Rename scRNA-seq schema from scRNALevel34 to scRNALevel3and4 (#130)

aditigopalan · actions-user · web-flow · commit ab9b1a0508a6 · 2026-01-23T10:55:23.000-05:00
* Rename scRNA-seq schema from scRNALevel34 to scRNALevel3and4

- Updated class name from scRNALevel34 to scRNALevel3and4 for better readability
- Updated enum name from scRNAseqWorkflowTypeEnumLevel34 to scRNAseqWorkflowTypeEnumLevel3and4
- Updated workflow to generate schema with new class name
- Updated test references to use new class name
- Avoids underscore parsing issues in Synapse while maintaining clarity

* chore: auto-generate Python classes from schema changes

Auto-generated Python classes from LinkML schema updates.

**Auto-generated by GitHub Actions workflow**
[skip ci]

---------

Co-authored-by: GitHub Action &lt;action@github.com&gt;
diff --git a/.github/workflows/json-schema-synapse.yml b/.github/workflows/json-schema-synapse.yml
@@ -157,8 +157,8 @@ jobs:
         # scRNA-seq Level 3/4
         poetry run python scripts/linkml_to_flat_synapse_jsonschema.py \
           "modules/scRNA-seq/domains/level_3_4.yaml" \
-          --class-name "scRNALevel34" \
-          --output "JSON_Schemas/${{ steps.version.outputs.version }}/HTAN.scRNALevel34-${{ steps.version.outputs.version }}-schema.json"
+          --class-name "scRNALevel3and4" \
+          --output "JSON_Schemas/${{ steps.version.outputs.version }}/HTAN.scRNALevel3and4-${{ steps.version.outputs.version }}-schema.json"
         
         # SpatialOmics Level 1
         echo "Generating SpatialOmics schemas..."
@@ -328,7 +328,7 @@ jobs:
         **scRNA-seq Module:**
         - scRNALevel1 Schema
         - scRNALevel2 Schema
-        - scRNALevel34 Schema
+        - scRNALevel3and4 Schema
         
         **SpatialOmics Module:**
         - SpatialLevel1 Schema
diff --git a/modules/Biospecimen/src/htan_biospecimen/datamodel/biospecimen.py b/modules/Biospecimen/src/htan_biospecimen/datamodel/biospecimen.py
@@ -1,5 +1,5 @@
 # Auto generated from biospecimen.yaml by pythongen.py version: 0.0.1
-# Generation date: 2026-01-22T10:32:44
+# Generation date: 2026-01-23T15:49:04
 # Schema: Biospecimen
 #
 # id: https://w3id.org/htan/biospecimen
diff --git a/modules/Clinical/src/htan_clinical/datamodel/clinical.py b/modules/Clinical/src/htan_clinical/datamodel/clinical.py
@@ -1,5 +1,5 @@
 # Auto generated from clinical.yaml by pythongen.py version: 0.0.1
-# Generation date: 2026-01-22T10:32:12
+# Generation date: 2026-01-23T15:48:34
 # Schema: Clinical
 #
 # id: https://w3id.org/htan/clinical
diff --git a/modules/DigitalPathology/src/htan_digitalpathology/datamodel/digital_pathology.py b/modules/DigitalPathology/src/htan_digitalpathology/datamodel/digital_pathology.py
@@ -1,5 +1,5 @@
 # Auto generated from digital_pathology.yaml by pythongen.py version: 0.0.1
-# Generation date: 2026-01-22T10:33:09
+# Generation date: 2026-01-23T15:49:23
 # Schema: DigitalPathology
 #
 # id: https://w3id.org/htan/digital_pathology
diff --git a/modules/Imaging/src/htan_imaging/datamodel/imaging.py b/modules/Imaging/src/htan_imaging/datamodel/imaging.py
@@ -1,5 +1,5 @@
 # Auto generated from imaging.yaml by pythongen.py version: 0.0.1
-# Generation date: 2026-01-22T10:33:04
+# Generation date: 2026-01-23T15:49:20
 # Schema: Imaging
 #
 # id: https://w3id.org/htan/imaging
diff --git a/modules/MultiplexMicroscopy/src/htan_multiplexmicroscopy/datamodel/multiplex_microscopy.py b/modules/MultiplexMicroscopy/src/htan_multiplexmicroscopy/datamodel/multiplex_microscopy.py
@@ -1,5 +1,5 @@
 # Auto generated from multiplex_microscopy.yaml by pythongen.py version: 0.0.1
-# Generation date: 2026-01-22T10:33:12
+# Generation date: 2026-01-23T15:49:25
 # Schema: MultiplexMicroscopy
 #
 # id: https://w3id.org/htan/multiplex_microscopy
diff --git a/modules/Sequencing/src/htan_sequencing/datamodel/sequencing.py b/modules/Sequencing/src/htan_sequencing/datamodel/sequencing.py
@@ -1,5 +1,5 @@
 # Auto generated from sequencing.yaml by pythongen.py version: 0.0.1
-# Generation date: 2026-01-22T10:33:02
+# Generation date: 2026-01-23T15:49:18
 # Schema: Sequencing
 #
 # id: https://w3id.org/htan/sequencing
diff --git a/modules/SpatialOmics/src/htan_spatial/datamodel/spatial.py b/modules/SpatialOmics/src/htan_spatial/datamodel/spatial.py
@@ -1,5 +1,5 @@
 # Auto generated from spatial.yaml by pythongen.py version: 0.0.1
-# Generation date: 2026-01-22T10:33:15
+# Generation date: 2026-01-23T15:49:27
 # Schema: SpatialOmics
 #
 # id: https://w3id.org/htan/spatial
diff --git a/modules/WES/src/htan_wes/datamodel/wes.py b/modules/WES/src/htan_wes/datamodel/wes.py
@@ -1,5 +1,5 @@
 # Auto generated from wes.yaml by pythongen.py version: 0.0.1
-# Generation date: 2026-01-22T10:32:42
+# Generation date: 2026-01-23T15:49:02
 # Schema: WES
 #
 # id: https://w3id.org/htan/wes
diff --git a/modules/scRNA-seq/domains/level_3_4.yaml b/modules/scRNA-seq/domains/level_3_4.yaml
@@ -1,4 +1,4 @@
-name: scRNALevel34
+name: scRNALevel3and4
 id: https://w3id.org/htan/scrna_seq/level_3_4
 description: Single-cell RNA-seq Level 3 and 4 - Gene expression files and cell relationships
 imports:
@@ -13,7 +13,7 @@ prefixes:
 default_prefix: htan
 
 enums:
-  scRNAseqWorkflowTypeEnumLevel34:
+  scRNAseqWorkflowTypeEnumLevel3and4:
     permissible_values:
       "Cell annotation":
         description: Cell annotation workflow
@@ -67,7 +67,7 @@ enums:
         description: Scaled count matrix
 
 classes:
-  scRNALevel34:
+  scRNALevel3and4:
     is_a: BaseSequencingAttributes
     description: Single-cell RNA-seq Level 3 and 4 - Gene expression files and cell relationships
     attributes:
@@ -87,7 +87,7 @@ classes:
       
       # scRNA-seq-specific attributes
       SCRNASEQ_WORKFLOW_TYPE:
-        range: scRNAseqWorkflowTypeEnumLevel34
+        range: scRNAseqWorkflowTypeEnumLevel3and4
         required: true
         title: "scRNAseq Workflow Type"
         description: Generic name for the workflow used to analyze a data set
diff --git a/modules/scRNA-seq/domains/scrna_seq.yaml b/modules/scRNA-seq/domains/scrna_seq.yaml
@@ -23,6 +23,6 @@ classes:
         range: scRNALevel2
         description: Level 2 scRNA-seq data
       level3_4_data:
-        range: scRNALevel34
+        range: scRNALevel3and4
         description: Level 3/4 scRNA-seq data
 
diff --git a/modules/scRNA-seq/src/htan_scrna_seq/datamodel/scrna_seq.py b/modules/scRNA-seq/src/htan_scrna_seq/datamodel/scrna_seq.py
@@ -1,5 +1,5 @@
 # Auto generated from scrna_seq.yaml by pythongen.py version: 0.0.1
-# Generation date: 2026-01-22T10:33:06
+# Generation date: 2026-01-23T15:49:22
 # Schema: scRNA-seq
 #
 # id: https://w3id.org/htan/scrna_seq
@@ -92,7 +92,7 @@ class ScRNALevel2HTANDATAFILEID(BaseSequencingAttributesHTANDATAFILEID):
     pass
 
 
-class ScRNALevel34HTANDATAFILEID(BaseSequencingAttributesHTANDATAFILEID):
+class ScRNALevel3and4HTANDATAFILEID(BaseSequencingAttributesHTANDATAFILEID):
     pass
 
 
@@ -110,7 +110,7 @@ class ScRNAseqData(YAMLRoot):
 
     level1_data: Optional[Union[str, ScRNALevel1HTANDATAFILEID]] = None
     level2_data: Optional[Union[str, ScRNALevel2HTANDATAFILEID]] = None
-    level3_4_data: Optional[Union[str, ScRNALevel34HTANDATAFILEID]] = None
+    level3_4_data: Optional[Union[str, ScRNALevel3and4HTANDATAFILEID]] = None
 
     def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         if self.level1_data is not None and not isinstance(self.level1_data, ScRNALevel1HTANDATAFILEID):
@@ -119,8 +119,8 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         if self.level2_data is not None and not isinstance(self.level2_data, ScRNALevel2HTANDATAFILEID):
             self.level2_data = ScRNALevel2HTANDATAFILEID(self.level2_data)
 
-        if self.level3_4_data is not None and not isinstance(self.level3_4_data, ScRNALevel34HTANDATAFILEID):
-            self.level3_4_data = ScRNALevel34HTANDATAFILEID(self.level3_4_data)
+        if self.level3_4_data is not None and not isinstance(self.level3_4_data, ScRNALevel3and4HTANDATAFILEID):
+            self.level3_4_data = ScRNALevel3and4HTANDATAFILEID(self.level3_4_data)
 
         super().__post_init__(**kwargs)
 
@@ -393,26 +393,26 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
 
 
 @dataclass(repr=False)
-class ScRNALevel34(BaseSequencingAttributes):
+class ScRNALevel3and4(BaseSequencingAttributes):
     """
     Single-cell RNA-seq Level 3 and 4 - Gene expression files and cell relationships
     """
     _inherited_slots: ClassVar[List[str]] = []
 
-    class_class_uri: ClassVar[URIRef] = HTAN["ScRNALevel34"]
-    class_class_curie: ClassVar[str] = "htan:ScRNALevel34"
-    class_name: ClassVar[str] = "scRNALevel34"
-    class_model_uri: ClassVar[URIRef] = HTAN.ScRNALevel34
+    class_class_uri: ClassVar[URIRef] = HTAN["ScRNALevel3and4"]
+    class_class_curie: ClassVar[str] = "htan:ScRNALevel3and4"
+    class_name: ClassVar[str] = "scRNALevel3and4"
+    class_model_uri: ClassVar[URIRef] = HTAN.ScRNALevel3and4
 
-    HTAN_DATA_FILE_ID: Union[str, ScRNALevel34HTANDATAFILEID] = None
+    HTAN_DATA_FILE_ID: Union[str, ScRNALevel3and4HTANDATAFILEID] = None
     HTAN_PARENT_ID: str = None
     LIBRARY_LAYOUT: Union[str, "LibraryLayoutEnum"] = None
     SEQUENCING_PLATFORM: Union[str, "SequencingPlatformEnum"] = None
     WORKFLOW_VERSION: str = None
     GENOMIC_REFERENCE: str = None
     FILE_FORMAT: str = None
     FILENAME: str = None
-    SCRNASEQ_WORKFLOW_TYPE: Union[str, "ScRNAseqWorkflowTypeEnumLevel34"] = None
+    SCRNASEQ_WORKFLOW_TYPE: Union[str, "ScRNAseqWorkflowTypeEnumLevel3and4"] = None
     SCRNASEQ_WORKFLOW_PARAMETERS_DESCRIPTION: str = None
     DATA_CATEGORY: Union[str, "DataCategoryEnum"] = None
     MATRIX_TYPE: Union[str, "MatrixTypeEnum"] = None
@@ -426,8 +426,8 @@ class ScRNALevel34(BaseSequencingAttributes):
     def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         if self._is_empty(self.HTAN_DATA_FILE_ID):
             self.MissingRequiredField("HTAN_DATA_FILE_ID")
-        if not isinstance(self.HTAN_DATA_FILE_ID, ScRNALevel34HTANDATAFILEID):
-            self.HTAN_DATA_FILE_ID = ScRNALevel34HTANDATAFILEID(self.HTAN_DATA_FILE_ID)
+        if not isinstance(self.HTAN_DATA_FILE_ID, ScRNALevel3and4HTANDATAFILEID):
+            self.HTAN_DATA_FILE_ID = ScRNALevel3and4HTANDATAFILEID(self.HTAN_DATA_FILE_ID)
 
         if self._is_empty(self.FILE_FORMAT):
             self.MissingRequiredField("FILE_FORMAT")
@@ -441,8 +441,8 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
 
         if self._is_empty(self.SCRNASEQ_WORKFLOW_TYPE):
             self.MissingRequiredField("SCRNASEQ_WORKFLOW_TYPE")
-        if not isinstance(self.SCRNASEQ_WORKFLOW_TYPE, ScRNAseqWorkflowTypeEnumLevel34):
-            self.SCRNASEQ_WORKFLOW_TYPE = ScRNAseqWorkflowTypeEnumLevel34(self.SCRNASEQ_WORKFLOW_TYPE)
+        if not isinstance(self.SCRNASEQ_WORKFLOW_TYPE, ScRNAseqWorkflowTypeEnumLevel3and4):
+            self.SCRNASEQ_WORKFLOW_TYPE = ScRNAseqWorkflowTypeEnumLevel3and4(self.SCRNASEQ_WORKFLOW_TYPE)
 
         if self._is_empty(self.SCRNASEQ_WORKFLOW_PARAMETERS_DESCRIPTION):
             self.MissingRequiredField("SCRNASEQ_WORKFLOW_PARAMETERS_DESCRIPTION")
@@ -687,7 +687,7 @@ def _addvals(cls):
                 text="HCA Optimus",
                 description="HCA Optimus workflow"))
 
-class ScRNAseqWorkflowTypeEnumLevel34(EnumDefinitionImpl):
+class ScRNAseqWorkflowTypeEnumLevel3and4(EnumDefinitionImpl):
 
     CellRanger = PermissibleValue(
         text="CellRanger",
@@ -712,7 +712,7 @@ class ScRNAseqWorkflowTypeEnumLevel34(EnumDefinitionImpl):
         description="dropEST workflow")
 
     _defn = EnumDefinition(
-        name="ScRNAseqWorkflowTypeEnumLevel34",
+        name="ScRNAseqWorkflowTypeEnumLevel3and4",
     )
 
     @classmethod
@@ -861,7 +861,7 @@ class slots:
                    model_uri=HTAN.scRNAseqData__level2_data, domain=None, range=Optional[Union[str, ScRNALevel2HTANDATAFILEID]])
 
 slots.scRNAseqData__level3_4_data = Slot(uri=HTAN.level3_4_data, name="scRNAseqData__level3_4_data", curie=HTAN.curie('level3_4_data'),
-                   model_uri=HTAN.scRNAseqData__level3_4_data, domain=None, range=Optional[Union[str, ScRNALevel34HTANDATAFILEID]])
+                   model_uri=HTAN.scRNAseqData__level3_4_data, domain=None, range=Optional[Union[str, ScRNALevel3and4HTANDATAFILEID]])
 
 slots.scRNALevel1__FILE_FORMAT = Slot(uri=HTAN.FILE_FORMAT, name="scRNALevel1__FILE_FORMAT", curie=HTAN.curie('FILE_FORMAT'),
                    model_uri=HTAN.scRNALevel1__FILE_FORMAT, domain=None, range=str,
@@ -915,44 +915,44 @@ class slots:
 slots.scRNALevel2__UMI_TAG = Slot(uri=HTAN.UMI_TAG, name="scRNALevel2__UMI_TAG", curie=HTAN.curie('UMI_TAG'),
                    model_uri=HTAN.scRNALevel2__UMI_TAG, domain=None, range=Optional[str])
 
-slots.scRNALevel34__FILE_FORMAT = Slot(uri=HTAN.FILE_FORMAT, name="scRNALevel34__FILE_FORMAT", curie=HTAN.curie('FILE_FORMAT'),
-                   model_uri=HTAN.scRNALevel34__FILE_FORMAT, domain=None, range=str,
+slots.scRNALevel3and4__FILE_FORMAT = Slot(uri=HTAN.FILE_FORMAT, name="scRNALevel3and4__FILE_FORMAT", curie=HTAN.curie('FILE_FORMAT'),
+                   model_uri=HTAN.scRNALevel3and4__FILE_FORMAT, domain=None, range=str,
                    pattern=re.compile(r'^h5ad$'))
 
-slots.scRNALevel34__FILENAME = Slot(uri=HTAN.FILENAME, name="scRNALevel34__FILENAME", curie=HTAN.curie('FILENAME'),
-                   model_uri=HTAN.scRNALevel34__FILENAME, domain=None, range=str,
+slots.scRNALevel3and4__FILENAME = Slot(uri=HTAN.FILENAME, name="scRNALevel3and4__FILENAME", curie=HTAN.curie('FILENAME'),
+                   model_uri=HTAN.scRNALevel3and4__FILENAME, domain=None, range=str,
                    pattern=re.compile(r'^.+\.h5ad$'))
 
-slots.scRNALevel34__SCRNASEQ_WORKFLOW_TYPE = Slot(uri=HTAN.SCRNASEQ_WORKFLOW_TYPE, name="scRNALevel34__SCRNASEQ_WORKFLOW_TYPE", curie=HTAN.curie('SCRNASEQ_WORKFLOW_TYPE'),
-                   model_uri=HTAN.scRNALevel34__SCRNASEQ_WORKFLOW_TYPE, domain=None, range=Union[str, "ScRNAseqWorkflowTypeEnumLevel34"])
+slots.scRNALevel3and4__SCRNASEQ_WORKFLOW_TYPE = Slot(uri=HTAN.SCRNASEQ_WORKFLOW_TYPE, name="scRNALevel3and4__SCRNASEQ_WORKFLOW_TYPE", curie=HTAN.curie('SCRNASEQ_WORKFLOW_TYPE'),
+                   model_uri=HTAN.scRNALevel3and4__SCRNASEQ_WORKFLOW_TYPE, domain=None, range=Union[str, "ScRNAseqWorkflowTypeEnumLevel3and4"])
 
-slots.scRNALevel34__SCRNASEQ_WORKFLOW_PARAMETERS_DESCRIPTION = Slot(uri=HTAN.SCRNASEQ_WORKFLOW_PARAMETERS_DESCRIPTION, name="scRNALevel34__SCRNASEQ_WORKFLOW_PARAMETERS_DESCRIPTION", curie=HTAN.curie('SCRNASEQ_WORKFLOW_PARAMETERS_DESCRIPTION'),
-                   model_uri=HTAN.scRNALevel34__SCRNASEQ_WORKFLOW_PARAMETERS_DESCRIPTION, domain=None, range=str)
+slots.scRNALevel3and4__SCRNASEQ_WORKFLOW_PARAMETERS_DESCRIPTION = Slot(uri=HTAN.SCRNASEQ_WORKFLOW_PARAMETERS_DESCRIPTION, name="scRNALevel3and4__SCRNASEQ_WORKFLOW_PARAMETERS_DESCRIPTION", curie=HTAN.curie('SCRNASEQ_WORKFLOW_PARAMETERS_DESCRIPTION'),
+                   model_uri=HTAN.scRNALevel3and4__SCRNASEQ_WORKFLOW_PARAMETERS_DESCRIPTION, domain=None, range=str)
 
-slots.scRNALevel34__DATA_CATEGORY = Slot(uri=HTAN.DATA_CATEGORY, name="scRNALevel34__DATA_CATEGORY", curie=HTAN.curie('DATA_CATEGORY'),
-                   model_uri=HTAN.scRNALevel34__DATA_CATEGORY, domain=None, range=Union[str, "DataCategoryEnum"])
+slots.scRNALevel3and4__DATA_CATEGORY = Slot(uri=HTAN.DATA_CATEGORY, name="scRNALevel3and4__DATA_CATEGORY", curie=HTAN.curie('DATA_CATEGORY'),
+                   model_uri=HTAN.scRNALevel3and4__DATA_CATEGORY, domain=None, range=Union[str, "DataCategoryEnum"])
 
-slots.scRNALevel34__MATRIX_TYPE = Slot(uri=HTAN.MATRIX_TYPE, name="scRNALevel34__MATRIX_TYPE", curie=HTAN.curie('MATRIX_TYPE'),
-                   model_uri=HTAN.scRNALevel34__MATRIX_TYPE, domain=None, range=Union[str, "MatrixTypeEnum"])
+slots.scRNALevel3and4__MATRIX_TYPE = Slot(uri=HTAN.MATRIX_TYPE, name="scRNALevel3and4__MATRIX_TYPE", curie=HTAN.curie('MATRIX_TYPE'),
+                   model_uri=HTAN.scRNALevel3and4__MATRIX_TYPE, domain=None, range=Union[str, "MatrixTypeEnum"])
 
-slots.scRNALevel34__LINKED_MATRICES = Slot(uri=HTAN.LINKED_MATRICES, name="scRNALevel34__LINKED_MATRICES", curie=HTAN.curie('LINKED_MATRICES'),
-                   model_uri=HTAN.scRNALevel34__LINKED_MATRICES, domain=None, range=Optional[str])
+slots.scRNALevel3and4__LINKED_MATRICES = Slot(uri=HTAN.LINKED_MATRICES, name="scRNALevel3and4__LINKED_MATRICES", curie=HTAN.curie('LINKED_MATRICES'),
+                   model_uri=HTAN.scRNALevel3and4__LINKED_MATRICES, domain=None, range=Optional[str])
 
-slots.scRNALevel34__CELL_MEDIAN_NUMBER_READS = Slot(uri=HTAN.CELL_MEDIAN_NUMBER_READS, name="scRNALevel34__CELL_MEDIAN_NUMBER_READS", curie=HTAN.curie('CELL_MEDIAN_NUMBER_READS'),
-                   model_uri=HTAN.scRNALevel34__CELL_MEDIAN_NUMBER_READS, domain=None, range=int)
+slots.scRNALevel3and4__CELL_MEDIAN_NUMBER_READS = Slot(uri=HTAN.CELL_MEDIAN_NUMBER_READS, name="scRNALevel3and4__CELL_MEDIAN_NUMBER_READS", curie=HTAN.curie('CELL_MEDIAN_NUMBER_READS'),
+                   model_uri=HTAN.scRNALevel3and4__CELL_MEDIAN_NUMBER_READS, domain=None, range=int)
 
-slots.scRNALevel34__CELL_MEDIAN_NUMBER_GENES = Slot(uri=HTAN.CELL_MEDIAN_NUMBER_GENES, name="scRNALevel34__CELL_MEDIAN_NUMBER_GENES", curie=HTAN.curie('CELL_MEDIAN_NUMBER_GENES'),
-                   model_uri=HTAN.scRNALevel34__CELL_MEDIAN_NUMBER_GENES, domain=None, range=int)
+slots.scRNALevel3and4__CELL_MEDIAN_NUMBER_GENES = Slot(uri=HTAN.CELL_MEDIAN_NUMBER_GENES, name="scRNALevel3and4__CELL_MEDIAN_NUMBER_GENES", curie=HTAN.curie('CELL_MEDIAN_NUMBER_GENES'),
+                   model_uri=HTAN.scRNALevel3and4__CELL_MEDIAN_NUMBER_GENES, domain=None, range=int)
 
-slots.scRNALevel34__CELL_TOTAL = Slot(uri=HTAN.CELL_TOTAL, name="scRNALevel34__CELL_TOTAL", curie=HTAN.curie('CELL_TOTAL'),
-                   model_uri=HTAN.scRNALevel34__CELL_TOTAL, domain=None, range=int)
+slots.scRNALevel3and4__CELL_TOTAL = Slot(uri=HTAN.CELL_TOTAL, name="scRNALevel3and4__CELL_TOTAL", curie=HTAN.curie('CELL_TOTAL'),
+                   model_uri=HTAN.scRNALevel3and4__CELL_TOTAL, domain=None, range=int)
 
-slots.scRNALevel34__ANNDATA_SCHEMA_VERSION = Slot(uri=HTAN.ANNDATA_SCHEMA_VERSION, name="scRNALevel34__ANNDATA_SCHEMA_VERSION", curie=HTAN.curie('ANNDATA_SCHEMA_VERSION'),
-                   model_uri=HTAN.scRNALevel34__ANNDATA_SCHEMA_VERSION, domain=None, range=str,
+slots.scRNALevel3and4__ANNDATA_SCHEMA_VERSION = Slot(uri=HTAN.ANNDATA_SCHEMA_VERSION, name="scRNALevel3and4__ANNDATA_SCHEMA_VERSION", curie=HTAN.curie('ANNDATA_SCHEMA_VERSION'),
+                   model_uri=HTAN.scRNALevel3and4__ANNDATA_SCHEMA_VERSION, domain=None, range=str,
                    pattern=re.compile(r'^0\.1$'))
 
-slots.scRNALevel34__ANNDATA_STRUCTURE_VALIDATED = Slot(uri=HTAN.ANNDATA_STRUCTURE_VALIDATED, name="scRNALevel34__ANNDATA_STRUCTURE_VALIDATED", curie=HTAN.curie('ANNDATA_STRUCTURE_VALIDATED'),
-                   model_uri=HTAN.scRNALevel34__ANNDATA_STRUCTURE_VALIDATED, domain=None, range=Union[bool, Bool])
+slots.scRNALevel3and4__ANNDATA_STRUCTURE_VALIDATED = Slot(uri=HTAN.ANNDATA_STRUCTURE_VALIDATED, name="scRNALevel3and4__ANNDATA_STRUCTURE_VALIDATED", curie=HTAN.curie('ANNDATA_STRUCTURE_VALIDATED'),
+                   model_uri=HTAN.scRNALevel3and4__ANNDATA_STRUCTURE_VALIDATED, domain=None, range=Union[bool, Bool])
 
 slots.baseSequencingAttributes__SEQUENCING_BATCH_ID = Slot(uri=HTAN.SEQUENCING_BATCH_ID, name="baseSequencingAttributes__SEQUENCING_BATCH_ID", curie=HTAN.curie('SEQUENCING_BATCH_ID'),
                    model_uri=HTAN.baseSequencingAttributes__SEQUENCING_BATCH_ID, domain=None, range=Optional[str])
diff --git a/modules/scRNA-seq/tests/test_scrna_seq.py b/modules/scRNA-seq/tests/test_scrna_seq.py
@@ -71,10 +71,10 @@ def test_level3_4_schema(self):
         sv = SchemaView(LEVEL3_4_PATH)
         
         # Check class exists
-        assert "scRNALevel34" in sv.all_classes()
+        assert "scRNALevel3and4" in sv.all_classes()
         
         # Check required attributes (base attributes come from inheritance)
-        level3_4_class = sv.get_class("scRNALevel34")
+        level3_4_class = sv.get_class("scRNALevel3and4")
         required_attrs = [
             "FILE_FORMAT",
             "SCRNASEQ_WORKFLOW_TYPE",
@@ -94,7 +94,7 @@ def test_h5ad_file_format_validation(self):
         """Test h5ad file format validation."""
         sv = SchemaView(LEVEL3_4_PATH)
         
-        level3_4_class = sv.get_class("scRNALevel34")
+        level3_4_class = sv.get_class("scRNALevel3and4")
         file_format_attr = level3_4_class.attributes["FILE_FORMAT"]
         
         # Check pattern validation
@@ -162,7 +162,7 @@ def test_ann_data_schema_compliance(self):
         """Test AnnData schema compliance validation."""
         sv = SchemaView(LEVEL3_4_PATH)
         
-        level3_4_class = sv.get_class("scRNALevel34")
+        level3_4_class = sv.get_class("scRNALevel3and4")
         
         # Check AnnData schema version pattern
         schema_version_attr = level3_4_class.attributes["ANNDATA_SCHEMA_VERSION"]
@@ -205,7 +205,7 @@ def test_enum_alphabetical_ordering(self):
         sv = SchemaView(LEVEL3_4_PATH)
         
         level3_4_enums = [
-            "scRNAseqWorkflowTypeEnumLevel34",
+            "scRNAseqWorkflowTypeEnumLevel3and4",
             "DataCategoryEnum",
             "MatrixTypeEnum"
         ]
@@ -220,7 +220,7 @@ def test_inheritance_from_base_sequencing(self):
         sv = SchemaView(SCHEMA_PATH)
         
         # Check inheritance for all levels
-        for level_class in ["scRNALevel1", "scRNALevel2", "scRNALevel34"]:
+        for level_class in ["scRNALevel1", "scRNALevel2", "scRNALevel3and4"]:
             class_def = sv.get_class(level_class)
             assert class_def.is_a == "BaseSequencingAttributes"
 

Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,5 @@`
`1`	`1`	`# Auto generated from biospecimen.yaml by pythongen.py version: 0.0.1`
`2`		`-# Generation date: 2026-01-22T10:32:44`
	`2`	`+# Generation date: 2026-01-23T15:49:04`
`3`	`3`	`# Schema: Biospecimen`
`4`	`4`	`#`
`5`	`5`	`# id: https://w3id.org/htan/biospecimen`
Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,5 @@`
`1`	`1`	`# Auto generated from clinical.yaml by pythongen.py version: 0.0.1`
`2`		`-# Generation date: 2026-01-22T10:32:12`
	`2`	`+# Generation date: 2026-01-23T15:48:34`
`3`	`3`	`# Schema: Clinical`
`4`	`4`	`#`
`5`	`5`	`# id: https://w3id.org/htan/clinical`
Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,5 @@`
`1`	`1`	`# Auto generated from digital_pathology.yaml by pythongen.py version: 0.0.1`
`2`		`-# Generation date: 2026-01-22T10:33:09`
	`2`	`+# Generation date: 2026-01-23T15:49:23`
`3`	`3`	`# Schema: DigitalPathology`
`4`	`4`	`#`
`5`	`5`	`# id: https://w3id.org/htan/digital_pathology`
Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,5 @@`
`1`	`1`	`# Auto generated from imaging.yaml by pythongen.py version: 0.0.1`
`2`		`-# Generation date: 2026-01-22T10:33:04`
	`2`	`+# Generation date: 2026-01-23T15:49:20`
`3`	`3`	`# Schema: Imaging`
`4`	`4`	`#`
`5`	`5`	`# id: https://w3id.org/htan/imaging`
Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,5 @@`
`1`	`1`	`# Auto generated from multiplex_microscopy.yaml by pythongen.py version: 0.0.1`
`2`		`-# Generation date: 2026-01-22T10:33:12`
	`2`	`+# Generation date: 2026-01-23T15:49:25`
`3`	`3`	`# Schema: MultiplexMicroscopy`
`4`	`4`	`#`
`5`	`5`	`# id: https://w3id.org/htan/multiplex_microscopy`
Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,5 @@`
`1`	`1`	`# Auto generated from sequencing.yaml by pythongen.py version: 0.0.1`
`2`		`-# Generation date: 2026-01-22T10:33:02`
	`2`	`+# Generation date: 2026-01-23T15:49:18`
`3`	`3`	`# Schema: Sequencing`
`4`	`4`	`#`
`5`	`5`	`# id: https://w3id.org/htan/sequencing`
Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,5 @@`
`1`	`1`	`# Auto generated from spatial.yaml by pythongen.py version: 0.0.1`
`2`		`-# Generation date: 2026-01-22T10:33:15`
	`2`	`+# Generation date: 2026-01-23T15:49:27`
`3`	`3`	`# Schema: SpatialOmics`
`4`	`4`	`#`
`5`	`5`	`# id: https://w3id.org/htan/spatial`
Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,5 @@`
`1`	`1`	`# Auto generated from wes.yaml by pythongen.py version: 0.0.1`
`2`		`-# Generation date: 2026-01-22T10:32:42`
	`2`	`+# Generation date: 2026-01-23T15:49:02`
`3`	`3`	`# Schema: WES`
`4`	`4`	`#`
`5`	`5`	`# id: https://w3id.org/htan/wes`