Augmentation Updates for V3 Spec Modifications

packages/augmentation/src/augmentation/models/application.py

@@ -9,7 +9,18 @@
 class ApplicationCode(StrEnum):
     """The list of applications that will leveraging Augmentation functionality."""
 
-    TEXT_TO_CODE = "text-to-code"
+    # element 0 - Application Code
+    # element 1 - Application Code Display Name (for human readability)
+    TEXT_TO_CODE = ("text-to-code", "Text-to-Code")
+
+    def __new__(cls, code: str, display: str) -> "ApplicationCode":
+        """Create a new instance of the ApplicationCode enum with code and display attributes."""
+        # use the base type's __new__ to create the enum instance
+        obj = str.__new__(cls, code)
+        obj._value_ = code
+        obj.display = display
+        obj.code = code
+        return obj
 
 
 class NonstandardCodeInstanceMetadata(NonstandardCodeInstance):

packages/augmentation/src/augmentation/models/config.py

@@ -51,7 +51,7 @@ class TTCAugmenterConfig(AugmenterConfig):
     }
     # TODO: The function code is currently a constant (used for both lab orders and results), but will need to be dynamic when additional fields with different function codes are introduced.
     author_function_code: str = "code-text-to-code"
-    author_function_code_system: str = "2.16.840.1.113663.10.20.15.2.7.1"
+    author_function_code_system: str = "2.16.840.1.113883.10.20.15.2.7.1"
     author_function_code_system_name: str = "eCRDataAugmentation"
 
     @model_validator(mode="after")

packages/augmentation/src/augmentation/services/augmenter.py

@@ -48,7 +48,16 @@ def document_payload_not_none(cls, v: str) -> Element:
         return clean_xml_tree(v)
 
     def _get_application_code_value(self) -> str:
-        return self.application_code.value
+        # added this check to satisfy the type checker
+        if hasattr(self.application_code, "code"):
+            return self.application_code.code
+        raise Exception("we will never return an ''")
+
+    def _get_application_code_display(self) -> str:
+        # added this check to satisfy the type checker
+        if hasattr(self.application_code, "display"):
+            return self.application_code.display
+        raise Exception("we will never return an ''")
 
     @abstractmethod
     def augment(self) -> Metadata:

packages/augmentation/src/augmentation/services/eicr_augmenter.py

@@ -229,24 +229,15 @@ def _get_old_xrfm_related_document(self) -> Element | None:
     def _generate_author(self, level: str = "header") -> Element:
         null_flavor_comment = " set to nullFlavor 'NA' "
         author = etree.Element("author")
-        function_code = etree.SubElement(author, "functionCode")
-        function_code.set("code", value=self.config.author_function_code)
-        function_code.set("codeSystem", value=self.config.author_function_code_system)
-        function_code.set("codeSystemName", value=self.config.author_function_code_system_name)
-        # TODO: Eventually we wwill not only separate by header vs. data_element
+        # TODO: Eventually we will not only separate by header vs. data_element
         # but will also separate out the various comments by the various data element
         # type being modified. This can easily be stored in the model for the data elemnts
         # For now we are hard coding for code-text-to-code and observation in the comment
-        if level == "header":
-            self._add_previous_element_comment(
-                (
-                    "functionCode specifies type of change "
-                    "'text-to-code' which signifies this document has been transformed using the "
-                    "text-to-code data augmentation tool "
-                ),
-                function_code,
-            )
-        else:
+        if level != "header":
+            function_code = etree.SubElement(author, "functionCode")
+            function_code.set("code", value=self.config.author_function_code)
+            function_code.set("codeSystem", value=self.config.author_function_code_system)
+            function_code.set("codeSystemName", value=self.config.author_function_code_system_name)
             self._add_previous_element_comment(
                 (
                     "functionCode specifies type of change "
@@ -283,7 +274,14 @@ def _generate_author(self, level: str = "header") -> Element:
             " set to 'Data Augmentation Tool' ", assigned_authoring_device
         )
         software_name = etree.SubElement(assigned_authoring_device, "softwareName")
-        software_name.set("displayName", "Data Augmentation Tool")
+        software_name.set("code", value=self._get_application_code_value())
+        software_name.set("codeSystem", value=self.config.author_function_code_system)
+        software_name.set("codeSystemName", value=self.config.author_function_code_system_name)
+        software_name.set("displayName", self._get_application_code_display())
+        self._add_previous_element_comment(
+            " assignedAuthoringDevice/softwareName specifies that this document has been transformed using the Text-to-Code data augmentation tool",
+            software_name,
+        )
 
         return author
 

packages/augmentation/tests/unit/snapshots/test_eicr_augmenter/test_basic_eicr/basic_eicr_augmented.xml

@@ -28,7 +28,7 @@
                                 </code>
                                 <author>
                                     <!--DATA AUGMENTATION: functionCode specifies type of change 'code-text-to-code' which signifies that the code in this observation has been augmented with a code derived from the text in the code element -->
-                                    <functionCode code="code-text-to-code" codeSystem="2.16.840.1.113663.10.20.15.2.7.1" codeSystemName="eCRDataAugmentation"/>
+                                    <functionCode code="code-text-to-code" codeSystem="2.16.840.1.113883.10.20.15.2.7.1" codeSystemName="eCRDataAugmentation"/>
                                     <!--DATA AUGMENTATION: time of data augmentation operation -->
                                     <effectiveTime value="20260213152757"/>
                                     <assignedAuthor>
@@ -40,7 +40,8 @@
                                         <telecom nullFlavor="NA"/>
                                         <!--DATA AUGMENTATION: set to 'Data Augmentation Tool' -->
                                         <assignedAuthoringDevice>
-                                            <softwareName displayName="Data Augmentation Tool"/>
+                                            <!--DATA AUGMENTATION: assignedAuthoringDevice/softwareName specifies that this document has been transformed using the Text-to-Code data augmentation tool -->
+                                            <softwareName code="text-to-code" codeSystem="2.16.840.1.113883.10.20.15.2.7.1" codeSystemName="eCRDataAugmentation" displayName="Text-to-Code"/>
                                         </assignedAuthoringDevice>
                                     </assignedAuthor>
                                 </author>
@@ -64,8 +65,6 @@
         </parentDocument>
     </relatedDocument>
     <author>
-        <!--DATA AUGMENTATION: functionCode specifies type of change 'text-to-code' which signifies this document has been transformed using the text-to-code data augmentation tool -->
-        <functionCode code="code-text-to-code" codeSystem="2.16.840.1.113663.10.20.15.2.7.1" codeSystemName="eCRDataAugmentation"/>
         <!--DATA AUGMENTATION: time of data augmentation operation -->
         <effectiveTime value="20260213152757"/>
         <assignedAuthor>
@@ -77,7 +76,8 @@
             <telecom nullFlavor="NA"/>
             <!--DATA AUGMENTATION: set to 'Data Augmentation Tool' -->
             <assignedAuthoringDevice>
-                <softwareName displayName="Data Augmentation Tool"/>
+                <!--DATA AUGMENTATION: assignedAuthoringDevice/softwareName specifies that this document has been transformed using the Text-to-Code data augmentation tool -->
+                <softwareName code="text-to-code" codeSystem="2.16.840.1.113883.10.20.15.2.7.1" codeSystemName="eCRDataAugmentation" displayName="Text-to-Code"/>
             </assignedAuthoringDevice>
         </assignedAuthor>
     </author>

packages/augmentation/tests/unit/snapshots/test_eicr_augmenter/test_eicr_related_doc/basic_eicr_related_doc_augmented.xml

@@ -35,7 +35,7 @@
                                 </code>
                                 <author>
                                     <!--DATA AUGMENTATION: functionCode specifies type of change 'code-text-to-code' which signifies that the code in this observation has been augmented with a code derived from the text in the code element -->
-                                    <functionCode code="code-text-to-code" codeSystem="2.16.840.1.113663.10.20.15.2.7.1" codeSystemName="eCRDataAugmentation"/>
+                                    <functionCode code="code-text-to-code" codeSystem="2.16.840.1.113883.10.20.15.2.7.1" codeSystemName="eCRDataAugmentation"/>
                                     <!--DATA AUGMENTATION: time of data augmentation operation -->
                                     <effectiveTime value="20260213152757"/>
                                     <assignedAuthor>
@@ -47,7 +47,8 @@
                                         <telecom nullFlavor="NA"/>
                                         <!--DATA AUGMENTATION: set to 'Data Augmentation Tool' -->
                                         <assignedAuthoringDevice>
-                                            <softwareName displayName="Data Augmentation Tool"/>
+                                            <!--DATA AUGMENTATION: assignedAuthoringDevice/softwareName specifies that this document has been transformed using the Text-to-Code data augmentation tool -->
+                                            <softwareName code="text-to-code" codeSystem="2.16.840.1.113883.10.20.15.2.7.1" codeSystemName="eCRDataAugmentation" displayName="Text-to-Code"/>
                                         </assignedAuthoringDevice>
                                     </assignedAuthor>
                                 </author>
@@ -71,8 +72,6 @@
         </parentDocument>
     </relatedDocument>
     <author>
-        <!--DATA AUGMENTATION: functionCode specifies type of change 'text-to-code' which signifies this document has been transformed using the text-to-code data augmentation tool -->
-        <functionCode code="code-text-to-code" codeSystem="2.16.840.1.113663.10.20.15.2.7.1" codeSystemName="eCRDataAugmentation"/>
         <!--DATA AUGMENTATION: time of data augmentation operation -->
         <effectiveTime value="20260213152757"/>
         <assignedAuthor>
@@ -84,7 +83,8 @@
             <telecom nullFlavor="NA"/>
             <!--DATA AUGMENTATION: set to 'Data Augmentation Tool' -->
             <assignedAuthoringDevice>
-                <softwareName displayName="Data Augmentation Tool"/>
+                <!--DATA AUGMENTATION: assignedAuthoringDevice/softwareName specifies that this document has been transformed using the Text-to-Code data augmentation tool -->
+                <softwareName code="text-to-code" codeSystem="2.16.840.1.113883.10.20.15.2.7.1" codeSystemName="eCRDataAugmentation" displayName="Text-to-Code"/>
             </assignedAuthoringDevice>
         </assignedAuthor>
     </author>

packages/augmentation/tests/unit/test_model_application.py

@@ -6,3 +6,5 @@ def test_application_code(self):
         """Basic unit test for ApplicationCode enum."""
         app_enum = ApplicationCode
         assert app_enum.TEXT_TO_CODE.value == "text-to-code"
+        assert app_enum.TEXT_TO_CODE.display == "Text-to-Code"
+        assert app_enum.TEXT_TO_CODE.code == "text-to-code"