REFORMATTING TOOLS Med2MedSDN and NEMO

OBSERVATIONS

& PRÉVISIONS CÔTIÈRES

www.seadatanet.org

Training Workshop – Ostende – 26-29 October 2009

REFORMATTING TOOLS

Med2MedSDN and NEMO

M. Fichaut

OBSERVATIONS


2www.seadatanet.org

3rd SeaDataNet training course – Ostende – 27 October 2009

CDI

CSR

EDMERP

EDMED

SEADATANET PORTAL

European portal

Collection of

ASCII filesFormat X

Data in Database

Metadata in

Database

Data Input

Metadata Input

MetadataIn

Excel files

Partner system : pilot data centre

SeaDatanet Vocabulary

NEMO

ODV

Med2MedSDN

Coupling table

Download

Manager

Collection of

ASCII filesFormat SDN

XML Metadata

Files

Local copy of data

to download

Data request

Data download

MIKADO

MIKADO

XML Validator

OBSERVATIONS


3www.seadatanet.org


Overview

• Med2MedSDN

• Objectives and main features

• NEMO

• Objectives, main features and principles

• Technical characteristics

• Description of the different steps to follow to be able to reformat ASCII files to SeaDataNet format

• Link between NEMO and MIKADO

• Link between NEMO and SDN Download Manager – coupling table

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www.seadatanet.org


Med2MedSDN

For MEDATLAS files

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Objectives of Med2MedSDN

• Translate MEDATLAS files to SeaDataNet MEDATLAS files - available under Windows

• Version 1.1.02 and user manual available at :

http://www.seadatanet.org/standards_software/software/Med2MedSDN

OBSERVATIONS


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Med2MedSDN main features

• Reformats MEDATLAS files to MEDATLAS SeaDataNet format

• Java tool, bilingual (French, English)

• Adds the additional SeaDataNet information : mapping for parameters and LOCAL_CDI_ID and EDMO_CODE

• Can reformat one file or a large number of files (in one directory)

• Generates a coupling file for the SeaDataNet download manager

• Linked to SeaDataNet vocabularies through Web services for parameters mapping and for list of EDMO codes

• Need of internet connexion while updating lists

OBSERVATIONS


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Med2MedSDN

Med2MedSDN vocabulary update

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Med2MedSDN main screen

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Med2MedSDN log files

• Errors (managed by Log4j) are registered in a log file in Med2MedSDN installation directory.

• One line in the log file is composed as following:• Date, Name of the Software, Error severity level, Error message

INFO Informative messages for starting of the conversion or successful conversion

ERROR For conversion errors : conversion is cancelled on the current file but continues on the other files

FATAL For conversion errors which stop the processing of the files

OBSERVATIONS


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Med2MedSDN - User manual

• User manual is provided :

File : sdn_Med2MedSDN_UserManual_V1.0.pdf

• Detailed explanation for Med2MedSDN installation and use, lots of snapshots

OBSERVATIONS




ANY QUESTION?

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NEMO

For ASCII files on any type

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Objectives

NEMO is a reformatting software used to

generate ASCII files at MEDATLAS or ODV formats which are defined as SeaDataNet formats for data exchange between SeaDataNet partners. Can be downloaded from SeaDataNet Web site :

http://www.seadatanet.org/standards_software/software/nemo

It was created in IFREMER for internal purposes, and adapted to take into account the SeaDataNet formats and vocabularies.

OBSERVATIONS




Technical characteristics• Written in Java Language (Version >= 1.6)

• Bilingual (French, English)

• Available under multiple environments :

• Microsoft : Windows 2000, XP, VISTA , APPLE

• Unix - Solaris

• Linux

• Use of SeaDataNet common vocabularies web services

• to update lists of values of the SeaDataNet common vocabularies

• need network connections in order to have up to date lists of values.

• But NEMO works offline once the lists are up-to-date

OBSERVATIONS




NEMO main features

• Reformat any ASCII file of vertical profiles, time-series or trajectories to a SeaDataNet ASCII format (ODV, MEDATLAS).

• The input ASCII files can be :

• one file per station for vertical profiles or time series

• one file for one cruise for vertical profiles, time series or trajectories

• Interact with Mikado, to be able to generate ISO-19115 XML descriptions of the data.

OBSERVATIONS




NEMO principles• NEMO must be able to read almost any ASCII format to

translate it to MEDATLAS, ODV• Users of NEMO describe the entry files format so that NEMO

is able to find the information which is necessary in the SeaDataNet formats

• One mandatory pre-requirement is that in the set of entry files the information about the stations must

• be located at the same position : same line in the file, same position on the line or same column if CSV format

• be in the same format• For example : for all the stations the latitude is

• on line 3 on the station header, • from character 21 to character 27, or 3rd column in CSV• the format is +DD.ddd

OBSERVATIONS




Running NEMO

• 4 or 5 steps to convert the entry files to a SeaDataNet format1. Describe the type of file(s)2. [Describe the cruise, if the files are related to 1 cruise]

• NEMO is able to read XML CSR generated with MIKADO

3. Describe the station information4. Describe the measured parameters5. Convert the file

• One more step to • Save the description of the format (Model)

OBSERVATIONS




NEMO - Description of entry files (1)

• Where are the files?

• Is it a cruise?

• Is it one file per cruise or one file per station ?

• Is it a collection of station files ?

• grouped by cruises or not?

• Are the files with separators?

• Tabulations? Semicolon? Comma?

• Are they vertical profiles, time series or trajectories data?

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NEMO - Description of entry files (2)

• File to convert is displayed in NEMO window

• The principle is to describe the input file by selecting the information in the file window

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Station header : constant number of lines

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Station header : number of lines not constant

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Cruise description

Can be

• Manually input

• Imported from a SeaDataNet XML CSR

• Imported from a database (IFREMER only)

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Station description

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Station description

• Select the date in the file, in the left part of the screen

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Station description

• Input the date format

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Station description

• Click on the Set button to tell NEMO the start and end position of the date

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Station description

• Click on the Test button to verify your input

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Station description

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Data description

• Give the position , the default value, the format of each parameter

• QC flags can also be described

• Pressure is mandatory for vertical profiles (MEDATLAS requirement) and cannot be deleted.

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Data description

• Select « Parameter list » in the context menu of the measured parameters table (right click to open the menu)

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Data description

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Data description

• Select the value of the measured parameter in the file, in the upper left part of the screen

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Data description

• Select « Set start /end » in the context menu of the measured parameters table

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Data description

• Start and End position of temperature are added in the table

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Data description

• Select « Update test » in the context menu of the measured parameters table

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Data description

• The values read by NEMO are displayed in the Test column of the table. User is able to check that his input is correct

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File conversion

Output formats

• MEDATLAS

• Multi-station

• ODV

• Mono-station

• Multi-station

OBSERVATIONS




While converting …

NEMO is able to

• Generate a SeaDataNet CDI Summary

• Text file containing the minimum mandatory information needed in the CDI ISO-19115 description

• This file can be converted to an Excel file

• Which can be read by MIKADO to generate the XML CDI files

• Generate a coupling table that will be used by the Download manager of SeaDataNet

• It is the link between the LOCAL_CDI_ID and the file

OBSERVATIONS




CDI summary

• Further information must be added in NEMO settings (menu Options of NEMO)

OBSERVATIONS




CDI SUMMARY FileText file

• Open it with Excel

• Rename the sheet : STATION

• Save the file as an EXCEL file

OBSERVATIONS




Interaction with MIKADO

Collection of

ASCII files

ODV files

CDI summaryCSV file

SeaDataNetCDI

MIKADO

XML CDI files

summary_CDI_NEMO.xml

OBSERVATIONS




Coupling table for Download Manager

• Further information must be added in NEMO settings (menu Options of NEMO)

• The coupling table makes the link between each LOCAL_CDI_ID and the file(s) which contains it

OBSERVATIONS




Coupling table

If the “Generate mapping” option is clicked :

• NEMO will insert a record in the coupling table for each vertical profile, time series or trajectory that it converts.

• The coupling table is managed by a local database imbedded in NEMO

• The coupling table can be :

• Edited (for modification, insertion or deletion)

• exported (to be used by the download manager)

• imported (from previous version of NEMO, for example)

OBSERVATIONS




Coupling table content (1)

LOCAL_CDI_ID

Modus

• 1 : mono-station

• 3 multi-station

Filename

Date of creation

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Coupling table content (2)

• One unique LOCAL_CDI_ID in one mono-station ODV file

• The same LOCAL_CDI_ID in 2 different files :

• One multi-station MEDATLAS file

• One mono-station ODV file

OBSERVATIONS




Downloading the data

CDI

CSR

EDMERP

EDMED

SEADATANET PORTAL

European portal

Collection of

ASCII filesFormat SDN

Local copy of data

to downloadData request

Data download

Coupling table

SeaDataNet Data Centre

List of LOCAL_CDI_IDs

DownloadManager

OBSERVATIONS




NEMO – User manual

• User manual is provided :

File : sdn_Nemo_UserManual_V1.2.pdf

• Detailed explanation for NEMO installation and use, lots of snapshots

OBSERVATIONS




And don’t forget that

• All software freely available at :

http://www.seadatanet.org/standards_software/software

• FAQ on the web site for MIKADO and NEMO

• Don’t forget to read the user manuals which are very detailed

• Any problems using the software

Mail to [email protected]

OBSERVATIONS




ANY QUESTION?

REFORMATTING TOOLS Med2MedSDN and NEMO

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