Merge pull request galaxyproject#18792 from arash77/update-fastapi-viz

Update Visualization FastAPI

client/src/api/schema/schema.ts

@@ -4689,11 +4689,8 @@ export interface paths {
         put?: never;
         /**
          * Create a new visualization.
-         * @description POST /api/visualizations
-         *     creates a new visualization using the given payload and does not require the import_id field
-         *
-         *     POST /api/visualizations?import_id={encoded_visualization_id}
-         *     imports a copy of an existing visualization into the user's workspace and does not require the rest of the payload
+         * @description Creates a new visualization using the given payload and does not require the import_id field.
+         *     If import_id given, it imports a copy of an existing visualization into the user's workspace and does not require the rest of the payload.
          */
         post: operations["create_api_visualizations_post"];
         delete?: never;
@@ -16850,12 +16847,6 @@ export interface components {
              * @description The database key of the visualization.
              */
             dbkey?: string | null;
-            /**
-             * Save
-             * @description Whether to save the visualization.
-             * @default true
-             */
-            save: boolean | null;
             /**
              * Slug
              * @description The slug of the visualization.
@@ -16871,7 +16862,7 @@ export interface components {
              * Type
              * @description The type of the visualization.
              */
-            type?: string | null;
+            type: string;
         };
         /** VisualizationCreateResponse */
         VisualizationCreateResponse: {

lib/galaxy/schema/visualization.py

@@ -298,15 +298,16 @@ class VisualizationUpdateResponse(Model):
 
 
 class VisualizationCreatePayload(Model):
-    type: Optional[SanitizedString] = Field(
-        None,
+    type: str = Field(
+        ...,
         title="Type",
         description="The type of the visualization.",
     )
     title: Optional[SanitizedString] = Field(
         SanitizedString("Untitled Visualization"),
         title="Title",
         description="The name of the visualization.",
+        min_length=3,
     )
     dbkey: Optional[SanitizedString] = Field(
         None,
@@ -328,11 +329,6 @@ class VisualizationCreatePayload(Model):
         title="Config",
         description="The config of the visualization.",
     )
-    save: Optional[bool] = Field(
-        True,
-        title="Save",
-        description="Whether to save the visualization.",
-    )
 
 
 class VisualizationUpdatePayload(Model):

lib/galaxy/webapps/galaxy/api/visualizations.py

@@ -256,11 +256,8 @@ def create(
         trans: ProvidesUserContext = DependsOnTrans,
     ) -> VisualizationCreateResponse:
         """
-        POST /api/visualizations
-        creates a new visualization using the given payload and does not require the import_id field
-
-        POST /api/visualizations?import_id={encoded_visualization_id}
-        imports a copy of an existing visualization into the user's workspace and does not require the rest of the payload
+        Creates a new visualization using the given payload and does not require the import_id field.
+        If import_id given, it imports a copy of an existing visualization into the user's workspace and does not require the rest of the payload.
         """
         return self.service.create(trans, import_id, payload)
 

lib/galaxy/webapps/galaxy/services/visualizations.py

@@ -44,7 +44,6 @@
 from galaxy.security.idencoding import IdEncodingHelper
 from galaxy.structured_app import StructuredApp
 from galaxy.util.hash_util import md5_hash_str
-from galaxy.util.sanitize_html import sanitize_html
 from galaxy.visualization.plugins.plugin import VisualizationPlugin
 from galaxy.visualization.plugins.registry import VisualizationsRegistry
 from galaxy.web import url_for
@@ -163,29 +162,24 @@ def create(
         if import_id:
             visualization = self._import_visualization(trans, import_id)
         else:
-            # must have a type (I've taken this to be the visualization name)
-            if not payload.type:
-                raise exceptions.RequestParameterMissingException("key/value 'type' is required")
             type = payload.type
             title = payload.title
             slug = payload.slug
             dbkey = payload.dbkey
             annotation = payload.annotation
             config = payload.config
-            save = payload.save
 
             # generate defaults - this will err if given a weird key?
-            visualization = self._create_visualization(trans, type, title, dbkey, slug, annotation, save)
+            visualization = self._create_visualization(trans, type, title, dbkey, slug, annotation)
 
             # Create and save first visualization revision
             revision = VisualizationRevision(visualization=visualization, title=title, config=config, dbkey=dbkey)
             visualization.latest_revision = revision
 
-            if save:
-                session = trans.sa_session
-                session.add(revision)
-                with transaction(session):
-                    session.commit()
+            session = trans.sa_session
+            session.add(revision)
+            with transaction(session):
+                session.commit()
 
         return VisualizationCreateResponse(id=str(visualization.id))
 
@@ -245,10 +239,7 @@ def _get_visualization(
         """
         Get a Visualization from the database by id, verifying ownership.
         """
-        try:
-            visualization = trans.sa_session.get(Visualization, visualization_id)
-        except TypeError:
-            visualization = None
+        visualization = trans.sa_session.get(Visualization, visualization_id)
         if not visualization:
             raise exceptions.ObjectNotFound("Visualization not found")
         else:
@@ -300,28 +291,26 @@ def _create_visualization(
         self,
         trans: ProvidesUserContext,
         type: str,
-        title: Optional[str] = None,
+        title: Optional[str] = "Untitled Visualization",
         dbkey: Optional[str] = None,
         slug: Optional[str] = None,
         annotation: Optional[str] = None,
-        save: Optional[bool] = True,
     ) -> Visualization:
         """Create visualization but not first revision. Returns Visualization object."""
         user = trans.get_user()
 
         # Error checking.
-        title_err = slug_err = ""
-        if not title:
-            title_err = "visualization name is required"
-        elif slug and not is_valid_slug(slug):
-            slug_err = "visualization identifier must consist of only lowercase letters, numbers, and the '-' character"
-        elif slug and slug_exists(trans.sa_session, Visualization, user, slug, ignore_deleted=True):
-            slug_err = "visualization identifier must be unique"
-
-        if title_err or slug_err:
-            # TODO: handle this error structure better
-            val_err = str(title_err or slug_err)
-            raise exceptions.RequestParameterMissingException(val_err)
+        if slug:
+            slug_err = ""
+            if not is_valid_slug(slug):
+                slug_err = (
+                    "visualization identifier must consist of only lowercase letters, numbers, and the '-' character"
+                )
+            elif slug_exists(trans.sa_session, Visualization, user, slug, ignore_deleted=True):
+                slug_err = "visualization identifier must be unique"
+            if slug_err:
+                # TODO: handle this error structure better
+                raise exceptions.RequestParameterMissingException(slug_err)
 
         # Create visualization
         visualization = Visualization(user=user, title=title, dbkey=dbkey, type=type)
@@ -331,16 +320,14 @@ def _create_visualization(
             slug_builder = SlugBuilder()
             slug_builder.create_item_slug(trans.sa_session, visualization)
         if annotation:
-            annotation = sanitize_html(annotation)
             # TODO: if this is to stay in the mixin, UsesAnnotations should be added to the superclasses
             #   right now this is depending on the classes that include this mixin to have UsesAnnotations
             add_item_annotation(trans.sa_session, trans.user, visualization, annotation)
 
-        if save:
-            session = trans.sa_session
-            session.add(visualization)
-            with transaction(session):
-                session.commit()
+        session = trans.sa_session
+        session.add(visualization)
+        with transaction(session):
+            session.commit()
 
         return visualization