jpayne@4: import pytest
jpayne@4: 
jpayne@4: from bio2srr import *
jpayne@4: 
jpayne@4: 
jpayne@4: def test_element_tree_xpath():
jpayne@4:     from xml.etree import ElementTree as xml
jpayne@4:     root = xml.fromstring(biosample_example)
jpayne@4:     assert root.find(".//Id[@db='BioSample']") is not None
jpayne@4: 
jpayne@4: def test_flatten_biosample_xml():
jpayne@4:     d = flatten_biosample_xml(biosample_example)
jpayne@4:     assert d['biosample_accession'] == 'SAMN17131268'
jpayne@4:     assert d['organism'] == 'Campylobacter jejuni'
jpayne@4:     assert d['isolate'] == 'CFSAN091032'
jpayne@4: 
jpayne@4: def test_flatten_runs():
jpayne@4:     d = list(flatten_runs(runs_example))
jpayne@4:     assert len(d) == 2
jpayne@4: 
jpayne@4: def test_header_sort_override_consistency():
jpayne@4:     import random
jpayne@4:     L = ["C", "B", "A", "taxid", "bioproject"]
jpayne@4:     L.sort(key=hso)
jpayne@4:     # assert L[0] == "bioproject"
jpayne@4:     A = L.copy()
jpayne@4:     assert A == L
jpayne@4:     R = []
jpayne@4:     for _ in range(100):
jpayne@4:         random.shuffle(A)
jpayne@4:         A.sort(key=hso)
jpayne@4:         R.append(A == L)
jpayne@4:     assert all(R)
jpayne@4: 
jpayne@4: def test_hso_override():
jpayne@4:     assert header_sort_override("bioproject", "taxid") < 0
jpayne@4:     assert header_sort_override("taxid", "bioproject") > 0
jpayne@4:     assert header_sort_override("taxid", "taxid") == 0
jpayne@4: 
jpayne@4: def test_hso_regular():
jpayne@4:     assert header_sort_override("A", "B") < 0
jpayne@4:     assert header_sort_override("B", "A") > 0