Optimize s3 url generation

charts/processed_data/charts/processed_data/Chart.yaml

@@ -5,4 +5,4 @@ type: application
 
 version: 0.1.0
 
-appVersion: 0.1.0-rc13
+appVersion: 0.2.0-rc2

charts/processed_data/templates/ispyb-secret.yaml

@@ -0,0 +1,19 @@
+apiVersion: bitnami.com/v1alpha1
+kind: SealedSecret
+metadata:
+  annotations:
+    sealedsecrets.bitnami.com/namespace-wide: "true"
+  creationTimestamp: null
+  name: ispyb
+  namespace: graph
+spec:
+  encryptedData:
+    password: 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
+  template:
+    metadata:
+      annotations:
+        sealedsecrets.bitnami.com/namespace-wide: "true"
+      creationTimestamp: null
+      name: ispyb
+      namespace: graph
+

charts/processed_data/values.yaml

@@ -8,3 +8,17 @@ processed-data:
       secretName: ispyb
       secretKey: password
   otelCollectorUrl: http://federation-opentelemetry-collector:4317
+  affinity:
+    podAffinity:
+      requiredDuringSchedulingIgnoredDuringExecution:
+        - labelSelector:
+            matchExpressions:
+              - key: app.kubernetes.io/instance
+                operator: In
+                values:
+                  - ispyb
+              - key: app.kubernetes.io/name
+                operator: In
+                values:
+                  - mariadb-galera
+          topologyKey: kubernetes.io/hostname

processed_data/src/graphql/entities.rs

@@ -117,6 +117,7 @@ impl From<Option<FileType>> for AttachmentFileType {
 #[graphql(name = "AutoProcFileAttachment", unresolvable, complex)]
 pub struct AutoProcFileAttachment {
     /// An opaque unique identifier for the autoproc file attachment
+    #[graphql(skip)]
     pub id: u32,
     /// An opaque unique identifier for auto proc program
     #[graphql(skip)]
@@ -130,7 +131,6 @@ pub struct AutoProcFileAttachment {
     #[graphql(skip)]
     pub file_path: Option<String>,
 }
-
 impl From<auto_proc_program_attachment::Model> for AutoProcFileAttachment {
     fn from(value: auto_proc_program_attachment::Model) -> Self {
         Self {
@@ -143,6 +143,19 @@ impl From<auto_proc_program_attachment::Model> for AutoProcFileAttachment {
     }
 }
 
+impl AutoProcFileAttachment {
+    /// S3 bucket object key
+    pub fn object_key(&self) -> String {
+        let mut key = std::path::PathBuf::from(
+            <Option<String> as Clone>::clone(&self.file_path)
+                .unwrap()
+                .to_string(),
+        );
+        key.push(<Option<String> as Clone>::clone(&self.file_name).unwrap());
+        key.to_string_lossy().to_string()
+    }
+}
+
 /// Represents a processing job
 #[derive(Clone, Debug, PartialEq, SimpleObject)]
 #[graphql(name = "ProcessingJobs", unresolvable)]
@@ -272,19 +285,6 @@ impl From<auto_proc_scaling_statistics::Model> for AutoProcScalingStatics {
     }
 }
 
-impl AutoProcFileAttachment {
-    /// S3 bucket object key
-    pub fn object_key(&self) -> String {
-        let mut key = std::path::PathBuf::from(
-            <Option<String> as Clone>::clone(&self.file_path)
-                .unwrap()
-                .to_string(),
-        );
-        key.push(<Option<String> as Clone>::clone(&self.file_name).unwrap());
-        key.to_string_lossy().to_string()
-    }
-}
-
 /// Datasets subgraph extension
 #[derive(SimpleObject)]
 #[graphql(name = "DataCollection", complex)]

processed_data/src/graphql/mod.rs

@@ -5,7 +5,7 @@ use async_graphql::{
     dataloader::{DataLoader, Loader},
     ComplexObject, Context, EmptyMutation, EmptySubscription, Object, Schema, SchemaBuilder,
 };
-use aws_sdk_s3::{presigning::PresigningConfig, Client};
+use aws_sdk_s3::presigning::PresigningConfig;
 use entities::{
     AutoProcFileAttachment, AutoProcScalingStatics, AutoProcessing, DataCollection, ProcessingJob,
     StatisticsType,
@@ -29,23 +29,13 @@ pub type RootSchema = Schema<Query, EmptyMutation, EmptySubscription>;
 /// router handler extension
 pub trait AddDataLoadersExt {
     /// Adds dataloader to graphql request
-    fn add_data_loaders(
-        self,
-        database: DatabaseConnection,
-        s3_client: Client,
-        s3_bucket: S3Bucket,
-    ) -> Self;
+    fn add_data_loaders(self, database: DatabaseConnection) -> Self;
 }
 
 impl AddDataLoadersExt for async_graphql::Request {
-    fn add_data_loaders(
-        self,
-        database: DatabaseConnection,
-        s3_client: Client,
-        s3_bucket: S3Bucket,
-    ) -> Self {
+    fn add_data_loaders(self, database: DatabaseConnection) -> Self {
         self.data(DataLoader::new(
-            FileAttachmentDataLoader::new(database.clone(), s3_client, s3_bucket),
+            FileAttachmentDataLoader::new(database.clone()),
             tokio::spawn,
         ))
         .data(DataLoader::new(
@@ -77,8 +67,6 @@ pub struct Query;
 pub struct FileAttachmentDataLoader {
     database: DatabaseConnection,
     parent_span: Span,
-    s3_client: Client,
-    s3_bucket: S3Bucket,
 }
 /// DataLoader for Process Job
 #[allow(clippy::missing_docs_in_private_items)]
@@ -111,12 +99,10 @@ impl ProcessingJobDataLoader {
 
 #[allow(clippy::missing_docs_in_private_items)]
 impl FileAttachmentDataLoader {
-    fn new(database: DatabaseConnection, s3_client: Client, s3_bucket: S3Bucket) -> Self {
+    fn new(database: DatabaseConnection) -> Self {
         Self {
             database,
             parent_span: Span::current(),
-            s3_client,
-            s3_bucket,
         }
     }
 }
@@ -372,25 +358,6 @@ impl DataCollection {
     }
 }
 
-#[ComplexObject]
-impl AutoProcFileAttachment {
-    /// Gives downloadable link for the processed image in the s3 bucket
-    async fn file_url(&self, ctx: &Context<'_>) -> async_graphql::Result<String> {
-        let s3_client = ctx.data::<aws_sdk_s3::Client>()?;
-        let bucket = ctx.data::<S3Bucket>()?;
-        let object_uri = s3_client
-            .get_object()
-            .bucket(bucket.clone())
-            .key(self.object_key())
-            .presigned(PresigningConfig::expires_in(Duration::from_secs(10 * 60))?)
-            .await?
-            .uri()
-            .clone();
-        let object_url = Url::parse(&object_uri.to_string())?;
-        Ok(object_url.to_string())
-    }
-}
-
 #[ComplexObject]
 impl AutoProcessing {
     /// Fetches the overall scaling statistics type
@@ -442,6 +409,25 @@ impl AutoProcessing {
     }
 }
 
+#[ComplexObject]
+impl AutoProcFileAttachment {
+    /// Gives downloadable link for the processed image in the s3 bucket
+    async fn file_url(&self, ctx: &Context<'_>) -> async_graphql::Result<String> {
+        let s3_client = ctx.data::<aws_sdk_s3::Client>()?;
+        let bucket = ctx.data::<S3Bucket>()?;
+        let object_uri = s3_client
+            .get_object()
+            .bucket(bucket.clone())
+            .key(self.object_key())
+            .presigned(PresigningConfig::expires_in(Duration::from_secs(10 * 60))?)
+            .await?
+            .uri()
+            .clone();
+        let object_url = Url::parse(&object_uri.to_string())?;
+        Ok(object_url.to_string())
+    }
+}
+
 #[Object]
 impl Query {
     /// Reference datasets resolver for the router

processed_data/src/main.rs

@@ -144,12 +144,7 @@ async fn setup_database(database_url: Url) -> Result<DatabaseConnection, Transac
 }
 
 /// Creates an [`axum::Router`] serving GraphiQL, synchronous GraphQL and GraphQL subscriptions
-fn setup_router(
-    schema: RootSchema,
-    database: DatabaseConnection,
-    s3_client: aws_sdk_s3::Client,
-    s3_bucket: S3Bucket,
-) -> Router {
+fn setup_router(schema: RootSchema, database: DatabaseConnection) -> Router {
     #[allow(clippy::missing_docs_in_private_items)]
     const GRAPHQL_ENDPOINT: &str = "/";
 
@@ -159,7 +154,7 @@ fn setup_router(
             get(Html(
                 GraphiQLSource::build().endpoint(GRAPHQL_ENDPOINT).finish(),
             ))
-            .post(GraphQLHandler::new(schema, database, s3_client, s3_bucket)),
+            .post(GraphQLHandler::new(schema, database)),
         )
         .layer(OtelInResponseLayer)
         .layer(OtelAxumLayer::default())
@@ -248,8 +243,11 @@ async fn main() {
             setup_telemetry(args.log_level, args.otel_collector_url).unwrap();
             let database = setup_database(args.database_url).await.unwrap();
             let s3_client = Client::from_s3_client_args(args.s3_client);
-            let schema = root_schema_builder().finish();
-            let router = setup_router(schema, database, s3_client, args.s3_bucket);
+            let schema = root_schema_builder()
+                .data(s3_client)
+                .data(args.s3_bucket)
+                .finish();
+            let router = setup_router(schema, database);
             serve(router, args.port).await.unwrap();
         }
         Cli::Schema(args) => {

processed_data/src/route_handlers.rs

@@ -10,7 +10,7 @@ use axum::{
 use sea_orm::DatabaseConnection;
 use std::{future::Future, pin::Pin};
 
-use crate::{graphql::AddDataLoadersExt, S3Bucket};
+use crate::graphql::AddDataLoadersExt;
 
 /// An [`Handler`] which executes an [`Executor`] including the [`Authorization<Bearer>`] in the [`async_graphql::Context`]
 #[derive(Debug, Clone)]
@@ -19,26 +19,12 @@ pub struct GraphQLHandler<E: Executor> {
     executor: E,
     /// Database connection
     database: DatabaseConnection,
-    /// S3 client
-    s3_client: aws_sdk_s3::Client,
-    /// S3 Bucket
-    s3_bucket: S3Bucket,
 }
 
 impl<E: Executor> GraphQLHandler<E> {
     /// Constructs an instance of the handler with the provided schema.
-    pub fn new(
-        executor: E,
-        database: DatabaseConnection,
-        s3_client: aws_sdk_s3::Client,
-        s3_bucket: S3Bucket,
-    ) -> Self {
-        Self {
-            executor,
-            database,
-            s3_client,
-            s3_bucket,
-        }
+    pub fn new(executor: E, database: DatabaseConnection) -> Self {
+        Self { executor, database }
     }
 }
 
@@ -54,11 +40,7 @@ where
             match request {
                 Ok(request) => GraphQLResponse::from(
                     self.executor
-                        .execute(request.into_inner().add_data_loaders(
-                            self.database,
-                            self.s3_client,
-                            self.s3_bucket,
-                        ))
+                        .execute(request.into_inner().add_data_loaders(self.database))
                         .await,
                 )
                 .into_response(),