fractal-server 2.10.1__py3-none-any.whl → 2.10.3__py3-none-any.whl

fractal_server/__init__.py

@@ -1 +1 @@
-__VERSION__ = "2.10.1"
+__VERSION__ = "2.10.3"

fractal_server/__main__.py

@@ -1,5 +1,6 @@
 import argparse as ap
 import asyncio
+import json
 import sys
 
 import uvicorn
@@ -62,6 +63,41 @@ update_db_data_parser = subparsers.add_parser(
     description="Apply data-migration script to an existing database.",
 )
 
+# fractalctl email-settings
+email_settings_parser = subparsers.add_parser(
+    "email-settings",
+    description=(
+        "Generate valid values for environment variables "
+        "`FRACTAL_EMAIL_SETTINGS` and `FRACTAL_EMAIL_SETTINGS_KEY`."
+    ),
+)
+email_settings_parser.add_argument(
+    "sender",
+    type=str,
+    help="Email of the sender",
+)
+email_settings_parser.add_argument(
+    "server",
+    type=str,
+    help="SMPT server used to send emails",
+)
+email_settings_parser.add_argument(
+    "port",
+    type=int,
+    help="Port of the SMPT server",
+)
+email_settings_parser.add_argument(
+    "instance",
+    type=str,
+    help="Name of the Fractal instance sending emails",
+)
+email_settings_parser.add_argument(
+    "--skip-starttls",
+    action="store_true",
+    default=False,
+    help="If set, skip the execution of `starttls` when sending emails",
+)
+
 
 def save_openapi(dest="openapi.json"):
     from fractal_server.main import start_application
@@ -188,6 +224,33 @@ def update_db_data():
     current_update_db_data_module.fix_db()
 
 
+def print_mail_settings(
+    sender: str,
+    server: str,
+    port: int,
+    instance: str,
+    skip_starttls: bool,
+):
+    from cryptography.fernet import Fernet
+
+    password = input(f"Insert email password for sender '{sender}': ")
+    key = Fernet.generate_key().decode("utf-8")
+    fractal_mail_settings = json.dumps(
+        dict(
+            sender=sender,
+            password=password,
+            smtp_server=server,
+            port=port,
+            instance_name=instance,
+            use_starttls=(not skip_starttls),
+        )
+    ).encode("utf-8")
+    email_settings = Fernet(key).encrypt(fractal_mail_settings).decode("utf-8")
+
+    print(f"\nFRACTAL_EMAIL_SETTINGS: {email_settings}")
+    print(f"FRACTAL_EMAIL_SETTINGS_KEY: {key}")
+
+
 def run():
     args = parser.parse_args(sys.argv[1:])
 
@@ -204,6 +267,14 @@ def run():
             port=args.port,
             reload=args.reload,
         )
+    elif args.cmd == "email-settings":
+        print_mail_settings(
+            sender=args.sender,
+            server=args.server,
+            port=args.port,
+            instance=args.instance,
+            skip_starttls=args.skip_starttls,
+        )
     else:
         sys.exit(f"Error: invalid command '{args.cmd}'.")
 

fractal_server/app/routes/api/v2/task_collection.py

@@ -56,6 +56,8 @@ router = APIRouter()
 
 logger = set_logger(__name__)
 
+FORBIDDEN_CHAR_WHEEL = [";", "/"]
+
 
 class CollectionRequestData(BaseModel):
     """
@@ -90,6 +92,14 @@ class CollectionRequestData(BaseModel):
                     f"provided (given package_version='{package_version}')."
                 )
             values["origin"] = TaskGroupV2OriginEnum.WHEELFILE
+
+            for forbidden_char in FORBIDDEN_CHAR_WHEEL:
+                if forbidden_char in file.filename:
+                    raise ValueError(
+                        "Wheel filename has forbidden characters, "
+                        f"{FORBIDDEN_CHAR_WHEEL}"
+                    )
+
         return values
 
 

fractal_server/app/routes/api/v2/workflowtask.py

@@ -6,7 +6,6 @@ from fastapi import Depends
 from fastapi import HTTPException
 from fastapi import Response
 from fastapi import status
-from sqlalchemy.orm.attributes import flag_modified
 
 from ....db import AsyncSession
 from ....db import get_async_db
@@ -89,8 +88,7 @@ async def replace_workflowtask(
                 _args_parallel = replace.args_parallel
 
     # If user's changes to `meta_non_parallel` are compatible with new task,
-    # keep them;
-    # else, get `meta_non_parallel` from new task
+    # keep them; else, get `meta_non_parallel` from new task
     if (
         old_workflow_task.meta_non_parallel
         != old_workflow_task.task.meta_non_parallel
@@ -107,12 +105,10 @@ async def replace_workflowtask(
         _meta_parallel = task.meta_parallel
 
     new_workflow_task = WorkflowTaskV2(
-        # new task
-        task_type=task.type,
         task_id=task.id,
+        task_type=task.type,
         task=task,
-        # old values
-        order=old_workflow_task.order,
+        # old-task values
         input_filters=old_workflow_task.input_filters,
         # possibly new values
         args_non_parallel=_args_non_parallel,
@@ -121,11 +117,11 @@ async def replace_workflowtask(
         meta_parallel=_meta_parallel,
     )
 
-    await db.delete(old_workflow_task)
-    workflow.task_list.insert(new_workflow_task.order, new_workflow_task)
-    flag_modified(workflow, "task_list")
+    workflow_task_order = old_workflow_task.order
+    workflow.task_list.remove(old_workflow_task)
+    workflow.task_list.insert(workflow_task_order, new_workflow_task)
     await db.commit()
-
+    await db.refresh(new_workflow_task)
     return new_workflow_task
 
 

fractal_server/app/runner/executors/slurm/sudo/_executor_wait_thread.py

@@ -9,6 +9,7 @@ from cfut import FileWaitThread
 
 from ......logger import set_logger
 from ._check_jobs_status import _jobs_finished
+from fractal_server.app.runner.exceptions import JobExecutionError
 
 logger = set_logger(__name__)
 
@@ -56,6 +57,10 @@ class FractalFileWaitThread(FileWaitThread):
         Note that (with respect to clusterfutures) we replaced `filename` with
         `filenames`.
         """
+        if self.shutdown:
+            error_msg = "Cannot call `wait` method after executor shutdown."
+            logger.warning(error_msg)
+            raise JobExecutionError(info=error_msg)
         with self.lock:
             self.waiting[filenames] = jobid
 

fractal_server/app/runner/executors/slurm/sudo/executor.py

@@ -331,6 +331,12 @@ class FractalSlurmExecutor(SlurmExecutor):
             Future representing the execution of the current SLURM job.
         """
 
+        # Do not continue if auxiliary thread was shut down
+        if self.wait_thread.shutdown:
+            error_msg = "Cannot call `submit` method after executor shutdown"
+            logger.warning(error_msg)
+            raise JobExecutionError(info=error_msg)
+
         # Set slurm_file_prefix
         slurm_file_prefix = task_files.file_prefix
 
@@ -395,6 +401,12 @@ class FractalSlurmExecutor(SlurmExecutor):
 
         """
 
+        # Do not continue if auxiliary thread was shut down
+        if self.wait_thread.shutdown:
+            error_msg = "Cannot call `map` method after executor shutdown"
+            logger.warning(error_msg)
+            raise JobExecutionError(info=error_msg)
+
         def _result_or_cancel(fut):
             """
             This function is based on the Python Standard Library 3.11.
@@ -546,6 +558,15 @@ class FractalSlurmExecutor(SlurmExecutor):
         Returns:
             Future representing the execution of the current SLURM job.
         """
+
+        # Prevent calling sbatch if auxiliary thread was shut down
+        if self.wait_thread.shutdown:
+            error_msg = (
+                "Cannot call `_submit_job` method after executor shutdown"
+            )
+            logger.warning(error_msg)
+            raise JobExecutionError(info=error_msg)
+
         fut: Future = Future()
 
         # Inject SLURM account (if set) into slurm_config
@@ -1207,6 +1228,9 @@ class FractalSlurmExecutor(SlurmExecutor):
                 logger.error(error_msg)
                 raise JobExecutionError(info=error_msg)
 
+        # Redudantly set thread shutdown attribute to True
+        self.wait_thread.shutdown = True
+
         logger.debug("Executor shutdown: end")
 
     def _stop_and_join_wait_thread(self):

fractal_server/app/security/__init__.py

@@ -59,7 +59,10 @@ from fractal_server.app.models import UserGroup
 from fractal_server.app.models import UserOAuth
 from fractal_server.app.models import UserSettings
 from fractal_server.app.schemas.user import UserCreate
+from fractal_server.app.security.signup_email import mail_new_oauth_signup
+from fractal_server.config import get_settings
 from fractal_server.logger import set_logger
+from fractal_server.syringe import Inject
 
 logger = set_logger(__name__)
 
@@ -211,8 +214,6 @@ class UserManager(IntegerIDMixin, BaseUserManager[UserOAuth, int]):
     async def on_after_register(
         self, user: UserOAuth, request: Optional[Request] = None
     ):
-        logger = set_logger("fractal_server.on_after_register")
-
         logger.info(
             f"New-user registration completed ({user.id=}, {user.email=})."
         )
@@ -248,6 +249,22 @@ class UserManager(IntegerIDMixin, BaseUserManager[UserOAuth, int]):
                 f"to '{this_user.email}'."
             )
 
+            # Send mail section
+            settings = Inject(get_settings)
+
+            if this_user.oauth_accounts and settings.MAIL_SETTINGS is not None:
+                try:
+                    mail_new_oauth_signup(
+                        msg=f"New user registered: '{this_user.email}'.",
+                        mail_settings=settings.MAIL_SETTINGS,
+                    )
+                except Exception as e:
+                    logger.error(
+                        "ERROR sending notification email after oauth "
+                        f"registration of {this_user.email}. "
+                        f"Original error: '{e}'."
+                    )
+
 
 async def get_user_manager(
     user_db: SQLModelUserDatabaseAsync = Depends(get_user_db),

fractal_server/app/security/signup_email.py

@@ -0,0 +1,39 @@
+import smtplib
+from email.message import EmailMessage
+from email.utils import formataddr
+
+from fractal_server.config import MailSettings
+
+
+def mail_new_oauth_signup(msg: str, mail_settings: MailSettings):
+    """
+    Send an email using the specified settings to notify a new OAuth signup.
+    """
+
+    mail_msg = EmailMessage()
+    mail_msg.set_content(msg)
+    mail_msg["From"] = formataddr((mail_settings.sender, mail_settings.sender))
+    mail_msg["To"] = ",".join(
+        [
+            formataddr((recipient, recipient))
+            for recipient in mail_settings.recipients
+        ]
+    )
+    mail_msg[
+        "Subject"
+    ] = f"[Fractal, {mail_settings.instance_name}] New OAuth signup"
+
+    with smtplib.SMTP(mail_settings.smtp_server, mail_settings.port) as server:
+        server.ehlo()
+        if mail_settings.use_starttls:
+            server.starttls()
+            server.ehlo()
+
+        server.login(
+            user=mail_settings.sender, password=mail_settings.password
+        )
+        server.sendmail(
+            from_addr=mail_settings.sender,
+            to_addrs=mail_settings.recipients,
+            msg=mail_msg.as_string(),
+        )

fractal_server/config.py

@@ -11,6 +11,7 @@
 # <exact-lab.it> under contract with Liberali Lab from the Friedrich Miescher
 # Institute for Biomedical Research and Pelkmans Lab from the University of
 # Zurich.
+import json
 import logging
 import shutil
 import sys
@@ -21,9 +22,11 @@ from typing import Literal
 from typing import Optional
 from typing import TypeVar
 
+from cryptography.fernet import Fernet
 from dotenv import load_dotenv
 from pydantic import BaseModel
 from pydantic import BaseSettings
+from pydantic import EmailStr
 from pydantic import Field
 from pydantic import root_validator
 from pydantic import validator
@@ -32,6 +35,29 @@ from sqlalchemy.engine import URL
 import fractal_server
 
 
+class MailSettings(BaseModel):
+    """
+    Schema for `MailSettings`
+
+    Attributes:
+        sender: Sender email address
+        recipients: List of recipients email address
+        smtp_server: SMTP server address
+        port: SMTP server port
+        password: Sender password
+        instance_name: Name of SMTP server instance
+        use_starttls: Using or not security protocol
+    """
+
+    sender: EmailStr
+    recipients: list[EmailStr] = Field(min_items=1)
+    smtp_server: str
+    port: int
+    password: str
+    instance_name: str
+    use_starttls: bool
+
+
 class FractalConfigurationError(RuntimeError):
     pass
 
@@ -492,6 +518,39 @@ class Settings(BaseSettings):
     Whether to include the v1 API.
     """
 
+    FRACTAL_PIP_CACHE_DIR: Optional[str] = None
+    """
+    Absolute path to the cache directory for `pip`; if unset,
+    `--no-cache-dir` is used.
+    """
+
+    @validator("FRACTAL_PIP_CACHE_DIR", always=True)
+    def absolute_FRACTAL_PIP_CACHE_DIR(cls, v):
+        """
+        If `FRACTAL_PIP_CACHE_DIR` is a relative path, fail.
+        """
+        if v is None:
+            return None
+        elif not Path(v).is_absolute():
+            raise FractalConfigurationError(
+                f"Non-absolute value for FRACTAL_PIP_CACHE_DIR={v}"
+            )
+        else:
+            return v
+
+    @property
+    def PIP_CACHE_DIR_ARG(self) -> str:
+        """
+        Option for `pip install`, based on `FRACTAL_PIP_CACHE_DIR` value.
+
+        If `FRACTAL_PIP_CACHE_DIR` is set, then return
+        `--cache-dir /somewhere`; else return `--no-cache-dir`.
+        """
+        if self.FRACTAL_PIP_CACHE_DIR is not None:
+            return f"--cache-dir {self.FRACTAL_PIP_CACHE_DIR}"
+        else:
+            return "--no-cache-dir"
+
     FRACTAL_MAX_PIP_VERSION: str = "24.0"
     """
     Maximum value at which to update `pip` before performing task collection.
@@ -527,9 +586,69 @@ class Settings(BaseSettings):
     FRACTAL_VIEWER_AUTHORIZATION_SCHEME is set to "users-folders".
     """
 
+    ###########################################################################
+    # SMTP SERVICE
+    ###########################################################################
+    FRACTAL_EMAIL_SETTINGS: Optional[str] = None
+    """
+    Encrypted version of settings dictionary, with keys `sender`, `password`,
+    `smtp_server`, `port`, `instance_name`, `use_starttls`.
+    """
+    FRACTAL_EMAIL_SETTINGS_KEY: Optional[str] = None
+    """
+    Key value for `cryptography.fernet` decrypt
+    """
+    FRACTAL_EMAIL_RECIPIENTS: Optional[str] = None
+    """
+    List of email receivers, separated with commas
+    """
+
+    @property
+    def MAIL_SETTINGS(self) -> Optional[MailSettings]:
+        if (
+            self.FRACTAL_EMAIL_SETTINGS is not None
+            and self.FRACTAL_EMAIL_SETTINGS_KEY is not None
+            and self.FRACTAL_EMAIL_RECIPIENTS is not None
+        ):
+            smpt_settings = (
+                Fernet(self.FRACTAL_EMAIL_SETTINGS_KEY)
+                .decrypt(self.FRACTAL_EMAIL_SETTINGS)
+                .decode("utf-8")
+            )
+            recipients = self.FRACTAL_EMAIL_RECIPIENTS.split(",")
+            mail_settings = MailSettings(
+                **json.loads(smpt_settings), recipients=recipients
+            )
+            return mail_settings
+        elif not all(
+            [
+                self.FRACTAL_EMAIL_RECIPIENTS is None,
+                self.FRACTAL_EMAIL_SETTINGS_KEY is None,
+                self.FRACTAL_EMAIL_SETTINGS is None,
+            ]
+        ):
+            raise ValueError(
+                "You must set all SMPT config variables: "
+                f"{self.FRACTAL_EMAIL_SETTINGS=}, "
+                f"{self.FRACTAL_EMAIL_RECIPIENTS=}, "
+                f"{self.FRACTAL_EMAIL_SETTINGS_KEY=}, "
+            )
+
     ###########################################################################
     # BUSINESS LOGIC
     ###########################################################################
+
+    def check_fractal_mail_settings(self):
+        """
+        Checks that the mail settings are properly set.
+        """
+        try:
+            self.MAIL_SETTINGS
+        except Exception as e:
+            raise FractalConfigurationError(
+                f"Invalid email configuration settings. Original error: {e}"
+            )
+
     def check_db(self) -> None:
         """
         Checks that db environment variables are properly set.
@@ -538,7 +657,6 @@ class Settings(BaseSettings):
             raise FractalConfigurationError("POSTGRES_DB cannot be None.")
 
     def check_runner(self) -> None:
-
         if not self.FRACTAL_RUNNER_WORKING_BASE_DIR:
             raise FractalConfigurationError(
                 "FRACTAL_RUNNER_WORKING_BASE_DIR cannot be None."
@@ -546,7 +664,6 @@ class Settings(BaseSettings):
 
         info = f"FRACTAL_RUNNER_BACKEND={self.FRACTAL_RUNNER_BACKEND}"
         if self.FRACTAL_RUNNER_BACKEND == "slurm":
-
             from fractal_server.app.runner.executors.slurm._slurm_config import (  # noqa: E501
                 load_slurm_config_file,
             )
@@ -637,12 +754,13 @@ class Settings(BaseSettings):
 
         self.check_db()
         self.check_runner()
+        self.check_fractal_mail_settings()
 
     def get_sanitized(self) -> dict:
         def _must_be_sanitized(string) -> bool:
             if not string.upper().startswith("FRACTAL") or any(
                 s in string.upper()
-                for s in ["PASSWORD", "SECRET", "PWD", "TOKEN"]
+                for s in ["PASSWORD", "SECRET", "PWD", "TOKEN", "KEY"]
             ):
                 return True
             else:

fractal_server/tasks/utils.py

@@ -6,6 +6,7 @@ from fractal_server.syringe import Inject
 COLLECTION_FILENAME = "collection.json"
 COLLECTION_LOG_FILENAME = "collection.log"
 COLLECTION_FREEZE_FILENAME = "collection_freeze.txt"
+FORBIDDEN_DEPENDENCY_STRINGS = ["github.com"]
 
 
 def get_absolute_venv_path_v1(venv_path: Path) -> Path:

fractal_server/tasks/v2/local/deactivate.py

@@ -15,6 +15,7 @@ from fractal_server.app.schemas.v2 import TaskGroupActivityActionV2
 from fractal_server.app.schemas.v2 import TaskGroupV2OriginEnum
 from fractal_server.app.schemas.v2.task_group import TaskGroupActivityStatusV2
 from fractal_server.logger import set_logger
+from fractal_server.tasks.utils import FORBIDDEN_DEPENDENCY_STRINGS
 from fractal_server.tasks.utils import get_log_path
 from fractal_server.tasks.v2.utils_background import get_current_log
 from fractal_server.tasks.v2.utils_templates import SCRIPTS_SUBFOLDER
@@ -189,6 +190,16 @@ def deactivate_local(
                             "task-group attributes."
                         )
 
+                # Fail if `pip_freeze` includes "github.com", see
+                # https://github.com/fractal-analytics-platform/fractal-server/issues/2142
+                for forbidden_string in FORBIDDEN_DEPENDENCY_STRINGS:
+                    if forbidden_string in task_group.pip_freeze:
+                        raise ValueError(
+                            "Deactivation and reactivation of task packages "
+                            f"with direct {forbidden_string} dependencies "
+                            "are not currently supported. Exit."
+                        )
+
                 # We now have all required information for reactivating the
                 # virtual environment at a later point
 

fractal_server/tasks/v2/local/reactivate.py

@@ -119,7 +119,6 @@ def reactivate_local(
                 )
                 logger.debug("end - create venv")
                 activity.log = get_current_log(log_file_path)
-                activity.timestamp_ended = get_timestamp()
                 activity = add_commit_refresh(obj=activity, db=db)
 
                 logger.debug("start - install from pip freeze")

fractal_server/tasks/v2/ssh/deactivate.py

@@ -16,6 +16,7 @@ from fractal_server.app.schemas.v2 import TaskGroupV2OriginEnum
 from fractal_server.app.schemas.v2.task_group import TaskGroupActivityStatusV2
 from fractal_server.logger import set_logger
 from fractal_server.ssh._fabric import FractalSSH
+from fractal_server.tasks.utils import FORBIDDEN_DEPENDENCY_STRINGS
 from fractal_server.tasks.utils import get_log_path
 from fractal_server.tasks.v2.utils_background import get_current_log
 from fractal_server.tasks.v2.utils_templates import SCRIPTS_SUBFOLDER
@@ -221,6 +222,16 @@ def deactivate_ssh(
                             "task-group attributes."
                         )
 
+                # Fail if `pip_freeze` includes "github", see
+                # https://github.com/fractal-analytics-platform/fractal-server/issues/2142
+                for forbidden_string in FORBIDDEN_DEPENDENCY_STRINGS:
+                    if forbidden_string in task_group.pip_freeze:
+                        raise ValueError(
+                            "Deactivation and reactivation of task packages "
+                            f"with direct {forbidden_string} dependencies "
+                            "are not currently supported. Exit."
+                        )
+
                 # We now have all required information for reactivating the
                 # virtual environment at a later point
 

fractal_server/tasks/v2/ssh/reactivate.py

@@ -159,7 +159,6 @@ def reactivate_ssh(
                 )
                 logger.debug("end - create venv")
                 activity.log = get_current_log(log_file_path)
-                activity.timestamp_ended = get_timestamp()
                 activity = add_commit_refresh(obj=activity, db=db)
 
                 logger.debug("start - install from pip freeze")

fractal_server/tasks/v2/templates/2_pip_install.sh

@@ -7,9 +7,10 @@ write_log(){
 
 # Variables to be filled within fractal-server
 PACKAGE_ENV_DIR=__PACKAGE_ENV_DIR__
-INSTALL_STRING=__INSTALL_STRING__
+INSTALL_STRING="__INSTALL_STRING__"
 PINNED_PACKAGE_LIST="__PINNED_PACKAGE_LIST__"
 FRACTAL_MAX_PIP_VERSION="__FRACTAL_MAX_PIP_VERSION__"
+FRACTAL_PIP_CACHE_DIR_ARG="__FRACTAL_PIP_CACHE_DIR_ARG__"
 
 TIME_START=$(date +%s)
 
@@ -17,8 +18,8 @@ VENVPYTHON=${PACKAGE_ENV_DIR}/bin/python
 
 # Upgrade `pip` and install `setuptools`
 write_log "START upgrade pip and install setuptools"
-"$VENVPYTHON" -m pip install --no-cache-dir "pip<=${FRACTAL_MAX_PIP_VERSION}" --upgrade
-"$VENVPYTHON" -m pip install --no-cache-dir setuptools
+"$VENVPYTHON" -m pip install ${FRACTAL_PIP_CACHE_DIR_ARG} "pip<=${FRACTAL_MAX_PIP_VERSION}" --upgrade
+"$VENVPYTHON" -m pip install ${FRACTAL_PIP_CACHE_DIR_ARG} setuptools
 write_log "END   upgrade pip and install setuptools"
 echo
 
@@ -41,7 +42,7 @@ if [ "$PINNED_PACKAGE_LIST" != "" ]; then
     done
 
     write_log "All packages in ${PINNED_PACKAGE_LIST} are already installed, proceed with specific versions."
-    "$VENVPYTHON" -m pip install --no-cache-dir "$PINNED_PACKAGE_LIST"
+    "$VENVPYTHON" -m pip install ${FRACTAL_PIP_CACHE_DIR_ARG} "$PINNED_PACKAGE_LIST"
     write_log "END installing pinned versions $PINNED_PACKAGE_LIST"
 else
     write_log "SKIP installing pinned versions $PINNED_PACKAGE_LIST (empty list)"

fractal_server/tasks/v2/templates/6_pip_install_from_freeze.sh

@@ -9,6 +9,7 @@ write_log(){
 PACKAGE_ENV_DIR=__PACKAGE_ENV_DIR__
 PIP_FREEZE_FILE=__PIP_FREEZE_FILE__
 FRACTAL_MAX_PIP_VERSION=__FRACTAL_MAX_PIP_VERSION__
+FRACTAL_PIP_CACHE_DIR_ARG="__FRACTAL_PIP_CACHE_DIR_ARG__"
 
 TIME_START=$(date +%s)
 
@@ -16,14 +17,14 @@ VENVPYTHON=${PACKAGE_ENV_DIR}/bin/python
 
 # Upgrade `pip` and install `setuptools`
 write_log "START upgrade pip and install setuptools"
-"$VENVPYTHON" -m pip install --no-cache-dir "pip<=${FRACTAL_MAX_PIP_VERSION}" --upgrade
-"$VENVPYTHON" -m pip install --no-cache-dir setuptools
+"$VENVPYTHON" -m pip install ${FRACTAL_PIP_CACHE_DIR_ARG} "pip<=${FRACTAL_MAX_PIP_VERSION}" --upgrade
+"$VENVPYTHON" -m pip install ${FRACTAL_PIP_CACHE_DIR_ARG} setuptools
 write_log "END   upgrade pip and install setuptools"
 echo
 
 # Install from pip-freeze file
 write_log "START installing requirements from ${PIP_FREEZE_FILE}"
-"$VENVPYTHON" -m pip install -r "${PIP_FREEZE_FILE}"
+"$VENVPYTHON" -m pip install ${FRACTAL_PIP_CACHE_DIR_ARG} -r "${PIP_FREEZE_FILE}"
 write_log "END   installing requirements from ${PIP_FREEZE_FILE}"
 echo
 

fractal_server/tasks/v2/utils_templates.py

@@ -81,6 +81,7 @@ def get_collection_replacements(
             "__FRACTAL_MAX_PIP_VERSION__",
             settings.FRACTAL_MAX_PIP_VERSION,
         ),
+        ("__FRACTAL_PIP_CACHE_DIR_ARG__", settings.PIP_CACHE_DIR_ARG),
         (
             "__PINNED_PACKAGE_LIST__",
             task_group.pinned_package_versions_string,

fractal_server/urls.py

@@ -2,12 +2,13 @@ from os.path import normpath
 
 
 def normalize_url(url: str) -> str:
+    url = url.strip()
     if url.startswith("/"):
         return normpath(url)
     elif url.startswith("s3"):
         # It would be better to have a NotImplementedError
         # but Pydantic Validation + FastAPI require
         # ValueError, TypeError or AssertionError
-        raise ValueError("S3 handling not implemented yet")
+        raise ValueError("S3 handling not implemented yet.")
     else:
         raise ValueError("URLs must begin with '/' or 's3'.")

{fractal_server-2.10.1.dist-info → fractal_server-2.10.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fractal-server
-Version: 2.10.1
+Version: 2.10.3
 Summary: Server component of the Fractal analytics platform
 Home-page: https://github.com/fractal-analytics-platform/fractal-server
 License: BSD-3-Clause
@@ -15,6 +15,7 @@ Classifier: Programming Language :: Python :: 3.12
 Requires-Dist: alembic (>=1.13.1,<2.0.0)
 Requires-Dist: cloudpickle (>=3.0.0,<3.1.0)
 Requires-Dist: clusterfutures (>=0.5,<0.6)
+Requires-Dist: cryptography (>=44.0.0,<44.1.0)
 Requires-Dist: fabric (>=3.2.2,<4.0.0)
 Requires-Dist: fastapi (>=0.115.0,<0.116.0)
 Requires-Dist: fastapi-users[oauth] (>=14,<15)

{fractal_server-2.10.1.dist-info → fractal_server-2.10.3.dist-info}/RECORD

@@ -1,5 +1,5 @@
-fractal_server/__init__.py,sha256=mGoPL5QC9hw_tGv5lsEM4M_0NMrtig40cMpwnjY5kto,23
-fractal_server/__main__.py,sha256=dEkCfzLLQrIlxsGC-HBfoR-RBMWnJDgNrxYTyzmE9c0,6146
+fractal_server/__init__.py,sha256=rYclpU8ceRdk5UXfl7ivOwKeHGWqQLFzTFUQXjy6mvA,23
+fractal_server/__main__.py,sha256=D2YTmSowmXNyvqOjW_HeItCZT2UliWlySl_owicaZg0,8026
 fractal_server/alembic.ini,sha256=MWwi7GzjzawI9cCAK1LW7NxIBQDUqD12-ptJoq5JpP0,3153
 fractal_server/app/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/app/db/__init__.py,sha256=wup2wcOkyOh8Vd0Xm76PZn_naxeMqaL4eF8DHHXTGlI,2889
@@ -53,13 +53,13 @@ fractal_server/app/routes/api/v2/project.py,sha256=eWYFJ7F2ZYQcpi-_n-rhPF-Q4gJhz
 fractal_server/app/routes/api/v2/status.py,sha256=6N9DSZ4iFqbZImorWfEAPoyoFUgEruo4Hweqo0x0xXU,6435
 fractal_server/app/routes/api/v2/submit.py,sha256=cQwt0oK8xjHMGA_bQrw4Um8jd_aCvgmWfoqSQDh12hQ,8246
 fractal_server/app/routes/api/v2/task.py,sha256=K0ik33t7vL8BAK5S7fqyJDNdRK4stGqb_73bSa8tvPE,7159
-fractal_server/app/routes/api/v2/task_collection.py,sha256=snX_E3OSBsgjbVwQMgKvV7pLmfNGD0OyqgAsxSGtB5E,12359
+fractal_server/app/routes/api/v2/task_collection.py,sha256=9p8w9UnN6RFszC1ohy9Uo3I4HIMVdfD8fYGWuQqzxMU,12682
 fractal_server/app/routes/api/v2/task_collection_custom.py,sha256=cctW61-C2QYF2KXluS15lLhZJS_kt30Ca6UGLFO32z0,6207
 fractal_server/app/routes/api/v2/task_group.py,sha256=4o2N0z7jK7VUVlJZMM4GveCCc4JKxYJx9-PMmsYIlJQ,8256
 fractal_server/app/routes/api/v2/task_group_lifecycle.py,sha256=3o9bCC8ubMwffQPPaxQZy-CjH9IB2RkIReIecI6L2_w,9300
 fractal_server/app/routes/api/v2/workflow.py,sha256=vjCNRzMHaAB4YWbAEWGlELHXDN4GjtE26IkIiB15RGM,8682
 fractal_server/app/routes/api/v2/workflow_import.py,sha256=-7Er3FWGF_1xI2qHFO9gfLVQAok5bojd7mbzQxa9Ofw,10858
-fractal_server/app/routes/api/v2/workflowtask.py,sha256=opA6hYfscPmoPhD-Xx1Z9DDeUf9Nnoo6jF2LUdNyGhM,10771
+fractal_server/app/routes/api/v2/workflowtask.py,sha256=dh8IxFSx50dY7kXldr9vC_NdQrFqv_heefOuZBX-7XE,10714
 fractal_server/app/routes/auth/__init__.py,sha256=fao6CS0WiAjHDTvBzgBVV_bSXFpEAeDBF6Z6q7rRkPc,1658
 fractal_server/app/routes/auth/_aux_auth.py,sha256=ifkNocTYatBSMYGwiR14qohmvR9SfMldceiEj6uJBrU,4783
 fractal_server/app/routes/auth/current_user.py,sha256=I3aVY5etWAJ_SH6t65Mj5TjvB2X8sAGuu1KG7FxLyPU,5883
@@ -90,9 +90,9 @@ fractal_server/app/runner/executors/slurm/ssh/_slurm_job.py,sha256=rwlqZzoGo4SAb
 fractal_server/app/runner/executors/slurm/ssh/executor.py,sha256=U2-tNE_5ECHFIoXjEvBlaSXKaIf-1IXZlDs0c34mab8,54110
 fractal_server/app/runner/executors/slurm/sudo/__init__.py,sha256=Cjn1rYvljddi96tAwS-qqGkNfOcfPzjChdaEZEObCcM,65
 fractal_server/app/runner/executors/slurm/sudo/_check_jobs_status.py,sha256=wAgwpVcr6JIslKHOuS0FhRa_6T1KCManyRJqA-fifzw,1909
-fractal_server/app/runner/executors/slurm/sudo/_executor_wait_thread.py,sha256=z5LlhaiqAb8pHsF1WwdzXN39C5anQmwjo1rSQgtRAYE,4422
+fractal_server/app/runner/executors/slurm/sudo/_executor_wait_thread.py,sha256=uRRyVHQtK9McHCB6OsjYfDnQsu2E8At9K_UYb_pe2pg,4682
 fractal_server/app/runner/executors/slurm/sudo/_subprocess_run_as_user.py,sha256=g8wqUjSicN17UZVXlfaMomYZ-xOIbBu1oE7HdJTzfvw,5218
-fractal_server/app/runner/executors/slurm/sudo/executor.py,sha256=CAIPFMmsjQLxmjN8Kdpq0OlZIX9PZIiRo0XO1quKWEM,46495
+fractal_server/app/runner/executors/slurm/sudo/executor.py,sha256=FVgx2mxqCLOhSoH3UTAeNc0BT0eJaxHMglGzGYePGPM,47439
 fractal_server/app/runner/executors/slurm/utils_executors.py,sha256=naPyJI0I3lD-sYHbSXbMFGUBK4h_SggA5V91Z1Ch1Xg,1416
 fractal_server/app/runner/extract_archive.py,sha256=tLpjDrX47OjTNhhoWvm6iNukg8KoieWyTb7ZfvE9eWU,2483
 fractal_server/app/runner/filenames.py,sha256=9lwu3yB4C67yiijYw8XIKaLFn3mJUt6_TCyVFM_aZUQ,206
@@ -161,9 +161,10 @@ fractal_server/app/schemas/v2/task_collection.py,sha256=9c_yyFcVBXdAZpQQniy1bROh
 fractal_server/app/schemas/v2/task_group.py,sha256=EPQ1WHjIA8WDrpsTfvfRESjwUVzu6jKiaKZx45b36N4,3215
 fractal_server/app/schemas/v2/workflow.py,sha256=-KWvXnbHBFA3pj5n7mfSyLKJQSqkJmoziIEe7mpLl3M,1875
 fractal_server/app/schemas/v2/workflowtask.py,sha256=FthKErVgx3a-k7WVk3nqJe1G-fl_iHND4rVrDXJ0F84,5942
-fractal_server/app/security/__init__.py,sha256=MlWVrLFPj9M2Gug-k8yATM-Cw066RugVU4KK6kMRbnQ,13019
+fractal_server/app/security/__init__.py,sha256=UmFnFFGM9WB_7b0itBi0b9uOIUWx_tcA2rCRaTNXErU,13778
+fractal_server/app/security/signup_email.py,sha256=hzzHxoEizl6IPVeB0j9Ek_tKIalGRxH6npzWUyGkCc4,1164
 fractal_server/app/user_settings.py,sha256=OP1yiYKtPadxwM51_Q0hdPk3z90TCN4z1BLpQsXyWiU,1316
-fractal_server/config.py,sha256=wRWJqyEeH4j2puH-fGlCYKLoKFh9pzRsQkS6q1VtO9M,23173
+fractal_server/config.py,sha256=9rAzw7OO6ZeHEz-I8NJHuGoHf4xCHxfFLyRNZQD9ytY,27019
 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
@@ -208,7 +209,7 @@ fractal_server/ssh/_fabric.py,sha256=lNy4IX1I4We6VoWa4Bz4fUPuApLMSoejpyE6I3jDZeM
 fractal_server/string_tools.py,sha256=XtMNsr5R7GmgzmFi68zkKMedHs8vjGoVMMCXqWhIk9k,2568
 fractal_server/syringe.py,sha256=3qSMW3YaMKKnLdgnooAINOPxnCOxP7y2jeAQYB21Gdo,2786
 fractal_server/tasks/__init__.py,sha256=kadmVUoIghl8s190_Tt-8f-WBqMi8u8oU4Pvw39NHE8,23
-fractal_server/tasks/utils.py,sha256=2ShlUSOXx53IiZT72dTCF31xXoLX9P8bY18vMj2m-mc,1059
+fractal_server/tasks/utils.py,sha256=gA9nYAviWKAMJmaF5RtoT2InddU6dCT2qA6fZTYNGO4,1105
 fractal_server/tasks/v1/_TaskCollectPip.py,sha256=ARq5AoHYXH0hziEsb-nFAqbsLA-VIddXOdXL38O6_zA,3746
 fractal_server/tasks/v1/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/tasks/v1/background_operations.py,sha256=0Zm8TT_RV0BxJCXbruYJCu1eXOkEcHpqnWn_BEe7huw,11829
@@ -219,29 +220,29 @@ fractal_server/tasks/v2/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG
 fractal_server/tasks/v2/local/__init__.py,sha256=9RVItnS7OyLsJOuJjWMCicaky4ASUPQEYD4SzDs0hOE,141
 fractal_server/tasks/v2/local/_utils.py,sha256=EvhmVwYjqaNyDCUMEsTWYOUXLgEwR1xr6bu32apCEI8,2491
 fractal_server/tasks/v2/local/collect.py,sha256=JuMplfREqrPvVEGlT5kJhcmZXC_iYlwvNlkgFrCaCC0,12107
-fractal_server/tasks/v2/local/deactivate.py,sha256=XR1nvJY3mKCRqwPwV79rVaQmtb3J83KdmJKjTOHD-cU,9250
-fractal_server/tasks/v2/local/reactivate.py,sha256=R3rArAzUpMGf6xa3dGVwwXHW9WVDi5ia28AFisZsqNc,6112
+fractal_server/tasks/v2/local/deactivate.py,sha256=SOFtOaR5yYm3IkbOw48TrQgzEpONQ9647KvyD_zImr8,9899
+fractal_server/tasks/v2/local/reactivate.py,sha256=MeUZHx8IKrfTEf-pXlfYms8I4o-26co3jdNgSNAvw60,6053
 fractal_server/tasks/v2/ssh/__init__.py,sha256=aSQbVi6Ummt9QzcSLWNmSqYjfdxrn9ROmqgH6bDpI7k,135
 fractal_server/tasks/v2/ssh/_utils.py,sha256=LjaEYVUJDChilu3YuhxuGWYRNnVJ_zqNE9SDHdRTIHY,2824
 fractal_server/tasks/v2/ssh/collect.py,sha256=2XXEPpl4LS22A75v_k4Bd46k46tmnLNZfceHyPi3kXo,13457
-fractal_server/tasks/v2/ssh/deactivate.py,sha256=Ffk_UuQSBUBNBCiviuKNhEUGyZPQa4_erJKFdwgMcE8,10616
-fractal_server/tasks/v2/ssh/reactivate.py,sha256=jdO8iyzavzSVPcOpIZrYSEkGPYTvz5XJ5h_5-nz9yzA,7896
+fractal_server/tasks/v2/ssh/deactivate.py,sha256=D8rfnC46davmDKZCipPdWZHDD4TIZ-4nr9vxZSV2aC0,11261
+fractal_server/tasks/v2/ssh/reactivate.py,sha256=cmdT2P1J0FwS1NYYRrhxHsSRyUZ5uu78hS3fDrSVbKo,7837
 fractal_server/tasks/v2/templates/1_create_venv.sh,sha256=PK0jdHKtQpda1zULebBaVPORt4t6V17wa4N1ohcj5ac,548
-fractal_server/tasks/v2/templates/2_pip_install.sh,sha256=RDDfbFnGOK3aRuHyXqDOUNCGullzAr0zS7BFqG1CJeE,1720
+fractal_server/tasks/v2/templates/2_pip_install.sh,sha256=Gpk2io8u9YaflFUlQu2NgkDQw5AA4m4AOVG1sB4yrHQ,1822
 fractal_server/tasks/v2/templates/3_pip_freeze.sh,sha256=JldREScEBI4cD_qjfX4UK7V4aI-FnX9ZvVNxgpSOBFc,168
 fractal_server/tasks/v2/templates/4_pip_show.sh,sha256=84NGHlg6JIbrQktgGKyfGsggPFzy6RBJuOmIpPUhsrw,1747
 fractal_server/tasks/v2/templates/5_get_venv_size_and_file_number.sh,sha256=q-6ZUvA6w6FDVEoSd9O63LaJ9tKZc7qAFH72SGPrd_k,284
-fractal_server/tasks/v2/templates/6_pip_install_from_freeze.sh,sha256=n9C8w76YraLbeTe7NhuLzvAQiJCm_akL3Mc3EMfxrHo,1007
+fractal_server/tasks/v2/templates/6_pip_install_from_freeze.sh,sha256=A2y8RngEjAcRhG-_owA6P7tAdrS_AszFuGXnaeMV8u0,1122
 fractal_server/tasks/v2/utils_background.py,sha256=tikXhggqxdU7EnKdx2co3UwinlDazEjfOPQOXtO58zs,4240
 fractal_server/tasks/v2/utils_database.py,sha256=g5m3sNPZKQ3AjflhPURDlAppQcIS5T1A8a1macdswBA,1268
 fractal_server/tasks/v2/utils_package_names.py,sha256=RDg__xrvQs4ieeVzmVdMcEh95vGQYrv9Hfal-5EDBM8,2393
 fractal_server/tasks/v2/utils_python_interpreter.py,sha256=5_wrlrTqXyo1YuLZvAW9hrSoh5MyLOzdPVUlUwM7uDQ,955
-fractal_server/tasks/v2/utils_templates.py,sha256=MS8zu24qimJSktZaHruPxkwIl81ZoUnIVGtnMHS4Y3o,2876
-fractal_server/urls.py,sha256=5o_qq7PzKKbwq12NHSQZDmDitn5RAOeQ4xufu-2v9Zk,448
+fractal_server/tasks/v2/utils_templates.py,sha256=07TZpJ0Mh_A4lXVXrrH2o1VLFFGwxeRumA6DdgMgCWk,2947
+fractal_server/urls.py,sha256=QjIKAC1a46bCdiPMu3AlpgFbcv6a4l3ABcd5xz190Og,471
 fractal_server/utils.py,sha256=utvmBx8K9I8hRWFquxna2pBaOqe0JifDL_NVPmihEJI,3525
 fractal_server/zip_tools.py,sha256=GjDgo_sf6V_DDg6wWeBlZu5zypIxycn_l257p_YVKGc,4876
-fractal_server-2.10.1.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
-fractal_server-2.10.1.dist-info/METADATA,sha256=r2HP2NsG-Jz9wcqob_X5XehPxQCzC8amUcW300aoPG4,4544
-fractal_server-2.10.1.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-fractal_server-2.10.1.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
-fractal_server-2.10.1.dist-info/RECORD,,
+fractal_server-2.10.3.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
+fractal_server-2.10.3.dist-info/METADATA,sha256=VeMNzjxlKvRgkyxQMzNMhNUArzpYkydFa7S4Fgcpaaw,4591
+fractal_server-2.10.3.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+fractal_server-2.10.3.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
+fractal_server-2.10.3.dist-info/RECORD,,