Merge pull request galaxyproject#18721 from arash77/FastAPI_Visualiza…

…tions

Migrate Visualizations API to FastAPI

lib/galaxy/schema/schema.py

@@ -28,6 +28,7 @@
     RootModel,
     UUID4,
 )
+from pydantic_core import core_schema
 from typing_extensions import (
     Annotated,
     Literal,
@@ -48,6 +49,7 @@
     OffsetNaiveDatetime,
     RelativeUrl,
 )
+from galaxy.util.sanitize_html import sanitize_html
 
 USER_MODEL_CLASS = Literal["User"]
 GROUP_MODEL_CLASS = Literal["Group"]
@@ -3814,3 +3816,23 @@ class PageSummaryList(RootModel):
 class MessageExceptionModel(BaseModel):
     err_msg: str
     err_code: int
+
+
+class SanitizedString(str):
+    @classmethod
+    def __get_validators__(cls):
+        yield cls.validate
+
+    @classmethod
+    def validate(cls, value):
+        if isinstance(value, str):
+            return cls(sanitize_html(value))
+        raise TypeError("string required")
+
+    @classmethod
+    def __get_pydantic_core_schema__(cls, source_type, handler):
+        return core_schema.no_info_after_validator_function(
+            cls.validate,
+            core_schema.str_schema(),
+            serialization=core_schema.to_string_ser_schema(),
+        )

lib/galaxy/schema/visualization.py

@@ -1,7 +1,9 @@
 from datetime import datetime
 from typing import (
+    Dict,
     List,
     Optional,
+    Union,
 )
 
 from pydantic import (
@@ -14,16 +16,22 @@
 from galaxy.schema.fields import (
     DecodedDatabaseIdField,
     EncodedDatabaseIdField,
+    ModelClassField,
 )
 from galaxy.schema.schema import (
     CreateTimeField,
     Model,
+    SanitizedString,
     TagCollection,
     UpdateTimeField,
+    WithModelClass,
 )
 
 VisualizationSortByEnum = Literal["create_time", "title", "update_time", "username"]
 
+VISUALIZATION_MODEL_CLASS = Literal["Visualization"]
+VISUALIZATION_REVISION_MODEL_CLASS = Literal["VisualizationRevision"]
+
 
 class VisualizationIndexQueryPayload(Model):
     deleted: bool = False
@@ -100,3 +108,251 @@ class VisualizationSummaryList(RootModel):
         default=[],
         title="List with detailed information of Visualizations.",
     )
+
+
+class VisualizationRevisionResponse(Model, WithModelClass):
+    model_class: VISUALIZATION_REVISION_MODEL_CLASS = ModelClassField(VISUALIZATION_REVISION_MODEL_CLASS)
+    id: EncodedDatabaseIdField = Field(
+        ...,
+        title="ID",
+        description="Encoded ID of the Visualization Revision.",
+    )
+    visualization_id: EncodedDatabaseIdField = Field(
+        ...,
+        title="Visualization ID",
+        description="Encoded ID of the Visualization.",
+    )
+    title: str = Field(
+        ...,
+        title="Title",
+        description="The name of the visualization revision.",
+    )
+    dbkey: Optional[str] = Field(
+        None,
+        title="DbKey",
+        description="The database key of the visualization.",
+    )
+    config: Dict = Field(
+        ...,
+        title="Config",
+        description="The config of the visualization revision.",
+    )
+
+
+class VisualizationPluginResponse(Model):
+    name: str = Field(
+        ...,
+        title="Name",
+        description="The name of the plugin.",
+    )
+    html: str = Field(
+        ...,
+        title="HTML",
+        description="The HTML of the plugin.",
+    )
+    description: str = Field(
+        ...,
+        title="Description",
+        description="The description of the plugin.",
+    )
+    logo: Optional[str] = Field(
+        None,
+        title="Logo",
+        description="The logo of the plugin.",
+    )
+    title: Optional[str] = Field(
+        None,
+        title="Title",
+        description="The title of the plugin.",
+    )
+    target: str = Field(
+        ...,
+        title="Target",
+        description="The target of the plugin.",
+    )
+    embeddable: bool = Field(
+        ...,
+        title="Embeddable",
+        description="Whether the plugin is embeddable.",
+    )
+    entry_point: Dict = Field(
+        ...,
+        title="Entry Point",
+        description="The entry point of the plugin.",
+    )
+    settings: List[Dict] = Field(
+        ...,
+        title="Settings",
+        description="The settings of the plugin.",
+    )
+    groups: Optional[List[Dict]] = Field(
+        None,
+        title="Groups",
+        description="The groups of the plugin.",
+    )
+    specs: Optional[Dict] = Field(
+        None,
+        title="Specs",
+        description="The specs of the plugin.",
+    )
+    href: str = Field(
+        ...,
+        title="Href",
+        description="The href of the plugin.",
+    )
+
+
+class VisualizationShowResponse(Model, WithModelClass):
+    model_class: VISUALIZATION_MODEL_CLASS = ModelClassField(VISUALIZATION_MODEL_CLASS)
+    id: EncodedDatabaseIdField = Field(
+        ...,
+        title="ID",
+        description="Encoded ID of the Visualization.",
+    )
+    title: str = Field(
+        ...,
+        title="Title",
+        description="The name of the visualization.",
+    )
+    type: str = Field(
+        ...,
+        title="Type",
+        description="The type of the visualization.",
+    )
+    user_id: EncodedDatabaseIdField = Field(
+        ...,
+        title="User ID",
+        description="The ID of the user owning this Visualization.",
+    )
+    dbkey: Optional[str] = Field(
+        None,
+        title="DbKey",
+        description="The database key of the visualization.",
+    )
+    slug: Optional[str] = Field(
+        None,
+        title="Slug",
+        description="The slug of the visualization.",
+    )
+    latest_revision: VisualizationRevisionResponse = Field(
+        ...,
+        title="Latest Revision",
+        description="The latest revision of this Visualization.",
+    )
+    revisions: List[EncodedDatabaseIdField] = Field(
+        ...,
+        title="Revisions",
+        description="A list of encoded IDs of the revisions of this Visualization.",
+    )
+    url: str = Field(
+        ...,
+        title="URL",
+        description="The URL of the visualization.",
+    )
+    username: str = Field(
+        ...,
+        title="Username",
+        description="The name of the user owning this Visualization.",
+    )
+    email_hash: str = Field(
+        ...,
+        title="Email Hash",
+        description="The hash of the email of the user owning this Visualization.",
+    )
+    tags: Optional[TagCollection] = Field(
+        None,
+        title="Tags",
+        description="A list of tags to add to this item.",
+    )
+    annotation: Optional[str] = Field(
+        None,
+        title="Annotation",
+        description="The annotation of this Visualization.",
+    )
+    plugin: Optional[VisualizationPluginResponse] = Field(
+        None,
+        title="Plugin",
+        description="The plugin of this Visualization.",
+    )
+
+
+class VisualizationCreateResponse(Model):
+    id: EncodedDatabaseIdField = Field(
+        ...,
+        title="ID",
+        description="Encoded ID of the Visualization.",
+    )
+
+
+class VisualizationUpdateResponse(Model):
+    id: EncodedDatabaseIdField = Field(
+        ...,
+        title="ID",
+        description="Encoded ID of the Visualization.",
+    )
+    revision: EncodedDatabaseIdField = Field(
+        ...,
+        title="Revision",
+        description="Encoded ID of the Visualization Revision.",
+    )
+
+
+class VisualizationCreatePayload(Model):
+    type: Optional[SanitizedString] = Field(
+        None,
+        title="Type",
+        description="The type of the visualization.",
+    )
+    title: Optional[SanitizedString] = Field(
+        SanitizedString("Untitled Visualization"),
+        title="Title",
+        description="The name of the visualization.",
+    )
+    dbkey: Optional[SanitizedString] = Field(
+        None,
+        title="DbKey",
+        description="The database key of the visualization.",
+    )
+    slug: Optional[SanitizedString] = Field(
+        None,
+        title="Slug",
+        description="The slug of the visualization.",
+    )
+    annotation: Optional[SanitizedString] = Field(
+        None,
+        title="Annotation",
+        description="The annotation of the visualization.",
+    )
+    config: Optional[dict] = Field(
+        {},
+        title="Config",
+        description="The config of the visualization.",
+    )
+    save: Optional[bool] = Field(
+        True,
+        title="Save",
+        description="Whether to save the visualization.",
+    )
+
+
+class VisualizationUpdatePayload(Model):
+    title: Optional[SanitizedString] = Field(
+        None,
+        title="Title",
+        description="The name of the visualization.",
+    )
+    dbkey: Optional[SanitizedString] = Field(
+        None,
+        title="DbKey",
+        description="The database key of the visualization.",
+    )
+    deleted: Optional[bool] = Field(
+        False,
+        title="Deleted",
+        description="Whether this Visualization has been deleted.",
+    )
+    config: Optional[Union[dict, bytes]] = Field(
+        {},
+        title="Config",
+        description="The config of the visualization.",
+    )