--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/irods_main.py	Wed Aug 04 12:01:55 2021 +0000
@@ -0,0 +1,633 @@
+___author___ = "Richard Hohensinner"
+___created___ = "04.02.2021"
+___last_modified___ = "20.05.2021"
+
+# general imports
+import os, sys, json
+
+from shutil import copyfile
+from datetime import datetime
+from irods_data import registry_content
+
+# irods-client imports
+from irods.session import iRODSSession
+from irods.models import Collection, DataObject
+from irods.query import SpecificQuery
+
+# Tkinter imports
+from tkinter import messagebox, Label, Button, Entry, Listbox, Tk, PhotoImage, Grid
+
+# global variables
+session = None
+file_path_list = []
+selected_file = ""
+session_success = False
+selection_success = False
+iRODSCredentials = {"host": "", "port": "", "user": "", "pw": "", "zone": ""}
+python_path = []
+
+with open("reg.xml", "w") as xf:
+    xf.write(registry_content)
+    xf.close()
+
+########################################################################################################################
+#   Main function of the iRODS tools
+#
+#   IN:
+#   JSON Object params (argv[1])
+#   OUT:
+#
+########################################################################################################################
+def main():
+
+    # check input parameters
+    if len(sys.argv) == 2:
+        params = json.loads(sys.argv[1])
+    else:
+        raise Exception("Invalid Parameters submitted!")
+
+    tool_type = params["tool_type"]
+
+    try:
+        if params["tool_type"] != "up" and params["tool_type"] != "down":
+            raise Exception("Invalid tool-type parameter submitted!")
+    except:
+        raise Exception("No tool-type parameter submitted!")
+    is_download_call = True
+    if tool_type == "up":
+        is_download_call = False
+
+    # check params for integrity
+    result_string, params_faulty = check_params(params)
+
+    if params_faulty:
+        raise Exception(result_string)
+
+    global iRODSCredentials, session_success, selected_file, selection_success
+    iRODSCredentials["host"] = params["irods_host"]
+    iRODSCredentials["port"] = params["irods_port"]
+    iRODSCredentials["zone"] = params["irods_zone"]
+
+    # create login window
+    ## 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":
+
+            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":
+
+            if session_success:
+                params["user"] = iRODSCredentials["pw"]
+                params["password"] = iRODSCredentials["user"]
+                # start upload routine
+                handle_upload_call(params)
+            else:
+                raise Exception("Logging into iRODS failed")
+    else:
+        raise Exception("Logging into iRODS failed")
+# -------------------------------------------------------------------------------------------------------------------- #
+
+
+########################################################################################################################
+#   Login Window class for Tkinter
+#
+#   IN:
+#   Tk Window win
+#   OUT:
+#   (sets global variables iRODSCredentials, session and session_success)
+#
+########################################################################################################################
+class LoginWindow:
+    def __init__(self, win):
+        self.window = win
+        self.lbl1 = Label(win, text='iRODS Username:')
+        self.lbl2 = Label(win, text='iRODS Password:')
+        self.t1 = Entry(bd=3)
+        self.t2 = Entry(show="*")
+        self.b1 = Button(win, text='Login', command=self.login)
+
+        self.window.grid()
+        Grid.rowconfigure(self.window, 0, weight=1)
+        Grid.rowconfigure(self.window, 1, weight=1)
+        Grid.rowconfigure(self.window, 2, weight=1)
+        Grid.rowconfigure(self.window, 3, weight=1)
+        Grid.rowconfigure(self.window, 4, weight=1)
+        Grid.columnconfigure(self.window, 0, weight=1)
+
+        self.lbl1.grid(row=0, column=0, padx="20", pady="1", sticky="w")
+        self.t1.grid(row=1, column=0, padx="10", pady="1", sticky="nsew")
+        self.lbl2.grid(row=2, column=0, padx="20", pady="1", sticky="w")
+        self.t2.grid(row=3, column=0, padx="10", pady="1", sticky="nsew")
+        self.b1.grid(row=4, column=0, padx="50", pady="10", sticky="nsew")
+
+    def login(self):
+        global iRODSCredentials
+        user = str(self.t1.get())
+        password = str(self.t2.get())
+        if user == "" or password == "":
+            self.window.iconify()
+            messagebox.showerror("Error", "Username or Password empty!")
+            self.window.deiconify()
+            return
+        else:
+            iRODSCredentials["user"] = user
+            iRODSCredentials["pw"] = password
+
+        get_irods_session(self.window)
+        if not session_success:
+            return
+
+        self.window.destroy()
+# -------------------------------------------------------------------------------------------------------------------- #
+
+
+########################################################################################################################
+#   File Selection Window class for Tkinter
+#
+#   IN:
+#   Tk Window win
+#   OUT:
+#   (sets global variables selected_file and selection_success)
+#
+########################################################################################################################
+class FileSelectWindow:
+    def __init__(self, win):
+        global session, iRODSCredentials
+        self.session = session
+        self.window = win
+        self.b1 = Button(win, text='Select', command=self.select)
+        self.lb1 = Listbox(win)
+
+        self.window.grid()
+        Grid.rowconfigure(self.window, 0, weight=1)
+        Grid.rowconfigure(self.window, 1, weight=1)
+        Grid.columnconfigure(self.window, 0, weight=1)
+
+        self.lb1.grid(row=0, column=0, padx="20", pady="1", sticky="nswe")
+        self.b1.grid(row=1, column=0, padx="50", pady="1", sticky="ew")
+
+        coll = session.collections.get("/" + iRODSCredentials["zone"] + "/" + "home" + "/" + iRODSCredentials["user"])
+        file_list = []
+
+        self.get_files_from_collections(coll, file_list)
+
+        for counter in range(len(file_list)):
+            self.lb1.insert(counter, file_list[counter])
+
+    def get_files_from_collections(self, coll, file_list):
+        for obj in coll.data_objects:
+            file_list.append(obj.path)
+
+        for col in coll.subcollections:
+            self.get_files_from_collections(col, file_list)
+
+    def select(self):
+        global session, selected_file, selection_success
+        try:
+            selection = self.lb1.get(self.lb1.curselection())
+        except:
+            self.window.iconify()
+            messagebox.showerror("Error", "No file selected!")
+            self.window.deiconify()
+            return
+
+        selected_file = selection
+        selection_success = True
+        self.window.destroy()
+# -------------------------------------------------------------------------------------------------------------------- #
+
+
+########################################################################################################################
+#   Creates an iRODS session and sets the global session variable
+#
+#   IN:
+#   Tk Window window
+#
+#   OUT:
+#
+########################################################################################################################
+def get_irods_session(window):
+    global iRODSCredentials
+    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:
+        window.iconify()
+        messagebox.showerror("Error", "Invalid Authentification")
+        window.deiconify()
+        return
+
+    if coll:
+        session = iRODSsession
+        session_success = True
+# -------------------------------------------------------------------------------------------------------------------- #
+
+
+########################################################################################################################
+#   Helper function to initialize Login Window classes and Tk windows
+#
+#   IN:
+#
+#   OUT:
+#
+########################################################################################################################
+def make_login_window(params):
+    #get login icon
+    log_img = ""
+    for dirpath, dirnames, filenames in os.walk(params["galaxy_root"]):
+        for fn in filenames:
+            if fn == "irods_galaxy_login.png":
+                log_img = os.path.join(dirpath, fn)
+            if log_img != "":
+                break
+        if log_img != "":
+            break
+    # print(log_img)
+    
+    window = Tk()
+    LoginWindow(window)
+    window.title('iRODS Login')
+    window.geometry("450x225+10+10")
+    window.minsize(450, 225)
+    window.tk.call('wm', 'iconphoto', window._w, PhotoImage(file=log_img))
+    # alternative options:
+    # window.iconphoto(False, PhotoImage(file='/path/to/ico/icon.png'))
+    # window.iconbitmap("/home/richard/git/galaxy_irods_tools/login.ico")
+    window.mainloop()
+# -------------------------------------------------------------------------------------------------------------------- #
+
+
+########################################################################################################################
+#   Helper function to initialize File Selection Window classes and Tk windows
+#
+#   IN:
+#
+#   OUT:
+#
+########################################################################################################################
+def make_file_select_window():
+    window = Tk()
+    FileSelectWindow(window)
+    window.title('iRODS File Select')
+    window.geometry("450x225+10+10")
+    window.minsize(450, 225)
+    window.mainloop()
+# -------------------------------------------------------------------------------------------------------------------- #
+
+
+########################################################################################################################
+#   Checks whether arguments are valid and returns true/false depending on params
+#
+#   IN:
+#   Dict params
+#
+#   OUT:
+#   String res_string
+#   Bool res_bool
+########################################################################################################################
+def check_params(params):
+    res_string = ""
+    res_bool = False
+
+    try:
+        if params["irods_host"] == "":
+            res_string += "Host empty!\n"
+            res_bool = True
+        if params["irods_port"] == "":
+            res_string += "Port empty!\n"
+            res_bool = True
+        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
+    except:
+        raise Exception("Invalid/Missing Parameters")
+
+    return res_string, res_bool
+# -------------------------------------------------------------------------------------------------------------------- #
+
+
+########################################################################################################################
+#   Function to handle iRODS download calls
+#
+#   IN:
+#   Dict params
+#
+#   OUT:
+#
+########################################################################################################################
+def handle_download_call(params):
+
+    global session, selected_file
+
+    # check if /ZONE/USER/...FILE... pattern is valid
+    if len(selected_file.split("/")) < 2:
+        raise Exception("Path to file is not valid in iRODS")
+
+    file_list = []
+
+    # check if file is a directory
+    if "." not in selected_file:
+        try:
+            coll = session.collections.get(selected_file)
+            for file in coll.data_objects:
+                file_list.append(file.path)
+        except:
+            raise Exception("Invalid directory path specified!")
+    else:
+        file_list.append(selected_file)
+
+    ## get registry file
+    #reg_file = ""
+    #for dirpath, dirnames, filenames in os.walk(params["galaxy_root"]):
+    #    for fn in filenames:
+    #        if fn == "irods_galaxy_registry.xml":
+    #            reg_file = os.path.join(dirpath, fn)
+    #        if reg_file != "":
+    #            break
+    #    if reg_file != "":
+    #        break
+    reg_file = "reg.xml"
+    
+    # print(file_list)
+    # print(os.getcwd())
+
+    # handle download for all files in file_list
+    for f in file_list:
+
+        file_to_get = f
+
+        # handle path and file name
+        name_file_to_get = file_to_get.split("/")[-1]
+        path_file_to_get = "/".join(file_to_get.split("/")[0:len(file_to_get.split("/")) - 1])
+
+        # check iRODS filesystem
+        check_iRODS_destination(session, path_file_to_get, name_file_to_get)
+
+        # get file object from iRODS
+        iRODS_file_object = session.data_objects.get(path_file_to_get + "/" + name_file_to_get)
+        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()
+
+        abs_file_path = os.path.abspath(name_file_to_get)
+
+        file_type = str(name_file_to_get.split(".")[-1])
+
+        file_content = {"uuid": None,
+                        "file_type": "auto",
+                        "space_to_tab": False,
+                        "dbkey": "?",
+                        "to_posix_lines": True,
+                        "ext": file_type,
+                        "path": abs_file_path,
+                        "in_place": True,
+                        "dataset_id": params["job_id"],
+                        "type": "file",
+                        "is_binary": False,
+                        "link_data_only": "copy_files",
+                        "name": name_file_to_get
+                        }
+
+        with open("temporal.json", "w") as fileParams:
+            fileParams.write(json.dumps(file_content))
+        fileParams.close()
+
+        # load file into Galaxy by using the integrated upload tool - Preparation
+        python_command = params["galaxy_root"] + "/tools/data_source/upload.py"
+        arg1 = params["galaxy_root"]
+        arg2 = params["galaxy_datatypes"]
+        arg3 = os.path.abspath(fileParams.name)
+        arg4 = params["job_id"] + ":" + params["out_dir"] + ":" + params["out_file"]
+        arg5 = params["galaxy_root"] + "/lib/galaxy"
+
+        # copy sample registry.xml to working directory
+        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\")\'" + "&& 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
+        sys.path.append(params["galaxy_root"] + "/lib")
+        #sys.path.append(params["galaxy_root"] + "/tools/data_source")
+        #sys.path.append(params["galaxy_root"] + "/.venv/lib/python3.8/site-packages")
+        with open("python__path.txt", "w") as pp:
+            pp.truncate(0)
+            for item in sys.path:
+                pp.write(item + ",")
+
+        os.system(params["galaxy_root"] + "/.venv/bin/python " +  upload_file + " " + arg1 + " " + arg2 + " " + arg3 + " " + arg4)
+    # close connection
+    session.cleanup()
+# -------------------------------------------------------------------------------------------------------------------- #
+
+
+########################################################################################################################
+#   Function to handle iRODS upload calls
+#
+#   IN:
+#   Dict params
+#
+#   OUT:
+#
+########################################################################################################################
+def handle_upload_call(params):
+
+    global session, iRODSCredentials
+
+    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:
+        coll = session.collections.get(coll_path)
+    except:
+        coll = session.collections.create(coll_path)
+
+    now = datetime.now()
+
+    # dd/mm/YY
+    day = now.strftime("%d%m%Y")
+    time = now.strftime("%H%M%S")
+
+    coll_path = coll_path + "/" + day
+
+    try:
+        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)
+
+    irods_file = iRODS_file_object.open("w")
+    galaxy_file = open(path_to_file, "rb")
+    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()
+
+    pass
+# -------------------------------------------------------------------------------------------------------------------- #
+
+
+########################################################################################################################
+#   Function to initialize an iRODS Session - will raise an Exception if timeout is longer than 2 seconds
+#
+#   IN:
+#   String host
+#   String port
+#   String user
+#   String password
+#   String zone
+#
+#   OUT:
+#   iRODSSession-object session
+########################################################################################################################
+def get_iRODS_connection(host, port, user, password, zone):
+
+    # initialize timeout checker - fires after 2 secs
+    import signal
+    signal.signal(signal.SIGALRM, timeout_checker)
+    signal.alarm(2)
+
+    try:
+        session = iRODSSession(host=host, port=port, user=user, password=password, zone=zone)
+    except Exception:
+        raise Exception("There was a timeout creating the iRODS session")
+
+    # void/reset alarm
+    signal.alarm(0)
+
+    return session
+# -------------------------------------------------------------------------------------------------------------------- #
+
+
+########################################################################################################################
+#   Helper function to raise timeout exception when SIGALRM fires
+#
+#   IN:
+#
+#   OUT:
+#
+########################################################################################################################
+def timeout_checker():
+
+    raise Exception("iRODS session timeout")
+# -------------------------------------------------------------------------------------------------------------------- #
+
+
+########################################################################################################################
+#   Function to check if file exists in iRODS
+#
+#   IN:
+#   String path
+#
+#   OUT:
+#   Bool ret_bool
+#
+########################################################################################################################
+def check_if_file_exists(path):
+
+    if os.path.isfile(path):
+        ret_bool = True
+    else:
+        ret_bool = False
+
+    return ret_bool
+# -------------------------------------------------------------------------------------------------------------------- #
+
+
+########################################################################################################################
+#   Function to check iRODS destination
+#
+#   IN:
+#   iRODSSession-object session
+#   String path
+#   String name
+#
+#   OUT:
+#   Bool ret_bool
+#
+########################################################################################################################
+def check_iRODS_destination(session, path, name):
+
+    try:
+        session.collections.get(path.rstrip("/"))
+    except Exception:
+        raise Exception("Collection doesn't exist in iRODS file system")
+
+    try:
+        session.data_objects.get(path.rstrip("/") + "/" + name)
+    except Exception:
+        raise Exception("File doesn't exist in iRODS file system")
+# -------------------------------------------------------------------------------------------------------------------- #
+
+
+if __name__ == "__main__":
+    main()