liminal-orm 1.0.2rc0__py3-none-any.whl → 1.0.3__py3-none-any.whl

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/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/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/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/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/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-1.0.2rc0.dist-info → liminal_orm-1.0.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: liminal-orm
-Version: 1.0.2rc0
+Version: 1.0.3
 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
@@ -12,8 +12,8 @@ Classifier: Programming Language :: Python :: 3.11
 Requires-Dist: benchling-sdk (>=1.8.0)
 Requires-Dist: bs4 (>=0.0.2,<0.0.3)
 Requires-Dist: lxml (>=5.3.0,<6.0.0)
-Requires-Dist: pandas (>=2.2.3,<3.0.0)
-Requires-Dist: pydantic (>=2,<2.7)
+Requires-Dist: pandas (>=1.5.3)
+Requires-Dist: pydantic (>=2,<=2.7)
 Requires-Dist: requests (>=2.32.3,<3.0.0)
 Requires-Dist: rich (>=13.9.2,<14.0.0)
 Requires-Dist: sqlalchemy (<2)

{liminal_orm-1.0.2rc0.dist-info → liminal_orm-1.0.3.dist-info}/RECORD

@@ -6,7 +6,7 @@ liminal/base/compare_operation.py,sha256=hkpv4ewHhxy4dlTPKgJuzBjsAqO6Km7OrrKB44p
 liminal/base/properties/base_field_properties.py,sha256=V9UlY_geSoOhx_Iwiw2eZ7kDKghYy4Xa5bbGcCOFDk8,4511
 liminal/base/properties/base_schema_properties.py,sha256=XIgTZvWYjqpSXJ-_uSew0sp-wWRb62-McmJtJ5rdNg0,3925
 liminal/base/str_enum.py,sha256=jF3d-Lo8zsHUe6GsctX2L-TSj92Y3qCYDrTD-saeJoc,210
-liminal/cli/cli.py,sha256=tIdepgPf3UoZcKec93rN6yc3JfOs-GA9SoIdGJs4fi8,8994
+liminal/cli/cli.py,sha256=Bv0H_RWLpPxaCNmD4X9l_0wYQ8VCDbAHwALvCTUxB1g,8998
 liminal/cli/controller.py,sha256=QNj3QO9TMb9hfc6U-VhLuFa0_aohOHZUmvY4XkATPhw,10118
 liminal/cli/live_test_dropdown_migration.py,sha256=i20JkY5xmLffHrB73WOl3Tjyb4V2RPb3rt7-wh-BwME,2826
 liminal/cli/live_test_entity_schema_migration.py,sha256=X03tEYYHYDXeXHWgLc9tcwksKVvr0b7nlYQndDS4MvA,5683
@@ -14,17 +14,17 @@ liminal/connection/__init__.py,sha256=3z4pSANIOkc9mh1Xp763oYQuJZDEh4lauN901PU4vq
 liminal/connection/benchling_connection.py,sha256=ZcKmaQE6T_yjAaSPF69e2PnhoZz5yZ_0TywjVykr0TM,2358
 liminal/connection/benchling_service.py,sha256=SEydyYUV3Zm55gAWs8tL2U9feLgbZITV_hH40aXIfBU,7397
 liminal/dropdowns/api.py,sha256=n5oxi1EhkmpmPpNi1LOI4xcIQmk1C069XFaGP5XSBx8,6959
-liminal/dropdowns/compare.py,sha256=N2niypG547k9e-iwWMi-TmlRDEiYAPkiVYaPRDVSXhU,6806
+liminal/dropdowns/compare.py,sha256=5cz8djtaStozUun_Cp8t_5PVjq-aovme2Qq5J8FXFg4,6829
 liminal/dropdowns/generate_files.py,sha256=IqnBs-IyLsIZE0NUkdB99zd5EAF-1f9CPBeblz-GzJE,2041
 liminal/dropdowns/operations.py,sha256=U1pHLVWEj4Rgms9sV4rpDuvCVm_NsQxJKLhsezx2bMw,13479
-liminal/dropdowns/utils.py,sha256=WGqF4WfPvk3SXg0106y7COGQep_Po8Y_mNsJI6Od-a8,3550
+liminal/dropdowns/utils.py,sha256=1-H7bTszCUeqeRBpiYXjRjreDzhn1Fd1MFwIsrEI-o4,4109
 liminal/entity_schemas/api.py,sha256=Dkd44NGJ4JqRTJLJtPsZ8Qan2owbEYf446A6EuP8iL0,2786
 liminal/entity_schemas/compare.py,sha256=EL5v82FEBxMIubhlQmsmQO7a-EZeMWXRU2pBt9HmzPI,13849
 liminal/entity_schemas/entity_schema_models.py,sha256=X2ouBUWIonrWeB3hMVj0bCqchbcztrp3joaftv8yHWo,5393
-liminal/entity_schemas/generate_files.py,sha256=XdnyoTDitQKUrC7xrYBWzyFWw_xHQgoS4UV-dtOqUuU,8389
+liminal/entity_schemas/generate_files.py,sha256=ZiTk_6wqnW_5_uW6gfCP13qUGd8uqlIh-wi7ydSk8N0,8442
 liminal/entity_schemas/operations.py,sha256=sub6rigZjro72EMqqsayOYNxPL6eDYwCCIlzMr9sNfQ,23306
 liminal/entity_schemas/tag_schema_models.py,sha256=VVqI9iC7T_p1RZJSu09AsptK7Cr-YQvXjYP5cjhpeBo,15979
-liminal/entity_schemas/utils.py,sha256=JkCns-RqyaGzQRYyWW0ma1yb7BBHoNxprw5MUbsspzY,4213
+liminal/entity_schemas/utils.py,sha256=tJVEfpJ6CtpuYI1_LWOE5-pGzNe0bsrGluLbU8sc9EM,4192
 liminal/enums/__init__.py,sha256=jz_c-B_fifatvrYoESlHZ9ljYdz-3rNl0sBazoESiHI,523
 liminal/enums/benchling_api_field_type.py,sha256=DEMlkvKuc8kaslnKdWsdB8Z70OY3CGwOHfZNC3a1SOE,528
 liminal/enums/benchling_entity_type.py,sha256=t00mcbzbfQ9oiHt8xPrmNYs9bK7Bmk6F1dcoQubzmUs,409
@@ -52,10 +52,10 @@ liminal/tests/conftest.py,sha256=kKli52zn-J48Tsqbqejyd8Mtref5gVg3_Qex6KbLHd8,160
 liminal/tests/from benchling_sdk.py,sha256=CjRUHFB3iaa4rUPLGOqDiBq5EPKldm-Fd8aQQr92zF4,147
 liminal/tests/test_dropdown_compare.py,sha256=yHB0ovQlBLRu8-qYkqIPd8VtYEOmOft_93FQM86g_z8,8198
 liminal/tests/test_entity_schema_compare.py,sha256=FBYxqIB9oeFArWYKnbGV8I7NPzv2syziaPjEQg-wZ1o,15529
-liminal/utils.py,sha256=8aY7jvSBd3P1NNenHp4cRCNmjApSBC6DdMuAZMcvGvw,2564
+liminal/utils.py,sha256=UT07vILwm9fu8DLgwIxMm1DxEPFIIsW-0mgBU8oNrNY,2566
 liminal/validation/__init__.py,sha256=SBd48xxBMJrBzI48G2RcK056EMlevt5YjmZMkfCWN1I,6924
-liminal_orm-1.0.2rc0.dist-info/LICENSE.md,sha256=oVA877F_D1AV44dpjsv4f-4k690uNGApX1EtzOo3T8U,11353
-liminal_orm-1.0.2rc0.dist-info/METADATA,sha256=f2riPIO-DL2a9H1AVYKssB1ZbXE3VYx4sj4OoinjxOA,11805
-liminal_orm-1.0.2rc0.dist-info/WHEEL,sha256=kLuE8m1WYU0Ig0_YEGrXyTtiJvKPpLpDEiChiNyei5Y,88
-liminal_orm-1.0.2rc0.dist-info/entry_points.txt,sha256=atIrU63rrzH81dWC2sjUbFLlc5FWMmYRdMxXEWexIZA,47
-liminal_orm-1.0.2rc0.dist-info/RECORD,,
+liminal_orm-1.0.3.dist-info/LICENSE.md,sha256=oVA877F_D1AV44dpjsv4f-4k690uNGApX1EtzOo3T8U,11353
+liminal_orm-1.0.3.dist-info/METADATA,sha256=kZKg7zRldnulEPHB9ryLiPzSs9EnRYil6QbJSBLJT48,11796
+liminal_orm-1.0.3.dist-info/WHEEL,sha256=kLuE8m1WYU0Ig0_YEGrXyTtiJvKPpLpDEiChiNyei5Y,88
+liminal_orm-1.0.3.dist-info/entry_points.txt,sha256=atIrU63rrzH81dWC2sjUbFLlc5FWMmYRdMxXEWexIZA,47
+liminal_orm-1.0.3.dist-info/RECORD,,