Merge pull request #940 from VisLab/develop

Minor update to support hed web

.codespellrc

@@ -0,0 +1,3 @@
+[codespell]
+skip = .git,*.pdf,*.svg,deprecated,*.xml,*.mediawiki,*.omn,*.toml
+ignore-words-list = covert,hed,assertIn,parms

hed/__init__.py

@@ -9,7 +9,7 @@
 from hed.models.sidecar import Sidecar
 from hed.models.definition_dict import DefinitionDict
 from hed.models.query_handler import QueryHandler
-from hed.models.query_service import get_query_handlers, search_strings
+from hed.models.query_service import get_query_handlers, search_hed_objs
 
 from hed.schema.hed_schema import HedSchema
 from hed.schema.hed_schema_group import HedSchemaGroup

hed/models/__init__.py

@@ -6,7 +6,7 @@
 from .definition_dict import DefinitionDict
 from .definition_entry import DefinitionEntry
 from .query_handler import QueryHandler
-from .query_service import get_query_handlers, search_strings
+from .query_service import get_query_handlers, search_hed_objs
 from .hed_group import HedGroup
 from .spreadsheet_input import SpreadsheetInput
 from .hed_string import HedString

hed/models/query_service.py

@@ -40,11 +40,11 @@ def get_query_handlers(queries, query_names=None):
     return expression_parsers, query_names, issues
 
 
-def search_strings(hed_strings, queries, query_names):
+def search_hed_objs(hed_objs, queries, query_names):
     """ Return a DataFrame of factors based on results of queries.
 
     Parameters:
-        hed_strings (list):  A list of HedString objects (empty entries or None entries are 0's
+        hed_objs (list):  A list of HedString objects (empty entries or None entries are 0's
         queries (list):  A list of query strings or QueryHandler objects.
         query_names (list): A list of column names for results of queries.
 
@@ -54,9 +54,9 @@ def search_strings(hed_strings, queries, query_names):
     :raises ValueError:
         - If query names are invalid or duplicated.
     """
-    df_factors = pd.DataFrame(0, index=range(len(hed_strings)), columns=query_names)
+    df_factors = pd.DataFrame(0, index=range(len(hed_objs)), columns=query_names)
     for parse_ind, parser in enumerate(queries):
-        for index, next_item in enumerate(hed_strings):
+        for index, next_item in enumerate(hed_objs):
             if next_item:
                 match = parser.search(next_item)
                 if match:

hed/tools/analysis/annotation_util.py

@@ -6,6 +6,7 @@
 import pandas as pd
 from pandas import DataFrame, Series
 from hed.models.sidecar import Sidecar
+from hed.models.hed_string import HedString
 from hed.models.tabular_input import TabularInput
 
 from hed.errors.exceptions import HedFileError
@@ -220,6 +221,27 @@ def str_to_tabular(tsv_str, sidecar=None):
     return TabularInput(file=io.StringIO(tsv_str), sidecar=sidecar)
 
 
+def strs_to_hed_objs(hed_strings, hed_schema):
+    """ Returns a list of HedString objects from a list of strings.
+
+     Parameters:
+         hed_strings (string or list):  String or strings representing HED annotations.
+         hed_schema (HedSchema or HedSchemaGroup): Schema version for the strings.
+         
+     Returns:
+         list or None:  list of HedString objects or None.
+     """
+
+    if not hed_strings:
+        return None
+    if not isinstance(hed_strings, list):
+        hed_strings = [hed_strings]
+    if hed_strings:
+        return [HedString(hed, hed_schema=hed_schema) for hed in hed_strings]
+    else:
+        return None
+
+
 def strs_to_sidecar(sidecar_strings):
     """ Return a Sidecar from a sidecar as string or as a list of sidecars as strings.
 
@@ -242,7 +264,6 @@ def strs_to_sidecar(sidecar_strings):
     else:
         return None
 
-
 def to_factor(data, column=None):
     """Convert data to an integer factor list.
 

hed/tools/remodeling/operations/factor_hed_tags_op.py

@@ -122,7 +122,7 @@ def do_op(self, dispatcher, df, name, sidecar=None):
         tag_man = HedTagManager(EventManager(input_data, dispatcher.hed_schema),
                                 remove_types=self.remove_types)
         hed_objs = tag_man.get_hed_objs(include_context=self.expand_context, replace_defs=self.replace_defs)
-        df_factors = query_service.search_strings(hed_objs, self.query_handlers, query_names=self.query_names)
+        df_factors = query_service.search_hed_objs(hed_objs, self.query_handlers, query_names=self.query_names)
         if len(df_factors.columns) > 0:
             df_list.append(df_factors)
         df_new = pd.concat(df_list, axis=1)

tests/tools/analysis/test_annotation_util.py

@@ -326,6 +326,16 @@ def test_series_to_factor(self):
         self.assertEqual(len(series2), len(factor2))
         self.assertEqual(sum(factor2), 1)
 
+    def test_strs_to_hed_objs(self):
+        self.assertIsNone(annotation_util.strs_to_hed_objs('', self.hed_schema))
+        self.assertIsNone(annotation_util.strs_to_hed_objs(None, self.hed_schema))
+        self.assertIsNone(annotation_util.strs_to_hed_objs([], self.hed_schema))
+        hed_objs1 = annotation_util.strs_to_hed_objs(['Sensory-event', 'Red'], self.hed_schema)
+        self.assertIsInstance(hed_objs1, list)
+        self.assertEqual(len(hed_objs1), 2)
+        self.assertEqual('Red', str(hed_objs1[1]))
+        hed_objs2 = annotation_util.strs_to_hed_objs(['Sensory-event', 'Blech'], self.hed_schema)
+
     def test_strs_to_sidecar(self):
         with open(self.json_path, 'r') as fp:
             sidecar_dict = json.load(fp)

tests/tools/analysis/test_temporal_event.py

@@ -27,21 +27,21 @@ def setUpClass(cls):
     def test_constructor_no_group(self):
         test1 = HedString("(Onset, def/blech)", hed_schema=self.schema)
         groups = test1.find_top_level_tags(["onset"], include_groups=1)
-        te = TemporalEvent(groups[0], 3, 4.5)
-        self.assertEqual(te.start_index, 3)
-        self.assertEqual(te.start_time, 4.5)
-        self.assertEqual(te.anchor, 'Def/blech')
-        self.assertFalse(te.internal_group)
+        temp_event = TemporalEvent(groups[0], 3, 4.5)
+        self.assertEqual(temp_event.start_index, 3)
+        self.assertEqual(temp_event.start_time, 4.5)
+        self.assertEqual(temp_event.anchor, 'Def/blech')
+        self.assertFalse(temp_event.internal_group)
 
     def test_constructor_group(self):
         test1 = HedString("(Onset, (Label/Apple, Blue), Def/Blech/54.3)", hed_schema=self.schema)
         groups = test1.find_top_level_tags(["onset"], include_groups=1)
-        te = TemporalEvent(groups[0], 3, 4.5)
-        self.assertEqual(te.start_index, 3)
-        self.assertEqual(te.start_time, 4.5)
-        self.assertTrue(te.internal_group)
-        self.assertEqual(te.anchor, 'Def/Blech/54.3')
-        self.assertIsInstance(te.internal_group, HedGroup)
+        temp_event = TemporalEvent(groups[0], 3, 4.5)
+        self.assertEqual(temp_event.start_index, 3)
+        self.assertEqual(temp_event.start_time, 4.5)
+        self.assertTrue(temp_event.internal_group)
+        self.assertEqual(temp_event.anchor, 'Def/Blech/54.3')
+        self.assertIsInstance(temp_event.internal_group, HedGroup)
 
     def test_constructor_on_files(self):
         manager1 = EventManager(self.input_data, self.schema)