Fix tests

mutacc_auto/cli/import_command.py

@@ -20,18 +20,23 @@ def parse_path(ctx, param, value):
     return value
 
 @click.command('import')
+@click.option('-C','--config-file',
+              type=click.Path(exists=True),
+              callback=parse_path,
+              help="configuration file used for mutacc")
 @click.option('-D','--dry',
-is_flag=True,
-help="dry run")
+              is_flag=True,
+              help="dry run")
 @click.option('-V','--verbose',
-is_flag=True,
-help="verbose")
+              is_flag=True,
+              help="verbose")
 @click.pass_context
 def import_command(ctx,
+                   config_file,
                    dry,
                    verbose):
 
-    mutacc_config = ctx.obj['mutacc_config']
+    mutacc_config = ctx.obj.get('mutacc_config') or config_file
     #Open and read config for mutacc
     with open(Path(mutacc_config)) as yaml_handle:
 

mutacc_auto/recipes/input_recipe.py

@@ -49,15 +49,15 @@ def get_bams(case_id, hk_config=None, hk_binary=None):
             bam_paths (dict): dict with paths to bam for each sample
     """
 
-    #housekeeper_command = HousekeeperCommand(
-    #    case_id=case_id,
-    #    config_file=hk_config,
-    #    hk_binary=hk_binary
-    #)
-    #hk_output = housekeeper_command.check_output()
+    housekeeper_command = HousekeeperCommand(
+        case_id=case_id,
+        config_file=hk_config,
+        hk_binary=hk_binary
+    )
+    hk_output = housekeeper_command.check_output()
     ###
-    hk_out = subprocess.check_output(['cat', '/Users/adam.rosenbaum/develop/mutacc_auto/tests/fixtures/HK_output_test.txt'])
-    hk_output = hk_out.decode('utf-8')
+    #hk_out = subprocess.check_output(['cat', '/Users/adam.rosenbaum/develop/mutacc_auto/tests/fixtures/HK_output_test.txt'])
+    #hk_output = hk_out.decode('utf-8')
     ###
     bam_paths = get_bams_from_housekeeper(hk_output)
 

tests/cli/test_extract_command.py

@@ -25,27 +25,24 @@ def test_extract_command(
 
     with open(tmp_dir.joinpath('tmp_conf.yaml'), 'w') as conf_handle:
 
-        conf_dict = {'case_dir': str(tmp_dir)}
+        conf_dict = {'case_dir': str(tmp_dir), 'root_dir': str(tmp_dir)}
         yaml.dump(conf_dict, conf_handle)
         conf_path = conf_handle.name
 
     with open(tmp_dir.joinpath('tmp_test.mutacc'), 'w') as handle:
         handle.write('\n')
 
     runner = CliRunner()
-    result = runner.invoke(cli, [
-            '--config-file', configuration_file,
-            'extract',
-            '--case-id', 'test_id',
-            '--environment', 'env',
-            '--mutacc-config', conf_path,
-            '--log-directory', str(tmp_dir),
-            '--email', 'email@email.com',
-            '--dry',
-            '--verbose'
-        ]
-    )
-
+    result = runner.invoke(cli, ['--config-file', configuration_file,
+                                 'extract',
+                                 '--case-id', 'test_id',
+                                 '--environment', 'env',
+                                 '--mutacc-config', conf_path,
+                                 '--log-directory', str(tmp_dir),
+                                 '--email', 'email@email.com',
+                                 '--dry',
+                                 '--verbose'])
+    #mock_mkdir.assert_called_with('dsa')
     assert result.exit_code == 0
 
     result = runner.invoke(cli, [

tests/fixtures/config_file.yaml

@@ -3,7 +3,7 @@ scout_config: /path/to/scout_config
 scout_binary: /path/to/scout
 housekeeper_config: /path/to/housekeeper_config
 housekeeper_binary: /path/to/housekeeper
-mutacc_config: /path/to/mutacc_config
+mutacc_config: /Users/adam.rosenbaum/develop/mutacc_auto/tests/fixtures/mutacc_config.yaml
 mutacc_binary: /path/to/mutacc
 
 slurm:

tests/fixtures/mutacc_config.yaml

@@ -0,0 +1 @@
+root_dir: path/to/root/

tests/utils/test_tmp_dir.py

@@ -4,20 +4,19 @@
 
 from mutacc_auto.utils.tmp_dir import TemporaryDirectory
 
-def test_TemporaryDirectory():
+def test_TemporaryDirectory(tmpdir):
 
-    with TemporaryDirectory() as tmp_dir:
+    with TemporaryDirectory(directory=tmpdir) as tmp_dir:
 
         assert Path(tmp_dir).exists()
         assert Path(tmp_dir).is_dir()
 
-    assert not Path(tmp_dir).exists()
+    assert Path(tmp_dir).exists()
+    rmtree(tmp_dir)
 
-    with TemporaryDirectory(delete_dir=False) as tmp_dir:
+    with TemporaryDirectory(directory=tmpdir, delete_dir=True) as tmp_dir:
 
         assert Path(tmp_dir).exists()
         assert Path(tmp_dir).is_dir()
 
-    assert Path(tmp_dir).exists()
-    rmtree(tmp_dir)
-
+    assert not Path(tmp_dir).exists()