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REFORMATTING TOOLS Med2MedSDN and NEMO

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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  1. Training Workshop – Ostende – 26-29 October 2009 REFORMATTING TOOLSMed2MedSDN and NEMO M. Fichaut

  2. 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

  3. 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

  4. Training Workshop – Ostende – 26-29 October 2009 Med2MedSDN For MEDATLAS files

  5. 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

  6. 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

  7. Med2MedSDN • Med2MedSDN vocabulary update

  8. Med2MedSDN main screen

  9. 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

  10. Med2MedSDN - User manual • User manual is provided : File : sdn_Med2MedSDN_UserManual_V1.0.pdf • Detailed explanation for Med2MedSDN installation and use, lots of snapshots

  11. ANY QUESTION?

  12. Training Workshop – Ostende – 26-29 October 2009 NEMO For ASCII files on any type

  13. 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.

  14. 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

  15. 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.

  16. 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

  17. 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)

  18. 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?

  19. 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

  20. Station header : constant number of lines

  21. Station header : number of lines not constant

  22. Cruise description • Can be • Manually input • Imported from a SeaDataNet XML CSR • Imported from a database (IFREMER only)

  23. Station description

  24. Station description • Select the date in the file, in the left part of the screen

  25. Station description • Input the dateformat

  26. Station description • Click on the Set button to tell NEMO the start and end position of the date

  27. Station description • Click on the Test button to verify your input

  28. Station description

  29. 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

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

  31. Data description

  32. Data description • Select the value of the measured parameter in the file, in the upper left part of the screen

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

  34. Data description • Start and End position of temperature are added in the table

  35. Data description • Select « Update test » in the context menu of the measured parameters table

  36. 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

  37. File conversion • Output formats • MEDATLAS • Multi-station • ODV • Mono-station • Multi-station

  38. 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

  39. CDI summary • Further information must be added in NEMO settings (menu Options of NEMO)

  40. CDI SUMMARY File • Text file • Open it with Excel • Rename the sheet : STATION • Save the file as an EXCEL file

  41. ODV files Collection of ASCII files XML CDI files SeaDataNet CDI summary_CDI_NEMO.xml CDI summary CSV file MIKADO Interaction with MIKADO

  42. 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

  43. 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)

  44. Coupling table content (1) • LOCAL_CDI_ID • Modus • 1 : mono-station • 3 multi-station • Filename • Date of creation

  45. 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

  46. 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

  47. NEMO – User manual • User manual is provided : File :sdn_Nemo_UserManual_V1.2.pdf • Detailed explanation for NEMO installation and use, lots of snapshots

  48. 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 sdn-userdesk@seadatanet.org

  49. ANY QUESTION?

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