Difference between revisions of "AquamapsServiceAdminGuide"

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<!-- CATEGORIES -->
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[[Category: Administrator's Guide]][[Category:TO_BE_REMOVED]]
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<!-- CATEGORIES -->
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== Aquamaps Service Installation ==
 
== Aquamaps Service Installation ==
  
Line 8: Line 12:
 
=== Aquamaps Service packages and dependencies installation ===
 
=== Aquamaps Service packages and dependencies installation ===
  
−
The current stable repository for gCube (v 2.2.1) can be found at :
+
==== gCube software ====
  
−
https://grids16.eng.it/BuildReport/browse/Recent_Builds/org.gcube.2-2-1/BUILD_6
+
The packages listed below can be found at
  
−
The following package has been released as part of gCube 2.2.1:
+
http://grids16.eng.it/BuildReport/browse/Recent_Builds/
  
−
* org.gcube.application.aquamaps.aquamapsservice-servicearchive-2.4.2-0 [https://grids16.eng.it/BuildReport/download/Recent_Builds/org.gcube.2-2-1/BUILD_6/dist/org.gcube/org.gcube.application.aquamaps.aquamapsservice-servicearchive/2.4.2/ubuntu8_ia32_gcc424/org.gcube.application.aquamaps.aquamapsservice-servicearchive-2.4.2-0.tar.gz]
+
We kindly recommend to download the software packages contained in the last Build of the last released version of gCube distribution.
  
 +
 +
The following package has been released as part of gCube :
 +
 +
* org.gcube.application.aquamaps.aquamapsservice-servicearchive
  
 
The tar archive contains the following packages to install:
 
The tar archive contains the following packages to install:
Line 26: Line 34:
  
 
* Aquamaps stubs
 
* Aquamaps stubs
−
The Aquamaps Service stubs library ( org.gcube.application.aquamapspublihser.stubs.jar ) [https://grids16.eng.it/BuildReport/download/Recent_Builds/org.gcube.2-2-1/BUILD_6/dist/org.gcube/org.gcube.application.aquamaps.aquamapspublisherservice-servicearchive/1.0.0/ubuntu8_ia32_gcc424/org.gcube.application.aquamaps.aquamapspublisherservice-servicearchive-1.0.0-0.tar.gz] to be copied inside the gHN library folder ( $GLOBUS_LOCATION/lib )
+
The Aquamaps Service stubs library ( org.gcube.application.aquamaps.stubs.jar ) to be copied inside the gHN library folder ( $GLOBUS_LOCATION/lib )
  
−
* Aquamaps Publisher Service stubs
+
In addition the following gCube libraries are needed( to be installed  into the $GLOBUS_LOCATION/lib folder )
−
The Aquamaps Publisher Service stubs library ( org.gcube.application.aquamaps.stubs.jar ) to be copied inside the gHN library folder ( $GLOBUS_LOCATION/lib )
+
  
−
* gCube GeoServer Interface library
+
* The Aquamaps Publisher Service stubs library
−
The geoserverInt.jar  automatically installed  into the $GLOBUS_LOCATION/lib folder when installing Aquamaps Service gar
+
  
−
* Third Party Libraries
+
* The Messaging Consumer library
−
The Following Third Party Libraries are automatically installed togheter with Aquamaps Service gar into the $GLOBUS_LOCATION/lib folder:
+
−
**commons-codec-1.3.jar
+
−
**commons-httpclient.jar
+
−
**csv4j_gcube.jar ( gCube specific extension to csv4j library)
+
−
In addition the following libraries need to be manually installed under $GLOBUS_LOCATION/lib
+
−
** Jetty v. 7.0.0 [https://grids16.eng.it/BuildReport/download/Recent_Builds/org.gcube.2-2-1/BUILD_6/dist/org.gcube/org.gcube.ext.jetty-servicearchive/7.0.0/ubuntu8_ia32_gcc424/org.gcube.ext.jetty-servicearchive-7.0.0-pre5.tar.gz]
+
−
** MySQL JDBC v 5.1.5 [https://grids16.eng.it/BuildReport/download/Recent_Builds/org.gcube.2-2-1/BUILD_6/dist/org.gcube/org.gcube.ext.mysql-jdbc-servicearchive/5.1.5/ubuntu8_ia32_gcc424/org.gcube.ext.mysql-jdbc-servicearchive-5.1.5-0.tar.gz]
+
  
 +
* The Aquamaps Data Model library
 +
 +
* The GIS Data Model library
 +
 +
* The GeoServer Interface library
 +
 +
==== Third Party Libraries ====
 +
 +
The following libraries need to be manually installed under $GLOBUS_LOCATION/lib:
 +
 +
* Geo Tools framework v 2.6
 +
 +
available from Geo Tools official website[http://www.geotools.org/], in particular the following library are needed:
 +
**geoapi-2.3-M1.jar
 +
**geoapi-pending-2.3-M1.jar
 +
**geodb-0.3.jar
 +
**gt-api-2.6.4.jar
 +
**gt-arcgrid-2.6.4.jar
 +
**gt-arcsde-2.6.4.jar
 +
**gt-arcsde-common-2.6.4.jar
 +
**gt-brewer-2.6.4.jar
 +
**gt-charts-2.6.4.jar
 +
**gt-coverage-2.6.4.jar
 +
**gt-cql-2.6.4.jar
 +
**gt-data-2.6.4.jar
 +
**gt-db2-2.6.4.jar
 +
**gt-directory-2.6.4.jar
 +
**gt-epsg-extension-2.6.4.jar
 +
**gt-epsg-hsql-2.6.4.jar
 +
**gt-epsg-postgresql-2.6.4.jar
 +
**gt-epsg-wkt-2.6.4.jar
 +
**gt-feature-pregeneralized-2.6.4.jar
 +
**gt-geotiff-2.6.4.jar
 +
**gt-graph-2.6.4.jar
 +
**gt-gtopo30-2.6.4.jar
 +
**gt-image-2.6.4.jar
 +
**gt-imageio-ext-gdal-2.6.4.jar
 +
**gt-imagemosaic-2.6.4.jar
 +
**gt-imagemosaic-jdbc-2.6.4.jar
 +
**gt-imagepyramid-2.6.4.jar
 +
**gt-jdbc-2.6.4.jar
 +
**gt-jdbc-db2-2.6.4.jar
 +
**gt-jdbc-h2-2.6.4.jar
 +
**gt-jdbc-mysql-2.6.4.jar
 +
**gt-jdbc-oracle-2.6.4.jar
 +
**gt-jdbc-postgis-2.6.4.jar
 +
**gt-jdbc-spatialite-2.6.4.jar
 +
**gt-jdbc-sqlserver-2.6.4.jar
 +
**gt-jp2k-2.6.4.jar
 +
**gt-legacy-2.6.4.jar
 +
**gt-main-2.6.4.jar
 +
**gt-metadata-2.6.4.jar
 +
**gt-postgis-2.6.4.jar
 +
**gt-property-2.6.4.jar
 +
**gt-referencing-2.6.4.jar
 +
**gt-referencing3D-2.6.4.jar
 +
**gt-render-2.6.4.jar
 +
**gt-sample-data-2.6.4.jar
 +
**gt-shapefile-2.6.4.jar
 +
**gt-svg-2.6.4.jar
 +
**gt-swing-2.6.4.jar
 +
**gt-validation-2.6.4.jar
 +
**gt-wfs-2.6.4.jar
 +
**gt-wms-2.6.4.jar
 +
**gt-xml-2.6.4.jar
 +
**gt-xsd-core-2.6.4.jar
 +
**gt-xsd-filter-2.6.4.jar
 +
**gt-xsd-gml2-2.6.4.jar
 +
**gt-xsd-gml3-2.6.4.jar
 +
**gt-xsd-kml-2.6.4.jar
 +
**gt-xsd-ows-2.6.4.jar
 +
**gt-xsd-sld-2.6.4.jar
 +
**gt-xsd-wfs-2.6.4.jar
 +
**gt-xsd-wps-2.6.4.jar
 +
 +
* Jetty v. 7.0.0 [https://grids16.eng.it/BuildReport/download/Recent_Builds/org.gcube.2-7-0/latest/dist/org.gcube/org.gcube.ext.jetty-servicearchive/7.0.0/ubuntu8_ia32_gcc424/org.gcube.ext.jetty-servicearchive-7.0.0-pre5.tar.gz]
 +
* MySQL JDBC v 5.1.5 [https://grids16.eng.it/BuildReport/download/Recent_Builds/org.gcube.2-7-0/latest/dist/org.gcube/org.gcube.ext.mysql-jdbc-servicearchive/5.1.5/ubuntu8_ia32_gcc424/org.gcube.ext.mysql-jdbc-servicearchive-5.1.5-0.tar.gz]
 +
* commons-dbcp[http://eticssoft.web.cern.ch/eticssoft/repository/externals/commons-dbcp/1.2.1/noarch/commons-dbcp.tar.gz]
 +
* commons-pool[http://eticssoft.web.cern.ch/eticssoft/repository/externals/commons-pool/1.3/noarch/commons-pool.tar.gz]
 +
* hsqldb[http://puzzle.dl.sourceforge.net/sourceforge/hsqldb/hsqldb_1_7_2_3.zip]
 +
* ostermillerutils[http://eticssoft.web.cern.ch/eticssoft/repository/externals/ostermillerutils/1.7.0/noarch/ostermillerutils-1.7.0.tar.gz]
 +
* Xstream[http://eticssoft.web.cern.ch/eticssoft/repository/externals/XStream/1.3.1/noarch/XStream-1.3.1.tar.gz]
 +
* Lucene
 +
* commons-codec 1.3
 +
* postgresql-8.4-701
 +
* csv-4j
 +
* commons-http-client 3.0.1
 +
* dom4j
 +
* hibernate
 +
* hsql
 +
* java-persistence
 +
* jts
 +
* sl4j
  
 
=== CMAR C-Square Mapper Software and dependencies Installation ===
 
=== CMAR C-Square Mapper Software and dependencies Installation ===
Line 50: Line 142:
 
The original version running as web application has been modified in order to run on a gCube Hosting Node as well as on a gLite Working node. This way the software can be exploited by the gCube Aquamaps Service Suite to plot Aquamaps Species Distribution and Biodiversity Maps.
 
The original version running as web application has been modified in order to run on a gCube Hosting Node as well as on a gLite Working node. This way the software can be exploited by the gCube Aquamaps Service Suite to plot Aquamaps Species Distribution and Biodiversity Maps.
  
−
The customized version of the software can be download from :
+
The customized version of the software can be download from [ http://shell.research-infrastructures.eu/c-squaresOnGrid.tar.gz]
  
−
-- Link to add --
 
  
 
The installation of the customized version of the C-Square Mapper on the gHN hosting the Aquamaps Service should be carried as follows:
 
The installation of the customized version of the C-Square Mapper on the gHN hosting the Aquamaps Service should be carried as follows:
Line 59: Line 150:
  
 
==== Dependencies Installation ====
 
==== Dependencies Installation ====
 +
 +
===== SL4 node =====
  
 
The C-Square Mapper software depends on third party libraries to be installed on the gHN host:
 
The C-Square Mapper software depends on third party libraries to be installed on the gHN host:
Line 66: Line 159:
 
* GD Library (http://www.libgd.org/Main_Page )
 
* GD Library (http://www.libgd.org/Main_Page )
 
* perl GD Library (http://search.cpan.org/dist/GD/)
 
* perl GD Library (http://search.cpan.org/dist/GD/)
 +
 +
 +
===== Ubuntu 64 =====
 +
 +
* perl GD Library
 +
** apt-get install libgd2-xpm-dev
 +
** sudo perl -MCPAN -e 'install GD'
 +
* xplanet software
 +
** apt-get install xplanet
 +
** N.B. workaround ->  cp /usr/share/xplanet/images/earth.jpg /usr/share/xplanet/images/earth.gif
 +
 +
 +
===== SUSE 64 =====
 +
 +
* perl GD Library
 +
** zypper  install gd-devel
 +
** zypper  install libjpeg-devel
 +
** zypper  install giflib-devel
 +
** perl -MCPAN -e 'install GD'
 +
* xplanet software
 +
** Download source [http://downloads.sourceforge.net/project/xplanet/xplanet/1.2.2/xplanet-1.2.2.tar.gz?r=http%3A%2F%2Fxplanet.sourceforge.net%2F&ts=1316678539&use_mirror=garr]
 +
** /configure --with-gif --with-jpeg
 +
** make && make install
  
 
=== Mysql Installation and Aquamaps DB Import ===
 
=== Mysql Installation and Aquamaps DB Import ===
  
−
TO DO
+
AquaMaps Service is designed to work with a MySQL DB server 4.1.22, which documentation is available at MySQL official website[http://www.mysql.com/].
  
 
=== Aquamaps Service Configuration ===
 
=== Aquamaps Service Configuration ===
Line 77: Line 193:
 
* $GLOBUS_LOCATION/etc/org.gcube.application.aquamaps/dbprop.properties: the credentials to contact the local mysql db need to be provided by specifying the ''dbusername'' and ''dbpassword'' values
 
* $GLOBUS_LOCATION/etc/org.gcube.application.aquamaps/dbprop.properties: the credentials to contact the local mysql db need to be provided by specifying the ''dbusername'' and ''dbpassword'' values
 
* $GLOBUS_LOCATION/etc/org.gcube.application.aquamaps/geoserver.properties: this file contains the configuration parameters needed to customize the integration with the GeoServer Service.  
 
* $GLOBUS_LOCATION/etc/org.gcube.application.aquamaps/geoserver.properties: this file contains the configuration parameters needed to customize the integration with the GeoServer Service.  
−
-- TO LIST PARAMETERS
+
* $GLOBUS_LOCATION/etc/org.gcube.application.aquamaps/pool.properties: performance configuration parameters regarding the size of the submitting queue
  
 
== Aquamaps Publisher Installation ==
 
== Aquamaps Publisher Installation ==
Line 94: Line 210:
 
In addition the following library need to be manually installed under $GLOBUS_LOCATION/lib
 
In addition the following library need to be manually installed under $GLOBUS_LOCATION/lib
 
* Jetty v. 7.0.0 [https://grids16.eng.it/BuildReport/download/Recent_Builds/org.gcube.2-2-1/BUILD_6/dist/org.gcube/org.gcube.ext.jetty-servicearchive/7.0.0/ubuntu8_ia32_gcc424/org.gcube.ext.jetty-servicearchive-7.0.0-pre5.tar.gz]
 
* Jetty v. 7.0.0 [https://grids16.eng.it/BuildReport/download/Recent_Builds/org.gcube.2-2-1/BUILD_6/dist/org.gcube/org.gcube.ext.jetty-servicearchive/7.0.0/ubuntu8_ia32_gcc424/org.gcube.ext.jetty-servicearchive-7.0.0-pre5.tar.gz]
 +
 +
 +
== Aquamaps batch Job Execution on the Grid ==
 +
 +
=== gLite WN configuration ===
 +
 +
The current version of the Batch Job Execution running on the gLite Grid needs the following packages to be installed:
 +
 +
* perl-XML-Writer
 +
* perl-DBI
 +
* perl-DBD-MySQL ( which depends on mysql client)
 +
* perl-GD
 +
 +
All needed packages can be installed by running ''yum install perl-XML-Writer perl-DBI perl-DBD-MySQL perl-GD''
 +
 +
In addition the following software:
 +
 +
* Xplanet v.1.2.1 (http://xplanet.sourceforge.net/) [http://shell.research-infrastructures.eu/xplanet.tar.gz]
 +
 +
should be installed under the /usr/local/share folder of the WN
 +
 +
As last steps, all WNs contacting the AquaMaps DB should be granted to access remotely the mysql instance running at shell.research-infrastructures.eu.

Latest revision as of 18:50, 6 July 2016


Aquamaps Service Installation

The Installation of the Aquamaps Service on top of a gCube container (gHN), cannot be performed by exploiting the dynamic deployment mechanism offered by the gCube framework.

Therefore a manual installation process need to be performed in order to install the service and its dependenceny and to correctly configure access to Aquamaps DB.


Aquamaps Service packages and dependencies installation

gCube software

The packages listed below can be found at

http://grids16.eng.it/BuildReport/browse/Recent_Builds/

We kindly recommend to download the software packages contained in the last Build of the last released version of gCube distribution.


The following package has been released as part of gCube :

  • org.gcube.application.aquamaps.aquamapsservice-servicearchive

The tar archive contains the following packages to install:

  • Aquamaps Service gar

The Aquamaps Service package, to be installed inside a gHN container using the following command: 

gcore-deploy-service org.gcube.application.aquamaps.gar
  • Aquamaps stubs

The Aquamaps Service stubs library ( org.gcube.application.aquamaps.stubs.jar ) to be copied inside the gHN library folder ( $GLOBUS_LOCATION/lib )

In addition the following gCube libraries are needed( to be installed into the $GLOBUS_LOCATION/lib folder )

  • The Aquamaps Publisher Service stubs library
  • The Messaging Consumer library
  • The Aquamaps Data Model library
  • The GIS Data Model library
  • The GeoServer Interface library

Third Party Libraries

The following libraries need to be manually installed under $GLOBUS_LOCATION/lib:

  • Geo Tools framework v 2.6

available from Geo Tools official website[1], in particular the following library are needed:

    • geoapi-2.3-M1.jar
    • geoapi-pending-2.3-M1.jar
    • geodb-0.3.jar
    • gt-api-2.6.4.jar
    • gt-arcgrid-2.6.4.jar
    • gt-arcsde-2.6.4.jar
    • gt-arcsde-common-2.6.4.jar
    • gt-brewer-2.6.4.jar
    • gt-charts-2.6.4.jar
    • gt-coverage-2.6.4.jar
    • gt-cql-2.6.4.jar
    • gt-data-2.6.4.jar
    • gt-db2-2.6.4.jar
    • gt-directory-2.6.4.jar
    • gt-epsg-extension-2.6.4.jar
    • gt-epsg-hsql-2.6.4.jar
    • gt-epsg-postgresql-2.6.4.jar
    • gt-epsg-wkt-2.6.4.jar
    • gt-feature-pregeneralized-2.6.4.jar
    • gt-geotiff-2.6.4.jar
    • gt-graph-2.6.4.jar
    • gt-gtopo30-2.6.4.jar
    • gt-image-2.6.4.jar
    • gt-imageio-ext-gdal-2.6.4.jar
    • gt-imagemosaic-2.6.4.jar
    • gt-imagemosaic-jdbc-2.6.4.jar
    • gt-imagepyramid-2.6.4.jar
    • gt-jdbc-2.6.4.jar
    • gt-jdbc-db2-2.6.4.jar
    • gt-jdbc-h2-2.6.4.jar
    • gt-jdbc-mysql-2.6.4.jar
    • gt-jdbc-oracle-2.6.4.jar
    • gt-jdbc-postgis-2.6.4.jar
    • gt-jdbc-spatialite-2.6.4.jar
    • gt-jdbc-sqlserver-2.6.4.jar
    • gt-jp2k-2.6.4.jar
    • gt-legacy-2.6.4.jar
    • gt-main-2.6.4.jar
    • gt-metadata-2.6.4.jar
    • gt-postgis-2.6.4.jar
    • gt-property-2.6.4.jar
    • gt-referencing-2.6.4.jar
    • gt-referencing3D-2.6.4.jar
    • gt-render-2.6.4.jar
    • gt-sample-data-2.6.4.jar
    • gt-shapefile-2.6.4.jar
    • gt-svg-2.6.4.jar
    • gt-swing-2.6.4.jar
    • gt-validation-2.6.4.jar
    • gt-wfs-2.6.4.jar
    • gt-wms-2.6.4.jar
    • gt-xml-2.6.4.jar
    • gt-xsd-core-2.6.4.jar
    • gt-xsd-filter-2.6.4.jar
    • gt-xsd-gml2-2.6.4.jar
    • gt-xsd-gml3-2.6.4.jar
    • gt-xsd-kml-2.6.4.jar
    • gt-xsd-ows-2.6.4.jar
    • gt-xsd-sld-2.6.4.jar
    • gt-xsd-wfs-2.6.4.jar
    • gt-xsd-wps-2.6.4.jar
  • Jetty v. 7.0.0 [2]
  • MySQL JDBC v 5.1.5 [3]
  • commons-dbcp[4]
  • commons-pool[5]
  • hsqldb[6]
  • ostermillerutils[7]
  • Xstream[8]
  • Lucene
  • commons-codec 1.3
  • postgresql-8.4-701
  • csv-4j
  • commons-http-client 3.0.1
  • dom4j
  • hibernate
  • hsql
  • java-persistence
  • jts
  • sl4j

CMAR C-Square Mapper Software and dependencies Installation

The CMAR C-Square Mapper software ( http://www.marine.csiro.au/csquares/about-mapper.htm) is a perl utility which plots dataset exents on a range of base maps, according to a string of c-squares.

The original version running as web application has been modified in order to run on a gCube Hosting Node as well as on a gLite Working node. This way the software can be exploited by the gCube Aquamaps Service Suite to plot Aquamaps Species Distribution and Biodiversity Maps.

The customized version of the software can be download from [ http://shell.research-infrastructures.eu/c-squaresOnGrid.tar.gz]


The installation of the customized version of the C-Square Mapper on the gHN hosting the Aquamaps Service should be carried as follows:

  • Untar the tar archive c-squaresOnGrid.tar.gz
  • Move the c-squaresOnGrid folder under the $GLOBUS_LOCATION folder

Dependencies Installation

SL4 node

The C-Square Mapper software depends on third party libraries to be installed on the gHN host:

The Xplanet tar archive should be installed under the /usr/local/share folder of the gHN host


Ubuntu 64
  • perl GD Library
    • apt-get install libgd2-xpm-dev
    • sudo perl -MCPAN -e 'install GD'
  • xplanet software
    • apt-get install xplanet
    • N.B. workaround -> cp /usr/share/xplanet/images/earth.jpg /usr/share/xplanet/images/earth.gif


SUSE 64
  • perl GD Library
    • zypper install gd-devel
    • zypper install libjpeg-devel
    • zypper install giflib-devel
    • perl -MCPAN -e 'install GD'
  • xplanet software
    • Download source [10]
    • /configure --with-gif --with-jpeg
    • make && make install

Mysql Installation and Aquamaps DB Import

AquaMaps Service is designed to work with a MySQL DB server 4.1.22, which documentation is available at MySQL official website[11].

Aquamaps Service Configuration

In order to configure the Aquamaps Service, the following configuration file need to be customized:

  • $GLOBUS_LOCATION/etc/org.gcube.application.aquamaps/dbprop.properties: the credentials to contact the local mysql db need to be provided by specifying the dbusername and dbpassword values
  • $GLOBUS_LOCATION/etc/org.gcube.application.aquamaps/geoserver.properties: this file contains the configuration parameters needed to customize the integration with the GeoServer Service.
  • $GLOBUS_LOCATION/etc/org.gcube.application.aquamaps/pool.properties: performance configuration parameters regarding the size of the submitting queue

Aquamaps Publisher Installation

The Installation of the Aquamaps Publisher Service on top of a gCube container (gHN), can be performed by exploiting the dynamic deployment mechianism offered by the gCube framework.

For a manual installation the following steps need to be followed:

  • Download the latest stable version of the Aquamaps Publisher [12]
  • Untar the archive
  • Deploy the Aquamaps Publisher gar file into the gHN container by typing:
gcore-deploy-service org.gcube.application.aquamaps.aquamapspublisher.gar
  • Copy the aquamaps-publisher-stubs library (org.gcube.application.aquamaps.aquamapspublisher.stubs.jar) into the $GLOBUS_LOCATION/lib folder

In addition the following library need to be manually installed under $GLOBUS_LOCATION/lib

  • Jetty v. 7.0.0 [13]


Aquamaps batch Job Execution on the Grid

gLite WN configuration

The current version of the Batch Job Execution running on the gLite Grid needs the following packages to be installed:

  • perl-XML-Writer
  • perl-DBI
  • perl-DBD-MySQL ( which depends on mysql client)
  • perl-GD

All needed packages can be installed by running yum install perl-XML-Writer perl-DBI perl-DBD-MySQL perl-GD

In addition the following software:

should be installed under the /usr/local/share folder of the WN

As last steps, all WNs contacting the AquaMaps DB should be granted to access remotely the mysql instance running at shell.research-infrastructures.eu.

Retrieved from "https://wiki.gcube-system.org/index.php?title=AquamapsServiceAdminGuide&oldid=25196"