feat!: remove file handling (#124)

* Updating dependencies.

* Upgrade strawberry-graphql.

* Allow Strawberry's GQL errors to pass through without changes.

* Remove file handling.

platformics/cli/main.py

@@ -43,20 +43,18 @@ def api() -> None:
 @api.command("generate")
 @click.option("--schemafile", type=str, required=True)
 @click.option("--output-prefix", type=str, required=True)
-@click.option("--render-files/--skip-render-files", type=bool, default=True, show_default=True)
 @click.option("--template-override-paths", type=str, multiple=True)
 @click.pass_context
 def api_generate(
     ctx: click.Context,
     schemafile: str,
     output_prefix: str,
-    render_files: bool,
     template_override_paths: tuple[str],
 ) -> None:
     """
     Launch code generation
     """
-    generate(schemafile, output_prefix, render_files, template_override_paths)
+    generate(schemafile, output_prefix, template_override_paths)
 
 
 @cli.group()

platformics/codegen/generator.py

@@ -62,7 +62,6 @@ def generate_entity_subclass_files(
     template_filename: str,
     environment: Environment,
     view: ViewWrapper,
-    render_files: bool,
 ) -> None:
     """
     Code generation for SQLAlchemy models, GraphQL types, Cerbos policies, and Factoryboy factories
@@ -76,13 +75,11 @@ def generate_entity_subclass_files(
             override_template = environment.get_template(f"{dest_filename}.j2")
             content = override_template.render(
                 cls=entity,
-                render_files=render_files,
                 view=view,
             )
         else:
             content = template.render(
                 cls=entity,
-                render_files=render_files,
                 view=view,
             )
         with open(os.path.join(output_prefix, dest_filename), mode="w", encoding="utf-8") as outfile:
@@ -94,7 +91,6 @@ def generate_entity_import_files(
     output_prefix: str,
     environment: Environment,
     view: ViewWrapper,
-    render_files: bool,
 ) -> None:
     """
     Code generation for database model imports, and GraphQL queries/mutations
@@ -116,7 +112,6 @@ def generate_entity_import_files(
         import_template = environment.get_template(f"{filename}.j2")
         content = import_template.render(
             classes=classes,
-            render_files=render_files,
             view=view,
         )
         with open(os.path.join(output_prefix, filename), mode="w", encoding="utf-8") as outfile:
@@ -134,7 +129,7 @@ def regex_replace(txt, rgx, val, ignorecase=False, multiline=False):
     return compiled_rgx.sub(val, txt)
 
 
-def generate(schemafile: str, output_prefix: str, render_files: bool, template_override_paths: tuple[str]) -> None:
+def generate(schemafile: str, output_prefix: str, template_override_paths: tuple[str]) -> None:
     """
     Launch code generation
     """
@@ -157,48 +152,42 @@ def generate(schemafile: str, output_prefix: str, render_files: bool, template_o
     # Generate enums and import files
     generate_enums(output_prefix, environment, wrapped_view)
     generate_limit_offset_type(output_prefix, environment)
-    generate_entity_import_files(output_prefix, environment, wrapped_view, render_files=render_files)
+    generate_entity_import_files(output_prefix, environment, wrapped_view)
 
     # Generate database models, GraphQL types, Cerbos policies, and Factoryboy factories
     generate_entity_subclass_files(
         output_prefix,
         "database/models/class_name.py",
         environment,
         wrapped_view,
-        render_files=render_files,
     )
     generate_entity_subclass_files(
         output_prefix,
         "graphql_api/types/class_name.py",
         environment,
         wrapped_view,
-        render_files=render_files,
     )
     generate_entity_subclass_files(
         output_prefix,
         "validators/class_name.py",
         environment,
         wrapped_view,
-        render_files=render_files,
     )
     generate_entity_subclass_files(
         output_prefix,
         "cerbos/policies/class_name.yaml",
         environment,
         wrapped_view,
-        render_files=render_files,
     )
     generate_entity_subclass_files(
         output_prefix,
         "test_infra/factories/class_name.py",
         environment,
         wrapped_view,
-        render_files=render_files,
     )
     generate_entity_subclass_files(
         output_prefix,
         "graphql_api/helpers/class_name.py",
         environment,
         wrapped_view,
-        render_files=render_files,
     )

platformics/codegen/lib/linkml_wrappers.py

@@ -5,6 +5,7 @@
 functions to keep complicated LinkML-specific logic out of our Jinja2 templates.
 """
 
+import contextlib
 from functools import cached_property
 
 import strcase
@@ -35,10 +36,19 @@ def identifier(self) -> str:
     def name(self) -> str:
         return self.wrapped_field.name.replace(" ", "_")
 
+    @cached_property
+    def description(self) -> str:
+        # Make sure to quote this so it's safe!
+        return repr(self.wrapped_field.description)
+
     @cached_property
     def camel_name(self) -> str:
         return strcase.to_lower_camel(self.name)
 
+    @cached_property
+    def type_designator(self) -> bool:
+        return bool(self.wrapped_field.designates_type)
+
     @cached_property
     def multivalued(self) -> str:
         return self.wrapped_field.multivalued
@@ -47,6 +57,10 @@ def multivalued(self) -> str:
     def required(self) -> bool:
         return self.wrapped_field.required or False
 
+    @cached_property
+    def designates_type(self) -> bool:
+        return self.wrapped_field.designates_type
+
     # Validation attributes
     @cached_property
     def minimum_value(self) -> float | int | None:
@@ -64,6 +78,11 @@ def maximum_value(self) -> float | int | None:
     def indexed(self) -> bool:
         if "indexed" in self.wrapped_field.annotations:
             return self.wrapped_field.annotations["indexed"].value
+        if self.identifier:
+            return True
+        with contextlib.suppress(NotImplementedError, AttributeError, ValueError):
+            if self.related_class.identifier:
+                return True
         return False
 
     @cached_property
@@ -94,9 +113,7 @@ def hidden(self) -> bool:
     @cached_property
     def readonly(self) -> bool:
         is_readonly = self.wrapped_field.readonly
-        if is_readonly:
-            return True
-        return False
+        return bool(is_readonly)
 
     # Whether these fields should be available to change via an `Update` mutation
     # All fields are mutable by default, so long as they're not marked as readonly
@@ -138,16 +155,12 @@ def inverse_field(self) -> str:
     @cached_property
     def is_enum(self) -> bool:
         field = self.view.get_element(self.wrapped_field.range)
-        if isinstance(field, EnumDefinition):
-            return True
-        return False
+        return bool(isinstance(field, EnumDefinition))
 
     @cached_property
     def is_entity(self) -> bool:
         field = self.view.get_element(self.wrapped_field.range)
-        if isinstance(field, ClassDefinition):
-            return True
-        return False
+        return bool(isinstance(field, ClassDefinition))
 
     @property
     def related_class(self) -> "EntityWrapper":
@@ -163,6 +176,17 @@ def factory_type(self) -> str | None:
             return self.wrapped_field.annotations["factory_type"].value
         return None
 
+    @cached_property
+    def is_single_parent(self) -> bool:
+        # TODO, this parameter probably needs a better name. It's entirely SA specific right now.
+        # Basically we need it to tell SQLAlchemy that we have a 1:many relationship without a backref.
+        # Normally that's fine on its own, but if SQLALchemy will not allow us to enable cascading
+        # deletes unless we promise it (with this flag) that a given "child" object has only one parent,
+        # thereby making it safe to delete when the parent is deleted
+        if "single_parent" in self.wrapped_field.annotations:
+            return self.wrapped_field.annotations["single_parent"].value
+        return False
+
     @cached_property
     def is_cascade_delete(self) -> bool:
         if "cascade_delete" in self.wrapped_field.annotations:
@@ -234,15 +258,15 @@ def writable_fields(self) -> list[FieldWrapper]:
         return [FieldWrapper(self.view, item) for item in self.view.class_induced_slots(self.name) if not item.readonly]
 
     @cached_property
-    def identifier(self) -> str:
-        # Prioritize sending back identifiers from the entity mixin instead of inherited fields.
+    def identifier(self) -> FieldWrapper:
+        # Prioritize sending back identifiers from the current class and mixins instead of inherited fields.
+        domains_owned_by_this_class = set(self.wrapped_class.mixins + [self.name])
         for field in self.all_fields:
-            # FIXME, the entity.id / entity_id relationship is a little brittle right now :(
-            if field.identifier and "EntityMixin" in field.wrapped_field.domain_of:
-                return field.name
+            if field.identifier and domains_owned_by_this_class.intersection(set(field.wrapped_field.domain_of)):
+                return field
         for field in self.all_fields:
-            if field.identifier:
-                return field.name
+            if field.identifier and self.name in field.wrapped_field.domain_of:
+                return field
         raise Exception("No identifier found")
 
     @cached_property
@@ -343,6 +367,9 @@ def enums(self) -> list[EnumWrapper]:
         enums = []
         for enum_name in self.view.all_enums():
             enum = self.view.get_element(enum_name)
+            # Don't codegen stuff that users asked us not to.
+            if enum.annotations.get("skip_codegen") and enum.annotations["skip_codegen"].value:
+                continue
             enums.append(EnumWrapper(self.view, enum))
         return enums
 

platformics/codegen/templates/database/models/__init__.py.j2

@@ -9,13 +9,11 @@ Make changes to the template codegen/templates/database/models/__init__.py.j2 in
 
 from sqlalchemy.orm import configure_mappers
 
-from platformics.database.models import Base, meta, Entity, File, FileStatus  # noqa: F401
+from platformics.database.models import Base, meta, Entity # noqa: F401
 {%- for class in classes %}
   {%- if class.snake_name != "Entity" %}
 from database.models.{{ class.snake_name }} import {{ class.name }}  # noqa: F401
   {%- endif %}
 {%- endfor %}
 
-from platformics.database.models.file import File, FileStatus  # noqa: F401
-
 configure_mappers()

platformics/codegen/templates/database/models/class_name.py.j2

@@ -6,7 +6,7 @@ Make changes to the template codegen/templates/database/models/class_name.py.j2
 """
 
 {% set related_fields = cls.related_fields | unique(attribute='related_class.name') | list %}
-{% set ignored_fields = ["File", "Entity", cls.name] %}
+{% set ignored_fields = ["Entity", cls.name] %}
 
 import uuid
 import datetime
@@ -26,19 +26,19 @@ from support.enums import
 {%- endfor %}
 
 if TYPE_CHECKING:
-    from database.models.file import File
     {%- for related_field in related_fields %}
         {%- if related_field.related_class.name not in ignored_fields %}
     from database.models.{{related_field.related_class.snake_name}} import {{related_field.related_class.name}}
         {%- endif %}
     {%- endfor %}
+    pass
 else:
-    File = "File"
     {%- for related_field in related_fields %}
         {%- if related_field.related_class.name not in ignored_fields %}
     {{related_field.related_class.name}} = "{{related_field.related_class.name}}"
         {%- endif %}
     {%- endfor %}
+    pass
 
 
 class {{cls.name}}(Entity):
@@ -65,12 +65,13 @@ class {{cls.name}}(Entity):
         {%- elif attr.type == "date" %}
     {{attr.name}}: Mapped[datetime.datetime] = mapped_column(DateTime(timezone=True), nullable={{ "False" if attr.required else "True"}}{%- if attr.indexed%}, index=True{%- endif %})
         {%- else %}
+            {%- if attr.is_single_parent -%}
+                {% set single_parent = 'single_parent=True,' %}
+            {%- else -%}
+                {% set single_parent = "" %}
+            {%- endif -%}
             {%- if attr.is_cascade_delete -%}
-                {%- if attr.type == "File" -%}
-                    {% set cascade = 'cascade="all, delete-orphan", single_parent=True, post_update=True' %}
-                {%- else -%}
-                    {% set cascade = 'cascade="all, delete-orphan"' %}
-                {%- endif -%}
+                {% set cascade = 'cascade="all, delete-orphan",' %}
             {%- else -%}
                 {% set cascade = "" %}
             {%- endif -%}
@@ -83,11 +84,12 @@ class {{cls.name}}(Entity):
         uselist=True,
         foreign_keys="{{attr.type}}.{{attr.inverse_field}}_id",
         {{cascade}}
+        {{single_parent}}
     )
             {%- else %}
     {{attr.name}}_id: Mapped[uuid.UUID] = mapped_column(
         UUID,
-        ForeignKey("{{attr.related_class.snake_name}}.{{attr.related_class.identifier}}"),
+        ForeignKey("{{attr.related_class.snake_name}}.{{attr.related_class.identifier.name}}"),
         nullable={{"False" if attr.required else "True"}},
         {%- if attr.identifier %}
         primary_key=True,
@@ -103,6 +105,7 @@ class {{cls.name}}(Entity):
         back_populates="{{attr.inverse_field}}",
         {%- endif %}
         {{cascade}}
+        {{single_parent}}
     )
               {%- endif %}
             {%- endif %}

platformics/codegen/templates/graphql_api/helpers/class_name.py.j2

@@ -5,7 +5,7 @@ Auto-gereanted by running 'make codegen'. Do not edit.
 Make changes to the template codegen/templates/graphql_api/groupby_helpers.py.j2 instead.
 """
 {% set related_fields = cls.related_fields | unique(attribute='related_class.name') | list %}
-{% set ignored_fields = ["File", "Entity", cls.name] %}
+{% set ignored_fields = ["Entity", cls.name] %}
 
 from typing import Any, Optional
 import strawberry
@@ -35,8 +35,8 @@ These are only used in aggregate queries.
 @strawberry.type
 class {{ cls.name }}GroupByOptions:
 {%- for attr in cls.visible_fields %}
-    {%- if attr.type != "File" and not attr.multivalued and not attr.is_virtual_relationship %}
-        {%- if attr.inverse %}
+    {%- if not attr.multivalued and not attr.is_virtual_relationship %}
+        {%- if attr.is_entity %}
     {{ attr.name }}: Optional[{{ attr.related_class.name }}GroupByOptions] = None
         {%- elif attr.type == cls.name %}
     {{ attr.name }}: Optional["{{ cls.name }}GroupByOptions"] = None
@@ -78,7 +78,7 @@ def build_{{ cls.snake_name }}_groupby_output(
     key = keys.pop(0)
     match key:
 {%- for attr in cls.visible_fields %}
-    {%- if attr.type != "File" and not attr.multivalued and not attr.is_virtual_relationship %}
+    {%- if not attr.multivalued and not attr.is_virtual_relationship %}
         {%- if attr.inverse %}
         case "{{ attr.related_class.snake_name }}":
             if getattr(group_object, key):

platformics/codegen/templates/graphql_api/mutations.py.j2

@@ -7,24 +7,13 @@ Make changes to the template codegen/templates/graphql_api/mutations.py.j2 inste
 
 import strawberry
 from typing import Sequence
-{%- if render_files %}
-from platformics.graphql_api.files import File, create_file, upload_file, upload_temporary_file, mark_upload_complete, concatenate_files, SignedURL, MultipartUploadResponse
-{%- endif %}
 
 {%- for class in classes %}
 from graphql_api.types.{{ class.snake_name }} import {{ class.name }}, {%- if class.create_fields %}create_{{ class.snake_name }}, {%- endif %}{%- if class.mutable_fields %}update_{{ class.snake_name }}, {%- endif %}delete_{{ class.snake_name }}
 {%- endfor %}
 
 @strawberry.type
 class Mutation:
-    {%- if render_files %}
-    # File mutations
-    create_file: File = create_file
-    upload_file: MultipartUploadResponse = upload_file
-    upload_temporary_file: MultipartUploadResponse = upload_temporary_file
-    mark_upload_complete: File = mark_upload_complete
-    concatenate_files: SignedURL = concatenate_files
-    {%- endif %}
 {%- for class in classes %}
 
     # {{ class.name }} mutations