Added draft (not tested yet!) starting code for flask migration.

mzmine · Mar 25, 2024 · 265df58 · 265df58
1 parent 1079e3b
commit 265df58
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Showing 18 changed files with 109 additions and 861 deletions.
diff --git a/.gitignore b/.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/
 
diff --git a/flask_app/app.py b/flask_app/app.py
@@ -0,0 +1,52 @@
+from flask import Flask
+from flask import request, render_template
+
+import pandas as pd
+from matplotlib.figure import Figure
+
+app = Flask(__name__)
+
+@app.route('/')
+def index():
+    return render_template('index.html')
+
+@app.route('/upload', methods=['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)
+
+@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"]
+
+    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')
+
+if __name__ == '__main__':
+    app.run(debug=True)
diff --git a/flask_app/services/plot_spectra.py b/flask_app/services/plot_spectra.py
@@ -0,0 +1,3 @@
+'''
+TODO Migrate here functionality to plot spectra
+'''
diff --git a/flask_app/templates/about.html b/flask_app/templates/about.html
@@ -0,0 +1,3 @@
+
+
+"# This is the creation and curation wizard for FAIR MS Libraries."
diff --git a/flask_app/templates/base.html b/flask_app/templates/base.html
@@ -0,0 +1,22 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>{% block title %}Order Service App{% endblock %}</title>
+    <link rel= "stylesheet" type= "text/css" href= "{{ url_for('static',filename='styles.css') }}">
+    <script type="text/javascript" src="http://ajax.googleapis.com/ajax/libs/jquery/1.6.2/jquery.min.js"></script>
+</head>
+<body>
+    <nav>
+        <ul>
+            <li><a href="{{ url_for('index') }}">Home</a></li>
+            <li><a href="https://github.com/mzmine/biohack23_p15">Get help</a></li>
+            <li><a href="https://github.com/mzmine/biohack23_p15/issues/new/choose">Report bug</a></li>
+            <li><a href="{{ url_for('about') }}">About</a></li>
+        </ul>
+    </nav>
+    {% block content %}
+    {% endblock %}
+</body>
+</html>
diff --git a/streamlit_app/__init__.py → flask_app/templates/index.html b/streamlit_app/__init__.py → flask_app/templates/index.html
diff --git a/flask_app/templates/plot_spectrum.html b/flask_app/templates/plot_spectrum.html
@@ -0,0 +1,11 @@
+<form action="/plot_spectrum" method="post">
+    <label for="compound_name">Select a compound name:</label>
+    <select id="compound_name" name="compound_name">
+        {% for cmp in cmp_list %}
+            <option value="{{ cmp }}">{{ cmp }}</option>
+        {% endfor %}
+    </select>
+    <input type="submit" value="Plot Spectrum">
+</form>
+
+<!-- <img src="{{ plot_path }}" alt="Spectrum Plot"> -->
diff --git a/flask_app/templates/preview.html b/flask_app/templates/preview.html
@@ -0,0 +1,13 @@
+{% if sheets %}
+<form action="/preview" method="post">
+    <select name="sheet">
+        {% for sheet in sheets %}
+            <option value="{{ sheet }}">{{ sheet }}</option>
+        {% endfor %}
+    </select>
+    <input type="submit" value="Preview">
+</form>
+{% endif %}
+{% if df %}
+{{ df | safe }}
+{% endif %}
diff --git a/flask_app/templates/upload_data.html b/flask_app/templates/upload_data.html
@@ -0,0 +1,4 @@
+<form action="/upload" method="post" enctype="multipart/form-data">
+    <input type="file" name="file" accept=".xls,.xlsx">
+    <input type="submit" value="Upload">
+</form>
diff --git a/library_spectra_validation/.gitignore b/library_spectra_validation/.gitignore
diff --git a/streamlit_app/requirements.txt → requirements.txt b/streamlit_app/requirements.txt → requirements.txt
diff --git a/streamlit_app/FAIR_MS_Library_Editor.py b/streamlit_app/FAIR_MS_Library_Editor.py
diff --git a/streamlit_app/README.md b/streamlit_app/README.md
diff --git a/streamlit_app/assets/.empty b/streamlit_app/assets/.empty
diff --git a/streamlit_app/config.json b/streamlit_app/config.json
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,3 @@


		"# This is the creation and curation wizard for FAIR MS Libraries."