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. There are multiple ways to access this software, as explained further below. Using FCHECK, contributors may evaluate the format of their SeaBASS-compatible files prior to submission.
 
FCHECK scans files for common syntax problems, missing header information, data values outside of typical ranges, nonstandard field names or units, and also detects various other issues. It will report a summary of the types of problems detected (if any) among all the files it scanned, as well as a more detailed breakdown of issues found in each individual file. Problems are classified as either errors or warnings, depending on their severity. Errors are critical problems that must be addressed before files can be archived. Warnings should be fixed if possible, but some of them are subjective or optional and may be disregarded.


Table of Contents


How does one use FCHECK?

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

Option 1: Email files as attachments

FCHECK can be run on one or more data files by attaching them to an email sent to fcheck@seabass.gsfc.nasa.gov.
 
There are 2 requirements to use this method
1. You must have already registered a submitter account with us. For details on how to apply for SFTP submitter account, please see our data submission page.
2. You must email FCHECK from the email address that you picked to be associated with your account.
 

Option 2: SFTP Method

FCHECK can be run on one or more data files by uploading them using your SeaBASS SFTP (SSH File Transfer Protocol) credentials. 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. Create a new subdirectory within your FCHECK directory. Use a simple folder name of your choice (but avoid spaces and special punctuation) and upload your SeaBASS data files within it. 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 email you the results.

 

The email results are typically returned within minutes, unless the total file size of your data files is large (dozens of megabytes or more could take longer). If you do not receive an email, check your spam folder, and also make sure you are using the email address you used to register your SFTP account.

SFTP example:
(A) Create a subdirectory within your SFTP account's FCHECK directory: ~/FCHECK/ocean_blue
(B) Upload several SeaBASS data 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

 

Option 3: 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

Download Source Code (.tar)
 
Last updated: 2020-11-02
 
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
2020-11-02
Minor header updates
2020-10-28
Minor field and headers updates, mostly related to archiving IFCB measurements
2020-08-18
Minor field updates
2020-07-08
Minor field updates, mostly related to archiving EXPORTS measurements
2020-06-18
Minor field updates, mostly related to archiving EXPORTS measurements
2020-05-04
Non-ASCII characters are now detected as errors
2020-04-22
Minor field updates
2020-04-04
Minor field updates, mostly related to archiving EXPORTS measurements
2019-09-25
Minor field updates, mostly related to archiving EXPORTS measurements
2019-09-06
Minor field updates
2019-08-06
Minor field updates
2019-07-03
Minor field updates
2019-05-22
Minor field updates including size fractionation suffixes (_#umfilt & _#umprefilt)
2019-04-25
Minor field updates
2019-03-22
Minor field updates
2019-02-08
Added support for one-to-many base-field suffix mapping.
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 Inia Soto Ramos on 2019-09-25
Created by Jason Lefler on 2012-05-23