corrections, test passing (new test)

isatools/convert/isatab2json.py

@@ -36,6 +36,7 @@ def convert(work_dir, identifier_type=IdentifierType.name,
             validate_first=True, config_dir=isatab.default_config_dir,
             use_new_parser=False):
     i_files = glob.glob(os.path.join(work_dir, 'i_*.txt'))
+
     if validate_first:
         log.info("Validating input ISA tab before conversion")
         if len(i_files) != 1:
@@ -120,6 +121,7 @@ def convert(self, work_dir):
             log.fatal("No ISA-Tab dataset found")
         else:
             isa_json = dict([])
+
             if isa_tab.metadata != {}:
                 isa_json = dict([
                     ("identifier",

isatools/isatab/load/core.py

@@ -201,7 +201,7 @@ def get_comments_row(cols, row):
                 file=row['Term Source File'],
                 version=row['Term Source Version'],
                 description=row['Term Source Description'])
-            ontology_source.comments = get_comments(df_dict['ontology_sources'])
+            ontology_source.comments = get_comments_row(df_dict['ontology_sources'].columns, row)
             investigation.ontology_source_references.append(ontology_source)
 
         ontology_source_map = dict(map(lambda x: (x.name, x), investigation.ontology_source_references))
@@ -317,8 +317,7 @@ def get_comments_row(cols, row):
                     row['Study Assay Technology Type Term Source REF']
                 )
                 assay.technology_platform = row['Study Assay Technology Platform']
-                assay.comments = get_comments(df_dict['s_assays'][i])
-
+                assay.comments = get_comments_row(df_dict['s_assays'][i].columns, row)
                 if skip_load_tables:
                     pass
                 else:

tests/isajson/test_isajson.py

@@ -420,6 +420,28 @@ def test_json_load_and_dump_bii_s_7(self):
             self.assertEqual(len(assay_gx['dataFiles']), 29)  # 29 data files  in a_matteo-assay-Gx.txt
             self.assertEqual(len(assay_gx['processSequence']), 116)  # 116 processes in in a_matteo-assay-Gx.txt
 
+    def test_json_load_and_dump_bii_s_test(self):
+        # Load into ISA objects
+        with open(os.path.join(utils.JSON_DATA_DIR, 'ISA-1', 'isa-test1.json')) as isajson_fp:
+            ISA = isajson.load(isajson_fp)
+
+            # Dump into ISA JSON from ISA objects
+            ISA_J = json.loads(json.dumps(ISA, cls=isajson.ISAJSONEncoder))
+            study_bii_s_test = [s for s in ISA_J['studies'] if s['filename'] == 's_study.txt'][0]
+            assay_gx = [a for a in study_bii_s_test['assays'] if a['filename'] == 'a_assay.txt'][0]
+
+
+    def test_json_load_and_dump_isa_le_test(self):
+        # Load into ISA objects
+        with open(os.path.join(utils.JSON_DATA_DIR, 'TEST-ISA-LabeledExtract1', 'isa-test-le1.json')) as isajson_fp:
+            ISA = isajson.load(isajson_fp)
+
+            # Dump into ISA JSON from ISA objects
+            ISA_J = json.loads(json.dumps(ISA, cls=isajson.ISAJSONEncoder))
+            study_bii_s_test = [s for s in ISA_J['studies'] if s['filename'] == 's_study.txt'][0]
+            assay_gx = [a for a in study_bii_s_test['assays'] if a['filename'] == 'a_assay.txt'][0]
+            self.assertEqual(assay_gx['materials']['otherMaterials'][3]["type"], "Labeled Extract Name")
+
     def test_json_load_from_file_and_create_isa_objects(self):
         # reading from file
         with open(os.path.join(utils.JSON_DATA_DIR, 'ISA-1', 'isa-test1.json')) as isajson_fp:

tests/isatab/test_isatab.py

@@ -1046,6 +1046,14 @@ def test_isatab_load_sdata201414_isa1(self):
             self.assertEqual(len(ISA.studies[0].contacts[1].comments), 5)  # 5 comments in contact
             self.assertListEqual([a.filename for a in ISA.studies[0].assays], ['a_chambers.txt'])  # 1 assays in s_chambers.txt
 
+    def test_isatab_load_bii_s_test(self):
+        with open(os.path.join(self._tab_data_dir, 'BII-S-TEST', 'i_test.txt')) as fp:
+            ISA = isatab.load(fp)
+
+            self.assertEqual(len(ISA.studies[0].assays[0].other_material), 8)
+            self.assertEqual(ISA.studies[0].assays[0].other_material[1].type, "Labeled Extract Name")
+
+
     def test_isatab_load_bii_i_1(self):
         with open(os.path.join(self._tab_data_dir, 'BII-I-1', 'i_investigation.txt')) as fp:
             ISA = isatab.load(fp)