Transcript practical_work File
Training Workshop – Ostende – 1-4 March 2010
Training course – Ostende – 2-6 July 2012
Practical work on NEMO
Converting files
M. Fichaut
Training course – Ostende – 2-6 July 2012
From ASCII data to XML files
Collection of ASCII files ODV files XML CDI files Coupling table Export Coupling table summary_CDI_NEMO.xml
Delivered with NEMO CDI summary CSV file
[email protected] – www.seadatanet.org
MIKADO SeaDataNet CDI
Training course – Ostende – 2-6 July 2012
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 • Don’t forget to add the NEMO shortcut on your desktop
[email protected] – www.seadatanet.org
Training course – Ostende – 2-6 July 2012
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
[email protected] – www.seadatanet.org
Training course – Ostende – 2-6 July 2012
First step : conversion to ODV with NEMO
•
Run NEMO
to convert the files to ODV format.
1. 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)
2. Proceed the 4 steps of NEMO [email protected] – www.seadatanet.org
Training course – Ostende – 2-6 July 2012
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 [email protected] – www.seadatanet.org
Training course – Ostende – 2-6 July 2012
• • • • • • • • •
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
[email protected] – www.seadatanet.org
Training course – Ostende – 2-6 July 2012
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 [email protected] – www.seadatanet.org
Training course – Ostende – 2-6 July 2012
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
[email protected] – www.seadatanet.org
Training course – Ostende – 2-6 July 2012
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
[email protected] – www.seadatanet.org
Training course – Ostende – 2-6 July 2012
Practical work on NEMO
Generating CDI summary and coupling table
M. Fichaut
Training course – Ostende – 2-6 July 2012
From ASCII data to XML files
Collection of ASCII files ODV files XML CDI files Coupling table Export Coupling table summary_CDI_NEMO.xml
Delivered with NEMO CDI summary CSV file
[email protected] – www.seadatanet.org
MIKADO SeaDataNet CDI
Training course – Ostende – 2-6 July 2012
•
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 Fulfill
in the box
Generate SeaDataNet CDI summary
all the mandatory fields (in red), using right click for the Search function
[email protected] – www.seadatanet.org
Training course – Ostende – 2-6 July 2012
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\file_name
–
and output directory prefix = C:\username\NEMO
–
file name in the mapping table will be : cruise_name\file_name
[email protected] – www.seadatanet.org
Training course – Ostende – 2-6 July 2012
CDI summary file
• Convert it to an EXCEL file (for future use by MIKADO) –
Open the CDI summary text file
delimited by tabulations) with EXCEL (field – –
Rename the folder into Save it under
:
STATION XLS or XLSX
format, it will be used later on during the practical work on MIKADO
[email protected] – www.seadatanet.org
Training course – Ostende – 2-6 July 2012
Coupling table
• •
Have a look
at the coupling table – Menu :
Coupling_table>Edit
– 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_table>Export
– Have a look at the flat coupling.txt file
[email protected] – www.seadatanet.org
Training Workshop – Ostende – 1-4 March 2010
Training course – Ostende – 2-6 July 2012
Practical work on MIKADO
Creation of XML files for CDI
M. Fichaut
Training course – Ostende – 2-6 July 2012
Exercise 1
a.CDI Automatic generation from the CDI summary file created this morning with NEMO – Validation of the XML files b.Creation
of the corresponding coupling file
[email protected] – www.seadatanet.org
Training course – Ostende – 2-6 July 2012
Collection of ASCII files
From ASCII data to XML files
a VALIDATOR ODV files b Coupling file for DM XML CDI files Coupling table Export Coupling table summary_CDI_NEMO.xml
Delivered with NEMO CDI summary CSV file
[email protected] – www.seadatanet.org
MIKADO SeaDataNet CDI
Training course – Ostende – 2-6 July 2012
• • • •
a) Configuration file for CDI XML
•
Run MIKADO
•
Open the configuration file delivered with NEMO :
–
MIKADO =>
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 [email protected] – www.seadatanet.org
Training course – Ostende – 2-6 July 2012
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
Manual>Open>File>CDI
[email protected] – www.seadatanet.org
Training course – Ostende – 2-6 July 2012
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.
[email protected] – www.seadatanet.org
Training course – Ostende – 2-6 July 2012
• • • • • • • •
b) Coupling configuration file
Run MIKADO Open the configuration file delivered with NEMO :
–
MIKADO =>
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_address.xls
Go to the main query tag
and a green message)
check the query (
you must have
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
Training course – Ostende – 2-6 July 2012
• • • • • •
b) Coupling file generation
Run the generation of the coupling file
–
MIKADO =>
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 [email protected] – www.seadatanet.org
Exercise 2
• EDIOS manual input of – 1 Program – 1 Series – 1 Platform
Training course – Ostende – 2-6 July 2012
[email protected] – www.seadatanet.org
Training course – Ostende – 2-6 July 2012
• • •
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 can’t you first enter a platform, then a series then a program?
[email protected] – www.seadatanet.org
Training course – Ostende – 2-6 July 2012
Exercise 3
• EDIOS Automatic generation of XML files for: – Program – Series – Platforms
[email protected] – www.seadatanet.org
Training course – Ostende – 2-6 July 2012
• • • • •
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_Example\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_Example\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_Example\queries\poseidon_edios_platform.xml
[email protected] – www.seadatanet.org
Training course – Ostende – 2-6 July 2012
Generate the XML EDIOS files
• EDIOS PROGRAM
– Run MIKADO : Automatic>Generate>EDIOS Program • Choose the \queries\poseidon_edios_program.xml
• Choose the export directory \results\program
• EDIOS SERIES
– Run MIKADO : Automatic>Generate>EDIOS Series • Choose the \queries\poseidon_edios_series.xml
• Choose the export directory \results\series
• EDIOS PLATFORMS
– Run MIKADO : Automatic>Generate>EDIOS platforms • Choose the \queries\poseidon_edios_platforms.xml
• Choose the export directory \results\platforms