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 ====
 +
 
 +
The packages listed below can be found at  
 +
 
 +
http://grids16.eng.it/BuildReport/browse/Recent_Builds/
  
−
https://grids16.eng.it/BuildReport/browse/Recent_Builds/org.gcube.2-2-1/BUILD_6
+
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 2.2.1:
 
  
−
* 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]
+
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 28: Line 36:
 
The Aquamaps Service stubs library ( org.gcube.application.aquamaps.stubs.jar )  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 )
  
 +
In addition the following gCube libraries are needed( to be installed  into the $GLOBUS_LOCATION/lib folder )
  
−
* 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, however it depends from the following packages which are distributed as part as the Geo Tools framework available from Geo Tools official website[http://www.geotools.org/]:
+
  
 +
* 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[http://www.geotools.org/], in particular the following library are needed:
 
**geoapi-2.3-M1.jar
 
**geoapi-2.3-M1.jar
 
**geoapi-pending-2.3-M1.jar
 
**geoapi-pending-2.3-M1.jar
Line 94: Line 117:
 
**gt-xsd-wps-2.6.4.jar
 
**gt-xsd-wps-2.6.4.jar
  
−
* Third Party Libraries
+
* 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]
−
The Following Third Party Libraries are automatically installed togheter with Aquamaps Service gar into the $GLOBUS_LOCATION/lib folder:
+
* 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-codec-1.3.jar[http://eticssoft.web.cern.ch/eticssoft/repository/externals/commons-codec/1.3.0/noarch/commons-codec-1.3.0-0.tar.gz]
+
* commons-dbcp[http://eticssoft.web.cern.ch/eticssoft/repository/externals/commons-dbcp/1.2.1/noarch/commons-dbcp.tar.gz]
−
**commons-httpclient.jar[http://eticssoft.web.cern.ch/eticssoft/repository/externals/commons-httpclient/3.0.1/noarch/commons-httpclient-3.0.1-0.tar.gz]
+
* commons-pool[http://eticssoft.web.cern.ch/eticssoft/repository/externals/commons-pool/1.3/noarch/commons-pool.tar.gz]
−
**csv4j_gcube.jar ( gCube specific extension to csv4j library)[http://grids16.eng.it/BuildReport/download/Recent_Builds/org.gcube.2-2-1/BUILD_6/dist/org.gcube/org.gcube.common.csv4j-custom-servicearchive/1.0.0/ubuntu8_ia32_gcc424/org.gcube.common.csv4j-custom-servicearchive-1.0.0-0.tar.gz]
+
* hsqldb[http://puzzle.dl.sourceforge.net/sourceforge/hsqldb/hsqldb_1_7_2_3.zip]
−
**postgresql-8.4-701.jdbc3.jar[http://eticssoft.web.cern.ch/eticssoft/repository/externals/postgresql-jdbc/8.4/noarch/postgresql-jdbc-8.4-701.tar.gz]
+
* 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]
−
In addition the following libraries need to be manually installed under $GLOBUS_LOCATION/lib:
+
* Lucene
−
 
+
* commons-codec 1.3
−
** The Aquamaps Publisher Service stubs library [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]( org.gcube.application.aquamapspublisher.stubs.jar )
+
* postgresql-8.4-701
−
** 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]
+
* csv-4j
−
** 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]
+
* commons-http-client 3.0.1
−
** commons-dbcp[http://sunsite.cnlab-switch.ch/www/mirror/apache/dist/jakarta/commons/dbcp/binaries/commons-dbcp-1.2.1.tar.gz]
+
* dom4j
−
** commons-pool[http://sunsite.cnlab-switch.ch/www/mirror/apache/dist/jakarta/commons/pool/binaries/commons-pool-1.3.tar.gz]
+
* hibernate
−
** hsqldb[http://puzzle.dl.sourceforge.net/sourceforge/hsqldb/hsqldb_1_7_2_3.zip]
+
* hsql
−
** ostermillerutils[http://eticssoft.web.cern.ch/eticssoft/repository/externals/ostermillerutils/1.7.0/noarch/ostermillerutils-1.7.0.tar.gz]
+
* java-persistence
−
** Xstream[http://eticssoft.web.cern.ch/eticssoft/repository/externals/XStream/1.3.1/noarch/XStream-1.3.1.tar.gz]
+
* jts
 +
* sl4j
  
 
=== CMAR C-Square Mapper Software and dependencies Installation ===
 
=== CMAR C-Square Mapper Software and dependencies Installation ===
Line 126: 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 133: 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 ===
Line 163: Line 212:
  
  
−
== Aquamaps on the Grid ==
+
== Aquamaps batch Job Execution on the Grid ==
  
 
=== gLite WN configuration ===
 
=== gLite WN configuration ===
  
−
The current version of the Batch Job Execution running on the gLite Grid, in addition to the software listed as C-Square Mapper dependency, needs the following packages to be installed:
+
The current version of the Batch Job Execution running on the gLite Grid needs the following packages to be installed:
  
 
* perl-XML-Writer
 
* perl-XML-Writer
 
* perl-DBI
 
* perl-DBI
 
* perl-DBD-MySQL ( which depends on mysql client)
 
* 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 17:50, 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://gcube.wiki.gcube-system.org/index.php?title=AquamapsServiceAdminGuide&oldid=25196"