Practical work on NEMO Converting files

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Practical work on NEMOConverting files

• M. Fichaut

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From ASCII data to XML files
Coupling table
Export
Coupling table
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NEMO installation

• Open the install_nemo_1.4.4_windows.zip file (on
  the desktop)
• Unzip it
• Double click on launcher_nemo.bat
• Follow the installation procedure
• Dont forget to add the NEMO shortcut on your
  desktop

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Collection of ASCII files

• Training data set
• 6 CTDs raw files under
• SDN tools/Practical work/data/input files
• ASCII files with measured parameters in column
• Measured parameters Depth, Temperature,
  Salinity, Fluorescence and Dissolved oxygen

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First step conversion to ODV with NEMO

• Run NEMO to convert the files to ODV format.
• Modify the settings of NEMO
• Default directories for data set to
• SDN tools/Practical work/data
• Default directories for data set to
• SDN tools/Practical work/models
• Enter your EDMO ID in the field below using the
  search function (right click)
• Proceed the 4 steps of NEMO

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NEMO File description

• Choose the type of file (cruise directory, cruise
  file, )
• Browse your PC to input the data files directory
• Once the file is open in NEMO, have a look to its
  content
• Choose file type Profile
• Choose the output format ODV, one unique file
  for all stations or One file per station
• Enter the Station header information
• there is a specific character string at the end
  of each Station header END
• The Data termination indicator is EOF (End of
  file)
• Validate the step when description is OK

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NEMO Station description

• Station number is given on line Station
• Data type is CTD stations
• Time is U.T.
• Latitude format is NDD MM.mm
• Longitude format is NDDD.MM.mm
• Bottom Depth is not available
• Input all the mandatory fields station number,
  time, date, latitude, longitude
• Use the Test function to verify your input
• Validate the step when description is OK

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NEMO Data description (1)

• Select the parameter list to use P011 via P021
• Add the parameters P021 codes are
• Depth AHGT, Temperature TEMP, Salinity
  PSAL, Fluorescence FVLT, Dissolved oxygen
  DOXY, Input the units of the parameters (for
  salinity, use Dimensionless)
• Add a text label to each parameter
• Set Start and End positions for the parameters
• Tell NEMO which code is the vertical reference

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NEMO Data description (2)

• Format is mandatory
• Describe the output format that you want
• 6.1f means 6 digits total (decimal point
  included), 1 digit for decimal, f for float
  (decimal number)
• Use the contextual menu Select the format for
  predefined format
• Use the test fields to validate your input
• Validate the step when description is OK
• Save you model in the model directory

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File conversion

• You will be asked to give
• A dataset reference (can be a cruise name, for
  example)
• A name for the output file (all the stations in
  the same file) or name for the output directory
  (one station per file) in the SDN
  tools\Practical work\output directory
• Have a look to the output files
• Drag and drop the ODV files in ODV to test their
  conformity

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Practical work on NEMOGenerating CDI summary and
coupling table

• M. Fichaut

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From ASCII data to XML files
Coupling table
Export
Coupling table
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Creation of the CDI-SUMMARY and the coupling table

• Input the information in NEMO SETTINGS
• Mapping
• Click in the box Generate mapping for SeaDataNet
  download Manager
• SeaDataNET CDI summary
• Unfold the SeaDataNet CDI Summary block
• Click in the box Generate SeaDataNet CDI summary
• Fulfill all the mandatory fields (in red), using
  right click for the Search function

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Run the file conversion

• Same file than in the previous exercise
• You will be asked to give
• A dataset reference (can be a cruise name, for
  example)
• A name for the CDI summary file
• A name for the output file (all the stations in
  the same file) or name for the output directory
  (one station per file)
• An output directory prefix (for the coupling
  table). This prefix will be subtracted from the
  file name in the mapping table.
• For example if
• output file name C\username\NEMO\cruise_name\fi
  le_name
• and output directory prefix C\username\NEMO
• file name in the mapping table will be
  cruise_name\file_name

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CDI summary file

• Convert it to an EXCEL file (for future use by
  MIKADO)
• Open the CDI summary text file with EXCEL (field
  delimited by tabulations)
• Rename the folder into STATION
• Save it under XLS or XLSX format, it will be used
  later on during the practical work on MIKADO

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Coupling table

• Have a look at the coupling table
• Menu Coupling_tablegtEdit
• It gives the link between the LOCAL_CDI_ID and
  the file in which the LOCAL_CDI_ID will be found
  by the download manager of SeaDataNet
• MODUS 1 if the LOCAL_CDI_ID is in a
  mono-station file
• MODUS 3 if the LOCAL_CDI_ID is in a
  multi-station file
• One LOCAL_CDI_ID and one format is unique in the
  coupling table
• Add and delete records
• Export the coupling table in a flat file
• Menu Coupling_tablegtExport
• Have a look at the flat coupling.txt file

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Practical work on MIKADOCreation of XML files
for CDI

• M. Fichaut

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Exercise 1

• CDI Automatic generation from the CDI summary
  file created this morning with NEMO Validation
  of the XML files
• Creation of the corresponding coupling file

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From ASCII data to XML files
VALIDATOR
a
b
Coupling file for DM
Coupling table
Export
Coupling table
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a) Configuration file for CDI XML

• Run MIKADO
• Open the configuration file delivered with NEMO
  
• MIKADO gt Automatic/Open/CDI
• the configuration file is in the
  HOME_DIRECTORY of NEMO, but for the training it
  is under \Practical work\config , file
  summary_CDI_NEMO.xml
• Make the connection with the Excel file that you
  have created with NEMO (the Excel file must be
  closed to avoid conflict access)
• Check the connection (you must have a green
  message)
• Go to the Queries tag and have a look at the
  queries
• Check them (green message after check all)
• Save your configuration file

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a) XML file generation

• Run Automatic/Generate/CDI
• Open the configuration file
• \Practical work\config\summary_CDI_NEMO.xml
• Choose the export directory (where CDI XML files
  will be written)
• Choose the type of export file you want
• XML files
• Zip file containing the XML files
• Both (XML and Zip)
• Open one XML export file to have a look at it
  with MIKADO ManualgtOpengtFilegtCDI

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a) Web validation service Validator

• Check the XML file with the Web validation
  Service at http//www.seadatanet.org/validator
• Select the CDI catalogue
• Validate file with CDI Xml schema
• Upload one of the XML file that has been
  generated
• Validate the file
• Look at the result of the validation you must
  have no error, you can have some warnings
  depending on the vocabulary versions.

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b) Coupling configuration file

• Run MIKADO
• Open the configuration file delivered with NEMO
  
• MIKADO gt Tools/Coupling table for download
  manager/ Import CDI configuration
• the configuration file is the same than in a)
  ) in the config directory
• Check the connection to the excel file
• \Practical work\config\CDI_summary_with_ad
  dress.xls
• Go to the main query tag and check the query (you
  must have a green message)
• Go to Modus 1 or Modus 3, choose the output
  format and fulfill the query which retrieve the
  file address in the excel file
• Check it
• Preview the coupling file
• Save your coupling configuration file

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b) Coupling file generation

• Run the generation of the coupling file
• MIKADO gt Tools/Coupling table for download
  manager/ generate/ Modus 1 or Modus 3 depending
  on your ODV file(s)
• Select the configuration file for coupling that
  you just create
• Select the output directory
• Choose the mode for writing
• Generate the coupling file
• Open it with a text editor

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Exercise 2

• EDIOS manual input of
• 1 Program
• 1 Series
• 1 Platform

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Under SDN_tools\practical_work

• Under \EDIOS__POSEIDON_Example\EDIOS_Data
• Open the EDIOS_POSEIDON.xls file describing the
  EDIOS program, series and platforms (1 program,
  15 series,15 platforms)
• Input the program information into MIKADO and
  create the corresponding XML file
• Input 1 series information into MIKADO and create
  the corresponding XML file
• Input the platform related to the previous series
  in MIKADO and create the corresponding XML file
• Why cant you first enter a platform, then a
  series then a program?

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Exercise 3

• EDIOS Automatic generation of XML files for
• Program
• Series
• Platforms

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Under SDN_tools\practical_work

• \EDIOS__POSEIDON_Example\EDIOS_Data
• Open the EDIOS_POSEIDON.xls file describing the
  EDIOS program, series and platforms (1 program,15
  series, 15 platforms)
• Run MIKADO to create the automatic query to
  retrieve the program information
• Or open the already written XML configuration for
  MIKADO for EDIOS program \EDIOS__POSEIDON_Exampl
  e\queries\poseidon_edios_program.xml
• Run MIKADO to create the automatic query to
  retrieve the series information
• Or open the already written XML configuration for
  MIKADO for EDIOS program \EDIOS__POSEIDON_Exampl
  e\queries\poseidon_edios_series.xml
• Run MIKADO to create the automatic query to
  retrieve the program information
• Or open the already written XML configuration for
  MIKADO for EDIOS platform \EDIOS__POSEIDON_Examp
  le\queries\poseidon_edios_platform.xml

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Generate the XML EDIOS files

• EDIOS PROGRAM
• Run MIKADO AutomaticgtGenerategtEDIOS Program
• Choose the \queries\poseidon_edios_program.xml
• Choose the export directory \results\program
• EDIOS SERIES
• Run MIKADO AutomaticgtGenerategtEDIOS Series
• Choose the \queries\poseidon_edios_series.xml
• Choose the export directory \results\series
• EDIOS PLATFORMS
• Run MIKADO AutomaticgtGenerategtEDIOS platforms
• Choose the \queries\poseidon_edios_platforms.xml
• Choose the export directory \results\platforms