Merge pull request #36 from jeromekelleher/cli-testing

Start on cli testing

Author: jeromekelleher

bio2zarr/cli.py

@@ -50,8 +50,7 @@ def explode(vcfs, out_path, verbose, worker_processes, column_chunk_size):
 @verbose
 def summarise(columnarised, verbose):
     setup_logging(verbose)
-    pcvcf = vcf.PickleChunkedVcf.load(columnarised)
-    data = pcvcf.summary_table()
+    data = vcf.summarise(columnarised)
     click.echo(tabulate.tabulate(data, headers="keys"))
 
 

bio2zarr/vcf.py

@@ -879,6 +879,11 @@ def explode(
     )
 
 
+def summarise(columnarised):
+    pcvcf = vcf.PickleChunkedVcf.load(columnarised)
+    return pcvcf.summary_table()
+
+
 @dataclasses.dataclass
 class ZarrColumnSpec:
     # TODO change to "variable_name"

tests/test_cli.py

@@ -1,11 +1,38 @@
+from unittest import mock
+
 import click.testing as ct
 
 from bio2zarr import cli
 
-# NOTE just putting things together here to see what works.
-# Probably want to mock the module functions here to
-# avoid testing any real functionality.
-def test_vcf_summarise():
-    runner = ct.CliRunner()
-    result = runner.invoke(cli.vcf2zarr, "summarise", "filename")
-    # FIXME not testing anything!
+class TestWithMocks:
+
+    def test_vcf_explode(self):
+        runner = ct.CliRunner(mix_stderr=False)
+        with mock.patch("bio2zarr.vcf.explode") as mocked:
+            result = runner.invoke(
+                cli.vcf2zarr, ["explode", "source", "dest"], catch_exceptions=False
+
+            )
+            assert result.exit_code == 0
+            assert len(result.stdout) == 0
+            assert len(result.stderr) == 0
+            mocked.assert_called_once_with(
+                ("source",),
+                "dest",
+                column_chunk_size=64,
+                worker_processes=1,
+                show_progress=True,
+            )
+
+    def test_summarise(self):
+        runner = ct.CliRunner(mix_stderr=False)
+        with mock.patch("bio2zarr.vcf.summarise", return_value={}) as mocked:
+            result = runner.invoke(
+                cli.vcf2zarr, ["summarise", "path"], catch_exceptions=False
+
+            )
+            assert result.exit_code == 0
+            assert result.stdout == "\n"
+            assert len(result.stderr) == 0
+            mocked.assert_called_once_with("path")
+