Draft: submit dummy Slurm job

README.md

@@ -98,6 +98,18 @@ docker exec -i <keycloak-container-name> bash /usr/scripts/bootstrap-keycloak.sh
 
 The keycloak admin portal can be accessed in the browser by navigating to localhost and the port specified by the `KEYCLOAK_PORT` env var, e.g., `localhost:9821`
 
+To request an access token to Keycloak: 
+```bash
+export TOKEN=$(curl --location --request POST 'http://localhost:9821/auth/realms/ssmp/protocol/openid-connect/token' --header 'Content-Type: application/x-www-form-urlencoded' --data-urlencode 'password=secret' --data-urlencode 'username=ssmp-user' --data-urlencode 'client_id=ssmp-backend' --data-urlencode 'realm=ssmp' --data-urlencode 'grant_type=password' | jq -r '.access_token')
+```
+
+To access a protected endpoint on the backend: 
+```bash
+curl -X POST http://localhost:5862/graphql -H "Authorization: Bearer '$TOKEN'" \
+--header 'Content-Type: application/json' \
+--data-raw <JSON>
+```
+
 ## Mongo
 
 Annotations can be imported into mongo using the following command. Note that that the headers should not be included in the csv and the order of the fields passed to the `fields` argument should match the order of the fields in the csv.

docker-compose.yaml

@@ -48,6 +48,9 @@ services:
       TEST_NODE_SSMP_TOKEN_ENDPOINT:
       TEST_NODE_TOKEN_AUDIENCE:
       MONGO_CONNECTION_STRING: mongodb://${MONGO_INITDB_ROOT_USERNAME}:${MONGO_INITDB_ROOT_PASSWORD}@mongo/${MONGO_INITDB_DATABASE}?authSource=admin
+      SLURM_USER:
+      SLURM_JWT:
+      SLURM_ENDPOINT:
   mongo:
     image: mongo:latest
     environment:

react/package.json

@@ -4,16 +4,24 @@
     "private": true,
     "proxy": "http://ssmp-server:3000",
     "dependencies": {
+        "@apollo/client": "^3.5.10",
+        "@apollo/link-error": "^2.0.0-beta.3",
         "@apollo/react-hooks": "^4.0.0",
+        "@graphql-tools/schema": "^8.3.10",
         "@react-keycloak/web": "^3.4.0",
         "@types/uuid": "^8.3.1",
         "apollo-client": "^2.6.10",
-        "apollo-link-rest": "^0.8.0-beta.0",
+        "apollo-link": "^1.2.14",
+        "apollo-link-rest": "^0.9.0-rc.1",
         "apollo-link-timeout": "^4.0.0",
+        "apollo-server-core": "^3.6.7",
+        "crypto": "^1.0.1",
+        "crypto-hash": "^2.0.1",
         "framer-motion": "^4.1.17",
         "gql-tag": "^1.0.1",
         "graphql": "^15.5.1",
         "graphql-anywhere": "^4.2.7",
+        "graphql-ws": "^5.8.1",
         "keycloak-js": "^15.0.0",
         "react": "^17.0.2",
         "react-beautiful-dnd": "^13.1.0",
@@ -25,7 +33,11 @@
         "react-router-dom": "^5.2.0",
         "react-table": "^7.7.0",
         "styled-components": "5.3.0",
-        "uuid": "^8.3.2"
+        "uuid": "^8.3.2",
+        "ws": "^8.5.0"
+    },
+    "resolutions": {
+        "apollo-link": "^1.2.14"
     },
     "devDependencies": {
         "@storybook/addon-actions": "^6.3.4",

react/src/apollo/client.ts

@@ -1,16 +1,28 @@
 import {
     ApolloClient,
+    ApolloLink,
     createHttpLink,
     from,
     InMemoryCache,
+    NextLink,
     Observable,
+    Operation,
+    QueryHookOptions,
+    split,
+    SubscriptionHookOptions,
     useLazyQuery,
+    useQuery,
+    useSubscription,
 } from '@apollo/client';
-import { onError } from '@apollo/client/link/error';
-import { ApolloLink, QueryHookOptions, useQuery } from '@apollo/react-hooks';
+
+import { GraphQLWsLink } from '@apollo/client/link/subscriptions';
+
+import { getMainDefinition } from '@apollo/client/utilities';
+import { onError } from '@apollo/link-error';
 import { RestLink } from 'apollo-link-rest';
 import ApolloLinkTimeout from 'apollo-link-timeout';
 import { DocumentNode } from 'graphql';
+import { createClient } from 'graphql-ws';
 import { makeGraphQLError, makeNetworkError, makeNodeError } from '../components';
 import { useErrorContext } from '../hooks';
 import { VariantQueryResponseError } from '../types';
@@ -27,12 +39,29 @@ export const buildLink = (token?: string) => {
         headers: { accept: 'application/json' },
     });
 
-    const remoteNodeErrorLink = new ApolloLink((operation, forward) => {
+    const wsLink = new GraphQLWsLink(
+        createClient({
+            url: `ws://localhost:5862/graphql`,
+        })
+    );
+
+    const splitLink = split(
+        ({ query }) => {
+            const definition = getMainDefinition(query);
+            return (
+                definition.kind === 'OperationDefinition' && definition.operation === 'subscription'
+            );
+        },
+        wsLink,
+        httpLink
+    );
+
+    const remoteNodeErrorLink = new ApolloLink((operation: Operation, forward: NextLink) => {
         return new Observable(observer => {
             const dispatcherContext = operation.getContext();
             const sub = forward(operation).subscribe({
                 next: response => {
-                    if (!!response?.data?.getVariants.errors.length) {
+                    if (!!response?.data?.getVariants?.errors.length) {
                         response?.data?.getVariants.errors.forEach(
                             (e: VariantQueryResponseError) => {
                                 dispatcherContext.dispatch(makeNodeError(e));
@@ -51,7 +80,7 @@ export const buildLink = (token?: string) => {
 
     const errorLink = onError(({ graphQLErrors, networkError, operation, response, forward }) => {
         const { dispatch } = operation.getContext();
-        const sources = operation.variables.input.sources;
+        const sources = operation.variables.input.sources || [];
 
         if (graphQLErrors) {
             graphQLErrors.forEach(graphQLError => {
@@ -73,7 +102,7 @@ export const buildLink = (token?: string) => {
         return forward(operation);
     });
 
-    const authLink = new ApolloLink((operation, forward) => {
+    const authLink = new ApolloLink((operation: Operation, forward: NextLink) => {
         operation.setContext(({ headers = {} }) => ({
             headers: {
                 ...headers,
@@ -84,7 +113,7 @@ export const buildLink = (token?: string) => {
         return forward(operation);
     });
 
-    return from([mygeneRestLink, authLink, errorLink, timeoutLink, remoteNodeErrorLink, httpLink]);
+    return from([mygeneRestLink, authLink, errorLink, timeoutLink, remoteNodeErrorLink, splitLink]);
 };
 
 export const client = new ApolloClient<any>({
@@ -108,6 +137,21 @@ export const useApolloQuery = <T, V>(query: DocumentNode, options: QueryHookOpti
     });
 };
 
+export const useApolloSubscription = <T, V>(
+    subscription: DocumentNode,
+    options: SubscriptionHookOptions<T, V> = {}
+) => {
+    const { dispatch } = useErrorContext();
+
+    return useSubscription<T, V>(subscription, {
+        client,
+        shouldResubscribe: true,
+        fetchPolicy: 'network-only',
+        context: { dispatch },
+        ...options,
+    });
+};
+
 export const useLazyApolloQuery = <T, V>(
     query: DocumentNode,
     options: QueryHookOptions<T, V> = {}

react/src/apollo/hooks/index.ts

@@ -1,4 +1,11 @@
 import useFetchAutocompleteQuery from './useFetchAutocompleteQuery';
 import useFetchVariantsQuery from './useFetchVariantsQuery';
+import useFetchVariantsSubscription from './useFetchVariantsSubscription';
+import useSlurmSubscription from './useSlurmSubscriptionQuery';
 
-export { useFetchAutocompleteQuery, useFetchVariantsQuery };
+export {
+    useFetchAutocompleteQuery,
+    useFetchVariantsQuery,
+    useFetchVariantsSubscription,
+    useSlurmSubscription,
+};

react/src/apollo/hooks/useFetchVariantsSubscription.ts

@@ -0,0 +1,97 @@
+import { gql } from '@apollo/react-hooks';
+import { CombinedVariantQueryResponse } from '../../types';
+import { useApolloSubscription } from '../client';
+
+export const fetchVariantsSubscription = gql`
+    subscription GetVariantsSubscription($id: String!) {
+        getVariantsSubscription(id: $id) {
+            data {
+                variant {
+                    alt
+                    callsets {
+                        callsetId
+                        individualId
+                        info {
+                            ad
+                            dp
+                            gq
+                            qual
+                            zygosity
+                        }
+                    }
+                    end
+                    info {
+                        af
+                        aaAlt
+                        aaPos
+                        aaRef
+                        cdna
+                        consequence
+                        geneName
+                        gnomadHet
+                        gnomadHom
+                        transcript
+                    }
+                    ref
+                    referenceName
+                    start
+                    variantId
+                }
+                individual {
+                    datasetId
+                    diseases {
+                        ageOfOnset {
+                            age
+                            ageGroup
+                        }
+                        description
+                        diseaseId
+                        diseaseLabel
+                        levelSeverity
+                        outcome
+                        stage
+                    }
+                    ethnicity
+                    geographicOrigin
+                    individualId
+                    info {
+                        diagnosis
+                        candidateGene
+                        solved
+                        classifications
+                    }
+                    phenotypicFeatures {
+                        ageOfOnset {
+                            age
+                            ageGroup
+                        }
+                        dateOfOnset
+                        levelSeverity
+                        onsetType
+                        phenotypeId
+                        phenotypeLabel
+                    }
+                    sex
+                }
+                contactInfo
+                source
+            }
+            errors {
+                error {
+                    id
+                    code
+                    message
+                }
+                source
+            }
+        }
+    }
+`;
+
+const useFetchVariantsSubscription = () =>
+    useApolloSubscription<{ getVariantsSubscription: CombinedVariantQueryResponse }, {}>(
+        fetchVariantsSubscription,
+        {}
+    );
+
+export default useFetchVariantsSubscription;

react/src/apollo/hooks/useSlurmSubscriptionQuery.ts

@@ -0,0 +1,42 @@
+import { gql } from '@apollo/react-hooks';
+import { SlurmVariantResponse } from '../../types';
+import { useApolloSubscription } from '../client';
+
+export const fetchSlurmSubscription = gql`
+    subscription OnSlurmResponse {
+        slurmResponse {
+            jobId
+            variants {
+                start
+                end
+                referenceName
+                ref
+                alt
+                Consequence
+                oAA
+                nAA
+                FeatureID
+                cDNApos
+                protPos
+                nhomalt
+                an
+                af
+                filter
+                transcript
+                cdna
+                amino_acids
+            }
+        }
+    }
+`;
+
+const useSlurmSubscription = () =>
+    useApolloSubscription<
+        {
+            jobId: number;
+            variants: SlurmVariantResponse[];
+        },
+        {}
+    >(fetchSlurmSubscription, {});
+
+export default useSlurmSubscription;