Federated compound soaking service

.devcontainer/Dockerfile.backend

@@ -7,3 +7,6 @@ RUN apt-get update \
     sqlite3 pre-commit \
     libopencv-dev clang libclang-dev \
     && rm -rf /var/lib/apt/lists/*
+
+# Install Rover CLI for composing subgraphs
+RUN curl -sSL https://rover.apollo.dev/nix/latest | sh

.devcontainer/docker-compose.yaml

@@ -1,6 +1,20 @@
 version: "3.8"
 
 services:
+  apollo-router:
+    image: ghcr.io/apollographql/router:v1.41.0-rc.2
+    volumes:
+      - ./supergraph.graphql:/dist/schema/supergraph.graphql
+      - ./router.yaml:/dist/config/router.yaml
+    ports:
+      - 4001:4000
+    command:
+      - --dev
+      - -config
+      - config/router.yaml
+      - -supergraph 
+      - schema/supergraph.graphql
+
   backend:
     build:
       context: .
@@ -12,6 +26,11 @@ services:
       OPA_URL: http://opa:8181
       DATABASE_URL: postgres://postgres:password@postgres
       RABBITMQ_URL: amqp://rabbitmq:password@rabbitmq
+      CRYSTAL_LIBRARY_PORT: 8000
+      COMPOUND_LIBRARY_PORT: 8001
+      COMPOUND_SOAKING_PORT: 8002
+      PIN_PACKING_PORT: 8003
+      TARGITING_PORT: 8004
 
   frontend:
     image: docker.io/library/node:20.6.0-bookworm

.devcontainer/router.yaml

@@ -0,0 +1,7 @@
+supergraph:
+  listen: 0.0.0.0:4000
+headers:
+  all:
+    request:
+      - propagate:
+          matching: .*

.github/workflows/container.yml

@@ -14,6 +14,7 @@ jobs:
           - chimp_chomp
           - chimp_controller
           - compound_library
+          - compound_soaking
           - crystal_library
           - pin_packing
           - soakdb_sync

.gitignore

@@ -3,3 +3,6 @@
 
 # Developer Tooling
 .vscode
+
+# Generated supergraph schema 
+.devcontainer/supergraph.graphql

backend/Cargo.toml

@@ -5,6 +5,7 @@ members = [
     "chimp_protocol", 
     "crystal_library",
     "compound_library",
+    "compound_soaking",
     "graphql_endpoints",
     "graphql_event_broker",
     "opa_client",

backend/Dockerfile

@@ -12,6 +12,7 @@ COPY chimp_chomp/Cargo.toml chimp_chomp/Cargo.toml
 COPY chimp_controller/Cargo.toml chimp_controller/Cargo.toml
 COPY chimp_protocol/Cargo.toml chimp_protocol/Cargo.toml
 COPY compound_library/Cargo.toml compound_library/Cargo.toml
+COPY compound_soaking/Cargo.toml compound_soaking/Cargo.toml
 COPY crystal_library/Cargo.toml crystal_library/Cargo.toml
 COPY graphql_endpoints/Cargo.toml graphql_endpoints/Cargo.toml
 COPY graphql_event_broker/Cargo.toml graphql_event_broker/Cargo.toml
@@ -29,6 +30,8 @@ RUN mkdir chimp_chomp/src \
     && echo "fn main() {}" > chimp_controller/src/main.rs \
     && mkdir compound_library/src \
     && echo "fn main() {}" > compound_library/src/main.rs \
+    && mkdir compound_soaking/src \
+    && echo "fn main() {}" > compound_soaking/src/main.rs \
     && mkdir crystal_library/src \
     && echo "fn main() {}" > crystal_library/src/main.rs \
     && mkdir graphql_endpoints/src \
@@ -56,6 +59,7 @@ RUN touch chimp_chomp/src/main.rs \
     && touch chimp_protocol/src/lib.rs \
     && touch chimp_controller/src/main.rs \
     && touch compound_library/src/main.rs \
+    && touch compound_soaking/src/main.rs \
     && touch crystal_library/src/main.rs \
     && touch graphql_endpoints/src/lib.rs \
     && touch graphql_event_broker/src/lib.rs \
@@ -101,6 +105,12 @@ COPY --from=build /app/target/release/compound_library /compound_library
 
 ENTRYPOINT ["/compound_library"]
 
+FROM gcr.io/distroless/cc as compound_soaking
+
+COPY --from=build /app/target/release/compound_soaking /compound_soaking
+
+ENTRYPOINT ["/compound_soaking"]
+
 FROM gcr.io/distroless/cc as crystal_library
 
 COPY --from=build /app/target/release/crystal_library /crystal_library

backend/compound_library/src/graphql/compound_instances_res.rs

@@ -1,4 +1,4 @@
-use crate::entities::{compound_instances, compound_types};
+use crate::tables::{compound_instances, compound_types};
 use async_graphql::{ComplexObject, Context, Object};
 use chrono::Utc;
 use opa_client::subject_authorization;
@@ -57,6 +57,23 @@ impl CompoundInstanceQuery {
             .one(db)
             .await?)
     }
+
+    /// Reference resolver for compound instance in compound library subgraph
+    #[graphql(entity)]
+    async fn route_compound_instance(
+        &self,
+        ctx: &Context<'_>,
+        plate_id: Uuid,
+        well_number: i16,
+    ) -> async_graphql::Result<Option<compound_instances::Model>> {
+        subject_authorization!("xchemlab.compound_library.read_compound", ctx).await?;
+        let db = ctx.data::<DatabaseConnection>()?;
+        Ok(compound_instances::Entity::find()
+            .filter(compound_instances::Column::PlateId.eq(plate_id))
+            .filter(compound_instances::Column::WellNumber.eq(well_number))
+            .one(db)
+            .await?)
+    }
 }
 
 #[Object]
@@ -66,7 +83,7 @@ impl CompoundInstanceMutation {
         &self,
         ctx: &Context<'_>,
         plate_id: Uuid,
-        well_number: i16,
+        #[graphql(validator(minimum = 1, maximum = 288))] well_number: i16,
         compound_type: String,
     ) -> async_graphql::Result<compound_instances::Model> {
         let operator_id =

backend/compound_library/src/graphql/compound_types_res.rs

@@ -1,4 +1,4 @@
-use crate::entities::{compound_instances, compound_types};
+use crate::tables::{compound_instances, compound_types};
 use async_graphql::{ComplexObject, Context, CustomValidator, InputValueError, Object};
 use chrono::Utc;
 use opa_client::subject_authorization;

backend/compound_library/src/graphql/mod.rs

@@ -22,5 +22,5 @@ pub type RootSchema = Schema<Query, Mutation, EmptySubscription>;
 /// This function initializes the schema with default instances of `Query`,
 /// `Mutation`, and `EmptySubscription`.
 pub fn root_schema_builder() -> SchemaBuilder<Query, Mutation, EmptySubscription> {
-    Schema::build(Query::default(), Mutation::default(), EmptySubscription)
+    Schema::build(Query::default(), Mutation::default(), EmptySubscription).enable_federation()
 }

backend/compound_library/src/main.rs

@@ -3,14 +3,14 @@
 #![warn(clippy::missing_docs_in_private_items)]
 #![doc=include_str!("../README.md")]
 
-/// This module defines the structure and schema of the database tables
-/// through various entity structs.
-mod entities;
 /// This module sets up the GraphQL schema, including queries, mutations,
 /// and subscriptions. It defines how data is queried and mutated through the API.
 mod graphql;
 /// This module is responsible for defining and applying database migrations.
 mod migrator;
+/// This module defines the structure and schema of the database tables
+/// through various entity structs.
+mod tables;
 
 use async_graphql::extensions::Tracing;
 use axum::{routing::get, Router, Server};
@@ -43,7 +43,7 @@ enum Cli {
 #[allow(clippy::missing_docs_in_private_items)]
 struct ServeArgs {
     /// The port number to serve on.
-    #[arg(short, long, default_value_t = 80)]
+    #[arg(short, long, default_value_t = 80, env = "COMPOUND_LIBRARY_PORT")]
     port: u16,
     /// URL for the OPA server
     #[arg(long, env)]

backend/compound_library/src/migrator.rs

@@ -1,4 +1,4 @@
-use crate::entities::{compound_instances, compound_types};
+use crate::tables::{compound_instances, compound_types};
 use axum::async_trait;
 use sea_orm::{DbErr, DeriveMigrationName, Schema};
 use sea_orm_migration::{MigrationTrait, MigratorTrait, SchemaManager};

backend/compound_library/src/entities/compound_instances.rs → backend/compound_library/src/tables/compound_instances.rs

@@ -10,7 +10,7 @@ use uuid::Uuid;
 /// Represents a compound instance within the database.
 #[derive(Clone, Debug, PartialEq, Eq, DeriveEntityModel, SimpleObject)]
 #[sea_orm(table_name = "compound_instances")]
-#[graphql(name = "compund_instances", complex)]
+#[graphql(name = "compound_instances", complex, shareable)]
 pub struct Model {
     /// ID of the plate on which the compound instance is located.
     #[sea_orm(primary_key, auto_increment = false)]

backend/compound_library/src/tables/mod.rs

@@ -0,0 +1,4 @@
+/// The table storing compound instances information
+pub mod compound_instances;
+/// The table storing the compound types information
+pub mod compound_types;

backend/compound_soaking/Cargo.toml

@@ -0,0 +1,23 @@
+[package]
+name = "compound_soaking"
+version = "0.1.0"
+edition = "2021"
+
+[dependencies]
+async-graphql = { workspace = true }
+axum = { workspace = true }
+clap = { workspace = true }
+chrono ={ workspace = true }
+dotenvy = { workspace = true }
+graphql_endpoints = { path = "../graphql_endpoints" }
+opa_client = { path = "../opa_client", features = ["graphql"] }
+sea-orm = { workspace = true, features = ["sqlx-postgres"] }
+sea-orm-migration = { workspace = true }
+the_paginator = { version = "0.1.0", path = "../the_paginator", features = [
+  "async-graphql",
+] }
+tracing = { workspace = true }
+tracing-subscriber = { workspace = true }
+tokio = { workspace = true }
+url = { workspace = true }
+uuid = { workspace = true }

backend/compound_soaking/README.md

@@ -0,0 +1,3 @@
+# Compound Soaking Service
+
+This service keeps track of all the soaked compounds by various projects at the Diamond Light Source.

backend/compound_soaking/src/graphql/mod.rs

@@ -0,0 +1,24 @@
+/// A collection of resolvers relating to soaked compounds
+mod soak_compound_res;
+/// A collection of subgraphs extended from other services
+mod subgraph_extensions;
+
+use async_graphql::{EmptySubscription, MergedObject, Schema, SchemaBuilder};
+use soak_compound_res::{SoakCompoundMutation, SoakCompoundQuery};
+
+/// Combines all query resolvers into a single GraphQL `Query` type.
+#[derive(Debug, Clone, MergedObject, Default)]
+pub struct Query(SoakCompoundQuery);
+
+/// Combines all mutations resolvers into a single GraphQL `Mutation` type.
+#[derive(Debug, Clone, MergedObject, Default)]
+pub struct Mutation(SoakCompoundMutation);
+
+/// Type alias for the complete GraphQL schema.
+pub type RootSchema = Schema<Query, Mutation, EmptySubscription>;
+
+/// Initializes the schema with default instances of `Query`,
+/// `Mutation`, and `EmptySubscription`.
+pub fn root_schema_builder() -> SchemaBuilder<Query, Mutation, EmptySubscription> {
+    Schema::build(Query::default(), Mutation::default(), EmptySubscription).enable_federation()
+}