Add begin sample file upload endpoint, decouple it from create sample…

… file

Signed-off-by: cosa65 <[email protected]>

src/api.v2/controllers/sampleFileController.js

@@ -13,7 +13,7 @@ const logger = getLogger('[SampleFileController] - ');
 const createFile = async (req, res) => {
   const {
     params: { experimentId, sampleId, sampleFileType },
-    body: { sampleFileId, size, metadata = {} },
+    body: { sampleFileId, size },
   } = req;
   logger.log(`Creating file ${sampleFileType} for sample ${sampleId} in experiment ${experimentId}`);
 
@@ -25,19 +25,31 @@ const createFile = async (req, res) => {
     upload_status: 'uploading',
   };
 
-  let uploadUrlParams;
+
 
   await sqlClient.get().transaction(async (trx) => {
     await new SampleFile(trx).create(newSampleFile);
     await new Sample(trx).setNewFile(sampleId, sampleFileId, sampleFileType);
-
-    logger.log(`Getting multipart upload urls for ${experimentId}, sample ${sampleId}, sampleFileType ${sampleFileType}`);
-    uploadUrlParams = await getFileUploadUrls(sampleFileId, metadata, size, bucketNames.SAMPLE_FILES);
   });
 
 
   logger.log(`Finished creating sample file for experiment ${experimentId}, sample ${sampleId}, sampleFileType ${sampleFileType}`);
-  res.json(uploadUrlParams);
+
+  res.json(OK());
+};
+
+const beginUpload = async (req, res) => {
+  const {
+    params: { experimentId, sampleFileId },
+    body: { metadata, size },
+  } = req;
+
+  logger.log(`Generating multipart upload urls for ${experimentId}, sample file ${sampleFileId}`);
+  const uploadParams = await getFileUploadUrls(
+    sampleFileId, metadata, size, bucketNames.SAMPLE_FILES,
+  );
+
+  res.json(uploadParams);
 };
 
 const patchFile = async (req, res) => {
@@ -66,5 +78,5 @@ const getS3DownloadUrl = async (req, res) => {
 };
 
 module.exports = {
-  createFile, patchFile, getS3DownloadUrl,
+  createFile, beginUpload, patchFile, getS3DownloadUrl,
 };

src/api.v2/routes/sampleFile.js

@@ -1,5 +1,5 @@
 const {
-  createFile, patchFile, getS3DownloadUrl,
+  createFile, patchFile, getS3DownloadUrl, beginUpload,
 } = require('../controllers/sampleFileController');
 
 const { expressAuthorizationMiddleware } = require('../middlewares/authMiddlewares');
@@ -13,6 +13,10 @@ module.exports = {
     expressAuthorizationMiddleware,
     (req, res, next) => patchFile(req, res).catch(next),
   ],
+  'sampleFile#beginUpload': [
+    expressAuthorizationMiddleware,
+    (req, res, next) => beginUpload(req, res).catch(next),
+  ],
   'sampleFile#downloadUrl': [
     expressAuthorizationMiddleware,
     (req, res, next) => getS3DownloadUrl(req, res).catch(next),

src/specs/api.v2.yaml

@@ -1439,7 +1439,7 @@ paths:
           content:
             application/json:
               schema:
-                type: object
+                $ref: "#/components/schemas/HTTPSuccess"
         "400":
           description: Bad Request
           content:
@@ -1537,6 +1537,75 @@ paths:
             application/json:
               schema:
                 $ref: "#/components/schemas/HTTPError"
+  "/experiments/{experimentId}/sampleFiles/{sampleFileId}/beginUpload":
+    post:
+      summary: Begins the multipart upload of a sample file
+      description: Begins the multipart upload of a sample file
+      operationId: beginUpload
+      x-eov-operation-id: sampleFile#beginUpload
+      x-eov-operation-handler: routes/sampleFile
+      parameters:
+        - name: experimentId
+          required: true
+          in: path
+          description: ID of the experiment.
+          schema:
+            type: string
+        - name: sampleFileId
+          in: path
+          description: Type of the file.
+          required: true
+          schema:
+            type: string
+      requestBody:
+        content:
+          application/json:
+            schema:
+              $ref: "#/components/schemas/BeginSampleFileUpload"
+      responses:
+        "200":
+          description: Success
+          content:
+            application/json:
+              schema:
+                type: object
+                properties:
+                  signedUrls: 
+                    type: array
+                    items:
+                      type: string
+                  uploadId: 
+                    type: string
+        "400":
+          description: Bad Request
+          content:
+            application/json:
+              schema:
+                $ref: "#/components/schemas/HTTPError"
+        "401":
+          description: The request lacks authentication credentials.
+          content:
+            application/json:
+              schema:
+                $ref: "#/components/schemas/HTTPError"
+        "403":
+          description: Forbidden request for this user.
+          content:
+            application/json:
+              schema:
+                $ref: "#/components/schemas/HTTPError"
+        "404":
+          description: Not found error.
+          content:
+            application/json:
+              schema:
+                $ref: "#/components/schemas/HTTPError"
+        "424":
+          description: Terms not accepted error.
+          content:
+            application/json:
+              schema:
+                $ref: "#/components/schemas/HTTPError"
   /completeMultipartUpload:
     post:
       summary: Complete a multipart upload
@@ -2481,6 +2550,8 @@ components:
       $ref: ./models/samples-bodies/CreateSampleFile.v2.yaml
     PatchSampleFile:
       $ref: ./models/samples-bodies/PatchSampleFile.v2.yaml
+    BeginSampleFileUpload: 
+      $ref: ./models/samples-bodies/BeginSampleFileUpload.v2.yaml
     UpdateSamplesOptions:
       $ref: ./models/samples-bodies/UpdateSamplesOptions.v2.yaml
     CellSets:

src/specs/models/samples-bodies/BeginSampleFileUpload.v2.yaml

@@ -0,0 +1,21 @@
+title: Begin sample file multipart upload
+description: 'Data to begin an s3 multipart upload'
+type: object
+properties:
+  size:
+    type: number
+  metadata:
+    description: Metadata to append to the s3 object on upload
+    type: object
+    properties:
+      cellrangerVersion:
+        type: string
+        oneOf:
+          - pattern: v2
+          - pattern: v3
+
+required:
+  - size
+  - metadata
+
+additionalProperties: false

src/specs/models/samples-bodies/CreateSampleFile.v2.yaml

@@ -6,15 +6,6 @@ properties:
     type: string
   size:
     type: number
-  metadata:
-    description: Metadata to append to the s3 object on upload
-    type: object
-    properties:
-      cellrangerVersion:
-        type: string
-        oneOf:
-          - pattern: v2
-          - pattern: v3
 
 required:
   - sampleFileId