Upload fasta files in results folder

application.properties

 [global]
-upload_folder = /home/fcabanettes/public_html/tmp
 data_folder = /home/fcabanettes/public_html/test
 # batch system type: local, sge, slurm
 batch_system_type = local

srv/config_reader.py

@@ -15,12 +15,6 @@ class AppConfigReader(object):
         self.reader = RawConfigParser()
         self.reader.read(os.path.join(os.path.dirname(inspect.getfile(self.__class__)), self.CONFIG_FILE_PATH))
 
-    def get_upload_folder(self):
-        try:
-            return self.reader.get("global", "upload_folder")
-        except NoOptionError:
-            raise Exception("No upload folder found in application.properties (global section)")
-
     def get_app_data(self):
         try:
             return self.reader.get("global", "data_folder")

srv/main.py

@@ -20,13 +20,10 @@ sqlite_file = os.path.join(app_folder, "database.sqlite")
 # Init config reader:
 config_reader = AppConfigReader()
 
-UPLOAD_FOLDER = config_reader.get_upload_folder()
-
 app_title = "D-GENIES - Dotplot for Genomes Interactive, E-connected and Speedy"
 
 # Init Flask:
 app = Flask(__name__, static_url_path='/static')
-app.config['UPLOAD_FOLDER'] = UPLOAD_FOLDER
 app.config['SECRET_KEY'] = 'dsqdsq-255sdA-fHfg52-25Asd5'
 
 # Folder containing data:
@@ -88,23 +85,26 @@ def launch_analysis():
             flash("Format of target fasta must be in fasta format (*.%s)" % ", *.".join(ALLOWED_EXTENSIONS))
             form_pass = False
         if form_pass:
+            # Get final job id:
+            id_job_orig = id_job
+            while os.path.exists(os.path.join(app_data, id_job)):
+                id_job = id_job_orig + "_2"
+
+            folder_files = os.path.join(app_data, id_job)
+            os.makedirs(folder_files)
+
             # Save files:
             query_name = os.path.splitext(os.path.basename(file_query.filename))[0]
-            filename_query = get_valid_uploaded_filename(secure_filename(file_query.filename), app.config["UPLOAD_FOLDER"])
+            filename_query = get_valid_uploaded_filename(secure_filename(file_query.filename), folder_files)
             target_name = os.path.splitext(os.path.basename(file_target.filename))[0]
-            query_path = os.path.join(app.config["UPLOAD_FOLDER"], filename_query)
+            query_path = os.path.join(folder_files, filename_query)
             file_query.save(query_path)
             target_path = None
             if file_target.filename != "":
-                filename_target = get_valid_uploaded_filename(secure_filename(file_target.filename), app.config["UPLOAD_FOLDER"])
-                target_path = os.path.join(app.config["UPLOAD_FOLDER"], filename_target)
+                filename_target = get_valid_uploaded_filename(secure_filename(file_target.filename), folder_files)
+                target_path = os.path.join(folder_files, filename_target)
                 file_target.save(target_path)
 
-            # Get final job id:
-            id_job_orig = id_job
-            while os.path.exists(os.path.join(app_data, id_job)):
-                id_job = id_job_orig + "_2"
-
             # Launch job:
             job = JobManager(id_job, email, query_path, target_path, query_name, target_name)
             job.launch()