fractal-server 2.15.0a3__py3-none-any.whl → 2.15.0a5__py3-none-any.whl

fractal_server/tasks/v2/ssh/_utils.py

@@ -1,6 +1,10 @@
 import os
 from pathlib import Path
 
+from sqlalchemy.ext.asyncio import AsyncSession
+
+from ..utils_background import fail_and_cleanup
+from fractal_server.app.models.v2 import TaskGroupActivityV2
 from fractal_server.app.models.v2 import TaskGroupV2
 from fractal_server.logger import get_logger
 from fractal_server.ssh._fabric import FractalSSH
@@ -10,7 +14,7 @@ from fractal_server.tasks.v2.utils_templates import customize_template
 def _customize_and_run_template(
     *,
     template_filename: str,
-    replacements: list[tuple[str, str]],
+    replacements: set[tuple[str, str]],
     script_dir_local: str,
     prefix: str,
     fractal_ssh: FractalSSH,
@@ -66,7 +70,10 @@ def _customize_and_run_template(
 
 
 def _copy_wheel_file_ssh(
-    *, task_group: TaskGroupV2, fractal_ssh: FractalSSH, logger_name: str
+    *,
+    task_group: TaskGroupV2,
+    fractal_ssh: FractalSSH,
+    logger_name: str,
 ) -> str:
     """
     Handle the situation where `task_group.archive_path` is not part of
@@ -81,7 +88,41 @@ def _copy_wheel_file_ssh(
         Path(task_group.path) / Path(task_group.archive_path).name
     ).as_posix()
     cmd = f"cp {source} {dest}"
-    logger.debug(f"[_copy_wheel_file] START {source=} {dest=}")
+    logger.debug(f"[_copy_wheel_file_ssh] START {source=} {dest=}")
     fractal_ssh.run_command(cmd=cmd)
-    logger.debug(f"[_copy_wheel_file] END {source=} {dest=}")
+    logger.debug(f"[_copy_wheel_file_ssh] END {source=} {dest=}")
     return dest
+
+
+def check_ssh_or_fail_and_cleanup(
+    *,
+    fractal_ssh: FractalSSH,
+    task_group: TaskGroupV2,
+    task_group_activity: TaskGroupActivityV2,
+    logger_name: str,
+    log_file_path: Path,
+    db: AsyncSession,
+) -> bool:
+    """
+    Check SSH connection.
+
+    Returns:
+        Whether SSH connection is OK.
+    """
+    try:
+        fractal_ssh.check_connection()
+        return True
+    except Exception as e:
+        logger = get_logger(logger_name=logger_name)
+        logger.error(
+            "Cannot establish SSH connection. " f"Original error: {str(e)}"
+        )
+        fail_and_cleanup(
+            task_group=task_group,
+            task_group_activity=task_group_activity,
+            logger_name=logger_name,
+            log_file_path=log_file_path,
+            exception=e,
+            db=db,
+        )
+        return False

fractal_server/tasks/v2/ssh/collect.py

@@ -2,11 +2,11 @@ import time
 from pathlib import Path
 from tempfile import TemporaryDirectory
 
-from ....ssh._fabric import SingleUseFractalSSH
 from ..utils_background import fail_and_cleanup
 from ..utils_background import get_activity_and_task_group
 from ..utils_background import prepare_tasks_metadata
 from ..utils_database import create_db_tasks_and_update_task_group_sync
+from ._utils import check_ssh_or_fail_and_cleanup
 from fractal_server.app.db import get_sync_db
 from fractal_server.app.schemas.v2 import FractalUploadedFile
 from fractal_server.app.schemas.v2 import TaskGroupActivityActionV2
@@ -14,6 +14,7 @@ from fractal_server.app.schemas.v2 import TaskGroupActivityStatusV2
 from fractal_server.app.schemas.v2.manifest import ManifestV2
 from fractal_server.logger import reset_logger_handlers
 from fractal_server.logger import set_logger
+from fractal_server.ssh._fabric import SingleUseFractalSSH
 from fractal_server.ssh._fabric import SSHConfig
 from fractal_server.tasks.v2.ssh._utils import _customize_and_run_template
 from fractal_server.tasks.v2.utils_background import add_commit_refresh
@@ -68,43 +69,39 @@ def collect_ssh(
             logger_name=LOGGER_NAME,
             log_file_path=log_file_path,
         )
-        with SingleUseFractalSSH(
-            ssh_config=ssh_config,
-            logger_name=LOGGER_NAME,
-        ) as fractal_ssh:
-
-            with next(get_sync_db()) as db:
-                success, task_group, activity = get_activity_and_task_group(
-                    task_group_activity_id=task_group_activity_id,
-                    task_group_id=task_group_id,
-                    db=db,
-                )
-                if not success:
-                    return
-
-                # Log some info
-                logger.info("START")
-                for key, value in task_group.model_dump().items():
-                    logger.debug(f"task_group.{key}: {value}")
-
-                # Check that SSH connection works
+        logger.info("START")
+        with next(get_sync_db()) as db:
+            db_objects_ok, task_group, activity = get_activity_and_task_group(
+                task_group_activity_id=task_group_activity_id,
+                task_group_id=task_group_id,
+                db=db,
+                logger_name=LOGGER_NAME,
+            )
+            if not db_objects_ok:
+                return
+
+            with SingleUseFractalSSH(
+                ssh_config=ssh_config,
+                logger_name=LOGGER_NAME,
+            ) as fractal_ssh:
+
                 try:
-                    fractal_ssh.check_connection()
-                except Exception as e:
-                    logger.error("Cannot establish SSH connection.")
-                    fail_and_cleanup(
+                    # Check SSH connection
+                    ssh_ok = check_ssh_or_fail_and_cleanup(
+                        fractal_ssh=fractal_ssh,
                         task_group=task_group,
                         task_group_activity=activity,
                         logger_name=LOGGER_NAME,
                         log_file_path=log_file_path,
-                        exception=e,
                         db=db,
                     )
-                    return
-
-                try:
+                    if not ssh_ok:
+                        return
 
                     # Check that the (remote) task_group path does not exist
+                    # NOTE: this is not part of the try/except below, in order
+                    # to avoid removing the existing folder (as part of the
+                    # exception-handling).
                     if fractal_ssh.remote_exists(task_group.path):
                         error_msg = f"{task_group.path} already exists."
                         logger.error(error_msg)
@@ -119,9 +116,7 @@ def collect_ssh(
                         return
 
                     # Create remote `task_group.path` and `script_dir_remote`
-                    # folders (note that because of `parents=True` we  are in
-                    # the `no error if existing, make parent directories as
-                    # needed` scenario for `mkdir`)
+                    # folders
                     script_dir_remote = (
                         Path(task_group.path) / SCRIPTS_SUBFOLDER
                     ).as_posix()
@@ -139,8 +134,7 @@ def collect_ssh(
                             Path(tmpdir) / wheel_filename
                         ).as_posix()
                         logger.info(
-                            "Write wheel-file contents into "
-                            f"{tmp_archive_path}"
+                            f"Write wheel file into {tmp_archive_path}"
                         )
                         with open(tmp_archive_path, "wb") as f:
                             f.write(wheel_file.contents)
@@ -161,8 +155,8 @@ def collect_ssh(
                     # Prepare common arguments for _customize_and_run_template
                     common_args = dict(
                         replacements=replacements,
-                        script_dir_local=(
-                            Path(tmpdir) / SCRIPTS_SUBFOLDER
+                        script_dir_local=Path(
+                            tmpdir, SCRIPTS_SUBFOLDER
                         ).as_posix(),
                         script_dir_remote=script_dir_remote,
                         prefix=(
@@ -187,6 +181,7 @@ def collect_ssh(
                     )
                     activity.log = get_current_log(log_file_path)
                     activity = add_commit_refresh(obj=activity, db=db)
+
                     # Run script 2
                     stdout = _customize_and_run_template(
                         template_filename="2_pip_install.sh",
@@ -315,7 +310,7 @@ def collect_ssh(
                     except Exception as e_rm:
                         logger.error(
                             "Removing folder failed. "
-                            f"Original error:\n{str(e_rm)}"
+                            f"Original error: {str(e_rm)}"
                         )
                     fail_and_cleanup(
                         task_group=task_group,

fractal_server/tasks/v2/ssh/collect_pixi.py

@@ -2,13 +2,13 @@ import time
 from pathlib import Path
 from tempfile import TemporaryDirectory
 
-from ....ssh._fabric import SingleUseFractalSSH
 from ..utils_background import fail_and_cleanup
 from ..utils_background import get_activity_and_task_group
 from ..utils_background import prepare_tasks_metadata
 from ..utils_database import create_db_tasks_and_update_task_group_sync
 from ..utils_pixi import parse_collect_stdout
 from ..utils_pixi import SOURCE_DIR_NAME
+from ._utils import check_ssh_or_fail_and_cleanup
 from fractal_server.app.db import get_sync_db
 from fractal_server.app.schemas.v2 import FractalUploadedFile
 from fractal_server.app.schemas.v2 import TaskGroupActivityActionV2
@@ -17,6 +17,7 @@ from fractal_server.app.schemas.v2.manifest import ManifestV2
 from fractal_server.config import get_settings
 from fractal_server.logger import reset_logger_handlers
 from fractal_server.logger import set_logger
+from fractal_server.ssh._fabric import SingleUseFractalSSH
 from fractal_server.ssh._fabric import SSHConfig
 from fractal_server.syringe import Inject
 from fractal_server.tasks.v2.ssh._utils import _customize_and_run_template
@@ -64,43 +65,34 @@ def collect_ssh_pixi(
             logger_name=LOGGER_NAME,
             log_file_path=log_file_path,
         )
-        with SingleUseFractalSSH(
-            ssh_config=ssh_config,
-            logger_name=LOGGER_NAME,
-        ) as fractal_ssh:
-
-            with next(get_sync_db()) as db:
-                success, task_group, activity = get_activity_and_task_group(
-                    task_group_activity_id=task_group_activity_id,
-                    task_group_id=task_group_id,
-                    db=db,
-                )
-                if not success:
-                    return
-
-                # Log some info
-                logger.info("START")
-                for key, value in task_group.model_dump(
-                    exclude={"env_info"}
-                ).items():
-                    logger.debug(f"task_group.{key}: {value}")
+        logger.info("START")
+        with next(get_sync_db()) as db:
+            db_objects_ok, task_group, activity = get_activity_and_task_group(
+                task_group_activity_id=task_group_activity_id,
+                task_group_id=task_group_id,
+                db=db,
+                logger_name=LOGGER_NAME,
+            )
+            if not db_objects_ok:
+                return
+
+            with SingleUseFractalSSH(
+                ssh_config=ssh_config,
+                logger_name=LOGGER_NAME,
+            ) as fractal_ssh:
 
-                # Check that SSH connection works
                 try:
-                    fractal_ssh.check_connection()
-                except Exception as e:
-                    logger.error("Cannot establish SSH connection.")
-                    fail_and_cleanup(
+                    # Check SSH connection
+                    ssh_ok = check_ssh_or_fail_and_cleanup(
+                        fractal_ssh=fractal_ssh,
                         task_group=task_group,
                         task_group_activity=activity,
                         logger_name=LOGGER_NAME,
                         log_file_path=log_file_path,
-                        exception=e,
                         db=db,
                     )
-                    return
-
-                try:
+                    if not ssh_ok:
+                        return
 
                     # Check that the (remote) task_group path does not exist
                     if fractal_ssh.remote_exists(task_group.path):
@@ -117,11 +109,9 @@ def collect_ssh_pixi(
                         return
 
                     # Create remote `task_group.path` and `script_dir_remote`
-                    # folders (note that because of `parents=True` we  are in
-                    # the `no error if existing, make parent directories as
-                    # needed` scenario for `mkdir`)
-                    script_dir_remote = (
-                        Path(task_group.path) / SCRIPTS_SUBFOLDER
+                    # folders
+                    script_dir_remote = Path(
+                        task_group.path, SCRIPTS_SUBFOLDER
                     ).as_posix()
                     fractal_ssh.mkdir(folder=task_group.path, parents=True)
                     fractal_ssh.mkdir(folder=script_dir_remote, parents=True)
@@ -133,9 +123,7 @@ def collect_ssh_pixi(
                         Path(task_group.path) / tar_gz_filename
                     ).as_posix()
                     tmp_archive_path = Path(tmpdir, tar_gz_filename).as_posix()
-                    logger.info(
-                        f"Write tar.gz-file contents into {tmp_archive_path}"
-                    )
+                    logger.info(f"Write tar.gz file into {tmp_archive_path}")
                     with open(tmp_archive_path, "wb") as f:
                         f.write(tar_gz_file.contents)
                     fractal_ssh.send_file(
@@ -145,19 +133,32 @@ def collect_ssh_pixi(
                     task_group.archive_path = archive_path
                     task_group = add_commit_refresh(obj=task_group, db=db)
 
-                    # Set `pixi_bin`
                     settings = Inject(get_settings)
-                    pixi_home = settings.pixi.versions[task_group.pixi_version]
-
                     replacements = {
-                        ("__PIXI_HOME__", pixi_home),
+                        (
+                            "__PIXI_HOME__",
+                            settings.pixi.versions[task_group.pixi_version],
+                        ),
                         ("__PACKAGE_DIR__", task_group.path),
-                        ("__TAR_GZ_PATH__", archive_path),
+                        ("__TAR_GZ_PATH__", task_group.archive_path),
                         (
                             "__IMPORT_PACKAGE_NAME__",
                             task_group.pkg_name.replace("-", "_"),
                         ),
                         ("__SOURCE_DIR_NAME__", SOURCE_DIR_NAME),
+                        ("__FROZEN_OPTION__", ""),
+                        (
+                            "__TOKIO_WORKER_THREADS__",
+                            str(settings.pixi.TOKIO_WORKER_THREADS),
+                        ),
+                        (
+                            "__PIXI_CONCURRENT_SOLVES__",
+                            str(settings.pixi.PIXI_CONCURRENT_SOLVES),
+                        ),
+                        (
+                            "__PIXI_CONCURRENT_DOWNLOADS__",
+                            str(settings.pixi.PIXI_CONCURRENT_DOWNLOADS),
+                        ),
                     }
 
                     logger.info("installing - START")
@@ -169,7 +170,7 @@ def collect_ssh_pixi(
 
                     common_args = dict(
                         script_dir_local=(
-                            Path(tmpdir) / SCRIPTS_SUBFOLDER
+                            Path(tmpdir, SCRIPTS_SUBFOLDER)
                         ).as_posix(),
                         script_dir_remote=script_dir_remote,
                         prefix=(
@@ -214,6 +215,11 @@ def collect_ssh_pixi(
                         "project_python_wrapper"
                     ]
 
+                    source_dir = Path(
+                        task_group.path, SOURCE_DIR_NAME
+                    ).as_posix()
+                    fractal_ssh.run_command(cmd=f"chmod 755 {source_dir} -R")
+
                     # Read and validate remote manifest file
                     manifest_path_remote = (
                         f"{package_root_remote}/__FRACTAL_MANIFEST__.json"
@@ -294,7 +300,7 @@ def collect_ssh_pixi(
                     except Exception as e_rm:
                         logger.error(
                             "Removing folder failed. "
-                            f"Original error:\n{str(e_rm)}"
+                            f"Original error: {str(e_rm)}"
                         )
                     fail_and_cleanup(
                         task_group=task_group,

fractal_server/tasks/v2/ssh/deactivate.py

@@ -8,6 +8,7 @@ from ..utils_background import get_activity_and_task_group
 from ..utils_templates import get_collection_replacements
 from ._utils import _copy_wheel_file_ssh
 from ._utils import _customize_and_run_template
+from ._utils import check_ssh_or_fail_and_cleanup
 from fractal_server.app.db import get_sync_db
 from fractal_server.app.schemas.v2 import TaskGroupActivityActionV2
 from fractal_server.app.schemas.v2 import TaskGroupV2OriginEnum
@@ -53,41 +54,33 @@ def deactivate_ssh(
             logger_name=LOGGER_NAME,
             log_file_path=log_file_path,
         )
-        with SingleUseFractalSSH(
-            ssh_config=ssh_config,
-            logger_name=LOGGER_NAME,
-        ) as fractal_ssh:
-
-            with next(get_sync_db()) as db:
-                success, task_group, activity = get_activity_and_task_group(
-                    task_group_activity_id=task_group_activity_id,
-                    task_group_id=task_group_id,
-                    db=db,
-                )
-                if not success:
-                    return
-
-                # Log some info
-                logger.debug("START")
-                for key, value in task_group.model_dump().items():
-                    logger.debug(f"task_group.{key}: {value}")
-
-                # Check that SSH connection works
+        logger.debug("START")
+        with next(get_sync_db()) as db:
+            db_objects_ok, task_group, activity = get_activity_and_task_group(
+                task_group_activity_id=task_group_activity_id,
+                task_group_id=task_group_id,
+                db=db,
+                logger_name=LOGGER_NAME,
+            )
+            if not db_objects_ok:
+                return
+
+            with SingleUseFractalSSH(
+                ssh_config=ssh_config,
+                logger_name=LOGGER_NAME,
+            ) as fractal_ssh:
                 try:
-                    fractal_ssh.check_connection()
-                except Exception as e:
-                    logger.error("Cannot establish SSH connection.")
-                    fail_and_cleanup(
+                    # Check SSH connection
+                    ssh_ok = check_ssh_or_fail_and_cleanup(
+                        fractal_ssh=fractal_ssh,
                         task_group=task_group,
                         task_group_activity=activity,
                         logger_name=LOGGER_NAME,
                         log_file_path=log_file_path,
-                        exception=e,
                         db=db,
                     )
-                    return
-
-                try:
+                    if not ssh_ok:
+                        return
 
                     # Check that the (local) task_group venv_path does exist
                     if not fractal_ssh.remote_exists(task_group.venv_path):

fractal_server/tasks/v2/ssh/deactivate_pixi.py

@@ -5,6 +5,7 @@ from ..utils_background import add_commit_refresh
 from ..utils_background import fail_and_cleanup
 from ..utils_background import get_activity_and_task_group
 from ..utils_pixi import SOURCE_DIR_NAME
+from ._utils import check_ssh_or_fail_and_cleanup
 from fractal_server.app.db import get_sync_db
 from fractal_server.app.schemas.v2.task_group import TaskGroupActivityStatusV2
 from fractal_server.logger import reset_logger_handlers
@@ -46,43 +47,34 @@ def deactivate_ssh_pixi(
             logger_name=LOGGER_NAME,
             log_file_path=log_file_path,
         )
-        with SingleUseFractalSSH(
-            ssh_config=ssh_config,
-            logger_name=LOGGER_NAME,
-        ) as fractal_ssh:
-
-            with next(get_sync_db()) as db:
-                success, task_group, activity = get_activity_and_task_group(
-                    task_group_activity_id=task_group_activity_id,
-                    task_group_id=task_group_id,
-                    db=db,
-                )
-                if not success:
-                    return
+        logger.debug("START")
+        with next(get_sync_db()) as db:
+            db_objects_ok, task_group, activity = get_activity_and_task_group(
+                task_group_activity_id=task_group_activity_id,
+                task_group_id=task_group_id,
+                db=db,
+                logger_name=LOGGER_NAME,
+            )
+            if not db_objects_ok:
+                return
 
-                # Log some info
-                logger.debug("START")
-                for key, value in task_group.model_dump(
-                    exclude={"env_info"}
-                ).items():
-                    logger.debug(f"task_group.{key}: {value}")
-
-                # Check that SSH connection works
+            with SingleUseFractalSSH(
+                ssh_config=ssh_config,
+                logger_name=LOGGER_NAME,
+            ) as fractal_ssh:
                 try:
-                    fractal_ssh.check_connection()
-                except Exception as e:
-                    logger.error("Cannot establish SSH connection.")
-                    fail_and_cleanup(
+                    # Check SSH connection
+                    ssh_ok = check_ssh_or_fail_and_cleanup(
+                        fractal_ssh=fractal_ssh,
                         task_group=task_group,
                         task_group_activity=activity,
                         logger_name=LOGGER_NAME,
                         log_file_path=log_file_path,
-                        exception=e,
                         db=db,
                     )
-                    return
+                    if not ssh_ok:
+                        return
 
-                try:
                     # Check that the (remote) task_group venv_path does exist
                     source_dir = Path(
                         task_group.path, SOURCE_DIR_NAME

fractal_server/tasks/v2/ssh/reactivate.py

@@ -7,6 +7,7 @@ from ..utils_background import fail_and_cleanup
 from ..utils_background import get_activity_and_task_group
 from ..utils_templates import get_collection_replacements
 from ._utils import _customize_and_run_template
+from ._utils import check_ssh_or_fail_and_cleanup
 from fractal_server.app.db import get_sync_db
 from fractal_server.app.schemas.v2 import TaskGroupActivityActionV2
 from fractal_server.app.schemas.v2.task_group import TaskGroupActivityStatusV2
@@ -54,41 +55,34 @@ def reactivate_ssh(
             log_file_path=log_file_path,
         )
 
-        with SingleUseFractalSSH(
-            ssh_config=ssh_config,
-            logger_name=LOGGER_NAME,
-        ) as fractal_ssh:
-
-            with next(get_sync_db()) as db:
-                success, task_group, activity = get_activity_and_task_group(
-                    task_group_activity_id=task_group_activity_id,
-                    task_group_id=task_group_id,
-                    db=db,
-                )
-                if not success:
-                    return
-
-                # Log some info
-                logger.info("START")
-                for key, value in task_group.model_dump().items():
-                    logger.debug(f"task_group.{key}: {value}")
-
-                # Check that SSH connection works
+        logger.info("START")
+        with next(get_sync_db()) as db:
+            db_objects_ok, task_group, activity = get_activity_and_task_group(
+                task_group_activity_id=task_group_activity_id,
+                task_group_id=task_group_id,
+                db=db,
+                logger_name=LOGGER_NAME,
+            )
+            if not db_objects_ok:
+                return
+
+            with SingleUseFractalSSH(
+                ssh_config=ssh_config,
+                logger_name=LOGGER_NAME,
+            ) as fractal_ssh:
                 try:
-                    fractal_ssh.check_connection()
-                except Exception as e:
-                    logger.error("Cannot establish SSH connection.")
-                    fail_and_cleanup(
+                    # Check SSH connection
+                    ssh_ok = check_ssh_or_fail_and_cleanup(
+                        fractal_ssh=fractal_ssh,
                         task_group=task_group,
                         task_group_activity=activity,
                         logger_name=LOGGER_NAME,
                         log_file_path=log_file_path,
-                        exception=e,
                         db=db,
                     )
-                    return
+                    if not ssh_ok:
+                        return
 
-                try:
                     # Check that the (remote) task_group venv_path does not
                     # exist
                     if fractal_ssh.remote_exists(task_group.venv_path):
@@ -192,8 +186,8 @@ def reactivate_ssh(
                         logger.info(f"Deleted folder {task_group.venv_path}")
                     except Exception as rm_e:
                         logger.error(
-                            "Removing folder failed.\n"
-                            f"Original error:\n{str(rm_e)}"
+                            "Removing folder failed. "
+                            f"Original error: {str(rm_e)}"
                         )
 
                     fail_and_cleanup(