How to place data on your own JGOFS Server
The JGOFS Data system was designed with the flexibility to serve
data from the Investigator's own workstation. The U.S. GLOBEC
Georges Bank Program encourages our scientific investigators
to serve their data from their own computers, ensuring that
the most up to date data are made available to others in the project.
Determine if your format can be read by the system
After data is ready to be shared with other Investigators in the
program, check its format against the samples provided by the DMO. If the
format of your data does not exactly match one of the existing
sample formats, a decision needs to be made to either change the
data format to conform to the most similar sample format or to
request a modification to one of the formats. If the data does
match one of the formats, note the name of the "method" or
translation program that can read that format. Now you know most of
the pieces required by our system: the method name, the name(s) of
the files to be served, and where they will reside on your system.
Install a JGOFS server
The next step is to download the
system software from the Distribution site. Follow the
instructions offered with the software for downloading the JGOFS
software as a tar file. We suggest that a new user be created on
your system with the username, 'jgofs'. This user can be the one
who installs and, therefore, owns the software. The user 'jgofs'
should have its own group id and a user id that differs from any
other user on your system. Install the JGOFS Data System according
to the directions online. If you have problems while installing the
software, contact the
DMO for assistance.
Placing data on the server
Once you have a working server installed on your workstation,
you are ready to tell it where your data are located. As user
'jgofs', make certain that you can read the data files [suggestion:
'more' one or more of the files]. This will ascertain that the
system (run as jgofs) will have permission to read and serve the
There are two files that tell the JGOFS system where to find data and how to read it:
These two files are located in the objects subdirectory tree of the
JGOFS Data System. For example, if you chose to install the system
at /home/machinename/globec, your data objects information will be
located starting at /home/machinename/globec/objects. Below this
level are the directories which are displayed by the system automatically.
- The .remoteobjects file contains a three line entry for
every object available through the JGOFS data system in a given
category. The three lines entered in the .remoteobjects file should
be inserted alphabetically by the Principal Investigator's last name
and will appear in this order on the system. The information given
by the 3 line entry is:
- Line 1:
- the name of the data object to display, limited to 18 characters
- the machine where the data is located, even if that machine is the local machine
- the location of the .objects file on the serving machine
- the name of the data object entry in the .objects file.
- Line 2: the name of the Principal Investigator responsible for collecting the data
- Line 3: a brief description of the contents of the data object
The structure of the 3-line entries in .remoteobjects is, where ^
indicates a required blank space:
- -^Brief description of the data
An example of an entry is:
- - James Manning
- - Wind Stress
- The .objects file contains a one (1) line entry for each
object that it serves. The object name in the .objects file must
exactly match the object name at the end of the URL-like entry
beginning with //machine in the corresponding .remoteobjects file.
This one line entry provides the following information:
- the exact directory and filename(s) of the data on the local system
- which method, or translation program, to use to access it
- optionally, limits the parameters displayed by the system
Structure of .objects is as follows:
An example of an entry is:
Optionally, one may restrict the parameters to be served.
For example, an extended syntax allows:
The existence of the item [,optional_list_parameters] indicated
above, identifies the parameters which will be served by the system
and may restrict which of these will be served, also. For example,
a line such as
displays only station, pressure, salinity, and PAR parameters,
excluding any others which may reside in the data file a119.ctd. A
further restriction to the parameters is made by specifying only
stations numbered less than 150 e.g. station<150.
Contact the DMO for correct syntax for your
object, if you are unsure.
The main U.S. GLOBEC Georges Bank server has as its top level, a /gb/
category, below which are the five categories, broadscale, modeling,
mooring, process, and satellite. We further divide these categories
by year. So, for example, CTD data from a 1996 process cruise would
Assume that you are serving data from Georges Bank, 1997 process cruises.
You would create a subdirectory structure like this:
indicating that you want to display /gb/process/1997 as your
category of data. The .remoteobjects and .objects files containing
the information about the process data from 1997 would be located in this
Documents detailing protocols of scientific methodology related to
sample or data collection, need to be available for proper
utilization of the data. We ask that these documents be submitted
to the DMO before you begin to serve your data.
Notes specific to a particular dataset, perhaps indicating anomalies
at the time of collection or during the processing of data can be
served with the information, documenting the parameter names used in
the data. We do require that the parameter names be defined and
that the units be clearly stated. The name of the object (from the
.remoteobjects file) is used to provide the filename for another
file that is also part of the system.
The objectname.info file is located in the same directory as
the .remoteobjects and .objects files. It provides information
related to data collection as well as the object's parameter names,
their descriptions and units. Also included are the ship name,
cruise identifier, the Principal Investigator(s)'s full name and
links to any additional notes. Place four spaces between the
longest parameter name and its description and keep lines to an 80
character maximum length to ensure the list will be visually
aesthetic. A template for the
objectname.info file is provided.
Spot-check the data
All the pieces required to display data on the system are now in
place. Using a browser, visually inspect the data to insure proper
alignment, etc. Use the "List all at next level" followed by the
"Flat listing" features of the system and refer to the original file
to insure that every record of the dataset is displayed.
Let the world know
data is ready to be incorporated into the category collection. In
other words, the data that you have prepared and are now serving
needs to be made available to the other Investigators as part of the
Process Study data set. To do this, send the .remoteobjects file to
the Data Management
Office to be added to its larger file of entries. The DMO
will update the List of Available Objects.
Note: If the above instructions were not clear,
here for another version of these instructions.
Last modified: August 29, 2005
Original text: C. Hammond