fractal-server 2.7.0a1__py3-none-any.whl → 2.7.0a3__py3-none-any.whl

fractal_server/migrations/versions/742b74e1cc6e_revamp_taskv2_and_taskgroupv2.py

@@ -0,0 +1,101 @@
+"""Revamp TaskV2 and TaskGroupV2
+
+Revision ID: 742b74e1cc6e
+Revises: df7cc3501bf7
+Create Date: 2024-10-07 16:56:37.399878
+
+"""
+import sqlalchemy as sa
+import sqlmodel
+from alembic import op
+
+
+# revision identifiers, used by Alembic.
+revision = "742b74e1cc6e"
+down_revision = "df7cc3501bf7"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("taskgroupv2", schema=None) as batch_op:
+        batch_op.add_column(
+            sa.Column(
+                "origin", sqlmodel.sql.sqltypes.AutoString(), nullable=False
+            )
+        )
+        batch_op.add_column(
+            sa.Column(
+                "pkg_name", sqlmodel.sql.sqltypes.AutoString(), nullable=False
+            )
+        )
+        batch_op.add_column(
+            sa.Column(
+                "version", sqlmodel.sql.sqltypes.AutoString(), nullable=True
+            )
+        )
+        batch_op.add_column(
+            sa.Column(
+                "python_version",
+                sqlmodel.sql.sqltypes.AutoString(),
+                nullable=True,
+            )
+        )
+        batch_op.add_column(
+            sa.Column(
+                "path", sqlmodel.sql.sqltypes.AutoString(), nullable=True
+            )
+        )
+        batch_op.add_column(
+            sa.Column(
+                "venv_path", sqlmodel.sql.sqltypes.AutoString(), nullable=True
+            )
+        )
+        batch_op.add_column(
+            sa.Column(
+                "pip_extras", sqlmodel.sql.sqltypes.AutoString(), nullable=True
+            )
+        )
+
+    with op.batch_alter_table("taskv2", schema=None) as batch_op:
+        batch_op.add_column(
+            sa.Column(
+                "category", sqlmodel.sql.sqltypes.AutoString(), nullable=True
+            )
+        )
+        batch_op.add_column(
+            sa.Column(
+                "modality", sqlmodel.sql.sqltypes.AutoString(), nullable=True
+            )
+        )
+        batch_op.add_column(
+            sa.Column(
+                "authors", sqlmodel.sql.sqltypes.AutoString(), nullable=True
+            )
+        )
+        batch_op.add_column(
+            sa.Column("tags", sa.JSON(), server_default="[]", nullable=False)
+        )
+
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("taskv2", schema=None) as batch_op:
+        batch_op.drop_column("tags")
+        batch_op.drop_column("authors")
+        batch_op.drop_column("modality")
+        batch_op.drop_column("category")
+
+    with op.batch_alter_table("taskgroupv2", schema=None) as batch_op:
+        batch_op.drop_column("pip_extras")
+        batch_op.drop_column("venv_path")
+        batch_op.drop_column("path")
+        batch_op.drop_column("python_version")
+        batch_op.drop_column("version")
+        batch_op.drop_column("pkg_name")
+        batch_op.drop_column("origin")
+
+    # ### end Alembic commands ###

fractal_server/tasks/v2/background_operations.py

@@ -172,6 +172,7 @@ def _prepare_tasks_metadata(
                 }
             ),
             **task_attributes,
+            authors=package_manifest.authors,
         )
         task_list.append(task_obj)
     return task_list
@@ -274,9 +275,19 @@ async def background_collect_pip(
             )
             _check_task_files_exist(task_list=task_list)
 
+            # Prepare some task-group attributes
+            task_group_attrs = dict(
+                pkg_name=task_pkg.package_name,
+                version=task_pkg.package_version,
+            )
+            if task_pkg.is_local_package:
+                task_group_attrs["origin"] = "wheel-file"
+            else:
+                task_group_attrs["origin"] = "pypi"
+
             task_group = create_db_task_group_and_tasks(
                 task_list=task_list,
-                task_group_obj=TaskGroupCreateV2(),
+                task_group_obj=TaskGroupCreateV2(**task_group_attrs),
                 user_id=user_id,
                 user_group_id=user_group_id,
                 db=db,

fractal_server/tasks/v2/background_operations_ssh.py

@@ -316,9 +316,19 @@ def background_collect_pip_ssh(
                     python_bin=Path(python_bin),
                 )
 
+                # Prepare some task-group attributes
+                task_group_attrs = dict(
+                    pkg_name=task_pkg.package_name,
+                    version=task_pkg.package_version,
+                )
+                if task_pkg.is_local_package:
+                    task_group_attrs["origin"] = "wheel-file"
+                else:
+                    task_group_attrs["origin"] = "pypi"
+
                 create_db_task_group_and_tasks(
                     task_list=task_list,
-                    task_group_obj=TaskGroupCreateV2(),
+                    task_group_obj=TaskGroupCreateV2(**task_group_attrs),
                     user_id=user_id,
                     user_group_id=user_group_id,
                     db=db,

fractal_server/tasks/v2/endpoint_operations.py

@@ -5,17 +5,24 @@ from typing import Optional
 from typing import Union
 from zipfile import ZipFile
 
+from fastapi import HTTPException
+from fastapi import status
+from httpx import AsyncClient
+from httpx import TimeoutException
+
 from ._TaskCollectPip import _TaskCollectPip
 from .utils import _parse_wheel_filename
 from .utils import get_python_interpreter_v2
 from fractal_server.app.schemas.v2 import ManifestV2
 from fractal_server.config import get_settings
 from fractal_server.logger import get_logger
+from fractal_server.logger import set_logger
 from fractal_server.syringe import Inject
 from fractal_server.utils import execute_command
 
 
 FRACTAL_PUBLIC_TASK_SUBDIR = ".fractal"
+logger = set_logger(__name__)
 
 
 async def download_package(
@@ -134,3 +141,38 @@ def create_package_dir_pip(
     if create:
         venv_path.mkdir(exist_ok=False, parents=True)
     return venv_path
+
+
+async def get_package_version_from_pypi(name: str) -> str:
+    """
+    Make a GET call to PyPI JSON API and get latest package version.
+
+    Ref https://warehouse.pypa.io/api-reference/json.html.
+
+    Arguments:
+        name: Package name.
+    """
+
+    url = f"https://pypi.org/pypi/{name}/json"
+    hint = f"Hint: specify the required version for '{name}'."
+    try:
+        async with AsyncClient(timeout=5.0) as client:
+            res = await client.get(url)
+            if res.status_code != 200:
+                raise HTTPException(
+                    status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
+                    detail=(
+                        f"Could not get {url} (status_code {res.status_code})."
+                        f"\n{hint}"
+                    ),
+                )
+            version = res.json()["info"]["version"]
+            return version
+    except (KeyError, TimeoutException) as e:
+        logger.warning(
+            f"An error occurred while getting {url}. Original error: {str(e)}."
+        )
+        raise HTTPException(
+            status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
+            detail=(f"An error occurred while getting {url}.\n{hint}"),
+        )

{fractal_server-2.7.0a1.dist-info → fractal_server-2.7.0a3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fractal-server
-Version: 2.7.0a1
+Version: 2.7.0a3
 Summary: Server component of the Fractal analytics platform
 Home-page: https://github.com/fractal-analytics-platform/fractal-server
 License: BSD-3-Clause

{fractal_server-2.7.0a1.dist-info → fractal_server-2.7.0a3.dist-info}/RECORD

@@ -1,5 +1,5 @@
-fractal_server/__init__.py,sha256=a93MyH1kQ9BKFlxzrvnhMDhXFBw7mHkaQCSrrhceInk,24
-fractal_server/__main__.py,sha256=WcBAkmVE9aH5mDI6wGkVmPAql2N5Vyk0A-7zuUl8WX0,6122
+fractal_server/__init__.py,sha256=8F5In7R-H4qg5Yf7sXXB43RixMlW4SOmaCR83lziaso,24
+fractal_server/__main__.py,sha256=KqGiemsvIhrBeUlFDzIQsMEjOJW2BsH4qo_a_ldRQok,6362
 fractal_server/alembic.ini,sha256=MWwi7GzjzawI9cCAK1LW7NxIBQDUqD12-ptJoq5JpP0,3153
 fractal_server/app/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/app/db/__init__.py,sha256=81rK9w1__Z6PJ5cEcChPVc-wI9YOK4fN--_5Opry0MQ,4119
@@ -20,13 +20,17 @@ fractal_server/app/models/v2/collection_state.py,sha256=nxb042i8tt8rCpmgbFJoBCYW
 fractal_server/app/models/v2/dataset.py,sha256=-7sxHEw4IIAvF_uSan7tA3o8hvoakBkQ0SRvqS2iOQU,1455
 fractal_server/app/models/v2/job.py,sha256=ypJmN-qspkKBGhBG7Mt-HypSQqcQ2EmB4Bzzb2-y550,1535
 fractal_server/app/models/v2/project.py,sha256=rAHoh5KfYwIaW7rTX0_O0jvWmxEvfo1BafvmcXuSSRk,786
-fractal_server/app/models/v2/task.py,sha256=JuRo18JBiHxuujux0Uw-AWzj8L0ln2ZMJA7zQn4KQU8,2074
+fractal_server/app/models/v2/task.py,sha256=SbTVkIUj7igL6-zhu8GigJK9oq4ddN4mXGvtlbjNbC0,2495
 fractal_server/app/models/v2/workflow.py,sha256=YBgFGCziUgU0aJ5EM3Svu9W2c46AewZO9VBlFCHiSps,1069
 fractal_server/app/models/v2/workflowtask.py,sha256=iDuJYk8kp4PNqGmbKRtGI7y-QsbjkNd_gDsbMzL4i-g,1274
 fractal_server/app/routes/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/app/routes/admin/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/app/routes/admin/v1.py,sha256=GIpZlwAwwwLGDWkBqywhtmp9TGsKLhGmZAdj1TDKJvE,13976
-fractal_server/app/routes/admin/v2.py,sha256=hoEbH_sRJ-MaKMwhFp8c7SNObP0-Kmtgw1zbs_Z3nLY,12971
+fractal_server/app/routes/admin/v2/__init__.py,sha256=zkdrk3mSQWfgTJugS8Sc_Q_xCAwfmHUfdRe0DTaYT80,521
+fractal_server/app/routes/admin/v2/job.py,sha256=JmNmF5MeHtcDQzGadCJWwFNDQvB5G8SwVABaL11S1Vc,8268
+fractal_server/app/routes/admin/v2/project.py,sha256=luy-yiGX1JYTdPm1hpIdDUUqPm8xHuipLy9k2X6zu74,1223
+fractal_server/app/routes/admin/v2/task.py,sha256=T0DNtc8d4jZYS0gGKBcz6pwoeh30WSgkMuIUEw_yBjo,4406
+fractal_server/app/routes/admin/v2/task_group.py,sha256=aJhizy-EhM0Iupxq19w0lam7Prs_xTnGxyLFaL8I_AE,4545
 fractal_server/app/routes/api/__init__.py,sha256=2IDheFi0OFdsUg7nbUiyahqybvpgXqeHUXIL2QtWrQQ,641
 fractal_server/app/routes/api/v1/__init__.py,sha256=Y2HQdG197J0a7DyQEE2jn53IfxD0EHGhzK1I2JZuEck,958
 fractal_server/app/routes/api/v1/_aux_functions.py,sha256=P9Q48thGH95w0h5cacYoibxqgiiLW4oqZ8rNJ2LIISY,13219
@@ -46,11 +50,11 @@ fractal_server/app/routes/api/v2/job.py,sha256=Bga2Kz1OjvDIdxZObWaaXVhNIhC_5JKhK
 fractal_server/app/routes/api/v2/project.py,sha256=eWYFJ7F2ZYQcpi-_n-rhPF-Q4gJhzYBsVGYFhHZZXAE,6653
 fractal_server/app/routes/api/v2/status.py,sha256=6N9DSZ4iFqbZImorWfEAPoyoFUgEruo4Hweqo0x0xXU,6435
 fractal_server/app/routes/api/v2/submit.py,sha256=h7mjmea_VNCriGiA4HRuyxLHlvd9aGfTAFXK3bSsvzc,9422
-fractal_server/app/routes/api/v2/task.py,sha256=CZQjI5IKxeN23YTu3eTjPuPcO6BSmcAXQR3Pcy0WSuQ,7828
+fractal_server/app/routes/api/v2/task.py,sha256=FRYHJTvr_tl62HvwKgHSayLrT0gCNeGwU9k9bsiSqws,8302
 fractal_server/app/routes/api/v2/task_collection.py,sha256=9trKrJDuaKKgdn-mG06VuFpyObhbcCD8AstaxN4lAOM,13507
-fractal_server/app/routes/api/v2/task_collection_custom.py,sha256=T3RoxQWmJVipEdXSjbD_Zdw_mc3IIYT3aDLZIQ_StIM,7272
+fractal_server/app/routes/api/v2/task_collection_custom.py,sha256=CIJ4ZYPRtKvC6JVkagQPVFm6A53mOeDIPD8-y1lPJLc,7433
 fractal_server/app/routes/api/v2/task_group.py,sha256=yRUCMZtXH9KdfD2pfdCKPBGf_eVn-S5CXFHCUyXAoJk,4078
-fractal_server/app/routes/api/v2/workflow.py,sha256=q4_sFCSw-_1oC4FENv_HIInDF_2uJG5QXqiH9Ns_ZK4,11330
+fractal_server/app/routes/api/v2/workflow.py,sha256=aG5hs7oj-em2EpydgBPE4xPKrlKxD6NXuLhKkfdG79c,12116
 fractal_server/app/routes/api/v2/workflowtask.py,sha256=TIOePM13uK3GKVhtGK2wBB341ZFheBYQKTfXuPfdymE,6999
 fractal_server/app/routes/auth/__init__.py,sha256=fao6CS0WiAjHDTvBzgBVV_bSXFpEAeDBF6Z6q7rRkPc,1658
 fractal_server/app/routes/auth/_aux_auth.py,sha256=6GERRDXK4P-2OA81bjxJZEw6hN4QCk5x7MqDNtN7VG4,4746
@@ -144,17 +148,18 @@ fractal_server/app/schemas/v2/__init__.py,sha256=BHbRPSBLjGaCpmjd8OJSycKhBLfZY5b
 fractal_server/app/schemas/v2/dataset.py,sha256=dLT52tV4dSf2HrFNak4vdQEn8PT_04IUrGnd2z-AXIU,2599
 fractal_server/app/schemas/v2/dumps.py,sha256=ZrJCHTv9oU2QMNjPUSBO3DIPRO3qDvbxpAGpernpf-Q,1720
 fractal_server/app/schemas/v2/job.py,sha256=zfF9K3v4jWUJ7M482ta2CkqUJ4tVT4XfVt60p9IRhP0,3250
-fractal_server/app/schemas/v2/manifest.py,sha256=N37IWohcfO3_y2l8rVM0h_1nZq7m4Izxk9iL1vtwBJw,6243
+fractal_server/app/schemas/v2/manifest.py,sha256=eHfDjth8cSDiuYeDMfBOte8sMHOI74DC0VlhebhUXvY,6545
 fractal_server/app/schemas/v2/project.py,sha256=u7S4B-bote1oGjzAGiZ-DuQIyeRAGqJsI71Tc1EtYE0,736
 fractal_server/app/schemas/v2/status.py,sha256=SQaUpQkjFq5c5k5J4rOjNhuQaDOEg8lksPhkKmPU5VU,332
-fractal_server/app/schemas/v2/task.py,sha256=TpMBinf3Mf2Kqlj1IgiHkf6Blob_bjXyIM-7xgK7XqY,4814
+fractal_server/app/schemas/v2/task.py,sha256=8iuugQR_ol-bP9nFkANt2JjjBtEzzTifrBmTWpV4QF4,6557
 fractal_server/app/schemas/v2/task_collection.py,sha256=_utBv7_kcRJCbPdWezasU8GrikI_QFPKeIl4vyAgDd4,6155
-fractal_server/app/schemas/v2/task_group.py,sha256=8A4MgLgSIRBdb5Q10Ae7RmsRdZkVtGRxD6cIdn8Gjho,419
+fractal_server/app/schemas/v2/task_group.py,sha256=LRW_sggWUqnXVkmicmwxMbxRRYbSJmzg0Np-Dm0uBDU,1217
 fractal_server/app/schemas/v2/workflow.py,sha256=7jqZhGn6plFSU8EkQsvvnDMh5N8m7GouRt1DIXmweIA,1986
 fractal_server/app/schemas/v2/workflowtask.py,sha256=t29n7TM2Z_bcFC8RKor694dcU_cGaasUSuX4Q9oQikY,5758
 fractal_server/app/security/__init__.py,sha256=V1NOWlmaFZHMR6SrkMl62jyAuqYONyo8lyGvR6UZesM,12312
 fractal_server/app/user_settings.py,sha256=aZgQ3i0JkHfgwLGW1ee6Gzr1ae3IioFfJKKSsSS8Svk,1312
 fractal_server/config.py,sha256=gX0aYwDwbC5y7JNorifON84YMveubb7XTb4sH14N3KM,23667
+fractal_server/data_migrations/2_7_0.py,sha256=ReB664szR2w9_mblfEilYYkVzs8Wi61O1_9G1gDtoQQ,9405
 fractal_server/data_migrations/README.md,sha256=_3AEFvDg9YkybDqCLlFPdDmGJvr6Tw7HRI14aZ3LOIw,398
 fractal_server/data_migrations/tools.py,sha256=LeMeASwYGtEqd-3wOLle6WARdTGAimoyMmRbbJl-hAM,572
 fractal_server/gunicorn_fractal.py,sha256=u6U01TLGlXgq1v8QmEpLih3QnsInZD7CqphgJ_GrGzc,1230
@@ -175,6 +180,7 @@ fractal_server/migrations/versions/50a13d6138fd_initial_schema.py,sha256=zwXegXs
 fractal_server/migrations/versions/5bf02391cfef_v2.py,sha256=axhNkr_H6R4rRbY7oGYazNbFvPXeSyBDWFVbKNmiqs8,8433
 fractal_server/migrations/versions/70e77f1c38b0_add_applyworkflow_first_task_index_and_.py,sha256=Q-DsMzG3IcUV2Ol1dhJWosDvKERamBE6QvA2zzS5zpQ,1632
 fractal_server/migrations/versions/71eefd1dd202_add_slurm_accounts.py,sha256=mbWuCkTpRAdGbRhW7lhXs_e5S6O37UAcCN6JfoY5H8A,1353
+fractal_server/migrations/versions/742b74e1cc6e_revamp_taskv2_and_taskgroupv2.py,sha256=CHihUE7dfHfVwweH_ijdGw_l7XGM0UfXDqXwAG9FKBg,3002
 fractal_server/migrations/versions/7cf1baae8fb4_task_group_v2.py,sha256=793xuEk8Pr28q1Hfe9_qNWWtU6ysXYdOFVRUPO_MB1o,1996
 fractal_server/migrations/versions/84bf0fffde30_add_dumps_to_applyworkflow.py,sha256=NSCuhANChsg76vBkShBl-9tQ4VEHubOjtAv1etHhlvY,2684
 fractal_server/migrations/versions/8f79bd162e35_add_docs_info_and_docs_link_to_task_.py,sha256=6pgODDtyAxevZvAJBj9IJ41inhV1RpwbpZr_qfPPu1A,1115
@@ -206,10 +212,10 @@ fractal_server/tasks/v1/utils.py,sha256=J9oKys-82OehBxOon5wWl3CxjVBgYWeVEEyWGVFn
 fractal_server/tasks/v2/_TaskCollectPip.py,sha256=kWQNMNZ8OEddkYhmhsk3E6ArcaD7qe4vsjYYx9vbrUg,4900
 fractal_server/tasks/v2/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/tasks/v2/_venv_pip.py,sha256=6NCItfeWgO9BDnlfhoCfiUG5UCGGz_SJz4Mfn4Jg_nk,6489
-fractal_server/tasks/v2/background_operations.py,sha256=Z-AlIIYGbwoZMQgpAM_4PDgh3w5xk-cwrJXwcOiJk_M,11171
-fractal_server/tasks/v2/background_operations_ssh.py,sha256=Tw-vuGbxjvXF90QSbkvoRzxSGYLdjGUDO6n0tKHML1s,14494
+fractal_server/tasks/v2/background_operations.py,sha256=CcaIzhQTqtw4wnlN3A-vLLSm6qOJvzrfG-12Jg0iC1I,11604
+fractal_server/tasks/v2/background_operations_ssh.py,sha256=9mj4t3cNJ8a268ykoj7lukXSojXi2dme7od1Uf_lVq4,14917
 fractal_server/tasks/v2/database_operations.py,sha256=_55kLUMWuOYQANuN0QDtDt-GWby4hDKPJp5NOB4ZoxA,1396
-fractal_server/tasks/v2/endpoint_operations.py,sha256=gT38pl5TEH6WNWOtg4Itegt2lTJJI6YRa7fEj9Y4x2s,4226
+fractal_server/tasks/v2/endpoint_operations.py,sha256=v1p3lFa3nuQ0ydv2T-cUQF42mZodz62C4tuiOKsA858,5637
 fractal_server/tasks/v2/templates/_1_create_venv.sh,sha256=5uW0ETYxl5xiQEXP107zgq8V_-vf3k5NzMMj1hSLjas,1015
 fractal_server/tasks/v2/templates/_2_upgrade_pip.sh,sha256=ca5Yng6JgJYu-a4QrsIsatwUmrLdRWBKw7_VJrY7WLY,555
 fractal_server/tasks/v2/templates/_3_pip_install.sh,sha256=T9sabeB9iQzVZpLfuLkKGz9EpfHkUrJHKWO4HNij6yM,595
@@ -219,8 +225,8 @@ fractal_server/tasks/v2/utils.py,sha256=JOyCacb6MNvrwfLNTyLwcz8y79J29YuJeJ2MK5kq
 fractal_server/urls.py,sha256=5o_qq7PzKKbwq12NHSQZDmDitn5RAOeQ4xufu-2v9Zk,448
 fractal_server/utils.py,sha256=b7WwFdcFZ8unyT65mloFToYuEDXpQoHRcmRNqrhd_dQ,2115
 fractal_server/zip_tools.py,sha256=xYpzBshysD2nmxkD5WLYqMzPYUcCRM3kYy-7n9bJL-U,4426
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