FCHECK

To assist with the standardization of SeaBASS data files, the SIMBIOS Project developed feedback software, named FCHECK, to evaluate the format of submitted data files. Since then, it has been rebuilt from the ground up by the SeaBASS development team to make it available to the end-users. Using FCHECK, contributors may evaluate the format of their SeaBASS-compatible files prior to submission.


Table of Contents


How does one use FCHECK?

There are three methods for users to check data via FCHECK:

FCHECK: Email Method (most common)

 One or more files may be checked by emailing them as attachments to fcheck@seabass.gsfc.nasa.gov. Upon receipt of the file(s), FCHECK parses the data and metadata and compares them to the required SeaBASS format. FCHECK will send a reply email reporting if the files passed or failed (the response email is generated within minutes for most submissions.) If the files contained errors, the email will describe the nature of the problems.

FCHECK: SFTP Method

 For checking large submissions (either a large number of files or files that are too large for email), you may run FCHECK by uploading the files to the SeaBASS SFTP (SSH File Transfer Protocol) site. The SeaBASS SFTP server requires individual accounts for use and utilizes the same authentication credentials as the data submission process. For details on how to apply for SFTP access, please see our data submission page.

 

Once access has been granted to the SeaBASS SFTP server by the SeaBASS Administrator, there will be an FCHECK directory within your SFTP account. Please create a new subdirectory within a simple name of your choice within your FCHECK directory and upload the SeaBASS files to this location. As a final step, please send an email to fcheck@seabass.gsfc.nasa.gov with the subject line: FTP: my_folder from the email address that was used to register for SeaBASS SFTP access (this is important, as your email address indicates to FCHECK which SFTP account to check). FCHECK will process all the files within your subdirectory and report via a single email the status of each file.

SFTP example:
(A) Create a subdirectory within your SFTP account's FCHECK directory: ~/FCHECK/ocean_blue
(B) Upload several files to that subdirectory: ~/FCHECK/ocean_blue
(C) Send an email from the email address used to register for SFTP access to FCHECK at fcheck@seabass.gsfc.nasa.gov with the subject: FTP: ocean_blue
(D) Receive an email back from FCHECK describing the status (pass, fail, comments) of each uploaded file 

FCHECK: Local Method (via Source Code)

 To run FCHECK locally, download the source, extract it to a folder, and run fcheck4.pl from the command line, giving any folders/files you want checked as an argument. No building or tedious installation is required, nor are any external packages, modules, etc. All you need is Perl (which most Mac and Linux machines already have by default). More information is available in the README provided with the source. The only feature that local FCHECK does not provide is the warning message if a measurement location might be incorrect because it appears to be over land (based on bathymetry references).

Additional Help

You may write to the SeaBASS Administrator with questions, comments, and bug reports.
 

Download Source Code

Source Code (.tar)
 
Last updated: 2018-11-27
 
If you plan to regularly run FCHECK locally in the future, keep in mind that you should periodically check back to see if the source code has been updated, since new fields and other changes are occasionally added. See the change log for details.

Change Log

Date Modifications
2018-11-27
Corrected the unit handling for _cv and _bincount field suffix modifiers
2018-10-22
Minor field updates
2018-02-21
Minor field updates and obsolete_field_warning support
2017-10-13
Minor field updates
2017-08-23
Updates to fields and headers; added support to catch byte order marks
2016-12-19
Minor updates to fields and headers
2016-07-29
Minor updates to fields and headers. Added better support for field name modifiers and suffixes.
2016-05-11   
Minor bug fixes
2016-01-19   
Minor updates to fields and headers
2015-10-05   
Added summary to display types of errors and warnings
2015-02-27   
Improved flagging of INF values and certain whitespace
Improved detection of certain suffixes in fields
2015-01-15   
Updated blank line detection
2014-11-13
Various minor updates to FCHECK and .ini file
2013-08-12   
Various minor updates.
2013-01-30
Fixed fatal error when months were not numerical.
2013-01-25
Fixed detection of a missing /end_header.
2013-01-17
Symbolic links to fcheck4.pl now work.
2012-12-19
Fixed improper checking of invalid number of fields.
Added abs_{ap,ag,ad}.
2012-12-04
Fixed improper handling of duplicate fields.
Fixed detection of oddly formed wavelengths.
2012-11-02 Bug fixes.
2012-05-23 Initial revision uploaded.
 
Tags:
Last edited by Joel Scott on 2018-11-27
Created by Jason Lefler on 2012-05-23