fractal-server 2.15.0a1__py3-none-any.whl → 2.15.0a3__py3-none-any.whl

fractal_server/__init__.py

@@ -1 +1 @@
-__VERSION__ = "2.15.0a1"
+__VERSION__ = "2.15.0a3"

fractal_server/tasks/v2/local/collect_pixi.py

@@ -57,7 +57,9 @@ def collect_local_pixi(
                 return
 
             logger.info("START")
-            for key, value in task_group.model_dump().items():
+            for key, value in task_group.model_dump(
+                exclude={"env_info"}
+            ).items():
                 logger.debug(f"task_group.{key}: {value}")
 
             if Path(task_group.path).exists():
@@ -73,9 +75,6 @@ def collect_local_pixi(
                 )
                 return
 
-            # Set `pixi_home`
-            pixi_home = settings.pixi.versions[task_group.pixi_version]
-
             try:
                 Path(task_group.path).mkdir(parents=True)
                 logger.info(f"Created {task_group.path}")
@@ -90,7 +89,10 @@ def collect_local_pixi(
 
                 common_args = dict(
                     replacements={
-                        ("__PIXI_HOME__", pixi_home),
+                        (
+                            "__PIXI_HOME__",
+                            settings.pixi.versions[task_group.pixi_version],
+                        ),
                         ("__PACKAGE_DIR__", task_group.path),
                         ("__TAR_GZ_PATH__", archive_path),
                         (

fractal_server/tasks/v2/local/deactivate_pixi.py

@@ -52,7 +52,9 @@ def deactivate_local_pixi(
             # Log some info
             logger.debug("START")
 
-            for key, value in task_group.model_dump().items():
+            for key, value in task_group.model_dump(
+                exclude={"env_info"}
+            ).items():
                 logger.debug(f"task_group.{key}: {value}")
 
             source_dir = Path(task_group.path, SOURCE_DIR_NAME)

fractal_server/tasks/v2/local/reactivate_pixi.py

@@ -1,6 +1,5 @@
-import shlex
 import shutil
-import subprocess  # nosec
+import time
 from pathlib import Path
 from tempfile import TemporaryDirectory
 
@@ -9,13 +8,16 @@ from ..utils_background import fail_and_cleanup
 from ..utils_background import get_activity_and_task_group
 from ..utils_pixi import SOURCE_DIR_NAME
 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
 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.syringe import Inject
 from fractal_server.tasks.utils import get_log_path
+from fractal_server.tasks.v2.local._utils import _customize_and_run_template
 from fractal_server.tasks.v2.utils_background import get_current_log
+from fractal_server.tasks.v2.utils_templates import SCRIPTS_SUBFOLDER
 from fractal_server.utils import get_timestamp
 
 
@@ -55,7 +57,9 @@ def reactivate_local_pixi(
             # Log some info
             logger.debug("START")
 
-            for key, value in task_group.model_dump().items():
+            for key, value in task_group.model_dump(
+                exclude={"env_info"}
+            ).items():
                 logger.debug(f"task_group.{key}: {value}")
 
             source_dir = Path(task_group.path, SOURCE_DIR_NAME).as_posix()
@@ -76,42 +80,61 @@ def reactivate_local_pixi(
                 activity.status = TaskGroupActivityStatusV2.ONGOING
                 activity = add_commit_refresh(obj=activity, db=db)
 
-                logger.debug("start - writing pixi lock")
-                with open(f"{task_group.path}/pixi.lock", "w") as f:
-                    f.write(task_group.env_info)
-                logger.debug("end - writing pixi lock")
-
-                subprocess.run(  # nosec
-                    shlex.split(
-                        f"tar xz -f {task_group.archive_path} "
-                        f"{Path(task_group.archive_path).name}"
+                settings = Inject(get_settings)
+                common_args = dict(
+                    replacements={
+                        (
+                            "__PIXI_HOME__",
+                            settings.pixi.versions[task_group.pixi_version],
+                        ),
+                        ("__PACKAGE_DIR__", task_group.path),
+                        ("__TAR_GZ_PATH__", task_group.archive_path),
+                        (
+                            "__IMPORT_PACKAGE_NAME__",
+                            task_group.pkg_name.replace("-", "_"),
+                        ),
+                        ("__SOURCE_DIR_NAME__", SOURCE_DIR_NAME),
+                        ("__FROZEN_OPTION__", "true"),
+                    },
+                    script_dir=Path(
+                        task_group.path, SCRIPTS_SUBFOLDER
+                    ).as_posix(),
+                    prefix=(
+                        f"{int(time.time())}_"
+                        f"{TaskGroupActivityActionV2.REACTIVATE}"
                     ),
-                    encoding="utf-8",
-                    cwd=task_group.path,
+                    logger_name=LOGGER_NAME,
                 )
 
-                subprocess.run(  # nosec
-                    shlex.split(
-                        f"mv {Path(task_group.archive_path).name} {source_dir}"
-                    ),
-                    encoding="utf-8",
-                    cwd=task_group.path,
+                # Run script 1 - extract tar.gz into `source_dir`
+                _customize_and_run_template(
+                    template_filename="pixi_1_extract.sh",
+                    **common_args,
                 )
+                activity.log = get_current_log(log_file_path)
+                activity = add_commit_refresh(obj=activity, db=db)
 
-                settings = Inject(get_settings)
-                pixi_home = settings.pixi.versions[task_group.pixi_version]
-                pixi_bin = Path(pixi_home, "bin/pixi").as_posix()
-
-                logger.debug("start - pixi install")
-                subprocess.run(  # nosec
-                    shlex.split(
-                        f"{pixi_bin} install "
-                        f"--manifest-path {source_dir}/pyproject.toml --frozen"
-                    ),
-                    encoding="utf-8",
-                    cwd=task_group.path,
+                # Write pixi.lock into `source_dir`
+                logger.debug(f"start - writing {source_dir}/pixi.lock")
+                with Path(source_dir, "pixi.lock").open("w") as f:
+                    f.write(task_group.env_info)
+                logger.debug(f"end - writing {source_dir}/pixi.lock")
+
+                # Run script 2 - run pixi-install command
+                _customize_and_run_template(
+                    template_filename="pixi_2_install.sh",
+                    **common_args,
+                )
+                activity.log = get_current_log(log_file_path)
+                activity = add_commit_refresh(obj=activity, db=db)
+
+                # Run script 3
+                _customize_and_run_template(
+                    template_filename="pixi_3_post_install.sh",
+                    **common_args,
                 )
-                logger.debug("end - pixi install")
+                activity.log = get_current_log(log_file_path)
+                activity = add_commit_refresh(obj=activity, db=db)
 
                 activity.log = get_current_log(log_file_path)
                 activity.status = TaskGroupActivityStatusV2.OK

fractal_server/tasks/v2/ssh/collect_pixi.py

@@ -80,7 +80,9 @@ def collect_ssh_pixi(
 
                 # Log some info
                 logger.info("START")
-                for key, value in task_group.model_dump().items():
+                for key, value in task_group.model_dump(
+                    exclude={"env_info"}
+                ).items():
                     logger.debug(f"task_group.{key}: {value}")
 
                 # Check that SSH connection works
@@ -130,9 +132,7 @@ def collect_ssh_pixi(
                     archive_path = (
                         Path(task_group.path) / tar_gz_filename
                     ).as_posix()
-                    tmp_archive_path = (
-                        Path(tmpdir) / 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}"
                     )
@@ -176,8 +176,8 @@ def collect_ssh_pixi(
                             f"{int(time.time())}_"
                             f"{TaskGroupActivityActionV2.COLLECT}"
                         ),
-                        fractal_ssh=fractal_ssh,
                         logger_name=LOGGER_NAME,
+                        fractal_ssh=fractal_ssh,
                     )
 
                     # Run the three pixi-related scripts

fractal_server/tasks/v2/ssh/deactivate_pixi.py

@@ -62,7 +62,9 @@ def deactivate_ssh_pixi(
 
                 # Log some info
                 logger.debug("START")
-                for key, value in task_group.model_dump().items():
+                for key, value in task_group.model_dump(
+                    exclude={"env_info"}
+                ).items():
                     logger.debug(f"task_group.{key}: {value}")
 
                 # Check that SSH connection works

fractal_server/tasks/v2/ssh/reactivate_pixi.py

@@ -58,7 +58,9 @@ def reactivate_ssh_pixi(
 
                 # Log some info
                 logger.info("START")
-                for key, value in task_group.model_dump().items():
+                for key, value in task_group.model_dump(
+                    exclude={"env_info"}
+                ).items():
                     logger.debug(f"task_group.{key}: {value}")
 
                 # Check that SSH connection works

{fractal_server-2.15.0a1.dist-info → fractal_server-2.15.0a3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: fractal-server
-Version: 2.15.0a1
+Version: 2.15.0a3
 Summary: Backend component of the Fractal analytics platform
 License: BSD-3-Clause
 Author: Tommaso Comparin

{fractal_server-2.15.0a1.dist-info → fractal_server-2.15.0a3.dist-info}/RECORD

@@ -1,4 +1,4 @@
-fractal_server/__init__.py,sha256=jqf_k5MzFRozDqpvzsTxEimwRfYyqB0UiYf2p5oD-pw,25
+fractal_server/__init__.py,sha256=tcBKTFic3HqyDYYBuQ8rt1m1EBOL362w1jDviQBo4aI,25
 fractal_server/__main__.py,sha256=rkM8xjY1KeS3l63irB8yCrlVobR-73uDapC4wvrIlxI,6957
 fractal_server/alembic.ini,sha256=MWwi7GzjzawI9cCAK1LW7NxIBQDUqD12-ptJoq5JpP0,3153
 fractal_server/app/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -193,19 +193,19 @@ fractal_server/tasks/v2/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG
 fractal_server/tasks/v2/local/__init__.py,sha256=S842wRersYKBKjc7xbmj0ov8b5i1YuCHa2f_yYuxcaI,312
 fractal_server/tasks/v2/local/_utils.py,sha256=n-w1IqgOTeeXLE0LoHBixrU7kkg-eYEPWepur6g7DQA,2664
 fractal_server/tasks/v2/local/collect.py,sha256=OIqvvXqI631MjHDGxYj3a7AmC0FhMZ2v2LD3RSZ18wU,12000
-fractal_server/tasks/v2/local/collect_pixi.py,sha256=0vHDSq34VMFExz_TX7hwd0WrXilIEvfHtrs107zjX9U,9847
+fractal_server/tasks/v2/local/collect_pixi.py,sha256=hm-57SixLujb6wGUI2RBOv49g3E14j80BxGpxhW5x50,9915
 fractal_server/tasks/v2/local/deactivate.py,sha256=jaJ-Ejq29JQTZpiQjWHCRf2yUPZUbnjvaQrqnNkmFuo,9836
-fractal_server/tasks/v2/local/deactivate_pixi.py,sha256=S3ipLVwpzkpGpSKVsDBdiv3RBt0DsVL_sGux3I5aSg8,3597
+fractal_server/tasks/v2/local/deactivate_pixi.py,sha256=JM5YM8HLd6YoJdkUH8k8WhXjpydfB3EIhbrL-6SdZgU,3647
 fractal_server/tasks/v2/local/reactivate.py,sha256=ZZhwyoQQ8Lzkk18BB4l3pr8x8VI-MnZSoClKnMvTy14,5860
-fractal_server/tasks/v2/local/reactivate_pixi.py,sha256=MRixXYbQPq3Cc47r0bBQc-4Spj8B1dgqn1uuQKrlPQA,5317
+fractal_server/tasks/v2/local/reactivate_pixi.py,sha256=wAUpGWS8mbWn78T2Eh-b6fRDAIIh_d60DUNsFAwN69I,6542
 fractal_server/tasks/v2/ssh/__init__.py,sha256=vX5aIM9Hbn2T_cIP_LrZ5ekRqJzYm_GSfp-4Iv7kqeI,300
 fractal_server/tasks/v2/ssh/_utils.py,sha256=VAagoseIQW_fSsbwLencqQGyPflQii-Tvzk-r58g478,2834
 fractal_server/tasks/v2/ssh/collect.py,sha256=4PwHLEBjY6CV0URHfin47YXPQnhcoizBug2-Syh1CKQ,14543
-fractal_server/tasks/v2/ssh/collect_pixi.py,sha256=C1hJE8GcROLFfPOT2YnmCDfCvO8jtaSsUzWlvxvSCQc,13273
+fractal_server/tasks/v2/ssh/collect_pixi.py,sha256=uzDVM3zN3m6U3uekH2qKjxQyeFOi9l_ZU5e-iExJCiw,13282
 fractal_server/tasks/v2/ssh/deactivate.py,sha256=A4v9pcualcGD7l-eWcnMbM0N0HEsectHFA9lJnDXlM0,12639
-fractal_server/tasks/v2/ssh/deactivate_pixi.py,sha256=qksD9ccpjy0v8ckhbZUfcuFVJf5iL25nj6wHNqvDkUg,4947
+fractal_server/tasks/v2/ssh/deactivate_pixi.py,sha256=18S9CQ7XA1YS4GHHFl-1HzHRtKnI2TNDSxvuFeA1HhM,5005
 fractal_server/tasks/v2/ssh/reactivate.py,sha256=IWekB37oCWzqiFvHe2ncsvL1qgM9RVCmqe3CMBaz5L8,8472
-fractal_server/tasks/v2/ssh/reactivate_pixi.py,sha256=khOJuLon3l_Vj6whJWkcw7w0rnUsp6cq2fIdTTsZuFY,3789
+fractal_server/tasks/v2/ssh/reactivate_pixi.py,sha256=Szs4yuDOp2kib1Sda7AFQsHtVQLJstGhtFSUjT9hZrs,3847
 fractal_server/tasks/v2/templates/1_create_venv.sh,sha256=PK0jdHKtQpda1zULebBaVPORt4t6V17wa4N1ohcj5ac,548
 fractal_server/tasks/v2/templates/2_pip_install.sh,sha256=jMJPQJXHKznO6fxOOXtFXKPdCmTf1VLLWj_JL_ZdKxo,1644
 fractal_server/tasks/v2/templates/3_pip_freeze.sh,sha256=JldREScEBI4cD_qjfX4UK7V4aI-FnX9ZvVNxgpSOBFc,168
@@ -229,8 +229,8 @@ fractal_server/types/validators/_workflow_task_arguments_validators.py,sha256=HL
 fractal_server/urls.py,sha256=QjIKAC1a46bCdiPMu3AlpgFbcv6a4l3ABcd5xz190Og,471
 fractal_server/utils.py,sha256=Vn35lApt1T1J8nc09sAVqd10Cy0sa3dLipcljI-hkuk,2185
 fractal_server/zip_tools.py,sha256=tqz_8f-vQ9OBRW-4OQfO6xxY-YInHTyHmZxU7U4PqZo,4885
-fractal_server-2.15.0a1.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
-fractal_server-2.15.0a1.dist-info/METADATA,sha256=BjMlnSvVc1DYozWmqOI19lWcVATlbEG_ELwzyvo4Hlc,4245
-fractal_server-2.15.0a1.dist-info/WHEEL,sha256=7dDg4QLnNKTvwIDR9Ac8jJaAmBC_owJrckbC0jjThyA,88
-fractal_server-2.15.0a1.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
-fractal_server-2.15.0a1.dist-info/RECORD,,
+fractal_server-2.15.0a3.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
+fractal_server-2.15.0a3.dist-info/METADATA,sha256=Ohmn8BKN9-iTrWF56LJDlUnfC7ZBCi_Y4jX6j0IwAt8,4245
+fractal_server-2.15.0a3.dist-info/WHEEL,sha256=7dDg4QLnNKTvwIDR9Ac8jJaAmBC_owJrckbC0jjThyA,88
+fractal_server-2.15.0a3.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
+fractal_server-2.15.0a3.dist-info/RECORD,,