fixes #569

Author: proccaserra

isatools/isatab/__init__.py

@@ -4,6 +4,8 @@
     write_study_table_files,
     write_assay_table_files,
     write_value_columns,
+    flatten,
+
     dump_tables_to_dataframes
 )
 from isatools.isatab.load import (
@@ -18,3 +20,4 @@
 from isatools.isatab.defaults import default_config_dir
 from isatools.isatab.utils import IsaTabDataFrame, TransposedTabParser
 from isatools.isatab.validate import validate, batch_validate
+

isatools/isatab/dump/__init__.py

@@ -1,2 +1,2 @@
 from isatools.isatab.dump.core import dump, dumps, dump_tables_to_dataframes
-from isatools.isatab.dump.write import write_study_table_files, write_assay_table_files, write_value_columns
+from isatools.isatab.dump.write import write_study_table_files, write_assay_table_files, write_value_columns, flatten

isatools/isatab/dump/write.py

@@ -26,6 +26,26 @@
 )
 
 
+def flatten(current_list) -> list:
+    """
+    :rtype: object
+    :param current_list: List
+    :return: flattened_listL: List
+    """
+    flattened_list = []
+    if current_list is not None:
+
+        for sublist in current_list:
+            if sublist is not None:
+                for item in sublist:
+                    flattened_list.append(item)
+            else:
+                raise ValueError
+    else:
+        raise ValueError
+    return flattened_list
+
+
 def write_study_table_files(inv_obj, output_dir):
     """Writes out study table files according to pattern defined by
 
@@ -49,10 +69,6 @@ def write_study_table_files(inv_obj, output_dir):
             break
         protrefcount = 0
         protnames = dict()
-
-        def flatten(current_list):
-            return [item for sublist in current_list for item in sublist]
-
         columns = []
 
         # start_nodes, end_nodes = _get_start_end_nodes(s_graph)
@@ -255,10 +271,6 @@ def write_assay_table_files(inv_obj, output_dir, write_factor_values=False):
                 break
             protrefcount = 0
             protnames = dict()
-
-            def flatten(current_list):
-                return [item for sublist in current_list for item in sublist]
-
             columns = []
 
             paths, indexes = _build_paths_and_indexes(assay_obj.process_sequence)

isatools/isatab/utils.py

@@ -388,10 +388,15 @@ def get_pv_columns(label, pv):
     """
     columns = None
     try:
-        columns = ["{0}.Parameter Value[{1}]".format(label, pv.category.parameter_name.term)]
+        if pv.category is not None:
+            columns = ["{0}.Parameter Value[{1}]".format(label, pv.category.parameter_name.term)]
+            print(columns)
+        else:
+            raise ValueError
     except AttributeError:
         log.fatal(label, pv)
-    columns.extend(get_value_columns(columns[0], pv))
+    if columns is not None:
+        columns.extend(get_value_columns(columns[0], pv))
     return columns
 
 

isatools/model/parameter_value.py

@@ -27,7 +27,7 @@ def __init__(self, category=None, value=None, unit=None, comments=None):
 
         # Shouldn't this be in the setter to avoid manually setting a non-numerical value when a unit is supplied ?
         if not isinstance(value, Number) and unit:
-            raise ValueError("ParameterValue value mus be quantitative (i.e. numeric) if a unit is supplied")
+            raise ValueError("ParameterValue value must be quantitative (i.e. numeric) if a unit is supplied")
         self.value = value
         self.unit = unit
 

isatools/net/mw2isa/__init__.py

@@ -60,7 +60,7 @@ def getblock(container, start_marker, end_marker):
 
 
 def get_archived_file(mw_study_id):
-    """A method of download Metabolomics Workbench archived data from their anonymous FTP site input: a valid Metabolomics
+    """ A method of download Metabolomics Workbench archived data from their anonymous FTP site input: a valid Metabolomics
     Workbench study accession number that should follow this pattern ^ST\d+[6]
     :param mw_study_id -> str
     :return: success -> boolean

isatools/resources/schemas/isa_model_version_1_0_schemas/core/comment_schema.json

@@ -1,4 +1,4 @@
-                {
+{
     "id": "https://raw.githubusercontent.com/ISA-tools/isa-api/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/comment_schema.json",
     "$schema": "https://json-schema.org/draft/2020-12/schema",
     "title": "ISA Comment schema - it corresponds to ISA Comment[] construct",

tests/isatab/test_isatab.py

@@ -18,8 +18,12 @@
 )
 from isatools.tests.utils import assert_tab_content_equal
 from isatools.tests import utils
-from isatools.isatab import IsaTabDataFrame
+from isatools.isatab import IsaTabDataFrame, flatten
 
+from isatools.isatab.utils import (
+    get_comment_column,
+    get_pv_columns
+)
 
 def setUpModule():
     if not os.path.exists(utils.DATA_DIR):
@@ -94,6 +98,22 @@ def setUp(self):
     def tearDown(self):
         shutil.rmtree(self._tmp_dir)
 
+    def test_isatab_flatten(self):
+        test_list = None
+        with self.assertRaises(ValueError):
+            flatten(test_list)
+
+    def test_isatab_get_pv_columns(self):
+        columns = []
+        pp = ProtocolParameter(parameter_name="test_parameter_name")
+        with self.assertRaises(AttributeError):
+            pv = ParameterValue(category="test_parameter_name", value=3)
+            get_pv_columns("Protocol REF", pv)
+
+        with self.assertRaises(AttributeError):
+            pv = ParameterValue(category=pp.parameter_name, value=3)
+            get_pv_columns("Protocol REF", pv)
+
     def test_isatab_bad_i_file_name(self):
         with self.assertRaises(NameError):
             isatab.dump(Investigation(), self._tmp_dir, i_file_name='investigation.txt')

tests/model/test_parameter_value.py

@@ -18,7 +18,7 @@ def test_init(self):
         with self.assertRaises(ValueError) as context:
             ParameterValue(unit=OntologyAnnotation())
         self.assertEqual(str(context.exception),
-                         "ParameterValue value mus be quantitative (i.e. numeric) if a unit is supplied")
+                         "ParameterValue value must be quantitative (i.e. numeric) if a unit is supplied")
 
     def test_category(self):
         self.assertIsNone(self.parameter.category)