[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

@@ -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
+### 0.2
-- html mail with recent status information
+
-- updated web page design
+* surveillance of mass, clock and gaps
-- restructured parameter file
+* individual mailing lists for different stations
-- recognize if PBox is disconnected
+* 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

@@ -1,9 +1,9 @@
 # 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", "LFKM", "GR19", "LAKA"]      # 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)
@@ -56,7 +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.:
@@ -117,6 +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)
@@ -130,17 +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"
+  # 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: []                     # do not send emails for specific stations
+  mailserver: "smtp.example.org"      # mail server
-  networks_blacklist: []                           # do not send emails for specific network
+  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
+#$ -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

@@ -1,8 +1,8 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-__version__ = '0.1'
+__version__ = '0.3'
-__author__ = 'Marcel Paffrath'
+__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
@@ -233,7 +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():
@@ -350,7 +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
@@ -594,6 +595,7 @@ class StationQC(object):
         self.status_track = status_track
 
         self.powbox_active = self.is_pbox_activated_check()
+        self.mass_active = self.is_mass_activated_check()
 
         self.start()
 
@@ -738,7 +740,6 @@ 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
@@ -757,8 +758,10 @@ 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()
 
@@ -1078,6 +1081,11 @@ 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:
@@ -1297,7 +1305,7 @@ 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()}: '
@@ -1339,6 +1347,12 @@ class StationQC(object):
         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."""
@@ -1393,15 +1407,15 @@ class StatusOK(Status):
 
 
 class StatusWarn(Status):
-    def __init__(self, message='WARN', count=1, last_occurence=None, detailed_messages=None, show_count=False):
+    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_occurence,
+        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):
+    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_occurence,
+        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
@@ -1418,8 +1432,8 @@ class StatusError(Status):
 
 
 class StatusOther(Status):
-    def __init__(self, messages=None, count=1, last_occurence=None, detailed_messages=None):
+    def __init__(self, messages=None, count=1, last_occurrence=None, detailed_messages=None):
-        super(StatusOther, self).__init__(count=count, last_occurrence=last_occurence,
+        super(StatusOther, self).__init__(count=count, last_occurrence=last_occurrence,
                                           detailed_messages=detailed_messages)
         if messages is None:
             messages = []

utils.py

@@ -5,6 +5,8 @@ import logging
 
 import matplotlib
 import numpy as np
+import smtplib
+import os
 
 from obspy import Stream
 
@@ -173,7 +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
 
@@ -279,3 +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

@@ -19,12 +19,13 @@ 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>']
     header = _convert_to_textstring(header)
     return header
@@ -86,7 +87,7 @@ def get_html_row(items, html_key='td'):
         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'
+                      + f'style="color:{font_color}">{text_str}</{html_key}>\n'
     row_string += default_space + '</tr>\n'
     return row_string