fractal-server 2.15.0a0__py3-none-any.whl → 2.15.0a2__py3-none-any.whl

fractal_server/tasks/v2/utils_background.py

@@ -1,3 +1,4 @@
+import logging
 from pathlib import Path
 from typing import TypeVar
 
@@ -24,6 +25,24 @@ def add_commit_refresh(*, obj: T, db: DBSyncSession) -> T:
     return obj
 
 
+def get_activity_and_task_group(
+    *,
+    task_group_activity_id: int,
+    task_group_id: int,
+    db: DBSyncSession,
+) -> tuple[bool, TaskGroupV2, TaskGroupActivityV2]:
+    task_group = db.get(TaskGroupV2, task_group_id)
+    activity = db.get(TaskGroupActivityV2, task_group_activity_id)
+    if activity is None or task_group is None:
+        logging.error(
+            "Cannot find database rows with "
+            f"{task_group_id=} and {task_group_activity_id=}:\n"
+            f"{task_group=}\n{activity=}. Exit."
+        )
+        return False, None, None
+    return True, task_group, activity
+
+
 def fail_and_cleanup(
     task_group: TaskGroupV2,
     task_group_activity: TaskGroupActivityV2,
@@ -53,8 +72,7 @@ def prepare_tasks_metadata(
     package_manifest: ManifestV2,
     package_root: Path,
     python_bin: Path | None = None,
-    pixi_bin: str | None = None,
-    pixi_manifest_path: str | None = None,
+    project_python_wrapper: Path | None = None,
     package_version: str | None = None,
 ) -> list[TaskCreateV2]:
     """
@@ -65,17 +83,19 @@ def prepare_tasks_metadata(
         package_root:
         package_version:
         python_bin:
-        pixi_bin:
+        project_python_wrapper:
     """
-    if bool(pixi_bin is None) == bool(python_bin is None):
-        raise UnreachableBranchError(
-            f"Either {pixi_bin} or {python_bin} must be set."
-        )
-    if pixi_bin is not None and pixi_manifest_path is None:
+
+    if bool(project_python_wrapper is None) == bool(python_bin is None):
         raise UnreachableBranchError(
-            f"If {pixi_bin} is set, pixi_manifest_path must be set."
+            f"Either {project_python_wrapper} or {python_bin} must be set."
         )
 
+    if python_bin is not None:
+        actual_python = python_bin
+    else:
+        actual_python = project_python_wrapper
+
     task_list = []
     for _task in package_manifest.task_list:
         # Set non-command attributes
@@ -89,28 +109,15 @@ def prepare_tasks_metadata(
         # Set command attributes
         if _task.executable_non_parallel is not None:
             non_parallel_path = package_root / _task.executable_non_parallel
-            if python_bin is not None:
-                cmd_non_parallel = (
-                    f"{python_bin.as_posix()} {non_parallel_path.as_posix()}"
-                )
-            else:
-                cmd_non_parallel = (
-                    f"{pixi_bin} run --manifest-path {pixi_manifest_path} "
-                    "--no-lockfile-update python "
-                    f"{non_parallel_path.as_posix()}"
-                )
+            cmd_non_parallel = (
+                f"{actual_python.as_posix()} {non_parallel_path.as_posix()}"
+            )
             task_attributes["command_non_parallel"] = cmd_non_parallel
         if _task.executable_parallel is not None:
             parallel_path = package_root / _task.executable_parallel
-            if python_bin is not None:
-                cmd_parallel = (
-                    f"{python_bin.as_posix()} {parallel_path.as_posix()}"
-                )
-            else:
-                cmd_parallel = (
-                    f"{pixi_bin} run --manifest-path {pixi_manifest_path} "
-                    f"--no-lockfile-update python {parallel_path.as_posix()}"
-                )
+            cmd_parallel = (
+                f"{actual_python.as_posix()} {parallel_path.as_posix()}"
+            )
             task_attributes["command_parallel"] = cmd_parallel
         # Create object
         task_obj = TaskCreateV2(

fractal_server/tasks/v2/utils_pixi.py

@@ -7,6 +7,7 @@ class ParsedOutput(TypedDict):
     package_root: str
     venv_size: str
     venv_file_number: str
+    project_python_wrapper: str
 
 
 def parse_collect_stdout(stdout: str) -> ParsedOutput:
@@ -17,6 +18,7 @@ def parse_collect_stdout(stdout: str) -> ParsedOutput:
         ("Package folder:", "package_root"),
         ("Disk usage:", "venv_size"),
         ("Number of files:", "venv_file_number"),
+        ("Project Python wrapper:", "project_python_wrapper"),
     ]
     stdout_lines = stdout.splitlines()
     attributes = dict()

{fractal_server-2.15.0a0.dist-info → fractal_server-2.15.0a2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: fractal-server
-Version: 2.15.0a0
+Version: 2.15.0a2
 Summary: Backend component of the Fractal analytics platform
 License: BSD-3-Clause
 Author: Tommaso Comparin

{fractal_server-2.15.0a0.dist-info → fractal_server-2.15.0a2.dist-info}/RECORD

@@ -1,4 +1,4 @@
-fractal_server/__init__.py,sha256=bRI_27InR891I2DVNDGmrq1dL1GzKxuY-VlNbPye6Eo,25
+fractal_server/__init__.py,sha256=p2CNc7pXWHJeIFFY2UyN5qnuVf1-pAw9mr2D7XjIBDI,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
@@ -47,9 +47,9 @@ fractal_server/app/routes/api/v2/submit.py,sha256=_BDkWtFdo8-p7kZ0Oxaidei04MfuBe
 fractal_server/app/routes/api/v2/task.py,sha256=ptS47XtxnHzk9bPNZV24Wfroo5sP19RE0-LsfX0ZvOc,7018
 fractal_server/app/routes/api/v2/task_collection.py,sha256=MRaf_-rI4dL6Sfn8XuDUZ-f9a_60V-ChPvPEEuzCzCc,12599
 fractal_server/app/routes/api/v2/task_collection_custom.py,sha256=3EZAzTVlt3wrHAuwxfcYo7LpHefLCcQUctZuolJOQHE,6728
-fractal_server/app/routes/api/v2/task_collection_pixi.py,sha256=aeosGRONv4C53uwb4sFMGIvPvjzi59d7CsxUv86D6N4,8218
+fractal_server/app/routes/api/v2/task_collection_pixi.py,sha256=oHTTB1gXoX2mbuQTvH7SuW4GYrGOfmb9xHZ8DwChmcE,8219
 fractal_server/app/routes/api/v2/task_group.py,sha256=M96VoKcLqOpZlY0RWnsHza8jN0dzAWK9lxw87Om3Fbw,9063
-fractal_server/app/routes/api/v2/task_group_lifecycle.py,sha256=MUtLo_XKoGQTV392dLlNgXuRkrbOTbrxUeyp5uPHgw8,9339
+fractal_server/app/routes/api/v2/task_group_lifecycle.py,sha256=vCIAuSkepwLZw05ZLn46MOB4x6ZN_v3tXXyjv4f6rJw,10070
 fractal_server/app/routes/api/v2/task_version_update.py,sha256=o8W_C0I84X0u8gAMnCvi8ChiVAKrb5WzUBuJLSuujCA,8235
 fractal_server/app/routes/api/v2/workflow.py,sha256=gwMtpfUY_JiTv5_R_q1I9WNkp6nTqEVtYx8jWNJRxcU,10227
 fractal_server/app/routes/api/v2/workflow_import.py,sha256=kOGDaCj0jCGK1WSYGbnUjtUg2U1YxUY9UMH-2ilqJg4,9027
@@ -184,36 +184,41 @@ fractal_server/migrations/versions/f384e1c0cf5d_drop_task_default_args_columns.p
 fractal_server/migrations/versions/fbce16ff4e47_new_history_items.py,sha256=TDWCaIoM0Q4SpRWmR9zr_rdp3lJXhCfBPTMhtrP5xYE,3950
 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=AK5E2LXVv0fNilSCy4Zufh0D5QdMozL4OtvNKgMSli4,24155
+fractal_server/ssh/_fabric.py,sha256=3Q0nlXctEXtRspQvg00wzCOyYK-0fAJlCowQuXEMk9I,25118
 fractal_server/string_tools.py,sha256=qLB5u6-4QxXPiZrUeWn_cEo47axj4OXFzDd47kNTIWw,1847
 fractal_server/syringe.py,sha256=3YJeIALH-wibuJ9R5VMNYUWh7x1-MkWT0SqGcWG5MY8,2795
 fractal_server/tasks/__init__.py,sha256=kadmVUoIghl8s190_Tt-8f-WBqMi8u8oU4Pvw39NHE8,23
 fractal_server/tasks/utils.py,sha256=V7dj8o2AnoHhGSTYlqJHcRFhCIpmOrMOUhtiE_DvRVA,291
 fractal_server/tasks/v2/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-fractal_server/tasks/v2/local/__init__.py,sha256=d8xO1H1kAGZFk707BKhNhjxPjdnoPGxHiNcsC_ZGcJE,253
+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=WOwLZwEH6ez-2fmjwZP7cXQ7KwktelUgsmMxOpwhsn0,12243
-fractal_server/tasks/v2/local/collect_pixi.py,sha256=qnw0AYT8upyhdxt6OmEMEM_nnqAehlStFxd1DdQYdWE,9510
-fractal_server/tasks/v2/local/deactivate.py,sha256=nACIpbo5guF3r3b0QUv7g6Yx-p37BHpvMvEZnxhs-qk,10164
-fractal_server/tasks/v2/local/deactivate_pixi.py,sha256=s6A7_HhTy6bSTE8vVgGGtAQfBtOdNtb-s9Yjv4wYc5g,3989
-fractal_server/tasks/v2/local/reactivate.py,sha256=go3q2QSD3L7FQP0yHmMBSw_z5y6gQyPFhwltv51aO5U,6189
-fractal_server/tasks/v2/ssh/__init__.py,sha256=GmhXfaoYv52FrjhEuOb8zrooFIgBDBf9odXSmeYsRBs,186
+fractal_server/tasks/v2/local/collect.py,sha256=OIqvvXqI631MjHDGxYj3a7AmC0FhMZ2v2LD3RSZ18wU,12000
+fractal_server/tasks/v2/local/collect_pixi.py,sha256=MAr48JqTbBIw72i2HC9NxgLjdu2Z76B_YlcOaiEb_UA,9865
+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/reactivate.py,sha256=ZZhwyoQQ8Lzkk18BB4l3pr8x8VI-MnZSoClKnMvTy14,5860
+fractal_server/tasks/v2/local/reactivate_pixi.py,sha256=T7Rviv-vifg3D1UxHf4aIc-6hG1HdZ4phEyYEZVX7vo,6378
+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=myqHfErAljmGLyp0g0nWHFdEbNDH40ipyQXIgHQuXh4,14886
-fractal_server/tasks/v2/ssh/collect_pixi.py,sha256=0a3HRiZqWMwdteZBmltbzJUUeySFW2YBOHnQkaxv4qE,12931
-fractal_server/tasks/v2/ssh/deactivate.py,sha256=J4ZsVpU7vvZF-9H2esPoOC8TfU0IvXziYAg4VtcCIbM,12983
-fractal_server/tasks/v2/ssh/reactivate.py,sha256=qVjPSbnYMITRL6c7SyC--_IiCGFz-NTj4ze-htwVunI,8816
+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/deactivate.py,sha256=A4v9pcualcGD7l-eWcnMbM0N0HEsectHFA9lJnDXlM0,12639
+fractal_server/tasks/v2/ssh/deactivate_pixi.py,sha256=qksD9ccpjy0v8ckhbZUfcuFVJf5iL25nj6wHNqvDkUg,4947
+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/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
 fractal_server/tasks/v2/templates/4_pip_show.sh,sha256=qm1vPy6AkKhWDjCJGXS8LqCLYO3KsAyRK325ZsFcF6U,1747
 fractal_server/tasks/v2/templates/5_get_venv_size_and_file_number.sh,sha256=q-6ZUvA6w6FDVEoSd9O63LaJ9tKZc7qAFH72SGPrd_k,284
 fractal_server/tasks/v2/templates/6_pip_install_from_freeze.sh,sha256=A2y8RngEjAcRhG-_owA6P7tAdrS_AszFuGXnaeMV8u0,1122
-fractal_server/tasks/v2/templates/pixi_1_collect.sh,sha256=RHlhkcaboHcFyxEb0DscHkOYWTA7GDmC19rEyQTQBRs,2014
-fractal_server/tasks/v2/utils_background.py,sha256=L-x7X69uorrtuV0SK2SenTT0CAcEerXiF4NRiwLJEro,4567
+fractal_server/tasks/v2/templates/pixi_1_extract.sh,sha256=1Z6sd_fTzqQkOfbFswaPZBNLUyv-OrS4euGlcoi8ces,1097
+fractal_server/tasks/v2/templates/pixi_2_install.sh,sha256=lvqIUH3zVr2fhZfoEwjBqAzvYhX9fID6Cea-fPTHbOI,1315
+fractal_server/tasks/v2/templates/pixi_3_post_install.sh,sha256=SfXl0l4wY1ygr-DErbaXrgg24UFU7wsz1O8zgbHV0NE,2618
+fractal_server/tasks/v2/utils_background.py,sha256=_62JAee3DltnQn14HVGfFosssgiDTyuzFkPbw2RNB8M,4575
 fractal_server/tasks/v2/utils_database.py,sha256=yi7793Uue32O59OBVUgomO42oUrVKdSKXoShBUNDdK0,1807
 fractal_server/tasks/v2/utils_package_names.py,sha256=RDg__xrvQs4ieeVzmVdMcEh95vGQYrv9Hfal-5EDBM8,2393
-fractal_server/tasks/v2/utils_pixi.py,sha256=eX9aUXJpnbp1EAt-xAgysHP6ngUcpGLCLL4EL_nP_1Y,1126
+fractal_server/tasks/v2/utils_pixi.py,sha256=QrRVtN8SZM_ZDoRadXK98R27irOvTJuZO4c_mCfJ92A,1221
 fractal_server/tasks/v2/utils_python_interpreter.py,sha256=5_wrlrTqXyo1YuLZvAW9hrSoh5MyLOzdPVUlUwM7uDQ,955
 fractal_server/tasks/v2/utils_templates.py,sha256=Kc_nSzdlV6KIsO0CQSPs1w70zLyENPqJeTQEFiz4bOg,3124
 fractal_server/types/__init__.py,sha256=aA_8J1xXzuiLqpwO_Qf18-qzaRcYkHzevhH_T-diXWM,2026
@@ -224,8 +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-2.15.0a0.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
-fractal_server-2.15.0a0.dist-info/METADATA,sha256=JqEKi9mWP2fp-0EXknj0OILaSBBOsuNdvSZSiZudDx8,4245
-fractal_server-2.15.0a0.dist-info/WHEEL,sha256=7dDg4QLnNKTvwIDR9Ac8jJaAmBC_owJrckbC0jjThyA,88
-fractal_server-2.15.0a0.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
-fractal_server-2.15.0a0.dist-info/RECORD,,
+fractal_server-2.15.0a2.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
+fractal_server-2.15.0a2.dist-info/METADATA,sha256=pPjPz3h14JS4StI6QZVCA4LU_9Yib5fDpINeID1PMv0,4245
+fractal_server-2.15.0a2.dist-info/WHEEL,sha256=7dDg4QLnNKTvwIDR9Ac8jJaAmBC_owJrckbC0jjThyA,88
+fractal_server-2.15.0a2.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
+fractal_server-2.15.0a2.dist-info/RECORD,,

fractal_server/tasks/v2/templates/pixi_1_collect.sh

@@ -1,70 +0,0 @@
-set -e
-
-write_log(){
-    TIMESTAMP=$(date -u +"%Y-%m-%dT%H:%M:%SZ")
-    echo "[collect-task-pixi, $TIMESTAMP] $1"
-}
-
-# Replacements
-PIXI_HOME="__PIXI_HOME__"
-PACKAGE_DIR="__PACKAGE_DIR__"
-TAR_GZ_PATH="__TAR_GZ_PATH__"
-IMPORT_PACKAGE_NAME="__IMPORT_PACKAGE_NAME__"
-SOURCE_DIR_NAME="__SOURCE_DIR_NAME__"
-
-# Strip trailing `/` from `PACKAGE_DIR`
-PIXI_HOME=${PIXI_HOME%/}
-PACKAGE_DIR=${PACKAGE_DIR%/}
-
-# Known paths
-PIXI_EXECUTABLE="${PIXI_HOME}/bin/pixi"
-SOURCE_DIR="${PACKAGE_DIR}/${SOURCE_DIR_NAME}"
-PYPROJECT_TOML="${SOURCE_DIR}/pyproject.toml"
-TAR_GZ_BASENAME=$(basename "$TAR_GZ_PATH" ".tar.gz")
-
-# Pixi env variable
-export PIXI_HOME="$PIXI_HOME"
-export PIXI_CACHE_DIR="${PIXI_HOME}/cache"
-export RATTLER_AUTH_FILE="${PIXI_HOME}/credentials.json"
-
-
-TIME_START=$(date +%s)
-
-cd "$PACKAGE_DIR"
-write_log "Changed working directory to $PACKAGE_DIR"
-
-
-write_log "START 'tar xz -f $TAR_GZ_PATH $TAR_GZ_BASENAME'"
-tar xz -f "$TAR_GZ_PATH" "$TAR_GZ_BASENAME"
-write_log "END   'tar xz -f $TAR_GZ_PATH $TAR_GZ_BASENAME'"
-echo
-
-write_log "START 'mv ${PACKAGE_DIR}/${TAR_GZ_BASENAME} $SOURCE_DIR'"
-mv "${PACKAGE_DIR}/${TAR_GZ_BASENAME}" "$SOURCE_DIR"
-write_log "END   'mv ${PACKAGE_DIR}/${TAR_GZ_BASENAME} $SOURCE_DIR'"
-echo
-write_log "END extract $TAR_GZ_PATH"
-TIME_END_TAR=$(date +%s)
-write_log "Elapsed: $((TIME_END_TAR - TIME_START)) seconds"
-echo
-
-write_log "START '$PIXI_EXECUTABLE install --manifest-path $PYPROJECT_TOML'"
-${PIXI_EXECUTABLE} install --manifest-path "$PYPROJECT_TOML"
-write_log "END   '$PIXI_EXECUTABLE install --manifest-path $PYPROJECT_TOML'"
-echo
-
-PACKAGE_FOLDER=$(
-    ${PIXI_EXECUTABLE} run --manifest-path "$PYPROJECT_TOML" python \
-    -c "import $IMPORT_PACKAGE_NAME as p, os; print(os.path.dirname(p.__file__))"
-)
-write_log "Package folder: $PACKAGE_FOLDER"
-echo
-
-ENV_DISK_USAGE=$(du -sk "${PACKAGE_DIR}" | cut -f1)
-ENV_FILE_NUMBER=$(find "${PACKAGE_DIR}" -type f | wc -l)
-
-write_log "Disk usage: $ENV_DISK_USAGE"
-write_log "Number of files: $ENV_FILE_NUMBER"
-
-write_log "All ok, exit."
-echo