add progress bars to output

luponzo86 · Nov 14, 2019 · ab3b4f3 · ab3b4f3
1 parent 52085b1
commit ab3b4f3
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Showing 5 changed files with 27 additions and 13 deletions.
diff --git a/html/navbar.php b/html/navbar.php
@@ -23,12 +23,12 @@
     <!-- left navbar -->
     <ul class="navbar-nav mr-auto">
       <li class="nav-item <?php echo $a['sat_mutagen'][0]?>">
-        <a class="nav-link" href="sat_mutagen.php">Saturation mutagenesis
+        <a class="nav-link" href="sat_mutagen.php">Run saturation mutagenesis
           <?php echo $a['sat_mutagen'][1]?>
         </a>
       </li>
       <li class="nav-item <?php echo $a['batch_query'][0]?>">
-        <a class="nav-link" href="batch_query.php">Batch query
+        <a class="nav-link" href="batch_query.php">Query single variants
           <?php echo $a['batch_query'][1]?>
         </a>
       </li>

diff --git a/index.php b/index.php
@@ -16,7 +16,8 @@
   <div class="jumbotron">
     <div class="container text-center">
       <h1>Rhapsody</h1>
-      computationally predicting effects of saturation mutagenesis
+      predicting the impact of human missense variants <br>
+      based on proteins' sequence, structure and dynamics
     </div>
   </div>
 
@@ -54,7 +55,7 @@ class="img-responsive border rounded" style="width:80%" alt="">
       </div>
 
       <div class="col-md py-2">
-        <h5>Batch query of mixed variants </h5>
+        <h5>Batch query of individual variants </h5>
         <small class="form-text text-muted px-5">
           obtain predictions for a list of human missense variants from
           various protein sequences. See an example

diff --git a/src/php/get_status.php b/src/php/get_status.php
@@ -14,16 +14,20 @@ function isProcessRunning($f) {
   return posix_kill((int)$pid, 0);
 }
 
-function tailShell($filepath, $lines = 13) {
+function tailShell($filepath, $lines = 10) {
   ob_start();
   passthru('tail -' . $lines . ' ' . escapeshellarg($filepath));
   return trim(ob_get_clean());
 }
 
 function returnStatus($status="") {
-  $logFile  = 'rhapsody-log.txt';
+  $logFile = 'rhapsody-log.txt';
+  $statusFile = 'rhapsody-status.txt';
   if ( file_exists($logFile) ) {
-    $logTail = tailShell($logFile);
+    $logTail = tailShell($logFile, 5);
+    if ( file_exists($statusFile) ) {
+      $logTail .= "\r\n\r\n" . tailShell($statusFile, 1);
+    }
   }
   else {
     $logTail = "";

diff --git a/src/python/protocols.py b/src/python/protocols.py
@@ -1,9 +1,17 @@
 import os
 import rhapsody as rd
 
+
 FIGURE_MAX_WIDTH = 100
 
 
+# define Rhapsody keyword arguments
+kwargs = {}
+for i, step in enumerate(['Uniprot', 'PDB', 'Pfam']):
+    kwargs[f'status_file_{step}'] = f'rhapsody-status.txt'
+    kwargs[f'status_prefix_{step}'] = f'STEP {i+1}: '
+
+
 def sat_mutagen():
 
     # import data
@@ -22,9 +30,9 @@ def sat_mutagen():
     # run RHAPSODY
     if os.path.isfile('pph2-full.txt'):
         rh = rd.rhapsody('pph2-full.txt', query_type='PolyPhen2',
-                         custom_PDB=pdb, log=False)
+                         custom_PDB=pdb, log=False, **kwargs)
     else:
-        rh = rd.rhapsody(input_query, custom_PDB=pdb, log=False)
+        rh = rd.rhapsody(input_query, custom_PDB=pdb, log=False, **kwargs)
 
     # write predictions on PDB file(s)
     rh.writePDBs()
@@ -51,8 +59,9 @@ def batch_query():
 
     # run RHAPSODY
     if os.path.isfile('pph2-full.txt'):
-        rh = rd.rhapsody('pph2-full.txt', query_type='PolyPhen2', log=False)
+        rh = rd.rhapsody(
+            'pph2-full.txt', query_type='PolyPhen2', log=False, **kwargs)
     else:
-        rh = rd.rhapsody('input-batch_query.txt', log=False)
+        rh = rd.rhapsody('input-batch_query.txt', log=False, **kwargs)
 
     return rh
diff --git a/status.php b/status.php
@@ -56,7 +56,7 @@
           </small></p>
         </div>
         <div id="logdiv">
-          <textarea class="form-control" id="log_update" cols="100" rows="14" readonly
+          <textarea class="form-control" id="log_update" cols="100" rows="7" readonly
                     style="font-family:monospace; font-size:12px; white-space:pre-wrap">
             ...
           </textarea>
@@ -92,7 +92,7 @@ function check_status() {
         setTimeout(check_status, 100);
       }
       else if (job_status == "running...") {
-        setTimeout(check_status, 1000);
+        setTimeout(check_status, 300);
       }
       else if (job_status == "completed") {
         $("#infodiv").hide();