.17.0a3__tar.gz → 2.17.0a4__tar.gz

{fractal_server-2.17.0a3 → fractal_server-2.17.0a4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: fractal-server
-Version: 2.17.0a3
+Version: 2.17.0a4
 Summary: Backend component of the Fractal analytics platform
 License-Expression: BSD-3-Clause
 License-File: LICENSE

fractal_server-2.17.0a4/fractal_server/__init__.py

@@ -0,0 +1 @@
+__VERSION__ = "2.17.0a4"

{fractal_server-2.17.0a3 → fractal_server-2.17.0a4}/fractal_server/__main__.py

@@ -62,14 +62,26 @@ init_db_data_parser = subparsers.add_parser(
 init_db_data_parser.add_argument(
     "--resource",
     type=str,
-    help=("Either `default` or path to the JSON file of the first resource."),
-    required=True,
+    help="Either `default` or path to the JSON file of the first resource.",
+    required=False,
 )
 init_db_data_parser.add_argument(
     "--profile",
     type=str,
-    help=("Either `default` or path to the JSON file of the first profile."),
-    required=True,
+    help="Either `default` or path to the JSON file of the first profile.",
+    required=False,
+)
+init_db_data_parser.add_argument(
+    "--admin-email",
+    type=str,
+    help="Email of the first admin user to create.",
+    required=False,
+)
+init_db_data_parser.add_argument(
+    "--admin-pwd",
+    type=str,
+    help="Password of the first admin user to create.",
+    required=False,
 )
 
 # fractalctl update-db-data
@@ -124,14 +136,13 @@ def set_db():
 
 
 def init_db_data(
-    *,
-    resource: str,
-    profile: str,
+    resource: str | None = None,
+    profile: str | None = None,
+    admin_email: str | None = None,
+    admin_password: str | None = None,
 ) -> None:
     from fractal_server.app.security import _create_first_user
     from fractal_server.app.security import _create_first_group
-    from fractal_server.syringe import Inject
-    from fractal_server.config import get_init_data_settings
     from fractal_server.app.db import get_sync_db
     from sqlalchemy import select, func
     from fractal_server.app.models.security import UserOAuth
@@ -139,104 +150,112 @@ def init_db_data(
     from fractal_server.app.schemas.v2.resource import cast_serialize_resource
     from fractal_server.app.schemas.v2.profile import cast_serialize_profile
 
-    init_data_settings = Inject(get_init_data_settings)
-
     # Create default group and user
     print()
     _create_first_group()
     print()
-    asyncio.run(
-        _create_first_user(
-            email=init_data_settings.FRACTAL_DEFAULT_ADMIN_EMAIL,
-            password=(
-                init_data_settings.FRACTAL_DEFAULT_ADMIN_PASSWORD.get_secret_value()  # noqa E501
-            ),
-            is_superuser=True,
-            is_verified=True,
-        )
-    )
-    print()
 
-    # Create resource and profile
-    with next(get_sync_db()) as db:
-        # Preliminary check
-        num_resources = db.execute(select(func.count(Resource.id))).scalar()
-        if num_resources != 0:
-            print(f"There exist already {num_resources=} resources. Exit.")
-            sys.exit(1)
-
-        # Get resource/profile data
-        if resource == "default":
-            _python_version = (
-                f"{sys.version_info.major}.{sys.version_info.minor}"
-            )
-            resource_data = {
-                "name": "Local resource",
-                "type": ResourceType.LOCAL,
-                "jobs_local_dir": (Path.cwd() / "data-jobs").as_posix(),
-                "tasks_local_dir": (Path.cwd() / "data-tasks").as_posix(),
-                "tasks_python_config": {
-                    "default_version": _python_version,
-                    "versions": {
-                        _python_version: sys.executable,
-                    },
-                },
-                "jobs_poll_interval": 0,
-                "jobs_runner_config": {},
-                "tasks_pixi_config": {},
-            }
-            print("Prepared default resource data.")
-        else:
-            with open(resource) as f:
-                resource_data = json.load(f)
-            print(f"Read resource data from {resource}.")
-        if profile == "default":
-            profile_data = {
-                "resource_type": "local",
-                "name": "Local profile",
-            }
-            print("Prepared default profile data.")
-        else:
-            with open(profile) as f:
-                profile_data = json.load(f)
-            print(f"Read profile data from {profile}.")
-
-        # Validate resource/profile data
-        try:
-            resource_data = cast_serialize_resource(resource_data)
-        except ValidationError as e:
-            sys.exit(
-                f"ERROR: Invalid resource data.\nOriginal error:\n{str(e)}"
-            )
-        try:
-            profile_data = cast_serialize_profile(profile_data)
-        except ValidationError as e:
-            sys.exit(
-                f"ERROR: Invalid profile data.\nOriginal error:\n{str(e)}"
+    # Create admin user if requested
+    if (admin_email is None) != (admin_password is None):
+        print("You must provide both --admin-email and --admin-pwd. Exit.")
+        sys.exit(1)
+    if admin_password and admin_email:
+        asyncio.run(
+            _create_first_user(
+                email=admin_email,
+                password=admin_password,
+                is_superuser=True,
+                is_verified=True,
             )
-
-        # Create resource/profile db objects
-        resource_obj = Resource(**resource_data)
-        db.add(resource_obj)
-        db.commit()
-        db.refresh(resource_obj)
-        profile_data["resource_id"] = resource_obj.id
-        profile_obj = Profile(**profile_data)
-        db.add(profile_obj)
-        db.commit()
-        db.refresh(profile_obj)
-
-        # Associate profile to users
-        res = db.execute(select(UserOAuth))
-        users = res.unique().scalars().all()
-        for user in users:
-            print(f"Now set profile_id={profile_obj.id} for {user.email}.")
-            user.profile_id = profile_obj.id
-            db.add(user)
-        db.commit()
-        db.expunge_all()
+        )
         print()
 
+    # Create resource and profile if requested
+    if (resource is None) != (profile is None):
+        print("You must provide both --resource and --profile. Exit.")
+        sys.exit(1)
+    if resource and profile:
+        with next(get_sync_db()) as db:
+            # Preliminary check
+            num_resources = db.execute(
+                select(func.count(Resource.id))
+            ).scalar()
+            if num_resources != 0:
+                print(f"There exist already {num_resources=} resources. Exit.")
+                sys.exit(1)
+
+            # Get resource/profile data
+            if resource == "default":
+                _python_version = (
+                    f"{sys.version_info.major}.{sys.version_info.minor}"
+                )
+                resource_data = {
+                    "name": "Local resource",
+                    "type": ResourceType.LOCAL,
+                    "jobs_local_dir": (Path.cwd() / "data-jobs").as_posix(),
+                    "tasks_local_dir": (Path.cwd() / "data-tasks").as_posix(),
+                    "tasks_python_config": {
+                        "default_version": _python_version,
+                        "versions": {
+                            _python_version: sys.executable,
+                        },
+                    },
+                    "jobs_poll_interval": 0,
+                    "jobs_runner_config": {},
+                    "tasks_pixi_config": {},
+                }
+                print("Prepared default resource data.")
+            else:
+                with open(resource) as f:
+                    resource_data = json.load(f)
+                print(f"Read resource data from {resource}.")
+            if profile == "default":
+                profile_data = {
+                    "resource_type": "local",
+                    "name": "Local profile",
+                }
+                print("Prepared default profile data.")
+            else:
+                with open(profile) as f:
+                    profile_data = json.load(f)
+                print(f"Read profile data from {profile}.")
+
+            # Validate resource/profile data
+            try:
+                resource_data = cast_serialize_resource(resource_data)
+            except ValidationError as e:
+                sys.exit(
+                    f"ERROR: Invalid resource data.\nOriginal error:\n{str(e)}"
+                )
+            try:
+                profile_data = cast_serialize_profile(profile_data)
+            except ValidationError as e:
+                sys.exit(
+                    f"ERROR: Invalid profile data.\nOriginal error:\n{str(e)}"
+                )
+
+            # Create resource/profile db objects
+            resource_obj = Resource(**resource_data)
+            db.add(resource_obj)
+            db.commit()
+            db.refresh(resource_obj)
+            profile_data["resource_id"] = resource_obj.id
+            profile_obj = Profile(**profile_data)
+            db.add(profile_obj)
+            db.commit()
+            db.refresh(profile_obj)
+
+            # Associate profile to users
+            res = db.execute(select(UserOAuth))
+            users = res.unique().scalars().all()
+            for user in users:
+                print(f"Now set profile_id={profile_obj.id} for {user.email}.")
+                user.profile_id = profile_obj.id
+                db.add(user)
+            db.commit()
+            db.expunge_all()
+            print()
+
 
 def update_db_data():
     """
@@ -328,6 +347,8 @@ def run():
         init_db_data(
             resource=args.resource,
             profile=args.profile,
+            admin_email=args.admin_email,
+            admin_password=args.admin_pwd,
         )
     elif args.cmd == "update-db-data":
         update_db_data()

{fractal_server-2.17.0a3 → fractal_server-2.17.0a4}/fractal_server/app/routes/admin/v2/resource.py

@@ -13,7 +13,9 @@ from fractal_server.app.db import AsyncSession
 from fractal_server.app.db import get_async_db
 from fractal_server.app.models import UserOAuth
 from fractal_server.app.models.v2 import Profile
+from fractal_server.app.models.v2 import ProjectV2
 from fractal_server.app.models.v2 import Resource
+from fractal_server.app.models.v2 import TaskGroupV2
 from fractal_server.app.routes.auth import current_active_superuser
 from fractal_server.app.schemas.v2 import ProfileCreate
 from fractal_server.app.schemas.v2 import ProfileRead
@@ -166,6 +168,38 @@ async def delete_resource(
             ),
         )
 
+    # Fail if at least one Project is associated with the Resource.
+    res = await db.execute(
+        select(func.count(ProjectV2.id)).where(
+            ProjectV2.resource_id == resource_id
+        )
+    )
+    associated_project_count = res.scalar()
+    if associated_project_count > 0:
+        raise HTTPException(
+            status_code=status.HTTP_422_UNPROCESSABLE_CONTENT,
+            detail=(
+                f"Cannot delete Resource {resource_id} because it's associated"
+                f" with {associated_project_count} Projects."
+            ),
+        )
+
+    # Fail if at least one TaskGroupV2 is associated with the Resource.
+    res = await db.execute(
+        select(func.count(TaskGroupV2.id)).where(
+            TaskGroupV2.resource_id == resource_id
+        )
+    )
+    associated_taskgroup_count = res.scalar()
+    if associated_taskgroup_count > 0:
+        raise HTTPException(
+            status_code=status.HTTP_422_UNPROCESSABLE_CONTENT,
+            detail=(
+                f"Cannot delete Resource {resource_id} because it's associated"
+                f" with {associated_taskgroup_count} TaskGroupV2."
+            ),
+        )
+
     # Delete
     await db.delete(resource)
     await db.commit()

{fractal_server-2.17.0a3 → fractal_server-2.17.0a4}/fractal_server/config/__init__.py

@@ -1,7 +1,6 @@
 from ._database import DatabaseSettings
 from ._email import EmailSettings
 from ._email import PublicEmailSettings  # noqa F401
-from ._init_data import InitDataSettings
 from ._main import Settings
 from ._oauth import OAuthSettings
 
@@ -18,11 +17,5 @@ def get_email_settings(email_settings=EmailSettings()) -> EmailSettings:
     return email_settings
 
 
-def get_init_data_settings(
-    init_data_settings=InitDataSettings(),
-) -> InitDataSettings:
-    return init_data_settings
-
-
 def get_oauth_settings(oauth_settings=OAuthSettings()) -> OAuthSettings:
     return oauth_settings

{fractal_server-2.17.0a3 → fractal_server-2.17.0a4}/fractal_server/runner/config/_slurm.py

@@ -3,6 +3,7 @@ from typing import Annotated
 from pydantic import AfterValidator
 from pydantic import BaseModel
 from pydantic import ConfigDict
+from pydantic import Field
 from pydantic.types import PositiveInt
 
 from fractal_server.runner.config.slurm_mem_to_MB import slurm_mem_to_MB
@@ -44,7 +45,7 @@ class _SlurmConfigSet(BaseModel):
     nodelist: NonEmptyStr | None = None
     time: NonEmptyStr | None = None
     account: NonEmptyStr | None = None
-    extra_lines: list[NonEmptyStr] | None = None
+    extra_lines: list[NonEmptyStr] = Field(default_factory=list)
     gpus: NonEmptyStr | None = None
 
 
@@ -125,4 +126,4 @@ class JobRunnerConfigSLURM(BaseModel):
     default_slurm_config: _SlurmConfigSet
     gpu_slurm_config: _SlurmConfigSet | None = None
     batching_config: _BatchingConfigSet
-    user_local_exports: DictStrStr | None = None
+    user_local_exports: DictStrStr = Field(default_factory=dict)

{fractal_server-2.17.0a3 → fractal_server-2.17.0a4}/fractal_server/runner/executors/slurm_common/base_slurm_runner.py

@@ -252,7 +252,7 @@ class BaseSlurmRunner(BaseRunner):
                 f"Add {self.common_script_lines} to "
                 f"{new_slurm_config.extra_lines=}."
             )
-            current_extra_lines = new_slurm_config.extra_lines or []
+            current_extra_lines = new_slurm_config.extra_lines
             new_slurm_config.extra_lines = (
                 current_extra_lines + self.common_script_lines
             )

{fractal_server-2.17.0a3 → fractal_server-2.17.0a4}/fractal_server/runner/executors/slurm_common/get_slurm_config.py

@@ -77,7 +77,7 @@ def _get_slurm_config_internal(
     else:
         needs_gpu = False
     logger.debug(f"[get_slurm_config] {needs_gpu=}")
-    if needs_gpu:
+    if needs_gpu and shared_config.gpu_slurm_config is not None:
         for key, value in shared_config.gpu_slurm_config.model_dump(
             exclude_unset=True, exclude={"mem"}
         ).items():

{fractal_server-2.17.0a3 → fractal_server-2.17.0a4}/fractal_server/runner/executors/slurm_common/slurm_config.py

@@ -83,10 +83,10 @@ class SlurmConfig(BaseModel):
 
     # Free-field attribute for extra lines to be added to the SLURM job
     # preamble
-    extra_lines: list[str] | None = Field(default_factory=list)
+    extra_lines: list[str] = Field(default_factory=list)
 
     # Variables that will be `export`ed in the SLURM submission script
-    user_local_exports: dict[str, str] | None = None
+    user_local_exports: dict[str, str] = Field(default_factory=dict)
 
     # Metaparameters needed to combine multiple tasks in each SLURM job
     tasks_per_job: int | None = None
@@ -152,9 +152,8 @@ class SlurmConfig(BaseModel):
                 "SlurmConfig.sbatch_preamble requires that "
                 f"{self.parallel_tasks_per_job=} is not None."
             )
-        if self.extra_lines:
-            if len(self.extra_lines) != len(set(self.extra_lines)):
-                raise ValueError(f"{self.extra_lines=} contains repetitions")
+        if len(self.extra_lines) != len(set(self.extra_lines)):
+            raise ValueError(f"{self.extra_lines=} contains repetitions")
 
         mem_per_job_MB = self.parallel_tasks_per_job * self.mem_per_task_MB
         lines = [
@@ -187,18 +186,16 @@ class SlurmConfig(BaseModel):
                 option = key.replace("_", "-")
                 lines.append(f"{self.prefix} --{option}={value}")
 
-        if self.extra_lines:
-            for line in self._sorted_extra_lines():
-                lines.append(line)
-
-        if self.user_local_exports:
-            if remote_export_dir is None:
-                raise ValueError(
-                    f"remote_export_dir=None 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}")
+        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}")
 
         """
         FIXME export SRUN_CPUS_PER_TASK

{fractal_server-2.17.0a3 → fractal_server-2.17.0a4}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "fractal-server"
-version = "2.17.0a3"
+version = "2.17.0a4"
 description = "Backend component of the Fractal analytics platform"
 authors = [
     { name="Tommaso Comparin", email="tommaso.comparin@exact-lab.it" },
@@ -96,7 +96,7 @@ filterwarnings = [
 markers = ["container", "ssh", "fails_on_macos"]
 
 [tool.bumpver]
-current_version = "2.17.0a3"
+current_version = "2.17.0a4"
 version_pattern = "MAJOR.MINOR.PATCH[PYTAGNUM]"
 commit_message = "bump version {old_version} -> {new_version}"
 commit = true

fractal_server-2.17.0a3/fractal_server/__init__.py

@@ -1 +0,0 @@
-__VERSION__ = "2.17.0a3"

fractal_server-2.17.0a3/fractal_server/config/_init_data.py

@@ -1,27 +0,0 @@
-from pydantic import SecretStr
-from pydantic_settings import BaseSettings
-from pydantic_settings import SettingsConfigDict
-
-from ._settings_config import SETTINGS_CONFIG_DICT
-
-
-class InitDataSettings(BaseSettings):
-    model_config = SettingsConfigDict(**SETTINGS_CONFIG_DICT)
-
-    FRACTAL_DEFAULT_ADMIN_EMAIL: str = "admin@fractal.xy"
-    """
-    Admin default email, used upon creation of the first superuser during
-    server startup.
-
-    ⚠️  **IMPORTANT**: After the server startup, you should always edit the
-    default admin credentials.
-    """
-
-    FRACTAL_DEFAULT_ADMIN_PASSWORD: SecretStr = "1234"
-    """
-    Admin default password, used upon creation of the first superuser during
-    server startup.
-
-    ⚠️ **IMPORTANT**: After the server startup, you should always edit the
-    default admin credentials.
-    """