empress/tests/python/test_cli.py at 9bc20575407d3f5f24378cb8e6cd269e0a7ba30f · biocore/empress · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
import os
import unittest

from click.testing import CliRunner
import pandas as pd

from empress.scripts._cli import empress
from .util import extract_q2_artifact_to_path


def files_present(output_dir):
    files = os.listdir(output_dir)
    assert "empress.html" in files
    assert os.path.isdir(f"{output_dir}/support_files")


class TestCLI(unittest.TestCase):

    @classmethod
    def setUpClass(cls):
        q2_tree_loc = os.path.abspath("docs/moving-pictures/rooted-tree.qza")
        q2_table_loc = os.path.abspath("docs/moving-pictures/table.qza")
        q2_fm_loc = os.path.abspath("docs/moving-pictures/taxonomy.qza")
        q2_pcoa_loc = os.path.abspath("docs/moving-pictures/biplot.qza")

        q2_sm_loc = os.path.abspath(
            "docs/moving-pictures/sample_metadata.tsv"
        )

        # create isolated filesystem for tests in this file
        # manually using __enter__ so that we can run all tests and close in
        # tearDown rather than use 'with runner.isolated_filesystem():'
        cls.runner = CliRunner()
        cls.iso_fs = cls.runner.isolated_filesystem()
        cls.iso_fs.__enter__()

        # extract Artifacts to temporary filesystem
        cls.tree_loc = extract_q2_artifact_to_path("tree", q2_tree_loc,
                                                   "tree.nwk")
        cls.table_loc = extract_q2_artifact_to_path("tbl", q2_table_loc,
                                                    "feature-table.biom")
        cls.fm_loc = extract_q2_artifact_to_path("fm", q2_fm_loc,
                                                 "taxonomy.tsv")
        cls.pcoa_loc = extract_q2_artifact_to_path("pcoa", q2_pcoa_loc,
                                                   "ordination.txt")
        # need to re-save sample metadata to remove q2:types row
        cls.sm_loc = "tmp_sample_metadata.tsv"
        pd.read_csv(q2_sm_loc, sep="\t", index_col=0, skiprows=[1]).to_csv(
            cls.sm_loc,
            sep="\t",
            index=True
        )

    @classmethod
    def tearDownClass(cls):
        # https://stackoverflow.com/questions/51706836/manually-open-context-manager
        cls.iso_fs.__exit__(None, None, None)

    def test_tree_plot_basic(cls):
        output_dir = "tree_plot_basic"
        result = cls.runner.invoke(
            empress,
            ["tree-plot", "--tree", cls.tree_loc, "--output-dir", output_dir]
        )
        assert result.exit_code == 0
        files_present(output_dir)

    def test_comm_plot_basic(cls):
        output_dir = "comm_plot_basic"
        result = cls.runner.invoke(
            empress,
            ["community-plot", "--tree", cls.tree_loc, "--table",
             cls.table_loc, "--sample-metadata", cls.sm_loc,
             "--output-dir", output_dir]
        )
        assert result.exit_code == 0
        files_present(output_dir)

    def test_comm_plot_pcoa(cls):
        output_dir = "comm_plot_pcoa"
        result = cls.runner.invoke(
            empress,
            ["community-plot", "--tree", cls.tree_loc, "--table",
             cls.table_loc, "--sample-metadata", cls.sm_loc,
             "--output-dir", output_dir, "--pcoa", cls.pcoa_loc,
             "--filter-extra-samples", "--feature-metadata", cls.fm_loc]
        )
        assert result.exit_code == 0
        files_present(output_dir)
        assert os.path.isdir(f"{output_dir}/emperor-resources")

    def test_existing_directory(cls):
        output_dir = "existing_dir"
        os.mkdir("existing_dir")
        result = cls.runner.invoke(
            empress,
            ["community-plot", "--tree", cls.tree_loc, "--table",
             cls.table_loc, "--sample-metadata", cls.sm_loc,
             "--output-dir", output_dir]
        )
        assert result.exit_code == 1
        error_class, value, _ = result.exc_info
        assert error_class == OSError
        assert str(value) == "Output directory already exists!"
        assert not os.path.isdir(f"{output_dir}/support_files")
        assert "empress.html" not in os.listdir(output_dir)

    def test_existing_directory_overwrite(cls):
        output_dir = "existing_dir_2"
        os.mkdir(output_dir)
        result = cls.runner.invoke(
            empress,
            ["community-plot", "--tree", cls.tree_loc, "--table",
             cls.table_loc, "--sample-metadata", cls.sm_loc,
             "--output-dir", output_dir, "--overwrite"]
        )
        assert result.exit_code == 0
        files_present(output_dir)

    def test_tree_plot_basic_cli_abbrev(cls):
        output_dir = "tree_plot_basic_cli_abbrev"
        result = cls.runner.invoke(
            empress,
            ["tree-plot", "-t", cls.tree_loc, "-o", output_dir]
        )
        assert result.exit_code == 0
        files_present(output_dir)