[bugfix] HTML faild validator.w3.org checks

Implements checks for mass channel activity to ensure proper functionality.

Introduces methods to verify if mass channels are active and to set errors when they are not connected.

Enhances reliability of data logging by avoiding unnecessary processing when mass channels are inactive.

.gitignore

@@ -211,3 +211,9 @@ flycheck_*.el
 /network-security.data
 
 
+/__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

@@ -1,9 +1,9 @@
 # survBot
 
-version: 0.1
+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
 
@@ -40,8 +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
+
+### 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>)
 
-November 2022
+Jan 2025

__init__.py

@@ -0,0 +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-docker"

mailing_list.yaml

@@ -0,0 +1,9 @@
+# specify mail addresses and station network ids for which information mails shall be sent, e.g.:
+# "mail.address@provider.com, mail.address2@provider2.com":
+#   - 1Y.GR01
+#   - 1Y.GR02
+# "mail.address3@provider.com":
+#   - 1Y.GR03
+
+#"kasper.fischer@rub.de":
+#    - 1Y.GR01

parameters.yaml

@@ -1,18 +1,18 @@
 # Parameters file for Surveillance Bot
-datapath: "/data/SDS/"                    # SC3 Datapath
+datapath: "/data/SDS/"                    # path to SDS data archive
-networks: ["1Y", "HA"]                    # select networks, list or str
+networks: ["1Y", "HA", "MK"]              # select networks, list or str
 stations: "*"                             # select stations, list or str
 locations: "*"                            # select locations, list or str
-channels: ["EX1", "EX2", "EX3", "VEI", "LCQ"]    # Specify SOH channels, currently supported EX[1-3], VEI and LCQ
+stations_blacklist: ["ATHR", "DOMV", "EREA", "GR19", "GR27", "HAVD", "LAKA", "LFKM", "TEST"]      # exclude these stations
-stations_blacklist: ["TEST", "EREA"]      # exclude these stations
 networks_blacklist: []                    # exclude these networks
 interval: 60               # Perform checks every x seconds
-n_track: 300               # wait n_track * intervals before performing an action (i.e. send mail/end highlight status)
+n_track: 360               # wait n_track * intervals before performing an action (i.e. send mail/end highlight status)
 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: 3              # minimum samples for raising Warn/FAIL
+min_sample: 5              # minimum samples for raising Warn/FAIL
 dt_thresh: [300, 1800]     # threshold (s) for timing delay colourisation (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)
@@ -40,13 +40,88 @@ 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
-  clockquality_warn: 90        # clock quality ranges from 0 % to 100 % with 100 % being the best level
+  max_vm_warn: 1.5             # threshold for mass offset (warn), fail)
-  clockquality_fail: 70
+  max_vm_fail: 2.5             # threshold for mass offset (warn), fail)
+  clockquality_warn: 90        # warn level - clock quality ranges from 0 % to 100 % with 100 % being the best level
+  clockquality_fail: 70        # fail level
+  min_gap: 0.1                 # minimum for gap declaration, should be > 0 [s]
+
+
+# ---------------------------------- Specification of input channels ---------------------------------------------------
+# Currently supported: EX[1-3], VEI, VM[1-3], LCQ
+#
+# 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 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]
+#             - ["-", 20]
+#  --> PBox EX1 V to deg C: 20 * x -20
+CHANNELS:
+  EX1:
+    unit: 1e-6
+    name: "PowBox Temperature (°C)"
+    ticks: [-10, 50, 10]
+    transform:
+      - ["*", 20]
+      - ["-", 20]
+    warn: "max_temp"
+  EX2:
+    unit: 1e-6
+    name: "PowBox 230V/12V (V)"
+    ticks: [0, 5, 1]
+    warn: "pb_SOH2"
+  EX3:
+    unit: 1e-6
+    name: "PowBox Router/Charger (V)"
+    ticks: [0, 5, 1]
+    warn: "pb_SOH3"
+  VEI:
+    unit: 1e-3
+    name: "Datalogger (V)"
+    ticks: [9, 15, 1]
+    warn: ["low_volt", "high_volt"]
+    fail: 10.5
+  VM1:
+    unit: 1e-6
+    name: "Mass position W (V)"
+    ticks: [-2.5, 2.5, 1]
+    warn: [-1.5, 1.5]
+    fail: [-2.5, 2.5]
+  VM2:
+    unit: 1e-6
+    name: "Mass position V (V)"
+    ticks: [-2.5, 2.5, 1]
+    warn: [-1.5, 1.5]
+    fail: [-2.5, 2.5]
+  VM3:
+    unit: 1e-6
+    name: "Mass position U (V)"
+    ticks: [-2.5, 2.5, 1]
+    warn: [-1.5, 1.5]
+    fail: [-2.5, 2.5]
+  LCQ:
+    name: "Clock quality (%)"
+    ticks: [0, 100, 20]
+    warn: "clockquality_warn"
+    fail: "clockquality_fail"
+
+# specify data channels (can be additional to the above). From these channels only headers will be read
+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)
@@ -54,34 +129,31 @@ 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:
+  # 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=osm"}
+
+# html logo at page bottom (path relative to html directory)
+html_logo: "logo.png"
 
 # E-mail notifications
 EMAIL:
-  mailserver: "localhost"
+  # specify mail server and credentials
-  addresses: ["marcel.paffrath@rub.de", "kasper.fischer@rub.de"]  # list of mail addresses for info mails
+  # port, auth_type, user and password are only required if mailserver is not set to "localhost"
-  sender: "webmaster@geophysik.ruhr-uni-bochum.de" # mail sender
+  # user and password can be set to "ENV" or "DOCKER" to read from environment variables or docker secrets
-  stations_blacklist: ['GR33']                     # do not send emails for specific stations
+  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])
-# names for plotting of the above defined parameter "channels" in the same order
+  external_mail_list: "conf/mailing_list.yaml"
-channel_names: ["Clock Quality (%)", "Temperature (°C)", "230V/12V Status (V)", "Router/Charger State (V)", "Logger Voltage (V)"] # names for plotting (optional)
-# specify y-ticks (and ylims) giving, (ymin, ymax, step) for each of the above channels (0: default)
-CHANNEL_TICKS:
-  - [0, 100, 20]
-  - [-10, 50, 10]
-  - [1, 5, 1]
-  - [1, 5, 1]
-  - [9, 15, 1]
-
-# Factor for channel to SI-units (for plotting)
-CHANNEL_UNITS:
-  EX1: 1e-6
-  EX2: 1e-6
-  EX3: 1e-6
-  VEI: 1e-3
-
-# Transform channel for plotting, perform arithmetic operations in given order, e.g.: PBox EX1 V to deg C: 20 * x -20
-CHANNEL_TRANSFORM:
-  EX1:
-    - ["*", 20]
-    - ["-", 20]

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

@@ -1,27 +1,36 @@
 body {
     background-color: #ffffff;
-    place-items: center;
     text-align: center;
+    padding-bottom: 30px;
+    font-family: "Helvetica", "sans-serif";
+}
+
+table {
+    position: relative
 }
 
 td {
-    border-radius: 4px;
+    border-radius: 2px;
     padding: 0px;
+    white-space: nowrap;
 }
 
 th {
-    background-color: #999;
+    background-color: #17365c;
-    border-radius: 4px;
+    color: #fff;
+    border-radius: 2px;
     padding: 3px 1px;
+    position: sticky;
+    top: 0;
 }
 
 a:link, a:visited {
-    background-color: #ccc;
+    background-color: #e8e8e8;
     color: #000;
     text-decoration: none;
     display: block;
     border-radius: 4px;
-    border: 1px solid #bbb;
+    border: 1px solid #ccc;
 }
 
 a:hover {
@@ -37,3 +46,12 @@ a:hover {
     50%		{ background-color: #ff3200;}
     100%	{ background-color: #ffcc00;}
 }
+
+.footer {
+   position: fixed;
+   left: 0;
+   bottom: 0;
+   width: 100%;
+   height: 50px;
+   text-align: center;
+}

stylesheets/mobile.css

@@ -1,27 +1,36 @@
 body {
     background-color: #ffffff;
-    place-items: center;
     text-align: center;
+    padding-bottom: 30px;
+    font-family: "Helvetica", "sans-serif";
+}
+
+table {
+    position: relative
 }
 
 td {
-    border-radius: 4px;
+    border-radius: 3px;
     padding: 10px 2px;
+    white-space: nowrap;
 }
 
 th {
-    background-color: #999;
+    background-color: #17365c;
-    border-radius: 4px;
+    color: #fff;
-    padding: 10px, 2px;
+    border-radius: 3px;
+    padding: 10px 2px;
+    position: sticky;
+    top: 0;
 }
 
-a:link {
+a:link, a:visited {
-    background-color: #ccc;
+    background-color: #e8e8e8;
     color: #000;
     text-decoration: none;
     display: block;
-    border-radius: 4px;
+    border-radius: 6px;
-    border: 1px solid #bbb;
+    border: 1px solid #ccc;
 }
 
 a:hover {
@@ -37,7 +46,16 @@ a:hover {
     animation: blinkingBackground 2s infinite;
 }
 @keyframes blinkingBackground{
-    0%		{ background-color: #ffee00;}
+    0%		{ background-color: #ffcc00;}
     50%		{ background-color: #ff3200;}
-    100%	{ background-color: #ffee00;}
+    100%	{ background-color: #ffcc00;}
+}
+
+.footer {
+   position: fixed;
+   left: 0;
+   bottom: 0;
+   width: 100%;
+   height: 50px;
+   text-align: center;
 }

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'

survBotGUI.py

@@ -11,6 +11,8 @@ import os
 import sys
 import traceback
 
+import logging
+
 try:
     from PySide2 import QtGui, QtCore, QtWidgets
 except ImportError:
@@ -34,14 +36,14 @@ from obspy import UTCDateTime
 
 from survBot import SurveillanceBot
 from write_utils import *
-from utils import get_bg_color, modify_stream_for_plot, trace_ylabels, trace_yticks
+from utils import get_bg_color, modify_stream_for_plot, set_axis_yticks, set_axis_color, plot_axis_thresholds
 
 try:
     from rest_api.utils import get_station_iccid
     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}')
@@ -316,8 +316,10 @@ class MainWindow(QtWidgets.QMainWindow):
             self.plot_widget.setWindowTitle(nwst_id)
             st = modify_stream_for_plot(st, parameters=self.parameters)
             st.plot(equal_scale=False, method='full', block=False, fig=self.plot_widget.canvas.fig)
-            trace_ylabels(fig=self.plot_widget.canvas.fig, parameters=self.parameters)
+            # set_axis_ylabels(fig=self.plot_widget.canvas.fig, parameters=self.parameters)
-            trace_yticks(fig=self.plot_widget.canvas.fig, parameters=self.parameters)
+            set_axis_yticks(fig=self.plot_widget.canvas.fig, parameters=self.parameters)
+            set_axis_color(fig=self.plot_widget.canvas.fig)
+            plot_axis_thresholds(fig=self.plot_widget.canvas.fig, parameters=self.parameters)
             self.plot_widget.show()
 
     def notification(self, text):

utils.py

@@ -1,7 +1,22 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
+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):
@@ -10,10 +25,15 @@ def get_bg_color(check_key, status, dt_thresh=None, hex=False):
         bg_color = get_time_delay_color(message, dt_thresh)
     elif check_key == 'temp':
         bg_color = get_temp_color(message)
+    elif check_key == 'mass':
+        bg_color = get_mass_color(message)
     else:
         if status.is_warn:
-            bg_color = get_color('WARNX')(status.count)
+            bg_color = get_warn_color(status.count)
         elif status.is_error:
+            if status.connection_error:
+                bg_color = get_color('disc')
+            else:
                 bg_color = get_color('FAIL')
         else:
             bg_color = get_color(message)
@@ -26,18 +46,26 @@ def get_bg_color(check_key, status, dt_thresh=None, hex=False):
 
 
 def get_color(key):
-    # some GUI default colors
+    # some old GUI default colors
-    colors_dict = {'FAIL': (255, 50, 0, 255),
+    # colors_dict = {'FAIL': (255, 85, 50, 255),
-                   'NO DATA': (255, 255, 125, 255),
+    #                'NO DATA': (255, 255, 125, 255),
-                   'WARN': (255, 255, 80, 255),
+    #                'WARN': (255, 255, 80, 255),
-                   'WARNX': lambda x: (min([255, 200 + x ** 2]), 255, 80, 255),
+    #                'OK': (173, 255, 133, 255),
-                   'OK': (125, 255, 125, 255),
+    #                'undefined': (230, 230, 230, 255),
-                   'undefined': (230, 230, 230, 255)}
+    #                'disc': (255, 160, 40, 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):
+    color_tup = get_color(key)
+    return np.array([color/255. for color in color_tup])
 
 
 def get_time_delay_color(dt, dt_thresh):
     """ Set color of time delay after thresholds specified in self.dt_thresh """
+    if isinstance(dt, type(dt_thresh[0])):
         if dt < dt_thresh[0]:
             return get_color('OK')
         elif dt_thresh[0] <= dt < dt_thresh[1]:
@@ -45,9 +73,25 @@ def get_time_delay_color(dt, dt_thresh):
     return get_color('FAIL')
 
 
+def get_warn_color(count, n_colors=20):
+    if count >= n_colors:
+        count = -1
+    gradient = np.linspace((240, 245, 110, 255), (250, 192, 63, 255), n_colors, dtype=int)
+    return tuple(gradient[count])
+
+
+def get_mass_color(message):
+    # can change this to something else if wanted. This way it always returns get_color (without warn count)
+    if isinstance(message, (float, int)):
+        return get_color('OK')
+    return get_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)
@@ -55,29 +99,61 @@ def get_temp_color(temp, vmin=-10, vmax=60, cmap='coolwarm'):
     return rgba
 
 
-def modify_stream_for_plot(st, parameters):
+def get_font_color(bg_color, hex=False):
+    if hex:
+        bg_color = matplotlib.colors.to_rgb(bg_color)
+    bg_color_hsv = matplotlib.colors.rgb_to_hsv(bg_color)
+    bg_color_hsl = hsv_to_hsl(bg_color_hsv)
+    font_color = (255, 255, 255, 255) if bg_color_hsl[2] < 0.6 else (0, 0, 0, 255)
+    if hex:
+        font_color = '#{:02x}{:02x}{:02x}'.format(*font_color[:3])
+    return font_color
+
+
+def hsv_to_hsl(hsv):
+    hue, saturation, value = hsv
+    lightness = value * (1 - saturation / 2)
+    saturation = 0 if lightness in (0, 1) else (value - lightness) / min(lightness, 1 - lightness)
+    return hue, saturation, lightness
+
+
+def modify_stream_for_plot(input_stream, parameters):
     """ copy (if necessary) and modify stream for plotting """
-    ch_units = parameters.get('CHANNEL_UNITS')
-    ch_transf = parameters.get('CHANNEL_TRANSFORM')
 
-    # if either of both are defined make copy
+    # make a copy
-    if ch_units or ch_transf:
+    st = Stream()
-        st = st.copy()
 
-    # modify trace for plotting by multiplying unit factor (e.g. 1e-3 mV to V)
+    channels_dict = parameters.get('CHANNELS')
-    if ch_units:
+
-        for tr in st:
+    # iterate over all channels and put them to new stream in order
-            channel = tr.stats.channel
+    for index, ch_tup in enumerate(channels_dict.items()):
-            unit_factor = ch_units.get(channel)
+        # unpack tuple from items
+        channel, channel_dict = ch_tup
+
+        # get correct channel from stream
+        st_sel = input_stream.select(channel=channel)
+        # in case there are != 1 there is ambiguity
+        if not len(st_sel) == 1:
+            continue
+
+        # make a copy to not modify original stream!
+        tr = st_sel[0].copy()
+
+        # multiply with conversion factor for unit
+        unit_factor = channel_dict.get('unit')
         if unit_factor:
             tr.data = tr.data * float(unit_factor)
-    # modify trace for plotting by other arithmetic expressions
+
-    if ch_transf:
+        # apply transformations if provided
-        for tr in st:
+        transform = channel_dict.get('transform')
-            channel = tr.stats.channel
+        if transform:
-            transf = ch_transf.get(channel)
+            tr.data = transform_trace(tr.data, transform)
-            if transf:
+
-                tr.data = transform_trace(tr.data, transf)
+        # modify trace id to maintain plotting order
+        name = channel_dict.get('name')
+        tr.id = f'{index + 1}: {name} - {tr.id}'
+
+        st.append(tr)
 
     return st
 
@@ -99,47 +175,156 @@ 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
 
 
-def trace_ylabels(fig, parameters, verbosity=0):
+def set_axis_ylabels(fig, parameters):
     """
     Adds channel names to y-axis if defined in parameters.
-    Can get mixed up if channel order in stream and channel names defined in parameters.yaml differ, but it is
-    difficult to assess the correct order from Obspy plotting routing.
     """
-    names = parameters.get('channel_names')
+    names = [channel.get('name') for channel in parameters.get('CHANNELS').values()]
     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 trace_yticks(fig, parameters, verbosity=0):
+def set_axis_color(fig, color='0.8', shade_color='0.95'):
+    """
+    Set all axes (frame) of figure to specific color. Shade every second axis.
+    """
+    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):
     """
     Adds channel names to y-axis if defined in parameters.
-    Can get mixed up if channel order in stream and channel names defined in parameters.yaml differ, but it is
-    difficult to assess the correct order from Obspy plotting routing.
     """
-    ticks = parameters.get('CHANNEL_TICKS')
+    ticks = [channel.get('ticks') for channel in parameters.get('CHANNELS').values()]
     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:
             continue
         ymin, ymax, step = ytick_tripple
 
-        yticks = list(range(ymin, ymax + step, step))
+        yticks = list(np.arange(ymin, ymax + step, step))
         ax.set_yticks(yticks)
-        ax.set_ylim(ymin - step, ymax + step)
+        ax.set_ylim(ymin - 0.33 * step, ymax + 0.33 * step)
+
+
+def plot_axis_thresholds(fig, parameters):
+    """
+    Adds channel thresholds (warn, fail) to y-axis if defined in parameters.
+    """
+    logging.info('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)}
+
+    for key, kwargs in keys_colors.items():
+        channel_threshold_list = [channel.get(key) for channel in parameters.get('CHANNELS').values()]
+        if not channel_threshold_list:
+            continue
+        plot_threshold_lines(fig, channel_threshold_list, parameters, **kwargs)
+
+
+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
+
+        if not isinstance(channel_thresholds, (list, tuple)):
+            channel_thresholds = [channel_thresholds]
+
+        for warn_thresh in channel_thresholds:
+            if isinstance(warn_thresh, str):
+                warn_thresh = parameters.get('THRESHOLDS').get(warn_thresh)
+            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(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

@@ -1,48 +1,78 @@
+from base64 import b64encode
 from datetime import timedelta
 
 
-def write_html_table_title(fobj, parameters):
+def _convert_to_textstring(lst):
+    return '\n'.join(lst)
+
+
+def get_html_table_title(parameters):
     title = get_print_title_str(parameters)
-    fobj.write(f'<h3>{title}</h3>\n')
+    return f'<h3>{title}</h3>\n'
 
 
-def write_html_text(fobj, text):
+def get_html_text(text):
-    fobj.write(f'<p>{text}</p>\n')
+    return f'<p>{text}</p>\n'
 
 
-def write_html_header(fobj, refresh_rate=10):
+def get_html_header(refresh_rate=10):
     header = ['<!DOCTYPE html>',
               '<html>',
               '<head>',
-              '  <link rel="stylesheet" media="only screen and (max-width: 400px)" href="mobile.css" />',
+              '  <title>SurvBot status</title>',
-              '  <link rel="stylesheet" media="only screen and (min-width: 401px)" href="desktop.css" />',
+              '  <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">',
               '</head>',
-              f'<meta http-equiv="refresh" content="{refresh_rate}" >',
-              '<meta charset="utf-8">',
-              '<meta name="viewport" content="width=device-width, initial-scale=1">',
               '<body>']
-    for item in header:
+    header = _convert_to_textstring(header)
-        fobj.write(item + '\n')
+    return header
 
 
-def init_html_table(fobj):
+def get_mail_html_header():
-    fobj.write('<table style="width:100%">\n')
+    header = ['<html>',
+              '<head>',
+              '</head>',
+              '<body>']
+    header = _convert_to_textstring(header)
+    return header
 
 
-def finish_html_table(fobj):
+def init_html_table():
-    fobj.write('</table>\n')
+    return '<table style="width:100%">\n'
 
 
-def write_html_footer(fobj):
+def finish_html_table():
-    footer = ['</body>',
+    return '</table>\n'
-              '</html>']
-    for item in footer:
-        fobj.write(item + '\n')
 
 
-def write_html_row(fobj, items, html_key='td'):
+def html_footer(footer_logo=None):
+    footer = ['</body>']
+    if footer_logo:
+        logo_items = [f'<div class="footer">',
+                      f'  <img style="float: right; padding: 10px;" src="{footer_logo}" height=30px>',
+                      f'</div>']
+        footer += logo_items
+    footer.append('</html>\n')
+
+    footer = _convert_to_textstring(footer)
+    return footer
+
+
+def add_html_image(img_data, img_format='png'):
+    return f"""<br>\n<img width="100%" src="data:image/{img_format};base64, {b64encode(img_data).decode('ascii')}">"""
+
+
+def get_html_link(text, link):
+    return f'<a href="{link}"> {text} </a>'
+
+
+def get_html_row(items, html_key='td'):
+    row_string = ''
     default_space = '  '
-    fobj.write(default_space + '<tr>\n')
+    row_string += default_space + '<tr>\n'
     for item in items:
         text = item.get('text')
         if item.get('bold'):
@@ -50,16 +80,16 @@ def write_html_row(fobj, items, html_key='td'):
         if item.get('italic'):
             text = '<i>' + text + '</i>'
         tooltip = item.get('tooltip')
-        color = item.get('color')
+        font_color = item.get('font_color')
-        # check for black background of headers (shouldnt happen anymore)
-        color = '#e6e6e6' if color == '#000000' else color
         hyperlink = item.get('hyperlink')
-        image_str = f'<a href="{hyperlink}">' if hyperlink else ''
+        color = 'transparent' if hyperlink else item.get('color')
+        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 ''
-        fobj.write(2 * default_space + f'<{html_key}{class_str} bgcolor="{color}" title="{tooltip}"> {image_str}'
+        row_string += 2 * default_space + f'<{html_key}{class_str} bgcolor="{color}" title="{tooltip}"' \
-                   + text + f'</{html_key}>\n')
+                      + f'style="color:{font_color}">{text_str}</{html_key}>\n'
-    fobj.write(default_space + '</tr>\n')
+    row_string += default_space + '</tr>\n'
+    return row_string
 
 
 def get_print_title_str(parameters):