fractal-server 2.16.2__tar.gz → 2.16.3__tar.gz

{fractal_server-2.16.2 → fractal_server-2.16.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: fractal-server
-Version: 2.16.2
+Version: 2.16.3
 Summary: Backend component of the Fractal analytics platform
 License: BSD-3-Clause
 Author: Tommaso Comparin
@@ -12,7 +12,7 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Requires-Dist: alembic (>=1.13.1,<2.0.0)
-Requires-Dist: cryptography (>=45.0.3,<45.1.0)
+Requires-Dist: cryptography (>=46.0.0,<47.0.0)
 Requires-Dist: fabric (>=3.2.2,<3.3.0)
 Requires-Dist: fastapi (>=0.116.0,<0.117.0)
 Requires-Dist: fastapi-users[oauth] (>=14,<15)

fractal_server-2.16.3/fractal_server/__init__.py

@@ -0,0 +1 @@
+__VERSION__ = "2.16.3"

{fractal_server-2.16.2 → fractal_server-2.16.3}/fractal_server/tasks/v2/ssh/_pixi_slurm_ssh.py

@@ -31,6 +31,36 @@ STATES_FINISHED = {
 }
 
 
+def _get_workdir_remote(script_paths: list[str]) -> str:
+    """
+    Check that there is one and only one `workdir`, and return it.
+
+    Note: The `is_absolute` check is to filter out a `chmod` command.
+    """
+    workdirs = [
+        Path(script_path).parent.as_posix()
+        for script_path in script_paths
+        if Path(script_path).is_absolute()
+    ]
+    if not len(set(workdirs)) == 1:
+        raise ValueError(f"Invalid {script_paths=}.")
+    return workdirs[0]
+
+
+def _read_file_if_exists(
+    *,
+    fractal_ssh: FractalSSH,
+    path: str,
+) -> str:
+    """
+    Read a remote file if it exists, or return an empty string.
+    """
+    if fractal_ssh.remote_exists(path=path):
+        return fractal_ssh.read_remote_text_file(path)
+    else:
+        return ""
+
+
 def _log_change_of_job_state(
     *,
     old_state: str | None,
@@ -99,15 +129,18 @@ def _verify_success_file_exists(
         logger = get_logger(logger_name=logger_name)
         error_msg = f"{success_file_remote=} missing."
         logger.info(error_msg)
-        if fractal_ssh.remote_exists(stderr_remote):
-            stderr = fractal_ssh.read_remote_text_file(stderr_remote)
+
+        stderr = _read_file_if_exists(
+            fractal_ssh=fractal_ssh, path=stderr_remote
+        )
+        if stderr:
             logger.info(f"SLURM-job stderr:\n{stderr}")
         raise RuntimeError(error_msg)
 
 
 def run_script_on_remote_slurm(
     *,
-    script_path: str,
+    script_paths: list[str],
     slurm_config: PixiSLURMConfig,
     fractal_ssh: FractalSSH,
     logger_name: str,
@@ -127,7 +160,7 @@ def run_script_on_remote_slurm(
     settings = Inject(get_settings)
 
     # (1) Prepare remote submission script
-    workdir_remote = Path(script_path).parent.as_posix()
+    workdir_remote = _get_workdir_remote(script_paths)
     submission_script_remote = os.path.join(
         workdir_remote, f"{prefix}-submit.sh"
     )
@@ -144,10 +177,11 @@ def run_script_on_remote_slurm(
         f"#SBATCH --out={stdout_remote}",
         f"#SBATCH -D {workdir_remote}",
         "",
-        f"bash {script_path}",
-        f"touch {success_file_remote}",
-        "",
     ]
+    for script_path in script_paths:
+        script_lines.append(f"bash {script_path}")
+    script_lines.append(f"touch {success_file_remote}")
+
     script_contents = "\n".join(script_lines)
     fractal_ssh.write_remote_file(
         path=submission_script_remote,
@@ -209,6 +243,13 @@ def run_script_on_remote_slurm(
         stderr_remote=stderr_remote,
     )
 
+    stdout = _read_file_if_exists(
+        fractal_ssh=fractal_ssh,
+        path=stdout_remote,
+    )
+
     logger.info("SLURM-job execution completed successfully, continue.")
     activity.log = get_current_log(log_file_path)
     activity = add_commit_refresh(obj=activity, db=db)
+
+    return stdout

{fractal_server-2.16.2 → fractal_server-2.16.3}/fractal_server/tasks/v2/ssh/collect_pixi.py

@@ -203,12 +203,21 @@ def collect_ssh_pixi(
                         pyproject_toml_path=pyproject_toml_path,
                     )
 
-                    # Run script 2 - run pixi-install command
+                    # Prepare scripts 2 and 3
                     remote_script2_path = _customize_and_send_template(
                         template_filename="pixi_2_install.sh",
                         replacements=replacements,
                         **common_args,
                     )
+                    remote_script3_path = _customize_and_send_template(
+                        template_filename="pixi_3_post_install.sh",
+                        replacements=replacements,
+                        **common_args,
+                    )
+                    logger.debug(
+                        "Post-installation script written to "
+                        f"{remote_script3_path=}."
+                    )
                     logger.debug(
                         "Installation script written to "
                         f"{remote_script2_path=}."
@@ -216,8 +225,13 @@ def collect_ssh_pixi(
                     activity.log = get_current_log(log_file_path)
                     activity = add_commit_refresh(obj=activity, db=db)
 
-                    run_script_on_remote_slurm(
-                        script_path=remote_script2_path,
+                    # Run scripts 2 and 3
+                    stdout = run_script_on_remote_slurm(
+                        script_paths=[
+                            remote_script2_path,
+                            remote_script3_path,
+                            f"chmod -R 755 {source_dir}",
+                        ],
                         slurm_config=settings.pixi.SLURM_CONFIG,
                         fractal_ssh=fractal_ssh,
                         logger_name=LOGGER_NAME,
@@ -229,16 +243,6 @@ def collect_ssh_pixi(
                     activity.log = get_current_log(log_file_path)
                     activity = add_commit_refresh(obj=activity, db=db)
 
-                    # Run script 3 - post-install
-                    stdout = _customize_and_run_template(
-                        template_filename="pixi_3_post_install.sh",
-                        replacements=replacements,
-                        **common_args,
-                    )
-                    logger.debug(f"STDOUT: {stdout}")
-                    activity.log = get_current_log(log_file_path)
-                    activity = add_commit_refresh(obj=activity, db=db)
-
                     # Parse stdout
                     parsed_output = parse_collect_stdout(stdout)
                     package_root_remote = parsed_output["package_root"]
@@ -248,8 +252,6 @@ def collect_ssh_pixi(
                         "project_python_wrapper"
                     ]
 
-                    fractal_ssh.run_command(cmd=f"chmod -R 755 {source_dir}")
-
                     # Read and validate remote manifest file
                     manifest_path_remote = (
                         f"{package_root_remote}/__FRACTAL_MANIFEST__.json"

{fractal_server-2.16.2 → fractal_server-2.16.3}/fractal_server/tasks/v2/ssh/reactivate_pixi.py

@@ -188,12 +188,21 @@ def reactivate_ssh_pixi(
                         remote=pixi_lock_remote,
                     )
 
-                    # Run script 2 - run pixi-install command
+                    # Prepare scripts 2 and 3
                     remote_script2_path = _customize_and_send_template(
                         template_filename="pixi_2_install.sh",
                         replacements=replacements,
                         **common_args,
                     )
+                    remote_script3_path = _customize_and_send_template(
+                        template_filename="pixi_3_post_install.sh",
+                        replacements=replacements,
+                        **common_args,
+                    )
+                    logger.debug(
+                        "Post-installation script written to "
+                        f"{remote_script3_path=}."
+                    )
                     logger.debug(
                         "Installation script written to "
                         f"{remote_script2_path=}."
@@ -201,8 +210,13 @@ def reactivate_ssh_pixi(
                     activity.log = get_current_log(log_file_path)
                     activity = add_commit_refresh(obj=activity, db=db)
 
-                    run_script_on_remote_slurm(
-                        script_path=remote_script2_path,
+                    # Run scripts 2 and 3
+                    stdout = run_script_on_remote_slurm(
+                        script_paths=[
+                            remote_script2_path,
+                            remote_script3_path,
+                            f"chmod -R 755 {source_dir}",
+                        ],
                         slurm_config=settings.pixi.SLURM_CONFIG,
                         fractal_ssh=fractal_ssh,
                         logger_name=LOGGER_NAME,
@@ -214,18 +228,6 @@ def reactivate_ssh_pixi(
                     activity.log = get_current_log(log_file_path)
                     activity = add_commit_refresh(obj=activity, db=db)
 
-                    # Run script 3 - post-install
-                    stdout = _customize_and_run_template(
-                        template_filename="pixi_3_post_install.sh",
-                        replacements=replacements,
-                        **common_args,
-                    )
-                    logger.debug(f"STDOUT: {stdout}")
-                    activity.log = get_current_log(log_file_path)
-                    activity = add_commit_refresh(obj=activity, db=db)
-
-                    fractal_ssh.run_command(cmd=f"chmod -R 755 {source_dir}")
-
                     # Finalize (write metadata to DB)
                     activity.status = TaskGroupActivityStatusV2.OK
                     activity.timestamp_ended = get_timestamp()

{fractal_server-2.16.2 → fractal_server-2.16.3}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "fractal-server"
-version = "2.16.2"
+version = "2.16.3"
 description = "Backend component of the Fractal analytics platform"
 authors = [
     { name="Tommaso Comparin", email="tommaso.comparin@exact-lab.it" },
@@ -26,7 +26,7 @@ dependencies = [
     "fabric >= 3.2.2, <3.3.0",
     "gunicorn >=23.0,<24.0",
     "psycopg[binary] >= 3.1.0, <4.0.0",
-    "cryptography >=45.0.3,<45.1.0",
+    "cryptography >=46.0.0,<47.0.0",
     "tomli_w >=1.2.0, <1.3.0 "
 ]
 
@@ -95,7 +95,7 @@ filterwarnings = [
 markers = ["container", "ssh", "fails_on_macos"]
 
 [tool.bumpver]
-current_version = "2.16.2"
+current_version = "2.16.3"
 version_pattern = "MAJOR.MINOR.PATCH[PYTAGNUM]"
 commit_message = "bump version {old_version} -> {new_version}"
 commit = true

fractal_server-2.16.2/fractal_server/__init__.py

@@ -1 +0,0 @@
-__VERSION__ = "2.16.2"