From 925614df39eeb57eaedc560935a7b7f053ee1602 Mon Sep 17 00:00:00 2001
From: cosa65 <martin@biomage.net>
Date: Tue, 28 Nov 2023 11:28:05 -0300
Subject: [PATCH] Change endpoint to update upload stauts of a file to require
 sample file id instead of type and sample id

Signed-off-by: cosa65 <martin@biomage.net>
---
 src/api.v2/controllers/sampleFileController.js |  8 ++++----
 src/api.v2/model/SampleFile.js                 | 12 +++---------
 src/specs/api.v2.yaml                          | 11 +++--------
 3 files changed, 10 insertions(+), 21 deletions(-)

diff --git a/src/api.v2/controllers/sampleFileController.js b/src/api.v2/controllers/sampleFileController.js
index 9bbb8a937..bfea1b9dd 100644
--- a/src/api.v2/controllers/sampleFileController.js
+++ b/src/api.v2/controllers/sampleFileController.js
@@ -65,14 +65,14 @@ const beginUpload = async (req, res) => {
 
 const patchFile = async (req, res) => {
   const {
-    params: { experimentId, sampleId, sampleFileType },
+    params: { experimentId, sampleFileId },
     body: { uploadStatus },
   } = req;
-  logger.log(`Patching file ${sampleFileType} for sample ${sampleId} in experiment ${experimentId}`);
+  logger.log(`Patching file ${sampleFileId} in experiment ${experimentId}`);
 
-  await new SampleFile().updateUploadStatus(sampleId, sampleFileType, uploadStatus);
+  await new SampleFile().updateUploadStatus(sampleFileId, uploadStatus);
 
-  logger.log(`Finished patching sample file for experiment ${experimentId}, sample ${sampleId}, sampleFileType ${sampleFileType}`);
+  logger.log(`Finished patching sample file for experiment ${experimentId}, file: ${sampleFileId}`);
   res.json(OK());
 };
 
diff --git a/src/api.v2/model/SampleFile.js b/src/api.v2/model/SampleFile.js
index 900bdafce..889152d13 100644
--- a/src/api.v2/model/SampleFile.js
+++ b/src/api.v2/model/SampleFile.js
@@ -33,16 +33,10 @@ class SampleFile extends BasicModel {
     return files;
   }
 
-  async updateUploadStatus(sampleId, sampleFileType, uploadStatus) {
-    await this.sql({ sf: tableNames.SAMPLE_FILE })
+  async updateUploadStatus(sampleFileId, uploadStatus) {
+    return this.sql({ sf: tableNames.SAMPLE_FILE })
       .update({ upload_status: uploadStatus })
-      .whereExists(
-        this.sql({ sf_map: tableNames.SAMPLE_TO_SAMPLE_FILE_MAP })
-          .select(['sample_file_id'])
-          .where('sf_map.sample_file_id', '=', this.sql.ref('sf.id'))
-          .where('sf_map.sample_id', '=', sampleId),
-      )
-      .andWhere({ sample_file_type: sampleFileType });
+      .where({ id: sampleFileId });
   }
 }
 
diff --git a/src/specs/api.v2.yaml b/src/specs/api.v2.yaml
index 65462810d..85dcabc52 100644
--- a/src/specs/api.v2.yaml
+++ b/src/specs/api.v2.yaml
@@ -1574,9 +1574,9 @@ paths:
             application/json:
               schema:
                 $ref: "#/components/schemas/HTTPError"
+  "/experiments/{experimentId}/sampleFiles/{sampleFileId}":
     patch:
       summary: Update a sample files property
-      description: Update property of a sample file
       operationId: patchFile
       x-eov-operation-id: sampleFile#patch
       x-eov-operation-handler: routes/sampleFile
@@ -1587,13 +1587,7 @@ paths:
           description: ID of the experiment.
           schema:
             type: string
-        - name: sampleId
-          in: path
-          description: ID of the sample.
-          required: true
-          schema:
-            type: string
-        - name: sampleFileType
+        - name: sampleFileId
           in: path
           description: Type of the file.
           required: true
@@ -1641,6 +1635,7 @@ paths:
             application/json:
               schema:
                 $ref: "#/components/schemas/HTTPError"
+    
   "/experiments/{experimentId}/sampleFiles/{sampleFileId}/beginUpload":
     post:
       summary: Begins the multipart upload of a sample file