stocke le fichier pdf dans le S3

.gitignore

@@ -29,3 +29,4 @@ yarn-error.log*
 /frontend/.env
 /dist/
 /local/
+/locals3root

README.md

@@ -20,6 +20,9 @@ La création des tables et autres structures SQL se fera automatiquement lors du
 
 Pour le stockage des fichiers, l'application utilise un service S3. 
 En local et pour les tests, il est possible d'utiliser https://github.com/adobe/S3Mock
+```bash
+docker compose up -d
+```
 
 
 ### Installation de l'application

docker-compose.yml

@@ -0,0 +1,14 @@
+#s3cmd --host http://localhost:9090 ls s3://maestro --no-ssl
+services:
+  s3mock:
+    image: adobe/s3mock:latest
+    container_name: maestro_s3
+    environment:
+      - debug=true
+      - retainFilesOnExit=true
+      - root=containers3root
+      - initialBuckets=maestro
+    ports:
+      - 9090:9090
+    volumes:
+      - ./locals3root:/containers3root

server/controllers/documentController.ts

@@ -1,14 +1,12 @@
 import {
   DeleteObjectCommand,
   GetObjectCommand,
-  PutObjectCommand,
   S3,
 } from '@aws-sdk/client-s3';
 import { getSignedUrl as getS3SignedUrl } from '@aws-sdk/s3-request-presigner';
 import { Request, Response } from 'express';
 import { AuthenticatedRequest } from 'express-jwt';
 import { constants } from 'http2';
-import { v4 as uuidv4 } from 'uuid';
 import DocumentMissingError from '../../shared/errors/documentMissingError';
 import {
   Document,
@@ -17,6 +15,7 @@ import {
 import { hasPermission } from '../../shared/schema/User/User';
 import documentRepository from '../repositories/documentRepository';
 import config from '../utils/config';
+import { getUploadSignedUrlS3 } from '../services/s3Service';
 
 const getDocument = async (request: Request, response: Response) => {
   const { documentId } = request.params;
@@ -37,30 +36,19 @@ const getUploadSignedUrl = async (request: Request, response: Response) => {
   const user = (request as AuthenticatedRequest).user;
 
   if (kind === 'Resource' && !hasPermission(user, 'createResource')) {
-    return response.sendStatus(constants.HTTP_STATUS_FORBIDDEN);
+    return { status: constants.HTTP_STATUS_FORBIDDEN}
   }
   if (
     kind === 'AnalysisReportDocument' &&
     !hasPermission(user, 'createAnalysis')
   ) {
-    return response.sendStatus(constants.HTTP_STATUS_FORBIDDEN);
+    return { status: constants.HTTP_STATUS_FORBIDDEN }
   }
 
-  console.log('Get signed url for file', filename);
-
-  const client = new S3(config.s3.client);
-  const id = uuidv4();
-  const key = `${id}_${filename}`;
+  const result: {url: string, documentId: string} = await getUploadSignedUrlS3(filename )
 
-  const command = new PutObjectCommand({
-    Bucket: config.s3.bucket,
-    Key: key,
-  });
-
-  const url = await getS3SignedUrl(client, command, { expiresIn: 3600 });
-
-  response.status(200).json({ url, documentId: id });
-};
+  return response.status(200).json(result)
+}
 
 const getDownloadSignedUrl = async (request: Request, response: Response) => {
   const { documentId } = request.params;

server/repositories/kysely.type.ts

@@ -6,6 +6,7 @@
 import type { ColumnType } from "kysely";
 import { UserRole } from '../../shared/schema/User/UserRole';
 import { Region } from '../../shared/referential/Region';
+import { DocumentKind } from '../../shared/schema/Document/DocumentKind';
 
 export type Generated<T> = T extends ColumnType<infer S, infer I, infer U>
   ? ColumnType<S, I | undefined, U>
@@ -90,7 +91,7 @@ export interface Documents {
   createdBy: string | null;
   filename: string;
   id: Generated<string>;
-  kind: string;
+  kind: DocumentKind;
 }
 
 export interface KnexMigrations {

server/services/imapService/girpa.ts

@@ -89,7 +89,7 @@ export const analyseXmlValidator = z.object({
   Substance_active_anglais: residueEnglishNameValidator
 });
 // Visible for testing
-export const extractSample = (obj: unknown): ExportSample[] | null => {
+export const extractSample = (obj: unknown): Omit<ExportSample, 'pdfFile'>[] | null => {
   const echantillonValidator = z.object({
     Code_échantillon: z.string(),
     Commentaire: z.string(),
@@ -155,12 +155,35 @@ const exportDataFromEmail: ExportDataFromEmail = (email) => {
   if (xmlFile !== undefined) {
     const parser = new XMLParser();
     const obj = parser.parse(xmlFile.content);
-    return extractSample(obj);
+
+    const extractAnalyse = extractSample(obj)
+
+    if( extractAnalyse === null ){
+      //FIXME error
+      return null
+    }
+
+    const analyseWithPdf: ExportSample[] = []
+
+    for (const analyse of extractAnalyse) {
+      const pdfAttachment = email.attachments.find(({ contentType, filename }) => contentType === 'application/pdf' && filename?.startsWith(analyse.sampleReference))
+
+      if (pdfAttachment === undefined) {
+        //FIXME error
+        return null
+      }
+
+      const pdfFile: File = new File([pdfAttachment.content], pdfAttachment.filename ?? '');
+      analyseWithPdf.push({...analyse, pdfFile})
+    }
+
+
+    return analyseWithPdf
   } else {
     console.log('Aucun XML', email.attachments);
+    return null
   }
 
-  return null;
 };
 
 export const girpaConf: LaboratoryConf = {

server/services/imapService/index.ts

@@ -2,29 +2,39 @@ import { ImapFlow } from 'imapflow';
 import { isNull } from 'lodash';
 import { ParsedMail, simpleParser } from 'mailparser';
 import { LaboratoryName } from '../../../shared/referential/Laboratory';
+import { Analyte } from '../../../shared/referential/Residue/Analyte';
+import { ComplexResidue } from '../../../shared/referential/Residue/ComplexResidue';
+import { SimpleResidue } from '../../../shared/referential/Residue/SimpleResidue';
+import { Sample } from '../../../shared/schema/Sample/Sample';
+import { initKysely, kysely } from '../../repositories/kysely';
 import config from '../../utils/config';
+import { getUploadSignedUrlS3 } from '../s3Service';
 import { girpaConf } from './girpa';
-import { Sample } from '../../../shared/schema/Sample/Sample';
-import { SimpleResidue } from '../../../shared/referential/Residue/SimpleResidue';
-import { ComplexResidue } from '../../../shared/referential/Residue/ComplexResidue';
-import { Analyte } from '../../../shared/referential/Residue/Analyte';
 
 const laboratoriesWithConf = ['GIR 49'] as const satisfies LaboratoryName[];
 type LaboratoryWithConf = (typeof laboratoriesWithConf)[number];
 
 export type ExportResidue =
-{ value: SimpleResidue, kind: 'SimpleResidue' } |
-{ value:ComplexResidue, kind: 'ComplexResidue' } |
-{ value: Analyte, kind: 'Analyte' }
+  | { value: SimpleResidue; kind: 'SimpleResidue' }
+  | { value: ComplexResidue; kind: 'ComplexResidue' }
+  | { value: Analyte; kind: 'Analyte' };
 
-export type ExportDataSubstance = {substance: ExportResidue} & ( {result_kind: 'NQ', result: null, lmr: null} | {result_kind: 'Q', result: number, lmr: number})
-export type IsSender = (senderAddress: string) => boolean
+export type ExportDataSubstance = { substance: ExportResidue } & (
+  | { result_kind: 'NQ'; result: null; lmr: null }
+  | {
+      result_kind: 'Q';
+      result: number;
+      lmr: number;
+    }
+);
+export type IsSender = (senderAddress: string) => boolean;
 export type ExportSample = {
-  sampleReference: Sample['reference'],
-  notes: string,
-  substances: ExportDataSubstance[]
+  sampleReference: Sample['reference'];
+  notes: string;
+  pdfFile: File;
+  substances: ExportDataSubstance[];
 };
-export type ExportDataFromEmail = (email: ParsedMail) => null | ExportSample[]
+export type ExportDataFromEmail = (email: ParsedMail) => null | ExportSample[];
 
 export type LaboratoryConf = {
   isSender: IsSender;
@@ -103,7 +113,7 @@ const run = async () => {
         }
       }
       for (const message of messagesToRead) {
-        const messageUid: string = `${message.messageUid}`
+        const messageUid: string = `${message.messageUid}`;
         //undefined permet de récupérer tout l'email
         const downloadObject = await client.download(messageUid, undefined, {
           uid: true
@@ -114,12 +124,47 @@ const run = async () => {
         //FIXME trash
         // await client.messageMove(messageUid, config.inbox.trashboxName, {uid: true})
 
-        const data =  laboratoriesConf[message.laboratoryName].exportDataFromEmail(
-            parsed
-          );
+        const data =
+          laboratoriesConf[message.laboratoryName].exportDataFromEmail(parsed);
 
-        console.log(JSON.stringify(data, null, 4))
-        // createWriteStream(parsed.attachments[2].filename ?? '').write(parsed.attachments[2].content)
+        if (data !== null) {
+          initKysely(config.databaseUrl)
+          for (const analyse of data) {
+            const { url, documentId } = await getUploadSignedUrlS3(
+              analyse.pdfFile.name
+            );
+
+            const uploadResult = await fetch(url, {
+              method: 'PUT',
+              body: analyse.pdfFile
+            });
+            if (!uploadResult.ok) {
+              //FIXME
+              // return {
+              //   error: {
+              //     status: uploadResult.status,
+              //     data: await uploadResult.json(),
+              //   } as FetchBaseQueryError,
+              // };
+            }
+            await kysely.transaction().execute(async (trx) => {
+              await trx
+                .insertInto('documents')
+                .values({
+                  id: documentId,
+                  filename: analyse.pdfFile.name,
+                  kind: 'AnalysisReportDocument',
+                  createdAt: new Date(),
+                  createdBy: null
+                })
+                .execute();
+            });
+            console.log(JSON.stringify(data, null, 4));
+            // createWriteStream(parsed.attachments[2].filename ?? '').write(parsed.attachments[2].content)
+          }
+        } else {
+          //FIXME
+        }
       }
     }
   } catch (e) {

server/services/s3Service.ts

@@ -0,0 +1,31 @@
+import { DocumentToCreate } from '../../shared/schema/Document/Document';
+import { PutObjectCommand, S3 } from '@aws-sdk/client-s3';
+import config from '../utils/config';
+import { v4 as uuidv4 } from 'uuid';
+
+import { getSignedUrl as getS3SignedUrl } from '@aws-sdk/s3-request-presigner';
+export const getUploadSignedUrlS3 = async (filename: DocumentToCreate['filename']): Promise<{url: string, documentId: string}> => {
+
+
+  console.log('Get signed url for file', filename);
+
+  const client = new S3({
+      ...config.s3.client,
+    //FIXME forcePathStyle for S3Mock
+    forcePathStyle: true
+    }
+  );
+  const id = uuidv4();
+  const key = `${id}_${filename}`;
+
+  const command = new PutObjectCommand({
+    Bucket: config.s3.bucket,
+    Key: key,
+  });
+
+  const url = await getS3SignedUrl(client, command, { expiresIn: 3600 });
+
+
+
+  return {url, documentId: id}
+};