--- a/main.py	Wed Jun 23 10:40:19 2021 +0000
+++ b/main.py	Fri Jul 02 09:40:25 2021 +0000
@@ -4,6 +4,8 @@
 
 # general imports
 import os, sys, json
+import irods_upload
+
 from shutil import copyfile
 from datetime import datetime
 
@@ -63,27 +65,38 @@
     iRODSCredentials["zone"] = params["irods_zone"]
 
     # create login window
-    make_login_window(params)
+    ## make_login_window(params)
+    iRODSCredentials["user"] = params["irods_user"]
+    iRODSCredentials["pw"] = params["irods_password"]
+    
+    host = iRODSCredentials["host"]
+    port = iRODSCredentials["port"]
+    user = iRODSCredentials["user"]
+    password = iRODSCredentials["pw"]
+    zone = iRODSCredentials["zone"]
+
+    iRODSsession = get_iRODS_connection(host=host, port=port, user=user, password=password, zone=zone)
+    global session, session_success
+    try:
+        coll = iRODSsession.collections.get("/" + zone + "/" + "home" + "/" + user)
+    except Exception:
+        raise Exception("Invalid Login")
+
+    if coll:
+        session = iRODSsession
+        session_success = True
+    
+    
     # check tool settings and start tool execution
     if session_success:
         # initialize download tool
         if params["tool_type"] == "down":
 
-            if params["selection_type"] == "explorer":
-                make_file_select_window()
-            else:
-                if (params["file_path"] != ""): #and ("/" in params["file_path"]):
-                    selected_file = params["file_path"]
-                else:
-                    raise Exception("Invalid File Path submitted!")
-
-            if selection_success or params["selection_type"] == "path":
-                params["user"] = iRODSCredentials["pw"]
-                params["password"] = iRODSCredentials["user"]
-                # start download routine
-                handle_download_call(params)
-            else:
-                raise Exception("File Selection failed (No file selected)")
+            selected_file = params["file_path"]
+            params["user"] = iRODSCredentials["pw"]
+            params["password"] = iRODSCredentials["user"]
+            # start download routine
+            handle_download_call(params)
 
         # initialize upload tool
         elif params["tool_type"] == "up":
@@ -261,7 +274,7 @@
                 break
         if log_img != "":
             break
-    print(log_img)
+    # print(log_img)
     
     window = Tk()
     LoginWindow(window)
@@ -318,9 +331,9 @@
         if params["irods_zone"] == "":
             res_string += "Zone empty!\n"
             res_bool = True
-        if params["selection_type"] == "path" and params["file_path"] == "":
-            res_string += "Missing file path!\n"
-            res_bool = True
+        ##if params["selection_type"] == "path" and params["file_path"] == "":
+        ##    res_string += "Missing file path!\n"
+        ##    res_bool = True
     except:
         raise Exception("Invalid/Missing Parameters")
 
@@ -369,10 +382,13 @@
         if reg_file != "":
             break
 
+    # print(file_list)
+    # print(os.getcwd())
+
     # handle download for all files in file_list
-    for file in file_list:
+    for f in file_list:
 
-        file_to_get = file
+        file_to_get = f
 
         # handle path and file name
         name_file_to_get = file_to_get.split("/")[-1]
@@ -386,7 +402,12 @@
         input_file = iRODS_file_object.open("r+")
         output_file = open(name_file_to_get, "wb")
         output_file.write(input_file.read())
-
+        #input_file.seek(0,0)
+        #print(input_file.read().decode("utf-8"))
+        #temp = open("/home/richard/test.txt", "w")
+        #input_file.seek(0,0)
+        #temp.write(input_file.read().decode("utf-8"))
+	
         input_file.close()
         output_file.close()
 
@@ -424,10 +445,22 @@
         copyfile(reg_file, params["galaxy_datatypes"])
 
         # activate environment for new process call and call the python upload command either both with
-        sys.path.append(params["galaxy_root"] + "/lib")
-        os.system("python -c \'import sys;sys.path.append(\"" + params["galaxy_root"] + "/lib\")\'" + " python " +
-                  python_command + " " + arg1 + " " + arg2 + " " + arg3 + " " + arg4)
-    
+        #sys.path.append(params["galaxy_root"] + "/lib")
+        #os.system("python -c \'import sys;sys.path.append(\"" + params["galaxy_root"] + "/lib\")\'" + "&& python3 " +
+        #          python_command + " " + arg1 + " " + arg2 + " " + arg3 + " " + arg4)
+        
+        # get upload file
+        upload_file = ""
+        for dirpath, dirnames, filenames in os.walk(params["galaxy_root"]):
+            for fn in filenames:
+                if fn == "irods_upload.py":
+                    upload_file = os.path.join(dirpath, fn)
+                if upload_file != "":
+                    break
+            if upload_file != "":
+                break
+                
+        os.system("python " +  upload_file + " " + arg1 + " " + arg2 + " " + arg3 + " " + arg4)
     # close connection
     session.cleanup()
 # -------------------------------------------------------------------------------------------------------------------- #
@@ -448,6 +481,8 @@
 
     path_to_file = params["up_file_path"]
     name_of_file = params["up_file"]
+    #print(path_to_file)
+    #print(name_of_file)
 
     coll_path = "/" + iRODSCredentials["zone"] + "/home/" + iRODSCredentials["user"] + "/galaxyupload"
     try:
@@ -467,7 +502,10 @@
         coll = session.collections.get(coll_path)
     except:
         coll = session.collections.create(coll_path)
-
+    
+    if "/" in name_of_file:
+        name_of_file = name_of_file.split("/")[-1]
+    
     irods_file_name = time + "_" + name_of_file
     iRODS_file_object = session.data_objects.create(coll_path + "/" + irods_file_name)
     iRODS_file_object = session.data_objects.get(coll_path + "/" + irods_file_name)
@@ -477,6 +515,7 @@
     content = galaxy_file.read()
     irods_file.write(content)
 
+    print("Successfully uploaded: " + name_of_file + "\n as: " + irods_file_name)
     # TODO can't close session without writing process finished - but reading/writing happens async.
     # session.cleanup()