From e68513f78274c9235db1285dde33fa70ef9991b7 Mon Sep 17 00:00:00 2001 From: Cyril Matthey-Doret Date: Fri, 2 Feb 2024 10:46:32 +0100 Subject: [PATCH] fix(cff): enforce valid urls as doi (#108) * fix(cff): parse yaml to handle quotes + prepend scheme to doi * chore(fmt): quotes * chore: update lock * docs(readme): update obsolete env var name * docs(readme): lighter fmt * test(cff): update doctest to include scheme * fix(cff): ensure doi is a valid url * fix: drop unused import * fix(cff): error handling on invalid yaml * refactor(cff): use regex + defensive prog * fix(cff): drop unused prefix var * test(cff): update test cases with valid doi * feat(cff): add warning when doi missing from cff * fix(log): replace deprecated logger.warn -> logger.warning * feat(log): format to include loglevel --- README.md | 8 +- gimie/__init__.py | 6 +- gimie/parsers/cff.py | 77 ++- poetry.lock | 1122 +++++++++++++++++++----------------------- 4 files changed, 573 insertions(+), 640 deletions(-) diff --git a/README.md b/README.md index 82283e64..ef023b58 100644 --- a/README.md +++ b/README.md @@ -12,7 +12,7 @@ Scientific code repositories contain valuable metadata which can be used to enri Using Gimie: easy peasy, it's a 3 step process. -## STEP 1: Installation +## 1: Installation To install the stable version on PyPI: @@ -32,10 +32,10 @@ Gimie is also available as a docker container hosted on the [Github container re docker pull ghcr.io/sdsc-ordes/gimie:latest # The access token can be provided as an environment variable -docker run -e ACCESS_TOKEN=$ACCESS_TOKEN ghcr.io/sdsc-ordes/gimie:latest gimie data +docker run -e GITHUB_TOKEN=$GITHUB_TOKEN ghcr.io/sdsc-ordes/gimie:latest gimie data ``` -## STEP 2 : Set your credentials +## 2 : Set your credentials In order to access the github api, you need to provide a github token with the `read:org` scope. @@ -61,7 +61,7 @@ and/or your Gitlab token: export GITLAB_TOKEN= ``` -## STEP 3: GIMIE info ! Run Gimie +## 3: GIMIE info ! Run Gimie ### As a command line tool diff --git a/gimie/__init__.py b/gimie/__init__.py index 18631bda..8bcdf9e2 100644 --- a/gimie/__init__.py +++ b/gimie/__init__.py @@ -22,4 +22,8 @@ __version__ = importlib_metadata.version(__name__) logger = logging.getLogger() -logger.setLevel(logging.WARNING) +stdout_formatter = logging.Formatter("%(levelname)s :: %(message)s") +stream_handler = logging.StreamHandler() +stream_handler.setLevel(logging.WARNING) +stream_handler.setFormatter(stdout_formatter) +logger.addHandler(stream_handler) diff --git a/gimie/parsers/cff.py b/gimie/parsers/cff.py index a00499a1..beeb5bca 100644 --- a/gimie/parsers/cff.py +++ b/gimie/parsers/cff.py @@ -17,15 +17,17 @@ from io import BytesIO import re from typing import List, Optional, Set +import yaml from rdflib.term import URIRef +from gimie import logger from gimie.graph.namespaces import SDO from gimie.parsers.abstract import Parser, Property class CffParser(Parser): - """Parse cff file to extract the doi into schema:citation .""" + """Parse DOI from CITATION.cff into schema:citation .""" def __init__(self): super().__init__() @@ -43,30 +45,81 @@ def parse(self, data: bytes) -> Set[Property]: return props +def doi_to_url(doi: str) -> str: + """Formats a doi to an https URL to doi.org. + + Parameters + ---------- + doi + doi where the scheme (e.g. https://) and + hostname (e.g. doi.org) may be missing. + + Returns + ------- + str + doi formatted as a valid url. Base url + is set to https://doi.org when missing. + + Examples + -------- + >>> doi_to_url("10.0000/example.abcd") + 'https://doi.org/10.0000/example.abcd' + >>> doi_to_url("doi.org/10.0000/example.abcd") + 'https://doi.org/10.0000/example.abcd' + >>> doi_to_url("https://doi.org/10.0000/example.abcd") + 'https://doi.org/10.0000/example.abcd' + """ + + # regex from: + # https://www.crossref.org/blog/dois-and-matching-regular-expressions + doi_match = re.search( + r"10.\d{4,9}/[-._;()/:A-Z0-9]+$", doi, flags=re.IGNORECASE + ) + + if doi_match is None: + raise ValueError(f"Not a valid DOI: {doi}") + + short_doi = doi_match.group() + + return f"https://doi.org/{short_doi}" + + def get_cff_doi(data: bytes) -> Optional[str]: """Given a CFF file, returns the DOI, if any. Parameters ---------- - data: + data The cff file body as bytes. + Returns + ------- + str, optional + doi formatted as a valid url + Examples -------- >>> get_cff_doi(bytes("doi: 10.5281/zenodo.1234", encoding="utf8")) - '10.5281/zenodo.1234' + 'https://doi.org/10.5281/zenodo.1234' >>> get_cff_doi(bytes("abc: def", encoding="utf8")) """ - matches = re.search( - r"^doi: *(.*)$", - data.decode(), - flags=re.IGNORECASE | re.MULTILINE, - ) try: - doi = matches.groups()[0] - except AttributeError: - doi = None + cff = yaml.safe_load(data.decode()) + except yaml.scanner.ScannerError: + logger.warning("cannot read CITATION.cff, skipped.") + return None + + try: + doi_url = doi_to_url(cff["doi"]) + # No doi in cff file + except (KeyError, TypeError): + logger.warning("CITATION.cff does not contain a 'doi' key.") + doi_url = None + # doi is malformed + except ValueError as err: + logger.warning(err) + doi_url = None - return doi + return doi_url diff --git a/poetry.lock b/poetry.lock index 8abc5c53..ebf897e0 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,22 +1,20 @@ -# This file is automatically @generated by Poetry and should not be changed by hand. +# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. [[package]] name = "alabaster" -version = "0.7.13" -description = "A configurable sidebar-enabled Sphinx theme" -category = "dev" +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", hash = "sha256:1ee19aca801bbabb5ba3f5f258e4422dfa86f82f3e9cefb0859b283cdd7f62a3"}, - {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"}, + {file = "alabaster-0.7.16-py3-none-any.whl", hash = "sha256:b46733c07dce03ae4e150330b975c75737fa60f0a7c591b6c8bf4928a28e2c92"}, + {file = "alabaster-0.7.16.tar.gz", hash = "sha256:75a8b99c28a5dad50dd7f8ccdd447a121ddb3892da9e53d1ca5cca3106d58d65"}, ] [[package]] name = "annotated-types" version = "0.6.0" description = "Reusable constraint types to use with typing.Annotated" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -26,14 +24,13 @@ files = [ [[package]] name = "babel" -version = "2.13.1" +version = "2.14.0" description = "Internationalization utilities" -category = "dev" optional = false python-versions = ">=3.7" files = [ - {file = "Babel-2.13.1-py3-none-any.whl", hash = "sha256:7077a4984b02b6727ac10f1f7294484f737443d7e2e66c5e4380e41a3ae0b4ed"}, - {file = "Babel-2.13.1.tar.gz", hash = "sha256:33e0952d7dd6374af8dbf6768cc4ddf3ccfefc244f9986d4074704f2fbd18900"}, + {file = "Babel-2.14.0-py3-none-any.whl", hash = "sha256:efb1a25b7118e67ce3a259bed20545c29cb68be8ad2c784c83689981b7a57287"}, + {file = "Babel-2.14.0.tar.gz", hash = "sha256:6919867db036398ba21eb5c7a0f6b28ab8cbc3ae7a73a44ebe34ae74a4e7d363"}, ] [package.extras] @@ -41,20 +38,22 @@ dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"] [[package]] name = "beautifulsoup4" -version = "4.12.2" +version = "4.12.3" description = "Screen-scraping library" -category = "dev" optional = false python-versions = ">=3.6.0" files = [ - {file = "beautifulsoup4-4.12.2-py3-none-any.whl", hash = "sha256:bd2520ca0d9d7d12694a53d44ac482d181b4ec1888909b035a3dbf40d0f57d4a"}, - {file = "beautifulsoup4-4.12.2.tar.gz", hash = "sha256:492bbc69dca35d12daac71c4db1bfff0c876c00ef4a2ffacce226d4638eb72da"}, + {file = "beautifulsoup4-4.12.3-py3-none-any.whl", hash = "sha256:b80878c9f40111313e55da8ba20bdba06d8fa3969fc68304167741bbf9e082ed"}, + {file = "beautifulsoup4-4.12.3.tar.gz", hash = "sha256:74e3d1928edc070d21748185c46e3fb33490f22f52a3addee9aee0f4f7781051"}, ] [package.dependencies] soupsieve = ">1.2" [package.extras] +cchardet = ["cchardet"] +chardet = ["chardet"] +charset-normalizer = ["charset-normalizer"] html5lib = ["html5lib"] lxml = ["lxml"] @@ -62,7 +61,6 @@ lxml = ["lxml"] name = "black" version = "22.12.0" description = "The uncompromising code formatter." -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -98,7 +96,6 @@ uvloop = ["uvloop (>=0.15.2)"] name = "cachetools" version = "5.3.2" description = "Extensible memoizing collections and decorators" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -110,7 +107,6 @@ files = [ name = "calamus" version = "0.4.2" description = "calamus is a library built on top of marshmallow to allow (de-)Serialization of Python classes to JSON-LD." -category = "main" optional = false python-versions = ">=3.7.1,<4.0.0" files = [ @@ -129,21 +125,19 @@ docs = ["Jinja2 (>=3.0.0,<3.1.0)", "sphinx (>=3.0.3,<4.0.0)", "sphinx-rtd-theme [[package]] name = "certifi" -version = "2023.7.22" +version = "2023.11.17" description = "Python package for providing Mozilla's CA Bundle." -category = "main" optional = false python-versions = ">=3.6" files = [ - {file = "certifi-2023.7.22-py3-none-any.whl", hash = "sha256:92d6037539857d8206b8f6ae472e8b77db8058fec5937a1ef3f54304089edbb9"}, - {file = "certifi-2023.7.22.tar.gz", hash = "sha256:539cc1d13202e33ca466e88b2807e29f4c13049d6d87031a3c110744495cb082"}, + {file = "certifi-2023.11.17-py3-none-any.whl", hash = "sha256:e036ab49d5b79556f99cfc2d9320b34cfbe5be05c5871b51de9329f0603b0474"}, + {file = "certifi-2023.11.17.tar.gz", hash = "sha256:9b469f3a900bf28dc19b8cfbf8019bf47f7fdd1a65a1d4ffb98fc14166beb4d1"}, ] [[package]] name = "cfgv" version = "3.4.0" description = "Validate configuration and produce human readable error messages." -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -155,7 +149,6 @@ files = [ name = "charset-normalizer" version = "3.3.2" description = "The Real First Universal Charset Detector. 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