[bugfix] fixed footer output to produce valid html when using a logo

new parameters in for paramters.yaml file:
  - added parameter logo_alt_text
  - added parameter logo_height

.gitignore

@@ -213,3 +213,7 @@ flycheck_*.el
 
 /__simulate_fail.json
 /mailing_list.yaml
+
+.vscode/
+
+*.code-workspace

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

@@ -3,7 +3,7 @@
 version: 0.2
 
 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.
+ by analyzing contents of a Seiscomp data archive.
 
 ## Requirements
 
@@ -40,16 +40,53 @@ 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` fields 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
-- surveillance of mass, clock and gaps
-- individual mailing lists for different stations
-- html mail with recent status information
-- updated web page design
-- restructured parameter file
-- recognize if PBox is disconnected
+
+### 0.2
+
+* surveillance of mass, clock and gaps
+* individual mailing lists for different stations
+* html mail with recent status information
+* updated web page design
+* 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)
+Original author: M.Paffrath (<marcel.paffrath@rub.de>)
+Contributions: 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

@@ -1,13 +1,13 @@
 # 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 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)
@@ -40,6 +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
@@ -55,7 +56,7 @@ 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.:
@@ -116,6 +117,11 @@ data_channels: ["HHZ", "HHN", "HHE"]
 
 
 # ---------------------------------------- OPTIONAL PARAMETERS ---------------------------------------------------------
+# deactivate powbox surveillance for stations (e.g. for solar powered), key: station, value: status message (abbr.)
+no_pbox_stations: {'GR33': 'SOL', 'GR27B': 'DCN', 'RP01': 'noPBox', 'RP02': 'noPBox', 'RP03': 'noPBox', 'RP04': 'noPBox', 'RP05B': 'noPBox', 'RP06': 'noPBox', 'RP07': 'noPBox', 'RP08': 'noPBox'}
+
+# deactivate mass position surveillance for stations without connected mass channels (e.g. STS-2 instruments), key: station, value: status message (abbr.)
+no_mass_stations: {'BIA': 'DCN', 'KNEZ': 'DCN', 'KRUS': 'DCN', 'OHR': 'DCN', 'OTOV': 'DCN', 'SKO': 'DCN', 'STIP': 'DCN', 'VAY': 'DCN', 'ZUPA': 'DCN'}
 
 # add links to html table with specified key as column and value as relative link, interpretable string parameters:
 # nw (e.g. 1Y), st (e.g. GR01A), nwst_id (e.g. 1Y.GR01A)
@@ -129,17 +135,25 @@ add_links:
 add_global_links:
   # for example: - {"text": "our homepage", "URL": "https://www.rub.de"}
   - {"text": "show recent events on map",
-     "URL": "https://fdsnws.geophysik.ruhr-uni-bochum.de/map/?lat=39.5&lon=21&zoom=7&baselayer=mapnik"}
+     "URL": "https://fdsnws.geophysik.ruhr-uni-bochum.de/map/?lat=39.5&lon=21&zoom=7&baselayer=osm"}
 
 # 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"
-  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
-  stations_blacklist: ['GR33']                     # do not send emails for specific stations
+  # 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.example.org"      # 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: ["test@example.org"]  # list of mail addresses for info mails
+  sender: "<test@example.org>"              # mail sender
+  stations_blacklist: []                                          # do not send emails for specific stations
   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";
@@ -17,10 +16,10 @@ td {
 }
 
 th {
-    background-color: #999;
+    background-color: #17365c;
     color: #fff;
     border-radius: 3px;
-    padding: 10px, 2px;
+    padding: 10px 2px;
     position: sticky;
     top: 0;
 }

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
-#$ -l os=*stretch
+#$ -binding linear:1
+#$ -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

@@ -1,8 +1,8 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-__version__ = '0.1'
-__author__ = 'Marcel Paffrath'
+__version__ = '0.3.1'
+__author__ = ['Marcel Paffrath <marcel.paffrath@rub.de>', 'Kasper D. Fischer <kasper.fischer@rub.de>']
 
 import os
 import io
@@ -23,7 +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
@@ -69,6 +70,7 @@ def set_logging_level(params: dict) -> None:
         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)
 
@@ -232,7 +234,7 @@ class SurveillanceBot(object):
         self.gaps = self.dataStream.get_gaps(min_gap=self.parameters['THRESHOLDS'].get('min_gap'))
         self.dataStream.merge()
 
-        # organise data in dictionary with key for each station
+        # organize data in dictionary with key for each station
         for trace in self.dataStream:
             nwst_id = get_nwst_id(trace)
             if not nwst_id in self.data.keys():
@@ -349,7 +351,7 @@ class SurveillanceBot(object):
             first_exec = False
 
     def console_print(self, itemlist, str_len=21, sep='|', seplen=3):
-        assert len(sep) <= seplen, f'Make sure seperator has less than {seplen} characters'
+        assert len(sep) <= seplen, f'Make sure separator has less than {seplen} characters'
         sl = sep.ljust(seplen)
         sr = sep.rjust(seplen)
         string = sl
@@ -535,11 +537,13 @@ class SurveillanceBot(object):
 
                 # write footer with optional logo
                 logo_file = self.parameters.get('html_logo')
+                logo_alt_text = self.parameters.get('logo_alt_text')
+                logo_height = self.parameters.get('logo_height')
                 if not os.path.isfile(pjoin(self.outpath_html, logo_file)):
                     logging.info(f'Specified file {logo_file} not found.')
                     logo_file = None
 
-                outfile.write(html_footer(footer_logo=logo_file))
+                outfile.write(html_footer(footer_logo=logo_file, alt_text=logo_alt_text, height=logo_height))
 
         except Exception as e:
             logging.info(f'Could not write HTML table to {fnout}:')
@@ -549,7 +553,8 @@ class SurveillanceBot(object):
 
     def update_status_message(self):
         timespan = timedelta(seconds=int(self.parameters.get('timespan') * 24 * 3600))
-        self.status_message = f'Program starttime (UTC) {self.starttime.strftime("%Y-%m-%d %H:%M:%S")} | ' \
+        self.status_message = f' Version {__version__} | ' \
+                              f'Program start time (UTC) {self.starttime.strftime("%Y-%m-%d %H:%M:%S")} | ' \
                               f'Current time (UTC) {UTCDateTime().strftime("%Y-%m-%d %H:%M:%S")} | ' \
                               f'Refresh period: {self.refresh_period}s | ' \
                               f'Showing data of last {timespan}'
@@ -573,8 +578,6 @@ class StationQC(object):
         :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
@@ -594,6 +597,9 @@ class StationQC(object):
             status_track = {}
         self.status_track = status_track
 
+        self.powbox_active = self.is_pbox_activated_check()
+        self.mass_active = self.is_mass_activated_check()
+
         self.start()
 
     @property
@@ -645,7 +651,8 @@ 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
@@ -736,7 +743,6 @@ 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:
             logging.info('Mail sender or addresses not (correctly) defined. Return')
             return
@@ -755,8 +761,10 @@ class StationQC(object):
         html_str = self.add_html_mail_body(text)
         msg.add_alternative(html_str, subtype='html')
 
-        # send message via SMTP server
-        s = smtplib.SMTP(server)
+        # connect to server, send mail and close connection
+        s = connect_to_mail_server(mail_params)
+        if not s: # if connection failed
+            return
         s.send_message(msg)
         s.quit()
 
@@ -1024,9 +1032,12 @@ 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:
@@ -1047,12 +1058,21 @@ class StationQC(object):
         logging.info(f'Average temperature at {np.nanmean(temp)}\N{DEGREE SIGN}')
         logging.info(f'Peak temperature at {max(temp)}\N{DEGREE SIGN}')
         logging.info(f'Min temperature at {min(temp)}\N{DEGREE SIGN}')
-        max_temp = thresholds.get('max_temp')
+        max_temp = thresholds.get('max_temp', t_max_default)
+        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()}: '
-                                       f'Temperature over {max_temp}\N{DEGREE SIGN} at {trace.get_id()}!'
+                      detailed_message=tcheck_message_template.format(id=trace.get_id(), tmax=max_temp_crit,
+                                                                      temp=cur_temp)
                                        + self.get_last_occurrence_timestring(trace, t_check),
                       last_occurrence=self.get_last_occurrence(trace, t_check))
         else:
@@ -1064,6 +1084,11 @@ class StationQC(object):
         """ Analyse datalogger mass channels. """
         key = 'mass'
 
+        # skip processing if mass is not active
+        if not self.mass_active:
+            self.set_mass_inactive_error(key)
+            return
+        
         # build stream with all channels
         st = Stream()
         for channel in channels:
@@ -1108,6 +1133,11 @@ class StationQC(object):
     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:
@@ -1129,7 +1159,11 @@ 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:
@@ -1243,6 +1277,10 @@ 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
@@ -1270,7 +1308,7 @@ class StationQC(object):
 
         # Warn in case of voltage under OK-level (1V)
         if len(under) > 0:
-            # try calculate number of occurences from gaps between indices
+            # try calculate number of occurrences from gaps between indices
             n_occurrences = len(np.where(np.diff(under) > 1)[0]) + 1
             voltage_dict[-1] = under
             self.status_other(detailed_message=f'Trace {trace.get_id()}: '
@@ -1305,6 +1343,19 @@ 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)
+
+    def is_mass_activated_check(self):
+        return self.station not in self.parameters.get('no_mass_stations', [])
+
+    def set_mass_inactive_error(self, key):
+        msg = self.parameters.get('no_mass_stations')[self.station]
+        self.error(key, detailed_message=f'Mass channels not connected', disc=msg)
 
 class Status(object):
     """ Basic Status class. All status classes are derived from this class."""
@@ -1359,21 +1410,23 @@ class StatusOK(Status):
 
 
 class StatusWarn(Status):
-    def __init__(self, message='WARN', count=1, last_occurence=None, detailed_messages=None, show_count=False):
-        super(StatusWarn, self).__init__(message=message, count=count, last_occurrence=last_occurence,
+    def __init__(self, message='WARN', count=1, last_occurrence=None, detailed_messages=None, show_count=False):
+        super(StatusWarn, self).__init__(message=message, count=count, last_occurrence=last_occurrence,
                                          detailed_messages=detailed_messages, show_count=show_count)
         self.set_warn()
 
 
 class StatusError(Status):
-    def __init__(self, message='FAIL', count=1, last_occurence=None, detailed_messages=None, show_count=False):
-        super(StatusError, self).__init__(message=message, count=count, last_occurrence=last_occurence,
+    def __init__(self, message='FAIL', count=1, last_occurrence=None, detailed_messages=None, show_count=False):
+        super(StatusError, self).__init__(message=message, count=count, last_occurrence=last_occurrence,
                                           detailed_messages=detailed_messages, show_count=show_count)
         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):
@@ -1382,8 +1435,8 @@ class StatusError(Status):
 
 
 class StatusOther(Status):
-    def __init__(self, messages=None, count=1, last_occurence=None, detailed_messages=None):
-        super(StatusOther, self).__init__(count=count, last_occurrence=last_occurence,
+    def __init__(self, messages=None, count=1, last_occurrence=None, detailed_messages=None):
+        super(StatusOther, self).__init__(count=count, last_occurrence=last_occurrence,
                                           detailed_messages=detailed_messages)
         if messages is None:
             messages = []

utils.py

@@ -5,10 +5,20 @@ import logging
 
 import matplotlib
 import numpy as np
+import smtplib
+import os
 
 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':
@@ -43,13 +53,9 @@ 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),
-                   '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), }
-    return colors_dict.get(key)
+    if not key in COLORS_DICT.keys():
+        key = 'undefined'
+    return COLORS_DICT.get(key)
 
 
 def get_color_mpl(key):
@@ -84,6 +90,8 @@ 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)
@@ -167,7 +175,7 @@ def transform_trace(data, transf):
         elif operator_str == '/':
             data = data / val
         else:
-            raise IOError(f'Unknown arithmethic operator string: {operator_str}')
+            raise IOError(f'Unknown arithmetic operator string: {operator_str}')
 
     return data
 
@@ -273,3 +281,50 @@ def annotate_voltage_states(ax, parameters, pb_key, color='0.75'):
 
         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(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(user, password)
+    return s

write_utils.py

@@ -17,15 +17,16 @@ def get_html_text(text):
 
 def get_html_header(refresh_rate=10):
     header = ['<!DOCTYPE html>',
-              '<html>',
+              '<html lang="en">',
               '<head>',
-              '  <link rel="stylesheet" media="only screen and (max-width: 400px)" href="mobile.css" />',
-              '  <link rel="stylesheet" media="only screen and (min-width: 401px)" href="desktop.css" />',
-              '</head>',
+              '  <title>SurvBot status</title>',
+              '  <link rel="stylesheet" media="only screen and (max-width: 400px)" href="mobile.css">',
+              '  <link rel="stylesheet" media="only screen and (min-width: 401px)" href="desktop.css">',
               f'  <meta http-equiv="refresh" content="{refresh_rate}">',
               '  <meta charset="utf-8">',
               '  <meta name="viewport" content="width=device-width, initial-scale=1">',
-              '<body>']
+              '</head>',
+              '<body>\n']
     header = _convert_to_textstring(header)
     return header
 
@@ -47,14 +48,15 @@ def finish_html_table():
     return '</table>\n'
 
 
-def html_footer(footer_logo=None):
-    footer = ['</body>']
+def html_footer(footer_logo=None, alt_text='Logo', height=30):
     if footer_logo:
-        logo_items = [f'<div class="footer">',
-                      f'  <img style="float: right; padding: 10px;" src="{footer_logo}" height=30px>',
+        footer = [f'<div class="footer">',
+                  f'  <img style="float: right; padding: 10px;" src="{footer_logo}" height={height} alt="{alt_text}">',
                   f'</div>']
-        footer += logo_items
-    footer.append('</html>\n')
+    else:
+        footer = []
+    footer.append('</body>')
+    footer.append('</html>')
 
     footer = _convert_to_textstring(footer)
     return footer
@@ -85,8 +87,14 @@ def get_html_row(items, html_key='td'):
         text_str = get_html_link(text, hyperlink) if hyperlink else text
         html_class = item.get('html_class')
         class_str = f' class="{html_class}"' if html_class else ''
-        row_string += 2 * default_space + f'<{html_key}{class_str} bgcolor="{color}" title="{tooltip}"' \
-                      + f'style="color:{font_color}"> {text_str}</{html_key}>\n'
+        row_string += 2 * default_space + f'<{html_key}{class_str} '
+        row_string += f'title="{tooltip}" ' if tooltip else ''
+        row_string += 'style="' if color or font_color else ''
+        row_string += f'background-color: {color};' if color else 'style="'
+        row_string += ' ' if font_color else ''
+        row_string += f'color: {font_color};' if font_color else ''
+        row_string += '" ' if color or font_color else '' 
+        row_string += f'>{text_str}</{html_key}>\n'
     row_string += default_space + '</tr>\n'
     return row_string