From df1a56e5a9ca4c5cb9c6c39b2a524f5f83e0cabb Mon Sep 17 00:00:00 2001 From: sneakers-the-rat Date: Tue, 2 Apr 2024 19:27:08 -0700 Subject: [PATCH] Correct URL_FOR - Unskip tests for URL resolution and correctness - Skip fail-prone and unused github URL tests - Add requests_cache --- .github/workflows/main.yaml | 2 +- linkml_runtime/linkml_model/linkml_files.py | 3 +- poetry.lock | 142 +++++++++++++------ pyproject.toml | 1 + tests/conftest.py | 22 +++ tests/test_linkml_model/test_linkml_files.py | 40 +++++- 6 files changed, 157 insertions(+), 53 deletions(-) create mode 100644 tests/conftest.py diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index 96b5949d..e4ea7a4b 100644 --- a/.github/workflows/main.yaml +++ b/.github/workflows/main.yaml @@ -50,7 +50,7 @@ jobs: #---------------------------------------------- - name: Generate coverage results run: | - poetry run coverage run -m unittest discover + poetry run coverage run -m pytest poetry run coverage xml poetry run coverage report -m diff --git a/linkml_runtime/linkml_model/linkml_files.py b/linkml_runtime/linkml_model/linkml_files.py index 198b052f..bce1ca5b 100644 --- a/linkml_runtime/linkml_model/linkml_files.py +++ b/linkml_runtime/linkml_model/linkml_files.py @@ -143,7 +143,8 @@ def _build_loc(base: str, source: Source, fmt: Format) -> str: def URL_FOR(source: Source, fmt: Format) -> str: """ Return the URL to retrieve source in format """ - return f"{LINKML_URL_BASE}{source.value}.{fmt.value}" + fmt_path: FormatPath = _Path.get(fmt.name) + return f"{LINKML_URL_BASE}{source.value}.{fmt_path.extension}" def LOCAL_PATH_FOR(source: Source, fmt: Format) -> str: diff --git a/poetry.lock b/poetry.lock index ee462d1d..afd28039 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,10 +1,9 @@ -# This file is automatically @generated by Poetry 1.4.0 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. 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-798,11 +816,40 @@ urllib3 = ">=1.21.1,<3" socks = ["PySocks (>=1.5.6,!=1.5.7)"] use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"] +[[package]] +name = "requests-cache" +version = "1.2.0" +description = "A persistent cache for python requests" +optional = false +python-versions = ">=3.8" +files = [ + {file = "requests_cache-1.2.0-py3-none-any.whl", hash = "sha256:490324301bf0cb924ff4e6324bd2613453e7e1f847353928b08adb0fdfb7f722"}, + {file = "requests_cache-1.2.0.tar.gz", hash = "sha256:db1c709ca343cc1cd5b6c8b1a5387298eceed02306a6040760db538c885e3838"}, +] + +[package.dependencies] +attrs = ">=21.2" +cattrs = ">=22.2" +platformdirs = ">=2.5" +requests = ">=2.22" +url-normalize = ">=1.4" +urllib3 = ">=1.25.5" + +[package.extras] +all = ["boto3 (>=1.15)", "botocore (>=1.18)", "itsdangerous (>=2.0)", "pymongo (>=3)", "pyyaml (>=6.0.1)", "redis (>=3)", "ujson (>=5.4)"] +bson = ["bson (>=0.5)"] +docs = ["furo (>=2023.3,<2024.0)", "linkify-it-py (>=2.0,<3.0)", "myst-parser (>=1.0,<2.0)", "sphinx (>=5.0.2,<6.0.0)", "sphinx-autodoc-typehints (>=1.19)", "sphinx-automodapi (>=0.14)", "sphinx-copybutton (>=0.5)", "sphinx-design (>=0.2)", "sphinx-notfound-page (>=0.8)", "sphinxcontrib-apidoc (>=0.3)", "sphinxext-opengraph (>=0.9)"] +dynamodb = ["boto3 (>=1.15)", "botocore (>=1.18)"] +json = ["ujson (>=5.4)"] +mongodb = ["pymongo (>=3)"] +redis = ["redis (>=3)"] +security = ["itsdangerous (>=2.0)"] +yaml = ["pyyaml (>=6.0.1)"] + [[package]] name = "rpds-py" version = "0.18.0" description = "Python bindings to Rust's persistent data structures (rpds)" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -911,7 +958,6 @@ files = [ name = "six" version = "1.16.0" description = "Python 2 and 3 compatibility utilities" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*" files = [ @@ -923,7 +969,6 @@ files = [ name = "sortedcontainers" version = "2.4.0" description = "Sorted Containers -- Sorted List, Sorted Dict, Sorted Set" -category = "main" optional = false python-versions = "*" files = [ @@ -935,7 +980,6 @@ files = [ name = "tomli" version = "2.0.1" description = "A lil' TOML parser" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -947,7 +991,6 @@ files = [ name = "typing-extensions" version = "4.9.0" description = "Backported and Experimental Type Hints for Python 3.8+" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -955,11 +998,24 @@ files = [ {file = "typing_extensions-4.9.0.tar.gz", hash = "sha256:23478f88c37f27d76ac8aee6c905017a143b0b1b886c3c9f66bc2fd94f9f5783"}, ] +[[package]] +name = "url-normalize" +version = "1.4.3" +description = "URL normalization for Python" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" +files = [ + {file = "url-normalize-1.4.3.tar.gz", hash = "sha256:d23d3a070ac52a67b83a1c59a0e68f8608d1cd538783b401bc9de2c0fac999b2"}, + {file = "url_normalize-1.4.3-py2.py3-none-any.whl", hash = "sha256:ec3c301f04e5bb676d333a7fa162fa977ad2ca04b7e652bfc9fac4e405728eed"}, +] + +[package.dependencies] +six = "*" + [[package]] name = "urllib3" version = "2.2.1" description = "HTTP library with thread-safe connection pooling, file post, and more." -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -977,7 +1033,6 @@ zstd = ["zstandard (>=0.18.0)"] name = "wrapt" version = "1.16.0" description = "Module for decorators, wrappers and monkey patching." -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -1057,7 +1112,6 @@ files = [ name = "zipp" version = "3.17.0" description = "Backport of pathlib-compatible object wrapper for zip files" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1072,4 +1126,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p [metadata] lock-version = "2.0" python-versions = "^3.8" -content-hash = "ee072611489b4293d1d155732995615e53afba728f652255af36f72826262f62" +content-hash = "fddd54f2e38fdce32a4236c283d5f4e141f897e6d7ed4aac4ce5dbb40c37e428" diff --git a/pyproject.toml b/pyproject.toml index bb504c1f..b50cba65 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -64,6 +64,7 @@ pydantic = ">=1.10.2, <3.0.0" [tool.poetry.dev-dependencies] coverage = "^6.2" +requests-cache = "^1.2.0" [build-system] requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning"] diff --git a/tests/conftest.py b/tests/conftest.py new file mode 100644 index 00000000..f0f30ec9 --- /dev/null +++ b/tests/conftest.py @@ -0,0 +1,22 @@ +from pathlib import Path +import pytest +import requests_cache + +@pytest.fixture(scope="session", autouse=True) +def patch_requests_cache(pytestconfig): + """ + Cache network requests - for each unique network request, store it in + an sqlite cache. only do unique requests once per session. + """ + cache_file = Path(__file__).parent / "output" / "requests-cache.sqlite" + cache_file.parent.mkdir(exist_ok=True) + requests_cache.install_cache( + str(cache_file), + backend="sqlite", + urls_expire_after={"localhost": requests_cache.DO_NOT_CACHE}, + ) + requests_cache.clear() + yield + # If we want to delete cache, this is how we might do it! + # if not pytestconfig.getoption("--with-output"): + # cache_file.unlink(missing_ok=True) \ No newline at end of file diff --git a/tests/test_linkml_model/test_linkml_files.py b/tests/test_linkml_model/test_linkml_files.py index 189f1fc3..5899950d 100644 --- a/tests/test_linkml_model/test_linkml_files.py +++ b/tests/test_linkml_model/test_linkml_files.py @@ -28,6 +28,26 @@ if (fmt not in META_ONLY or source == Source.META) ] +W3ID_EXTENSIONS = ( + 'html', + 'yaml', + 'graphql', + 'context.json', + 'context.jsonld', + 'schema.json', + 'json', + 'ttl', + 'owl', + 'shex', + 'shexc', + 'shexj' +) +W3ID_FORMATS = [ + (source, fmt) for source, fmt in EXPECTED_FORMATS + if _Path.get(fmt.name).extension in W3ID_EXTENSIONS +] +"""The formats that have rewrite rules at https://github.com/perma-id/w3id.org/blob/master/linkml/.htaccess""" + @pytest.mark.parametrize( 'source,fmt', EXPECTED_FORMATS @@ -66,7 +86,7 @@ def test_no_unmapped_dirs(): # URLs # -------------------------------------------------- -@pytest.mark.skipif(not HAVE_REQUESTS_CACHE, reason='We need to cache this...') +@pytest.mark.skip("github paths largely unused and expensive to test due to ratelimiting") @pytest.mark.parametrize( 'release_type', ReleaseTag.__iter__() @@ -78,7 +98,7 @@ def test_no_unmapped_dirs(): def test_github_path_exists(source,fmt, release_type): url = GITHUB_PATH_FOR(source, fmt, release_type) res = requests.get(url) - assert res.status_code != 404 + assert res.status_code != 404, url @pytest.mark.parametrize( @@ -99,8 +119,7 @@ def test_github_path_format(source,fmt, release_type): # for windows... assert '\\' not in url - -@pytest.mark.skipif(not HAVE_REQUESTS_CACHE,reason= "Need to cache this") +@pytest.mark.skip("github paths largely unused") @pytest.mark.parametrize( 'source,fmt', EXPECTED_FORMATS @@ -108,18 +127,25 @@ def test_github_path_format(source,fmt, release_type): def test_github_io_path(source,fmt): url = GITHUB_IO_PATH_FOR(source, fmt) res = requests.get(url) - assert res.status_code != 404 + assert res.status_code != 404, url @pytest.mark.skipif(not HAVE_REQUESTS_CACHE,reason= 'Need to cache this') @pytest.mark.parametrize( 'source,fmt', - EXPECTED_FORMATS + W3ID_FORMATS ) def test_url_for_format(source,fmt): url = URL_FOR(source, fmt) res = requests.get(url) - assert res.status_code != 404 + assert res.status_code != 404, url + +def test_fixed_meta_url(): + """ + One fixed canary value - the METAMODEL_URI as used in linkml main shouldn't change + """ + assert URL_FOR(Source.META, Format.YAML) == 'https://w3id.org/linkml/meta.yaml' + assert URL_FOR(Source.META, Format.JSONLD) == 'https://w3id.org/linkml/meta.context.jsonld'