bioproject_to_srr_2: tests.py annotate

planemo upload for repository https://toolrepo.galaxytrakr.org/view/jpayne/bioproject_to_srr_2/556cac4fb538

rev	line source
jpayne@4	1 import pytest
jpayne@4	2
jpayne@4	3 from bio2srr import *
jpayne@4	4
jpayne@4	5
jpayne@4	6 def test_element_tree_xpath():
jpayne@4	7 from xml.etree import ElementTree as xml
jpayne@4	8 root = xml.fromstring(biosample_example)
jpayne@4	9 assert root.find(".//Id[@db='BioSample']") is not None
jpayne@4	10
jpayne@4	11 def test_flatten_biosample_xml():
jpayne@4	12 d = flatten_biosample_xml(biosample_example)
jpayne@4	13 assert d['biosample_accession'] == 'SAMN17131268'
jpayne@4	14 assert d['organism'] == 'Campylobacter jejuni'
jpayne@4	15 assert d['isolate'] == 'CFSAN091032'
jpayne@4	16
jpayne@4	17 def test_flatten_runs():
jpayne@4	18 d = list(flatten_runs(runs_example))
jpayne@4	19 assert len(d) == 2
jpayne@4	20
jpayne@4	21 def test_header_sort_override_consistency():
jpayne@4	22 import random
jpayne@4	23 L = ["C", "B", "A", "taxid", "bioproject"]
jpayne@4	24 L.sort(key=hso)
jpayne@4	25 # assert L[0] == "bioproject"
jpayne@4	26 A = L.copy()
jpayne@4	27 assert A == L
jpayne@4	28 R = []
jpayne@4	29 for _ in range(100):
jpayne@4	30 random.shuffle(A)
jpayne@4	31 A.sort(key=hso)
jpayne@4	32 R.append(A == L)
jpayne@4	33 assert all(R)
jpayne@4	34
jpayne@4	35 def test_hso_override():
jpayne@4	36 assert header_sort_override("bioproject", "taxid") < 0
jpayne@4	37 assert header_sort_override("taxid", "bioproject") > 0
jpayne@4	38 assert header_sort_override("taxid", "taxid") == 0
jpayne@4	39
jpayne@4	40 def test_hso_regular():
jpayne@4	41 assert header_sort_override("A", "B") < 0
jpayne@4	42 assert header_sort_override("B", "A") > 0

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