diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml index 57fa983..f59a0c9 100644 --- a/.github/workflows/pytest.yml +++ b/.github/workflows/pytest.yml @@ -5,19 +5,6 @@ on: branches: [ main ] workflow_dispatch: -env: - MB__BATCH_SIZE: 10_000 - MB__BACKEND_TYPE: postgres - MB__DATASETS_CONFIG: datasets.toml - # PostgreSQL backend settings - MB__POSTGRES__HOST: localhost - MB__POSTGRES__PORT: 5432 - MB__POSTGRES__USER: matchbox_user - MB__POSTGRES__PASSWORD: matchbox_password - MB__POSTGRES__DATABASE: matchbox - MB__POSTGRES__DB_SCHEMA: mb - - jobs: run-unit-tests: name: tests @@ -34,8 +21,11 @@ jobs: - name: Install the project run: uv sync --all-extras --dev + + - name: Copy environment variables + run: cp environments/dev_docker.env .env - - name: Set up PostgreSQL + - name: Run DBs and API run: | docker compose up -d --wait diff --git a/.gitignore b/.gitignore index 831b7c8..c3ccc86 100644 --- a/.gitignore +++ b/.gitignore @@ -177,6 +177,9 @@ dmypy.json # Cython debug symbols cython_debug/ +# Mac things +.DS_Store + # PyCharm # JetBrains specific template is maintained in a separate JetBrains.gitignore that can # be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore diff --git a/.gitlab/merge_request_templates/merge_template.md b/.gitlab/merge_request_templates/merge_template.md deleted file mode 100644 index 5ad0049..0000000 --- a/.gitlab/merge_request_templates/merge_template.md +++ /dev/null @@ -1,11 +0,0 @@ -### Description of change - - -### Checklist -This pull/merge request meets the following requirements: - -* [ ] The code runs and you have made proportionate checks that it works correctly -* [ ] No application secrets or sensitive outputs have been committed -* [ ] The README and other documentation files have been updated (if needed) -* [ ] requirements.txt has been updated (if needed) -* [ ] .env.sample has been updated (if needed) diff --git a/docker-compose.yml b/docker-compose.yml index 044c536..e36db21 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -21,6 +21,26 @@ services: - "5432:5432" volumes: - matchbox_data:/var/lib/postgresql/data + api: + build: + context: . + dockerfile: src/matchbox/server/Dockerfile + ports: + - "8000:8000" + depends_on: + - matchbox-postgres + + develop: + # https://docs.docker.com/compose/file-watch/#compose-watch-versus-bind-mounts + watch: + # Sync the working directory with the `/app` directory in the container + - action: sync + path: ./src/matchbox/server + target: /code/src/matchbox/server + + # Rebuild the image on changes to the `pyproject.toml` + - action: rebuild + path: ./pyproject.toml volumes: warehouse_data: diff --git a/environments/dev_docker.env b/environments/dev_docker.env new file mode 100644 index 0000000..82a8998 --- /dev/null +++ b/environments/dev_docker.env @@ -0,0 +1,12 @@ +MB__BATCH_SIZE=250_000 +MB__BACKEND_TYPE=postgres +MB__DATASETS_CONFIG=datasets.toml + +MB__POSTGRES__HOST=matchbox-postgres +MB__POSTGRES__PORT=5432 +MB__POSTGRES__USER=matchbox_user +MB__POSTGRES__PASSWORD=matchbox_password +MB__POSTGRES__DATABASE=matchbox +MB__POSTGRES__DB_SCHEMA=mb + +API__ROOT=http://localhost:8000 \ No newline at end of file diff --git a/environments/dev_local.env b/environments/dev_local.env new file mode 100644 index 0000000..508bd1f --- /dev/null +++ b/environments/dev_local.env @@ -0,0 +1,12 @@ +MB__BATCH_SIZE=250_000 +MB__BACKEND_TYPE=postgres +MB__DATASETS_CONFIG=datasets.toml + +MB__POSTGRES__HOST=localhost +MB__POSTGRES__PORT=5432 +MB__POSTGRES__USER=matchbox_user +MB__POSTGRES__PASSWORD=matchbox_password +MB__POSTGRES__DATABASE=matchbox +MB__POSTGRES__DB_SCHEMA=mb + +API__ROOT=http://localhost:8000 \ No newline at end of file diff --git a/environments/sample.env b/environments/sample.env new file mode 100644 index 0000000..07c8f21 --- /dev/null +++ b/environments/sample.env @@ -0,0 +1,12 @@ +MB__BATCH_SIZE= +MB__BACKEND_TYPE= +MB__DATASETS_CONFIG= + +MB__POSTGRES__HOST= +MB__POSTGRES__PORT= +MB__POSTGRES__USER= +MB__POSTGRES__PASSWORD= +MB__POSTGRES__DATABASE= +MB__POSTGRES__DB_SCHEMA= + +API__ROOT= \ No newline at end of file diff --git a/justfile b/justfile index e9b74b1..34427a6 100644 --- a/justfile +++ b/justfile @@ -19,8 +19,4 @@ scan: # Run Python tests test: docker compose up -d --wait - uv run pytest - -# Run development version of API -api: - uv run fastapi dev src/matchbox/server/api.py \ No newline at end of file + uv run pytest \ No newline at end of file diff --git a/pyproject.toml b/pyproject.toml index 08063a3..a7a39e9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -10,6 +10,7 @@ dependencies = [ "click>=8.1.7", "connectorx>=0.3.3", "duckdb>=1.1.1", + "httpx>=0.28.0", "matplotlib>=3.9.2", "pandas>=2.2.3", "psycopg2>=2.9.10", @@ -38,6 +39,7 @@ dev = [ "pytest-env>=1.1.5", "ruff>=0.6.8", "docker>=7.1.0", + "vcrpy>=6.0.2", ] typing = [ "polars>=1.11.0", @@ -89,7 +91,3 @@ log_cli = false log_cli_level = "INFO" log_cli_format = "%(asctime)s [%(levelname)8s] %(message)s (%(filename)s:%(lineno)s)" log_cli_date_format = "%Y-%m-%d %H:%M:%S" - -[tool.pytest_env] -MB__POSTGRES__SCHEMA = "test" -MB__BATCH_SIZE = "400" diff --git a/sample.env b/sample.env deleted file mode 100644 index 999b098..0000000 --- a/sample.env +++ /dev/null @@ -1,10 +0,0 @@ -MB__BATCH_SIZE=250_000 -MB__BACKEND_TYPE=postgres -MB__DATASETS_CONFIG=datasets.toml - -MB__POSTGRES__HOST= -MB__POSTGRES__PORT= -MB__POSTGRES__USER= -MB__POSTGRES__PASSWORD= -MB__POSTGRES__DATABASE= -MB__POSTGRES__DB_SCHEMA=mb diff --git a/src/matchbox/client/__init__.py b/src/matchbox/client/__init__.py new file mode 100644 index 0000000..d83d27f --- /dev/null +++ b/src/matchbox/client/__init__.py @@ -0,0 +1,6 @@ +from matchbox.client.visualisation import draw_resolution_graph + +__all__ = ( + # Visualisation + draw_resolution_graph, +) diff --git a/src/matchbox/client/_handler.py b/src/matchbox/client/_handler.py new file mode 100644 index 0000000..3726d6b --- /dev/null +++ b/src/matchbox/client/_handler.py @@ -0,0 +1,21 @@ +from os import getenv + +import httpx + +from matchbox.common.graph import ResolutionGraph + + +def url(path: str) -> str: + """ + Return path prefixed by API root, determined from environment + """ + api_root = getenv("API__ROOT") + if api_root is None: + raise RuntimeError("API__ROOT needs to be defined in the environment") + + return api_root + path + + +def get_resolution_graph() -> str: + res = httpx.get(url("/report/resolutions")).json() + return ResolutionGraph.model_validate(res) diff --git a/src/matchbox/helpers/visualisation.py b/src/matchbox/client/visualisation.py similarity index 63% rename from src/matchbox/helpers/visualisation.py rename to src/matchbox/client/visualisation.py index ff41d59..9f78d92 100644 --- a/src/matchbox/helpers/visualisation.py +++ b/src/matchbox/client/visualisation.py @@ -2,29 +2,28 @@ from matplotlib.figure import Figure from rustworkx.visualization import mpl_draw -from matchbox.server.base import MatchboxDBAdapter, inject_backend +from matchbox.client._handler import get_resolution_graph -@inject_backend -def draw_model_tree(backend: MatchboxDBAdapter) -> Figure: +def draw_resolution_graph() -> Figure: """ - Draws the model subgraph. + Draws the resolution graph. """ - G = backend.get_model_subgraph() + G: rx.PyDiGraph = get_resolution_graph().to_rx() node_indices = G.node_indices() datasets = { G[node_indices[i]]["id"]: i for i in node_indices - if G[node_indices[i]]["type"] == "dataset" + if G[node_indices[i]]["kind"] == "dataset" } colours = [] for i in node_indices: - type = G[node_indices[i]]["type"] - if type == "dataset": + kind = G[node_indices[i]]["kind"] + if kind == "dataset": colours.append((0, 0, 1, 0.2)) - elif type == "model": + elif kind == "model": colours.append((1, 0, 0, 0.2)) return mpl_draw( @@ -37,6 +36,5 @@ def draw_model_tree(backend: MatchboxDBAdapter) -> Figure: node_color=colours, with_labels=True, labels=lambda node: node["name"], - edge_labels=lambda edge: edge["type"], font_size=8, ) diff --git a/src/matchbox/common/graph.py b/src/matchbox/common/graph.py new file mode 100644 index 0000000..21e9030 --- /dev/null +++ b/src/matchbox/common/graph.py @@ -0,0 +1,43 @@ +from enum import StrEnum + +import rustworkx as rx +from matchbox.common.hash import hash_to_str +from pydantic import BaseModel + + +class ResolutionNodeKind(StrEnum): + DATASET = "dataset" + MODEL = "model" + HUMAN = "human" + + +class ResolutionNode(BaseModel): + hash: bytes + name: str + kind: ResolutionNodeKind + + def __hash__(self): + return hash(self.hash) + + +class ResolutionEdge(BaseModel): + parent: bytes + child: bytes + + def __hash__(self): + return hash((self.parent, self.child)) + + +class ResolutionGraph(BaseModel): + nodes: set[ResolutionNode] + edges: set[ResolutionEdge] + + def to_rx(self) -> rx.PyDiGraph: + nodes = {} + G = rx.PyDiGraph() + for n in self.nodes: + node_data = {"id": hash_to_str(n.hash), "name": n.name, "kind": str(n.kind)} + nodes[n.hash] = G.add_node(node_data) + for e in self.edges: + G.add_edge(nodes[e.parent], nodes[e.child], {}) + return G diff --git a/src/matchbox/common/hash.py b/src/matchbox/common/hash.py index 4ce9c07..9cb81ef 100644 --- a/src/matchbox/common/hash.py +++ b/src/matchbox/common/hash.py @@ -1,3 +1,4 @@ +import base64 import hashlib from typing import TYPE_CHECKING, Any, TypeVar from uuid import UUID @@ -17,6 +18,10 @@ HASH_FUNC = hashlib.sha256 +def hash_to_str(hash: bytes) -> str: + return base64.b64encode(hash).decode("utf-8") + + def dataset_to_hashlist(dataset: Source, model_hash: bytes) -> list[dict[str, Any]]: """Retrieve and hash a dataset from its warehouse, ready to be inserted.""" with Session(dataset.database.engine) as warehouse_session: diff --git a/src/matchbox/helpers/__init__.py b/src/matchbox/helpers/__init__.py index 10b3a3e..5295521 100644 --- a/src/matchbox/helpers/__init__.py +++ b/src/matchbox/helpers/__init__.py @@ -1,7 +1,6 @@ from matchbox.helpers.cleaner import cleaner, cleaners from matchbox.helpers.comparison import comparison from matchbox.helpers.selector import selector, selectors -from matchbox.helpers.visualisation import draw_model_tree __all__ = ( # Cleaners @@ -12,6 +11,4 @@ # Selectors "selector", "selectors", - # Visualisation - "draw_model_tree", ) diff --git a/src/matchbox/server/Dockerfile b/src/matchbox/server/Dockerfile new file mode 100644 index 0000000..7281a3a --- /dev/null +++ b/src/matchbox/server/Dockerfile @@ -0,0 +1,35 @@ +# connectorx won't work on ARM or python-alpine +FROM --platform=amd64 python:3.11 + +COPY --from=ghcr.io/astral-sh/uv:latest /uv /uvx /bin/ + +WORKDIR /code + +# Enable bytecode compilation +ENV UV_COMPILE_BYTECODE=1 + +# Copy from the cache instead of linking since it's a mounted volume +ENV UV_LINK_MODE=copy + +# Install the project's dependencies using the lockfile and settings +RUN --mount=type=cache,target=/root/.cache/uv \ + --mount=type=bind,source=uv.lock,target=uv.lock \ + --mount=type=bind,source=pyproject.toml,target=pyproject.toml \ + uv sync --frozen --all-extras --no-install-project --no-dev + +COPY ./environments/dev_docker.env /code/.env +COPY ./uv.lock /code/uv.lock +COPY ./pyproject.toml /code/pyproject.toml +COPY ./src/matchbox /code/src/matchbox + +# Then, add the rest of the project source code and install it +# Installing separately from its dependencies allows optimal layer caching +RUN --mount=type=cache,target=/root/.cache/uv \ + uv sync --frozen --all-extras --no-dev + +# Place executables in the environment at the front of the path +ENV PATH="/code/.venv/bin:$PATH" + +# Uses `fastapi dev` to enable hot-reloading when the `watch` sync occurs +# Uses `--host 0.0.0.0` to allow access from outside the container +CMD ["fastapi", "dev", "--host", "0.0.0.0", "src/matchbox/server/api.py"] \ No newline at end of file diff --git a/src/matchbox/server/api.py b/src/matchbox/server/api.py index 80b84bb..71da31c 100644 --- a/src/matchbox/server/api.py +++ b/src/matchbox/server/api.py @@ -5,6 +5,7 @@ from fastapi import Depends, FastAPI, HTTPException from pydantic import BaseModel +from matchbox.common.graph import ResolutionGraph from matchbox.server.base import BackendManager, MatchboxDBAdapter dotenv_path = find_dotenv(usecwd=True) @@ -154,6 +155,8 @@ async def validate_hashes(): raise HTTPException(status_code=501, detail="Not implemented") -@app.get("/report/models") -async def get_model_subgraph(): - raise HTTPException(status_code=501, detail="Not implemented") +@app.get("/report/resolutions") +async def get_resolutions( + backend: Annotated[MatchboxDBAdapter, Depends(get_backend)], +) -> ResolutionGraph: + return backend.get_resolution_graph() diff --git a/src/matchbox/server/base.py b/src/matchbox/server/base.py index 24f3c6b..5b38057 100644 --- a/src/matchbox/server/base.py +++ b/src/matchbox/server/base.py @@ -17,10 +17,10 @@ from dotenv import find_dotenv, load_dotenv from pydantic import Field from pydantic_settings import BaseSettings, SettingsConfigDict -from rustworkx import PyDiGraph from sqlalchemy import Engine from matchbox.common.db import Source +from matchbox.common.graph import ResolutionGraph if TYPE_CHECKING: from pandas import DataFrame as PandasDataFrame @@ -261,7 +261,7 @@ def validate_hashes(self, hashes: list[bytes]) -> bool: ... def get_dataset(self, db_schema: str, db_table: str, engine: Engine) -> Source: ... @abstractmethod - def get_model_subgraph(self) -> PyDiGraph: ... + def get_resolution_graph(self) -> ResolutionGraph: ... @abstractmethod def get_model(self, model: str) -> MatchboxModelAdapter: ... diff --git a/src/matchbox/server/postgresql/adapter.py b/src/matchbox/server/postgresql/adapter.py index 54dbe45..f5fc386 100644 --- a/src/matchbox/server/postgresql/adapter.py +++ b/src/matchbox/server/postgresql/adapter.py @@ -1,7 +1,6 @@ from typing import TYPE_CHECKING, Any, Literal from pydantic import BaseModel -from rustworkx import PyDiGraph from sqlalchemy import Engine, and_, bindparam, delete, func, or_, select from sqlalchemy.orm import Session @@ -11,6 +10,7 @@ MatchboxDatasetError, MatchboxModelError, ) +from matchbox.common.graph import ResolutionGraph from matchbox.common.results import ClusterResults, ProbabilityResults, Results from matchbox.server.base import MatchboxDBAdapter, MatchboxModelAdapter from matchbox.server.postgresql.db import MBDB, MatchboxPostgresSettings @@ -22,7 +22,7 @@ Probabilities, Sources, ) -from matchbox.server.postgresql.utils.db import get_model_subgraph +from matchbox.server.postgresql.utils.db import get_resolution_graph from matchbox.server.postgresql.utils.insert import ( insert_dataset, insert_model, @@ -363,9 +363,9 @@ def get_dataset(self, db_schema: str, db_table: str, engine: Engine) -> Source: else: raise MatchboxDatasetError(db_schema=db_schema, db_table=db_table) - def get_model_subgraph(self) -> PyDiGraph: + def get_resolution_graph(self) -> ResolutionGraph: """Get the full subgraph of a model.""" - return get_model_subgraph(engine=MBDB.get_engine()) + return get_resolution_graph(engine=MBDB.get_engine()) def get_model(self, model: str) -> MatchboxPostgresModel: """Get a model from the database. diff --git a/src/matchbox/server/postgresql/orm.py b/src/matchbox/server/postgresql/orm.py index 8f1c667..6e4051d 100644 --- a/src/matchbox/server/postgresql/orm.py +++ b/src/matchbox/server/postgresql/orm.py @@ -1,5 +1,3 @@ -from enum import Enum - from sqlalchemy import ( FLOAT, INTEGER, @@ -12,16 +10,11 @@ from sqlalchemy.dialects.postgresql import ARRAY, BYTEA from sqlalchemy.orm import Session, relationship +from matchbox.common.graph import ResolutionNodeKind from matchbox.server.postgresql.db import MBDB from matchbox.server.postgresql.mixin import CountMixin -class ModelType(Enum): - MODEL = "model" - DATASET = "dataset" - HUMAN = "human" - - class ModelsFrom(CountMixin, MBDB.MatchboxBase): """Model lineage closure table with cached truth values.""" @@ -109,7 +102,7 @@ def get_lineage_to_dataset( self, model: "Models" ) -> tuple[bytes, dict[bytes, float]]: """Returns the model lineage and cached truth values to a dataset.""" - if model.type != ModelType.DATASET.value: + if model.type != ResolutionNodeKind.DATASET.value: raise ValueError( f"Target model must be of type 'dataset', got {model.type}" ) @@ -135,7 +128,7 @@ def get_lineage_to_dataset( lineage = { parent: truth for parent, truth, type in results - if type != ModelType.DATASET.value + if type != ResolutionNodeKind.DATASET.value } lineage[self.hash] = self.truth diff --git a/src/matchbox/server/postgresql/utils/db.py b/src/matchbox/server/postgresql/utils/db.py index 1cd90f5..9931b14 100644 --- a/src/matchbox/server/postgresql/utils/db.py +++ b/src/matchbox/server/postgresql/utils/db.py @@ -5,47 +5,37 @@ from itertools import islice from typing import Any, Callable, Iterable, Tuple -import rustworkx as rx from pg_bulk_ingest import Delete, Upsert, ingest from sqlalchemy import Engine, MetaData, Table from sqlalchemy.engine.base import Connection from sqlalchemy.orm import DeclarativeMeta, Session -from matchbox.server.postgresql.orm import Models, ModelsFrom, ModelType, Sources +from matchbox.common.graph import ( + ResolutionEdge, + ResolutionGraph, + ResolutionNode, + ResolutionNodeKind, +) +from matchbox.server.postgresql.orm import Models, ModelsFrom # Retrieval -def get_model_subgraph(engine: Engine) -> rx.PyDiGraph: - """Retrieves the model subgraph as a PyDiGraph.""" - G = rx.PyDiGraph() - models = {} - datasets = {} - +def get_resolution_graph(engine: Engine) -> ResolutionGraph: + """Retrieves the resolution graph.""" + G = ResolutionGraph(nodes=set(), edges=set()) with Session(engine) as session: - for dataset in session.query(Sources).all(): - dataset_idx = G.add_node( - { - "id": str(dataset.model), - "name": f"{dataset.schema}.{dataset.table}", - "type": "dataset", - } + for resolution in session.query(Models).all(): + G.nodes.add( + ResolutionNode( + hash=resolution.hash, + name=resolution.name, + kind=ResolutionNodeKind(resolution.type), + ) ) - datasets[dataset.model] = dataset_idx - for model in session.query(Models).all(): - model_idx = G.add_node( - {"id": str(model.hash), "name": model.name, "type": "model"} - ) - models[model.hash] = model_idx - if model.type == ModelType.DATASET: - dataset_idx = datasets.get(model.hash) - _ = G.add_edge(model_idx, dataset_idx, {"type": "deduplicates"}) - - for edge in session.query(ModelsFrom).all(): - parent_idx = models.get(edge.parent) - child_idx = models.get(edge.child) - _ = G.add_edge(parent_idx, child_idx, {"type": "from"}) + for edge in session.query(ModelsFrom).filter(ModelsFrom.level == 1).all(): + G.edges.add(ResolutionEdge(parent=edge.parent, child=edge.child)) return G diff --git a/src/matchbox/server/postgresql/utils/insert.py b/src/matchbox/server/postgresql/utils/insert.py index c58abd8..1715e46 100644 --- a/src/matchbox/server/postgresql/utils/insert.py +++ b/src/matchbox/server/postgresql/utils/insert.py @@ -11,6 +11,7 @@ from sqlalchemy.orm import Session from matchbox.common.db import Source +from matchbox.common.graph import ResolutionNodeKind from matchbox.common.hash import dataset_to_hashlist, list_to_value_ordered_hash from matchbox.common.results import ClusterResults, ProbabilityResults, Results from matchbox.server.postgresql.orm import ( @@ -18,7 +19,6 @@ Contains, Models, ModelsFrom, - ModelType, Probabilities, Sources, ) @@ -41,7 +41,7 @@ def insert_dataset(dataset: Source, engine: Engine, batch_size: int) -> None: model_data = { "hash": model_hash, - "type": ModelType.DATASET.value, + "type": ResolutionNodeKind.DATASET.value, "name": f"{dataset.db_schema}.{dataset.db_table}", } @@ -139,7 +139,7 @@ def insert_model( insert(Models) .values( hash=model_hash, - type=ModelType.MODEL.value, + type=ResolutionNodeKind.MODEL.value, name=model, description=description, truth=1.0, diff --git a/test/client/test_handler.py b/test/client/test_handler.py new file mode 100644 index 0000000..1661a25 --- /dev/null +++ b/test/client/test_handler.py @@ -0,0 +1,23 @@ +from functools import wraps +from pathlib import Path +from typing import Callable + +from matchbox.client._handler import get_resolution_graph +from vcr import use_cassette + + +def vcr_cassette(func: Callable) -> Callable: + test_dir = Path(__file__).resolve().parents[1] + cassette_name = f"{func.__name__}.yaml" + + @wraps(func) + @use_cassette(test_dir / "fixtures" / "vcr_cassettes" / cassette_name) + def wrapper(*args, **kwargs): + return func(*args, **kwargs) + + return wrapper + + +@vcr_cassette +def test_get_resolution_graph(): + assert get_resolution_graph() diff --git a/test/client/test_helpers.py b/test/client/test_helpers.py index 2e0855b..b2f7975 100644 --- a/test/client/test_helpers.py +++ b/test/client/test_helpers.py @@ -8,12 +8,10 @@ cleaner, cleaners, comparison, - draw_model_tree, selector, selectors, ) from matchbox.server.postgresql import MatchboxPostgres -from matplotlib.figure import Figure from pandas import DataFrame from ..fixtures.db import AddIndexedDataCallable @@ -106,8 +104,3 @@ def test_comparisons(): ) assert comparison_name_id is not None - - -def test_draw_model_tree(matchbox_postgres: MatchboxPostgres): - plt = draw_model_tree(backend=matchbox_postgres) - assert isinstance(plt, Figure) diff --git a/test/client/test_visualisation.py b/test/client/test_visualisation.py new file mode 100644 index 0000000..bf6ce5c --- /dev/null +++ b/test/client/test_visualisation.py @@ -0,0 +1,12 @@ +from unittest.mock import patch + +from matchbox.client.visualisation import draw_resolution_graph +from matplotlib.figure import Figure + + +@patch("matchbox.client.visualisation.get_resolution_graph") +def test_draw_resolution_graph(handler_func, resolution_graph): + handler_func.return_value = resolution_graph + + plt = draw_resolution_graph() + assert isinstance(plt, Figure) diff --git a/test/common/test_graph.py b/test/common/test_graph.py new file mode 100644 index 0000000..114da9f --- /dev/null +++ b/test/common/test_graph.py @@ -0,0 +1,13 @@ +from typing import Any + +from matchbox.common.graph import ResolutionGraph +from rustworkx import PyDiGraph, is_isomorphic + + +def test_res_graph_to_rx(resolution_graph: ResolutionGraph, pydigraph: PyDiGraph): + G: PyDiGraph = resolution_graph.to_rx() + + def same(x: Any, y: Any) -> bool: + return x == y + + assert is_isomorphic(G, pydigraph, node_matcher=same, edge_matcher=same) diff --git a/test/conftest.py b/test/conftest.py index 091c458..7c82675 100644 --- a/test/conftest.py +++ b/test/conftest.py @@ -1,4 +1,5 @@ pytest_plugins = [ "test.fixtures.data", "test.fixtures.db", + "test.fixtures.graph", ] diff --git a/test/fixtures/graph.py b/test/fixtures/graph.py new file mode 100644 index 0000000..124acc9 --- /dev/null +++ b/test/fixtures/graph.py @@ -0,0 +1,50 @@ +import pytest +from matchbox.common.graph import ( + ResolutionEdge, + ResolutionGraph, + ResolutionNode, +) +from matchbox.common.graph import ( + ResolutionNodeKind as ResKind, +) +from matchbox.common.hash import hash_to_str +from rustworkx import PyDiGraph + + +@pytest.fixture +def resolution_graph() -> ResolutionGraph: + res_graph = ResolutionGraph( + nodes={ + ResolutionNode(hash=bytes(1), name="1", kind=ResKind.DATASET), + ResolutionNode(hash=bytes(2), name="2", kind=ResKind.DATASET), + ResolutionNode(hash=bytes(3), name="3", kind=ResKind.MODEL), + ResolutionNode(hash=bytes(4), name="4", kind=ResKind.MODEL), + ResolutionNode(hash=bytes(5), name="5", kind=ResKind.MODEL), + }, + edges={ + ResolutionEdge(parent=bytes(2), child=bytes(1)), + ResolutionEdge(parent=bytes(4), child=bytes(3)), + ResolutionEdge(parent=bytes(5), child=bytes(2)), + ResolutionEdge(parent=bytes(5), child=bytes(4)), + }, + ) + + return res_graph + + +@pytest.fixture +def pydigraph() -> PyDiGraph: + def make_id(n: int) -> str: + return hash_to_str(bytes(n)) + + G = PyDiGraph() + n1 = G.add_node({"id": make_id(1), "name": "1", "kind": str(ResKind.DATASET)}) + n2 = G.add_node({"id": make_id(2), "name": "2", "kind": str(ResKind.DATASET)}) + n3 = G.add_node({"id": make_id(3), "name": "3", "kind": str(ResKind.MODEL)}) + n4 = G.add_node({"id": make_id(4), "name": "4", "kind": str(ResKind.MODEL)}) + n5 = G.add_node({"id": make_id(5), "name": "5", "kind": str(ResKind.MODEL)}) + G.add_edge(n2, n1, {}) + G.add_edge(n4, n3, {}) + G.add_edge(n5, n2, {}) + G.add_edge(n5, n4, {}) + return G diff --git a/test/fixtures/vcr_cassettes/test_get_resolution_graph.yaml b/test/fixtures/vcr_cassettes/test_get_resolution_graph.yaml new file mode 100644 index 0000000..1c81026 --- /dev/null +++ b/test/fixtures/vcr_cassettes/test_get_resolution_graph.yaml @@ -0,0 +1,32 @@ +interactions: +- request: + body: '' + headers: + accept: + - '*/*' + accept-encoding: + - gzip, deflate + connection: + - keep-alive + host: + - localhost:8000 + user-agent: + - python-httpx/0.28.0 + method: GET + uri: http://localhost:8000/report/resolutions + response: + body: + string: '{"nodes":[],"edges":[]}' + headers: + content-length: + - '23' + content-type: + - application/json + date: + - Sun, 08 Dec 2024 16:55:39 GMT + server: + - uvicorn + status: + code: 200 + message: OK +version: 1 diff --git a/test/server/test_adapter.py b/test/server/test_adapter.py index c369691..898d327 100644 --- a/test/server/test_adapter.py +++ b/test/server/test_adapter.py @@ -1,7 +1,6 @@ from typing import Callable import pytest -import rustworkx as rx from dotenv import find_dotenv, load_dotenv from matchbox.common.db import Source from matchbox.common.exceptions import ( @@ -9,6 +8,7 @@ MatchboxDatasetError, MatchboxModelError, ) +from matchbox.common.graph import ResolutionGraph from matchbox.common.hash import HASH_FUNC from matchbox.common.results import ( ClusterResults, @@ -124,15 +124,20 @@ def test_get_dataset(self): engine=crn.database.engine, ) - def test_get_model_subgraph(self): - """Test getting model from the model subgraph.""" - self.setup_database("link") + def test_get_resolution_graph(self): + """Test getting model from the resolution graph.""" + graph = self.backend.get_resolution_graph() + assert len(graph.nodes) == 0 + assert len(graph.edges) == 0 + assert isinstance(graph, ResolutionGraph) - subgraph = self.backend.get_model_subgraph() + self.setup_database("link") - assert isinstance(subgraph, rx.PyDiGraph) - assert subgraph.num_nodes() > 0 - assert subgraph.num_edges() > 0 + graph = self.backend.get_resolution_graph() + # Nodes: 3 datasets, 3 dedupers, and 2 linkers + # Edges: 1 per deduper, 2 per linker + assert len(graph.nodes) == 8 + assert len(graph.edges) == 7 def test_get_model(self): """Test getting a model from the database.""" diff --git a/test/server/test_api.py b/test/server/test_api.py index 4c87189..81b47a8 100644 --- a/test/server/test_api.py +++ b/test/server/test_api.py @@ -1,6 +1,9 @@ from unittest.mock import Mock, patch from fastapi.testclient import TestClient +from matchbox.common.graph import ( + ResolutionGraph, +) from matchbox.server import app client = TestClient(app) @@ -112,6 +115,12 @@ def test_count_backend_item(self, get_backend): # response = client.get("/validate/hash") # assert response.status_code == 200 - # def test_get_model_subgraph(): - # response = client.get("/report/models") - # assert response.status_code == 200 + @patch("matchbox.server.base.BackendManager.get_backend") + def test_get_resolution_graph(self, get_backend, resolution_graph): + mock_backend = Mock() + mock_backend.get_resolution_graph = Mock(return_value=resolution_graph) + get_backend.return_value = mock_backend + + response = client.get("/report/resolutions") + assert response.status_code == 200 + assert ResolutionGraph.model_validate(response.json()) diff --git a/uv.lock b/uv.lock index 2fdc60e..362b6be 100644 --- a/uv.lock +++ b/uv.lock @@ -1,9 +1,12 @@ version = 1 requires-python = ">=3.11" resolution-markers = [ - "python_full_version < '3.12'", - "python_full_version == '3.12.*'", - "python_full_version >= '3.13'", + "python_full_version < '3.12' and platform_python_implementation == 'PyPy'", + "python_full_version < '3.12' and 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