Reformatting tools med2medsdn and nemo
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REFORMATTING TOOLS Med2MedSDN and NEMO. M. Fichaut. SeaDatanet Vocabulary. XML Validator. Metadata in Database. XML Metadata Files. Metadata Input. MIKADO. Metadata In Excel files. CSR. MIKADO. Coupling table. Data in Database. EDMED. Collection of ASCII files

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REFORMATTING TOOLS Med2MedSDN and NEMO

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Reformatting tools med2medsdn and nemo

Training Workshop – Ostende – 26-29 October 2009

REFORMATTING TOOLSMed2MedSDN and NEMO

M. Fichaut


Reformatting tools med2medsdn and nemo

SeaDatanet Vocabulary

XML Validator

Metadata

in

Database

XML

Metadata

Files

Metadata

Input

MIKADO

Metadata

In

Excel files

CSR

MIKADO

Coupling table

Data in

Database

EDMED

Collection

of

ASCII files

Format SDN

Data Input

Collection

of

ASCII files

Format X

SEADATANET

PORTAL

NEMO

EDMERP

Med2MedSDN

CDI

Download

Manager

Local copy

of data

to download

Data request

ODV

Data download

Partner system : pilot data centre

European portal


Overview

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


Med2medsdn

Training Workshop – Ostende – 26-29 October 2009

Med2MedSDN

For MEDATLAS files


Objectives of med2medsdn

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


Med2medsdn main features

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


Med2medsdn1

Med2MedSDN

  • Med2MedSDN vocabulary update


Med2medsdn main screen

Med2MedSDN main screen


Med2medsdn log files

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


Med2medsdn user manual

Med2MedSDN - User manual

  • User manual is provided :

    File : sdn_Med2MedSDN_UserManual_V1.0.pdf

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


Reformatting tools med2medsdn and nemo

  • ANY QUESTION?


Reformatting tools med2medsdn and nemo

Training Workshop – Ostende – 26-29 October 2009

NEMO

For ASCII files on any type


Objectives

Objectives

  • NEMOis 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.


Technical characteristics

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


Reformatting tools med2medsdn and nemo

  • 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.


Nemo principles

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


Running nemo

Running NEMO

  • 4 or 5 steps to convert the entry files to a SeaDataNet format

    • Describe the type of file(s)

    • [Describe the cruise, if the files are related to 1 cruise]

      • NEMO is able to read XML CSR generated with MIKADO

    • Describe the station information

    • Describe the measured parameters

    • Convert the file

  • One more step to

    • Save the description of the format (Model)


  • Nemo description of entry files 1

    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?


    Nemo description of entry files 2

    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


    Station header constant number of lines

    Station header : constant number of lines


    Station header number of lines not constant

    Station header : number of lines not constant


    Cruise description

    Cruise description

    • Can be

    • Manually input

    • Imported from a SeaDataNet XML CSR

    • Imported from a database (IFREMER only)


    Station description

    Station description


    Station description1

    Station description

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


    Station description2

    Station description

    • Input the dateformat


    Station description3

    Station description

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


    Station description4

    Station description

    • Click on the Test button to verify your input


    Station description5

    Station description


    Data description

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

    Data description

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

    • QC flags can also be described


    Data description1

    Data description

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


    Data description2

    Data description


    Data description3

    Data description

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


    Data description4

    Data description

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


    Data description5

    Data description

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


    Data description6

    Data description

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


    Data description7

    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


    Reformatting tools med2medsdn and nemo

    • File conversion

    • Output formats

    • MEDATLAS

      • Multi-station

    • ODV

      • Mono-station

      • Multi-station


    While converting

    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


    Cdi summary

    CDI summary

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


    Cdi summary file

    CDI SUMMARY File

    • Text file

    • Open it with Excel

    • Rename the sheet : STATION

    • Save the file as an EXCEL file


    Interaction with mikado

    ODV

    files

    Collection

    of

    ASCII files

    XML

    CDI files

    SeaDataNet

    CDI

    summary_CDI_NEMO.xml

    CDI summary

    CSV file

    MIKADO

    Interaction with MIKADO


    Coupling table for download manager

    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


    Coupling table

    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)


    Coupling table content 1

    Coupling table content (1)

    • LOCAL_CDI_ID

    • Modus

    • 1 : mono-station

    • 3 multi-station

    • Filename

    • Date of creation


    Coupling table content 2

    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


    Downloading the data

    Coupling table

    Downloading the data

    CSR

    EDMED

    Collection

    of

    ASCII files

    Format SDN

    EDMERP

    SEADATANET

    PORTAL

    Download

    Manager

    List of LOCAL_CDI_IDs

    CDI

    Local copy

    of data

    to download

    Data request

    Data download

    European portal

    SeaDataNet Data Centre


    Nemo user manual

    NEMO – User manual

    • User manual is provided :

      File :sdn_Nemo_UserManual_V1.2.pdf

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


    And don t forget that

    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]


    Reformatting tools med2medsdn and nemo

    • ANY QUESTION?


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