[update] html output from GUI in background possible but maybe not optimal (needs display to work in bg)

parameters.yaml

@@ -1,6 +1,5 @@
 # Parameters file for Surveillance Bot
 datapath: '/data/SDS/'      # SC3 Datapath
-outpath_html: '/home/marcel/tmp/survBot_out.html' # output of HTML table
 networks: ['1Y', 'HA']
 stations: '*'
 locations: '*'

submit_bot.sh

@@ -2,15 +2,20 @@
 ulimit -s 8192
 
 #$ -l low
-#$ -l os=*stretch
+#$ -l h_vmem=5G
 #$ -cwd
 #$ -pe smp 1
-##$ -q "*@minos15"
+#$ -N survBot_bg
 
-export PYTHONPATH="$PYTHONPATH:/home/marcel/git/"
 export PYTHONPATH="$PYTHONPATH:/home/marcel/git/code_base/"
 
 source /opt/anaconda3/etc/profile.d/conda.sh
 conda activate py37
 
-python survBot.py
+# environment variables for numpy to prevent multi threading
+export MKL_NUM_THREADS=1
+export NUMEXPR_NUM_THREADS=1
+export OMP_NUM_THREADS=1
+
+
+python survBotGUI.py -html '/home/marcel/public_html/survBot_out.html' --background

survBot.py

@@ -1,4 +1,5 @@
-#! /usr/bin/env python
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
 
 __version__ = '0.1'
 __author__ = 'Marcel Paffrath'
@@ -510,7 +511,7 @@ class StationQC(object):
                 self.warn(key=key,
                           message=f'Trace {trace.get_id()}: '
                                   f'Voltage below {pb_ok}V {len(under)} times. '
-                                  f'Mean voltage: {np.mean(voltage)}'
+                                  f'Mean voltage: {np.mean(voltage):.2}'
                                   + self.get_last_occurrence_timestring(trace, under),
                           status_message='WARN ({})'.format(n_occurrences))
 

survBotGUI.py

@@ -1,4 +1,5 @@
-#! /usr/bin/env python
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
 """
 GUI overlay for the main survBot to show quality control of different stations specified in parameters.yaml file.
 """
@@ -77,7 +78,7 @@ class Thread(QtCore.QThread):
 
 
 class MainWindow(QtWidgets.QMainWindow):
-    def __init__(self, parameters='parameters.yaml', dt_thresh=(300, 1800)):
+    def __init__(self, parameters='parameters.yaml', outpath_html=None, dt_thresh=(300, 1800)):
         """
         Main window of survBot GUI.
         :param parameters: Parameters dictionary file (yaml format)
@@ -98,6 +99,7 @@ class MainWindow(QtWidgets.QMainWindow):
         self.last_mouse_loc = None
         self.status_message = ''
         self.starttime = UTCDateTime()
+        self.outpath_html = outpath_html
 
         # setup main layout of the GUI
         self.main_layout = QtWidgets.QVBoxLayout()
@@ -184,12 +186,12 @@ class MainWindow(QtWidgets.QMainWindow):
         return super(QtWidgets.QMainWindow, self).eventFilter(object, event)
 
     def write_html_table(self):
-        fnout = self.parameters.get('outpath_html')
+        fnout = self.outpath_html
         if not fnout:
             return
         try:
             with open(fnout, 'w') as outfile:
-                write_html_header(outfile)
+                write_html_header(outfile, self.refresh_period)
                 #write_html_table_title(outfile, self.parameters)
                 init_html_table(outfile)
                 nrows = self.table.rowCount()
@@ -272,6 +274,10 @@ class MainWindow(QtWidgets.QMainWindow):
 
     def fill_table(self):
         """ Fills the table with most recent information. Executed after execute_qc thread is done or on refresh. """
+
+        # fill status bar first with new time
+        self.fill_status_bar()
+
         for col_ind, check_key in enumerate(self.survBot.keys):
             for row_ind, st_id in enumerate(self.survBot.station_list):
                 status_dict, detailed_dict = self.survBot.analysis_results.get(st_id)
@@ -501,9 +507,15 @@ class SendSMSWidget(QtWidgets.QDialog):
 
 
 if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description='Call survBot GUI')
+    parser.add_argument('-html', dest='html_filename', default=None, help='filename for HTML output')
+    parser.add_argument('--background', dest='background', default=False, action='store_true', help='run in background')
+    args = parser.parse_args()
+
     program_path = sys.path[0]
     parameters = os.path.join(program_path, 'parameters.yaml')
     app = QtWidgets.QApplication([])
-    window = MainWindow(parameters=parameters)
+    window = MainWindow(parameters=parameters, outpath_html=args.html_filename)
+    if not args.background:
         window.showMaximized()
     sys.exit(app.exec_())

write_utils.py

@@ -7,15 +7,17 @@ def write_html_table_title(fobj, parameters):
 def write_html_text(fobj, text):
     fobj.write(f'<p>{text}</p>\n')
 
-def write_html_header(fobj):
+def write_html_header(fobj, refresh_rate=10):
     header = ['<!DOCTYPE html>',
               '<html>',
-              '<style>',
-              'table, th, td {',
-              'border:1px solid black;',
-              '}',
-              '</style>',
+              f'<meta http-equiv="refresh" content="{refresh_rate}" >',
+              '<meta charset="utf-8">',
               '<body>']
+    # style = ['<style>',
+    #           'table, th, td {',
+    #           'border:1px solid black;',
+    #           '}',
+    #           '</style>',]
     for item in header:
         fobj.write(item + '\n')
 
@@ -32,14 +34,16 @@ def write_html_footer(fobj):
         fobj.write(item + '\n')
 
 def write_html_row(fobj, items, html_key='td'):
-    fobj.write('<tr>\n')
+    default_space = '  '
+    fobj.write(default_space + '<tr>\n')
     for item in items:
         text = item.text()
+        tooltip = item.toolTip()
         color = item.backgroundColor().name()
         # fix for black background of headers
         color = '#e6e6e6' if color == '#000000' else color
-        fobj.write(f'<{html_key} bgcolor="{color}">' + text + f'</{html_key}>\n')
-    fobj.write('</tr>\n')
+        fobj.write(2 * default_space + f'<{html_key} bgcolor="{color}" title="{tooltip}">' + text + f'</{html_key}>\n')
+    fobj.write(default_space + '</tr>\n')
 
 def get_print_title_str(parameters):
     timespan = parameters.get('timespan') * 24 * 3600