cdi implementation

Pan-European infrastructure for Ocean & Marine Data management

An EU Integrated research Infrastructure Initiative (I3)

How to implement CDI ?M. Fichaut, V. Tosello

Training course - June 2007, Oostende, Belgium

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How to proceed with the fi les for trainingIn the shared directory :With 2 f i les CDI_implementation.ppt : this presentation training2_programme.doc : programme sent by email

And 5 directories :

CDI documentation Detailed documentation on CDI and mapping

Example database3 directories for ACCESS, MySQL and EXCEL database

Exercises Mikado

Mikado software and configuration files

SolutionsSolution of the exercises, empty now, will be filled during the training after each exercises session

Now : Copy the common directory on your computer

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Example database (1)

10 tables describing : the stations of datasets collected during cruises 5 cruises on 2 ships, 10 datasets, 1399 stations the datasets are either CTD or Bottle stations (mikado_dataset.database_id) Measured parameters are linked to the datasets (mikado_dataset_parameter) Mapping with common vocabularies is made through mapping tables

(mikado_map_…)

Document : \example_database\example_database_description.rtf

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Example database (1)

One database in several environmentsOn Microsoft ACCESS \access\cdi_training_course_2.mdb

On MySQL Name of the database : mikado, user : mikado, password :

mikadoOn EXCEL \excel\ cdi_training_course_2.xls

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First set of Exercises

Manipulate the example database in different environments

Exercise 1 : MySQL database

Exercise 2 : ACCESS database

Exercise 3 : Excel file

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CDI implementation progress

USER LOCAL

DATABASEACCESS

MYSQL

EXCEL

EXCEL FILES

STATION METADATA(CTDs, Bottles, Current meters, …)

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Generating the CDI - First STEP

MAP YOUR DATABASE to THE CDI FIELDS

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Database mapping to XML schema (1)

Using the documents : \CDI documentation\ CDI_XML_V0_documentation_3_00_June2007.doc:

Metadata Format and full description of XML schema version 2.04 – as prepared in Sea-Search

\CDI documentation\ CDI_V1_04_mapping.xls : Excel file describing the mapping between the CDI fields, ISO-19115 and the local database

\example_database\example_database_description.rtf :Description of the tables of the example database

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On the right hand side : local database reference Table_name.field_name


Level 2 Level 3 Level 4 …WHERE Latitude1 (var1) <dataIdInfo> (15) <geoBox> (42) <southBL> (346)WHERE Longitude1 (var2) <dataIdInfo> (15) <geoBox> (42) <westBL> (344)WHERE Latitude2 (var3) <dataIdInfo> (15) <geoBox> (42) <northBL> (347)WHERE Longitude2 (var4) <dataIdInfo> (15) <geoBox> (42) <eastBL> (345) WHERE Measuring area type (var5) <spatRepInfo> (12) <VectSpatRep> (176) <geometObjs> (178) WHERE Data Coordinate system (var6) <refSysInfo> (13) <MdCoRefSys> (189) <datum> (192)

… WHEN Start date (var12) <dataIdInfo> (15) <dataExt> (45) <tempEle> (337) WHEN Start time (UT) var(12) see Start date WHAT Parameters measured (var50) <dataIdInfo> (15) <descKeys> (33) <keyword> (53)

<KeyTyp> (54)

HOW Instrument or gear type (var42) <dataIdInfo> (15) <descKeys> (33) <keyword> (53)<KeyTyp> (54)

HOW Type of platform (var43) <dataIdInfo> (15) <descKeys> (33) <keyword> (53)<KeyTyp> (54)

WHO Originator (var16) <dataIdInfo> (15) <idPoc> (29) <rpOrgNameId> (not ISO)<role> (379)

PART CDI FIELD XML TAGS LOCAL DATABASE FIELD(TABLE_NAME.FIELD_NAME)

On the left hand side : CDI reference For each : XML tree (XML tags, with ISO-19115 number)

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WHERE Latitude1 (var1) MIKADO_STATION.STATION_LATWHERE Longitude1 (var2) MIKADO_STATION.STATION_LONWHERE Latitude2 (var3) not relevantWHERE Longitude2 (var4) not relevantWHERE Measuring area type (var5)WHERE Data Coordinate system (var6)

… WHEN Start date (var12)WHEN Start time (UT) var(12)WHAT Parameters measured (var50)HOW Instrument or gear type (var42)

HOW Type of platform (var43)WHO Originator (var16)

PART CDI FIELD LOCAL DATABASE FIELD(TABLE_NAME.FIELD_NAME)

Mandatory CDI f ields in bold characters

Example of mapping

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Second set of Exercises

Map the local database to the CDI f ields

Exercise 4 : Find all CDI fields mapping with MIKADO_CRUISE table

Exercise 5 : Find the mapping for the CDI field Data Coordinate system and Sampling Interval

Exercise 6 : Full mapping Look at the final mapping file. Questions?

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ISO-19115

XML SCHEMA

defined for the CDI

by SDN – TTT

USER LOCAL

DATABASEORACLE

MSSERVER

MYSQL

…

EXCEL FILES


MAPPING

Common vocabularies

MA

PP

ING

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Principles of the CDI

ISO-19115

XML SCHEMA

defined for the CDI

by SDN – TTT

USER LOCAL

DATABASEORACLE

MSSERVER

MYSQL

…

EXCEL FILES


MAPPING

Central CDI

Common vocabularies

MA

PP

ING

TOOLSMikadoOthers

Configuration Files

Compliant to

XML CDI fi les

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Configure Mikado - Second STEP


MIKADO CONFIGURATION

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MIKADO : Reminder

MIKADO has been developed by IFREMER in the framework of the SEA-SEARCH project.

MIKADO can be used to generate EDMED, CSR and CDI XML files.

MIKADO can be used into 2 different ways : One manual way, to input manually information for EDMED,

CSR and CDI fields in order to generate XML files. One automatic way, to generate these descriptions automatically

if information is catalogued in a relational database.

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MIKADO principle

MIKADOJava code

JDBCJava DataBase Connectivity

JVM – Java Virtual Machine

Native DriversMYSQL

ORACLEPOSTGRESSQLServer

Bridge Driversusing Microsoft ODBC

(ACCESS, EXCEL, SQL SERVER)

DATABASEConfigurat ion

Fi les(*.properties)

Download driversfrom web sites

if not provided with Mikado

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List of drivers provided with Mikado

ODBC Bridge (from Java JDK 1.5) MS Access 97, 2000, 2003 MS Excel

JTDS 1.1 (Open Source licence) Sybase 10, 11, 12, 15 SQL Server

MySQL 3.1.10 (GPL licence) MySQL 4.1, 5.x

Oracle 14 (Oracle Technology Network Development and Distribution License) Oracle 8.1.7, 9i, 10i (with restrictions)

PostgreSQL 8.0.312 (BSD licence) PostgreSQL

MS SQL server 2005 driver (Microsoft download) SQL Server 2000 with Service Pack 1 or higher

Please note that Mikado source level is JDK 1.5

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How to find the appropriate JDBC driver?

Native drivers must be downloaded from the appropriate vendors websites(i.e Oracle, Sybase, MySQL, PostGres, …) It must f i t with the database and the JDBC versions.

This l ink may help you to find out the native drivers you need : http:/ /developers.sun.com/product/ jdbc/drivers

For Oracle RDBMS , a native driver may be found on http:/ /www.oracle.com/technology/software/tech/ java/sqlj_jdbc/ index.html

For Microsoft SQL server, a native driver may be found on Microsoft MSDN http://msdn2.microsoft .com/en-us/data/default.aspx

Bridge drivers (using Microsoft-ODBC Open DataBase Connectivity) are bundled with the Java 2 SDK.

http:// java.sun.com/j2se/1.3/docs/guide/jdbc/getstart/bridge.doc.htmlDrivers have then to be installed following the given recommendations The corresponding .jar files must be copied in the \mikado\dist directory

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MIKADO configuration f i les

See Mikado user manual \mikado\sdn_Mikado_Manual_V0.1.doc

Mikado needs 2 configuration fi les in the \mikado\conf directory files.properties file which contains

all the information about the name and the location of the files used by the software

Cdi.properties file which contains:Database connection parametersQueries to retrieve data from the database Mapping between the queries results (SQL variables) and the CDI fields

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Mikado fi les.properties f i le All the information about the name and the location of

the f i les used by the softwareName of the files containing the list of

values for CDI [and EDMED and CSR] : Parameters codes, platforms codes, …

############### CDI###############cdiPartnerCodescdiPartnerCodes.f i le = ./conf/cdi_partner_codes.csv#cdiMeasurementAreaTypeCodescdiMeasurementAreaTypeCodes.f i le = ./conf/cdi_measurement_codes.csv

Name of XML schemas used for CDI [and EDMED and CSR]

#xsdxsd.cdi = . /conf/CDI_V1_04.xsdxsd.cdi_mult irecords = . /conf/CDI_V2_01_mult irecords.xsd

Name of the files used for CDI XML automatic generation [and EDMED and CSR]

#mapping.cdi = . /conf/cdi_training2_access.propert ies#mapping.cdi = . /conf/cdi_training2_mysql.propert iesmapping.cdi = . /conf/cdi_training2_excel.properties

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Mikado cdi.properties f i le

3 parts in the f i le Database connection parameters

Depending on the DATABASE : ACCESS, MySQL, ORACLE …

Queries to extract data from the database To be written from the mapping

Mapping between the queries results (SQL variables) and the CDI fields

Must not be modified!!!

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cdi.properties fi le : database connection (1)

DATABASE ACCESS JDBC (Java Data Base Connectivity) connection parameters

###############################JDBC parameters for querying database###############################bdd.query.timeout = database connection time outbdd.className= driver Java Class Name (the *.jar file which

implement this Class Name must exist in the mikado\conf\dist directory)

bdd.connectURL = connect string to the databasebdd.user.name = user namebdd.user.password = user password

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Examples of ODBC bridge drivers ACCESS database

bdd.className = sun.jdbc.odbc.JdbcOdbcDriverbdd.connectURL =jdbc:odbc:Driver={Microsoft Access Driver

(*.mdb)};DBQ=N://example_database/access/cdi_training_course_2.mdbbdd.user.name =bdd.user.password =

EXCEL filebdd.className = sun.jdbc.odbc.JdbcOdbcDriverbdd.connectURL =jdbc:odbc:Driver={Microsoft Excel Driver

(*.xls)};DBQ=X:/example_database/excel/cdi_training_course_2.xlsbdd.user.name =bdd.user.password =

MS SERVEUR Not recommended, use nat ive driver

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Examples of Native driversMySQL database

bdd.className = com.mysql. jdbc.Driverbdd.connectURL = jdbc:mysql: / / localhost/mikadobdd.user.name = mikadobdd.user.password = mikado

ORACLEbdd.className = oracle.jdbc.OracleDriver bdd.connectURL = jdbc:oracle:thin:@server:port:instance User and password must be providedExample : jdbc:oracle:thin:@josephine. ifremer.fr:1521:btest920

• MS SERVERbdd.className = com.microsoft. jdbc.sqlserver. SQLServerDriver bdd.connectURL =

jdbc:sqlserver://serverName;instanceName:portNumber;property=value[;property=value]

User and password must be providedExample : jdbc:sqlserveur:/ /www.bkrclass.org:1065;databaseName=io_mikado;

integratedSecurity=false;

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cdi.properties fi le : mapping

Mapping of the query results to the CDI f ieldsMapping table : SQL variables = CDI fields

var1 = southLatitudevar2 = westLongitudevar3 = northLati tude…..var42 = instrumentOrGearTypevar43 = typeOfPlatformvar50 = parametersMeasured.value

WHERE Latitude1 (var1) MIKADO_STATION.STATION_LATWHERE Longitude1 (var2) MIKADO_STATION.STATION_LONWHERE Latitude2 (var3) not relevantWHERE Longitude2 (var4) not relevant

PART CDI FIELD LOCAL DATABASE FIELD(TABLE_NAME.FIELD_NAME)

Must not bechanged

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cdi.properties fi le : SQL queries (1)

Main query

It is the query which identifies all CDI entries that must be exported. This request must return only one column which is the identifier of each entry and that will be used for sub-queries.

SQL syntax must be adapted to your local database############################# Main query (station identifier list)############################query.=select mikado_station.station_id from mikado_station

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Sub-queries For each row of the main query, it is possible to define single or

multi sub-queries.Single sub-queries : return one row for each row of the main query (ex: dataset_id, cruise_name)Multi sub-queries : return several rows for each row of the main query (ex: parameters).

The links between the fields of the database and the variables of the mapping (var1 to varN) table have to be defined in theses sub-queries as synonyms of the selected columns

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Single Sub-queries : return one row

The number of single sub-queries must be defined

queries.single.number=5

The keyword for single sub-queries is :queries.single.i= where i varies from 1 to queries.single.number

Example : queries.single.1 = select tabA.colX var1 from tabA where

tableA.colY= :$var1 = synonym for the column name from the mapping table:$ = the identifier of the row returned by the main query

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Mult iple Sub-queries : return several rows

All the names of the multi sub-queries are defined and must not be changed

For CDI one multi sub-query is defined

The keyword is :queries.multi.parametersMeasured =

Example : queries.multi.parametersMeasured =select tabA.colX var50 from

tabA, tabB where tabB.colX = :$ and tabB.colY = tabA.colZ

var50 = synonym for the column name from the mapping table:$ = the identifier of the row returned by the main query

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Third set of Exercises

Write the cdi.properties f i les for ACCESS or MY SQL or EXCEL fi les In the exercises only the stations of the Cruise « CITHER2 LEG 1 » will

selected to have a smaller number of stations

Exercise 7 : Look at the main query. Questions?

Exercise 8 : Fulfil the missing information in query.single.1.

Query on MIKADO_DATASET table

Exercise 9 : Fulfil the missing information in query.single.2.

Query on MIKADO_STATION table

Exercise 10 : Write the query.single.4 to f ind the datum coordinate system

Exercise 11 : Have a look at the final property f i le, questions?

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ISO date format

Date format must have the following syntax YYYY-MM-DD YYYY-MM-DDTHH24:MI YYYY-MM-DDTHH24:MI:SS

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ISO-19115

XML SCHEMA

defined for the CDI

by SDN – TTT

USER LOCAL

DATABASEORACLE

MSSERVER

MYSQL

…

EXCEL FILES


MAPPING

Common vocabularies

MA

PP

ING

TOOLSMikadoOthers

Configuration Files

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XML fi les generation - Third STEP



Generate the XML fi les

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XML CDI f i les generation

Use the Mikado software to create the XML CDI f i les Make sure that you have the right « properties » files in the

\mikado\conf directory files before running the software Change the connection to the database in the

CDI.properties file, with the path to your local database Run Mikado Import the common vocabularies lists for CDI using Mikado

: Menu configuration, library, CDI Create and output directory for your XML files

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XML fi les check - Fourth STEP




Check the XML fi les

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ISO-19115

XML SCHEMA

defined for the CDI

by SDN – TTT

USER LOCAL

DATABASEORACLE

MSSERVER

MYSQL

…

EXCEL FILES


MAPPING

Common vocabularies

MA

PP

ING

TOOLSMikadoOthers

Configuration Files

Compliant to

XML CDI fi les

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Send XML fi les - Fifth STEP




Check the XML fi les

Send the XML fi lesto central CDI

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Fourth set of Exercises

Generate the XML CDI f i les and check them

Exercise 12 : Generate the XML files with Mikado

Exercise 13 : Check the XML files