Added table rendering for spectra. Modified templates.

flask_app/app.py

@@ -1,52 +1,71 @@
+import os,sys
+
+sys.path.append('../')
+sys.path.append('../library_spectra_validation')
+
 from flask import Flask
-from flask import request, render_template
+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=['POST'])
+@app.route('/upload', methods=['GET','POST'])
 def upload():
-    uploaded_file = request.files['file']
-    uploaded_file.save(uploaded_file.filename)  # Save the file
-    xl = pd.ExcelFile(uploaded_file.filename)
-    sheets = xl.sheet_names
-    return render_template('preview.html', sheets=sheets)
-
+    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():
-    cmp_selector = request.form['compound_name']
-    cmp_id = cmp_list.index(cmp_selector)
-    cmp_smile = df_spectra.loc[cmp_id]["smiles"]
+# @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]
 
-    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])
 
-    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")
 
-    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])
 
-    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')
 
-    # 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

@@ -0,0 +1,19 @@
+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