Dockerfile

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

README.md

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

__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-docker"
+__version__ = "0.2"

mailing_list.yaml

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

parameters.yaml

@@ -3,7 +3,7 @@ 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: ["ATHR", "DOMV", "EREA", "GR19", "GR27", "HAVD", "LAKA", "LFKM", "TEST"]      # exclude these stations
+stations_blacklist: ["DOMV", "EREA", "GR19", "GR27", "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)
@@ -133,22 +133,14 @@ add_global_links:
      "URL": "https://fdsnws.geophysik.ruhr-uni-bochum.de/map/?lat=39.5&lon=21&zoom=7&baselayer=mapnik"}
 
 # html logo at page bottom (path relative to html directory)
-html_logo: "logo.png"
+html_logo: "figures/Logo_RUB_BLAU_rgb.png"
 
 # E-mail notifications
 EMAIL:
-  # specify mail server and credentials
-  # port, auth_type, user and password are only required if mailserver is not set to "localhost"
-  # user and password can be set to "ENV" or "DOCKER" to read from environment variables or docker secrets
-  mailserver: "smtp.rub.de"           # mail server
-  auth_type: "SSL"                    # mail authentication type, can be "SSL", "TLS" or "None"
-  port: 465                           # mail port, default 465 for SSL, 587 for TLS
-  user: "DOCKER"                      # mail user, read from environment variable if set to "ENV" or from docker secret if set to "DOCKER"
-  password: "DOCKER"                  # mail password, read from environment variable if set to "ENV" or from docker secret if set to "DOCKER"
-  # specify mail recipients, sender and blacklists
+  mailserver: "localhost"
   addresses: ["marcel.paffrath@rub.de", "kasper.fischer@rub.de"]  # list of mail addresses for info mails
-  sender: "RUB SeisObs <seisobs@ruhr-uni-bochum.de>"              # mail sender
-  stations_blacklist: []                                          # do not send emails for specific stations
-  networks_blacklist: []                                          # do not send emails for specific network
+  sender: "webmaster@geophysik.ruhr-uni-bochum.de" # 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: "conf/mailing_list.yaml"
+  external_mail_list: "mailing_list.yaml"

requirements.txt

@@ -1,36 +0,0 @@
-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

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

stylesheets/mobile.css

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

submit_bot.sh

@@ -1,24 +1,19 @@
 #!/bin/bash
+ulimit -s 8192
 
 #$ -l low
-#$ -l h_vmem=2.5G
-#$ -l mem=2.5G
-#$ -l h_stack=INFINITY
+#$ -l h_vmem=5G
 #$ -cwd
 #$ -pe smp 1
-#$ -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
+#$ -N survBot_bg
+#$ -l os=*stretch
 
 source /opt/anaconda3/etc/profile.d/conda.sh
-conda activate survBot
+conda activate py37
 
 # 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/~kasper/survBot'
+python survBot.py -html '/data/www/~marcel/'

survBot.py

@@ -1,8 +1,8 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-__version__ = '0.2-docker'
-__author__ = 'Marcel Paffrath <marcel.paffrath@rub.de>'
+__version__ = '0.1'
+__author__ = 'Marcel Paffrath'
 
 import os
 import io
@@ -23,8 +23,7 @@ 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, \
-    connect_to_mail_server
+from utils import get_bg_color, get_font_color, modify_stream_for_plot, set_axis_yticks, set_axis_color, plot_axis_thresholds
 
 try:
     import smtplib
@@ -739,6 +738,7 @@ 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
@@ -757,10 +757,8 @@ class StationQC(object):
         html_str = self.add_html_mail_body(text)
         msg.add_alternative(html_str, subtype='html')
 
-        # connect to server, send mail and close connection
-        s = connect_to_mail_server(mail_params)
-        if not s: # if connection failed
-            return
+        # send message via SMTP server
+        s = smtplib.SMTP(server)
         s.send_message(msg)
         s.quit()
 

utils.py

@@ -5,7 +5,6 @@ import logging
 
 import matplotlib
 import numpy as np
-import smtplib
 
 from obspy import Stream
 
@@ -280,50 +279,3 @@ 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(self, mail_params):
-    """
-    Connect to mail server and return server object.
-    """
-    # get server from parameters
-    server = mail_params.get('mailserver')
-    # get auth_type from parameters
-    auth_type = mail_params.get('auth_type')
-    # set up connection to mail server
-    if auth_type == 'None':
-        s = smtplib.SMTP(server)
-    else:
-        # user and password from parameters, docker secret or environment variable
-        user = get_credential(mail_params.get('user'), 'mail_user')
-        password = get_credential(mail_params.get('password'), 'mail_password')
-        # create secure connection to server
-        if auth_type == 'SSL':
-            s = smtplib.SMTP_SSL(server, mail_params.get('port'))
-        elif auth_type == 'TLS':
-            s = smtplib.SMTP(server, mail_params.get('port'))
-            s.starttls()
-        else:
-            logging.error('Unknown authentication type. Mails can not be sent')
-            return
-        s.login(mail_params.get('user'), mail_params.get('password'))
-    return s