Merge pull request #1183: Cram-ify "functional" pytests

tests/filter/test_relative_dates.py

@@ -0,0 +1,172 @@
+# This file contains functional tests that would normally be written as
+# Cram-style tests. However, pytest is nice here since it is easy to use with
+# parameterized inputs/outputs and mocked system time (things that are not
+# straightforward to set up for Cram tests¹).
+# ¹ https://github.com/nextstrain/augur/pull/1183#discussion_r1142687476
+
+import argparse
+from freezegun import freeze_time
+import pytest
+import shlex
+
+from augur.filter import register_arguments
+from augur.filter._run import run
+
+
+def parse_args(args):
+    parser = argparse.ArgumentParser()
+    register_arguments(parser)
+    return parser.parse_args(shlex.split(args))
+
+
+def write_metadata(tmpdir, metadata):
+    fn = str(tmpdir / "metadata.tsv")
+    with open(fn, "w") as fh:
+        fh.write("\n".join(("\t".join(md) for md in metadata)))
+    return fn
+
+
+@freeze_time("2020-03-25")
+@pytest.mark.parametrize(
+    "argparse_params, metadata_rows, output_sorted_expected",
+    [
+        (
+            "--min-date 1D",
+            (
+                ("SEQ_1","2020-03-23"),
+                ("SEQ_2","2020-03-24"),
+                ("SEQ_3","2020-03-25"),
+            ),
+            ["SEQ_2", "SEQ_3"],
+        ),
+        (
+            "--max-date 1D",
+            (
+                ("SEQ_1","2020-03-23"),
+                ("SEQ_2","2020-03-24"),
+                ("SEQ_3","2020-03-25"),
+            ),
+            ["SEQ_1", "SEQ_2"],
+        ),
+        (
+            "--min-date 4W",
+            (
+                ("SEQ_1","2020-02-25"),
+                ("SEQ_2","2020-02-26"),
+                ("SEQ_3","2020-03-25"),
+            ),
+            ["SEQ_2", "SEQ_3"],
+        ),
+        (
+            "--max-date 4W",
+            (
+                ("SEQ_1","2020-02-25"),
+                ("SEQ_2","2020-02-26"),
+                ("SEQ_3","2020-03-25"),
+            ),
+            ["SEQ_1", "SEQ_2"],
+        ),
+        (
+            "--min-date 1M",
+            (
+                ("SEQ_1","2020-01-25"),
+                ("SEQ_2","2020-02-25"),
+                ("SEQ_3","2020-03-25"),
+            ),
+            ["SEQ_2", "SEQ_3"],
+        ),
+        (
+            "--max-date 1M",
+            (
+                ("SEQ_1","2020-01-25"),
+                ("SEQ_2","2020-02-25"),
+                ("SEQ_3","2020-03-25"),
+            ),
+            ["SEQ_1", "SEQ_2"],
+        ),
+        (
+            "--min-date P1M",
+            (
+                ("SEQ_1","2020-01-25"),
+                ("SEQ_2","2020-02-25"),
+                ("SEQ_3","2020-03-25"),
+            ),
+            ["SEQ_2", "SEQ_3"],
+        ),
+        (
+            "--max-date P1M",
+            (
+                ("SEQ_1","2020-01-25"),
+                ("SEQ_2","2020-02-25"),
+                ("SEQ_3","2020-03-25"),
+            ),
+            ["SEQ_1", "SEQ_2"],
+        ),
+        (
+            "--min-date 2Y",
+            (
+                ("SEQ_1","2017-03-25"),
+                ("SEQ_2","2018-03-25"),
+                ("SEQ_3","2019-03-25"),
+            ),
+            ["SEQ_2", "SEQ_3"],
+        ),
+        (
+            "--max-date 2Y",
+            (
+                ("SEQ_1","2017-03-25"),
+                ("SEQ_2","2018-03-25"),
+                ("SEQ_3","2019-03-25"),
+            ),
+            ["SEQ_1", "SEQ_2"],
+        ),
+        (
+            "--min-date 1Y2W5D",
+            (
+                ("SEQ_1","2019-03-05"),
+                ("SEQ_2","2019-03-06"),
+                ("SEQ_3","2019-03-07"),
+            ),
+            ["SEQ_2", "SEQ_3"],
+        ),
+        (
+            "--max-date 1Y2W5D",
+            (
+                ("SEQ_1","2019-03-05"),
+                ("SEQ_2","2019-03-06"),
+                ("SEQ_3","2019-03-07"),
+            ),
+            ["SEQ_1", "SEQ_2"],
+        ),
+    ],
+)
+def test_filter_relative_dates(tmpdir, argparse_params, metadata_rows, output_sorted_expected):
+    """Test that various relative dates work"""
+    out_fn = str(tmpdir / "filtered.txt")
+    meta_fn = write_metadata(tmpdir, (("strain","date"),
+                                      *metadata_rows))
+    args = parse_args(f'--metadata {meta_fn} --output-strains {out_fn} {argparse_params}')
+    run(args)
+    with open(out_fn) as f:
+        output_sorted = sorted(line.rstrip() for line in f)
+    assert output_sorted == output_sorted_expected
+
+
+@freeze_time("2020-03-25")
+@pytest.mark.parametrize(
+    "argparse_flag, argparse_value",
+    [
+        ("--min-date", "3000Y"),
+        ("--max-date", "3000Y"),
+        ("--min-date", "invalid"),
+        ("--max-date", "invalid"),
+    ],
+)
+def test_filter_relative_dates_error(tmpdir, argparse_flag, argparse_value):
+    """Test that invalid dates fail"""
+    out_fn = str(tmpdir / "filtered.txt")
+    meta_fn = write_metadata(tmpdir, (("strain","date"),
+                                      ("SEQ_1","2020-03-23")))
+    with pytest.raises(SystemExit) as e_info:
+        parse_args(f'--metadata {meta_fn} --output-strains {out_fn} {argparse_flag} {argparse_value}')
+    assert f"Invalid date '{argparse_value}'" in e_info.value.__context__.message