Pad out basic cli testing

Author: jeromekelleher

bio2zarr/cli.py

@@ -85,15 +85,14 @@ def encode(if_path, zarr_path, verbose, schema, worker_processes):
 @worker_processes
 def convert_vcf(vcfs, out_path, verbose, worker_processes):
     setup_logging(verbose)
-    vcf.convert(
-        vcfs, out_path, show_progress=True, worker_processes=worker_processes
-    )
+    vcf.convert(vcfs, out_path, show_progress=True, worker_processes=worker_processes)
 
 
 @click.command
 @click.argument("vcfs", nargs=-1, required=True)
 @click.argument("out_path", type=click.Path())
 def validate(vcfs, out_path):
+    # FIXME! Will silently not look at remaining VCFs
     vcf.validate(vcfs[0], out_path, show_progress=True)
 
 

bio2zarr/vcf.py

@@ -923,7 +923,9 @@ def asjson(self):
     @staticmethod
     def fromdict(d):
         ret = ZarrConversionSpec(**d)
-        ret.columns = {key: ZarrColumnSpec(**value) for key,value in d["columns"].items()}
+        ret.columns = {
+            key: ZarrColumnSpec(**value) for key, value in d["columns"].items()
+        }
         return ret
 
     @staticmethod
@@ -1326,9 +1328,7 @@ def mkschema(if_path, out):
     out.write(spec.asjson())
 
 
-def encode(
-    if_path, zarr_path, schema_path, worker_processes=1, show_progress=False
-):
+def encode(if_path, zarr_path, schema_path, worker_processes=1, show_progress=False):
     pcvcf = PickleChunkedVcf.load(if_path)
     if schema_path is None:
         schema = ZarrConversionSpec.generate(pcvcf)

tests/test_cli.py

@@ -65,11 +65,13 @@ def test_encode(self):
                 show_progress=True,
             )
 
-    def test_convert(self):
+    def test_convert_vcf(self):
         runner = ct.CliRunner(mix_stderr=False)
         with mock.patch("bio2zarr.vcf.convert") as mocked:
             result = runner.invoke(
-                cli.vcf2zarr, ["convert", "vcf_path", "zarr_path"], catch_exceptions=False
+                cli.vcf2zarr,
+                ["convert", "vcf_path", "zarr_path"],
+                catch_exceptions=False,
             )
             assert result.exit_code == 0
             assert len(result.stdout) == 0
@@ -80,3 +82,38 @@ def test_convert(self):
                 worker_processes=1,
                 show_progress=True,
             )
+
+    def test_validate(self):
+        runner = ct.CliRunner(mix_stderr=False)
+        with mock.patch("bio2zarr.vcf.validate") as mocked:
+            result = runner.invoke(
+                cli.vcf2zarr,
+                ["validate", "vcf_path", "zarr_path"],
+                catch_exceptions=False,
+            )
+            assert result.exit_code == 0
+            assert len(result.stdout) == 0
+            assert len(result.stderr) == 0
+            mocked.assert_called_once_with(
+                "vcf_path",
+                "zarr_path",
+                show_progress=True,
+            )
+
+    def test_convert_plink(self):
+        runner = ct.CliRunner(mix_stderr=False)
+        with mock.patch("bio2zarr.plink.convert") as mocked:
+            result = runner.invoke(
+                cli.plink2zarr, ["convert", "in", "out"], catch_exceptions=False
+            )
+            assert result.exit_code == 0
+            assert len(result.stdout) == 0
+            assert len(result.stderr) == 0
+            mocked.assert_called_once_with(
+                "in",
+                "out",
+                worker_processes=1,
+                chunk_width=None,
+                chunk_length=None,
+                show_progress=True,
+            )