updating PUDU_implementation

Dockerfile

@@ -14,9 +14,6 @@ EXPOSE 5003
 COPY requirements.txt /app/
 RUN /usr/local/bin/python -m pip install --upgrade pip
 RUN pip install --no-cache-dir -r requirements.txt
-RUN pip list -V
-RUN pip show pudupy
-RUN pip show sbol2build
 
 # Create uploads directory
 RUN mkdir -p /app/uploads && \

sbs_server/app/views.py

@@ -23,12 +23,6 @@ def pin():
 def get_data():
     return app.send_static_file("data.json")
 
-@app.route('/api/test_metadata_upload', methods = ['POST'])
-def test_metadata_upload():
-    if request.method == 'POST':
-        f = request.files['file']
-
-
 @app.route('/api/upload_sbs', methods = ['POST'])
 def upload_file_from_sbs_post():
     if 'Metadata' not in request.files:
@@ -44,6 +38,10 @@ def upload_file_from_sbs_post():
     if params_file.filename == '':
         return 'No selected Params file', 400
     params_from_request = json.loads(params_file.read())
+    expected_params = ['fj_url', 'fj_token', 'sbh_url', 'sbh_token', 'sbh_collec', 'sbh_collec_desc', 'sbh_overwrite', 'fj_overwrite']
+    for param in expected_params:
+        if param not in params_from_request:
+            return 'Parameter ' + param + ' not found in request', 400
 
     # instantiate the XDC class using the params_from_request dictionary
     print(request.files['Metadata'])
@@ -62,13 +60,17 @@ def upload_file_from_sbs_post():
             sbh_token = params_from_request['sbh_token'],
             homespace = "https://synbiohub.org/gonza10v"
             )
-
 
-
-    xdc.initialize()
-    xdc.log_in_sbh()
-    xdc.convert_to_sbol()
-    sbh_url = xdc.upload_to_sbh()
+    try:
+        xdc.initialize()
+        xdc.log_in_sbh()
+        xdc.log_in_fj()
+        xdc.convert_to_sbol()
+        xdc.generate_sbol_hash_map()
+        sbh_url = xdc.upload_to_sbh()
+        xdc.upload_to_fj()
+    except AttributeError as e:
+        return jsonify({"error": str(e)}), 400
 
     sbs_upload_response_dict ={
         "sbh_url": sbh_url,
@@ -91,6 +93,10 @@ def upload_file_from_sbs_post_up():
     if params_file.filename == '':
         return 'No selected Params file', 400
     params_from_request = json.loads(params_file.read())
+    expected_params = ['fj_url', 'fj_user', 'fj_pass', 'sbh_url', 'sbh_user', 'sbh_pass', 'sbh_collec', 'sbh_collec_desc', 'sbh_overwrite', 'fj_overwrite']
+    for param in expected_params:
+        if param not in params_from_request:
+            return 'Parameter ' + param + ' not found in request', 400
 
     # instantiate the XDC class using the params_from_request dictionary
     print(request.files['Metadata'])
@@ -108,64 +114,25 @@ def upload_file_from_sbs_post_up():
             fj_token = None, 
             sbh_token = None,
             homespace = "https://synbiohub.org/gonza10v"
-            )
-
-
-
-    xdc.initialize()
-    xdc.log_in_sbh()
-    xdc.convert_to_sbol()
-    xdc.generate_sbol_hash_map()
-    sbh_url = xdc.upload_to_sbh()
+            )            
 
-    sbs_upload_response_dict ={
+    try:
+        xdc.initialize()
+        xdc.log_in_fj()
+        xdc.log_in_sbh()
+        xdc.convert_to_sbol()
+        xdc.generate_sbol_hash_map()
+        sbh_url = xdc.upload_to_sbh()
+        xdc.upload_to_fj()
+    except AttributeError as e:
+        return jsonify({"error": str(e)}), 400
+
+    sbs_upload_response_dict = {
         "sbh_url": sbh_url,
         "status": "success"
     }
     return jsonify(sbs_upload_response_dict)
 
-@app.route('/extract_data', methods=['POST'])
-def process_files():
-    if 'Metadata' not in request.files:
-        print(request)
-        return 'No file part', 400
-    metadata_file = request.files['Metadata']
-    if metadata_file.filename == '':
-        return 'No selected file', 400
-
-    if 'platereader_output' not in request.files:
-        print(request)
-        return 'No file part', 400
-    file = request.files['platereader_output']
-    if file.filename == '':
-        return 'No selected file', 400
-    # Get uploaded files from request
-    platereader_output_files = [file] #request.files.getlist('platereader_output') #[file] #TODO: see how to iterate through files 
-    # Get selected preset from request
-    preset = request.form.get('preset')
-
-    print(platereader_output_files)
-    print(preset)
-    # Call the process_files_with_script function
-    modified_file_path = process_files_with_script(platereader_output_files, metadata_file, preset)
-
-    # Return the modified file as a response
-    with open(modified_file_path, 'rb') as f:
-        modified_file_data = f.read()
-    #os.remove(modified_file_path)  # Optional: Remove the temporary file
-    print('finished')
-    # save modified file to disk
-
-
-
-    return modified_file_data
-
-@app.route('/return_info', methods=['POST'])
-def return_info():
-    # Return the profile information of the logged in user
-
-
-    return
 
 
 @app.route('/sbol_2_build_golden_gate', methods=['POST'])
@@ -267,5 +234,17 @@ def build_pudu():
         return jsonify({"error": f"Unexpected server error: {str(e)}"}), 500
 
 
+@app.route('/api/inspect_request', methods=['POST'])
+def inspect_request():
+    files = {}
+    for name in request.files:
+        file = request.files[name]
+        try:
+            files[name] = json.loads(file.read())
+        except Exception as e:
+            return jsonify({"error": str(e)}), 400
+
+    return jsonify({
+        "message": "Request received successfully", 
+        "files": files}), 200
 
-

sbs_server/files/files.md

@@ -0,0 +1 @@
+folder for files

sbs_server/files/sbs_params_up.json

@@ -0,0 +1,12 @@
+{
+    "fj_url": "charmmefj-api.synbiohub.org",
+    "fj_user": "test",
+    "fj_pass": "test123",
+    "sbh_url": "https://synbiohub.org",
+    "sbh_user": "test@test.test",
+    "sbh_pass": "test123",
+    "sbh_collec": "xdc_sbs_test_uploader_file",
+    "sbh_collec_desc": "xdc_sbs_test_uploader_file_description",
+    "fj_overwrite": false,
+    "sbh_overwrite": false
+}