BioMCP

import json import shlex from pytest_bdd import given, parsers, scenarios, then from typer.testing import CliRunner from biomcp.cli.main import app scenarios("fetch.feature") runner = CliRunner() @given(parsers.parse('I run "{command}"'), target_fixture="cli_result") def cli_result(command): """Run the given CLI command and return the parsed JSON output.""" args = shlex.split(command)[1:] result = runner.invoke(app, args) return json.loads(result.stdout) @then("the JSON output should be a non-empty list") def check_non_empty_list(cli_result): """Check that the JSON output is a list with at least one article.""" assert isinstance(cli_result, list), "Expected JSON output to be a list" assert len(cli_result) > 0, "Expected at least one article in the output" @then("the first article's abstract should be populated") def check_abstract_populated(cli_result): """Check that the first article has a non-empty abstract.""" article = cli_result[0] abstract = article.get("abstract") assert abstract is not None, "Abstract field is missing" assert abstract.strip() != "", "Abstract field is empty" @then("the application should return an error") def step_impl(cli_result): assert cli_result == [ {"error": 'Error 400: {"detail":"Could not retrieve publications"}'} ] @then("the first article should have a DOI field") def check_doi_field(cli_result): """Check that the first article has a DOI field.""" article = cli_result[0] doi = article.get("doi") assert doi is not None, "DOI field is missing" assert doi.startswith("10."), f"Invalid DOI format: {doi}" @then("the source should be Europe PMC") def check_europe_pmc_source(cli_result): """Check that the article source is Europe PMC.""" article = cli_result[0] source = article.get("source") assert ( source == "Europe PMC" ), f"Expected source 'Europe PMC', got '{source}'"