From e34687554a5feddec5e4e100b23a2e97e0396876 Mon Sep 17 00:00:00 2001 From: Glass Date: Fri, 17 May 2024 11:28:37 -0600 Subject: [PATCH] Fix api call for compact associations (#696) Closes #687 --- backend/poetry.lock | 3296 +++++++++++---------- backend/pyproject.toml | 38 +- backend/src/monarch_py/api/association.py | 4 +- backend/src/monarch_py/cli.py | 8 +- backend/tests/api/test_api.py | 3 +- 5 files changed, 1711 insertions(+), 1638 deletions(-) diff --git a/backend/poetry.lock b/backend/poetry.lock index 18fe99cca..267c7a528 100644 --- a/backend/poetry.lock +++ b/backend/poetry.lock @@ -17,13 +17,13 @@ parse = ["beautifulsoup4 (>=4.10.0,<5.0)", "requests (>=2.12.0,<3)"] [[package]] name = "alabaster" -version = "0.7.13" -description = "A configurable sidebar-enabled Sphinx theme" +version = "0.7.16" +description = "A light, configurable Sphinx theme" optional = false -python-versions = ">=3.6" +python-versions = ">=3.9" files = [ - {file = "alabaster-0.7.13-py3-none-any.whl", 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"jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"] +docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] +testing = ["big-O", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"] [metadata] lock-version = "2.0" python-versions = "^3.9" -content-hash = "ad4f1fc499b4214baffd62fd9c46e7421849b7547641e129991ebe594930f199" +content-hash = "b6333105d2d7b667b8d451386ff86db368efe6607739bd9629b04d32f6189b43" diff --git a/backend/pyproject.toml b/backend/pyproject.toml index 3eb9eb47b..2d1c66852 100644 --- a/backend/pyproject.toml +++ b/backend/pyproject.toml @@ -20,36 +20,34 @@ curies = "<1" linkml = "^1.6" prefixmaps = "^0.2" bioregistry = "^0.10.57" -oaklib = ">=0.5.22" +oaklib = ">=0.6.6" -docker = "^6.0.1" -fastapi = "^0.103.1" -gunicorn = "^21.2.0" +docker = "^7.0.0" +fastapi = "^0.111.0" +gunicorn = "^22.0.0" loguru = "*" -pystow = ">=0.5.0" -requests = "^2.28.1" +pystow = ">=0.5.4" +requests = "^2.31.0" rich = "*" -typer = "^0.7.0" -typer-cli = "^0.0.13" -spacy = ">=3.6.1,<3.8.0" +typer = "^0.12" +# spacy = ">=3.7.5,<3.8.0" +spacy = { git = "https://github.com/explosion/spaCy.git", branch = "master" } beautifulsoup4 = "^4.12.3" [tool.poetry.dependencies.en_core_sci_sm] -url = "https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.5.3/en_core_sci_sm-0.5.3.tar.gz" +url = "https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.5.4/en_core_sci_sm-0.5.4.tar.gz" [tool.poetry.group.dev.dependencies] -pytest = "^7.2.0" -mkdocs = ">=1.4.2" -mkdocs-material = ">=9.1.16" -mkdocstrings = { extras = ["python"], version = ">=0.22.0" } -black = "^22.10.0" +pytest = "^8.2.0" +mkdocs = ">=1.6.0" +mkdocs-material = ">=9.5.23" +mkdocstrings = { version = ">=0.25.1", extras = ["python"] } +black = "^24.4.2" ruff = "*" -uvicorn = { extras = ["standard"], version = "^0.20.0" } -httpx = "^0.24.1" +uvicorn = { extras = ["standard"], version = "^0.29.0" } +httpx = "^0.27" scholarly = "*" -habanero = "*" -manubot = "*" -coverage = "^7.4.1" +coverage = "^7.5.1" [tool.poetry.scripts] diff --git a/backend/src/monarch_py/api/association.py b/backend/src/monarch_py/api/association.py index 372595c01..992198037 100644 --- a/backend/src/monarch_py/api/association.py +++ b/backend/src/monarch_py/api/association.py @@ -4,7 +4,7 @@ from monarch_py.api.additional_models import OutputFormat, PaginationParams from monarch_py.api.config import solr -from monarch_py.datamodels.model import AssociationResults, MultiEntityAssociationResults +from monarch_py.datamodels.model import AssociationResults, CompactAssociationResults, MultiEntityAssociationResults from monarch_py.datamodels.category_enums import AssociationCategory, AssociationPredicate, EntityCategory from monarch_py.utils.format_utils import to_tsv @@ -36,7 +36,7 @@ async def _get_associations( title="Output format for the response", examples=["json", "tsv"], ), -) -> Union[AssociationResults, str]: +) -> Union[AssociationResults, CompactAssociationResults, str]: """Retrieves all associations for a given entity, or between two entities.""" response = solr().get_associations( category=category, diff --git a/backend/src/monarch_py/cli.py b/backend/src/monarch_py/cli.py index 6797dabff..3f2150194 100644 --- a/backend/src/monarch_py/cli.py +++ b/backend/src/monarch_py/cli.py @@ -387,7 +387,7 @@ def releases( @app.command("release") def release( - version: str = typer.Argument(None, help="The release version to get metadata for"), + release_ver: str = typer.Argument(None, help="The release version to get metadata for"), fmt: str = typer.Option( "json", "--format", @@ -400,12 +400,12 @@ def release( Retrieve metadata for a specific release Args: - version: The release version to get metadata for + release_ver: The release version to get metadata for fmt: The format of the output (json, yaml, tsv, table) output: The path to the output file (stdout if not specified) """ - release_info = get_release_metadata(version) - format_output(fmt, release_info) + release_info = get_release_metadata(release_ver) + format_output(fmt, release_info, output) if __name__ == "__main__": diff --git a/backend/tests/api/test_api.py b/backend/tests/api/test_api.py index 606ecd015..7de821ec3 100644 --- a/backend/tests/api/test_api.py +++ b/backend/tests/api/test_api.py @@ -33,7 +33,8 @@ def test_releases(): response = client.get("/v3/api/releases?limit=2") assert response.status_code == 200 releases = [release["version"] for release in response.json()] - assert [i in ["latest", "previous"] for i in releases] + assert [i in ["latest", "previous"] for i in releases] + def test_release_metadata(): response = client.get("/v3/api/releases?release=latest")