fixed ref guide nesting, removed operators/ations (#1282)

Author: SFJohnson24

cdisc_rules_engine/check_operators/dataframe_operators.py

@@ -1526,36 +1526,6 @@ def target_is_sorted_by(self, other_value: dict):
     def target_is_not_sorted_by(self, other_value: dict):
         return ~self.target_is_sorted_by(other_value)
 
-    @log_operator_execution
-    @type_operator(FIELD_DATAFRAME)
-    def variable_metadata_equal_to(self, other_value: dict):
-        """
-        Validates the metadata for variables,
-        provided in the metadata column, is equal to
-        the comparator.
-        Ex.
-        target: STUDYID
-        comparator: "Exp"
-        metadata_column: {"STUDYID": "Req", "DOMAIN": "Req"}
-        result: False
-        """
-        target = self.replace_prefix(other_value.get("target"))
-        comparator = other_value.get(
-            "comparator"
-        )  # Assumes the comparator is a value not a column
-        metadata_column = self.replace_prefix(other_value.get("metadata"))
-        result = np.where(
-            vectorized_get_dict_key(self.value[metadata_column], target) == comparator,
-            True,
-            False,
-        )
-        return self.value.convert_to_series(result)
-
-    @log_operator_execution
-    @type_operator(FIELD_DATAFRAME)
-    def variable_metadata_not_equal_to(self, other_value: dict):
-        return ~self.variable_metadata_equal_to(other_value)
-
     @log_operator_execution
     @type_operator(FIELD_DATAFRAME)
     def shares_at_least_one_element_with(self, other_value: dict):

cdisc_rules_engine/operations/operations_factory.py

@@ -56,9 +56,6 @@
 from cdisc_rules_engine.operations.whodrug_hierarchy_validator import (
     WhodrugHierarchyValidator,
 )
-from cdisc_rules_engine.operations.variable_library_metadata import (
-    VariableLibraryMetadata,
-)
 from cdisc_rules_engine.operations.variable_count import VariableCount
 from cdisc_rules_engine.operations.variable_is_null import VariableIsNull
 from cdisc_rules_engine.operations.required_variables import RequiredVariables
@@ -117,7 +114,6 @@ class OperationsFactory(FactoryInterface):
         "valid_meddra_code_term_pairs": MedDRACodeTermPairsValidator,
         "variable_exists": VariableExists,
         "variable_names": VariableNames,
-        "variable_library_metadata": VariableLibraryMetadata,
         "variable_value_count": VariableValueCount,
         "variable_count": VariableCount,
         "variable_is_null": VariableIsNull,

cdisc_rules_engine/operations/variable_library_metadata.py

@@ -369,15 +369,6 @@
       "required": ["id", "operator"],
       "type": "object"
     },
-    {
-      "properties": {
-        "operator": {
-          "const": "variable_library_metadata"
-        }
-      },
-      "required": ["id", "operator", "name"],
-      "type": "object"
-    },
     {
       "properties": {
         "operator": { "const": "variable_names" }

resources/schema/Operations.json

@@ -875,6 +875,63 @@ will return:
 ["2023-05-19", "2023-10-26", "2023-12-13"]
 ```
 
+## variable_count
+
+Returns a mapping of variable names to the number of times that variable appears in a domain within the study.
+
+- Input
+
+  ```json
+  {
+    "AE": ["STUDYID", "DOMAIN", "USUBJID", "AETERM", "AEENDTC"],
+    "LB": ["STUDYID", "DOMAIN", "USUBJID", "LBTESTCD", "LBENDTC"]
+  }
+  ```
+
+- Output
+
+  ```json
+  {
+    "STUDYID": 2,
+    "DOMAIN": 2,
+    "USUBJID": 2,
+    "--TERM": 1,
+    "--TESTCD": 1,
+    "--ENDTC": 2
+  }
+  ```
+
+## variable_exists
+
+Flag an error if MIDS is in the dataset currently being evaluated and the TM domain is not present in the study
+
+```yaml
+Rule Type: Domain Presence Check
+Check:
+  all:
+    - name: $MIDS_EXISTS
+      operator: equal_to
+      value: true
+    - name: TM
+      operator: not_exists
+Operations:
+  - id: $MIDS_EXISTS
+    name: MIDS
+    operator: variable_exists
+```
+
+## variable_is_null
+
+True if variable is missing or if all values within a variable are null or empty string
+
+## variable_names
+
+Return the set of variable names from the library for the given standard
+
+## variable_value_count
+
+Given a variable `name`, returns a mapping of variable values to the number of times that value appears in the variable within all datasets in the study.
+
 # External Dictionary Validation Operations
 
 ## Supported External Dictionary Types
@@ -1087,95 +1144,3 @@ Operations:
   - id: $valid_whodrug_codes
     operator: whodrug_code_hierarchy
 ```
-
-## variable_count
-
-Returns a mapping of variable names to the number of times that variable appears in a domain within the study.
-
-- Input
-
-  ```json
-  {
-    "AE": ["STUDYID", "DOMAIN", "USUBJID", "AETERM", "AEENDTC"],
-    "LB": ["STUDYID", "DOMAIN", "USUBJID", "LBTESTCD", "LBENDTC"]
-  }
-  ```
-
-- Output
-
-  ```json
-  {
-    "STUDYID": 2,
-    "DOMAIN": 2,
-    "USUBJID": 2,
-    "--TERM": 1,
-    "--TESTCD": 1,
-    "--ENDTC": 2
-  }
-  ```
-
-## variable_exists
-
-Flag an error if MIDS is in the dataset currently being evaluated and the TM domain is not present in the study
-
-```yaml
-Rule Type: Domain Presence Check
-Check:
-  all:
-    - name: $MIDS_EXISTS
-      operator: equal_to
-      value: true
-    - name: TM
-      operator: not_exists
-Operations:
-  - id: $MIDS_EXISTS
-    name: MIDS
-    operator: variable_exists
-```
-
-## variable_is_null
-
-True if variable is missing or if all values within a variable are null or empty string
-
-## variable_names
-
-Return the set of variable names from the library for the given standard
-
-## variable_library_metadata
-
-Get the metadata value from the library for all variables in the current dataset. Metadata attribute is specified by the `name`.
-
-Result
-
-```json
-{
-  "STUDYID": "Req",
-  "DOMAIN": "Req",
-  "AEGRPID": "Perm",
-  "AETERM": "Req",
-  "AELLT": "Exp",
-  "...": "..."
-}
-```
-
-> Condition: Variable Core Status = Required
-
-> Rule: Variable ^= null
-
-```yaml
-Check:
-  any:
-    - all:
-        - operator: variable_metadata_equal_to
-          value: Req
-          metadata: $var_perm
-        - operator: empty
-Operations:
-  - id: $var_perm
-    operator: variable_library_metadata
-    name: core
-```
-
-## variable_value_count
-
-Given a variable `name`, returns a mapping of variable values to the number of times that value appears in the variable within all datasets in the study.

resources/schema/Operations.md

@@ -804,24 +804,6 @@
       "required": ["operator", "value"],
       "type": "object"
     },
-    {
-      "properties": {
-        "operator": {
-          "const": "variable_metadata_equal_to"
-        }
-      },
-      "required": ["operator", "metadata", "value"],
-      "type": "object"
-    },
-    {
-      "properties": {
-        "operator": {
-          "const": "variable_metadata_not_equal_to"
-        }
-      },
-      "required": ["operator", "metadata", "value"],
-      "type": "object"
-    },
     {
       "properties": {
         "operator": {

resources/schema/Operator.json

@@ -563,27 +563,6 @@ Check:
       operator: "inconsistent_enumerated_columns"
 ```
 
-## variable_metadata_equal_to
-
-Could be useful, for example, in checking variable permissibility in conjunction with the `variable_library_metadata` operation:
-
-```yaml
-Check:
-  all:
-    - operator: variable_metadata_equal_to
-      value: Exp
-      metadata: $permissibility
-    - operator: not_exists
-Operations:
-  - id: $permissibility
-    operator: variable_library_metadata
-    name: core
-```
-
-## variable_metadata_not_equal_to
-
-Complement of `variable_metadata_equal_to`
-
 # Relationship & Set
 
 ## is_contained_by