Cli tests

Author: benjeffery

bio2zarr/cli.py

@@ -84,15 +84,15 @@ def explode(vcfs, out_path, verbose, worker_processes, column_chunk_size):
 @click.option("-n", "--target_num_partitions", type=int, required=True)
 @verbose
 @worker_processes
-def explode_init(vcfs, out_path, num_partitions, verbose, worker_processes):
+def explode_init(vcfs, out_path, target_num_partitions, verbose, worker_processes):
     """
     Initial step for parallel conversion of VCF(s) to columnar intermediate format
     """
     setup_logging(verbose)
     vcf.explode_init(
         vcfs,
         out_path,
-        num_partitions=num_partitions,
+        target_num_partitions=target_num_partitions,
         worker_processes=worker_processes,
         show_progress=True,
     )

bio2zarr/vcf.py

@@ -1108,17 +1108,17 @@ def explode(
     )
     return PickleChunkedVcf.load(out_path)
 
-def explode_init(vcfs, out_path, *, num_partitions=1, worker_processes=1, show_progress=False):
+def explode_init(vcfs, out_path, *, target_num_partitions=1, worker_processes=1, show_progress=False):
     out_path = pathlib.Path(out_path)
     if out_path.exists():
         shutil.rmtree(out_path)
     # Error if num_parts less than number of files
-    if num_partitions < len(vcfs):
+    if target_num_partitions < len(vcfs):
         raise ValueError("num_partitions must be greater than or equal to the number of input VCFs")
     return PickleChunkedVcf.convert_init(
         vcfs,
         out_path,
-        num_partitions=num_partitions,
+        num_partitions=target_num_partitions,
         worker_processes=worker_processes,
         show_progress=show_progress,
     )

tests/test_cli.py

@@ -26,6 +26,63 @@ def test_vcf_explode(self, mocked):
             show_progress=True,
         )
 
+    def test_vcf_explode_init(self):
+        runner = ct.CliRunner(mix_stderr=False)
+        with mock.patch("bio2zarr.vcf.explode_init") as mocked:
+            result = runner.invoke(
+                cli.vcf2zarr, ["explode-init", "source", "dest", "-n", "5"], 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",
+                target_num_partitions=5,
+                worker_processes=1,
+                show_progress=True,
+            )
+
+    def test_vcf_explode_partition_count(self):
+        runner = ct.CliRunner(mix_stderr=False)
+        with mock.patch("bio2zarr.vcf.explode_partition_count", return_value=5) as mocked:
+            result = runner.invoke(
+                cli.vcf2zarr, ["explode-partition-count", "path"], catch_exceptions=False
+            )
+            assert result.exit_code == 0
+            assert result.stdout == "5\n"
+            assert len(result.stderr) == 0
+            mocked.assert_called_once_with("path")
+
+    def test_vcf_explode_slice(self):
+        runner = ct.CliRunner(mix_stderr=False)
+        with mock.patch("bio2zarr.vcf.explode_slice") as mocked:
+            result = runner.invoke(
+                cli.vcf2zarr, ["explode-slice", "path", "-s", "1", "-e", "2"], catch_exceptions=False
+            )
+            assert result.exit_code == 0
+            assert len(result.stdout) == 0
+            assert len(result.stderr) == 0
+            mocked.assert_called_once_with(
+                "path",
+                1,
+                2,
+                column_chunk_size=64,
+                worker_processes=1,
+                show_progress=True,
+            )
+
+    def test_vcf_explode_finalise(self):
+        runner = ct.CliRunner(mix_stderr=False)
+        with mock.patch("bio2zarr.vcf.explode_finalise") as mocked:
+            result = runner.invoke(
+                cli.vcf2zarr, ["explode-finalise", "path"], catch_exceptions=False
+            )
+            assert result.exit_code == 0
+            assert len(result.stdout) == 0
+            assert len(result.stderr) == 0
+            mocked.assert_called_once_with("path")
+
     @mock.patch("bio2zarr.vcf.inspect")
     def test_inspect(self, mocked):
         runner = ct.CliRunner(mix_stderr=False)