fractal-server 2.3.1a0__tar.gz → 2.3.3__tar.gz

{fractal_server-2.3.1a0 → fractal_server-2.3.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fractal-server
-Version: 2.3.1a0
+Version: 2.3.3
 Summary: Server component of the Fractal analytics platform
 Home-page: https://github.com/fractal-analytics-platform/fractal-server
 License: BSD-3-Clause

fractal_server-2.3.3/fractal_server/__init__.py

@@ -0,0 +1 @@
+__VERSION__ = "2.3.3"

{fractal_server-2.3.1a0 → fractal_server-2.3.3}/fractal_server/app/routes/admin/v1.py

@@ -387,9 +387,7 @@ async def download_job_logs(
     # Create and return byte stream for zipped log folder
     PREFIX_ZIP = Path(job.working_dir).name
     zip_filename = f"{PREFIX_ZIP}_archive.zip"
-    byte_stream = _zip_folder_to_byte_stream(
-        folder=job.working_dir, zip_filename=zip_filename
-    )
+    byte_stream = _zip_folder_to_byte_stream(folder=job.working_dir)
     return StreamingResponse(
         iter([byte_stream.getvalue()]),
         media_type="application/x-zip-compressed",

{fractal_server-2.3.1a0 → fractal_server-2.3.3}/fractal_server/app/routes/admin/v2.py

@@ -274,9 +274,7 @@ async def download_job_logs(
     # Create and return byte stream for zipped log folder
     PREFIX_ZIP = Path(job.working_dir).name
     zip_filename = f"{PREFIX_ZIP}_archive.zip"
-    byte_stream = _zip_folder_to_byte_stream(
-        folder=job.working_dir, zip_filename=zip_filename
-    )
+    byte_stream = _zip_folder_to_byte_stream(folder=job.working_dir)
     return StreamingResponse(
         iter([byte_stream.getvalue()]),
         media_type="application/x-zip-compressed",

{fractal_server-2.3.1a0 → fractal_server-2.3.3}/fractal_server/app/routes/api/v1/job.py

@@ -128,9 +128,7 @@ async def download_job_logs(
     # Create and return byte stream for zipped log folder
     PREFIX_ZIP = Path(job.working_dir).name
     zip_filename = f"{PREFIX_ZIP}_archive.zip"
-    byte_stream = _zip_folder_to_byte_stream(
-        folder=job.working_dir, zip_filename=zip_filename
-    )
+    byte_stream = _zip_folder_to_byte_stream(folder=job.working_dir)
     return StreamingResponse(
         iter([byte_stream.getvalue()]),
         media_type="application/x-zip-compressed",

{fractal_server-2.3.1a0 → fractal_server-2.3.3}/fractal_server/app/routes/api/v2/job.py

@@ -131,9 +131,7 @@ async def download_job_logs(
     # Create and return byte stream for zipped log folder
     PREFIX_ZIP = Path(job.working_dir).name
     zip_filename = f"{PREFIX_ZIP}_archive.zip"
-    byte_stream = _zip_folder_to_byte_stream(
-        folder=job.working_dir, zip_filename=zip_filename
-    )
+    byte_stream = _zip_folder_to_byte_stream(folder=job.working_dir)
     return StreamingResponse(
         iter([byte_stream.getvalue()]),
         media_type="application/x-zip-compressed",

{fractal_server-2.3.1a0 → fractal_server-2.3.3}/fractal_server/app/routes/aux/_job.py

@@ -1,3 +1,4 @@
+import os
 from io import BytesIO
 from pathlib import Path
 from typing import Union
@@ -25,19 +26,20 @@ def _write_shutdown_file(*, job: Union[ApplyWorkflow, JobV2]):
         f.write(f"Trigger executor shutdown for {job.id=}.")
 
 
-def _zip_folder_to_byte_stream(*, folder: str, zip_filename: str) -> BytesIO:
+def _zip_folder_to_byte_stream(*, folder: str) -> BytesIO:
     """
     Get byte stream with the zipped log folder of a job.
 
     Args:
         folder: the folder to zip
-        zip_filename: name of the zipped archive
     """
-    working_dir_path = Path(folder)
 
     byte_stream = BytesIO()
     with ZipFile(byte_stream, mode="w", compression=ZIP_DEFLATED) as zipfile:
-        for fpath in working_dir_path.glob("*"):
-            zipfile.write(filename=str(fpath), arcname=str(fpath.name))
+        for root, dirs, files in os.walk(folder):
+            for file in files:
+                file_path = os.path.join(root, file)
+                archive_path = os.path.relpath(file_path, folder)
+                zipfile.write(file_path, archive_path)
 
     return byte_stream

{fractal_server-2.3.1a0 → fractal_server-2.3.3}/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.

{fractal_server-2.3.1a0 → fractal_server-2.3.3}/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-2.3.1a0 → fractal_server-2.3.3}/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-2.3.1a0 → fractal_server-2.3.3}/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-2.3.1a0 → fractal_server-2.3.3}/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-2.3.1a0 → fractal_server-2.3.3}/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-2.3.1a0 → fractal_server-2.3.3}/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-2.3.1a0 → fractal_server-2.3.3}/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-2.3.1a0 → fractal_server-2.3.3}/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-2.3.1a0 → fractal_server-2.3.3}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "fractal-server"
-version = "2.3.1a0"
+version = "2.3.3"
 description = "Server component of the Fractal analytics platform"
 authors = [
     "Tommaso Comparin <tommaso.comparin@exact-lab.it>",
@@ -91,7 +91,7 @@ filterwarnings = [
 ]
 
 [tool.bumpver]
-current_version = "2.3.1a0"
+current_version = "2.3.3"
 version_pattern = "MAJOR.MINOR.PATCH[PYTAGNUM]"
 commit_message = "bump version {old_version} -> {new_version}"
 commit = true

fractal_server-2.3.1a0/fractal_server/__init__.py

@@ -1 +0,0 @@
-__VERSION__ = "2.3.1a0"