liminal-orm 1.0.3.dev1__tar.gz → 1.0.4.dev1__tar.gz

{liminal_orm-1.0.3.dev1 → liminal_orm-1.0.4.dev1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: liminal-orm
-Version: 1.0.3.dev1
+Version: 1.0.4.dev1
 Summary: An ORM and toolkit that builds on top of Benchling's platform to keep your schemas and downstream code dependencies in sync.
 Author: DynoTx Open Source
 Author-email: opensource@dynotx.com

{liminal_orm-1.0.3.dev1 → liminal_orm-1.0.4.dev1}/liminal/cli/cli.py

@@ -78,8 +78,8 @@ def generate_files(
     benchling_tenant: str = typer.Argument(
         ..., help="Benchling tenant (or alias) to connect to."
     ),
-    write_path: Path = typer.Argument(
-        ..., help="The path to write the generated files to."
+    write_path: Path = typer.Option(
+        Path("."), help="The path to write the generated files to."
     ),
 ) -> None:
     current_revision_id, benchling_connection = read_local_env_file(

{liminal_orm-1.0.3.dev1 → liminal_orm-1.0.4.dev1}/liminal/dropdowns/compare.py

@@ -19,7 +19,7 @@ def compare_dropdowns(
 ) -> dict[str, list[CompareOperation]]:
     dropdown_operations: dict[str, list[CompareOperation]] = {}
     benchling_dropdowns: dict[str, Dropdown] = get_benchling_dropdowns_dict(
-        benchling_service
+        benchling_service, include_archived=True
     )
     processed_benchling_names = set()
     model_dropdowns = BaseDropdown.get_all_subclasses(dropdown_names)

{liminal_orm-1.0.3.dev1 → liminal_orm-1.0.4.dev1}/liminal/dropdowns/utils.py

@@ -57,15 +57,15 @@ def get_benchling_dropdown_by_name(
 
 def get_benchling_dropdowns_dict(
     benchling_service: BenchlingService,
+    include_archived: bool = False,
 ) -> dict[str, Dropdown]:
-    with requests.Session() as session:
-        request = session.get(
-            f"https://{benchling_service.benchling_tenant}.benchling.com/1/api/schema-field-selectors/?registryId={benchling_service.registry_id}",
-            headers=benchling_service.custom_post_headers,
-            cookies=benchling_service.custom_post_cookies,
-        )
-    return {
-        d["name"]: Dropdown(
+    def _convert_dropdown_from_json(
+        d: dict[str, Any], include_archived: bool = False
+    ) -> Dropdown:
+        all_options = d["allSchemaFieldSelectorOptions"]
+        if not include_archived:
+            all_options = [o for o in all_options if not o["archiveRecord"]]
+        return Dropdown(
             id=d["id"],
             name=d["name"],
             archive_record=BenchlingArchiveRecord(reason=d["archiveRecord"]["purpose"])
@@ -81,11 +81,26 @@ def get_benchling_dropdowns_dict(
                     if o["archiveRecord"]
                     else None,
                 )
-                for o in d["allSchemaFieldSelectorOptions"]
+                for o in all_options
             ],
         )
-        for d in request.json()["selectorsByRegistryId"][benchling_service.registry_id]
+
+    with requests.Session() as session:
+        request = session.get(
+            f"https://{benchling_service.benchling_tenant}.benchling.com/1/api/schema-field-selectors/?registryId={benchling_service.registry_id}",
+            headers=benchling_service.custom_post_headers,
+            cookies=benchling_service.custom_post_cookies,
+        )
+        all_dropdowns = request.json()["selectorsByRegistryId"][
+            benchling_service.registry_id
+        ]
+        if not include_archived:
+            all_dropdowns = [d for d in all_dropdowns if not d["archiveRecord"]]
+    dropdowns = {
+        d["name"]: _convert_dropdown_from_json(d, include_archived)
+        for d in all_dropdowns
     }
+    return dropdowns
 
 
 def dropdown_exists_in_benchling(

{liminal_orm-1.0.3.dev1 → liminal_orm-1.0.4.dev1}/liminal/entity_schemas/generate_files.py

@@ -90,7 +90,7 @@ def generate_all_entity_schema_files(
                 dropdown_classname = dropdown_name_to_classname_map[col.dropdown_link]
                 dropdowns.append(dropdown_classname)
             column_strings.append(
-                f"""{tab}{col_name}: SqlColumn = Column(name="{col.name}", type={str(col.type)}, required={col.required}{', is_multi=True' if col.is_multi else ''}{', parent_link=True' if col.parent_link else ''}{f', entity_link="{col.entity_link}"' if col.entity_link else ''}{f', dropdown={dropdown_classname}' if dropdown_classname else ''})"""
+                f"""{tab}{col_name}: SqlColumn = Column(name="{col.name}", type={str(col.type)}, required={col.required}{', is_multi=True' if col.is_multi else ''}{', parent_link=True' if col.parent_link else ''}{f', entity_link="{col.entity_link}"' if col.entity_link else ''}{f', dropdown={dropdown_classname}' if dropdown_classname else ''}{f', tooltip="{col.tooltip}"' if col.tooltip else ''})"""
             )
             if col.required and col.type:
                 init_strings.append(

{liminal_orm-1.0.3.dev1 → liminal_orm-1.0.4.dev1}/liminal/entity_schemas/utils.py

@@ -41,6 +41,9 @@ def convert_tag_schema_to_internal_schema(
     dropdowns_map: dict[str, str],
     include_archived_fields: bool = False,
 ) -> tuple[SchemaProperties, dict[str, BaseFieldProperties]]:
+    all_fields = tag_schema.allFields
+    if not include_archived_fields:
+        all_fields = [f for f in all_fields if not f.archiveRecord]
     return (
         SchemaProperties(
             name=tag_schema.name,
@@ -63,11 +66,7 @@ def convert_tag_schema_to_internal_schema(
         ).set_archived(tag_schema.archiveRecord is not None),
         {
             f.systemName: convert_tag_schema_field_to_field_properties(f, dropdowns_map)
-            for f in (
-                tag_schema.allFields
-                if include_archived_fields
-                else [f for f in tag_schema.allFields if not f.archiveRecord]
-            )
+            for f in all_fields
         },
     )
 

{liminal_orm-1.0.3.dev1 → liminal_orm-1.0.4.dev1}/liminal/utils.py

@@ -9,14 +9,14 @@ from liminal.connection.benchling_service import BenchlingService
 
 def pascalize(input_string: str) -> str:
     return "".join(
-        re.sub(r"[\[\]{}()]", "", word).capitalize()
+        re.sub(r"[\[\]{}():]", "", word).capitalize()
         for word in re.split(r"[ /_\-]", input_string)
     )
 
 
 def to_snake_case(input_string: str) -> str:
     return "_".join(
-        re.sub(r"[\[\]{}()]", "", word).lower()
+        re.sub(r"[\[\]{}():]", "", word).lower()
         for word in re.split(r"[ /_\-]", input_string)
     )
 

{liminal_orm-1.0.3.dev1 → liminal_orm-1.0.4.dev1}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "liminal-orm"
-version = "1.0.3.dev1"
+version = "1.0.4.dev1"
 description = "An ORM and toolkit that builds on top of Benchling's platform to keep your schemas and downstream code dependencies in sync."
 authors = ["DynoTx Open Source <opensource@dynotx.com>"]
 readme = "README.md"
@@ -22,7 +22,7 @@ lxml = "^5.3.0"
 [tool.poetry.group.dev.dependencies]
 ipykernel = "^6.29.5"
 mkdocs-material = "^9.5.41"
-mypy = "^1.11.2"
+mypy = "^1.1.1"
 pre-commit = "^4.0.1"
 pytest = "^8.3.3"
 ruff = "^0.6.9"