R2R Event Logger User Guide  

Version 1 of this file: 20130719
This is version 2.

R2R ECFM Admin

 FAQ 

This FAQ list that may prove helpful for ship techs and administrators of R2R Elog.

Problems that users may encounter

Q: Elog isn't working. What is wrong and what can I do?
Q: How to get to the configure page (and also to control the Operational State)
Q: Users may find they are 'kicked out' to the(often empty) list of events when trying to enter an event(probably the first time) or add instruments or participants. What is going on?
Q: The 'submit final config' button was hit prematurely
Q: The 'end event logging' button was hit prematurely
Q: When I go to start my cruise, I get stuck on the 'create new cruise' page. What is wrong and what can I do?
Q: What actions should I add for a custom instrument? Can I add more actions for instruments from the database?
Q: Lat, Lon or GPS_Time is Nan. Can this be fixed?
Q: I forgot to enter an event a while ago. Can I enter it now? or later?
Q: Can I edit an event? How?
Q: I want to be able to view my events off the ship using elog. Can I do this? How?

Problems that administrators and techs may encounter

Q: Serial GPS is being used but baud rate is other than 4800. How do I change the baud rate?
Q: What to do in case of GPS UDP port change (this may occur on Endeavor if there is a problem with the primary GPS feed)?
Q: How to switch between edist installations (in case a new distribution doesn't work and you want to go back to a previous version)
Q: How does GPS work in the R2R Eventlogger?
Q: What is a dreamplug?
Q: How do I log onto the dreamplug command line?
Q: How to perform system operations on the dreamplug?



Q: Elog isn't working. What is wrong and what can I do?

A: Many things can cause the eventlogger to have problems. Some are simple and others are very complicated. The list below is roughly in order of complexity of the problem.



Q: How to get to the configure page (and also to control the Operational State)

A: The URL is:

http://[elog server name or IP address]:8090/[cruiseID]-SE/?cmd=ecfmhome

Note that without the cruiseID many aspects of configuration and event entry will fail.
A hint for how to figure out the cruiseID is to first go to http://[elog server]:8090/ which will complete itself to include the cruiseID and be directed to the configuration page.
Then to get to the logbook, use the link on the configuration page to 'Show Eventlog' which will open a new tab with the logbook(list of events).


Q: Users may find they are 'kicked out' to the(often empty) list of events when trying to enter an event(probably the first time) or add instruments or participants. What is going on? Is elog broken?

A: This is caused by a URL that doesn't include the cruiseID. The URL format is:

    http://[elog server name or IP address]:8090/[CRUISEID]-SE/

Using the part of the name up to and including the port is enough to get started. When this is entered, the cruiseID will be added automatically and the browser is directed to the configuration page. Without the cruiseID in the URL, many aspects of configuration and event entry will not work.


Q: The 'submit final config' button was hit prematurely. What are the consequences and how to recover?

A: Instruments and Participants can be edited but will not be in the configuration zip file to be carried to the ship. A new zip file cannot be created. This is only an issue when using the shore server to make a preconfiguration file to be loaded on the ship.(CHECK THIS!!!! Maybe on ship, the final config file will not include instruments/participant changes made after submit?)
To recover, remove the lock file: /shipdata/[cruiseID]/r2r/eventlog/elog/ecfm/ecfm_lock_precruise_complete.lck and ecfm is returned to the 'Configuration in Progress' state.


Q: The 'end event logging' button was hit prematurely. What are the consequenses and how to recover?

A: Events can still be entered but will not be part of the cruise zip and csv files which have already been created at this point and will be available for download after selecting 'End Cruise'.
To recover remove the lock file: ecfm_lock_cruise_complete.lck and ecfm is returned to the 'Event Collection in Progress' state.


Q: When I go to start my cruise, I get stuck on the 'create new cruise' page. What is wrong and what can I do?

A: Once a cruise name has been entered, it can not be reused. This is to ensure a logbook does not get inadvertantly deleted or overwritten.
If there is success creating the new cruise, the page changes to the ECFMHome page.
If you are stuck on the 'create new cruise' page there is some problem creating the cruise. It is possible the problem is a duplicate cruise number.
No error is shown if <cruiseID> exists when trying to use 'create new cruise', but you stay on that page.
The fix requires that someone log onto the
dreamplug command line and perform the following steps (as root using sudo): Now the cruise can be started from 'create new cruise'. Care must be taken ensure the file associated with the cruise linked to /shipdata/cruise_cfg/current_cfg does NOT get changed. Note that case(upper/lower) matters with cruise names. If the cruiseID you want is already used, you can change the case to create it without having to use the command line.
There may be other issues that cause this problem. Check other answers or send email to elog@rvdata.us for more help.


Q: What actions should I add for a custom instrument? Can I add more actions for instruments from the database?

A: A good practice is to anticipate all actions that might be performed for a particular instrument and put them into the configuration. Bad practice is to have a limited list of actions and using 'other' with repetative text in the comments. This leads to an inconsistent logbook which is difficult to sort.
But a balance must be struck. Too few actions and 'other' will be used too much. Too many actions can also be a problem as users try to navigate a long list. Consider adding more actions to instruments like 'ship' (startTransit/endTransit) and sorting the actions for ease of use. To handle all situations, each instrument should have 'Other' as an action and there should be an instrument 'other' with action 'other'.
Check out these
sample configurations.


Q: Lat, Lon or GPS_Time is Nan. Can this be fixed?

A: Yes, this can be fixed by editing the event. Select Edit and make sure the GPS_Time contains the desired value(no need to change it if it is not NaN) and select Submit. The Lat and Lon will be filled in from the GPS database.
One caveat is that the database must have been started before the time being entered. The database is started when 'Create New Cruise' is pressed.
Occasionally this occurs because the program doesn't get a reply to the query to the UDP port within the timeout period. If it occurs a lot there may be a problem with a lot of network traffic causing a timeout. There is a separate query for Lat, Lon and GPS_Time so some of these may be nan when others contain a valid value.
If all three fields are Nan there may be a problem with the UDP packets containing the GPS data.



Q: I forgot to enter an event a while ago. Can I enter it now? or later?

A: An event can be entered later than it happened by entering the GPS_Time in the field on the
New event form


Q: Can I edit an event? How?

A: Select an event and then select
Edit at the top of the page. Editable fields are changable.


Q: I want to be able to view my events off the ship using elog. Can I do this? How?
A: Yes, you can install elog on your own computer to do this. Go to
https://midas.psi.ch/elog/download.html to get the source code and install it using directions here.


Q: Serial GPS is being used but baud rate is other than 4800. How do I change the baud rate?

A: The script collecting serial data is:
/home/r2root/current/bin/elog/redirect_serial.pl
Around line 30 is the setting for baud rate. Change the value and save the file. Then look for the process running the script redirect_serial.pl (Hint: ps auxw | grep redirect_serial) and kill the process. It will be restarted on next :10 minute interval by crontab and should come up running with the new baud rate which can be checked by: ps auxw | grep elog.

This change will only be in effect for the current cruise. To make the change permanent. Edit the value of GPSUDP in the file:
/home/r2root/CRUISE_TEMPLATE/r2r/info/cruise_cfg/[shipID]_cruise.cfg
When the next cruise is started, this value will be used.
Ths requires logging onto the
.


Q: What to do in case of GPS UDP port change?

A: A cron job restarts the elogd process every 30 minutes. Changes made to the ship's config file will take effect at that time.
To avoid waiting until the next 1/2 hour restart of the process, reboot the dreamplug. Reboot takes a few minutes.
A command line can also be used to restart the process. The process must be run as r2relog, so to run the command as the r2relog user:
  
    > sudo su - r2relog
    > /home/r2root/current/bin/elog/restart_elog >> /dev/null 2>&1
    > exit


Q: How to switch between edist installations (in case a new distribution doesn't work and you want to go back to a previous version)

A: Sample listing of an r2root home directory:
current -> r2r_edist-1.3.12/
dist/
ecfm_install
r2r_edist-1.3.12/
r2r_edist-1.3.11/
This above installation is running edist version r2r_edist-1.3.12. The symbolic link current points to this distribution.
To change back to distribution r2r_edist-1.3.11 the steps are:
  1. Stop the current elog process.
    In the browser go to:
    http://[servername or IP]/r2r-bin/manage_elog
    Under 'Elog Processes Running' click 'stop' (select 'refresh' to update page).

  2. On the command line, remove the original link: current:
    from /home/r2root/:
        % rm current
        
  3. Add a new symbolic link pointing to the desired distribution:
    from /home/r2root:
        % ln -s r2r_edist-1.3.11 current
        
  4. Start the elog process:
    In the browser go to:
     http://[servername or IP]/r2r-bin/manage_elog
    click 'start' next to the cruise you want to start
    click 'refresh' next to 'Elog Processes Running'
    see the new elog process running
    You are now running the r2r_edist-1.3.11 distribution
Note: You can also stop/start the elog process from the command line:
sudo /home/r2root/current/bin/elog/restart_elog


Q: How does GPS work in the R2R Eventlogger?

A: The R2R Eventlogger expects ship's GPS data to be broadcast on a UDP port (e.g. 55150).
If the ship does not support this, then a process is run on the dreamplug to read serial GPS and redirect it to a UDP port (55000 by default).
Each ship has a specific configuration file which contains the default value for the GPSUDP port for that ship.
If a ship is known to use serial GPS only, this port is set to 55000 which is the default for redirecting serial to UDP by the R2R Eventlogger.
Process 'rt_datalog.pl' runs in the background (owned by r2relog) and:
Routine 'get_gps_latlon' is called from the elog cfg file whenever an event is entered.

Q: What is a dreamplug?

A:
Dreamplug is the name of the hardware the the R2R Eventlogger is running on for Ship Resident installations. More information is available at Global Scale Technologies


Q: How do I log onto the dreamplug command line?

A: Use ssh from another Linux system on the ship's network. If no Linux system is available on the same network as the dreamplug, a program called
putty.exe can be used to access the dreamplug command line from a Windows system.



Q: How to perform system operations on the dreamplug?

A: The dreamplug or netbook running the R2R elog server is running the
Ubuntu(a form of Linux) operating system.
Without some basic understanding of Linux commands, caution is advised to avoid creating problems.
See the question above this one for how to log onto the dreamplug. Many of the commands to run need to be run as root so familiarity with sudo is advised.
Some of the Linux commands used include: ls, cd, ps, rm, grep, vi.
If none of these commands are familiar, contact the R2R elog team at elog@rvdata.us for help.

 Sample Configurations 

These sample configurations files may be useful:

This configuration is rather complex with several types of incubations.
Instrument              Actions
CTD911                  deploy,maxDepth,recover,abort,other
Net_trap                deploy,recover,abort,other
PIT_trap                deploy,recover,abort,other
NetPIT_trap             deploy,recover,abort,other
planktonNetTow          deploy,recover,abort,other
McLanePump              deploy,recover,abort,other
EIMS_O2/Ar              start,end,abort,calibrate,service,other
SeaFlowCyto             start,sample,end,abort,other
Air_HOCs                start,end,abort,other
Water_HOCs              start,end,abort,other
Water_TOX               start,end,abort,other
incubation_Kuj          start,sample,abort,other
incubation_VM           start,sample,abort,other
incubation_Dyhr         start,sample,abort,other
incubation_Arn          start,sample,abort,other
incubation_Hew          start,sample,abort,other
incubation_multi        start,sample,abort,other
incubation_other        start,sample,abort,other
ADCP75                  start,stop,service,other
ADCP300                 start,stop,service,other
MeteorologicalSensor    start,stop,other,
Thermosalinograph SBE45 startLine,endLine,abortLine,sampleLine
XBT                     release
Mooring                 recover,other
Ship                    startCruise,endCruise,other
Other                   start,end,other

This configuration is somewhat simpler. Notice the custom actions for the two types of OBS's. Also notice the different order of the instruments.
Instrument              Actions
CTD911                  deploy,maxDepth,recover,abort,other
Thermosalinograph SBE45 startLine,endLine,abortLine,sampleLine
ADCP150                 start,stop,service,other
MeteorologicalSensor    start,stop,other,
Other                   start,end,other
Ship                    startCruise,endCruise,other
XBT                     release,other
Fluorometer             startLine,endLine,abortLine,sampleLine
Echosounder12           startLine,endLine,abortLine
Echosounder3.5          startLine,endLine,abortLine
LDEO APG Deepwater OBS  other,deploy,recover,startStation,endStation,start acoustic survey,end acoustic survey,On Bottom
LDEO TRM OBS            other,deploy,recover,startStation,endStation,On Bottom,Released from winch,start acoustic survey,end acoustic survey

Here is another configuration with a few different instruments in a different order.
Instrument              Actions
Ship                     startCruise,endCruise,other
Mooring                  deploy,service,recover,startLine,endLine,abortLine,other
CTD911                   deploy,maxDepth,recover,abort,other
ADCP75                   start,stop,service,other
Echosounder3.5           startLine,endLine,abortLine
Other                    start,end
Thermosalinograph SBE45  startLine,endLine,abortLine,sampleLine
XBT                      release
MeteorologicalSensor     start,stop,other
Fluorometer              startLine,endLine,abortLine,sampleLine
12 kHz pinger            deploy,recover,start,end,service,other
Echosounder12            startLine,endLine,abortLine
Seabeam                  start,stop,other
ADCP300                  start,stop,service,other


 More information 

For more information or if you have additional questions about the current cruise ELOG send email to: elog@rvdata.us

   

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