fixes issue #323, addresses use of a deprecated call in isatab2w4m

isatools/convert/isatab2w4m.py

@@ -304,8 +304,7 @@ def make_variable_names(assay_df):
 
     # Make variable names from data values
     for col in ['mass_to_charge', 'retention_time', 'chemical_shift']:
-        # if assay_df.keys().contains(col):
-        if col in assay_df.keys():    
+        if col in assay_df.keys():
             for i, v in enumerate(assay_df[col].values):
                 if type(v) == str or not numpy.isnan(v):
                     x = var_names[i]

isatools/isatab.py

@@ -1791,8 +1791,7 @@ def _build_section_df(f):
         :return: A DataFrame corresponding to the file section
         """
         df = pd.read_csv(f, names=range(0, 128), sep='\t', engine='python',
-                         encoding='utf-8', comment='#').dropna(
-            axis=1, how='all')
+                         encoding='utf-8').dropna(axis=1, how='all')
         df = df.T
         df.replace(np.nan, '', regex=True, inplace=True)
         #  Strip out the nan entries

tests/test_isatab.py

@@ -18,7 +18,7 @@
 
 def setUpModule():
     if not os.path.exists(utils.DATA_DIR):
-        raise FileNotFoundError("Could not fine test data directory in {0}. Ensure you have cloned the ISAdatasets "
+        raise FileNotFoundError("Could not find test data directory in {0}. Ensure you have cloned the ISAdatasets "
                                 "repository using "
                                 "git clone -b tests --single-branch git@github.com:ISA-tools/ISAdatasets {0}"
                                 .format(utils.DATA_DIR))
@@ -726,6 +726,18 @@ def setUp(self):
     def tearDown(self):
         shutil.rmtree(self._tmp_dir)
 
+    def test_isatab_load_issue323(self):
+        with open(os.path.join(self._tab_data_dir, 'issue323', 'i_05.txt')) as fp:
+            ISA = isatab.load(fp)
+            print(ISA.studies[0].protocols[0].description)
+            self.assertEqual(len(ISA.studies[0].protocols[0].description), 70)
+
+        protocol = Protocol(description="some description containing a # character that should not be picked up", name="", protocol_type=OntologyAnnotation(term=""))
+        print("test protocol description", protocol.description)
+
+        self.assertEqual(len(protocol.description),70)
+
+
     def test_isatab_load_issue200(self):
         with open(os.path.join(self._tab_data_dir, 'issue200', 'i_Investigation.txt')) as fp:
             ISA = isatab.load(fp)