# HG changeset patch # User rhohensinner # Date 1621590690 0 # Node ID 7d8912d20007ff1859c7ad0a227e762362c1572a "planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty" diff -r 000000000000 -r 7d8912d20007 irods_download.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/irods_download.xml Fri May 21 09:51:30 2021 +0000 @@ -0,0 +1,82 @@ + + Download your files from iRODS into Galaxy + + python-irodsclient + tk + + + + ### using CHEETAH ### + ## Set up iRODS params + #import json + #set params = {} + #set params["irods_host"] = str($custom_host) + #set params["irods_port"] = str($custom_port) + #set params["irods_zone"] = str($custom_zone) + ##set params["filepath"] = str($file_path) + + #if $file_select_config.selection_type == "use_path" + #set params["selection_type"] = "path" + #set params["file_path"] = str($file_select_config.file_path) + #set params["expl_path"] = "" + #end if + #if $file_select_config.selection_type == "use_explorer" + #set params["selection_type"] = "explorer" + #set params["file_path"] = "" + #set params["expl_path"] = str($file_select_config.explorer_entrypoint) + #end if + ## set up Galaxy params + #set params["galaxy_user"] = str($__user_name__) + #set params["job_id"] = str($output.creating_job.id) + #set params["out_dir"] = str($output.files_path) + #set params["out_file"] = str($output) + #set params["galaxy_root"] = str($GALAXY_ROOT_DIR) + #set params["galaxy_datatypes"] = str($GALAXY_DATATYPES_CONF_FILE) + ##import os + ##import glob + ##set $test = glob.glob("os.getcwd()" + "/**/irods_galaxy_registry.xml", recursive=True) + ##set params["reg_file"] + #set params["tool_type"] = "down" + #set $params=json.dumps($params) + main.py '$params' + + + + + + + + + + + + + + + + + + + + + + + + + +Download iRODS + + + + +@misc{Download-iRODS, + author = {Hohensinner, Richard}, + year = {2021}, + title = {iRODSTools}, + publisher = {GitLab}, + journal = {GitLab repository}, + url = {https://gitlab.tugraz.at/D463A320ED7901AB/galaxy_irods_tools}, +} + + + diff -r 000000000000 -r 7d8912d20007 irods_galaxy_registry.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/irods_galaxy_registry.xml Fri May 21 09:51:30 2021 +0000 @@ -0,0 +1,10 @@ + + + + + + + + + \ No newline at end of file diff -r 000000000000 -r 7d8912d20007 irods_upload.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/irods_upload.xml Fri May 21 09:51:30 2021 +0000 @@ -0,0 +1,66 @@ + + Upload your files to iRODS from Galaxy + + python-irodsclient + tk + + + + ## using CHEETAH + #import json + #set params = {} + #set params["irods_host"] = str($custom_host) + #set params["irods_port"] = str($custom_port) + #set params["irods_zone"] = str($custom_zone) + ##if $irods_config.typeiRODS == "use_any_irods" + ##set params["irods_host"] = str($irods_config.custom_host) + ##set params["irods_port"] = str($irods_config.custom_port) + ##set params["irods_zone"] = str($irods_config.custom_zone) + ##end if + ##if $irods_config.typeiRODS == "use_tug_irods" + ##set params["irods_host"] = "data.cyverse.tugraz.at" + ##set params["irods_port"] = "1247" + ##set params["irods_zone"] = "TUG" + ##end if + ## set up Galaxy params + #set params["galaxy_user"] = str($__user_name__) + #set params["job_id"] = str($output.creating_job.id) + #set params["out_dir"] = str($output.files_path) + #set params["out_file"] = str($output) + #set params["up_file"] = str($up_file.name) + #set params["up_file_path"] = str($up_file) + #set params["galaxy_root"] = str($GALAXY_ROOT_DIR) + #set params["galaxy_datatypes"] = str($GALAXY_DATATYPES_CONF_FILE) + #set params["tool_type"] = "up" + #set $params=json.dumps($params) + main.py '$params' + + + + + + + + + + + + + + +Upload RODS + + + + +@misc{Upload-iRODS, + author = {Hohensinner, Richard}, + year = {2021}, + title = {iRODSTools}, + publisher = {GitLab}, + journal = {GitLab repository}, + url = {https://gitlab.tugraz.at/D463A320ED7901AB/galaxy_irods_tools}, +} + + + diff -r 000000000000 -r 7d8912d20007 login.png Binary file login.png has changed diff -r 000000000000 -r 7d8912d20007 main.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/main.py Fri May 21 09:51:30 2021 +0000 @@ -0,0 +1,569 @@ +___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 + +# 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": ""} + + +######################################################################################################################## +# 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() + # 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)") + + # 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(): + 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='/home/richard/git/galaxy_irods_tools/login.png')) + # 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 + + # handle download for all files in file_list + for file in file_list: + + file_to_get = file + + # 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.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"] + + # 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\")\'" + " python " + + python_command + " " + 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"] + + 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) + + 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) + + # 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() diff -r 000000000000 -r 7d8912d20007 registry.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/registry.xml Fri May 21 09:51:30 2021 +0000 @@ -0,0 +1,10 @@ + + + + + + + + + \ No newline at end of file