Fixed #393

peppy/project.py

@@ -1316,7 +1316,10 @@ def _read_sample_data(self):
         if self[SUBSAMPLE_TABLES_FILE_KEY] is not None:
             sst = self[SUBSAMPLE_TABLES_FILE_KEY]
         else:
-            if CONFIG_KEY in self and CFG_SUBSAMPLE_TABLE_KEY in self[CONFIG_KEY]:
+            if (
+                CONFIG_KEY in self
+                and self[CONFIG_KEY].get(CFG_SUBSAMPLE_TABLE_KEY) is not None
+            ):
                 sst = make_list(self[CONFIG_KEY][CFG_SUBSAMPLE_TABLE_KEY], str)
             else:
                 sst = None

peppy/utils.py

@@ -2,7 +2,7 @@
 
 import logging
 import os
-from typing import Dict, Mapping
+from typing import Dict, Mapping, Type, Union
 from urllib.request import urlopen
 
 import yaml
@@ -76,14 +76,16 @@ def grab_project_data(prj):
         raise KeyError("Project lacks section '{}'".format(CONFIG_KEY))
 
 
-def make_list(arg, obj_class):
+def make_list(arg: Union[list, str], obj_class: Type) -> list:
     """
     Convert an object of predefined class to a list of objects of that class or
     ensure a list is a list of objects of that class
 
     :param list[obj] | obj arg: string or a list of strings to listify
     :param str obj_class: name of the class of intrest
+
     :return list: list of objects of the predefined class
+
     :raise TypeError: if a faulty argument was provided
     """
 

tests/data/example_peps-master/example_subsamples_none/project_config.yaml

@@ -0,0 +1,3 @@
+pep_version: "2.0.0"
+sample_table: sample_table.csv
+subsample_table: null

tests/data/example_peps-master/example_subsamples_none/sample_table.csv

@@ -0,0 +1,4 @@
+sample_name,protocol,file
+frog_1,anySampleType,multi
+frog_2,anySampleType,multi
+frog_3,anySampleType,multi

tests/test_Project.py

@@ -715,3 +715,11 @@ def test_sample_len(self, example_pep_cfg_path):
         """
         p = Project(cfg=example_pep_cfg_path)
         assert len(p.samples[0]) == 4
+
+    @pytest.mark.parametrize("example_pep_cfg_path", ["subsamples_none"], indirect=True)
+    def test_config_with_subsample_null(self, example_pep_cfg_path):
+        """
+        Tests if config can have value with subsample=null
+        """
+        p = Project(cfg=example_pep_cfg_path)
+        assert p.subsample_table is None