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If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/checknmr.py b/checknmr.py new file mode 100644 index 0000000..1e9ccb7 --- /dev/null +++ b/checknmr.py @@ -0,0 +1,357 @@ +""" +Mora the Explorer checks for new NMR spectra at the Organic Chemistry department at the WWU Münster. +Copyright (C) 2023 Matthew J. Milner + +This program is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with this program. If not, see . +""" + +import filecmp +import json +import logging +import os +import platform +import subprocess +import shutil +import sys +from datetime import date, datetime, timedelta +from pathlib import Path + + +# Checks that two spectra with the same name are actually identical and not e.g. different proton measurements +def identical_spectra(mora_folder, dest_folder): + # Read original folder path (i.e. the experiment no) of spectrum + audit_path_mora = mora_folder / "audita.txt" + try: + with open(audit_path_mora, encoding="utf-8") as audit_file_mora: + audit_mora = audit_file_mora.readlines() + exp_mora = audit_mora[4] + except FileNotFoundError: + print( + "no audita.txt file found in " + + mora_folder + + " - presumably measurement was unsuccessful. Spectrum skipped." + ) + # Return True so that the spectrum on mora is treated as identical and not copied + return True + # Do same for existing spectrum in destination + audit_path_dest = dest_folder / "audita.txt" + try: + with open(audit_path_dest, encoding="utf-8") as audit_file_dest: + audit_dest = audit_file_dest.readlines() + exp_dest = audit_dest[4] + # The first spectrum with a given title is always copied, so it is possible that it doesn't have an audit file + except FileNotFoundError: + exp_dest = None + # Compare experiment nos + if exp_mora == exp_dest: + return True + else: + return False + + +# Define main checking function for Mora the Explorer +def check_nmr(fed_options, check_day, mora_path, spec_paths, wild_group, prog_bar, progress_callback): + logging.info(f"Beginning check of {check_day} with the options:") + logging.info(fed_options) + # Initialize list that will be returned as output + output_list = ["no new spectra"] + # Confirm destination directory exists + if Path(fed_options["dest_path"]).exists() is False: + output_list.append("given destination folder not found!") + logging.info("given destination folder not found!") + return output_list + # Confirm mora can be reached + if mora_path.exists() is False: + output_list.append("the mora server could not be reached!") + logging.info("the mora server could not be reached!") + return output_list + # Format paths of spectrometer folders + spectrometer = fed_options["spec"] + if spectrometer == "300er": + # Add fix here to use folder where spectra from 2022 were moved to in Jan 2023 + #if check_day[-4:] == "2022": + # primary_check_path = spec_paths[spectrometer] / "22-av300_2022" / check_day + #else: + primary_check_path = spec_paths[spectrometer] / check_day + # Give message if folder for the given date doesn't exist yet + if primary_check_path.exists() is False: + output_list.append("no folder exists for this date!") + return output_list + check_path_list = [primary_check_path] + # If main folder exists, check if other folders are available for same day (generated on mora when two samples are submitted with same exp. no.) + for num in range(2, 10): + alt_path = primary_check_path.with_name(primary_check_path.name + "_" + str(num)) + if alt_path.exists() is True: + check_path_list.append(alt_path) + logging.info("The following paths will be checked:") + logging.info(check_path_list) + elif spectrometer == "400er": + check_day_a = "neo400a_" + check_day + check_day_b = "neo400b_" + check_day + check_day_c = "neo400c_" + check_day + # Add fix here to use folder where spectra from 2022 were moved to in Jan 2023 + #if check_day[-4:] == "2022": + # check_path_a = spec_paths[spectrometer] / "22-neo400a_2022" / check_day_a + # check_path_b = spec_paths[spectrometer] / "22-neo400b_2022" / check_day_b + # check_path_c = spec_paths[spectrometer] / "22-neo400c_2022" / check_day_c + #else: + check_path_a = spec_paths[spectrometer] / check_day_a + check_path_b = spec_paths[spectrometer] / check_day_b + check_path_c = spec_paths[spectrometer] / check_day_c + check_path_300er = spec_paths["300er"] / check_day + check_path_list = [check_path_a, check_path_b, check_path_c, check_path_300er] + # Add any extra folders for this date beyond the expected four to check list + unchanging_check_path_list = check_path_list + for entry in unchanging_check_path_list: + for num in range(2, 20): + alt_path = entry.with_name(entry.name + "_" + str(num)) + if alt_path.exists() is True: + check_path_list.append(alt_path) + logging.info("The following paths will be checked:") + logging.info(check_path_list) + elif spectrometer == "hf": + # Code to check folders of all groups when the nmr group is chosen and the wild group option is invoked + if wild_group is True: + check_list = [] + # Slightly complicated bit of code here but it just goes through all folders in 500-600er folder + logging.info("The following paths will be checked:") + logging.info(spec_paths[spectrometer].parent.iterdir()) + for group_folder in spec_paths[spectrometer].parent.iterdir(): + if group_folder.is_dir() and (group_folder.name[0] != "."): + try: + for spectrum_folder in list((group_folder / check_day).iterdir()): + check_list.append(spectrum_folder) + except FileNotFoundError: + logging.info(f"No spectra in {group_folder}") + continue + # Normal behaviour for all other users + else: + logging.info("The following paths will be checked:") + logging.info(spec_paths[spectrometer] / check_day) + # Try to get list of spectrum folders in folder for requested spectrometer, group and date + # Display message to user if it doesn't exist yet + try: + check_list = list((spec_paths[spectrometer] / check_day).iterdir()) + except FileNotFoundError: + output_list.append("no folder exists for this date!") + logging.info("no folder exists for this date!") + return output_list + # Now process needs to be slightly different depending on the spectrometer, as the directory structures are different + if spectrometer == "300er" or spectrometer == "400er": + # Initialize progress bar + if spectrometer == "300er": + prog_bar.setMaximum(100) + elif spectrometer == "400er": + prog_bar.setMaximum(100 * len(check_path_list)) + prog_state = 0 + progress_callback.emit(prog_state) + # Loop through each folder in check_path_list (usually only one for 300er, several for 400er as separate ones are generated for each spectrometer) + for check_path in check_path_list: + try: + check_list = list(check_path.iterdir()) + except FileNotFoundError: + continue + # Loop through list of spectra in spectrometer folder + logging.info("The following spectra were checked for potential matches:") + for folder in check_list: + logging.info(folder) + # Extract title and experiment details from title file in spectrum folder + title_file_path = folder / "pdata" / "1" / "title" + try: + with open(title_file_path, encoding="utf-8") as title_file: + title_contents = title_file.readlines() + title = title_contents[0] + details = title_contents[1] + except FileNotFoundError: + output_list.append(f"{folder} had no title file!") + logging.info("No title file found") + continue + split_title = title.split() + split_details = details.split() + logging.info(" " + str(split_title)) + logging.info(" " + str(split_details)) + # Look for search string in extracted title, then copy matching spectra + # Confirm that the title is even long enough to avoid IndexErrors + if (len(split_title) < 2) or (len(split_title[1]) < 3) or ((wild_group is True) and len(split_title) < 3): + logging.info("Title doesn't have enough parts") + continue + # Add nmr to front of spectrum title so that the group initials get matched to the "initials" provided by the user, allowing Klaus to download all spectra from a specific group + if (fed_options["group"] == "nmr") and (split_title[0] != "nmr"): + split_title.insert(0, "nmr") + # Check if spectrum is a match for search term, including the wild option for the nmr group + if (split_title[1][0:3] == fed_options["initials"]) or ((wild_group is True) and (split_title[2][0:3] == fed_options["initials"])): + logging.info("Spectrum matches search query!") + # Formatting options specifically for nmr group, include everything - even date and spec via parent folder name + if fed_options["group"] == "nmr": + new_folder_name = ( + ("-".join(split_title[1:])) + "-" + ("-".join(split_details[:2])) + "_" + check_path.name + "_" + folder.name + ) + # Otherwise format spectrum name according to user's choices + else: + # Format in the style of NMRCheck if requested i.e. using underscores, including initials and spectrometer and date and exp no + if fed_options["nmrcheck_style"] is True: + if len(split_title) > 2: + hyphenated_title = "_".join(split_title[1:]) + "_" + check_path.name + "_" + folder.name + else: + hyphenated_title = "_".join(split_title) + "_" + check_path.name + "_" + folder.name + # Length checks above and below are to account for the possibility that the user might have forgotten to separate with spaces + # Principle applied is that if the information being dropped isn't 100% definitely what we think it is (i.e. the group name), play it safe and don't drop it + # Now the formatting for most cases (NMRCheck style is legacy) + elif len(split_title) > 2: + if fed_options["inc_init"] is True: + hyphenated_title = "-".join(split_title[1:]) + else: + hyphenated_title = "-".join(split_title[2:]) + else: + hyphenated_title = "-".join(split_title) + # Append experiment type e.g. proton to end of name, and solvent if requested + if fed_options["inc_solv"] is True: + new_folder_name = ( + hyphenated_title + "-" + split_details[0] + "-" + split_details[1] + ) + else: + new_folder_name = hyphenated_title + "-" + split_details[0] + new_folder_path = Path(fed_options["dest_path"]) / new_folder_name + # Check that spectrum hasn't been copied before + if new_folder_path.exists() is True: + logging.info("Spectrum with this name already exists in destination") + # Check that the spectra are actually identical and not e.g. different proton measurements + # If confirmed to be unique spectra, need to extend spectrum name with -2, -3 etc. to avoid conflict with spectra already in dest + identical_spectrum_found = False + if identical_spectra(folder, new_folder_path) is False: + new_folder_name = new_folder_path.name + "-2" + new_folder_path = new_folder_path.parent / new_folder_name + # While loop that will eventually settle on a new unique name + while new_folder_path.exists() is True: + # Do whole procedure again as long as name has a match in the destination + if identical_spectra(folder, new_folder_path) == True: + identical_spectrum_found = True + new_folder_name = ( + new_folder_path.name[:-2] + + "-" + + str(int(new_folder_path.name[-1]) + 1) + ) + new_folder_path = new_folder_path.parent / new_folder_name + if identical_spectrum_found is not True: + logging.info("but the spectrum itself has not been copied before.") + logging.info(f"Copying with the new name: {new_folder_path.stem}") + try: + shutil.copytree(folder, new_folder_path) + except PermissionError: + output_list.append( + "you do not have permission to write to the given folder" + ) + logging.info("No write permission for destination") + return output_list + text_to_add = "spectrum found: " + new_folder_name + output_list.append(text_to_add) + # Otherwise there is no existing spectrum in the destination so straightforward copy + else: + try: + shutil.copytree(folder, new_folder_path) + except PermissionError: + output_list.append( + "you do not have permission to write to the given folder" + ) + return output_list + text_to_add = "spectrum found: " + new_folder_name + logging.info(f"Spectrum saved to {new_folder_path}") + output_list.append(text_to_add) + # Update progress bar + prog_state += 100 / len(check_list) + progress_callback.emit(round(prog_state)) + elif spectrometer == "hf": + # Initialize progress bar + max_progress = len(check_list) + prog_bar.setMaximum(max_progress) + prog_state = 0 + progress_callback.emit(prog_state) + # Look for spectra + logging.info("The following spectra were checked for potential matches:") + for folder in check_list: + logging.info(folder) + # Check for initials at start of folder name, as folders are given the name of the sample on 500 and 600 MHz spectrometers + if folder.name[:3] == fed_options["initials"]: + logging.info("Spectrum matches search query!") + # Find out magnet strength, set to initial false value as flag + magnet_freq = "x" + contents_list = list(folder.iterdir()) + while magnet_freq == "x": + for cont_folder in contents_list: + text_file_path = cont_folder / "text" + if text_file_path.exists() is True: + with open(text_file_path, encoding="utf-8") as spectrum_text: + spectrum_info = spectrum_text.readlines() + line_with_freq_split = spectrum_info[3].split(",") + magnet_freq = line_with_freq_split[0] + if fed_options["group"] == "nmr": + new_folder_name = folder.parent.parent.name + "_" + folder.parent.name + "_" + folder.name + "_" + magnet_freq + elif fed_options["nmrcheck_style"] is True: + new_folder_name = fed_options["initials"] + "_" + folder.name[3:] + "_" + magnet_freq + elif fed_options["inc_init"] is True: + new_folder_name = fed_options["initials"] + "-" + folder.name[3:] + "_" + magnet_freq + else: + new_folder_name = folder.name[3:] + "_" + magnet_freq + new_folder_path = Path(fed_options["dest_path"]) / new_folder_name + # Check that spectrum hasn't been copied before + # Begin by setting check number to >0 so that if nothing has ever been copied the spectrum gets copied + new_spectra = True + partial_copy = False + if new_folder_path.exists() is True: + logging.info("Spectrum already exists in destination") + comparison = filecmp.dircmp(folder, new_folder_path) + if len(comparison.left_only) == 0: + new_spectra = False + elif len(comparison.left_only) > 0: + partial_copy = True + logging.info("but only a partial copy") + # Only copy if new spectra in folder + if new_spectra is True: + if partial_copy is True: + for cont_folder in contents_list: + new_spectrum_path = new_folder_path / cont_folder.name + if new_spectrum_path.exists() is False: + try: + shutil.copytree(cont_folder, new_spectrum_path) + except PermissionError: + output_list.append( + "you do not have permission to write to the given folder" + ) + return output_list + text_to_add = "spectra found: " + new_folder_name + output_list.append(text_to_add) + else: + try: + shutil.copytree(folder, new_folder_path) + except PermissionError: + output_list.append( + "you do not have permission to write to the given folder" + ) + return output_list + text_to_add = "spectra found: " + new_folder_name + output_list.append(text_to_add) + logging.info(f"Spectrum saved to {new_folder_path}") + # Make progress bar move noticeably while checking/copying users' spectra so it doesn't look like it has crashed + max_progress += 20 + prog_bar.setMaximum(max_progress) + prog_state += 20 + progress_callback.emit(prog_state) + # Update progress bar + prog_state += 1 + progress_callback.emit(prog_state) + now = datetime.now().strftime("%H:%M:%S") + completed_statement = f"check of {check_day} completed at " + now + output_list.append(completed_statement) + logging.info(completed_statement) + return output_list diff --git a/explorer.ico b/explorer.ico new file mode 100644 index 0000000..cee4f18 Binary files /dev/null and b/explorer.ico differ diff --git a/groups.json b/groups.json new file mode 100644 index 0000000..be8b205 --- /dev/null +++ b/groups.json @@ -0,0 +1,20 @@ +{ + "fer": "fernandez", + "gar": "garcia", + "gil": "gilmour", + "glo": "glorius", + "nae": "naesborg", + "rav": "ravoo", + "stu": "studer", + "other": { + "ac": "ac", + "biochemie": "biochemie", + "extern": "extern", + "ipc": "ipc", + "kb": "kb", + "meet": "meet", + "nmr": "nmr", + "nuk": "nuk", + "pharmazie": "pharmazie" + } +} diff --git a/mora_path.txt b/mora_path.txt new file mode 100644 index 0000000..21dea55 --- /dev/null +++ b/mora_path.txt @@ -0,0 +1,3 @@ +//mora/nmr +/Volumes/nmr +overwrite this line with the mount point on Linux diff --git a/mora_the_explorer.py b/mora_the_explorer.py new file mode 100644 index 0000000..102d050 --- /dev/null +++ b/mora_the_explorer.py @@ -0,0 +1,773 @@ +""" +Mora the Explorer checks for new NMR spectra at the Organic Chemistry department at the WWU Münster. +Copyright (C) 2023 Matthew J. Milner + +This program is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with this program. If not, see . +""" + +import filecmp +import json +import logging +import os +import platform +import subprocess +import shutil +import sys +from datetime import date, datetime, timedelta +from pathlib import Path + +import darkdetect +import platformdirs +import plyer + +from PySide6.QtCore import QSize, QTimer, Qt, QRunnable, Signal, Slot, QThreadPool, QObject +from PySide6.QtGui import QIcon, QPalette, QColor +from PySide6.QtWidgets import ( + QApplication, + QMainWindow, + QPushButton, + QRadioButton, + QButtonGroup, + QComboBox, + QLabel, + QLineEdit, + QDateEdit, + QCheckBox, + QSpinBox, + QProgressBar, + QScrollArea, + QHBoxLayout, + QVBoxLayout, + QGridLayout, + QWidget, + QMessageBox, +) + +from checknmr import check_nmr as checknmr + + +# Assign directory containing the various supporting files to a variable so we can use it whenever necessary. For whatever reason __file__ doesn't give the right location on a mac when a .app has been generated with pyinstaller +if platform.system() == "Darwin" and getattr(sys, "frozen", False): + rsrc_dir = Path(sys._MEIPASS) +else: + rsrc_dir = Path(__file__).parent + +# Set up logging +log = rsrc_dir / "log.log" +logging.basicConfig(filename=log, filemode="w", format="%(asctime)s %(message)s", encoding="utf-8", level=logging.INFO) + +class WorkerSignals(QObject): + progress = Signal(int) + result = Signal(object) + completed = Signal() + +class Worker(QRunnable): + def __init__(self, fn, *args, **kwargs): + super(Worker, self).__init__() + + # Pass function itself, along with provided arguments, to new function within the Checker instance + self.fn = fn + self.args = args + self.kwargs = kwargs + # Give the Checker signals + self.signals = WorkerSignals() + # Add the callback to kwargs + self.kwargs["progress_callback"] = self.signals.progress + + @Slot() + def run(self): + # Run the Worker function with passed args, kwargs, including progress_callback + output = self.fn(*self.args, **self.kwargs) + # Emit the output of the function as the result signal so that it can be picked up + self.signals.result.emit(output) + self.signals.completed.emit() + + +class MainWindow(QMainWindow): + def __init__(self): + super().__init__() + + # Check for updates + update_return = self.update_check() + if update_return == "permission_error": + sys.exit() + + # Set up multithreading; MaxThreadCount limited to 1 as checks don't run properly if multiple run concurrently + self.threadpool = QThreadPool() + self.threadpool.setMaxThreadCount(1) + + # Load initial options from config file, or make one if it doesn't exist yet + # platformdirs automatically saves the config file in the place appropriate to the os + self.config_file_path = Path(platformdirs.user_config_dir("mora_the_explorer", roaming=True)) / "config.json" + old_config_path = rsrc_dir / "config.json" + if self.config_file_path.exists() is True: + with open(self.config_file_path, encoding="utf-8") as config_file: + self.options = json.load(config_file) + # If a config file from version <1.4.9 exists in program folder, copy it across to the proper location. Delete later, after everyone has migrated + elif old_config_path.exists() is True: + self.config_file_path.parent.mkdir(parents=True, exist_ok=True) + shutil.copyfile(old_config_path, self.config_file_path) + with open(self.config_file_path, encoding="utf-8") as config_file: + self.options = json.load(config_file) + else: + self.options = { + "initials": "mjm", + "group": "gil", + "dest_path": "copy full path here", + "inc_init": False, + "inc_solv": False, + "nmrcheck_style": False, + "spec": "400er", + "repeat_switch": False, + "repeat_delay": 5, + } + self.config_file_path.parent.mkdir(parents=True, exist_ok=True) + with open(self.config_file_path, "w", encoding="utf-8") as config_file: + json.dump(self.options, config_file) + + # For users upgrading from <1.5.2, add nmrcheck_style to options + if "nmrcheck_style" not in self.options: + self.options["nmrcheck_style"] = False + with open(self.config_file_path, "w", encoding="utf-8") as config_file: + json.dump(self.options, config_file) + + # Load path to mora from file. If none is found, set to default path on Windows, or require user input on other OSes + self.mora_location_file_path = rsrc_dir / "mora_path.txt" + if self.mora_location_file_path.exists() is True: + with open(self.mora_location_file_path, encoding="utf-8") as mora_location_file: + mora_path_dict = {} + mora_path_dict["Windows"] = Path(mora_location_file.readline().rstrip()) + mora_path_dict["Darwin"] = Path(mora_location_file.readline().rstrip()) + mora_path_dict["Linux"] = Path(mora_location_file.readline().rstrip()) + self.mora_path = mora_path_dict[platform.system()] + + # Load available groups from groups.json + with open(rsrc_dir / "groups.json", encoding="utf-8") as groups_file: + self.groups_dict = json.load(groups_file) + + # Define paths to spectrometers based on loaded mora_path + self.path_300er = self.mora_path / "300er" + self.path_400er = self.mora_path / "400er" + #self.path_hf = self.mora_path / "500-600er" / self.groups_dict[self.options["group"]] + self.spectrometer_paths = { + "300er": self.path_300er, + "400er": self.path_400er, + } + + # Title and version info header + self.setWindowTitle("Mora the Explorer") + with open(rsrc_dir / "version.txt", encoding="utf-8") as version_file: + version_info = version_file.read() + version_box = QLabel(version_info) + version_box.setAlignment(Qt.AlignHCenter) + + # Setup layouts + layout = QVBoxLayout() + layout.addWidget(version_box) + options_layout = QGridLayout() + groups_layout = QHBoxLayout() + groups_overflow = QHBoxLayout() + spec_layout = QVBoxLayout() + options_layout.addLayout(groups_layout, 1, 1) + options_layout.addLayout(groups_overflow, 2, 1) + options_layout.addLayout(spec_layout, 6, 1, 1, 2) + layout.addLayout(options_layout) + # Add central widget and give it parent layout + layout_widget = QWidget() + layout_widget.setLayout(layout) + self.setCentralWidget(layout_widget) + + # Initials entry box + initials_label = QLabel("initials:") + initials_label.setAlignment(Qt.AlignRight | Qt.AlignVCenter) + options_layout.addWidget(initials_label, 0, 0) + + self.initials_entry = QLineEdit() + self.initials_entry.setMaxLength(3) + self.initials_entry.setText(self.options["initials"]) + # Initialize wild option for later (see initials_changed function) + self.wild_group = False + self.initials_entry.textChanged.connect(self.initials_changed) + options_layout.addWidget(self.initials_entry, 0, 1) + + initials_hint = QLabel("(lowercase!)") + initials_hint.setAlignment(Qt.AlignCenter) + options_layout.addWidget(initials_hint, 0, 2) + + # Research group selection buttons + group_label = QLabel("group:") + group_label.setAlignment(Qt.AlignRight | Qt.AlignVCenter) + options_layout.addWidget(group_label, 1, 0) + + # Add radio button for each group in groups_dict (loaded earlier) + self.AKlist = list(self.groups_dict.keys()) + self.AK_button_group = QButtonGroup(layout_widget) + self.button_list = [] + for AK in self.AKlist: + AKbutton = QRadioButton(AK) + self.button_list.append(AKbutton) + if (AK == self.options["group"]) or (AK == "other" and self.AK_button_group.checkedButton() is None): + AKbutton.setChecked(True) + self.AK_button_group.addButton(AKbutton) + if len(self.AKlist) <= 4 or self.AKlist.index(AK) < (len(self.AKlist) / 2): + groups_layout.addWidget(AKbutton) + elif len(self.AKlist) > 4 and self.AKlist.index(AK) >= (len(self.AKlist) / 2): + groups_overflow.addWidget(AKbutton) + self.AK_button_group.buttonClicked.connect(self.group_changed) + + # Drop down list for further options that appears only when "other" radio button is clicked + self.AKlist_other = list(self.groups_dict["other"]) + self.other_box = QComboBox() + self.other_box.addItems(self.AKlist_other) + if self.options["group"] in self.AKlist_other: + self.other_box.setCurrentText(self.options["group"]) + else: + self.other_box.hide() + self.other_box.currentTextChanged.connect(self.group_changed) + options_layout.addWidget(self.other_box, 2, 2) + + + # Destination path entry box + dest_path_label = QLabel("save in:") + dest_path_label.setAlignment(Qt.AlignRight | Qt.AlignVCenter) + options_layout.addWidget(dest_path_label, 3, 0) + + dest_path_input = QLineEdit() + dest_path_input.setText(self.options["dest_path"]) + dest_path_input.textChanged.connect(self.dest_path_changed) + options_layout.addWidget(dest_path_input, 3, 1) + + self.open_button = QPushButton("go to") + self.open_button.clicked.connect(self.open_path) + self.open_button.setShortcut("Ctrl+G") + options_layout.addWidget(self.open_button, 3, 2) + # Disable button if path hasn't yet been specified to stop new users thinking it should be used to select a folder + if self.options["dest_path"] == "copy full path here": + self.open_button.hide() + + # File naming options + file_naming_layout = QHBoxLayout() + + include_label = QLabel("include:") + include_label.setAlignment(Qt.AlignRight | Qt.AlignVCenter) + options_layout.addWidget(include_label, 4, 0) + + self.inc_init_checkbox = QCheckBox("initials") + self.inc_init_checkbox.setChecked(self.options["inc_init"]) + self.inc_init_checkbox.stateChanged.connect(self.inc_init_switched) + if self.options["nmrcheck_style"] is True: + self.inc_init_checkbox.setEnabled(False) + file_naming_layout.addWidget(self.inc_init_checkbox) + + self.inc_solv_checkbox = QCheckBox("solvent") + self.inc_solv_checkbox.setChecked(self.options["inc_solv"]) + self.inc_solv_checkbox.stateChanged.connect(self.inc_solv_switched) + if self.options["spec"] == "hf": + self.inc_solv_checkbox.setEnabled(False) + file_naming_layout.addWidget(self.inc_solv_checkbox) + + options_layout.addLayout(file_naming_layout, 4, 1) + + in_filename_label = QLabel("...in filename") + in_filename_label.setAlignment(Qt.AlignCenter) + options_layout.addWidget(in_filename_label, 4, 2) + + # Option to use NMRCheck-style formatting of folder names + self.nmrcheck_style_checkbox = QCheckBox("use comprehensive (NMRCheck) style") + self.nmrcheck_style_checkbox.setChecked(self.options["nmrcheck_style"]) + self.nmrcheck_style_checkbox.stateChanged.connect(self.nmrcheck_style_switched) + options_layout.addWidget(self.nmrcheck_style_checkbox, 5, 1, 1, 2) + + # Spectrometer selection buttons + spec_label = QLabel("search:") + spec_label.setAlignment(Qt.AlignRight | Qt.AlignTop) + options_layout.addWidget(spec_label, 6, 0) + + self.spectrometer_text = { + "300er": "Studer group NMR only (300 MHz)", + "400er": "routine NMR (300 && 400 MHz)", + "hf": "high-field spectrometers (500 && 600 MHz)", + } + self.spec_list = list(self.spectrometer_text.keys()) + self.spec_button_group = QButtonGroup(layout_widget) + self.spec_button_dict = {} + self.spec_button_list = [] + for spec in self.spec_list: + spec_button = QRadioButton(self.spectrometer_text[spec]) + if self.options["spec"] == spec: + spec_button.setChecked(True) + self.spec_button_group.addButton(spec_button) + self.spec_button_dict[spec_button] = spec + self.spec_button_list.append(spec_button) + spec_button.toggled.connect(self.spec_changed) + spec_layout.addWidget(spec_button) + + # Checkbox to instruct to repeat after chosen interval + repeat_layout = QHBoxLayout() + + repeat_label = QLabel("repeat:") + repeat_label.setAlignment(Qt.AlignRight | Qt.AlignVCenter) + options_layout.addWidget(repeat_label, 7, 0) + + self.repeat_check_checkbox = QCheckBox("check every") + self.repeat_check_checkbox.setChecked(self.options["repeat_switch"]) + self.repeat_check_checkbox.stateChanged.connect(self.repeat_switched) + repeat_layout.addWidget(self.repeat_check_checkbox) + + repeat_interval = QSpinBox() + repeat_interval.setMinimum(1) + repeat_interval.setValue(self.options["repeat_delay"]) + repeat_interval.valueChanged.connect(self.repeat_delay_changed) + repeat_layout.addWidget(repeat_interval) + + repeat_mins = QLabel("mins") + repeat_layout.addWidget(repeat_mins) + + options_layout.addLayout(repeat_layout, 7, 1) + + # Button to save all options for future + self.save_button = QPushButton("save options as defaults for next time") + self.save_button.clicked.connect(self.save) + options_layout.addWidget(self.save_button, 8, 0, 1, 3) + self.save_button.setEnabled(False) + + # Initialize date variable + self.date_selected = date.today() + + # Date selection tool for 300er and 400er + date_label = QLabel("when?") + date_label.setAlignment(Qt.AlignRight | Qt.AlignVCenter) + options_layout.addWidget(date_label, 9, 0) + + date_layout = QHBoxLayout() + options_layout.addLayout(date_layout, 9, 1) + self.only_button = QRadioButton("only") + self.since_button = QRadioButton("since") + date_layout.addWidget(self.only_button, 0) + date_layout.addWidget(self.since_button, 1) + self.date_button_group = QButtonGroup(layout_widget) + self.date_button_group.addButton(self.only_button) + self.date_button_group.addButton(self.since_button) + self.date_button_list = [self.only_button, self.since_button] + self.since_button.toggled.connect(self.since_function_activated) + self.only_button.setChecked(True) + + self.date_selector = QDateEdit() + self.date_selector.setDisplayFormat("dd MMM yyyy") + self.date_selector.setDate(date.today()) + self.date_selector.dateChanged.connect(self.date_changed) + date_layout.addWidget(self.date_selector, 2) + + self.today_button = QPushButton("today") + options_layout.addWidget(self.today_button, 9, 2) + self.today_button.clicked.connect(self.set_date_as_today) + + # Date selection tool for hf (only needs year) + self.hf_date_selector = QDateEdit() + self.hf_date_selector.setDisplayFormat("yyyy") + self.hf_date_selector.setDate(date.today()) + self.hf_date_selector.dateChanged.connect(self.hf_date_changed) + options_layout.addWidget(self.hf_date_selector, 9, 1) + + # Button to begin check + self.start_check_button = QPushButton("start check now") + self.start_check_button.setStyleSheet("background-color : #b88cce") + layout.addWidget(self.start_check_button) + self.start_check_button.clicked.connect(self.started) + + # Button to cancel pending repeat check + self.interrupt_button = QPushButton("cancel repeat check") + self.interrupt_button.setStyleSheet("background-color : #cc0010; color : white") + layout.addWidget(self.interrupt_button) + self.interrupt_button.clicked.connect(self.interrupted) + self.interrupt_button.hide() + + # Timer for repeat check, starts checking function when timer runs out + self.timer = QTimer() + self.timer.setSingleShot(True) + self.timer.timeout.connect(self.started) + + # Progress bar for check + self.prog_bar = QProgressBar() + self.prog_bar.setAlignment(Qt.AlignCenter | Qt.AlignVCenter) + layout.addWidget(self.prog_bar) + + # Box to display output of check function (list of copied spectra) + self.copied_list = [] + self.display_layout = QVBoxLayout() + self.display = QWidget() + self.display.setLayout(self.display_layout) + self.display_scroll = QScrollArea() + self.display_scroll.setWidgetResizable(True) + self.display_scroll.setWidget(self.display) + layout.addWidget(self.display_scroll) + + # Extra notification that spectra have been found, dismissable + self.notification = QPushButton() + layout.addWidget(self.notification) + self.notification.clicked.connect(self.notification_clicked) + self.notification.hide() + + # Trigger function to adapt which spectrometers are shown to the user based on their selected group + self.refresh_visible_specs() + # Trigger function to adapt date selector and naming options to the selected spectrometer + self.adapt_to_spec() + # Trigger function that normally activates when the group is changed so that the hf path is generated + self.group_changed() + + # Set up window. macos spaces things out more than windows so give it a bigger window + if platform.system() == "Windows": + self.setMinimumSize(QSize(380, 650)) + else: + self.setMinimumSize(QSize(450, 780)) + + # Now come all the other functions + + # Define function to check for updates at location specified in update_path.txt + def update_check(self): + logging.info("Checking for updates at:") + with open(rsrc_dir / "update_path.txt", encoding="utf-8") as update_path_file: + self.update_path = Path(update_path_file.readline().rstrip()) + update_path_version_file = self.update_path / "version.txt" + logging.info(self.update_path) + with open(rsrc_dir / "version.txt", encoding="utf-8") as version_file: + self.version_no = version_file.readlines()[2].rstrip() + logging.info(f"Current version: {self.version_no}") + try: + if update_path_version_file.exists() is True: + with open(update_path_version_file, encoding="utf-8") as newest_version_file: + self.newest_version_no = newest_version_file.readlines()[2].rstrip() + if self.version_no != self.newest_version_no: + self.notify_update() + return "remote_version_found" + else: + return "no_remote_version" + except PermissionError: + failed_permission_dialog = QMessageBox(self) + failed_permission_dialog.setWindowTitle("Access to mora server denied") + failed_permission_dialog.setText(""" +You have been denied permission to access the mora server. +Check the connection and your authentication details and try again. +The program will now close. + """) + failed_permission_dialog.exec() + logging.info("Permission to access server denied") + return "permission_error" + + # Popup to notify user that an update is available, with version info + def notify_update(self): + update_dialog = QMessageBox(self) + update_dialog.setWindowTitle("Update available") + update_dialog.setText( + f"There appears to be a new update available at:\n{self.update_path}" + ) + update_dialog.setInformativeText(f"Your version is {self.version_no}\nThe version on the server is {self.newest_version_no}") + update_dialog.setStandardButtons(QMessageBox.Ignore | QMessageBox.Open) + update_dialog.setDefaultButton(QMessageBox.Ignore) + choice = update_dialog.exec() + if choice == QMessageBox.Open: + if self.update_path.exists() is True: + # Extra quotes necessary because cmd.exe can't handle spaces in path names otherwise + os.system(f'start "" "{self.update_path}"') + + # Spawn popup dialog that dissuades user from using the "since" function regularly, unless the nmr group has been selected + def since_function_activated(self): + since_message = """ +The function to check multiple days at a time should not be used on a regular basis. +Please switch back to a single-day check once your search is finished. +The repeat function is also disabled as long as this option is selected. + """ + if self.since_button.isChecked() is True and self.options["group"] != "nmr": + since_warning = QMessageBox.warning(self, "Warning", since_message) + self.repeat_check_checkbox.setEnabled(False) + self.options["repeat_switch"] = False + else: + self.repeat_check_checkbox.setEnabled(True) + self.options["repeat_switch"] = self.repeat_check_checkbox.isChecked() + + def initials_changed(self, new_initials): + # Allow initials entry to take five characters total if the nmr group is chosen and the wild group option is invoked + if len(new_initials) > 0: + if (self.options["group"] == "nmr") and (new_initials.split()[0] == "*"): + self.initials_entry.setMaxLength(5) + if (len(new_initials.split()) > 1): + self.wild_group = True + self.options["initials"] = new_initials.split()[1] + else: + self.options["initials"] = "" + else: + self.options["initials"] = new_initials + else: + self.initials_entry.setMaxLength(3) + self.options["initials"] = new_initials + self.save_button.setEnabled(True) + + def group_changed(self): + if self.AK_button_group.checkedButton().text() == "other": + self.other_box.show() + self.options["group"] = self.other_box.currentText() + self.path_hf = ( + self.mora_path / "500-600er" / self.groups_dict["other"][self.options["group"]] + ) + else: + self.other_box.hide() + self.options["group"] = self.AK_button_group.checkedButton().text() + self.path_hf = ( + self.mora_path / "500-600er" / self.groups_dict[self.options["group"]] + ) + self.spectrometer_paths["hf"] = self.path_hf + self.refresh_visible_specs() + # If nmr group has been selected, disable the naming option checkboxes as they will be treated as selected anyway. Also make sure wild option is turned off + if self.options["group"] == "nmr": + self.inc_init_checkbox.setEnabled(False) + self.nmrcheck_style_checkbox.setEnabled(False) + else: + # Only enable initials checkbox if nmrcheck_style option is not selected, disable otherwise + self.inc_init_checkbox.setEnabled(not self.options["nmrcheck_style"]) + self.nmrcheck_style_checkbox.setEnabled(True) + self.wild_group = False + if self.options["group"] == "nmr" or self.options["spec"] == "hf": + self.inc_solv_checkbox.setEnabled(False) + else: + self.inc_solv_checkbox.setEnabled(True) + self.save_button.setEnabled(True) + + def dest_path_changed(self, new_path): + formatted_path = new_path + # Best way to ensure cross-platform compatibility is to avoid use of backslashes and then let pathlib.Path take care of formatting + if "\\" in formatted_path: + formatted_path = formatted_path.replace("\\", "/") + # If the option "copy path" is used in Windows Explorer and then pasted into the box, the path will be surrounded by quotes, so remove them if there + if formatted_path[0] == '"': + formatted_path = formatted_path.replace('"', "") + self.options["dest_path"] = formatted_path + self.open_button.show() + self.save_button.setEnabled(True) + + def open_path(self): + if Path(self.options["dest_path"]).exists() is True: + if platform.system() == "Windows": + # Extra quotes necessary because cmd.exe can't handle spaces in path names otherwise + os.system(f'start "" "{self.options["dest_path"]}"') + elif platform.system() == "Darwin": + subprocess.Popen(["open", self.options["dest_path"]]) + elif platform.system() == "Linux": + subprocess.Popen(["xdg-open", self.options["dest_path"]]) + + def inc_init_switched(self): + self.options["inc_init"] = self.inc_init_checkbox.isChecked() + self.save_button.setEnabled(True) + + def inc_solv_switched(self): + self.options["inc_solv"] = self.inc_solv_checkbox.isChecked() + self.save_button.setEnabled(True) + + def nmrcheck_style_switched(self): + self.options["nmrcheck_style"] = self.nmrcheck_style_checkbox.isChecked() + self.save_button.setEnabled(True) + self.inc_init_checkbox.setEnabled(not self.nmrcheck_style_checkbox.isChecked()) + self.adapt_to_spec() + + def refresh_visible_specs(self): + if self.options["group"] in ["stu", "nae", "nmr"]: + self.spec_button_list[0].show() + else: + self.spec_button_list[0].hide() + + def spec_changed(self): + self.options["spec"] = self.spec_button_dict[self.spec_button_group.checkedButton()] + self.adapt_to_spec() + self.save_button.setEnabled(True) + + def adapt_to_spec(self): + if self.options["spec"] == "hf": + # Including the solvent in the title is not supported for high-field measurements so disable option + self.inc_solv_checkbox.setEnabled(False) + self.repeat_check_checkbox.setEnabled(False) + self.date_selector.hide() + self.today_button.setEnabled(False) + self.hf_date_selector.show() + else: + if self.options["group"] != "nmr" and self.options["nmrcheck_style"] is False: + self.inc_solv_checkbox.setEnabled(True) + self.repeat_check_checkbox.setEnabled(True) + self.hf_date_selector.hide() + self.date_selector.show() + self.today_button.setEnabled(True) + + def repeat_switched(self): + self.options["repeat_switch"] = self.repeat_check_checkbox.isChecked() + self.save_button.setEnabled(True) + + def repeat_delay_changed(self, new_delay): + self.options["repeat_delay"] = new_delay + self.save_button.setEnabled(True) + + def save(self): + with open(self.config_file_path, "w", encoding="utf-8") as config_file: + json.dump(self.options, config_file) + self.save_button.setEnabled(False) + + def date_changed(self): + self.date_selected = self.date_selector.date().toPython() + + def hf_date_changed(self): + self.date_selected = self.hf_date_selector.date().toPython() + + def set_date_as_today(self): + self.date_selector.setDate(date.today()) + + # Converts Python datetime.date object to the same format used in the folder names on Mora + def format_date(self, input_date): + if self.options["spec"] == "hf": + formatted_date = input_date.strftime("%Y") + else: + formatted_date = input_date.strftime("%b%d-%Y") + return formatted_date + + def started(self): + if self.only_button.isChecked() is True or self.options["spec"] == "hf": + self.queued_checks = 1 + self.single_check(self.date_selected) + elif self.since_button.isChecked() is True: + # Give number of checks initial value of zero so it can be added to iteratively below + self.queued_checks = 0 + self.multiday_check(self.date_selected) + + def single_check(self, date): + self.start_check_button.setEnabled(False) + formatted_date = self.format_date(date) + # Start main checking function in worker thread + worker = Worker(checknmr, self.options, formatted_date, self.mora_path, self.spectrometer_paths, self.wild_group, self.prog_bar) + worker.signals.progress.connect(self.update_progress) + worker.signals.result.connect(self.handle_output) + worker.signals.completed.connect(self.check_ended) + self.threadpool.start(worker) + + def multiday_check(self, initial_date): + end_date = date.today() + timedelta(days=1) + date_to_check = initial_date + while date_to_check != end_date: + self.single_check(date_to_check) + date_to_check += timedelta(days=1) + self.queued_checks += 1 + + def update_progress(self, prog_state): + self.prog_bar.setValue(prog_state) + + def handle_output(self, final_output): + self.copied_list = final_output + + def check_ended(self): + # Set progress to 100% just in case it didn't reach it for whatever reason + self.prog_bar.setMaximum(1) + self.prog_bar.setValue(1) + # Will only not be true if an unknown error occurred, in all cases len will be at least 2 + if len(self.copied_list) > 1: + # At least one spectrum was found + if self.copied_list[1][:5] == "spect": + self.copied_list.pop(0) + self.notify(self.copied_list) + # No spectra were found but check completed successfully + elif self.copied_list[1][:5] == "check": + pass + # Known error occurred + else: + self.copied_list.pop(0) + self.notify(self.copied_list) + else: + # Unknown error occurred, output of check function was returned without appending anything to copied_list + self.copied_list.pop(0) + self.notify(self.copied_list) + # Display output + for entry in self.copied_list: + entry_label = QLabel(entry) + self.display_layout.addWidget(entry_label) + # Move scroll area so that the user sees immediately which spectra were found or what the error was - but only the first time this happens (haven't been able to make this work) + #if entry == self.copied_list[0] and self.copied_list[0][:5] != "check": + #QApplication.processEvents() + #self.display_scroll.ensureWidgetVisible(entry_label, ymargin=50) + # Behaviour for repeat check function. Deactivate for hf spectrometer. See also self.timer in init function + if (self.options["repeat_switch"] is True) and (self.options["spec"] != "hf"): + self.start_check_button.hide() + self.interrupt_button.show() + self.timer.start(int(self.options["repeat_delay"]) * 60 * 1000) + # Enable start check button again, but only if all queued checks have finished + self.queued_checks -= 1 + if self.queued_checks == 0: + self.start_check_button.setEnabled(True) + + # I suspect this duplicates the functionality above, and doesn't seem to be used anywhere? Consider removal + def start_timer(self): + self.start_check_button.hide() + self.interrupt_button.show() + self.timer.start(int(self.options["repeat_delay"]) * 60 * 1000) + + def interrupted(self): + self.timer.stop() + self.start_check_button.show() + self.interrupt_button.hide() + + def notify(self, copied_list): + # If spectra were found, the list will have len > 1, if a known error occurred, the list will have len 1, if an unknown error occurred, the list will be empty + if len(copied_list) > 1: + notification_text = "Spectra have been found!" + self.notification.setText(notification_text + " Ctrl+G to go to. Click to dismiss") + self.notification.setStyleSheet("background-color : limegreen") + else: + self.notification.setStyleSheet("background-color : #cc0010; color : white") + try: + notification_text = "Error: " + copied_list[0] + except: + notification_text = "Unknown error occurred." + self.notification.setText(notification_text + " Click to dismiss") + self.notification.show() + # Display system notification - doesn't seem to be implemented for macOS currently + try: + plyer.notification.notify(title="Hola!", message=notification_text, app_name="Mora the Explorer", timeout=120) + except: + pass + + def notification_clicked(self): + self.notification.hide() + +logging.info("Initializing program") +app = QApplication(sys.argv) + +# Create instance of MainWindow as defined above, then show it +window = MainWindow() +window.show() + + +# Make dark mode less black because Windows dark mode looks bad +dark_palette = QPalette() +dark_palette.setColor(QPalette.Window, QColor(53, 53, 53)) +dark_palette.setColor(QPalette.WindowText, Qt.white) +dark_palette.setColor(QPalette.Base, QColor(25, 25, 25)) +dark_palette.setColor(QPalette.AlternateBase, QColor(53, 53, 53)) +dark_palette.setColor(QPalette.ToolTipBase, Qt.black) +dark_palette.setColor(QPalette.ToolTipText, Qt.white) +dark_palette.setColor(QPalette.Text, Qt.white) +dark_palette.setColor(QPalette.Button, QColor(53, 53, 53)) +dark_palette.setColor(QPalette.ButtonText, Qt.white) +dark_palette.setColor(QPalette.BrightText, Qt.red) +dark_palette.setColor(QPalette.Link, QColor(42, 130, 218)) +dark_palette.setColor(QPalette.Highlight, QColor(42, 130, 218)) +dark_palette.setColor(QPalette.HighlightedText, Qt.black) +if darkdetect.isDark() is True and platform.system() == "Windows": + app.setStyle("Fusion") + app.setPalette(dark_palette) + +app.setWindowIcon(QIcon("explorer.ico")) +app.exec() diff --git a/mora_the_explorer.spec b/mora_the_explorer.spec new file mode 100644 index 0000000..2a3cf58 --- /dev/null +++ b/mora_the_explorer.spec @@ -0,0 +1,57 @@ +# -*- mode: python ; coding: utf-8 -*- + + +block_cipher = None + + +a = Analysis( + ['mora_the_explorer.py'], + pathex=[], + binaries=[], + datas=[('LICENSE.md', '.'), ('README.md', '.'), ('explorer.ico', '.'), ('requirements.txt', '.'), ('update_path.txt', '.'), ('mora_path.txt', '.'), ('version.txt', '.'), ('groups.json', '.')], + hiddenimports=['plyer.platforms.win.notification', 'plyer.platforms.macosx.notification', 'plyer.platforms.linux.notification'], + hookspath=[], + hooksconfig={}, + runtime_hooks=[], + excludes=[], + win_no_prefer_redirects=False, + win_private_assemblies=False, + cipher=block_cipher, + noarchive=False, +) +pyz = PYZ(a.pure, a.zipped_data, cipher=block_cipher) + +exe = EXE( + pyz, + a.scripts, + [], + exclude_binaries=True, + name='mora_the_explorer', + icon='explorer.ico', + debug=False, + bootloader_ignore_signals=False, + strip=False, + upx=True, + console=False, + disable_windowed_traceback=False, + argv_emulation=False, + target_arch=None, + codesign_identity=None, + entitlements_file=None, +) +coll = COLLECT( + exe, + a.binaries, + a.zipfiles, + a.datas, + strip=False, + upx=True, + upx_exclude=[], + name='mora_the_explorer', +) +app = BUNDLE( + coll, + name='mora_the_explorer.app', + icon='explorer.ico', + bundle_identifier=None, +) diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 0000000..5cb6d71 --- /dev/null +++ b/requirements.txt @@ -0,0 +1,8 @@ +darkdetect>=0.8.0 +platformdirs>=3.2.0 +plyer>=2.1.0 +Pillow>=9.2.0 +PySide6>=6.4.2 +PySide6-Addons>=6.4.2 +PySide6-Essentials>=6.4.2 +shiboken6>=6.4.2 diff --git a/update_path.txt b/update_path.txt new file mode 100644 index 0000000..f95ade3 --- /dev/null +++ b/update_path.txt @@ -0,0 +1 @@ +//mora/nmr/mnova/mora_the_explorer diff --git a/version.txt b/version.txt new file mode 100644 index 0000000..7125320 --- /dev/null +++ b/version.txt @@ -0,0 +1,5 @@ +Mora the Explorer +Matt Milner +v1.5.3 +License: GPLv3 +Please report any bugs to milner@uni-muenster.de!