#318 - Address linter issues

cassis/cas.py

@@ -13,6 +13,8 @@
 
 from cassis.typesystem import (
     FEATURE_BASE_NAME_HEAD,
+    FEATURE_BASE_NAME_LANGUAGE,
+    TYPE_NAME_DOCUMENT_ANNOTATION,
     TYPE_NAME_FS_ARRAY,
     TYPE_NAME_FS_LIST,
     TYPE_NAME_SOFA,
@@ -21,8 +23,6 @@
     TypeCheckError,
     TypeSystem,
     TypeSystemMode,
-    TYPE_NAME_DOCUMENT_ANNOTATION,
-    FEATURE_BASE_NAME_LANGUAGE,
 )
 
 _validator_optional_string = validators.optional(validators.instance_of(str))

cassis/json.py

@@ -1,12 +1,42 @@
 import base64
 import json
 import math
-from collections import OrderedDict
+from collections import OrderedDict, defaultdict
 from io import TextIOBase, TextIOWrapper
 from math import isnan
+from typing import Union, IO, Optional, Dict, List
+from toposort import toposort_flatten
 
 from cassis.cas import NAME_DEFAULT_SOFA, Cas, IdGenerator, Sofa, View
-from cassis.typesystem import *
+from cassis.typesystem import (
+    TYPE_NAME_ANNOTATION,
+    TypeSystem,
+    is_predefined,
+    merge_typesystems,
+    TYPE_NAME_SOFA,
+    FEATURE_BASE_NAME_SOFAARRAY,
+    array_type_name_for_type,
+    FEATURE_BASE_NAME_SOFASTRING,
+    FEATURE_BASE_NAME_SOFAID,
+    FEATURE_BASE_NAME_SOFAMIME,
+    FEATURE_BASE_NAME_SOFANUM,
+    FEATURE_BASE_NAME_SOFAURI,
+    TYPE_NAME_FS_ARRAY,
+    TYPE_NAME_BYTE_ARRAY,
+    TYPE_NAME_FLOAT_ARRAY,
+    TYPE_NAME_DOUBLE_ARRAY,
+    TypeSystemMode,
+    TYPE_NAME_DOCUMENT_ANNOTATION,
+    Type,
+    Feature,
+    TYPE_NAME_TOP,
+    is_primitive_array,
+    TYPE_NAME_FLOAT,
+    TYPE_NAME_DOUBLE,
+    element_type_name_for_array_type,
+    is_primitive,
+    is_array,
+)
 
 RESERVED_FIELD_PREFIX = "%"
 REF_FEATURE_PREFIX = "@"

cassis/xmi.py

@@ -12,7 +12,6 @@
 from cassis.typesystem import (
     _LIST_TYPES,
     _PRIMITIVE_ARRAY_TYPES,
-    _PRIMITIVE_LIST_TYPES,
     FEATURE_BASE_NAME_BEGIN,
     FEATURE_BASE_NAME_END,
     FEATURE_BASE_NAME_HEAD,
@@ -295,7 +294,8 @@ def deserialize(self, source: Union[IO, str], typesystem: TypeSystem, lenient: b
             else:
                 view = cas.create_view(sofa.sofaID, xmiID=sofa.xmiID, sofaNum=sofa.sofaNum)
 
-            # Directly set the sofaString and offsetConverter for the sofa to avoid recomputing the offset convertion (slow!) when using the setter
+            # Directly set the sofaString and offsetConverter for the sofa to avoid recomputing the offset convertion
+            # (slow!) when using the setter
             view.get_sofa()._sofaString = sofa.sofaString
             view.get_sofa()._offset_converter = sofa._offset_converter
             view.sofa_mime = sofa.mimeType

tests/test_cas.py

@@ -20,17 +20,17 @@ def test_default_typesystem_is_not_shared():
     cas1 = Cas()
     cas2 = Cas()
 
-    t1 = cas1.typesystem.create_type(name="test.Type")
-    t2 = cas2.typesystem.create_type(name="test.Type")
+    cas1.typesystem.create_type(name="test.Type")
+    cas2.typesystem.create_type(name="test.Type")
 
 
 def test_default_typesystem_is_not_shared_load_from_xmi(empty_cas_xmi):
     # https://github.com/dkpro/dkpro-cassis/issues/67
     cas1 = load_cas_from_xmi(empty_cas_xmi)
     cas2 = load_cas_from_xmi(empty_cas_xmi)
 
-    t1 = cas1.typesystem.create_type(name="test.Type")
-    t2 = cas2.typesystem.create_type(name="test.Type")
+    cas1.typesystem.create_type(name="test.Type")
+    cas2.typesystem.create_type(name="test.Type")
 
 
 # View

tests/test_json.py

@@ -1,6 +1,6 @@
 import json
 
-from cassis.typesystem import TYPE_NAME_ANNOTATION, TypeSystemMode, TYPE_NAME_DOCUMENT_ANNOTATION
+from cassis.typesystem import TYPE_NAME_ANNOTATION, TYPE_NAME_DOCUMENT_ANNOTATION, TypeSystemMode
 from tests.fixtures import *
 from tests.test_files.test_cas_generators import MultiFeatureRandomCasGenerator, MultiTypeRandomCasGenerator
 from tests.util import assert_json_equal

tests/test_typesystem.py

@@ -10,14 +10,14 @@
     TYPE_NAME_ANNOTATION_BASE,
     TYPE_NAME_ARRAY_BASE,
     TYPE_NAME_BOOLEAN,
+    TYPE_NAME_DOCUMENT_ANNOTATION,
     TYPE_NAME_INTEGER,
     TYPE_NAME_SOFA,
     TYPE_NAME_STRING,
     TYPE_NAME_STRING_ARRAY,
     TYPE_NAME_TOP,
     TypeCheckError,
     is_predefined,
-    TYPE_NAME_DOCUMENT_ANNOTATION,
 )
 from tests.fixtures import *
 from tests.util import assert_xml_equal
@@ -315,7 +315,6 @@ def test_type_inherits_from_annotation():
     ],
 )
 def test_is_predefined(type_name: str, expected: bool):
-
     assert is_predefined(type_name) == expected
 
 
@@ -498,7 +497,7 @@ def test_is_primitive_collection(type_name: str, expected: bool):
         ("uima.cas.DoubleArray", True),
     ],
 )
-def test_is_primitive_collection(type_name: str, expected: bool):
+def test_is_primitive_array(type_name: str, expected: bool):
     typesystem = TypeSystem()
 
     assert typesystem.is_primitive_array(type_name) == expected
@@ -883,9 +882,9 @@ def test_that_merging_types_creates_self_contained_type_system():
 def test_that_dkpro_core_typeystem_can_be_loaded():
     ts = load_dkpro_core_typesystem()
 
-    POS = ts.get_type("de.tudarmstadt.ukp.dkpro.core.api.lexmorph.type.pos.POS")
-    NamedEntity = ts.get_type("de.tudarmstadt.ukp.dkpro.core.api.ner.type.NamedEntity")
-    CoreferenceLink = ts.get_type("de.tudarmstadt.ukp.dkpro.core.api.coref.type.CoreferenceLink")
+    assert ts.get_type("de.tudarmstadt.ukp.dkpro.core.api.lexmorph.type.pos.POS") is not None
+    assert ts.get_type("de.tudarmstadt.ukp.dkpro.core.api.ner.type.NamedEntity") is not None
+    assert ts.get_type("de.tudarmstadt.ukp.dkpro.core.api.coref.type.CoreferenceLink") is not None
 
 
 # Type checking

tests/test_util.py

@@ -1,5 +1,3 @@
-from pathlib import Path
-
 from cassis.typesystem import TYPE_NAME_ANNOTATION, TYPE_NAME_FS_ARRAY
 from tests.fixtures import *
 from tests.test_files.test_cas_generators import MultiFeatureRandomCasGenerator, MultiTypeRandomCasGenerator

tests/test_xmi.py

@@ -65,7 +65,7 @@ def test_deserializing_from_string(small_typesystem_xml):
         <cas:Sofa xmi:id="1" sofaNum="1" sofaID="mySofa" mimeType="text/plain"
                   sofaString="Joe waited for the train . The train was late ."/>
         <cas:View sofa="1" members="8 79 84"/>
-    </xmi:XMI>    
+    </xmi:XMI>
     """
     load_cas_from_xmi(cas_xmi, typesystem=typesystem)
 
@@ -102,7 +102,7 @@ def test_views_are_parsed(small_xmi, small_typesystem_xml):
         <cas:Sofa xmi:id="2" sofaNum="2" sofaID="sofa2" mimeType="text/plain"
                   sofaString="The train was late ."/>
         <cas:View sofa="2" members="84"/>
-    </xmi:XMI>    
+    </xmi:XMI>
     """
     cas = load_cas_from_xmi(cas_xmi, typesystem=typesystem)
 
@@ -302,11 +302,11 @@ def test_offsets_are_recomputed_when_sofa_string_changes(cas_with_smileys_xmi, d
 
 def test_offsets_work_for_empty_sofastring():
     xmi = """<?xml version="1.0" encoding="UTF-8"?>
-        <xmi:XMI xmlns:xmi="http://www.omg.org/XMI" xmlns:tcas="http:///uima/tcas.ecore" 
-            xmlns:cas="http:///uima/cas.ecore" xmi:version="2.0"> 
-            <cas:NULL xmi:id="0" /> 
-            <tcas:DocumentAnnotation xmi:id="2" sofa="1" begin="0" end="0" language="en" /> 
-            <cas:Sofa xmi:id="1" sofaNum="1" sofaID="_InitialView" mimeType="text" sofaString="" /> 
+        <xmi:XMI xmlns:xmi="http://www.omg.org/XMI" xmlns:tcas="http:///uima/tcas.ecore"
+            xmlns:cas="http:///uima/cas.ecore" xmi:version="2.0">
+            <cas:NULL xmi:id="0" />
+            <tcas:DocumentAnnotation xmi:id="2" sofa="1" begin="0" end="0" language="en" />
+            <cas:Sofa xmi:id="1" sofaNum="1" sofaID="_InitialView" mimeType="text" sofaString="" />
             <cas:View sofa="1" members="2" />
         </xmi:XMI>"""
 
@@ -316,14 +316,15 @@ def test_offsets_work_for_empty_sofastring():
 
 def test_that_invalid_offsets_remain_unmapped_on_import():
     xmi = """<?xml version="1.0" encoding="UTF-8"?>
-        <xmi:XMI xmlns:xmi="http://www.omg.org/XMI" xmlns:tcas="http:///uima/tcas.ecore" 
-            xmlns:cas="http:///uima/cas.ecore" xmi:version="2.0"> 
-            <cas:NULL xmi:id="0" /> 
-            <tcas:DocumentAnnotation xmi:id="2" sofa="1" begin="0" end="4" language="en" /> 
-            <tcas:Annotation xmi:id="3" sofa="1" begin="100" end="200" /> 
-            <cas:Sofa xmi:id="1" sofaNum="1" sofaID="_InitialView" mimeType="text" sofaString="Test" /> 
+        <xmi:XMI xmlns:xmi="http://www.omg.org/XMI" xmlns:tcas="http:///uima/tcas.ecore"
+            xmlns:cas="http:///uima/cas.ecore" xmi:version="2.0">
+            <cas:NULL xmi:id="0" />
+            <tcas:DocumentAnnotation xmi:id="2" sofa="1" begin="0" end="4" language="en" />
+            <tcas:Annotation xmi:id="3" sofa="1" begin="100" end="200" />
+            <cas:Sofa xmi:id="1" sofaNum="1" sofaID="_InitialView" mimeType="text" sofaString="Test" />
             <cas:View sofa="1" members="2 3" />
-        </xmi:XMI>"""
+        </xmi:XMI>
+        """
 
     # assert no exception
     with warnings.catch_warnings(record=True) as ws:
@@ -361,14 +362,14 @@ def test_leniency_type_not_in_typesystem_lenient(cas_with_leniency_xmi, small_ty
     typesystem = load_typesystem(small_typesystem_xml)
 
     with pytest.warns(UserWarning):
-        cas = load_cas_from_xmi(cas_with_leniency_xmi, typesystem=typesystem, lenient=True)
+        load_cas_from_xmi(cas_with_leniency_xmi, typesystem=typesystem, lenient=True)
 
 
 def test_leniency_type_not_in_typesystem_not_lenient(cas_with_leniency_xmi, small_typesystem_xml):
     typesystem = load_typesystem(small_typesystem_xml)
 
     with pytest.raises(TypeNotFoundError):
-        cas = load_cas_from_xmi(cas_with_leniency_xmi, typesystem=typesystem, lenient=False)
+        load_cas_from_xmi(cas_with_leniency_xmi, typesystem=typesystem, lenient=False)
 
 
 def test_multiple_references_allowed_true():