fractal-server 2.3.2__py3-none-any.whl → 2.3.4__py3-none-any.whl

fractal_server/__init__.py

@@ -1 +1 @@
-__VERSION__ = "2.3.2"
+__VERSION__ = "2.3.4"

fractal_server/app/routes/api/__init__.py

@@ -2,9 +2,12 @@
 `api` module
 """
 from fastapi import APIRouter
+from fastapi import Depends
 
 from ....config import get_settings
 from ....syringe import Inject
+from ...models.security import UserOAuth
+from ...security import current_active_superuser
 
 
 router_api = APIRouter()
@@ -17,3 +20,9 @@ async def alive():
         alive=True,
         version=settings.PROJECT_VERSION,
     )
+
+
+@router_api.get("/settings/")
+async def view_settings(user: UserOAuth = Depends(current_active_superuser)):
+    settings = Inject(get_settings)
+    return settings.get_sanitized()

fractal_server/app/routes/api/v1/project.py

@@ -250,9 +250,18 @@ async def apply_workflow(
     db: AsyncSession = Depends(get_async_db),
 ) -> Optional[ApplyWorkflowReadV1]:
 
+    settings = Inject(get_settings)
+    if settings.FRACTAL_API_V1_MODE == "include_without_submission":
+        raise HTTPException(
+            status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
+            detail=(
+                "Legacy API is still accessible, "
+                "but the submission of legacy jobs is not available."
+            ),
+        )
+
     # Remove non-submitted V1 jobs from the app state when the list grows
     # beyond a threshold
-    settings = Inject(get_settings)
     if (
         len(request.app.state.jobsV1)
         > settings.FRACTAL_API_MAX_JOB_LIST_LENGTH

fractal_server/app/runner/compress_folder.py

@@ -1,120 +1,132 @@
-import shlex
-import subprocess  # nosec
+"""
+Wrap `tar` compression command.
+
+This module is used both locally (in the environment where `fractal-server`
+is running) and remotely (as a standalon Python module, executed over SSH).
+
+This is a twin-module of `extract_archive.py`.
+
+The reason for using the `tar` command via `subprocess` rather than Python
+built-in `tarfile` library has to do with performance issues we observed
+when handling files which were just created within a SLURM job, and in the
+context of a CephFS filesystem.
+"""
+import shutil
 import sys
-import tarfile
-import time
 from pathlib import Path
-from typing import Optional
 
+from fractal_server.app.runner.run_subprocess import run_subprocess
+from fractal_server.logger import get_logger
+from fractal_server.logger import set_logger
+
+
+def copy_subfolder(src: Path, dest: Path, logger_name: str):
+    cmd_cp = f"cp -r {src.as_posix()} {dest.as_posix()}"
+    logger = get_logger(logger_name=logger_name)
+    logger.debug(f"{cmd_cp=}")
+    res = run_subprocess(cmd=cmd_cp, logger_name=logger_name)
+    return res
+
+
+def create_tar_archive(
+    tarfile_path: Path,
+    subfolder_path_tmp_copy: Path,
+    logger_name: str,
+    remote_to_local: bool,
+):
+    logger = get_logger(logger_name)
+
+    if remote_to_local:
+        exclude_options = "--exclude *sbatch --exclude *_in_*.pickle "
+    else:
+        exclude_options = ""
+
+    cmd_tar = (
+        f"tar czf {tarfile_path} "
+        f"{exclude_options} "
+        f"--directory={subfolder_path_tmp_copy.as_posix()} "
+        "."
+    )
+    logger.debug(f"cmd tar:\n{cmd_tar}")
+    run_subprocess(cmd=cmd_tar, logger_name=logger_name)
 
-# COMPRESS_FOLDER_MODALITY = "python"
-COMPRESS_FOLDER_MODALITY = "cp-tar-rmtree"
 
+def remove_temp_subfolder(subfolder_path_tmp_copy: Path, logger_name: str):
+    logger = get_logger(logger_name)
+    try:
+        logger.debug(f"Now remove {subfolder_path_tmp_copy}")
+        shutil.rmtree(subfolder_path_tmp_copy)
+    except Exception as e:
+        logger.debug(f"ERROR during shutil.rmtree: {e}")
 
-def _filter(info: tarfile.TarInfo) -> Optional[tarfile.TarInfo]:
-    if info.name.endswith(".pickle"):
-        filename = info.name.split("/")[-1]
-        parts = filename.split("_")
-        if len(parts) == 3 and parts[1] == "in":
-            return None
-        elif len(parts) == 5 and parts[3] == "in":
-            return None
-    elif info.name.endswith("slurm_submit.sbatch"):
-        return None
-    return info
 
+def compress_folder(
+    subfolder_path: Path, remote_to_local: bool = False
+) -> str:
+    """
+    Compress e.g. `/path/archive` into `/path/archive.tar.gz`
 
-if __name__ == "__main__":
-    help_msg = (
-        "Expected use:\n"
-        "python -m fractal_server.app.runner.compress_folder "
-        "path/to/folder"
-    )
+    Note that `/path/archive.tar.gz` may already exist. In this case, it will
+    be overwritten.
 
-    if len(sys.argv[1:]) != 1:
-        raise ValueError(
-            "Invalid argument(s).\n" f"{help_msg}\n" f"Provided: {sys.argv=}"
-        )
+    Args:
+        subfolder_path: Absolute path to the folder to compress.
+        remote_to_local: If `True`, exclude some files from the tar.gz archive.
+
+    Returns:
+        Absolute path to the tar.gz archive.
+    """
 
-    subfolder_path = Path(sys.argv[1])
-    t_0 = time.perf_counter()
-    print("[compress_folder.py] START")
-    print(f"[compress_folder.py] {COMPRESS_FOLDER_MODALITY=}")
-    print(f"[compress_folder.py] {subfolder_path=}")
+    logger_name = "compress_folder"
+    logger = set_logger(logger_name)
 
-    job_folder = subfolder_path.parent
+    logger.debug("START")
+    logger.debug(f"{subfolder_path=}")
+    parent_dir = subfolder_path.parent
     subfolder_name = subfolder_path.name
-    tarfile_path = (job_folder / f"{subfolder_name}.tar.gz").as_posix()
-    print(f"[compress_folder.py] {tarfile_path=}")
-
-    if COMPRESS_FOLDER_MODALITY == "python":
-        raise NotImplementedError()
-        with tarfile.open(tarfile_path, "w:gz") as tar:
-            tar.add(
-                subfolder_path,
-                arcname=".",  # ????
-                recursive=True,
-                filter=_filter,
-            )
-    elif COMPRESS_FOLDER_MODALITY == "cp-tar-rmtree":
-        import shutil
-        import time
-
-        subfolder_path_tmp_copy = (
-            subfolder_path.parent / f"{subfolder_path.name}_copy"
-        )
+    tarfile_path = (parent_dir / f"{subfolder_name}.tar.gz").as_posix()
+    logger.debug(f"{tarfile_path=}")
 
-        t0 = time.perf_counter()
-        # shutil.copytree(subfolder_path, subfolder_path_tmp_copy)
-        cmd_cp = (
-            "cp -r "
-            f"{subfolder_path.as_posix()} "
-            f"{subfolder_path_tmp_copy.as_posix()}"
-        )
-        res = subprocess.run(  # nosec
-            shlex.split(cmd_cp),
-            check=True,
-            capture_output=True,
-            encoding="utf-8",
+    subfolder_path_tmp_copy = (
+        subfolder_path.parent / f"{subfolder_path.name}_copy"
+    )
+    try:
+        copy_subfolder(
+            subfolder_path, subfolder_path_tmp_copy, logger_name=logger_name
         )
-        t1 = time.perf_counter()
-        print("[compress_folder.py] `cp -r` END - " f"elapsed: {t1-t0:.3f} s")
-
-        cmd_tar = (
-            "tar czf "
-            f"{tarfile_path} "
-            "--exclude *sbatch --exclude *_in_*.pickle "
-            f"--directory={subfolder_path_tmp_copy.as_posix()} "
-            "."
+        create_tar_archive(
+            tarfile_path,
+            subfolder_path_tmp_copy,
+            logger_name=logger_name,
+            remote_to_local=remote_to_local,
         )
+        return tarfile_path
 
-        print(f"[compress_folder.py] cmd tar:\n{cmd_tar}")
-        t0 = time.perf_counter()
-        res = subprocess.run(  # nosec
-            shlex.split(cmd_tar),
-            capture_output=True,
-            encoding="utf-8",
-        )
-        t1 = time.perf_counter()
-        t_1 = time.perf_counter()
-        print(f"[compress_folder.py] tar END - elapsed: {t1-t0:.3f} s")
+    except Exception as e:
+        logger.debug(f"ERROR: {e}")
+        sys.exit(1)
 
-        print(f"[compress_folder] END - elapsed {t_1 - t_0:.3f} seconds")
+    finally:
+        remove_temp_subfolder(subfolder_path_tmp_copy, logger_name=logger_name)
 
-        if res.returncode != 0:
-            print("[compress_folder.py] ERROR in tar")
-            print(f"[compress_folder.py] tar stdout:\n{res.stdout}")
-            print(f"[compress_folder.py] tar stderr:\n{res.stderr}")
 
-            shutil.rmtree(subfolder_path_tmp_copy)
-            sys.exit(1)
+def main(sys_argv: list[str]):
+
+    help_msg = (
+        "Expected use:\n"
+        "python -m fractal_server.app.runner.compress_folder "
+        "path/to/folder [--remote-to-local]\n"
+    )
+    num_args = len(sys_argv[1:])
+    if num_args == 0:
+        sys.exit(f"Invalid argument.\n{help_msg}\nProvided: {sys_argv[1:]=}")
+    elif num_args == 1:
+        compress_folder(subfolder_path=Path(sys_argv[1]))
+    elif num_args == 2 and sys_argv[2] == "--remote-to-local":
+        compress_folder(subfolder_path=Path(sys_argv[1]), remote_to_local=True)
+    else:
+        sys.exit(f"Invalid argument.\n{help_msg}\nProvided: {sys_argv[1:]=}")
 
-        t0 = time.perf_counter()
-        shutil.rmtree(subfolder_path_tmp_copy)
-        t1 = time.perf_counter()
-        print(
-            f"[compress_folder.py] shutil.rmtree END - elapsed: {t1-t0:.3f} s"
-        )
 
-    t_1 = time.perf_counter()
-    print(f"[compress_folder] END - elapsed {t_1 - t_0:.3f} seconds")
+if __name__ == "__main__":
+    main(sys.argv)

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

@@ -13,7 +13,6 @@
 import json
 import math
 import sys
-import tarfile
 import threading
 import time
 from concurrent.futures import Future
@@ -38,9 +37,11 @@ from ...slurm._slurm_config import SlurmConfig
 from .._batching import heuristics
 from ._executor_wait_thread import FractalSlurmWaitThread
 from fractal_server.app.runner.components import _COMPONENT_KEY_
+from fractal_server.app.runner.compress_folder import compress_folder
 from fractal_server.app.runner.exceptions import JobExecutionError
 from fractal_server.app.runner.exceptions import TaskExecutionError
 from fractal_server.app.runner.executors.slurm.ssh._slurm_job import SlurmJob
+from fractal_server.app.runner.extract_archive import extract_archive
 from fractal_server.config import get_settings
 from fractal_server.logger import set_logger
 from fractal_server.ssh._fabric import FractalSSH
@@ -822,17 +823,12 @@ class FractalSlurmSSHExecutor(SlurmExecutor):
 
         # Create compressed subfolder archive (locally)
         local_subfolder = self.workflow_dir_local / subfolder_name
-        tarfile_name = f"{subfolder_name}.tar.gz"
-        tarfile_path_local = (
-            self.workflow_dir_local / tarfile_name
-        ).as_posix()
+        tarfile_path_local = compress_folder(local_subfolder)
+        tarfile_name = Path(tarfile_path_local).name
+        logger.info(f"Subfolder archive created at {tarfile_path_local}")
         tarfile_path_remote = (
             self.workflow_dir_remote / tarfile_name
         ).as_posix()
-        with tarfile.open(tarfile_path_local, "w:gz") as tar:
-            for this_file in local_subfolder.glob("*"):
-                tar.add(this_file, arcname=this_file.name)
-        logger.info(f"Subfolder archive created at {tarfile_path_local}")
 
         # Transfer archive
         t_0_put = time.perf_counter()
@@ -1222,7 +1218,8 @@ class FractalSlurmSSHExecutor(SlurmExecutor):
         tar_command = (
             f"{self.python_remote} "
             "-m fractal_server.app.runner.compress_folder "
-            f"{(self.workflow_dir_remote / subfolder_name).as_posix()}"
+            f"{(self.workflow_dir_remote / subfolder_name).as_posix()} "
+            "--remote-to-local"
         )
         stdout = self.fractal_ssh.run_command(cmd=tar_command)
         print(stdout)
@@ -1240,8 +1237,7 @@ class FractalSlurmSSHExecutor(SlurmExecutor):
         )
 
         # Extract tarfile locally
-        with tarfile.open(tarfile_path_local) as tar:
-            tar.extractall(path=(self.workflow_dir_local / subfolder_name))
+        extract_archive(Path(tarfile_path_local))
 
         t_1 = time.perf_counter()
         logger.info("[_get_subfolder_sftp] End - " f"elapsed: {t_1-t_0:.3f} s")

fractal_server/app/runner/extract_archive.py

@@ -1,7 +1,22 @@
+"""
+Wrap `tar` extraction command.
+
+This module is used both locally (in the environment where `fractal-server`
+is running) and remotely (as a standalon Python module, executed over SSH).
+
+This is a twin-module of `compress_folder.py`.
+
+The reason for using the `tar` command via `subprocess` rather than Python
+built-in `tarfile` library has to do with performance issues we observed
+when handling files which were just created within a SLURM job, and in the
+context of a CephFS filesystem.
+"""
 import sys
-import tarfile
 from pathlib import Path
 
+from .run_subprocess import run_subprocess
+from fractal_server.logger import set_logger
+
 
 def _remove_suffix(*, string: str, suffix: str) -> str:
     if string.endswith(suffix):
@@ -10,29 +25,61 @@ def _remove_suffix(*, string: str, suffix: str) -> str:
         raise ValueError(f"Cannot remove {suffix=} from {string=}.")
 
 
-if __name__ == "__main__":
+def extract_archive(archive_path: Path):
+    """
+    Extract e.g. `/path/archive.tar.gz` archive into `/path/archive` folder
+
+    Note that `/path/archive` may already exist. In this case, files with
+    the same name are overwritten and new files are added.
+
+    Arguments:
+        archive_path: Absolute path to the archive file.
+    """
+
+    logger_name = "extract_archive"
+    logger = set_logger(logger_name)
+
+    logger.debug("START")
+    logger.debug(f"{archive_path.as_posix()=}")
+
+    # Check archive_path is valid
+    if not archive_path.exists():
+        sys.exit(f"Missing file {archive_path.as_posix()}.")
+
+    # Prepare subfolder path
+    parent_dir = archive_path.parent
+    subfolder_name = _remove_suffix(string=archive_path.name, suffix=".tar.gz")
+    subfolder_path = parent_dir / subfolder_name
+    logger.debug(f"{subfolder_path.as_posix()=}")
+
+    # Create subfolder
+    subfolder_path.mkdir(exist_ok=True)
+
+    # Run tar command
+    cmd_tar = (
+        f"tar -xzvf {archive_path} "
+        f"--directory={subfolder_path.as_posix()} "
+        "."
+    )
+    logger.debug(f"{cmd_tar=}")
+    run_subprocess(cmd=cmd_tar, logger_name=logger_name)
+
+    logger.debug("END")
+
+
+def main(sys_argv: list[str]):
     help_msg = (
         "Expected use:\n"
         "python -m fractal_server.app.runner.extract_archive "
         "path/to/archive.tar.gz"
     )
 
-    if len(sys.argv[1:]) != 1:
-        raise ValueError(
-            f"Invalid argument.\n{help_msg}\nProvided: {sys.argv=}"
-        )
-    elif not sys.argv[1].endswith(".tar.gz"):
-        raise ValueError(
-            f"Invalid argument.\n{help_msg}\nProvided: {sys.argv=}"
-        )
-
-    tarfile_path = Path(sys.argv[1])
-
-    print(f"[extract_archive.py] {tarfile_path=}")
+    if len(sys_argv[1:]) != 1 or not sys_argv[1].endswith(".tar.gz"):
+        sys.exit(f"Invalid argument.\n{help_msg}\nProvided: {sys_argv[1:]=}")
+    else:
+        tarfile_path = Path(sys_argv[1])
+        extract_archive(tarfile_path)
 
-    job_folder = tarfile_path.parent
-    subfolder_name = _remove_suffix(string=tarfile_path.name, suffix=".tar.gz")
-    with tarfile.open(tarfile_path) as tar:
-        tar.extractall(path=Path(job_folder, subfolder_name).as_posix())
 
-    print(f"[extract_archive.py] {tarfile_path=}")
+if __name__ == "__main__":
+    main(sys.argv)

fractal_server/app/runner/run_subprocess.py

@@ -0,0 +1,27 @@
+import shlex
+import subprocess  # nosec
+from typing import Optional
+
+from fractal_server.logger import get_logger
+
+
+def run_subprocess(
+    cmd: str, logger_name: Optional[str] = None
+) -> subprocess.CompletedProcess:
+    logger = get_logger(logger_name)
+    try:
+        res = subprocess.run(  # nosec
+            shlex.split(cmd), check=True, capture_output=True, encoding="utf-8"
+        )
+        return res
+    except subprocess.CalledProcessError as e:
+        logger.debug(
+            f"Command '{e.cmd}' returned non-zero exit status {e.returncode}."
+        )
+        logger.debug(f"stdout: {e.stdout}")
+        logger.debug(f"stderr: {e.stderr}")
+        raise e
+    except Exception as e:
+        logger.debug(f"An error occurred while running command: {cmd}")
+        logger.debug(str(e))
+        raise e

fractal_server/config.py

@@ -497,7 +497,7 @@ class Settings(BaseSettings):
     [`clusterfutures`](https://github.com/sampsyo/clusterfutures/blob/master/cfut/__init__.py)).
     """
 
-    FRACTAL_SLURM_SBATCH_SLEEP: int = 0
+    FRACTAL_SLURM_SBATCH_SLEEP: float = 0
     """
     Interval to wait (in seconds) between two subsequent `sbatch` calls, when
     running a task that produces multiple SLURM jobs.
@@ -546,7 +546,9 @@ class Settings(BaseSettings):
     attribute in their input-arguments JSON file.
     """
 
-    FRACTAL_API_V1_MODE: Literal["include", "exclude"] = "include"
+    FRACTAL_API_V1_MODE: Literal[
+        "include", "include_without_submission", "exclude"
+    ] = "include"
     """
     Whether to include the v1 API.
     """
@@ -685,6 +687,25 @@ class Settings(BaseSettings):
         self.check_db()
         self.check_runner()
 
+    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"]
+            ):
+                return True
+            else:
+                return False
+
+        sanitized_settings = {}
+        for k, v in self.dict().items():
+            if _must_be_sanitized(k):
+                sanitized_settings[k] = "***"
+            else:
+                sanitized_settings[k] = v
+
+        return sanitized_settings
+
 
 def get_settings(settings=Settings()) -> Settings:
     return settings

fractal_server/main.py

@@ -49,7 +49,7 @@ def collect_routers(app: FastAPI) -> None:
     settings = Inject(get_settings)
 
     app.include_router(router_api, prefix="/api")
-    if settings.FRACTAL_API_V1_MODE == "include":
+    if settings.FRACTAL_API_V1_MODE.startswith("include"):
         app.include_router(router_api_v1, prefix="/api/v1")
         app.include_router(
             router_admin_v1, prefix="/admin/v1", tags=["V1 Admin area"]

fractal_server/ssh/_fabric.py

@@ -286,7 +286,6 @@ class FractalSSH(object):
             folder: Absolute path to a folder that should be removed.
             safe_root: If `folder` is not a subfolder of the absolute
                 `safe_root` path, raise an error.
-            fractal_ssh:
         """
         invalid_characters = {" ", "\n", ";", "$", "`"}
 

fractal_server/string_tools.py

@@ -9,12 +9,12 @@ def sanitize_string(value: str) -> str:
 
     Make the string lower-case, and replace any special character with an
     underscore, where special characters are:
-    ```python repl
-    >>> string.punctuation
-    '!"#$%&\'()*+,-./:;<=>?@[\\]^_`{|}~'
-    >>> string.whitespace
-    ' \t\n\r\x0b\x0c'
-    ```
+
+
+        >>> string.punctuation
+        '!"#$%&\'()*+,-./:;<=>?@[\\\\]^_`{|}~'
+        >>> string.whitespace
+        ' \\t\\n\\r\\x0b\\x0c'
 
     Args:
         value: Input string
@@ -35,5 +35,11 @@ def slugify_task_name_for_source(task_name: str) -> str:
     from `fractal_server.string_tools.sanitize_string`, nor we can remove it.
     As 2.3.1, we are renaming it to `slugify_task_name_for_source`, to make
     it clear that it should not be used for other purposes.
+
+    Args:
+        task_name:
+
+    Return:
+        Slug-ified task name.
     """
     return task_name.replace(" ", "_").lower()

fractal_server/tasks/v2/background_operations_ssh.py

@@ -167,7 +167,7 @@ def background_collect_pip_ssh(
                     / ".fractal"
                     / f"{task_pkg.package_name}{package_version}"
                 ).as_posix()
-
+                logger.debug(f"{package_env_dir=}")
                 replacements = [
                     ("__PACKAGE_NAME__", task_pkg.package_name),
                     ("__PACKAGE_ENV_DIR__", package_env_dir),
@@ -197,10 +197,18 @@ def background_collect_pip_ssh(
                 # long operations that do not use the db
                 db.close()
 
+                # `remove_venv_folder_upon_failure` is set to True only if
+                # script 1 goes through, which means that the remote folder
+                # `package_env_dir` did not already exist. If this remote
+                # folder already existed, then script 1 fails and the boolean
+                # flag `remove_venv_folder_upon_failure` remains false.
+                remove_venv_folder_upon_failure = False
                 stdout = _customize_and_run_template(
                     script_filename="_1_create_venv.sh",
                     **common_args,
                 )
+                remove_venv_folder_upon_failure = True
+
                 stdout = _customize_and_run_template(
                     script_filename="_2_upgrade_pip.sh",
                     **common_args,
@@ -294,6 +302,7 @@ def background_collect_pip_ssh(
 
                 # Finalize (write metadata to DB)
                 logger.debug("finalising - START")
+
                 collection_state = db.get(CollectionStateV2, state_id)
                 collection_state.data["log"] = log_file_path.open("r").read()
                 collection_state.data["freeze"] = stdout_pip_freeze
@@ -312,16 +321,26 @@ def background_collect_pip_ssh(
                     exception=e,
                     db=db,
                 )
-                try:
-                    logger.info(f"Now delete remote folder {package_env_dir}")
-                    fractal_ssh.remove_folder(
-                        folder=package_env_dir,
-                        safe_root=settings.FRACTAL_SLURM_SSH_WORKING_BASE_DIR,
-                    )
-                    logger.info(f"Deleted remoted folder {package_env_dir}")
-                except Exception as e:
-                    logger.error(
-                        f"Deleting remote folder failed.\n"
-                        f"Original error:\n{str(e)}"
-                    )
+                if remove_venv_folder_upon_failure:
+                    try:
+                        logger.info(
+                            f"Now delete remote folder {package_env_dir}"
+                        )
+                        fractal_ssh.remove_folder(
+                            folder=package_env_dir,
+                            safe_root=settings.FRACTAL_SLURM_SSH_WORKING_BASE_DIR,  # noqa: E501
+                        )
+                        logger.info(
+                            f"Deleted remoted folder {package_env_dir}"
+                        )
+                    except Exception as e:
+                        logger.error(
+                            f"Removing remote folder failed.\n"
+                            f"Original error:\n{str(e)}"
+                        )
+                    else:
+                        logger.info(
+                            "Not trying to remove remote folder "
+                            f"{package_env_dir}."
+                        )
                 return

fractal_server/tasks/v2/templates/_1_create_venv.sh

@@ -12,12 +12,12 @@ PYTHON=__PYTHON__
 
 TIME_START=$(date +%s)
 
-
-# Create main folder
+# Check that package folder does not exist
 if [ -d "$PACKAGE_ENV_DIR" ]; then
     write_log "ERROR: Folder $PACKAGE_ENV_DIR already exists. Exit."
     exit 1
 fi
+
 write_log "START mkdir -p $PACKAGE_ENV_DIR"
 mkdir -p $PACKAGE_ENV_DIR
 write_log "END   mkdir -p $PACKAGE_ENV_DIR"

fractal_server/tasks/v2/templates/_2_upgrade_pip.sh

@@ -7,10 +7,6 @@ write_log(){
 
 # Variables to be filled within fractal-server
 PACKAGE_ENV_DIR=__PACKAGE_ENV_DIR__
-PACKAGE_NAME=__PACKAGE_NAME__
-PACKAGE=__PACKAGE__
-PYTHON=__PYTHON__
-INSTALL_STRING=__INSTALL_STRING__
 
 TIME_START=$(date +%s)
 

fractal_server/tasks/v2/templates/_3_pip_install.sh

@@ -8,12 +8,8 @@ write_log(){
 
 # Variables to be filled within fractal-server
 PACKAGE_ENV_DIR=__PACKAGE_ENV_DIR__
-PACKAGE_NAME=__PACKAGE_NAME__
-PACKAGE=__PACKAGE__
-PYTHON=__PYTHON__
 INSTALL_STRING=__INSTALL_STRING__
 
-
 TIME_START=$(date +%s)
 
 VENVPYTHON=${PACKAGE_ENV_DIR}/bin/python

fractal_server/tasks/v2/templates/_4_pip_freeze.sh

@@ -9,12 +9,6 @@ write_log(){
 
 # Variables to be filled within fractal-server
 PACKAGE_ENV_DIR=__PACKAGE_ENV_DIR__
-PACKAGE_NAME=__PACKAGE_NAME__
-PACKAGE=__PACKAGE__
-PYTHON=__PYTHON__
-INSTALL_STRING=__INSTALL_STRING__
-
-
 
 VENVPYTHON=${PACKAGE_ENV_DIR}/bin/python
 

fractal_server/tasks/v2/templates/_5_pip_show.sh

@@ -9,9 +9,7 @@ write_log(){
 # Variables to be filled within fractal-server
 PACKAGE_ENV_DIR=__PACKAGE_ENV_DIR__
 PACKAGE_NAME=__PACKAGE_NAME__
-PACKAGE=__PACKAGE__
-PYTHON=__PYTHON__
-INSTALL_STRING=__INSTALL_STRING__
+
 
 
 TIME_START=$(date +%s)

{fractal_server-2.3.2.dist-info → fractal_server-2.3.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fractal-server
-Version: 2.3.2
+Version: 2.3.4
 Summary: Server component of the Fractal analytics platform
 Home-page: https://github.com/fractal-analytics-platform/fractal-server
 License: BSD-3-Clause

{fractal_server-2.3.2.dist-info → fractal_server-2.3.4.dist-info}/RECORD

@@ -1,4 +1,4 @@
-fractal_server/__init__.py,sha256=rXqFcllf2dozijOCAlnZWvgsFpCEMVhBtm66tw0cp-A,22
+fractal_server/__init__.py,sha256=eG9nilkh3fQGESwdGxiBx9bAq-mIR2ueRWgDXGopc1M,22
 fractal_server/__main__.py,sha256=CocbzZooX1UtGqPi55GcHGNxnrJXFg5tUU5b3wyFCyo,4958
 fractal_server/alembic.ini,sha256=MWwi7GzjzawI9cCAK1LW7NxIBQDUqD12-ptJoq5JpP0,3153
 fractal_server/app/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -25,12 +25,12 @@ fractal_server/app/routes/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJW
 fractal_server/app/routes/admin/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/app/routes/admin/v1.py,sha256=ShmsUFtfyRqP84QScqmRDVrJFpbR4p-8baLxAkI3n1U,13926
 fractal_server/app/routes/admin/v2.py,sha256=JuG1qqVeQIgVJgPyqrB1053il22mGPGpKBiJi6zVsqQ,13687
-fractal_server/app/routes/api/__init__.py,sha256=EVyZrEq3I_1643QGTPCC5lgCp4xH_auYbrFfogTm4pc,315
+fractal_server/app/routes/api/__init__.py,sha256=XlJUFd-0FossfyKyJti4dmwY6SMysQn1yiisMrNzgBE,615
 fractal_server/app/routes/api/v1/__init__.py,sha256=Y2HQdG197J0a7DyQEE2jn53IfxD0EHGhzK1I2JZuEck,958
 fractal_server/app/routes/api/v1/_aux_functions.py,sha256=CeaVrNVYs_lEbiJbu4uaTeeiajljeXfdq1iLkt5RoRo,12636
 fractal_server/app/routes/api/v1/dataset.py,sha256=HRE-8vPmVkeXf7WFYkI19mDtbY-iJZeJ7PmMiV0LMgY,16923
 fractal_server/app/routes/api/v1/job.py,sha256=217fGh7U37esib1JG8INpLhE0W88t9X0fFwCNVt2r_M,5313
-fractal_server/app/routes/api/v1/project.py,sha256=MxbJUc9H14ZZ8mmMbX3LXGTVR3sHdD26YSw4TKI7WtU,16108
+fractal_server/app/routes/api/v1/project.py,sha256=0DavnACBDr8-BHWGQ0YPfxVNJLsYmbuo-TeKJk1s3Hw,16436
 fractal_server/app/routes/api/v1/task.py,sha256=udbKnenzc-Q10elYCVB9JmOPWATraa9tZi0AaByvWo0,6129
 fractal_server/app/routes/api/v1/task_collection.py,sha256=82XBsJHlPiDPCbpLa-16ojKDpj2LYj9_jFSZt0t58bQ,8911
 fractal_server/app/routes/api/v1/workflow.py,sha256=7r9IoIevg_rvYCrerMOsIsUabSOQatxdPCfLdkP0dRs,10942
@@ -57,7 +57,7 @@ fractal_server/app/runner/.gitignore,sha256=ytzN_oyHWXrGU7iFAtoHSTUbM6Rn6kG0Zkdd
 fractal_server/app/runner/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/app/runner/async_wrap.py,sha256=_O6f8jftKYXG_DozkmlrDBhoiK9QhE9MablOyECq2_M,829
 fractal_server/app/runner/components.py,sha256=ZF8ct_Ky5k8IAcrmpYOZ-bc6OBgdELEighYVqFDEbZg,119
-fractal_server/app/runner/compress_folder.py,sha256=6UD9qo-ssPp6OBAZpQuCypJNINamzN5JVkyvqB2b9jU,3717
+fractal_server/app/runner/compress_folder.py,sha256=zmxo2EFkSaO4h3GnMRi9DYaf62bxy4zznZZGfmq-n68,3975
 fractal_server/app/runner/exceptions.py,sha256=_qZ_t8O4umAdJ1ikockiF5rDJuxnEskrGrLjZcnQl7A,4159
 fractal_server/app/runner/executors/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/app/runner/executors/slurm/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -67,14 +67,15 @@ fractal_server/app/runner/executors/slurm/remote.py,sha256=wLziIsGdSMiO-jIXM8x77
 fractal_server/app/runner/executors/slurm/ssh/__init__.py,sha256=Cjn1rYvljddi96tAwS-qqGkNfOcfPzjChdaEZEObCcM,65
 fractal_server/app/runner/executors/slurm/ssh/_executor_wait_thread.py,sha256=jM4G-wiHynZhNERusVGLtDTepJDiYjCDloWZyflaMV0,3482
 fractal_server/app/runner/executors/slurm/ssh/_slurm_job.py,sha256=rwlqZzoGo4SAb4nSlFjsQJdaCgfM1J6YGcjb8yYxlqc,4506
-fractal_server/app/runner/executors/slurm/ssh/executor.py,sha256=FMS0lvb9-pPk8mTkgfLDwljnKq2J_yDqpwth9GZmOOM,55475
+fractal_server/app/runner/executors/slurm/ssh/executor.py,sha256=O3BV7Qo7W8qEJmIeaajxtCCbkbYQDEXZbfS7GKCO5LQ,55338
 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/_subprocess_run_as_user.py,sha256=uZgmxP0ZneGpzTVt-GT-6EgNKUh1sW2-QH7LFYc1tNI,5132
 fractal_server/app/runner/executors/slurm/sudo/executor.py,sha256=nu1mcg3veOEaDwqPLyrf9_pMUc34-uXhd8er3IsMQZw,48236
-fractal_server/app/runner/extract_archive.py,sha256=JDK6wtTFdE7Cf1kGaJajLxNoMmhzweP6YyxdPCm65fc,1095
+fractal_server/app/runner/extract_archive.py,sha256=tLpjDrX47OjTNhhoWvm6iNukg8KoieWyTb7ZfvE9eWU,2483
 fractal_server/app/runner/filenames.py,sha256=9lwu3yB4C67yiijYw8XIKaLFn3mJUt6_TCyVFM_aZUQ,206
+fractal_server/app/runner/run_subprocess.py,sha256=KTkJnWLrLQdR2WRJ3jGu0RBu4330L3mtCAE_B0wDx3M,818
 fractal_server/app/runner/set_start_and_last_task_index.py,sha256=-q4zVybAj8ek2XlbENKlfOAJ39hT_zoJoZkqzDqiAMY,1254
 fractal_server/app/runner/shutdown.py,sha256=I_o2iYKJwzku0L3E85ETjrve3QPECygR5xhhsAo5huM,2910
 fractal_server/app/runner/task_files.py,sha256=sd_MpJ01C8c9QTO8GzGMidFGdlq_hXX_ARDRhd_YMnI,3762
@@ -138,14 +139,14 @@ fractal_server/app/schemas/v2/task_collection.py,sha256=8PG1bOqkfQqORMN0brWf6mHD
 fractal_server/app/schemas/v2/workflow.py,sha256=Zzx3e-qgkH8le0FUmAx9UrV5PWd7bj14PPXUh_zgZXM,1827
 fractal_server/app/schemas/v2/workflowtask.py,sha256=atVuVN4aXsVEOmSd-vyg-8_8OnPmqx-gT75rXcn_AlQ,6552
 fractal_server/app/security/__init__.py,sha256=2-QbwuR-nsuHM_uwKS_WzYvkhnuhO5jUv8UVROetyVk,11169
-fractal_server/config.py,sha256=SCKJrGQeKkWxyz-kT7sCjcxwKwidR1bT0hi0KEj0sV0,24282
+fractal_server/config.py,sha256=KOa2jrsbx0H6zG2ItNZkLiKqbuOkV3aUYKFuIN3FIyE,24921
 fractal_server/data_migrations/README.md,sha256=_3AEFvDg9YkybDqCLlFPdDmGJvr6Tw7HRI14aZ3LOIw,398
 fractal_server/gunicorn_fractal.py,sha256=2AOkgxu-oQ-XB578_voT0VuhmAXFTmb0c-nYn1XLy_Q,1231
 fractal_server/images/__init__.py,sha256=xO6jTLE4EZKO6cTDdJsBmK9cdeh9hFTaSbSuWgQg7y4,196
 fractal_server/images/models.py,sha256=9ipU5h4N6ogBChoB-2vHoqtL0TXOHCv6kRR-fER3mkM,4167
 fractal_server/images/tools.py,sha256=gxeniYy4Z-cp_ToK2LHPJUTVVUUrdpogYdcBUvBuLiY,2209
 fractal_server/logger.py,sha256=56wfka6fHaa3Rx5qO009nEs_y8gx5wZ2NUNZZ1I-uvc,5130
-fractal_server/main.py,sha256=CTWA_EJBaSO7hty6AdAenFQjbNE4Chr1U-sZ2qsPDmw,5289
+fractal_server/main.py,sha256=Kmty1C9jPfH101nP3b82u9H9QvT-5Z-8Dd60wf9S5h0,5298
 fractal_server/migrations/README,sha256=4rQvyDfqodGhpJw74VYijRmgFP49ji5chyEemWGHsuw,59
 fractal_server/migrations/env.py,sha256=Bvg-FJzRJZIH_wqS_ZyZNXANIaathjo22_IY7c3fCjo,2636
 fractal_server/migrations/script.py.mako,sha256=oMXw9LC3zRbinWWPPDgeZ4z9FJrV2zhRWiYdS5YgNbI,526
@@ -167,8 +168,8 @@ 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=GsiB3wrNfIkDmXr5A3qjkXhUAaRCyAT4VJRHIAbI1gM,10764
-fractal_server/string_tools.py,sha256=AwwDb-wtgGQeGdZjZQKgtYCmWbFHGNk_DzaCnYerRAY,1197
+fractal_server/ssh/_fabric.py,sha256=4B6D0F2bWWho1V_xdDDBWYAHno9h_6Smp7_FP2n8jYo,10739
+fractal_server/string_tools.py,sha256=KThgTLn_FHNSuEUGLabryJAP6DaFd7bpi-hF5FgkBjw,1268
 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
@@ -182,18 +183,18 @@ fractal_server/tasks/v2/_TaskCollectPip.py,sha256=kWQNMNZ8OEddkYhmhsk3E6ArcaD7qe
 fractal_server/tasks/v2/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/tasks/v2/_venv_pip.py,sha256=xm4XClWYbhXQRqDxYxM9cP7ZCnx-8b078fuVUL12D2M,6286
 fractal_server/tasks/v2/background_operations.py,sha256=CQwQon5RKAXrjsN255Okh5dcT0R45axgqoPW3EB-v_Q,11527
-fractal_server/tasks/v2/background_operations_ssh.py,sha256=Zjoo3UZQD97INksFkhkTMHYHDltDADs8MbWyAWJtjO8,12926
+fractal_server/tasks/v2/background_operations_ssh.py,sha256=3TJp2NW2CJ9KlghWDEhTQ4HDZxmbrLHjb0OQJI3ALo0,13892
 fractal_server/tasks/v2/endpoint_operations.py,sha256=gT38pl5TEH6WNWOtg4Itegt2lTJJI6YRa7fEj9Y4x2s,4226
-fractal_server/tasks/v2/templates/_1_create_venv.sh,sha256=_Lr1UCWQycqea07YZFICxiwQVz9YZHYS-AaVFjNLUyQ,993
-fractal_server/tasks/v2/templates/_2_upgrade_pip.sh,sha256=45CPrRxxNBq1ujDA8m1_LWt6QaN1G29mda_LbW2EjN8,626
-fractal_server/tasks/v2/templates/_3_pip_install.sh,sha256=ViAf3KKtk8YnEkrhybPV8ZZdmZJ0g2l4zkoVnmXbAKw,664
-fractal_server/tasks/v2/templates/_4_pip_freeze.sh,sha256=SHndmLn5daT_lg6rnhNPMrRiPAIbGUlMUBIDDLniVOg,372
-fractal_server/tasks/v2/templates/_5_pip_show.sh,sha256=3onbKZ0PJkkYronP4_tdMBoAe3GqxVQFH-L4dUqSkQY,1825
+fractal_server/tasks/v2/templates/_1_create_venv.sh,sha256=5uW0ETYxl5xiQEXP107zgq8V_-vf3k5NzMMj1hSLjas,1015
+fractal_server/tasks/v2/templates/_2_upgrade_pip.sh,sha256=hVqwgWuNOxr6ck-0FklpcF0o7q-vQXQasYNNaPSxlKM,524
+fractal_server/tasks/v2/templates/_3_pip_install.sh,sha256=T9sabeB9iQzVZpLfuLkKGz9EpfHkUrJHKWO4HNij6yM,595
+fractal_server/tasks/v2/templates/_4_pip_freeze.sh,sha256=6BIOVYBPZmaaOuaDwNirt1iHWjj2oDjViUDvQaL_f6Y,268
+fractal_server/tasks/v2/templates/_5_pip_show.sh,sha256=GrJ19uHYQxANEy9JaeNJZVTquY9c8Ww9eCdnC7eLVr0,1754
 fractal_server/tasks/v2/utils.py,sha256=JOyCacb6MNvrwfLNTyLwcz8y79J29YuJeJ2MK5kqXRM,1657
 fractal_server/urls.py,sha256=5o_qq7PzKKbwq12NHSQZDmDitn5RAOeQ4xufu-2v9Zk,448
 fractal_server/utils.py,sha256=b7WwFdcFZ8unyT65mloFToYuEDXpQoHRcmRNqrhd_dQ,2115
-fractal_server-2.3.2.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
-fractal_server-2.3.2.dist-info/METADATA,sha256=UMmVY5UM3tc8mAtvtT1dncFUsRJgvSOXY3wSYVGTrjw,4425
-fractal_server-2.3.2.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-fractal_server-2.3.2.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
-fractal_server-2.3.2.dist-info/RECORD,,
+fractal_server-2.3.4.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
+fractal_server-2.3.4.dist-info/METADATA,sha256=mfO_uoRAUY2bfiBN0AU1exGu0orny30foijJx6SR1Xc,4425
+fractal_server-2.3.4.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+fractal_server-2.3.4.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
+fractal_server-2.3.4.dist-info/RECORD,,