fractal-server 2.11.0a10__py3-none-any.whl → 2.12.0__py3-none-any.whl

fractal_server/__init__.py

@@ -1 +1 @@
-__VERSION__ = "2.11.0a10"
+__VERSION__ = "2.12.0"

fractal_server/app/models/__init__.py

@@ -4,9 +4,7 @@ thus we should always export all relevant database models from here or they
 will not be picked up by alembic.
 """
 from .linkusergroup import LinkUserGroup  # noqa: F401
-from .linkuserproject import LinkUserProject  # noqa: F401
 from .linkuserproject import LinkUserProjectV2  # noqa: F401
 from .security import *  # noqa
 from .user_settings import UserSettings  # noqa
-from .v1 import *  # noqa
 from .v2 import *  # noqa

fractal_server/app/models/linkuserproject.py

@@ -2,15 +2,6 @@ from sqlmodel import Field
 from sqlmodel import SQLModel
 
 
-class LinkUserProject(SQLModel, table=True):
-    """
-    Crossing table between User and Project
-    """
-
-    project_id: int = Field(foreign_key="project.id", primary_key=True)
-    user_id: int = Field(foreign_key="user_oauth.id", primary_key=True)
-
-
 class LinkUserProjectV2(SQLModel, table=True):
     """
     Crossing table between User and ProjectV2

fractal_server/app/models/v2/dataset.py

@@ -1,6 +1,5 @@
 from datetime import datetime
 from typing import Any
-from typing import Literal
 from typing import Optional
 
 from sqlalchemy import Column
@@ -42,9 +41,6 @@ class DatasetV2(SQLModel, table=True):
         sa_column=Column(JSON, server_default="[]", nullable=False)
     )
 
-    filters: Optional[
-        dict[Literal["attributes", "types"], dict[str, Any]]
-    ] = Field(sa_column=Column(JSON, nullable=True, server_default="null"))
     type_filters: dict[str, bool] = Field(
         sa_column=Column(JSON, nullable=False, server_default="{}")
     )

fractal_server/app/models/v2/workflowtask.py

@@ -1,5 +1,4 @@
 from typing import Any
-from typing import Literal
 from typing import Optional
 
 from sqlalchemy import Column
@@ -25,9 +24,6 @@ class WorkflowTaskV2(SQLModel, table=True):
     args_parallel: Optional[dict[str, Any]] = Field(sa_column=Column(JSON))
     args_non_parallel: Optional[dict[str, Any]] = Field(sa_column=Column(JSON))
 
-    input_filters: Optional[
-        dict[Literal["attributes", "types"], dict[str, Any]]
-    ] = Field(sa_column=Column(JSON, nullable=True, server_default="null"))
     type_filters: dict[str, bool] = Field(
         sa_column=Column(JSON, nullable=False, server_default="{}")
     )

fractal_server/app/routes/aux/_job.py

@@ -1,12 +1,10 @@
 from pathlib import Path
-from typing import Union
 
-from ...models.v1 import ApplyWorkflow
 from ...models.v2 import JobV2
 from ...runner.filenames import SHUTDOWN_FILENAME
 
 
-def _write_shutdown_file(*, job: Union[ApplyWorkflow, JobV2]):
+def _write_shutdown_file(*, job: JobV2):
     """
     Write job's shutdown file.
 

fractal_server/app/runner/executors/slurm/ssh/executor.py

@@ -385,9 +385,7 @@ class FractalSlurmSSHExecutor(SlurmExecutor):
         args_batches = []
         batch_size = tasks_per_job
         for ind_chunk in range(0, tot_tasks, batch_size):
-            args_batches.append(
-                list_args[ind_chunk : ind_chunk + batch_size]  # noqa
-            )
+            args_batches.append(list_args[ind_chunk : ind_chunk + batch_size])
         if len(args_batches) != math.ceil(tot_tasks / tasks_per_job):
             raise RuntimeError("Something wrong here while batching tasks")
 
@@ -536,10 +534,15 @@ class FractalSlurmSSHExecutor(SlurmExecutor):
             _prefixes = []
             _subfolder_names = []
             for component in components:
-                if isinstance(component, dict):
+                # In Fractal, `component` is `dict` by construction (e.g.
+                # `component = {"zarr_url": "/something", "param": 1}``). The
+                # try/except covers the case of e.g. `executor.map([1, 2])`,
+                # which is useful for testing.
+                try:
                     actual_component = component.get(_COMPONENT_KEY_, None)
-                else:
-                    actual_component = component
+                except AttributeError:
+                    actual_component = str(component)
+
                 _task_file_paths = get_task_file_paths(
                     workflow_dir_local=task_files.workflow_dir_local,
                     workflow_dir_remote=task_files.workflow_dir_remote,

fractal_server/app/runner/executors/slurm/sudo/executor.py

@@ -608,11 +608,7 @@ class FractalSlurmExecutor(SlurmExecutor):
             _prefixes = []
             _subfolder_names = []
             for component in components:
-                if isinstance(component, dict):
-                    # This is needed for V2
-                    actual_component = component.get(_COMPONENT_KEY_, None)
-                else:
-                    actual_component = component
+                actual_component = component.get(_COMPONENT_KEY_, None)
                 _task_file_paths = get_task_file_paths(
                     workflow_dir_local=task_files.workflow_dir_local,
                     workflow_dir_remote=task_files.workflow_dir_remote,

fractal_server/app/runner/filenames.py

@@ -1,4 +1,2 @@
-HISTORY_FILENAME_V1 = "history.json"
-METADATA_FILENAME_V1 = "metadata.json"
 SHUTDOWN_FILENAME = "shutdown"
 WORKFLOW_LOG_FILENAME = "workflow.log"

fractal_server/app/runner/shutdown.py

@@ -3,8 +3,6 @@ import time
 from sqlmodel import select
 
 from fractal_server.app.db import get_async_db
-from fractal_server.app.models.v1 import ApplyWorkflow
-from fractal_server.app.models.v1.job import JobStatusTypeV1
 from fractal_server.app.models.v2 import JobV2
 from fractal_server.app.models.v2.job import JobStatusTypeV2
 from fractal_server.app.routes.aux._job import _write_shutdown_file
@@ -13,9 +11,7 @@ from fractal_server.logger import get_logger
 from fractal_server.syringe import Inject
 
 
-async def cleanup_after_shutdown(
-    *, jobsV1: list[int], jobsV2: list[int], logger_name: str
-):
+async def cleanup_after_shutdown(*, jobsV2: list[int], logger_name: str):
     logger = get_logger(logger_name)
     logger.info("Cleanup function after shutdown")
     stm_v2 = (
@@ -24,22 +20,12 @@ async def cleanup_after_shutdown(
         .where(JobV2.status == JobStatusTypeV2.SUBMITTED)
     )
 
-    stm_v1 = (
-        select(ApplyWorkflow)
-        .where(ApplyWorkflow.id.in_(jobsV1))
-        .where(ApplyWorkflow.status == JobStatusTypeV1.SUBMITTED)
-    )
-
     async for session in get_async_db():
         jobsV2_db = (await session.execute(stm_v2)).scalars().all()
-        jobsV1_db = (await session.execute(stm_v1)).scalars().all()
 
         for job in jobsV2_db:
             _write_shutdown_file(job=job)
 
-        for job in jobsV1_db:
-            _write_shutdown_file(job=job)
-
         settings = Inject(get_settings)
 
         t_start = time.perf_counter()
@@ -49,9 +35,8 @@ async def cleanup_after_shutdown(
             logger.info("Waiting 3 seconds before checking")
             time.sleep(3)
             jobsV2_db = (await session.execute(stm_v2)).scalars().all()
-            jobsV1_db = (await session.execute(stm_v1)).scalars().all()
 
-            if len(jobsV2_db) == 0 and len(jobsV1_db) == 0:
+            if len(jobsV2_db) == 0:
                 logger.info(
                     (
                         "All jobs associated to this app are "
@@ -61,10 +46,7 @@ async def cleanup_after_shutdown(
                 return
             else:
                 logger.info(
-                    (
-                        f"Some jobs are still 'submitted' "
-                        f"{jobsV1_db=}, {jobsV2_db=}"
-                    )
+                    (f"Some jobs are still 'submitted' " f"{jobsV2_db=}")
                 )
         logger.info(
             (
@@ -79,10 +61,4 @@ async def cleanup_after_shutdown(
             session.add(job)
         await session.commit()
 
-        for job in jobsV1_db:
-            job.status = "failed"
-            job.log = (job.log or "") + "\nJob stopped due to app shutdown\n"
-            session.add(job)
-        await session.commit()
-
         logger.info("Exit from shutdown logic")

fractal_server/app/schemas/_validators.py

@@ -48,25 +48,6 @@ def valdict_keys(attribute: str):
     return val
 
 
-def valint(attribute: str, min_val: int = 1):
-    """
-    Check that an integer attribute (e.g. if it is meant to be the ID of a
-    database entry) is greater or equal to min_val.
-    """
-
-    def val(integer: Optional[int]) -> Optional[int]:
-        if integer is None:
-            raise ValueError(f"Integer attribute '{attribute}' cannot be None")
-        if integer < min_val:
-            raise ValueError(
-                f"Integer attribute '{attribute}' cannot be less than "
-                f"{min_val} (given {integer})"
-            )
-        return integer
-
-    return val
-
-
 def val_absolute_path(attribute: str, accept_none: bool = False):
     """
     Check that a string attribute is an absolute path

fractal_server/config.py

@@ -338,7 +338,7 @@ class Settings(BaseSettings):
 
     FRACTAL_API_MAX_JOB_LIST_LENGTH: int = 50
     """
-    Number of ids that can be stored in the `jobsV1` and `jobsV2` attributes of
+    Number of ids that can be stored in the `jobsV2` attribute of
     `app.state`.
     """
 
@@ -496,13 +496,6 @@ class Settings(BaseSettings):
     `JobExecutionError`.
     """
 
-    FRACTAL_API_SUBMIT_RATE_LIMIT: int = 2
-    """
-    Interval to wait (in seconds) to be allowed to call again
-    `POST api/v1/{project_id}/workflow/{workflow_id}/apply/`
-    with the same path and query parameters.
-    """
-
     FRACTAL_RUNNER_TASKS_INCLUDE_IMAGE: str = (
         "Copy OME-Zarr structure;Convert Metadata Components from 2D to 3D"
     )
@@ -511,13 +504,6 @@ class Settings(BaseSettings):
     attribute in their input-arguments JSON file.
     """
 
-    FRACTAL_API_V1_MODE: Literal[
-        "include", "include_read_only", "exclude"
-    ] = "include"
-    """
-    Whether to include the v1 API.
-    """
-
     FRACTAL_PIP_CACHE_DIR: Optional[str] = None
     """
     Absolute path to the cache directory for `pip`; if unset,

fractal_server/main.py

@@ -39,20 +39,11 @@ def collect_routers(app: FastAPI) -> None:
             The application to register the routers to.
     """
     from .app.routes.api import router_api
-    from .app.routes.api.v1 import router_api_v1
     from .app.routes.api.v2 import router_api_v2
-    from .app.routes.admin.v1 import router_admin_v1
     from .app.routes.admin.v2 import router_admin_v2
     from .app.routes.auth.router import router_auth
 
-    settings = Inject(get_settings)
-
     app.include_router(router_api, prefix="/api")
-    if settings.FRACTAL_API_V1_MODE.startswith("include"):
-        app.include_router(router_api_v1, prefix="/api/v1")
-        app.include_router(
-            router_admin_v1, prefix="/admin/v1", tags=["V1 Admin area"]
-        )
     app.include_router(router_api_v2, prefix="/api/v2")
     app.include_router(
         router_admin_v2, prefix="/admin/v2", tags=["V2 Admin area"]
@@ -84,7 +75,6 @@ def check_settings() -> None:
 
 @asynccontextmanager
 async def lifespan(app: FastAPI):
-    app.state.jobsV1 = []
     app.state.jobsV2 = []
     logger = set_logger("fractal_server.lifespan")
     logger.info("Start application startup")
@@ -123,12 +113,11 @@ async def lifespan(app: FastAPI):
 
     logger.info(
         f"Current worker with pid {os.getpid()} is shutting down. "
-        f"Current jobs: {app.state.jobsV1=}, {app.state.jobsV2=}"
+        f"Current jobs: {app.state.jobsV2=}"
     )
     if _backend_supports_shutdown(settings.FRACTAL_RUNNER_BACKEND):
         try:
             await cleanup_after_shutdown(
-                jobsV1=app.state.jobsV1,
                 jobsV2=app.state.jobsV2,
                 logger_name="fractal_server.lifespan",
             )

fractal_server/migrations/versions/1eac13a26c83_drop_v1_tables.py

@@ -0,0 +1,67 @@
+"""Drop V1 tables
+
+Revision ID: 1eac13a26c83
+Revises: af8673379a5c
+Create Date: 2025-01-10 13:17:47.838607
+
+"""
+import logging
+
+from alembic import op
+from sqlmodel import SQLModel
+
+from fractal_server.migrations.naming_convention import NAMING_CONVENTION
+
+# revision identifiers, used by Alembic.
+revision = "1eac13a26c83"
+down_revision = "af8673379a5c"
+branch_labels = None
+depends_on = None
+
+
+TABLES_V1 = [
+    "resource",
+    "applyworkflow",
+    "task",
+    "workflow",
+    "workflowtask",
+    "linkuserproject",
+    "dataset",
+    "project",
+    "state",
+]
+
+
+def upgrade() -> None:
+
+    logger = logging.getLogger("alembic.runtime.migration")
+
+    target_metadata = SQLModel.metadata
+    target_metadata.naming_convention = NAMING_CONVENTION
+
+    connection = op.get_bind()
+    target_metadata.reflect(
+        bind=connection,
+        extend_existing=True,
+        only=TABLES_V1,
+    )
+
+    logger.info("Starting non-reversible upgrade")
+    logger.info("Dropping all V1 ForeignKey constraints")
+    fk_names = []
+    for table_name in TABLES_V1:
+        table = target_metadata.tables[table_name]
+        for fk in table.foreign_keys:
+            op.drop_constraint(fk.name, table_name, type_="foreignkey")
+            fk_names.append(fk.name)
+    logger.info(f"Dropped all V1 ForeignKey constraints: {fk_names}")
+    logger.info(f"Dropping all V1 tables: {TABLES_V1}")
+    for table_name in TABLES_V1:
+        op.drop_table(table_name)
+
+
+def downgrade() -> None:
+    raise RuntimeError(
+        "Cannot downgrade from 1eac13a26c83 to db09233ad13a, "
+        "because it's fully breaking."
+    )

fractal_server/migrations/versions/af8673379a5c_drop_old_filter_columns.py

@@ -0,0 +1,54 @@
+"""drop old filter columns
+
+Revision ID: af8673379a5c
+Revises: db09233ad13a
+Create Date: 2025-01-30 14:44:04.302795
+
+"""
+import sqlalchemy as sa
+from alembic import op
+from sqlalchemy.dialects import postgresql
+
+# revision identifiers, used by Alembic.
+revision = "af8673379a5c"
+down_revision = "db09233ad13a"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("datasetv2", schema=None) as batch_op:
+        batch_op.drop_column("filters")
+
+    with op.batch_alter_table("workflowtaskv2", schema=None) as batch_op:
+        batch_op.drop_column("input_filters")
+
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("workflowtaskv2", schema=None) as batch_op:
+        batch_op.add_column(
+            sa.Column(
+                "input_filters",
+                postgresql.JSON(astext_type=sa.Text()),
+                server_default=sa.text("'null'::json"),
+                autoincrement=False,
+                nullable=True,
+            )
+        )
+
+    with op.batch_alter_table("datasetv2", schema=None) as batch_op:
+        batch_op.add_column(
+            sa.Column(
+                "filters",
+                postgresql.JSON(astext_type=sa.Text()),
+                server_default=sa.text("'null'::json"),
+                autoincrement=False,
+                nullable=True,
+            )
+        )
+
+    # ### end Alembic commands ###

fractal_server/string_tools.py

@@ -33,27 +33,6 @@ def sanitize_string(value: str) -> str:
     return new_value
 
 
-def slugify_task_name_for_source_v1(task_name: str) -> str:
-    """
-    NOTE: this function is used upon creation of tasks' sources, therefore
-    for the moment we cannot replace it with its more comprehensive version
-    from `fractal_server.string_tools.sanitize_string`, nor we can remove it.
-
-    As of 2.3.1, we are renaming it to `slugify_task_name_for_source`, to make
-    it clear that it should not be used for other purposes.
-
-    As of 2.7.0, we are renaming it to `slugify_task_name_for_source_v1`, to
-    make it clear that it is not used for v2.
-
-    Args:
-        task_name:
-
-    Return:
-        Slug-ified task name.
-    """
-    return task_name.replace(" ", "_").lower()
-
-
 def validate_cmd(
     command: str,
     *,

fractal_server/tasks/utils.py

@@ -1,7 +1,5 @@
 from pathlib import Path
 
-from fractal_server.config import get_settings
-from fractal_server.syringe import Inject
 
 COLLECTION_FILENAME = "collection.json"
 COLLECTION_LOG_FILENAME = "collection.log"
@@ -9,31 +7,5 @@ COLLECTION_FREEZE_FILENAME = "collection_freeze.txt"
 FORBIDDEN_DEPENDENCY_STRINGS = ["github.com"]
 
 
-def get_absolute_venv_path_v1(venv_path: Path) -> Path:
-    """
-    If a path is not absolute, make it a relative path of FRACTAL_TASKS_DIR.
-
-    As of v2.7.0, we rename this to v1 since it is only to be used in v1.
-    """
-    if venv_path.is_absolute():
-        package_path = venv_path
-    else:
-        settings = Inject(get_settings)
-        package_path = settings.FRACTAL_TASKS_DIR / venv_path
-    return package_path
-
-
-def get_collection_path(base: Path) -> Path:
-    return base / COLLECTION_FILENAME
-
-
 def get_log_path(base: Path) -> Path:
     return base / COLLECTION_LOG_FILENAME
-
-
-def get_collection_log_v1(path: Path) -> str:
-    package_path = get_absolute_venv_path_v1(path)
-    log_path = get_log_path(package_path)
-    with log_path.open("r") as f:
-        log = f.read()
-    return log

{fractal_server-2.11.0a10.dist-info → fractal_server-2.12.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: fractal-server
-Version: 2.11.0a10
+Version: 2.12.0
 Summary: Backend component of the Fractal analytics platform
 Home-page: https://github.com/fractal-analytics-platform/fractal-server
 License: BSD-3-Clause