Merge pull request #40 from safeinsights/file-drop

Replace container push screen with file upload

bin/prod-docker-build

@@ -7,8 +7,11 @@ if [ -z "$$DOCKER_TAG" ]; then
     exit 1
 fi
 
+# provenence is disabled because without it docker generates a "multi-platform index" that is incompatible with lambda
+# https://github.com/docker/buildx/issues/1509#issuecomment-1378538197
 docker build \
     --file Dockerfile.prod \
+    --provenance=false \
     --platform=linux/amd64 \
     --secret id=envs,src=.env \
     --progress=plain \

package.json

@@ -31,11 +31,13 @@
         "@aws-sdk/client-s3": "^3.722.0",
         "@aws-sdk/credential-provider-ini": "^3.721.0",
         "@aws-sdk/lib-storage": "^3.722.0",
+        "@aws-sdk/s3-presigned-post": "^3.697.0",
         "@aws-sdk/s3-request-presigner": "^3.722.0",
         "@clerk/nextjs": "^6.9.6",
         "@faker-js/faker": "^9.3.0",
         "@hookform/resolvers": "^3.9.1",
         "@mantine/core": "^7.15",
+        "@mantine/dropzone": "^7.14.1",
         "@mantine/form": "^7.15",
         "@mantine/modals": "^7.15",
         "@mantine/notifications": "^7.15.2",
@@ -100,6 +102,5 @@
         "typescript-eslint": "^8.19.1",
         "vite-tsconfig-paths": "^5.1.4",
         "vitest": "*"
-    },
-    "overrides": {}
+    }
 }

src/app/api/dev/upload-code/[studyRunIdentifier]/route.ts

@@ -0,0 +1,47 @@
+import { db } from '@/database'
+import { NextResponse } from 'next/server'
+import { PROD_ENV } from '@/server/config'
+import { getUploadTmpDirectory } from '@/server/config'
+import { pathForStudyRunCode } from '@/lib/paths'
+import path from 'path'
+import fs from 'fs'
+
+export const dynamic = 'force-dynamic' // defaults to auto
+
+export async function POST(req: Request, { params }: { params: Promise<{ studyRunIdentifier: string }> }) {
+    const { studyRunIdentifier } = await params
+    if (PROD_ENV) {
+        return NextResponse.json({ error: 'This route is only available in development' }, { status: 403 })
+    }
+
+    const info = await db
+        .selectFrom('studyRun')
+        .innerJoin('study', 'study.id', 'studyRun.studyId')
+        .innerJoin('member', 'member.id', 'study.memberId')
+        .select(['studyRun.id as studyRunId', 'studyId', 'member.identifier as memberIdentifier'])
+        .where('studyRun.id', '=', studyRunIdentifier)
+        .executeTakeFirst()
+
+    if (!info) {
+        return NextResponse.json({ status: 'fail', error: 'run not found' }, { status: 404 })
+    }
+
+    const formData = await req.formData()
+    const file = formData.get('file') as File
+
+    const dir = path.join(getUploadTmpDirectory(), pathForStudyRunCode(info), path.dirname(file.name))
+    fs.mkdirSync(dir, { recursive: true })
+    const filePath = path.join(dir, path.basename(file.name))
+    const buffer = await file.arrayBuffer()
+    await fs.promises.writeFile(filePath, Buffer.from(buffer))
+
+    await db
+        .updateTable('studyRun')
+        .set({
+            status: 'CODE-SUBMITTED',
+        })
+        .where('id', '=', info.studyRunId)
+        .executeTakeFirstOrThrow()
+
+    return new NextResponse('ok', { status: 200 })
+}

src/app/api/run/[runId]/results/route.ts

@@ -20,7 +20,7 @@ export const POST = wrapApiMemberAction(async (req: Request, { params }: { param
         }
 
         // join is a security check to ensure the run is owned by the member
-        const run = await db
+        const info = await db
             .selectFrom('studyRun')
             .innerJoin('study', (join) =>
                 join.onRef('study.id', '=', 'studyRun.studyId').on('study.memberId', '=', member.id),
@@ -29,13 +29,13 @@ export const POST = wrapApiMemberAction(async (req: Request, { params }: { param
             .where('studyRun.id', '=', runId)
             .executeTakeFirst()
 
-        if (!run) {
+        if (!info) {
             return NextResponse.json({ status: 'fail', error: 'run not found' }, { status: 404 })
         }
 
         await attachResultsToStudyRun(
             {
-                ...run,
+                ...info,
                 memberIdentifier: member.identifier,
             },
             contents,

src/app/api/services/code-push/route.ts

@@ -6,7 +6,6 @@ import { NextResponse } from 'next/server'
 
 const schema = z.object({
     runId: z.string().uuid(),
-    codePath: z.string(),
     fileSize: z.number(),
     fileCount: z.number(),
 })
@@ -20,7 +19,6 @@ export async function POST(req: Request) {
         .where('status', '=', 'INITIATED')
         .set({
             status: 'CODE-SUBMITTED',
-            codePath: body.codePath,
             uploadedAt: new Date(),
             fileSize: body.fileSize,
             fileCount: body.fileCount,

src/app/layout.tsx

@@ -1,9 +1,9 @@
 import type { Metadata } from 'next'
 
 import './globals.css'
-
 import '@mantine/core/styles.layer.css'
 import 'mantine-datatable/styles.layer.css'
+import '@mantine/dropzone/styles.layer.css'
 
 import { Providers } from './providers'
 import { AppLayout } from '@/components/app-layout'

src/app/member/[memberIdentifier]/study/[studyIdentifier]/run/[studyRunIdentifier]/review/actions.ts

@@ -16,6 +16,7 @@ export const updateStudyRunStatusAction = async (info: MinimalRunInfo, status: S
 }
 
 export const dataForRunAction = async (studyRunIdentifier: string) => {
+    const runId = b64toUUID(studyRunIdentifier)
     const run = await db
         .selectFrom('studyRun')
         .innerJoin('study', 'study.id', 'studyRun.studyId')
@@ -27,10 +28,12 @@ export const dataForRunAction = async (studyRunIdentifier: string) => {
             'study.title as studyTitle',
             'member.identifier as memberIdentifier',
         ])
-        .where('studyRun.id', '=', b64toUUID(studyRunIdentifier))
+        .where('studyRun.id', '=', runId)
         .executeTakeFirst()
 
     let manifest: CodeManifest = {
+        runId,
+        language: 'r',
         files: {},
         size: 0,
         tree: { label: '', value: '', size: 0, children: [] },

src/app/providers.tsx

@@ -42,17 +42,6 @@ function getQueryClient() {
     }
 }
 
-export const TestingProviders: React.FC<Props> = ({ children }) => {
-    const queryClient = getQueryClient()
-    return (
-        <MantineProvider theme={theme}>
-            <QueryClientProvider client={queryClient}>
-                <ModalsProvider>{children}</ModalsProvider>
-            </QueryClientProvider>
-        </MantineProvider>
-    )
-}
-
 export const Providers: React.FC<Props> = ({ children }) => {
     const queryClient = getQueryClient()
 

src/app/researcher/study/[encodedStudyId]/review/actions.ts

@@ -7,8 +7,8 @@ import { uuidToB64 } from '@/lib/uuid'
 import { revalidatePath } from 'next/cache'
 import { attachSimulatedResultsToStudyRun, storageForResultsFile } from '@/server/results'
 import { sleep } from '@/lib/util'
-import { SIMULATE_RESULTS_UPLOAD, USING_CONTAINER_REGISTRY } from '@/server/config'
 import { queryRunResult } from '@/server/queries'
+import { SIMULATE_RESULTS_UPLOAD, USING_CONTAINER_REGISTRY } from '@/server/config'
 import { fetchStudyRunResults } from '@/server/aws'
 
 const AllowedStatusChanges: Array<StudyStatus> = ['APPROVED', 'REJECTED'] as const

src/app/researcher/study/[encodedStudyId]/upload/actions.ts

@@ -2,6 +2,9 @@
 
 import { b64toUUID } from '@/lib/uuid'
 import { db } from '@/database'
+import { MinimalRunInfo } from '@/lib/types'
+import { urlForStudyRunCodeUpload, type PresignedPost } from '@/server/aws'
+import { USING_S3_STORAGE } from '@/server/config'
 
 export const getLatestStudyRunAction = async ({ encodedStudyId }: { encodedStudyId: string }) => {
     return await db
@@ -11,6 +14,7 @@ export const getLatestStudyRunAction = async ({ encodedStudyId }: { encodedStudy
             'study.id',
             'study.title',
             'study.containerLocation',
+            'member.identifier as memberIdentifier',
             'member.name as memberName',
             ({ selectFrom }) =>
                 selectFrom('studyRun')
@@ -23,3 +27,14 @@ export const getLatestStudyRunAction = async ({ encodedStudyId }: { encodedStudy
         .where('study.id', '=', b64toUUID(encodedStudyId))
         .executeTakeFirst()
 }
+
+export async function getUploadUrlForStudyRunCodeAction(info: MinimalRunInfo): Promise<PresignedPost> {
+    if (USING_S3_STORAGE) {
+        return urlForStudyRunCodeUpload(info)
+    } else {
+        return {
+            url: `/api/dev/upload-code/${info.studyRunId}`,
+            fields: {},
+        }
+    }
+}

src/app/researcher/study/[encodedStudyId]/upload/page.tsx

@@ -2,8 +2,9 @@ import React from 'react'
 import { Button, Flex, Text, Title, Container } from '@mantine/core'
 import { getLatestStudyRunAction } from './actions'
 import Link from 'next/link'
-import { PushInstructions } from '@/components/push-instructions'
+import { UploadStudyRunCode } from '@/components/upload-study-run-code'
 import { AlertNotFound } from '@/components/errors'
+import { getUploadUrlForStudyRunCodeAction } from './actions'
 
 export default async function UploadPage(props: { params: Promise<{ encodedStudyId: string }> }) {
     const params = await props.params
@@ -19,15 +20,18 @@ export default async function UploadPage(props: { params: Promise<{ encodedStudy
 
     return (
         <Container w="100%">
-            <Title mb="lg">OpenStax Study Proposal Step 2)</Title>
+            <Title mb="lg">{study.memberName} Study Proposal Step 2)</Title>
             <Text
                 pt={10}
                 fs="italic"
             >{`{ For the Pilot, communications steps and member review/approval are skipped }`}</Text>
             <Text mb="xl" mt="lg" fw="bold">
                 For the Pilot, engineers use the following to containerize and upload code:
             </Text>
-            <PushInstructions containerLocation={study.containerLocation} runId={study.pendingRunId} />
+            <UploadStudyRunCode
+                run={{ memberIdentifier: study.memberIdentifier, studyId: study.id, studyRunId: study.pendingRunId }}
+                getSignedURL={getUploadUrlForStudyRunCodeAction}
+            />
             <Flex justify="end" mt="lg">
                 <Link href="edit" passHref>
                     <Button>Next</Button>

src/app/researcher/study/request/[memberIdentifier]/form.test.tsx

@@ -1,7 +1,7 @@
 import { expect, describe, it, vi } from 'vitest'
 import { render } from '@testing-library/react'
 import { Form } from './form'
-import { TestingProviders } from '@/app/providers'
+import { TestingProvidersWrapper } from '@/tests/providers'
 import userEvent from '@testing-library/user-event'
 
 import { onCreateStudyAction } from './actions'
@@ -14,9 +14,7 @@ describe('Member Start Page Form', () => {
     it('submits form', async () => {
         const { getByLabelText, getByRole, container } = render(
             <Form memberId="1234" memberIdentifier="hello-world" />,
-            {
-                wrapper: TestingProviders,
-            },
+            TestingProvidersWrapper,
         )
         let title = '2srt'