Resource workflow v2

backend/requirements.txt

@@ -5,8 +5,8 @@ numpy==1.26.1
 pandas==1.3.3
 pyflapjack @ git+https://github.com/flapjacksynbio/pyFlapjack@xdc_features2
 excel2flapjack==1.0.11
-tricahue==0.0b6
-# tricahue @ git+https://github.com/MyersResearchGroup/Tricahue/@dev
+# tricahue==0.0b6
+tricahue @ git+https://github.com/MyersResearchGroup/Tricahue/@dev
 sbol2build
 flask_swagger_ui
 xlsxwriter

backend/sbs_server/app/views.py

@@ -7,7 +7,6 @@
 import os
 import json
 import xml.etree.ElementTree as ET
-
 import tricahue
 import sbol2 as sb2
 import pudu
@@ -39,9 +38,7 @@ def upload_experiment():
 Helper function to upload to SynBioHub and Flapjack using XDC/XDE
 '''
 def sbh_fj_upload(files):
-
     if 'Metadata' not in files:
-        print(request)
         return 'No file part', 400
     metadata_file = files['Metadata']
     if metadata_file.filename == '':
@@ -65,6 +62,10 @@ def sbh_fj_upload(files):
     if params_file.filename == '':
         return 'No selected Params file', 400
     params_from_request = json.loads(params_file.read())
+    sbh_url = params_from_request.get('sbh_url')
+    if sbh_url and not (sbh_url.startswith('http://') or sbh_url.startswith('https://')):
+        params_from_request['sbh_url'] = 'https://' + sbh_url
+
     required_params = ['sbh_url', 'sbh_token', 'sbh_user', 'sbh_pass', 
                        'fj_url', 'fj_token', 'fj_user', 'fj_pass', 
                        'sbh_collec', 'sbh_collec_desc', 
@@ -78,26 +79,18 @@ def sbh_fj_upload(files):
         return 'No SBH credentials provided', 400
 
     # Attachment files to upload to SBH
-    attachments = None
-    if 'Attachments' in files:
+    if 'Attachments' in files and 'attachments' in params_from_request:
         attachment_files = files.getlist("Attachments")
-        attachment_metadata = params_from_request.get('attachments')
-
-        if attachment_metadata is None:
-            return 'Attachment metadata not provided', 400
-        if not isinstance(attachment_metadata, dict):
-            return 'Attachment metadata must be a JSON object keyed by filename', 400
-
         attachments = {}
-        missing_metadata = [file.filename for file in attachment_files if file.filename not in attachment_metadata]
-        if missing_metadata:
-            missing_list = ', '.join(missing_metadata)
-            return f'Missing attachment metadata for files: {missing_list}', 400
-
         for file in attachment_files:
-            attachments[attachment_metadata[file.filename]] = file
-
-        print(attachments)
+            if file.filename not in params_from_request['attachments']:
+                return (
+                    f"Attachment metadata for file '{file.filename}' not found in request",
+                    400,
+                )
+            attachments[params_from_request['attachments'][file.filename]] = file
+    else:
+        attachments = None
 
     # instantiate the XDC class using the params_from_request dictionary
     xdc = tricahue.XDC(input_excel_path = files['Metadata'],
@@ -113,8 +106,8 @@ def sbh_fj_upload(files):
             fj_overwrite = params_from_request['fj_overwrite'], 
             fj_token = params_from_request['fj_token'], 
             sbh_token = params_from_request['sbh_token'],
+            attachments = attachments,
             homespace = "https://example.org/", 
-            attachments = attachments
             )
 
     try:

backend/sbs_server/files/sbs_params.json

@@ -1,10 +1,16 @@
 {
+    "attachments": {"ExpNOTs_GFP_trans.xlsx": "LB", "example.jpg": "ExampleMedia"},
+    "fj_overwrite": 1,
+    "fj_pass": null,
+    "fj_token": null,
     "fj_url": "charmmefj-api.synbiohub.org",
-    "fj_token": "eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJ0b2tlbl90eXBlIjoicmVmcmVzaCIsImV4cCI6MTc1Mzk4MDI2NywianRpIjoiNTg5MTFmM2IxZTlhNGZlN2FjOTA2YzI2NmIwYzJmMjUiLCJ1c2VyX2lkIjoyfQ.hYVb65i4XinKOMsRgCG2EHrvFcYDx4vvzWg_wImDsDA",
+    "fj_user": null,
+    "sbh_collec": "sbs_backend_test",
+    "sbh_collec_desc": "Uploaded via SBS_server using XDC to SBH",
+    "sbh_overwrite": 1,
+    "sbh_pass": null,
+    "sbh_token": "REPLACE_WITH_SYN_BIO_HUB_TOKEN",
     "sbh_url": "https://synbiohub.org",
-    "sbh_token": "37ae0d50-ba67-4f66-bb06-79619d8ba7d3",
-    "sbh_collec": "xdc_sbs_test_uploader_file",
-    "sbh_collec_desc": "xdc_sbs_test_uploader_file_description",
-    "fj_overwrite": false,
-    "sbh_overwrite": false
+    "sbh_user": null,
+    "version": ""
 }

frontend/src/API.js

@@ -37,7 +37,7 @@ export async function upload_resource(
     sbh_collec,
     sbh_collec_desc,
     workingDirectory = null,
-    sbh_overwrite = false
+    sbh_overwrite = 0
 ) {
     try {
         let data = new FormData();
@@ -57,15 +57,15 @@ export async function upload_resource(
         const paramsObj = {
             sbh_url: sbh_url,
             sbh_token: sbh_token,
+            fj_url: "charmmefj-api.synbiohub.org",
             sbh_user: null,
             sbh_pass: null,
-            fj_url: "charmmefj-api.synbiohub.org",
             fj_token: null,
             fj_user: null,
             fj_pass: null,
             sbh_collec: sbh_collec,
             sbh_collec_desc: sbh_collec_desc,
-            sbh_overwrite: sbh_overwrite ? 2 : 0,
+            sbh_overwrite: sbh_overwrite,
             fj_overwrite: 1,
             version: "",
             attachments: {}
@@ -88,7 +88,6 @@ export async function upload_resource(
         return response.data;
     } catch (error) {
         console.error("Upload Resource error:", error);
-        showErrorNotification('Error', error.message);
         throw error;
     }
 }