fractal-server 2.6.0a1__py3-none-any.whl → 2.6.2__py3-none-any.whl

fractal_server/__init__.py

@@ -1 +1 @@
-__VERSION__ = "2.6.0a1"
+__VERSION__ = "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/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/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/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/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/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/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/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.dist-info → fractal_server-2.6.2.dist-info}/METADATA

@@ -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-2.6.0a1.dist-info → fractal_server-2.6.2.dist-info}/RECORD

@@ -1,4 +1,4 @@
-fractal_server/__init__.py,sha256=V37BdMJAncuN7d1NxAYcAAW3NwjqA3Vl-LqN_PhaVrc,24
+fractal_server/__init__.py,sha256=zk2Mr_vPWXiYjT0KF9CbddwUnuJ011NmmqEbItcDUz4,22
 fractal_server/__main__.py,sha256=WcBAkmVE9aH5mDI6wGkVmPAql2N5Vyk0A-7zuUl8WX0,6122
 fractal_server/alembic.ini,sha256=MWwi7GzjzawI9cCAK1LW7NxIBQDUqD12-ptJoq5JpP0,3153
 fractal_server/app/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -6,7 +6,7 @@ fractal_server/app/db/__init__.py,sha256=81rK9w1__Z6PJ5cEcChPVc-wI9YOK4fN--_5Opr
 fractal_server/app/models/__init__.py,sha256=aG7mf1zZbsgzDSp7GHEcZhdjHfW3TGPOLCI8MrvYhPw,500
 fractal_server/app/models/linkusergroup.py,sha256=ufthlbLFAWMU_dJmsVZzVlQa_D9C9SmgydxypQ2Xq1U,309
 fractal_server/app/models/linkuserproject.py,sha256=eQaourbGRshvlMVlKzLYJKHEjfsW1CbWws9yW4eHXhA,567
-fractal_server/app/models/security.py,sha256=DY1JGS11pdlFXTValt86hNcL6a6kLRZ5xkOhhZJ8c1U,3831
+fractal_server/app/models/security.py,sha256=xeR_3Wb5Epn2fvNgEuTKibzMkMybVogACpUvrP1J1b8,3625
 fractal_server/app/models/user_settings.py,sha256=0YXCAwoAVGqI2irRLdXgr9-JS0STtHhSaoFENigAnrk,1312
 fractal_server/app/models/v1/__init__.py,sha256=hUI7dEbPaiZGN0IbHW4RSmSicyvtn_xeuevoX7zvUwI,466
 fractal_server/app/models/v1/dataset.py,sha256=99GDgt7njx8yYQApkImqp_7bHA5HH3ElvbR6Oyj9kVI,2017
@@ -125,10 +125,10 @@ fractal_server/app/runner/v2/runner_functions_low_level.py,sha256=1fWvQ6YZUUnDhO
 fractal_server/app/runner/v2/task_interface.py,sha256=myS-kT0DsJ8xIJZBVEzgD8g54VbiwL6i7Im3e1zcVHQ,1866
 fractal_server/app/runner/versions.py,sha256=dSaPRWqmFPHjg20kTCHmi_dmGNcCETflDtDLronNanU,852
 fractal_server/app/schemas/__init__.py,sha256=stURAU_t3AOBaH0HSUbV-GKhlPKngnnIMoqWc3orFyI,135
-fractal_server/app/schemas/_validators.py,sha256=1dTOYr1IZykrxuQSV2-zuEMZbKe_nGwrfS7iUrsh-sE,3461
+fractal_server/app/schemas/_validators.py,sha256=XKEGEHxp3H6YSJewtFWXe_2Nh7SDdNtAXmlEmJO6Vb0,3606
 fractal_server/app/schemas/user.py,sha256=VNnAPnAVK6X0PZlw7XehocAshVNuUHdDwiZVWCCor6Y,2156
 fractal_server/app/schemas/user_group.py,sha256=2f9XQ6kIar6NMY4UCN0yOnve6ZDHUVZaHv1dna1Vfjg,1446
-fractal_server/app/schemas/user_settings.py,sha256=E9O4NAyxr1NpnO39MZ-AlYvEe-pielFYmerVLNJR9Do,2879
+fractal_server/app/schemas/user_settings.py,sha256=UEST1MSmd9w2YypCji3SONSFlJcr2u4uG3bTczZy_Pk,3102
 fractal_server/app/schemas/v1/__init__.py,sha256=CrBGgBhoemCvmZ70ZUchM-jfVAICnoa7AjZBAtL2UB0,1852
 fractal_server/app/schemas/v1/applyworkflow.py,sha256=uuIh7fHlHEL4yLqL-dePI6-nfCsqgBYATmht7w_KITw,4302
 fractal_server/app/schemas/v1/dataset.py,sha256=n71lNUO3JLy2K3IM9BZM2Fk1EnKQOTU7pm2s2rJ1FGY,3444
@@ -147,13 +147,12 @@ fractal_server/app/schemas/v2/manifest.py,sha256=N37IWohcfO3_y2l8rVM0h_1nZq7m4Iz
 fractal_server/app/schemas/v2/project.py,sha256=u7S4B-bote1oGjzAGiZ-DuQIyeRAGqJsI71Tc1EtYE0,736
 fractal_server/app/schemas/v2/status.py,sha256=SQaUpQkjFq5c5k5J4rOjNhuQaDOEg8lksPhkKmPU5VU,332
 fractal_server/app/schemas/v2/task.py,sha256=XsN8w1Szs8BrxxRtKyWCHKjN4Od-Kmlhi769JEplL-M,4804
-fractal_server/app/schemas/v2/task_collection.py,sha256=8PG1bOqkfQqORMN0brWf6mHDmijt0bBW-mZsF7cSxUs,6129
+fractal_server/app/schemas/v2/task_collection.py,sha256=_utBv7_kcRJCbPdWezasU8GrikI_QFPKeIl4vyAgDd4,6155
 fractal_server/app/schemas/v2/workflow.py,sha256=Zzx3e-qgkH8le0FUmAx9UrV5PWd7bj14PPXUh_zgZXM,1827
 fractal_server/app/schemas/v2/workflowtask.py,sha256=TN-mdkuE_EWet9Wk-xFrUwIt_tXYcw88WOKMnUcchKk,5665
 fractal_server/app/security/__init__.py,sha256=V1NOWlmaFZHMR6SrkMl62jyAuqYONyo8lyGvR6UZesM,12312
 fractal_server/app/user_settings.py,sha256=aZgQ3i0JkHfgwLGW1ee6Gzr1ae3IioFfJKKSsSS8Svk,1312
-fractal_server/config.py,sha256=NucdVswA4MJpgeePDqSsU01I893Bn_hqWUrxrax83Ls,24257
-fractal_server/data_migrations/2_6_0.py,sha256=Vl17mFiOF5jQsktOnog5vnaXXcUXOJRa-ljas9kUX0E,1863
+fractal_server/config.py,sha256=gX0aYwDwbC5y7JNorifON84YMveubb7XTb4sH14N3KM,23667
 fractal_server/data_migrations/README.md,sha256=_3AEFvDg9YkybDqCLlFPdDmGJvr6Tw7HRI14aZ3LOIw,398
 fractal_server/data_migrations/tools.py,sha256=LeMeASwYGtEqd-3wOLle6WARdTGAimoyMmRbbJl-hAM,572
 fractal_server/gunicorn_fractal.py,sha256=u6U01TLGlXgq1v8QmEpLih3QnsInZD7CqphgJ_GrGzc,1230
@@ -176,6 +175,7 @@ fractal_server/migrations/versions/70e77f1c38b0_add_applyworkflow_first_task_ind
 fractal_server/migrations/versions/71eefd1dd202_add_slurm_accounts.py,sha256=mbWuCkTpRAdGbRhW7lhXs_e5S6O37UAcCN6JfoY5H8A,1353
 fractal_server/migrations/versions/84bf0fffde30_add_dumps_to_applyworkflow.py,sha256=NSCuhANChsg76vBkShBl-9tQ4VEHubOjtAv1etHhlvY,2684
 fractal_server/migrations/versions/8f79bd162e35_add_docs_info_and_docs_link_to_task_.py,sha256=6pgODDtyAxevZvAJBj9IJ41inhV1RpwbpZr_qfPPu1A,1115
+fractal_server/migrations/versions/94a47ea2d3ff_remove_cache_dir_slurm_user_and_slurm_.py,sha256=yL3-Hvzw5jBLKj4LFP1z5ofZE9L9W3tLwYtPNW7z4ko,1508
 fractal_server/migrations/versions/97f444d47249_add_applyworkflow_project_dump.py,sha256=eKTZm3EgUgapXBxO0RuHkEfTKic-TZG3ADaMpGLuc0k,1057
 fractal_server/migrations/versions/99ea79d9e5d2_add_dataset_history.py,sha256=0im6TxDr53sKKcjiPgeH4ftVRGnRXZSh2lPbRQ1Ir9w,883
 fractal_server/migrations/versions/9c5ae74c9b98_add_user_settings_table.py,sha256=syONdZNf4-OnAcWIsbzXpYwpXPsXZ4SsmjwVvmVG0PU,2256
@@ -187,8 +187,8 @@ fractal_server/migrations/versions/efa89c30e0a4_add_project_timestamp_created.py
 fractal_server/migrations/versions/f384e1c0cf5d_drop_task_default_args_columns.py,sha256=9BwqUS9Gf7UW_KjrzHbtViC880qhD452KAytkHWWZyk,746
 fractal_server/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/ssh/__init__.py,sha256=sVUmzxf7_DuXG1xoLQ1_00fo5NPhi2LJipSmU5EAkPs,124
-fractal_server/ssh/_fabric.py,sha256=B9C7Cj9ibrT1_OGlu38Jz94elNofLvkP1pxf0Tv8Eic,16140
-fractal_server/string_tools.py,sha256=YyopB2ZZ8iL9JLDXUA8PI0hahivqLiohir2HsAlEzqE,2170
+fractal_server/ssh/_fabric.py,sha256=Fw6NZl8YnlShYTL-jmuPpbJ_Kn2pDRAIRY3bbDcnMA8,16214
+fractal_server/string_tools.py,sha256=bEcGNzlZJ3fj4IjRBXM34Klt25Amfx5AbeTHqPwnAqM,2264
 fractal_server/syringe.py,sha256=3qSMW3YaMKKnLdgnooAINOPxnCOxP7y2jeAQYB21Gdo,2786
 fractal_server/tasks/__init__.py,sha256=kadmVUoIghl8s190_Tt-8f-WBqMi8u8oU4Pvw39NHE8,23
 fractal_server/tasks/utils.py,sha256=wucz57I7G0Vd8hvtmvonlryACx9zIVlqfxG5I87MJ80,1820
@@ -213,8 +213,8 @@ fractal_server/tasks/v2/utils.py,sha256=JOyCacb6MNvrwfLNTyLwcz8y79J29YuJeJ2MK5kq
 fractal_server/urls.py,sha256=5o_qq7PzKKbwq12NHSQZDmDitn5RAOeQ4xufu-2v9Zk,448
 fractal_server/utils.py,sha256=b7WwFdcFZ8unyT65mloFToYuEDXpQoHRcmRNqrhd_dQ,2115
 fractal_server/zip_tools.py,sha256=xYpzBshysD2nmxkD5WLYqMzPYUcCRM3kYy-7n9bJL-U,4426
-fractal_server-2.6.0a1.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
-fractal_server-2.6.0a1.dist-info/METADATA,sha256=vgfTZcfqQkzjshalFqzIv5UXRWGbsd5rRLbxyJkFbL4,4630
-fractal_server-2.6.0a1.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-fractal_server-2.6.0a1.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
-fractal_server-2.6.0a1.dist-info/RECORD,,
+fractal_server-2.6.2.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
+fractal_server-2.6.2.dist-info/METADATA,sha256=hlWGMOKcA-SXQpW1tlXMo9zfn6lKs31rl-byf88u8Bs,4628
+fractal_server-2.6.2.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+fractal_server-2.6.2.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
+fractal_server-2.6.2.dist-info/RECORD,,

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")