1047 define variable has method

cdisc_rules_engine/dataset_builders/define_variables_with_library_metadata.py

@@ -24,6 +24,7 @@ def build(self):
         "define_variable_codelist_coded_codes",
         "define_variable_mandatory",
         "define_variable_has_comment",
+        "define_variable_has_method",
         "library_variable_name",
         "library_variable_label",
         "library_variable_data_type",

cdisc_rules_engine/dataset_builders/variables_metadata_with_define_dataset_builder.py

@@ -28,8 +28,9 @@ def build(self):
         define_variable_has_codelist,
         define_variable_codelist_coded_values,
         define_variable_codelist_coded_codes,
-        define_variable_mandatory
-        define_variable_has_comment
+        define_variable_mandatory,
+        define_variable_has_comment,
+        define_variable_has_method
         """
         # get Define XML metadata for domain and use it as a rule comparator
         variable_metadata: List[dict] = self.get_define_xml_variables_metadata()

cdisc_rules_engine/services/define_xml/base_define_xml_reader.py

@@ -382,6 +382,7 @@ def _get_item_def_representation(self, itemdef, itemref, codelists, index) -> di
             "define_variable_codelist_coded_codes": [],
             "define_variable_mandatory": None,
             "define_variable_has_comment": False,
+            "define_variable_has_method": False,
         }
         if itemdef:
             data["define_variable_mandatory"] = itemref.Mandatory
@@ -418,6 +419,7 @@ def _get_item_def_representation(self, itemdef, itemref, codelists, index) -> di
                 itemref, index
             )
             data["define_variable_has_comment"] = itemdef.CommentOID is not None
+            data["define_variable_has_method"] = itemref.MethodOID is not None
         return data
 
     def _get_codelist_ccode(self, codelist):

resources/schema/rule-merged/MetaVariables.json

@@ -82,6 +82,10 @@
       "const": "define_variable_has_comment",
       "markdownDescription": "\nItemGroupDef.ItemDef.CommentOID exists\n"
     },
+    {
+      "const": "define_variable_has_method",
+      "markdownDescription": "\nItemGroupDef.ItemRef.MethodOID exists\n"
+    },
     {
       "const": "define_variable_has_no_data",
       "markdownDescription": "\nItemGroupDef.ItemRef.HasNoData\n"
@@ -198,6 +202,14 @@
       "const": "library_variable_core",
       "markdownDescription": "\ncore attribute of a variable from the CDISC Library\n"
     },
+    {
+      "const": "library_variable_has_codelist",
+      "markdownDescription": "\nIndicates whether a variable has an associated codelist in the CDISC Library\n"
+    },
+    {
+      "const": "library_variable_ccode",
+      "markdownDescription": "\nccode attribute of a variable from the CDISC Library\n"
+    },
     {
       "const": "library_variable_data_type",
       "markdownDescription": "\nsimpleDatatype attribute of a variable from the CDISC Library\n"

resources/schema/rule-merged/Rule_Type.json

@@ -20,7 +20,7 @@
     {
       "const": "Define Item Metadata Check against Library Metadata",
       "title": "Define xml metadata at variable level and corresponding library variable metadata",
-      "markdownDescription": "\n#### Columns\n\n- `define_variable_name`\n- `define_variable_label`\n- `define_variable_data_type`\n- `define_variable_role`\n- `define_variable_size`\n- `define_variable_ccode`\n- `define_variable_format`\n- `define_variable_allowed_terms`\n- `define_variable_origin_type`\n- `define_variable_is_collected`\n- `define_variable_has_no_data`\n- `define_variable_order_number`\n- `define_variable_has_codelist`\n- `define_variable_codelist_coded_values`\n- `define_variable_codelist_coded_codes`\n- `define_variable_mandatory`\n- `define_variable_has_comment`\n- `library_variable_name`\n- `library_variable_order_number`\n- `library_variable_label`\n- `library_variable_data_type`\n- `library_variable_role`\n- `library_variable_core`\n- `library_variable_ccode`\n\n#### Rule Macro\n\nChecks variable-level metadata, codelists, and codelist terms from Define-XML against the corresponding standard variable definitions from the CDISC Library.\n"
+      "markdownDescription": "\n#### Columns\n\n- `define_variable_name`\n- `define_variable_label`\n- `define_variable_data_type`\n- `define_variable_role`\n- `define_variable_size`\n- `define_variable_ccode`\n- `define_variable_format`\n- `define_variable_allowed_terms`\n- `define_variable_origin_type`\n- `define_variable_is_collected`\n- `define_variable_has_no_data`\n- `define_variable_order_number`\n- `define_variable_has_codelist`\n- `define_variable_codelist_coded_values`\n- `define_variable_codelist_coded_codes`\n- `define_variable_mandatory`\n- `define_variable_has_comment`\n- `define_variable_has_method`\n- `library_variable_name`\n- `library_variable_order_number`\n- `library_variable_label`\n- `library_variable_data_type`\n- `library_variable_role`\n- `library_variable_core`\n- `library_variable_has_codelist`\n- `library_variable_ccode`\n\n#### Rule Macro\n\nChecks variable-level metadata, codelists, and codelist terms from Define-XML against the corresponding standard variable definitions from the CDISC Library.\n"
     },
     {
       "const": "Domain Presence Check",
@@ -65,7 +65,7 @@
     {
       "const": "Variable Metadata Check against Define XML",
       "title": "Content metadata at variable level and define xml metadata at variable level",
-      "markdownDescription": "\n#### Columns\n\n- `variable_name`\n- `variable_order_number`\n- `variable_label`\n- `variable_size`\n- `variable_data_type`\n- `define_variable_name`\n- `define_variable_label`\n- `define_variable_data_type`\n- `define_variable_is_collected`\n- `define_variable_role`\n- `define_variable_size`\n- `define_variable_ccode`\n- `define_variable_format`\n- `define_variable_allowed_terms`\n- `define_variable_origin_type`\n- `define_variable_has_no_data`\n- `define_variable_order_number`\n- `define_variable_length`\n- `define_variable_has_codelist`\n- `define_variable_codelist_coded_values`\n- `define_variable_codelist_coded_codes`\n- `define_variable_mandatory`\n- `define_variable_has_comment`\n\n#### Rule Macro\n\nCombines variable-level metadata from submission dataset contents against the matching variable definitions in Define-XML.\n\n#### Example\n\n```yaml\n- name: variable_name\n  operator: not_equal_to\n  value: define_variable_name\n```\n"
+      "markdownDescription": "\n#### Columns\n\n- `variable_name`\n- `variable_order_number`\n- `variable_label`\n- `variable_size`\n- `variable_data_type`\n- `define_variable_name`\n- `define_variable_label`\n- `define_variable_data_type`\n- `define_variable_is_collected`\n- `define_variable_role`\n- `define_variable_size`\n- `define_variable_ccode`\n- `define_variable_format`\n- `define_variable_allowed_terms`\n- `define_variable_origin_type`\n- `define_variable_has_no_data`\n- `define_variable_order_number`\n- `define_variable_length`\n- `define_variable_has_codelist`\n- `define_variable_codelist_coded_values`\n- `define_variable_codelist_coded_codes`\n- `define_variable_mandatory`\n- `define_variable_has_comment`\n- `define_variable_has_method`\n\n#### Rule Macro\n\nCombines variable-level metadata from submission dataset contents against the matching variable definitions in Define-XML.\n\n#### Example\n\n```yaml\n- name: variable_name\n  operator: not_equal_to\n  value: define_variable_name\n```\n"
     },
     {
       "const": "Variable Metadata Check against Library Metadata",

resources/schema/rule/MetaVariables.json

@@ -56,6 +56,9 @@
     {
       "const": "define_variable_has_comment"
     },
+    {
+      "const": "define_variable_has_method"
+    },
     {
       "const": "define_variable_has_no_data"
     },

resources/schema/rule/MetaVariables.md

@@ -86,6 +86,10 @@ ItemGroupDef.ItemDef.CodeListRef exists
 
 ItemGroupDef.ItemDef.CommentOID exists
 
+## define_variable_has_method
+
+ItemGroupDef.ItemRef.MethodOID exists
+
 ## define_variable_has_no_data
 
 ItemGroupDef.ItemRef.HasNoData

resources/schema/rule/Rule_Type.md

@@ -191,6 +191,7 @@ Columns are the columns within the original dataset along with the following col
 - `define_variable_codelist_coded_values`
 - `define_variable_codelist_coded_values`
 - `define_variable_has_comment`
+- `define_variable_has_method`
 
 #### Rule Macro
 
@@ -309,6 +310,7 @@ all:
 - `define_variable_codelist_coded_codes`
 - `define_variable_mandatory`
 - `define_variable_has_comment`
+- `define_variable_has_method`
 - `library_variable_name`
 - `library_variable_order_number`
 - `library_variable_label`
@@ -498,6 +500,7 @@ all:
 - `define_variable_codelist_coded_codes`
 - `define_variable_mandatory`
 - `define_variable_has_comment`
+- `define_variable_has_method`
 
 #### Rule Macro
 
@@ -561,6 +564,7 @@ Combines variable-level metadata from submission dataset contents against the co
 - `define_variable_codelist_coded_codes`
 - `define_variable_mandatory`
 - `define_variable_has_comment`
+- `define_variable_has_method`
 - `library_variable_name`
 - `library_variable_role`
 - `library_variable_label`

tests/unit/test_dataset_builders/test_define_variables_with_library_metadata.py

@@ -227,6 +227,7 @@ def test_define_variables_metadata_with_library_metadata_dataset_builder(
         "define_variable_codelist_coded_codes",
         "define_variable_mandatory",
         "define_variable_has_comment",
+        "define_variable_has_method",
         "library_variable_name",
         "library_variable_role",
         "library_variable_label",

tests/unit/test_dataset_builders/test_variables_metadata_with_define_and_library_dataset_builder.py

@@ -176,6 +176,7 @@ def test_build_combined_metadata(
         "define_variable_codelist_coded_codes",
         "define_variable_mandatory",
         "define_variable_has_comment",
+        "define_variable_has_method",
         "library_variable_name",
         "library_variable_label",
         "library_variable_data_type",

tests/unit/test_define_xml_reader.py

@@ -223,6 +223,15 @@ def test_extract_variable_metadata(filename):
             "define_variable_is_collected": False,
             "define_variable_order_number": 11,
             "define_variable_has_comment": True,
+            "define_variable_has_method": False,
+        }
+        expected_exdose_metadata = {
+            "define_variable_name": "EXDOSE",
+            "define_variable_data_type": "integer",
+            "define_variable_origin_type": "Derived",
+            "define_variable_is_collected": False,
+            "define_variable_has_comment": False,
+            "define_variable_has_method": True,
         }
         for index, variable in enumerate(variable_metadata):
             assert variable["define_variable_name"] in expected_variables
@@ -232,6 +241,12 @@ def test_extract_variable_metadata(filename):
             ):
                 for key in expected_exroute_metadata.keys():
                     assert variable[key] == expected_exroute_metadata[key]
+            if (
+                variable["define_variable_name"]
+                == expected_exdose_metadata["define_variable_name"]
+            ):
+                for key in expected_exdose_metadata.keys():
+                    assert variable[key] == expected_exdose_metadata[key]
 
             assert variable["define_variable_order_number"] == index + 1