Flask app

.gitignore

@@ -157,5 +157,5 @@ cython_debug/
 #  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
-#.idea/
+.idea/
 

flask_app/app.py

@@ -0,0 +1,71 @@
+import os,sys
+
+sys.path.append('../')
+sys.path.append('../library_spectra_validation')
+
+from flask import Flask
+from flask import request, render_template, redirect, url_for
+
+import pandas as pd
+import numpy as np
+from matplotlib.figure import Figure
+
+from library_spectra_validation.library_handler import LibraryHandler
+
+
+app = Flask(__name__)
+app.config.from_pyfile("config.py")
+
+@app.route('/')
+def index():
+    return render_template('index.html')
+
+@app.route('/upload', methods=['GET','POST'])
+def upload():
+    if request.method == 'POST':
+        file = request.files['file']
+        file.save(os.path.join(app.config['UPLOAD_FOLDER'], file.filename))
+        fpath = os.path.join(app.config['UPLOAD_FOLDER'], file.filename)
+        if file:
+            library_handler = LibraryHandler(fpath)
+            df_spectra = pd.DataFrame({"spectrum": library_handler.spectra}) #TODO 
+            return render_template("preview.html", data=df_spectra.to_html())
+    return render_template('upload_data.html')
+
+@app.route('/preview', methods=['POST'])
+def preview():
+    sheet_name = request.form['sheet']
+    df = pd.read_excel(request.files['file'], sheet_name=sheet_name)
+    return render_template('preview.html', df=df.to_html(), sheet_name=sheet_name)
+
+# @app.route('/plot_spectrum', methods=['POST'])
+# def plot_spectrum():
+#     # TODO plotly??
+#     cmp_selector = request.form['compound_name']
+#     cmp_id = cmp_list.index(cmp_selector)
+#     cmp_smile = df_spectra.loc[cmp_id]["smiles"]
+
+#     plt_spectrum = spectra[cmp_id]
+
+#     fig, axs = plt.subplots(1, 2, figsize=(12.8, 4.2), gridspec_kw={'width_ratios': [2, 5]}, sharey=False)
+#     cmp_img = Chem.Draw.MolToImage(Chem.MolFromSmiles(cmp_smile), ax=axs[0])
+
+#     axs[0].grid(False)
+#     axs[0].tick_params(axis='both', bottom=False, labelbottom=False, left=False, labelleft=False)
+#     axs[0].set_title(cmp_smile)
+#     axs[0].imshow(cmp_img)
+#     axs[0].axis("off")
+
+#     plot_spectrum(plt_spectrum, axs[1])
+
+#     # Save the plot to a temporary file or convert it to a base64 string to embed in HTML
+#     # Example: plt.savefig('static/plot.png')
+#     # Pass the path or base64 string to the template
+#     return render_template('plot_spectrum.html', plot_path='static/plot.png')
+
+@app.route('/about')
+def about():
+    return render_template('about.html')
+
+if __name__ == '__main__':
+    app.run(debug=True)

flask_app/config.py

@@ -0,0 +1 @@
+UPLOAD_FOLDER = 'resources'

flask_app/resources/Broken_records.txt

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+I clean all the 12 mass spectra in the "test_case_correct.mgf", in terms of 
+--> adding inchikey
+--> cleaning the inchi
+--> adding formula
+
+So all mass spectra in the "test_case_wrong.mgf" are missing formula and inchikey
+
+mass spectrum 1: no change
+mass spectrum 2: wrong adduct
+mass spectrum 3: wrong pepmass (precursor)
+mass spectrum 4: wrong smiles
+mass spectrum 5: missing adduct
+mass spectrum 6: no change (share the same compound name as mass spectrum 5, but different adduct)
+mass spectrum 7: missing adduct
+mass spectrum 8: missing adduct
+mass spectrum 9: no change
+mass spectrum 10: missing compound name and adduct
+mass spectrum 11: no change
+mass spectrum 12: wroing inchi