fractal-server 1.4.10__py3-none-any.whl → 2.0.0a1__py3-none-any.whl

fractal_server/images/tools.py

@@ -0,0 +1,85 @@
+from copy import copy
+from typing import Any
+from typing import Literal
+from typing import Optional
+from typing import Union
+
+from fractal_server.images import Filters
+
+
+ImageSearch = dict[Literal["image", "index"], Union[int, dict[str, Any]]]
+
+
+def find_image_by_path(
+    *,
+    images: list[dict[str, Any]],
+    path: str,
+) -> Optional[ImageSearch]:
+    """
+    Return a copy of the image with a given path, and its positional index.
+
+    Arguments:
+        images: List of images.
+        path: Path that the returned image must have.
+
+    Returns:
+        The first image from `images` which has path equal to `path`.
+    """
+    image_paths = [img["path"] for img in images]
+    try:
+        ind = image_paths.index(path)
+    except ValueError:
+        return None
+    return dict(image=copy(images[ind]), index=ind)
+
+
+# FIXME: what is filters
+def match_filter(image: dict[str, Any], filters: Filters) -> bool:
+    """
+    Find whether an image matches a filter set.
+
+    Arguments:
+        image: A single image.
+        filters: A set of filters.
+
+    Returns:
+        Whether the image matches the filter set.
+    """
+    # Verify match with types (using a False default)
+    for key, value in filters.types.items():
+        if image["types"].get(key, False) != value:
+            return False
+    # Verify match with attributes (only for non-None filters)
+    for key, value in filters.attributes.items():
+        if value is None:
+            continue
+        if image["attributes"].get(key) != value:
+            return False
+    return True
+
+
+def filter_image_list(
+    images: list[dict[str, Any]],
+    filters: Filters,
+) -> list[dict[str, Any]]:
+    """
+    Compute a sublist with images that match a filter set.
+
+    Arguments:
+        images: A list of images.
+        filters: A set of filters.
+
+    Returns:
+        List of the `images` elements which match the filter set.
+    """
+
+    # When no filter is provided, return all images
+    if filters.attributes == {} and filters.types == {}:
+        return images
+
+    filtered_images = [
+        copy(this_image)
+        for this_image in images
+        if match_filter(this_image, filters=filters)
+    ]
+    return filtered_images

fractal_server/main.py

@@ -32,13 +32,21 @@ def collect_routers(app: FastAPI) -> None:
     """
     from .app.routes.api import router_api
     from .app.routes.api.v1 import router_api_v1
-    from .app.routes.admin import router_admin
+    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 import router_auth
 
     app.include_router(router_api, prefix="/api")
     app.include_router(router_api_v1, prefix="/api/v1")
-    app.include_router(router_admin, prefix="/admin", tags=["Admin area"])
-    app.include_router(router_auth, prefix="/auth", tags=["auth"])
+    app.include_router(router_api_v2, prefix="/api/v2")
+    app.include_router(
+        router_admin_v1, prefix="/admin/v1", tags=["V1 Admin area"]
+    )
+    app.include_router(
+        router_admin_v2, prefix="/admin/v2", tags=["V2 Admin area"]
+    )
+    app.include_router(router_auth, prefix="/auth", tags=["Authentication"])
 
 
 def check_settings() -> None:

fractal_server/migrations/env.py

@@ -58,7 +58,6 @@ def run_migrations_offline() -> None:
         target_metadata=target_metadata,
         literal_binds=True,
         dialect_opts={"paramstyle": "named"},
-        render_as_batch=True,
     )
 
     with context.begin_transaction():
@@ -69,7 +68,6 @@ def do_run_migrations(connection: Connection) -> None:
     context.configure(
         connection=connection,
         target_metadata=target_metadata,
-        render_as_batch=True,
     )
 
     with context.begin_transaction():

fractal_server/migrations/versions/d71e732236cd_v2.py

@@ -0,0 +1,239 @@
+"""v2
+
+Revision ID: d71e732236cd
+Revises: 9fd26a2b0de4
+Create Date: 2024-04-05 11:09:17.639183
+
+"""
+import sqlalchemy as sa
+import sqlmodel
+from alembic import op
+
+
+# revision identifiers, used by Alembic.
+revision = "d71e732236cd"
+down_revision = "9fd26a2b0de4"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_table(
+        "projectv2",
+        sa.Column("id", sa.Integer(), nullable=False),
+        sa.Column("name", sqlmodel.sql.sqltypes.AutoString(), nullable=False),
+        sa.Column("read_only", sa.Boolean(), nullable=False),
+        sa.Column(
+            "timestamp_created", sa.DateTime(timezone=True), nullable=False
+        ),
+        sa.PrimaryKeyConstraint("id"),
+    )
+    op.create_table(
+        "taskv2",
+        sa.Column("id", sa.Integer(), nullable=False),
+        sa.Column("name", sqlmodel.sql.sqltypes.AutoString(), nullable=False),
+        sa.Column("type", sqlmodel.sql.sqltypes.AutoString(), nullable=False),
+        sa.Column(
+            "command_non_parallel",
+            sqlmodel.sql.sqltypes.AutoString(),
+            nullable=True,
+        ),
+        sa.Column(
+            "command_parallel",
+            sqlmodel.sql.sqltypes.AutoString(),
+            nullable=True,
+        ),
+        sa.Column(
+            "source", sqlmodel.sql.sqltypes.AutoString(), nullable=False
+        ),
+        sa.Column(
+            "meta_non_parallel", sa.JSON(), server_default="{}", nullable=False
+        ),
+        sa.Column(
+            "meta_parallel", sa.JSON(), server_default="{}", nullable=False
+        ),
+        sa.Column("owner", sqlmodel.sql.sqltypes.AutoString(), nullable=True),
+        sa.Column(
+            "version", sqlmodel.sql.sqltypes.AutoString(), nullable=True
+        ),
+        sa.Column("args_schema_non_parallel", sa.JSON(), nullable=True),
+        sa.Column("args_schema_parallel", sa.JSON(), nullable=True),
+        sa.Column(
+            "args_schema_version",
+            sqlmodel.sql.sqltypes.AutoString(),
+            nullable=True,
+        ),
+        sa.Column(
+            "docs_info", sqlmodel.sql.sqltypes.AutoString(), nullable=True
+        ),
+        sa.Column(
+            "docs_link", sqlmodel.sql.sqltypes.AutoString(), nullable=True
+        ),
+        sa.Column("input_types", sa.JSON(), nullable=True),
+        sa.Column("output_types", sa.JSON(), nullable=True),
+        sa.PrimaryKeyConstraint("id"),
+        sa.UniqueConstraint("source"),
+    )
+    op.create_table(
+        "datasetv2",
+        sa.Column("id", sa.Integer(), nullable=False),
+        sa.Column("name", sqlmodel.sql.sqltypes.AutoString(), nullable=False),
+        sa.Column("project_id", sa.Integer(), nullable=False),
+        sa.Column("history", sa.JSON(), server_default="[]", nullable=False),
+        sa.Column("read_only", sa.Boolean(), nullable=False),
+        sa.Column(
+            "timestamp_created", sa.DateTime(timezone=True), nullable=False
+        ),
+        sa.Column(
+            "zarr_dir", sqlmodel.sql.sqltypes.AutoString(), nullable=False
+        ),
+        sa.Column("images", sa.JSON(), server_default="[]", nullable=False),
+        sa.Column(
+            "filters",
+            sa.JSON(),
+            server_default='{"attributes": {}, "types": {}}',
+            nullable=False,
+        ),
+        sa.ForeignKeyConstraint(
+            ["project_id"],
+            ["projectv2.id"],
+        ),
+        sa.PrimaryKeyConstraint("id"),
+    )
+    op.create_table(
+        "linkuserprojectv2",
+        sa.Column("project_id", sa.Integer(), nullable=False),
+        sa.Column("user_id", sa.Integer(), nullable=False),
+        sa.ForeignKeyConstraint(
+            ["project_id"],
+            ["projectv2.id"],
+        ),
+        sa.ForeignKeyConstraint(
+            ["user_id"],
+            ["user_oauth.id"],
+        ),
+        sa.PrimaryKeyConstraint("project_id", "user_id"),
+    )
+    op.create_table(
+        "workflowv2",
+        sa.Column("id", sa.Integer(), nullable=False),
+        sa.Column("name", sqlmodel.sql.sqltypes.AutoString(), nullable=False),
+        sa.Column("project_id", sa.Integer(), nullable=False),
+        sa.Column(
+            "timestamp_created", sa.DateTime(timezone=True), nullable=False
+        ),
+        sa.ForeignKeyConstraint(
+            ["project_id"],
+            ["projectv2.id"],
+        ),
+        sa.PrimaryKeyConstraint("id"),
+    )
+    op.create_table(
+        "jobv2",
+        sa.Column("id", sa.Integer(), nullable=False),
+        sa.Column("project_id", sa.Integer(), nullable=True),
+        sa.Column("workflow_id", sa.Integer(), nullable=True),
+        sa.Column("dataset_id", sa.Integer(), nullable=True),
+        sa.Column(
+            "user_email", sqlmodel.sql.sqltypes.AutoString(), nullable=False
+        ),
+        sa.Column(
+            "slurm_account", sqlmodel.sql.sqltypes.AutoString(), nullable=True
+        ),
+        sa.Column("dataset_dump", sa.JSON(), nullable=False),
+        sa.Column("workflow_dump", sa.JSON(), nullable=False),
+        sa.Column("project_dump", sa.JSON(), nullable=False),
+        sa.Column(
+            "worker_init", sqlmodel.sql.sqltypes.AutoString(), nullable=True
+        ),
+        sa.Column(
+            "working_dir", sqlmodel.sql.sqltypes.AutoString(), nullable=True
+        ),
+        sa.Column(
+            "working_dir_user",
+            sqlmodel.sql.sqltypes.AutoString(),
+            nullable=True,
+        ),
+        sa.Column("first_task_index", sa.Integer(), nullable=False),
+        sa.Column("last_task_index", sa.Integer(), nullable=False),
+        sa.Column(
+            "start_timestamp", sa.DateTime(timezone=True), nullable=False
+        ),
+        sa.Column("end_timestamp", sa.DateTime(timezone=True), nullable=True),
+        sa.Column(
+            "status", sqlmodel.sql.sqltypes.AutoString(), nullable=False
+        ),
+        sa.Column("log", sqlmodel.sql.sqltypes.AutoString(), nullable=True),
+        sa.ForeignKeyConstraint(
+            ["dataset_id"],
+            ["datasetv2.id"],
+        ),
+        sa.ForeignKeyConstraint(
+            ["project_id"],
+            ["projectv2.id"],
+        ),
+        sa.ForeignKeyConstraint(
+            ["workflow_id"],
+            ["workflowv2.id"],
+        ),
+        sa.PrimaryKeyConstraint("id"),
+    )
+    op.create_table(
+        "workflowtaskv2",
+        sa.Column("id", sa.Integer(), nullable=False),
+        sa.Column("workflow_id", sa.Integer(), nullable=False),
+        sa.Column("order", sa.Integer(), nullable=True),
+        sa.Column("meta_parallel", sa.JSON(), nullable=True),
+        sa.Column("meta_non_parallel", sa.JSON(), nullable=True),
+        sa.Column("args_parallel", sa.JSON(), nullable=True),
+        sa.Column("args_non_parallel", sa.JSON(), nullable=True),
+        sa.Column(
+            "input_filters",
+            sa.JSON(),
+            server_default='{"attributes": {}, "types": {}}',
+            nullable=False,
+        ),
+        sa.Column("is_legacy_task", sa.Boolean(), nullable=False),
+        sa.Column(
+            "task_type", sqlmodel.sql.sqltypes.AutoString(), nullable=False
+        ),
+        sa.Column("task_id", sa.Integer(), nullable=True),
+        sa.Column("task_legacy_id", sa.Integer(), nullable=True),
+        sa.ForeignKeyConstraint(
+            ["task_id"],
+            ["taskv2.id"],
+        ),
+        sa.ForeignKeyConstraint(
+            ["task_legacy_id"],
+            ["task.id"],
+        ),
+        sa.ForeignKeyConstraint(
+            ["workflow_id"],
+            ["workflowv2.id"],
+        ),
+        sa.PrimaryKeyConstraint("id"),
+    )
+    op.add_column(
+        "task",
+        sa.Column(
+            "is_v2_compatible",
+            sa.Boolean(),
+            server_default=sa.text("false"),
+            nullable=False,
+        ),
+    )
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_column("task", "is_v2_compatible")
+    op.drop_table("workflowtaskv2")
+    op.drop_table("jobv2")
+    op.drop_table("workflowv2")
+    op.drop_table("linkuserprojectv2")
+    op.drop_table("datasetv2")
+    op.drop_table("taskv2")
+    op.drop_table("projectv2")
+    # ### end Alembic commands ###

fractal_server/tasks/__init__.py

@@ -1,8 +1,3 @@
 """
 `tasks` module
-
-Submodules:
-    * [Endpoint functions](background_operations)
-    * [Background-task functions](endpoint_operations)
-    * [Auxiliary functions](utils)
 """

fractal_server/tasks/endpoint_operations.py

@@ -4,35 +4,26 @@ from typing import Optional
 from typing import Union
 from zipfile import ZipFile
 
-from fractal_server.app.schemas import ManifestV1
-from fractal_server.app.schemas import TaskCollectStatus
+from .utils import _normalize_package_name
+from .utils import get_python_interpreter
+from .v1._TaskCollectPip import _TaskCollectPip as _TaskCollectPipV1
+from .v2._TaskCollectPip import _TaskCollectPip as _TaskCollectPipV2
+from fractal_server.app.schemas.v1 import ManifestV1
+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.syringe import Inject
-from fractal_server.tasks._TaskCollectPip import _TaskCollectPip
-from fractal_server.tasks.utils import _normalize_package_name
-from fractal_server.tasks.utils import get_absolute_venv_path
-from fractal_server.tasks.utils import get_collection_path
-from fractal_server.tasks.utils import get_python_interpreter
 from fractal_server.utils import execute_command
 
 
 FRACTAL_PUBLIC_TASK_SUBDIR = ".fractal"
 
 
-def get_collection_data(venv_path: Path) -> TaskCollectStatus:
-    package_path = get_absolute_venv_path(venv_path)
-    collection_path = get_collection_path(package_path)
-    with collection_path.open() as f:
-        data = json.load(f)
-    return TaskCollectStatus(**data)
-
-
 async def download_package(
     *,
-    task_pkg: _TaskCollectPip,
+    task_pkg: Union[_TaskCollectPipV1, _TaskCollectPipV2],
     dest: Union[str, Path],
-):
+) -> Path:
     """
     Download package to destination
     """
@@ -52,7 +43,7 @@ async def download_package(
 
 def _load_manifest_from_wheel(
     path: Path, wheel: ZipFile, logger_name: Optional[str] = None
-) -> ManifestV1:
+) -> Union[ManifestV1, ManifestV2]:
     logger = get_logger(logger_name)
     namelist = wheel.namelist()
     try:
@@ -69,6 +60,9 @@ def _load_manifest_from_wheel(
     if manifest_version == "1":
         pkg_manifest = ManifestV1(**manifest_dict)
         return pkg_manifest
+    elif manifest_version == "2":
+        pkg_manifest = ManifestV2(**manifest_dict)
+        return pkg_manifest
     else:
         msg = f"Manifest version {manifest_version=} not supported"
         logger.error(msg)
@@ -146,7 +140,7 @@ def inspect_package(path: Path, logger_name: Optional[str] = None) -> dict:
 
 def create_package_dir_pip(
     *,
-    task_pkg: _TaskCollectPip,
+    task_pkg: Union[_TaskCollectPipV1, _TaskCollectPipV2],
     create: bool = True,
 ) -> Path:
     """

fractal_server/tasks/utils.py

@@ -5,7 +5,9 @@ from pathlib import Path
 from typing import Optional
 
 from fractal_server.config import get_settings
+from fractal_server.logger import get_logger
 from fractal_server.syringe import Inject
+from fractal_server.utils import execute_command
 
 COLLECTION_FILENAME = "collection.json"
 COLLECTION_LOG_FILENAME = "collection.log"
@@ -84,3 +86,36 @@ def _normalize_package_name(name: str) -> str:
         The normalized package name.
     """
     return re.sub(r"[-_.]+", "-", name).lower()
+
+
+async def _init_venv(
+    *,
+    path: Path,
+    python_version: Optional[str] = None,
+    logger_name: str,
+) -> Path:
+    """
+    Set a virtual environment at `path/venv`
+
+    Args:
+        path : Path
+            path to directory in which to set up the virtual environment
+        python_version : default=None
+            Python version the virtual environment will be based upon
+
+    Returns:
+        python_bin : Path
+            path to python interpreter
+    """
+    logger = get_logger(logger_name)
+    logger.debug(f"[_init_venv] {path=}")
+    interpreter = get_python_interpreter(version=python_version)
+    logger.debug(f"[_init_venv] {interpreter=}")
+    await execute_command(
+        cwd=path,
+        command=f"{interpreter} -m venv venv",
+        logger_name=logger_name,
+    )
+    python_bin = path / "venv/bin/python"
+    logger.debug(f"[_init_venv] {python_bin=}")
+    return python_bin

fractal_server/tasks/{_TaskCollectPip.py → v1/_TaskCollectPip.py}

@@ -3,11 +3,11 @@ from typing import Optional
 
 from pydantic import root_validator
 
-from fractal_server.app.schemas import ManifestV1
-from fractal_server.app.schemas import TaskCollectPip
+from fractal_server.app.schemas.v1 import ManifestV1
+from fractal_server.app.schemas.v1 import TaskCollectPipV1
 
 
-class _TaskCollectPip(TaskCollectPip):
+class _TaskCollectPip(TaskCollectPipV1):
     """
     Internal TaskCollectPip schema
 

fractal_server/tasks/{background_operations.py → v1/background_operations.py}

@@ -5,61 +5,27 @@ is used as a background task for the task-collection endpoint.
 import json
 from pathlib import Path
 from shutil import rmtree as shell_rmtree
-from typing import Optional
 
+from ..utils import _init_venv
+from ..utils import _normalize_package_name
+from ..utils import get_collection_log
+from ..utils import get_collection_path
+from ..utils import get_log_path
+from ..utils import slugify_task_name
+from ._TaskCollectPip import _TaskCollectPip
 from fractal_server.app.db import DBSyncSession
 from fractal_server.app.db import get_sync_db
 from fractal_server.app.models import State
 from fractal_server.app.models import Task
-from fractal_server.app.schemas import TaskCollectStatus
-from fractal_server.app.schemas import TaskCreate
-from fractal_server.app.schemas import TaskRead
+from fractal_server.app.schemas.v1 import TaskCollectStatusV1
+from fractal_server.app.schemas.v1 import TaskCreateV1
+from fractal_server.app.schemas.v1 import TaskReadV1
 from fractal_server.logger import close_logger
 from fractal_server.logger import get_logger
 from fractal_server.logger import set_logger
-from fractal_server.tasks._TaskCollectPip import _TaskCollectPip
-from fractal_server.tasks.utils import _normalize_package_name
-from fractal_server.tasks.utils import get_collection_log
-from fractal_server.tasks.utils import get_collection_path
-from fractal_server.tasks.utils import get_log_path
-from fractal_server.tasks.utils import get_python_interpreter
-from fractal_server.tasks.utils import slugify_task_name
 from fractal_server.utils import execute_command
 
 
-async def _init_venv(
-    *,
-    path: Path,
-    python_version: Optional[str] = None,
-    logger_name: str,
-) -> Path:
-    """
-    Set a virtual environment at `path/venv`
-
-    Args:
-        path : Path
-            path to directory in which to set up the virtual environment
-        python_version : default=None
-            Python version the virtual environment will be based upon
-
-    Returns:
-        python_bin : Path
-            path to python interpreter
-    """
-    logger = get_logger(logger_name)
-    logger.debug(f"[_init_venv] {path=}")
-    interpreter = get_python_interpreter(version=python_version)
-    logger.debug(f"[_init_venv] {interpreter=}")
-    await execute_command(
-        cwd=path,
-        command=f"{interpreter} -m venv venv",
-        logger_name=logger_name,
-    )
-    python_bin = path / "venv/bin/python"
-    logger.debug(f"[_init_venv] {python_bin=}")
-    return python_bin
-
-
 async def _pip_install(
     venv_path: Path,
     task_pkg: _TaskCollectPip,
@@ -218,7 +184,7 @@ async def create_package_environment_pip(
     task_pkg: _TaskCollectPip,
     venv_path: Path,
     logger_name: str,
-) -> list[TaskCreate]:
+) -> list[TaskCreateV1]:
     """
     Create environment, install package, and prepare task list
     """
@@ -263,7 +229,7 @@ async def create_package_environment_pip(
                 )
             else:
                 additional_attrs = {}
-            this_task = TaskCreate(
+            this_task = TaskCreateV1(
                 **t.dict(),
                 command=cmd,
                 version=task_pkg.package_version,
@@ -279,7 +245,7 @@ async def create_package_environment_pip(
 
 
 async def _insert_tasks(
-    task_list: list[TaskCreate],
+    task_list: list[TaskCreateV1],
     db: DBSyncSession,
 ) -> list[Task]:
     """
@@ -319,7 +285,7 @@ async def background_collect_pip(
 
     with next(get_sync_db()) as db:
         state: State = db.get(State, state_id)
-        data = TaskCollectStatus(**state.data)
+        data = TaskCollectStatusV1(**state.data)
         data.info = None
 
         try:
@@ -347,9 +313,11 @@ async def background_collect_pip(
             # finalise
             logger.debug("Task-collection status: finalising")
             collection_path = get_collection_path(venv_path)
-            data.task_list = [TaskRead(**task.model_dump()) for task in tasks]
+            data.task_list = [
+                TaskReadV1(**task.model_dump()) for task in tasks
+            ]
             with collection_path.open("w") as f:
-                json.dump(data.sanitised_dict(), f)
+                json.dump(data.sanitised_dict(), f, indent=2)
 
             # Update DB
             data.status = "OK"

fractal_server/tasks/v1/get_collection_data.py

@@ -0,0 +1,14 @@
+import json
+from pathlib import Path
+
+from fractal_server.app.schemas.v1 import TaskCollectStatusV1
+from fractal_server.tasks.utils import get_absolute_venv_path
+from fractal_server.tasks.utils import get_collection_path
+
+
+def get_collection_data(venv_path: Path) -> TaskCollectStatusV1:
+    package_path = get_absolute_venv_path(venv_path)
+    collection_path = get_collection_path(package_path)
+    with collection_path.open() as f:
+        data = json.load(f)
+    return TaskCollectStatusV1(**data)