fractal-server 2.2.0a0__py3-none-any.whl → 2.2.0a1__py3-none-any.whl

fractal_server/__init__.py

@@ -1 +1 @@
-__VERSION__ = "2.2.0a0"
+__VERSION__ = "2.2.0a1"

fractal_server/app/db/__init__.py

@@ -63,7 +63,7 @@ class DB:
             }
 
         cls._engine_async = create_async_engine(
-            settings.DATABASE_URL,
+            settings.DATABASE_ASYNC_URL,
             echo=settings.DB_ECHO,
             future=True,
             **engine_kwargs_async,

fractal_server/app/runner/v2/__init__.py

@@ -126,41 +126,57 @@ async def submit_workflow(
             db_sync.close()
             return
 
-        # Create WORKFLOW_DIR
-        original_umask = os.umask(0)
-        WORKFLOW_DIR_LOCAL.mkdir(parents=True, mode=0o755)
-        os.umask(original_umask)
-
-        # Define and create WORKFLOW_DIR_REMOTE
-        if FRACTAL_RUNNER_BACKEND == "local":
-            WORKFLOW_DIR_REMOTE = WORKFLOW_DIR_LOCAL
-        elif FRACTAL_RUNNER_BACKEND == "local_experimental":
-            WORKFLOW_DIR_REMOTE = WORKFLOW_DIR_LOCAL
-        elif FRACTAL_RUNNER_BACKEND == "slurm":
-            WORKFLOW_DIR_REMOTE = (
-                Path(user_cache_dir) / WORKFLOW_DIR_LOCAL.name
-            )
-            _mkdir_as_user(folder=str(WORKFLOW_DIR_REMOTE), user=slurm_user)
-
-        # Create all tasks subfolders
-        for order in range(job.first_task_index, job.last_task_index + 1):
-            this_wftask = workflow.task_list[order]
-            if this_wftask.is_legacy_task:
-                task_name = this_wftask.task_legacy.name
-            else:
-                task_name = this_wftask.task.name
-            subfolder_name = task_subfolder_name(
-                order=order,
-                task_name=task_name,
-            )
+        try:
+
+            # Create WORKFLOW_DIR
             original_umask = os.umask(0)
-            (WORKFLOW_DIR_LOCAL / subfolder_name).mkdir(mode=0o755)
+            WORKFLOW_DIR_LOCAL.mkdir(parents=True, mode=0o755)
+
             os.umask(original_umask)
-            if FRACTAL_RUNNER_BACKEND == "slurm":
+
+            # Define and create WORKFLOW_DIR_REMOTE
+            if FRACTAL_RUNNER_BACKEND == "local":
+                WORKFLOW_DIR_REMOTE = WORKFLOW_DIR_LOCAL
+            elif FRACTAL_RUNNER_BACKEND == "local_experimental":
+                WORKFLOW_DIR_REMOTE = WORKFLOW_DIR_LOCAL
+            elif FRACTAL_RUNNER_BACKEND == "slurm":
+                WORKFLOW_DIR_REMOTE = (
+                    Path(user_cache_dir) / WORKFLOW_DIR_LOCAL.name
+                )
                 _mkdir_as_user(
-                    folder=str(WORKFLOW_DIR_REMOTE / subfolder_name),
-                    user=slurm_user,
+                    folder=str(WORKFLOW_DIR_REMOTE), user=slurm_user
+                )
+
+            # Create all tasks subfolders
+            for order in range(job.first_task_index, job.last_task_index + 1):
+                this_wftask = workflow.task_list[order]
+                if this_wftask.is_legacy_task:
+                    task_name = this_wftask.task_legacy.name
+                else:
+                    task_name = this_wftask.task.name
+                subfolder_name = task_subfolder_name(
+                    order=order,
+                    task_name=task_name,
                 )
+                original_umask = os.umask(0)
+                (WORKFLOW_DIR_LOCAL / subfolder_name).mkdir(mode=0o755)
+                os.umask(original_umask)
+                if FRACTAL_RUNNER_BACKEND == "slurm":
+                    _mkdir_as_user(
+                        folder=str(WORKFLOW_DIR_REMOTE / subfolder_name),
+                        user=slurm_user,
+                    )
+        except Exception as e:
+            job.status = JobStatusTypeV2.FAILED
+            job.end_timestamp = get_timestamp()
+            job.log = (
+                "An error occurred while creating job folder and subfolders.\n"
+                f"Original error: {str(e)}"
+            )
+            db_sync.merge(job)
+            db_sync.commit()
+            db_sync.close()
+            return
 
         # After Session.commit() is called, either explicitly or when using a
         # context manager, all objects associated with the Session are expired.

fractal_server/config.py

@@ -166,7 +166,7 @@ class Settings(BaseSettings):
     ###########################################################################
     # DATABASE
     ###########################################################################
-    DB_ENGINE: Literal["sqlite", "postgres"] = "sqlite"
+    DB_ENGINE: Literal["sqlite", "postgres", "postgres-psycopg"] = "sqlite"
     """
     Select which database engine to use (supported: `sqlite` and `postgres`).
     """
@@ -201,39 +201,51 @@ class Settings(BaseSettings):
     """
 
     @property
-    def DATABASE_URL(self) -> URL:
-        if self.DB_ENGINE == "sqlite":
-            if not self.SQLITE_PATH:
-                raise FractalConfigurationError(
-                    "SQLITE_PATH path cannot be None"
-                )
-            sqlite_path = abspath(self.SQLITE_PATH)
+    def DATABASE_ASYNC_URL(self) -> URL:
+        if self.DB_ENGINE == "postgres":
             url = URL.create(
-                drivername="sqlite+aiosqlite",
-                database=sqlite_path,
+                drivername="postgresql+asyncpg",
+                username=self.POSTGRES_USER,
+                password=self.POSTGRES_PASSWORD,
+                host=self.POSTGRES_HOST,
+                port=self.POSTGRES_PORT,
+                database=self.POSTGRES_DB,
             )
-            return url
-        elif "postgres":
+        elif self.DB_ENGINE == "postgres-psycopg":
             url = URL.create(
-                drivername="postgresql+asyncpg",
+                drivername="postgresql+psycopg",
                 username=self.POSTGRES_USER,
                 password=self.POSTGRES_PASSWORD,
                 host=self.POSTGRES_HOST,
                 port=self.POSTGRES_PORT,
                 database=self.POSTGRES_DB,
             )
-            return url
+        else:
+            if not self.SQLITE_PATH:
+                raise FractalConfigurationError(
+                    "SQLITE_PATH path cannot be None"
+                )
+            sqlite_path = abspath(self.SQLITE_PATH)
+            url = URL.create(
+                drivername="sqlite+aiosqlite",
+                database=sqlite_path,
+            )
+        return url
 
     @property
     def DATABASE_SYNC_URL(self):
-        if self.DB_ENGINE == "sqlite":
+        if self.DB_ENGINE == "postgres":
+            return self.DATABASE_ASYNC_URL.set(
+                drivername="postgresql+psycopg2"
+            )
+        elif self.DB_ENGINE == "postgres-psycopg":
+            return self.DATABASE_ASYNC_URL.set(drivername="postgresql+psycopg")
+        else:
             if not self.SQLITE_PATH:
                 raise FractalConfigurationError(
                     "SQLITE_PATH path cannot be None"
                 )
-            return self.DATABASE_URL.set(drivername="sqlite")
-        elif self.DB_ENGINE == "postgres":
-            return self.DATABASE_URL.set(drivername="postgresql+psycopg2")
+            return self.DATABASE_ASYNC_URL.set(drivername="sqlite")
 
     ###########################################################################
     # FRACTAL SPECIFIC
@@ -420,6 +432,14 @@ class Settings(BaseSettings):
                     "DB engine is `postgres` but `psycopg2` or `asyncpg` "
                     "are not available"
                 )
+        elif self.DB_ENGINE == "postgres-psycopg":
+            try:
+                import psycopg  # noqa: F401
+            except ModuleNotFoundError:
+                raise FractalConfigurationError(
+                    "DB engine is `postgres-psycopg` but `psycopg` is not "
+                    "available"
+                )
         else:
             if not self.SQLITE_PATH:
                 raise FractalConfigurationError(

fractal_server/migrations/env.py

@@ -54,7 +54,7 @@ def run_migrations_offline() -> None:
     settings = Inject(get_settings)
     settings.check_db()
     context.configure(
-        url=settings.DATABASE_URL,
+        url=settings.DATABASE_ASYNC_URL,
         target_metadata=target_metadata,
         literal_binds=True,
         dialect_opts={"paramstyle": "named"},

{fractal_server-2.2.0a0.dist-info → fractal_server-2.2.0a1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fractal-server
-Version: 2.2.0a0
+Version: 2.2.0a1
 Summary: Server component of the Fractal analytics platform
 Home-page: https://github.com/fractal-analytics-platform/fractal-server
 License: BSD-3-Clause
@@ -15,6 +15,7 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Provides-Extra: gunicorn
 Provides-Extra: postgres
+Provides-Extra: postgres-psycopg-binary
 Requires-Dist: aiosqlite (>=0.19.0,<0.20.0)
 Requires-Dist: alembic (>=1.13.1,<2.0.0)
 Requires-Dist: asyncpg (>=0.29.0,<0.30.0) ; extra == "postgres"
@@ -26,6 +27,7 @@ Requires-Dist: fastapi-users[oauth] (>=12.1.0,<13.0.0)
 Requires-Dist: gunicorn (>=21.2,<23.0) ; extra == "gunicorn"
 Requires-Dist: packaging (>=23.2,<24.0)
 Requires-Dist: psycopg2 (>=2.9.5,<3.0.0) ; extra == "postgres"
+Requires-Dist: psycopg[binary] (>=3.1.0,<4.0.0) ; extra == "postgres-psycopg-binary"
 Requires-Dist: pydantic (>=1.10.8,<2)
 Requires-Dist: python-dotenv (>=1.0.0,<2.0.0)
 Requires-Dist: sqlalchemy[asyncio] (>=2.0.23,<2.1)

{fractal_server-2.2.0a0.dist-info → fractal_server-2.2.0a1.dist-info}/RECORD

@@ -1,8 +1,8 @@
-fractal_server/__init__.py,sha256=SlW0tbws1kw-jGFxFPps51tRVcdJnYWiGo7Se8A6BwY,24
+fractal_server/__init__.py,sha256=OybDAJMDuOmSHsn4iMvNgAcwadADya5I7nZmG0SV3VY,24
 fractal_server/__main__.py,sha256=CocbzZooX1UtGqPi55GcHGNxnrJXFg5tUU5b3wyFCyo,4958
 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=WZEVfdJAX7ZyBM1ngfEGeqWWcjK_NygtCbawpmbwGpU,4042
+fractal_server/app/db/__init__.py,sha256=KpS_mfmRfew0kieFDlwkSrDFvpzxftcvPALBBZ0LxsY,4048
 fractal_server/app/models/__init__.py,sha256=QGRjxBgk6GzHyyXh_7RuHvpLoe5PTl1g5KLkGqhFYMQ,199
 fractal_server/app/models/linkuserproject.py,sha256=eQaourbGRshvlMVlKzLYJKHEjfsW1CbWws9yW4eHXhA,567
 fractal_server/app/models/security.py,sha256=0oYj_cqPcQFsPFDyN4OTsqbXsLlXRcweawjP_iSiRI0,2900
@@ -81,7 +81,7 @@ fractal_server/app/runner/v1/_slurm/_submit_setup.py,sha256=KO9c694d318adoPQh9UG
 fractal_server/app/runner/v1/_slurm/get_slurm_config.py,sha256=6pQNNx997bLIfLp0guF09t_O0ZYRXnbEGLktSAcKnic,5999
 fractal_server/app/runner/v1/common.py,sha256=_L-vjLnWato80VdlB_BFN4G8P4jSM07u-5cnl1T3S34,3294
 fractal_server/app/runner/v1/handle_failed_job.py,sha256=bHzScC_aIlU3q-bQxGW6rfWV4xbZ2tho_sktjsAs1no,4684
-fractal_server/app/runner/v2/__init__.py,sha256=blmnUJTpZn8uYPbQIb0xmwB93xNKpEoFIAi4UDqKbWM,13418
+fractal_server/app/runner/v2/__init__.py,sha256=989hkJIy601BewBtpl0w_cL_wBKhDmKJq4N3idLbD5s,13999
 fractal_server/app/runner/v2/_local/__init__.py,sha256=KTj14K6jH8fXGUi5P7u5_RqEE1zF4aXtgPxCKzw46iw,5971
 fractal_server/app/runner/v2/_local/_local_config.py,sha256=9oi209Dlp35ANfxb_DISqmMKKc6DPaMsmYVWbZLseME,3630
 fractal_server/app/runner/v2/_local/_submit_setup.py,sha256=MucNOo8Er0F5ZIwH7CnTeXgnFMc6d3pKPkv563QNVi0,1630
@@ -126,7 +126,7 @@ fractal_server/app/schemas/v2/task_collection.py,sha256=sY29NQfJrbjiidmVkVjSIH-2
 fractal_server/app/schemas/v2/workflow.py,sha256=Zzx3e-qgkH8le0FUmAx9UrV5PWd7bj14PPXUh_zgZXM,1827
 fractal_server/app/schemas/v2/workflowtask.py,sha256=atVuVN4aXsVEOmSd-vyg-8_8OnPmqx-gT75rXcn_AlQ,6552
 fractal_server/app/security/__init__.py,sha256=2-QbwuR-nsuHM_uwKS_WzYvkhnuhO5jUv8UVROetyVk,11169
-fractal_server/config.py,sha256=ZRD-Mwim6gmWnL2JKT2v6KS3uRgthd1FZQRHwN7MYOE,16392
+fractal_server/config.py,sha256=XiSTdx7wI2Eem-lzeMQhhGAwUwsACCKdUnbiGqDIChY,17219
 fractal_server/data_migrations/README.md,sha256=_3AEFvDg9YkybDqCLlFPdDmGJvr6Tw7HRI14aZ3LOIw,398
 fractal_server/gunicorn_fractal.py,sha256=2AOkgxu-oQ-XB578_voT0VuhmAXFTmb0c-nYn1XLy_Q,1231
 fractal_server/images/__init__.py,sha256=xO6jTLE4EZKO6cTDdJsBmK9cdeh9hFTaSbSuWgQg7y4,196
@@ -135,7 +135,7 @@ fractal_server/images/tools.py,sha256=gxeniYy4Z-cp_ToK2LHPJUTVVUUrdpogYdcBUvBuLi
 fractal_server/logger.py,sha256=56wfka6fHaa3Rx5qO009nEs_y8gx5wZ2NUNZZ1I-uvc,5130
 fractal_server/main.py,sha256=U50BfL1cxpkSMglRmEHILZE1yDpiUhyb4tlrNuE3j6s,4417
 fractal_server/migrations/README,sha256=4rQvyDfqodGhpJw74VYijRmgFP49ji5chyEemWGHsuw,59
-fractal_server/migrations/env.py,sha256=bsl0HGZpjhommztgcs7wQ94sJzI1Orgnij97K8P_uyo,2630
+fractal_server/migrations/env.py,sha256=Bvg-FJzRJZIH_wqS_ZyZNXANIaathjo22_IY7c3fCjo,2636
 fractal_server/migrations/script.py.mako,sha256=oMXw9LC3zRbinWWPPDgeZ4z9FJrV2zhRWiYdS5YgNbI,526
 fractal_server/migrations/versions/4c308bcaea2b_add_task_args_schema_and_task_args_.py,sha256=-wHe-fOffmYeAm0JXVl_lxZ7hhDkaEVqxgxpHkb_uL8,954
 fractal_server/migrations/versions/4cedeb448a53_workflowtask_foreign_keys_not_nullables.py,sha256=Mob8McGYAcmgvrseyyYOa54E6Gsgr-4SiGdC-r9O4_A,1157
@@ -168,8 +168,8 @@ fractal_server/tasks/v2/background_operations.py,sha256=MAMBn6W2bhkdK59kfUGiD7a1
 fractal_server/tasks/v2/get_collection_data.py,sha256=Qhf2T_aaqAfqu9_KpUSlXsS7EJoZQbEPEreHHa2jco8,502
 fractal_server/urls.py,sha256=5o_qq7PzKKbwq12NHSQZDmDitn5RAOeQ4xufu-2v9Zk,448
 fractal_server/utils.py,sha256=b7WwFdcFZ8unyT65mloFToYuEDXpQoHRcmRNqrhd_dQ,2115
-fractal_server-2.2.0a0.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
-fractal_server-2.2.0a0.dist-info/METADATA,sha256=0lsKheVy4TMM296RuFQsLpVjEh4dhdeYzTi6pTTzrCw,4224
-fractal_server-2.2.0a0.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-fractal_server-2.2.0a0.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
-fractal_server-2.2.0a0.dist-info/RECORD,,
+fractal_server-2.2.0a1.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
+fractal_server-2.2.0a1.dist-info/METADATA,sha256=_EjXCIJCW7vFuEVg66y-Px3GUfi-ynAEPuNVJwg2dZo,4349
+fractal_server-2.2.0a1.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+fractal_server-2.2.0a1.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
+fractal_server-2.2.0a1.dist-info/RECORD,,