diff --git a/.flake8 b/.flake8 new file mode 100644 index 0000000..59ba6d8 --- /dev/null +++ b/.flake8 @@ -0,0 +1,7 @@ +[flake8] +# uv creates the virtual environment inside the repository, so a bare `flake8 .` +# would otherwise descend into the installed dependencies and report their issues. +extend-exclude = + .venv + build + dist diff --git a/.github/workflows/publish_pypi.yaml b/.github/workflows/publish_pypi.yaml index 3087d6c..a9925c6 100644 --- a/.github/workflows/publish_pypi.yaml +++ b/.github/workflows/publish_pypi.yaml @@ -10,7 +10,12 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@v6 - - name: Build and publish to pypi - uses: JRubics/poetry-publish@v2.1 + - name: Install uv + uses: astral-sh/setup-uv@v10.3.3 + - name: Build sdist and wheel + run: | + uv build + - name: Publish to PyPI + uses: pypa/gh-action-pypi-publish@release/v1 with: - pypi_token: ${{ secrets.PYPI_API_TOKEN }} + password: ${{ secrets.PYPI_API_TOKEN }} diff --git a/.github/workflows/test-package.yml b/.github/workflows/test-package.yml index 52cc473..a6dba42 100644 --- a/.github/workflows/test-package.yml +++ b/.github/workflows/test-package.yml @@ -13,23 +13,22 @@ jobs: steps: - uses: actions/checkout@v6 - - name: Set up Python 3.12 - uses: actions/setup-python@v6 + - name: Install uv + uses: astral-sh/setup-uv@v10.3.3 with: - python-version: 3.12 + python-version: "3.12" - name: Install dependencies run: | - pip install poetry - poetry install --with=dev + uv sync --frozen - name: Lint with ruff run: | - poetry run ruff check . --fix --exit-non-zero-on-fix + uv run ruff check . --fix --exit-non-zero-on-fix - name: Lint with flake8 run: | # stop the build if there are Python syntax errors or undefined names - poetry run flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics + uv run flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide - poetry run flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics + uv run flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics - name: Test with pytest run: | - poetry run pytest --cov --cov-report term --cov-report xml --junitxml=xunit-result.xml + uv run pytest --cov --cov-report term --cov-report xml --junitxml=xunit-result.xml diff --git a/.gitignore b/.gitignore index edeaf81..10ef512 100644 --- a/.gitignore +++ b/.gitignore @@ -5,4 +5,9 @@ MSMetaEnhancer_*.log dist MSMetaEnhancer.egg-info .vscode -poetry.lock \ No newline at end of file +.venv +# copied into the docs source tree by docs/source/conf.py at build time +docs/source/readme.md +docs/source/CHANGELOG.md +docs/source/CONTRIBUTING.md +docs/build \ No newline at end of file diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 55e4f98..6f8a9b4 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -10,17 +10,15 @@ build: os: ubuntu-22.04 tools: python: "3.12" - jobs: - post_create_environment: - # Install poetry - # https://python-poetry.org/docs/#installing-manually - - pip install poetry - post_install: - # Install dependencies with 'docs' dependency group - # https://python-poetry.org/docs/managing-dependencies/#dependency-groups - # VIRTUAL_ENV needs to be set manually for now. - # See https://github.com/readthedocs/readthedocs.org/pull/11152/ - - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install --with docs + +# Install the project and the 'docs' dependency group with uv. +# https://docs.readthedocs.com/platform/stable/config-file/v2.html#python-install +python: + install: + - method: uv + command: sync + groups: + - docs # Build documentation in the docs/ directory with Sphinx sphinx: diff --git a/CHANGELOG.md b/CHANGELOG.md index d84b0bc..8220a23 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,22 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## Unreleased +### Added +- Added a `ChEBI` web converter querying the ChEBI service (https://www.ebi.ac.uk/chebi/) + - Supports `compound_name`, `iupac_name`, `inchikey`, `inchi`, `smiles`, and `chebiid` as source attributes and returns `chebiid`, `compound_name`, `iupac_name`, `inchikey`, `inchi`, `smiles`, and `formula` + - Structure search from SMILES uses the ChEBI `structure_search` endpoint with `type=similarity` and a similarity threshold of 1 +- Declared `pytest-asyncio` explicitly instead of relying on it arriving transitively, and moved `myst-parser` from the `dev` to the `docs` group so the documentation dependencies are self-contained + +### Changed +- Project management moved from Poetry to [uv](https://docs.astral.sh/uv/): metadata converted to PEP 621, `uv_build` is the build backend, and `uv` now handles virtual environments, tests, linting, the docs build, and the package build +- `uv.lock` is committed and used as the source of truth; CI installs with `uv sync --frozen`, so a dependency change without a refreshed lock now fails instead of silently re-resolving +- Read the Docs installs with uv natively, which removes the `pip install poetry` step and its `VIRTUAL_ENV` workaround +- PyPI publishing builds with `uv build` and uploads with `pypa/gh-action-pypi-publish` in place of `JRubics/poetry-publish` +- `docs/source/conf.py` resolves its paths relative to itself rather than to the working directory, so the documentation also builds from the repository root + +### Fixed +- Normalize unhyphenated CAS numbers in the `Wikidata` converter before querying: Wikidata stores `P231` hyphenated only, so a source `casno` such as `50782` previously matched nothing. `fix_cas_number` moved to `libs.utils.Generic` and now leaves values that cannot be CAS numbers untouched instead of inserting dashes into them + ## [0.6.1] - 2026-10-22 ### Added diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 346b5c4..215d577 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -29,7 +29,7 @@ In case you feel like you've made a valuable contribution, but you don't know ho 1. (**important**) announce your plan to the rest of the community *before you start working*. This announcement should be in the form of a (new) issue; 1. (**important**) wait until some kind of consensus is reached about your idea being a good idea; 1. if needed, fork the repository to your own Github profile and create your own feature branch off of the latest master commit. While working on your feature branch, make sure to stay up to date with the main branch by pulling in changes, possibly from the 'upstream' repository (follow the instructions [here](https://help.github.com/articles/configuring-a-remote-for-a-fork/) and [here](https://help.github.com/articles/syncing-a-fork/)); -1. make sure the existing tests still work by running ``pytest``; +1. make sure the existing tests still work by running ``uv run pytest`` (see the [setup instructions](README.md#developer-documentation)); 1. add your own tests (if necessary); 1. update or expand the documentation; 1. update the [CHANGELOG](CHANGELOG.md) file with change; @@ -259,12 +259,12 @@ After implementing your converter: 1. Run the existing tests to ensure you haven't broken anything: ```bash - pytest tests/ + uv run pytest tests/ ``` 2. Run your specific tests: ```bash - pytest tests/test_YourService.py -v + uv run pytest tests/test_YourService.py -v ``` 3. Test the integration by using the converter in a real scenario diff --git a/MSMetaEnhancer/libs/Curator.py b/MSMetaEnhancer/libs/Curator.py index 358f1ac..2576fe7 100644 --- a/MSMetaEnhancer/libs/Curator.py +++ b/MSMetaEnhancer/libs/Curator.py @@ -4,6 +4,7 @@ is_valid_inchikey, ) from MSMetaEnhancer.libs.utils.Errors import InvalidAttributeFormat +from MSMetaEnhancer.libs.utils.Generic import fix_cas_number as add_cas_dashes # Example usage @@ -55,10 +56,7 @@ def fix_cas_number(cas_number): :param cas_number: given CAS number :return: CAS number enriched by dashes (if needed) """ - if isinstance(cas_number, str): - if "-" not in cas_number: - return f"{cas_number[:-3]}-{cas_number[-3:-1]}-{cas_number[-1]}" - return cas_number + return add_cas_dashes(cas_number) @staticmethod def filter_invalid_metadata(metadata, log, job): diff --git a/MSMetaEnhancer/libs/converters/web/ChEBI.py b/MSMetaEnhancer/libs/converters/web/ChEBI.py new file mode 100644 index 0000000..8240e3f --- /dev/null +++ b/MSMetaEnhancer/libs/converters/web/ChEBI.py @@ -0,0 +1,283 @@ +import json +from urllib.parse import quote + +from frozendict import frozendict + +from MSMetaEnhancer.libs.converters.web.WebConverter import WebConverter + + +class ChEBI(WebConverter): + """ + ChEBI (Chemical Entities of Biological Interest) is a freely available dictionary of + molecular entities focused on small chemical compounds. + + ChEBI service: https://www.ebi.ac.uk/chebi/ + API documentation: https://www.ebi.ac.uk/chebi/backend/api/docs/ + + Identifiers and names are resolved by the `es_search` endpoint, structures by the + `structure_search` endpoint. Both only return the fields of a compound summary, so the + obtained accession is used to retrieve the whole record from the `compound` endpoint, + which is the only one reporting the IUPAC name. + """ + + SEARCH_SIZE = 15 + """Number of search results requested from the ChEBI search endpoints.""" + + IDENTIFIER_FIELDS = ("chebi_accession", "inchikey", "inchi", "smiles") + """Fields used to positively identify a search result by the searched identifier.""" + + NAME_FIELDS = ("ascii_name", "name") + """Fields used to positively identify a search result by the searched name.""" + + def __init__(self, session): + super().__init__(session) + # service URLs + self.endpoints = { + "ChEBI": "https://www.ebi.ac.uk/chebi/backend/api/public/", + } + + # attributes as reported by the compound endpoint + self.attributes = [ + {"code": "chebiid", "paths": [("chebi_accession",)]}, + {"code": "compound_name", "paths": [("ascii_name",), ("name",)]}, + {"code": "formula", "paths": [("chemical_data", "formula")]}, + {"code": "smiles", "paths": [("default_structure", "smiles")]}, + {"code": "inchi", "paths": [("default_structure", "standard_inchi")]}, + { + "code": "inchikey", + "paths": [("default_structure", "standard_inchi_key")], + }, + ] + + # generate top level methods defining allowed conversions + conversions = [ + ("compound_name", "chebiid", "from_name"), + ("compound_name", "iupac_name", "from_name"), + ("compound_name", "inchikey", "from_name"), + ("compound_name", "inchi", "from_name"), + ("compound_name", "smiles", "from_name"), + ("compound_name", "formula", "from_name"), + ("iupac_name", "chebiid", "from_iupac_name"), + ("iupac_name", "compound_name", "from_iupac_name"), + ("iupac_name", "inchikey", "from_iupac_name"), + ("iupac_name", "inchi", "from_iupac_name"), + ("iupac_name", "smiles", "from_iupac_name"), + ("iupac_name", "formula", "from_iupac_name"), + ("inchikey", "chebiid", "from_inchikey"), + ("inchikey", "compound_name", "from_inchikey"), + ("inchikey", "iupac_name", "from_inchikey"), + ("inchikey", "inchi", "from_inchikey"), + ("inchikey", "smiles", "from_inchikey"), + ("inchikey", "formula", "from_inchikey"), + ("inchi", "chebiid", "from_inchi"), + ("inchi", "compound_name", "from_inchi"), + ("inchi", "iupac_name", "from_inchi"), + ("inchi", "inchikey", "from_inchi"), + ("inchi", "smiles", "from_inchi"), + ("inchi", "formula", "from_inchi"), + ("smiles", "chebiid", "from_smiles"), + ("smiles", "compound_name", "from_smiles"), + ("smiles", "iupac_name", "from_smiles"), + ("smiles", "inchikey", "from_smiles"), + ("smiles", "inchi", "from_smiles"), + ("smiles", "formula", "from_smiles"), + ("chebiid", "compound_name", "from_chebiid"), + ("chebiid", "iupac_name", "from_chebiid"), + ("chebiid", "inchikey", "from_chebiid"), + ("chebiid", "inchi", "from_chebiid"), + ("chebiid", "smiles", "from_chebiid"), + ("chebiid", "formula", "from_chebiid"), + ] + self.create_top_level_conversion_methods(conversions) + + async def from_name(self, name): + """ + Convert compound name to all possible attributes using ChEBI service. + + Only compounds reported under the given name by ChEBI are accepted, common names + present in ChEBI merely as synonyms are not resolved by the search endpoint. + + :param name: given compound name + :return: all found data + """ + return await self._from_es_search(name) + + async def from_iupac_name(self, iupac_name): + """ + Convert IUPAC name to all possible attributes using ChEBI service. + + :param iupac_name: given IUPAC name + :return: all found data + """ + return await self._from_es_search(iupac_name, by_term=False) + + async def from_inchikey(self, inchikey): + """ + Convert InChIKey to all possible attributes using ChEBI service. + + :param inchikey: given InChIKey + :return: all found data + """ + return await self._from_es_search(inchikey) + + async def from_inchi(self, inchi): + """ + Convert InChI to all possible attributes using ChEBI service. + + Only standard InChIs are accepted by the ChEBI search endpoint. + + :param inchi: given InChI string + :return: all found data + """ + return await self._from_es_search(inchi) + + async def _from_es_search(self, term, by_term=True): + """ + Search ChEBI for the given term and return the attributes of the matching compound. + + :param term: search term (name, IUPAC name, InChIKey or InChI) + :param by_term: whether the reported fields of a result are compared to the searched + term; IUPAC names are not reported by the search endpoint, so searches by IUPAC + name accept a single unambiguous result instead + :return: all found data + """ + args = f"es_search/?term={quote(term)}&page=1&size={self.SEARCH_SIZE}" + response = await self.query_the_service("ChEBI", args) + if not response: + return None + chebiid = self.extract_chebiid(response, term if by_term else None) + if chebiid is None: + return None + return await self.from_chebiid(chebiid) + + async def from_smiles(self, smiles): + """ + Convert SMILES to all possible attributes using ChEBI structure search service. + + ChEBI scores the submitted structure without re-canonicalising it, so the similarity + threshold of 1 accepts structures that ChEBI reports in the submitted form. + + :param smiles: given SMILES string + :return: all found data + """ + data = frozendict({"structure": smiles, "type": "similarity", "similarity": 1}) + response = await self.query_the_service( + "ChEBI", "structure_search/", method="POST", data=data + ) + if not response: + return None + chebiid = self.extract_chebiid(response) + if chebiid is None: + return None + return await self.from_chebiid(chebiid) + + async def from_chebiid(self, chebiid): + """ + Convert ChEBI ID to all possible attributes using ChEBI service. + + :param chebiid: given ChEBI ID (e.g. 'CHEBI:60888') + :return: all found data + """ + args = f"compound/{chebiid}/" + response = await self.query_the_service("ChEBI", args) + if response: + return self.parse_entity(response) + + def parse_entity(self, response): + """ + Parse attributes from a single ChEBI compound response. + + :param response: JSON string from /compound/{chebiId}/ endpoint + :return: dict of parsed attributes + """ + return self._extract_attributes(json.loads(response)) + + def extract_chebiid(self, response, term=None): + """ + Obtain the ChEBI accession of the search result corresponding to the searched term. + + ChEBI searches are ranked by relevance and report related compounds first (searching + for 'bapta' ranks '5,5'-dibromo-BAPTA above 'BAPTA'), so a result is accepted only + when it can be positively identified - either its reported accession, identifier or + name equals the searched term, or, when no term is given, the search returned a + single compound. + + :param response: JSON string from a ChEBI search endpoint + :param term: term that was used for the search, None to require a single result + :return: ChEBI accession of the matching compound or None + """ + entities = [ + result.get("_source", result) + for result in json.loads(response).get("results", []) + if isinstance(result, dict) + ] + entities = [entity for entity in entities if isinstance(entity, dict)] + if not entities: + return None + if term is None: + # structure searches are not ranked by a term, a single hit is required + return entities[0].get("chebi_accession") if len(entities) == 1 else None + searched = term.strip().casefold() + for field in self.IDENTIFIER_FIELDS + self.NAME_FIELDS: + for entity in entities: + value = entity.get(field) + if isinstance(value, str) and value.strip().casefold() == searched: + return entity.get("chebi_accession") + return None + + def _extract_attributes(self, entity): + """ + Extract known attributes from a ChEBI compound dict. + + :param entity: dict representing a ChEBI compound + :return: dict of parsed attributes + """ + if not isinstance(entity, dict): + return None + result = {} + for att in self.attributes: + value = self._get_first_value(entity, att["paths"]) + if value is not None: + result[att["code"]] = value + iupac_name = self._extract_iupac_name(entity) + if iupac_name is not None: + result["iupac_name"] = iupac_name + return result if result else None + + @staticmethod + def _extract_iupac_name(entity): + """ + Extract the IUPAC name from the names of a ChEBI compound. + + :param entity: dict representing a ChEBI compound + :return: IUPAC name string or None + """ + names = entity.get("names") + if not isinstance(names, dict): + return None + for entry in names.get("IUPAC NAME", []): + if isinstance(entry, dict): + value = entry.get("ascii_name") or entry.get("name") + if value: + return value + return None + + def _get_first_value(self, entity, paths): + """ + Return the first non-empty value found in the given candidate paths. + Paths that yield no value are skipped and the following ones are tried. + + :param entity: dict representing a ChEBI compound + :param paths: candidate key paths to try + :return: first non-empty value or None + """ + for path in paths: + value = entity + for key in path: + if not isinstance(value, dict): + value = None + break + value = value.get(key) + if value: + return value + return None diff --git a/MSMetaEnhancer/libs/converters/web/Wikidata.py b/MSMetaEnhancer/libs/converters/web/Wikidata.py index 6d6a34b..b7e0f8d 100644 --- a/MSMetaEnhancer/libs/converters/web/Wikidata.py +++ b/MSMetaEnhancer/libs/converters/web/Wikidata.py @@ -4,6 +4,7 @@ from frozendict import frozendict from MSMetaEnhancer.libs.converters.web.WebConverter import WebConverter +from MSMetaEnhancer.libs.utils.Generic import fix_cas_number, USER_AGENT class Wikidata(WebConverter): @@ -91,6 +92,9 @@ async def from_name(self, name): return await self.call_service(query) async def from_casno(self, casno): + # Wikidata stores CAS numbers (P231) in the hyphenated form only, so an + # exact match on an unhyphenated input such as '50782' returns nothing. + casno = fix_cas_number(casno) query = f""" PREFIX rdfs: PREFIX wdt: @@ -150,13 +154,7 @@ async def call_service(self, query): response = await self.query_the_service( "Wikidata", args, - headers=frozendict( - { - "User-Agent": ( - "MSMetaEnhancer (https://github.com/RECETOX/MSMetaEnhancer)" - ) - } - ), + headers=frozendict({"User-Agent": USER_AGENT}), ) if response: return self.parse_attributes(response) diff --git a/MSMetaEnhancer/libs/converters/web/__init__.py b/MSMetaEnhancer/libs/converters/web/__init__.py index 8b86930..d4d87d1 100644 --- a/MSMetaEnhancer/libs/converters/web/__init__.py +++ b/MSMetaEnhancer/libs/converters/web/__init__.py @@ -3,6 +3,7 @@ from MSMetaEnhancer.libs.converters.web.CIR import CIR from MSMetaEnhancer.libs.converters.web.PubChem import PubChem from MSMetaEnhancer.libs.converters.web.BridgeDb import BridgeDb +from MSMetaEnhancer.libs.converters.web.ChEBI import ChEBI from MSMetaEnhancer.libs.converters.web.Wikidata import Wikidata -__all__ = ["IDSM", "CTS", "CIR", "PubChem", "BridgeDb", "Wikidata"] +__all__ = ["IDSM", "CTS", "CIR", "PubChem", "BridgeDb", "Wikidata", "ChEBI"] diff --git a/MSMetaEnhancer/libs/utils/Generic.py b/MSMetaEnhancer/libs/utils/Generic.py index 0b177bf..e7da3c9 100644 --- a/MSMetaEnhancer/libs/utils/Generic.py +++ b/MSMetaEnhancer/libs/utils/Generic.py @@ -2,7 +2,7 @@ NA_STRING_VALUES = {"na", "n/a", "nan", "none", ""} - +USER_AGENT = "MSMetaEnhancer (https://github.com/RECETOX/MSMetaEnhancer)" def is_na_value(value) -> bool: """Check if a value should be treated as NA/missing (e.g. empty, None, NaN, 'NA').""" @@ -15,6 +15,29 @@ def is_na_value(value) -> bool: return False +CAS_MIN_DIGITS = 5 +CAS_MAX_DIGITS = 10 + + +def fix_cas_number(cas_number): + """ + Add dashes to an unhyphenated CAS number. + + '50782' becomes '50-78-2'. Anything that cannot be a CAS number is returned + unchanged: values that are not strings, that already contain dashes, or that + are not made up of the 5-10 digits a CAS RN contains (2-7 digits, 2 digits, + 1 check digit). + + :param cas_number: given CAS number + :return: CAS number enriched by dashes (if needed) + """ + if isinstance(cas_number, str): + digits = cas_number.strip() + if digits.isdigit() and CAS_MIN_DIGITS <= len(digits) <= CAS_MAX_DIGITS: + return f"{digits[:-3]}-{digits[-3:-1]}-{digits[-1]}" + return cas_number + + def escape_single_quotes(f): async def wrapper(self, arg): return await f(self, arg.replace("'", "\\'")) diff --git a/MSMetaEnhancer/libs/utils/Monitor.py b/MSMetaEnhancer/libs/utils/Monitor.py index 7ec4fcd..9c3d1fa 100644 --- a/MSMetaEnhancer/libs/utils/Monitor.py +++ b/MSMetaEnhancer/libs/utils/Monitor.py @@ -2,7 +2,7 @@ from urllib.parse import urlparse import time import requests - +from MSMetaEnhancer.libs.utils.Generic import USER_AGENT class Monitor(Thread): """ @@ -32,13 +32,15 @@ def get_base_url(converter): @staticmethod def check_service(url): """ - Send a GET request to given URL with 5 sec timeout. + Send a GET request to given URL with 5 sec timeout and a User-Agent + identifying MSMetaEnhancer (some services, e.g. Wikidata, reject + requests with generic user agents). :param url: given URL :return: True if request is successful with status code 200 """ try: - result = requests.get(url, timeout=5) + result = requests.get(url, timeout=5, headers={"User-Agent": USER_AGENT}) return result.status_code == 200 except ( requests.exceptions.ConnectionError, diff --git a/README.md b/README.md index 3db0baa..4f6f0d4 100644 --- a/README.md +++ b/README.md @@ -7,7 +7,7 @@ [![DOI](https://joss.theoj.org/papers/10.21105/joss.04494/status.svg)](https://doi.org/10.21105/joss.04494) **MSMetaEnhancer** is a tool used for `.msp` files annotation. -It adds metadata like SMILES, InChI, and CAS number fetched from the following services: [CIR](https://cactus.nci.nih.gov/chemical/structure_documentation), [CTS](https://cts.fiehnlab.ucdavis.edu/), [PubChem](https://pubchem.ncbi.nlm.nih.gov/), [IDSM](https://idsm.elixir-czech.cz/), [BridgeDb](https://bridgedb.github.io/), and [Wikidata](https://www.wikidata.org/). +It adds metadata like SMILES, InChI, and CAS number fetched from the following services: [CIR](https://cactus.nci.nih.gov/chemical/structure_documentation), [CTS](https://cts.fiehnlab.ucdavis.edu/), [PubChem](https://pubchem.ncbi.nlm.nih.gov/), [IDSM](https://idsm.elixir-czech.cz/), [BridgeDb](https://bridgedb.github.io/), [Wikidata](https://www.wikidata.org/), and [ChEBI](https://www.ebi.ac.uk/chebi/). The app uses asynchronous implementation of annotation process allowing for optimal fetching speed. If you use MSMetaEnhancer in your work, please cite the following publication: @@ -27,11 +27,12 @@ from MSMetaEnhancer.libs.converters.web import ( PubChem, BridgeDb, Wikidata, + ChEBI, ) from MSMetaEnhancer.libs.converters.compute import RDKit from MSMetaEnhancer.libs.utils.ConverterBuilder import ConverterBuilder -ConverterBuilder.register([CTS, CIR, IDSM, PubChem, BridgeDb, Wikidata, RDKit]) +ConverterBuilder.register([CTS, CIR, IDSM, PubChem, BridgeDb, Wikidata, ChEBI, RDKit]) app = Application() @@ -42,7 +43,7 @@ app.load_data('sample.msp', file_format='msp') app.curate_metadata() # specify requested services (these are supported) -services = ['CTS', 'CIR', 'IDSM', 'PubChem', 'BridgeDb', 'Wikidata', 'RDKit'] +services = ['CTS', 'CIR', 'IDSM', 'PubChem', 'BridgeDb', 'Wikidata', 'ChEBI', 'RDKit'] # specify requested jobs jobs = [('name', 'inchi', 'IDSM'), ('inchi', 'formula', 'IDSM'), ('inchi', 'inchikey', 'IDSM'), @@ -59,23 +60,52 @@ app.save_data('sample_out.msp', file_format='msp') Prerequisites: -- Python 3.9+ -- Anaconda +- Python 3.10 - 3.13 Install `MSMetaEnhancer` from Bioconda with: ``` # install MSMetaEnhancer in a new virtual environment to avoid dependency clashes -conda create --name MSMetaEnhancer python=3.9 +conda create --name MSMetaEnhancer python=3.12 conda activate MSMetaEnhancer conda install --channel bioconda --channel conda-forge MSMetaEnhancer ``` +Alternatively, install it from PyPI into any environment of your choice: + +``` +pip install msmetaenhancer +``` + ### Developer Documentation #### Setup -Create your development environment using the provided [script](conda/environment-dev.yml) via conda to install all required dependencies. +Development dependencies, the virtual environment and the package itself are all managed +by [uv](https://docs.astral.sh/uv/). Install uv once (e.g. `pip install uv`, or +`conda install --channel conda-forge uv`), clone the repository and run: + +``` +uv sync +``` + +This creates `.venv` in the repository root, installs the locked dependencies together with +the `dev` group, and installs `MSMetaEnhancer` in editable mode. A conda environment can +still be created from the provided [script](conda/environment-dev.yml) if you prefer conda; +it provides `uv` and Python, and `uv sync` then fills in the rest. + +Run everything through `uv run` so that it uses this environment: + +``` +uv run pytest # tests +uv run ruff check . # lint +uv run pre-commit install # git hooks +uv run --group docs sphinx-build -b html docs/source docs/build/html # documentation +``` + +Dependencies are pinned in the committed `uv.lock`. After changing the dependencies in +`pyproject.toml`, refresh the lock with `uv lock` and reinstall with `uv sync` — CI installs +with `uv sync --frozen` and therefore fails if the two are out of sync. #### Contributing @@ -86,3 +116,4 @@ For more information see [here](CONTRIBUTING.md). #### Testing All functionality is tested with the [pytest](https://docs.pytest.org/en/6.2.x/contents.html) framework. +Run the test suite with `uv run pytest`. diff --git a/conda/environment-dev.yml b/conda/environment-dev.yml index bf6e2a3..6bd8b9c 100644 --- a/conda/environment-dev.yml +++ b/conda/environment-dev.yml @@ -3,6 +3,4 @@ channels: - conda-forge dependencies: - python=3.12 - - pip - - pip: - - poetry \ No newline at end of file + - uv \ No newline at end of file diff --git a/docs/source/MSMetaEnhancer.libs.webConverters.rst b/docs/source/MSMetaEnhancer.libs.webConverters.rst index 26ee3d5..2deca68 100644 --- a/docs/source/MSMetaEnhancer.libs.webConverters.rst +++ b/docs/source/MSMetaEnhancer.libs.webConverters.rst @@ -49,6 +49,14 @@ Wikidata :undoc-members: :show-inheritance: +ChEBI +----- + +.. automodule:: MSMetaEnhancer.libs.converters.web.ChEBI + :members: + :undoc-members: + :show-inheritance: + General Web Converter --------------------- diff --git a/docs/source/conf.py b/docs/source/conf.py index e841ca8..f55d36a 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -10,16 +10,21 @@ # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. # -import os import sys +from pathlib import Path +from shutil import copyfile -sys.path.insert(0, os.path.abspath("../../")) +# Anchor every path to this file rather than to the working directory, so that +# the documentation builds from any invocation directory (repository root, docs/, +# or the directory Sphinx was started in by a hosting service). +docs_dir = Path(__file__).resolve().parent +repo_dir = docs_dir.parent.parent -from shutil import copyfile +sys.path.insert(0, str(repo_dir)) -copyfile("../../README.md", "readme.md") -copyfile("../../CHANGELOG.md", "CHANGELOG.md") -copyfile("../../CONTRIBUTING.md", "CONTRIBUTING.md") +copyfile(repo_dir / "README.md", docs_dir / "readme.md") +copyfile(repo_dir / "CHANGELOG.md", docs_dir / "CHANGELOG.md") +copyfile(repo_dir / "CONTRIBUTING.md", docs_dir / "CONTRIBUTING.md") # -- Project information ----------------------------------------------------- diff --git a/galaxy/generate_options.py b/galaxy/generate_options.py index 5474747..cea4410 100644 --- a/galaxy/generate_options.py +++ b/galaxy/generate_options.py @@ -11,6 +11,7 @@ PubChem, BridgeDb, Wikidata, + ChEBI, ) from MSMetaEnhancer.libs.converters.compute import RDKit from MSMetaEnhancer.libs.utils.ConverterBuilder import ConverterBuilder @@ -20,7 +21,7 @@ def generate_options(): - ConverterBuilder.register([CTS, CIR, IDSM, PubChem, BridgeDb, Wikidata, RDKit]) + ConverterBuilder.register([CTS, CIR, IDSM, PubChem, BridgeDb, Wikidata, ChEBI, RDKit]) jobs = [] converters = web_converters + compute_converters diff --git a/pyproject.toml b/pyproject.toml index aec973e..345f8bb 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,50 +1,57 @@ -[tool.poetry] +[project] name = "msmetaenhancer" version = "0.6.1" description = "Repository for tool that adds more annotations (e.g. SMILES, InChI, CAS number) to MSP files (Python version)." +readme = "README.md" +license = "MIT" +license-files = ["LICENSE"] +requires-python = ">=3.10,<3.14" authors = [ - "Helge Hecht ", - "Matej Trojak " + { name = "Helge Hecht", email = "helge.hecht@recetox.muni.cz" }, + { name = "Matej Trojak", email = "matej.trojak@recetox.muni.cz" }, ] -license = "MIT" -readme = "README.md" -packages = [ - { include = "MSMetaEnhancer" }, +dependencies = [ + "matchms>=0.30.0", + "pandas>=2.2.1,<3.0", + "scipy>=1.12.0,<2.0", + "requests>=2.31.0,<3.0", + "aiohttp>=3.9.3,<4.0", + "asyncstdlib>=3.12.0,<4.0", + "frozendict>=2.4.0,<3.0", + "twine>=5.0.0,<6.0", + "tabulate>=0.9.0,<0.10.0", + "rdkit>=2024.3.5,<2025.0.0", + "multidict>=6.0.5,<7.0", + "aiocircuitbreaker>=2.0.0,<3.0", + "openpyxl>=3.1.2,<4.0", ] -[tool.poetry.dependencies] -python = ">=3.10,<3.14" -matchms = ">=0.30.0" -pandas = "^2.2.1" -scipy = "^1.12.0" -requests = "^2.31.0" -aiohttp = "^3.9.3" -asyncstdlib = "^3.12.0" -frozendict = "^2.4.0" -twine = "^5.0.0" -tabulate = "^0.9.0" -rdkit = ">=2024.3.5,<2025.0.0" -multidict = "^6.0.5" -aiocircuitbreaker = "^2.0.0" -openpyxl = "^3.1.2" - -[tool.poetry.group.dev.dependencies] -mock = "^5.1.0" -pytest = "^8.0.2" -pytest-cov = "^4.1.0" -pytest-aiohttp = "^1.0.5" -pytest-dependency = "^0.6.0" -myst-parser = "^2.0.0" -ruff = "^0.11.13" -pre-commit = "^4.2.0" -flake8 = "^7.2.0" +[dependency-groups] +dev = [ + "mock>=5.1.0,<6.0", + "pytest>=8.0.2,<9.0", + "pytest-asyncio>=0.25", + "pytest-cov>=4.1.0,<5.0", + "pytest-aiohttp>=1.0.5,<2.0", + "pytest-dependency>=0.6.0,<0.7.0", + "ruff>=0.11.13,<0.12.0", + "pre-commit>=4.2.0,<5.0", + "flake8>=7.2.0,<8.0", +] +docs = [ + "sphinx>=7.2.6,<8.0", + "sphinx-rtd-theme>=2.0.0,<3.0", + "readthedocs-sphinx-ext>=2.2.5,<3.0", + "myst-parser>=2.0.0,<3.0", +] +[build-system] +requires = ["uv_build>=0.13.5,<0.14"] +build-backend = "uv_build" -[tool.poetry.group.docs.dependencies] -sphinx = "^7.2.6" -sphinx-rtd-theme = "^2.0.0" -readthedocs-sphinx-ext = "^2.2.5" +[tool.uv] +required-version = ">=0.13.5" -[build-system] -requires = ["poetry-core"] -build-backend = "poetry.core.masonry.api" +[tool.uv.build-backend] +module-name = "MSMetaEnhancer" +module-root = "" diff --git a/pytest.ini b/pytest.ini index 2f4c80e..ed84f89 100644 --- a/pytest.ini +++ b/pytest.ini @@ -1,2 +1,5 @@ [pytest] asyncio_mode = auto +addopts = -v -ra --showlocals +log_level = INFO +log_format = %(asctime)s %(levelname)s %(name)s: %(message)s \ No newline at end of file diff --git a/tests/test_ChEBI.py b/tests/test_ChEBI.py new file mode 100644 index 0000000..f02f75a --- /dev/null +++ b/tests/test_ChEBI.py @@ -0,0 +1,503 @@ +import asyncio +import json +import pytest + +from rdkit.Chem import MolFromInchi, MolFromSmiles, MolToInchi, MolToSmiles +from rdkit.Chem.inchi import InchiToInchiKey + +from MSMetaEnhancer.libs.converters.web import ChEBI +from MSMetaEnhancer.libs.utils.Errors import UnknownResponse +from tests.utils import wrap_with_session + + +CHEBI_ID = "CHEBI:60888" +INCHIKEY = "FTEDXVNDVHYDQW-UHFFFAOYSA-N" +INCHI = "InChI=1S/C22H24N2O10/c25-19(26)11-23(12-20(27)28)15-5-1-3-7-17(15)33-9-10-34-18-8-4-2-6-16(18)24(13-21(29)30)14-22(31)32/h1-8H,9-14H2,(H,25,26)(H,27,28)(H,29,30)(H,31,32)" +COMPOUND_NAME = "bapta" +CHEBI_NAME = "BAPTA" +IUPAC_NAME = ( + "2,2',2'',2'''-[ethane-1,2-diylbis(oxy-2,1-phenylenenitrilo)]tetraacetic acid" +) +SMILES = "O=C(O)CN(CC(=O)O)c1ccccc1OCCOc1ccccc1N(CC(=O)O)CC(=O)O" +FORMULA = "C22H24N2O10" + + +# Responses below were recorded from the ChEBI API on 2026-10-29 and shortened to the +# fields the converter reads, the reported keys and values were not altered. + +ENTITY_RESPONSE = json.dumps( + { + "id": 60888, + "chebi_accession": CHEBI_ID, + "name": CHEBI_NAME, + "stars": 3, + "ascii_name": CHEBI_NAME, + "names": { + "SYNONYM": [ + { + "name": "1,2-Bis(2-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid", + "status": "C", + "type": "SYNONYM", + "source": "ChemIDplus", + "ascii_name": "1,2-Bis(2-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid", + "adapted": False, + "language_code": "en", + } + ], + "IUPAC NAME": [ + { + "name": IUPAC_NAME, + "status": "C", + "type": "IUPAC NAME", + "source": "IUPAC", + "ascii_name": IUPAC_NAME, + "adapted": False, + "language_code": "en", + } + ], + }, + "chemical_data": { + "formula": FORMULA, + "charge": 0, + "mass": "476.438", + "monoisotopic_mass": "476.14309", + }, + "default_structure": { + "id": 2706518, + "smiles": SMILES, + "standard_inchi": INCHI, + "standard_inchi_key": INCHIKEY, + "wurcs": None, + "is_r_group": False, + }, + "secondary_ids": [], + } +) + +SEARCH_BAPTA_RESPONSE = json.dumps( + { + "results": [ + { + "_index": "chebi-prod-compounds-29102026", + "_type": "_doc", + "_id": "60890", + "_score": 67.00641, + "_source": { + "chebi_accession": "CHEBI:60890", + "name": "5,5'-dibromo-BAPTA", + "ascii_name": "5,5'-dibromo-BAPTA", + "stars": 3, + "default_structure": 2706528, + "charge": 0, + "formula": "C22H22Br2N2O10", + "inchikey": "KCTRRYZOCJDOTC-UHFFFAOYSA-N", + }, + }, + { + "_index": "chebi-prod-compounds-29102026", + "_type": "_doc", + "_id": "60889", + "_score": 65.14058, + "_source": { + "chebi_accession": "CHEBI:60889", + "name": "5,5'-dimethyl-BAPTA", + "ascii_name": "5,5'-dimethyl-BAPTA", + "stars": 3, + "default_structure": 2706524, + "charge": 0, + "formula": "C24H28N2O10", + "inchikey": "BOMWLYNXTGNSSE-UHFFFAOYSA-N", + }, + }, + { + "_index": "chebi-prod-compounds-29102026", + "_type": "_doc", + "_id": "60888", + "_score": 35.251152, + "_source": { + "chebi_accession": CHEBI_ID, + "name": CHEBI_NAME, + "ascii_name": CHEBI_NAME, + "stars": 3, + "default_structure": 2706518, + "charge": 0, + "formula": FORMULA, + "inchikey": INCHIKEY, + }, + }, + ], + "total": 3, + "number_pages": 1, + } +) + +SEARCH_INCHIKEY_RESPONSE = json.dumps( + { + "results": [ + { + "_index": "chebi-prod-compounds-29102026", + "_type": "_doc", + "_id": "60888", + "_score": 11.740927, + "_source": { + "chebi_accession": CHEBI_ID, + "name": CHEBI_NAME, + "ascii_name": CHEBI_NAME, + "stars": 3, + "default_structure": 2706518, + "charge": 0, + "formula": FORMULA, + "inchikey": INCHIKEY, + "inchi": INCHI, + "smiles": SMILES, + }, + } + ], + "total": 1, + "number_pages": 1, + } +) + +SEARCH_IUPAC_RESPONSE = json.dumps( + { + "results": [ + { + "_index": "chebi-prod-compounds-29102026", + "_type": "_doc", + "_id": "60888", + "_score": 117.740105, + "_source": { + "chebi_accession": CHEBI_ID, + "name": CHEBI_NAME, + "ascii_name": CHEBI_NAME, + "stars": 3, + "default_structure": 2706518, + "charge": 0, + "formula": FORMULA, + "inchikey": INCHIKEY, + "inchi": INCHI, + "smiles": SMILES, + }, + } + ], + "total": 1, + "number_pages": 1, + } +) + +STRUCTURE_SEARCH_RESPONSE = json.dumps( + { + "results": [ + { + "_index": "chebi-prod-compounds-29102026", + "_type": "_doc", + "_id": "60888", + "_score": 1.0, + "_source": { + "chebi_accession": CHEBI_ID, + "name": CHEBI_NAME, + "ascii_name": CHEBI_NAME, + "stars": 3, + "default_structure": 2706518, + "charge": 0, + "formula": FORMULA, + "inchikey": INCHIKEY, + "inchi": INCHI, + "smiles": SMILES, + }, + } + ], + "total": 1, + "number_pages": 1, + } +) + + +@pytest.mark.dependency() +def test_service_available(): + asyncio.run(wrap_with_session(ChEBI, "chebiid_to_inchikey", [CHEBI_ID])) + + +@pytest.mark.dependency(depends=["test_service_available"]) +def test_chebiid_to_inchikey(): + result = asyncio.run(wrap_with_session(ChEBI, "chebiid_to_inchikey", [CHEBI_ID])) + assert result is not None + assert result["inchikey"] == INCHIKEY + + +@pytest.mark.dependency(depends=["test_service_available"]) +def test_chebiid_to_inchi(): + result = asyncio.run(wrap_with_session(ChEBI, "chebiid_to_inchi", [CHEBI_ID])) + assert result is not None + assert result["inchi"] == INCHI + + +@pytest.mark.dependency(depends=["test_service_available"]) +def test_chebiid_to_smiles(): + result = asyncio.run(wrap_with_session(ChEBI, "chebiid_to_smiles", [CHEBI_ID])) + assert result is not None + assert result["smiles"] == SMILES + + +@pytest.mark.dependency(depends=["test_service_available"]) +def test_chebiid_to_formula(): + result = asyncio.run(wrap_with_session(ChEBI, "chebiid_to_formula", [CHEBI_ID])) + assert result is not None + assert result["formula"] == FORMULA + + +@pytest.mark.dependency(depends=["test_service_available"]) +def test_chebiid_to_compound_name(): + result = asyncio.run( + wrap_with_session(ChEBI, "chebiid_to_compound_name", [CHEBI_ID]) + ) + assert result is not None + assert result["compound_name"] == CHEBI_NAME + + +@pytest.mark.dependency(depends=["test_service_available"]) +def test_chebiid_to_iupac_name(): + result = asyncio.run(wrap_with_session(ChEBI, "chebiid_to_iupac_name", [CHEBI_ID])) + assert result is not None + assert result["iupac_name"] == IUPAC_NAME + + +@pytest.mark.dependency(depends=["test_service_available"]) +def test_compound_name_to_chebiid(): + result = asyncio.run( + wrap_with_session(ChEBI, "compound_name_to_chebiid", [COMPOUND_NAME]) + ) + assert result is not None + assert result["chebiid"] == CHEBI_ID + assert result["compound_name"] == CHEBI_NAME + + +@pytest.mark.dependency(depends=["test_service_available"]) +def test_compound_name_to_iupac_name(): + result = asyncio.run( + wrap_with_session(ChEBI, "compound_name_to_iupac_name", [COMPOUND_NAME]) + ) + assert result is not None + assert result["iupac_name"] == IUPAC_NAME + + +@pytest.mark.dependency(depends=["test_service_available"]) +def test_inchikey_to_chebiid(): + result = asyncio.run(wrap_with_session(ChEBI, "inchikey_to_chebiid", [INCHIKEY])) + assert result is not None + assert result["chebiid"] == CHEBI_ID + + +@pytest.mark.dependency(depends=["test_service_available"]) +def test_inchikey_to_iupac_name(): + result = asyncio.run(wrap_with_session(ChEBI, "inchikey_to_iupac_name", [INCHIKEY])) + assert result is not None + assert result["iupac_name"] == IUPAC_NAME + + +@pytest.mark.dependency(depends=["test_service_available"]) +def test_inchi_to_chebiid(): + result = asyncio.run(wrap_with_session(ChEBI, "inchi_to_chebiid", [INCHI])) + assert result is not None + assert result["chebiid"] == CHEBI_ID + + +@pytest.mark.dependency(depends=["test_service_available"]) +def test_iupac_name_to_chebiid(): + result = asyncio.run( + wrap_with_session(ChEBI, "iupac_name_to_chebiid", [IUPAC_NAME]) + ) + assert result is not None + assert result["chebiid"] == CHEBI_ID + + +@pytest.mark.dependency(depends=["test_service_available"]) +def test_smiles_to_chebiid(): + result = asyncio.run(wrap_with_session(ChEBI, "smiles_to_chebiid", [SMILES])) + assert result is not None + assert result["chebiid"] == CHEBI_ID + assert result["inchikey"] == INCHIKEY + + +@pytest.mark.dependency(depends=["test_service_available"]) +def test_unknown_compound_raises(): + with pytest.raises(UnknownResponse): + asyncio.run( + wrap_with_session( + ChEBI, "from_name", ["not-a-compound-name-msmetaenhancer"] + ) + ) + + +@pytest.mark.dependency(depends=["test_service_available"]) +def test_format_search_response(): + args = f"es_search/?term={INCHIKEY}&page=1&size=15" + response = asyncio.run( + wrap_with_session(ChEBI, "query_the_service", ["ChEBI", args]) + ) + + assert isinstance(response, str) + data = json.loads(response) + assert {"results", "total", "number_pages"} <= data.keys() + assert "_source" in data["results"][0] + + +@pytest.mark.dependency(depends=["test_service_available"]) +def test_format_structure_search_response(): + from frozendict import frozendict + + data = frozendict({"structure": SMILES, "type": "similarity", "similarity": 1}) + response = asyncio.run( + wrap_with_session( + ChEBI, "query_the_service", ["ChEBI", "structure_search/", "POST", data] + ) + ) + + assert isinstance(response, str) + data = json.loads(response) + assert {"results", "total", "number_pages"} <= data.keys() + assert data["results"][0]["_source"]["chebi_accession"] == CHEBI_ID + + +@pytest.mark.dependency(depends=["test_service_available"]) +def test_format_entity_response(): + args = f"compound/{CHEBI_ID}/" + response = asyncio.run( + wrap_with_session(ChEBI, "query_the_service", ["ChEBI", args]) + ) + + assert isinstance(response, str) + data = json.loads(response) + assert data["chebi_accession"] == CHEBI_ID + assert data["names"]["IUPAC NAME"][0]["name"] == IUPAC_NAME + + +def test_parse_entity(): + parsed = ChEBI(None).parse_entity(ENTITY_RESPONSE) + + assert parsed == { + "chebiid": CHEBI_ID, + "compound_name": CHEBI_NAME, + "iupac_name": IUPAC_NAME, + "formula": FORMULA, + "smiles": SMILES, + "inchi": INCHI, + "inchikey": INCHIKEY, + } + + +def test_parse_entity_without_structures(): + response = json.dumps( + { + "id": 26649, + "chebi_accession": "CHEBI:26649", + "name": "serine derivative", + "ascii_name": "serine derivative", + "stars": 3, + "names": { + "SYNONYM": [ + { + "name": "serine derivatives", + "status": "C", + "type": "SYNONYM", + "source": "ChEBI", + "ascii_name": "serine derivatives", + "adapted": False, + "language_code": "en", + } + ] + }, + "chemical_data": None, + "default_structure": None, + "secondary_ids": [], + } + ) + + parsed = ChEBI(None).parse_entity(response) + + assert parsed == { + "chebiid": "CHEBI:26649", + "compound_name": "serine derivative", + } + + +def test_extract_chebiid_prefers_matching_name(): + # ChEBI ranks '5,5'-dibromo-BAPTA highest for the term 'bapta' + assert ChEBI(None).extract_chebiid(SEARCH_BAPTA_RESPONSE, COMPOUND_NAME) == CHEBI_ID + + +def test_extract_chebiid_matching_identifier(): + assert ChEBI(None).extract_chebiid(SEARCH_INCHIKEY_RESPONSE, INCHIKEY) == CHEBI_ID + + +def test_extract_chebiid_matching_identifier_from_multiple_results(): + assert ChEBI(None).extract_chebiid(SEARCH_BAPTA_RESPONSE, INCHIKEY) == CHEBI_ID + + +def test_extract_chebiid_rejects_unmatched_multiple_results(): + # related compounds are reported for terms ChEBI does not know as names + assert ChEBI(None).extract_chebiid(SEARCH_BAPTA_RESPONSE, "bapta acid") is None + + +def test_extract_chebiid_rejects_other_identifier(): + assert ( + ChEBI(None).extract_chebiid( + SEARCH_INCHIKEY_RESPONSE, "UNSRVVFXOFNFJF-UHFFFAOYSA-N" + ) + is None + ) + + +def test_extract_chebiid_accepts_single_unmatched_result(): + # IUPAC names are not reported by the search endpoint, a single result identifies them + assert ChEBI(None).extract_chebiid(SEARCH_IUPAC_RESPONSE) == CHEBI_ID + + +def test_extract_chebiid_without_term_requires_single_result(): + assert ChEBI(None).extract_chebiid(SEARCH_BAPTA_RESPONSE) is None + + +def test_extract_chebiid_from_structure_search_response(): + assert ChEBI(None).extract_chebiid(STRUCTURE_SEARCH_RESPONSE) == CHEBI_ID + + +def test_extract_chebiid_without_results(): + assert ChEBI(None).extract_chebiid(json.dumps({"results": [], "total": 0})) is None + + +def test_get_first_value_skips_unusable_paths(): + converter = ChEBI(None) + entity = {"default_structure": 2706518, "name": CHEBI_NAME} + paths = [("default_structure", "smiles"), ("name",)] + + assert converter._get_first_value(entity, paths) == CHEBI_NAME + + +def test_get_first_value_missing_paths(): + converter = ChEBI(None) + + assert ( + converter._get_first_value({"name": None}, [("name",), ("ascii_name",)]) is None + ) + assert converter._get_first_value({}, [("default_structure", "smiles")]) is None + + +def test_reference_data_describes_single_compound(): + # the constants above are recorded from ChEBI and must describe one structure + mol = MolFromSmiles(SMILES) + assert MolToSmiles(mol) == MolToSmiles(MolFromInchi(INCHI)) + assert MolToInchi(MolFromSmiles(SMILES)) == INCHI + assert InchiToInchiKey(INCHI) == INCHIKEY + + +def test_get_conversions(): + jobs = ChEBI(None).get_conversion_functions() + assert ("chebiid", "inchikey", "ChEBI") in jobs + assert ("inchikey", "chebiid", "ChEBI") in jobs + assert ("compound_name", "chebiid", "ChEBI") in jobs + assert ("compound_name", "iupac_name", "ChEBI") in jobs + assert ("chebiid", "iupac_name", "ChEBI") in jobs + assert ("inchikey", "iupac_name", "ChEBI") in jobs + assert ("iupac_name", "chebiid", "ChEBI") in jobs + assert ("inchi", "chebiid", "ChEBI") in jobs + assert ("smiles", "chebiid", "ChEBI") in jobs diff --git a/tests/test_Monitor.py b/tests/test_Monitor.py new file mode 100644 index 0000000..4952d9b --- /dev/null +++ b/tests/test_Monitor.py @@ -0,0 +1,71 @@ +import mock +import pytest +import requests + +from MSMetaEnhancer.libs.converters.web import ( + BridgeDb, + ChEBI, + CIR, + CTS, + IDSM, + PubChem, + Wikidata, +) +from MSMetaEnhancer.libs.utils.Generic import USER_AGENT +from MSMetaEnhancer.libs.utils.Monitor import Monitor + + +@pytest.mark.parametrize( + "status_code, expected", + [ + (200, True), + (301, False), + (403, False), + (500, False), + ], +) +def test_check_service_interprets_status_codes(status_code, expected): + with mock.patch("MSMetaEnhancer.libs.utils.Monitor.requests.get") as get: + get.return_value = mock.Mock(status_code=status_code) + + assert Monitor.check_service("https://example.org") is expected + + get.assert_called_once_with( + "https://example.org", timeout=5, headers={"User-Agent": USER_AGENT} + ) + + +@pytest.mark.parametrize( + "exception", + [ + requests.exceptions.ConnectionError, + requests.exceptions.ReadTimeout, + TimeoutError, + ], +) +def test_check_service_handles_request_failures(exception): + with mock.patch("MSMetaEnhancer.libs.utils.Monitor.requests.get") as get: + get.side_effect = exception + + assert Monitor.check_service("https://example.org") is False + + +def test_get_base_url(): + assert Monitor.get_base_url(Wikidata(None)) == "https://query.wikidata.org" + +@pytest.mark.parametrize( + "converter_class", + [BridgeDb, CIR, CTS, ChEBI, IDSM, PubChem, Wikidata], +) +def test_run(converter_class): + converter = converter_class(None) + monitor = Monitor() + monitor.set_converters({converter_class.__name__: converter}) + + try: + monitor.start() + assert monitor.first_check.wait(timeout=10) + assert converter.is_available is True + finally: + monitor.join() + assert monitor.stop_request.is_set() \ No newline at end of file diff --git a/tests/test_Wikidata.py b/tests/test_Wikidata.py index fad080b..3d5cc28 100644 --- a/tests/test_Wikidata.py +++ b/tests/test_Wikidata.py @@ -6,7 +6,7 @@ import pytest from MSMetaEnhancer.libs.converters.web import Wikidata -from MSMetaEnhancer.libs.utils.Errors import UnknownResponse +from MSMetaEnhancer.libs.utils.Monitor import Monitor from tests.utils import wrap_with_session @@ -125,6 +125,44 @@ def test_from_casno_queries_cas_property(): assert result == {"compound_name": "Aspirin", "casno": "50-78-2"} +def test_from_casno_queries_hyphenated_form_of_unhyphenated_input(): + converter = Wikidata(None) + converter.query_the_service = mock.AsyncMock( + return_value=json.dumps( + { + "results": { + "bindings": [ + { + "compound_name": {"value": "aspirin"}, + "casno": {"value": "50-78-2"}, + } + ] + } + } + ) + ) + + result = asyncio.run(converter.from_casno("50782")) + + _, args = converter.query_the_service.call_args.args[:2] + query = parse_qs(args)["query"][0] + assert 'FILTER(?casno = "50-78-2")' in query + assert result == {"compound_name": "aspirin", "casno": "50-78-2"} + + +def test_from_casno_keeps_unparsable_input_unchanged(): + converter = Wikidata(None) + converter.query_the_service = mock.AsyncMock( + return_value='{"results": {"bindings": []}}' + ) + + asyncio.run(converter.from_casno("not-a-cas-number")) + + _, args = converter.query_the_service.call_args.args[:2] + query = parse_qs(args)["query"][0] + assert 'FILTER(?casno = "not-a-cas-number")' in query + + @pytest.mark.parametrize( "method, identifier, query_fragment", [ @@ -188,6 +226,11 @@ def test_from_wikidataid_rejects_invalid_ids(): @pytest.mark.dependency() +def test_service_available(): + assert Monitor.check_service(Monitor.get_base_url(Wikidata(None))) + + +@pytest.mark.dependency(depends=["test_service_available"]) def test_aspirin_name_lookup_live(): result = asyncio.run(wrap_with_session(Wikidata, "from_name", ["aspirin"])) @@ -204,7 +247,6 @@ def test_aspirin_cas_lookup_live(): @pytest.mark.dependency(depends=["test_aspirin_name_lookup_live"]) -@pytest.mark.xfail(raises=UnknownResponse) @pytest.mark.parametrize( "method, identifier", [ @@ -222,3 +264,17 @@ def test_aspirin_identifier_lookup_live(method, identifier): assert result["casno"] == "50-78-2" assert result["canonical_smiles"] == "CC(=O)OC1=CC=CC=C1C(=O)O" + assert result["wikidataid"] == "Q18216" + + +@pytest.mark.dependency(depends=["test_aspirin_name_lookup_live"]) +def test_aspirin_unhyphenated_cas_lookup_live(): + """ + Wikidata stores CAS numbers hyphenated only, so the unhyphenated form has to + be normalised before querying - without it this lookup returns no item. + """ + result = asyncio.run(wrap_with_session(Wikidata, "from_casno", ["50782"])) + + assert result["wikidataid"] == "Q18216" + assert result["casno"] == "50-78-2" + assert result["compound_name"].casefold() == "aspirin" diff --git a/tests/test_curator.py b/tests/test_curator.py index 311f80f..ca7d450 100644 --- a/tests/test_curator.py +++ b/tests/test_curator.py @@ -11,6 +11,25 @@ def test_fix_cas_number(): assert curator.fix_cas_number("7783-89-3") == "7783-89-3" +@pytest.mark.parametrize( + "cas_number, expected", + [ + ("50782", "50-78-2"), + ("7647145", "7647-14-5"), + (" 50782 ", "50-78-2"), + ("7783-89-3", "7783-89-3"), + ("not-a-cas-number", "not-a-cas-number"), + ("5078 2", "5078 2"), + ("123", "123"), + ("", ""), + (50782, 50782), + (None, None), + ], +) +def test_fix_cas_number_leaves_non_cas_input_untouched(cas_number, expected): + assert Curator().fix_cas_number(cas_number) == expected + + @pytest.mark.parametrize( "metadata, validated_metadata, logs_size", [ diff --git a/tests/test_data/sample.json b/tests/test_data/sample.json index a8ac8c4..d0cba82 100644 --- a/tests/test_data/sample.json +++ b/tests/test_data/sample.json @@ -1 +1 @@ -[{"formula": "H2", "mw": "2", "casno": "1333740", "id": "1", "num_peaks": "2", "compound_name": "Hydrogen", "peaks_json": [[1.0, 20.98], [2.0, 999.0]]}, {"formula": "D2", "mw": "4", "casno": "7782390", "id": "2", "num_peaks": "2", "compound_name": "Deuterium", "peaks_json": [[2.0, 14.99], [4.0, 999.0]]}, {"formula": "CH4", "mw": "16", "casno": "74828", "id": "3", "num_peaks": "6", "compound_name": "Methane", "peaks_json": [[12.0, 37.97], [13.0, 105.9], [14.0, 203.82], [15.0, 886.2], [16.0, 999.0], [17.0, 15.99]]}] \ No newline at end of file +[{"formula": "H2", "mw": "2", "casno": "1333740", "id": "1", "num_peaks": "2", "compound_name": "Dihydrogen", "peaks_json": [[1.0, 20.98], [2.0, 999.0]]}, {"formula": "D2", "mw": "4", "casno": "7782390", "id": "2", "num_peaks": "2", "compound_name": "Dideuterium", "peaks_json": [[2.0, 14.99], [4.0, 999.0]]}, {"formula": "CH4", "mw": "16", "casno": "74828", "id": "3", "num_peaks": "6", "compound_name": "Methane", "peaks_json": [[12.0, 37.97], [13.0, 105.9], [14.0, 203.82], [15.0, 886.2], [16.0, 999.0], [17.0, 15.99]]}] \ No newline at end of file diff --git a/tests/test_data/sample.mgf b/tests/test_data/sample.mgf index f93ecd8..05efef9 100644 --- a/tests/test_data/sample.mgf +++ b/tests/test_data/sample.mgf @@ -4,7 +4,7 @@ MW=2 CASNO=1333740 ID=1 NUM_PEAKS=2 -COMPOUND_NAME=Hydrogen +COMPOUND_NAME=Dihydrogen 1.0 20.98 2.0 999.0 END IONS @@ -15,7 +15,7 @@ MW=4 CASNO=7782390 ID=2 NUM_PEAKS=2 -COMPOUND_NAME=Deuterium +COMPOUND_NAME=Dideuterium 2.0 14.99 4.0 999.0 END IONS diff --git a/tests/test_data/sample.msp b/tests/test_data/sample.msp index d7cb67b..2215c3b 100644 --- a/tests/test_data/sample.msp +++ b/tests/test_data/sample.msp @@ -1,4 +1,4 @@ -NAME: Hydrogen +NAME: Dihydrogen FORMULA: H2 MW: 2 CASNO: 1333740 @@ -7,7 +7,7 @@ NUM PEAKS: 2 1.0 20.98 2.0 999.0 -NAME: Deuterium +NAME: Dideuterium FORMULA: D2 MW: 4 CASNO: 7782390 diff --git a/tests/test_data/sample_metadata.csv b/tests/test_data/sample_metadata.csv index 3c0718f..0e6bed9 100644 --- a/tests/test_data/sample_metadata.csv +++ b/tests/test_data/sample_metadata.csv @@ -1,4 +1,4 @@ formula,mw,casno,id,num_peaks,compound_name -H2,2,1333740,1,2,"Hydrogen" -D2,4,7782390,2,2,"Deuterium" +H2,2,1333740,1,2,"Dihydrogen" +D2,4,7782390,2,2,"Dideuterium" CH4,16,74828,3,6,"Methane" diff --git a/tests/test_data/sample_metadata.tsv b/tests/test_data/sample_metadata.tsv index 6d99052..5a1b0d8 100644 --- a/tests/test_data/sample_metadata.tsv +++ b/tests/test_data/sample_metadata.tsv @@ -1,4 +1,4 @@ formula mw casno id num_peaks compound_name -H2 2 1333740 1 2 "Hydrogen" -D2 4 7782390 2 2 "Deuterium" +H2 2 1333740 1 2 "Dihydrogen" +D2 4 7782390 2 2 "Dideuterium" CH4 16 74828 3 6 "Methane" diff --git a/tests/test_data/sample_metadata.xlsx b/tests/test_data/sample_metadata.xlsx index e14f3c1..10c57bf 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