Merge main

CHANGELOG.md

@@ -55,6 +55,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Add schema mapper for the `REC/2024/06/plate-reader` schema.
 - Checks for missing well item amplification and results data in quantstudio
 - Add csv support to ThermoFisher Nanodrop One
+- Add Thermo SkanIt adapter
 - Made Agilent Gen5 adapter compatible with the new REC schema
 
 ### Fixed

CODEOWNERS

@@ -1,7 +1,9 @@
 # Everything else is jointly owned by senior parser developers and Benchling Connect team
-*			            @slopez-b @alejandro-salgado @Benchling-Open-Source/benchling-connect
+*			            	@slopez-b @alejandro-salgado @Benchling-Open-Source/benchling-connect
 # Limit allotrope schema code and CODEOWNERS to Benchling Connect team
-src/allotropy/allotrope @Benchling-Open-Source/benchling-connect
-CODEOWNERS              @Benchling-Open-Source/benchling-connect
+src/allotropy/allotrope 		@Benchling-Open-Source/benchling-connect
+CODEOWNERS              		@Benchling-Open-Source/benchling-connect
 # Give ASM experts ownership over docs (Benchling Connect as backup)
-docs			        @james-leinas @Benchling-Open-Source/benchling-connect
+docs			        	@james-leinas @Benchling-Open-Source/benchling-connect
+src/allotropy/allotrope/schemas/schemas	@james-leinas @Benchling-Open-Source/benchling-connect
+src/allotropy/allotrope/schemas/models	@james-leinas @Benchling-Open-Source/benchling-connect

README.md

@@ -47,6 +47,7 @@ We currently have parser support for the following instruments:
 ### Candidate Release
 
 ### Working Draft
+  - Thermo SkanIt
   - Revvity Matrix
 
 The parsers follow maturation levels of: Recommended, Candidate Release, Working Draft - see [release_state.py](https://github.com/Benchling-Open-Source/allotropy/blob/main/src/allotropy/parsers/release_state.py) for additional details.

docs/tutorial.md

@@ -166,7 +166,7 @@ and *must* define set `DISPLAY_NAME`, `RELEASE_STATE`, and `SCHEMA_MAPPER` and i
 `create_data` that takes a `NamedFileContents` objects as input and produces an instance of (something derived from) `Data` as a result:
 
 ```python
-class ExampleWeylandYutaniParser(MapperVendorParser[Data, Model]):
+class ExampleWeylandYutaniParser(VendorParser[Data, Model]):
     DISPLAY_NAME = DISPLAY_NAME
     RELEASE_STATE = ReleaseState.WORKING_DRAFT
     SCHEMA_MAPPER = Mapper

scripts/templates/parser_template

@@ -16,10 +16,10 @@ from allotropy.parsers.$PARSER_NAME$.$PARSER_NAME$_structure import (
     create_metadata,
 )
 from allotropy.parsers.utils.pandas import map_rows
-from allotropy.parsers.vendor_parser import MapperVendorParser
+from allotropy.parsers.vendor_parser import VendorParser
 
 
-class $CLASS_NAME_PREFIX$Parser(MapperVendorParser[Data, Model]):
+class $CLASS_NAME_PREFIX$Parser(VendorParser[Data, Model]):
     DISPLAY_NAME = DISPLAY_NAME
     RELEASE_STATE = ReleaseState.WORKING_DRAFT
     SUPPORTED_EXTENSIONS = $CLASS_NAME_PREFIX$Reader.SUPPORTED_EXTENSIONS

src/allotropy/allotrope/converter.py

@@ -111,18 +111,32 @@ def add_custom_information_document(
     if not custom_info_doc:
         return model
 
-    if isinstance(custom_info_doc, dict):
-        custom_info_doc = structure_custom_information_document(
-            custom_info_doc, "custom information document"
-        )
-    if not is_dataclass(custom_info_doc):
+    # Convert to a dictionary first, so we can clean up values.
+    if is_dataclass(custom_info_doc):
+        custom_info_dict = asdict(custom_info_doc)
+    elif isinstance(custom_info_doc, dict):
+        custom_info_dict = custom_info_doc
+    else:
         msg = f"Invalid custom_info_doc: {custom_info_doc}"
         raise ValueError(msg)
 
-    # Do not add custom info doc if all values are None
-    if all(value is None for value in asdict(custom_info_doc).values()):
+    # Remove None and {"value": None, "unit"...} values
+    cleaned_dict = {}
+    for key, value in custom_info_dict.items():
+        if value is None:
+            continue
+        if isinstance(value, dict) and "value" in value and value["value"] is None:
+            continue
+        cleaned_dict[key] = value
+
+    # If dict is empty after cleaning, do not attach.
+    if not cleaned_dict:
         return model
 
+    custom_info_doc = structure_custom_information_document(
+        cleaned_dict, "custom information document"
+    )
+
     model.custom_information_document = custom_info_doc  # type: ignore
     return model