[update] README.md

- add section on running survBot in a Docker container
- add explaination of mal server settings in parameters.yaml

Dockerfile

@@ -0,0 +1,40 @@
+FROM python:3
+
+# metadata
+LABEL maintainer="Kasper D. Fischer <kasper.fischer@rub.de>"
+LABEL version="0.2-docker"
+LABEL description="Docker image for the survBot application"
+
+# install required system packages
+RUN apt update && apt install -y bind9-host iputils-ping
+
+# create user and group and home directory
+RUN groupadd -r survBot && useradd -r -g survBot survBot
+RUN mkdir -p /home/survBot && chown -R survBot:survBot /home/survBot
+
+# change working directory
+WORKDIR /usr/src/app
+
+# install required python packages
+RUN --mount=type=bind,source=requirements.txt,target=/tmp/requirements.txt \
+    pip install --no-cache-dir --requirement /tmp/requirements.txt
+
+# copy application files
+COPY survBot.py utils.py write_utils.py LICENSE README.md ./
+
+# copy configuration files
+VOLUME /usr/src/app/conf
+COPY parameters.yaml mailing_list.yam[l] simulate_fail.jso[n] conf/
+RUN ln -s conf/simulate_fail.json simulate_fail.json
+
+# copy www files
+VOLUME /usr/src/app/www
+COPY logo.pn[g] stylesheets/desktop.css stylesheets/mobile.css www/
+RUN ln -s www/survBot_out.html www/index.html
+
+# change ownership of working directory
+RUN chown -R survBot:survBot /usr/src/app
+
+# run the application as user survBot
+USER survBot
+CMD [ "python", "./survBot.py", "-html", "www", "-parfile", "conf/parameters.yaml" ]

README.md

@@ -40,7 +40,38 @@ The GUI can be loaded via
 python survBotGui.py
 ```
 
+### Docker
+
+To run the program in a Docker container, first build the image:
+
+```shell script
+docker build -t survbot .
+```
+
+Then run the container:
+
+```shell script
+docker run -v /path/to/conf-dir:/usr/src/app/conf -v /path/to/output:/usr/src/app/www survbot
+```
+
+The directory `/path/to/conf-dir` should contain the `parameters.yaml` file, and the directory `/path/to/output` will contain the output HTML files.
+
+### Configuration of the e-mail server settings
+
+The e-mail server settings can be configured in the `parameters.yaml` file. The following settings are available:
+
+- `mailserver`: the address of the mail server
+- `auth_type`: the authentication type for the mail server (`None`, `SSL`, `TLS`)
+- `port`: the port of the mail server
+- `user`: the username for the mail server (if required)
+- `password`: the password for the mail server (if required)
+
+The `user` and `password` fields are optional, and can be left empty if the mail server does not require authentication. The `auth_type` field can be set to `None` if no authentication is required, `SSL` if the mail server requires SSL authentication, or `TLS` if the mail server requires TLS authentication. If the `user` or `password` fileds are set to `Docker` ore `ENV` the program will try to read the values from the docker secrets `mail_user` and `mail_password` or environment variables `MAIL_USER` and `MAIL_PASSWORD` respectively. Docker secrets are only available in Docker Swarm mode, i.e. if the program is run as a service.
+
 ## Version Changes
+
+### 0.2
+
 - surveillance of mass, clock and gaps
 - individual mailing lists for different stations
 - html mail with recent status information
@@ -48,8 +79,14 @@ python survBotGui.py
 - restructured parameter file
 - recognize if PBox is disconnected
 
+### 0.2-docker
+
+- added Dockerfile for easy deployment
+- added more settings for connection to a mail server
+
 ## Staff
 
 Original author: M.Paffrath (marcel.paffrath@rub.de)
+Contributions by: Kasper D. Fischer (kasper.fischer@rub.de)
 
-June 2023
+Jan 2025

__init__.py

@@ -1,3 +1,3 @@
 # survBot is a small program used to track station quality channels of DSEBRA stations via PowBox output
 # over SOH channels by analysing contents of a Seiscomp3 datapath.
-__version__ = "0.2"
+__version__ = "0.2-docker"

mailing_list.yaml

@@ -2,7 +2,7 @@
 # "mail.address@provider.com, mail.address2@provider2.com":
 #   - 1Y.GR01
 #   - 1Y.GR02
-# "mail.address3@provder.com":
+# "mail.address3@provider.com":
 #   - 1Y.GR03
 
 #"kasper.fischer@rub.de":

parameters.yaml

@@ -1,18 +1,19 @@
 # Parameters file for Surveillance Bot
-datapath: "/data/SDS/"                    # SC3 Datapath
+datapath: "/data/SDS/"                    # path to SDS data archive
 networks: ["1Y", "HA", "MK"]              # select networks, list or str
 stations: "*"                             # select stations, list or str
 locations: "*"                            # select locations, list or str
-stations_blacklist: ["TEST", "EREA", "DOMV"]      # exclude these stations
+stations_blacklist: ["ATHR", "DOMV", "EREA", "GR19", "GR27", "HAVD", "LAKA", "LFKM", "TEST"]      # exclude these stations
 networks_blacklist: []                    # exclude these networks
 interval: 60               # Perform checks every x seconds
 n_track: 360               # wait n_track * intervals before performing an action (i.e. send mail/end highlight status)
-timespan: 3                # Check data of the recent x days
+timespan: 7                # Check data of the recent x days
-verbosity: 0               # verbosity flag
+verbosity: 0               # verbosity flag for program console output (not logging)
+logging_level: WARN        # set logging level (info, warning, debug)
 track_changes: True        # tracks all changes since GUI startup by text highlighting (GUI only)
 warn_count: False          # show number of warnings and errors in table
 min_sample: 5              # minimum samples for raising Warn/FAIL
-dt_thresh: [300, 1800]     # threshold (s) for timing delay colourisation (yellow/red)
+dt_thresh: [300, 1800]     # threshold (s) for timing delay colorization (yellow/red)
 html_figures: True         # Create html figure directory and links
 reread_parameters: True    # reread parameters file (change parameters on runtime, not for itself/GUI refresh/datapath)
 
@@ -39,6 +40,7 @@ POWBOX:
 THRESHOLDS:
   pb_thresh: 0.2               # Threshold for PowBox Voltage check +/- (V)
   max_temp: 50                 # max temperature for temperature warning
+  critical_temp: 65            # max temperature for critical warning (fail)
   low_volt: 12                 # min voltage for low voltage warning
   high_volt: 14.8              # max voltage for over voltage warning
   unclassified: 5              # min voltage samples not classified for warning
@@ -54,7 +56,8 @@ THRESHOLDS:
 #
 # For each channel a factor 'unit' for unit conversion (e.g. to SI) can be provided, as well as a 'name'
 # and 'ticks' [ymin, ymax, ystep] for plotting.
-# 'warn' and 'fail' plot horizontal lines in corresponding colors (can be str in TRESHOLDS, int/float or iterable)
+# 'warn' and 'fail' plot horizontal lines in corresponding colors (can be str in THRESHOLDS, int/float or iterable)
+# keyword "pb_SOH2" or "pb_SOH3" can be used to extract warning values from above POWBOX parameter definition
 #
 # 'transform' can be provided for plotting to perform arithmetic operations in given order, e.g.:
 #  transform: - ["*", 20]
@@ -73,12 +76,12 @@ CHANNELS:
     unit: 1e-6
     name: "PowBox 230V/12V (V)"
     ticks: [0, 5, 1]
-    warn: [2, 3, 4, 4.5, 5]
+    warn: "pb_SOH2"
   EX3:
     unit: 1e-6
     name: "PowBox Router/Charger (V)"
     ticks: [0, 5, 1]
-    warn: [2, 2.5, 3, 4, 5]
+    warn: "pb_SOH3"
   VEI:
     unit: 1e-3
     name: "Datalogger (V)"
@@ -121,6 +124,7 @@ add_links:
   # for example: slmon: {"URL": "path/{nw}_{st}.html", "text": "link"}
   slmon: {"URL": "../slmon/{nw}_{st}.html", "text": "show"}
   24h-plot: {"URL": "../scheli/{nw}/{st}.png", "text": "plot"}
+  ppsd: {"URL": "../ppsd/{nw}.{st}.html", "text": "show"}
 
 # add station-independent links below html table (list items separated with -)
 add_global_links:
@@ -129,14 +133,22 @@ add_global_links:
      "URL": "https://fdsnws.geophysik.ruhr-uni-bochum.de/map/?lat=39.5&lon=21&zoom=7&baselayer=mapnik"}
 
 # html logo at page bottom (path relative to html directory)
-html_logo: "figures/Logo_RUB_BLAU_rgb.png"
+html_logo: "logo.png"
 
 # E-mail notifications
 EMAIL:
-  mailserver: "localhost"
+  # specify mail server and credentials
+  # port, auth_type, user and password are only required if mailserver is not set to "localhost"
+  # user and password can be set to "ENV" or "DOCKER" to read from environment variables or docker secrets
+  mailserver: "smtp.rub.de"           # mail server
+  auth_type: "SSL"                    # mail authentication type, can be "SSL", "TLS" or "None"
+  port: 465                           # mail port, default 465 for SSL, 587 for TLS
+  user: "DOCKER"                      # mail user, read from environment variable if set to "ENV" or from docker secret if set to "DOCKER"
+  password: "DOCKER"                  # mail password, read from environment variable if set to "ENV" or from docker secret if set to "DOCKER"
+  # specify mail recipients, sender and blacklists
   addresses: ["marcel.paffrath@rub.de", "kasper.fischer@rub.de"]  # list of mail addresses for info mails
-  sender: "webmaster@geophysik.ruhr-uni-bochum.de" # mail sender
+  sender: "RUB SeisObs <seisobs@ruhr-uni-bochum.de>"              # mail sender
-  stations_blacklist: ['GR33']                     # do not send emails for specific stations
+  stations_blacklist: []                                          # do not send emails for specific stations
-  networks_blacklist: []                           # do not send emails for specific network
+  networks_blacklist: []                                          # do not send emails for specific network
   # specify recipients for single stations in a yaml: key = email-address, val = station list (e.g. [1Y.GR01, 1Y.GR02])
-  external_mail_list: "mailing_list.yaml"
+  external_mail_list: "conf/mailing_list.yaml"

requirements.txt

@@ -0,0 +1,36 @@
+Brotli==1.1.0
+certifi==2025.1.31
+cffi==1.17.1
+charset-normalizer==3.4.1
+contourpy==1.3.1
+cycler==0.12.1
+decorator==5.2.1
+fonttools==4.56.0
+greenlet==3.1.1
+h2==4.2.0
+hpack==4.1.0
+hyperframe==6.1.0
+idna==3.10
+kiwisolver==1.4.8
+lxml==5.3.1
+matplotlib==3.8.4
+munkres==1.1.4
+numpy==1.26.4
+obspy==1.4.1
+packaging==24.2
+pillow==11.1.0
+pip==25.0.1
+pycparser==2.22
+pyparsing==3.2.1
+PySocks==1.7.1
+python-dateutil==2.9.0.post0
+PyYAML==6.0.2
+requests==2.32.3
+scipy==1.15.2
+setuptools==75.8.2
+six==1.17.0
+SQLAlchemy==1.4.54
+unicodedata2==16.0.0
+urllib3==2.3.0
+wheel==0.45.1
+zstandard==0.23.0

stylesheets/desktop.css

@@ -1,6 +1,5 @@
 body {
     background-color: #ffffff;
-    place-items: center;
     text-align: center;
     padding-bottom: 30px;
     font-family: "Helvetica", "sans-serif";
@@ -17,7 +16,7 @@ td {
 }
 
 th {
-    background-color: #999;
+    background-color: #17365c;
     color: #fff;
     border-radius: 2px;
     padding: 3px 1px;

stylesheets/mobile.css

@@ -1,6 +1,5 @@
 body {
     background-color: #ffffff;
-    place-items: center;
     text-align: center;
     padding-bottom: 30px;
     font-family: "Helvetica", "sans-serif";
@@ -17,7 +16,7 @@ td {
 }
 
 th {
-    background-color: #999;
+    background-color: #17365c;
     color: #fff;
     border-radius: 3px;
     padding: 10px, 2px;

submit_bot.sh

@@ -1,19 +1,24 @@
 #!/bin/bash
-ulimit -s 8192
 
 #$ -l low
-#$ -l h_vmem=5G
+#$ -l h_vmem=2.5G
+#$ -l mem=2.5G
+#$ -l h_stack=INFINITY
 #$ -cwd
 #$ -pe smp 1
-#$ -N survBot_bg
+#$ -binding linear:1
-#$ -l os=*stretch
+#$ -N survBot
+#$ -o /data/www/~kasper/survBot/survBot_bg.log
+#$ -e /data/www/~kasper/survBot/survBot_bg.err
+#$ -m e
+#$ -M kasper.fischer@rub.de
 
 source /opt/anaconda3/etc/profile.d/conda.sh
-conda activate py37
+conda activate survBot
 
 # environment variables for numpy to prevent multi threading
 export MKL_NUM_THREADS=1
 export NUMEXPR_NUM_THREADS=1
 export OMP_NUM_THREADS=1
 
-python survBot.py -html '/data/www/~marcel/'
+python survBot.py -html '/data/www/~kasper/survBot'

survBot.py

@@ -1,12 +1,13 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-__version__ = '0.1'
+__version__ = '0.2-docker'
-__author__ = 'Marcel Paffrath'
+__author__ = 'Marcel Paffrath <marcel.paffrath@rub.de>'
 
 import os
 import io
 import copy
+import logging
 import traceback
 import yaml
 import argparse
@@ -22,7 +23,8 @@ from obspy.clients.filesystem.sds import Client
 
 from write_utils import get_html_text, get_html_link, get_html_row, html_footer, get_html_header, get_print_title_str, \
     init_html_table, finish_html_table, get_mail_html_header, add_html_image
-from utils import get_bg_color, get_font_color, modify_stream_for_plot, set_axis_yticks, set_axis_color, plot_axis_thresholds
+from utils import get_bg_color, get_font_color, modify_stream_for_plot, set_axis_yticks, set_axis_color, plot_axis_thresholds, \
+    connect_to_mail_server
 
 try:
     import smtplib
@@ -31,27 +33,48 @@ try:
 
     mail_functionality = True
 except ImportError:
-    print('Could not import smtplib or mail. Disabled sending mails.')
+    logging.warning('Could not import smtplib or mail. Disabled sending mails.')
     mail_functionality = False
 
 pjoin = os.path.join
 UP = "\x1B[{length}A"
 CLR = "\x1B[0K"
-deg_str = '\N{DEGREE SIGN}C'
+DEG_STR = '\N{DEGREE SIGN}C'
 
 
-def read_yaml(file_path, n_read=3):
+def read_yaml(file_path: str, n_read: int = 3) -> dict:
     for index in range(n_read):
         try:
             with open(file_path, "r") as f:
                 params = yaml.safe_load(f)
+            set_logging_level(params)
         except Exception as e:
-            print(f'Could not read parameters file: {e}.\nWill try again {n_read - index - 1} time(s).')
+            logging.warning(f'Could not read parameters file: {e}.\nWill try again {n_read - index - 1} time(s).')
             time.sleep(10)
             continue
         return params
 
 
+def set_logging_level(params: dict) -> None:
+    logging_levels = {'info': logging.INFO,
+                      'warning': logging.WARNING,
+                      'warn': logging.WARNING,
+                      'debug': logging.DEBUG,
+                      'error': logging.ERROR,
+                      'critical': logging.CRITICAL}
+    logging_level_str = params.get('logging_level')
+    if not logging_level_str:
+        logging.warning('Could not set logging level. Parameter not set')
+        return
+    if not isinstance(logging_level_str, str):
+        logging.warning(
+            f'Could not set logging level. Parameter logging_level = {logging_level_str} could not be interpreted.')
+        return
+    logging.info(f'Setting logging level to {logging_level_str}')
+    logging_level = logging_levels.get(logging_level_str.lower())
+    logging.basicConfig(level=logging_level)
+
+
 def nsl_from_id(nwst_id):
     nwst_id = get_full_seed_id(nwst_id)
     network, station, location = nwst_id.split('.')
@@ -115,7 +138,6 @@ class SurveillanceBot(object):
         self.parameters['channels'] = channels
         self.reread_parameters = self.parameters.get('reread_parameters')
         self.dt_thresh = [int(val) for val in self.parameters.get('dt_thresh')]
-        self.verbosity = self.parameters.get('verbosity')
         self.stations_blacklist = self.parameters.get('stations_blacklist')
         self.networks_blacklist = self.parameters.get('networks_blacklist')
         self.refresh_period = self.parameters.get('interval')
@@ -196,8 +218,7 @@ class SurveillanceBot(object):
         for filename in self.filenames:
             # if file already read and last modification time is the same as of last read operation: continue
             if self.filenames_read_last_modif.get(filename) == os.path.getmtime(filename):
-                if self.verbosity > 0:
+                logging.info(f'Continue on file {filename}')
-                    print('Continue on file', filename)
                 continue
             try:
                 # read only header of wf_data
@@ -207,7 +228,7 @@ class SurveillanceBot(object):
                     st_new = read(filename, dtype=float)
                 self.filenames_read_last_modif[filename] = os.path.getmtime(filename)
             except Exception as e:
-                print(f'Could not read file {filename}:', e)
+                logging.warning(f'Could not read file {filename}: {e}')
                 continue
             self.dataStream += st_new
         self.gaps = self.dataStream.get_gaps(min_gap=self.parameters['THRESHOLDS'].get('min_gap'))
@@ -234,8 +255,7 @@ class SurveillanceBot(object):
             if stream:
                 nsl = nsl_from_id(nwst_id)
                 station_qc = StationQC(self, stream, nsl, self.parameters, self.keys, qc_starttime,
-                                       self.verbosity, print_func=self.print,
+                                       print_func=self.print, status_track=self.status_track.get(nwst_id))
-                                       status_track=self.status_track.get(nwst_id))
                 analysis_print_result = station_qc.return_print_analysis()
                 station_dict = station_qc.return_analysis()
             else:
@@ -388,13 +408,13 @@ class SurveillanceBot(object):
                 st = modify_stream_for_plot(st, parameters=self.parameters)
                 st.plot(fig=fig, show=False, draw=False, block=False, equal_scale=False, method='full',
                         starttime=starttime, endtime=endtime)
-                # set_axis_ylabels(fig, self.parameters, self.verbosity)
+                # set_axis_ylabels(fig, self.parameters)
-                set_axis_yticks(fig, self.parameters, self.verbosity)
+                set_axis_yticks(fig, self.parameters)
                 set_axis_color(fig)
-                plot_axis_thresholds(fig, self.parameters, self.verbosity)
+                plot_axis_thresholds(fig, self.parameters)
             except Exception as e:
-                print(f'Could not generate plot for {nwst_id}:')
+                logging.error(f'Could not generate plot for {nwst_id}: {e}')
-                print(traceback.format_exc())
+                logging.error(traceback.format_exc())
             if len(fig.axes) > 0:
                 ax = fig.axes[0]
                 ax.set_title(f'Plot refreshed at (UTC) {UTCDateTime.now().strftime("%Y-%m-%d %H:%M:%S")}. '
@@ -402,7 +422,10 @@ class SurveillanceBot(object):
                 for ax in fig.axes:
                     ax.grid(True, alpha=0.1)
                 for fnout in fnames_out:
-                    fig.savefig(fnout, dpi=150., bbox_inches='tight')
+                    try:
+                        fig.savefig(fnout, dpi=150., bbox_inches='tight')
+                    except IOError as e:
+                        logging.warning('Could not save figure with IO error. Disk quota exceeded?\nError message: {e}')
                 # if needed save figure as virtual object (e.g. for mailing)
                 if save_bytes:
                     fnames_out[-1].seek(0)
@@ -458,7 +481,7 @@ class SurveillanceBot(object):
                 # add degree sign for temp
                 if check_key == 'temp':
                     if not type(message) in [str]:
-                        message = str(message) + deg_str
+                        message = str(message) + DEG_STR
 
                 html_class = self.get_html_class(hide_keys_mobile, status=status, check_key=check_key)
                 item = dict(text=str(message), tooltip=str(detailed_message), color=bg_color,
@@ -515,17 +538,16 @@ class SurveillanceBot(object):
                 # write footer with optional logo
                 logo_file = self.parameters.get('html_logo')
                 if not os.path.isfile(pjoin(self.outpath_html, logo_file)):
-                    print(f'Specified file {logo_file} not found.')
+                    logging.info(f'Specified file {logo_file} not found.')
                     logo_file = None
 
                 outfile.write(html_footer(footer_logo=logo_file))
 
         except Exception as e:
-            print(f'Could not write HTML table to {fnout}:')
+            logging.info(f'Could not write HTML table to {fnout}:')
-            print(traceback.format_exc())
+            logging.debug(traceback.format_exc())
 
-        if self.verbosity:
+        logging.info(f'Wrote html table to {fnout}')
-            print(f'Wrote html table to {fnout}')
 
     def update_status_message(self):
         timespan = timedelta(seconds=int(self.parameters.get('timespan') * 24 * 3600))
@@ -540,7 +562,6 @@ class SurveillanceBot(object):
         string.replace('\n', clear_end)
         print(string, end=clear_end, **kwargs)
         self.print_count += n_nl + 1  # number of newlines + actual print with end='\n' (no check for kwargs end!)
-        # print('pc:', self.print_count)
 
     def clear_prints(self):
         print(UP.format(length=self.print_count), end='')
@@ -548,14 +569,12 @@ class SurveillanceBot(object):
 
 
 class StationQC(object):
-    def __init__(self, parent, stream, nsl, parameters, keys, starttime, verbosity, print_func, status_track=None):
+    def __init__(self, parent, stream, nsl, parameters, keys, starttime, print_func, status_track=None):
         """
         Station Quality Check class.
         :param nsl: dictionary containing network, station and location (key: str)
         :param parameters: parameters dictionary from parameters.yaml file
         """
-        if status_track is None:
-            status_track = {}
         self.parent = parent
         self.stream = stream
         self.nsl = nsl
@@ -565,7 +584,6 @@ class StationQC(object):
         # make a copy of parameters object to prevent accidental changes
         self.parameters = copy.deepcopy(parameters)
         self.program_starttime = starttime
-        self.verbosity = verbosity
         self.last_active = False
         self.print = print_func
 
@@ -576,6 +594,8 @@ class StationQC(object):
             status_track = {}
         self.status_track = status_track
 
+        self.powbox_active = self.is_pbox_activated_check()
+
         self.start()
 
     @property
@@ -598,8 +618,7 @@ class StationQC(object):
         current_status = self.status_dict.get(key)
 
         # change this to something more useful, SMS/EMAIL/PUSH
-        if self.verbosity:
+        logging.info(f'{UTCDateTime()}: {detailed_message}')
-            self.print(f'{UTCDateTime()}: {detailed_message}', flush=False)
 
         # if error, do not overwrite with warning
         if current_status.is_error:
@@ -628,7 +647,8 @@ class StationQC(object):
         send_mail = False
         new_error = StatusError(count=count, show_count=self.parameters.get('warn_count'))
         if disc:
-            new_error.set_disconnected()
+            msg = disc if type(disc) == str else None
+            new_error.set_disconnected(msg)
         current_status = self.status_dict.get(key)
         if current_status.is_error:
             current_status.count += count
@@ -638,8 +658,7 @@ class StationQC(object):
             if self.status_track.get(key) and not self.status_track.get(key)[-1]:
                 self.parent.write_html_figure(self.nwst_id, save_bytes=True)
 
-        if self.verbosity:
+        logging.info(f'{UTCDateTime()}: {detailed_message}')
-            self.print(f'{UTCDateTime()}: {detailed_message}', flush=False)
 
         # do not send error mail if this is the first run (e.g. program startup) or state was already error (unchanged)
         if self.search_previous_errors(key) is True:
@@ -671,7 +690,7 @@ class StationQC(object):
 
         # simulate an error specified in json file (dictionary: {nwst_id: key} )
         if self._simulated_error_check(key) is True:
-            print(f'Simulating Error on {self.nwst_id}, {key}')
+            logging.info(f'Simulating Error on {self.nwst_id}, {key}')
             return True
 
         previous_errors = self.status_track.get(key)
@@ -696,26 +715,22 @@ class StationQC(object):
     def send_mail(self, key, status_type, additional_message=''):
         """ Send info mail using parameters specified in parameters file """
         if not mail_functionality:
-            if self.verbosity:
+            logging.info('Mail functionality disabled. Return')
-                print('Mail functionality disabled. Return')
             return
 
         mail_params = self.parameters.get('EMAIL')
         if not mail_params:
-            if self.verbosity:
+            logging.info('parameter "EMAIL" not set in parameter file. Return')
-                print('parameter "EMAIL" not set in parameter file. Return')
             return
 
         stations_blacklist = mail_params.get('stations_blacklist')
         if stations_blacklist and self.station in stations_blacklist:
-            if self.verbosity:
+            logging.info(f'Station {self.station} listed in blacklist. Return')
-                print(f'Station {self.station} listed in blacklist. Return')
             return
 
         networks_blacklist = mail_params.get('networks_blacklist')
         if networks_blacklist and self.network in networks_blacklist:
-            if self.verbosity:
+            logging.info(f'Station {self.station} of network {self.network} listed in blacklist. Return')
-                print(f'Station {self.station} of network {self.network} listed in blacklist. Return')
             return
 
         sender = mail_params.get('sender')
@@ -724,10 +739,8 @@ class StationQC(object):
         if add_addresses:
             # create copy of addresses ( [:] ) to prevent changing original, general list with addresses
             addresses = addresses[:] + list(add_addresses)
-        server = mail_params.get('mailserver')
         if not sender or not addresses:
-            if self.verbosity:
+            logging.info('Mail sender or addresses not (correctly) defined. Return')
-                print('Mail sender or addresses not (correctly) defined. Return')
             return
         dt = self.get_dt_for_action()
         text = f'{key}: Status {status_type} longer than {dt}: ' + additional_message
@@ -744,8 +757,10 @@ class StationQC(object):
         html_str = self.add_html_mail_body(text)
         msg.add_alternative(html_str, subtype='html')
 
-        # send message via SMTP server
+        # connect to server, send mail and close connection
-        s = smtplib.SMTP(server)
+        s = connect_to_mail_server(mail_params)
+        if not s: # if connection failed
+            return
         s.send_message(msg)
         s.quit()
 
@@ -790,20 +805,16 @@ class StationQC(object):
                         yield address
             # file not existing
             except FileNotFoundError as e:
-                if self.verbosity:
+                logging.warning(e)
-                    print(e)
             # no dictionary
             except AttributeError as e:
-                if self.verbosity:
+                logging.warning(f'Could not read dictionary from file {eml_filename}: {e}')
-                    print(f'Could not read dictionary from file {eml_filename}: {e}')
             # other exceptions
             except Exception as e:
-                if self.verbosity:
+                logging.warning(f'Could not open file {eml_filename}: {e}')
-                    print(f'Could not open file {eml_filename}: {e}')
         # no file specified
         else:
-            if self.verbosity:
+            logging.info('No external mail list set.')
-                print('No external mail list set.')
 
         return []
 
@@ -877,9 +888,8 @@ class StationQC(object):
         timespan = self.parameters.get('timespan') * 24 * 3600
         self.analysis_starttime = self.program_starttime - timespan
 
-        if self.verbosity > 0:
+        logging.info(150 * '#')
-            self.print(150 * '#')
+        logging.info('This is StationQC. Calculating quality for station'
-            self.print('This is StationQT. Calculating quality for station'
                        ' {network}.{station}.{location}'.format(**self.nsl))
         self.voltage_analysis()
         self.pb_temp_analysis()
@@ -907,7 +917,7 @@ class StationQC(object):
             if key == 'last active':
                 items.append(fancy_timestr(message))
             elif key == 'temp':
-                items.append(str(message) + deg_str)
+                items.append(str(message) + DEG_STR)
             else:
                 items.append(str(message))
         return items
@@ -946,9 +956,8 @@ class StationQC(object):
         clock_quality_warn_level = self.parameters.get('THRESHOLDS').get('clockquality_warn')
         clock_quality_fail_level = self.parameters.get('THRESHOLDS').get('clockquality_fail')
 
-        if self.verbosity > 1:
+        logging.info(40 * '-')
-            self.print(40 * '-')
+        logging.info('Performing Clock Quality check')
-            self.print('Performing Clock Quality check', flush=False)
 
         clockQuality_warn = np.where(clock_quality < clock_quality_warn_level)[0]
         clockQuality_fail = np.where(clock_quality < clock_quality_fail_level)[0]
@@ -992,9 +1001,8 @@ class StationQC(object):
         low_volt = self.parameters.get('THRESHOLDS').get('low_volt')
         high_volt = self.parameters.get('THRESHOLDS').get('high_volt')
 
-        if self.verbosity > 1:
+        logging.info(40 * '-')
-            self.print(40 * '-')
+        logging.info('Performing Voltage check')
-            self.print('Performing Voltage check', flush=False)
 
         overvolt = np.where(voltage > high_volt)[0]
         undervolt = np.where(voltage < low_volt)[0]
@@ -1020,9 +1028,12 @@ class StationQC(object):
             self.warn(key, detailed_message=detailed_message, count=n_undervolt,
                       last_occurrence=self.get_last_occurrence(trace, undervolt))
 
-    def pb_temp_analysis(self, channel='EX1'):
+    def pb_temp_analysis(self, channel='EX1', t_max_default=50, t_crit_default=70):
         """ Analyse PowBox temperature output. """
         key = 'temp'
+        if not self.powbox_active:
+            self.set_pbox_inactive_error(key)
+            return
         st = self.stream.select(channel=channel)
         trace = self.get_trace(st, key)
         if not trace:
@@ -1033,23 +1044,31 @@ class StationQC(object):
         # average temp
         timespan = min([self.parameters.get('timespan') * 24 * 3600, int(len(temp) / trace.stats.sampling_rate)])
         nsamp_av = int(trace.stats.sampling_rate) * timespan
-        av_temp_str = str(round(np.nanmean(temp[-nsamp_av:]), 1)) + deg_str
+        av_temp_str = str(round(np.nanmean(temp[-nsamp_av:]), 1)) + DEG_STR
         # dt of average
         dt_t_str = str(timedelta(seconds=int(timespan))).replace(', 0:00:00', '')
         # current temp
         cur_temp = round(temp[-1], 1)
-        if self.verbosity > 1:
+        logging.info(40 * '-')
-            self.print(40 * '-')
+        logging.info('Performing PowBox temperature check (EX1)')
-            self.print('Performing PowBox temperature check (EX1)', flush=False)
+        logging.info(f'Average temperature at {np.nanmean(temp)}\N{DEGREE SIGN}')
-            self.print(f'Average temperature at {np.nanmean(temp)}\N{DEGREE SIGN}', flush=False)
+        logging.info(f'Peak temperature at {max(temp)}\N{DEGREE SIGN}')
-            self.print(f'Peak temperature at {max(temp)}\N{DEGREE SIGN}', flush=False)
+        logging.info(f'Min temperature at {min(temp)}\N{DEGREE SIGN}')
-            self.print(f'Min temperature at {min(temp)}\N{DEGREE SIGN}', flush=False)
+        max_temp = thresholds.get('max_temp', t_max_default)
-        max_temp = thresholds.get('max_temp')
+        max_temp_crit = thresholds.get('critical_temp', t_crit_default)
         t_check = np.where(temp > max_temp)[0]
-        if len(t_check) > 0:
+        t_check_crit = np.where(temp > max_temp_crit)[0]
+        tcheck_message_template = ('Trace {id}: Temperature over {tmax}' + f'\N{DEGREE SIGN}'
+                                   + '! Current temperature: {temp}' + f'\N{DEGREE SIGN}')
+        if len(t_check_crit) > 0:
+            self.error(key=key,
+                      detailed_message=tcheck_message_template.format(id=trace.get_id(), tmax=max_temp, temp=cur_temp)
+                                       + self.get_last_occurrence_timestring(trace, t_check_crit),
+                      last_occurrence=self.get_last_occurrence(trace, t_check_crit))
+        elif len(t_check) > 0:
             self.warn(key=key,
-                      detailed_message=f'Trace {trace.get_id()}: '
+                      detailed_message=tcheck_message_template.format(id=trace.get_id(), tmax=max_temp_crit,
-                                       f'Temperature over {max_temp}\N{DEGREE SIGN} at {trace.get_id()}!'
+                                                                      temp=cur_temp)
                                        + self.get_last_occurrence_timestring(trace, t_check),
                       last_occurrence=self.get_last_occurrence(trace, t_check))
         else:
@@ -1098,23 +1117,26 @@ class StationQC(object):
             self.error(key=key,
                       detailed_message=f'Fail status for mass centering. Highest val (abs) {common_highest_val}V',)
 
-        if self.verbosity > 1:
+        logging.info(40 * '-')
-            self.print(40 * '-')
+        logging.info('Performing mass position check')
-            self.print('Performing mass position check', flush=False)
+        logging.info(f'Average mass position at {common_highest_val}')
-            self.print(f'Average mass position at {common_highest_val}', flush=False)
 
     def pb_power_analysis(self, channel='EX2', pb_dict_key='pb_SOH2'):
         """ Analyse EX2 channel of PowBox """
         keys = ['230V', '12V']
+        if not self.powbox_active:
+            for key in keys:
+                self.set_pbox_inactive_error(key)
+            return
+
         st = self.stream.select(channel=channel)
         trace = self.get_trace(st, keys)
         if not trace:
             return
 
         voltage = trace.data * self.get_unit_factor(channel)
-        if self.verbosity > 1:
+        logging.info(40 * '-')
-            self.print(40 * '-')
+        logging.info('Performing PowBox 12V/230V check (EX2)')
-            self.print('Performing PowBox 12V/230V check (EX2)', flush=False)
         voltage_check, voltage_dict, last_val = self.pb_voltage_ok(trace, voltage, pb_dict_key, channel=channel)
 
         if voltage_check:
@@ -1128,16 +1150,19 @@ class StationQC(object):
     def pb_rout_charge_analysis(self, channel='EX3', pb_dict_key='pb_SOH3'):
         """ Analyse EX3 channel of PowBox """
         keys = ['router', 'charger']
-        pb_thresh = self.parameters.get('THRESHOLDS').get('pb_1v')
+        if not self.powbox_active:
+            for key in keys:
+                self.set_pbox_inactive_error(key)
+            return
+
         st = self.stream.select(channel=channel)
         trace = self.get_trace(st, keys)
         if not trace:
             return
 
         voltage = trace.data * self.get_unit_factor(channel)
-        if self.verbosity > 1:
+        logging.info(40 * '-')
-            self.print(40 * '-')
+        logging.info('Performing PowBox Router/Charger check (EX3)')
-            self.print('Performing PowBox Router/Charger check (EX3)', flush=False)
         voltage_check, voltage_dict, last_val = self.pb_voltage_ok(trace, voltage, pb_dict_key, channel=channel)
 
         if voltage_check:
@@ -1243,6 +1268,10 @@ class StationQC(object):
         with each voltage value associated to the different steps specified in POWBOX > pb_steps. Also raises
         self.warn in case there are unassociated voltage values recorded.
         """
+        
+        if not self.powbox_active:
+            return
+
         pb_thresh = self.parameters.get('THRESHOLDS').get('pb_thresh')
         pb_ok = self.parameters.get('POWBOX').get('pb_ok')
         # possible voltage levels are keys of pb voltage level dict
@@ -1305,6 +1334,13 @@ class StationQC(object):
         """ get UTCDateTime from trace and index"""
         return trace.stats.starttime + trace.stats.delta * index
 
+    def is_pbox_activated_check(self):
+        return self.station not in self.parameters.get('no_pbox_stations', [])
+
+    def set_pbox_inactive_error(self, key):
+        msg = self.parameters.get('no_pbox_stations')[self.station]
+        self.error(key, detailed_message=f'PowBox not connected', disc=msg)
+
 
 class Status(object):
     """ Basic Status class. All status classes are derived from this class."""
@@ -1372,8 +1408,10 @@ class StatusError(Status):
         self.set_error()
         self.default_message = message
 
-    def set_disconnected(self, message='DCN'):
+    def set_disconnected(self, message=None):
         self.connection_error = True
+        if not message:
+            message = 'DCN'
         self.message = message
 
     def set_connected(self):

survBotGUI.py

@@ -11,6 +11,8 @@ import os
 import sys
 import traceback
 
+import logging
+
 try:
     from PySide2 import QtGui, QtCore, QtWidgets
 except ImportError:
@@ -41,7 +43,7 @@ try:
     from rest_api.rest_api_utils import get_last_messages, send_message, get_default_params
     sms_funcs = True
 except ImportError:
-    print('Could not load rest_api utils, SMS functionality disabled.')
+    logging.warning('Could not load rest_api utils, SMS functionality disabled.')
     sms_funcs = False
 
 deg_str = '\N{DEGREE SIGN}C'
@@ -54,10 +56,9 @@ class Thread(QtCore.QThread):
     """
     update = QtCore.Signal()
 
-    def __init__(self, parent, runnable, verbosity=0):
+    def __init__(self, parent, runnable):
         super(Thread, self).__init__(parent=parent)
         self.setParent(parent)
-        self.verbosity = verbosity
         self.runnable = runnable
         self.is_active = True
 
@@ -69,11 +70,10 @@ class Thread(QtCore.QThread):
             self.update.emit()
         except Exception as e:
             self.is_active = False
-            print(e)
+            logging.error(e)
-            print(traceback.format_exc())
+            logging.debug(traceback.format_exc())
         finally:
-            if self.verbosity > 0:
+            logging.info(f'Time for Thread execution: {UTCDateTime() - t0}')
-                print(f'Time for Thread execution: {UTCDateTime() - t0}')
 
 
 class MainWindow(QtWidgets.QMainWindow):
@@ -195,7 +195,7 @@ class MainWindow(QtWidgets.QMainWindow):
         station = nwst_id.split('.')[1]
         iccid = get_station_iccid(station)
         if not iccid:
-            print('Could not find iccid for station', nwst_id)
+            logging.info(f'Could not find iccid for station: {nwst_id}')
             return
         sms_widget = ReadSMSWidget(parent=self, iccid=iccid)
         sms_widget.setWindowTitle(f'Recent SMS of station: {nwst_id}')

utils.py

@@ -1,12 +1,23 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
+import logging
+
 import matplotlib
 import numpy as np
+import smtplib
 
 from obspy import Stream
 
 
+COLORS_DICT = {'FAIL': (195, 29, 14, 255),
+               'NO DATA': (255, 255, 125, 255),
+               'WARN': (250, 192, 63, 255),
+               'OK': (185, 245, 145, 255),
+               'undefined': (240, 240, 240, 255),
+               'disc': (126, 127, 131, 255), }
+
+
 def get_bg_color(check_key, status, dt_thresh=None, hex=False):
     message = status.message
     if check_key == 'last active':
@@ -41,13 +52,9 @@ def get_color(key):
     #                'OK': (173, 255, 133, 255),
     #                'undefined': (230, 230, 230, 255),
     #                'disc': (255, 160, 40, 255),}
-    colors_dict = {'FAIL': (195, 29, 14, 255),
+    if not key in COLORS_DICT.keys():
-                   'NO DATA': (255, 255, 125, 255),
+        key = 'undefined'
-                   'WARN': (250, 192, 63, 255),
+    return COLORS_DICT.get(key)
-                   'OK': (185, 245, 145, 255),
-                   'undefined': (240, 240, 240, 255),
-                   'disc': (126, 127, 131, 255), }
-    return colors_dict.get(key)
 
 
 def get_color_mpl(key):
@@ -82,6 +89,8 @@ def get_mass_color(message):
 def get_temp_color(temp, vmin=-10, vmax=60, cmap='coolwarm'):
     """ Get an rgba temperature value back from specified cmap, linearly interpolated between vmin and vmax. """
     if type(temp) in [str]:
+        if temp in COLORS_DICT.keys():
+            return get_color(temp)
         return get_color('undefined')
     cmap = matplotlib.cm.get_cmap(cmap)
     val = (temp - vmin) / (vmax - vmin)
@@ -170,7 +179,7 @@ def transform_trace(data, transf):
     return data
 
 
-def set_axis_ylabels(fig, parameters, verbosity=0):
+def set_axis_ylabels(fig, parameters):
     """
     Adds channel names to y-axis if defined in parameters.
     """
@@ -178,24 +187,25 @@ def set_axis_ylabels(fig, parameters, verbosity=0):
     if not names: # or not len(st.traces):
         return
     if not len(names) == len(fig.axes):
-        if verbosity:
+        logging.info('Mismatch in axis and label lengths. Not adding plot labels')
-            print('Mismatch in axis and label lengths. Not adding plot labels')
         return
     for channel_name, ax in zip(names, fig.axes):
         if channel_name:
             ax.set_ylabel(channel_name)
 
 
-def set_axis_color(fig, color='0.8'):
+def set_axis_color(fig, color='0.8', shade_color='0.95'):
     """
-    Set all axes of figure to specific color
+    Set all axes (frame) of figure to specific color. Shade every second axis.
     """
-    for ax in fig.axes:
+    for i, ax in enumerate(fig.axes):
         for key in ['bottom', 'top', 'right', 'left']:
             ax.spines[key].set_color(color)
+        if i % 2:
+            ax.set_facecolor(shade_color)
 
 
-def set_axis_yticks(fig, parameters, verbosity=0):
+def set_axis_yticks(fig, parameters):
     """
     Adds channel names to y-axis if defined in parameters.
     """
@@ -203,8 +213,7 @@ def set_axis_yticks(fig, parameters, verbosity=0):
     if not ticks:
         return
     if not len(ticks) == len(fig.axes):
-        if verbosity:
+        logging.info('Mismatch in axis tick and label lengths. Not changing plot ticks.')
-            print('Mismatch in axis tick and label lengths. Not changing plot ticks.')
         return
     for ytick_tripple, ax in zip(ticks, fig.axes):
         if not ytick_tripple:
@@ -216,12 +225,11 @@ def set_axis_yticks(fig, parameters, verbosity=0):
         ax.set_ylim(ymin - 0.33 * step, ymax + 0.33 * step)
 
 
-def plot_axis_thresholds(fig, parameters, verbosity=0):
+def plot_axis_thresholds(fig, parameters):
     """
     Adds channel thresholds (warn, fail) to y-axis if defined in parameters.
     """
-    if verbosity > 0:
+    logging.info('Plotting trace thresholds')
-        print('Plotting trace thresholds')
 
     keys_colors = {'warn': dict(color=0.8 * get_color_mpl('WARN'), linestyle=(0, (5, 10)), alpha=0.5, linewidth=0.7),
                    'fail': dict(color=0.8 * get_color_mpl('FAIL'), linestyle='solid', alpha=0.5, linewidth=0.7)}
@@ -235,6 +243,10 @@ def plot_axis_thresholds(fig, parameters, verbosity=0):
 
 def plot_threshold_lines(fig, channel_threshold_list, parameters, **kwargs):
     for channel_thresholds, ax in zip(channel_threshold_list, fig.axes):
+        if channel_thresholds in ['pb_SOH2', 'pb_SOH3']:
+            annotate_voltage_states(ax, parameters, channel_thresholds)
+            channel_thresholds = get_warn_states_pbox(channel_thresholds, parameters)
+
         if not channel_thresholds:
             continue
 
@@ -244,5 +256,74 @@ def plot_threshold_lines(fig, channel_threshold_list, parameters, **kwargs):
         for warn_thresh in channel_thresholds:
             if isinstance(warn_thresh, str):
                 warn_thresh = parameters.get('THRESHOLDS').get(warn_thresh)
-            if type(warn_thresh in (float, int)):
+            if isinstance(warn_thresh, (float, int)):
                 ax.axhline(warn_thresh, **kwargs)
+
+
+def get_warn_states_pbox(soh_key: str, parameters: dict) -> list:
+    pb_dict = parameters.get('POWBOX').get(soh_key)
+    if not pb_dict:
+        return []
+    return [key for key in pb_dict.keys() if key > 1]
+
+
+def annotate_voltage_states(ax, parameters, pb_key, color='0.75'):
+    for voltage, voltage_dict in parameters.get('POWBOX').get(pb_key).items():
+        if float(voltage) < 1:
+            continue
+        out_string = ''
+        for key, val in voltage_dict.items():
+            if val != 'OK':
+                if out_string:
+                    out_string += ' | '
+                out_string += f'{key}: {val}'
+
+        ax.annotate(out_string, (ax.get_xlim()[-1], voltage), color=color, fontsize='xx-small',
+                    horizontalalignment='right')
+
+def get_credential(source, param):
+    """
+    Retrieve a credential from a Docker secret or environment variable.
+    """
+    if source == 'DOCKER':
+        try:
+            with open('/run/secrets/'+param.lower(), 'r') as f:
+                return f.read().strip()
+        except FileNotFoundError as e:
+            logging.error(f'Could not read from Docker secret at /run/secrets/{param.lower()}')
+            logging.error(e)
+    elif source == 'ENV':
+        try:
+            return os.environ.get(param.upper())
+        except Exception as e:
+            logging.error(f'Could not read from environment variable {param.upper()}')
+            logging.error(e)
+    # return source if no credential was found
+    return source
+
+def connect_to_mail_server(self, mail_params):
+    """
+    Connect to mail server and return server object.
+    """
+    # get server from parameters
+    server = mail_params.get('mailserver')
+    # get auth_type from parameters
+    auth_type = mail_params.get('auth_type')
+    # set up connection to mail server
+    if auth_type == 'None':
+        s = smtplib.SMTP(server)
+    else:
+        # user and password from parameters, docker secret or environment variable
+        user = get_credential(mail_params.get('user'), 'mail_user')
+        password = get_credential(mail_params.get('password'), 'mail_password')
+        # create secure connection to server
+        if auth_type == 'SSL':
+            s = smtplib.SMTP_SSL(server, mail_params.get('port'))
+        elif auth_type == 'TLS':
+            s = smtplib.SMTP(server, mail_params.get('port'))
+            s.starttls()
+        else:
+            logging.error('Unknown authentication type. Mails can not be sent')
+            return
+        s.login(mail_params.get('user'), mail_params.get('password'))
+    return s