Mercurial > repos > rhohensinner > galaxy_irods_interface
changeset 1:19c1cecdfdfd draft
"planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
| author | rhohensinner |
|---|---|
| date | Wed, 23 Jun 2021 10:40:19 +0000 |
| parents | 7d8912d20007 |
| children | 0641ea2f75b1 |
| files | irods_galaxy_login.png login.png main.py |
| diffstat | 3 files changed, 581 insertions(+), 569 deletions(-) [+] |
line wrap: on
line diff
--- a/main.py Fri May 21 09:51:30 2021 +0000 +++ b/main.py Wed Jun 23 10:40:19 2021 +0000 @@ -1,569 +1,581 @@ -___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() +___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(params) + # 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(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 + + # 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()