fractal-server 2.2.0a0__tar.gz → 2.2.0a1__tar.gz

{fractal_server-2.2.0a0 → fractal_server-2.2.0a1}/PKG-INFO

@@ -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-2.2.0a1/fractal_server/__init__.py

@@ -0,0 +1 @@
+__VERSION__ = "2.2.0a1"

{fractal_server-2.2.0a0 → fractal_server-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-2.2.0a0 → fractal_server-2.2.0a1}/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-2.2.0a0 → fractal_server-2.2.0a1}/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-2.2.0a0 → fractal_server-2.2.0a1}/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 → fractal_server-2.2.0a1}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "fractal-server"
-version = "2.2.0a0"
+version = "2.2.0a1"
 description = "Server component of the Fractal analytics platform"
 authors = [
     "Tommaso Comparin <tommaso.comparin@exact-lab.it>",
@@ -40,12 +40,14 @@ clusterfutures = "^0.5"
 cloudpickle = ">=3.0.0,<3.1.0"
 
 asyncpg = { version = "^0.29.0", optional = true }
-psycopg2 = { version = "^2.9.5", optional = true }
 gunicorn = { version = ">=21.2,<23.0", optional = true }
+psycopg = { version = "^3.1.0", extras=["binary"], optional=true }
+psycopg2 = { version = "^2.9.5", optional = true }
 
 [tool.poetry.extras]
 postgres = ["asyncpg", "psycopg2"]
 gunicorn = ["gunicorn"]
+postgres-psycopg-binary = ["psycopg"]
 
 [tool.poetry.group.dev.dependencies]
 asgi-lifespan = "^2"
@@ -88,7 +90,7 @@ filterwarnings = [
 ]
 
 [tool.bumpver]
-current_version = "2.2.0a0"
+current_version = "2.2.0a1"
 version_pattern = "MAJOR.MINOR.PATCH[PYTAGNUM]"
 commit_message = "bump version {old_version} -> {new_version}"
 commit = true

fractal_server-2.2.0a0/fractal_server/__init__.py

@@ -1 +0,0 @@
-__VERSION__ = "2.2.0a0"