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"""Test cases for procedures defined in llms """
# pylint: disable=C0301
import pytest
from gn3.llms.process import fetch_pubmed
from gn3.llms.process import parse_context
from gn3.llms.process import format_bibliography_info
@pytest.mark.unit_test
def test_parse_context():
"""test for parsing doc id context"""
def mock_get_info(doc_id):
return f"Info for {doc_id}"
def mock_format_bib(doc_info):
return f"Formatted Bibliography: {doc_info}"
parsed_result = parse_context({
"doc1": [{"text": "Summary 1"}, {"text": "Summary 2"}],
"doc2": [{"text": "Summary 3"}, {"text": "Summary 4"}],
}, mock_get_info, mock_format_bib)
expected_result = [
{
"doc_id": "doc1",
"bibInfo": "Formatted Bibliography: Info for doc1",
"comboTxt": "\tSummary 1\tSummary 2",
},
{
"doc_id": "doc2",
"bibInfo": "Formatted Bibliography: Info for doc2",
"comboTxt": "\tSummary 3\tSummary 4",
},
]
assert parsed_result == expected_result
@pytest.mark.unit_test
def test_format_bib_info():
"""Test for formatting bibliography info """
mock_fahamu_bib_info = [
{
"author": "J.m",
"firstName": "john",
"title": "Genes and aging",
"year": 2013,
"doi": "https://Articles.com/12231"
},
"2019-Roy-Evaluation of Sirtuin-3 probe quality and co-expressed genes",
"2015 - Differential regional and cellular distribution of TFF3 peptide in the human brain.txt"]
expected_result = [
"J.m.Genes and aging.2013.https://Articles.com/12231 ",
"2019-Roy-Evaluation of Sirtuin-3 probe quality and co-expressed genes",
"2015 - Differential regional and cellular distribution of TFF3 peptide in the human brain"
]
assert all((format_bibliography_info(data) == expected
for data, expected
in zip(mock_fahamu_bib_info, expected_result)))
@pytest.mark.unit_test
def test_fetching_pubmed_info(monkeypatch):
"""Test for fetching and populating pubmed data with pubmed info"""
def mock_load_file(_filename, _dir_path):
return {
"12121": {
"Abstract": "items1",
"Author": "A1"
}
}
# patch the module with the mocked function
monkeypatch.setattr("gn3.llms.process.load_file", mock_load_file)
expected_results = [
{
"title": "Genes",
"year": "2014",
"doi": "https/article/genes/12121",
"doc_id": "12121",
"pubmed": {
"Abstract": "items1",
"Author": "A1"
}
},
{
"title": "Aging",
"year": "2014",
"doc_id": "12122"
}
]
data = [{
"title": "Genes",
"year": "2014",
"doi": "https/article/genes/12121",
"doc_id": "12121",
},
{
"title": "Aging",
"year": "2014",
"doc_id": "12122"
}]
assert (fetch_pubmed(data, "/pubmed.json", "data/")
== expected_results)
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