diff --git a/.github/workflows/remote-tests.yaml b/.github/workflows/remote-tests.yaml index 25e2a4d..84d8719 100644 --- a/.github/workflows/remote-tests.yaml +++ b/.github/workflows/remote-tests.yaml @@ -9,7 +9,7 @@ jobs: max-parallel: 4 fail-fast: false matrix: - python-version: ['3.10', '3.11', '3.12', '3.13'] + python-version: ['3.11', '3.12', '3.13'] steps: - name: Checkout diff --git a/.github/workflows/unit-tests.yaml b/.github/workflows/unit-tests.yaml index 245d773..eb10321 100644 --- a/.github/workflows/unit-tests.yaml +++ b/.github/workflows/unit-tests.yaml @@ -9,7 +9,7 @@ jobs: max-parallel: 4 fail-fast: false matrix: - python-version: ['3.10', '3.11', '3.12', '3.13'] + python-version: ['3.11', '3.12', '3.13'] steps: - name: Checkout diff --git a/pyenzyme/fetcher/chebi.py b/pyenzyme/fetcher/chebi.py index 6cd3752..6e62296 100644 --- a/pyenzyme/fetcher/chebi.py +++ b/pyenzyme/fetcher/chebi.py @@ -6,10 +6,10 @@ """ import re -from typing import Dict, List, Optional +from typing import List, Optional import httpx -from pydantic import BaseModel, ConfigDict, RootModel +from pydantic import BaseModel, ConfigDict, Field from pyenzyme.versions import v2 @@ -24,73 +24,61 @@ def __init__(self, message: str, cause: Optional[Exception] = None): self.cause = cause -class ChEBIStructure(BaseModel): - """Chemical structure information.""" - - model_config = ConfigDict(extra="ignore") - - smiles: Optional[str] = None - standard_inchi: Optional[str] = None - standard_inchi_key: Optional[str] = None - - -class ChEBIEntryData(BaseModel): - """Core data structure for a ChEBI entry.""" +class ChebiSearchSource(BaseModel): + """Source data structure from ChEBI search API result.""" model_config = ConfigDict(extra="ignore") + chebi_accession: str + name: Optional[str] = None ascii_name: str - default_structure: Optional[ChEBIStructure] = None - - -class ChEBIEntryResult(BaseModel): - """Individual ChEBI entry result.""" - - model_config = ConfigDict(extra="ignore") - - standardized_chebi_id: str - data: ChEBIEntryData - - -class ChEBIApiResponse(RootModel[Dict[str, ChEBIEntryResult]]): - """Top-level response structure from ChEBI API. Maps ChEBI IDs to their corresponding entry data.""" - - root: Dict[str, ChEBIEntryResult] + smiles: Optional[str] = None + inchi: Optional[str] = None + inchikey: Optional[str] = None + definition: Optional[str] = None + formula: Optional[str] = None + charge: Optional[int] = None + mass: Optional[float] = None + monoisotopicmass: Optional[float] = None + stars: Optional[int] = None + default_structure: Optional[int] = None + structures: Optional[List[int]] = None class ChebiSearchResult(BaseModel): """Individual search result structure.""" - model_config = ConfigDict(extra="ignore") + model_config = ConfigDict(extra="ignore", populate_by_name=True) - _source: Dict[str, str] # Contains chebi_accession field + source: ChebiSearchSource = Field(alias="_source") class ChebiSearchResponse(BaseModel): """Search response structure from ChEBI search API.""" results: List[ChebiSearchResult] + total: int + number_pages: int class ChEBIClient: """Client for accessing the ChEBI API to fetch chemical entity data.""" - BASE_URL = "https://www.ebi.ac.uk/chebi/backend/api/public/compounds/" SEARCH_URL = "https://www.ebi.ac.uk/chebi/backend/api/public/es_search/" def __init__(self): """Initialize the ChEBI client.""" pass - def get_entry_by_id(self, chebi_id: str) -> ChEBIEntryResult: + def get_entry_by_id(self, chebi_id: str) -> ChebiSearchSource: """ - Fetch a ChEBI entry by its ID. + Fetch a ChEBI entry by its ID using the search API. Args: chebi_id: The ChEBI ID to fetch, can be with or without the 'CHEBI:' prefix Returns: - ChEBIEntryResult object with the parsed response data + ChebiSearchSource object with the parsed response data Raises: ChEBIError: If the ChEBI ID is invalid or not found @@ -101,21 +89,18 @@ def get_entry_by_id(self, chebi_id: str) -> ChEBIEntryResult: try: with httpx.Client(timeout=DEFAULT_TIMEOUT) as client: - url = self.BASE_URL.format(chebi_id) - response = client.get(url) + params = {"term": chebi_id, "page": "1", "size": "1"} + response = client.get(self.SEARCH_URL, params=params) response.raise_for_status() if response.status_code == 200: try: - raw_response_data = response.json() + search_response = ChebiSearchResponse(**response.json()) - if not raw_response_data or len(raw_response_data) == 0: + if not search_response.results or len(search_response.results) == 0: raise ChEBIError(f"No data found for ChEBI ID {chebi_id}") - chebi_response = ChEBIApiResponse(raw_response_data) - - entry = list(chebi_response.root.values())[0] - return entry + return search_response.results[0].source except Exception as e: if isinstance(e, ChEBIError): @@ -127,15 +112,15 @@ def get_entry_by_id(self, chebi_id: str) -> ChEBIEntryResult: except httpx.HTTPStatusError as e: raise ChEBIError(f"Failed to fetch ChEBI ID {chebi_id}: {str(e)}", e) - def get_entries_batch(self, chebi_ids: List[str]) -> List[ChEBIEntryResult]: + def get_entries_batch(self, chebi_ids: List[str]) -> List[ChebiSearchSource]: """ - Fetch multiple ChEBI entries by their IDs. + Fetch multiple ChEBI entries by their IDs using the search API. Args: chebi_ids: List of ChEBI IDs to fetch Returns: - List of ChEBIEntryResult objects with data from ChEBI + List of ChebiSearchSource objects with data from ChEBI Raises: ChEBIError: If any ChEBI ID is invalid or not found @@ -144,74 +129,51 @@ def get_entries_batch(self, chebi_ids: List[str]) -> List[ChEBIEntryResult]: if not chebi_ids: return [] - formatted_ids = [] + results = [] for chebi_id in chebi_ids: - if not chebi_id.startswith("CHEBI:"): - formatted_ids.append(f"CHEBI:{chebi_id}") - else: - formatted_ids.append(chebi_id) - - try: - with httpx.Client(timeout=DEFAULT_TIMEOUT) as client: - url = self.BASE_URL.format(chebi_id) - response = client.get(url) - response.raise_for_status() - - if response.status_code == 200: - try: - raw_response_data = response.json() - chebi_response = ChEBIApiResponse(raw_response_data) - return list(chebi_response.root.values()) - - except Exception as e: - raise ChEBIError( - f"Failed to parse ChEBI batch response: {str(e)}", e - ) - else: - raise ChEBIError(f"HTTP {response.status_code}: {response.text}") + try: + entry = self.get_entry_by_id(chebi_id) + results.append(entry) + except ChEBIError as e: + # Continue with other IDs even if one fails + raise ChEBIError(f"Failed to fetch ChEBI ID {chebi_id}: {str(e)}", e) - except httpx.HTTPStatusError as e: - raise ChEBIError(f"Failed to fetch ChEBI batch: {str(e)}", e) + return results def search_entries( - self, query: str, size: Optional[int] = None - ) -> List[ChEBIEntryResult]: + self, query: str, size: Optional[int] = None, page: int = 1 + ) -> List[ChebiSearchSource]: """ Search for ChEBI entries by query string. Args: query: The search query string to find ChEBI entries size: The maximum number of search results to return + page: The page number to retrieve (default: 1) Returns: - List of ChEBIEntryResult objects for matching entries + List of ChebiSearchSource objects for matching entries Raises: ChEBIError: If the search request fails or the API is unavailable """ - params = {"term": query} + params = {"term": query, "page": str(page)} if size: params["size"] = str(size) try: with httpx.Client(timeout=DEFAULT_TIMEOUT) as client: - url = self.SEARCH_URL - response = client.get(url, params=params) + response = client.get(self.SEARCH_URL, params=params) response.raise_for_status() if response.status_code == 200: try: - search_results = ChebiSearchResponse(**response.json()) + search_response = ChebiSearchResponse(**response.json()) - if not search_results.results: + if not search_response.results: return [] - chebi_ids = [ - result._source["chebi_accession"] - for result in search_results.results - ] - - return self.get_entries_batch(chebi_ids) + return [result.source for result in search_response.results] except Exception as e: if isinstance(e, ChEBIError): @@ -226,44 +188,39 @@ def search_entries( raise ChEBIError(f"Failed to search ChEBI: {str(e)}", e) -def process_chebi_entry(entry: ChEBIEntryResult) -> v2.SmallMolecule: +def process_search_result(source: ChebiSearchSource) -> v2.SmallMolecule: """ - Process a ChEBI entry result and convert it to a SmallMolecule object. + Process a ChEBI search result source and convert it to a SmallMolecule object. Args: - entry: The ChEBI entry result from the API + source: The ChEBI search result source from the API Returns: A SmallMolecule object with mapped data """ - smallmol_id = process_id(entry.data.ascii_name) - - structure = entry.data.default_structure - canonical_smiles = structure.smiles if structure else None - inchi = structure.standard_inchi if structure else None - inchikey = structure.standard_inchi_key if structure else None + smallmol_id = process_id(source.ascii_name) small_molecule = v2.SmallMolecule( id=smallmol_id, - name=entry.data.ascii_name, - canonical_smiles=canonical_smiles, - inchi=inchi, - inchikey=inchikey, + name=source.ascii_name, + canonical_smiles=source.smiles, + inchi=source.inchi, + inchikey=source.inchikey, constant=False, vessel_id=None, synonymous_names=[], references=[ - f"https://www.ebi.ac.uk/chebi/searchId.do?chebiId={entry.standardized_chebi_id}" + f"https://www.ebi.ac.uk/chebi/searchId.do?chebiId={source.chebi_accession}" ], ) small_molecule.add_type_term( - term=f"OBO:{entry.standardized_chebi_id.replace(':', '_')}", + term=f"OBO:{source.chebi_accession.replace(':', '_')}", prefix="OBO", iri="http://purl.obolibrary.org/obo/", ) - small_molecule.ld_id = f"OBO:{entry.standardized_chebi_id.replace(':', '_')}" + small_molecule.ld_id = f"OBO:{source.chebi_accession.replace(':', '_')}" return small_molecule @@ -290,9 +247,9 @@ def fetch_chebi( """ try: client = ChEBIClient() - chebi_entry = client.get_entry_by_id(chebi_id) + chebi_source = client.get_entry_by_id(chebi_id) - small_molecule = process_chebi_entry(chebi_entry) + small_molecule = process_search_result(chebi_source) if smallmol_id is not None: small_molecule.id = smallmol_id @@ -325,9 +282,9 @@ def fetch_chebi_batch(chebi_ids: List[str]) -> List[v2.SmallMolecule]: return [] client = ChEBIClient() - chebi_entries = client.get_entries_batch(chebi_ids) + chebi_sources = client.get_entries_batch(chebi_ids) - return [process_chebi_entry(entry) for entry in chebi_entries] + return [process_search_result(source) for source in chebi_sources] def search_chebi(query: str, size: Optional[int] = None) -> List[v2.SmallMolecule]: @@ -355,9 +312,9 @@ def search_chebi(query: str, size: Optional[int] = None) -> List[v2.SmallMolecul atp_results = search_chebi('ATP', 5) """ client = ChEBIClient() - chebi_entries = client.search_entries(query, size) + chebi_sources = client.search_entries(query, size) - return [process_chebi_entry(entry) for entry in chebi_entries] + return [process_search_result(source) for source in chebi_sources] def process_id(name: str) -> str: diff --git a/pyenzyme/fetcher/pubchem.py b/pyenzyme/fetcher/pubchem.py index 77e36bc..d8be93e 100644 --- a/pyenzyme/fetcher/pubchem.py +++ b/pyenzyme/fetcher/pubchem.py @@ -98,9 +98,6 @@ def from_cid(cid: int) -> PubChemQuery: response = client.get(url) response.raise_for_status() - if response.status_code != 200: - raise ValueError(f"Failed to fetch PubChem data for CID {cid}") - return PubChemQuery(**response.json()) @staticmethod diff --git a/pyproject.toml b/pyproject.toml index 9692638..5de3231 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -3,7 +3,7 @@ name = "pyenzyme" version = "2.2.1" description = "A Python library for EnzymeML" authors = [{ name = "Jan Range", email = "range.jan@web.de" }] -requires-python = ">=3.10,<4" +requires-python = ">=3.11,<4" readme = "README.md" license = { text = "BSD-2-Clause" } dependencies = [ @@ -17,7 +17,7 @@ dependencies = [ "fastobo>=0.13.0,<0.14", "pymetadata>=0.5.3,<0.6", "httpx>=0.27", - "mdmodels>=0.2.1,<0.3", + "mdmodels>=0.2.4,<0.3", "joblib>=1.5.0,<2", "bokeh>=3.7.3,<4", "matplotlib>=3.10,<4", diff --git a/tests/integration/test_fetcher.py b/tests/integration/test_fetcher.py index 10c8b63..a34fed0 100644 --- a/tests/integration/test_fetcher.py +++ b/tests/integration/test_fetcher.py @@ -1,3 +1,4 @@ +import httpx import pytest from pyenzyme.fetcher.chebi import fetch_chebi @@ -155,7 +156,7 @@ def test_fetch_pubchem_to_small_molecule_with_prefix(self): @pytest.mark.remote def test_fetch_pubchem_to_small_molecule_invalid_id(self): - with pytest.raises(ValueError): + with pytest.raises(httpx.HTTPStatusError): fetch_pubchem(cid="162176127617627") @pytest.mark.remote diff --git a/tests/integration/test_legacy.py b/tests/integration/test_legacy.py deleted file mode 100644 index 987fded..0000000 --- a/tests/integration/test_legacy.py +++ /dev/null @@ -1,22 +0,0 @@ -from pyenzyme.v1 import EnzymeMLDocument - - -class TestLegacy: - """Test class for legacy functionality of EnzymeML v1.""" - - def test_legacy(self): - """Test that EnzymeML documents can be loaded from OMEX files and converted to XML. - - This test verifies backward compatibility by: - 1. Loading an EnzymeML document from an OMEX archive - 2. Converting it to XML string format - 3. Comparing the output with expected XML content - - The test ensures that the XML serialization process produces - consistent and expected output for legacy OMEX files. - """ - enzmldoc = EnzymeMLDocument.fromFile("tests/fixtures/sbml/v1_example.omex") - expected = open("tests/fixtures/sbml/v1_sbml.xml", "r", encoding="utf-8").read() - actual = enzmldoc.toXMLString() - - assert actual == expected diff --git a/uv.lock b/uv.lock index c7db0af..b7c8d0b 100644 --- a/uv.lock +++ b/uv.lock @@ -1,10 +1,9 @@ version = 1 revision = 2 -requires-python = ">=3.10, <4" +requires-python = ">=3.11, <4" resolution-markers = [ "python_full_version >= '3.12'", - "python_full_version == '3.11.*'", - "python_full_version < '3.11'", + "python_full_version < '3.12'", ] [[package]] @@ -21,7 +20,6 @@ name = "anyio" version = "4.12.1" source = { registry = "https://pypi.org/simple" } dependencies = [ - { name = "exceptiongroup", marker = "python_full_version < '3.11'" }, { name = "idna" }, { name = "typing-extensions", marker = "python_full_version < '3.13'" }, ] @@ -41,46 +39,25 @@ wheels = [ [[package]] name = "astropy" -version = "6.1.7" +version = "7.2.0" source = { registry = "https://pypi.org/simple" } dependencies = [ { name = "astropy-iers-data" }, - 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