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Directory Structure

This is the recommended (not required) cruise data directory structure for R2R participants, intended as guidance when designing or updating your vessel acquisition system.

(last updated 2012-03-22)

DESIGN GOALS

  1. Preserve original “full”-resolution data from the instruments — especially primary navigation.
  2. Organize files in a fleet-standard directory structure that can be routinely “broken out” shoreside by regular expression matching against vessel instrument profile.
    • Segregate the “routine underway” data (resident digital instrument systems) from everything else (science party files, visiting national facility data, etc).
    • Segregate data from documentation.
    • Segregate the original instrument data from secondary products and/or processed data.
  3. Preserve an “exact copy” of what the science party took home.

 

DIRECTORY TREE

      CRUISEID/

        docs/ – personnel list, cruise report, vessel diagrams, etc.

        r2r/
              eventlogs/ – produced by (or formatted for) the R2R Event Logger
              info/ – controlled vocabularies, etc. synced from shore
              www/ – HTML pages and associated content synced from shore

        system/   where system is either the vessel's native serial acquisition system (scs, calliope, vids, etc, or simply "das") or a standalone system (adcp, ctd, multibeam, xbt, etc)
              docs/ – manuals, photos, calibration sheets, etc. specific to this instrument system
              raw/
                    devicetype[_[make][model]][_location][_mnemonic]–dateTtimeZ
              proc/
        where mnemonic allows finer-grained separation of device interfaces - could be serial number, datatype (“centerbeam”), or just a number

        science/ – “dropbox” files created by the science party

 

BEST PRACTICES

  • Cruise IDs are unique within R2R. The exact naming style is each operator's prerogative, but IDs should begin with the vessel's unique prefix.
  • Directory and file names use standard vocabulary of device type, make, and model. Names are lower case, with no spaces or non-alphanumeric characters except nonconsecutive underscores and periods. R2R will never chop up, recombine, or rename files.
  • Write all data from the same “talker” (instrument interface) (i.e. multiple NMEA sentences from the same GNSS receiver port) to the same file. Data file granularity is daily where possible.
  • Individual files are not compressed. If compression is required, create a tarball of the entire cruise distro and zip that tarball using GNU gzip (.gz.). Alternatively, zip on-the-fly during network transfer.
  • Operator delivers a checksum manifest with each distro so that R2R can re-validate shoreside, using the "md5deep" program:
                    md5deep -c -r -l -o f -t -z cruise > cruise.md5deep
  • Cruise distros are posted for R2R to download via network transfer (rsync) or shipped on a USB portable drive with NTFS/EXT* filesystem.