diff --git a/alembic/versions/b2c52ee8ff12_add_ingestion_status.py b/alembic/versions/b2c52ee8ff12_add_ingestion_status.py new file mode 100644 index 00000000..b9861c90 --- /dev/null +++ b/alembic/versions/b2c52ee8ff12_add_ingestion_status.py @@ -0,0 +1,71 @@ +"""Add ingestion status + +Revision ID: b2c52ee8ff12 +Revises: 28bee3aa2429 +Create Date: 2026-05-11 16:16:03.768893 + +""" + +from typing import Sequence, Union + +import sqlalchemy as sa + +from alembic import op + +# revision identifiers, used by Alembic. +revision: str = "b2c52ee8ff12" +down_revision: Union[str, Sequence[str], None] = "28bee3aa2429" +branch_labels: Union[str, Sequence[str], None] = None +depends_on: Union[str, Sequence[str], None] = None + + +def upgrade() -> None: + """Upgrade schema.""" + conn = op.get_bind() + dialect = conn.dialect.name + if dialect == "postgresql": + op.execute( + "CREATE TYPE ingestionstatus AS ENUM ('QUEUED', 'COPYING', 'COPIED', " + "'VALIDATING', 'VALIDATED', 'COMPLETED', 'COPY_FAILED', " + "'VALIDATION_FAILED')" + ) + with op.batch_alter_table("simulations", schema=None) as batch_op: + batch_op.add_column( + sa.Column( + "ingestion_status", + sa.Enum( + "QUEUED", + "COPYING", + "COPIED", + "VALIDATING", + "VALIDATED", + "COMPLETED", + "COPY_FAILED", + "VALIDATION_FAILED", + name="ingestionstatus", + ), + nullable=True, + ) + ) + batch_op.add_column(sa.Column("ingestion_version", sa.Integer(), nullable=True)) + op.execute( + "UPDATE simulations SET ingestion_status = 'COMPLETED' WHERE ingestion_status " + "IS NULL" + ) + op.execute( + "UPDATE simulations SET ingestion_version = 0 WHERE ingestion_version IS NULL" + ) + with op.batch_alter_table("simulations", schema=None) as batch_op: + batch_op.alter_column("ingestion_status", nullable=False) + batch_op.alter_column("ingestion_version", nullable=False) + + +def downgrade() -> None: + """Downgrade schema.""" + with op.batch_alter_table("simulations", schema=None) as batch_op: + batch_op.drop_column("ingestion_version") + batch_op.drop_column("ingestion_status") + conn = op.get_bind() + dialect = conn.dialect.name + if dialect == "postgresql": + op.execute("DROP TYPE ingestionstatus") diff --git a/docs/celery.md b/docs/celery.md new file mode 100644 index 00000000..d06ea512 --- /dev/null +++ b/docs/celery.md @@ -0,0 +1,77 @@ +# Celery async task processing + +SimDB uses [Celery](https://docs.celeryproject.org/) to run asynchronous background +tasks such as copying simulation files and completing the ingestion pipeline. + +## Overview + +When simulations are uploaded via the REST API, the server offloads heavy operations +to Celery workers instead of blocking the HTTP request. Tasks are defined in +`src/simdb/workers/tasks.py`: + +- `copy_files_task` — copies input/output files from source locations to the server's + upload folder and updates the simulation's ingestion status. +- `complete_ingestion_task` — marks a simulation as fully ingested. +- `validate_imas_task` — runs validation checks on IMAS data (placeholder). +- `send_email_task` — sends email notifications. + +Tasks can be chained in the API endpoint: + +```python +copy_files = copy_files_task.si(simulation.uuid, ...) +complete = complete_ingestion_task.si(simulation.uuid) +_ = (copy_files | complete).apply_async() +``` + +## Configuration + +Celery is configured via `app.cfg`: + +| Section | Option | Required | Description | +|---------|----------------|----------|--------------------------------------------------| +| celery | broker_url | no | Redis URL for the message broker. Defaults to `redis://localhost:6379/0` | +| celery | result_backend | no | Redis URL for results storage. Defaults to `redis://localhost:6379/0` | + +Example: + +```ini +[celery] +broker_url = redis://localhost:6379/0 +result_backend = redis://localhost:6379/0 +``` + +## Running workers + +### Standalone worker + +Start a Celery worker using the built-in CLI: + +```bash +simdb_worker +``` + +### Worker with beat scheduler + +For periodic tasks (e.g. cleanup, reports), run both the worker and beat: + +```bash +# Terminal 1: worker +simdb_worker + +# Terminal 2: beat scheduler +simdb_beat +``` + +### Flower monitoring + +[Flower](https://flower.readthedocs.io/) provides a web UI for monitoring Celery +workers and tasks: + +```bash +celery -A simdb.workers.celery flower --port=5555 +``` + +## Testing with eager mode + +In tests, set `task_always_eager = True` to run tasks synchronously without a +broker. diff --git a/docs/developer_guide.md b/docs/developer_guide.md index d3e5259f..28b8a036 100644 --- a/docs/developer_guide.md +++ b/docs/developer_guide.md @@ -45,6 +45,22 @@ simdb_server This will start a server on port 5000. You can test this server is running by opening http://localhost:5000 in a browser. +## Running Celery workers + +For development, you typically want to run Celery tasks synchronously. This is +enabled by setting `task_always_eager = True` in tests (see `tests/remote/api/v1.3/test_simulations3.py`). + +To run actual background workers during development: + +```bash +# Worker +simdb_worker + +# Beat scheduler (if needed) +simdb_beat +``` + +See the [Celery documentation](celery.md) for full details. ## Swagger API documentation SimDB provides interactive Swagger API documentation for each API version. The documentation is automatically generated and accessible at different endpoints depending on the API version you want to explore. diff --git a/docs/maintenance_guide.md b/docs/maintenance_guide.md index e5664af2..9774d80e 100644 --- a/docs/maintenance_guide.md +++ b/docs/maintenance_guide.md @@ -332,6 +332,12 @@ service nginx restart You should now be able to check the simdb server is running by going to the http address defined in your nginx site (localhost:80 in the example above). +## Celery background workers + +SimDB uses Celery to run asynchronous background tasks such as copying simulation +files. See the [Celery documentation](celery.md) for details on configuration and +running workers. + #### Nginx Request Entity Size You may need to increase the size of uploaded files that Nginx will accept. For SimDB this should be at least 100MB. diff --git a/pyproject.toml b/pyproject.toml index e8f6d099..8d6f99a9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -91,13 +91,19 @@ build-docs = [ postgres = [ "psycopg2-binary>=2.8.0", ] +celery = [ + "celery>=5.3.0", + "redis>=5.0.0", +] all = [ - "imas-simdb[server, imas-validator, postgres]" + "imas-simdb[server, imas-validator, postgres, celery]", ] [project.scripts] simdb = "simdb.cli.simdb:main" simdb_server = "simdb.remote.wsgi:run" +simdb_worker = "simdb.workers.cli:worker" +simdb_beat = "simdb.workers.cli:beat" [project.urls] Homepage = "https://simdb.iter.org/dashboard/" @@ -167,5 +173,5 @@ dev = [ "pytest-cov>=5.0.0", "ruff~=0.15.0", "ty==0.0.34", - "imas-simdb[server, imas-validator, postgres, auth]" + "imas-simdb[server, imas-validator, postgres, auth, celery]" ] diff --git a/scripts/test_v13_ingestion.py b/scripts/test_v13_ingestion.py new file mode 100755 index 00000000..630a1dfc --- /dev/null +++ b/scripts/test_v13_ingestion.py @@ -0,0 +1,239 @@ +#!/usr/bin/env python3 +"""Test script for v1.3 simulation ingestion against a running server.""" +from simdb.workers.tasks import _calculate_checksum +from pathlib import Path + +import base64 +import sys +import time +import uuid +from datetime import datetime, timezone + +import requests +from pydantic import TypeAdapter + +try: + from simdb.remote.models import ( + FileData, + FileDataList, + MetadataData, + MetadataDataList, + SimulationData, + SimulationPostData, + SimulationPostResponse, + SimulationStatusResponse, + ) +except ImportError: + print("ERROR: simdb package not installed. Run: pip install -e .") + sys.exit(1) + +SERVER_URL = "http://localhost:5000" +API_VERSION = "v1.3" +API_VERSION_V12 = "v1.2" +TEST_PASSWORD = "CHANGE_ME" + +CREDENTIALS = base64.b64encode(f"admin:{TEST_PASSWORD}".encode()).decode() +HEADERS = {"Authorization": f"Basic {CREDENTIALS}"} + + +def generate_simulation_file(): + checksum = _calculate_checksum(Path("tmp/partition_data/subdir/test_file.txt")) + return FileData( + type="FILE", + uri="data:///subdir/test_file.txt", + checksum=checksum, + datetime=datetime.now(timezone.utc), + ) + +def generate_imas_file(relative_path): + checksum = _calculate_checksum(Path(f"tmp/partition_data/subdir/{relative_path}")) + return FileData( + type="IMAS", + uri=f"data:///subdir/{relative_path}", + checksum=checksum, + datetime=datetime.now(timezone.utc), + ) + + +def generate_imas_netcdf_file(): + return generate_imas_file("test_imas_data/test.nc") + + +def generate_imas_hdf5_files(): + return [ + generate_imas_file("test_imas_data/test_hdf5/master.h5"), + generate_imas_file("test_imas_data/test_hdf5/summary.h5"), + ] + + +def generate_imas_mdsplus_files(): + return [ + generate_imas_file("test_imas_data/test_mdsplus/ids_001.characteristics"), + generate_imas_file("test_imas_data/test_mdsplus/ids_001.datafile"), + generate_imas_file("test_imas_data/test_mdsplus/ids_001.tree"), + ] + + +def generate_all_imas_files(): + return [ + generate_imas_file("test_imas_data/test.nc"), + *generate_imas_hdf5_files(), + *generate_imas_mdsplus_files(), + ] + + +def generate_simulation_data( + alias=None, + inputs=None, + outputs=None, + metadata=None, + add_watcher=False, + uploaded_by=None, +): + if alias is None: + alias = f"test-{uuid.uuid4().hex[:8]}" + if inputs is None: + inputs = [generate_simulation_file()] + if outputs is None: + outputs = [generate_simulation_file()] + + simulation = SimulationData( + alias=alias, + inputs=FileDataList(root=inputs), + outputs=FileDataList(root=outputs), + ) + + if metadata: + simulation.metadata = MetadataDataList(root=metadata) + + data = SimulationPostData( + simulation=simulation, + add_watcher=add_watcher, + uploaded_by=uploaded_by, + ) + return data + + +def post_simulation(simulation_data, retries=5, delay=2): + url = f"{SERVER_URL}/{API_VERSION}/simulations" + for attempt in range(retries): + try: + response = requests.post( + url, + json=simulation_data.model_dump(mode="json"), + headers={**HEADERS, "Content-Type": "application/json"}, + ) + response.raise_for_status() + return response + except requests.exceptions.RequestException as e: + if attempt < retries - 1: + print(f"Attempt {attempt + 1} failed: {e}. Retrying in {delay}s...") + time.sleep(delay) + else: + raise + + +def get_simulation_status(sim_id): + url = f"{SERVER_URL}/{API_VERSION}/simulation/status/{sim_id}" + response = requests.get(url, headers=HEADERS) + response.raise_for_status() + return response + + +def get_simulation(sim_id): + url = f"{SERVER_URL}/{API_VERSION_V12}/simulation/{sim_id}" + response = requests.get(url, headers=HEADERS) + response.raise_for_status() + return response + + +def verify_files_in_database(sim_id, expected_files): + response = get_simulation(sim_id) + sim_data = response.json() + all_files = sim_data.get("inputs", []) + sim_data.get("outputs", []) + stored_uris = {f["uri"] for f in all_files} + expected_uris = expected_files + missing = expected_uris - stored_uris + return stored_uris, missing + + +def wait_for_completion(sim_id, timeout=60, interval=2): + start = time.time() + while time.time() - start < timeout: + response = get_simulation_status(sim_id) + status_data = SimulationStatusResponse.model_validate(response.json()) + print(f" Status: {status_data.status}") + if status_data.status.name in ("COMPLETED", "COPY_FAILED"): + return status_data + time.sleep(interval) + raise TimeoutError(f"Simulation {sim_id} did not complete within {timeout}s") + + +def main(): + print("=" * 60) + print("v1.3 Simulation Ingestion Test") + print("=" * 60) + print(f"Server: {SERVER_URL}") + print(f"API Version: {API_VERSION}") + print() + + print("Generating simulation data...") + imas_files = generate_all_imas_files() + simulation_data = generate_simulation_data( + alias=f"test-ingestion-{uuid.uuid4().hex}", + inputs=[generate_simulation_file()], + outputs=imas_files, + uploaded_by="test-script", + ) + print(f" Alias: {simulation_data.simulation.alias}") + print(f" UUID: {simulation_data.simulation.uuid}") + print(f" Files: {len(simulation_data.simulation.inputs.root)+len(simulation_data.simulation.outputs.root)}") + print() + + print("Posting simulation for ingestion...") + try: + response = post_simulation(simulation_data, retries=1) + except requests.exceptions.RequestException as e: + print(f"ERROR: Failed to post simulation: {e}") + sys.exit(1) + + result = SimulationPostResponse.model_validate(response.json()) + print(f" Ingested UUID: {result.ingested}") + if result.error: + print(f" Error: {result.error}") + print() + + print("Waiting for ingestion to complete...") + try: + final_status = wait_for_completion(result.ingested) + print() + print("=" * 60) + print(f"SUCCESS: Ingestion completed with status {final_status.status}") + print("=" * 60) + + print() + print("Verifying files in database via v1.2 API...") + imas_paths = { + f"file:/data/simdb/simulations/{result.ingested.hex}/test_file.txt", + f"file:/data/simdb/simulations/{result.ingested.hex}/test_imas_data/test.nc", + f"imas:hdf5?path=/data/simdb/simulations/{result.ingested.hex}/test_imas_data/test_hdf5", + f"imas:mdsplus?path=/data/simdb/simulations/{result.ingested.hex}/test_imas_data/test_mdsplus", + } + stored_uris, missing = verify_files_in_database(result.ingested, imas_paths) + print(f" Stored URIs: {len(stored_uris)}") + for uri in sorted(stored_uris): + print(f" {uri}") + if missing: + print(f" MISSING files: {missing}") + else: + print(" All files verified!") + except TimeoutError as e: + print() + print("=" * 60) + print(f"WARNING: {e}") + print("=" * 60) + sys.exit(1) + + +if __name__ == "__main__": + main() diff --git a/src/simdb/config/config.py b/src/simdb/config/config.py index 1b04d749..774b82e8 100644 --- a/src/simdb/config/config.py +++ b/src/simdb/config/config.py @@ -304,6 +304,23 @@ def get_string_option( ) return value + def get_int_option( + self, name: str, default: Union[int, None, _NothingSentinel] = NOTHING + ) -> int: + """ + Returns the value for the option with the given name from the configuration but + also ensures the resulting value is an integer. + + @see get_option + @raise TypeError if the found value was not an integer + """ + value = self.get_option(name, default) + if value is not None and not isinstance(value, int): + raise TypeError( + f"Invalid type of option {name}: expected int, got {type(value)}" + ) + return value + def delete_option(self, name: str) -> None: """ Delete the option with the given name from the configuration. diff --git a/src/simdb/database/database.py b/src/simdb/database/database.py index 356bb73e..da3a9f77 100644 --- a/src/simdb/database/database.py +++ b/src/simdb/database/database.py @@ -203,7 +203,6 @@ def __init__(self, db_type: DBMS, scopefunc=None, **kwargs) -> None: json_serializer=lambda obj: json.dumps(obj, cls=CustomEncoder), json_deserializer=lambda s: json.loads(s, cls=CustomDecoder), ) - elif db_type == Database.DBMS.MSSQL: if "user" not in kwargs: raise ValueError("Missing user parameter for MSSQL database") @@ -214,10 +213,8 @@ def __init__(self, db_type: DBMS, scopefunc=None, **kwargs) -> None: self.engine: sqlalchemy.engine.Engine = create_engine( "mssql+pyodbc://{user}:{password}@{dsnname}".format(**kwargs) ) - else: raise ValueError("Unknown database type: " + db_type.name) - Base.metadata.bind = self.engine if scopefunc is None: @@ -892,6 +889,24 @@ def get_local_db(config: Config) -> Database: return database +def get_db(config: Config) -> Database: + db_type = config.get_option("database.type") + if db_type == "postgres": + args = config.get_section("database") + return Database( + Database.DBMS.POSTGRESQL, + **args, + ) + elif db_type == "sqlite": + db_dir = appdirs.user_data_dir("simdb") + file_str = config.get_string_option("database.file", default=None) + file = Path(file_str) if file_str else Path(db_dir, "remote.db") + file.parent.mkdir(parents=True, exist_ok=True) + return Database(Database.DBMS.SQLITE, file=file) + else: + raise RuntimeError(f"Unknown database type in configuration: {db_type}.") + + def backup_local_db(config: Config): db_file = Path( config.get_string_option("db.file", default=None) diff --git a/src/simdb/database/models/file.py b/src/simdb/database/models/file.py index 6cb8a561..df5f3ddb 100644 --- a/src/simdb/database/models/file.py +++ b/src/simdb/database/models/file.py @@ -144,7 +144,7 @@ def to_model_with_path(self) -> FileGetDataResponse: files = [FileInfo(path=self.uri.path, checksum=self.checksum)] else: files = [ - FileInfo(path=path, checksum=sha1_checksum(URI(f"file:{path}"))) + FileInfo(path=path, checksum=sha1_checksum(urilib.URI(f"file:{path}"))) for path in imas_files(self.uri) ] return FileGetDataResponse( diff --git a/src/simdb/database/models/simulation.py b/src/simdb/database/models/simulation.py index 201e9bfc..103fb099 100644 --- a/src/simdb/database/models/simulation.py +++ b/src/simdb/database/models/simulation.py @@ -7,6 +7,7 @@ from pathlib import Path from typing import Any, Dict, List, Optional, Set, Union +from simdb.enums import IngestionStatus from simdb.remote.models import ( FileDataList, MetadataData, @@ -140,6 +141,13 @@ class Status(Enum): "Watcher", secondary=simulation_watchers, lazy="dynamic" ) + ingestion_status = Column( + sql_types.Enum(IngestionStatus), + nullable=False, + default=IngestionStatus.COMPLETED, + ) + ingestion_version = Column(sql_types.Integer, nullable=False, default=0) + @property def meta(self) -> List[MetaDataWrapper]: """ diff --git a/src/simdb/enums.py b/src/simdb/enums.py new file mode 100644 index 00000000..e5ce01d6 --- /dev/null +++ b/src/simdb/enums.py @@ -0,0 +1,13 @@ +from enum import Enum + + +class IngestionStatus(str, Enum): + QUEUED = "QUEUED" + COPYING = "COPYING" + COPIED = "COPIED" + VALIDATING = "VALIDATING" + VALIDATED = "VALIDATED" + COMPLETED = "COMPLETED" + + COPY_FAILED = "COPY_FAILED" + VALIDATION_FAILED = "VALIDATION_FAILED" diff --git a/src/simdb/imas/utils.py b/src/simdb/imas/utils.py index 0cc80c43..09825a13 100644 --- a/src/simdb/imas/utils.py +++ b/src/simdb/imas/utils.py @@ -280,6 +280,11 @@ def imas_files(uri: URI) -> List[Path]: @return: a list of files which contains the IDS data for the backend specified in the URI """ + + # Early exit for NetCDF files + if uri.scheme == "file" and uri.path and uri.path.suffix == ".nc": + return [uri.path] + backend = str(uri.path) if backend.startswith("/"): backend = backend[1:] diff --git a/src/simdb/remote/apis/__init__.py b/src/simdb/remote/apis/__init__.py index ca03561e..b75a9680 100644 --- a/src/simdb/remote/apis/__init__.py +++ b/src/simdb/remote/apis/__init__.py @@ -19,6 +19,8 @@ from .v1_1 import namespaces as namespaces_v1_1 from .v1_2 import api as api_v1_2 from .v1_2 import namespaces as namespaces_v1_2 +from .v1_3 import api as api_v1_3 +from .v1_3 import namespaces as namespaces_v1_3 def error(message: str) -> Response: @@ -145,3 +147,4 @@ def get(self, user: User): register(api_v1, "v1", namespaces_v1) register(api_v1_1, "v1.1", namespaces_v1_1) register(api_v1_2, "v1.2", namespaces_v1_2) +register(api_v1_3, "v1.3", namespaces_v1_3) diff --git a/src/simdb/remote/apis/v1_3/__init__.py b/src/simdb/remote/apis/v1_3/__init__.py new file mode 100644 index 00000000..732b2611 --- /dev/null +++ b/src/simdb/remote/apis/v1_3/__init__.py @@ -0,0 +1,28 @@ +from flask_restx import Api + +from simdb.remote.apis.files import api as file_ns +from simdb.remote.apis.metadata import api as metadata_ns +from simdb.remote.apis.watchers import api as watcher_ns +from simdb.remote.core.auth import TokenAuthenticator + +from .simulations import api as sim_ns + +api = Api( + title="SimDB REST API", + version="1.3", + description="SimDB REST API", + authorizations={ + "basicAuth": { + "type": "basic", + }, + "apiToken": { + "type": "apiKey", + "in": "header", + "name": TokenAuthenticator.TOKEN_HEADER_NAME, + }, + }, + security=["basicAuth", "apiToken"], + doc="/docs", +) + +namespaces = [metadata_ns, watcher_ns, file_ns, sim_ns] diff --git a/src/simdb/remote/apis/v1_3/simulations.py b/src/simdb/remote/apis/v1_3/simulations.py new file mode 100644 index 00000000..c265d279 --- /dev/null +++ b/src/simdb/remote/apis/v1_3/simulations.py @@ -0,0 +1,113 @@ +import datetime +from typing import Annotated, Optional + +from flask_restx import Namespace, Resource + +from simdb.database.models import metadata as models_meta +from simdb.database.models import simulation as models_sim +from simdb.enums import IngestionStatus +from simdb.remote.core.auth import User, requires_auth +from simdb.remote.core.cache import clear_cache +from simdb.remote.core.pydantic_utils import ( + Body, + pydantic_validate, +) +from simdb.remote.core.typing import current_app +from simdb.remote.models import ( + FileDataList, + SimulationPostData, + SimulationPostResponse, + SimulationStatusResponse, +) +from simdb.workers.tasks import ( + complete_ingestion_task, + copy_files_task, +) + +api = Namespace("simulations", path="/") + + +def _set_alias(simulation: models_sim.Simulation, alias: Optional[str]): + if alias is None: + simulation.alias = simulation.uuid.hex + return + + character = None + if alias.endswith("-"): + character = "-" + elif alias.endswith("#"): + character = "#" + + if not character: + simulation.alias = alias + return + + aliases = current_app.db.get_aliases(alias) + last_id = max( + (int(existing_alias.split(character)[-1]) for existing_alias in aliases), + default=0, + ) + next_id = last_id + 1 + simulation.alias = f"{alias}{next_id}" + simulation.meta.append(models_meta.MetaData("seqid", next_id)) + + +@api.route("/simulations") +class SimulationList(Resource): + @requires_auth() + @pydantic_validate(api) + def post( + self, + user: User, + body: Annotated[SimulationPostData, Body()], + ) -> SimulationPostResponse: + simulation_data = body.model_copy(deep=True) + + # Clear the file inputs and outputs. + # The files will be added by the job. + simulation_data.simulation.outputs = FileDataList() + simulation_data.simulation.inputs = FileDataList() + simulation = models_sim.Simulation.from_data_model(simulation_data.simulation) + + # Simulation Upload (Push) Date + simulation.datetime = datetime.datetime.now() + + uploaded_by = body.uploaded_by or user.email or user.name or "anonymous" + + simulation.set_meta("uploaded_by", uploaded_by) + + _set_alias(simulation, body.simulation.alias) + + simulation.ingestion_status = IngestionStatus.QUEUED + current_app.db.insert_simulation(simulation) + + # This job will copy and add the files to the simulation + copy_files = copy_files_task.si( + simulation.uuid, + body.simulation.inputs.model_dump(), + body.simulation.outputs.model_dump(), + ) + + # The complete job will set simulation.ingestion_status = Completed + complete = complete_ingestion_task.si(simulation.uuid) + + _ = (copy_files | complete).apply_async() + + result = SimulationPostResponse(ingested=simulation.uuid) + + clear_cache() + + return result + + +@api.route("/simulation/status/") +class SimulationIngestionStatus(Resource): + @requires_auth() + @pydantic_validate(api) + def get( + self, + sim_id: str, + user: User, + ) -> SimulationStatusResponse: + simulation = current_app.db.get_simulation(sim_id) + return SimulationStatusResponse(status=simulation.ingestion_status) diff --git a/src/simdb/remote/models.py b/src/simdb/remote/models.py index d8d2d2d0..981a27d7 100644 --- a/src/simdb/remote/models.py +++ b/src/simdb/remote/models.py @@ -34,6 +34,7 @@ ) from simdb.cli.manifest import DataObject +from simdb.enums import IngestionStatus HexUUID = Annotated[UUID, PlainSerializer(lambda x: x.hex, return_type=str)] """UUID serialized as a hex string.""" @@ -577,3 +578,9 @@ class ErrorResponse(BaseModel): error: str """Error description.""" + + +class SimulationStatusResponse(BaseModel): + """Response from the get simulation status endpoint.""" + + status: IngestionStatus diff --git a/src/simdb/workers/__init__.py b/src/simdb/workers/__init__.py new file mode 100644 index 00000000..8c83779f --- /dev/null +++ b/src/simdb/workers/__init__.py @@ -0,0 +1,4 @@ +from simdb.workers import tasks +from simdb.workers.celery import celery_app, make_celery + +__all__ = ["celery_app", "make_celery", "tasks"] diff --git a/src/simdb/workers/celery.py b/src/simdb/workers/celery.py new file mode 100644 index 00000000..66b2dede --- /dev/null +++ b/src/simdb/workers/celery.py @@ -0,0 +1,30 @@ +from typing import Optional + +from celery import Celery + +from simdb.config import Config + + +def make_celery(config: Optional[Config] = None) -> Celery: + if config is None: + config = Config() + config.load() + + broker_url = config.get_string_option( + "celery.broker_url", default="redis://localhost:6379/0" + ) + result_backend = config.get_string_option( + "celery.result_backend", default="redis://localhost:6379/0" + ) + + celery_app = Celery( + "simdb", + broker=broker_url, + backend=result_backend, + include=["simdb.workers.tasks"], + ) + + return celery_app + + +celery_app = make_celery() diff --git a/src/simdb/workers/cli.py b/src/simdb/workers/cli.py new file mode 100644 index 00000000..d33c206c --- /dev/null +++ b/src/simdb/workers/cli.py @@ -0,0 +1,81 @@ +import click + +from simdb.workers.celery import celery_app + + +@click.group() +def cli(): + """SimDB Celery worker management.""" + pass + + +@cli.command() +@click.option( + "--concurrency", + type=int, + default=None, + help="Number of concurrent worker processes", +) +@click.option( + "--loglevel", + default="INFO", + type=click.Choice(["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"]), + help="Logging level", +) +@click.option( + "--hostname", + default=None, + help="Set custom hostname (worker@FQHN)", +) +@click.option( + "--queues", + default=None, + help="Comma-separated list of queues to consume from", +) +def worker(concurrency, loglevel, hostname, queues): + """Start a Celery worker.""" + argv = ["worker", "--loglevel", loglevel] + if concurrency is not None: + argv.extend(["--concurrency", str(concurrency)]) + if hostname is not None: + argv.extend(["--hostname", hostname]) + if queues is not None: + argv.extend(["--queues", queues]) + celery_app.worker_main(argv) + + +@cli.command() +@click.option( + "--loglevel", + default="INFO", + type=click.Choice(["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"]), + help="Logging level", +) +@click.option( + "--schedule-file", + default="celerybeat-schedule", + help="Path to the schedule file", +) +@click.option( + "--max-interval", + type=int, + default=300, + help="Maximum interval between iterations (seconds)", +) +def beat(loglevel, schedule_file, max_interval): + """Start the Celery beat scheduler.""" + celery_app.start( + [ + "beat", + "--loglevel", + loglevel, + "--schedule", + schedule_file, + "--max-interval", + str(max_interval), + ] + ) + + +if __name__ == "__main__": + cli() diff --git a/src/simdb/workers/tasks.py b/src/simdb/workers/tasks.py new file mode 100644 index 00000000..2118c47e --- /dev/null +++ b/src/simdb/workers/tasks.py @@ -0,0 +1,256 @@ +import hashlib +import itertools +import logging +import os +import shutil +from pathlib import Path +from typing import Iterable, List +from uuid import UUID + +from simdb.config import Config +from simdb.database.database import get_db +from simdb.database.models import File +from simdb.email.server import EmailServer +from simdb.enums import IngestionStatus +from simdb.remote.models import FileData, FileDataList +from simdb.uri import URI +from simdb.workers.celery import celery_app + +logger = logging.getLogger(__name__) + + +@celery_app.task +def send_email_task( + subject: str, + body: str, + to_addresses: List[str], +) -> dict: + config = Config() + config.load() + + email_server = EmailServer(config) + email_server.send_message(subject, body, to_addresses) + + return { + "status": "sent", + "subject": subject, + "recipients": to_addresses, + } + + +def _imas_path_to_uri(imas_path: Path) -> URI: + if imas_path.suffix == ".nc": + return URI(scheme="file", path=imas_path) + + children = set(imas_path.iterdir()) + + if any(child.suffix == ".ids" for child in children): + u = URI(scheme="imas", path="ascii") + u.query.set("path", str(imas_path)) + return u + + if any(child.suffix == ".h5" for child in children) and any( + child.name == "master.h5" for child in children + ): + u = URI(scheme="imas", path="hdf5") + u.query.set("path", str(imas_path)) + return u + + if {p.name for p in children} >= { + "ids_001.tree", + "ids_001.characteristics", + "ids_001.datafile", + }: + u = URI(scheme="imas", path="mdsplus") + u.query.set("path", str(imas_path)) + return u + + raise ValueError("IMAS backend could not be identified.") + + +def _resolve_uri_to_path(uri: URI, config: Config) -> Path: + partition = uri.scheme + if not partition: + raise ValueError("Partition not given") + partition_path_str = config.get_string_option( + f"partition.{partition}", default=None + ) + if not partition_path_str: + raise ValueError(f"Partition '{partition}' not found in config") + partition_path = Path(partition_path_str) + path = uri.path + if not path: + raise ValueError("Path not given") + path = path.relative_to(path.anchor) + target = (partition_path / path).resolve() + if not target.is_relative_to(partition_path): + raise ValueError("Access denied.") + return target + + +def _resolve_paths(files_data: list[FileData], config: Config) -> list[Path]: + return [_resolve_uri_to_path(URI(f.uri), config) for f in files_data] + + +def _resolve_destination_path(source: Path, common_root: Path, dst_basepath: Path): + return dst_basepath / source.relative_to(common_root) + + +def _copy_files( + paths: Iterable[Path], + common_root: Path, + dst_basepath: Path, +): + for source in paths: + destination = _resolve_destination_path(source, common_root, dst_basepath) + destination.parent.mkdir(exist_ok=True, parents=True) + shutil.copy2(source, destination) + + +def _calculate_checksum(path: Path) -> str: + sha1 = hashlib.sha1() + with path.open("rb") as f: + for chunk in iter(lambda: f.read(4096), b""): + sha1.update(chunk) + return sha1.hexdigest() + + +def _get_imas_identifier_path(path: Path) -> Path: + if path.suffix == ".nc": + return path + return path.parent + + +def _create_file_from_data( + data: FileData, config: Config, imas_identifier_path: Path +) -> File: + uri = URI(data.uri) + path = _resolve_uri_to_path(uri, config) + + checksum = _calculate_checksum(path) + if data.checksum != checksum: + raise ValueError("Hash of file does not match provided checksum") + + file = File.from_data_model(data) + file.uri = _imas_path_to_uri(imas_identifier_path) + + return file + + +def _create_files_from_data_list( + files_data: list[FileData], config: Config, common_root: Path, dst_basepath: Path +) -> list[File]: + seen_imas_paths: set[Path] = set() + files: list[File] = [] + + for file_data in files_data: + uri = URI(file_data.uri) + path = _resolve_destination_path( + _resolve_uri_to_path(uri, config), common_root, dst_basepath + ) + + if file_data.type == "IMAS": + imas_path = _get_imas_identifier_path(path) + if imas_path in seen_imas_paths: + continue + seen_imas_paths.add(imas_path) + file = _create_file_from_data(file_data, config, imas_path) + else: + checksum = _calculate_checksum(path) + if file_data.checksum != checksum: + raise ValueError("Hash of file does not match provided checksum") + file = File.from_data_model(file_data) + file.uri = URI(scheme="file", path=path) + + files.append(file) + + return files + + +@celery_app.task +def copy_files_task( + simulation_uuid: UUID, + input_files_d: list[FileData], + output_files_d: list[FileData], +): + input_files = FileDataList.model_validate(input_files_d).root + output_files = FileDataList.model_validate(output_files_d).root + config = Config() + config.load() + database = get_db(config) + + simulation = database.get_simulation(simulation_uuid.hex) + simulation.ingestion_status = IngestionStatus.COPYING + database.session.commit() + + try: + input_paths = _resolve_paths(input_files, config) + output_paths = _resolve_paths(output_files, config) + paths = set(input_paths + output_paths) + if len(paths) == 0: + common_root = Path() + elif len(paths) == 1: + common_root = next(iter(paths)).parent + else: + common_root = Path(os.path.commonpath(paths)) + dst_basepath: Path = ( + Path(config.get_string_option("server.upload_folder")) / simulation_uuid.hex + ) + + _copy_files(paths, common_root, dst_basepath) + + inputs = _create_files_from_data_list( + input_files, config, common_root, dst_basepath + ) + outputs = _create_files_from_data_list( + output_files, config, common_root, dst_basepath + ) + + for f in [*inputs, *outputs]: + database.session.add(f) + + simulation.inputs = inputs + simulation.outputs = outputs + simulation.ingestion_status = IngestionStatus.COPIED + database.session.commit() + except Exception: + simulation.ingestion_status = IngestionStatus.COPY_FAILED + database.session.commit() + raise + finally: + database.close() + + +@celery_app.task +def validate_imas_task(simulation_uuid: UUID): + config = Config() + config.load() + database = get_db(config) + + try: + simulation = database.get_simulation(simulation_uuid.hex) + simulation.ingestion_status = IngestionStatus.VALIDATING + database.session.commit() + + for _file in itertools.chain(simulation.inputs, simulation.outputs): + # TODO + pass + + simulation.ingestion_status = IngestionStatus.VALIDATED + database.session.commit() + finally: + database.close() + + +@celery_app.task +def complete_ingestion_task(simulation_uuid: UUID): + config = Config() + config.load() + database = get_db(config) + + try: + simulation = database.get_simulation(simulation_uuid.hex) + simulation.ingestion_status = IngestionStatus.COMPLETED + database.session.commit() + finally: + database.close() diff --git a/tests/remote/api/test_simulations.py b/tests/remote/api/v1.2/test_simulations.py similarity index 100% rename from tests/remote/api/test_simulations.py rename to tests/remote/api/v1.2/test_simulations.py diff --git a/tests/remote/api/v1.3/test_simulations3.py b/tests/remote/api/v1.3/test_simulations3.py new file mode 100644 index 00000000..222a6b91 --- /dev/null +++ b/tests/remote/api/v1.3/test_simulations3.py @@ -0,0 +1,112 @@ +from datetime import datetime, timezone +from unittest import mock +from uuid import UUID + +import pytest +from conftest import ( + HEADERS, + generate_simulation_data, +) + +from simdb.config import Config +from simdb.enums import IngestionStatus +from simdb.remote.models import ( + FileData, + SimulationPostResponse, +) +from simdb.workers import tasks as simdb_tasks +from simdb.workers.celery import celery_app +from simdb.workers.tasks import _calculate_checksum + + +@pytest.fixture(autouse=True) +def celery_eager_config(): + + celery_app.conf.task_always_eager = True + celery_app.conf.task_eager_propagates = True + celery_app.conf.result_backend = None + yield + + +@pytest.fixture +def client_with_task_mock(client, monkeypatch, tmp_path): + db_file = tmp_path / "test.db" + db_file.write_text("") + upload_dir = tmp_path / "uploads" + upload_dir.mkdir() + + def mock_config(): + cfg = mock.MagicMock(spec=Config) + cfg.get_option.side_effect = lambda key, **kwargs: { + "database.type": "sqlite", + "database.file": str(db_file), + "server.upload_folder": str(upload_dir), + }.get(key, kwargs.get("default")) + cfg.get_string_option.side_effect = lambda key, **kwargs: { + "database.type": "sqlite", + "database.file": str(db_file), + "server.upload_folder": str(upload_dir), + "partition.data": str(tmp_path / "partition"), + }.get(key, kwargs.get("default")) + cfg.load = mock.MagicMock() + return cfg + + monkeypatch.setattr(simdb_tasks, "Config", mock_config) + monkeypatch.setattr(simdb_tasks, "get_db", lambda cfg: client.application.db) + monkeypatch.setattr(client.application.db, "close", lambda: None) + + return client + + +def post_simulation_v13(client, simulation_data, headers=HEADERS): + rv_post = client.post( + "/v1.3/simulations", + json=simulation_data.model_dump(mode="json"), + headers=headers, + content_type="application/json", + ) + return rv_post + + +def get_simulation_status(client, simulation_uuid: UUID, headers=HEADERS): + rv_get = client.get( + f"/v1.3/simulation/status/{simulation_uuid.hex}", headers=headers + ) + return rv_get + + +def generate_simulation_file(path) -> FileData: + file_path = path / "partition/file.txt" + file_path.parent.mkdir(exist_ok=True) + file_path.write_text("test data") + checksum = _calculate_checksum(file_path) + return FileData( + type="FILE", + uri="data:///file.txt", + checksum=checksum, + datetime=datetime.now(timezone.utc), + ) + + +def test_post_simulations_v13(client_with_task_mock, tmp_path): + """Test POST endpoint for creating a new simulation.""" + client = client_with_task_mock + simulation_data = generate_simulation_data( + alias="test-simulation-v13", + inputs=[generate_simulation_file(tmp_path)], + outputs=[generate_simulation_file(tmp_path)], + ) + + rv = post_simulation_v13(client, simulation_data) + + assert rv.status_code == 200 + + result = SimulationPostResponse.model_validate(rv.json) + assert result.ingested == simulation_data.simulation.uuid + + simulation = client.application.db.get_simulation(result.ingested.hex) + assert simulation.ingestion_status == IngestionStatus.COMPLETED + assert ( + simulation.inputs[0].uri.path + == tmp_path / "uploads" / result.ingested.hex / "file.txt" + ) diff --git a/tests/workers/test_tasks.py b/tests/workers/test_tasks.py new file mode 100644 index 00000000..c8187617 --- /dev/null +++ b/tests/workers/test_tasks.py @@ -0,0 +1,207 @@ +from datetime import datetime, timezone +from unittest import mock +from uuid import uuid1 + +import pytest + +from simdb.config import Config +from simdb.enums import IngestionStatus +from simdb.remote.models import FileData +from simdb.uri import URI +from simdb.workers.tasks import ( + _calculate_checksum, + _copy_files, + _create_file_from_data, + _get_imas_identifier_path, + _imas_path_to_uri, + _resolve_paths, + _resolve_uri_to_path, + copy_files_task, +) + + +def _make_file_data(uri: str, checksum: str = "abc") -> FileData: + return FileData( + type="FILE", + uri=uri, + checksum=checksum, + datetime=datetime.now(timezone.utc), + ) + + +def test_get_imas_identifier_path_returns_file_for_netcdf(tmp_path): + nc_file = tmp_path / "data.nc" + nc_file.touch() + + assert _get_imas_identifier_path(nc_file) == nc_file + + +def test_get_imas_identifier_path_returns_parent_for_directory(tmp_path): + ids_dir = tmp_path / "ids_dir" + ids_dir.mkdir() + + assert _get_imas_identifier_path(ids_dir) == tmp_path + + +@pytest.mark.parametrize( + "files,expected_backend", + [ + (["summary.ids"], "ascii"), + (["master.h5", "summary.h5"], "hdf5"), + (["ids_001.tree", "ids_001.characteristics", "ids_001.datafile"], "mdsplus"), + ], +) +def test_imas_path_to_uri_detects_backend_from_directory( + tmp_path, files, expected_backend +): + ids_dir = tmp_path / "ids_dir" + ids_dir.mkdir() + for f in files: + (ids_dir / f).touch() + + uri = _imas_path_to_uri(ids_dir) + + assert uri.scheme == "imas" + assert str(uri.path) == expected_backend + assert uri.query.get("path") == str(ids_dir) + + +def test_imas_path_to_uri_unknown_backend_raises(tmp_path): + ids_dir = tmp_path / "ids_dir" + ids_dir.mkdir() + (ids_dir / "file1.txt").touch() + + with pytest.raises(ValueError, match="IMAS backend could not be identified"): + _imas_path_to_uri(ids_dir) + + +@pytest.fixture +def config_with_partition(tmp_path): + config = Config() + partition_path = tmp_path / "partition_data" + partition_path.mkdir() + config.set_option("partition.data", str(partition_path)) + return config, partition_path + + +def test_resolve_uri_to_path_returns_partition_relative_path(config_with_partition): + config, partition_path = config_with_partition + + result = _resolve_uri_to_path(URI("data:/subdir/file.txt"), config) + + assert result == partition_path / "subdir" / "file.txt" + + +def test_resolve_uri_to_path_unknown_partition_raises(config_with_partition): + config, _ = config_with_partition + + with pytest.raises(ValueError, match="Partition 'unknown' not found"): + _resolve_uri_to_path(URI("unknown:/file.txt"), config) + + +def test_resolve_paths_resolves_multiple_files(config_with_partition): + config, partition_path = config_with_partition + files = [_make_file_data("data:/file1.txt"), _make_file_data("data:/file2.txt")] + + result = _resolve_paths(files, config) + + assert result == [partition_path / "file1.txt", partition_path / "file2.txt"] + + +@pytest.mark.parametrize( + "relative_source,common_root_subpath,expected_dst_subpath", + [ + ("source.txt", "", "source.txt"), + ("source/subdir/file.txt", "source", "subdir/file.txt"), + ("source/nested/file.txt", "source", "nested/file.txt"), + ], +) +def test_copy_files_preserves_relative_layout( + tmp_path, relative_source, common_root_subpath, expected_dst_subpath +): + source = tmp_path / relative_source + source.parent.mkdir(parents=True, exist_ok=True) + source.write_text("content") + + common_root = tmp_path / common_root_subpath + dst_basepath = tmp_path / "dest" + + _copy_files([source], common_root, dst_basepath) + + destination = dst_basepath / expected_dst_subpath + assert destination.exists() + assert destination.read_text() == "content" + + +def test_create_file_from_data_raises_on_checksum_mismatch(tmp_path): + config = Config() + partition_path = tmp_path / "partition_data" + partition_path.mkdir() + config.set_option("partition.data", str(partition_path)) + data_file = partition_path / "testfile.txt" + data_file.write_text("content") + + file_data = _make_file_data("data:testfile.txt", checksum="wrong_checksum") + + with pytest.raises(ValueError, match="Hash of file does not match"): + _create_file_from_data(file_data, config, data_file) + + +@pytest.fixture +def task_environment(tmp_path): + """Set up Config, mocked DB, and directory layout for copy_files_task tests.""" + config = Config() + upload_dir = tmp_path / "uploads" + upload_dir.mkdir() + partition_dir = tmp_path / "partition" + partition_dir.mkdir() + + config.set_option("database.type", "sqlite") + config.set_option("database.file", str(tmp_path / "test.db")) + config.set_option("server.upload_folder", str(upload_dir)) + config.set_option("partition.data", str(partition_dir)) + config.load = mock.MagicMock() + + simulation_uuid = uuid1() + mock_simulation = mock.MagicMock(uuid=simulation_uuid, inputs=[], outputs=[]) + mock_db = mock.MagicMock() + mock_db.get_simulation.return_value = mock_simulation + + with mock.patch("simdb.workers.tasks.Config", return_value=config), mock.patch( + "simdb.workers.tasks.get_db", return_value=mock_db + ): + yield { + "config": config, + "upload_dir": upload_dir, + "partition_dir": partition_dir, + "simulation_uuid": simulation_uuid, + "simulation": mock_simulation, + "db": mock_db, + } + + +def test_copy_files_task_copies_inputs_and_marks_copied(task_environment): + env = task_environment + source_file = env["partition_dir"] / "source.txt" + source_file.write_text("test content") + + input_files = [ + _make_file_data( + f"data:/{source_file.name}", checksum=_calculate_checksum(source_file) + ) + ] + + copy_files_task(env["simulation_uuid"], input_files, []) + + expected_destination = env["upload_dir"] / env["simulation_uuid"].hex / "source.txt" + assert expected_destination.read_text() == "test content" + assert env["simulation"].ingestion_status == IngestionStatus.COPIED + env["db"].session.add.assert_called() + + +def test_copy_files_task_with_no_files_marks_copied(task_environment): + env = task_environment + + copy_files_task(env["simulation_uuid"], [], []) + + assert env["simulation"].ingestion_status == IngestionStatus.COPIED diff --git a/uv.lock b/uv.lock index 3aca3c3b..032200bd 100644 --- a/uv.lock +++ b/uv.lock @@ -111,7 +111,7 @@ wheels = [ [[package]] name = "alembic" -version = "1.18.4" +version = "1.18.5" source = { registry = "https://pypi.org/simple" } resolution-markers = [ "python_full_version >= '3.13' and platform_machine == 'ARM64' and sys_platform == 'win32'", @@ -129,9 +129,21 @@ dependencies = [ { name = "tomli", marker = "python_full_version == '3.10.*'" }, { name = "typing-extensions", version = "4.15.0", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.10'" }, ] -sdist = { url = "https://files.pythonhosted.org/packages/94/13/8b084e0f2efb0275a1d534838844926f798bd766566b1375174e2448cd31/alembic-1.18.4.tar.gz", hash = "sha256:cb6e1fd84b6174ab8dbb2329f86d631ba9559dd78df550b57804d607672cedbc", size = 2056725, upload-time = 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