Merge pull request #611 from ISA-tools/table_headers_609

Changed tests to reflect changed table headers. #609

Author: proccaserra

isatools/constants.py

@@ -23,6 +23,7 @@
     "Acquisition Parameter Data File",
     "Metabolite Assignment File",
     "Metabolite Identification File",
+    "Normalization Name"
 ]
 
 _LABELS_DATA_NODES = [

isatools/isatab/validate/rules/rules_40xx.py

@@ -448,6 +448,7 @@ def load_table_checks(df, filename):
                         "Hybridization Assay Name",
                         "Array Design REF",
                         "Scan Name",
+                        "Normalization Name",
                         "Data Transformation Name",
                     ]
                     and not _RX_PARAMETER_VALUE.match(col)

tests/convert/test_mzml2isa.py

@@ -24,7 +24,7 @@ def test_mzml2isa_convert_investigation(self):
             os.path.join(self._mzml_data_dir, study_id + "-partial"), self._tmp_dir, study_id, validate_output=True
         )
         self.assertEqual(len(report["warnings"]), 8)
-        self.assertEqual(len(report["errors"]), 3)
+        self.assertEqual(len(report["errors"]), 2)
 
         # Strip out the line with Comment[Created With Tool] to avoid changes in version number generated by mzml2isa
         with open(os.path.join(self._tmp_dir, "i_Investigation.txt")) as in_fp, StringIO() as stripped_actual_file:
@@ -45,7 +45,7 @@ def test_mzml2isa_convert_study_table(self):
             os.path.join(self._mzml_data_dir, study_id + "-partial"), self._tmp_dir, study_id, validate_output=True
         )
         self.assertEqual(len(report["warnings"]), 8)
-        self.assertEqual(len(report["errors"]), 3)
+        self.assertEqual(len(report["errors"]), 2)
         with open(os.path.join(self._tmp_dir, "s_{}.txt".format(study_id))) as out_fp:
             with open(
                 os.path.join(self._tab_data_dir, study_id + "-partial", "s_{}.txt".format(study_id))
@@ -59,7 +59,7 @@ def test_mzml2isa_convert_assay_table(self):
         )
         self.assertTrue(report["validation_finished"])
         self.assertEqual(len(report["warnings"]), 8)
-        self.assertEqual(len(report["errors"]), 3)
+        self.assertEqual(len(report["errors"]), 2)
         with open(
             os.path.join(self._tmp_dir, "a_{}_metabolite_profiling_mass_spectrometry.txt".format(study_id))
         ) as out_fp:

tests/isatab/validate/test_core.py

@@ -23,13 +23,13 @@ def test_mtbls267(self):
         with open(path.join(data_path, "i_Investigation.txt"), "r") as data_file:
             r = validate(fp=data_file, config_dir=self.default_conf, origin="mzml2isa")
         print(r["warnings"])
-        self.assertEqual(len(r["errors"]), 4)
+        self.assertEqual(len(r["errors"]), 3)
 
     def test_mtbls_1846(self):
         data_path = path.join(path.dirname(path.abspath(__file__)), "..", "..", "data", "mtbls", "MTBLS1846")
         with open(path.join(data_path, "i_Investigation.txt"), "r") as data_file:
             r = validate(fp=data_file, config_dir=self.default_conf)
-        self.assertEqual(len(r["errors"]), 20)
+        self.assertEqual(len(r["errors"]), 18)
 
     def test_bii_i_1(self):
         data_path = path.join(path.dirname(path.abspath(__file__)), "..", "..", "data", "tab", "BII-I-1")