add .exe test

ms_sample_list_creator/csv_batch.py

@@ -1,8 +1,12 @@
+import csv
 import os
 import tkinter as tk
 from datetime import datetime
 from tkinter import filedialog
 
+import pandas as pd
+import requests
+
 
 class csvBatch(tk.Frame):
     def __init__(self, csv_batch_window: tk.Toplevel, root: tk.Tk):
@@ -32,7 +36,7 @@ def __init__(self, csv_batch_window: tk.Toplevel, root: tk.Tk):
         self.pre_blk = int(str(os.environ.get("PRE_BLK")))
         self.post_blk = int(str(os.environ.get("POST_BLK")))
         self.blk_name = str(os.environ.get("BLK_NAME"))
-        self.blk_pos = str(os.environ.get("LK_POS"))
+        self.blk_pos = str(os.environ.get("BLK_POS"))
         self.inj_volume = int(str(os.environ.get("INJ_VOLUME")))
         self.access_token = str(os.environ.get("ACCESS_TOKEN"))
         self.method_file = str(os.environ.get("METHOD_FILE"))
@@ -41,14 +45,14 @@ def __init__(self, csv_batch_window: tk.Toplevel, root: tk.Tk):
         self.file = str(os.environ.get("FILE"))
         self.current_position = 1
         self.current_row = 1
-        self.timestamp = datetime.now().strftime("%Y%m%d%H%M")
+        self.timestamp = "202404101527"#datetime.now().strftime("%Y%m%d%H%M")
         self.csv_path = f"{self.output_folder}/{datetime.now().strftime('%Y%m%d')}_{self.operator}_dbgi_{self.file}.csv"
 
-        warning_label = tk.Label(
+        self.warning_label = tk.Label(
             self.csv_batch_window,
             text="Warning, this mode is exclusively made to submit sample lists that have already been made using this tool.",
         )
-        warning_label.pack()
+        self.warning_label.pack()
 
         label = tk.Label(self.csv_batch_window, text="Search for your CSV:", pady=10)
         label.pack()
@@ -99,4 +103,117 @@ def submit_result(self) -> None:
         Returns:
             None
         """
-        print("correctly written")
+        # Retrieves file path and method name given by the user
+        file_path = os.environ.get("FILE_PATH")
+        self.file = str(os.environ.get("FILE"))
+
+        # Converts the CSV to a dataframe
+        df = pd.read_csv(str(file_path), skiprows=1)
+
+        # Delete standby row
+        df = df.drop(df.index[-1])
+
+        # Remove blanks
+        patterns = ["pre", "post"]
+        combined_patterns = "|".join(patterns)
+        filtered_df = df[~df["File Name"].str.contains(combined_patterns, regex=True)]
+
+        # Update data path, instrument method and injection volume
+        path = self.data_path.replace("/", "\\")
+        instrument_method = self.method_file.replace("/", "\\")
+        filtered_df["Path"] = path
+        filtered_df["Instrument Method"] = instrument_method
+        filtered_df["Inj Vol"] = self.inj_volume
+
+        # Change timestamp and operator initials
+        filtered_df["File Name"] = df["File Name"].apply(
+            lambda x: "_".join([self.timestamp, self.operator] + x.split("_")[2:])
+        )
+
+        # Prepare data for directus
+        directus_df = filtered_df
+        directus_df = directus_df.drop(columns=["Path", "Position"])
+        directus_df["aliquot_id"] = ""
+        directus_df["ms_id"] = self.ms_id
+        directus_df = directus_df.rename(columns={"File Name": "mass_spec_id"})
+        directus_df = directus_df.rename(columns={"Inj Vol": "injection_volume"})
+        directus_df = directus_df.rename(columns={"Instrument Method": "injection_method"})
+        directus_df["injection_method"] = self.file
+        for index, row in directus_df.iterrows():  # Iterate over rows using iterrows()
+            parts = row["mass_spec_id"].split("_")  # Split the "File Name" column by underscores
+            aliquot_id = "_".join(parts[2:])  # Extract the desired parts of the split string
+            directus_df.at[index, "aliquot_id"] = aliquot_id
+
+        # Send data to directus
+        records = directus_df.to_json(orient="records")
+        base_url = "http://directus.dbgi.org"
+        collection_url = base_url + "/items/Mass_Spectrometry_Analysis"
+        session = requests.Session()
+        headers = {"Content-Type": "application/json"}
+        session.headers.update({"Authorization": f"Bearer {self.access_token}"})
+        response = session.post(url=collection_url, headers=headers, data=records)
+
+        # Check if correctly added to directus
+        if response.status_code == 200:
+            self.warning_label.config(text="Success!! Writing CSV...", foreground="green")
+            # Write data to the CSV file
+            with open(self.csv_path, "w", newline="") as csv_file:
+                csv_writer = csv.writer(csv_file)
+                # Write headers
+                csv_writer.writerow(["Bracket Type=4", "", "", "", ""])
+                csv_writer.writerow(["File Name", "Path", "Instrument Method", "Position", "Inj Vol"])
+
+                # Write pre blanks
+                if self.pre_blk > 0:
+                    for i in range(1, self.pre_blk + 1):
+                        padded_number = str(i).zfill(2)
+                        filename = (
+                            self.timestamp + "_" + self.operator + "_dbgi_" + self.blk_name + "_blk_pre" + padded_number
+                        )
+                        path = self.data_path.replace("/", "\\")
+                        instrument_method = self.method_file.replace("/", "\\")
+                        position = self.blk_pos
+                        inj_volume = self.inj_volume
+                        csv_writer.writerow([filename, path, instrument_method, position, inj_volume])
+                else:
+                    print("no pre blanks")
+
+                # Write data
+                csv_writer.writerows(filtered_df.values)
+
+                # Write post blanks
+                if self.post_blk > 0:
+                    for i in range(1, self.post_blk + 1):
+                        padded_number = str(i).zfill(2)
+                        filename = (
+                            self.timestamp
+                            + "_"
+                            + self.operator
+                            + "_dbgi_"
+                            + self.blk_name
+                            + "_blk_post"
+                            + padded_number
+                        )
+                        path = self.data_path.replace("/", "\\")
+                        instrument_method = self.method_file.replace("/", "\\")
+                        position = self.blk_pos
+                        inj_volume = self.inj_volume
+                        csv_writer.writerow([filename, path, instrument_method, position, inj_volume])
+                else:
+                    print("no post blanks")
+
+                # Write standby line
+                parts = self.standby_file.split("/")
+                file = parts[-1]
+                filename = self.timestamp + "_" + self.operator + "_" + file
+                path = self.data_path.replace("/", "\\")
+                standby = self.standby_file.replace("/", "\\")
+                position = self.blk_pos
+                inj_volume = self.inj_volume
+                csv_writer.writerow([filename, path, standby, position, inj_volume])
+
+            # Close the Tkinter window
+            self.csv_batch_window.destroy()
+            self.root.destroy()
+        else:
+            self.warning_label.config(text="Directus error, please check your CSV.", foreground="red")

ms_sample_list_creator/home_page.py

@@ -50,8 +50,10 @@ def __init__(self, parent: tk.Tk, *args: Any, **kwargs: Any):
         frame_entries_up.pack(fill="x", pady=5)
 
         entry_username = tk.Entry(frame_entries_up, textvariable=self.username)
+        self.username.set("edouard.bruelhart@unifr.ch")
         entry_username.pack(side="left", anchor="center")
         entry_password = tk.Entry(frame_entries_up, textvariable=self.password, show="*")
+        self.password.set("861510Eb.98")
         entry_password.pack(side="right", anchor="center")
 
         frame_labels_om = tk.Frame(self)
@@ -67,9 +69,11 @@ def __init__(self, parent: tk.Tk, *args: Any, **kwargs: Any):
         frame_entries_om.pack(fill="x", pady=(5, 0))
 
         entry_operator = tk.Entry(frame_entries_om, textvariable=self.operator)
+        self.operator.set("EB")
         entry_operator.pack(side="left", anchor="center")
 
         entry_ms = tk.Entry(frame_entries_om, textvariable=self.ms_id)
+        self.ms_id.set("ms_000001")
         entry_ms.pack(side="right", anchor="center")
 
         frame_label_rack = tk.Frame(self)

ms_sample_list_creator/ms_sample_list_creator.py

@@ -1,8 +1,8 @@
-# To generate binaries for this script, install pyinstaller (pip install pyinstaller) and run "pyinstaller --onefile main.py"
+# To generate binaries for this script, install pyinstaller (pip install pyinstaller) and run "pyinstaller --onefile ms_sample_list_creator.py"
 # Generated binaries are made for the native system where the pyinstaller command is run.
 
 # You can generate windows executable from linux using wine, by previously installing wine, python 3.8.19, pyinstaller and
-# other non-built-in packages (here requests) inside wine. Then run: wine pyinstaller --onefile main.py
+# other non-built-in packages (here requests and pandas) inside wine. Then run: wine pyinstaller --onefile ms_sample_list_creator.py
 
 import tkinter as tk
 
@@ -29,6 +29,7 @@ def submit_results(clicked_button: str) -> None:
 def handle_user_choice() -> None:
     """
     Collect user choice and transmits it to de function that shows the correct window.
+    ;C:\users\edouard\Local Settings\Application Data\Programs\Python\Python38\Scripts
 
     Args:
         None
@@ -43,15 +44,6 @@ def handle_user_choice() -> None:
 
 
 def show_selected_window(choice: str) -> None:
-    """
-    Accepts user choice and launches the correct window.
-
-    Args:
-        choice (str): Retrieves the user choice.
-
-    Returns:
-        None
-    """
     if choice == "new":
         # Create a new Toplevel window for the new batch
         new_batch_window = tk.Toplevel(root)

ms_sample_list_creator/new_batch.py

@@ -36,7 +36,7 @@ def __init__(self, new_batch_window: tk.Toplevel, root: tk.Tk):
         self.pre_blk = int(str(os.environ.get("PRE_BLK")))
         self.post_blk = int(str(os.environ.get("POST_BLK")))
         self.blk_name = str(os.environ.get("BLK_NAME"))
-        self.blk_pos = str(os.environ.get("LK_POS"))
+        self.blk_pos = str(os.environ.get("BLK_POS"))
         self.inj_volume = int(str(os.environ.get("INJ_VOLUME")))
         self.access_token = str(os.environ.get("ACCESS_TOKEN"))
         self.method_file = str(os.environ.get("METHOD_FILE"))
@@ -165,7 +165,7 @@ def add_row(self, event: Optional[tk.Event] = None) -> None:
 
         self.label.config(text="")
 
-        if response.status_code == 200:
+        if response.status_code != 200:
             # Check if it is the first run or not the first position in the rack
             if (self.current_position > self.col_rack_size and self.current_position > self.col_rack_size) or (
                 self.current_position == 1 and self.current_row == 1