Collecting instrument data using BioBeamer

Install

• ensure you have python 2.7.*
• pip install PyFGCZ
• git clone [email protected]:fgcz/BioBeamer.git

Configure

BioBeamer xml configuration file

<?xml-stylesheet type="text/xsl" href="BioBeamer.xsl"?>
<BioBeamerHosts>
<host name="fgcz-i-180" 
    instrument="TRIPLETOF_1"
    min_size="1024" 
    min_time_diff="10800" 
    max_time_diff="2419200" 
    simulate='false' 
    func_target_mapping="map_data_analyst_tripletof1" 
    robocopy_args="/E /Z /NP /R:0 /LOG+:C:\\Progra~1\\BioBeamer\\robocopy.log"
    pattern=".+" 
    source_path="D:/Analyst Data/Projects/" 
    target_path="\\130.60.81.21\\Data2San">
    <b-fabric>
        <applicationID>93</applicationID>
    </b-fabric>
</host>
</BioBeamerHosts>

the xml can be validated using

xmllint --noout --schema BioBeamer.xsd BioBeamer.xml

or

xmlstarlet val --xsd BioBeamer.xsd BioBeamer.xml

Deploy @ new location

• change syslog host
• change configuration url

Configure Syslog '/etc/rsyslog.conf'

$template tplremote,"%timegenerated% %HOSTNAME% %fromhost-ip% %syslogtag%%msg:::drop-last-lf%\n"
$template RemoteHost,"/var/log/remote/%HOSTNAME%_%fromhost-ip%.log"

if ($fromhost-ip != '127.0.0.1') then ?RemoteHost;tplremote  
& ~

Configure logrotate '/etc/logrotate.d/remote'

/var/log/remote/*
{
        rotate 13
        monthly
        missingok
        notifempty
        compress
}

Run

@ FGCZ

just 'run as administrator' justBeamFiles.exe.

justBeamFiles.exe is an autoitscript. In our case the justBeamFiles.exe maps the storage and runs the fgcz_biobeamer.py script which uses robocopy.exe on Micorsoft installed PCs to sync the files.

otherwise

• ensure that SAN is mounted

python BioBeamer.py

BioBeamer class

Author

Christian Panse 🚀

See also

• fgcz-intranet wiki page
• FGCZ configuration

TODO

• munin plugin �