fractal-server 2.18.1__tar.gz → 2.18.3__tar.gz

{fractal_server-2.18.1 → fractal_server-2.18.3}/PKG-INFO

@@ -1,35 +1,29 @@
 Metadata-Version: 2.4
 Name: fractal-server
-Version: 2.18.1
+Version: 2.18.3
 Summary: Backend component of the Fractal analytics platform
+Author: Tommaso Comparin, Marco Franzon, Yuri Chiucconi, Jacopo Nespolo
+Author-email: Tommaso Comparin <tommaso.comparin@exact-lab.it>, Marco Franzon <marco.franzon@exact-lab.it>, Yuri Chiucconi <yuri.chiucconi@exact-lab.it>, Jacopo Nespolo <jacopo.nespolo@exact-lab.it>
 License-Expression: BSD-3-Clause
-License-File: LICENSE
-Author: Tommaso Comparin
-Author-email: tommaso.comparin@exact-lab.it
-Requires-Python: >=3.11,<3.15
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
-Classifier: Programming Language :: Python :: 3.13
-Classifier: Programming Language :: Python :: 3.14
-Requires-Dist: alembic (>=1.13.1,<2.0.0)
-Requires-Dist: fabric (>=3.2.2,<3.3.0)
-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: 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 (>=0.38.0,<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
-Project-URL: Repository, https://github.com/fractal-analytics-platform/fractal-server
+Requires-Dist: fastapi>=0.120.0,<0.121.0
+Requires-Dist: sqlmodel==0.0.27
+Requires-Dist: sqlalchemy[asyncio]>=2.0.23,<2.1
+Requires-Dist: fastapi-users[oauth]>=15,<16
+Requires-Dist: alembic>=1.13.1,<2.0.0
+Requires-Dist: uvicorn>=0.38.0,<0.39.0
+Requires-Dist: uvicorn-worker==0.4.0
+Requires-Dist: pydantic>=2.12.0,<2.13.0
+Requires-Dist: pydantic-settings==2.11.0
+Requires-Dist: packaging>=25.0.0,<26.0.0
+Requires-Dist: fabric>=3.2.2,<3.3.0
+Requires-Dist: gunicorn>=23.0,<24.0
+Requires-Dist: psycopg[binary]>=3.1.0,<4.0.0
+Requires-Dist: tomli-w>=1.2.0,<1.3.0
+Requires-Python: >=3.11, <3.15
 Project-URL: changelog, https://github.com/fractal-analytics-platform/fractal-server/blob/main/CHANGELOG.md
+Project-URL: documentation, https://fractal-analytics-platform.github.io/fractal-server
+Project-URL: homepage, https://github.com/fractal-analytics-platform/fractal-server
+Project-URL: repository, https://github.com/fractal-analytics-platform/fractal-server
 Description-Content-Type: text/markdown
 
 # Fractal Server
@@ -63,4 +57,3 @@ See https://fractal-analytics-platform.github.io/fractal-server.
 Fractal was conceived in the Liberali Lab at the Friedrich Miescher Institute for Biomedical Research and in the Pelkmans Lab at the University of Zurich by [@jluethi](https://github.com/jluethi) and [@gusqgm](https://github.com/gusqgm). The Fractal project is now developed at the [BioVisionCenter](https://www.biovisioncenter.uzh.ch/en.html) at the University of Zurich and the project lead is with [@jluethi](https://github.com/jluethi). The core development is done under contract by [eXact lab S.r.l.](https://www.exact-lab.it).
 
 Unless otherwise specified, Fractal components are released under the BSD 3-Clause License, and copyright is with the BioVisionCenter at the University of Zurich.
-

fractal_server-2.18.3/fractal_server/__init__.py

@@ -0,0 +1 @@
+__VERSION__ = "2.18.3"

{fractal_server-2.18.1 → fractal_server-2.18.3}/fractal_server/app/models/v2/task_group.py

@@ -71,8 +71,6 @@ class TaskGroupV2(SQLModel, table=True):
     )
     env_info: str | None = None
     venv_path: str | None = None
-    venv_size_in_kB: int | None = None
-    venv_file_number: int | None = None
 
     active: bool = True
     timestamp_created: datetime = Field(

{fractal_server-2.18.1 → fractal_server-2.18.3}/fractal_server/app/routes/admin/v2/job.py

@@ -17,6 +17,7 @@ from fractal_server.app.models import UserOAuth
 from fractal_server.app.models.v2 import HistoryRun
 from fractal_server.app.models.v2 import HistoryUnit
 from fractal_server.app.models.v2 import JobV2
+from fractal_server.app.models.v2.project import ProjectV2
 from fractal_server.app.routes.auth import current_superuser_act
 from fractal_server.app.routes.aux._job import _write_shutdown_file
 from fractal_server.app.routes.aux._runner import _check_shutdown_is_supported
@@ -37,6 +38,7 @@ router = APIRouter()
 @router.get("/", response_model=PaginationResponse[JobRead])
 async def view_job(
     id: int | None = None,
+    resource_id: int | None = None,
     user_id: int | None = None,
     project_id: int | None = None,
     dataset_id: int | None = None,
@@ -84,6 +86,13 @@ async def view_job(
     if id is not None:
         stm = stm.where(JobV2.id == id)
         stm_count = stm_count.where(JobV2.id == id)
+    if resource_id is not None:
+        stm = stm.join(ProjectV2, ProjectV2.id == JobV2.project_id).where(
+            ProjectV2.resource_id == resource_id
+        )
+        stm_count = stm_count.join(
+            ProjectV2, ProjectV2.id == JobV2.project_id
+        ).where(ProjectV2.resource_id == resource_id)
     if user_id is not None:
         stm = (
             stm.join(

{fractal_server-2.18.1 → fractal_server-2.18.3}/fractal_server/app/routes/api/v2/_aux_functions_history.py

@@ -19,6 +19,7 @@ from fractal_server.app.routes.api.v2._aux_functions import _get_workflow_or_404
 from fractal_server.app.routes.api.v2._aux_functions import (
     _get_workflowtask_or_404,
 )
+from fractal_server.app.schemas.v2.job import JobStatusType
 from fractal_server.app.schemas.v2.sharing import ProjectPermissions
 from fractal_server.logger import set_logger
 from fractal_server.zip_tools import _read_single_file_from_zip
@@ -70,6 +71,7 @@ def read_log_file(
     dataset_id: int,
     logfile: str,
     job_working_dir: str,
+    job_status: JobStatusType,
 ) -> str:
     """
     Returns the contents of a Job's log file, either directly from the working
@@ -93,12 +95,18 @@ def read_log_file(
             return _read_single_file_from_zip(
                 file_path=relative_logfile, archive_path=archive_path
             )
-
         else:
-            logger.error(
-                f"Error while retrieving logs for {logfile=} and "
-                f"{archive_path=}: both files do not exist."
-            )
+            match job_status:
+                case JobStatusType.SUBMITTED:
+                    logger.info(
+                        f"Neither {logfile=} nor {archive_path=} exist "
+                        "(for submitted job)."
+                    )
+                case _:
+                    logger.warning(
+                        f"Error while retrieving logs for {logfile=} and "
+                        f"{archive_path=}."
+                    )
             return (
                 f"Logs for task '{task_name}' in dataset "
                 f"{dataset_id} are not available."

{fractal_server-2.18.1 → fractal_server-2.18.3}/fractal_server/app/routes/api/v2/history.py

@@ -458,11 +458,11 @@ async def get_image_log(
 
     # Get job.working_dir
     res = await db.execute(
-        select(JobV2.working_dir)
+        select(JobV2.working_dir, JobV2.status)
         .join(HistoryRun, HistoryRun.job_id == JobV2.id)
         .where(HistoryRun.id == history_unit.history_run_id)
     )
-    job_working_dir = res.scalar_one_or_none()
+    job_working_dir, job_status = res.one()
 
     # Get log or placeholder text
     log = read_log_file(
@@ -470,6 +470,7 @@ async def get_image_log(
         task_name=wftask.task.name,
         dataset_id=request_data.dataset_id,
         job_working_dir=job_working_dir,
+        job_status=job_status,
     )
     return JSONResponse(content=log)
 
@@ -525,6 +526,7 @@ async def get_history_unit_log(
         task_name=wftask.task.name,
         dataset_id=dataset_id,
         job_working_dir=job.working_dir,
+        job_status=job.status,
     )
     return JSONResponse(content=log)
 

{fractal_server-2.18.1 → fractal_server-2.18.3}/fractal_server/app/routes/api/v2/job.py

@@ -54,7 +54,8 @@ async def get_user_jobs(
             LinkUserProjectV2, LinkUserProjectV2.project_id == JobV2.project_id
         )
         .where(LinkUserProjectV2.user_id == user.id)
-        .where(LinkUserProjectV2.is_owner.is_(True))
+        .where(LinkUserProjectV2.is_verified.is_(True))
+        .order_by(JobV2.start_timestamp.desc())
     )
     res = await db.execute(stm)
     job_list = res.scalars().all()
@@ -86,8 +87,11 @@ async def get_workflow_jobs(
         required_permissions=ProjectPermissions.READ,
         db=db,
     )
-    stm = select(JobV2).where(JobV2.workflow_id == workflow_id)
-    res = await db.execute(stm)
+    res = await db.execute(
+        select(JobV2)
+        .where(JobV2.workflow_id == workflow_id)
+        .order_by(JobV2.start_timestamp.desc())
+    )
     job_list = res.scalars().all()
     return job_list
 
@@ -212,8 +216,11 @@ async def get_job_list(
         db=db,
     )
 
-    stm = select(JobV2).where(JobV2.project_id == project.id)
-    res = await db.execute(stm)
+    res = await db.execute(
+        select(JobV2)
+        .where(JobV2.project_id == project.id)
+        .order_by(JobV2.start_timestamp.desc())
+    )
     job_list = res.scalars().all()
     await db.close()
     if not log:

{fractal_server-2.18.1 → fractal_server-2.18.3}/fractal_server/app/routes/auth/oauth.py

@@ -3,6 +3,8 @@ from httpx_oauth.clients.github import GitHubOAuth2
 from httpx_oauth.clients.google import GoogleOAuth2
 from httpx_oauth.clients.openid import OpenID
 from httpx_oauth.clients.openid import OpenIDConfigurationError
+from httpx_oauth.exceptions import GetIdEmailError
+from httpx_oauth.exceptions import GetProfileError
 
 from fractal_server.config import OAuthSettings
 from fractal_server.config import get_oauth_settings
@@ -13,6 +15,29 @@ from . import cookie_backend
 from . import fastapi_users
 
 
+class FractalOpenID(OpenID):
+    """
+    Subclass of `httpx_oauth.clients.openid.OpenID` with customizable name for
+    the `"email"` claim.
+    """
+
+    def __init__(self, *, email_claim: str, **kwargs):
+        super().__init__(**kwargs)
+        self.email_claim = email_claim
+
+    # TODO-requires-py312: add `@override` decorator
+    async def get_id_email(self, token: str) -> tuple[str, str | None]:
+        """
+        Identical to the parent-class method (httpx-oauth version 0.16.1),
+        apart from making `"email"` configurable.
+        """
+        try:
+            profile = await self.get_profile(token)
+        except GetProfileError as e:
+            raise GetIdEmailError(response=e.response) from e
+        return str(profile["sub"]), profile.get(self.email_claim)
+
+
 def _create_client_github(cfg: OAuthSettings) -> GitHubOAuth2:
     return GitHubOAuth2(
         client_id=cfg.OAUTH_CLIENT_ID.get_secret_value(),
@@ -29,10 +54,11 @@ def _create_client_google(cfg: OAuthSettings) -> GoogleOAuth2:
 
 def _create_client_oidc(cfg: OAuthSettings) -> OpenID:
     try:
-        open_id = OpenID(
+        open_id = FractalOpenID(
             client_id=cfg.OAUTH_CLIENT_ID.get_secret_value(),
             client_secret=cfg.OAUTH_CLIENT_SECRET.get_secret_value(),
             openid_configuration_endpoint=cfg.OAUTH_OIDC_CONFIG_ENDPOINT.get_secret_value(),  # noqa
+            email_claim=cfg.OAUTH_EMAIL_CLAIM,
         )
     except OpenIDConfigurationError as e:
         OAUTH_OIDC_CONFIG_ENDPOINT = (

{fractal_server-2.18.1 → fractal_server-2.18.3}/fractal_server/app/schemas/v2/task_group.py

@@ -84,9 +84,6 @@ class TaskGroupRead(BaseModel):
     pinned_package_versions_pre: dict[str, str] = Field(default_factory=dict)
     pinned_package_versions_post: dict[str, str] = Field(default_factory=dict)
 
-    venv_size_in_kB: int | None = None
-    venv_file_number: int | None = None
-
     active: bool
     timestamp_created: AwareDatetime
     timestamp_last_used: AwareDatetime

{fractal_server-2.18.1 → fractal_server-2.18.3}/fractal_server/config/_oauth.py

@@ -28,6 +28,11 @@ class OAuthSettings(BaseSettings):
             String to be used as `redirect_url` argument in
             `fastapi_users.get_oauth_router`, and then in
             `httpx_oauth.integrations.fastapi.OAuth2AuthorizeCallback`.
+        OAUTH_EMAIL_CLAIM:
+            Name of the OIDC claim with the user's email address. This is
+            `"email"` by default, but can be customized (e.g. to `"mail"`) to
+            fit with the response from the userinfo endpoint - see
+            https://openid.net/specs/openid-connect-core-1_0.html#UserInfoResponse
     """
 
     model_config = SettingsConfigDict(**SETTINGS_CONFIG_DICT)
@@ -43,6 +48,7 @@ class OAuthSettings(BaseSettings):
     OAUTH_CLIENT_SECRET: SecretStr | None = None
     OAUTH_OIDC_CONFIG_ENDPOINT: SecretStr | None = None
     OAUTH_REDIRECT_URL: str | None = None
+    OAUTH_EMAIL_CLAIM: str = "email"
 
     @model_validator(mode="after")
     def check_configuration(self: Self) -> Self:

fractal_server-2.18.3/fractal_server/migrations/versions/068496367952_drop_taskgroup_venv_size_and_files_.py

@@ -0,0 +1,48 @@
+"""Drop TaskGroup venv size and files number
+
+Revision ID: 068496367952
+Revises: b7477cc98f45
+Create Date: 2025-12-10 15:24:47.720796
+
+"""
+
+import sqlalchemy as sa
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision = "068496367952"
+down_revision = "b7477cc98f45"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("taskgroupv2", schema=None) as batch_op:
+        batch_op.drop_column("venv_size_in_kB")
+        batch_op.drop_column("venv_file_number")
+
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("taskgroupv2", schema=None) as batch_op:
+        batch_op.add_column(
+            sa.Column(
+                "venv_file_number",
+                sa.INTEGER(),
+                autoincrement=False,
+                nullable=True,
+            )
+        )
+        batch_op.add_column(
+            sa.Column(
+                "venv_size_in_kB",
+                sa.INTEGER(),
+                autoincrement=False,
+                nullable=True,
+            )
+        )
+
+    # ### end Alembic commands ###

{fractal_server-2.18.1 → fractal_server-2.18.3}/fractal_server/runner/config/_slurm.py

@@ -35,6 +35,7 @@ class SlurmConfigSet(BaseModel):
         extra_lines:
         gpus:
         shebang_line: The shell shebang to use for SLURM jobs.
+        use_mem_per_cpu:
     """
 
     model_config = ConfigDict(extra="forbid")
@@ -51,6 +52,7 @@ class SlurmConfigSet(BaseModel):
     extra_lines: list[NonEmptyStr] = Field(default_factory=list)
     gpus: NonEmptyStr | None = None
     shebang_line: str = "#!/bin/sh"
+    use_mem_per_cpu: bool = False
 
 
 class BatchingConfigSet(BaseModel):

{fractal_server-2.18.1 → fractal_server-2.18.3}/fractal_server/runner/executors/call_command_wrapper.py

@@ -6,6 +6,18 @@ import subprocess  # nosec
 from fractal_server.runner.exceptions import TaskExecutionError
 from fractal_server.string_tools import validate_cmd
 
+MAX_LEN_STDERR = 100_000
+
+
+def placeholder_if_too_long(stderr: str) -> str:
+    """Returns a placeholder if the string is too long"""
+    if len(stderr) > MAX_LEN_STDERR:
+        return (
+            f"Cannot display stderr of length {len(stderr)}. You can find the "
+            "detailed logs by downloading the job-log folder."
+        )
+    return stderr
+
 
 def call_command_wrapper(*, cmd: str, log_path: str) -> None:
     """
@@ -46,6 +58,7 @@ def call_command_wrapper(*, cmd: str, log_path: str) -> None:
         if os.path.isfile(log_path):
             with open(log_path) as fp_stderr:
                 stderr = fp_stderr.read()
+            stderr = placeholder_if_too_long(stderr)
         raise TaskExecutionError(
             f"Task failed with returncode={result.returncode}.\n"
             f"STDERR: {stderr}"

{fractal_server-2.18.1 → fractal_server-2.18.3}/fractal_server/runner/executors/slurm_common/base_slurm_runner.py

@@ -365,7 +365,8 @@ class BaseSlurmRunner(BaseRunner):
 
         # Prepare SLURM preamble based on SlurmConfig object
         script_lines = slurm_config.to_sbatch_preamble(
-            remote_export_dir=self.user_cache_dir
+            remote_export_dir=self.user_cache_dir,
+            use_mem_per_cpu=slurm_config.use_mem_per_cpu,
         )
 
         # Extend SLURM preamble with variable which are not in SlurmConfig, and
@@ -389,11 +390,14 @@ class BaseSlurmRunner(BaseRunner):
         script_lines.append("\n")
 
         # Include command lines
-        mem_per_task_MB = slurm_config.mem_per_task_MB
         for cmd in cmdlines:
+            if slurm_config.use_mem_per_cpu:
+                mem_specific = f"--mem-per-cpu={slurm_config.mem_per_cpu_MB}MB"
+            else:
+                mem_specific = f"--mem={slurm_config.mem_per_task_MB}MB"
             script_lines.append(
                 "srun --ntasks=1 --cpus-per-task=$SLURM_CPUS_PER_TASK "
-                f"--mem={mem_per_task_MB}MB "
+                f"{mem_specific} "
                 f"{cmd} &"
             )
         script_lines.append("wait\n\n")

{fractal_server-2.18.1 → fractal_server-2.18.3}/fractal_server/runner/executors/slurm_common/slurm_config.py

@@ -42,6 +42,9 @@ class SlurmConfig(BaseModel):
         exclude: Corresponds to SLURM option.
         prefix: Prefix of configuration lines in SLURM submission scripts.
         shebang_line: Shebang line for SLURM submission scripts.
+        use_mem_per_cpu:
+            If `True`, use `--mem-per-cpu` rather than `--mem`, both at the job
+            level and for `srun` statements.
         extra_lines: Additional lines to include in SLURM submission scripts.
         tasks_per_job: Number of tasks for each SLURM job.
         parallel_tasks_per_job: Number of tasks to run in parallel for
@@ -70,9 +73,12 @@ class SlurmConfig(BaseModel):
     partition: str
     cpus_per_task: int
     mem_per_task_MB: int
+
     prefix: str = "#SBATCH"
     shebang_line: str = "#!/bin/sh"
 
+    use_mem_per_cpu: bool = False
+
     # Optional SLURM parameters
     job_name: str | None = None
     constraint: str | None = None
@@ -139,6 +145,7 @@ class SlurmConfig(BaseModel):
     def to_sbatch_preamble(
         self,
         remote_export_dir: str,
+        use_mem_per_cpu: bool = False,
     ) -> list[str]:
         """
         Compile `SlurmConfig` object into the preamble of a SLURM submission
@@ -148,6 +155,8 @@ class SlurmConfig(BaseModel):
             remote_export_dir:
                 Base directory for exports defined in
                 `self.user_local_exports`.
+            use_mem_per_cpu:
+                If `True`, use `--mem-per-cpu` rather than `--mem`.
         """
         if self.parallel_tasks_per_job is None:
             raise ValueError(
@@ -157,13 +166,18 @@ class SlurmConfig(BaseModel):
         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
+        if use_mem_per_cpu:
+            memory_line = f"{self.prefix} --mem-per-cpu={self.mem_per_cpu_MB}M"
+        else:
+            mem_per_job_MB = self.parallel_tasks_per_job * self.mem_per_task_MB
+            memory_line = f"{self.prefix} --mem={mem_per_job_MB}M"
+
         lines = [
             self.shebang_line,
             f"{self.prefix} --partition={self.partition}",
             f"{self.prefix} --ntasks={self.parallel_tasks_per_job}",
             f"{self.prefix} --cpus-per-task={self.cpus_per_task}",
-            f"{self.prefix} --mem={mem_per_job_MB}M",
+            memory_line,
         ]
         for key in [
             "job_name",
@@ -214,3 +228,7 @@ class SlurmConfig(BaseModel):
     @property
     def batch_size(self) -> int:
         return self.tasks_per_job
+
+    @property
+    def mem_per_cpu_MB(self) -> int:
+        return int(self.mem_per_task_MB / self.cpus_per_task)

{fractal_server-2.18.1 → fractal_server-2.18.3}/fractal_server/tasks/v2/local/collect.py

@@ -174,15 +174,6 @@ def collect_local(
                 activity.log = get_current_log(log_file_path)
                 activity = add_commit_refresh(obj=activity, db=db)
 
-                # Run script 5
-                venv_info = _customize_and_run_template(
-                    template_filename="5_get_venv_size_and_file_number.sh",
-                    **common_args,
-                )
-                venv_size, venv_file_number = venv_info.split()
-                activity.log = get_current_log(log_file_path)
-                activity = add_commit_refresh(obj=activity, db=db)
-
                 pkg_attrs = parse_script_pip_show_stdout(stdout)
                 for key, value in pkg_attrs.items():
                     logger.debug(f"Parsed from pip-show: {key}={value}")
@@ -241,18 +232,10 @@ def collect_local(
                 logger.info("create_db_tasks_and_update_task_group - end")
 
                 # Update task_group data
-                logger.info(
-                    "Add env_info, venv_size and venv_file_number "
-                    "to TaskGroupV2 - start"
-                )
+                logger.info("Add env_info to TaskGroupV2 - start")
                 task_group.env_info = pip_freeze_stdout
-                task_group.venv_size_in_kB = int(venv_size)
-                task_group.venv_file_number = int(venv_file_number)
                 task_group = add_commit_refresh(obj=task_group, db=db)
-                logger.info(
-                    "Add env_info, venv_size and venv_file_number "
-                    "to TaskGroupV2 - end"
-                )
+                logger.info("Add env_info to TaskGroupV2 - end")
 
                 # Finalize (write metadata to DB)
                 logger.info("finalising - START")

{fractal_server-2.18.1 → fractal_server-2.18.3}/fractal_server/tasks/v2/local/collect_pixi.py

@@ -175,8 +175,6 @@ def collect_local_pixi(
                 # Parse stdout
                 parsed_output = parse_collect_stdout(stdout)
                 package_root = parsed_output["package_root"]
-                venv_size = parsed_output["venv_size"]
-                venv_file_number = parsed_output["venv_file_number"]
                 project_python_wrapper = parsed_output["project_python_wrapper"]
 
                 # Make task folder 755
@@ -220,23 +218,15 @@ def collect_local_pixi(
                 logger.info("create_db_tasks_and_update_task_group - end")
 
                 # Update task_group data
-                logger.info(
-                    "Add env_info, venv_size and venv_file_number "
-                    "to TaskGroupV2 - start"
-                )
+                logger.info("Add env_info to TaskGroupV2 - start")
                 with Path(source_dir, "pixi.lock").open() as f:
                     pixi_lock_contents = f.read()
 
                 # NOTE: see issue 2626 about whether to keep `pixi.lock` files
                 # in the database
                 task_group.env_info = pixi_lock_contents
-                task_group.venv_size_in_kB = int(venv_size)
-                task_group.venv_file_number = int(venv_file_number)
                 task_group = add_commit_refresh(obj=task_group, db=db)
-                logger.info(
-                    "Add env_info, venv_size and venv_file_number "
-                    "to TaskGroupV2 - end"
-                )
+                logger.info("Add env_info to TaskGroupV2 - end")
 
                 # Finalize (write metadata to DB)
                 logger.info("finalising - START")

{fractal_server-2.18.1 → fractal_server-2.18.3}/fractal_server/tasks/v2/local/reactivate.py

@@ -121,7 +121,7 @@ def reactivate_local(
 
                 logger.debug("start - install from pip freeze")
                 _customize_and_run_template(
-                    template_filename="6_pip_install_from_freeze.sh",
+                    template_filename="5_pip_install_from_freeze.sh",
                     **common_args,
                 )
                 logger.debug("end - install from pip freeze")

{fractal_server-2.18.1 → fractal_server-2.18.3}/fractal_server/tasks/v2/ssh/collect.py

@@ -211,15 +211,6 @@ def collect_ssh(
                     activity.log = get_current_log(log_file_path)
                     activity = add_commit_refresh(obj=activity, db=db)
 
-                    # Run script 5
-                    venv_info = _customize_and_run_template(
-                        template_filename="5_get_venv_size_and_file_number.sh",
-                        **common_args,
-                    )
-                    venv_size, venv_file_number = venv_info.split()
-                    activity.log = get_current_log(log_file_path)
-                    activity = add_commit_refresh(obj=activity, db=db)
-
                     pkg_attrs = parse_script_pip_show_stdout(stdout)
 
                     for key, value in pkg_attrs.items():
@@ -275,18 +266,10 @@ def collect_ssh(
                     logger.info("create_db_tasks_and_update_task_group - end")
 
                     # Update task_group data
-                    logger.info(
-                        "Add env_info, venv_size and venv_file_number "
-                        "to TaskGroupV2 - start"
-                    )
+                    logger.info("Add env_info to TaskGroupV2 - start")
                     task_group.env_info = pip_freeze_stdout
-                    task_group.venv_size_in_kB = int(venv_size)
-                    task_group.venv_file_number = int(venv_file_number)
                     task_group = add_commit_refresh(obj=task_group, db=db)
-                    logger.info(
-                        "Add env_info, venv_size and venv_file_number "
-                        "to TaskGroupV2 - end"
-                    )
+                    logger.info("Add env_info to TaskGroupV2 - end")
 
                     # Finalize (write metadata to DB)
                     logger.info("finalising - START")

{fractal_server-2.18.1 → fractal_server-2.18.3}/fractal_server/tasks/v2/ssh/collect_pixi.py

@@ -266,8 +266,6 @@ def collect_ssh_pixi(
                     # Parse stdout
                     parsed_output = parse_collect_stdout(stdout)
                     package_root_remote = parsed_output["package_root"]
-                    venv_size = parsed_output["venv_size"]
-                    venv_file_number = parsed_output["venv_file_number"]
                     project_python_wrapper = parsed_output[
                         "project_python_wrapper"
                     ]
@@ -312,18 +310,10 @@ def collect_ssh_pixi(
                     )
 
                     # Update task_group data
-                    logger.info(
-                        "Add env_info, venv_size and venv_file_number "
-                        "to TaskGroupV2 - start"
-                    )
+                    logger.info("Add env_info to TaskGroupV2 - start")
                     task_group.env_info = pixi_lock_contents
-                    task_group.venv_size_in_kB = int(venv_size)
-                    task_group.venv_file_number = int(venv_file_number)
                     task_group = add_commit_refresh(obj=task_group, db=db)
-                    logger.info(
-                        "Add env_info, venv_size and venv_file_number "
-                        "to TaskGroupV2 - end"
-                    )
+                    logger.info("Add env_info to TaskGroupV2 - end")
 
                     # Finalize (write metadata to DB)
                     logger.info("finalising - START")

{fractal_server-2.18.1 → fractal_server-2.18.3}/fractal_server/tasks/v2/ssh/reactivate.py

@@ -167,7 +167,7 @@ def reactivate_ssh(
 
                     logger.info("start - install from pip freeze")
                     _customize_and_run_template(
-                        template_filename="6_pip_install_from_freeze.sh",
+                        template_filename="5_pip_install_from_freeze.sh",
                         **common_args,
                     )
                     logger.info("end - install from pip freeze")