Mercurial > repos > jpayne > bioproject2srr

comparison tests.py @ 0:79fa4330f2c9 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 27af5cba48986d508a67a5024a3bd35dd47bee15-dirty
author jpayne
date Mon, 08 Dec 2025 20:18:03 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:79fa4330f2c9
1 import pytest
2
3 from bio2srr import *
4
5
6 def test_element_tree_xpath():
7 from xml.etree import ElementTree as xml
8 root = xml.fromstring(biosample_example)
9 assert root.find(".//Id[@db='BioSample']") is not None
10
11 def test_flatten_biosample_xml():
12 d = flatten_biosample_xml(biosample_example)
13 assert d['biosample_accession'] == 'SAMN17131268'
14 assert d['organism'] == 'Campylobacter jejuni'
15 assert d['isolate'] == 'CFSAN091032'
16
17 def test_flatten_runs():
18 d = list(flatten_runs(runs_example))
19 assert len(d) == 2
20
21 def test_header_sort_override_consistency():
22 import random
23 L = ["C", "B", "A", "taxid", "bioproject"]
24 L.sort(key=hso)
25 # assert L[0] == "bioproject"
26 A = L.copy()
27 assert A == L
28 R = []
29 for _ in range(100):
30 random.shuffle(A)
31 A.sort(key=hso)
32 R.append(A == L)
33 assert all(R)
34
35 def test_hso_override():
36 assert header_sort_override("bioproject", "taxid") < 0
37 assert header_sort_override("taxid", "bioproject") > 0
38 assert header_sort_override("taxid", "taxid") == 0
39
40 def test_hso_regular():
41 assert header_sort_override("A", "B") < 0
42 assert header_sort_override("B", "A") > 0