Retain formatting of Display name for annotations and table column names

schematic/help.py

@@ -101,11 +101,6 @@
                 "The component or data type from the data model which you can use to validate the "
                 "data filled in your manifest template."
             ),
-            "use_schema_label": (
-                "Store attributes using the schema label (--use_schema_label, default) or store attributes using the display label "
-                "(--use_display_label). Attribute display names in the schema must not only include characters that are "
-                "not accepted by Synapse. Annotation names may only contain: letters, numbers, '_' and '.'"
-            ),
             "hide_blanks": (
                 "This is a boolean flag. If flag is provided when command line utility is executed, annotations with blank values will be hidden from a dataset's annotation list in Synaspe."
                 "If not, annotations with blank values will be displayed."
@@ -127,7 +122,16 @@
                 "'upsert' should be used for initial table uploads if users intend to upsert into them at a later time."
                 "Using 'upsert' at creation will generate the metadata necessary for upsert functionality."
                 "Upsert functionality requires primary keys to be specified in the data model and manfiest as <component>_id."
-                "Currently it is required to use -dl/--use_display_label with table upserts."
+                "Currently it is required to use --table_column_names = display_name with table upserts."
+            ),
+            "annotation_keys": (
+                "Store attributes using the class label (default) or store attributes using the display label. "
+                "Attribute display names in the schema must not only include characters that are "
+                "not accepted by Synapse. Annotation names may only contain: letters, numbers, '_' and '.'"
+            ),
+            "table_column_names": (
+                "class_label, display_label, display_name, default, class_label. When true annotations and table columns will be uploaded with the display name formatting with blacklisted characters removed. "
+                "To use for tables, use in conjunction with the use_schema_label flag."
             ),
         },
         "validate": {

schematic/models/commands.py

@@ -72,12 +72,6 @@ def model(ctx, config):  # use as `schematic model ...`
     "--validate_component",
     help=query_dict(model_commands, ("model", "submit", "validate_component")),
 )
-@click.option(
-    "--use_schema_label/--use_display_label",
-    "-sl/-dl",
-    default=True,
-    help=query_dict(model_commands, ("model", "submit", "use_schema_label")),
-)
 @click.option(
     "--hide_blanks",
     "-hb",
@@ -114,18 +108,35 @@ def model(ctx, config):  # use as `schematic model ...`
     type=click.Choice(["replace", "upsert"], case_sensitive=True),
     help=query_dict(model_commands, ("model", "submit", "table_manipulation")),
 )
+@click.option(
+    "--table_column_names",
+    "-tcn",
+    default="class_label",
+    type=click.Choice(
+        ["class_label", "display_label", "display_name"], case_sensitive=True
+    ),
+    help=query_dict(model_commands, ("model", "submit", "table_column_names")),
+)
+@click.option(
+    "--annotation_keys",
+    "-ak",
+    default="class_label",
+    type=click.Choice(["class_label", "display_label"], case_sensitive=True),
+    help=query_dict(model_commands, ("model", "submit", "annotation_keys")),
+)
 @click.pass_obj
 def submit_manifest(
     ctx,
     manifest_path,
     dataset_id,
     validate_component,
     manifest_record_type,
-    use_schema_label,
     hide_blanks,
     restrict_rules,
     project_scope,
     table_manipulation,
+    table_column_names,
+    annotation_keys,
 ):
     """
     Running CLI with manifest validation (optional) and submission options.
@@ -145,10 +156,11 @@ def submit_manifest(
         validate_component=validate_component,
         manifest_record_type=manifest_record_type,
         restrict_rules=restrict_rules,
-        use_schema_label=use_schema_label,
         hide_blanks=hide_blanks,
         project_scope=project_scope,
         table_manipulation=table_manipulation,
+        table_column_names=table_column_names,
+        annotation_keys=annotation_keys,
     )
 
     if manifest_id:

schematic/models/metadata.py

@@ -1,6 +1,7 @@
 import os
 import logging
 import networkx as nx
+from os.path import exists
 from jsonschema import ValidationError
 
 # allows specifying explicit variable types
@@ -11,7 +12,6 @@
 from schematic.schemas.data_model_parser import DataModelParser
 from schematic.schemas.data_model_json_schema import DataModelJSONSchema
 
-
 # TODO: This module should only be aware of the store interface
 # we shouldn't need to expose Synapse functionality explicitly
 from schematic.store.synapse import SynapseStorage
@@ -322,10 +322,11 @@ def submit_metadata_manifest(
         restrict_rules: bool,
         access_token: Optional[str] = None,
         validate_component: Optional[str] = None,
-        use_schema_label: bool = True,
         hide_blanks: bool = False,
         project_scope: List = None,
         table_manipulation: str = "replace",
+        table_column_names: str = "class_label",
+        annotation_keys: str = "class_label",
     ) -> str:
         """Wrap methods that are responsible for validation of manifests for a given component, and association of the
         same manifest file with a specified dataset.
@@ -382,9 +383,10 @@ def submit_metadata_manifest(
                         metadataManifestPath=censored_manifest_path,
                         datasetId=dataset_id,
                         manifest_record_type=manifest_record_type,
-                        useSchemaLabel=use_schema_label,
                         hideBlanks=hide_blanks,
                         table_manipulation=table_manipulation,
+                        table_column_names=table_column_names,
+                        annotation_keys=annotation_keys,
                     )
                     restrict_maniest = True
 
@@ -393,10 +395,11 @@ def submit_metadata_manifest(
                     metadataManifestPath=manifest_path,
                     datasetId=dataset_id,
                     manifest_record_type=manifest_record_type,
-                    useSchemaLabel=use_schema_label,
                     hideBlanks=hide_blanks,
                     restrict_manifest=restrict_maniest,
                     table_manipulation=table_manipulation,
+                    table_column_names=table_column_names,
+                    annotation_keys=annotation_keys,
                 )
 
                 logger.info(f"No validation errors occured during validation.")
@@ -415,9 +418,10 @@ def submit_metadata_manifest(
                 metadataManifestPath=censored_manifest_path,
                 datasetId=dataset_id,
                 manifest_record_type=manifest_record_type,
-                useSchemaLabel=use_schema_label,
                 hideBlanks=hide_blanks,
                 table_manipulation=table_manipulation,
+                table_column_names=table_column_names,
+                annotation_keys=annotation_keys,
             )
             restrict_maniest = True
 
@@ -426,10 +430,11 @@ def submit_metadata_manifest(
             metadataManifestPath=manifest_path,
             datasetId=dataset_id,
             manifest_record_type=manifest_record_type,
-            useSchemaLabel=use_schema_label,
             hideBlanks=hide_blanks,
             restrict_manifest=restrict_maniest,
             table_manipulation=table_manipulation,
+            table_column_names=table_column_names,
+            annotation_keys=annotation_keys,
         )
 
         logger.debug(