update app

Author: dsmutin

README.md

@@ -17,11 +17,15 @@ At the core of PROBEst is an AI-enhanced workflow that combines Primer3 for init
 ```bash
 git clone https://github.com/CTLab-ITMO/PROBEst.git
 cd PROBEst
-conda env create -f environment.yml
-conda activate probest
 python setup.py install
 ```
 
+## Dependencies
+```bash
+conda install bioconda::primer3
+conda install bioconda::blast
+```
+
 ### Validate installation
 
 ```bash

app/app.py

@@ -360,7 +360,7 @@ def process():
         # Optional parameters
         args_dict['threads'] = request.form.get('threads', '1')
         args_dict['algorithm'] = request.form.get('algorithm', 'FISH')
-        args_dict['iterations'] = request.form.get('iterations', '5')
+        args_dict['iterations'] = request.form.get('iterations', '10')
         args_dict['top'] = request.form.get('top', '10')
         args_dict['mutation_rate'] = request.form.get('mutation_rate', '0.05')
         args_dict['indel_rate'] = request.form.get('indel_rate', '0.05')

app/static/ctlab_probest.jpg

@@ -5,6 +5,8 @@ document.addEventListener('DOMContentLoaded', function() {
     const resultsSection = document.getElementById('resultsSection');
     const resultsContent = document.getElementById('resultsContent');
     const downloadBtn = document.getElementById('downloadBtn');
+    const statusText = document.getElementById('statusText');
+    const progressContainer = document.getElementById('progressContainer');
 
     form.addEventListener('submit', async function(e) {
         e.preventDefault();
@@ -13,6 +15,8 @@ document.addEventListener('DOMContentLoaded', function() {
         loadingOverlay.style.display = 'flex';
         resultsSection.style.display = 'none';
         submitBtn.disabled = true;
+        statusText.textContent = 'Waiting to finish...';
+        progressContainer.style.display = 'block';
 
         // Create FormData
         const formData = new FormData(form);
@@ -39,6 +43,7 @@ document.addEventListener('DOMContentLoaded', function() {
         } finally {
             loadingOverlay.style.display = 'none';
             submitBtn.disabled = false;
+            progressContainer.style.display = 'none';
         }
     });
 
@@ -78,6 +83,7 @@ document.addEventListener('DOMContentLoaded', function() {
 
     function displayResults(topProbes, totalProbes) {
         resultsContent.innerHTML = '';
+        statusText.textContent = 'Completed.';
 
         // Add summary
         const summary = document.createElement('div');
@@ -148,6 +154,7 @@ document.addEventListener('DOMContentLoaded', function() {
         resultsContent.appendChild(errorDiv);
         resultsSection.style.display = 'block';
         resultsSection.scrollIntoView({ behavior: 'smooth' });
+        statusText.textContent = 'Error during generation.';
     }
 });
 

app/static/ctlab_probest_white.png

@@ -6,7 +6,7 @@
 
 body {
     font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, 'Helvetica Neue', Arial, sans-serif;
-    background: linear-gradient(135deg, #667eea 0%, #764ba2 100%);
+    background: linear-gradient(135deg, #0f5390 0%, #127ed1 100%);
     min-height: 100vh;
     padding: 20px;
     color: #333;
@@ -21,11 +21,31 @@ body {
     overflow: hidden;
 }
 
+.logo-title {
+    display: flex;
+    align-items: center;
+    gap: 16px;
+}
+
+.logo {
+    width: 56px;
+    height: 56px;
+    border-radius: 12px;
+    background: rgba(255, 255, 255, 0.15);
+    padding: 6px;
+    object-fit: contain;
+}
+
 header {
-    background: linear-gradient(135deg, #667eea 0%, #764ba2 100%);
+    background: linear-gradient(135deg, #0f5390 0%, #127ed1 100%);
     color: white;
-    padding: 40px;
-    text-align: center;
+    padding: 24px 40px;
+}
+
+.header-inner {
+    display: flex;
+    align-items: center;
+    justify-content: space-between;
 }
 
 header h1 {
@@ -51,7 +71,7 @@ header h1 {
 .form-section h2 {
     font-size: 1.5em;
     margin-bottom: 20px;
-    color: #667eea;
+    color: #0f5390;
     font-weight: 600;
 }
 
@@ -97,15 +117,15 @@ input[type="file"] {
 }
 
 input[type="file"]:hover {
-    border-color: #667eea;
+    border-color: #0f5390;
 }
 
 input[type="text"]:focus,
 input[type="number"]:focus,
 select:focus {
     outline: none;
-    border-color: #667eea;
-    box-shadow: 0 0 0 3px rgba(102, 126, 234, 0.1);
+    border-color: #0f5390;
+    box-shadow: 0 0 0 3px rgba(15, 83, 144, 0.12);
 }
 
 small {
@@ -117,8 +137,55 @@ small {
 
 .form-actions {
     padding: 30px 40px;
-    text-align: center;
     background: #f8f9fa;
+    border-top: 1px solid #e0e0e0;
+}
+
+.action-row {
+    display: flex;
+    align-items: center;
+    justify-content: flex-end;
+    gap: 24px;
+}
+
+.status-area {
+    display: flex;
+    flex-direction: column;
+    align-items: flex-start;
+    gap: 6px;
+}
+
+.status-text {
+    font-size: 0.9em;
+    color: #555;
+    min-height: 1.2em;
+}
+
+.progress-container {
+    width: 180px;
+    height: 6px;
+    border-radius: 999px;
+    background: #e1e9f2;
+    overflow: hidden;
+}
+
+.progress-bar {
+    width: 40%;
+    height: 100%;
+    background: linear-gradient(90deg, #0f5390, #127ed1);
+    animation: progress-indeterminate 1.2s infinite;
+}
+
+@keyframes progress-indeterminate {
+    0% {
+        transform: translateX(-100%);
+    }
+    50% {
+        transform: translateX(0%);
+    }
+    100% {
+        transform: translateX(100%);
+    }
 }
 
 .btn {
@@ -134,13 +201,13 @@ small {
 }
 
 .btn-primary {
-    background: linear-gradient(135deg, #667eea 0%, #764ba2 100%);
+    background: linear-gradient(135deg, #0f5390 0%, #127ed1 100%);
     color: white;
 }
 
 .btn-primary:hover {
     transform: translateY(-2px);
-    box-shadow: 0 10px 20px rgba(102, 126, 234, 0.3);
+    box-shadow: 0 10px 20px rgba(15, 83, 144, 0.35);
 }
 
 .btn-primary:active {
@@ -160,11 +227,11 @@ small {
 .results-section {
     padding: 40px;
     background: #f8f9fa;
-    border-top: 3px solid #667eea;
+    border-top: 3px solid #0f5390;
 }
 
 .results-section h2 {
-    color: #667eea;
+    color: #0f5390;
     margin-bottom: 30px;
     font-size: 2em;
 }
@@ -188,7 +255,7 @@ small {
 }
 
 .probe-card h3 {
-    color: #667eea;
+    color: #0f5390;
     margin-bottom: 15px;
     font-size: 1.3em;
 }
@@ -227,7 +294,7 @@ small {
     font-size: 14px;
     word-break: break-all;
     color: #2c3e50;
-    border-left: 4px solid #667eea;
+    border-left: 4px solid #0f5390;
 }
 
 .results-actions {
@@ -280,11 +347,68 @@ small {
 
 .success-message {
     background: #efe;
-    color: #3c3;
+    color: #248a3d;
     padding: 15px;
     border-radius: 8px;
     margin-bottom: 20px;
-    border-left: 4px solid #3c3;
+    border-left: 4px solid #248a3d;
+}
+
+.advanced-section {
+    margin: 0 40px 30px 40px;
+    border-radius: 12px;
+    border: 1px dashed #c5d3e3;
+    background: #f7f9fc;
+    padding: 0 0 10px 0;
+}
+
+.advanced-section > summary {
+    padding: 14px 20px;
+    cursor: pointer;
+    font-weight: 600;
+    color: #0f5390;
+    list-style: none;
+}
+
+.advanced-section[open] > summary {
+    border-bottom: 1px solid #dde5f0;
+}
+
+.advanced-section > summary::marker,
+.advanced-section > summary::-webkit-details-marker {
+    display: none;
+}
+
+.advanced-section > summary::before {
+    content: '▸';
+    display: inline-block;
+    margin-right: 8px;
+    transition: transform 0.2s ease;
+}
+
+.advanced-section[open] > summary::before {
+    transform: rotate(90deg);
+}
+
+.advanced-section .form-section {
+    padding: 20px 20px 10px 20px;
+}
+
+.footer {
+    padding: 20px 40px 24px 40px;
+    font-size: 0.9em;
+    color: #666;
+    border-top: 1px solid #e0e0e0;
+    background: #fff;
+}
+
+.footer a {
+    color: #0f5390;
+    text-decoration: none;
+}
+
+.footer a:hover {
+    text-decoration: underline;
 }
 
 @media (max-width: 768px) {
@@ -294,11 +418,16 @@ small {
     }
 
     header {
-        padding: 20px;
+        padding: 16px 20px;
     }
 
     header h1 {
-        font-size: 1.8em;
+        font-size: 1.6em;
+    }
+
+    .logo {
+        width: 44px;
+        height: 44px;
     }
 
     .form-section {
@@ -308,6 +437,24 @@ small {
     .form-row {
         grid-template-columns: 1fr;
     }
+
+    .advanced-section {
+        margin: 0 20px 20px 20px;
+    }
+
+    .form-actions {
+        padding: 20px;
+    }
+
+    .action-row {
+        flex-direction: column-reverse;
+        align-items: stretch;
+        gap: 12px;
+    }
+
+    .status-area {
+        align-items: flex-start;
+    }
 }